syedzayyan/paper_mill_benchmark huggingface dataset:
C9orf16 represents the aberrant genetic programs and drives the progression of PDAC.

Pancreatic ductal adenocarcinoma (pdac), constituting 90% of pancreatic cancers, is the fourth leading cause of cancer-related deaths in the world.Lack of early detection of pdac contributes to its poor prognosis as patients are often diagnosed at an advanced stage of disease.This is mostly due to the lack of promising diagnostic and therapeutic targets and corresponding drugs.Methods and results here, by bioinformatic analysis of single cell rna-sequencing data on normal pancreas tissues, primary and metastatic pdac tumors, we identified a promising pdac biomarker, c9orf16.The expression of c9orf16, rarely detectable in normal epithelial cells, was upregulated in primary pdac cancer cells and was further elevated in metastatic pdac cancer cells.Gain or loss of function of c9orf16 demonstrated its critical functions in regulating the cell proliferation, invasion and chemotherapy resistance of cancer cells.Pathway analysis and functional studies identified myc signaling pathways as the most activated pathways in regulating c9orf16 expression and in mediating the development and progression of pdac.Conclusions these data suggested a crucial gene regulation system, myc-c9orf16, which is actively involved in pdac development and progression, and targeting this system should be a novel diagnostic and therapeutic target for pdac.

Journal: BMC cancer (2022)
Publication types: Journal Article
Tumor Microenvironment and its Implications for Antitumor Immunity in Cholangiocarcinoma: Future Perspectives for Novel Therapies.

The incidence of cholangiocarcinoma (cca) has been increasing over the past few years.Although there are surgery, chemotherapy and other conventional treatment methods, the effect is not as expected.At present, immunotherapy has become the research frontier of cancer treatment, and cca tumor microenvironment (tme) is becoming a hot exploration direction of immunobiology.Tme can affect tumor progression through changes in metabolism, secretion and immunity.Accordingly, understanding the role played by immune cells and stromal cells in tme is important for the study of cca immunotherapy.This review will discuss the interactions between immune cells (including cd8+t cells, cd4+t cells, macrophages, natural killer cells, dendritic cells, myeloid suppressor cells, mast cells, and neutrophils) and stromal cells (including cancer-associated fibroblasts, endothelial cells) in the tme of cca.In addition, we will also discuss current research results on tme of cca and recent advances in immunotherapy.

Journal: International journal of biological sciences (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Changes of Circulating Extracellular Vesicles from the Liver after Roux-en-Y Bariatric Surgery.

Circulating extracellular vesicles are small particles enclosed by a phospholipid bilayer.Vesicles deriving directly from the cellular membrane by an active budding process retain cell origin specific proteins and rna.These vesicles carry pathophysiological information from their parental cell and hold the potential to allow analysis of organs without the need for a biopsy.We included in our study 27 patients undergoing bariatric surgery.Hepatic extracellular vesicles were determined by flow cytometry.M rna specific for hepatic cellular origin was determined in the extracellular vesicle fraction using q pcr.Surgery led to a massive reduction of weight and overall hepatic stress as determined by alanine transaminase (alt), aspartate transaminase (ast) and γ-glutamyltransferase (ggt).Total extracellular vesicle numbers were reduced after bariatric surgery.Liver specific vesicles identified by hep par1 or asialoglycoprotein receptor (asgpr) were significantly reduced after bariatric surgery in both annexin v+and annexin v-subgroups.When analyzing circulating liver-specific m rnas, we found reduced levels of these m rnas after surgery even though total circulating rna remained unchanged.We conclude that circulating hepatic extracellular vesicles are detectable in samples from patients undergoing gastric bypass surgery.These vesicles are reduced after a reduction of hepatic stress also observed with classic liver enzyme measurements.We conclude that asgpr or hep par positive vesicles hold the potential to serve as liver specific vesicle markers.

Journal: International journal of molecular sciences (2019)
Publication types: Journal Article
The levels of bioactive compounds found in raw and cooked Canadian pulses.

The effect of cooking on the levels of bioactive compounds (oligosaccharides, polyphenols and saponins, and vicine/convicine for faba bean only) were examined in a wide range of canadian pulses.The total oligosaccharide concentrations were reduced ∼40% for chickpea, 11-81% for lentils, 41-43% for faba beans, 10-51% for beans, and 20-44% for peas.Individual oligosaccharides, raffinose, ciceritol, stachyose and verbascose, increased or decreased in the cooked samples depending on each pulse sample.Cooking reduced the total polyphenol content by 13-25% for chickpeas, 0-83% for lentils, 47-54% for faba beans, 47-54% for beans, and 48-70% for peas.And, the total saponin concentrations were reduced by 11-30% for chickpeas, 0-40% for lentils, 32-46% for beans, 14-30% for peas and increased by 8-26% in faba bean.The vicine and convicine levels in faba bean were reduced by 26-38% with cooking.The reduction in bioactive compounds after cooking depended on the specific compound and specific type of pulse.This large analyses of 20 different pulse samples allows for comparison between and within different types of pulses.

Journal: Food science and technology international = Ciencia y tecnologia de los alimentos internacional (2021)
Publication types: Journal Article
Toll like receptor 7 expressed by malignant cells promotes tumor progression and metastasis through the recruitment of myeloid derived suppressor cells.

In non-small cell lung carcinoma (nsclc), stimulation of toll-like receptor 7 (tlr7), a receptor for single stranded rna, is linked to tumor progression and resistance to anticancer chemotherapy.However, the mechanism of this effect has been elusive.Here, using a murine model of lung adenocarcinoma, we demonstrate a key role for tlr7 expressed by malignant (rather than by stromal and immune) cells, in the recruitment of myeloid derived suppressor cells (mdscs), induced after tlr7 stimulation, resulting in accelerated tumor growth and metastasis.In adenocarcinoma patients, high tlr7 expression on malignant cells was associated with poor clinical outcome, as well as with a gene expression signature linked to aggressiveness and metastastic dissemination with high abundance of m rna encoding intercellular adhesion molecule 1 (icam-1), cytokeratins 7 and 19 (krt-7 and 19), syndecan 4 (sdc4), and p53.In addition, lung tumors expressing high levels of tlr7 have a phenotype of epithelial mesenchymal transition with high expression of vimentin and low abundance of e-cadherin.These data reveal a crucial role for cancer cell-intrinsic tlr7 expression in lung adenocarcinoma progression.

Journal: Oncoimmunology (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
3-(3-Hydroxyphenyl)-Propionic Acid (PPA) Suppresses Osteoblastic Cell Senescence to Promote Bone Accretion in Mice.

Phenolic acids (pas) are metabolites derived from polyphenolic compounds found in fruits and vegetables resulting from the actions of gut bacteria.Previously, we reported that the levels of seven individual pas were found to be at least 10 times higher in the serum of rats fed a blueberry (bb)-containing diet compared to those fed a control diet.We have characterized the effects of one such bb-associated serum pa, 3-(3-hydroxyphenyl)-propionic acid (ppa), on senescence signaling and promotion of mesenchymal stem cell differentiation toward osteoblasts, while suppressing adipogenesis in the stem cells.To better understand the mechanistic actions of ppa on bone formation in vivo, we administered four doses of ppa (0.1, 0.5, 1, and 5 mg/kg/day; daily i.p.) to 1-month-old female c57bl6/j mice for 30 days.We did not observe significant effects of ppa on cortical bone; however, there were significantly higher bone volume and trabecular thickness and increased osteoblastic cell number, but decreased osteoclastic cell number in ppa-treated groups compared to controls.These morphological and cellular outcomes of bone were reflected in changes of bone formation markers in serum and bone marrow plasma.Ppa treatment reduced senescence signaling as evaluated by senescence-associated β-galactosidase activity, pparγ, p53, and p21 expression in bone.In conclusion, ppa is capable of altering the mesenchymal stem cell differentiation program and bone cell senescence.This raises the possibility that bb-rich diets promote bone growth through increasing systemic pas, a question that merits additional investigation.© 2019 the authors.jbmr pluspublished by wiley periodicals, inc.On behalf of american society for bone and mineral research.

Journal: JBMR plus (2019)
Publication types: Journal Article
Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards.

Muscles facilitate most animal behavior, from eating to fleeing.However, to generate the variation in behavior necessary for survival, different muscles must perform differently; for instance, sprinting requires multiple rapid muscle contractions, whereas biting may require fewer contractions but greater force.Here, we use a transcriptomic approach to identify genes associated with variation in muscle contractile physiology among different muscles from the same individual.We measured differential gene expression between a leg and jaw muscle of anolis lizards known to differ in muscle contractile physiology and performance.For each individual, one muscle was used to measure muscle contractile physiology, including contractile velocity (vmaxand v40), specific tension, power ratio, and twitch time, whereas the contralateral muscle was used to extract rna for transcriptomic sequencing.Using the transcriptomic data, we found clear clustering of muscle type.Expression of genes clustered in gene ontology (go) terms related to muscle contraction and extracellular matrix was, on average, negatively correlated with vmaxand slower twitch times but positively correlated to power ratio and v40.Conversely, genes related to the go terms related to aerobic respiration were downregulated in muscles with higher power ratio and v40, and over-expressed as twitch time decreased.Determining the molecular mechanisms that underlie variation in muscle contractile physiology can begin to explain how organisms are able to optimize behavior under variable conditions.Future studies pursuing the effects of differential gene expression across muscle types in different environments might inform researchers about how differences develop across species, populations, and individuals varying in ecological history.

Journal: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology (2022)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.;Research Support, Non-U.S. Gov't
Type I multivariate zero-inflated COM-Poisson regression model.

In this paper, we present the type i multivariate zero-inflated conway-maxwell-poisson distribution, whose development is based on the extension of the type i multivariate zero-inflated poisson distribution.We developed important properties of the distribution and present a regression model.The aic and bic criteria are used to select the best fitted model.Two real data sets have been used to illustrate the proposed model.Moreover, we conclude by stating that the type i multivariate zero-inflated conway-maxwell-poisson distribution produces a better fitted model for multivariate count data with excess of zeros.

Journal: Biometrical journal. Biometrische Zeitschrift (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
A time-frequency denoising method for single-channel event-related EEG.

Introduction electroencephalogram (eeg) acquisition is easily affected by various noises, including those from electrocardiogram (ecg), electrooculogram (eog), and electromyogram (emg).Because noise interference can significantly limit the study and analysis of brain signals, there is a significant need for the development of improved methods to remove this interference for more accurate measurement of eeg signals.Methods based on the non-linear and non-stationary characteristics of brain signals, a strategy was developed to denoise brain signals using a time-frequency denoising algorithm framework of short-time fourier transform (stft), bidimensional empirical mode decomposition (bemd), and non-local means (nlm).Time-frequency analysis can reveal the signal frequency component and its evolution process, allowing the elimination of noise according to the signal and noise distribution.Bemd can be used to decompose the time-frequency signals into sub-time-frequency signals for noise removal at different scales.Nlm relies on structural self-similarity to locally smooth an image to remove noise and restore its main geometric structure, making this method appropriate for time-frequency signal denoising.Results the experimental results show that the proposed method can effectively suppress the high-frequency components of brain signals, resulting in a smoother brain signal waveform after denoising.The correlation coefficient of the reference signal, a superposition average of multiple trial signals, and the original single trial signal was determined, and then correlation coefficients were calculated between the reference signal and single trial signals processed by time-frequency denoising, ensemble empirical mode decomposition (eemd)-independent component analysis (ica), eemd-canonical correlation analysis (cca), and wavelet threshold denoising methods.The correlation coefficient was highest for the signal processed by the time-frequency denoising method and the reference signal, indicating that the single trial signal after time-frequency denoising was most similar to the waveform of the reference signal and suggesting this is a feasible strategy to effectively reduce noise and more accurately determine signals.Discussion the proposed time-frequency denoising method exhibits excellent performance with promising potential for practical application.

Journal: Frontiers in neuroscience (2022)
Publication types: Journal Article
Short and mid-term SARS-CoV-2 antibody response after inactivated COVID-19 vaccine in hemodialysis and kidney transplant patients.

The efficacy of the inactivated severe acute respiratory syndrome coronavirus 2 (sars-co v-2) vaccine has not been fully elucidated across the whole spectrum of patients on kidney replacement therapy.We aimed to characterize the long-term antibody response of inactivated sars-co v-2 vaccine administered in kidney transplant recipients (ktrs) and hemodialysis (hd) patients.We performed this prospective observational study in 50 hd, 64 ktr, and 41 healthy control groups (hg) given two doses of corona vac.We measured anti-spike antibodies after 28 days of every vaccine dose, 3rd and 6th months after the first dose, and compared them between cohorts.After two doses, an anti-spike immunoglobulin g of ≥50 au/ml was present in hd, ktr, and hg as 44%, 7.2%, and 58.5%, respectively (p < 0.001).Furthermore, the proportion of antibody titers peaked at 86.5%, 23%, and 97.6% (p < 0.001) at the 3rd month and decreased significantly at the 6th month in most hd and hg participants, whereas this effect was not observed in ktrs from basal until the 6th month (p < 0.001).During the follow-up, the incidence of coronavirus disease 2019 disease was higher (p < 0.003) in ktrs compared to the other groups, but there was no requirement for an intensive care unit and no death was recorded.We found a negative correlation between antibody seroconversion and age (p < 0.016).The antibody response following inactivated vaccine in dialysis patients is almost comparable to controls for 6 months.In contrast, kidney transplant patients have a poor response.These findings reinforce the need to discuss the vaccination strategy in immunocompromised patients, including the third dose with homologous or heterologous vaccines.

Journal: Journal of medical virology (2022)
Publication types: Journal Article;Observational Study;Research Support, Non-U.S. Gov't
In vivo and in vitro aging of common carp Cyprinus carpio sperm after multiple hormonal application and stripping of males.

The present study was designed to evaluate sperm phenotypic variables during in vivo and in vitro storage following multiple sperm stripping in common carp (cyprinus carpio l.).Each male was injected 3 times with carp pituitary 3 days apart.Sperm was stored in vivo in the body cavity for 0.5 days (fresh sperm) and 3 days (old sperm) after hormonal stimulation.Then sperm was collected and diluted with a carp extender at a ratio of 1:1, and stored in vitro on ice for 0, 3, and 6 days.The phenotypic parameters, including the number of total motile spermatozoa, number of fast motile spermatozoa, number of motile spermatozoa, percentage of fast motile spermatozoa, and percentage of spermatozoa motility were the major components of principal component analysis (pca).In general, fresh sperm from the first stripping showed slightly better quality than old sperm from the second and third stripping, especially in the phenotypic parameters of a number of total spermatozoa and a number of total motile spermatozoa (p < 0.05).The highest kinetic and quantitative spermatozoa variables were obtained in fresh and old sperm just after sperm collection (0-day storage in vitro), and then they were decreased during the period of in vitro storage up to 6 days (p < 0.05).However, the fertilization, hatching, and malformation rates from fresh sperm were similar compared with the old sperm.Sperm could be stripped 0.5 days post hormonal treatment and stored in vitro up to 6 days with good fertilization performance (fertility, hatching, and malformation rates were 92.5%, 91.5%, and 1.3%, respectively).Therefore, our results suggested that multiple hormonal treatments with multiple stripping could be used in artificial reproduction in common carp.

Journal: Fish physiology and biochemistry (2022)
Publication types: Journal Article
Revisiting the role ofAkkermansia muciniphilaas a therapeutic bacterium.

Despite a short history since its first isolation,akkermansia muciniphilahas been extensively studied in relation to its effects on human metabolism.A recent human intervention study also demonstrated that the bacterium is safe to use for therapeutic purposes.The best-known effects of a.Muciniphilain human health and disease relate to its ability to strengthen gut integrity, modulate insulin resistance, and protect the host from metabolic inflammation.A further molecular mechanism, induction of glp-1 secretion through icam-2 receptor, was recently discovered with the identification of a new bacterial protein produced by a.Muciniphila.However, other studies have suggested a detrimental role for a.Muciniphilain specific host immune settings.Here, we evaluate the molecular, mechanistic effects of a.Muciniphilain host health and suggest some of the missing links to be connected before the organism should be considered as a next-generation biotherapeutic agent.

Journal: Gut microbes (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The Effect of C/Si Ratio and Fluorine Doping on the Gas Permeation Properties of Pendant-Type and Bridged-Type Organosilica Membranes.

A series of pendant-type alkoxysilane structures with various carbon numbers (c1-c8) were used to fabricate sol-gel derived organosilica membranes to evaluate the effects of the c/si ratio and fluorine doping.Initially, this investigation was focused on the effect that carbon-linking (pendant-type) units exert on a microporous structure and how this affects the gas-permeation properties of pendant-type organosilica membranes.Gas permeation results were compared with those of bridged-type organosilica membranes (c1-c8).Network pore size evaluation was conducted based on the selectivity of h2/n2and the activation energy (ep) of h2permeation.Consequently,ep(h2) was increased as the c/si ratio increased from c1to c8, which could have been due to the aggregation of pendant side chains that occupied the available micropore channel space and resulted in the reduced pore size.By comparison, these permeation results indicate that pendant-type organosilica membranes showed a somewhat loose network structure in comparison with bridged-type organosilica membranes by following the lower values of activation energies (ep).Subsequently, we also evaluated the effect that fluorine doping (nh4f) exerts on pendant-type [methytriethoxysilane (mtes), propyltrimethoxysilane (ptms)] and bridged-type [1,2-bis(triethoxysilyl)methane (btesm) bis(triethoxysilyl)propane (btesp)] organosilica structures with similar carbon numbers (c1and c3).The gas-permeation properties of f-doped pendant network structures revealed values for pore size, h2/n2selectivity, and ep(h2) that were comparable to those of pristine organosilica membranes.This could be ascribed to the pendant side chains, which might have hindered the effectiveness of fluorine in pendant-type organosilica structures.The f-doped bridged-type organosilica (btesm and btesp) membranes, on the other hand, exhibited a looser network formation as the fluorine concentration increased.

Journal: Membranes (2022)
Publication types: Journal Article
Dual molecular diagnosis of tricho-rhino-phalangeal syndrome type I and Okur-Chung neurodevelopmental syndrome in one Chinese patient: a case report.

Okur-chung neurodevelopmental syndrome (ocnds) and tricho-rhino-phalangeal syndrome type i (trpsi) are rare mendelian diseases.Ocnds is caused by csnk2a1 gene variants and trpsi is caused by the trps1gene.However, to have two mendelian diseases in one patient is even rarer.Case presentation a 6-year-10-month-old boy characterized by special facial features, short stature and mental retardation was referred to our pediatric endocrinology department.Whole-exome sequencing (wes) was done to detect the molecular basis of his disease.This patient was confirmed to carry two variants in the csnk2a1 gene and one in the trps1 gene.The variant in the csnk2a1 gene was vertically transmitted from his father, and the variant in trps1 gene from his mother.These two variants are classified as pathogenic and the causes of the presentation in this child.This patient's father and mother have subsequently been diagnosed as having ocnds and trpsi respectively.Conclusion this is the first reported case of a dual molecular diagnosis of tricho-rhino-phalangeal syndrome type i and okur-chung neurodevelopmental syndrome in the same patient.This patient is the first published example of vertical transmission of this recurrent csn2a1 variant from parent to child.A novel variant in the trps1 gene that is pathogenic was also identified.In conclusion, identification of the variants in this patient expands the phenotypes and molecular basis of dual mendelian diseases.

Journal: BMC medical genetics (2020)
Publication types: Case Reports;Journal Article