syedzayyan/paper_mill_benchmark huggingface dataset:
Do endotherms have thermal performance curves?

Temperature is an important environmental factor governing the ability of organisms to grow, survive and reproduce.Thermal performance curves (tpcs), with some caveats, are useful for charting the relationship between body temperature and some measure of performance in ectotherms, and provide a standardized set of characteristics for interspecific comparisons.Endotherms, however, have a more complicated relationship with environmental temperature, as endothermy leads to a decoupling of body temperature from external temperature through use of metabolic heat production, large changes in insulation and variable rates of evaporative heat loss.This has impeded our ability to model endothermic performance in relation to environmental temperature as well as to readily compare performance between species.In this commentary, we compare the strengths and weaknesses of potential tpc analogues (including other useful proxies for linking performance to temperature) in endotherms and suggest several ways forward in the comparative ecophysiology of endotherms.Our goal is to provide a common language with which ecologists and physiologists can evaluate the effects of temperature on performance.Key directions for improving our understanding of endotherm thermoregulatory physiology include a comparative approach to the study of the level and precision of body temperature, measuring performance directly over a range of body temperatures and building comprehensive mechanistic models of endotherm responses to environmental temperatures.We believe the answer to the question posed in the title could be 'yes', but only if 'performance' is well defined and understood in relation to body temperature variation, and the costs and benefits of endothermy are specifically modelled.

Journal: The Journal of experimental biology (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.;Review
Hydrophobic cue-induced appressorium formation depends on MoSep1-mediated MoRgs7 phosphorylation and internalization in Magnaporthe oryzae.

The rice blast fungus magnaporthe oryzae forms specialized infectious structures called appressoria that breach host cells to initiate infection.Previous studies demonstrated that the regulator of g-protein signaling (rgs)-like protein mo rgs7 undergoes endocytosis upon fungal sensing of hydrophobic environmental cues to activate c amp signaling required for appressorium formation.However, the mechanism by which mo rgs7 internalizes and its fate remains undetermined.We here show that mo sep1, a conserved protein kinase of mitotic exit network (men), phosphorylates mo rgs7 to regulate its function.Mo rgs7 phosphorylation determines its interaction with mo crn1, a coronin-like actin-binding protein homolog that also modulates the internalization of mo rgs7.Importantly, the endocytic transport of mo rgs7 is critical for its gtpase-activating protein (gap) function important in c amp signaling.Together, our findings revealed a novel mechanism by which m.Oryzae activates mo rgs7-mediated hydrophobic cue-sensing signal transduction involving protein phosphorylation and endocytic transport to govern appressorium formation and fungal pathogenicity.

Journal: PLoS genetics (2023)
Publication types: Journal Article
Acute appendicitis during coronavirus disease 2019 in Türkiye: Changes in clinical approach, treatment, and diagnosis modalities: A retrospective and cohort study.

The novel coronavirus disease 2019 (covid-19) has resulted in major changes in health-care systems and emer-gency surgical interventions.Here, we examined patients with acute appendicitis who presented to emergency departments and com-pared diagnosis, treatment, and post-treatment processes before and during the pandemic period and investigated how the pandemic affected management of acute appendicitis.Methods a national, multicenter, and cohort study model was designed that included patients older than 18 years of age diag-nosed with acute appendicitis clinically and/or radiologically, with patients compared before (pre-pandemic period: january 1-april 30, 2019) and after (pandemic period: january 1-april 30, 2020) the pandemic.Our investigation included comparisons of pre-operative imaging methods, presence of plastron appendicitis/abscess, conservative/surgical approach, type of anesthesia given, laparoscopic/open surgical approach, bowel resection rates, drain insertion rates, and presence of post-operative complications results: for the two study groups, 8972 patients from 69 centers were examined, with 4582 patients operated in the pre-pan-demic period and 4234 patients operated in the pandemic period.During the pandemic period, 63.6% of patients underwent open surgery, whereas 34.4% had laparoscopic surgery.Although 60 patients (1.3%) requested non-operative follow-up in the pre-pandemic period, 94 patients (2.2%) requested this in the pandemic period.When conditions of patients were evaluated regardless of their own wishes, 114 patients (2.4%) before and 163 patients (3.8%) during the pandemic received non-operative follow-up.Conclusion our study did not show the direct correlation between the application of covid-19-related restrictions and the severity of acute appendicitis.Although non-operative management rates have been increased during the covid-19 period, the incidences of both complicated and the uncomplicated appendicitis were similar during the covid-19 crisis period.Given this infor-mation non-operative management can be employed for patients diagnosed with appendicitis.

Journal: Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma & emergency surgery : TJTES (2022)
Publication types: Multicenter Study;Journal Article
Differences in Electromygraphic Activity of the Middle and the Lower Serratus Anterior Fibers During Open and Closed Kinematics Exercises.

Ratanapinunchai, j and madeeyoh, i.Differences in electromygraphic activity of the middle and the lower serratus anterior fibers during open and closed kinematics exercises.J strength cond res 36(7): 1788-1792, 2022-this paper seeks to determine differences in muscle activation between the middle (msa) and the lower serratus anterior (lsa) fibers during 3 exercises.Fifteen healthy men were recruited for the study.Bench push-up plus (bpup), unstable bpup (upup), and resisted shoulder flexion (rsf) with 10 repetitions at maximum weight were tested.The normalized electromyographic (emg) activity of the msa and the lsa was recorded during isometric scapular protraction for bpup and upup or at 150° shoulder flexion for rsf.Normalization was calculated using maximum voluntary isometric scapular protraction activity (%emg).The results showed that the ratio of %emg of msa:lsa was higher than one in bpup (1.41 ± 0.36) and upup (1.81 ± 0.47), but less than one (0.86 ± 0.27) in rsf.These ratios were statistically significantly different (p < 0.05).The activity of msa and lsa in rsf was significantly (p < 0.002) higher than that of bpup and upup (%emg of the msa = 80.53 ± 26.07, 64.75 ± 23.19 and 55.62 ± 25.56 for the rsf, bpup, and upup, respectively; %emg of lsa = 95.54 ± 24.15, 50.71 ± 26.32, and 32.26 ± 16.14 for the rsf, bpup, and upup, respectively).There was no difference in the %emg of msa and lsa between bpup and upup.The msa worked more than the lsa in the push-up plus (pup), but the opposite was found in the rsf exercise.The study suggests different functions of the msa and the lsa.Different exercises should be used, including a pup for the msa and rsf for the lsa, or a combination to emphasize both parts of the sa.

Journal: Journal of strength and conditioning research (2022)
Publication types: Journal Article
Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives.

Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time.Such a procedure is especially suited for automation and miniaturization.Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation.Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (maldi-ms) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences.Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized.This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts.Herein, different technologies are discussed that might be involved in this endeavor.A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.

Journal: Advanced materials (Deerfield Beach, Fla.) (2019)
Publication types: Journal Article;Review
Towards unravelling the Rosette agent enigma: Spread and emergence of the co-invasive host-pathogen complex, Pseudorasbora parva-Sphaerothecum destruens.

The emergence of non-native fungal pathogens is a growing threat to global health, biodiversity, conservation biology, food security and the global economy.Moreover, a thorough understanding of the spread and emergence of pathogens among invasive and native host populations, as well as genetic analysis of the structure of co-invasive host populations, is crucial in terms of conservation biology and management strategies.Here we combined extensive catchment sampling, molecular detection tools and genomic signatures to i) assess the prevalence of the rosette agent sphaerothecum destruens in invasive and native fish populations in contrasting french regions, and ii) characterize the genetic diversity and population structure of its co-invasive and asymptomatic carrier pseudorasbora parva.Although s.Destruens was not detected in all the fish collected its presence in contrasting freshwater ecosystems suggests that the disease may already be widespread in france.Furthermore, our results show that the detection of s.Destruens dna in its asymptomatic carrier p.Parva is still limited.Finally, we found that p.Parva populations show a homogeneous genetic and geographical structuring, which raises the possibility of the occurrence of successive introduction events in france from their native and invasive range.

Journal: The Science of the total environment (2022)
Publication types: Journal Article
Head & neck melanoma: A 22-year experience of recurrence following sentinel lymph node biopsy.

To examine the clinicopathologic factors that contribute to regional and distant recurrence in intermediate to high risk head and neck melanoma patients after sentinel lymph node biopsy (slnb).Methods this study is a retrospective review from an academic tertiary care center.Patients treated with slnb for head and neck melanoma from 1997 to 2019 were reviewed and characterized by sentinel lymph node (sln) status.Clinical variables were examined for the impact on regional and distant recurrence in slnb-negative patients using univariable and multivariable cox regression analysis.Results one hundred and fifty four patients were included.Of note, 127 (82.5 %) were men, and the average age was 61.3 years.Median follow-up was 68.6 weeks.Pathologic review of slns found 3.9% positive for metastatic melanoma; 96.1% were negative.Regional recurrence was significantly associated with tumor stage and age on multivariate analysis.A total of 4.5% of patients recurred in a previously labeled negative basin.Scalp subsite accounted for 30.5% of primary tumors and was more likely to yield a positive sln on univariate analysis (p= .023).Tumor stage and age were significantly associated with distant metastasis on multivariable analysis (p= .026,p< .001 respectively).Conclusion we report a number of prognostic trends in head and neck melanoma.Sln positivity was found more often in patients with a primary tumor of the scalp.Regional recurrence was significantly associated with age and tumor stage, whereas distant recurrence was significantly associated with tumor staging and scalp subsite.Scalp subsite was associated with an increased risk for nodal metastasis and distant recurrence.Level of evidence 3.

Journal: Laryngoscope investigative otolaryngology (2021)
Publication types: Journal Article
Update on the roles of imaging in the management of chronic thromboembolic pulmonary hypertension.

Chronic thromboembolic pulmonary hypertension (cteph), classified as group 4 pulmonary hypertension (ph), is caused by stenosis and obstruction of the pulmonary arteries by organized thrombi that are incompletely resolved after acute pulmonary embolism.The prognosis of patients with cteph is poor if untreated; however, in expert centers with multidisciplinary teams, a treatment strategy for cteph has been established, dramatically improving its prognosis.Cteph is currently not a fatal disease and is the only curable form of ph.Despite these advances and the establishment of treatment approaches, early diagnosis is still challenging, especially for non-experts, for several reasons.One of the reasons for this is insufficient knowledge of the various diagnostic imaging modalities, which are essential in the clinical practice of cteph.Imaging modalities should detect the following pathological findings: lung perfusion defects, thromboembolic lesions in pulmonary arteries, and right ventricular remodeling and dysfunction.Perfusion lung scintigraphy and catheter angiography have long been considered gold standards for the detection of perfusion defects and assessment of vascular lesions, respectively.However, advances in imaging technology of computed tomography and magnetic resonance imaging have enabled the non-invasive detection of these abnormal findings in a single examination.Cardiac magnetic resonance (cmr) is the gold standard for evaluating the morphology and function of the right heart; however, state-of-the-art techniques in cmr allow the assessment of cardiac tissue characterization and hemodynamics in the pulmonary arteries.Comprehensive knowledge of the role of imaging in cteph enables appropriate use of imaging modalities and accurate image interpretation, resulting in early diagnosis, determination of treatment strategies, and appropriate evaluation of treatment efficacy.This review summarizes the current roles of imaging in the clinical practice for cteph, demonstrating the characteristic findings observed in each modality.

Journal: Journal of cardiology (2023)
Publication types: Journal Article;Review
The effect of obstructive sleep apnea on the increased risk of cardiovascular disease: a systematic review and meta-analysis.

Obstructive sleep apnea (osa) is a disorder characterized by intermittent airway obstruction during sleep.The association between osa and the incidence of cardiovascular disease (cvd) has been investigated in many studies; however, the results are not entirely consistent between studies.The aim of this study was to investigate the relationship between osa and the risk of cvd through a meta-analysis of cohort studies.Methods a systematic review and meta-analysis of literature was conducted using the pub med, wo s, embase, science direct, scopus, and web of science databases up to the year 2020.In order to analyze the eligible studies, the stochastic effects model was used and the heterogeneity of the studies with the i2index was investigated.Data analysis was performed with comprehensive meta-analysis software (version 2).Results a total of 24 studies were included in the meta-analysis according to the inclusion criteria.Twelve studies reported cvd results, 11 studies reported stroke results, 9 studies reported mortality results, and 8 studies reported cvd results.The odds ratio of cvd in patients with osa 1.71 (1.17-2.27: 95% confidence interval) stroke in patients with osa, 1.86 (1.28-2.69: 95% confidence interval), mortality in patients with osa, 1.77 (1.37-2.29: 95% confidence interval) and chd in patients with osa, and 1.48 (1.06-2.28: 95% confidence interval) was obtained.Conclusion osa is considered a cardiovascular risk factor.There is a relationship between the severity of osa and the risk of cardiovascular disease.Osa increases the risk of heart attack, chd, and death from cardiovascular disease.

Journal: Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology (2022)
Publication types: Journal Article;Meta-Analysis;Review;Systematic Review
Chimeric Investigations into the Diamide Binding Site on the Lepidopteran Ryanodine Receptor.

Alterations to amino acid residues g4946 and i4790, associated with resistance to diamide insecticides, suggests a location of diamide interaction within the p vsd voltage sensor-like domain of the insect ryanodine receptor (ry r).To further delineate the interaction site(s), targeted alterations were made within the same p vsd region on the diamondback moth (plutella xylostella) ry r channel.The editing of five amino acid positions to match those found in the diamide insensitive skeletal ry r1 of humans (h ry r1) in order to generate a human-plutellachimeric construct showed that these alterations strongly reduce diamide efficacy when introduced in combination but cause only minor reductions when introduced individually.It is concluded that the sites of diamide interaction on insect ry rs lie proximal to the voltage sensor-like domain of the ry r and that the main site of interaction is at residues k4700, y4701, i4790 and s4919 in the s1 to s4 transmembrane domains.

Journal: International journal of molecular sciences (2021)
Publication types: Journal Article
Identification and validation of a ferroptosis-related prognostic risk-scoring model and key genes in small cell lung cancer.

Small cell lung cancer (sclc) is an aggressive lung malignancy with high relapse rates and poor survival outcomes.Ferroptosis is a recently identified type of cell death caused by excessive intracellular iron accumulation and lipid peroxidation, which may mediate tumor-infiltrating immune cells to influence anti-cancer immunity.But prognostic value of ferroptosis-related genes and its relationship with the treatment response of immunotherapies in sclc have not been elucidated.Methods the rna-sequencing and clinical data of sclc patients were downloaded from the c bio portal database.A ferroptosis-related prognostic risk-scoring model was constructed based on univariable and multivariable cox-regression analysis.Kaplan-meier (k-m) survival curves and receiver operating characteristics (roc) curves were constructed to assess the sensitivity and specificity of the risk-scoring model.And the correlations between ferroptosis-related prognostic genes and immune microenvironment were explored.The ic50 values of anti-cancer drugs were downloaded from the genomics of drug sensitivity in cancer (gdsc) database and the correlation analysis with the key gene thioredoxin-interacting protein (txnip) was performed.In addition, immunohistochemistry (ihc) staining was employed to detect the expression of txnipin 20 sclc patients who received first-line chemo-immunotherapy.Immunotherapeutic response according to i recist (response evaluation criteria in solid tumours for immunotherapy trials) were recorded.Results we constructed a risk-score successfully dividing patients in the low- and high-risk groups (with better and worse prognosis, respectively).The area under the curve (auc) of this risk-scoring model was 0.812, showing it had good utility in predicting the prognosis of sclc.Moreover, ferroptosis-related genes were associated with the degree of immune infiltration of sclc.Most importantly, we found that the txnipexpression was highly correlated with the degree of immune invasion and the efficacy of chemotherapy in combination with immunotherapy in sclc patients.Conclusions the ferroptosis-related prognostic risk-scoring model proposed in this study can potentially predict the prognosis of sclc patients.txnipmay serve as a potential biomarker to predict the prognosis and efficacy of chemotherapy combined with immunotherapy in sclc patients.

Journal: Translational lung cancer research (2022)
Publication types: Journal Article
Prognostic Factors for Immune Thrombocytopenic Purpura Remission after Laparoscopic Splenectomy: A Cohort Study.

And objectives laparoscopic splenectomy (ls) has become the gold standard for patients with immune thrombocytopenic purpura (itp).The total remission rate after splenectomy is 70%-90%, of which 66% is long-term.Despite this high response rate, some patients do not benefit from surgery.It is therefore important to try to identify risk factors for an unsatisfactory clinical response.The aim of this study was to assess long-term outcomes of ls for itp and identify factors associated with increased disease remission rates.Materials and methods we retrospectively studied consecutive patients with itp undergoing ls in a tertiary referral surgical center prospectively recorded in a database.Inclusion criteria were: elective, laparoscopic splenectomy for diagnosed itp, and complete follow-up.The cohort was divided into two groups-group 1 (g1) patients with itp remission after splenectomy and group 2 (g2) patients without remission.There were 113 g1 patients and 52 g2 patients.Median follow-up was 9.5 (iqr: 5-15) years.Results in univariate analysis, patient's age, body mass index (bmi), preoperative platelet count, the need for platelet transfusions, and presence of hemorrhagic diathesis were shown to be statistically significant factors.Next, we built a multivariate logistic regression model using factors significant in univariate analysis.Age <41 years (odds ratio (or) 4.49; 95% ci: 1.66-12.09), bmi <24.3 kg/m2(or: 4.67; 95% ci: 1.44-15.16), and preoperative platelet count ≥97 × 103/mm3(or: 3.50; 95% ci: 1.30-9.47) were shown to be independent prognostic factors for itp remission after ls.Conclusion the independent prognostic factors for itp remission after ls revealed in our study are: age <41 years, bmi <24.3 kg/m2, and preoperative platelet count ≥97 × 103/mm3.Duration of the itp and the time of treatment are not related to remission after ls.

Journal: Medicina (Kaunas, Lithuania) (2019)
Publication types: Journal Article
Clinical Anatomy of Feeding Artery of the Submandibular Gland.

The purpose of this study was to investigate the clinical anatomy of the feeding artery of the submandibular gland (smg).A total of 199 smg removals were performed in extraoral or intraoral approach with/without endoscopic assistance by a single surgeon.The feeding artery of the smg was always identified intraoperatively and recorded in the operation record.The clinical anatomy of the feeding artery of the smg was investigated based on the intraoperative findings.The facial artery was ligated and transected for the involvement of tumor or severe inflammation in 16 (8.0%) procedures.The feeding artery was investigated in the remaining 183 procedures.The mean number of the glandular branch was 1.5.There were 1 branch in 98 procedures (53.6%), 2 branches in 80 procedures (43.7%), and 3 branches in 5 procedures (2.7%).Detailed anatomical knowledge of the feeding artery of the smg is useful for proper dissection of the smg and preservation of the facial artery.

Journal: The Journal of craniofacial surgery (2022)
Publication types: Journal Article