Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction of Arabidopsis Tryptophan Pathway Enzymes and Camalexin by Amino Acid Starvation, Oxidative Stress, and an Abiotic Elicitor

The tryptophan (Trp) biosynthetic pathway leads to the production of many secondary metabolites with diverse functions, and its regulation is predicted to respond to the needs for both protein synthesis and secondary metabolism. We have tested the response of the Trp pathway enzymes and three other amino acid biosynthetic enzymes to starvation for aromatic amino acids, branched-chain amino acids, or methionine. The Trp pathway enzymes and cytosolic glutamine synthetase were induced under all of the amino acid starvation test conditions, whereas methionine synthase and acetolactate synthase were not. The mRNAs for two stress-inducible enzymes unrelated to amino acid biosynthesis and accumulation of the indolic phytoalexin camalexin were also induced by amino acid starvation. These results suggest that regulation of the Trp pathway enzymes under amino acid deprivation conditions is largely a stress response to allow for increased biosynthesis of secondary metabolites. Consistent with this hypothesis, treatments with the oxidative stress-inducing herbicide acifluorfen and the abiotic elicitor α-amino butyric acid induced responses similar to those induced by the amino acid starvation treatments. The role of salicylic acid in herbicide-mediated Trp and camalexin induction was investigated.
OSTEOPOROSIS: A NECROPSY STUDY OF VERTEBRAE AND ILIAC CRESTS.

Osteoporosis is a diminution of hard bone substance without obvious changes in its chemical or histologic composition. Generalized osteoporosis is evident most readily in those bone regions which are predominantly cancellous, such as the vertebrae, sacrum, sternum, ribs and iliac crests. While osteoporosis may be secondary to other diseases, as in thyrotoxicosis and Cushing's syndrome, the etiology, for the most part, is obscure. Study of this disease has been hindered by the difficulty in its quantitative assessment. It has been shown that the calcium content of bone salt is remarkably constant,L and the expression of calcium weight per unit volume of bone remains the parameter by which other measurements should be judged. Radiologic examination of vertebral bone slabs has been closely correlated with calcium analysis by Caldwell and Collins in ioo necropsied patients.2 The normal interposition of soft tissues has been shown by Fusi3 to require the extraction of 6o per cent of calcium from vertebrae before marked radiologic changes appear. For clinical purposes there have been developed methods using ratios of cortical thickness to shaft diameter of tubular bones and of anterior to central vertebral body heights.4 Bone biopsy using trephined material from the iliac crest has been graded visually by Beck and Nordin, as an index of osteoporosis.5 The crude assessment of vertebrae at necropsy by visual examination and finger pressure is unreliable, and the histologic examinations of routine bone sections is also suspect. The purpose of the present study was to examine the vertebrae and iliac crests in a random necropsy series using a histologic method with a minimum of subjective interpretation and one which would show a significant correlation with vertebral calcium concentration.
Micronutrient composition and acceptability of Moringa oleifera leaf‐fortified dishes by children in Ada‐East district, Ghana

Abstract Moringa oleifera (M. oleifera), a green leafy vegetable, is a good source of minerals and vitamins which could be consumed as part of diet to improve human health and well‐being. Drying M. oleifera leaves could make it readily available for use as a food fortificant. The objectives of the study were to determine micromineral and β ‐carotene content of dried M. oleifera leaves, and leaf‐incorporated local dishes, and also assess school children's (4‐12 yr) acceptability of dried M. oleifera leaf‐incorporated local dishes and feasibility of introducing dried leaves into a school lunch menu. M. oleifera leaves were solar dried, milled into powder, and packaged into polythene bags. Moisture level in the dried leaves and pH were determined. Minerals in the leaf powder were determined by Atomic Absorption Spectrophotometry (AAS). Beta‐carotene levels were determined by spectrophotometry. Acceptability tests of dishes fortified with M. oleifera leaf powder were conducted with score sheets (Smileys) on a 5‐point hedonic scale of “Like Extremely” to “Dislike Extremely”, and dishes ranked to determine preference. Dried M. oleifera leaves contained high levels of micronutrients: 0.36 ± 0.04 mg/100 g Copper (Cu); 5.80 ± 0.68 mg/100 g Manganese (Mn); 20.96 ± 1.37 mg/100 g Iron (Fe); 6.79 ± 1.82 mg/100 g Zn; and 21.42 ± 1.67 mg/100 g β‐carotene. The dishes showed significant levels of these minerals compared to the nonfortified dishes (P < 0.05). M. oleifera leaf‐fortified dishes were also highly acceptable to the children (highest mean score of 5.0 ± 0 of 5 and lowest of 3.50 ± 1.43 of 5). M. oleifera leaf powder contains high levels of the micronutrients β‐carotene, Zn, Mn, and Fe, comparable to levels found in amaranth and spinach. M. oleifera leaf‐fortified local dishes were well accepted by children in Ada‐East district. M. oleifera leaf fortified dishes could be good sources of β‐carotene and other minerals for children vulnerable to malnutrition in Ghana.
A wide-bandwidth Si/SiGe HBT direct conversion sub-harmonic mixer/downconverter

A wideband sub-harmonic mixer/direct-conversion downconverter is implemented in a Si/SiGe HBT technology, with improved rejection of the local oscillator (LO), high input intercept point, and low current requirements. The circuit utilizes a combination of phase shifters operating at 45/spl deg/ and 90/spl deg/ to achieve better than 33-dB input-referred rejection of the LO. The measured third-order input intercept point (IIP3) was approximately -3 dBm and the second-order input intercept point (IIP2) was roughly 35 dBm, with a measured double sideband (DSB) noise figure of 7.8 dB. A comparison was made between devices of differing germanium concentration in the base, and the devices with higher Ge content exhibited improved noise figure and gain. Each mixer required approximately 2.8 mA from a 3.3 V supply.
Enhanced Deep Residual Networks for Single Image Super-Resolution

Recent research on super-resolution has progressed with the development of deep convolutional neural networks (DCNN). In particular, residual learning techniques exhibit improved performance. In this paper, we develop an enhanced deep super-resolution network (EDSR) with performance exceeding those of current state-of-the-art SR methods. The significant performance improvement of our model is due to optimization by removing unnecessary modules in conventional residual networks. The performance is further improved by expanding the model size while we stabilize the training procedure. We also propose a new multi-scale deep super-resolution system (MDSR) and training method, which can reconstruct high-resolution images of different upscaling factors in a single model. The proposed methods show superior performance over the state-of-the-art methods on benchmark datasets and prove its excellence by winning the NTIRE2017 Super-Resolution Challenge[26].
Not Welcome Anymore: The Effect of Electoral Incentives on the Reception of Refugees

Do electoral incentives affect immigration policies? Exploiting the Italian system for refugees’ reception and data from Italian municipalities, we show that proximity to elections reduces the probability that a municipality applies to host a refugee center by 26%, despite the economic benefits arising from these centers. Low electoral competition and high shares of extreme-right voters drive the effect. Our results are rationalized by a theoretical model and can explain the unequal distribution of refugees across and within countries.
Revisiting Embedding Features for Simple Semi-supervised Learning

Recent work has shown success in using continuous word embeddings learned from unlabeled data as features to improve supervised NLP systems, which is regarded as a simple semi-supervised learning mechanism. However, fundamental problems on effectively incorporating the word embedding features within the framework of linear models remain. In this study, we investigate and analyze three different approaches, including a new proposed distributional prototype approach, for utilizing the embedding features. The presented approaches can be integrated into most of the classical linear models in NLP. Experiments on the task of named entity recognition show that each of the proposed approaches can better utilize the word embedding features, among which the distributional prototype approach performs the best. Moreover, the combination of the approaches provides additive improvements, outperforming the dense and continuous embedding features by nearly 2 points of F1 score.
Common amino acid domain among endopolygalacturonases of ascomycete fungi

The endopolygalacturonase (EC 3.2.1.15) enzymes produced in vitro by three ascomycete fungi, Aspergillus niger, Sclerotinia sclerotiorum, and Colletotrichum lindemuthianum were studied by using thin-layer isoelectric focusing and activity stain overlay techniques. The polygalacturonases from A. niger and S. sclerotiorum consisted of numerous isoforms, whereas the endopolygalacturonase from C. lindemuthianum consisted of a single protein species. The most abundant endopolygalacturonase isoform produced by each of these organisms was purified and characterized. Biochemical parameters, including molecular weight, isoelectric point, kinetic parameters, temperature and pH optima, and thermal stability, were determined. Considerable differences in physical and chemical properties were demonstrated among these fungal polygalacturonases. Antibodies raised against individual proteins exhibited little cross-reaction, suggesting that these enzymes differ structurally as well as biochemically. In contrast, the analysis of the N-terminal amino acid sequences of the three proteins showed extensive homology, particularly in a region labeled domain 1 in which 84% of the amino acids were conserved.
Biological Signatures of Brain Damage Associated with High Serum Ferritin Levels in Patients with Acute Ischemic Stroke and Thrombolytic Treatment

Background and purpose: Increased body iron stores have been related to greater oxidative stress and brain injury in clinical and experimental cerebral ischemia and reperfusion. We aimed to investigate the biological signatures of excitotoxicity, inflammation and blood brain barrier disruption potentially associated with high serum ferritin levels-related damage in acute stroke patients treated with i.v. t-PA. Methods: Serum levels of ferritin (as index of increased cellular iron stores), glutamate, interleukin-6, matrix metalloproteinase-9 and cellular fibronectin were determined in 134 patients treated with i.v. t-PA within 3 hours from stroke onset in blood samples obtained before t-PA treatment, at 24 and 72 hours. Results: Serum ferritin levels before t-PA infusion correlated to glutamate (r = 0.59, p < 0.001) and interleukin-6 (r = 0.55, p <0.001) levels at baseline, and with glutamate (r = 0.57,p <0.001), interleukin-6 (r = 0.49,p <0.001), metalloproteinase-9 (r = 0.23, p = 0.007) and cellular fibronectin (r = 0.27, p = 0.002) levels measured at 24 hours and glutamate (r = 0.415, p < 0.001), interleukin-6 (r = 0.359, p < 0.001) and metalloproteinase-9 (r = 0.261, p = 0.004) at 72 hours. The association between ferritin and glutamate levels remained after adjustment for confounding factors in generalized linear models. Conclusions: Brain damage associated with increased iron stores in acute ischemic stroke patients treated with iv. tPA may be mediated by mechanisms linked to excitotoxic damage. The role of inflammation, blood brain barrier disruption and oxidative stress in this condition needs further research.
Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays

Background In addition to SARS associated coronaviruses, 4 non-SARS related human coronaviruses (HCoVs) are recognized as common respiratory pathogens. The etiology and clinical impact of HCoVs in Chinese adults with acute upper respiratory tract infection (URTI) needs to be characterized systematically by molecular detection with excellent sensitivity. Methodology/Principal Findings In this study, we detected 4 non-SARS related HCoV species by real-time RT-PCR in 981 nasopharyngeal swabs collected from March 2009 to February 2011. All specimens were also tested for the presence of other common respiratory viruses and newly identified viruses, human metapneumovirus (hMPV) and human bocavirus (HBoV). 157 of the 981 (16.0%) nasopharyngeal swabs were positive for HCoVs. The species detected were 229E (96 cases, 9.8%), OC43 (42 cases, 4.3%), HKU1 (16 cases, 1.6%) and NL63 (11 cases, 1.1%). HCoV-229E was circulated in 21 of the 24 months of surveillance. The detection rates for both OC43 and NL63 were showed significantly year-to-year variation between 2009/10 and 2010/11, respectively (P<0.001 and P = 0.003), and there was a higher detection frequency of HKU1 in patients aged over 60 years (P = 0.03). 48 of 157(30.57%) HCoV positive patients were co-infected. Undifferentiated human rhinoviruses and influenza (Flu) A were the most common viruses detected (more than 35%) in HCoV co-infections. Respiratory syncytial virus (RSV), human parainfluenza virus (PIV) and HBoV were detected in very low rate (less than 1%) among adult patients with URTI. Conclusions/Significance All 4 non-SARS-associated HCoVs were more frequently detected by real-time RT-PCR assay in adults with URTI in Beijing and HCoV-229E led to the most prevalent infection. Our study also suggested that all non-SARS-associated HCoVs contribute significantly to URTI in adult patients in China.
The Relationship between Student Engagement and Professionalism in Pharmacy Students.

This study investigates the relationship between student engagement (as measured by the National Survey of Student Engagement benchmarks) and pharmacy student professionalism (as measured by the Pharmacy Professionalism Domain instrument) in first and third year pharmacy students at seven different schools of pharmacy. Engagement provides the conceptual framework. Data were analyzed from 1,405 first and third year pharmacy students at seven different schools of pharmacy during spring 2010. Factor validity of the scales was assessed using Structural Equation modeling and model fit was established at RMSEA . 052. The parameter estimates suggest convergent and divergent validity of the instruments. Mean level differences in professionalism were found by year with higher means for third year students in all of the professionalism domains except Reliability, Responsibility, and Accountability. Among first year students, the Enriching Educational Experience benchmark was the most important predictor of professionalism. Among third year students, the Student-Faculty Interaction was the most important predictor of professionalism.
Sugared water consumption by adult offspring of mothers fed a protein-restricted diet during pregnancy results in increased offspring adiposity: the second hit effect

Poor maternal nutrition predisposes offspring to metabolic disease. This predisposition is modified by various postnatal factors. We hypothesised that coupled to the initial effects of developmental programming due to a maternal low-protein diet, a second hit resulting from increased offspring postnatal sugar consumption would lead to additional changes in metabolism and adipose tissue function. The objective of the present study was to determine the effects of sugared water consumption (5 % sucrose in the drinking-water) on adult offspring adiposity as a ‘second hit’ following exposure to maternal protein restriction during pregnancy. We studied four offspring groups: (1) offspring of mothers fed the control diet (C); (2) offspring of mothers fed the restricted protein diet (R); (3) offspring of control mothers that drank sugared water (C-S); (4) offspring of restricted mothers that drank sugared water (R-S). Maternal diet in pregnancy was considered the first factor and sugared water consumption as the second factor – the second hit. Body weight and total energy consumption, before and after sugared water consumption, were similar in all the groups. Sugared water consumption increased TAG, insulin and cholesterol concentrations in both the sexes of the C-S and R-S offspring. Sugared water consumption increased leptin concentrations in the R-S females and males but not in the R offspring. There was also an interaction between sugared water and maternal diet in males. Sugared water consumption increased adipocyte size and adiposity index in both females and males, but the interaction with maternal diet was observed only in females. Adiposity index and plasma leptin concentrations were positively correlated in both the sexes. The present study shows that a second hit during adulthood can amplify the effects of higher adiposity arising due to poor maternal pregnancy diet in an offspring sex dependent fashion.
Acute Effects of Nicotine Amplify Accumbal Neural Responses during Nicotine-Taking Behavior and Nicotine-Paired Environmental Cues

Nicotine self-administration (SA) is maintained by several variables, including the reinforcing properties of nicotine-paired cues and the nicotine-induced amplification of those cue properties. The nucleus accumbens (NAc) is implicated in mediating the influence of these variables, though the underlying neurophysiological mechanisms are not yet understood. In the present study, Long-Evans rats were trained to self-administer nicotine. During SA sessions each press of a lever was followed by an intravenous infusion of nicotine (30 µg/kg) paired with a combined light-tone cue. Extracellular recordings of single-neuron activity showed that 20% of neurons exhibited a phasic change in firing during the nicotine-directed operant, the light-tone cue, or both. The phasic change in firing for 98% of neurons was an increase. Sixty-two percent of NAc neurons additionally or alternatively showed a sustained decrease in average firing during the SA session relative to a presession baseline period. These session decreases in firing were significantly less prevalent in a group of neurons that were activated during either the operant or the cue than in a group of neurons that were nonresponsive during those events (referred to as task-activated and task-nonactivated neurons, respectively). Moreover, the session decrease in firing was dose-dependent for only the task-nonactivated neurons. The data of the present investigation provide supportive correlational evidence for two hypotheses: (1) excitatory neurophysiological mechanisms mediate the NAc role in cue-maintenance of nicotine SA, and (2) a differential nicotine-induced inhibition of task-activated and task-nonactivated neurons mediates the NAc role in nicotine-induced amplification of cue effects on nicotine SA.
Evaluating Composition Techniques for Architectural Specifications: A Comparative Study

Techniques for composing architectural specifications are emerging in order to facilitate software architecture evolution. However, there is little empirical understanding on whether such techniques scale when they are used to express different types of architectural changes. This paper presents a first comparative evaluation of two significantly-different composition techniques for architectural descriptions. The first technique is fully based on heuristic composition operators, while the second one demands explicit composition specification. Several releases of a software product line were used in our evaluation, and their designs were expressed with an architectural description language, called ACME. Some metrics were used to compute the number of required modifications, syntactic conflicts, and semantic conflicts in composed (output) models produced with both heuristic and non-heuristic compositions. We observed that, in general, the heuristic composition approach outperformed the non-heuristic one mainly due to the narrow set of composition operators supported by the latter.
Parallel breadth-first search on distributed memory systems

Data-intensive, graph-based computations are pervasive in several scientific applications, and are known to to be quite challenging to implement on distributed memory systems. In this work, we explore the design space of parallel algorithms for Breadth-First Search (BFS), a key subroutine in several graph algorithms. We present two highly-tuned parallel approaches for BFS on large parallel systems: a level-synchronous strategy that relies on a simple vertex-based partitioning of the graph, and a two-dimensional sparse matrix partitioning-based approach that mitigates parallel communication overhead. For both approaches, we also present hybrid versions with intra-node multithreading. Our novel hybrid two-dimensional algorithm reduces communication times by up to a factor of 3.5, relative to a common vertex based approach. Our experimental study identifies execution regimes in which these approaches will be competitive, and we demonstrate extremely high performance on leading distributed-memory parallel systems. For instance, for a 40,000-core parallel execution on Hopper, an AMD MagnyCours based system, we achieve a BFS performance rate of 17.8 billion edge visits per second on an undirected graph of 4.3 billion vertices and 68.7 billion edges with skewed degree distribution.
Usefulness of carotid plaque (sum and maximum of plaque thickness) in combination with intima‐media thickness for the detection of coronary artery disease in asymptomatic patients with diabetes

The usefulness of markers of carotid plaque, such as sum (PS) and maximum (P‐max) of the plaque thickness, in combination with intima‐media thickness in the common carotid artery (CIMT) for the detection of obstructive coronary artery disease (CAD) was investigated in patients with type 2 diabetes without known CAD.
Insertion and Deletion Processes in Recent Human History

Background Although insertions and deletions (indels) account for a sizable portion of genetic changes within and among species, they have received little attention because they are difficult to type, are alignment dependent and their underlying mutational process is poorly understood. A fundamental question in this respect is whether insertions and deletions are governed by similar or different processes and, if so, what these differences are. Methodology/Principal Findings We use published resequencing data from Seattle SNPs and NIEHS human polymorphism databases to construct a genomewide data set of short polymorphic insertions and deletions in the human genome (n = 6228). We contrast these patterns of polymorphism with insertions and deletions fixed in the same regions since the divergence of human and chimpanzee (n = 10546). The macaque genome is used to resolve all indels into insertions and deletions. We find that the ratio of deletions to insertions is greater within humans than between human and chimpanzee. Deletions segregate at lower frequency in humans, providing evidence for deletions being under stronger purifying selection than insertions. The insertion and deletion rates correlate with several genomic features and we find evidence that both insertions and deletions are associated with point mutations. Finally, we find no evidence for a direct effect of the local recombination rate on the insertion and deletion rate. Conclusions/Significance Our data strongly suggest that deletions are more deleterious than insertions but that insertions and deletions are otherwise generally governed by the same genomic factors.