Zebrafish (Danio rerio) associative responses are useful for pharmaceutical and toxicology screen... more Zebrafish (Danio rerio) associative responses are useful for pharmaceutical and toxicology screening, behavioral genetics, and discovering neural mechanisms involved in behavioral modulation. In novel environments, zebrafish swim to tank bottoms and dark backgrounds, behaviors attributed to anxiety associated with threat of predation. To examine possible genetic effects of inbreeding and segregation on this behavior, we compared Zebrafish International Resource Center (ZIRC) AB and WIK lines to zebrafish and GloFish® from a pet store (PETCO) in two qualitatively different novel environments: the dive tank and aquatic light/dark plus maze. Behavior was observed in the dive tank for 5 min, immediately followed by 5 min in the light/dark plus maze. Among strains, WIK spent more time in the dive tank top than AB (76 + 30 vs. 17 + 11 sec), and AB froze in the plus maze center for longer than PETCO or GloFish® (162 + 61 vs. 72 + 29 or 27 + 27 sec). Further, behavior of zebrafish exposed for 3 min to 25 mg/L nicotine, desipramine, chlordiazepoxide, yohimbine, 100 mg/L citalopram, 0.05% DMSO, or 0.5% ethanol was compared to controls. Approximately 0.1% of drug is available in brain after such exposures. Desipramine or citalopramexposed fish spent more time in the dive tank top, and both reuptake inhibitors bound to serotonin transporters in zebrafish brain with high affinity (K i = 7 + 5 and 9 + 5 nM). In the plus maze, chlordiazepoxide, ethanol and DMSO-exposed fish crossed more lines and spent more time in white arms. Neither 25 mg/L nicotine nor yohimbine altered zebrafish behavior in novel environments, but nicotine was anxiolytic at higher doses. Overall, the light/dark plus maze and dive tank are distinct behavioral measures that are sensitive to treatment with anxiolytic compounds, but zebrafish line selection and solvents can influence baseline behavior in these tests.
We propose a general matrix-valued multiple kernel learning framework for highdimensional nonline... more We propose a general matrix-valued multiple kernel learning framework for highdimensional nonlinear multivariate regression problems. This framework allows a broad class of mixed norm regularizers, including those that induce sparsity, to be imposed on a dictionary of vector-valued Reproducing Kernel Hilbert Spaces. We develop a highly scalable and eigendecompositionfree algorithm that orchestrates two inexact solvers for simultaneously learning both the input and output components of separable matrix-valued kernels. As a key application enabled by our framework, we show how high-dimensional causal inference tasks can be naturally cast as sparse function estimation problems, leading to novel nonlinear extensions of a class of Graphical Granger Causality techniques. Our algorithmic developments and extensive empirical studies are complemented by theoretical analyses in terms of Rademacher generalization bounds.
The accumulation of organic contaminants including dyes in aquatic systems is of significant envi... more The accumulation of organic contaminants including dyes in aquatic systems is of significant environmental concern, necessitating the development of affordable and sustainable materials for the treatment/elimination of these hazardous pollutants. Here, a green synthesis strategy has been used to develop a self-assembled gum kondagogu-sodium alginate bioconjugate sponge adorned with silver nanoparticles, for the first time. The properties of the nanocomposite sponge were then analyzed using FTIR, TGA, SEM, and MicroCT. The ensued biobased sponge exhibited hierarchical microstructure, open cellular pores, good shape memory, and mechanical properties. It merges the attributes of an open cellular porous structure with metal nanoparticles and are envisaged to be deployed as a sustainable catalytic system for reducing contaminants in the aqueous environment. This nanocomposite sponge showed enhanced catalytic effectiveness (km values up to 37 min−1 g−1 and 44 min−1 g−1 for methylene blue ...
Point cloud data of cracks can be used for various purposes such as crack detection, depth calcul... more Point cloud data of cracks can be used for various purposes such as crack detection, depth calculation and crack segmentation. Upsampling low-density point clouds can help to improve the performance of those tasks. Building on existing methods that upsample point clouds from low-resolution point cloud input, to improve feature definition, this paper proposes a new method for upsampling low-density point clouds using a combination of these point clouds and corresponding 2D images of the original objects as input data. We use an architecture based on Generative Adversarial Networks (GAN) for training input point clouds with additional information from the corresponding 2D images. The key idea is to exploit features from both 2D images and point clouds to enrich point clouds in both the training and testing phases. Our method takes advantage of the combination of 2D images and point clouds using a GAN framework. Experimental results show our proposed method achieves a higher effectiveness compared with previous upsampling methods. INDEX TERMS Point cloud upsampling, generative adversarial network, crack point cloud, enrichment point cloud, combining point clouds and images.
MicroRNAs (miRNAs) are essential post-transcriptional gene regulators involved in various neurona... more MicroRNAs (miRNAs) are essential post-transcriptional gene regulators involved in various neuronal and non-neuronal cell functions and play a key role in pathological conditions. Numerous studies have demonstrated that miRNAs are dysregulated in major neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, or Huntington’s disease. Hence, in the present work, we constructed a comprehensive overview of individual microRNA alterations in various models of the above neurodegenerative diseases. We also provided evidence of miRNAs as promising biomarkers for prognostic and diagnostic approaches. In addition, we summarized data from the literature about miRNA-based therapeutic applications via inhibiting or promoting miRNA expression. We finally identified the overlapping miRNA signature across the diseases, including miR-128, miR-140-5p, miR-206, miR-326, and miR-155, associated with multiple etiological cellular mec...
Foreign language teaching and learning, especially English language for communication as sea is a... more Foreign language teaching and learning, especially English language for communication as sea is a part of curriculum in all maritime colleges. This is because English has been used as the sea language in a whole world. As a foreign language in Indonesia, it requires more skills to be able to teach it because besides teaching the subject matters, the lecturer’s competence is necessary for the successful learning process. The research aimed at finding out: (1) the profile of students’ writing skill at deck department of Politeknik Ilmu Pelayaran Makassar, (2) the influence of pedagogic competence toward students’ writing proficiency at Deck Department of Politeknik Ilmu Pelayaran Makassar, (3) the influence of professional competence toward students’ writing proficiency at Deck Department of Politeknik Ilmu Pelayaran Makassar. The research applied quantitative design with applying the ex post facto method. The subject of this research consists of second semester of Deck (Nautical) dep...
As we approach the era of quantum advantage, when quantum computers (QCs) can outperform any clas... more As we approach the era of quantum advantage, when quantum computers (QCs) can outperform any classical computer on particular tasks, there remains the difficult challenge of how to validate their performance. While algorithmic success can be easily verified in some instances such as number factoring or oracular algorithms, these approaches only provide pass/fail information for a single QC. On the other hand, a comparison between different QCs on the same arbitrary circuit provides a lower-bound for generic validation: a quantum computation is only as valid as the agreement between the results produced on different QCs. Such an approach is also at the heart of evaluating metrological standards such as disparate atomic clocks. In this paper, we report a cross-platform QC comparison using randomized and correlated measurements that results in a wealth of information on the QC systems. We execute several quantum circuits on widely different physical QC platforms and analyze the cross-p...
BioTuring’s BBrowser is a software solution that helps scientists effectively analyze single-cell... more BioTuring’s BBrowser is a software solution that helps scientists effectively analyze single-cell omics data. It combines big data with big computation and modern data visualization to create a unique platform where scientists can interact and obtain important biological insights from the massive amounts of single-cell data. BBrowser has three main components: a curated single-cell database, a big-data analytics layer, and a data visualization module. BBrowser is available for download at:https://bioturing.com/bbrowser/download.
We present our approach for the identification of cited text spans in scientific literature, usin... more We present our approach for the identification of cited text spans in scientific literature, using pre-trained encoders (BERT) in combination with different neural networks. We further experiment to assess the impact of using these cited text spans as input in BERT-based extractive summarisation methods. Inspired and motivated by the CL-SciSumm shared tasks, we explore different methods to adapt pre-trained models which are tuned for generic domain to scientific literature. For the identification of cited text spans, we assess the impact of different configurations in terms of learning from augmented data and using different features and network architectures (BERT, XLNET, CNN, and BiMPM) for training. We show that identifying and fine-tuning the language models on unlabelled or augmented domain specific data can improve the performance of cited text span identification models. For the scientific summarisation we implement an extractive summarisation model adapted from BERT. With re...
This study compares the effect of nanoscale and microscale zerovalent iron on natural freshwater ... more This study compares the effect of nanoscale and microscale zerovalent iron on natural freshwater microplankton over 21 days.
Store-operated Ca² entry (SOCE) constitutes a major Ca influx pathway in mammals to regulate a my... more Store-operated Ca² entry (SOCE) constitutes a major Ca influx pathway in mammals to regulate a myriad of physiological processes, including muscle contraction, synaptic transmission, gene expression, and metabolism. In non-excitable cells, the Ca² release-activated Ca² (CRAC) channel, composed of ORAI and stromal interaction molecules (STIM), constitutes a prototypical example of SOCE to mediate Ca entry at specialized membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and the plasma membrane (PM). The key steps of SOCE activation include the oligomerization of the luminal domain of the ER-resident Ca sensor STIM1 upon Ca² store depletion, subsequent signal propagation toward the cytoplasmic domain to trigger a conformational switch and overcome the intramolecular autoinhibition, and ultimate exposure of the minimal ORAI-activating domain to directly engage and gate ORAI channels in the plasma membrane. This exquisitely coordinated cellular event is also facilitate...
Simple methods with straightforward readouts that enable real-time interrogation of protein quate... more Simple methods with straightforward readouts that enable real-time interrogation of protein quaternary structure are much needed to facilitate the physicochemical characterization of proteins at the single-cell level. After screening over a series of microtubule (MT) binders, we report herein the development of two genetically encoded tags (designated as "MoTags" for the monomer/oligomer detection tag) that can be conveniently fused to a given protein to probe its oligomeric state when combined with routine fluorescence microscopy. In their monomeric form, MoTags are evenly distributed in the cytosol; whereas oligomerization enables MoTags to label MT or track MT tips in an oligomeric state-dependent manner. We demonstrate here the broad utility of engineered MoTags to aid the determination of protein oligomeric states, dissection of protein structure and function, and monitoring of protein-target interactions under physiological conditions in living cells.
The calcium release-activated calcium (CRAC) channel, composed of ORAI and stromal interaction mo... more The calcium release-activated calcium (CRAC) channel, composed of ORAI and stromal interaction molecules (STIM), represents a prototypical example of store-operated calcium entry in mammals. The ORAI-STIM signaling occurs at membrane contact sites formed by close appositions between the endoplasmic reticulum (ER) and the plasma membrane. ORAI1 is a four-pass transmembrane protein that forms a highly calcium-selective ion channel in the plasma membrane. STIM1 is an ER-resident, a single-pass transmembrane protein that serves as a calcium sensor within the ER lumen and a potent activator of ORAI1 calcium channels. The intricate interplay between ORAI and STIM controls calcium entry into cells to regulate a myriad of physiological processes. We highlight herein the current knowledge on the structure-function relationship of CRAC channel, with a focus on key structural elements that mediate STIM1 conformational switch and the dynamic coupling between STIM1 and ORAI1. Furthermore, we dis...
Pflugers Archiv : European journal of physiology, Jan 22, 2018
Mediated through the combined action of STIM proteins and Orai channels, store-operated Ca entry ... more Mediated through the combined action of STIM proteins and Orai channels, store-operated Ca entry (SOCE) functions ubiquitously among different cell types. The existence of multiple STIM and Orai genes has made it difficult to assign specific roles of each STIM and Orai homolog in mediating Ca signals. Using CRISPR/Cas9 gene editing tools, we generated cells with both STIM or all three Orai homologs deleted and directly monitored store Ca and Ca signals. We found that unstimulated, SOCE null KO cells still retain 50~70% of ER Ca stores of wildtype (wt) cells. After brief exposure to store-emptying conditions, acute refilling of ER Ca stores was totally blocked in KO cells. However, after 24 h in culture, stores were eventually refilled. Thus, SOCE is critical for immediate refilling of ER Ca but is dispensable for the maintenance of long-term ER Ca homeostasis. Using the Orai null background triple Orai-KO cells, we examined the plasma membrane translocation properties of a series of...
International journal of radiation oncology, biology, physics, 2018
To assess the safety and efficacy of upfront treatment using bortezomib combined with standard ra... more To assess the safety and efficacy of upfront treatment using bortezomib combined with standard radiation therapy (RT) and temozolomide (TMZ), followed by adjuvant bortezomib and TMZ for ≤24 cycles, in patients with newly diagnosed glioblastoma multiforme (GBM). Twenty-four patients with newly diagnosed GBM were enrolled. The patients received standard external beam regional RT with concurrent TMZ beginning 3 to 6 weeks after surgery, followed by adjuvant TMZ and bortezomib for ≤24 cycles or until tumor progression. During RT, bortezomib was given at 1.3 mg/m on days 1, 4, 8, 11, 29, 32, 36, and 39. After RT, bortezomib was given at 1.3 mg/m on days 1, 4, 8, and 11 every 4 weeks. No unexpected adverse events occurred from the addition of bortezomib. The efficacy analysis showed a median progression-free survival (PFS) of 6.2 months (95% confidence interval [CI] 3.7-8.8), with promising PFS rates at ≥18 months compared with historical norms (25.0% at 18 and 24 months; 16.7% at 30 mont...
Recently, the green synthesis of metal nanoparticles has attracted wide attention due to its feas... more Recently, the green synthesis of metal nanoparticles has attracted wide attention due to its feasibility and very low environmental impact. This approach was applied in this study to synthesise nanoscale gold (Au), platinum (Pt), palladium (Pd), silver (Ag) and copper oxide (CuO) materials in simple aqueous media using the natural polymer gum karaya as a reducing and stabilising agent. The nanoparticles' (NPs) zeta-potential, stability and size were characterised by Zetasizer Nano, UV-Vis spectroscopy and by electron microscopy. Moreover, the biological effect of the NPs (concentration range 1.0-20.0 mg/L) on a unicellular green alga (Chlamydomonas reinhardtii) was investigated by assessing algal growth, membrane integrity, oxidative stress, chlorophyll (Chl) fluorescence and photosystem II photosynthetic efficiency. The resulting NPs had a mean size of 42 (Au), 12 (Pt), 1.5 (Pd), 5 (Ag) and 180 (CuO) nm and showed high stability over 6 months. At concentrations of 5 mg/L, Au an...
Mutant isocitrate dehydrogenase (IDH) 1/2 converts α-ketoglutarate (α-KG) to D-2 hydroxyglutarate... more Mutant isocitrate dehydrogenase (IDH) 1/2 converts α-ketoglutarate (α-KG) to D-2 hydroxyglutarate (D-2-HG), a putative oncometabolite that can inhibit α-KG dependent enzymes, including ten-eleven translocation methylcytosine dioxygenase (TET) DNA demethylases. We recently established that miRNAs are components of the IDH1 mutant-associated glioma CpG island methylator phenotype (G-CIMP), and specifically identified MIR148A as a tumor-suppressive miRNA within G-CIMP. However, the precise mechanism by which mutant IDH induces hypermethylation of MIR148A and other G-CIMP promoters remains to be elucidated. In this study, we demonstrate that treatment with exogenous D-2-HG induces MIR148A promoter methylation and transcriptional silencing in human embryonic kidney 293T (293T) cells and primary normal human astrocytes. Conversely, we show that the development of MIR148A promoter methylation in mutant IDH1 over-expressing 293T cells is abrogated via treatment with C227, an inhibitor of mu...
The most challenging task in the preparation of magnetic poly(N-isopropylacrylamide) (Fe3O4-PNIPA... more The most challenging task in the preparation of magnetic poly(N-isopropylacrylamide) (Fe3O4-PNIPAAm) nanocomposites for bio-applications is to maximise their reactivity and stability. Emulsion polymerisation, in situ precipitation and physical addition were used to produce Fe3O4-PNIPAAm-1, Fe3O4-PNIPAAm-2 and Fe3O4-PNIPAAm-3, respectively. Their properties were characterised using scanning electron microscopy (morphology), zeta-potential (surface charge), thermogravimetric analysis (stability), vibrating sample magnetometry (magnetisation) and dynamic light scattering. Moreover, we investigated the antibacterial effect of each nanocomposite against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. Both Fe3O4-PNIPAAm-1 and Fe3O4-PNIPAAm-2 nanocomposites displayed high thermal stability, zeta potential and magnetisation values, suggesting stable colloidal systems. Overall, the presence of Fe3O4-PNIPAAm nanocomposites, even at lower concentrations, caused signific...
Die nichtinvasive Laser-Tyndallometrie erlaubt eine quantifizierende Untersuchung der Integritat ... more Die nichtinvasive Laser-Tyndallometrie erlaubt eine quantifizierende Untersuchung der Integritat der Blut-Kammerwasser-Schranke. In der vorliegenden Arbeit werden-anhand von Kasuistiken-die Einsatzmoglichkeiten dieser Methode bei Patienten nach perforierender Keratoplastik and mit akuten endothelialen Transplantatreaktionen illustriert. Patienten and Methoden: Frinf retrospektiv ausgewahlte Patienten wurden nach perforierender Keratoplastik regel-mal3ig klinisch and tyndallometrisch mit dem Laser Flare-Cell Meter (Kowa FC-1000) untersucht. Bei vier der Patienten entwickelten sich Episoden akuter diffuser endothelialer Transplantatreaktionen, welche unter lokaler and systemischer Steroidtherapie reversibel waren. Ergebnisse: Wahrend sich die Tyndallometrie-Werte bei komplikationslosem Verlauf postoperativ rasch normalisieren, konnte bei manifester Transplantatreaktion eine deutliche Storung der Blut-Kammerwasser-Schranke nachgewiesen werden. Hierbei korrelierten die Tyndallometrie-Werte gut mit dem klinischen spaltlampenmikroskopischen Eindruck der Schwere der Transplantatreaktion. Schlufifolgerungen: Die nichtinvasive Tyndallometrie erscheint uns wertvoll fur Verlaufs-and Therapiekontrolle nach perforierender Keratoplastik.
Zebrafish (Danio rerio) associative responses are useful for pharmaceutical and toxicology screen... more Zebrafish (Danio rerio) associative responses are useful for pharmaceutical and toxicology screening, behavioral genetics, and discovering neural mechanisms involved in behavioral modulation. In novel environments, zebrafish swim to tank bottoms and dark backgrounds, behaviors attributed to anxiety associated with threat of predation. To examine possible genetic effects of inbreeding and segregation on this behavior, we compared Zebrafish International Resource Center (ZIRC) AB and WIK lines to zebrafish and GloFish® from a pet store (PETCO) in two qualitatively different novel environments: the dive tank and aquatic light/dark plus maze. Behavior was observed in the dive tank for 5 min, immediately followed by 5 min in the light/dark plus maze. Among strains, WIK spent more time in the dive tank top than AB (76 + 30 vs. 17 + 11 sec), and AB froze in the plus maze center for longer than PETCO or GloFish® (162 + 61 vs. 72 + 29 or 27 + 27 sec). Further, behavior of zebrafish exposed for 3 min to 25 mg/L nicotine, desipramine, chlordiazepoxide, yohimbine, 100 mg/L citalopram, 0.05% DMSO, or 0.5% ethanol was compared to controls. Approximately 0.1% of drug is available in brain after such exposures. Desipramine or citalopramexposed fish spent more time in the dive tank top, and both reuptake inhibitors bound to serotonin transporters in zebrafish brain with high affinity (K i = 7 + 5 and 9 + 5 nM). In the plus maze, chlordiazepoxide, ethanol and DMSO-exposed fish crossed more lines and spent more time in white arms. Neither 25 mg/L nicotine nor yohimbine altered zebrafish behavior in novel environments, but nicotine was anxiolytic at higher doses. Overall, the light/dark plus maze and dive tank are distinct behavioral measures that are sensitive to treatment with anxiolytic compounds, but zebrafish line selection and solvents can influence baseline behavior in these tests.
We propose a general matrix-valued multiple kernel learning framework for highdimensional nonline... more We propose a general matrix-valued multiple kernel learning framework for highdimensional nonlinear multivariate regression problems. This framework allows a broad class of mixed norm regularizers, including those that induce sparsity, to be imposed on a dictionary of vector-valued Reproducing Kernel Hilbert Spaces. We develop a highly scalable and eigendecompositionfree algorithm that orchestrates two inexact solvers for simultaneously learning both the input and output components of separable matrix-valued kernels. As a key application enabled by our framework, we show how high-dimensional causal inference tasks can be naturally cast as sparse function estimation problems, leading to novel nonlinear extensions of a class of Graphical Granger Causality techniques. Our algorithmic developments and extensive empirical studies are complemented by theoretical analyses in terms of Rademacher generalization bounds.
The accumulation of organic contaminants including dyes in aquatic systems is of significant envi... more The accumulation of organic contaminants including dyes in aquatic systems is of significant environmental concern, necessitating the development of affordable and sustainable materials for the treatment/elimination of these hazardous pollutants. Here, a green synthesis strategy has been used to develop a self-assembled gum kondagogu-sodium alginate bioconjugate sponge adorned with silver nanoparticles, for the first time. The properties of the nanocomposite sponge were then analyzed using FTIR, TGA, SEM, and MicroCT. The ensued biobased sponge exhibited hierarchical microstructure, open cellular pores, good shape memory, and mechanical properties. It merges the attributes of an open cellular porous structure with metal nanoparticles and are envisaged to be deployed as a sustainable catalytic system for reducing contaminants in the aqueous environment. This nanocomposite sponge showed enhanced catalytic effectiveness (km values up to 37 min−1 g−1 and 44 min−1 g−1 for methylene blue ...
Point cloud data of cracks can be used for various purposes such as crack detection, depth calcul... more Point cloud data of cracks can be used for various purposes such as crack detection, depth calculation and crack segmentation. Upsampling low-density point clouds can help to improve the performance of those tasks. Building on existing methods that upsample point clouds from low-resolution point cloud input, to improve feature definition, this paper proposes a new method for upsampling low-density point clouds using a combination of these point clouds and corresponding 2D images of the original objects as input data. We use an architecture based on Generative Adversarial Networks (GAN) for training input point clouds with additional information from the corresponding 2D images. The key idea is to exploit features from both 2D images and point clouds to enrich point clouds in both the training and testing phases. Our method takes advantage of the combination of 2D images and point clouds using a GAN framework. Experimental results show our proposed method achieves a higher effectiveness compared with previous upsampling methods. INDEX TERMS Point cloud upsampling, generative adversarial network, crack point cloud, enrichment point cloud, combining point clouds and images.
MicroRNAs (miRNAs) are essential post-transcriptional gene regulators involved in various neurona... more MicroRNAs (miRNAs) are essential post-transcriptional gene regulators involved in various neuronal and non-neuronal cell functions and play a key role in pathological conditions. Numerous studies have demonstrated that miRNAs are dysregulated in major neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, or Huntington’s disease. Hence, in the present work, we constructed a comprehensive overview of individual microRNA alterations in various models of the above neurodegenerative diseases. We also provided evidence of miRNAs as promising biomarkers for prognostic and diagnostic approaches. In addition, we summarized data from the literature about miRNA-based therapeutic applications via inhibiting or promoting miRNA expression. We finally identified the overlapping miRNA signature across the diseases, including miR-128, miR-140-5p, miR-206, miR-326, and miR-155, associated with multiple etiological cellular mec...
Foreign language teaching and learning, especially English language for communication as sea is a... more Foreign language teaching and learning, especially English language for communication as sea is a part of curriculum in all maritime colleges. This is because English has been used as the sea language in a whole world. As a foreign language in Indonesia, it requires more skills to be able to teach it because besides teaching the subject matters, the lecturer’s competence is necessary for the successful learning process. The research aimed at finding out: (1) the profile of students’ writing skill at deck department of Politeknik Ilmu Pelayaran Makassar, (2) the influence of pedagogic competence toward students’ writing proficiency at Deck Department of Politeknik Ilmu Pelayaran Makassar, (3) the influence of professional competence toward students’ writing proficiency at Deck Department of Politeknik Ilmu Pelayaran Makassar. The research applied quantitative design with applying the ex post facto method. The subject of this research consists of second semester of Deck (Nautical) dep...
As we approach the era of quantum advantage, when quantum computers (QCs) can outperform any clas... more As we approach the era of quantum advantage, when quantum computers (QCs) can outperform any classical computer on particular tasks, there remains the difficult challenge of how to validate their performance. While algorithmic success can be easily verified in some instances such as number factoring or oracular algorithms, these approaches only provide pass/fail information for a single QC. On the other hand, a comparison between different QCs on the same arbitrary circuit provides a lower-bound for generic validation: a quantum computation is only as valid as the agreement between the results produced on different QCs. Such an approach is also at the heart of evaluating metrological standards such as disparate atomic clocks. In this paper, we report a cross-platform QC comparison using randomized and correlated measurements that results in a wealth of information on the QC systems. We execute several quantum circuits on widely different physical QC platforms and analyze the cross-p...
BioTuring’s BBrowser is a software solution that helps scientists effectively analyze single-cell... more BioTuring’s BBrowser is a software solution that helps scientists effectively analyze single-cell omics data. It combines big data with big computation and modern data visualization to create a unique platform where scientists can interact and obtain important biological insights from the massive amounts of single-cell data. BBrowser has three main components: a curated single-cell database, a big-data analytics layer, and a data visualization module. BBrowser is available for download at:https://bioturing.com/bbrowser/download.
We present our approach for the identification of cited text spans in scientific literature, usin... more We present our approach for the identification of cited text spans in scientific literature, using pre-trained encoders (BERT) in combination with different neural networks. We further experiment to assess the impact of using these cited text spans as input in BERT-based extractive summarisation methods. Inspired and motivated by the CL-SciSumm shared tasks, we explore different methods to adapt pre-trained models which are tuned for generic domain to scientific literature. For the identification of cited text spans, we assess the impact of different configurations in terms of learning from augmented data and using different features and network architectures (BERT, XLNET, CNN, and BiMPM) for training. We show that identifying and fine-tuning the language models on unlabelled or augmented domain specific data can improve the performance of cited text span identification models. For the scientific summarisation we implement an extractive summarisation model adapted from BERT. With re...
This study compares the effect of nanoscale and microscale zerovalent iron on natural freshwater ... more This study compares the effect of nanoscale and microscale zerovalent iron on natural freshwater microplankton over 21 days.
Store-operated Ca² entry (SOCE) constitutes a major Ca influx pathway in mammals to regulate a my... more Store-operated Ca² entry (SOCE) constitutes a major Ca influx pathway in mammals to regulate a myriad of physiological processes, including muscle contraction, synaptic transmission, gene expression, and metabolism. In non-excitable cells, the Ca² release-activated Ca² (CRAC) channel, composed of ORAI and stromal interaction molecules (STIM), constitutes a prototypical example of SOCE to mediate Ca entry at specialized membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and the plasma membrane (PM). The key steps of SOCE activation include the oligomerization of the luminal domain of the ER-resident Ca sensor STIM1 upon Ca² store depletion, subsequent signal propagation toward the cytoplasmic domain to trigger a conformational switch and overcome the intramolecular autoinhibition, and ultimate exposure of the minimal ORAI-activating domain to directly engage and gate ORAI channels in the plasma membrane. This exquisitely coordinated cellular event is also facilitate...
Simple methods with straightforward readouts that enable real-time interrogation of protein quate... more Simple methods with straightforward readouts that enable real-time interrogation of protein quaternary structure are much needed to facilitate the physicochemical characterization of proteins at the single-cell level. After screening over a series of microtubule (MT) binders, we report herein the development of two genetically encoded tags (designated as "MoTags" for the monomer/oligomer detection tag) that can be conveniently fused to a given protein to probe its oligomeric state when combined with routine fluorescence microscopy. In their monomeric form, MoTags are evenly distributed in the cytosol; whereas oligomerization enables MoTags to label MT or track MT tips in an oligomeric state-dependent manner. We demonstrate here the broad utility of engineered MoTags to aid the determination of protein oligomeric states, dissection of protein structure and function, and monitoring of protein-target interactions under physiological conditions in living cells.
The calcium release-activated calcium (CRAC) channel, composed of ORAI and stromal interaction mo... more The calcium release-activated calcium (CRAC) channel, composed of ORAI and stromal interaction molecules (STIM), represents a prototypical example of store-operated calcium entry in mammals. The ORAI-STIM signaling occurs at membrane contact sites formed by close appositions between the endoplasmic reticulum (ER) and the plasma membrane. ORAI1 is a four-pass transmembrane protein that forms a highly calcium-selective ion channel in the plasma membrane. STIM1 is an ER-resident, a single-pass transmembrane protein that serves as a calcium sensor within the ER lumen and a potent activator of ORAI1 calcium channels. The intricate interplay between ORAI and STIM controls calcium entry into cells to regulate a myriad of physiological processes. We highlight herein the current knowledge on the structure-function relationship of CRAC channel, with a focus on key structural elements that mediate STIM1 conformational switch and the dynamic coupling between STIM1 and ORAI1. Furthermore, we dis...
Pflugers Archiv : European journal of physiology, Jan 22, 2018
Mediated through the combined action of STIM proteins and Orai channels, store-operated Ca entry ... more Mediated through the combined action of STIM proteins and Orai channels, store-operated Ca entry (SOCE) functions ubiquitously among different cell types. The existence of multiple STIM and Orai genes has made it difficult to assign specific roles of each STIM and Orai homolog in mediating Ca signals. Using CRISPR/Cas9 gene editing tools, we generated cells with both STIM or all three Orai homologs deleted and directly monitored store Ca and Ca signals. We found that unstimulated, SOCE null KO cells still retain 50~70% of ER Ca stores of wildtype (wt) cells. After brief exposure to store-emptying conditions, acute refilling of ER Ca stores was totally blocked in KO cells. However, after 24 h in culture, stores were eventually refilled. Thus, SOCE is critical for immediate refilling of ER Ca but is dispensable for the maintenance of long-term ER Ca homeostasis. Using the Orai null background triple Orai-KO cells, we examined the plasma membrane translocation properties of a series of...
International journal of radiation oncology, biology, physics, 2018
To assess the safety and efficacy of upfront treatment using bortezomib combined with standard ra... more To assess the safety and efficacy of upfront treatment using bortezomib combined with standard radiation therapy (RT) and temozolomide (TMZ), followed by adjuvant bortezomib and TMZ for ≤24 cycles, in patients with newly diagnosed glioblastoma multiforme (GBM). Twenty-four patients with newly diagnosed GBM were enrolled. The patients received standard external beam regional RT with concurrent TMZ beginning 3 to 6 weeks after surgery, followed by adjuvant TMZ and bortezomib for ≤24 cycles or until tumor progression. During RT, bortezomib was given at 1.3 mg/m on days 1, 4, 8, 11, 29, 32, 36, and 39. After RT, bortezomib was given at 1.3 mg/m on days 1, 4, 8, and 11 every 4 weeks. No unexpected adverse events occurred from the addition of bortezomib. The efficacy analysis showed a median progression-free survival (PFS) of 6.2 months (95% confidence interval [CI] 3.7-8.8), with promising PFS rates at ≥18 months compared with historical norms (25.0% at 18 and 24 months; 16.7% at 30 mont...
Recently, the green synthesis of metal nanoparticles has attracted wide attention due to its feas... more Recently, the green synthesis of metal nanoparticles has attracted wide attention due to its feasibility and very low environmental impact. This approach was applied in this study to synthesise nanoscale gold (Au), platinum (Pt), palladium (Pd), silver (Ag) and copper oxide (CuO) materials in simple aqueous media using the natural polymer gum karaya as a reducing and stabilising agent. The nanoparticles' (NPs) zeta-potential, stability and size were characterised by Zetasizer Nano, UV-Vis spectroscopy and by electron microscopy. Moreover, the biological effect of the NPs (concentration range 1.0-20.0 mg/L) on a unicellular green alga (Chlamydomonas reinhardtii) was investigated by assessing algal growth, membrane integrity, oxidative stress, chlorophyll (Chl) fluorescence and photosystem II photosynthetic efficiency. The resulting NPs had a mean size of 42 (Au), 12 (Pt), 1.5 (Pd), 5 (Ag) and 180 (CuO) nm and showed high stability over 6 months. At concentrations of 5 mg/L, Au an...
Mutant isocitrate dehydrogenase (IDH) 1/2 converts α-ketoglutarate (α-KG) to D-2 hydroxyglutarate... more Mutant isocitrate dehydrogenase (IDH) 1/2 converts α-ketoglutarate (α-KG) to D-2 hydroxyglutarate (D-2-HG), a putative oncometabolite that can inhibit α-KG dependent enzymes, including ten-eleven translocation methylcytosine dioxygenase (TET) DNA demethylases. We recently established that miRNAs are components of the IDH1 mutant-associated glioma CpG island methylator phenotype (G-CIMP), and specifically identified MIR148A as a tumor-suppressive miRNA within G-CIMP. However, the precise mechanism by which mutant IDH induces hypermethylation of MIR148A and other G-CIMP promoters remains to be elucidated. In this study, we demonstrate that treatment with exogenous D-2-HG induces MIR148A promoter methylation and transcriptional silencing in human embryonic kidney 293T (293T) cells and primary normal human astrocytes. Conversely, we show that the development of MIR148A promoter methylation in mutant IDH1 over-expressing 293T cells is abrogated via treatment with C227, an inhibitor of mu...
The most challenging task in the preparation of magnetic poly(N-isopropylacrylamide) (Fe3O4-PNIPA... more The most challenging task in the preparation of magnetic poly(N-isopropylacrylamide) (Fe3O4-PNIPAAm) nanocomposites for bio-applications is to maximise their reactivity and stability. Emulsion polymerisation, in situ precipitation and physical addition were used to produce Fe3O4-PNIPAAm-1, Fe3O4-PNIPAAm-2 and Fe3O4-PNIPAAm-3, respectively. Their properties were characterised using scanning electron microscopy (morphology), zeta-potential (surface charge), thermogravimetric analysis (stability), vibrating sample magnetometry (magnetisation) and dynamic light scattering. Moreover, we investigated the antibacterial effect of each nanocomposite against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. Both Fe3O4-PNIPAAm-1 and Fe3O4-PNIPAAm-2 nanocomposites displayed high thermal stability, zeta potential and magnetisation values, suggesting stable colloidal systems. Overall, the presence of Fe3O4-PNIPAAm nanocomposites, even at lower concentrations, caused signific...
Die nichtinvasive Laser-Tyndallometrie erlaubt eine quantifizierende Untersuchung der Integritat ... more Die nichtinvasive Laser-Tyndallometrie erlaubt eine quantifizierende Untersuchung der Integritat der Blut-Kammerwasser-Schranke. In der vorliegenden Arbeit werden-anhand von Kasuistiken-die Einsatzmoglichkeiten dieser Methode bei Patienten nach perforierender Keratoplastik and mit akuten endothelialen Transplantatreaktionen illustriert. Patienten and Methoden: Frinf retrospektiv ausgewahlte Patienten wurden nach perforierender Keratoplastik regel-mal3ig klinisch and tyndallometrisch mit dem Laser Flare-Cell Meter (Kowa FC-1000) untersucht. Bei vier der Patienten entwickelten sich Episoden akuter diffuser endothelialer Transplantatreaktionen, welche unter lokaler and systemischer Steroidtherapie reversibel waren. Ergebnisse: Wahrend sich die Tyndallometrie-Werte bei komplikationslosem Verlauf postoperativ rasch normalisieren, konnte bei manifester Transplantatreaktion eine deutliche Storung der Blut-Kammerwasser-Schranke nachgewiesen werden. Hierbei korrelierten die Tyndallometrie-Werte gut mit dem klinischen spaltlampenmikroskopischen Eindruck der Schwere der Transplantatreaktion. Schlufifolgerungen: Die nichtinvasive Tyndallometrie erscheint uns wertvoll fur Verlaufs-and Therapiekontrolle nach perforierender Keratoplastik.
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