syedzayyan/paper_mill_benchmark huggingface dataset:
Circuit Integration Initiation of New Hippocampal Neurons in the Adult Brain.

In the adult brain, new dentate granule cells integrate into neural circuits and participate in hippocampal functioning.However, when and how they initiate this integration remain poorly understood.Using retroviral and live-imaging methods, we find that new neurons undergo neurite remodeling for competitive horizontal-to-radial repositioning in the dentate gyrus prior to circuit integration.Gene expression profiling, lipidomics analysis, and molecular interrogation of new neurons during this period reveal a rapid activation of sphingolipid signaling mediated by sphingosine-1-phosphate receptor 1.Genetic manipulation of this g protein-coupled receptor reveals its requirement for successful repositioning of new neurons.This receptor is also activated by hippocampus-engaged behaviors, which enhances repositioning efficiency.These findings reveal that activity-dependent sphingolipid signaling regulates cellular repositioning of new dentate granule cells.The competitive horizontal-to-radial repositioning of new neurons may provide a gating strategy in the adult brain to limit the integration of new neurons into pre-existing circuits.

Journal: Cell reports (2020)
Publication types: Journal Article
Identification of Mellein as a Pathogenic Substance ofBotryosphaeria dothideaby UPLC-MS/MS Analysis and Phytotoxic Bioassay.

Botryosphaeria dothideais a pathogenic fungus that can cause apple ring rot, a destructive apple disease in china.There have been reports on its molecular pathogenesis, but the pathogenic substances still remain unknown.In the present study, instrument analysis including uplc-high-resolution mass spectrometry (hrms) and nuclear magnetic resonance showed that b.Dothideafermentation broth contained (r)-(-)-mellein, a well-known fungal enantiomer of mellein.For further confirmation, a uplc-ms/ms method for the determination of mellein was developed and validated.By this method, mellein was found to also exist in b.Dothidea-infected apple fruits and branches with concentration ranges of 0.14-0.94 and 5.88-80.29 mg/kg, respectively.The concentration in fruits reached a peak at 48 h after pathogen inoculation, while a sustained concentration increase was achieved within 11 days for branches.Simultaneously, it was evident that there was a relation between disease spot expansion and mellein production kinetics in apple tissue.Phytotoxic bioassay showed that mellein could cause discoloration and death of apple leaves and browning in stems.Therefore, we confirmed that mellein was one of the pathogenic substances of b.Dothidea.The present study provided additional data for the research on the pathogenesis of this pathogen.

Journal: Journal of agricultural and food chemistry (2021)
Publication types: Journal Article
Baghel Prakash Prognosis Scoring System - Conceptual framework and preliminary psychometric validation.

The assessment of prognosis in a patient using a rigorous methodology is documented in old ayurveda texts.But in present times, practitioners employ varied clinical assessment methods, which results in low inter-observer agreement.Objectives this study proposes a conceptual framework for developing a prognosis scoring system, which we refer to as the "baghel prakash prognosis scoring system" (bppss), and presents its preliminary psychometric validation.Materials and methods classics of ayurveda were extensively reviewed for item generation.Thirty-nine items were pooled initially.The content validity index for items (i-cvi), scale-level content validity index (s-cvi), and content validity ratio (cvr) were calculated.The final framework contained 30 items.The scoring system was pilot-tested in a sample of 30 patients with various disease conditions.The reliability checks were done to evaluate internal consistency.Inter-item correlations, item-total correlations, and cronbach's alpha (if an item is deleted) were used to conduct item analysis for the instrument.Results the framework developed includes a set of early clinical warning signs and a prognosis scoring system of 30 items with a provision for clinical adjustment of scores for selected items.Internal consistency of the scoring system during the initial psychometric validation revealed a value of .761 for cronbach's alpha (based on standardized items), and item analysis revealed that most of the items had acceptable correlation coefficients between .3 and .7.Conclusion based on this preliminary validation study, we found that this prognosis framework, based on the principles of ayurveda, may be used in varied clinical situations.The preliminary psychometric validation experiments yielded satisfactory results.The framework also has potential in clinical research, such as selecting patients with similar prognostic scores for comparability in case and control groups of clinical trials.This tool can be utilized as a reliable outcome measure after conducting enough validation studies.

Journal: Journal of Ayurveda and integrative medicine (2022)
Publication types: Journal Article
The Glycolytic Enzyme Triosephosphate Isomerase of Trichomonas vaginalis Is a Surface-Associated Protein Induced by Glucose That Functions as a Laminin- and Fibronectin-Binding Protein.

Triosephosphate isomerase of trichomonas vaginalis (tv tim) is a 27-k da cytoplasmic protein encoded by two genes, tvtim1 and tvtim2, that participates in glucose metabolism.Tv tim is also localized to the parasite surface.Thus, the goal of this study was to identify the novel functions of the surface-associated tv tim in t.Vaginalis and to assess the effect of glucose as an environmental factor that regulates its expression and localization.Reverse transcription-pcr (rt-pcr) showed that the tvtim genes were differentially expressed in response to glucose concentration.Tvtim1 was overexpressed under glucose-restricted (gr) conditions, whereas tvtim2 was overexpressed under glucose-rich, or high-glucose (hg), conditions.Western blot and indirect immunofluorescence assays also showed that glucose positively affected the amount and surface localization of tv tim in t.Vaginalis affinity ligand assays demonstrated that the recombinant tv tim1 and tv tim2 proteins bound to laminin (lm) and fibronectin (fn) but not to plasminogen.Moreover, higher levels of adherence to lm and fn were detected in parasites grown under hg conditions than in those grown under gr conditions.Furthermore, pretreatment of trichomonads with an anti-tv timr polyclonal antibody or pretreatment of lm- or fn-coated wells with both recombinant proteins (tv tim1r and tv tim2r) specifically reduced the binding of live parasites to lm and fn in a concentration-dependent manner.Moreover, t.Vaginalis was exposed to different glucose concentrations during vaginal infection of women with trichomoniasis.Our data indicate that tv tim is a surface-associated protein under hg conditions that mediates specific binding to lm and fn as a novel virulence factor of t.Vaginalis.

Journal: Infection and immunity (2016)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Association Between Monocyte Count and Preoperative Deep Venous Thrombosis in Older Patients with hip Fracture: A Retrospective Study.

To analyze the relationship between monocyte count and preoperative deep venous thrombosis (dvt) in older patients with hip fracture.Methods consecutive older patients with hip fracture undergoing surgery were included from january 2014 to december 2021.Monocyte count was measured on admission, and doppler ultrasonography was performed for dvt screening prior to surgery.Univariate and multivariate logistic regression analyses were used to assess the association between monocyte count and dvt.Results a total of 674 patients were finally included, and 128 patients (19.0%) were diagnosed with preoperative dvt.Patients with dvt exhibited a higher monocyte count than patients without dvt [0.55 (0.43-0.72) × 109/l versus 0.49 (0.38-0.63) × 109/l,p= 0.007].Multivariate logistic regression analysis showed that a high monocyte count (> 0.6 × 109/l) was independently associated with a higher risk of dvt (or = 1.705, 95%ci: 1.121-2.593,p= 0.013), and for every 0.1 × 109/l increase in monocyte count, the risk of dvt increased by 8.5% (or = 1.085, 95%ci: 1.003-1.174,p= 0.041).Other risk factors associated with dvt included intertrochanteric fracture (or = 1.596, 95%ci: 1.022-2.492,p= 0.040), and elevated fibrinogen level (or = 1.236, 95%ci: 1.029-1.484,p= 0.023).Conclusion a high monocyte count is associated with an increased risk of dvt in older patients with hip fracture.Future studies should evaluate the potential role of monocyte in the prevention and treatment of thrombosis.

Journal: Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis (2022)
Publication types: Journal Article
Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum.

Gleason score, a measure of prostate tumor differentiation, is the strongest predictor of lethal prostate cancer at the time of diagnosis.Metabolomic profiling of tumor and of patient serum could identify biomarkers of aggressive disease and lead to the development of a less-invasive assay to perform active surveillance monitoring.Metabolomic profiling of prostate tissue and serum samples was performed.Metabolite levels and metabolite sets were compared across gleason scores.Machine learning algorithms were trained and tuned to predict transformation or differentiation status from metabolite data.A total of 135 metabolites were significantly different (padjusted< 0.05) in tumor versus normal tissue, and pathway analysis identified one sugar metabolism pathway (padjusted= 0.03).Machine learning identified profiles that predicted tumor versus normal tissue (auc of 0.82 ± 0.08).In tumor tissue, 25 metabolites were associated with gleason score (unadjusted p< 0.05), 4 increased in high grade while the remainder were enriched in low grade.While pyroglutamine and 1,5-anhydroglucitol were correlated (0.73 and 0.72, respectively) between tissue and serum from the same patient, no metabolites were consistently associated with gleason score in serum.Previously reported as well as novel metabolites with differing abundance were identified across tumor tissue.However, a "metabolite signature" for gleason score was not obtained.This may be due to study design and analytic challenges that future studies should consider.Implications: metabolic profiling can distinguish benign and neoplastic tissues.A novel unsupervised machine learning method can be utilized to achieve this distinction.

Journal: Molecular cancer research : MCR (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Protein Phosphatase PP1 Negatively Regulates IRF3 in Response to GCRV Infection in Grass Carp (Ctenopharyngodon idella).

Protein phosphatase-1 (pp1) has an important role in many cell functions, such as cell differentiation, development, immune response and tumorigenesis.However, the specific role of pp1 in the antiviral response in fish remains to be elucidated.In this study, the ppp1r3ghomolog was identified in the grass carp (ctenopharyngodon idella) and its role in defence against the gcrv infection was investigated.Phylogenetic analysis demonstrated that ci ppp1r3g clustered with homologues from other teleosts.Temporal expression analysisin vivorevealed that the expression level of ci ppp1r3gwas significantly up-regulated in response to gcrv infection in grass carps, especially in the intestine and head-kidney.Cellular distribution analysis revealed that ci ppp1r3g was located in the nucleus and cytoplasm.Overexpression of ci ppp1r3gsignificantly negatively regulated the expression of ci irf3, thus inhibiting its activation.In summary, we systematically analyzed the ppp1r3ggene in grass carp and illustrated its function as a negative regulator in the anti-gcrv immune responses.

Journal: Frontiers in immunology (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Lessons learned and keys to success: Provider experiences during the implementation of virtual oncology tumor boards in the era of COVID-19.

And objectives the covid-19 pandemic required rapid adaptation of multidisciplinary tumor board conferences to a virtual setting; however, there are little data describing the benefits and challenges of using such a platform.Methods an anonymous quality improvement survey was sent to participants of tumor board meetings at a large academic institution.Participants answered questions pertaining to the relative strengths and weaknesses of in-person and virtual settings.Results a total of 335 responses (23.3% response rate) were recorded, and 253 met inclusion criteria.Respondents represented 25 different tumor board meetings, with colorectal, breast, and liver (18.6%, 17.0%, and 13.0%, respectively) being the most commonly attended.Virtual tumor boards were equivalent to in-person across 9 of 10 domains queried, while a virtual format was preferred for participation in off-site tumor boards.The lack of networking opportunities was ranked by physicians to be a significant challenge of the virtual format.Consistent leadership and organization, engaged participation of all attendees, and upgrading technology infrastructure were considered critical for success of virtual meetings.Conclusions the implementation of virtual tumor board meetings has been associated with numerous challenges.However, improving several key aspects can improve participant satisfaction and ensure excellent patient care.

Journal: Journal of surgical oncology (2022)
Publication types: Journal Article
A Review of Factors AffectingGanodermaBasal Stem Rot Disease Progress in Oil Palm.

In recent years, oil palm has grown on a major scale as it is a prominent commodity crop that contributes the most to almost every producing country's gross domestic product (gdp).Nonetheless, existing threats such as the ganodermabasal stem rot (bsr) disease have been deteriorating the oil palm plantations and suitable actions to overcome the issue are still being investigated.The bsr disease progression in oil palm is being studied using the disease progression through the plant disease triangle idea.This concept looks at all potential elements that could affect the transmission and development of the disease.The elements include pathogenic, with their mode of infection in each studied factor.

Journal: Plants (Basel, Switzerland) (2022)
Publication types: Journal Article;Review
M probe comes first: Impact of initial probe choice on diagnostic performance of vibration controlled transient elastography.

& aims probe choice (m or xl) in transient elastography can be made by the user's own measure of skin-to-liver-capsule distance (scd) or with an automated tool (auto).We studied how auto depends on initial probe choice.Methods three fictive clinics were considered: the "m-first clinic" uses auto from the m probe, the "xl-first clinic" uses auto from the xl probe and a "reference clinic" measures scd independently.Agreement and discrepancies to the reference clinic were measured.Results 200 patients with chronic liver disease were prospectively included (58% female, 56 years, bmi 28.1 kg/m2).Fleiss' kappa for agreement in probe selection was 0.11 (95% ci -0.09 to 0.31), but accuracy was above 0.8 for both.Probe failure occurred for 16 (m-first clinic), 4 (xl-first clinic) and 3 patients (reference clinic).Use of xl probe given m probe failure improved performance of the m-first approach.The odds ratio for discrepancy in the xl-first vs m-first clinic is 2.4 (95% ci 1.2 to 5.2, p = 0.012) for liver fibrosis and 4.8 (95% ci 1.8 to 16.1, p < 0.001) for steatosis.Conclusions agreement in auto between m and xl probes is poor although each has acceptable accuracy.The m-first approach leads to fewer discrepancies and should be adopted as a standard.

Journal: Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver (2022)
Publication types: Journal Article
Differential Responses of Wheat (Triticum aestivumL.) and Cotton (Gossypium hirsutumL.) to Nitrogen Deficiency in the Root Morpho-Physiological Characteristics and Potential MicroRNA-Mediated Mechanisms.

Understanding the mechanism of crop response to nitrogen (n) deficiency is very important for developing sustainable agriculture.In addition, it is unclear if the micro rna-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under n deficiency.Therefore, the root morpho-physiological characteristics and micro rna-mediated mechanisms were studied under n deficiency in wheat (triticum aestivum l.) and cotton (gossypium hirsutum l.).For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of n deficiency.Although n deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton.After 8 days of treatment with n deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton.At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of n deficiency treatment.Additionally, the two crops had different root regulatory mechanisms of micro rnas (mi rnas) to n deficiency.In wheat, the expressions of mi r167, mi r319, mi r390, mi r827, mi r847, and mi r165/166 were induced by n treatment; these mi rnas inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate n deficiency.In cotton, the expressions of mi r156, mi r167, mi r171, mi r172, mi r390, mi r396 were induced and the expressions of mi r162 and mi r393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the n deficiency.In conclusion, n deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by mi rnas, but the mi rna-mediated mechanisms were different in wheat and cotton.

Journal: Frontiers in plant science (2022)
Publication types: Journal Article
Fully integrated photoacoustic microscopy and photoplethysmography of humanin vivo.

Photoacoustic microscopy (pam) is used to visualize blood vessels and to monitor their time-dependent changes.Photoplethysmography (ppg) measures hemodynamic time-series changes such as heart rate.However, ppg's limited visual access to the dynamic changes of blood vessels has prohibited further understanding of hemodynamics.Here, we propose a novel, fully integrated pam and photoplethysmography (pam-ppg) system to understand hemodynamic features in detail.Using the pam-ppg system, we simultaneously acquire vascular images (by pam) and changes in the blood volume (by ppg) from human fingers.Next, we determine the heart rate from changes in the pa signals, which match well with the ppg signals.These changes can be measured if the blood flow is not blocked.From the results, we believe that pam-ppg could be a useful clinical tool in various clinical fields such as cardiology and endocrinology.

Journal: Photoacoustics (2022)
Publication types: Journal Article
Prevalence of Statin Use for Primary Prevention of Atherosclerotic Cardiovascular Disease by Race, Ethnicity, and 10-Year Disease Risk in the US: National Health and Nutrition Examination Surveys, 2013 to March 2020.

Importance the burden of atherosclerotic cardiovascular disease (ascvd) in the us is higher among black and hispanic vs white adults.Inclusion of race in guidance for statin indication may lead to decreased disparities in statin use.Objective to evaluate prevalence of primary prevention statin use by race and ethnicity according to 10-year ascvd risk.Design, setting, and participants this serial, cross-sectional analysis performed in may 2022 used data from the national health and nutrition examination survey, a nationally representative sample of health status in the us, from 2013 to march 2020 (limited cycle due to the covid-19 pandemic), to evaluate statin use for primary prevention of ascvd and to estimate 10-year ascvd risk.Participants aged 40 to 75 years without ascvd, diabetes, low-density lipoprotein cholesterol levels 190 mg/d l or greater, and with data on medication use were included.Exposures self-identified race and ethnicity (asian, black, hispanic, and white) and 10-year ascvd risk category (5%-<7.5%, 7.5%-<20%, ≥20%).Main outcomes and measures prevalence of statin use, defined as identification of statin use on pill bottle review.Results a total of 3417 participants representing 39.4 million us adults after applying sampling weights (mean [sd] age, 61.8 [8.0] years; 1289 women [weighted percentage, 37.8%] and 2128 men [weighted percentage, 62.2%]; 329 asian [weighted percentage, 4.2%], 1032 black [weighted percentage, 12.7%], 786 hispanic [weighted percentage, 10.1%], and 1270 white [weighted percentage, 73.0%]) were included.Compared with white participants, statin use was lower in black and hispanic participants and comparable among asian participants in the overall cohort (asian, 25.5%; black, 20.0%; hispanic, 15.4%; white, 27.9%) and within ascvd risk strata.Within each race and ethnicity group, a graded increase in statin use was observed across increasing ascvd risk strata.Statin use was low in the highest risk stratum overall with significantly lower rates of use among black (23.8%; prevalence ratio [pr], 0.90; 95% ci, 0.82-0.98 vs white) and hispanic participants (23.9%; pr, 0.90; 95% ci, 0.81-0.99 vs white).Among other factors, routine health care access and health insurance were significantly associated with higher statin use in black, hispanic, and white adults.Prevalence of statin use did not meaningfully change over time by race and ethnicity or by ascvd risk stratum.Conclusions and relevance in this study, statin use for primary prevention of ascvd was low among all race and ethnicity groups regardless of ascvd risk, with the lowest use occurring among black and hispanic adults.Improvements in access to care may promote equitable use of primary prevention statins in black and hispanic adults.

Journal: JAMA cardiology (2023)
Publication types: Journal Article