Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a PCR methodology to distinguish species members of Culex vishnui subgroup (Diptera: Culicidae), based on DNA Barcodes

“DNA Barcoding” has emerged as a very efficient tool for species identification of diverse group of animals and plants (Stoeckle & Hebert, 2008). This methodology was proposed as a universal approach for species identification about a decade back (Hebert et al, 2003). Realizing its importance towards description of global biodiversity, a global consortium of DNA Barcoding of life (CBOL) was launched under the auspices of the Smithsonian Institution, U.S.A. and about 0.175 million species of plants and animals have been DNA barcoded so far, globally (Barcode of life data systems [BOLD]) (Ratnasingham & Hebert, 2007). Utility of DNA Barcoding methodology for species identification of economically important insects, the mosquitoes have been recorded (Cywinska et al., 2006; Kumar et al., 2007; Kumar et al., 2009; Rajavel et al., 2015). Culex vishnui subgroup of mosquitoes prevalent in Southeast Asian countries are important vectors of arboviral diseases such as Japanese encephalitis, Chandipura virus, etc. Three major species of this subgroup Culex vishnui, Culex pseudovishnui, and Culex tritaeniorhynchus are reported to be prevalent in India (Reuben et al., 1969; Sirivanakarn, 1975). The taxonomic identification of these species had been extremely difficult or impossible in adult stages and the larval exuviae were normally used for the same (Bram, 1967). Later, Reuben et al. (1994) described adult morphological characteristics, towards their species identification. However, these being very minute (scale distribution and color of the proboscis,
Transparent nanostructured metal oxides for chemical biosensors: towards point-of-care environments

Existe una creciente necesidad de desarrollar sistemas de punto de cuidado (POC) innovadores, versatiles y de bajo coste, capaces de detectar enfermedades en estadios de desarrollo tempranos. Un sistema POC consiste en un biosensor integrado en un sistema electronico y eventualmente un sistema microfluidico que gestione las muestras de fluidos biologicos. El objetivo general de esta tesis es investigar distintas posibilidades de mejorar la tecnologia POC. Los sistemas biosensores actualmente integrados en sistemas POC son limitados, y requieren de metodos que se apoyen en un potente sistema electronico. Para esto, se requiere por un lado de sustratos adecuados que permitan tanto el acoplo de biomoleculas como la deteccion de reacciones quimicas ocurridas en su superficie; por otro lado, es necesaria una potente circuiteria electronica que pueda ser miniaturizada y de bajo consumo. Los biosensores electroquimicos y opticos han tomado mucha relevancia en sistemas POC debido a su alta sensibilidad y especificidad, aunque estas pueden verse gravemente afectadas por la miniaturizacion de los dispositivos. Por ello, la elevada relacion superficie-volumen que presentan las nanoestructuras las hace especialmente interesantes para biodeteccion. En esta tesis, se propone el oxido de indio dopado con estano (ITO) nanoestructurado como material de electrodo de trabajo en biosensores electroquimicos. En la primera parte de esta tesis se han estudiado las propiedades del ITO, y se ha caracterizado electrica, optica, electroquimica y estructuralmente, a partir de muestras preparadas sobre silicio y sobre vidrio mediante evaporacion por haz de electrones. Se ha estudiado su interaccion con moleculas crosslinkers, y se han realizado varios inmunoensayos usando el ITO nanoestructurado como sustrato. Se han estudiado distintos mecanismos de medida de sensores electroquimicos; por espectroscopia de impedancias se han detectado distintas concentraciones del biomarcador TNF-a. Se ha disenado la electronica necesaria para realizar medidas de amperometria con dos electrodos, asi como de potenciometria, ensayando este ultimo sistema con ITO nanoestructurado y modificado sensible a cambios de pH. En sintesis, esta tesis recoge algunas propuestas para la mejora de los sistemas POC actuales, tanto en la cuestion biosensora como en la parte electronica, usando para las medidas y pruebas de concepto un biomarcador importante en el ambito biomedico.
A TOP at the Synapse

Editor's Note: These short reviews of a recent paper in the Journal, written exclusively by graduate students or postdoctoral fellows, are intended to mimic the journal clubs that exist in your own departments or institutions. For more information on the format and purpose of the Journal Club, please see Review of Huang et al. 5ЈTOP mRNA species contain a short 5Ј Tract rich in OligoPyrimidines that encode for translation factors and vertebrate ribosomal protein subunits. Because 5ЈTOP mRNAs are rapidly translated, they are attractive candidates for dendriti-cally localized molecules that could enhance protein synthesis in activated syn-apses, leading to the expression of long-term plasticity. The 5ЈTOP-encoded protein eukaryotic elongation factor 1A (eEF1A, also known as EF1␣) is an essential factor that joins aminoacyl-tRNA to the ribosome during translation. Interestingly , eEF1A performs many extratransla-tional functions including the binding of mRNA transcripts and bundling of fila-mentous actin (F-actin) (Liu et al., 2002). Notably, eEF1A mRNA is transported and docked to activated synapses during long-term facilitation in Aplysia, and the synthesis of eEF1A coincides with the maintenance phase of plasticity (Giu-stetto et al.acterize the localization of eEF1A transcript and protein in models of mamma-lian synaptic plasticity. The authors began their studies by examining the basal expression of eEF1A mRNA in the brain. eEF1A transcript was observed to be ubiquitously expressed. Although neuronal somata were highly enriched , only specific dendritic regions expressed moderate levels of the transcript [Huang et al. In contrast to other known dendritic mRNAs, a developmental decline of eEF1A transcript levels in synaptic terminals was observed. This suggests that eEF1A mRNA is restricted to subserve specific types of synaptic activation in the developing and adult brain. To evaluate eEF1A transcript distribution during synaptic activation, a long-term potentiation (LTP)-inducing protocol known to cause induction and subsequent transport of Arc mRNA, a dendritically translated transcript, to the middle molecular layers of the dentate gy-rus (DG) was used. Although changes were described for Arc, no alterations in eEF1A transcripts could be detected in the DG [Huang et al. (2005), their Fig. 4 Similarly, treatment of dendritic laminas with the group I metabotropic glutamate receptor (mGluR) agonist (R, S)-3,5-dihydroxy-phenylglycine (DHPG), which induces long-term depression (LTD), did not alter eEF1A transcript distribution. It is important to consider that the in situ hybridiza-tion techniques used in these experiments are appropriate for the detection of robust signals, and that, as the authors acknowledge , microcellular changes …
High Prevalence of Hyperuricemia and Gout inNorth American Patients with IgA Nephropathy

Objectives: To determine the prevalence of hyperuricemia (HU) and gout in 153 adult IgAN patients in North America (NA) and to compare this with the prevalence in the USA general population and with IgAN patients in Asia and Europe. Methods: Serum creatinine and serum uric acid (SUA) concentrations were measured in a central laboratory. Estimated glomerular filtration rates (eGFR) were determined in 109 of the patients and the prevalence of HU (SUA>7 mg/dl in men; >5.7 mg/dl in women) was correlated with chronic kidney disease (CKD) Stages 1 (eGFR ≥ 90 ml/min/1.73m2), 2 (eGFR 60-89 ml/min/1.73m2), 3 (eGFR 30-59 ml/min/1.73m2), and 4 (eGFR<30ml/min/1.73m2). Results: Seven patients (all males with a median age 50 years, range 33-63 years), who had been diagnosed with gout, were receiving allopurinol. The SUA levels in these patients were not used in defining the prevalence of HU. They all had reduced eGFRs (30-90 ml/min/1.73m2). HU was detected in 96 (65.8%) of the other 146 patients. SUA was >9mg/dl in 30 of these patients. HU was present in 43.2% of CKD1 patients; 67.6% of CKD2 patients, 85.7% of CKD3 patients, and both of the two CKD4 patients. Conclusions: Persistent HU and gout occur more frequently in IgAN patients in NA compared with the general population and with IgAN patients in other parts of the world.
Constraint-Based Entity Matching

Entity matching is the problem of deciding if two given mentions in the data, such as "Helen Hunt" and "H. M. Hunt", refer to the same real-world entity. Numerous solutions have been developed, but they have not considered in depth the problem of exploiting integrity constraints that frequently exist in the domains. Examples of such constraints include "a mention with age two cannot match a mention with salary 200K" and "if two paper citations match, then their authors are likely to match in the same order". In this paper we describe a probabilistic solution to entity matching that exploits such constraints to improve matching accuracy. At the heart of the solution is a generative model that takes into account the constraints during the generation process, and provides well-defined interpretations of the constraints. We describe a novel combination of EM and relaxation labeling algorithms that efficiently learns the model, thereby matching mentions in an unsupervised way, without the need for annotated training data. Experiments on several real-world domains show that our solution can exploit constraints to significantly improve matching accuracy, by 3-12% F-1, and that the solution scales up to large data sets.
Environmental Endocrine-Disrupting Chemical Exposure: Role in Non-Communicable Diseases

The exponential growth of pollutant discharges into the environment due to increasing industrial and agricultural activities is a rising threat for human health and a biggest concern for environmental health globally. Several synthetic chemicals, categorized as potential environmental endocrine-disrupting chemicals (EDCs), are evident to affect the health of not only livestock and wildlife but also humankind. In recent years, human exposure to environmental EDCs has received increased awareness due to their association with altered human health as documented by several epidemiological and experimental studies. EDCs are associated with deleterious effects on male and female reproductive health; causes diabetes, obesity, metabolic disorders, thyroid homeostasis and increase the risk of hormone-sensitive cancers. Sewage effluents are a major source of several EDCs, which eventually reach large water bodies and potentially contaminate the drinking water supply. Similarly, water storage material such as different types of plastics also leaches out EDCs in drinking Water. Domestic wastewater containing pharmaceutical ingredients, metals, pesticides and personal care product additives also influences endocrine activity. These EDCs act via various receptors through a variety of known and unknown mechanisms including epigenetic modification. They differ from classic toxins in several ways such as low-dose effect, non-monotonic dose and trans-generational effects. This review aims to highlight the hidden burden of EDCs on human health and discusses the non-classical toxic properties of EDCs in an attempt to understand the magnitude of the exposome on human health. Present data on the environmental EDCs advocate that there may be associations between human exposure to EDCs and several undesirable health outcomes that warrants further human bio-monitoring of EDCs.
Protein expression after gingival injection of messenger RNA encoding platelet-derived growth factor-bb in ligature-induced rat periodontitis

As a new class of medicines, mRNA platform has proven to be safe and effective. The objective of this study was to investigate the effect of local inflammation on platelet derived growth factor-BB (PDGF-BB) expression after gingival injection of PDGF-BB mRNA in lipid nanoparticles (LNPs) in ligature-induced rat periodontitis and to examine the dose-dependent effect of gingival delivery of mRNA. �3-0 silk was placed around maxillary left second molar for two weeks and removed, while the corresponding molar on the right was non-ligated. Under stereomicroscope, a significant bone loss at ligature sites was observed as compared to the non-ligature sites, indicating established periodontitis. However, there were no differences in inflammatory cytokine levels (IL-1? , TNF-? and IL-17a) and cellular infiltrates between the two sites. The local inflammation may occur at earlier time point in this ligature model. Different doses of PDGF-BB mRNA (low (3 ? g), medium (10 ? g), high (30 ? g)),�DPBS (control) and LNPs alone were injected into palatal gingiva upon ligature removal. After 24 hour of mRNA delivery, we found high levels of translated PDGF-BB protein at both ligature and non-ligature sites, demonstrating a trend of dose response. �In addition, some amount of inflammatory cytokine including IL-1? , and IL-17a was detected. In conclusion, this study of 24 hour-local delivery of PDGF mRNA-LNPs into gingiva using ligature-induced rat periodontitis model results in high translated PDGF protein. Even though, local gingival inflammation was not detected in this established periodontitis model, this model may be useful for future testing of mRNA therapeutic effects.
Observing the Effects of Mindfulness-Based Meditation on Anxiety and Depression in Chronic Pain Patients

Background: People whose chronic pain limits their independence are especially likely to become anxious and depressed. Mindfulness training has shown promise for stress-related disorders. Methods: Chronic pain patients who complained of anxiety and depression and who scored higher than moderate in the Hamilton Depression Rating Scale (HDRS) and Hospital Anxiety and Depression Scale (HADS) as well as moderate in Quality of Life Scale (QOLS) were observed for eight weeks, three days a week for an hour of Mindfulness Meditation training with an hour daily home Mindfulness Meditation practice. Pain was evaluated on study entry and completion, and patients were given the Patients’ Global Impression of Change (PGIC) to score at the end of the training program. Results: Forty-seven (47) patients completed the Mindfulness Meditation Training program. Over the year-long observation, patients demonstrated noticeable improvement in depression, anxiety, pain, and global impression of change. Conclusions: Chronic pain patients who suffer with anxiety and depression may benefit from incorporating Mindfulness Meditation into their treatment plans.
Hierarchical Cooperative Tracking of Vehicles and People Using Laser Scanners Mounted on Multiple Mobile Robots

—This paper presents a tracking (estimation of the pose and size) of moving objects such as pedestrians, cars, motorcycles, and bicycles, using multiple mobile robots as sensor nodes. In this cooperative-tracking method, nearby sensor nodes share their tracking information, enabling the tracking of objects that are invisible or partially visible to an individual sensor node. The cooperative-tacking method can then make the tracking system more reliable than the conventional individual tracking method by a single robot. We previously presented a centralized architecture of cooperative tracking. Each sensor node detected moving objects in its own laser-scanned images captured by a single-layer laser scanner. It then sent measurement information related to the moving objects to a central server. The central server estimated the objects’ poses (positions and velocities) and sizes from the measurement information using Bayesian filter. However, such a centralized method might have poor dependability and impose a computational burden upon the central server. To address this problem, this paper presents hierarchical architecture of cooperative tracking. Each sensor node locally estimates the poses and sizes of moving objects and then sends these estimates to the central server, which then merges the pose and size estimates. Experimental results using two sensor nodes in outdoor environments show that the proposed hierarchical cooperative-tracking method provides slightly inferior tracking accuracy and has a smaller computational cost in the central server than a previous centralized method.
A reciprocating twin-channel model for ABC transporters

Abstract ABC transporters comprise a large, diverse, and ubiquitous superfamily of membrane active transporters. Their core architecture is a dimer of dimers, comprising two transmembrane (TM) domains that bind substrate, and two ATP-binding cassettes, which use the cell's energy currency to couple substrate translocation to ATP hydrolysis. Despite the availability of over a dozen resolved structures and a wealth of biochemical and biophysical data, this field is bedeviled by controversy and long-standing mechanistic questions remain unresolved. The prevailing paradigm for the ABC transport mechanism is the Switch Model, in which the ATP-binding cassettes dimerize upon binding two ATP molecules, and thence dissociate upon sequential ATP hydrolysis. This cycle of nucleotide-binding domain (NBD) dimerization and dissociation is coupled to a switch between inward- or outward facing conformations of a single TM channel; this alternating access enables substrate binding on one face of the membrane and its release at the other. Notwithstanding widespread acceptance of the Switch Model, there is substantial evidence that the NBDs do not separate very much, if at all, and thus physical separation of the ATP cassettes observed in crystallographic structures may be an artefact. An alternative Constant Contact Model has been proposed, in which ATP hydrolysis occurs alternately at the two ATP-binding sites, with one of the sites remaining closed and containing occluded nucleotide at all times. In this model, the cassettes remain in contact and the active sites swing open in an alternately seesawing motion. Whilst the concept of NBD association/dissociation in the Switch Model is naturally compatible with a single alternating-access channel, the asymmetric functioning proposed by the Constant Contact model suggests an alternating or reciprocating function in the TMDs. Here, a new model for the function of ABC transporters is proposed in which the sequence of ATP binding, hydrolysis, and product release in each active site is directly coupled to the analogous sequence of substrate binding, translocation and release in one of two functionally separate substrate translocation pathways. Each translocation pathway functions 180° out of phase. A wide and diverse selection of data for both ABC importers and exporters is examined, and the ability of the Switch and Reciprocating Models to explain the data is compared and contrasted. This analysis shows that not only can the Reciprocating Model readily explain the data; it also suggests straightforward explanations for the function of a number of atypical ABC transporters. This study represents the most coherent and complete attempt at an all-encompassing scheme to explain how these important proteins work, one that is consistent with sound biochemical and biophysical evidence.
The Future of Creditor Protection Through Capital Maintenance Rules in European Company Law

Accounting-based profit distribution restrictions have been a key issue of the EU’s company law harmonisation efforts. At present, the concept of creditor protection via the maintenance of a minimum level of nominal capital is challenged in several respects: (i) With its recent rulings, the European Court of Justice has introduced corporate charter competition. Thus, domestic capital maintenance rules can no longer be enforced for all domestic limited liability companies. (ii) The move toward EU accounting harmonisation towards IAS/IFRS challenges the effectiveness of accounting-based creditor protection because the regulation of profit distribution is not an objective of the IAS/IFRS. (iii) Ongoing discussion focuses on abolishing capital maintenance rules in order to render EU company law more flexible. In this context, this paper provides an economic analysis, comparing the costs and benefits of accounting-based profit distribution to those of alternative rules, notably the solvency test. The efficiency of creditor protection rules is addressed as a problem of optimal precision of legal standards.
Detection of EXP1-Specific CD4+ T Cell Responses Directed Against a Broad Range of Epitopes Including Two Promiscuous MHC Class II Binders During Acute Plasmodium falciparum Malaria

Background: T cells are thought to play a major role in conferring immunity against malaria. This study aimed to comprehensively define the breadth and specificity of the Plasmodium falciparum (P. falciparum)-specific CD4+ T cell response directed against the exported protein 1 (EXP1) in a cohort of patients diagnosed with acute malaria. Methods: Peripheral blood mononuclear cells of 44 patients acutely infected with P. falciparum, and of one patient infected with P. vivax, were stimulated and cultured in vitro with an overlapping set of 31 P. falciparum-specific 13-17-mer peptides covering the entire EXP1 sequence. EXP1-specific T cell responses were analyzed by ELISPOT and intracellular cytokine staining for interferon-γ production after re-stimulation with individual peptides. For further characterization of the epitopes, in silico and in vitro human leukocyte antigen (HLA) binding studies and fine mapping assays were performed. Results: We detected one or more EXP1-specific CD4+ T cell responses (mean: 1.09, range 0–5) in 47% (21/45) of our patients. Responses were directed against 15 of the 31 EXP1 peptides. Peptides EXP1-P13 (aa60-74) and P15 (aa70-85) were detected by 18% (n = 8) and 27% (n = 12) of the 45 patients screened. The optimal length, as well as the corresponding most likely HLA-restriction, of each of these two peptides was assessed. Interestingly, we also identified one CD4+ T cell response against peptide EXP1-P15 in a patient who was infected with P. vivax but not falciparum. Conclusions: This first detailed characterization of novel EXP1-specific T cell epitopes provides important information for future analysis with major histocompatibility complex-multimer technology as well as for immunomonitoring and vaccine design.