Miracle-dz/UniFAR-FTUs huggingface dataset:
The Dynamics of Plasma Membrane, Metabolism and Respiration (PM-M-R) in Penicillium ochrochloron CBS 123824 in Response to Different Nutrient Limitations—A Multi-level Approach to Study Organic Acid Excretion in Filamentous Fungi

Filamentous fungi are important cell factories. In contrast, we do not understand well even basic physiological behavior in these organisms. This includes the widespread phenomenon of organic acid excretion. One strong hurdle to fully exploit the metabolic capacity of these organisms is the enormous, highly environment sensitive phenotypic plasticity. In this work we explored organic acid excretion in Penicillium ochrochloron from a new point of view by simultaneously investigating three essential metabolic levels: the plasma membrane H+-ATPase (PM); energy metabolism, in particular adenine and pyridine nucleotides (M); and respiration, in particular the alternative oxidase (R). This was done in strictly standardized chemostat culture with different nutrient limitations (glucose, ammonium, nitrate, and phosphate). These different nutrient limitations led to various quantitative phenotypes (as represented by organic acid excretion, oxygen consumption, glucose consumption, and biomass formation). Glucose-limited grown mycelia were used as the reference point (very low organic acid excretion). Both ammonium and phosphate grown mycelia showed increased organic acid excretion, although the patterns of excreted acids were different. In ammonium-limited grown mycelia amount and activity of the plasma membrane H+-ATPase was increased, nucleotide concentrations were decreased, energy charge (EC) and catabolic reduction charge (CRC) were unchanged and alternative respiration was present but not quantifiable. In phosphate-limited grown mycelia (no data on the H+-ATPase) nucleotide concentrations were still lower, EC was slightly decreased, CRC was distinctly decreased and alternative respiration was present and quantifiable. Main conclusions are: (i) the phenotypic plasticity of filamentous fungi demands adaptation of sample preparation and analytical methods at the phenotype level; (ii) each nutrient condition is unique and its metabolic situation must be considered separately; (iii) organic acid excretion is inversely related to nucleotide concentration (but not EC); (iv) excretion of organic acids is the outcome of a simultaneous adjustment of several metabolic levels to nutrient conditions.
What's New in Shock, May 2017?

This issue of Shock offers another special collection of superb scientific articles spanning from authoritative reviews of current clinical paradigms of resuscitation to the description of novel diagnostic and therapeutic tools in surgical and critical care settings. Five basic science articles are also included in this issue and cover the latest advances in fundamental mechanisms of cell signaling, immune regulation and host–pathogen interactions during sepsis, trauma, and ischemia and reperfusion injury. On a final note, this issue concludes with an editorial comment that poses important questions confronting investigators on sepsis research. The first article by Etchill et al. (1) is an extensive review that deals with the important topic of thrombocytopenia and platelet transfusion practices in surgical and critical care settings. Thrombocytopenia is a common problem in critically ill patients and an independent predictor of mortality. The authors provide a critical appraisal of data reported by 153 manuscripts focusing on transfusion practices in different settings of thrombocytopenia. A highlight of the study is the description of point-of-care laboratory assays, which emphasizes the importance of platelet function testing. The authors also provide a synopsis of recent advances in transfusion medicine and research into synthetic platelet substitutes that may overcome some of the complications and critical contraindications associated with platelet transfusion. The study by Long et al. (2) of the Paediatric Research in Emergency Departments International Collaborative is a systematic review and meta-analysis of data on respiratory variation in the inferior vena cava (IVC) diameter as a predictor of fluid responsiveness in patients with acute circulatory failure. Assessment for volume responsiveness prior to fluid resuscitation is already recommended by the European Society of Intensive Care Medicine, since prediction of fluid responsiveness would allow for resuscitation with fluids to patients who would benefit, while it would reduce adverse effects of fluid overload. A noninvasive tool, such as the measurement of respiratory variation in IVC diameter, would, therefore, provide additional benefit without added risk. After a critical analysis of 17 studies assessed for the design and reporting quality and the risk of bias, the authors conclude that respiratory variation in IVC diameter is moderately predictive of fluid responsiveness. This noninvasive test is most useful in
Touch detection method for non-display surface using multiple shadows of finger

Our objective is to create a system that enables users to interact with surrounding surfaces by using touch interactions. In this work, we propose a touch detection method that utilizes the shadows of a finger for use with a system featuring an infrared (IR) camera and two IR lights. Since the shape of a finger's shadow varies depending on the distance between the surface and the finger, the system can recognize a touch by detecting this phenomenon. Evaluations showed that a touch can be detected with high accuracy over an entire large (80 inches wide) operating surface.
Cerebellar neurodegeneration in a new rat model of episodic hepatic encephalopathy

Hepatic encephalopathy has traditionally been considered a reversible disorder. However, recent studies suggested that repeated episodes of hepatic encephalopathy cause persistent impairment leading to neuronal loss. The aims of our study were the development of a new animal model that reproduces the course of episodic hepatic encephalopathy and the identification of neurodegeneration evidences. Rats with portacaval anastomosis underwent simulated episodes of hepatic encephalopathy, triggered by the regular administration of ammonium acetate, and/or lipopolysaccharide. The neurological status was assessed and neuronal loss stereologically quantified in motor areas. During the simulated episodes, ammonia induced reversible motor impairment in portacaval anastomosis rats. In cerebellum, stereology showed a reduction in Purkinje cell population in portacaval anastomosis and PCA+NH3 groups and morphological changes. An increase in astrocyte size in PCA+NH3 group and activated microglia in groups treated with ammonium acetate and/or lipopolysaccharide was observed. A modulation of neurodegeneration-related genes and the presence of apoptosis in Bergmann glia were observed. This new animal model reproduces the clinical course of episodic hepatic encephalopathy when ammonia is the precipitant factor and demonstrates the existence of neuronal loss in cerebellum. The persistence of over-activated microglia and reactive astrocytes could participate in the apoptosis of Bergmann glia and therefore Purkinje cell degeneration.
Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study

MOTIVATION In this study, we address the problem of estimating the parameters of regulatory networks and provide the first application of Markov chain Monte Carlo (MCMC) methods to experimental data. As a case study, we consider a stochastic model of the Hes1 system expressed in terms of stochastic differential equations (SDEs) to which rigorous likelihood methods of inference can be applied. When fitting continuous-time stochastic models to discretely observed time series the lengths of the sampling intervals are important, and much of our study addresses the problem when the data are sparse. RESULTS We estimate the parameters of an autoregulatory network providing results both for simulated and real experimental data from the Hes1 system. We develop an estimation algorithm using MCMC techniques which are flexible enough to allow for the imputation of latent data on a finer time scale and the presence of prior information about parameters which may be informed from other experiments as well as additional measurement error.
Vaccination Confidence and Parental Refusal/Delay of Early Childhood Vaccines

Objective To support efforts to address parental hesitancy towards early childhood vaccination, we sought to validate the Vaccination Confidence Scale using data from a large, population-based sample of U.S. parents. Methods We used weighted data from 9,354 parents who completed the 2011 National Immunization Survey. Parents reported on the immunization history of a 19- to 35-month-old child in their households. Healthcare providers then verified children’s vaccination status for vaccines including measles, mumps, and rubella (MMR), varicella, and seasonal flu. We used separate multivariable logistic regression models to assess associations between parents’ mean scores on the 8-item Vaccination Confidence Scale and vaccine refusal, vaccine delay, and vaccination status. Results A substantial minority of parents reported a history of vaccine refusal (15%) or delay (27%). Vaccination confidence was negatively associated with refusal of any vaccine (odds ratio [OR] = 0.58, 95% confidence interval [CI], 0.54–0.63) as well as refusal of MMR, varicella, and flu vaccines specifically. Negative associations between vaccination confidence and measures of vaccine delay were more moderate, including delay of any vaccine (OR = 0.81, 95% CI, 0.76–0.86). Vaccination confidence was positively associated with having received vaccines, including MMR (OR = 1.53, 95% CI, 1.40–1.68), varicella (OR = 1.54, 95% CI, 1.42–1.66), and flu vaccines (OR = 1.32, 95% CI, 1.23–1.42). Conclusions Vaccination confidence was consistently associated with early childhood vaccination behavior across multiple vaccine types. Our findings support expanding the application of the Vaccination Confidence Scale to measure vaccination beliefs among parents of young children.
The relationship between caregivers' subjective social status and asthma symptoms and management for urban children

ABSTRACT Objective: Subjective social status (SSS) is a person's perception of his/her social standing among others. We explored the relationship between caregivers' SSS and asthma symptoms, visits, and medication use among children with persistent asthma. Methods: We analyzed baseline data of children (3–10 years) from the SB-TEAM trial in Rochester, NY. Using a modified MacArthur Scale of SSS, caregivers rated themselves “a lot worse off” to “a lot better off” compared to 4 groups (e.g., neighbors). “Low SSS” was defined by a response of “a lot worse off” or “somewhat worse off” for any of the referent groups. Caregivers reported their child's asthma symptoms, healthcare visits for asthma, and medication use. Bivariate and multivariate statistics were used. Results: We found that, of the 230 children enrolled (participation rate:78%, 62% Black, 72% Medicaid), 29% of caregivers had low SSS. Caregivers with low SSS had more depressive symptoms (46% vs. 28%) and lower social support (69.1 vs. 77.7). In multivariable analyses, children of caregivers with low SSS had fewer symptom-free days/2 weeks (5.8 vs. 7.9, p = .01). While they were more likely to have a routine asthma visit in the past year (35% vs. 23%, adjusted p = .03), there was no difference in their use of preventive medication. Conclusions: Many caregivers of children with persistent asthma report low SSS. While children of these caregivers had fewer symptom-free days, they were not more likely to use preventive medications. Efforts are needed to support these caregivers to ensure optimal preventive care and reduce morbidity.
High-speed through-silicon via filling method using Cu-cored solder balls

A novel low-cost and high-speed via filling method using Cu-cored solder balls was investigated for through-silicon via manufacture.Cu-cored solder balls with a total diameter of 100μm were used to fill 150μm deep,110μm wide vias in silicon.The wafer-level filling process can be completed in a few seconds,which is much faster than using the traditional electroplating process.Thermo-mechanical analysis of via filling using solder,Cu and Cu-cored solder was carried out to assess the thermo-mechanical properties of the different filling materials.It was found that the vias filled with Cu-cored solder exhibit less thermal-mechanical stresses than solder-filled vias, but more than Cu-filled vias.
Prediction of outcome in internet‐delivered cognitive behaviour therapy for paediatric obsessive‐compulsive disorder: A machine learning approach

There are no consistent predictors of treatment outcome in paediatric obsessive–compulsive disorder (OCD). One reason for this might be the use of suboptimal statistical methodology. Machine learning is an approach to efficiently analyse complex data. Machine learning has been widely used within other fields, but has rarely been tested in the prediction of paediatric mental health treatment outcomes.
Fate of 15N-urea applied to wheat-soybean succession crop

The wheat crop in Sao Paulo State, Brazil, is fertilized with N, P and K. The rate of applied N (0 to 120 kg.ha -1 ) depends on the previous grown crop and the irrigation possibility. The response of wheat to rates and time of N application and the fate of N applied to irrigated wheat were studied during two years. Residual N recovery by soybean grown after the wheat was also studied. The maximum grain productivity was obtained with 92 kg.ha -1 of N. The efficiency of 15 N-urea utilization ranged from 52% to 85%. The main loss of applied 15 N, 5% to 12% occurred as ammonia volatilized from urea applied on soil surface. The N loss by leaching even at the N rate of 135 kg.ha -1 , was less than 1% of applied 15 N, due to the low amount of rainfall during the wheat grown season and a controlled amount of irrigated water, that were sufficient to moisten only the wheat root zone. The residual 15 N after wheat harvest represents around 40% of N applied as urea: 20% in soil, 3% in wheat root system and 16% in the wheat straw. Soybean recovered less than 2% of the 15 N applied to wheat at sowing or at tillering stage.
Lipid metabolic perturbation is an early-onset phenotype in adult spinster mutants: a Drosophila model for lysosomal storage disorders

Intracellular accumulation of lipids and swollen dysfunctional lysosomes are linked to several neurodegenerative diseases including lysosomal storage disorders (LSD). A detailed characterization of lipid metabolic changes in relation to the onset and progression of neurodegeneration is currently missing. In this study, we systematically analyzed lipid perturbations in spinster (spin) mutants, a Drosophila model of neurodegeneration associated with LSD. Our results highlight an imbalance in brain ceramide and sphingosine as a crucial phenotype in the early stages of neurodegeneration. This perturbation in ceramide metabolism precedes the accumulation of endomembranous structures, manifestation of altered behavior and buildup of lipofuscin (the ageing pigment). Manipulating levels of ceramidase, and, consequently further altering these lipids in spin mutants have allowed us to conclude that ceramide/sphingosine homeostasis is the driving force in disease progression and is integral to spin function in the adult nervous system. Furthermore, we have identified 29 novel and direct interaction partners of Spin. We specifically focused on the lipid carrier protein, Lipophorin (Lpp), and demonstrate its localization with Spin in the adult nervous system and in organs specialized for lipid metabolism including fat bodies and oenocytes. Our observations in spin mutants of altered Lpp immunostaining, and of increased levels of lipid metabolites produced by oenocytes, allude to a functional relevance of the Spin-Lpp interaction. Overall, these results detailing the kinetics of ceramide perturbations in the context of lipofuscin accumulation, as well as the proteomics experiment, represent a valuable resource to further unravel the mechanistic link between systemic changes in lipid metabolism and lysosomal storage disorders. Summary Statement Elevations in specific brain lipids and connections to relevant metabolic genes are identified in a fly model for lysosomal storage disorders. This enables a better understanding of disease progression.
Perceived Risk Among Human Immunodeficiency Virus Serodiscordant Couples in East Africa Taking Oral Pre-Exposure Prophylaxis

Objectives Perceived risk of human immunodeficiency virus (HIV) infection is thought to drive low adherence in pre-exposure prophylaxis (PrEP) trials. We explored the level of perceived risk of incident HIV infection in the Partners PrEP Study, in which adherence was generally high. Methods A cross-sectional questionnaire assessed perceived risk of HIV at 12 months after enrollment. Logistic regression was used to analyze the relationship between perceived risk and other demographic and behavioral variables. Results Three thousand two hundred twenty-six couples from the Partners PrEP Study were included in this analysis. Only 15.4% of participants reported high or moderate perceived risk. Participants at high risk of acquiring HIV were slightly more likely to report high perceived risk (odds ratio, 1.60; 95% confidence interval, 1.30–1.95; P < 0.001); nevertheless, only 20% of participants with high-risk reported high perceived risk. Conclusions Participants reported low perceived risk of HIV but were adherent to PrEP. Perceptions of risk are likely socially determined and more complex than Likert scale questionnaires capture.
Automated volumetry of temporal horn of lateral ventricle for detection of Alzheimer's disease in CT scan

The rapid increase in the incidence of Alzheimer’s disease (AD) has become a critical issue in low and middle income countries. In general, MR imaging has become sufficiently suitable in clinical situations, while CT scan might be uncommonly used in the diagnosis of AD due to its low contrast between brain tissues. However, in those countries, CT scan, which is less costly and readily available, will be desired to become useful for the diagnosis of AD. For CT scan, the enlargement of the temporal horn of the lateral ventricle (THLV) is one of few findings for the diagnosis of AD. In this paper, we present an automated volumetry of THLV with segmentation based on Bayes’ rule on CT images. In our method, first, all CT data sets are normalized into an atlas by using linear affine transformation and non-linear wrapping techniques. Next, a probability map of THLV is constructed in the normalized data. Then, THLV regions are extracted based on Bayes’ rule. Finally, the volume of the THLV is evaluated. This scheme was applied to CT scans from 20 AD patients and 20 controls to evaluate the performance of the method for detecting AD. The estimated THLV volume was markedly increased in the AD group compared with the controls (P < .0001), and the area under the receiver operating characteristic curve (AUC) was 0.921. Therefore, this computerized method may have the potential to accurately detect AD on CT images.
Crowdclustering with Sparse Pairwise Labels: A Matrix Completion Approach

Crowdsourcing utilizes human ability by distributing tasks to a large number of workers. It is especially suitable for solving data clustering problems because it provides a way to obtain a similarity measure between objects based on manual annotations, which capture the human perception of similarity among objects. This is in contrast to most clustering algorithms that face the challenge of finding an appropriate similarity measure for the given dataset. Several algorithms have been developed for crowdclustering that combine partial clustering results, each obtained by annotations provided by a different worker, into a single data partition. However, existing crowdclustering approaches require a large number of annotations, due to the noisy nature of human annotations, leading to a high computational cost in addition to the large cost associated with annotation. We address this problem by developing a novel approach for crowclustering that exploits the technique of matrix completion. Instead of using all the annotations, the proposed algorithm constructs a partially observed similarity matrix based on a subset of pairwise annotation labels that are agreed upon by most annotators. It then deploys the matrix completion algorithm to complete the similarity matrix and obtains the final data partition by applying a spectral clustering algorithm to the completed similarity matrix. We show, both theoretically and empirically, that the proposed approach needs only a small number of manual annotations to obtain an accurate data partition. In effect, we highlight the trade-off between a large number of noisy crowdsourced labels and a small number of high quality labels.
Input-Aware Auto-Tuning of Compute-Bound HPC Kernels

Efficient implementations of HPC applications for parallel architectures generally rely on external software packages (e.g., BLAS, LAPACK, CUDNN). While these libraries provide highly optimized routines for certain characteristics of inputs (e.g., square matrices), they generally do not retain optimal performance across the wide range of problems encountered in practice. In this paper, we present an input-aware autotuning framework for matrix multiplications and convolutions, ISAAC, which uses predictive modeling techniques to drive highly parameterized PTX code templates towards not only hardware-, but also application-specific kernels. Numerical experiments on the NVIDIA Maxwell and Pascal architectures show up to 3xperformance gains over both cuBLAS and cuDNN after only a few hours of auto-tuning.
Safety‐critical Java for embedded systems

This paper presents the motivation for and outcomes of an engineering research project on certifiable Java for embedded systems. The project supports the upcoming standard for safety‐critical Java, which defines a subset of Java and libraries aiming for development of high criticality systems. The outcome of this project include prototype safety‐critical Java implementations, a time‐predictable Java processor, analysis tools for memory safety, and example applications to explore the usability of safety‐critical Java for this application area. The text summarizes developments and key contributions and concludes with the lessons learned. Copyright © 2016 John Wiley & Sons, Ltd.