Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Cord Blood Derived Immature Basophils Show Dual Characteristics, Expressing Both Basophil and Eosinophil Associated Proteins

Basophils are blood cells of low abundance associated with allergy, inflammation and parasite infections. To study the transcriptome of mature circulating basophils cells were purified from buffy coats by density gradient centrifugations and two-step magnetic cell sorting. However, after extensive analysis the cells were found to be transcriptionally inactive and almost completely lack functional mRNA. In order to obtain transcriptionally active immature basophils for analysis of their transcriptome, umbilical cord blood cells were therefore cultured in the presence of interleukin (IL)-3 for 9 days and basophils were enriched by removing non-basophils using magnetic cell sorting. The majority of purified cells demonstrated typical metachromatic staining with Alcian blue dye (95%) and expression of surface markers FcεRI and CD203c, indicating a pure population of cells with basophil-like phenotype. mRNA was extracted from these cells and used to construct a cDNA library with approximately 600 000 independent clones. This library served as tool to determine the mRNA frequencies for a number of hematopoietic marker proteins. It was shown that these cells express basophil/mast cell-specific transcripts, i.e. β-tryptase, serglycin and FcεRI α-chain, to a relatively low degree. In contrast, the library contained a high number of several eosinophil-associated transcripts such as: major basic protein (MBP), charcot leyden crystal (CLC), eosinophil cationic protein (ECP), eosinophil derived neurotoxin (EDN) and eosinophil peroxidase (EPO). Out of these transcripts, MBP and EPO were the most frequently observed, representing 8% and 3.2% of the total mRNA pool, respectively. Moreover, in a proteome analysis of cultured basophils we identified MBP and EPO as the two most prominent protein bands, suggesting a good correlation between protein and mRNA analyses of these cells. The mixed phenotype observed for these cells strengthens the conclusion that eosinophils and basophils are closely linked during human hematopoietic development. The dual phenotype also indicates that other cytokines than IL-3 or cell surface interactions are needed to obtain the full basophil specific phenotype in vivo.
Dissimilarity in the Frequency of Venous Thromboembolism Risk Factors among Studies, a Commentary

Venous Thromboembolism (VTE) is the 3rd most prevalent vascular disease behind myocardial infarction and cerebrovascular ischemic attack. This disorder has received attention from health policy makers because of its major complications including recurrent VTE, post thrombotic syndrome, sudden cardiac death and high mortality rate. In the United States, VTE was reported in approximately 201000 cases annually, 25% of which expired within 7 days after diagnosis and 22% of mortalities did not have a definitive diagnosis. Despite the progression in diagnosis and treatment of VTE since 1979, its incidence did not decrease dramatically. This gap declares that VTE risk factors, especially transient ones, have not been detected completely. Obesity, history of VTE, family history of VTE, recent surgery, malignancy, myeloproliferative disorders, trauma, pregnancy, post-menopausal hormone therapy, hereditary syndromes like anti phospholipid syndrome (APS), chronic kidney disease (CKD), chronic obstructive pulmonary disease (COPD), blood transfusion and older age are determined as major risk factors. These factors can be categorized into two major subgroups as intrinsic and predisposing. Recent investigations focused on predisposing ones, which can be justified. Designing a cross sectional study in Imam Hossein Hospital, Tehran, Iran, from 2016 to 2017, we found that inactivity due to disability (30.9%), smoking (29.3%), and active malignancy (18.1%), were the most prevalent transient risks factor of VTE in our sample, respectively. Similar to our results, Kesieme et al. and Cushman et al. declared that VTE is more diagnosed in the elderly. Park MS et al. introduced recent surgery, trauma (73%), and disability to walk (62%) as major independent risk factors of VTE. Fuji T et al. introduced malignancy, recent infectious disease, and obesity as the factors predisposing patients who were admitted for orthopedic surgery to VTE. As can be seen, despite the risk factors of VTE being the same in various studies, their frequency varied between the studies. Population and cultural characteristics and various habits may have an effect in this regard. Therefore, it is suggested to performa multi-center, comprehensive study considering all the racial and ethnic in order to have a correct pattern of the frequency of predisposing factors of this disease in the Iranian population for health and prevention programs.
A comparison of methods for organ-weight data adjustment in chicks.

An experiment was conducted with 168 Arbor Acre X Peterson unsexed, crossbred broiler chicks to compare methods of expressing organ-weight data and to assess changes in organ weights and physiological parameters as body weight (97 to 791 g) and age (5 to 26 days) increased. Actual wet weight of liver, heart, intestine, spleen, and pancreas and percent bone ash increased (P less than .01) as age and body weight increased. Tibia length-to-width ratio decreased (P less than .01) as age and body weight increased. Blood hemoglobin, hematocrit, and plasma protein were not affected (P greater than .1) by age or by body weight. Liver, heart, and intestinal weight decreased (P less than .01) and spleen weight increased (P less than .01) as body weight and age increased when these tissue weights were expressed as percent of body weight. Liver weight adjusted for body weight by covariance analysis, however, remained constant; adjusted heart and intestinal weights decreased (P less than .01), and adjusted spleen weights increased (P less than .01) with increasing age and body weight. The covariate, body weight, was not significant (P greater than .1) for pancreas weight, tibia length-to-width ratio, and percent bone ash. Except for spleen, adjustment by covariance analysis more effectively reduced variation due to body weight than did expression as percent of body weight. (ABSTRACT TRUNCATED AT 250 WORDS)
Prevalence of Helicobacter Pylori Infection Among Patients Undergoing Upper Gastrointestinal Endoscopy in a Medical College Hospital in Kerala, India

Background: Helicobacter pylori related gastritis is a major health ailment in developing nations. There is high morbidity and mortality ranging from chronic gastritis to gastric malignancies. Prevalence of H. pylori infection varies markedly from country to country and in a country, region to region. Aim: To study the prevalence of H. pylori gastritis in patients undergoing endoscopy and its association with the development of gastrointestinal diseases. Subjects and Methods: The study was carried out in a Medical College Hospital in Kerala, India. Patients presenting with dyspeptic symptoms were subjected to upper gastrointestinal endoscopy and investigated for H. pylori infection through histopathological examination and rapid urease test of biopsy specimen. Diagnosis of H. pylori infection was made if one or both diagnostic test results were positive. Data analysis was carried out using the statistical package for social sciences, for Windows version 16.0 (SPSS 16; Chicago, IL, USA). Results: H. pylori infection was diagnosed in 62.0% (329/530) of patients screened. There was no statistically significant difference in sex and age related distribution (<50 year age group and >50 year age group) of H. pylori infection. However, a statistically significant association of H. pylori infection with the presence of endoscopic abnormalities, peptic ulcer, and dysplasia/cancer was seen. Conclusion: The prevalence of H. pylori infection is significantly high in rural and suburban population of Ernakulam district, Kerala. Early detection and prompt treatment are essential for prevention of serious complications.
Pearl millet in diets of white Pekin ducks.

In two 21-d experiments, the performance, nutrient utilization, and carcass composition of ducks fed diets containing pearl millet were compared with those fed diets containing corn. Corn, in diets at two protein levels (22 vs 18% in Experiment 1 and 22 vs 16% in Experiment 2), was replaced by pearl millet either on an equal-weight or isonitrogenous basis. During the first 2 wk of the first experiment, corn diets compared on an isonitrogenous basis were superior (P < .05) to the millet diets in promoting weight gain (666 vs 633 g per duck) and feed consumption (965 vs 914 g per duck); but when compared on an equal-weight basis, the millet diets were similar to the corn diets in promoting growth. No significant differences were observed for weight gain, feed consumption, or feed efficiency at the end of 3 wk. Over the 21-d study, the higher protein diets were more efficiently (P < .05) converted to weight gain than the lower protein diets (.63 vs .60 g gain:g feed). Carcass protein in ducks fed the corn diets was greater (P < .05) than in those fed the pearl millet diets. In Experiment 2, growth performance differences across dietary protein levels were similar to those in Experiment 1. However in contrast to Experiment 1, feed consumption was similar for corn and pearl millet diets (776 vs 786 g per duck, respectively), and ducks fed the corn diets gained less (P < .05) than those fed the pearl millet diets (590 vs 622 g per duck) during the first 2 wk of Experiment 2. Results of the nutrient utilization trial conducted at the end of Experiment 2 revealed that diets containing pearl millet were higher (P < .05) in AME than those containing corn (3,300 vs 3,100 kcal/kg). These results indicate that pearl millet has a higher energy value and appears to be at least equal to corn in promoting weight gains in ducks.
Paper ) Recommendations and the Impact of Labeling

In this paper we show that organic recommendations are preferred over commercial recommendations even when they point to the same freely downloadable research papers. Simply the fact that users perceive recommendations as commercial decreased their willingness to accept them. It is further shown that the exact labeling of recommendations matters. For instance, recommendations labeled as ‘advertisement’ performed worse than those labeled as ‘sponsored’. Similarly, recommendations labeled as ‘Free Research Papers’ performed better than those labeled as ‘Research Papers’. However, whatever the differences between the labels were – the best performing recommendations were those with no label at all.
Learning and Feature Selection under Budget Constraints in Crowdsourcing

The cost of data acquisition limits the amount of labeled data available for machine learning algorithms, both at the training and the testing phase. This problem is further exacerbated in real-world crowdsourcing applications where labels are aggregated from multiple noisy answers. We tackle classification problems where the underlying feature labels are unknown to the algorithm and a (noisy) label of the desired feature can be acquired at a fixed cost. This problem has two types of budget constraints - the total cost of feature labels available for learning at the training phase, and the cost of features to use during the testing phase for classification. We propose a novel budgeted learning and feature selection algorithm, B-LEAFS, for jointly tackling this problem in the presence of noise. Experimental evaluation on synthetic and real-world crowdsourcing data demonstrate the practical applicability of our approach.
Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework

MOTIVATION Like most human diseases, tumors are complex traits, the genesis and development of which recruit a number of genes and several important biological processes. As proteins involved in common processes tend to be centralized in the same local area of protein-protein interaction networks, here a novel framework has been developed to identify which areas of the networks are most relevant to a phenotype. RESULTS These areas termed 'coherent modules' can be regarded as gene sets dynamically defined in the networks. Compared with previous analogous approaches, one critical feature of our method is the optimization of coherent modules for two distinct aspects balanced by tuning a parameter in the framework. First, we seek the low coupling between coherent modules and then maximize the intrinsic similarity within a module. The framework has good expansibility, with classical expression data analysis methods generalized as particular cases. This coherent module approach was applied to an oral cavity tumor dataset with 18 significant coherent modules identified, which could indicate the presence of lymph node metastasis. Further examination shows that most of the modules are responsible for comparatively independent biological processes. Our framework is helpful for the prognosis of tumors and offers a new perspective for tumor research. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Preparation of High‐Percentage 1T‐Phase Transition Metal Dichalcogenide Nanodots for Electrochemical Hydrogen Evolution

Nanostructured transition metal dichalcogenides (TMDs) are proven to be efficient and robust earth‐abundant electrocatalysts to potentially replace precious platinum‐based catalysts for the hydrogen evolution reaction (HER). However, the catalytic efficiency of reported TMD catalysts is still limited by their low‐density active sites, low conductivity, and/or uncleaned surface. Herein, a general and facile method is reported for high‐yield, large‐scale production of water‐dispersed, ultrasmall‐sized, high‐percentage 1T‐phase, single‐layer TMD nanodots with high‐density active edge sites and clean surface, including MoS2, WS2, MoSe2, Mo0.5W0. 5S2, and MoSSe, which exhibit much enhanced electrochemical HER performances as compared to their corresponding nanosheets. Impressively, the obtained MoSSe nanodots achieve a low overpotential of −140 mV at current density of 10 mA cm−2, a Tafel slope of 40 mV dec−1, and excellent long‐term durability. The experimental and theoretical results suggest that the excellent catalytic activity of MoSSe nanodots is attributed to the high‐density active edge sites, high‐percentage metallic 1T phase, alloying effect and basal‐plane Se‐vacancy. This work provides a universal and effective way toward the synthesis of TMD nanostructures with abundant active sites for electrocatalysis, which can also be used for other applications such as batteries, sensors, and bioimaging.
An approximate joint model for multiple paired longitudinal outcomes and time‐to‐event data

Joint modeling of multivariate paired longitudinal data and time‐to‐event data presents computational challenges that supersede full likelihood estimation due to the large dimensional random effects vector needed to capture correlation due to clustering with respect to pairs, subjects, and outcomes. We propose an alternative, computationally simpler approach to estimation of complex shared parameter models where missing data is imputed based on the Posterior Predictive Distribution from a Conditional Linear Model (CLM) approximation. Existing methods for complete data are then implemented to obtain estimates of the event time model parameters. Our method is applied to examine the effects of discordant growth in anthropometric measures of longitudinal fetal growth in twin fetuses and the timing of birth. Simulation results are presented to show that our method performs relatively well with moderate measurement errors under certain CLM approximations.
The ecology, geopolitics, and economics of managing Lymantria dispar in the United States

Increases in global trade and travel have resulted in a number of species being inadvertently (or, in a few cases, deliberately) introduced into new geographical locations. In most cases, there is generally a lack of information regarding a species' biology and ecology, and its potential to cause environmental and economic harm. Regardless, management decisions concerning these new species often need to be made rapidly, even in the absence of this information. The gypsy moth, Lymantria dispar (L.), is an exception insofar as it is a non-native species that, due to its considerable potential for damage, has been extensively studied and managed in the United States following its introduction in 1869. In this review, we attempt to highlight the ecology, geopolitics, and economics of managing L. dispar in the United States, integrating the lessons learned from over 100 years of research and management. In doing so, we attempt to provide a framework that could be applicable to the management of other non-native insect species, for which we often lack information upon which to develop and implement management strategies.
TrkB-Target Galectin-1 Impairs Immune Activation and Radiation Responses in Neuroblastoma: Implications for Tumour Therapy

Galectin-1 (Gal-1) has been described to promote tumour growth by inducing angiogenesis and to contribute to the tumour immune escape. We had previously identified up-regulation of Gal-1 in preclinical models of aggressive neuroblastoma (NB), the most common extracranial tumour of childhood. While Gal-1 did not confer a survival advantage in the absence of exogenous stressors, Gal-1 contributed to enhanced cell migratory and invasive properties. Here, we review these findings and extend them by analyzing Gal-1 mediated effects on immune cell regulation and radiation resistance. In line with previous results, cell autonomous effects as well as paracrine functions contribute to Gal-1 mediated pro-tumourigenic functions. Interfering with Gal-1 functions in vivo will add to a better understanding of the role of the Gal-1 axis in the complex tumour-host interaction during immune-, chemo- and radiotherapy of neuroblastoma.
Incentive Mechanisms for Motivating Mobile Data Offloading in Heterogeneous Networks: A Salary-Plus-Bonus Approach

In this paper, a salary-plus-bonus incentive mechanism is proposed to motivate WiFi Access Points (APs) to provide data offloading service for mobile network operators (MNOs). Under the proposed salary-plus-bonus scheme, WiFi APs are rewarded not only based on offloaded data volume but also based on the quality of their offloading service. The interactions between WiFi APs and the MNO under this incentive mechanism are then studied using Stackelberg game. By differentiating whether WiFi APs are of the same type (e.g. offloading cost and quality), two cases (homogeneous and heterogeneous) are studied. For both cases, we derive the best response functions for WiFi APs (i.e. the optimal amount of data to offload), and show that the Nash Equilibrium (NE) always exists for the subgame. Then, given WiFi APs' strategies, we investigate the optimal strategy (i.e. the optimal salary and bonus) for the MNO to maximize its utility. Then, two simple incentive mechanisms, referred to as the salary-only scheme and the bonus-only scheme, are presented and studied using Stackelberg game. For both of them, it is shown that the Stackelberg Equilibrium (SE) exists and is unique. We also show that the salary-only scheme is more effective in offloading more data, and the bonus-only scheme is more effective in selecting premium APs (i.e. providing high-quality offloading service at low cost), while the salary-plus-bonus scheme can strike a well balance between the offloaded data volume and the offloading quality.
Negative Pressure Therapy in the Regeneration of the Sciatic Nerve Using Vacuum – Assisted Closure in a Rabbit Model

Background The aim of this study was to investigate the effects of negative pressure therapy in the regeneration of the rabbit sciatic nerve using vacuum assisted closure (VAC). Material/Methods Thirty male New Zealand white rabbits underwent surgical injury of the sciatic nerve, followed by negative pressure therapy using vacuum assisted closure (VAC), in three treatment groups: Group A: 0 kPa; Group B: −20 kPa; Group C: −40 kPa. At 12 weeks following surgery, the following factors were studied: motor nerve conduction velocity (MNCV); the number of myelinated nerve fibers; the wet weight of the gastrocnemius muscle. Gastrocnemius muscle and sciatic nerve tissue samples were studied for the expression of S100, and brain-derived neurotrophic factor (BDNF) using Western blot. Results At 12 weeks following VAC treatment, the MNCV, number of myelinated nerve fibers, and wet weight of the gastrocnemius muscle showed significant differences between the groups (p<0.05), in the following order: Group B >Group A >Group C. The sciatic nerve at 12 weeks following VAC in Group B and Group C showed a significant increase in expression of S100 and BDNF when compared with Group A; no significant differences were detected between Group B and Group C results from Western blot at 12 weeks. Conclusions The findings of this study, using negative pressure therapy in VAC in a rabbit model of sciatic nerve damage, have shown that moderate negative pressure was beneficial, but high values did not benefit sciatic nerve repair.
Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach

Gene duplication is a major source of functional innovations and genome complexity, albeit this evolutionary process requires the preservation of duplicates in the genomes for long time. However, the population genetic mechanisms governing this preservation, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy enhances the information transfer from the environmental signal to the phenotypic response by reducing gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such a phenotypic accuracy yields a selective advantage in the order of 0.1% on average, which would allow the positive selection of gene duplication in populations with moderate or large sizes. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we show that the genome rearrangement rates greatly condition the eventual fixation of duplicated genes, either by natural selection or by random genetic drift. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication. SIGNIFICANCE Gene duplication is considered a major driver for the evolution of biological complexity. However, it is still enigmatic to what extent natural selection and genetic drift have governed this evolutionary process. This work uncovers a selective advantage for genotypes carrying duplicates, called phenotypic accuracy, widely characterized thanks to a multi-scale mathematical model coupling gene regulation with population genetics. Importantly, the integrative results presented here provide a detailed mechanistic description for the fixation of duplicates, which allows making predictions about the genome architectures, and which is relevant to understand the origins of complexity.