syedzayyan/paper_mill_benchmark huggingface dataset:
Deep Learning-Aided Automated Pneumonia Detection and Classification Using CXR Scans.

The covid-19 pandemic has caused a worldwide catastrophe and widespread devastation that reeled almost all countries.The pandemic has mounted pressure on the existing healthcare system and caused panic and desperation.The gold testing standard for covid-19 detection, reverse transcription-polymerase chain reaction (rt-pcr), has shown its limitations with 70% accuracy, contributing to the incorrect diagnosis that exaggerated the complexities and increased the fatalities.The new variations further pose unseen challenges in terms of their diagnosis and subsequent treatment.The covid-19 virus heavily impacts the lungs and fills the air sacs with fluid causing pneumonia.Thus, chest x-ray inspection is a viable option if the inspection detects covid-19-induced pneumonia, hence confirming the exposure of covid-19.Artificial intelligence and machine learning techniques are capable of examining chest x-rays in order to detect patterns that can confirm the presence of covid-19-induced pneumonia.This research used cnn and deep learning techniques to detect covid-19-induced pneumonia from chest x-rays.Transfer learning with fine-tuning ensures that the proposed work successfully classifies covid-19-induced pneumonia, regular pneumonia, and normal conditions.Xception, visual geometry group 16, and visual geometry group 19 are used to realize transfer learning.The experimental results were promising in terms of precision, recall, f1 score, specificity, false omission rate, false negative rate, false positive rate, and false discovery rate with a covid-19-induced pneumonia detection accuracy of 98%.Experimental results also revealed that the proposed work has not only correctly identified covid-19 exposure but also made a distinction between covid-19-induced pneumonia and regular pneumonia, as the latter is a very common disease, while covid-19 is more lethal.These results mitigated the concern and overlap in the diagnosis of covid-19-induced pneumonia and regular pneumonia.With further integrations, it can be employed as a potential standard model in differentiating the various lung-related infections, including covid-19.

Journal: Computational intelligence and neuroscience (2022)
Publication types: Journal Article
Synergistic efficacy of homoharringtonine and venetoclax on acute myeloid leukemia cells and the underlying mechanisms.

To evaluate whether homoharringtonine (hht) combined with venetoclax could produce a synergistic anti-acute myeloid leukemia (aml) effect and determine the underlying mechanisms.Methods the effect of hht and venetoclax combination on cell viability, apoptosis, and mitochondrial membrane potential was investigatedin vitrousing aml cell lines and primary cells.High-throughput m rna sequencing was used to analyze m rna level changes after the application of hht and venetoclax on oci-aml3 cells.Western blotting was used to verify the changes in protein expression within the mitogen-activated protein kinases/extracellular signal-regulated kinase (mapk/erk), phosphatidylinositiol 3-kinase (pi3k)/akt and p53 pathway.The efficacy of hht and venetoclaxin vivoand their effects on survival time were evaluated in a xenograft model established in severe immunodeficiency (nod/scid) mice.Results venetoclax and hht synergistically inhibited the proliferation of aml cells, decreased the mitochondrial membrane potential, and promoted aml cell apoptosis in a time- and concentration-dependent manner.Venetoclax combined with hht increased the expression of the caspase-3, poly (adp-ribose) polymerase (parp), and γh2ax proteins.Hht enhanced the proapoptotic effect of venetoclax by reducing the expression of myeloid cell leukemia sequence 1 (mcl-1).Hht arrested aml cells in g1 phase of the cell cycle.Hht enhanced the proapoptotic effect of venetoclax by inhibiting the activation of the mapk/erk and pi3k/akt pathways and activating the p53 pathway.in vivoexperiments confirmed that the combination of hht and venetoclax could inhibit the growth of tumors in aml xenotransplanted mice and prolong the survival time of tumor-bearing mice.Conclusions hht combined with venetoclax synergistically promoted apoptosis in aml cell lines and primary cells by inhibiting the activation of the mapk/erk and pi3k/akt pathways and activating the p53 pathway.

Journal: Annals of translational medicine (2022)
Publication types: Journal Article
Melatonin as a Smart Protector of Pregnancy in Dairy Cows.

The experimental objective was to examine the role of melatonin and its pathways in the maintenance of pregnancy in lactating dairy cows.Blood samples were collected at days 0, 16 and 32 after timed ai from cows (n = 200) in order to consider plasma melatonin concentrations and to conduct aopp (advanced oxidation products of proteins) and tbars (thiobarbituric acid reactive substances) tests.Luminal endometrial cells were collected at day 16 using a cytobrush in all cows to determine m rna expressions of melatonin receptor 1 (mt1), mouse double minute 2 (mdm2), mdm2 binding protein (mtbp),bcl2-associated x, apoptosis regulator (bax), p53 upregulated modulator of apoptosis (puma, gene symbol bbc3), mucin 1 (muc1) and leukemia inhibitory factor (lif).Plasma concentrations of melatonin were significantly greater in pregnant cows diagnosed pregnant at day 16 who sustained pregnancy to day 32 compared to nonpregnant cows at day 16, or pregnant at day 16 and who lost embryos by days 32.Concentrations of aopp and tbars were greater in nonpregnant cows at day 16 or pregnant at day 16 and who lost embryos by days 32 compared to those diagnosed pregnant at day 16 and who sustained pregnancy to day 32.In pregnant cows, endometrial m rna expressions of mdm2,mtbp,mtr1and lifwere higher compared to pregnant-embryo-loss cows (p< 0.05).In contrast, m rna expressions of bbc3and muc1were greater at day 16 in pregnant-embryo-loss cows compared to pregnant cows (p< 0.05).In conclusion, melatonin status is a modulator of embryo well-being and maintenance of pregnancy in lactating dairy cows.

Journal: Antioxidants (Basel, Switzerland) (2022)
Publication types: Journal Article
Machine learning approaches to explore digenic inheritance.

Some rare genetic disorders, such as retinitis pigmentosa or alport syndrome, are caused by the co-inheritance of dna variants at two different genetic loci (digenic inheritance).To capture the effects of these disease-causing variants and their possible interactive effects, various statistical methods have been developed in human genetics.Analogous developments have taken place in the field of machine learning, particularly for the field that is now called big data.In the past, these two areas have grown independently and have started to converge only in recent years.We discuss an overview of each of the two fields, paying special attention to machine learning methods for uncovering the combined effects of pairs of variants on human disease.

Journal: Trends in genetics : TIG (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Urachal mucinous cystic tumor of low malignant potential in a polymorbid female: a case report and review of the literature.

Neoplasms of the urachus are exceedingly rare, representing 0.17% of all bladder cancers.The mucinous cystic tumor of low malignant potential (mctlmp) subtype is particularly rare with just 25 previous cases reported in the literature.Although rare, mctlmps are important to identify due to potential devastating complications and good cure rates with surgical removal.We present a 43 year old female with a nuanced constellation of comorbidities and confirmed mctlmp following a workup for abdominal pain and irritative lower urinary tract symptoms.Notably, this tumor did not change in size over a 3-year course of serial imaging prior to surgical excision.This urachal mctlmp represents roughly the 26th and one of the smallest of its subtype reported in the literature.This case illustrates the diagnosis and management of this rare urachal mctlmp.Individual patient medical history, clinical considerations, and neoplasm characteristics are examined.Although rare, the potential for increased malignancy and potential complications necessitates surgical management and further investigation by the academic community.

Journal: International cancer conference journal (2022)
Publication types: Case Reports;Journal Article
An Unusual Presentation of Extramedullary Relapse Following Blinatumomab in Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia.

In adult patients, extramedullary relapse (emr) in b-acute lymphoblastic leukemia (b-all) has a pejorative prognosis, especially after allogeneic hematopoietic stem cell transplantation (allo-hsct).Blinatumomab, a bispecific cd3/cd19 antibody, is approved for relapsed/refractory acute lymphoblastic leukemia (all) and has proven its efficacy with good complete response (cr) rates and molecular responses in several trials.Unusual sites of relapse following treatment with blinatumomab for all are rarely reported.We describe the case of a 23-year-old male with b-all characterized as philadelphia chromosome-positive without extramedullary lesions at diagnosis.He benefited from a matched-related donor allo-hsct at first remission.A relapse in the bone marrow and central nervous system was diagnosed four months later.A treatment with blinatumomab was initiated with the obtention of cr after one cycle.During the third cycle of blinatumomab, multiple sites of emr occurred initially with a painless swelling appearing in the areolas and the nipples, followed by bilateral testicular hypertrophy and moderate paraplegia.A diagnosis of leukemic infiltration on the areola-nipple complex was made by cytological analysis of the fine-needle aspiration of the left areola.The analysis of bone marrow was normal, but molecular bcr-abl was positive.Systemic chemotherapy with hyper-cvad (cyclophosphamide, vincristine, doxorubicin, and dexamethasone) and cycles of blinatumomab with nilotinib was initiated in association with intrathecal chemotherapy and whole-brain radiation therapy.Clinical, molecular, and central nervous remissions were obtained.We report this case to describe multiple sites of emr of b-all with atypical breast infiltration in an adult male patient following treatment with blinatumomab.

Journal: Cureus (2022)
Publication types: Case Reports;Journal Article
The relationships between the gut microbiota and its metabolites with thyroid diseases.

Emerging studies have provided a preliminary understanding of the thyroid-gut axis, indicating that intestinal microbiota and its metabolites may act directly or indirectly on the thyroid by influencing intestinal microelements uptake, iodothyronine conversion and storage, and immune regulation, providing new insights into the pathogenesis of thyroid disorders and clinical management strategies.However, the research on gut microbiota and thyroid has only presented the tip of the iceberg.More robust clinical data and basic experiments are still required to elucidate the specific relationships and mechanisms in the future.Here we will characterize the associations between the microbiota and thyroid diseases to evaluate their potential implications in the pathophysiology and open up scientific avenues for future precision studies of the thyroid-gut axis.

Journal: Frontiers in endocrinology (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't
Suicide Typologies in the United States Air Force: A Hierarchical Cluster Analysis.

This study describes characteristics of united states air force (usaf) suicide decedents and determines subgroups.Method retrospective review of demographic, psychiatric, event-related, and psychosocial variables for usaf suicide decedents in the suicide event surveillance system database was conducted between february 1999 and july 2009 (n = 376).Hierarchical cluster analysis was used to determine initial clusters and cluster centroids.Results analyses identified three clusters.Cluster 1 (n = 149) individuals were mostly single or divorced, e-1-e-6 rank, living alone, and less likely to have psychiatric disorder diagnoses or engage with most helping resources.Cluster 2 (n = 126) decedents were mostly married, living with a partner, higher ranking, and least likely to communicate suicide intent.Cluster 3 (n = 101) individuals were mostly e-4-e-6 rank, with the highest rates of most psychiatric diagnoses, previous suicide-related events, engagement with multiple helping resources, communication of intent, and psychosocial precipitants.Clusters differed significantly in marital status, rank, psychiatric diagnoses, precipitants, service utilization, previous suicide-related events, risk factors, communication of intent, location and method of death, and residential status.Conclusions this study identifies empirically based suicide typologies within a military decedent sample.While further research and replications of findings are needed, these typologies have clinical and policy implications for military suicide prevention.

Journal: Suicide & life-threatening behavior (2019)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.
Effects of CDKN2B-AS1 on cellular proliferation, invasion and AKT3 expression are attenuated by miR-424-5p in a model of ovarian endometriosis.

Research question endometriosis is a common and complicated gynaecologic disease.Long non-coding rna cdkn2b-as1 plays a crucial role in the development and progression of several cancers.Whether cdkn2b-as1 contributes to endometriosis, however, remains unknown.Design cellular proliferation, invasion and dna synthesis abilities were assessed by cck8, transwell and 5-ethynyle-2'-deoxyuridine assays.The expression of epithelial-mesenchymal transition markers and three isoforms of akt was detected using western blot.Real-time polymerase chain reaction was used to determine the relative expression levels of cdkn2b-as1 and candidate mi rnas in ectopic, eutopic endometria and normal endometrial tissues.The relationship between cdkn2b-as1 and mi rna was determined by luciferase reporter assays.Results the relative expression level of cdkn2b-as1 was up-regulated in eutopic and ectopic endometria.In endometrial stromal cells and ishikawa cells, cdkn2b-as1 overexpression promoted cellular proliferation and invasion, and increased the protein expression of vimentin but decreased the expression of e-cadherin.Mi r-424-5p was confirmed the target of cdkn2b-as1 through bioinformatics tools and luciferase reporter assays.In addition, the enhanced effect of cellular phenotype of cdkn2b-as1 overexpression was significantly attenuated by mi r-424-5p overexpression.Furthermore, mi r-424-5p was able to directly target akt3 through luciferase reporter assay.Mechanistically, cdkn2b-as1 acts as a ce rna by sponging mi r-424-5p and targets akt3.Conclusions the cellular mechanism of cdkn2b-as1 in endometriosis was confirmed; cdkn2b-as1 may be a potential target for ovarian endometriosis therapy.

Journal: Reproductive biomedicine online (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Decreased reward circuit connectivity during reward anticipation in major depression.

An important symptom of major depressive disorder (mdd) is the inability to experience pleasure, possibly due to a dysfunction of the reward system.Despite promising insights regarding impaired reward-related processing in mdd, circuit-level abnormalities remain largely unexplored.Furthermore, whereas studies contrasting experimental conditions from incentive tasks have revealed important information about reward processing, temporal difference modeling of reward-related prediction error (pe) signals might give a more accurate representation of the reward system.We used a monetary incentive delay task during functional mri scanning to explore pe-related striatal and ventral tegmental area (vta) activation in response to anticipation and delivery of monetary rewards in 24 individuals with mdd versus 24 healthy controls (hcs).Furthermore, we investigated group differences in temporal difference related connectivity with a generalized psychophysiological interaction (g ppi) analysis with the vta, ventral striatum (vs) and dorsal striatum (ds) as seeds during reward versus neutral, both in anticipation and delivery.Relative to hcs, mdd patients displayed a trend-level (p = 0.052) decrease in temporal difference-related activation in the vs during reward anticipation and delivery combined.Moreover, g ppi analyses revealed that during reward anticipation, mdd patients exhibited decreased functional connectivity between the vs and anterior cingulate cortex / medial prefrontal cortex, anterior cingulate gyrus, angular/middle orbital gyrus, left insula, superior/middle frontal gyrus (sfg/mfg) and precuneus/superior occipital gyrus/cerebellum compared to hc.Moreover, mdd patients showed decreased functional connectivity between the vta and left insula compared to hc during reward anticipation.Exploratory analysis separating medication free patients from patients using antidepressant revealed that these decreased functional connectivity patterns were mainly apparent in the mdd group that used antidepressants.These results suggest that mdd is characterized by alterations in reward circuit connectivity rather than isolated activation impairments.These findings represent an important extension of the existing literature since improved understanding of neural pathways underlying depression-related reward dysfunctions, may help currently unmet diagnostic and therapeutic efforts.

Journal: NeuroImage. Clinical (2022)
Publication types: Journal Article
A framework for understanding the functions of biomolecular condensates across scales.

Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes.They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from rna metabolism to signalling to gene regulation.Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents.Recent years have brought a focus on understanding condensate functions.Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses).In this roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales.We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.

Journal: Nature reviews. Molecular cell biology (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't;Review
Interstitial pneumonia with autoimmune features: A case series and overview.

The topic of interstitial pneumonia with autoimmune features (ipaf) is a research classification proposed by the european respiratory society/american thoracic society task force: this includes patients with idiopathic interstitial pneumonia (iip) and clinical features, suggesting an underlying autoimmune process, but who do not meet established criteria for a connective tissue disease (ctd).We aimed to perform a detailed characterization of clinical, serological, and radiological features for our patients with ipaf criteria.Six patients were included, and a comprehensive description of these cases revealed a heterogeneous group in terms of clinical and treatment options.In most patients, it was possible to identify other features and disorders with an autoimmune "background," which may support the inclusion of these patients in the ipaf classification.No deaths or significant decline in lung function occurred, and thus no definitive diagnosis of ctd could be found over 35 months of median follow-up.Therefore, ipaf is a recent concept, with many questions still open in regard to its usage in the ild field.

Journal: Respiratory medicine case reports (2021)
Publication types: Case Reports;Journal Article
Physical, Physiological, and Technical Demands in Ultimate Frisbee Small-Sided Games: Influence of Pitch Size.

Small-sided games (ssgs) are common drills used in various team sports, but the exercise intensity in ultimate frisbee ssg has not yet been investigated.To clarify the physical, physiological, and technical demands of ultimate frisbee ssg, we investigated the influence of pitch size on exercise intensity during ssg.Nine male college ultimate frisbee players played (3 vs.3) ssg on small (ssgs: 30 × 15 m) and large (ssgl: 40 × 20 m) pitches; both ssgs comprised of four 4 min periods, interspersed by 5 min of passive recovery.Players' mean heart rate (170 ± 8 and 171 ± 7 bpm), peak heart rate (184 ± 7 and 184 ± 5 bpm), and blood lactate concentration (11.3 ± 4.7 and 11.8 ± 4.6 mmol/l) were similar in ssgsand ssgl, respectively.The total distance covered (1984 ± 166 m and 1702 ± 80 m) and the distance covered during quick (860 ± 112 m and 696 ± 69 m) and high-intensity running (439 ± 95 and 255 ± 44) in ssglwere significantly longer than those in ssgs(p< 0.05).Conversely, the number of accelerations (45 ± 3 and 41 ± 3) and decelerations (44 ± 3 and 40 ± 4), catching errors (2 ± 1 and 1 ± 1), and turnovers (8 ± 2 and 6 ± 2) in ssgswere significantly greater than those in ssgl(p< 0.05).This study suggests that ultimate frisbee ssg provides high-intensity training, which stimulates the glycolytic pathway.Furthermore, manipulating ssg pitch size effectively modulates the physical demands of ssg.

Journal: Sports (Basel, Switzerland) (2021)
Publication types: Journal Article
1,3,2-Diheterophospholane complexes: access to new tuneable precursors of phosphanoxyl complexes and P-functional polymers.

Synthesis of a testbed of p-h functional diheterophospholane complexes (3 and 6a,b) with no or little steric bulk at the α-position was achieved using [net4][wh(co)5] as a combined reductant and complexation reagent.Reaction with tempo leads to p-otemp substituted tungsten complexes (4 and 7a,b) possessing different thermostabilities towards n-o bond cleavage.The transient phosphanoxyl complexes obtained were used for the polymerisation of styrene and acrylonitrile.Dft calculations were performed on the formation of various open-shell complexes and loewdin spin density distributions.

Journal: Dalton transactions (Cambridge, England : 2003) (2022)
Publication types: Journal Article