Miracle-dz/UniFAR-FTUs huggingface dataset:
The Type II NADPH Dehydrogenase Facilitates Cyclic Electron Flow, Energy-Dependent Quenching, and Chlororespiratory Metabolism during Acclimation of Chlamydomonas reinhardtii to Nitrogen Deprivation1[OPEN]

A NADPH dehydrogenase is critical for balancing electron flow between energy-dissipating and energy-generating pathways during the acclimation to photoautotrophic nitrogen deprivation. When photosynthetic organisms are deprived of nitrogen (N), the capacity to grow and assimilate carbon becomes limited, causing a decrease in the productive use of absorbed light energy and likely a rise in the cellular reduction state. Although there is a scarcity of N in many terrestrial and aquatic environments, a mechanistic understanding of how photosynthesis adjusts to low-N conditions and the enzymes/activities integral to these adjustments have not been described. In this work, we use biochemical and biophysical analyses of photoautotrophically grown wild-type and mutant strains of Chlamydomonas reinhardtii to determine the integration of electron transport pathways critical for maintaining active photosynthetic complexes even after exposure of cells to N deprivation for 3 d. Key to acclimation is the type II NADPH dehydrogenase, NDA2, which drives cyclic electron flow (CEF), chlororespiration, and the generation of an H+ gradient across the thylakoid membranes. N deprivation elicited a doubling of the rate of NDA2-dependent CEF, with little contribution from PGR5/PGRL1-dependent CEF. The H+ gradient generated by CEF is essential to sustain nonphotochemical quenching, while an increase in the level of reduced plastoquinone would promote a state transition; both are necessary to down-regulate photosystem II activity. Moreover, stimulation of NDA2-dependent chlororespiration affords additional relief from the elevated reduction state associated with N deprivation through plastid terminal oxidase-dependent water synthesis. Overall, rerouting electrons through the NDA2 catalytic hub in response to photoautotrophic N deprivation sustains cell viability while promoting the dissipation of excess excitation energy through quenching and chlororespiratory processes.
Temporal trends in early clinical manifestations of perinatal HIV infection in a population-based cohort.

CONTEXT The effect of early antiretroviral therapy (ART) on the early progression of perinatal human immunodeficiency virus (HIV) infection is not well defined. OBJECTIVE To examine early disease progression and survival in a population-based cohort with perinatal HIV infection in relation to year of birth and use of ART. DESIGN, SETTING, AND PATIENTS Retrospective study of temporal trends in early progression of perinatal HIV infection among 205 HIV-infected children in Northern California born between January 1, 1988, and December 31, 2001, and followed up through age 3 years. MAIN OUTCOME MEASURES Prevalence of and age at progression to a first US Centers for Disease Control and Prevention category C diagnosis relative to year of birth, type of ART, and age at initiation of therapy. RESULTS Of 205 children, 134 (65%) received ART and/or Pneumocystis jiroveci pneumonia prophylaxis. By age 3 years, 81 (40%) progressed to a category C diagnosis, 41 (51%) of whom died. Untreated children were significantly more likely to progress to a category C diagnosis (62% [44/71] untreated vs 28% [37/134] treated children, P<.001); none of 23 infants who received triple ART progressed to category C. However, even without triple ART, very early mono/dual ART (by age 2 months vs 3-4 months) was associated with delayed and decreased progression to category C (P = .02). Of 33 children born between January 1, 1996, and December 31, 2001, only 7 (21%) progressed to category C (P = .02 compared with 1988-1995), 6 of 7 of whom received no therapy. More recent year of birth and more advanced therapy were associated with improved survival. CONCLUSIONS This population-based cohort demonstrated decreased early HIV progression and improved survival at age 3 years, associated with more advanced therapy. Although limited by small sample size, the findings suggest that very early treatment, even without triple ART, was associated with improved outcome.
Activity of Heat Shock Genes’ Promoters in Thermally Contrasting Animal Species

Heat shock gene promoters represent a highly conserved and universal system for the rapid induction of transcription after various stressful stimuli. We chose pairs of mammalian and insect species that significantly differ in their thermoresistance and constitutive levels of Hsp70 to compare hsp promoter strength under normal conditions and after heat shock (HS). The first pair includes the HSPA1 gene promoter of camel (Camelus dromedarius) and humans. It was demonstrated that the camel HSPA1A and HSPA1L promoters function normally in vitro in human cell cultures and exceed the strength of orthologous human promoters under basal conditions. We used the same in vitro assay for Drosophila melanogaster Schneider-2 (S2) cells to compare the activity of the hsp70 and hsp83 promoters of the second species pair represented by Diptera, i.e., Stratiomys singularior and D. melanogaster, which dramatically differ in thermoresistance and the pattern of Hsp70 accumulation. Promoter strength was also monitored in vivo in D. melanogaster strains transformed with constructs containing the S. singularior hsp70 ORF driven either by its own promoter or an orthologous promoter from the D. melanogaster hsp70Aa gene. Analysis revealed low S. singularior hsp70 promoter activity in vitro and in vivo under basal conditions and after HS in comparison with the endogenous promoter in D. melanogaster cells, which correlates with the absence of canonical GAGA elements in the promoters of the former species. Indeed, the insertion of GAGA elements into the S. singularior hsp70 regulatory region resulted in a dramatic increase in promoter activity in vitro but only modestly enhanced the promoter strength in the larvae of the transformed strains. In contrast with hsp70 promoters, hsp83 promoters from both of the studied Diptera species demonstrated high conservation and universality.
The ImageCLEF 2012 Plant Identification Task

The ImageCLEF's plant identification task provides a testbed for the system-oriented evaluation of plant identification, more precisely on the 126 tree species identification based on leaf images. Three types of image content are considered: Scan, Scan-like (leaf photographs with a white uniform background), and Photograph (unconstrained leaf with natural background). The main originality of this data is that it was specifically built through a citizen sciences initiative conducted by Tela Botanica, a French social network of amateur and expert botanists. This makes the task closer to the conditions of a real-world application. This overview presents more precisely the resources and assessments of task, summarizes the retrieval approaches employed by the participating groups, and provides an analysis of the main evaluation results. With a total of eleven groups from eight countries and with a total of 30 runs submitted, involving distinct and original methods, this second year pilot task confirms Image Retrieval community interest for biodiversity and botany, and highlights further challenging studies in plant identification.
Changes in heart rate and blood lactate concentration as intensity parameters during simulated Taekwondo competition.

AIM The absence of studies related to physiological responses in athletes during Taekwondo competition makes this the first attempt to investigate the physical aspects of this relative new Olympic sport event. Therefore, the aim of this study was to record and analyze heart rate (HR) and blood lactate (BL) levels of elite male Taekwondo athletes during multiple competition bouts in a single day. METHODS EXPERIMENTAL DESIGN prospective. SETTING competition simulation. PARTICIPANTS 24 elite male athletes, aged 20 to 24 years. MEASURES HR and BL responses were studied on 24 national level Taekwondo players in multiple competition bouts to explore the aerobic-anaerobic metabolism, as well as the physical demands of the players. The aerobic capacity (VO(2max)) of the players were determined using a 20 m shuttle run test. HR and BL concentration levels were measured during warm up and fighting rounds in every competition bout. RESULTS The mean VO(2max) ability for all subjects was 53.92 mL/kg/min and there was no significant difference between groups. Only the heavy weight division (+80 kg) players demonstrated a significant higher HRmax (P<0.05) than the other two divisions. No inter-weight division, as well as inter-round differences, were observed in the HR and BL concentration levels of the players. After all divisions were recorded and analyzed the mean HR and BL levels during competition were 158 beats/min and 3.35 mmol/L, respectively. CONCLUSION The study highlights that in competitive Taekwondo, irrespective of the weight division or aerobic capacity, the anaerobic adaptability of the subjects is the same.
Distinct Intracellular Trafficking of Hepatitis C Virus in Myeloid and Plasmacytoid Dendritic Cells

ABSTRACT Dendritic cells (DCs) are of pivotal importance for the initiation of immune responses to control and eliminate viral infections. The molecular mechanisms of hepatitis C virus (HCV) antigen uptake and processing by blood DCs are poorly defined. Here we show that human blood DC subsets acquire HCV independent of the classical HCV entry factors. Following HCV uptake, human plasmacytoid and myeloid DC subsets deliver HCV antigen into distinct endocytotic compartments, which are dedicated to presentation to CD4+ or CD8+ T cells. Our findings support a model of HCV antigen processing and presentation in which DC subsets fulfill distinct functions.
Selection-free predictions in global games with endogenous information and multiple equilibria

Global games with endogenous information often exhibit multiple equilibria. In this paper we show how one can nevertheless identify useful predictions that are robust across all equilibria and that could not have been delivered in the common-knowledge counterparts of these games. Our analysis is conducted within a flexible family of games of regime change, which have been used to model, inter alia, speculative currency attacks, debt crises, and political change. The endogeneity of information originates in the signaling role of policy choices. A novel procedure of iterated elimination of non-equilibrium strategies is used to deliver probabilistic predictions that an outside observer—an econometrician—can form under arbitrary equilibrium selections. The sharpness of these predictions improves as the noise gets smaller, but disappears in the complete-information version of the model.
Temperature Sensor Based on Colloidal Quantum Dots–PMMA Nanocomposite Waveguides

In this paper, integrated temperature sensors based on active nanocomposite planar waveguides are presented. The nanocomposites consist of cadmium selenide (CdSe) and cadmium telluride (CdTe) quantum dots (QDs) embedded in a polymethylmethacrylate (PMMA) matrix. When the samples are heated in a temperature range from 25<formula formulatype="inline"><tex Notation="TeX">$^{\circ}{\rm C}$</tex></formula> to 50<formula formulatype="inline"> <tex Notation="TeX">$^{\circ}{\rm C}$</tex></formula>, the waveguided photoluminescence of QDs suffers from a strong intensity decrease, which is approximately quadratic dependent on temperature. Moreover, the wavelength peak of the waveguided emission spectrum of CdTe-PMMA shows a blue shift of 0.25 <formula formulatype="inline"><tex Notation="TeX">${\rm nm}/^{\circ}{\rm C}$</tex></formula>, whereas it remains constant in the case of CdSe-PMMA. A temperature resolution of 0.1<formula formulatype="inline"><tex Notation="TeX">$^{\circ}{\rm C}$</tex></formula> is obtained. QD waveguides have great potential for the development of photonic sensors because of their integration, multiplexing, and roll-to-roll fabrication capabilities.
Using ENVI-met to simulate the impact of global warming on the mi- croclimate in central European cities

Within the BMBF joint research project KLIMES, the micro scale climate model ENVI-met is used by the subproject KLIMES JGU to simulate the effects of global warming on heat stress in central European cities and to evaluate possible countermeasures proposed by urban planners. In this study two simulations run with a model that contains structures which can be found in most central European cities. The first simulation runs with boundary conditions that are typical for central European summer days, the second simulation with boundary conditions that can be expected at the end of an extreme, longer lasting summer heat wave like 2003. The simulations are compared and the results are discussed. In the last years much effort has been put into meso scale simulations of climate change (e.g. Jacob, 2008). With resolutions of several kilometres, these simulations only display the climate within the main human habitat – the city which creates its own distinct urban climate - very coarsely. Due to their specific albedo, roughness length and soil sealing, cities create their own micro climate, mostly referred to as the urban heat island effect (Grimmond, 2006). Summerly heat-waves are aggravated within cities and the thermal discomfort and the health of the population is deteriorated. As regional climate models for central Europe predict heat waves to occur more often, be more intensive and longer lasting (e.g. Meehl and Tebaldi, 2004), it is necessary to study the effect of cities on heat waves in order to identify possible countermeasures. The joint research project “Development of strategies to mitigate enhanced heat stress in urban quarters due to regional climate change in Central Europe”, abbreviated by KLIMES, has the goal to study and quantify this urban heat island effect on human health and to propose possible countermeasures for urban planners. Within the KLIMES project the micro climate simulation ENVI-met is used to simulate and study the interaction of cities on the human thermal comfort and to predict how it will be affected by climate change. In this study the effects of the more extreme summerly weather conditions on an exemplary quarter of a central European city are investigated by comparing two simulations with different boundary conditions, one presenting an average European summer day, the other representing the conditions of an extreme summer heat wave.
A model to calculate dynamical and steady-state behavior of ice particles in ice slurry storage tank

Storage of ice slurries is advantageous to save energy and to produce a continuous controlled long-time operation of an ice-slurry system. To guarantee homogeneous ice particle fields and to prevent a system of blocking by ice clusters, up-to-present a good mixing of the slurries was proposed. But mixing can lead to twenty percent energy demand of the total energy con-sumption of an ice slurry system, including the production of cold. Therefore, new methods are invented to operate systems without a mixing in the storage tank, but still with a control of the fluid and flow conditions in the piping circuits. The theoretical basis to calculate distributions of ice particle fields, respectively ice concentration distributions in unmixed ice slurry storage tanks with stratifications is given and first numerical simulation results are presented.
Shape descriptors for non-rigid shapes with a single closed contour

The Core Experiment CE-Shape-1 for shape descriptors performed for the MPEG-7 standard gave a unique opportunity to compare various shape descriptors for non-rigid shapes with a single closed contour. There are two main differences with respect to other comparison results reported in the literature: (1) For each shape descriptor the experiments were carried out by an institute that is in favor of this descriptor. This implies that the parameters for each system were optimally determined and the implementations were thoroughly rested. (2) It was possible to compare the performance of shape descriptors based on totally different mathematical approaches. A more theoretical comparison of these descriptors seems to be extremely hard. In this paper we report on the MPEG-7 Core Experiment CE-Shape.
The Metabolomic Profile of Umbilical Cord Blood in Neonatal Hypoxic Ischaemic Encephalopathy

Background Hypoxic ischaemic encephalopathy (HIE) in newborns can cause significant long-term neurological disability. The insult is a complex injury characterised by energy failure and disruption of cellular homeostasis, leading to mitochondrial damage. The importance of individual metabolic pathways, and their interaction in the disease process is not fully understood. The aim of this study was to describe and quantify the metabolomic profile of umbilical cord blood samples in a carefully defined population of full-term infants with HIE. Methods and Findings The injury severity was defined using both the modified Sarnat score and continuous multichannel electroencephalogram. Using these classification systems, our population was divided into those with confirmed HIE (n = 31), asphyxiated infants without encephalopathy (n = 40) and matched controls (n = 71). All had umbilical cord blood drawn and biobanked at −80°C within 3 hours of delivery. A combined direct injection and LC-MS/MS assay (AbsolutIDQ p180 kit, Biocrates Life Sciences AG, Innsbruck, Austria) was used for the metabolomic analyses of the samples. Targeted metabolomic analysis showed a significant alteration between study groups in 29 metabolites from 3 distinct classes (Amino Acids, Acylcarnitines, and Glycerophospholipids). 9 of these metabolites were only significantly altered between neonates with Hypoxic ischaemic encephalopathy and matched controls, while 14 were significantly altered in both study groups. Multivariate Discriminant Analysis models developed showed clear multifactorial metabolite associations with both asphyxia and HIE. A logistic regression model using 5 metabolites clearly delineates severity of asphyxia and classifies HIE infants with AUC = 0.92. These data describe wide-spread disruption to not only energy pathways, but also nitrogen and lipid metabolism in both asphyxia and HIE. Conclusion This study shows that a multi-platform targeted approach to metabolomic analyses using accurately phenotyped and meticulously biobanked samples provides insight into the pathogenesis of perinatal asphyxia. It highlights the potential for metabolomic technology to develop a diagnostic test for HIE.
Correspondence analysis applied to microarray data

Correspondence analysis is an explorative computational method for the study of associations between variables. Much like principal component analysis, it displays a low-dimensional projection of the data, e.g., into a plane. It does this, though, for two variables simultaneously, thus revealing associations between them. Here, we demonstrate the applicability of correspondence analysis to and high value for the analysis of microarray data, displaying associations between genes and experiments. To introduce the method, we show its application to the well-known Saccharomyces cerevisiae cell-cycle synchronization data by Spellman et al. [Spellman, P. T. , Sherlock, G. , Zhang, M. Q. , Iyer, V. R. , Anders, K. , Eisen, M. B. , Brown, P. O. , Botstein, D. & Futcher, B. (1998) Mol. Biol. Cell 9, 3273–3297], allowing for comparison with their visualization of this data set. Furthermore, we apply correspondence analysis to a non-time-series data set of our own, thus supporting its general applicability to microarray data of different complexity, underlying structure, and experimental strategy (both two-channel fluorescence-tag and radioactive labeling).
Expertise Training with Novel Objects Leads to Left-Lateralized Facelike Electrophysiological Responses

Scalp event-related potentials (ERPs) in humans indicate that face and object processing differ approximately 170 ms following stimulus presentation, at the point of the N170 occipitotemporal component. The N170 is delayed and enhanced to inverted faces but not to inverted objects. We tested whether this inversion effect reflects early mechanisms exclusive to faces or whether it generalizes to other stimuli as a function of visual expertise. ERPs to upright and inverted faces and novel objects (Greebles) were recorded in 10 participants before and after 2 weeks of expertise training with Greebles. The N170 component was observed for both faces and Greebles. The results are consistent with previous reports in that the N170 was delayed and enhanced for inverted faces at recording sites in both hemispheres. For Greebles, the same effect of inversion was observed only for experts, primarily in the left hemisphere. These results suggest that the mechanisms underlying the electrophysiological face-inversion effect extend to visually homogeneous nonface object categories, at least in the left hemisphere, but only when such mechanisms are recruited by expertise.
“Every Male in There Is Your Competition”: Young Men's Perceptions Regarding the Role of the Drinking Setting in Male-to-Male Barroom Aggression

The present paper explores young men's perceptions regarding the influence of the bar setting on male-to-male barroom aggression. Focus group interviews were conducted with 27 young men aged 18–25 in London, Ontario, Canada. Participants were given a description of a typical incident of aggression between men in bars and asked to discuss why the incident happened. The following themes pertaining to the role of the setting were identified: (1) sexual competition and male rivalry; (2) heightened concerns with image and social pressure to fight; (3) anonymity and taking on a different identity; (4) provocation and negative stimuli; (5) bar staff behavior; (6) acceptance and expectation of aggression; (7) high level of drunkenness; and (8) thrill, excitement, high energy level, and uncertainty of what might happen. These findings are discussed within a situational/crime prevention framework and prevention implications are highlighted.
Joint Learning with Global Inference for Comment Classification in Community Question Answering

This paper addresses the problem of comment classiﬁcation in community Question Answering. Following the state of the art, we approach the task with a global inference process to exploit the information of all comments in the answer-thread in the form of a fully connected graph. Our contribution comprises two novel joint learning models that are on-line and integrate inference within learning. The ﬁrst one jointly learns two node - and edge -level MaxEnt classiﬁers with stochastic gradient descent and integrates the inference step with loopy belief propagation. The second model is an instance of fully connected pairwise CRFs (FCCRF). The FCCRF model signiﬁcantly outperforms all other approaches and yields the best results on the task to date. Crucial elements for its success are the global normalization and an Ising-like edge potential.