syedzayyan/paper_mill_benchmark huggingface dataset:
Gastric alarmin release: A warning signal in the development of gastric mucosal diseases.

Alarmins exist outside cells and are early warning signals to the immune system; as such, alarmin receptors are widely distributed on various immune cells.Alarmins, proinflammatory molecular patterns associated with tissue damage, are usually released into the extracellular space, where they induce immune responses and participate in the damage and repair processes of mucosal diseases.in the stomach, gastric alarmin release has been shown to be involved in gastric mucosal inflammation, antibacterial defense, adaptive immunity, and wound healing; moreover, this release causes damage and results in the development of gastric mucosal diseases, including various types of gastritis, ulcers, and gastric cancer.Therefore, it is necessary to understand the role of alarmins in gastric mucosal diseases.This review focuses on the contribution of alarmins, including il33, hmgb1, defensins and cathelicidins, to the gastric mucosal barrier and their role in gastric mucosal diseases.Here, we offer a new perspective on the prevention and treatment of gastric mucosal diseases.

Journal: Frontiers in immunology (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
A Systems-Based Key Innovation-Driven Approach Infers Co-option of Jaw Developmental Programs During Cancer Progression.

Cancer acquires metastatic potential and evolves via co-opting gene regulatory networks (grn) of embryonic development and tissue homeostasis.Such grns are encoded in the genome and frequently conserved among species.Considering that all metazoa have evolved from a common ancestor via major macroevolutionary events which shaped those grns and increased morphogenetic complexity, we sought to examine whether there are any key innovations that may be consistently and deterministically linked with metastatic potential across the metazoa clades.To address tumor evolution relative to organismal evolution, we revisited and retrospectively juxtaposed seminal laboratory and field cancer studies across taxa that lie on the evolutionary lineage from cnidaria to humans.We subsequently applied bioinformatics to integrate species-specific cancer phenotypes, multiomics data from up to 42 human cancer types, developmental phenotypes of knockout mice, and molecular phylogenetics.We found that the phenotypic manifestations of metastasis appear to coincide with agnatha-to-gnathostome transition.Genes indispensable for jaw development, a key innovation of gnathostomes, undergo mutations or methylation alterations, are aberrantly transcribed during tumor progression and are causatively associated with invasion and metastasis.There is a preference for deregulation of gnathostome-specific versus pre-gnathostome genes occupying hubs of the jaw development network.According to these data, we propose our systems-based model as anin silicotool the prediction of likely tumor evolutionary trajectories and therapeutic targets for metastasis prevention, on the rationale that the same genes which are essential for key innovations that catalyzed vertebrate evolution, such as jaws, are also important for tumor evolution.

Journal: Frontiers in cell and developmental biology (2021)
Publication types: Journal Article
Second-line palliative chemotherapy, survival, and prognostic factors in patients with advanced pancreatic cancer.

Introduction pancreatic cancer is a highly lethal disease with a close association between incidence and mortality.First-line (fl) palliative chemotherapy prolongs survival and alleviates cancer-related symptoms.However, the survival benefit of second-line (sl) treatment is uncertain, as studies fail to consistently show prolonged survival for any given sl treatment, and in the absence of prognostic factors patients will receive a futile treatment.The aim of this study was to examine prognostic factors and survival in patients with pancreatic cancer, with special reference to sl therapy.Material and methods this retrospective study included all patients with histopathologically verified pancreatic adenocarcinoma who received palliative chemotherapy at skåne university hospital and died between 1 feb 2015 and 31 dec 2017.Results during the study period, a total of 170 patients with pancreatic cancer died after receiving palliative chemotherapy.Of these, 72 had received sl treatment after progression on fl treatment.Median overall survival (os) from the start of sl treatment was 5.0 months (95% ci: 4.0-6.1).Median os was 2.9 months for patients with performance status 2 at start of sl treatment compared to 5.3 months for patients with performance status 0-1 (p= .03), and 3.5 months (95% ci: 3.0-5.4) in patients with hypoalbuminemia (<36 g/l) at the start of sl therapy compared to 8.0 months (95% ci: 5.3-11.1) for patients with normal albumin levels (p= .009).Weight loss during fl therapy, a doubling of ca 19-9 after fl therapy, and length of progression-free survival during fl treatment were not associated with survival following sl therapy.Conclusion poor performance status and hypoalbuminemia are negative prognostic factors for survival on sl palliative treatment in patients with advanced pancreatic cancer.Possible gain in survival should be carefully considered before initiating sl chemotherapy.

Journal: Acta oncologica (Stockholm, Sweden) (2021)
Publication types: Journal Article
Emotion Processing Dysfunction in Alzheimer's Disease: An Overview of Behavioral Findings, Systems Neural Correlates, and Underlying Neural Biology.

We described behavioral studies to highlight emotional processing deficits in alzheimer's disease (ad).The findings suggest prominent deficit in recognizing negative emotions, pronounced effect of positive emotion on enhancing memory, and a critical role of cognitive deficits in manifesting emotional processing dysfunction in ad.We reviewed imaging studies to highlight morphometric and functional markers of hippocampal circuit dysfunction in emotional processing deficits.Despite amygdala reactivity to emotional stimuli, hippocampal dysfunction conduces to deficits in emotional memory.Finally, the reviewed studies implicating major neurotransmitter systems in anxiety and depression in ad supported altered cholinergic and noradrenergic signaling in ad emotional disorders.Overall, the studies showed altered emotions early in the course of illness and suggest the need of multimodal imaging for further investigations.Particularly, longitudinal studies with multiple behavioral paradigms translatable between preclinical and clinical models would provide data to elucidate the time course and underlying neurobiology of emotion processing dysfunction in ad.

Journal: American journal of Alzheimer's disease and other dementias (2022)
Publication types: Journal Article;Review
Dietary β-conglycinin prevents acute ethanol-induced fatty liver in mice.

Alcoholic fatty liver is the earliest stage of alcohol-induced liver disease leading to liver cirrhosis.Β-conglycinin, one of the soy proteins, is known to prevent non-alcoholic fatty liver, hyperlipidemia and obesity.Therefore, we examined whether β-conglycinin feeding has an effect on the prevention of acute ethanol-induced fatty liver in mice.Male c57bl/6j mice were fed with 20 energy% β-conglycinin or casein for 4 weeks prior to ethanol administration and were then given ethanol or glucose, as a control, by gavage.Ethanol significantly increased liver triglyceride (tg) in mice fed casein due to the activation of peroxisome proliferator-activated receptor (ppar) γ2, a nuclear transcription factor known for regulating lipid metabolism and de novo lipogenesis.The liver tg of ethanol-administered β-conglycinin-fed mice was significantly lower than that in those fed casein, although ethanol increased the amount of liver tg in mice fed β-conglycinin.The increased levels of pparγ2 protein and its target gene cd36 in response to an ethanol were not observed in mice fed β-conglycinin.Moreover, β-conglycinin decreased the basal expression of de novo lipogenesis-related genes such as stearoyl-co a desaturase-1, and therefore, the expressions of these genes were lower in the ethanol-administered β-conglycinin-fed mice than in the casein-fed mice.In conclusion, β-conglycinin supplementation appears to prevent the development of fatty liver in mice caused by ethanol consumption via the suppression of alcohol-induced activation of pparγ2 and the downregulation of the basal expression of de novo lipogenesis.

Journal: Biochemical and biophysical research communications (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Correlating clinical and laboratory diagnostic modalities in the diagnosis of epidermolysis bullosa in a resource-poor setting.

Mutational analysis and immunofluorescence antigen mapping (ifm) are recommended as the laboratory tools of choice for diagnosing eb.In the past, transmission electron microscopy (tem) was considered the gold standard, and more recently, clinical diagnostic matrix (cdm) has shown good concordance with next-generation sequencing (ngs).Methods in this prospective diagnostic study, a skin biopsy was taken for tem and ifm in consecutive patients with eb (aged >6 months) diagnosed clinically with cdm.Wherever possible, mutational analysis was done using targeted ngs.Results of the 80 patients diagnosed with cdm, skin biopsy specimens of 42 patients were assessed using tem, and of 59 patients using ifm.Ngs was done in 39 patients.Taking ngs as the gold standard for diagnosing eb (n = 39 patients), the concordance with cdm, tem, and ifm were estimated at 84.6% (33/39), 78.5% (11/14), and 76% (19/25) respectively.Cdm showed a substantial agreement with ngs (k = 0.69, p < 0.001).Conclusions in comparison to ngs, the highest concordance was seen with cdm followed by tem and ifm in diagnosing major subtypes of eb.

Journal: Journal of cutaneous pathology (2022)
Publication types: Journal Article
Polymorphism of Type I-F CRISPR/Cas system in Escherichia coli of phylogenetic group B2 and its application in genotyping.

E.Coli of phylogenetic group b2 is responsible for many extraintestinal infections, posing a great threat to health.The relatively polymorphic nature of crispr in phylogenetically related e.Coli strains makes them potential markers for bacterial typing and evolutionary studies.In the current work, we investigated the occurrence and diversity of crispr/cas system and explored its potential for genotyping.Type i-f crispr/cas systems were found in 413 of 1190 strains of e.Coli and exhibited the clustering within certain ccs and sts.And crispr spacer contents correlated well with mlst types.The divergence analysis of crispr showed stronger discriminatory power than mlst, and crispr polymorphism was instrumental for differentiating highly closely related strains.The timeline of spacer acquisition and deletion provided important information for inferring the evolution model between distinct serotypes.Identical spacer sequences were shared by strains with the same h-antigen type but not strains with the same o-antigen type.The homology between spacers and antibiotic-resistant plasmids demonstrated the role of type i-f system in limiting the acquisition of antimicrobial resistance.Collectively, our data presents the dynamic nature of type i-f crispr in e.Coli of phylogenetic group b2 and provides new insights into the application of crispr-based typing in the species.

Journal: Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases (2019)
Publication types: Comparative Study;Journal Article;Research Support, Non-U.S. Gov't
Preservation solutions for attenuation of ischemia-reperfusion injury in vascularized composite allotransplantation.

Vascularized composite allotransplantation represents the final level of the reconstructive ladder, offering treatment options for severe tissue loss and functional deficiencies.Vascularized composite allotransplantation is particularly susceptible to ischemia-reperfusion injury and requires preservation techniques when subjected to extended storage times prior to transplantation.While static cold storage functions to reduce ischemic damage and is widely employed in clinical settings, there exists no consensus on the ideal preservation solution for vascularized composite allotransplantation.This review aims to highlight current clinical and experimental advances in preservation solution development and their critical role in attenuating ischemia-reperfusion injury in the context of vascularized composite allotransplantation.

Journal: SAGE open medicine (2021)
Publication types: Journal Article
De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection.

The adaptive immune system recognizes tumor antigens at an early stage to eradicate cancer cells.This process is accompanied by systemic proliferation of the tumor antigen-specific t lymphocytes.While detection of asymptomatic early-stage cancers is challenging due to small tumor size and limited somatic alterations, tracking peripheral t cell repertoire changes may provide an attractive solution to cancer diagnosis.Here, we developed a deep learning method called deep cat to enable de novo prediction of cancer-associated t cell receptors (tcrs).We validated deep cat using cancer-specific or non-cancer tcrs obtained from multiple major histocompatibility complex i (mhc-i) multimer-sorting experiments and demonstrated its prediction power for tcrs specific to cancer antigens.We blindly applied deep cat to distinguish over 250 patients with cancer from over 600 healthy individuals using blood tcr sequences and observed high prediction accuracy, with area under the curve (auc) ≥ 0.95 for multiple early-stage cancers.This work sets the stage for using the peripheral blood tcr repertoire for noninvasive cancer detection.

Journal: Science translational medicine (2020)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Malignant metastatic steroid cell tumor NOS: A rare presentation of a subtype of sex cord stromal tumor.

Steroid cell tumors - not otherwise specified (nos) - are rare sex cord stromal tumors that lack characteristic histology, are benign, and usually present with androgenic manifestations.Metastatic malignant steroid cell tumors pose treatment challenges due to their chemoresistance nature.This is a case report of a metastatic steroid cell tumor - nos with extensive peritoneal disease.

Journal: Gynecologic oncology reports (2023)
Publication types: Journal Article
Neuropsychological and neuropsychiatric recovery from mild traumatic brain injury.

Of review mild traumatic brain injury (m tbi) is a significant public health concern for children.This review summarizes recent literature on early symptoms and neuropsychiatric and neuropsychological outcomes following pediatric m tbi and highlights factors that predict prolonged recovery.Evidence-based recommendations for assessment and treatment are also discussed.Recent findings whereas most children recover within 1 month after m tbi, 10-30% of children experience lingering neuropsychiatric or neuropsychological symptoms 3 months or more after injury.For the subset who experience prolonged recovery, new or worsening emotional and behavioral symptoms are the most frequent concerns.Recent research has suggested that specific factors, including preinjury mental health concerns, female sex, and family characteristics, are associated with increased risk of experiencing prolonged recovery.Early management includes reassurance, brief rest (1-3 days), and gradual return to typical activities.When symptoms linger for more than 4 weeks, evaluation in a specialty clinic is recommended and multimodal therapies are considered.Active recovery models, which include gradual return to aerobic exercise and cognitive behavioral approaches, are promising for the management of prolonged symptoms.Summary a minority of children with m tbi experience prolonged neuropsychiatric or neuropsychological concerns.While our understanding of pediatric m tbi is growing, and recommendations for assessment and management have been developed, many gaps remain.

Journal: Current opinion in psychiatry (2022)
Publication types: Journal Article;Review
Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol.

Multiple primary tumor (mpt) is a special and rare cancer type, defined as more than two primary tumors presenting at the diagnosis in a single patient.The molecular characteristics and tumorigenesis of mpt remain unclear due to insufficient approaches.Here, we present mptevol, a practical computational framework for comprehensively exploring the mpt from multiregion sequencing (mrs) experiments.To verify the utility of mptevol, we performed whole-exome mrs for 33 samples of a rare patient with triple-primary tumors and three metastatic sites and systematically investigated clonal dynamics and metastatic routines.Mptevol assists in comparing genomic profiles across samples, detecting clonal evolutionary history and metastatic routines and quantifying the metastatic history.All triple-primary tumors were independent origins and their genomic characteristics were consistent with corresponding sporadic tumors, strongly supporting their independent tumorigenesis.We further showed two independent early monoclonal seeding events for the metastases in the ovary and uterus.We revealed that two ovarian metastases were disseminated from the same subclone of the primary tumor through undergoing whole-genome doubling processes, suggesting metastases-to-metastases seeding occurred when tumors had similar microenvironments.Surprisingly, according to the metastasis timing model of mptevol, we found that primary tumors of about 0.058-0.124 cm diameter have been disseminating to distant organs, which is much earlier than conventional clinical views.We developed mpt-specialized analysis framework mptevol and demonstrated its utility in explicitly resolving clonal evolutionary history and metastatic seeding routines with a rare mpt case.Mptevol is implemented in r and is available at under the gpl v3 license.

Journal: Briefings in bioinformatics (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Association Among Geriatric Nutritional Risk Index and Functional Prognosis in Elderly Patients with Osteoporotic Vertebral Compression Fractures.

Osteoporotic vertebral compression fractures (ovcf) are common among the elderly, and malnutrition has also been identified as a poor prognostic factor in elderly patients with fractures.However, the relationship between nutrition status and functional prognosis in ovcf is unclear.The aim of this study was to investigate the association between nutritional status using geriatric nutritional risk index (gnri), activities of daily living (adl), and fall after fracture in patients with ovcf.Methods the clinical information of 187 conservatively treated ovcf patients was retrospectively examined.This information included: age, sex, body mass index, total number of drugs used for treatment at admission, bone mineral density, use of drugs for osteoporosis, fracture type, comorbidity severity, nutritional status, barthel index (bi), and fall after ovcf.Subjects were divided into two groups according to their gnri.Propensity score matching was used to confirm factors affecting bi and falls after ovcf.Results sixty-eight patients (36.4%) presented with malnutrition at fracture.According to multiple linear regression analysis, gnri positively affected bi gain (β= 0.283, 95% confidence interval [ci] - 122.2 to - 0.706,p= 0.001).Furthermore, on logistic regression analysis, fall after ovcf was associated with gnri (odds ratio = 0.896, 95% ci 0.832-0.964,p= 0.003).Conclusions malnutrition in elderly ovcf patients decreases the acquisition of adl and increases fall risk.Improvement of nutritional status during ovcf treatment may lead to improvement of adl and prevention of falls.

Journal: Indian journal of orthopaedics (2022)
Publication types: Journal Article
Biological denitrification potential as an indicator for measuring digestate stability.

Biological stability is an essential parameter for assessing the environmental impact from the land application of digestate as organic amendment.In this paper, a new indicator, biological denitrification potential (bdp), was developed for evaluating the biological stability of digestate.Digestate samples collected along the digestion process from a mesophilic anaerobic batch digester fed with food waste were investigated under different solid retention time.The value of bdp based on nitrate removal ranged from 176.3 to 48.3 mg-n/g-vsdigestate, corresponding well to the digestion time, and strongly correlated with total organic carbon content.Evolution trends similar to respiration index (ri) and biochemical methane potential (bmp) can be also observed for bdp, indicating that values presented of these stability indices decreased with the degree of digestate stabilization.The mass balance of the bdp process indicated that nitrate was mainly converted into n2gas with mineralizing organic carbon from digestate, implying that biostability evaluated by bdp depends on carbon source and denitrification activity in digestate.The denitrifying bacteria thiopseudomonas and pseudomonas accounted for the majority of microorganisms.These findings of this study concluded that bdp can be an efficient indicator to assess the bio-stability of digestate planned for agricultural or land use.Compared with the existing biostability index, bdp has the additional advantage of no exogenous inoculum addition, homogenous test condition and possibility of shortening incubation time.

Journal: The Science of the total environment (2021)
Publication types: Journal Article
Ecotoxicity of two organic UV-filters to the freshwater caddisfly Sericostoma vittatum.

Organic ultraviolet filters (uv-filters) used for protection against radiation in personal care products and other materials (e.g.Textiles, plastic products) are considered emerging contaminants of aquatic ecosystem.Benzophenone-3 (bp3) and 3-(4-methylbenzylidene)camphor (4-mbc) are the most commonly used organic uv-filters and have been reported in freshwater environments due to contamination through discharges from wastewater treatment plants and swimming pools or by direct contamination from recreational activities.Our aim was to evaluate the ecotoxicological effects of these uv-filters using the freshwater caddisfly sericostoma vittatum' biochemical biomarkers and energy processing related endpoints (feeding behaviour, energy reserves and cellular metabolism).In laboratory trials, both compounds induced feeding inhibition of s.Vittatum at 3.55 mg/kg of bp3 and at concentrations ≥2.57 mg/kg of 4-mbc, decreased carbohydrates content at 3.55 and 6.95 mg/kg of bp3 and 4-mbc respectively, and increased total glutathione levels at concentrations ≥1.45 and 1.35 mg/kg of bp3 and 4-mbc respectively.No significant effects were observed on endpoints associated with oxidative stress, antioxidant defences, phase ii biotransformation or neurotoxicity after exposure to the two uv-filters.Our results show that environmental relevant concentrations of bp3 and 4-mbc, can negatively impact freshwater insects and demonstrate the importance of monitoring the ecological effects of organic uv-filters using non-model invertebrate species.

Journal: Environmental pollution (Barking, Essex : 1987) (2017)
Publication types: Journal Article