Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative approaches to vertebrate ecotoxicity tests in the 21st century: A review of developments over the last 2 decades and current status

The need for alternative approaches to the use of vertebrate animals for hazard assessment of chemicals and pollutants has become of increasing importance. It is now the first consideration when initiating a vertebrate ecotoxicity test, to ensure that unnecessary use of vertebrate organisms is minimized wherever possible. For some regulatory purposes, the use of vertebrate organisms for environmental risk assessments has been banned; in other situations, the number of organisms tested has been dramatically reduced or the severity of the procedure refined. However, there is still a long way to go to achieve a complete replacement of vertebrate organisms to generate environmental hazard data. The development of animal alternatives is based not just on ethical considerations but also on reducing the cost of performing vertebrate ecotoxicity tests and in some cases on providing better information aimed at improving environmental risk assessments. The present Focus article provides an overview of the considerable advances that have been made toward alternative approaches for ecotoxicity assessments over the last few decades. Environ Toxicol Chem 2016;35:2637–2646. © 2016 SETAC
Analysis of mechanical behavior of two parameters, collagen fiber direction and increased concentration of mineral in direct insertion tendon to bone

Tendons and ligaments have a regular hierarchical structure and play a vital role in transferring muscle forces along the tendon length to the skeleton. In this way, tendon is considered as an interface of soft (muscle) and hard (bone) tissue. Such interface causes stress concentration at the osteotendinous junction (insertion site of the tendon to bone) and could cause failure and fracture of the attachment. Collagen fibers are the main load bearing components along the tendon length. While approaching to the insertion site, gradual increase of minerals contribute as the principal strength factor. Hence, the transition of load-bearing from tensile elements (collagen fibers) to tension-compression crystals (minerals) leads to more strength of the insertion site and reduction of the stress concentration. The current study evaluates the role of mineralization and fiber distribution on performance of tendon to bone insertion by simulation of a representative volume element (RVE) in the attachment site. Comparison of models without and with insertion site indicate interesting deviations in stress concentration.
Energy efficient algorithm for SDWSNs based on DACR and energy hierarchy

Software defined wireless sensing network (SDWSN) has gained wide attention on account of overcoming the storage and computational restrictions. SDWSN, an ultramodern architecture, still has crippling roadblocks. One of the toughest aspects is energy confinement and imbalanced consumption. In this paper, we propose an energy efficient algorithm based on energy shell and dynamically adjusting communication radius. In our algorithm, nodes in higher energy shells have higher priority to relay data. Having several candidate nodes to relay data, nodes prefer to relay data through the nodes with the highest RSSI. Compared to most other algorithms the algorithm we are proposing performs better in reducing energy expenditure and balancing energy consumption.
Improving Dependency Parsing with Semantic Classes

This paper presents the introduction of WordNet semantic classes in a dependency parser, obtaining improvements on the full Penn Treebank for the first time. We tried different combinations of some basic semantic classes and word sense disambiguation algorithms. Our experiments show that selecting the adequate combination of semantic features on development data is key for success. Given the basic nature of the semantic classes and word sense disambiguation algorithms used, we think there is ample room for future improvements.
Neuroprotective effects of Rhizoma Dioscoreae polysaccharides against neuronal apoptosis induced by in vitro hypoxia

Rhizoma Dioscoreae polysaccharides (RDPS) are the primary active ingredient of Rhizoma Dioscoreae, which is a traditional Chinese medicine. RDPS have previously been shown to scavenge reactive oxygen species, and protect against D-galactose-induced mimetic aging. The present study aimed to investigate the neuroprotective effects of RDPS against hypoxia-induced neuronal cell apoptosis. Neuronal cells harvested from pregnant Sprague-Dawley rats were divided into groups, as follows: i) Normal control group; ii) hypoxia-induced apoptosis neuronal cell model; iii) 0.025 g/l RDPS-treated group; iv) 0.05 g/l RDPS-treated group; v) 0.1 g/l RDPS-treated group; and vi) 0.25 g/l RDPS treated group. Neuronal cell viability was investigated using an MTT assay, and neuronal cell apoptosis was analyzed using Annexin V-fluorescein isothiocyanate/propidium iodide double-staining, Hoechst 33342 fluorescent staining, Rhodamine 123 staining, polymerase chain reaction and immunocytochemical staining. The RDPS-treated neuronal cells exhibited improved viability, and decreased hypoxia-induced mitochondrial injury and apoptosis. In addition, the mRNA and protein expression levels of caspase-3 and B-cell lymphoma (Bcl)-2-associated X protein (Bax) were significantly downregulated, whereas the mRNA and protein expression levels of Bcl-2 were significantly upregulated, in the RDPS-treated hypoxic neurons, as compared with the apoptosis model (P<0.05). Furthermore, the ratio of Bcl-2 expression:Bax expression significantly increased following RDPS treatment, as compared with the apoptosis model (P<0.05). The results of the present study suggested that RDPS may attenuate hypoxia-induced neuronal cell apoptosis by altering the expression levels of key apoptosis-regulating proteins in hypoxic neurons.
Hepatitis C in Hemodialysis Patients: Current Global Magnitude, Natural History, Diagnostic Difficulties, and Preventive Measures

Hepatitis C virus (HCV) infection is a significant cause of morbidity and mortality in hemodialysis (HD) patients. The reported prevalence of HCV among the HD population has varied greatly from 1.9 to 84.6% in different countries in recent years. The length of time on HD is generally believed to be associated with HCV acquisition in HD subjects. Nevertheless, several recent reports failed to recognize any significant role of blood transfusion. Although there are some considerations about the accuracy of serologic testing in detecting HCV in HD patients, the accumulated data in this review suggest the false-negativity rate to be not more than 1.66% (153/9,220). Therefore, substituting virologic for serologic testing in the routine diagnosis of HCV infection in HD patients seems unreasonable. Several phylogenetic analyzes of viral isolates suggested nosocomial patient-to-patient transmission of HCV among HD patients for which the main potential source is believed to be contaminated hands and articles. However, isolation of HCV-infected HD patients and use of dedicated machines are currently unjustified while strict adherence to universal precautions seems to be enough to control disease spread in HD units. The present article is an update on epidemiological and clinical features of HCV in HD population.
Extracellular HtrA serine proteases: An emerging new strategy in bacterial pathogenesis

The HtrA family of chaperones and serine proteases is important for regulating stress responses and controlling protein quality in the periplasm of bacteria. HtrA is also associated with infectious diseases since inactivation of htrA genes results in significantly reduced virulence properties by various bacterial pathogens. These virulence features of HtrA can be attributed to reduced fitness of the bacteria, higher susceptibility to environmental stress and/or diminished secretion of virulence factors. In some Gram‐negative and Gram‐positive pathogens, HtrA itself can be exposed to the extracellular environment promoting bacterial colonisation and invasion of host tissues. Most of our knowledge on the function of exported HtrAs stems from research on Helicobacter pylori, Campylobacter jejuni, Borrelia burgdorferi, Bacillus anthracis, and Chlamydia species. Here, we discuss recent progress showing that extracellular HtrAs are able to cleave cell‐to‐cell junction factors including E‐cadherin, occludin, and claudin‐8, as well as extracellular matrix proteins such as fibronectin, aggrecan, and proteoglycans, disrupting the epithelial barrier and producing substantial host cell damage. We propose that the export of HtrAs is a newly discovered strategy, also applied by additional bacterial pathogens. Consequently, exported HtrA proteases represent highly attractive targets for antibacterial treatment by inhibiting their proteolytic activity or application in vaccine development.
Cardioprotective Effects of Nicorandil on Coronary Heart Disease Patients Undergoing Elective Percutaneous Coronary Intervention

Background Nicorandil is a nicotinamide ester commonly prescribed for treatment of patients with coronary heart disease (CHD). In the present study, we aimed to explore the cardioprotective effects of nicorandil on CHD patients undergoing elective percutaneous coronary intervention (PCI). Material/Methods One hundred patients with CHD undergoing PCI were randomly divided into a control group (n=48) and a nicorandil group (n=52). Patients in the control group received traditional therapy, and while patients in the nicorandil group received nicorandil before PCI in addition to the traditional therapy. After PCI, all patients underwent coronary angiogram, and TIMI frame count (TFC) was calculated. Plasma levels of cardiac troponin I (cTnI), creatine kinase-MB (CK-MB), myeloperoxidase (MPO), and malondialdehyde (MDA) were determined before and at 6, 18, and 24 h after PCI. Moreover, systolic blood pressure (SBP), mean blood pressure (DBP), heart rate (HR), and left ventricular ejection fractions (LVEF) were recorded before and 3 months after PCI. Results There was a significant difference in the rate of no-reflow (P=0.036) between the 2 groups. The blood frames and levels of cTnI, CK-MB, MPO, and MDA in the nicorandil group were significantly decreased compared to the control group (all P<0.05). Moreover, administration of nicorandil markedly decreased SBP, MBP, and HR, but obviously increased LVEF at 3 months after PCI (P<0.05 or P<0.01). Conclusions Nicorandil exerts cardioprotective effects on CHD patients undergoing elective PCI by decreasing PCI-related myocardial injury and rate of no-reflow and improvement of LVEF.
Moving Beyond ERP Components: A Selective Review of Approaches to Integrate EEG and Behavior

Relationships between neuroimaging measures and behavior provide important clues about brain function and cognition in healthy and clinical populations. While electroencephalography (EEG) provides a portable, low cost measure of brain dynamics, it has been somewhat underrepresented in the emerging field of model-based inference. We seek to address this gap in this article by highlighting the utility of linking EEG and behavior, with an emphasis on approaches for EEG analysis that move beyond focusing on peaks or “components” derived from averaging EEG responses across trials and subjects (generating the event-related potential, ERP). First, we review methods for deriving features from EEG in order to enhance the signal within single-trials. These methods include filtering based on user-defined features (i.e., frequency decomposition, time-frequency decomposition), filtering based on data-driven properties (i.e., blind source separation, BSS), and generating more abstract representations of data (e.g., using deep learning). We then review cognitive models which extract latent variables from experimental tasks, including the drift diffusion model (DDM) and reinforcement learning (RL) approaches. Next, we discuss ways to access associations among these measures, including statistical models, data-driven joint models and cognitive joint modeling using hierarchical Bayesian models (HBMs). We think that these methodological tools are likely to contribute to theoretical advancements, and will help inform our understandings of brain dynamics that contribute to moment-to-moment cognitive function.
3'-Azido-3'-deoxythymidine triphosphate as an inhibitor and substrate of purified human immunodeficiency virus reverse transcriptase

Reverse transcriptase was purified from human immunodeficiency virus (HIV). It utilized the artificial primer-template poly(rA)-oligo(dT)12-18 more efficiently than activated calf thymus DNA, poly(rI)-oligo(dC)12-18, poly(rC)-oligo(dG)12-18, or poly(rCm)-oligo(dG)12-18. Maximum activity was observed at pH 7.0 to 7.6 in the presence of 5 mM MgCl2 and 100 mM KCl. 3'-Azido-3'-deoxythymidine triphosphate competed with dTTP for binding to HIV reverse transcriptase. Different kinetic constants were obtained with different primer-templates. Km and Ki values of 2.8 and 0.04 microM, respectively, were obtained with poly(rA)-oligo(dT)12-18. The corresponding values were 1.2 and 0.3 microM, respectively, with activated calf thymus DNA and 0.3 and 0.01 microM, respectively, with extracted virus and native template. Inhibition of the host cell DNA polymerases alpha and beta was considerably weaker. The Km and Ki values obtained with activated calf thymus DNA as the primer-template were 2.4 and 230 microM, respectively, for DNA polymerase alpha and 6.0 and 73 microM, respectively, for DNA polymerase beta. 3'-Azido-3'-deoxythymidine triphosphate could also serve as an alternate substrate for HIV reverse transcriptase. The resulting incorporation of 3'-azido-3'-deoxythymidine triphosphate into poly(rA)-oligo(dT)12-18 caused chain termination and premature deceleration of the reaction. The terminated primer could not be elongated when incubated with dTTP and HIV reverse transcriptase.
On the Optimality of Reflection Control, with Production-Inventory Applications

We study the control of a Brownian motion (BM) with a negative drift, so as to minimize a long-run average cost objective. We show the optimality of a class of reflection controls that prevent the BM from dropping below some negative level r, by cancelling out from time to time part of the negative drift; and this optimality is established for any holding cost function h(x) that is increasing in x ? 0 and decreasing in x ? 0. Furthermore, we show the optimal reflection level can be derived as the fixed point that equates the long-run average cost to the holding cost. We also show the asymptotic optimality of this reflection control when it is applied to production-inventory systems driven by discrete counting processes.
The herbicide atrazine induces hyperactivity and compromises tadpole detection of predator chemical cues

The ability to detect chemical cues is often critical for freshwater organisms to avoid predation and find food and mates. In particular, reduced activity and avoidance of chemical cues signaling predation risk are generally adaptive behaviors that reduce prey encounter rates with predators. The present study examined the effects of the common herbicide atrazine on the ability of Cuban tree frog (Osteopilus septentrionalis) tadpoles to detect and respond to chemical cues from larval dragonfly (Libellulidae sp.) predators. Tadpoles exposed to an estimated environmental concentration of atrazine (calculated using US Environmental Protection Agency software; measured concentration, 178 μg/L) were significantly hyperactive relative to those exposed to solvent control. In addition, control tadpoles significantly avoided predator chemical cues, but tadpoles exposed to atrazine did not. These results are consistent with previous studies that have demonstrated that ecologically relevant concentrations of atrazine can induce hyperactivity and impair the olfactory abilities of other freshwater vertebrates. The authors call for additional studies examining the role of chemical contaminants in disrupting chemical communication and the quantification of subsequent impacts on the fitness and population dynamics of wildlife. Environ Toxicol Chem 2016;35:2239–2244. © 2016 SETAC
Quantal Release of ATP in Mouse Cortex

Transient currents occur at rest in cortical neurones that reflect the quantal release of transmitters such as glutamate and γ-aminobutyric acid (GABA). We found a bimodal amplitude distribution for spontaneously occurring inward currents recorded from mouse pyramidal neurones in situ, in acutely isolated brain slices superfused with picrotoxin. Larger events were blocked by glutamate receptor (AMPA, kainate) antagonists; smaller events were partially inhibited by P2X receptor antagonists suramin and PPADS. The decay of the larger events was selectively prolonged by cyclothiazide. Stimulation of single intracortical axons elicited quantal glutamate-mediated currents and also quantal currents with amplitudes corresponding to the smaller spontaneous inward currents. It is likely that the lower amplitude spontaneous events reflect packaged ATP release. This occurs with a lower probability than that of glutamate, and evokes unitary currents about half the amplitude of those mediated through AMPA receptors. Furthermore, the packets of ATP appear to be released from vesicle in a subset of glutamate-containing terminals.
Ultrasonographic Evaluation of Cervical Lymph Nodes in Thyroid Cancer

Objective To determine what ultrasonographic features can identify metastatic cervical lymph nodes, both preoperatively and in recurrences after complete thyroidectomy. Study Design Prospective. Setting Outpatient clinic, Department of Head and Neck Surgery, School of Medicine, University of São Paulo, Brazil. Subjects and Methods A total of 1976 lymph nodes were evaluated in 118 patients submitted to total thyroidectomy with or without cervical lymph node dissection. All the patients were examined by cervical ultrasonography, preoperatively and/or postoperatively. The following factors were assessed: number, size, shape, margins, presence of fatty hilum, cortex, echotexture, echogenicity, presence of microcalcification, presence of necrosis, and type of vascularity. The specificity, sensitivity, positive predictive value, and negative predictive value of each variable were calculated. Univariate and multivariate logistic regression analyses were conducted. A receiver operator characteristic (ROC) curve was plotted to determine the best cutoff value for the number of variables to discriminate malignant lymph nodes. Results Significant differences were found between metastatic and benign lymph nodes with regard to all of the variables evaluated (P < .05). Logistic regression analysis revealed that size and echogenicity were the best combination of altered variables (odds ratio, 40.080 and 7.288, respectively) in discriminating malignancy. The ROC curve analysis showed that 4 was the best cutoff value for the number of altered variables to discriminate malignant lymph nodes, with a combined specificity of 85.7%, sensitivity of 96.4%, and efficiency of 91.0%. Conclusion Greater diagnostic accuracy was achieved by associating the ultrasonographic variables assessed rather than by considering them individually.
Poster: Communication in Open-Source Projects–End of the E-mail Era?

Communication is essential in software engineering. Especially in distributed open-source teams, communication needs to be supported by channels including mailing lists, forums, issue trackers, and chat systems. Yet, we do not have a clear understanding of which communication channels stakeholders in open-source projects use. In this study, we fill the knowledge gap by investigating a statistically representative sample of 400 GitHub projects. We discover the used communication channels by regular expressions on project data. We show that (1) half of the GitHub projects use observable communication channels; (2) GitHub Issues, e-mail addresses, and the modern chat system Gitter are the most common channels; (3) mailing lists are only in place five and have a lower market share than all modern chat systems combined.
Vascular smooth muscle contraction in hypertension

Abstract Hypertension is a major risk factor for many common chronic diseases, such as heart failure, myocardial infarction, stroke, vascular dementia, and chronic kidney disease. Pathophysiological mechanisms contributing to the development of hypertension include increased vascular resistance, determined in large part by reduced vascular diameter due to increased vascular contraction and arterial remodelling. These processes are regulated by complex-interacting systems such as the renin-angiotensin-aldosterone system, sympathetic nervous system, immune activation, and oxidative stress, which influence vascular smooth muscle function. Vascular smooth muscle cells are highly plastic and in pathological conditions undergo phenotypic changes from a contractile to a proliferative state. Vascular smooth muscle contraction is triggered by an increase in intracellular free calcium concentration ([Ca2+]i), promoting actin–myosin cross-bridge formation. Growing evidence indicates that contraction is also regulated by calcium-independent mechanisms involving RhoA-Rho kinase, protein Kinase C and mitogen-activated protein kinase signalling, reactive oxygen species, and reorganization of the actin cytoskeleton. Activation of immune/inflammatory pathways and non-coding RNAs are also emerging as important regulators of vascular function. Vascular smooth muscle cell [Ca2+]i not only determines the contractile state but also influences activity of many calcium-dependent transcription factors and proteins thereby impacting the cellular phenotype and function. Perturbations in vascular smooth muscle cell signalling and altered function influence vascular reactivity and tone, important determinants of vascular resistance and blood pressure. Here, we discuss mechanisms regulating vascular reactivity and contraction in physiological and pathophysiological conditions and highlight some new advances in the field, focusing specifically on hypertension.
Driving information logger with in-vehicle communication for autonomous vehicle research

In this paper, we describe in detail the driving information logging used in developing an autonomous vehicle. The recorded vehicle information is used to identify the cause of problems in the system or undesired operations. Driving information logging can be used in many areas such as analysis of problems in the study of autonomous driving system and analysis of accident risk.
Clinical Practice and Epidemiology in Mental Health Asthma and Depression: a Pragmatic Review of the Literature and Recommendations for Future Research

Background: Although the association between asthma and psychosocial factors has long been recognised, it is only in the last decade that the impact of coexisting asthma and depression has become the focus of considerable research interest. However, the findings so far have been confusing and often contradictory. This paper sets out a methodical review and appraisal of the literature to date, including suggestions for future research.
Quantitative Receptor Autoradiography

This collection of writings reflects the author's unique capacity to choose a topic, to mull over it gracefully, and to evoke the perplexing nature of a number of fundamental notions (and the sentiments which these themes engender) regarding the human experience, i.e., life and death. While the writing style and diction are often in and of themselves as complex and intricate as any textbook description of a pathologic process, the expansive spectrum of queries and conclusions which Gonzalez-Crussi presents are gossamer-like and continually uplift the reader and nourish the spirit.