Miracle-dz/UniFAR-FTUs huggingface dataset:
REGIONAL DIFFERENCES IN RATES OF PLANT SPECIATION AND MOLECULAREVOLUTION: A COMPARISON BETWEEN EASTERN ASIA AND EASTERN NORTH AMERICA

Abstract The eastern Asian (EAS)‐eastern North American (ENA) floristic disjunction is one of the best‐known biogeographic patterns in the Northern Hemisphere. Recent paleontological and molecular analyses have illuminated the origins of the biogeographic pattern, but subsequent diversification and evolution of the disjunct floras in each of the two continents after isolation remains poorly understood. Although similar in climate and floristic composition, EAS has twice as many species as ENA in genera occurring in both regions. Explaining such differences in species diversity between regions with similar environmental conditions (diversity anomalies) is an important goal of the study of the global patterns of biodiversity. We used a phylogenetic approach to compare rates of net speciation and molecular evolution between the two regions. We first identified EAS‐ENA disjunct sister clades from ten genera (Asarum, Buckleya, Carpinus, Carya, Cornus, Hamamelis, Illicium, Panax, Stewartia, and Styrax) that represent diverse angiosperm lineages using phylogenetic analyses of ITS (internal transcribed spacer of nuclear ribosomal DNA) sequence data. Species richness and substitution rate of ITS between sister clades were compared. The results revealed a pattern of greater species diversity in the EAS counterparts. A positive relationship between species diversity and ITS substitution rate was also documented. These results suggest greater net speciation and accelerated molecular evolution in EAS. The data support the idea that a regional difference in net speciation rate related to topographic heterogeneity contributes to the diversity anomaly between EAS and ENA. The close relationship between rates of ITS evolution and species richness further suggests that species production may be directly linked to rate of nucleotide substitution.
Regulatory T cells in the central nervous system

Summary: Regulatory T cells (Tregs) are critical to the human immune system, providing appropriately scaled immune responses and mediating peripheral tolerance. A central role for forkhead box protein 3 (FoxP3)+ Tregs has been shown in the pathogenesis of mechanistically diverse central nervous system (CNS) diseases from autoimmune diseases such as multiple sclerosis to glioblastomas. Understanding how tumors induce Treg function to escape immune surveillance in marked contrast to autoimmune diseases, where there is loss of Treg function, will provide valuable lessons regarding Treg biology and potential therapeutic targets for CNS diseases.
On the Analysis of Impulse Test Results on Grounding Systems

In this paper, an analysis of experimental results on the behavior under impulse currents of various grounding electrodes: rod and horizontal electrodes, a ground grid, and tower footings, is presented. The parameters used for analyzing transient performance are reviewed, and the differences are highlighted based on test data. The analysis is extended to the following: 1) to quantify the effect of impulse shape; 2) to quantify the effect of current magnitude; 3) to compare low-frequency and impulse performances; 4) to compare impulse and high-frequency performances; and 5) to examine the effects of the test setup on measured results, e.g., in the case of field tests, the effect of current return leads, and proximity and extent of return electrodes. A generalized impulse index is introduced to help elucidate the differences between different parameters used for the analysis of transient test results on ground electrodes. It is found that the analysis of test data based on different parameters may lead to different assessments of impulse performance. The results also show that the impulse parameters used for the analysis of test data can be influenced by several factors such as electrode length, impulse current rise time, and experimental setup. In addition, variable-frequency test results are analyzed by introducing a “harmonic coefficient” which quantifies the deviations of the harmonic impedance from the low-frequency resistance over different frequency ranges covering the entire lightning frequency spectrum. Significant variations of the harmonic coefficient with frequency were observed, highlighting the importance of taking the frequency dependence of soil properties when modeling the impulse and high-frequency behavior of grounding systems.
Parallel multi-material decomposition of Dual-Energy CT data

Dual-Energy Computed Tomography (DECT) is a new modality of CT where two images are acquired simultaneously at two energy levels, and then decomposed into two material density images. It is also possible to further decompose these images into volume fraction images that approximate the percentage of a given material at each pixel. Here, we describe a novel parallel version of the multilateral decomposition algorithm proposed by Mendonça et al., which is used to obtain volume fraction images. Our parallel version accelerates decomposition by 200x. We also discuss some of the algorithm limitations.
Neuropeptide‐Metabolizing Peptidases in Neuro‐2a Neuroblastoma and C6 Glioma Cells

Abstract: Mouse Neuro‐2a neuroblastoma and rat C6 glioma cloned cells were screened for neuropeptide‐metabolizing peptidases using a kininase bioassay combined with a time‐course bradykinin‐product analysis, and a fluorimetnc assay for prolyl endopeptidase. The complementary peptide products Arg1→ Phe5/Ser6→ Arg9 and Arg1→ Pro7/Phe8‐Arg9 were released during bradykinin (Arg1‐Pro2‐Pro3‐Gly4‐Phe5‐Ser6‐Pro7‐Phe8‐Arg9) inactivation by homogenates of Neuro‐2a and C6 cells. The 1:1 stoichiometry of the complementary fragments and their high yields, at 10% bradykinin inactivation, demonstrated the sites of hydrolysis. The initial rate of Phe5‐Ser6 bond cleavage was six‐fold higher than that of the Pro7‐Phe8 bond. These sites of cleavage can be attributed to enzymes similar to endqpeptidase A (Phe5‐Ser6) and prolyl endopeptidase (Pro7‐Phe8) on the basis of the specificity and sensitivity to inhibitors of the kininase activity in Neuro‐2a and C6 cell homogenates. Kininase and prolyl endopeptidase specific activities (fmol/min/cell) were 10.5 and 12.4 for Neuro‐2a, and 1.5 and 2 for C6 homogenate, respectively. The recovery of kininase activity was 2.2‐fold higher in the particulate than in the soluble (105,000 g for 1 h) neuronal fraction, whereas the amount of prolyl endopeptidase activity was about the same in both fractions. Kininase and prolyl endopeptidase activities in C6 cells were recovered mostly in the soluble fraction. Prolyl endopeptidase specific activity decreased 10‐fold in serum‐starved Neuro‐2a cultured cells, with no change in activity in similarly treated C6 cells. In contrast, kininase specific activity in both cell types was essentially unaffected on serum‐deprivationinduced differentiation.
A hydrous melting and fractionation model for mid‐ocean ridge basalts: Application to the Mid‐Atlantic Ridge near the Azores

The major element, trace element, and isotopic composition of mid‐ocean ridge basalt glasses affected by the Azores hotspot are strongly correlated with H2O content of the glass. Distinguishing the relative importance of source chemistry and potential temperature in ridge‐hotspot interaction therefore requires a comprehensive model that accounts for the effect of H2O in the source on melting behavior and for the effect of H2O in primitive liquids on the fractionation path. We develop such a model by coupling the latest version of the MELTS algorithm to a model for partitioning of water among silicate melts and nominally anhydrous minerals. We find that much of the variation in all major oxides except TiO2 and a significant fraction of the crustal thickness anomaly at the Azores platform are explained by the combined effects on melting and fractionation of up to ∼700 ppm H2O in the source with only a small thermal anomaly, particularly if there is a small component of buoyantly driven active flow associated with the more H2O‐rich melting regimes. An on‐axis thermal anomaly of ∼35°C in potential temperature explains the full crustal thickness increase of ∼4 km approaching the Azores platform, whereas a ≥75°C thermal anomaly would be required in the absence of water or active flow. The polybaric hydrous melting and fractionation model allows us to solve for the TiO2, trace element and isotopic composition of the H2O‐rich component in a way that self‐consistently accounts for the changes in the melting and fractionation regimes resulting from enrichment, although the presence and concentration in the enriched component of elements more compatible than Dy cannot be resolved.
A Complexity Trichotomy for Approximately Counting List H-Colorings

We examine the computational complexity of approximately counting the list H-colorings of a graph. We discover a natural graph-theoretic trichotomy based on the structure of the graph H. If H is an irreflexive bipartite graph or a reflexive complete graph, then counting list H-colorings is trivially in polynomial time. Otherwise, if H is an irreflexive bipartite permutation graph or a reflexive proper interval graph, then approximately counting list H-colorings is equivalent to #BIS, the problem of approximately counting independent sets in a bipartite graph. This is a well-studied problem that is believed to be of intermediate complexity—it is believed that it does not have an FPRAS, but that it is not as difficult as approximating the most difficult counting problems in #P. For every other graph H, approximately counting list H-colorings is complete for #P with respect to approximation-preserving reductions (so there is no FPRAS unless NP = RP). Two pleasing features of the trichotomy are (1) it has a natural formulation in terms of hereditary graph classes, and (2) the proof is largely self-contained and does not require any universal algebra (unlike similar dichotomies in the weighted case). We are able to extend the hardness results to the bounded-degree setting, showing that all hardness results apply to input graphs with maximum degree at most 6.
Impaired executive functions in paediatric obsessive-compulsive disorder patients

Isık Taner Y, Erdogan Bakar E, Oner O. Impaired executive functions in paediatric obsessive-compulsive disorder patients. Objective: There are only few studies which investigated the neuropsychological performances of paediatric patients with obsessive-compulsive disorder (OCD). Previous studies show that most of adult OCD patients had an onset of their first symptoms before the age of 15. Our objective was to evaluate the neuropsychological functions in paediatric patients with OCD. Methods: We compared the executive functions and general intelligence of child and adolescent OCD patients (n = 20) with age- and gender-matched healthy controls (n = 20). To compare mentioned skills, a neuropsychological test battery including Wechsler Intelligence Scale for Children-Revised (WISC-R), Wisconsin Card Sorting Test (WCST), Stroop Test and Verbal Fluency Test was performed. Result: Performances of the OCD and control subjects on neuropsychological tests were statistically analysed by using multivariate analysis of covariance (MANCOVA), in which Full Scale Intelligence Quotient (FSIQ) results were taken into consideration as a covariate to observe FSIQ's effect on test scores. Our results showed that the differences in WISC-R Picture Arrangement and Coding scores remained significant when co-analysed with FSIQ scores. In a similar manner, the OCD group exhibited worse performances on STR1-duration, STR3-duration, STR3-error, STR4-duration, STR4-error, STR5-correct response, and STR5-error as compared with the control group when FSIQ scores were taken into calculation. Some variables of the WCST (perseverative responses, percent errors, abstraction-flexibility and categories completed) also yield lower test scores in the OCD group. There was no significant difference between the groups regarding Verbal Fluency Test scores. Conclusion: Our results suggested that paediatric OCD patients had worse abstraction-flexibility, mental set-shifting, verbal comprehension and visuospatial/construction abilities.
Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis

MicroRNAs (miRNAs) regulate gene expression directly through base pairing to their targets or indirectly through participating in multi-scale regulatory networks. Often miRNAs take part in feed-forward motifs where a miRNA and a transcription factor act on shared targets to achieve accurate regulation of processes such as cell differentiation. Here we show that the expression levels of miR-27a and miR-29a inversely correlate with the mRNA levels of lipoprotein lipase (Lpl), their predicted combinatorial target, and its key transcriptional regulator peroxisome proliferator-activated receptor gamma (Pparg) during 3T3-L1 adipocyte differentiation. More importantly, we show that Lpl, a key lipogenic enzyme, can be negatively regulated by the two miRNA families in a combinatorial fashion on the mRNA and functional level in maturing adipocytes. This regulation is mediated through the Lpl 3′UTR as confirmed by reporter gene assays. In addition, a small mathematical model captures the dynamics of this feed-forward motif and predicts the changes in Lpl mRNA levels upon network perturbations. The obtained results might offer an explanation to the dysregulation of LPL in diabetic conditions and could be extended to quantitative modeling of regulation of other metabolic genes under similar regulatory network motifs.
Influence of and Optimal Insulin Therapy for a Low–Glycemic Index Meal in Children With Type 1 Diabetes Receiving Intensive Insulin Therapy

OBJECTIVE—The purpose of this study was to quantify the effects of glycemic index on postprandial glucose excursion (PPGE) in children with type 1 diabetes receiving multiple daily injections and to determine optimal insulin therapy for a low–glycemic index meal. RESEARCH DESIGN AND METHODS—Twenty subjects consumed test breakfasts with equal macronutrient contents on 4 consecutive days; high–and low–glycemic index meals (glycemic index 84 vs. 48) were consumed with preprandial ultra-short-acting insulin, and the low–glycemic index meal was also consumed with preprandial regular insulin and postprandial ultra-short-acting insulin. Each child's insulin dose was standardized. Continuous glucose monitoring was used. RESULTS—The PPGE was significantly lower for the low–glycemic index meal compared with the high–glycemic index meal at 30–180 min (P < 0.02) when preprandial ultra-short-acting insulin was administered. The maximum difference occurred at 60 min (4.2 mmol/l, P < 0.0001). Regular insulin produced a 1.1 mmol/l higher PPGE at 30 min compared with ultra-short-acting insulin (P = 0.015) when the low–glycemic index meal was consumed. Postprandial ultra-short-acting insulin produced a higher PPGE at 30 and 60 min compared with preprandial administration when the low–glycemic index meal was consumed. The maximum difference was 2.5 mmol/l at 60 min (P < 0.0001). CONCLUSIONS—Low–glycemic index meals produce a lower PPGE than high–glycemic index meals. Preprandial ultra-short-acting insulin is the optimal therapy for a low–glycemic index meal.
Studies on optoelectronic properties of DC reactive magnetron sputtered CdTe thin films

Cadmium telluride continues to be a leading candidate for the development of cost effective photovoltaics for terrestrial applications. In the present work two individual metallic targets of Cd and Te were used for the deposition of CdTe thin films on mica substrates from room temperature to 300 °C by DC reactive magnetron sputtering method. XRD patterns of CdTe thin films deposited on mica substrates exhibit peaks at 2θ = 27.7°, 46.1° and 54.6°, which corresponds to reflection on (1 1 1), (2 2 0) and (3 1 1) planes of CdTe cubic structure. The intensities of XRD patterns increases with the increase of substrate temperature upto 150 °C and then it decreases at higher substrate temperatures. The conductivity of CdTe thin films measured from four probe method increases with the increase of substrate temperature. The activation energies (ΔE) are found to be decrease with the increase of substrate temperature. The optical transmittance spectra of CdTe thin films deposited on mica have a clear interference pat.
Evidence for Independent Heritability of the Glycation Gap (Glycosylation Gap) Fraction of HbA1c in Nondiabetic Twins

I have read with interest the article by Cohen et al. (1) in Diabetes Care . In this article, the authors reported a significant effect of heredity on the A1C values in twin subjects. This hereditary effect was attributed to “genes that preferentially affect erythrocyte lifespan or glucose and/or nonenzymatic glycation or deglycation in the intracellular rather …
Automatic query generation using word embeddings for retrieving passages describing experimental methods

Information regarding the physical interactions among proteins is crucial, since protein–protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing the reliability of the identified PPIs. A lot of information about PPIs and the experimental methods are only available in the text of the scientific publications that report them. In this study, we approach the problem of identifying passages with experimental methods for physical interactions between proteins as an information retrieval search task. The baseline system is based on query matching, where the queries are generated by utilizing the names (including synonyms) of the experimental methods in the Proteomics Standard Initiative–Molecular Interactions (PSI-MI) ontology. We propose two methods, where the baseline queries are expanded by including additional relevant terms. The first method is a supervised approach, where the most salient terms for each experimental method are obtained by using the term frequency–relevance frequency (tf.rf) metric over 13 articles from our manually annotated data set of 30 full text articles, which is made publicly available. On the other hand, the second method is an unsupervised approach, where the queries for each experimental method are expanded by using the word embeddings of the names of the experimental methods in the PSI-MI ontology. The word embeddings are obtained by utilizing a large unlabeled full text corpus. The proposed methods are evaluated on the test set consisting of 17 articles. Both methods obtain higher recall scores compared with the baseline, with a loss in precision. Besides higher recall, the word embeddings based approach achieves higher F-measure than the baseline and the tf.rf based methods. We also show that incorporating gene name and interaction keyword identification leads to improved precision and F-measure scores for all three evaluated methods. The tf.rf based approach was developed as part of our participation in the Collaborative Biocurator Assistant Task of the BioCreative V challenge assessment, whereas the word embeddings based approach is a novel contribution of this article. Database URL: https://github.com/ferhtaydn/biocemid/
An Event-Related Functional Magnetic Resonance Imaging Study of Voluntary and Stimulus-Driven Orienting of Attention

Attention can be voluntarily directed to a location or automatically summoned to a location by a salient stimulus. We compared the effects of voluntary and stimulus-driven shifts of spatial attention on the blood oxygenation level-dependent signal in humans, using a method that separated preparatory activity related to the initial shift of attention from the subsequent activity caused by target presentation. Voluntary shifts produced greater preparatory activity than stimulus-driven shifts in the frontal eye field (FEF) and intraparietal sulcus, core regions of the dorsal frontoparietal attention network, demonstrating their special role in the voluntary control of attention. Stimulus-driven attentional shifts to salient color singletons recruited occipitotemporal regions, sensitive to color information and part of the dorsal network, including the FEF, suggesting a partly overlapping circuit for endogenous and exogenous orienting. The right temporoparietal junction (TPJ), a core region of the ventral frontoparietal attention network, was strongly modulated by stimulus-driven attentional shifts to behaviorally relevant stimuli, such as targets at unattended locations. However, the TPJ did not respond to salient, task-irrelevant color singletons, indicating that behavioral relevance is critical for TPJ modulation during stimulus-driven orienting. Finally, both ventral and dorsal regions were modulated during reorienting but significantly only by reorienting after voluntary shifts, suggesting the importance of a mismatch between expectation and sensory input.
Sleep Disruption and Daytime Sleepiness Correlating with Disease Severity and Insulin Resistance in Non-Alcoholic Fatty Liver Disease: A Comparison with Healthy Controls

Background & Aims Sleep disturbance is associated with the development of obesity, diabetes and hepatic steatosis in murine models. Hepatic triglyceride accumulation oscillates in a circadian rhythm regulated by clock genes, light-dark cycle and feeding time in mice. The role of the sleep-wake cycle in the pathogenesis of human non-alcoholic fatty liver disease (NAFLD) is indeterminate. We sought to detail sleep characteristics, daytime sleepiness and meal times in relation to disease severity in patients with NAFLD. Methods Basic Sleep duration and latency, daytime sleepiness (Epworth sleepiness scale), Pittsburgh sleep quality index, positive and negative affect scale, Munich Chronotype Questionnaire and an eating habit questionnaire were assessed in 46 patients with biopsy-proven NAFLD and 22 healthy controls, and correlated with biochemical and histological parameters. Results In NAFLD compared to healthy controls, time to fall asleep was vastly prolonged (26.9 vs. 9.8 min., p = 0.0176) and sleep duration was shortened (6.3 vs. 7.2 hours, p = 0.0149). Sleep quality was poor (Pittsburgh sleep quality index 8.2 vs. 4.7, p = 0.0074) and correlated with changes in affect. Meal frequency was shifted towards night-times (p = 0.001). In NAFLD but not controls, daytime sleepiness significantly correlated with liver enzymes (ALAT [r = 0.44, p = 0.0029], ASAT [r = 0.46, p = 0.0017]) and insulin resistance (HOMA-IR [r = 0.5, p = 0.0009]) independent of cirrhosis. In patients with fibrosis, daytime sleepiness correlated with the degree of fibrosis (r = 0.364, p = 0.019). Conclusions In NAFLD sleep duration was shortened, sleep onset was delayed and sleep quality poor. Food-intake was shifted towards the night. Daytime sleepiness was positively linked to biochemical and histologic surrogates of disease severity. The data may indicate a role for sleep-wake cycle regulation and timing of food-intake in the pathogenesis of human NAFLD as suggested from murine models.
Nutritional recovery with rice bran did not modify energy balance and leptin and insulin levels.

OBJECTIVE To investigate the effect of nutritional recovery with rice bran on energy balance, leptin and insulin levels. METHODS Weaned Wistar rats were fed on a 17% (Control - C) or 0.5% (Aproteic - A) protein diet for 12d. After this, rats were kept on a C diet (C) or recovered with control (Recovered Control - RC) or control plus recovered rice bran diet (Recovered Rice Bran - RRB). RESULTS Despite the increased food intake, group A exhibited lower carcass fat associated to low serum leptin. RRB and RC groups showed lower carcass weight and energy intake and expenditure. Energy expenditure was positively associated with food intake and carcass weight. Negative correlations between HOMA-IR and energy expenditure and energy intake were observed. CONCLUSION Nutritional recovery with rice bran did not modify energy balance, leptin and insulin levels.