Miracle-dz/UniFAR-FTUs huggingface dataset:
De Novo Assembly and Characterization of Stress Transcriptome in a Salinity-Tolerant Variety CS52 of Brassica juncea

Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars for salinity tolerance, B. juncea and B. nigra. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52.
Efficient Multilevel Brain Tumor Segmentation With Integrated Bayesian Model Classification

We present a new method for automatic segmentation of heterogeneous image data that takes a step toward bridging the gap between bottom-up affinity-based segmentation methods and top-down generative model based approaches. The main contribution of the paper is a Bayesian formulation for incorporating soft model assignments into the calculation of affinities, which are conventionally model free. We integrate the resulting model-aware affinities into the multilevel segmentation by weighted aggregation algorithm, and apply the technique to the task of detecting and segmenting brain tumor and edema in multichannel magnetic resonance (MR) volumes. The computationally efficient method runs orders of magnitude faster than current state-of-the-art techniques giving comparable or improved results. Our quantitative results indicate the benefit of incorporating model-aware affinities into the segmentation process for the difficult case of glioblastoma multiforme brain tumor.
Viscoelastic Methods of Blood Clotting Assessment – A Multidisciplinary Review

Viscoelastic methods (VEM) made available the bedside assessment of blood clotting. Unlike standard laboratory tests, the results are based on the whole blood coagulation and are available in real time at a much faster turnaround time. In combination with our new knowledge about pathophysiology of the trauma-induced coagulopathy, the goal-oriented treatment protocols have been recently proposed for the initial management of bleeding in trauma victims. Additionally, the utility of viscoelastic monitoring devices has been proved even outside this setting in cardiosurgical patients or those undergoing liver transplantation. Many other situations were described in literature showing the potential use of bedside analysis of coagulation for the management of bleeding or critically ill patients. In the near future, we may expect further improvement in current bedside diagnostic tools enabling not only the assessment of secondary hemostasis but also the platelet aggregation. More sensitive assays for new anticoagulants are underway. Aim of this review is to offer the reader a multidisciplinary overview of VEM and their potential use in anesthesiology and critical care.
Feedback effects between similarity and social influence in online communities

A fundamental open question in the analysis of social networks is to understand the interplay between similarity and social ties. People are similar to their neighbors in a social network for two distinct reasons: first, they grow to resemble their current friends due to social influence; and second, they tend to form new links to others who are already like them, a process often termed selection by sociologists. While both factors are present in everyday social processes, they are in tension: social influence can push systems toward uniformity of behavior, while selection can lead to fragmentation. As such, it is important to understand the relative effects of these forces, and this has been a challenge due to the difficulty of isolating and quantifying them in real settings. We develop techniques for identifying and modeling the interactions between social influence and selection, using data from online communities where both social interaction and changes in behavior over time can be measured. We find clear feedback effects between the two factors, with rising similarity between two individuals serving, in aggregate, as an indicator of future interaction -- but with similarity then continuing to increase steadily, although at a slower rate, for long periods after initial interactions. We also consider the relative value of similarity and social influence in modeling future behavior. For instance, to predict the activities that an individual is likely to do next, is it more useful to know the current activities of their friends, or of the people most similar to them?
Exploring relationships among distress, psychological growth, motivation, and physical activity among transplant recipients

Abstract Purpose: To examine relationships among transplant-specific psychological growth and distress, motivational regulations and health-enhancing physical activity (HEPA) among transplant recipients. Methods: Participants (N = 138; Mage = 48 years; 58% male), who were primarily heart, liver, lung, and kidney transplant recipients, completed scientifically-supported questionnaires. The associations among transplant-specific emotional health, motivation, and HEPA were examined in a path model. Results: In the path model (Χ2(3) = 2.12, RMSEA = 0.02, CFI = 0.98, NNFI = 0.97, SRMR = 0.04), distress was significantly related to introjected regulation and psychological growth was associated with autonomous self-regulation (a combined score of identified and intrinsic regulations), which was a significant correlate of HEPA (R2 = 0.12). There were no significant direct associations between distress, psychological growth, and HEPA. Conclusion: Transplant-specific distress and psychological growth may be factors to target in clinical intervention and rehabilitation. Furthermore, exercise motivation regulations are modifiable factors that relate to HEPA among transplant recipients and could be targeted in the development of rehabilitation strategies aimed at enhancing physical activity in this population. Implications for Rehabilitation Organ transplant recipients should maintain a healthy lifestyle in order to prevent rejection and other risk factors associated with transplantation. Physical activity is a promising lifestyle factor linked to many health benefits. This study shows how a mix of stress and growth following transplantation is related to physical activity motivation and behavior.
Influence of Age and Nutritional Status on Flight Performance of the Asian Tiger Mosquito Aedes albopictus (Diptera: Culicidae)

The Asian tiger mosquito, Aedes albopictus, is a competent vector for arboviruses and recently was implicated as the vector of the first autochthonous cases of dengue and chikungunya in southern Europe. The objective of this study was to analyze the flight performance of female Ae. albopictus of different ages that were starved, sugar-fed, or sugar-fed and blood-fed, using flight mills. After three days of starvation post emergence, females flew an average distance of 0.7 ± 0.5 km in 1.9 ± 1.5 h during a 16 h trial period, whereas sugar- or sugar- and blood-fed females of this age covered a significantly higher distance of around 3 km with a mean total flight time of around 6 h. The age of females (up to four weeks) had no effect on performance. The average of maximal continuous flight segments of sugar-fed (2.14 ± 0.69 h) and blood-fed (3.17 ± 0.82 h) females was distinctly higher than of starved females (0.38 ± 0.15 h) of which most flyers (83%) performed maximal flight segments that lasted no longer than 0.5 h. Overall, the results for the laboratory monitored flight performance of Ae. albopictus confirm their ability to disperse a few kilometres between breeding site and host.
A modular approach to build structured event-based systems

Event-based systems are developed and used as a coordination model to integrate components in loosely coupled systems. Research and product development focused so far on efficiency issues but neglected methodological support to build such systems. In this paper, we present the modular design and implementation of an event system which supports scopes and event mappings, two new and powerful structuring methods that facilitate engineering and coordination of components in event-based systems. The approach is based on a trace-based specification method adapted from temporal logic.
Season, Sex, Age, and Education as Modifiers of the Effects of Outdoor Air Pollution on Daily Mortality in Shanghai, China: The Public Health and Air Pollution in Asia (PAPA) Study

Background Various factors can modify the health effects of outdoor air pollution. Prior findings about modifiers are inconsistent, and most of these studies were conducted in developed countries. Objectives We conducted a time-series analysis to examine the modifying effect of season, sex, age, and education on the association between outdoor air pollutants [particulate matter < 10 μm in aerodynamic diameter (PM10), sulfur dioxide, nitrogen dioxide, and ozone] and daily mortality in Shanghai, China, using 4 years of daily data (2001–2004). Methods Using a natural spline model to analyze the data, we examined effects of air pollution for the warm season (April–September) and cool season (October–March) separately. For total mortality, we examined the association stratified by sex and age. Stratified analysis by educational attainment was conducted for total, cardiovascular, and respiratory mortality. Results Outdoor air pollution was associated with mortality from all causes and from cardiorespiratory diseases in Shanghai. An increase of 10 μg/m3 in a 2-day average concentration of PM10, SO2, NO2, and O3 corresponds to increases in all-cause mortality of 0.25% [95% confidence interval (CI), 0.14–0.37), 0.95% (95% CI, 0.62–1.28), 0.97% (95% CI, 0.66–1.27), and 0.31% (95% CI, 0.04–0.58), respectively. The effects of air pollutants were more evident in the cool season than in the warm season, and females and the elderly were more vulnerable to outdoor air pollution. Effects of air pollution were generally greater in residents with low educational attainment (illiterate or primary school) compared with those with high educational attainment (middle school or above). Conclusions Season, sex, age, and education may modify the health effects of outdoor air pollution in Shanghai. These findings provide new information about the effects of modifiers on the relationship between daily mortality and air pollution in developing countries and may have implications for local environmental and social policies.
Functional analysis of pattern recognition receptors in miniature dachshunds with inflammatory colorectal polyps

Inflammatory colorectal polyps (ICRPs) frequently occur in miniature dachshunds (MDs) in Japan. MDs with ICRPs develop multiple polyps with severe neutrophil infiltration that respond to immunosuppressive therapy. Therefore, ICRPs are thought to constitute a novel, breed-specific form of canine inflammatory bowel disease (IBD). Pattern recognition receptors (PRRs) play a key role in the distinction of pathogens from commensal bacteria and food antigens. Dysfunction resulting from genetic disorders of PRRs have been linked to human and canine IBD. Therefore, we analyzed the reactivity of PRRs in MDs with ICRPs. Twenty-six MDs with ICRPs and 16 control MDs were recruited. Peripheral blood-derived monocytes were obtained from each dog and then stimulated with PRR ligands for 6 and 24 hr; subsequently, messenger RNA (mRNA) expression levels and protein secretion of IL-1β were quantified using quantitative real-time PCR and ELISA, respectively. The levels of IL-1β mRNA and protein secretion after stimulation with a nucleotide-binding oligomerization domain 2 (NOD2) ligand were significantly greater in monocytes from ICRP-affected MDs than in those from control MDs. In addition, IL-1β protein secretion induced by toll-like receptor (TLR) 1/2, TLR2 and TLR2/6 stimulation was also significantly greater in ICRP-affected MDs. These results suggest that reactivity against NOD2, TLR1/2, TLR2 and TLR2/6 signals is enhanced in ICRP-affected MDs and may play a role in the pathogenesis of ICRPs in MDs. Additional studies of the genetic background of these PRRs should be performed.
Should Malaria Treatment Be Guided by a Point of Care Rapid Test? A Threshold Approach to Malaria Management in Rural Burkina Faso

Background In Burkina Faso, rapid diagnostic tests for malaria have been made recently available. Previously, malaria was managed clinically. This study aims at assessing which is the best management option of a febrile patient in a hyperendemic setting. Three alternatives are: treating presumptively, testing, or refraining from both test and treatment. The test threshold is the tradeoff between refraining and testing, the test-treatment threshold is the tradeoff between testing and treating. Only if the disease probability lies between the two should the test be used. Methods and Findings Data for this analysis was obtained from previous studies on malaria rapid tests, involving 5220 patients. The thresholds were calculated, based on disease risk, treatment risk and cost, test accuracy and cost. The thresholds were then matched against the disease probability. For a febrile child under 5 in the dry season, the pre-test probability of clinical malaria (3.2%), was just above the test/treatment threshold. In the rainy season, that probability was 63%, largely above the test/treatment threshold. For febrile children >5 years and adults in the dry season, the probability was 1.7%, below the test threshold, while in the rainy season it was higher (25.1%), and situated between the two thresholds (3% and 60.9%), only if costs were not considered. If they were, neither testing nor treating with artemisinin combination treatments (ACT) would be recommended. Conclusions A febrile child under 5 should be treated presumptively. In the dry season, the probability of clinical malaria in adults is so low, that neither testing nor treating with any regimen should be recommended. In the rainy season, if costs are considered, a febrile adult should not be tested, nor treated with ACT, but a possible alternative would be a presumptive treatment with amodiaquine plus sulfadoxine-pyrimethamine. If costs were not considered, testing would be recommended.
Cryoprecipitate poor plasma does not improve early response in primary adult thrombotic thrombocytopenic purpura (TTP)

Thrombotic thrombocytopenic purpura (TTP) is a potentially fatal disease that is treated with plasma exchange and typically with replacement with fresh frozen plasma (FFP). This approach results in an approximate 50% response rate following 1 week of therapy and 80% survival. Cryoprecipitate poor plasma (CPP) is plasma from which the cryoprecipitate fraction is removed. CPP has been reported to be successful as salvage therapy in refractory TTP and has been suggested to be superior to FFP in retrospective studies. The present report compares initial therapy of TTP with exchange using replacement with either FFP or CPP in a multi‐institutional prospective randomized study performed by the North American TTP Group (NATG Group) from 1993 to 1995. Initial therapy also included corticosteroids. Antiplatelet drugs or vinca alkaloids were not employed. A severity score index, response score, and individual clinical parameters (platelet count, LDH × upper limit of normal, hemoglobin level, and creatinine) were compared at their nadir or peak values, baseline, and days +6 and +13 of therapy. Thirteen patients were randomized to FFP exchange and 14 to CPP exchange. Results were equivalent for all parameters. Survival was equal with three deaths in each group. These data indicate that the efficacy of FFP and CPP are the same in the initial treatment of TTP in adults. J. Clin. Apheresis. 16:19–22, 2001. © 2001 Wiley‐Liss, Inc.
Regulation of rat liver glycogen synthetase. Relationship of the hormonal activation and the time-dependent in vitro activation.

Abstract The activation of glycogen synthetase by insulin proceeds via the transformation of the less active D form to the active I form, with essentially no change in total activity. Although the enhancement of glycogen deposition has also been attributed to glucocorticoid activation of glycogen synthetase, insulin-induced activation is counteracted by hydrocortisone in diabetic and starved rats. The time-dependent activation of glycogen synthetase in crude liver extracts, which has been used as a model for activation of the enzyme by various agents, has now been demonstrated with more purified preparations. With the purified system the characteristics of the in vitro activation have been compared to the in vivo hormonally induced activation. In contrast to the in vivo case, the total activity of glycogen synthetase increased during activation in vitro in addition to the increase in the I activity. The effect of various cellular metabolites on the in vitro activation kinetics is profoundly altered by EDTA. Certain properties of the synthetase system, such as the ratio of D to I form, the Km for UDP-glucose, and the in vitro activation, are temperature-dependent.
A mesh-size-objective modeling of quasi-brittle material using micro-cell informed damage law

A multi-scale approach for mesh size independent finite element analysis of quasi-brittle material is proposed in this article. The homogenization based multi-scale damage representation is first introduced in obtaining the damage law from micro-cell simulation with consideration of microscopic crack propagation. The key idea to remedy the mesh size sensitivity in the 2D macroscopic finite element analysis is to introduce a damage law directly from the micro-cell simulation, where the micro-cell size should be identical to the macroscopic mesh size. The micro-cells with different sizes are generated and the corresponding simulations are presented in the numerical tests to obtain the micro-cell dependent damage law. The mesh independent finite element analysis results of the notched beam and the double-edge notched specimen affirm the strategy of correcting the mesh sensitivity.
Prematurity does not markedly affect intestinal sensitivity to endotoxins and feeding in pigs

Preterm neonates show enhanced sensitivity to nutrient maldigestion and bacteria-mediated gut inflammatory disorders, such as necrotising enterocolitis (NEC). We hypothesised that preterm birth increases the sensitivity of intestinal nutrient absorption to endotoxins and that feeding after birth reduces this response. Hence, we investigated the postnatal development of nutrient digestive and absorptive capacity in the preterm and term pig intestine, and its responsiveness to endotoxins. Pigs were delivered by caesarean section at preterm (n 20) or term (n 17) gestation, and the small intestine was collected at birth or after 2 d of colostrum feeding, followed by ex vivo stimulation with lipopolysaccharide endotoxins and mixed gut contents collected from pigs with NEC. Brush border enzyme activities were reduced in newborn preterm v. term pigs (39–45 % reduction, P < 0·05), but normalised after 2 d of feeding. Ex vivo leucine and glucose uptake increased with prenatal age. Bacterial stimulation reduced the nutrient uptake similarly at birth and after 2 d in preterm and term pigs (23–41 % reduction, P < 0·05), whereas IL-6 and TNF-α expression was stimulated only at birth. Toll-like receptor-4 expression increased markedly at day 2 for preterm and term pigs (22–33-fold, P < 0·05) but with much lower expression levels in newborn preterm pigs (approximately 95 %, P < 0·01). In conclusion, digestive and absorptive functions mature in the prenatal period, but are similarly affected by postnatal feeding and bacterial exposure in both preterm and term pigs. Nutrient maldigestion may contribute to NEC development, while a prematurity-related hyper-responsiveness to endotoxins could be less important, at least in pigs.
Cytoplasmic Phospholipase A2 Levels Correlate with Apoptosis in Human Colon Tumorigenesis

Colon cancers often display perturbations in arachidonic acid metabolism, with elevated levels of cyclooxygenase (COX)-2 expression and prostaglandin E2 (PGE2) production frequently observed. Whereas COX-2 and PGE2 are associated with cancer cell survival and tumor angiogenesis, arachidonic acid itself is a strong apoptotic signal that may facilitate cancer cell death. To further explore how cancer cells exploit the progrowth actions of prostaglandins while suppressing the proapoptotic actions of intracellular arachidonic acid, we determined the cytoplasmic phospholipase A2 (cPLA2) and COX-2 expression levels in a panel of human colon tumors by immunohistochemistry. Although high levels of cPLA2 and COX-2 expression are predicted to facilitate maximal prostaglandin production, tumors frequently displayed a high-COX-2/low-cPLA2 phenotype. The least represented phenotype was the high expression of cPLA2, a characteristic predicted to generate the highest levels of intracellular arachidonic acid. The potential proapoptotic role of cPLA2 was supported by a higher frequency of terminal deoxynucleotidyl transferase–mediated nick end labeling staining in cPLA2-positive tumors. Moreover, analysis of preneoplastic aberrant crypt foci from high-risk patients suggests that acquisition of the high-COX-2/low-cPLA2 phenotype may arise at an early stage of colon carcinogenesis. We additionally inhibited cPLA2 in HT-29 cells using antisense oligonucleotides. Our results indicate that cPLA2 plays an important role in tumor necrosis factor α–induced apoptosis in human colon cancer cells. Our data further support the model in which colon cancer growth is favored when intracellular arachidonic acid levels are suppressed by inhibition of cPLA2 or by a high-COX-2/low-cPLA2 phenotype.