syedzayyan/paper_mill_benchmark huggingface dataset:
Dietary taurine supplementation counteracts deoxynivalenol-induced liver injury via alleviating oxidative stress, mitochondrial dysfunction, apoptosis, and inflammation in piglets.

Deoxynivalenol (don), as a widespread fusarium mycotoxin in cereals, food products, and animal feed, is detrimental to both human and animal health.The liver is not only the primary organ responsible for don metabolism but also the principal organ affected by don toxicity.Taurine is well known to display various physiological and pharmacological functions due to its antioxidant and anti-inflammatory properties.However, the information regarding taurine supplementation counteracting don-induced liver injury in piglets is still unclear.In our work, twenty-four weaned piglets were subjected to four groups for a 24-day period, including the bd group (a basal diet), the don group (3 mg/kg don-contaminated diet), the don+lt group (3 mg/kg don-contaminated diet + 0.3% taurine), and the don+ht group (3 mg/kg don-contaminated diet + 0.6% taurine).Our findings indicated that taurine supplementation improved growth performance and alleviated don-induced liver injury, as evidenced by the reduced pathological and serum biochemical changes (alt, ast, alp, and ldh), especially in the group with the 0.3% taurine.Taurine could counteract hepatic oxidative stress in piglets exposed to don, as it reduced ros, 8-ohd g, and mda concentrations and improved the activity of antioxidant enzymes.Concurrently, taurine was observed to upregulate the expression of key factors involved in mitochondrial function and the nrf2 signaling pathway.Furthermore, taurine treatment effectively attenuated don-induced hepatocyte apoptosis, as verified through the decreased proportion of tunel-positive cells and regulation of the mitochondria-mediated apoptosis pathway.Finally, the administration of taurine was able to reduce liver inflammation due to don, by inactivating the nf-κb signaling pathway and declining the production of pro-inflammatory cytokines.In summary, our results implied that taurine effectively improved don-induced liver injury.The underlying mechanism should be that taurine restored mitochondrial normal function and antagonized oxidative stress, thereby reducing apoptosis and inflammatory responses in the liver of weaned piglets.

Journal: Ecotoxicology and environmental safety (2023)
Publication types: Journal Article
Manual stabilization reveals a transient role for balance control during locomotor adaptation.

A fundamental feature of human locomotor control is the need to adapt walking patterns in response to changes in the environment.For example, when people walk on a split-belt treadmill, which has belts that move at different speeds, they adapt to the asymmetric speed constraints by reducing spatiotemporal asymmetry.Here, we aim to understand the role of balance control as a potential factor driving this adaptation process.We recruited 24 healthy, young adults to adapt to walking on a split-belt treadmill while either holding on to a handrail or walking with free arm swing.We measured whole body angular momentum and step length asymmetry as measures of dynamic balance and spatiotemporal asymmetry, respectively.To understand how changes in intersegmental coordination influenced whole body angular momentum, we also measured segmental angular momenta and the coefficient of cancellation.When participants were initially exposed to the asymmetry in belt speeds, we observed an increase in whole body angular momentum that was due to both an increase in the momentum of individual segments and a reduction in the coefficient of cancellation.Holding on to a handrail reduced the perturbation to asymmetry during the early phase of adaptation and resulted in a smaller aftereffect during early postadaptation.In addition, the stabilization provided by holding on to a handrail led to reductions in the coupling between angular momentum and asymmetry.These results suggest that regulation of dynamic balance is most important during the initial, transient phase of adaptation to walking on a split-belt treadmill.new & noteworthywe investigated the role of dynamic balance during adaptation to a split-belt treadmill by measuring whole body angular momentum with or without holding on to a handrail.The initial step length asymmetry and associations between balance and asymmetry reduced when holding on to a handrail during early adaptation.These findings indicate that dynamic balance mostly contributes to the initial phase of adaptation when people are exposed to an asymmetric walking constraint.

Journal: Journal of neurophysiology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Molecular ontology of the parabrachial nucleus.

Diverse neurons in the parabrachial nucleus (pb) communicate with widespread brain regions.Despite evidence linking them to a variety of homeostatic functions, it remains difficult to determine which pb neurons influence which functions because their subpopulations intermingle extensively.An improved framework for identifying these intermingled subpopulations would help advance our understanding of neural circuit functions linked to this region.Here, we present the foundation of a developmental-genetic ontology that classifies pb neurons based on their intrinsic, molecular features.By combining transcription factor labeling with cre fate-mapping, we find that the pb is a blend of two, developmentally distinct macropopulations of glutamatergic neurons.Neurons in the first macropopulation express lmx1b (and, to a lesser extent, lmx1a) and are mutually exclusive with those in a second macropopulation, which derive from precursors expressing atoh1.This second, atoh1-derived macropopulation includes many foxp2-expressing neurons, but foxp2 also identifies a subset of lmx1b-expressing neurons in the kölliker-fuse nucleus (kf) and a population of gabaergic neurons ventrolateral to the pb ("caudal kf").Immediately ventral to the pb, phox2b-expressing glutamatergic neurons (some coexpressing lmx1b) occupy the kf, supratrigeminal nucleus, and reticular formation.We show that this molecular framework organizes subsidiary patterns of adult gene expression (including satb2, calca, grp, and pdyn) and predicts output projections to the amygdala (lmx1b), hypothalamus (atoh1), and hindbrain (phox2b/lmx1b).Using this molecular ontology to organize, interpret, and communicate pb-related information could accelerate the translation of experimental findings from animal models to human patients.

Journal: The Journal of comparative neurology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Dosimetric analysis of MR-LINAC treatment plans for salvage spine SBRT re-irradiation.

We investigated the feasibility of thoracic spine stereotactic body radiotherapy (sbrt) using the elekta unity magnetic resonance-guided linear accelerator (mrl) in patients who received prior radiotherapy.We hypothesized that monaco treatment plans can improve the gross tumor volume minimum dose (gtvmin) with spinal cord preservation and maintain consistent plan quality during daily adaptation.Methods pinnacle clinical plans for 10 patients who underwent thoracic spine sbrt (after prior radiotherapy) were regenerated in the monaco treatment planning system for the elekta unity mrl using 9 and 13 intensity-modulated radiotherapy (imrt) beams.Monaco adapt-to-position (atp) and adapt-to-shape (ats) workflow plans were generated using magnetic resonance imaging with a simulated daily positional setup deviation, and these adaptive plans were compared with monaco reference plans.Plan quality measures included target coverage, paddick conformity index, gradient index, homogeneity index, spinal cord d0.01cc, esophagus d0.01cc, lung v10, and skin d0.01cc.Results gtvmin values from the monaco 9-beam and 13-beam plans were significantly higher than those from pinnacle plans (p < 0.01) with similar spinal cord dose.Spinal cord d0.01cc, esophagus d0.01cc, and lung v10 did not statistically differ among the three plans.The electron-return effect did not induce remarkable dose effects around the lungs or skin.While in the atp workflow, a large increase in gtvmin was observed at the cost of a 10%-50% increase in spinal cord d0.01cc, in the ats workflow, the spinal cord dose increase was maintained within 3% of the reference plan.Conclusion these findings show that mrl plans for thoracic spine sbrt are safe and feasible, allowing tumor dose escalation with spinal cord preservation and consistent daily plan adaptation using the ats workflow.Careful plan review of hot spots and lung dose is necessary for safe mrl-based treatment.

Journal: Journal of applied clinical medical physics (2022)
Publication types: Journal Article
An ominous cause of back pain: Vertebral Osteomyelitis.

The authors present the case of a patient seen for back pain in the emergency department, initially discharged home with a diagnosis of musculoskeletal pain.He returned a week later and was found to have vertebral osteomyelitis based on a thorough neurologic exam.A review of ominous causes of back pain, including the elusive nature of vertebral osteomyelitis/diskitis is discussed.

Journal: Orthopedic reviews (2022)
Publication types: Journal Article
Selective adsorption of lead(II) from aqueous solution.

Adsorptive separation of pb(ii) from aqueous solution containing pb(ii) and other heavy metals (cu(ii), zn(ii) and cd(ii)) has been investigated, using three adsorbents, such as an iminodiacetic acid-chelating resin (cr11) and fe-based adsorbents (goethite and magnetite).Batchwise adsorption of pb(ii) and other metal ions in single metal system and multi-components system was carried out with varying parameters, such as p h, time and initial concentrations of metals.Cr11 possesses the highest adsorption ability for these metals, while the selectivity of individual metal is little.Goethite possesses selectivity for pb(ii) and cu(ii), and magnetite possesses selectivity for pb(ii), though the adsorption capacity for the metals is less than those with cr11.The kinetics of the adsorption of metals with all adsorbents is of pseudo-second-order, and the magnetite is revealed to have the fastest adsorption kinetics.The three adsorbents can be applied for chromatographic separation for these metals.The magnetite is feasible for selective separation of pb(ii), although complete elution cannot be achieved.

Journal: Environmental technology (2022)
Publication types: Journal Article
Opportunities and challenges in machine learning-based newborn screening-A systematic literature review.

The development and continuous optimization of newborn screening (nbs) programs remains an important and challenging task due to the low prevalence of screened diseases and high sensitivity requirements for screening methods.Recently, different machine learning (ml) methods have been applied to support nbs.However, most studies only focus on single diseases or specific ml techniques making it difficult to draw conclusions on which methods are best to implement.Therefore, we performed a systematic literature review of peer-reviewed publications on ml-based nbs methods.Overall, 125 related papers, published in the past two decades, were collected for the study, and 17 met the inclusion criteria.We analyzed the opportunities and challenges of ml methods for nbs including data preprocessing, classification models and pattern recognition methods based on their underlying approaches, data requirements, interpretability on a modular level, and performance.In general, ml methods have the potential to reduce the false positive rate and identify so far unknown metabolic patterns within nbs data.Our analysis revealed, that, among the presented, logistic regression analysis and support vector machines seem to be valuable candidates for nbs.However, due to the variety of diseases and methods, a general recommendation for a single method in nbs is not possible.Instead, these methods should be further investigated and compared to other approaches in comprehensive studies as they show promising results in nbs applications.

Journal: JIMD reports (2022)
Publication types: Journal Article
Colorimetric Detection of SARS-CoV-2 Using Plasmonic Biosensors and Smartphones.

Low-cost, instrument-free colorimetric tests were developed to detect sars-co v-2 using plasmonic biosensors with au nanoparticles functionalized with polyclonal antibodies (f-au nps).Intense color changes were noted with the naked eye owing to plasmon coupling when f-au nps form clusters on the virus, with high sensitivity and a detection limit of 0.28 pfu m l-1(pfu stands for plaque-forming units) in human saliva.Plasmon coupling was corroborated with computer simulations using the finite-difference time-domain (fdtd) method.The strategies based on preparing plasmonic biosensors with f-au nps are robust to permit sars-co v-2 detection via dynamic light scattering and uv-vis spectroscopy without interference from other viruses, such as influenza and dengue viruses.The diagnosis was made with a smartphone app after processing the images collected from the smartphone camera, measuring the concentration of sars-co v-2.Both image processing and machine learning algorithms were found to provide covid-19 diagnosis with 100% accuracy for saliva samples.In subsidiary experiments, we observed that the biosensor could be used to detect the virus in river waters without pretreatment.With fast responses and requiring small sample amounts (only 20 μl), these colorimetric tests can be deployed in any location within the point-of-care diagnosis paradigm for epidemiological control.

Journal: ACS applied materials & interfaces (2022)
Publication types: Journal Article
Applications of node-based resilience graph theoretic framework to clustering autism spectrum disorders phenotypes.

With the growing ubiquity of data in network form, clustering in the context of a network, represented as a graph, has become increasingly important.Clustering is a very useful data exploratory machine learning tool that allows us to make better sense of heterogeneous data by grouping data with similar attributes based on some criteria.This paper investigates the application of a novel graph theoretic clustering method, node-based resilience clustering (nbr-clust), to address the heterogeneity of autism spectrum disorder (asd) and identify meaningful subgroups.The hypothesis is that analysis of these subgroups would reveal relevant biomarkers that would provide a better understanding of asd phenotypic heterogeneity useful for further asd studies.We address appropriate graph constructions suited for representing the asd phenotype data.The sample population is drawn from a very large rigorous dataset: simons simplex collection (ssc).Analysis of the results performed using graph quality measures, internal cluster validation measures, and clinical analysis outcome demonstrate the potential usefulness of resilience measure clustering for biomedical datasets.We also conduct feature extraction analysis to characterize relevant biomarkers that delineate the resulting subgroups.The optimal results obtained favored predominantly a 5-cluster configuration.

Journal: Applied network science (2018)
Publication types: Journal Article
Renal localization and regulation by dietary phosphate of the MCT14 orphan transporter.

Mct14 is an orphan transporter belonging to the slc16 transporter family mediating the transport of monocarboxylates, aromatic amino acids, creatine, and thyroid hormones.The expression, tissue localization, regulation, and function of mct14 are unknown.In mouse mct14 m rna abundance is highest in kidney.Using a newly developed and validated antibody, mct14 was localized to the luminal membrane of the thick ascending limb of the loop of henle colocalizing in the same cells with uromodulin and nkcc2.Mct14 m rna and protein was found to be highly regulated by dietary phosphate intake in mice being increased by high dietary phosphate intake at both m rna and protein level.In order to identify the transport substrate(s), we expressed mct14 in xenopus laevis oocytes where mct14 was integrated into the plasma membrane.However, no transport was discovered for the classic substrates of the slc16 family nor for phosphate.In summary, mct14 is an orphan transporter regulated by phosphate and highly enriched in kidney localizing to the luminal membrane of one specific nephron segment.

Journal: PloS one (2017)
Publication types: Journal Article
Hallmark microRNA signature in liquid biopsy identifies hepatocellular carcinoma and differentiates it from liver metastasis.

This study aims to develop a liquid biopsy assay to identify hcc and differentially diagnose hepatocellular carcinoma (hcc) from colorectal carcinoma (crc) liver metastasis.methods:thirty-two micro rnas ("hall mark-32" panel) were designed to target the ten cancer hallmarks in hcc.Quantitative pcr and supervised machine learning models were applied to develop an hcc-specific diagnostic model.One hundred thirty-three plasma samples from intermediate-stage hcc patients, colorectal cancer (crc) patients with liver metastasis, and healthy individuals were examined.results:six differentially expressed micro rnas ("signature-six" panel) were identified after comparing hcc and healthy individuals.The micro rna mi r-221-3p, mi r-223-3p, mi r-26a-5p, and mi r-30c-5p were significantly down-regulated in the plasma of hcc samples, while mi r-365a-3p and mi r-423-3p were significantly up-regulated.Machine learning models combined with hall mark-32 and signature-six panels demonstrated promising performance with an auc of 0.85-0.96 (p≤ 0.018) and 0.84-0.93 (p≤ 0.021), respectively.Further modeling improvement by adjusting sample quality variation in the hall mark-32 panel boosted the accuracy to 95% ± 0.01 and auc to 0.991 (95% ci 0.96-1,p= 0.001), respectively.Even in alpha fetoprotein (afp)-negative (< 20ng/m l) hcc samples, hall mark-32 still achieved 100% sensitivity in identifying hcc.The cancer genome atlas (tcga, n=372) analysis demonstrated a significant association between hall mark-32 and hcc patient survival.conclusion:to the best of our knowledge, this is the first report to utilize circulating mi rnas and machine learning to differentiate hcc from crc liver metastasis.In this setting, hall mark-32 and signature-six are promising non-invasive tests for hcc differential diagnosis and distinguishing hcc from healthy individuals.

Journal: Journal of Cancer (2021)
Publication types: Journal Article
Tacrolimus time-in-therapeutic range is associated with freedom from acute rejection and graft failure following intestinal transplantation.

Trough-adjusted tacrolimus is commonly prescribed following intestinal transplantation to prevent allograft rejection.Despite established practice, there remains limited direct evidence linking tacrolimus levels with improved clinical outcomes.Methods this was a single-center review of all adult non-liver containing intestinal allograft recipients from 2011 to 2018.Patients received lymphocyte depleting induction and maintenance immunosuppression consisting of tacrolimus and a corticosteroid taper.Tacrolimus time-in-therapeutic range (tac-ttr) was calculated for all patients from the date of transplant until 1-year post-transplant using rosendaal's method.Cox-proportional hazards modeling was utilized to assess freedom from acute rejection and graft failure stratified by tac-ttr quartile.Results 47 patients were included in the review.Mean tac-ttr for the cohort was 30.2% ± 11.4.Fifteen episodes of acute rejection were observed, 8 of which were severe.Patients in the highest tac-ttr quartile >36% had a lower incidence of acute rejection and graft failure relative to patients with a tac-ttr <20%.Cox-proportional hazards modeling found a 10% decrease in tac-ttr was associated with an increased hazard for acute rejection (2.03), severe acute rejection (2.19), and graft loss (3.33).Conclusion the results of this study suggest that decreasing tac-ttr is a risk factor for both acute rejection as well as intestinal allograft failure.

Journal: Clinical transplantation (2021)
Publication types: Journal Article
Comparison of a Minimally Invasive Tissue-Sparing Posterior Superior (TSPS) Approach and the Standard Posterior Approach for Hip Replacement.

The purpose of this study is to compare the functional and clinical outcomes, blood loss, complication rate, and hospital length of stay (los) of total hip replacement (thr) using a minimally invasive tissue-sparing posterior superior (tsps) approach and the standard posterior approach.Materials and methods this retrospective, observational, double-centered study included 38 patients undergoing hip replacement.The patents were divided into two groups: control group (19 patients), who underwent surgery with the standard posterior approach, and treatment group (19 patients), who received the same type of implant with ceramic-on-ceramic bearing via the tsps approach.Hemoglobin level was assessed preoperatively, on first and second postoperative days, and on discharge day.Harris hip score and western ontario and mc master universities arthritis index were used to measure the clinical and functional outcomes.Hospital los and incidence of early and late complications were assessed in both groups.Postoperative anteroposterior pelvis x-ray was performed to assess the correct positioning of implants.Results better early clinical outcomes (p= 0.0155), lesser blood loss (p< 0.0001), and reduced hospital los (p< 0.0001) were observed in the tsps group than in the control group.No major adverse effects occurred in both groups, and a satisfactory implant orientation was achieved in all patients.Conclusions the tsps approach is a reliable minimally invasive procedure for thr as it allows an accurate orientation of the components and provides better early postoperative functional outcomes, faster recovery, significantly lower blood loss, and shorter hospital los than the standard posterior approach.However, further research is needed to confirm the promising results and cost-effectiveness of the tsps approach in larger cohorts with a longer follow-up period.

Journal: BioMed research international (2022)
Publication types: Journal Article;Observational Study