Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytochrome controls alternative splicing to mediate light responses in Arabidopsis

Significance Plants adapt to their fluctuating environment by monitoring surrounding light conditions through several photoreceptors, such as phytochrome. It is widely believed that upon absorbing red light, phytochrome induces plant light responses by regulating the transcription of numerous target genes. In this study, we provide clear evidence that phytochrome controls not only transcription, but also alternative splicing in Arabidopsis. We reveal that 6.9% of the annotated genes in the Arabidopsis genome undergo rapid changes in their alternative splicing patterns in a red light- and phytochrome-dependent manner. Our results demonstrate that phytochrome simultaneously regulates two different aspects of gene expression, namely transcription and alternative splicing to mediate light responses in plants. Plants monitor the ambient light conditions using several informational photoreceptors, including red/far-red light absorbing phytochrome. Phytochrome is widely believed to regulate the transcription of light-responsive genes by modulating the activity of several transcription factors. Here we provide evidence that phytochrome significantly changes alternative splicing (AS) profiles at the genomic level in Arabidopsis, to approximately the same degree as it affects steady-state transcript levels. mRNA sequencing analysis revealed that 1,505 and 1,678 genes underwent changes in their AS and steady-state transcript level profiles, respectively, within 1 h of red light exposure in a phytochrome-dependent manner. Furthermore, we show that splicing factor genes were the main early targets of AS control by phytochrome, whereas transcription factor genes were the primary direct targets of phytochrome-mediated transcriptional regulation. We experimentally validated phytochrome-induced changes in the AS of genes that are involved in RNA splicing, phytochrome signaling, the circadian clock, and photosynthesis. Moreover, we show that phytochrome-induced AS changes of SPA1-RELATED 3, the negative regulator of light signaling, physiologically contributed to promoting photomorphogenesis. Finally, photophysiological experiments demonstrated that phytochrome transduces the signal from its photosensory domain to induce light-dependent AS alterations in the nucleus. Taking these data together, we show that phytochrome directly induces AS cascades in parallel with transcriptional cascades to mediate light responses in Arabidopsis.
An equalization technique for orthogonal frequency-division multiplexing systems in time-variant multipath channels

A loss of subchannel orthogonality due to time-variant multipath channels in orthogonal frequency division multiplexing (OFDM) systems leads to interchannel interference (ICI) which increases the error floor in proportion to the Doppler frequency. A simple frequency-domain equalization technique which can compensate for the effect of ICI in a multipath fading channel is proposed. In this technique, the equalization of the received OFDM signal is achieved by using the assumption that the channel impulse response (CIR) varies in a linear fashion during a block period and by compensating for the ICI terms that significantly affect the bit-error rate (BER) performance.
Conjunctival hyperaemia with the use of latanoprost versus other prostaglandin analogues in patients with ocular hypertension or glaucoma: a meta-analysis of randomised clinical trials

Aim: To conduct a meta-analysis of randomised clinical trials (RCTs) in order to evaluate the development of conjunctival hyperaemia after the use of latanoprost versus travoprost and bimatoprost, in patients with ocular hypertension or glaucoma. Methods: In order to identify the potentially relevant RCTs, a systematic literature retrieval was conducted in Medline, Embase and Cochrane Controlled Trials Register (1995–April 2007) databases The outcome measure was the appearance of conjunctival hyperaemia during the study. Statistical analyses included the calculation of odds ratio (OR) and its respective confidence interval, along with intertrial statistical heterogeneity. Publication bias was evaluated through a funnel plot, and a sensitivity analysis was also performed. Results: In total, 13 RCTs involving 2222 patients with ocular hypertension or glaucoma were included, five comparing latanoprost versus travoprost, seven comparing latanoprost versus bimatoprost and one comparing latanoprost versus travoprost and bimatoprost. The combined results showed that latanoprost produced lower occurrence of conjunctival hyperaemia than both travoprost (OR = 0.51; 95% CI 0.39 to 0.67, p<0.0001) and bimatoprost (OR = 0.32; 95% CI 0.24 to 0.42, p<0.0001). No significant heterogeneity was found between the included RCTs. There was no evidence of publication bias. In the sensitivity analysis performed, none of the clinical trials included in this meta-analysis has an important impact in the global estimation of OR. Conclusions: According to available data, the use of latanoprost is associated with a lower incidence of conjunctival hyperaemia when compared with travoprost and bimatoprost in the treatment of patients with ocular hypertension or glaucoma.
[Pegylated interferon-alfa 2a with ribavirin in chronic viral hepatitis C (final report)].

UNLABELLED We evaluated the efficacy and safety of peginterferon alfa-2a [40KD] (Peg-IFNalpha-2a) plus ribavirin in patients with chronic hepatitis C in an open-label programme in a routine clinical setting in Poland. Patients received Peg-IFNalpha-2a 180mg/week plus ribavirin 800-1200 mg/d for 48 weeks. Sustained virological response (SVR) was defined as undetectable HCV RNA (<50IU/mL) at the end of follow-up (week 72). 466 adults were enrolled. Most patients (87.3%) had genotype 1 infection. 440 subjects (94,4%) completed treatment. The overall SVR rate was 55.7%. A higher SVR rate was obtained in treatment-naïve patients (58.7%) than in relapsers (47.8%; p=0,048). SVR rates in genotype 1 and non-1 patients were 51.1% and 88.5%, respectively (p<0.001). There were significant higher SVR rates in patients with lower baseline fibrosis (p=0,01). There were no differences in SVRs by gender or viral load. Hemoglobin, leukocyte and neutrophil levels decreased significantly during treatment, but returned to baseline after the end of treatment. ALT levels decreased significantly during treatment in patients with and without an SVR. 38.4% of patients experienced adverse events like neutropenia, anemia, thrombocytopenia, and other. There was one death (severe thrombocytopenia). CONCLUSIONS The overall SVR achieved in this predominantly genotype 1 population was 55.7%. SVR rates were significantly higher in treatment-naïve patients, those with non-1 genotypes, and in patients with lower baseline fibrosis scores.
Training‐induced mitochondrial adaptation: role of peroxisome proliferator‐activated receptor γ coactivator‐1α, nuclear factor‐κB and β‐blockade

• What is the central question of this study? The peroxisome proliferator‐activated receptor γ coactivator‐1α (PGC‐1α) signalling pathway plays an important role in mitochondrial biogenesis and has been shown to be activated both by an acute bout of exercise and by long‐term training. However, the upstream signals and control mechanisms causing the adaptation and its interaction with other signalling pathways during exercise are not clear. • What is the main finding and its importance? Our main finding was that PGC‐1α‐controlled mitochondrial training adaptation was attenuated by pyrolidine dithiocarbamate, an antioxidant known to block nuclear factor‐κB signalling, which indicates that PGC‐1α signalling is redox sensitive and can be influenced by nuclear factor‐κB. We also found that the β‐adrenergic blocker propranolol did not prevent the training‐induced adaptation of muscle mitochondrial protein under our experimental conditions.
China's Empty Nest Elderly Need Better Care

To the Editor: Elderly “empty nesters” are elderly adults with no children around to relieve their solitude, who thus live alone or with a spouse. China has the world’s largest number of elderly adults and the number of empty nest families is rapidly increasing. Empty nest elderly households in China account for almost 25% of older adult families, with the percentage in Beijing exceeding 35%. All current elderly families will become empty nesters by 2030, according to estimate data that suggest that the percentage of this group will reach 90%. The empty nest phenomenon has become an important social concern in China that cannot be ignored. Unaccompanied and unattended, empty nest elderly adults are vulnerable and usually experience the physical, psychological, and social problems associated with old age. One highlighted problem in China is dementia. It is estimated that the economic effect of dementia will be greater than that of cancer, heart disease, and stroke combined. A recent study revealed that, in 2010, 9.9 million people in China had dementia, with a prevalence of 2.6% for those aged 65 to 69 and 60.5% for those aged 95 to 99. Influenced by Chinese traditional ideas and insufficient social supports, immediate family members take care of more than 90% of individuals with dementia at home until the end of their lives. The one-child policy and large internal migration may exacerbate the problem of dementia, with decreasing continuing care to individuals with dementia. Additionally, Chinese empty nesters experience psychosocial problems such as depression, loneliness, and anxiety. The term “empty nest syndrome” is used to describe this condition. Depression is one of the most frequent psychiatric disorders in old age. A survey of 4,265 Chinese adults aged 60 and older showed that the prevalence of depressive symptoms for empty nest elderly adults was 8.18%, significantly higher than that for those who are not empty nesters. Factors such as being female, being single, and having poor self-rated health and life status were reported to be associated with depression. Lack of social support is one of the main causes of depression. Depression has negative effects on elderly adults, such as decreasing social and physical activities, generating unsociability and self-grief, and reducing the quality of life. The empty nest phenomenon has been more severe in rural areas than in urban areas, derived from the differences in things such as economic level, culture, lifestyle, and geographic location. Economic development differs between inland and coastal regions, and there is a flow of rural surplus labor to large, eastern coastal cities. Among a series of social problems that the population aging trend has brought about, the most prominent may be the elderly care problem. Despite great economic achievements, China’s social security provision for elderly adults remains underfunded, underdeveloped, and geographically unevenly distributed. Collectively, empty nest elderly adults in China need better care, especially those in rural areas.
quinoa , coeliac disease and gluten-free diet *

Quinoa is an Andean crop with multiple agronomical, nutritional and industrial applications. Coeliac disease (CD) is a condition characterized by an inappropriate immune response to dietary gluten leading to histological damage of the small intestine, and an effective treatment is a lifelong gluten-free diet (GFD). Quinoa contains low concentrations of gluten and has a distant phylogenetic link with gluten-containing cereals (wheat, rye and barley). This prompted consideration of quinoa as a naturally gluten-free product, suitable for patients with CD, although evidence is scant. The present chapter aims to review the current scientific literature pertaining quinoa and coeliac disease. Initial in vitro studies examined the suitability of quinoa for patients with CD using the agglutination activity of undifferentiated myeloid leukaemia cells (De Vincenzi et al., 1999), measuring the concentration of coeliac-toxic peptides (Berti et al., 2004) and analysing immune reactivity in T-cell-proliferation studies and organ culture explants (Bergamo et al., 2011). The main limitation of these studies was the use of one non-described cultivar. Recently, cultivars have been identified with putative toxic quinoa peptides that seem to elicit immunological activation of gliadin-specific CD4+ T-cells, as well as elicit secretion of cytokines when cultured with coeliac duodenal biopsies (Zevallos et al., 2012). In vivo studies are almost absent – with the exception of a retrospective review of dietary history of patients eating quinoa (Lee et al., 2009) and our feeding study (Zevallos et al., 2013) – which show that short-term consumption of quinoa is well tolerated among individuals with CD and has a mild hypocholesterolemic effect that could also be relevant for a non-CD subject at risk of obesity. To conclude, results from in vitro and in vivo studies indicate that some quinoa cultivars have small amounts of gluten-like proteins which can stimulate immune cells in vitro, but that do not exacerbate coeliac disease when eating as part of a GFD. However, further studies evaluating the long-term effects of quinoa consumption are needed. On the basis of current literature, it is anticipated that quinoa can be safely consumed by CD patients.
Fecal indicators and bacterial pathogens in bottled water from Dhaka, Bangladesh

Forty-six bottled water samples representing 16 brands from Dhaka, Bangladesh were tested for the numbers of total coliforms, fecal indicator bacteria (i.e., thermotolerant Escherichia coli and Enterococcus spp.) and potential bacterial pathogens (i.e., Aeromonas hydrophila, Pseudomonas aeruginosa, Salmonella spp., and Shigella spp.). Among the 16 brands tested, 14 (86%), ten (63%) and seven (44%) were positive for total coliforms, E. coil and Enterococcus spp. , respectively. Additionally, a further nine (56%), eight (50%), six (37%), and four (25%) brands were PCR positive for A. hydrophila lip, P. aeruginosa ETA, Salmonella spp. invA, and Shigella spp. ipaH genes, respectively. The numbers of bacterial pathogens in bottled water samples ranged from 28 ± 12 to 600 ± 45 (A. hydrophila lip gene), 180 ± 40 to 900 ± 200 (Salmonella spp. invA gene), 180 ± 40 to 1,300 ± 400 (P. aeruginosa ETA gene) genomic units per L of water. Shigella spp. ipaH gene was not quantifiable. Discrepancies were observed in terms of the occurrence of fecal indicators and bacterial pathogens. No correlations were observed between fecal indicators numbers and presence/absence of A. hydrophila lip (p = 0.245), Salmonella spp. invA (p = 0.433), Shigella spp. ipaH gene (p = 0.078), and P. aeruginosa ETA (p = 0.059) genes. Our results suggest that microbiological quality of bottled waters sold in Dhaka, Bangladesh is highly variable. To protect public health, stringent quality control is recommended for the bottled water industry in Bangladesh.
Linear bilevel programming solution by genetic algorithm

Bilevel programming, a tool for modeling decentralized decisions, consists of the objective of the leader at its 1rst level and that of the follower at the second level. Bilevel programming has been proved to be NP-hard problem. Numerous algorithms have been developed so far for solving bilevel programming problem. In this paper, an attempt has been made to develop an e6cient approach based on genetic algorithm. The e6ciency of the algorithm is ascertained by comparing the results with Gendreau et al. (J. Global Optimization 8 (1996) 217–233) method.
Distribution of Traction Forces and Intracellular Markers Associated with Shape Changes During Amoeboid Cell Migration

, on top of which are imposed smaller random ﬂuctuations. The fact that a considerable portion of the changes in cell shape are due to periodic repetitive events enables the use of conditional statistics methods to analyze the network of biochemical processes involved in cell motility. Taking advan-tage of this cyclic nature, we apply Principal Component Analysis (PCA) and phase-average statistics to analyze the dominant modes of shape change and their association to the activity and localization of molecular motors. We analyze time-lapse measure -ments of cell shape, traction forces and ﬂuorescence from green ﬂuorescent protein (GFP) reporters for F-actin in
The effect of a checklist on the quality of post-anaesthesia patient handover: a randomized controlled trial.

OBJECTIVE Patient handover is an important element of continuity, quality and safety in patient care. Handover without standardized protocols is prone to information loss and might be a possible danger to patient safety. Checklists are established methods that help to structure complex processes in other high-risk fields such as aviation. In the past few years, their implementation has attracted research interest in medicine. We hypothesize that a checklist for handover between anaesthesiologist and post-anaesthesia care unit nurse will increase the amount of information transfer during patient handover after anaesthesia. DESIGN AND SETTING A total of 120 post-anaesthesia patient handovers were recorded on video and analyzed. Forty handovers before the implementation of the checklist and 80 after the implementation of the checklist, randomized into two groups: with and without the use of the checklist. MAIN OUTCOME MEASURES An overall number of items handed over, handover of specific items and duration of the handover were analyzed. RESULTS With the use of the written checklist, the overall items handed over increased significantly from a median of 32.4-48.7%. The duration of handover increased from a median of 86-121 s. Instructions about items that should be included in handovers, but without the use of a written checklist, was not associated with an increase in the number of items handed over or duration of the interview. CONCLUSIONS This study suggests that the use of a checklist for post-anaesthesia handover might improve the quality of patient handover by increasing the information handed over.
Human Inferences about Sequences: A Minimal Transition Probability Model

The brain constantly infers the causes of the inputs it receives and uses these inferences to generate statistical expectations about future observations. Experimental evidence for these expectations and their violations include explicit reports, sequential effects on reaction times, and mismatch or surprise signals recorded in electrophysiology and functional MRI. Here, we explore the hypothesis that the brain acts as a near-optimal inference device that constantly attempts to infer the time-varying matrix of transition probabilities between the stimuli it receives, even when those stimuli are in fact fully unpredictable. This parsimonious Bayesian model, with a single free parameter, accounts for a broad range of findings on surprise signals, sequential effects and the perception of randomness. Notably, it explains the pervasive asymmetry between repetitions and alternations encountered in those studies. Our analysis suggests that a neural machinery for inferring transition probabilities lies at the core of human sequence knowledge. Author Summary We explore the possibility that the computation of time-varying transition probabilities may be a core building block of sequence knowledge in humans. Humans may then use these estimates to predict future observations. Expectations derived from such a model should conform to several properties. We list six such properties and we test them successfully against various experimental findings reported in distinct fields of the literature over the past century. We focus on five representative studies by other groups. Such findings include the “sequential effects” evidenced in many behavioral tasks, i.e. the pervasive fluctuations in performance induced by the recent history of observations. We also consider the “surprise-like” signals recorded in electrophysiology and even functional MRI, that are elicited by a random stream of observations. These signals are reportedly modulated in a quantitative manner by both the local and global statistics of observations. Last, we consider the notoriously biased subjective perception of randomness, i.e. whether humans think that a given sequence of observations has been generated randomly or not. Our model therefore unifies many previous findings and suggest that a neural machinery for inferring transition probabilities must lie at the core of human sequence knowledge.
Systematic Characterization of the Computed Tomography Angiography Spot Sign in Primary Intracerebral Hemorrhage Identifies Patients at Highest Risk for Hematoma Expansion: The Spot Sign Score

Background and Purpose— The presence of active contrast extravasation (the spot sign) on computed tomography (CT) angiography has been recognized as a predictor of hematoma expansion in patients with intracerebral hemorrhage. We aim to systematically characterize the spot sign to identify features that are most predictive of hematoma expansion and construct a spot sign scoring system. Methods— We retrospectively reviewed CT angiograms performed in all patients who presented to our emergency department over a 9-year period with primary intracerebral hemorrhage and had a follow-up noncontrast head CT within 48 hours of the baseline CT angiogram. Three neuroradiologists reviewed the CT angiograms and determined the presence and characteristics of spot signs according to strict radiological criteria. Baseline and follow-up intracerebral hemorrhage volumes were determined by computer-assisted volumetric analysis. Results— We identified spot signs in 71 of 367 CT angiograms (19%), 6 of which were delayed spot signs (8%). The presence of any spot sign increased the risk of significant hematoma expansion (69%, OR=92, P<0.0001). Among the spot sign characteristics examined, the presence of ≥3 spot signs, a maximum axial dimension ≥5 mm, and maximum attenuation ≥180 Hounsfield units were independent predictors of significant hematoma expansion, and these were subsequently used to construct the spot sign score. In multivariate analysis, the spot sign score was the strongest predictor of significant hematoma expansion, independent of time from ictus to CT angiogram evaluation. Conclusion— The spot sign score predicts significant hematoma expansion in primary intracerebral hemorrhage. If validated in other data sets, it could be used to select patients for early hemostatic therapy.
Project Nick: meetings augmentation and analysis

The Software Technology Program of MCC is investigating the early part of the design process, before requirements are established, for large-scale distributed systems. Face-to-face meetings are an important activity during this phase of a project since they provide a medium for direction, exploration, and consensus building. Project Nick is attempting to apply automated facilities to the process, conduct, and semantic capture of design meetings. Primary topics covered in this paper are meeting analysis, meeting augmentation, and a model of meeting progression that serves as the framework for our work.
Orchitis and testicular abscess formation caused by non‐typhoid Salmonellosis

The case of a 36‐year‐old man with epididymo‐orchitis followed by testicular abscess formation 4 weeks later due to Salmonella berta is reported, and the literature on orchitis and testicular abscesses caused by non‐typhoid Salmonella is reviewed.