(Q64082624)

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Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis

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Transcriptome analysis of rumen epithelium and meta-transcriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis (English)

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author name string

Wenli Li

1

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Sonia Gelsinger

2

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Andrea Edwards

3

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Christina Riehle

4

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Daniel Koch

5

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language of work or name

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publication date

18 March 2019

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Scientific Reports

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9

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1

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4744

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describes a project that uses

object named as

DESeq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

An evaluation of parameters for the detection of subclinical rumen acidosis in dairy herds.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Subacute ruminal acidosis (SARA): a review

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Subacute ruminal acidosis induces ruminal lipopolysaccharide endotoxin release and triggers an inflammatory response

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Modeling the adequacy of dietary fiber in dairy cows based on the responses of ruminal pH and milk fat production to composition of the diet.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Bovine rumen epithelium undergoes rapid structural adaptations during grain-induced subacute ruminal acidosis

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Incidence of ruminal parakeratosis in calves fed different rations and its relation to volatile fatty acid absorption

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Relation of Ruminal Parakeratosis Development to Volatile Fatty Acid Absorption

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

A grain-based subacute ruminal acidosis challenge causes translocation of lipopolysaccharide and triggers inflammation

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Ruminal acidosis in beef cattle: the current microbiological and nutritional outlook

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Diagnostic methods for the detection of subacute ruminal acidosis in dairy cows

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Ruminal lipopolysaccharide concentration and inflammatory response during grain-induced subacute ruminal acidosis in dairy cows.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Severity of ruminal acidosis in primiparous holstein cows during the periparturient period

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Replacing chopped alfalfa hay with alfalfa silage in barley grain and alfalfa-based total mixed rations for lactating dairy cows

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Subacute ruminal acidosis in dairy cows: the physiological causes, incidence and consequences

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Ruminal microbial development in conventionally or early-weaned calves

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Digestive development in neonatal dairy calves with either whole or ground oats in the calf starter

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effects of form of the diet on anatomical, microbial, and fermentative development of the rumen of neonatal calves

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Straw particle size in calf starters: Effects on digestive system development and rumen fermentation

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Butyric acid stimulates rumen mucosa development in the calf mainly by a reduction of apoptosis

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Short communication: Effect of calf starter on rumen pH of Holstein dairy calves at weaning

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The impact of a monensin controlled-release capsule on subclinical ketosis in the transition dairy cow.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The importance of pH in the regulation of ruminal acetate to propionate ratio and methane production in vitro

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Changes in rumen microbial fermentation are due to a combined effect of type of diet and pH.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Alfalfa pellet-induced subacute ruminal acidosis in dairy cows increases bacterial endotoxin in the rumen without causing inflammation

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Expression and localization of monocarboxylate transporters and sodium/proton exchangers in bovine rumen epithelium

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Use of Isolated Ruminal Epithelial Cells in the Study of Rumen Metabolism

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effects of varying dietary forage particle size in two concentrate levels on chewing activity, ruminal mat characteristics, and passage in dairy cows.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The effect of diet, intraruminal pH and osmolarity on sodium, chloride and magnesium absorption from the temporarily isolated and washed reticulo-rumen of sheep

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effects of dietary forage and calf starter on ruminal pH and transcriptomic adaptation of the rumen epithelium in Holstein calves during the weaning transition.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effects of Dietary Forage and Calf Starter Diet on Ruminal pH and Bacteria in Holstein Calves during Weaning Transition.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effect of grains differing in expected ruminal fermentability on the productivity of lactating dairy cows

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effect of forage level and replacing canola meal with dry distillers grains with solubles in precision-fed heifer diets: Digestibility and rumen fermentation

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effect and absorption of histamine in sheep rumen: significance of acidotic epithelial damage.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Glucose uptake via SGLT-1 is stimulated by beta(2)-adrenoceptors in the ruminal epithelium of sheep

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Energy contributions of volatile fatty acids from the gastrointestinal tract in various species

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Vesicular trafficking machinery, the actin cytoskeleton, and H+-K+-ATPase recycling in the gastric parietal cell

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Relationship Between Fermentation Acid Production in the Rumen and the Requirement for Physically Effective Fiber

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Ruminant Nutrition Symposium: Role of fermentation acid absorption in the regulation of ruminal pH.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Long-term management of gastroesophageal reflux disease with pantoprazole

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

On-demand therapy with pantoprazole 20 mg as effective long-term management of reflux disease in patients with mild GERD: the ORION trial

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Some effects of diet on the mitotic index and the cell cycle of the ruminal epithelium of sheep.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Rumen epithelial cell proliferation accelerated by rapid increase in intraruminal butyrate

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

An energy-rich diet causes rumen papillae proliferation associated with more IGF type 1 receptors and increased plasma IGF-1 concentrations in young goats

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Ruminal acidosis and the rapid onset of ruminal parakeratosis in a mature dairy cow: a case report

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The mechanics of microtubule networks in cell division.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Microtubule organization: A complex solution

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The polarisation of the anterior-posterior and dorsal-ventral axes during Drosophila oogenesis

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Axis development and early asymmetry in mammals

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Comparative analysis of gene expression profiles in ruminal tissue from Holstein dairy cows fed high or low concentrate diets

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Intraruminal infusion of n-butyric acid induces an increase of ruminal papillae size independent of IGF-1 system in castrated bulls

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Symposium: Nitrogen utilization by the ruminant nitrogen metabolism in the ruminant

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Glycoprotein biosynthesis during the acute-phase response to inflammation

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Glycosylation and the immune system

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Acute-phase proteins and other systemic responses to inflammation

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Feeding high proportions of barley grain stimulates an inflammatory response in dairy cows

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The mechanism of passage of endogenous urea through the rumen wall and the role of ureolytic epithelial bacteria in the urea flux

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Adherent bacterial populations on the bovine rumen wall: distribution patterns of adherent bacteria.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Evidence of Endotoxins in the Rumen Bacteria of Cattle Fed Hay or Grain

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Relationships between rumen lipopolysaccharide and mediators of inflammatory response with milk fat production and efficiency in dairy cows

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Effects of subacute ruminal acidosis challenges on fermentation and endotoxins in the rumen and hindgut of dairy cows

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Fusobacterium necrophorum: a ruminal bacterium that invades liver to cause abscesses in cattle

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Adherence of Fusobacterium necrophorum subsp. necrophorum to ruminal cells derived from bovine rumenitis

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Ruminal in situ disappearance and whole-tract digestion of starter feeds in calves before, during, and after weaning

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Characteristics of Water Soluble Markers for Measuring Rumen Liquid Volume and Dilution Rate

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Fast gapped-read alignment with Bowtie 2

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

HTSeq--a Python framework to work with high-throughput sequencing data

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

DAVID: Database for Annotation, Visualization, and Integrated Discovery

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

STAR: ultrafast universal RNA-seq aligner

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Kraken: ultrafast metagenomic sequence classification using exact alignments

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Modulation of STAT signaling by STAT-interacting proteins

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium.

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

1 reference

https://api.crossref.org/works/10.1038%2FS41598-019-40375-2

7 January 2021

based on heuristic

inferred from DOI database lookup

Adhesion of bacteria to epithelial cell surfaces within the reticulo-rumen of cattle

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ultrastructural changes in oxyntic cells associated with secretory function: a membrane-recycling hypothesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A net carbohydrate and protein system for evaluating cattle diets: II. Carbohydrate and protein availability

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

[Morphology of the rumen mucosa and fatty acid absorption in cattle--important factors for health and production]

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Digestion of epithelial tissue of the rumen wall by adherent bacteria in infused and conventionally fed sheep.

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Studies of Fusobacterium necrophorum from bovine hepatic abscesses: biotypes, quantitation, virulence, and antibiotic susceptibility

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Endotoxin and arachidonic acid metabolites in portal, hepatic and arterial blood of cattle with acute ruminal acidosis

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Adherence of Fusobacterium necrophorum subspecies necrophorum to different animal cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Symptom relief in gastroesophageal reflux disease: a randomized, controlled comparison of pantoprazole and nizatidine in a mixed patient population with erosive esophagitis or endoscopy-negative reflux disease

1 reference

https://pubmed.ncbi.nlm.nih.gov/30894588

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1038/S41598-019-40375-2

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