syedzayyan/paper_mill_benchmark huggingface dataset:
Molecular biomarkers, network biomarkers, and dynamic network biomarkers for diagnosis and prediction of rare diseases.

The difficulty of converting scientific research findings into novel pharmacological treatments for rare and life-threatening diseases is enormous.Biomarkers related to multiple biological processes involved in cell growth, proliferation, and disease occurrence have been identified in recent years with the development of immunology, molecular biology, and genomics technologies.Biomarkers are capable of reflecting normal physiological processes, pathological processes, and the response to therapeutic intervention; as such, they play vital roles in disease diagnosis, prevention, drug response, and other aspects of biomedicine.The discovery of valuable biomarkers has become a focal point of current research.Numerous studies have identified molecular biomarkers based on the differential expression/concentration of molecules (e.g., genes/proteins) for disease state diagnosis, characterization, and treatment.Although technological breakthroughs in molecular analysis platforms have enabled the identification of a large number of candidate biomarkers for rare diseases, only a small number of these candidates have been properly validated for use in patient treatment.The traditional molecular biomarkers may lose vital information by ignoring molecular associations/interactions, and thus the concept of network biomarkers based on differential associations/correlations of molecule pairs has been established.This approach promises to be more stable and reliable in diagnosing disease states.Furthermore, the newly-emerged dynamic network biomarkers (dnbs) based on differential fluctuations/correlations of molecular groups are able to recognize pre-disease states or critical states instead of disease states, thereby achieving rare disease prediction or predictive/preventative medicine and providing deep insight into the dynamic characteristics of disease initiation and progression.

Journal: Fundamental research (2022)
Publication types: Journal Article;Review
The impact of genetic polymorphisms on weight regain after successful weight loss.

Obesity is associated with an increased risk of various diseases and mortality.Although nearly 50 % of adults have been reported trying to lose weight, the prevalence of obesity has increased.One factor that hinders weight loss-induced decrease in obesity prevalence is weight regain.Although behavioural, psychological and physiological factors associated with weight regain have been reviewed, the information regarding the relationship between weight regain and genetics has not been previously summarised.In this paper, we comprehensively review the association between genetic polymorphisms and weight regain in adults and children with obesity after weight loss.Based on this information, identification of genetic polymorphism in patients who undergo weight loss intervention might be used to estimate their risks of weight regain.Additionally, the genetic-based risk estimation may be used as a guide for physicians and dietitians to provide each of their patients with the most appropriate strategies for weight loss and weight maintenance.

Journal: The British journal of nutrition (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Cold-Responsive Regions of Paradigm Cold-Shock and Non-Cold-Shock mRNAs Responsible for Cold Shock Translational Bias.

In escherichia coli, the m rna transcribed from the main cold-shock genecsp ais a thermosensor, which at low temperature adopts a conformation particularly suitable for translation in the cold.Unlikecsp a, its paraloguecsp dis expressed only at 37 °c, is toxic so cannot be hyper-expressed in e.Coliand is poorly translated in vitro, especially at low temperature.In this work, chimeric m rnas consisting of different segments ofcsp aandcsp dwere constructed to determine if parts ofcsp acould confer cold-responsive properties to csp d to improve its expression.The activities of these chimeric m rnas in translation and in partial steps of translation initiation such as formation of 30s initiation complexes and 50s subunits docking to 30s complexes to yield 70s initiation complexes were analyzed.We show that the 5' untranslated region (5'utr) ofcsp am rna is sufficient to improve the translation ofcsp dm rna at 37 °c whereas both the 5'utr and the region immediately downstream thecsp am rna initiation triplet are essential for translation at low temperature.Furthermore, the translational apparatus of cold-stressed cells contains trans-active elements targeting both 5'utr and downstream regions ofcsp am rna, thereby improving translation of specific chimeric constructs at both 15 and 37 °c.

Journal: International journal of molecular sciences (2019)
Publication types: Journal Article
Re-appraising the role of flavonols, flavones and flavonones on osteoblasts and osteoclasts- A review on its molecular mode of action.

Bone disorders have become a global concern illustrated with decreased bone mineral density and disruption in microarchitecture of natural bone tissue organization.Natural compounds that promote bone health by augmenting osteoblast functions and suppressing osteoclast functions has gained much attention and offer greater therapeutic value compared to conventional therapies.Amongst several plant-based molecules, flavonoids act as a major combatant in promoting bone health through their multi-faceted biological activities such as antioxidant, anti-inflammatory, and osteogenic properties.They protect bone loss by regulating the signalling cascades involved in osteoblast and osteoclast functions.Flavonoids augment osteoblastogenesis and inhibits osteoclastogenesis through their modulation of various signalling pathways.This review discusses the role of various flavonoids and their molecular mechanisms involved in maintaining bone health by regulating osteoblast and osteoclast functions.

Journal: Chemico-biological interactions (2022)
Publication types: Journal Article;Review
The Strategies to Support the COVID-19 Vaccination with Evidence-Based Communication and Tackling Misinformation.

Covid-19 vaccinations are about to begin in various countries or are already ongoing.This is an unprecedented operation that is also met with a loud response from anti-vaccine communities-currently using all available channels to manipulate public opinion.At the same time, the strategy to educate on vaccinations, explain their mechanism of action, and build trust in science is subdued in different world parts.Such actions should go much beyond campaigns promoting the covid-19 vaccines solely on the information provided by the health institutions and national authorities.In this paper, actions provided by independent expert groups needed to counteract the anti-vaccine propaganda and provide scientific-based information to the general public are offered.These actions encompass organizing groups continuously communicating science on covid-19 vaccines to the general public; tracking and tackling emerging and circulating fake news; and equipping celebrities and politicians with scientific information to ensure the quality of messages they communicate, as well as public letters, and statements of support for vaccination by healthcare workers, recognized scientists, vips, and scientific societies; and no tolerance to false and manipulated claims on vaccination spread via traditional and social media as well as by health professionals, scientists, and academics.These activities should be promptly implemented worldwide, regardless of the current status and availability of the covid-19 vaccine in a particular region.If we are about to control the pandemic for the sake of public benefit, it is high time to collectively speak out as academic and medical societies with support from decision-makers.Otherwise, the battle will be lost to those who stand against scientific evidence while offering no feasible solution to the problem.

Journal: Vaccines (2021)
Publication types: Journal Article;Review
TP63 Is Significantly Upregulated in Diabetic Kidney.

The role of tumor protein 63 (tp63) in regulating insulin receptor substrate 1 (irs-1) and other downstream signal proteins in diabetes has not been characterized.Rnas extracted from kidneys of diabetic mice (db/db) were sequenced to identify genes that are involved in kidney complications.Rna sequence analysis showed more than 4- to 6-fold increases in tp63 expression in the diabetic mice's kidneys, compared to wild-type mice at age 10 and 12 months old.In addition, the kidneys from diabetic mice showed significant increases in tp63 m rna and protein expression compared to wt mice.Mouse proximal tubular cells exposed to high glucose (hg) for 48 h showed significant decreases in irs-1 expression and increases in tp63, compared to cells grown in normal glucose (ng).When tp63 was downregulated by si rna, significant increases in irs-1 and activation of amp-activated protein kinase (ampk (p-ampk-th172)) occurred under ng and hg conditions.Moreover, activation of ampk by pretreating the cells with aicar resulted in significant downregulation of tp63 and increased irs-1 expression.Ad-c dna-mediated over-expression of tuberin resulted in significantly decreased tp63 levels and upregulation of irs-1 expression.Furthermore, tp63 knockdown resulted in increased glucose uptake, whereas irs-1 knockdown resulted in a decrease in the glucose uptake.Altogether, animal and cell culture data showed a potential role of tp63 as a new candidate gene involved in regulating irs-1 that may be used as a new therapeutic target to prevent kidney complications in diabetes.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
RNA-induced initiation of transcriptional silencing (RITS) complex structure and function.

Heterochromatic regions of the genome are epigenetically regulated to maintain a heritable '"silent state"'.In fission yeast and other organisms, epigenetic silencing is guided by nascent transcripts, which are targeted by the rna interference pathway.The key effector complex of the rna interference pathway consists of small interfering rna molecules (si rnas) associated with argonaute, assembled into the rna-induced transcriptional silencing (rits) complex.This review focuses on our current understanding of how rits promotes heterochromatin formation, and in particular on the role of argonaute-containing complexes in many other functions such as quelling, release of rna polymerases, cellular quiescence and genome defense.

Journal: RNA biology (2019)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Review
The Use of Gas Chromatography Coupled with High-Resolution Mass Spectrometry-Based Untargeted Metabolomics to Discover Metabolic Changes and Help in the Determination of Complex Causes of Death: A Preliminary Study.

The determination of cause of death (cod) is one of the most important tasks in forensic practice and is mainly based on macroscopical and microscopical morphological signatures.However, some cods are hard to determine because the significant morphological signatures can be nonspecific, variable, subjective, or even absent in the real world.In this study, gas chromatography coupled with high-resolution mass spectrometry (gc-hrms)-based untargeted metabolomics was employed to obtain plasma metabolic profiles of rats that died from anaphylactic shock (as), mechanical asphyxia (ma), or sudden cardiac death (scd).The metabolic alterations of each cod group compared to the control group were investigated using a principal component analysis, partial least-squares discriminant analysis, the wilcoxon test, and fold change analysis.A range of differential features was screened, and 11, 8, and 7 differential metabolites were finally verified for the as, ma, and scd groups, respectively.We proposed some explanations that may account for these metabolic differences, including glucose metabolism, the tricarboxylic acid cycle, glycolysis, lipid metabolism, creatinine catabolism, and purine metabolism.Next, for each cod, we used its differential metabolites, which were obtained through comparisons of each cod group to the control group and represented the metabolic changes of the individual cod, to perform a receiver operating characteristic (roc) analysis to preliminarily evaluate their ability to discriminate each cod group from the other cod groups.We found that creatinine in the as group and malic acid and uric acid in the ma group might represent some specific metabolic changes for the relevant cod with high areas under the curve in the roc curve analysis.Moreover, the combination panel for as or ma also showed a good ability to discriminate it from the others.However, scd had fewer metabolic signatures and was relatively harder to discriminate from the other cods in our work.The preliminary study demonstrates the feasibility of gc-hrms-based untargeted metabolomics as a promising tool to reveal metabolic changes in different death processes and to determine the complex cods.

Journal: ACS omega (2021)
Publication types: Journal Article
Correcting spelling mistakes in Persian texts with rules and deep learning methods.

This study aims to develop a system for automatically correcting spelling errors in persian texts using two approaches: one that relies on rules and a common spelling mistake list and another that uses a deep neural network.The list of 700 common misspellings was compiled, and a database of 55,000 common persian words was used to identify spelling errors in the rule-based approach.112 rules were implemented for spelling correction, each providing suggested words for misspelled words.2500 sentences were used for evaluation, with the word with the shortest levenshtein distance selected for evaluation.In the deep learning approach, a deep encoder-decoder network that utilized long short-term memory (lstm) with a word embedding layer was used as the base network, with fast text chosen as the word embedding layer.The base network was enhanced by adding convolutional and capsule layers.A database of 1.2 million sentences was created, with 800,000 for training, 200,000 for testing, and 200,000 for evaluation.The results showed that the network's performance with capsule and convolutional layers was similar to that of the base network.The network performed well in evaluation, achieving accuracy, precision, recall, f-measure, and bilingual evaluation understudy (bleu) scores of 87%, 70%, 89%, 78%, and 84%, respectively.

Journal: Scientific reports (2023)
Publication types: Journal Article
Anterolateral upper cervical approach for ventral C1-C2 meningioma.

The surgical management of ventral upper cervical meningiomas poses significant challenges due to their deep location and limited accessibility.These tumors have the potential to compress or involve nearby neurovascular structures, leading to various neurological complications including inferior cranial nerve palsy, motor deficits, and sensory disturbances such as hypoesthesia, paresthesia, and impaired coordination.To address this issue, surgical intervention through an anterolateral or far lateral approach has been recognized as the optimal treatment strategy.In this video, the authors present a detailed demonstration of the operative technique using an anterolateral upper cervical approach to safely resect a ventrally located c1-2 meningioma.

Journal: Neurosurgical focus: Video (2023)
Publication types: Journal Article
Artificial Insemination as an Alternative Transmission Route for African Swine Fever Virus.

The rapid spread of the african swine fever virus (asfv), causing severe disease with often high fatality rates in eurasian suids, prevails as a threat for pig populations and dependent industries worldwide.Although advancing scientific progress continually enhances our understanding of asfv pathogenesis, alternative transmission routes for asfv have yet to be assessed.Here, we demonstrate that asfv can efficiently be transferred from infected boars to naïve recipient gilts through artificial insemination (ai).In modern pig production, semen from boar studs often supplies many sow herds.Thus, the infection of a boar stud presents the risk of rapidly and widely distributing asfv within or between countries.Daily blood and semen collection from four boars after intramuscular inoculation with asfv strain 'estonia 2014' resulted in the detection of asfv genomes in the semen as early as 2 dpi, in blood at 1 dpi while semen quality remained largely unaffected.Ultimately, after insemination with extended semen, 7 of 14 gilts were asfv positive by 7 days post insemination, and all gilts were asfv positive by 35 days post insemination.Twelve out of 13 pregnant gilts aborted or resorbed at the onset of fever.A proportion of fetuses originating from the remaining gilt showed both abnormalities and replication of asfv in fetal tissues.Thus, we present evidence for the efficient transmission of asfv to gilts via ai and also to implanted embryos.These results underline the critical role that boar semen could play in asfv transmission.

Journal: Pathogens (Basel, Switzerland) (2022)
Publication types: Journal Article
The Frequency and Form of Controls by HIIS over Primary Health Care Physicians in Slovenia.

The aim of this study was to evaluate the pattern of controls and sanctions by the health insurance institute (hiis) over primary healthcare practitioners (phcps) in slovenia, the reasons for sanctions and the violence against phcps if they followed the hiis rules.Materials and methods we performed analyses using survey data from a cross-sectional study, across public health centres and individual contractors in which 1,458 phcps were invited to answer a questionnaire anonymously via an online system used to collect data for the slovenian medical chamber and the association of general practice/family medicine of south-east europe.Quantitative data were presented by descriptive statistics and analysed using pearson's chisquared test.Results responses were obtained from 462 female and 138 male phcps.Of the total number of 600 participants, 430 were family medicine specialists.263 (43.8%) responded that they have been sanctioned for various reasons.Phcps that are more likely to be sanctioned include family medicine specialists and individual contractors.Phcps working in areas smaller than 20 000 inhabitants were sanctioned in a bigger proportion than their counterparts.Monetary penalties levied against those working at health centres were usually covered by the health centre.Family medicine specialists, more often than other phcps experienced violence from patients or patients' relatives if they followed hiis rules.Conclusion family medicine specialists are sanctioned more frequently than other phcps, individual contractors are sanctioned more frequently than public healthcare phcps and phcps in working area with a population less than 20.000 are more frequently sanctioned than those working in an area with a bigger population count.

Journal: Acta medica academica (2021)
Publication types: Journal Article
Apicobasal Surfaceome Architecture Encodes for Polarized Epithelial Functionality and Depends on Tumor Suppressor PTEN.

The loss of apicobasal polarity during the epithelial-to-mesenchymal transition (emt) is a hallmark of cancer and metastasis.The key feature of this polarity in epithelial cells is the subdivision of the plasma membrane into apical and basolateral domains, with each orchestrating specific intra- and extracellular functions.Epithelial transport and signaling capacities are thought to be determined largely by the quality, quantity, and nanoscale organization of proteins residing in these membrane domains, the apicobasal surfaceomes.Despite its implications for cancer, drug uptake, and infection, our current knowledge of how the polarized surfaceome is organized and maintained is limited.Here, we used chemoproteomic surfaceome scanning to establish proteotype maps of apicobasal surfaceomes and reveal quantitative distributions of, i.e., surface proteases, phosphatases, and tetraspanins as potential key regulators of polarized cell functionality.We show further that the tumor suppressor pten regulates polarized surfaceome architecture and uncover a potential role in collective cell migration.Our differential surfaceome analysis provides a molecular framework to elucidate polarized protein networks regulating epithelial functions and pten-associated cancer progression.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Sensory-motor response elicited by first time intraoral administered ethanol after trigeminal neuropathic injury.

Recent findings have shown a relationship between alcohol use disorders (aud) and chronic pain.Preclinical models have demonstrated that chronic pain, including trigeminal nerve injury, increases ethanol consumption throughout extended administration periods.Nevertheless, it remains unclear whether chronic pain induces a greater susceptibility to developing aud by altering motor control consumption regardless of the symptomatology of neuropathic pain, and whether sex influences this susceptibility.We used a former prolonged pain experience model induced by a constriction of the mental nerve (m nc) to answer this question.We analyzed ethanol consumption in a short-access protocol to reduce the post-ingestional effects and compared licking microstructure between groups.The constriction of the mental nerve induced evoked and spontaneous pain and reduction in the hedonic value of sucrose.The differences in alcohol consumption were not reflective of the former prolonged pain experience.Female mice showed a more efficient dynamic of consumption of alcohol, reflected in a long burst of licking and a less variable licking rate within a cluster.

Journal: Alcohol (Fayetteville, N.Y.) (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Effects of dioxins on animal spermatogenesis: A state-of-the-art review.

The male reproductive system is especially affected by dioxins, a group of persistent environmental pollutants, resulting in irreversible abnormalities including effects on sexual function and fertility in adult males and possibly on the development of male offspring.The reproductive toxicity caused by dioxins is mostly mediated by an aryl hydrocarbon receptor (ah r).In animals, spermatogenesis is a highly sensitive and dynamic process that includes proliferation and maturation of germ cells.Spermatogenesis is subject to multiple endogenous and exogenous regulatory factors, including a wide range of environmental toxicants such as dioxins.This review discusses the toxicological effects of dioxins on spermatogenesis and their relevance to male infertility.After a detailed categorization of the environmental contaminants affecting the spermatogenesis, the exposure pathways and bioavailability of dioxins in animals was briefly reviewed.The effects of dioxins on spermatogenesis are then outlined in detail.The endocrine-disrupting effects of dioxins in animals and humans are discussed with a particular focus on their effects on the expression of spermatogenesis-related genes.Finally, the impacts of dioxins on the ratio of x and y chromosomes, the status of serum sex hormones, the quality and fertility of sperm, and the transgenerational effects of dioxins on male reproduction are reviewed.

Journal: Frontiers in reproductive health (2022)
Publication types: Journal Article;Review