Miracle-dz/UniFAR-FTUs huggingface dataset:
Live Cell Imaging of Germination and Outgrowth of Individual Bacillus subtilis Spores; the Effect of Heat Stress Quantitatively Analyzed with SporeTracker

Spore-forming bacteria are a special problem for the food industry as some of them are able to survive preservation processes. Bacillus spp. spores can remain in a dormant, stress resistant state for a long period of time. Vegetative cells are formed by germination of spores followed by a more extended outgrowth phase. Spore germination and outgrowth progression are often very heterogeneous and therefore, predictions of microbial stability of food products are exceedingly difficult. Mechanistic details of the cause of this heterogeneity are necessary. In order to examine spore heterogeneity we made a novel closed air-containing chamber for live imaging. This chamber was used to analyze Bacillus subtilis spore germination, outgrowth, as well as subsequent vegetative growth. Typically, we examined around 90 starting spores/cells for ≥4 hours per experiment. Image analysis with the purposely built program “SporeTracker” allows for automated data processing from germination to outgrowth and vegetative doubling. In order to check the efficiency of the chamber, growth and division of B. subtilis vegetative cells were monitored. The observed generation times of vegetative cells were comparable to those obtained in well-aerated shake flask cultures. The influence of a heat stress of 85°C for 10 min on germination, outgrowth, and subsequent vegetative growth was investigated in detail. Compared to control samples fewer spores germinated (41.1% less) and fewer grew out (48.4% less) after the treatment. The heat treatment had a significant influence on the average time to the start of germination (increased) and the distribution and average of the duration of germination itself (increased). However, the distribution and the mean outgrowth time and the generation time of vegetative cells, emerging from untreated and thermally injured spores, were similar.
Sex and spouse conditions influence symptoms of anxiety, depression, and posttraumatic stress disorder in both patients admitted to intensive care units and their spouses.

OBJECTIVES To assess the effect of sex and spouse condition on symptoms of anxiety, depression and posttraumatic stress symptoms in patients and their spouses. METHODS A prospective study conducted in a 22-bed adult mixed intensive care unit in a tertiary hospital in São Paulo, Brazil. Patients and their spouses were enrolled 2 days after intensive care unit admission. They were interviewed while in the intensive care unit using the Hospital Anxiety and Depression Scale. At 30 and 90 days after intensive care unit discharge, they completed the Impact of Event Scale and Hospital Anxiety and Depression Scale by phone. RESULTS From March 2011 to March 2013, we analyzed 118 patients and their spouses. We observed that female sex was associated with higher scores than male sex was in terms of the anxiety Hospital Anxiety and Depression Scale - subscale (p = 0.032) and depression (p = 0.034). There was no association between sex and posttraumatic stress disorder symptoms. However, spouses had higher Impact of Event Scale points compared with patients (p = 0.001). CONCLUSIONS Female sex was associated with anxiety and depression, and spouses were more vulnerable to post-traumatic stress symptoms than the patients were. Increasing age and a later time of assessment were also associated with lower scores on the Impact of Event Scale.
UIDELINES ercutaneous occlusion of the left atrial appendage : n expert consensus statement onsensus d ’ experts sur les modalités de l ’ occlusion percutanée de l ’ auricule auche

a Heart Rhythm Unit, Heart Hospital, CHRU de Lille, 59037 Lille, France b Department of Cardiology and Interventional Vascular Radiology, Polyclinique Les Fleurs, Ollioules, France c Heart Rhythm Unit, University Cardiology Clinic, CHU de Grenoble, Grenoble, France d Congenital Heart Disease of the Foetus, Child and Adult, Haut Levêque Heart Hospital, Pessac, France e Heart Rhythm Unit, Department of Cardiology, Nouvelles Cliniques Nantaises, Nantes, France f Department of Cardiology, Bichat-Claude Bernard Hospital Group, Paris, France g Heart Rhythm and Heart Failure Unit, Department of Cardiology and Vascular Diseases, Inserm U1046, Arnaud Villeneuve Hospital, CHU de Montpellier, Montpellier, France h Haemodynamic and Interventional Cardiovascular Unit, Cardiology Clinic, Guillaume and René Laennec Hospital, CHU North, Nantes, France i Cardiology Division, CHU Henri-Mondor, Créteil, France j Cardiology Division, Saint-Hilaire Clinic, Rouen, France k Cardiology Division 2—Arrhythmia Centre, North Cardiology Centre, Saint-Denis, France
Essential role of immobilized chemokine CXCL12 in the regulation of the humoral immune response

Significance High-affinity antibodies confer protective immunity against external antigens and are generated during germinal center (GC) reactions when B-lymphocytes, migrating between the dark zone (DZ) and light zone (LZ) of the GC, accumulate mutations in their immunoglobulin genes and are selected for high affinity to antigen. B cells move between DZ and LZ, guided by gradients of CXCL12 and CXCL13 chemokines. We show that immobilized CXCL12 is essential for the correct positioning of B-lymphocytes during the GC reaction and for the production of high-affinity antibodies. Our results provide fundamental insights into the role of surface-immobilized chemokines, molecules that regulate the migration of many cell types, thus controlling homeostasis in multiple tissues. Chemokines control the migration of a large array of cells by binding to specific receptors on cell surfaces. The biological function of chemokines also depends on interactions between nonreceptor binding domains and proteoglycans, which mediate chemokine immobilization on cellular or extracellular surfaces and formation of fixed gradients. Chemokine gradients regulate synchronous cell motility and integrin-dependent cell adhesion. Of the various chemokines, CXCL12 has a unique structure because its receptor-binding domain is distinct and does not overlap with the immobilization domains. Although CXCL12 is known to be essential for the germinal center (GC) response, the role of its immobilization in biological functions has never been addressed. In this work, we investigated the unexplored paradigm of CXCL12 immobilization during the germinal center reaction, a fundamental process where cellular traffic is crucial for the quality of humoral immune responses. We show that the structure of murine germinal centers and the localization of GC B cells are impaired when CXCL12 is unable to bind to cellular or extracellular surfaces. In such mice, B cells carry fewer somatic mutations in Ig genes and are impaired in affinity maturation. Therefore, immobilization of CXCL12 is necessary for proper trafficking of B cells during GC reaction and for optimal humoral immune responses.
How Can We Improve Osteoporosis Care? A Systematic Review and Meta‐Analysis of the Efficacy of Quality Improvement Strategies for Osteoporosis

Although osteoporosis affects 10 million people in the United States, screening and treatment rates remain low. We performed a systematic review and meta‐analysis of the efficacy of quality improvement strategies to improve osteoporosis screening (bone mineral density [BMD]/dual‐energy X‐ray absorptiometry [DXA] testing) and/or treatment (pharmacotherapy) initiation rates. We developed broad literature search strategies for PubMed, Embase, and Cochrane Library databases, and applied inclusion/exclusion criteria to select relevant studies. Random‐effects meta‐analyses were performed for outcomes of BMD/DXA testing and/or osteoporosis treatment. Forty‐three randomized clinical studies met inclusion criteria. For increasing BMD/DXA testing in patients with recent or prior fracture, meta‐analyses demonstrated several efficacious strategies, including orthopedic surgeon or fracture clinic initiation of osteoporosis evaluation or management (risk difference 44%, 95% confidence interval [CI] 26%–63%), fracture liaison service/case management (risk difference 43%, 95% CI 23%–64%), multifaceted interventions targeting providers and patients (risk difference 24%, 95% CI 15%–32%), and patient education and/or activation (risk difference 16%, 95% CI 6%–26%). For increasing osteoporosis treatment in patients with recent or prior fracture, meta‐analyses demonstrated significant efficacy for interventions of fracture liaison service/case management (risk difference 20%, 95% CI 1%–40%) and multifaceted interventions targeting providers and patients (risk difference 12%, 95% CI 6%–17%). The only quality improvement strategy for which meta‐analysis findings demonstrated significant improvement of osteoporosis care for patient populations including individuals without prior fracture was patient self‐scheduling of DXA plus education, for increasing the outcome of BMD testing (risk difference 13%, 95% CI 7%–18%). The meta‐analyses findings were limited by small number of studies in each analysis; high between‐study heterogeneity; sensitivity to removal of individual studies; and unclear risk of bias of included studies. Despite the limitations of the current body of evidence, our findings indicate there are several strategies that appear worthwhile to enact to try to improve osteoporosis screening and/or treatment rates. © 2018 American Society for Bone and Mineral Research.
Toward Generating a New Intrusion Detection Dataset and Intrusion Traffic Characterization

: With exponential growth in the size of computer networks and developed applications, the signiﬁcant in-creasing of the potential damage that can be caused by launching attacks is becoming obvious. Meanwhile, Intrusion Detection Systems (IDSs) and Intrusion Prevention Systems (IPSs) are one of the most important defense tools against the sophisticated and ever-growing network attacks. Due to the lack of adequate dataset, anomaly-based approaches in intrusion detection systems are suffering from accurate deployment, analysis and evaluation. There exist a number of such datasets such as DARPA98, KDD99, ISC2012, and ADFA13 that have been used by the researchers to evaluate the performance of their proposed intrusion detection and intrusion prevention approaches. Based on our study over eleven available datasets since 1998, many such datasets are out of date and unreliable to use. Some of these datasets suffer from lack of trafﬁc diversity and volumes, some of them do not cover the variety of attacks, while others anonymized packet information and payload which cannot reﬂect the current trends, or they lack feature set and metadata. This paper produces a reliable dataset that contains benign and seven common attack network ﬂows, which meets real world criteria and is publicly avaliable. Consequently, the paper evaluates the performance of a comprehensive set of network trafﬁc features and machine learning algorithms to indicate the best set of features for detecting the certain attack categories.
DISPERSAL OF STEGODYPHUS DUMICOLA (ARANEAE, ERESIDAE): THEY DO BALLOON AFTER ALL!

Abstract There has been some controversy about whether adult females of social Stegodyphus disperse by ballooning. Here we show that adult Stegodyphus dumicola (Eresidae) Pocock 1898 are able to gain up-lift by releasing a very large number of threads. The threads fan out widely from the spider's body and form a triangular sheet. This previously unknown ballooning mechanism, enables even large spiders to disperse over large distances.
Novel multi-kinase inhibitor, T03 inhibits Taxol-resistant breast cancer

Activation of kinase-associated signaling pathways is one of the leading causes of various malignant phenotypes in breast tumors. Strategies of drug discovery and development have investigated approaches to target the inhibition of protein kinase signaling. In the current study, the anti-tumor activities of a novel multi-kinase inhibitor, T03 were evaluated in breast cancer. T03 inhibited Taxol-resistant breast cancer cell proliferation and induced cell cycle arrest and apoptosis in vitro and in vivo. The current results demonstrated that T03 downregulated c-Raf, platelet-derived growth factor receptor-β and other kinases, thus inhibited Raf/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase and Akt/mechanistic target of rapamycin survival pathways in MCF-7 and MCF-7/Taxol xenograft tumors. At a dose of 100 mg/kg, T03 inhibited tumor growth by 62.90 and 59.98% in tumor weight in MX-1 and MX-1/T xenograft models, respectively and by 62.60 and 60.22% in MCF-7 and MCF-7/T tumors, respectively. These data indicate that the novel multi-kinase inhibitor, T03, may present as a potential compound to develop novel treatments against breast cancer and Taxol-resistant breast tumors.
TBD: Benchmarking and Analyzing Deep Neural Network Training

The recent popularity of deep neural networks (DNNs) has generated a lot of research interest in performing DNN-related computation efficiently. However, the primary focus is usually very narrow and limited to (i) inference -- i.e. how to efficiently execute already trained models and (ii) image classification networks as the primary benchmark for evaluation. Our primary goal in this work is to break this myopic view by (i) proposing a new benchmark for DNN training, called TBD (TBD is short for Training Benchmark for DNNs), that uses a representative set of DNN models that cover a wide range of machine learning applications: image classification, machine translation, speech recognition, object detection, adversarial networks, reinforcement learning, and (ii) by performing an extensive performance analysis of training these different applications on three major deep learning frameworks (TensorFlow, MXNet, CNTK) across different hardware configurations (single-GPU, multi-GPU, and multi-machine). TBD currently covers six major application domains and eight different state-of-the-art models. We present a new toolchain for performance analysis for these models that combines the targeted usage of existing performance analysis tools, careful selection of new and existing metrics and methodologies to analyze the results, and utilization of domain specific characteristics of DNN training. We also build a new set of tools for memory profiling in all three major frameworks; much needed tools that can finally shed some light on precisely how much memory is consumed by different data structures (weights, activations, gradients, workspace) in DNN training. By using our tools and methodologies, we make several important observations and recommendations on where the future research and optimization of DNN training should be focused.
Decoding two-dimensional movement trajectories using electrocorticographic signals in humans

Signals from the brain could provide a non-muscular communication and control system, a brain–computer interface (BCI), for people who are severely paralyzed. A common BCI research strategy begins by decoding kinematic parameters from brain signals recorded during actual arm movement. It has been assumed that these parameters can be derived accurately only from signals recorded by intracortical microelectrodes, but the long-term stability of such electrodes is uncertain. The present study disproves this widespread assumption by showing in humans that kinematic parameters can also be decoded from signals recorded by subdural electrodes on the cortical surface (ECoG) with an accuracy comparable to that achieved in monkey studies using intracortical microelectrodes. A new ECoG feature labeled the local motor potential (LMP) provided the most information about movement. Furthermore, features displayed cosine tuning that has previously been described only for signals recorded within the brain. These results suggest that ECoG could be a more stable and less invasive alternative to intracortical electrodes for BCI systems, and could also prove useful in studies of motor function.
Are We Eating Our Way to Prostate Cancer—A Hypothesis Based on the Evolution, Bioaccumulation, and Interspecific Transfer of miR-150

MicroRNAs (miRNAs) are well established epigenetic modifiers. There is a lot of work being done to identify the evolutionary transfer of miRNAs both at intra- and interspecific levels. In this hypothesis-driven review, we have suggested a possible reason as to why miR-150 can be a promising diagnostic biomarker for prostate cancer using theories of evolution, bio-accumulation, and interspecific transfer of miRNAs.
Prevalence of menstrual problems and their association with psychological stress in young female students studying health sciences

Objectives: To identify the prevalence of various menstrual problems in young females studying health sciences and to identify their association with academic stress. Methods: This was a cross-sectional study, conducted in the health colleges of Immam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia between February 2015 and February 2016. Seven hundred and thirty-eight female students aged 18-25 years anonymously completed menstrual problem identification and perceived stress scale questionnaire. The data was analyzed using the Statistical Package for Social Sciences version 16.0. Results: Ninety-one percent of the students were suffering from some kind of menstrual problem. The different menstrual problems reported, and their incidences included irregular menstruation (27%), abnormal vaginal bleeding (9.3%), amenorrhea (9.2%), menorrhagia (3.4%), dysmenorrhea (89.7%), and premenstrual symptoms (46.7%). High perceived stress (HPS) was identified in 39% of the students. A significant positive correlation was found between HPS and menstrual problems. Students with HPS had 4 times, 2 times, and 2.8 times increased odds ratio for experiencing amenorrhea, dysmenorrhea, and premenstrual syndrome (p<0.05). Conclusion: The most prevalent menstrual problems (dysmenorrhea and premenstrual symptoms) in the target population were strongly associated with stress. Therefore, it is recommended that health science students should be provided with early psychological and gynecological counselling to prevent future complications.
Geoelectrochemical CO production: Implications for the autotrophic origin of life

Efficient CO production realizing Wächtershäuser’s scenario was demonstrated in simulated early ocean hydrotherm systems. Wächtershäuser’s proposal of the autotrophic origin of life theory and subsequent laboratory demonstrations of relevant organic reactions have opened a new gate for the exploration of the origin of life. However, this scenario remains controversial because, at present, it requires a high pressure of CO as a source of carbon and reducing energy, although CO must have been a trace C species on the Hadean Earth. We show that, simulating a geoelectrochemical environment in deep-sea hydrothermal fields, CO production with up to ~40% Faraday efficiency was attainable on CdS in CO2-saturated NaCl solution at ≤–1 V (versus the standard hydrogen electrode). The threshold potential is readily generated in the H2-rich, high-temperature, and alkaline hydrothermal vents that were probably widespread on the early komatiitic and basaltic ocean crust. Thus, Wächtershäuser’s scenario starting from CO2 was likely to be realized in the Hadean ocean hydrothermal systems.
An Algorithm for Automatically Calculating Component Current Ratings in Switched-Capacitor DC-DC Converters

Switched capacitor (SC) dc–dc converters, which have traditionally been used for on-chip power supplies, are now being considered for medium to high-power applications. This paper presents a method for automatically synthesizing SC converters as well as deriving the expressions for their charge-multipliers. Charge multipliers can be used to calculate important design characteristics such as converter output voltage regulation, efficiency, and component current ratings, which can then be used to appraise different topologies. However, whilst a full appraisal of converters also requires component voltage ratings, this work is the first step in developing an automatic software tool that will employ a search-based algorithm to generate optimum SC topologies for a given application. The method is based on the proposition that all SC converters can be synthesized from a so-called “basic cell”. The automatic derivation and solution of the charge transfer equations for a traditional Fibonacci SC converter is presented as an example of the proposed method, which is validated against existing analytic equations as well as a detailed Spice simulation. The automatic calculation of the charge-multipliers for two other well-known SC converters is also demonstrated, including a new, arbitrarily generated circuit, which again is validated against detailed spice simulations.
Probing the Timing Recruitment of Broca’s Area in Speech Production for Mandarin Chinese: A TMS Study

Although Broca’s area is widely recognized to play an important role in speech production, neuroscientists still debate on its timing recruitment across different languages. In order to investigate the precise time course of phonological encoding for Mandarin Chinese, we applied real triple-pulse transcranial magnetic stimulation (tpTMS) and sham tpTMS within Broca’s area at five different time windows respectively (150 ms, 225 ms, 300 ms, 400 ms and 500 ms) in picture naming task in Mandarin Chinese. To exclude unspecific TMS effects and to make sure that the effects observed in the study were really due to stimulation at Broca’s area, we also conducted a control experiment by a different group of subjects. Significant increases in reaction times (RTs) were observed when real TMS stimulation at Broca’s area was applied at 225 ms, 300 ms and 400 ms time windows with a peak at 225 ms, compared with sham TMS stimulation at other time windows. Our findings support the hypothesis that the phonological encoding in speech production for Chinese language may approximately start from 200 ms and end around 400 ms post target onset, a little earlier than that from 355 ms to 455 ms for Indo-European languages.
Supraglacial Streams on the Greenland Ice Sheet Delineated From Combined Spectral–Shape Information in High-Resolution Satellite Imagery

Supraglacial meltwater streams and lakes that form each summer across large expanses of the Greenland Ice Sheet (GrIS) ablation zone have global implications for sea level rise but remain one of the least studied hydrologic systems on Earth. Remote sensing of supraglacial streams is challenging owing to their narrow width (~1-30 m) and proximity to other features having similar visible/near-infrared reflectance (lakes and slush) or shape (dry stream channels, crevasses, and fractures). This letter presents a new automated “spectral-shape” procedure for delineating actively flowing streams in high-resolution satellite imagery, utilizing both spectral and pattern information. First, a modified normalized difference water index adapted for ice ( NDWIice) enhances the spectral contrast between open water and drier snow/ice surfaces. Next, three NDWIice thresholds are used to mask deep-water lakes and discern open water from slush, in concert with a multipoints fast marching method to rejoin resulting stream fragments. Comparison of this procedure with manual digitization for six WorldView-2 images in southwestern Greenland demonstrates its value for detecting actively flowing supraglacial streams, particularly in slushy areas where classification performance dramatically improves (85.2% success) versus simple threshold methods (52.9% and 59.4% success for low and moderate thresholds, respectively). While a simple threshold approach is satisfactory for areas known to be slush free, the procedure outlined here enables comprehensive stream mapping across the GrIS ablation zone, regardless of slush conditions and/or the presence of similarly shaped glaciological features.