syedzayyan/paper_mill_benchmark huggingface dataset:
Selection of Genome-Wide SNPs for Pooled Allelotyping Assays Useful for Population Monitoring.

Parasitic worms are serious pests of humans, livestock, and crops worldwide.Multiple management strategies are employed in order to reduce their impact, and some of these may affect their genome and population allelic frequency distribution.The evolution of chemical resistance, ecological changes, and pest dispersal has allowed an increasing number of pests to become difficult to control with current management methods.Their lifestyle limits the use of ecological and individual-based management of populations.There is a need to develop rapid, affordable, and simple diagnostics to assess the efficacy of management strategies and delay the evolution of resistance to these strategies.This study presents a multilocus, equal-representation, whole-genome pooled single nucleotide polymorphisms (snps) selection approach as a monitoring tool for the ovine nematode parasite haemonchus contortus.The snp selection method used two reference genomes of different quality, then validated these snps against a high-quality recent genome assembly.From over 11 million high-quality snps identified, 334 snps were selected, of which 262 were species-specific, yielded similar allele frequencies when assessed as multiple individuals or as pools of individuals, and suitable to distinguish mixed nematode isolate pools from single isolate pools.As a proof-of-concept, 21 australian h.Contortus populations with various phenotypes and genotypes were screened.This analysis confirmed the overall low level of genetic differentiation between populations collected from the field, but clearly identifying highly inbred populations, and populations showing genetic signatures associated with chemical resistance.The analysis showed that 66% of the snps were necessary for stability in assessing population genetic patterns, and snp pairs did not show linkage according to allelic frequencies across the 21 populations.This method demonstrates that ongoing monitoring of parasite allelic frequencies and genetic changes can be achieved as a management assessment tool to identify drug-treatment failure, population incursions, and inbreeding signatures due to selection.The snp selection method could also be applied to other parasite species.

Journal: Genome biology and evolution (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
LiveLighter® 'Junk Food' mass media campaign increases behavioural strategies to reduce consumption.

The live lighter® 2016 'junk food' campaign ran for 5 weeks in western australia (wa) and urged adults to reduce their junk food consumption to avoid weight gain and associated chronic disease.A cohort design assessed campaign impact on knowledge, beliefs and behaviour.Pre-campaign (n = 1501) and post-campaign (n = 737) telephone surveys of wa adults aged 25-49 were undertaken.A post-campaign-only sample (n = 501) controlled for pre-test effects.The campaign reached 57% of respondents and increased knowledge of the link between overweight and non-alcoholic fatty liver disease (78% cf.87%; p < 0.01).Following campaign activity, respondents were more likely to avoid purchasing food from settings depicted in the advertisements (fast food outlets: 63% cf.77%; service stations: 82% cf.93%; vending machines: 87% cf.96%; all p < 0.001), particularly among pre-campaign consumers of fast food and salty snacks (≤2 times/week).Weight-loss self-efficacy increased among adults with higher body weight and campaign exposure (89% cf.97%; p < 0.01), and there was no increased endorsement of overweight stereotypes among the full sample.Support for fiscal disincentives and nutritional disclosure policies increased among healthy weight adults.Live lighter® positively influenced knowledge, beliefs and behaviours, along with attitudes towards policies to encourage healthy eating, supporting live lighter® as an advocacy campaign.

Journal: Health education research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
What's the Big IDEA? A Preliminary Analysis of Behavior Analysts' Self-Reported Training in and Knowledge of Federal Special Education Law.

Many behavior analysts currently work in school settings or with individuals who may qualify for educational services through federal special education law.However, it remains unclear what training, if any, behavior analysts receive in this law.Behavior analysts have an ethical responsibility to practice within their scope of competency and in compliance with legal regulations.Thus, it is important to determine whether behavior analysts practicing in the united states are adequately prepared and familiar with federal special education law.The current study consisted of a survey wherein respondents answered questions pertaining to the relevance of federal special education law, their familiarity with core terminology, and the alignment between the law and the professional and ethical compliance code for behavior analysts(behavior analyst certification board, 2016).Respondents' self-report indicates that behavior analysts hold conflicting views on how federal special education law aligns with and influences their role as service providers.As such, practitioners and agencies alike may benefit from explicit clarification of the responsibility board certified behavior analysts have to seek training in and adhere to federal special education law.

Journal: Behavior analysis in practice (2022)
Publication types: Journal Article
Perioperative Resumption of Direct Oral Anticoagulants: Review of the Mayo Clinic Experience.

We aimed to review recommendations for the postoperative resumption of direct oral anticoagulants (doacs) and report complications 30 days postoperatively.Methods we retrospectively reviewed patients receiving doac therapy who underwent preoperative evaluations from january 1, 2015 through may 30, 2018.We noted days that doac therapy was withheld, postoperative time until resumption of the doac, and complications within 30 postoperative days.Results a total of 317 patients were included.Ten had complications.Complication rates among patients stratified by time to resumption were not significantly different, except for the deep vein thrombosis rate when doacs were resumed after 72 hours (n = 2 [4.17%];p =0.02).The total time without doacs did not affect the complication rates.Conclusions we suggest withholding doacs for 48 to 72 hours before surgery and resuming them 48 to 72 hours after surgery, if safe.The interruption of therapy was not associated with an increase in thrombotic events for patients who resumed doacs within 72 hours postoperatively.Patients who resumed doacs after 72 hours postoperatively had a low rate of thrombotic complications.

Journal: Southern medical journal (2021)
Publication types: Journal Article;Review
Myeloid-derived suppressor cells regulate the immunosuppressive functions of PD-1-PD-L1+Bregs through PD-L1/PI3K/AKT/NF-κB axis in breast cancer.

Myeloid-derived suppressor cells (mdscs) are a heterogeneous group of myeloid cells that are closely related to tumor immune escape, but the mechanism by which mdscs regulate b cells has not been elucidated.Our previous studies revealed that breast cancer-derived mdscs could induce a group of pd-1-pd-l1+bregs with immunosuppressive functions.Here, we reported that blocking pd-1/pd-l1 interaction between mdscs and b cells could reverse the immunosuppressive functions of pd-1-pd-l1+bregs.The activation of pi3k/akt/nf-κb signaling pathway is essential for pd-1-pd-l1+bregs to exert immunosuppressive effects.Mdscs activated the pi3k/akt/nf-κb pathway in b cells via the pd-1/pd-l1 axis.Furthermore, inhibition of pd-1/pd-l1 or pi3k/akt signaling suppressed both tumor growth and the immunosuppressive functions of pd-1-pd-l1+bregs.Dual suppression of pd-1/pd-l1 and pi3k/akt exerted better antitumor effect.Finally, mdscs and pd-1-pd-l1+bregs were colocalized in breast cancer tissues and pd-1-pd-l1+bregs were positively correlated with poor prognosis.Thus, mdsc-educated pd-1-pd-l1+bregs and their regulatory mechanisms could contribute to the immunosuppressive tumor microenvironment.Our study proposes a novel mechanism for mdsc-mediated regulation of b cell immunity, which might shed new light on tumor immunotherapy.

Journal: Cell death & disease (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
The impact of entrepreneurs' cognitive flexibility on the business performance of New Ventures: an empirical study based on Chinese New Ventures.

We developed a "thinking-behavior-outcome" logical framework to explore the effect of entrepreneurs' cognitive flexibility on dual innovation and the performance of new ventures, drawing on social cognitive theory, and collected data from a sample of 293 new ventures through a questionnaire to conduct an empirical analysis.We find that entrepreneurs' cognitive flexibility may indirectly affect the performance of new ventures by influencing their dual innovation activities; resource management capabilities positively moderate the relationship between entrepreneurs' cognitive flexibility and dual innovation.In addition, our study demonstrates that dual innovation equilibrium has a stronger effect on the performance of new ventures than single-dimensional innovation activities.Our study highlights the importance of entrepreneurial cognitive flexibility for new ventures to implement innovation strategies and improve performance.The findings not only help to clarify the relationship between entrepreneurs' cognitive flexibility and new venture performance and to enrich social cognitive theory, but they also provide new perspectives on responses to enhance dual innovation capabilities of new ventures under the influence of covid-19.Supplementary information the online version contains supplementary material available at .

Journal: Current psychology (New Brunswick, N.J.) (2022)
Publication types: Journal Article
Effects of vitamin D receptor gene polymorphisms on the prognosis of COVID-19.

Vitamin d deficiency has emerged as another potential risk factor for coronavirus disease (covid-19) due to the immunomodulatory effects of 25 hydroxyvitamin d [25 (oh)d].Vitamin d receptor (vdr) gene polymorphisms such as fok i, bsm i, apa i, and taq i are also associated with different courses of viral infections.This study aimed to evaluate the association between the vdr gene polymorphism at fok i, taq i, bsm i, and apa i genotypes and the prognosis of covid-19 in respect to vitamin d deficiency.Methods two-hundred ninety-seven patients with covid-19 were enrolled.Serum 25 (oh)d levels were measured.Four variant regions of the vdr gene, fok i, bsm i, apa i, and taq i were determined.Results eighty-three percent of subjects had vitamin d deficiency, and 40.7% of the whole group had severe deficiency.Median 25 (oh)d level was 11.97 ng/ml.Vitamin d levels were not related to inflammatory markers, disease severity, admission to intensive care unit (icu), and mortality.While disease severity was related to fok i ff genotype, it was taq tt genotype for icu admission.Moreover, the apa i aa genotype was common among the patients who were died.None of the deceased subjects had the fok i ff genotype.Conclusion 25 (oh)d levels were not related to the severity and mortality of covid-19.Vdr gene polymorphisms are independently associated with the severity of covid-19 and the survival of patients.

Journal: Clinical endocrinology (2022)
Publication types: Journal Article
A high level of lncFGD5-AS1 inhibits epithelial-to-Mesenchymal transition by regulating the miR-196a-5p/SMAD6/BMP axis in gastric Cancer.

Long non-coding rna (lnc rna) was a vital factor in the progression and initiation of human cancers.This study found a new lnc rna, fgd5-as1, which can inhibit emt process, proliferation, and metastasis in vitro and in vivo.Methods q rt-pcr was employed to test the expression of lnc fgd5-as1 in 30 gastric cancer patients' cancer tissue and para-cancer tissue.Overexpressed lnc fgd5-as1 cells shown sharply decrease of proliferation, migration, and epithelial-mesenchymal transition (emt).Mi r-196a-5p/smad6 was confirmed as downstream molecular mechanism of lnc fgd5-as1 by expression correlation analysis and mechanism experiments.In vivo study illustrated overexpression of lnc fgd5-as1 suppression tumor growth.Results lnc fgd5-as1 served as a ce rna of mi r-196a-5p to release its inhibition on smad6, a conventional inhibitor on the bmp pathway.Comparing with normal gastric cancer cells, fgd5-as1 overexpressed group had fewer migration cells, lower cell viability, and lower emt transformation rate.Meanwhile, xenografts nude mice injecting with overexpressed-fgd5-as1 cells also shown smaller tumor weight and volume.Conclusion in conclusion, this research supported the first evidence that fgd5-as1 suppressed proliferation and metastasis in gastric cancer by regulating mi r-196a-5p/smad6/bmp axis and suggested a potential therapeutic candidate for gastric cancer.

Journal: BMC cancer (2021)
Publication types: Journal Article
Experimental study of the influence of dental restorations on thermal and fast photo-neutron production in radiotherapy with a high-energy photon beam.

In head and neck radiation therapy, the presence of dental restorations can increase unwanted neutron dose to the patient.This study aimed at the measurement of secondary neutron production induced by irradiation of a healthy tooth, amalgam, ni-cr alloy and ceramco with a photon beam generated in the treatment head of a siemens primus linac at a voltage of 15 mv.The irradiation field amounted to 10 × 10 cm2.The measurements of thermal and fast-neutron equivalent doses were performed by means of cr-39 detectors positioned in various depths of a perspex (polymethyl methacrylate) phantom as at open field as at presence of corresponding dental restorations.The general trend of thermal neutron as well as fast-neutron equivalent dose behind the denture samples reveals their reduction with increasing depth.The maximum values of thermal-neutron dose related to amalgam, ceramco and ni-cr alloy amount to 1.45 m sv/100 mu, 1.38 m sv/100 mu and 1.32 m sv/100 mu, whereas the corresponding maximum values of fast-neutron dose at the depth of 1.8 cm amount to 0.19 m sv/100 mu, 1.04 m sv/100 mu and 0.97 m sv/100 mu, respectively.The present study investigates the neutron dose accompanied with radiotherapy.It is recommended that attempts have to be made to ensure that dental restorations are not in the path of the primary high-energy photon beam.Considering treatment planning, the guidelines of radiation protection should be improved.

Journal: Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine (2019)
Publication types: Journal Article
Hyperammonemia Alters the Function of AMPA and NMDA Receptors in Hippocampus: Extracellular cGMP Reverses Some of These Alterations.

Chronic hyperammonemia alters membrane expression of ampa and nmda receptors subunits in hippocampus leading to impaired memory and learning.Increasing extracellular c gmp normalizes these alterations.However, it has not been studied whether hyperammonemia alters the function of ampa and nmda receptors.The aims of this work were: (1) assess if hyperammonemia alters ampa and nmda receptors function; (2) analyze if extracellular c gmp reverses these alterations.A multielectrode array device was used to stimulate schäffer collaterals and record postsynaptic currents in the ca1 region in hippocampal slices from control and hyperammonemic rats and analyze different features of the excitatory postsynaptic potentials.Hyperammonemia reduces the amplitude and delays appearance of ampa epsps, whereas increases amplitude, hyperpolarization, depolarization and desensitization area of the nmda epsps.These alterations in ampa and nmda function are accentuated as the stimulation intensity increases.Adding extracellular c gmp reverses the alteration in amplitude in both, ampa and nmda epsps.In control slices extracellular c gmp decreases the ampa and nmda epsps amplitude and delays the response of neurons and the return to the resting potential at all stimulation intensities.In conclusion, hyperammonemia decreases the ampa response, whereas increases the nmda response and extracellular c gmp reverses these alterations.

Journal: Neurochemical research (2022)
Publication types: Journal Article
Automated multicolor mesoscopic imaging for the 3-dimensional reconstruction of fluorescent biomarker distribution in large tissue specimens.

Research in translational medicine often requires high-resolution characterization techniques to visualize or quantify the fluorescent probes.For example, drug delivery systems contain fluorescent molecules enabling in vitro and in vivo tracing to determine biodistribution or plasma disappearance.Albeit fluorescence imaging systems with sufficient resolution exist, the sample preparation is typically too complex to image a whole organism of the size of a mouse.This article established a mesoscopic imaging technique utilizing a commercially available cryo-microtome and an in-house built episcopic imaging add-on to perform imaging during serial sectioning.Here we demonstrate that our automated red, green, blue (rgb) and fluorescence mesoscope can generate sequential block-face and 3-dimensional anatomical images at variable thickness with high quality of 6 μm × 6 μm pixel size.In addition, this mesoscope features a numerical aperture of 0.10 and a field-of-view of up to 21.6 mm × 27 mm × 25 mm (width, height, depth).

Journal: Biomedical optics express (2022)
Publication types: Journal Article
NEDD4 attenuates phosgene-induced acute lung injury through the inhibition of Notch1 activation.

Phosgene gas leakage can cause life-threatening acute lung injury (ali), which is characterized by inflammation, increased vascular permeability, pulmonary oedema and oxidative stress.Although the downregulation of neuronal precursor cell-expressed developmentally downregulated 4 (nedd4) is known to be associated with inflammation and oxidative damage, its functions in phosgene-induced ali remain unclear.In this study, rats with phosgene-induced ali were intravenously injected with nedd4-overexpressing lentiviruses to determine the functions of nedd4 in this inflammatory condition.Nedd4 expression was decreased in the lung parenchyma of phosgene-exposed control rats, whereas its expression level was high in the nedd4-overexpressing rats.Phosgene exposure increased the wet-to-dry lung weight ratio, but nedd4 abrogated this effect.Nedd4 overexpression attenuated phosgene-induced lung inflammation, lowering the high lung injury score (based on total protein, inflammatory cells and inflammatory factors in bronchoalveolar lavage fluid) and also reduced phosgene-induced oxidative stress and cell apoptosis.Finally, nedd4 was found to interact with notch1, enhancing its ubiquitination and thereby its degradation, thus attenuating the inflammatory responses to ali.Therefore, we demonstrated that nedd4 plays a protective role in alleviating phosgene-induced ali, suggesting that enhancing the effect of nedd4 may be a new approach for treating phosgene-induced ali.

Journal: Journal of cellular and molecular medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Drained and undrained heat capacity of swelling clays.

In microporous materials, poromechanical drained (open pore) and undrained (close pore) conditions play a role in the thermo-mechanical properties, which can also be affected by specific ion effects.Heat capacity is a key property to understanding the thermo-hydro-mechanical behavior of clays.However, there is a lack of bottom-up approaches aiming at capturing the influence of confined water and ion effects on the heat capacity of clays.We perform molecular dynamics simulations to obtain the heat capacity of na- and ca-montmorillonite using classical and semi-classical approaches.The heat of adsorption is computed from grand canonical monte carlo (gcmc) simulations under ambient conditions.We provide the theoretical framework to compute thedrainedheat capacity using the undrained heat capacity and the heat of adsorption.The semi-classical approach is required to capture the heat capacity of the solid mineral but cannot properly capture that of the inter-layer electrolyte.A hybrid approach is proposed, which combines the semi-classical approach for the mineral and the classical approach for the electrolyte.The undrained and drained heat capacities of clays evolve linearly with the water content, which leads to the conclusion that the effects of the mixing of hydration states are not significant.Undrained heat capacity is almost independent of the counterion nature.In contrast, the overall trends of drained heat capacity plotted against the water content exhibit larger values for na-mmt than for ca-mmt.Our results are in agreement with experimental data for a variety of smectites.

Journal: Physical chemistry chemical physics : PCCP (2022)
Publication types: Journal Article
Development of a prognostic nomogram based on an eight-gene signature for esophageal squamous cell carcinoma by weighted gene co-expression network analysis (WGCNA).

Esophageal squamous cell carcinoma (escc) is a highly aggressive malignant tumor.This study aims to develop a robust prognostic model for escc.Methods expression profiles of escc were downloaded from the gene expression omnibus (geo) and the cancer genome atlas (tcga) databases.Co-expressed modules were constructed by weighted gene co-expression network analysis (wgcna).Differentially expressed genes (degs) between escc and normal samples were identified with the screening criteria of adjusted p value 1.After univariate and multivariate cox regression analysis, an 8-gene module was constructed.A receiver operating characteristic (roc) curve for overall survival (os) was used to assess the prediction efficacy of the risk score.A nomogram was developed based on the risk score, age, gender, and stage for 1-, 2- and 3-year survival.The potential biological functions and pathways of the 8 genes were predicted using the metascape database.Results the 2 escc-related co-expression modules were built via wgcna.Among all degs, 55 survival-related genes were identified for escc.Based on these genes, an 8-gene module was constructed, composed of cfap53, fcgr2a, fcgr3a, gngt1, igf2, linc01524, magea3,and magea6.The area under the curve (auc) was 0.961, suggesting that the risk score could effectively predict the os of patients with escc.Furthermore, the nomogram exhibited high accuracy in predicting the survival rate of escc patients at 1, 2, and 3 years.These genes were mainly involved in escc-related pathways such as extracellular matrix organization, collagen formation, and blood vessel development.Conclusions our nomogram based on the 8-gene risk score could be a reliable prognostic tool for escc.

Journal: Annals of translational medicine (2022)
Publication types: Journal Article