Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxygen-Dependent Growth of the Sulfate-Reducing Bacterium Desulfovibrio oxyclinae in Coculture withMarinobacter sp. Strain MB in an Aerated Sulfate-Depleted Chemostat

ABSTRACT A chemostat coculture of the sulfate-reducing bacteriumDesulfovibrio oxyclinae and the facultatively aerobic heterotroph Marinobacter sp. strain MB was grown for 1 week under anaerobic conditions at a dilution rate of 0.05 h−1. It was then exposed to an oxygen flux of 223 μmol min−1by gassing the growth vessel with 5% O2. Sulfate reduction persisted under these conditions, though the amount of sulfate reduced decreased by 45% compared to the amount reduced during the initial anaerobic mode. After 1 week of growth under these conditions, sulfate was excluded from the incoming medium. The sulfate concentration in the growth vessel decreased exponentially from 4.1 mM to 2.5 μM. The coculture consumed oxygen effectively, and no residual oxygen was detected during either growth mode in which oxygen was supplied. The proportion of D. oxyclinae cells in the coculture as determined by in situ hybridization decreased from 86% under anaerobic conditions to 70% in the microaerobic sulfate-reducing mode and 34% in the microaerobic sulfate-depleted mode. As determined by the most-probable-number (MPN) method, the numbers of viable D. oxyclinae cells during the two microaerobic growth modes decreased compared to the numbers during the anaerobic growth mode. However, there was no significant difference between the MPN values for the two modes when oxygen was supplied. The patterns of consumption of electron donors and acceptors suggested that when oxygen was supplied in the absence of sulfate and thiosulfate, D. oxyclinaeperformed incomplete aerobic oxidation of lactate to acetate. This is the first observation of oxygen-dependent growth of a sulfate-reducing bacterium in the absence of either sulfate or thiosulfate. Cells harvested during the microaerobic sulfate-depleted stage and exposed to sulfate and thiosulfate in a respiration chamber were capable of anaerobic sulfate and thiosulfate reduction.
Temperature has a causal effect on avian timing of reproduction

Many bird species reproduce earlier in years with high spring temperatures, but little is known about the causal effect of temperature. Temperature may have a direct effect on timing of reproduction but the correlation may also be indirect, for instance via food phenology. As climate change has led to substantial shifts in timing, it is essential to understand this causal relationship to predict future impacts of climate change. We tested the direct effect of temperature on laying dates in great tits (Parus major) using climatized aviaries in a 6-year experiment. We mimicked the temperature patterns from two specific years in which our wild population laid either early (‘warm’ treatment) or late (‘cold’ treatment). Laying dates were affected by temperature directly. As the relevant temperature period started three weeks prior to the mean laying date, with a range of just 4°C between the warm and the cold treatments, and as the birds were fed ad libitum, it is likely that temperature acted as a cue rather than lifting an energetic constraint on the onset of egg production. We furthermore show a high correlation between the laying dates of individuals reproducing both in aviaries and in the wild, validating investigations of reproduction of wild birds in captivity. Our results demonstrate that temperature has a direct effect on timing of breeding, an important step towards assessing the implication of climate change on seasonal timing.
Rescoring and Linearly Combining: A Highly Effective Consensus Strategy for Virtual Screening Campaigns

The study proposes a novel consensus strategy based on linear combinations of different docking scores to be used in the evaluation of virtual screening campaigns. The consensus models are generated by applying the recently proposed Enrichment Factor Optimization (EFO) method, which develops the linear equations by exhaustively combining the available docking scores and by optimizing the resulting enrichment factors. The performances of such a consensus strategy were evaluated by simulating the entire Directory of Useful Decoys (DUD datasets). In detail, the poses were initially generated by the PLANTS docking program and then rescored by ReScore+ with and without the minimization of the complexes. The so calculated scores were then used to generate the mentioned consensus models including two or three different scoring functions. The reliability of the generated models was assessed by a per target validation as performed by default by the EFO approach. The encouraging performances of the here proposed consensus strategy are emphasized by the average increase of the 17% in the Top 1% enrichment factor (EF) values when comparing the single best score with the linear combination of three scores. Specifically, kinases offer a truly convincing demonstration of the efficacy of the here proposed consensus strategy since their Top 1% EF average ranges from 6.4 when using the single best performing primary score to 23.5 when linearly combining scoring functions. The beneficial effects of this consensus approach are clearly noticeable even when considering the entire DUD datasets as evidenced by the area under the curve (AUC) averages revealing a 14% increase when combining three scores. The reached AUC values compare very well with those reported in literature by an extended set of recent benchmarking studies and the three-variable models afford the highest AUC average.
Provenance Integration Requires Reconciliation

While there has been a great deal of research on provenance systems, there has been little discussion about challenges that arise when making different provenance systems interoperate. In fact, most of the literature focuses on provenance systems in isolation and does not discuss interoperability – what it means, its requirements, and how to achieve it. We designed the Provenance-Aware Storage System to be a generalpurpose substrate on top of which it would be “easy” to add other provenance-aware systems in a way that would provide “seamless integration” for the provenance captured at each level. While the system did exactly what we wanted on toy problems, when we began integrating StarFlow, a Python-based workflow/provenance system, we discovered that integration is far trickier and more subtle than anyone has suggested in the literature. This work describes our experience undertaking the integration of StarFlow and PASS, identifying several important additions to existing provenance models necessary for interoperability among provenance systems.
Benchmarking Energy Efficiency, Power Costs and Carbon Emissions on Heterogeneous Systems

With the advent of heterogeneous computing systems consisting of multi-core central processing units (CPUs) and many-core graphics processing units (GPUs), robust methods are needed to facilitate fair benchmark comparisons between different systems. In this paper, we present a benchmarking methodology for measuring a number of performance metrics for heterogeneous systems. Methods for comparing performance and energy efficiency are included. Consideration is given to further metrics, such as associated running costs and carbon emissions. We give a case study for these metrics applied to Bristol University Docking engine, a molecular mechanics-based docking application that has been ported to open computing language at the University of Bristol. Results are included for both AMD and NVIDIA GPUs, and for a highly optimized code on the latest x86 CPUs.
Sustained Attention to Science: A Tribute to the Life and Scholarship of Joel Warm

Objective: To provide an evaluative synthesis of the life and scientific contributions of the late Joel Warm. Background: As the doyen of vigilance research, Joel Warm expanded our understanding and horizons concerning this critical response capacity. However, he also made widespread and profound contributions to many other areas of perception and applied psychology, as we elucidate here. Method: Using archival sources, personal histories, and analysis of extant literature documenting Warm’s own productivity, we articulate his life in science. Results: Our synthesis illustrates the continued, broad, influential, and expanding impact that one individual can exert on diverse fields of study. Whole bodies of understanding of human behavior have been illuminated by his exemplary career. Application By understanding his path to success in applied experimental psychology, we anticipate that others will be motivated, inspired, and guided to replicate and even outstrip a lifetime of such seminal and influential contributions. The presence of individuals such as Warm serves as a primary motive in enhancing Humans Factors/Ergonomics Science.
Volume estimation of apple fruits using image processing

The present paper describes analytical methods for estimation of volume of axi-symmetric fruits like apples based on single view fruit images and the shape-based analytical models. The fruits are categorized into spherical, ellipsoid and paraboloid shapes with appropriate analytical models for their volume estimation. The methods analyze the single view fruit images to extract the eccentricity and shape related parameters and use appropriate shape models for estimating the volume. The proposed methods were tested in the laboratory and found to be reasonably accurate.
Identifying sources, pathways and risk drivers in ecosystems of Japanese Encephalitis in an epidemic-prone north Indian district

Japanese Encephalitis (JE) has caused repeated outbreaks in endemic pockets of India. This study was conducted in Kushinagar, a highly endemic district, to understand the human-animal-ecosystem interactions, and the drivers that influence disease transmission. Utilizing the ecosystems approach, a cross-sectional, descriptive study, employing mixed methods design was employed. Four villages (two with pig-rearing and two without) were randomly selected from a high, a medium and a low burden (based on case counts) block of Kushinagar. Children, pigs and vectors were sampled from these villages. A qualitative arm was incorporated to explain the findings from the quantitative surveys. All human serum samples were screened for JE-specific IgM using MAC ELISA and negative samples for JE RNA by rRT-PCR in peripheral blood mononuclear cells. In pigs, IgG ELISA and rRT-PCR for viral RNA were used. Of the 242 children tested, 24 tested positive by either rRT-PCR or MAC ELISA; in pigs, 38 out of the 51 pigs were positive. Of the known vectors, Culex vishnui was most commonly isolated across all biotopes. Analysis of 15 blood meals revealed human blood in 10 samples. Univariable analysis showed that gender, religion, lack of indoor residual spraying of insecticides in the past year, indoor vector density (all species), and not being vaccinated against JE in children were significantly associated with JE positivity. In multivariate analysis, only male gender remained as a significant risk factor. Based on previous estimates of symptomatic: asymptomatic cases of JE, we estimate that there should have been 618 cases from Kushinagar, although only 139 were reported. Vaccination of children and vector control measures emerged as major control activities; they had very poor coverage in the studied villages. In addition, lack of awareness about the cause of JE, lack of faith in the conventional medical healthcare system and multiple referral levels causing delay in diagnosis and treatment emerged as factors likely to result in adverse clinical outcomes.
Response of Climate Change on Urban Watersheds: A Case Study for Las Vegas, NV

The current research is a partnering effort between Southern Illinois University Carbondale and City of Las Vegas to assess the vulnerability to drought, extreme heat, and extreme precipitation. This study focuses on precipitation and uses different climate scenarios from the high-resolution North American Regional Climate Change Assessment Program (NARCCAP) climate model data to evaluate the existing stormwater infrastructure of the Gowan watershed in the Las Vegas valley. Six NARCCAP models considered in the study have shown the Gamma distribution as the best fitted from Kolmogorov Smirnov best fit test. Delta change method is adopted to quantify the effect of climate change on storm depth. U.S. Army Corps of Engineers HEC-HMS model is used to evaluate the changes in peak flow, storage, and outflow within the watershed. The findings of the analysis show that the drainage facility of the study area is vulnerable to the related climate change impacts. This study helps to quantify the effect of climate change on design storm depth of urban watershed.
Molecular Dynamics Study on Mechanical Responses of Circular Graphene Nanoflake under Nanoindentation

Authors : Jeong-Won Kang Abstract : Graphene, a single-atom sheet, has been considered as the most promising material for making future nanoelectromechanical systems as well as purely electrical switching with graphene transistors. Graphene-based devices have advantages in scaled-up device fabrication due to the recent progress in large area graphene growth and lithographic patterning of graphene nanostructures. Here we investigated its mechanical responses of circular graphene nanoflake under the nanoindentation using classical molecular dynamics simulations. A correlation between the load and the indentation depth was constructed. The nanoindented force in this work was applied to the center point of the circular graphene nanoflake and then, the resonance frequency could be tuned by a nanoindented depth. We found the hardening or the softening of the graphene nanoflake during its nanoindented-deflections, and such properties were recognized by the shift of the resonance frequency. The calculated mechanical parameters in the force vs deflection plot were in good agreement with previous experimental and theoretical works. This proposed schematics can detect the pressure via the deflection change or/and the resonance frequency shift, and also have great potential for versatile applications in nanoelectromechanical systems.
Software Release Planning

One of the most critical activities in software product development is the decisional process that assigns features to subsequent releases under technical, resource, risk, and budget constraints. This decision-centric process is referred to as software release planning (SRP). This briefing will expose a state of the art on SRP. A survey of the most relevant approaches will be presented. Emphasis will be made on their applicability (concerning e.g. type of development process – being more predictive versus more adaptive, type of system – commercial, open source product or mobile app), tool support and degree of validation in industry. One of these approaches, EVOLVE, will be analysed in detail.
Effects of on-pump versus off-pump coronary artery bypass grafting on myocardial metabolism

Background: On-pump coronary artery bypass grafting (ON-PCABG) and off-pump coronary artery bypass grafting (OF-PCABG) greatly affect myocardial metabolism (MCMB). However, no study has systematically explored and compared the impacts of ON-PCABG and OF-PCABG on MCMB. This study will aim to explore and to compare the effects of ON-PCABG and OF-PCABG on MCMB systematically. Methods: We will conduct the comprehensive literature search from the following electronic databases from inception to the present: Cochrane Library, EMBASE, MEDILINE, CINAHL, AMED and 4 Chinese databases without language restrictions. This systematic review will only concern randomized controlled trials (RCTs) and case-control studies of ON-PCABG and OF-PCABG on MCMB. The methodological quality of each entered study will be assessed by using Cochrane risk of bias tool. Results: Primary outcomes include myocardial cellular markers, myocardial lactate, oxygen utilization, pyruvate, and intramyocardial concentrations of glucose, urea and lactate. Secondary outcome comprises of glutathione, superoxide dismutase, myeloperoxidase, and oxidative stress and any other complications post surgery. Conclusion: This study will provide a high-quality synthesis and will assess and compare the effects of ON-PCABG and OF-PCABG on MCMB based on the current relevant literature evidence. Dissemination and ethics: The results will be submitted to peer-reviewed journals for publication. This study does not require ethic approval, because it only analyzes the data from published literature. Systematic review registration: PROSPERO CRD42019125381.
Kalman-Bucy filtering for linear systems driven by the Cox process with shot noise intensity and its application to the pricing of reinsurance contracts

In practical situations, we observe the number of claims to an insurance portfolio but not the claim intensity. It is therefore of interest to try to solve the 'filtering problem'; that is, to obtain the best estimate of the claim intensity on the basis of reported claims. In order to use the Kalman-Bucy filter, based on the Cox process incorporating a shot noise process as claim intensity, we need to approximate it by a Gaussian process. We demonstrate that, if the primary-event arrival rate of the shot noise process is reasonably large, we can then approximate the intensity, claim arrival, and aggregate loss processes by a three-dimensional Gaussian process. We establish weak-convergence results. We then use the Kalman-Bucy filter and we obtain the price of reinsurance contracts involving high-frequency events.
Numerical performance evaluation for Alamouti space time coded OFDM under receiver impairments

We present a methodology for the analysis of the capacity and symbol/bit error rate performance of Alamouti space time coded OFDM links that jointly captures the aggregate effects of real life receiver imperfections and mobile channel effects. Specifically, we investigate carrier frequency offset, channel estimation error, outdated channel state information due to time selective channel properties and flat receiver I/Q imbalance. Hence, we provide a numerical tool for realistic Alamouti space time coded (STC) OFDM performance evaluation. The main contribution of this work is the derivation of the probability density function of the received frequency domain signal with respect to the mentioned impairments. The density function is then used for numerical calculations of both the symbol and bit error rates, as well as the capacity for Alamouti STC OFDM links. Finally, we illustrate which of the mentioned impairments has the most severe impact on the overall STC OFDM system performance. The abstract goes here.
Interstitial CT lymphography-guided localization of breast sentinel lymph node: preliminary results.

BACKGROUND Accurate localization of the breast sentinel lymph node (SLN) can be challenging as a minimally invasive approach to the treatment of early-stage breast cancer. We tested the potential capability of interstitial computed tomographic lymphography (CT-LG) using a conventional contrast agent (iopamidol) for SLN mapping. METHODS In 14 female dogs, 0.5 and 1 mL of undiluted iopamidol was injected subcutaneously into the 2 skin areas overlying the mammary gland. Contiguous, 2 mm-thick multidetector helical CT images were obtained through the upper breast and axilla before, and for 60 minutes after, gentle massage at the injection site. Three-dimensional (3D) CT images were obtained from the postcontrast images showing the greatest SLN enhancement. This CT-LG with 2 mL of iopamidol was also evaluated in 5 human female volunteers. RESULTS The direct connection of SLN and lymphatic vessels draining from the injection sites in the animal models was clearly visualized, even with 0.5 mL of iopamidol. With this dose, the SLN attenuation was maximally enhanced, with a mean of 274 Hounsfield units (HU) on the first postcontrast images. The topographic 3D images provided the comprehensive anatomy of these lymphatic pathways. Of the 28 SLNs and 184 distant nodes visualized on CT images, all of the SLNs (100%) and 161 (87.5%) of the distant nodes could be resected at premortem and/or postmortem, with a good correlation in the locations and sizes with those on the CT images. The CT-LG effectively localized 5 SLNs with averaged maximum attenuation of 223 HU in the human volunteers, without any significant adverse effects. CONCLUSION Interstitial CT-LG using small volumes of iopamidol can sufficiently visualize breast lymphatic drainage and may have potential utility for breast SLN mapping.
Gaussian Process for Regression in Business Intelligence: A Fraud Detection Application

Business Intelligence (BI) systems are designed to provide information to support the decision making process in companies and governmental institutions. In this scenario, future events depend on the decisions and on the previous events. Therefore, the mathematical analysis of past data can be an important tool for the decision making process and to detect anomalies. Depending on the amount and the type of data to be analyzed, techniques from statistics, Machine Learning (ML), data mining and signal processing can be used to automate all or part of the system. In this paper, we propose to incorporate Gaussian Process for Regression (GPR) in BI systems in order to predict the data. As presented in this work, fraud detection is one important application of BI systems. We show that such application is possible with the use of GPR in the predictive stage, considering that GPR natively returns a full statistical description of the estimated variable, which can be used as a trigger measure to classify trusted and untrusted data. We validate our proposal with real world BI data provided by the Brazilian Federal Patrimony Department (SPU), regarding the monthly collection of federal taxes. In order to take into account the multidimensional structure of this specific data, we propose a pre-processing stage for reshaping the original time series into a bidimensional structure. The resulting algorithm, with GPR at its core, outperforms classical predictive schemes such as Artificial Neural Network (ANN).
Differential Activation of ERK Signaling in HPV-Related Oropharyngeal Squamous Cell Carcinoma

Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) forms a distinct tumor entity with better survival clinical outcome. Numerous underlying molecular mechanisms have been postulated for differences in treatment response, but the impact of MEK/ERK signaling, a main driver of carcinogenesis in various cancers including OPSCC and key player mediating therapy resistance remains elusive. In a retrospective experimental cohort study, primary tumor samples from OPSCC patients (n = 124) were available on tissue microarrays (TMAs) and expression levels of phosphorylated ERK1/2 (pERK1/2) were detected by immunohistochemical staining. Correlations of pERK1/2 expression patterns with clinicopathological features and clinical outcome were evaluated by statistical analysis. A low pERK1/2 expression was strongly associated with HPV-related OPSCC, while primary tumors with high pERK1/2 staining showed a distinctly worse survival outcome and were associated with higher cellular differentiation. Co-activation of both ERK1/2 and AKT was a common event and was associated with unfavorable prognosis in our cohort. However, the combinatorial analysis of pAKT (Ser473) and pERK1/2 did not strengthen the predictive power of pERK1/2, suggesting that pERK1/2 plays a more significant function in OPSCC. In summary, our data provide a compelling experimental and statistical evidence that low levels of tumor cell intrinsic ERK1/2 activation contribute at least in part to the favorable outcome of HPV-related OPSCC. On the other hand, presented findings indicate that non-HPV-related OPSCC with elevated ERK phosphorylation are at high risk for treatment failure and might benefit from targeted therapy of MEK/ERK signaling.