syedzayyan/paper_mill_benchmark huggingface dataset:
Differential gene expression analysis following olfactory learning in honeybee (Apis mellifera L.).

Insects change their stimulus-response through the perception of associating these stimuli with important survival events such as rewards, threats, and mates.Insects develop strong associations and relate them to their experiences through several behavioral procedures.Among the insects, apis species, apis mellifera ligustica are known for their outstanding ability to learn with tremendous economic importance.Apis mellifera ligustica has a strong cognitive ability and promising model species for investigating the neurobiological basis of remarkable olfactory learning abilities.Here we evaluated the olfactory learning ability of a.Mellifera by using the proboscis extension reflex (per) protocol.The brains of the learner and failed-learner bees were examined for comparative transcriptome analysis by rna-seq to explain the difference in the learning capacity.In this study, we used an appetitive olfactory learning paradigm in the same age of a.Mellifera bees to examine the differential gene expression in the brain of the learner and failed-learner.Bees that respond in 2nd and 3rd trials or only responded to 3rd trials were defined as learned bees, failed-learner individuals were those bees that did not respond in all learning trials the results indicate that the learning ability of learner bees was significantly higher than failed-learner bees for 12 days.We obtained approximately 46.7 and 46.4 million clean reads from the learner bees failed-learner bees, respectively.Gene expression profile between learners' bees and failed-learners bees identified 74 differentially expressed genes, 57 genes up-regulated in the brains of learners and 17 genes were down-regulated in the brains of the bees that fail to learn.The q rt-pcr validated the differently expressed genes.Transcriptome analyses revealed that specific genes in learner and failed-learner bees either down-regulated or up-regulated play a crucial role in brain development and learning behavior.Our finding suggests that down-regulated genes of the brain involved in the integumentary system, storage proteins, brain development, sensory processing, and neurodegenerative disorder may result in reduced olfactory discrimination and olfactory sensitivity in failed-learner bees.This study aims to contribute to a better understanding of the olfactory learning behavior and gene expression information, which opens the door for understanding of the molecular mechanism of olfactory learning behavior in honeybees.

Journal: PloS one (2022)
Publication types: Journal Article
Does asymmetry in patient recruitment in large critical care trials follow the Pareto principle?

Randomised controlled trials (rct) may be hindered by slow recruitment rates, particularly in critically ill patients.While statistical models to predict recruitment rates have been described, no systematic assessment has been conducted of the distribution of recruitment across sites, temporal trends in site participation and impact of competing trials on patient recruitment.Methods we used recruitment and screening logs from the safe, nice-sugar, renal, chest and adrenal trials, five of the largest critical care rcts.We quantified the extent of recruitment asymmetry between sites using lorenz curves and gini coefficients and assessed whether the recruitment distribution across sites follow the pareto principle, which states that 80% of effects come from 20% of causes.Peak recruitment rates and growth in participating sites were calculated.Results in total, 25,412 patients were randomised in 99 intensive care units (icus) for the five trials.Distribution of recruitment was asymmetric, with a small number of icus recruiting a large proportion of the patients.The gini coefficients ranged from 0.14 to 0.52.The time to peak recruitment rate ranged from 7 to 41 months and was variable (7, 31, 41, 10 and 40 months).Over time, the proportion of recruitment at non-tertiary icus increased from 15% to 34%.Conclusions there is asymmetry of recruitment with a small proportion of icus recruiting a large proportion of patients.The distributions of recruitment were not consistent with the pareto principle.There has been increasing participation of non-tertiary icus in clinical trials.

Journal: Trials (2020)
Publication types: Journal Article
Effect of resistance training with and without vitamin D calcium chitosan nanoparticle supplements on apoptosis markers in ovariectomized rats: An experimental study.

Hormone therapy is one of the most effective treatments for menopausal disorders, but it may increase the risk of breast cancer, coronary heart disease, and pulmonary embolism.Objective the present study investigated the effect of resistance training with and without vitamin d calcium(ca++) chitosan nanoparticles on apoptosis markers in ovariectomized rats.Materials and methods 42 female wistar rats were divided into 7 groups (n = 6/each).One group was assigned as the healthy controls to show the induction of menopause.The other 6 groups comprised ovariectomized (ovx) animals including: 1) vitamin d + calcium + chitosan + resistance training, 2) saline + estrogen + resistance training, 3) saline + resistance training, 4) vitamin d + calcium + chitosan, 5) saline + estrogen, and 6) ovx + control.48 hr after the last intervention, the hippocampus tissue was extracted to measure the bcl-2-associated x (bax), b-cell lymphoma 2 (bcl-2), and caspase-3 gene expression as well as the percentage of dead cells.Results ovx rats demonstrated increased baxgene expression, ratio of baxgene expression to bcl-2, caspase-3 gene expression, and percentage of dead cells of hippocampal tissue, but decreased bcl-2gene expression.Resistance training and vitamin d ca++chitosan nanoparticle supplements seemed to reverse these changes.Conclusion the combination of resistance training and vitamin d ca++chitosan nanoparticle supplements may be considered a non-pharmacological treatment for ovx-induced apoptosis.

Journal: International journal of reproductive biomedicine (2022)
Publication types: Journal Article
Investigation of blood leptin and adropin levels in patients with multiple sclerosis: A CONSORT-clinical study.

The effects of adipokines have been investigated in multiple sclerosis (ms) in the literature.Results are uncertain, and subgroups like adropin have not been previously studied.We primarily aimed to determine leptin and adropin levels in ms and their potential use as a biomarker.Methods this study was an experimental research.While 44 ms patients diagnosed according to mc donald criteria were included in the patient group, 40 people without ms diagnosis and risk factors took part in the control group.Demographic data, height, weight, body mass index, blood glucose, thyroid-stimulating hormone, alanine transaminase, aspartate transaminase, creatinine, low-density lipoprotein, leptin, adropin levels, presence of hypertension, diabetes mellitus, coronary artery disease were recorded.Expanded disability status scale and disease duration were also evaluated in the patient group.Our data were presented as mean ± standard deviations.Results the mean blood leptin value of the patient group (6.12 ± 5.34 ng/m l) was significantly lower than the value of the control group (13.02 ± 8.25 ng/m l) (p .001).Conclusion this is the first study that has evaluated adropin levels in patients with ms.The relationship between ms and leptin levels is still unclear.Therefore, our study might be helpful to elucidate ms pathogenesis and provide supportive criteria for diagnosis.

Journal: Medicine (2021)
Publication types: Journal Article
Revealing the Mechanism of Irreversible Binding of Antifreeze Glycoproteins to Ice.

Antifreeze glycoproteins (afgps) are a special kind of antifreeze proteins with strong flexibility.Whether their antifreeze activity is achieved by reversibly or irreversibly binding to ice is widely debated, and the molecular mechanism of irreversible binding remains unclear.In this work, the antifreeze mechanism of the smallest afgp isoform, afgp8, is investigated at the atomic level.The results indicate that afgp8 can bind to ice both reversibly through its hydrophobic methyl groups (peptide binding) and irreversibly through its hydrophilic disaccharide moieties (saccharide binding).Although peptide binding occurs faster than saccharide binding, free-energy calculations indicate that the latter is energetically more favorable.In saccharide binding, at least one disaccharide moiety is frozen in the grown ice, resulting in irreversible binding, while the other moieties significantly perturb the water hydrogen-bonding network, thus inhibiting ice growth more effectively.The present study reveals the coexistence of reversible and irreversible bindings of afgp8, both contributing to the inhibition of ice growth and further provides molecular mechanism of irreversible binding.

Journal: The journal of physical chemistry. B (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
New class of benzothiophene morpholine analogues with high selectivity and affinity were designed and evaluated for anti-drug addiction.

To probe the mechanism of dopamine receptors in drug addiction and look for potential new methods for treating this disease, we have designed and synthesized benzothiophene morpholine analogues that were considered as dopamine d3 receptor-selective ligands.Radioligand binding assay was used to determine the binding affinity of target compounds.Members of this class have great selectivity and binding affinity in d3 receptor.In addition, the ability of these compounds to mitigate the symptoms of addiction from opioids was investigated in animal behavior patterns, and we have found that two compounds (18a and 18d) have good affinity in the d3r and exhibit the efficacy of anti-drug addiction in morphine-dependent mice induced by naloxone.

Journal: Chemical biology & drug design (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Late sequelae of drug reaction with eosinophilia and systemic symptoms (DRESS) cause thyroid dysfunction and thyroiditis: review of literature.

Drug reaction with eosinophilia and systemic symptoms (dress) is one of the severe cutaneous adverse drug reactions (scars) with high mortality rate and variable long term sequelae, especially in thyroid dysfunction and thyroiditis.In this article, we review clinical course, culprit drugs, onset of diagnosis, and type of thyroid dysfunction in dress patients.There were a total of 51 cases including 12 children (aged less than 18 years old) and 39 adults from our review.The most common thyroid dysfunction was hashimoto's thyroiditis (41/51=80.4%) including anti-thyroid antibody positive (29/51=56.9%), possible/compatible with hashimoto's thyroiditis (12/51=23.5%) both in the children (n=12) and adult (n=39), graves' disease/hyperthyroidism (7/51=13.7%) and non-specific hypothyroidism (3/51=5.9%), respectively.The most common culprit drugs and onset of thyroid dysfunction after dress diagnosis in children aged less than 18 years include antiepileptic drugs (phenytoin, phenobarbital, carbamazepine) (range 0-8 months, median 2 months) and sulfa groups (sulfasalazine, sulfamethoxazole, sulfonamide) (range 1-4 months, median 2 months).Data of prevalence, type, and clinical course of thyroid dysfunction from dress is important for clinicians to recognize for monitoring its sequelae and provide plans for treatment.

Journal: Journal of pediatric endocrinology & metabolism : JPEM (2022)
Publication types: Journal Article;Review
In Silico Analysis and Synthesis of Nafamostat Derivatives and Evaluation of Their Anti-SARS-CoV-2 Activity.

Inhibition of transmembrane serine protease 2 (tmprss2) is expected to block the spike protein-mediated fusion of severe acute respiratory syndrome coronavirus 2 (sars-co v-2).Nafamostat, a potent tmprss2 inhibitor as well as a candidate for anti-sars-co v-2 drug, possesses the same acyl substructure as camostat, but is known to have a greater antiviral effect.A unique aspect of the molecular binding of nafamostat has been recently reported to be the formation of a covalent bond between its acyl substructure and ser441 in tmprss2.In this study, we investigated crucial elements that cause the difference in anti-sars-co v-2 activity of nafamostat and camostat.In silico analysis showed that asp435 significantly contributes to the binding of nafamostat and camostat to tmprss2, while glu299 interacts strongly only with nafamostat.The estimated binding affinity for each compound with tmprss2 was actually consistent with the higher activity of nafamostat; however, the evaluation of the newly synthesized nafamostat derivatives revealed that the predicted binding affinity did not correlate with their anti-sars-co v-2 activity measured by the cytopathic effect (cpe) inhibition assay.It was further shown that the substitution of the ester bond with amide bond in nafamostat resulted in significantly weakened anti-sars-co v-2 activity.These results strongly indicate that the ease of covalent bond formation with ser441 in tmprss2 possibly plays a major role in the anti-sars-co v-2 effect of nafamostat and its derivatives.

Journal: Viruses (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Biophysical tools to study the oligomerization dynamics of Prx1-class peroxiredoxins.

Peroxiredoxins (prx) are ubiquitous, highly conserved peroxidases whose activity depends on catalytic cysteine residues.The prx1-class of the peroxiredoxin family, also called typical 2-cys prx, organize as head-to-tail homodimers containing two active sites.The peroxidatic cysteine cpof one monomer reacts with the peroxide substrate to form sulfenic acid that reacts with the resolving cysteine (cr) of the adjacent subunit to form an intermolecular disulfide, that is reduced back by the thioredoxin/thioredoxin reductase/nadph system.Although the minimal catalytic unit is the dimer, these prx oligomerize into (do)decamers.In addition, these ring-shaped decamers can pile-up into high molecular weight structures.Prx not only display peroxidase activity reducing h2o2, peroxynitrous acid and lipid hydroperoxides (antioxidant enzymes), but also exhibit holdase activity protecting other proteins from unfolding (molecular chaperones).Highly relevant is their participation in redox cellular signaling that is currently under active investigation.The different activities attributed to prx are strongly ligated to their quaternary structure.In this review, we will describe different biophysical approaches used to characterize the oligomerization dynamics of prx that include the classical size-exclusion chromatography, analytical ultracentrifugation, calorimetry, and also fluorescence anisotropy and lifetime measurements, as well as mass photometry.

Journal: Biophysical reviews (2023)
Publication types: Journal Article;Review
Infant and young child nutritional status and their caregivers' feeding knowledge and hygiene practices in internally displaced person camps, Somalia.

In an attempt to design an educational programme targeting caregivers of children aged 6 to 59 months in internally displaced persons camps in somalia, the objective of this study was twofold.First, to explore the nutritional situation of all children aged 6-59 months enrolled in a nutrition programme provided by save the children in 2017 in internally displaced persons camps.Second, to identify gaps in the caregivers' hygiene and feeding practices.Methods in a study of 1655 households, 1655 caregivers for 2370 children aged 6 to 59 months enrolled in a nutrition programme provided by save the children answered an adapted questionnaire on hygiene and feeding practices.At the same time, based on standard criteria in the questionnaire, naturalistic observations of caregivers' hygiene practices were conducted.Every child in the study was measured with anthropometric mid-upper-arm circumference measurements for the classification of moderate acute malnutrition, severe acute malnutrition and global acute malnutrition.Descriptive statistics were used for analysis.Results 1) there was severe (12.1%) and global acute (19.9%) malnutrition among children included in the nutrition programme, more frequently in the 6-24 month age group compared to the 25-59 month age group (p< 0.01).2).The practices in the households were below what could generally be considered hygienic.3) there was poor caregivers' knowledge of breastfeeding benefits and complementary foods.Conclusion child malnutrition might derive from gaps in the caregiver's knowledge, attitudes, and practices regarding hygiene and infant feeding.An awareness of these gaps can be helpful in designing future educational programmes that target caregivers, particularly in at-risk population groups.

Journal: BMC nutrition (2019)
Publication types: Journal Article
House Dust Mite Sublingual Immunotherapy in Children Versus Adults With Allergic Rhinitis.

There are only a few studies in which the clinical efficacy of slit has been compared between children and adults.In addition, there is a lack of research on other factors, associated with the treatment, including immunological parameters and quality of life (qol).Objective to compare the effects of sublingual immunotherapy (slit) in adults and children on various factors: clinical efficacy, quality of life (qol), satisfaction, immunological parameters, and adverse events.Methods subjects who were sensitized to house dust mites and treated with slit for at least 2 years were enrolled.Seventy patients who completed questionnaires measuring nasal symptoms and rhinoconjunctivitis quality of life questionnaire (rqlq) scores and underwent serologic tests for immunological parameters at initial, 1-year, and 2-year follow-up were selected and divided into two groups based on age: a child group (age 4-12 years, n = 44) and an adult group (age 19-59 years, n = 26).Results the total nasal symptom score (tnss) was significantly decreased after 2 years of slit in both the child and adult groups (p < 0.001, both); however, changes in tnss from baseline did not significantly differ between the two groups (p = 0.365).More patients in adult group were satisfied with slit than those in child group (p = 0.050), and changes in rqlq score from baseline tended to be larger in adult group (p = 0.089).The levels of immunological parameters at baseline were significantly higher in the child group than in the adult group; however, changes in the levels of these parameters were not significantly different.Conclusion although more adult patients were satisfied with slit, the clinical effects of slit on nasal symptoms were comparable between child and adult groups.Despite different immunological values at baseline between the two groups, changing patterns of immunological parameters did not differ.

Journal: American journal of rhinology & allergy (2021)
Publication types: Journal Article
A self-perpetuating repressive state of a viral replication protein blocks superinfection by the same virus.

Diverse animal and plant viruses block the re-infection of host cells by the same or highly similar viruses through superinfection exclusion (sie), a widely observed, yet poorly understood phenomenon.Here we demonstrate that sie of turnip crinkle virus (tcv) is exclusively determined by p28, one of the two replication proteins encoded by this virus.P28 expressed from a tcv replicon exerts strong sie to a different tcv replicon.Transiently expressed p28, delivered simultaneously with, or ahead of, a tcv replicon, largely recapitulates this repressive activity.Interestingly, p28-mediated sie is dramatically enhanced by c-terminally fused epitope tags or fluorescent proteins, but weakened by n-terminal modifications, and it inversely correlates with the ability of p28 to complement the replication of a p28-defective tcv replicon.Strikingly, p28 in sie-positive cells forms large, mobile punctate inclusions that trans-aggregate a non-coalescing, sie-defective, yet replication-competent p28 mutant.These results support a model postulating that tcv sie is caused by the formation of multimeric p28 complexes capable of intercepting fresh p28 monomers translated from superinfector genomes, thereby abolishing superinfector replication.This model could prove to be applicable to other rna viruses, and offer novel targets for antiviral therapy.

Journal: PLoS pathogens (2017)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Characterization of Moyamoya and Middle Cerebral Artery Diseases by Carotid Canal Diameter and RNF213 p.R4810K Genotype.

S it is sometimes difficult to differentiate middle cerebral artery disease from moyamoya disease because the two can present similarly yet have different treatment strategies.We investigated whether the presence of a narrow carotid canal and the rnf213 mutation can help differentiate between the two phenotypes.Population and methods we analyzed 78 patients with moyamoya disease, 27 patients with middle cerebral artery disease, and 79 controls from 2 facilities.The carotid canal diameter was measured using computed tomography.The p.r4810k mutation was genotyped by taq man assay.A receiver operating characteristics analysis was performed to assess the significance of the carotid canal diameter for the accurate diagnosis of moyamoya disease.Results the carotid canal diameter was significantly narrower in patients with moyamoya disease than in controls.The optimal cutoff values were 5.0 mm for adult males and 4.5 mm for adult females and children (sensitivity: 0.82; specificity: 0.92).Among the patients with middle cerebral artery disease, 18.5% and 25.0% of the affected hemispheres had the p.r4810k mutation and narrow canal (i.e., below the cutoff), respectively, whereas only 3.1% of those had both.Contrastingly, 68.8% of the affected hemispheres in patients with moyamoya disease had both these characteristics.Among the patients with moyamoya disease, those with the p.r4810k mutation tended to have narrower carotid canals.Conclusions although the presence of a narrow carotid canal or the p.r4810k mutation alone could not be used to distinguish those with moyamoya disease from those with middle cerebral artery disease, the combination of these factors could better characterize the two phenotypes.

Journal: Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association (2022)
Publication types: Journal Article
Two robust long short-term memory frameworks for trading stocks.

This paper aims to find a superior strategy for the daily trading on a portfolio of stocks for which traditional trading strategies perform poorly due to the low frequency of new information.The experimental work is divided into a set of traditional trading strategies and a set of long short-term memory networks.The networks incorporate general and specific trading patterns, where the former takes into account the universal decision factors for trading across many stocks, while the latter takes into account stock-specific decision factors.Our research shows that both long short-term memory networks, regardless of whether they are based on universal or stock-specific decision factors, significantly outperform traditional trading strategies.Interestingly, however, on average neither has the edge compared to the other, thus remaining ambivalent as to whether universality or specificality is to be preferred when it comes to designing long short-term memory networks for optimal trading.

Journal: Applied intelligence (Dordrecht, Netherlands) (2021)
Publication types: Journal Article