Miracle-dz/UniFAR-FTUs huggingface dataset:
Invasion Genetics of the Western Flower Thrips in China: Evidence for Genetic Bottleneck, Hybridization and Bridgehead Effect

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. F. occidentalis, which is endemic to North America, was initially detected in Kunming in southwestern China in 2000 and since then it has rapidly invaded several other localities in China where it has greatly damaged greenhouse vegetables and ornamental crops. Controlling this invasive pest in China requires an understanding of its genetic makeup and migration patterns. Using the mitochondrial COI gene and 10 microsatellites, eight of which were newly isolated and are highly polymorphic, we investigated the genetic structure and the routes of range expansion of 14 F. occidentalis populations in China. Both the mitochondrial and microsatellite data revealed that the genetic diversity of F. occidentalis of the Chinese populations is lower than that in its native range. Two previously reported cryptic species (or ecotypes) were found in the study. The divergence in the mitochondrial COI of two Chinese cryptic species (or ecotypes) was about 3.3% but they cannot be distinguished by nuclear markers. Hybridization might produce such substantial mitochondrial-nuclear discordance. Furthermore, we found low genetic differentiation (global F ST = 0.043, P<0.001) among all the populations and strong evidence for gene flow, especially from the three southwestern populations (Baoshan, Dali and Kunming) to the other Chinese populations. The directional gene flow was further supported by the higher genetic diversity of these three southwestern populations. Thus, quarantine and management of F. occidentalis should focus on preventing it from spreading from the putative source populations to other parts of China.
ReliaCloud‐NS: A scalable web‐based simulation platform for evaluating the reliability of cloud computing systems

This paper discusses the implementation, architecture, and use of a graphical web‐based application called ReliaCloud‐NS that allows users to (1) evaluate the reliability of a cloud computing system (CCS) and (2) design a CCS to a specified reliability level for both public and private clouds. The software was designed with a RESTful application programming interface for performing nonsequential Monte Carlo simulations to perform reliability evaluations of a CCS. Simulation results are stored and presented to the user in the form of interactive charts and graphs from within a web browser. The software contains multiple types of CCS components, simulations, and virtual machine allocation schemes. ReliaCloud‐NS also contains a novel feature that evaluates CCS reliability across a range of varying virtual machine allocations and establishes and graphs a CCS reliability curve. This paper discusses the software architecture, the interactive web‐based interface, and the different types of simulations available in ReliaCloud‐NS and presents an overview of the results generated from a simulation.
Columbia-Jadavpur submission for EMNLP 2016 Code-Switching Workshop Shared Task: System description

We describe our present system for language identiﬁcation as a part of the EMNLP 2016 Shared Task. We were provided with the Spanish-English corpus composed of tweets. We have employed a predictor-corrector algo-rithm to accomplish the goals of this shared task and analyzed the results obtained.
The regulation of human mesenchymal stem cell chondrogenesis through multiaxial load

The repair of damaged articular cartilage remains a clinical problem despite the development of numerous surgical approaches for cartilage regeneration. As result new options for therapeutic approaches are being sought. One of the candidate cell types for cartilage repair are mesenchymal stem cells (MSCs). These cells can be isolated from a number of different tissues and have the ability to differentiate down several different mesenchymal lineages. This thesis focused on the use of MSCs for repairing damaged articular cartilage. Specifically I investigated the effect of producing regenerative medicine type constructs containing different populations of MSCs on the induction of chondrogenesis in response to mechanical load, compared the induction of chondrogenesis in MSCs through the application of exogenous TGF-β1 and multiaxial mechanical load and identified potentially novel markers of MSC chondrogenesis. The results presented in this thesis show that the induction of chondrogenesis in MSCs can be manipulated by producing constructs that contain separate populations of MSCs. The work demonstrated that seeding a layer of MSCs on the loaded surface of a fibrin-poly(ester-urethane) scaffold could increase the deposition of histologically detectable matrix. However, it was not possible to determine the mechanism responsible for this. Comparison of the secretomes of MSCs stimulated with TGF-β1 and mechanical load showed that these two forms of chondrogenic stimulation are not analogous and that a number of markers, including GRO and MMP13 may be useful for monitoring the progression of MSCs through chondrogenesis and hypertrophy. These data provide further insights into the effect of joint-like load on MSCs within tissue engineering/regenerative medicine style constructs, and the chondrogenic response of MSCs to this stimulation, which may prove to be useful for the development of constructs for cartilage repair.
Intracellular calcium increases in vascular smooth muscle cells with progression of chronic kidney disease in a rat model

Background: Vascular smooth muscle cells (VSMCs) exhibit phenotypic plasticity, promoting vascular calcification and increasing cardiovascular risk. Changes in VSMC intracellular calcium ([Ca2+]i) are a major determinant of plasticity, but little is known about changes in [Ca2+]i in chronic kidney disease (CKD). We have previously demonstrated such plasticity in aortas from our rat model of CKD and therefore sought to examine changes in [Ca2+]i during CKD progression. Materials and Methods: We examined freshly isolated VSMCs from aortas of normal rats, Cy/+ rats (CKD) with early and advanced CKD, and advanced CKD rats treated without and with 3% calcium gluconate (CKD + Ca2+) to lower parathyroid hormone (PTH) levels. [Ca2+]i was measured with fura‐2. Results: Cy/+ rats developed progressive CKD, as assessed by plasma levels of blood urea nitrogen, calcium, phosphorus, parathyroid hormone and fibroblast growth factor 23. VSMCs isolated from rats with CKD demonstrated biphasic alterations in resting [Ca2+]i: VSMCs from rats with early CKD exhibited reduced resting [Ca2+]i, while VSMCs from rats with advanced CKD exhibited elevated resting [Ca2+]i. Caffeine‐induced sarcoplasmic reticulum (SR) Ca2+ store release was modestly increased in early CKD and was more drastically increased in advanced CKD. The advanced CKD elevation in SR Ca2+ store release was associated with a significant increase in the activity of the sarco‐endoplasmic reticulum Ca2+ ATPase (SERCA); however, SERCA2a protein expression was decreased in advanced CKD. Following SR Ca2+ store release, recovery of [Ca2+]i in the presence of caffeine and extracellular Ca2+ was attenuated in VSMCs from rats with advanced CKD. This impairment, together with reductions in expression of the Na+/Ca2+ exchanger, suggest a reduction in Ca2+ extrusion capability. Finally, store‐operated Ca2+ entry (SOCE) was assessed following SR Ca2+ store depletion. Ca2+ entry during recovery from caffeine‐induced SR Ca2+ store release was elevated in advanced CKD, suggesting a role for exacerbated SOCE with progressing CKD. Conclusions: With progressive CKD in the Cy/+ rat there is increased resting [Ca2+]i in VSMCs due, in part, to increased SOCE and impaired calcium extrusion from the cell. Such changes may predispose VSMCs to phenotypic changes that are a prerequisite to calcification.
Fluorescence-Reported Allelic Exchange Mutagenesis Reveals a Role for Chlamydia trachomatis TmeA in Invasion That Is Independent of Host AHNAK

ABSTRACT Development of approaches to genetically manipulate Chlamydia is fostering important advances in understanding pathogenesis. Fluorescence-reported allelic exchange mutagenesis (FRAEM) now enables the complete deletion of specific genes in C. trachomatis L2. We have leveraged this technology to delete the coding sequences for a known type III effector. The evidence provided here indicates that CT694/CTL0063 is a virulence protein involved in chlamydial invasion. Based on our findings, we designate the gene product corresponding to ct694-ctl0063translocated membrane-associated effector A (TmeA). Deletion of tmeA did not impact development of intracellular chlamydiae. However, the absence of TmeA manifested as a decrease in infectivity in both tissue culture and murine infection models. The in vitro defect was reflected by impaired invasion of host cells. TmeA binds human AHNAK, and we demonstrate here that AHNAK is transiently recruited by invading chlamydiae. TmeA, however, is not required for endogenous AHNAK recruitment. TmeA also impairs AHNAK-dependent actin bundling activity. This TmeA-mediated effect likely does not explain impaired invasion displayed by the tmeA strain of Chlamydia, since AHNAK-deficient cells revealed no invasion phenotype. Overall, our data indicate the efficacy of FRAEM and reveal a role of TmeA during chlamydial invasion that manifests independently of effects on AHNAK.
Hepatocyte Differentiation from Human ES Cells using the Simple Embryoid Body Formation Method and the Staged-Additional Cocktail

To induce hepatocytes from human embryonic stem (hES) cells easily and effectively, a simple suspension culture method that separates ES colonies with a scraper and transfers them into newly developed, nonadherent MPC (2-methacryloyloxyethyl phosphorylcholine) plates, and the staged-additional cocktail method, including growth factors, cytokines, and Lanford serum-free medium, were developed and evaluated mainly by morphological analysis. The formed embryoid bodies (EBs) showed compact cellular agglomeration until day 4 and later formed coeloms in their interior. RT-PCR (reverse transcriptase-polymerase chain reaction) analysis showed that they are gene markers of the three germ layers. Mesenchymal cells with rough endoplasmic reticulum (rER) and extracellular matrix (ECM), and without junctions, were recognized in the interior of the EBs by transmission electron microscopy (TEM) in addition to epithelial cells. When they were stimulated by the staged-additional cocktail, they expressed albumin-positive immunoreactivity, indocyanine green (ICG) uptake, and typical ultrastructures of the hepatocytes, including bile canaliculi. These results indicate that these combined methods promote EB formation and hepatocyte differentiation from hES cells.
Effects of Noise Bandwidth and Amplitude Modulation on Masking in Frog Auditory Midbrain Neurons

Natural auditory scenes such as frog choruses consist of multiple sound sources (i.e., individual vocalizing males) producing sounds that overlap extensively in time and spectrum, often in the presence of other biotic and abiotic background noise. Detection of a signal in such environments is challenging, but it is facilitated when the noise shares common amplitude modulations across a wide frequency range, due to a phenomenon called comodulation masking release (CMR). Here, we examined how properties of the background noise, such as its bandwidth and amplitude modulation, influence the detection threshold of a target sound (pulsed amplitude modulated tones) by single neurons in the frog auditory midbrain. We found that for both modulated and unmodulated masking noise, masking was generally stronger with increasing bandwidth, but it was weakened for the widest bandwidths. Masking was less for modulated noise than for unmodulated noise for all bandwidths. However, responses were heterogeneous, and only for a subpopulation of neurons the detection of the probe was facilitated when the bandwidth of the modulated masker was increased beyond a certain bandwidth – such neurons might contribute to CMR. We observed evidence that suggests that the dips in the noise amplitude are exploited by TS neurons, and observed strong responses to target signals occurring during such dips. However, the interactions between the probe and masker responses were nonlinear, and other mechanisms, e.g., selective suppression of the response to the noise, may also be involved in the masking release.
Title Total Dual Integrality in Some Facility Location Problems

Facility location, arising in a rich variety of applications, has been studied extensively in the fields of operations research and computer science. In this paper we consider the classical uncapacitated facility location problem and its “prize-collecting” variant introduced by Bäıou and Barahona, and we show that the linear systems associated with these problems are totally dual integral if and only if the input graphs do not contain a certain type of odd cycles. As corollaries, we get structural characterizations of two min-max relations on facility location. Our results strengthen the integrality theorems on facility location polytopes proved by Bäıou and Barahona; our proofs lead to combinatorial polynomial-time algorithms for the facility location problems that we consider.
Pim kinase inhibition sensitizes FLT3-ITD acute myeloid leukemia cells to topoisomerase 2 inhibitors through increased DNA damage and oxidative stress

Internal tandem duplication of fms-like tyrosine kinase-3 (FLT3-ITD) is frequent (30 percent) in acute myeloid leukemia (AML), and is associated with short disease-free survival following chemotherapy. The serine threonine kinase Pim-1 is a pro-survival oncogene transcriptionally upregulated by FLT3-ITD that also promotes its signaling in a positive feedback loop. Thus inhibiting Pim-1 represents an attractive approach in targeting FLT3-ITD cells. Indeed, co-treatment with the pan-Pim kinase inhibitor AZD1208 or expression of a kinase-dead Pim-1 mutant sensitized FLT3-ITD cell lines to apoptosis triggered by chemotherapy drugs including the topoisomerase 2 inhibitors daunorubicin, etoposide and mitoxantrone, but not the nucleoside analog cytarabine. AZD1208 sensitized primary AML cells with FLT3-ITD to topoisomerase 2 inhibitors, but did not sensitize AML cells with wild-type FLT3 or remission bone marrow cells, supporting a favorable therapeutic index. Mechanistically, the enhanced apoptosis observed with AZD1208 and topoisomerase 2 inhibitor combination treatment was associated with increased DNA double-strand breaks and increased levels of reactive oxygen species (ROS), and co-treatment with the ROS scavenger N-acetyl cysteine rescued FLT3-ITD cells from AZD1208 sensitization to topoisomerase 2 inhibitors. Our data support testing of Pim kinase inhibitors with topoisomerase 2 inhibitors, but not with cytarabine, to improve treatment outcomes in AML with FLT3-ITD.
Classification and gender recognition from veiled-faces

This study aims to investigate to what extent a computer system can identify veiled-human and recognise gender using eyes and the uncovered part of the face. For the purpose of this study, we have created a new veiled persons image (VPI) database shot using a mobile phone camera, imaging 100 different veiled-persons over two sessions. After preprocessing and segmentation we used a fused method for feature extraction. The fusion occurs between geometrical (edge ratio) and textural (probability density function of the colour moments) features. The experimental results using different classifiers were ranging from 88:63% to 97:22% for person identification accuracy before feature selection and up to 97:55% after feature selection. The proposed method achieved up to 99:41% success rate for gender classification.
The Development of Producing Expanded Graphite Via Chemical Oxidization Method

The development of graphite materials,oxidant,extrusion temperature and expanded method of chemical oxidization method are analyzed.Then putting forward the expanded graphite research direction: fine crystalline flake graphite is used to prepare the the high rate of low sulfur and even without sulfur low temperature expanded graphite in little even without sulfuric acid and low extrusion temperature.
CMOL implementation of spiking neurons and spike‐timing dependent plasticity

Successful implementation of spiking neural networks onto CMOS‐Molecular (CMOL) architecture has already been proposed, but the ability of dynamic learning has not yet been addressed. Here, we propose a spiking neural topology with spike‐timing‐dependent learning ability and provide its basic building blocks that are easily mapped onto CMOL architecture. The learning method modifies state of synaptic switches, using spatially and temporally local information which is available at the synapse when state modification is performed.
The Candida albicans Ku70 Modulates Telomere Length and Structure by Regulating Both Telomerase and Recombination

The heterodimeric Ku complex has been shown to participate in DNA repair and telomere regulation in a variety of organisms. Here we report a detailed characterization of the function of Ku70 in the diploid fungal pathogen Candida albicans. Both ku70 heterozygous and homozygous deletion mutants have a wild-type colony and cellular morphology, and are not sensitive to MMS or UV light. Interestingly, we observed complex effects of KU70 gene dosage on telomere lengths, with the KU70/ku70 heterozygotes exhibiting slightly shorter telomeres, and the ku70 null strain exhibiting long and heterogeneous telomeres. Analysis of combination mutants suggests that the telomere elongation in the ku70 null mutant is due mostly to unregulated telomerase action. In addition, elevated levels of extrachromosomal telomeric circles were detected in the null mutant, consistent with activation of aberrant telomeric recombination. Altogether, our observations point to multiple mechanisms of the Ku complex in telomerase regulation and telomere protection in C. albicans, and reveal interesting similarities and differences in the mechanisms of the Ku complex in disparate systems.
A Stretchable Alternating Current Electroluminescent Fiber

Flexible, stretchable electroluminescent fibers are of significance to meet the escalating requirements of increasing complexity and multifunctionality of smart electronics. We report a stretchable alternating current electroluminescent (ACEL) fiber by a low-cost and all solution-processed scalable process. The ACEL fiber provides high stretchability, decent light-emitting performance, with excellent stability and nearly zero hysteresis. It can be stretched up to 80% strain. Our ACEL fiber device maintained a stable luminance for over 6000 stretch-release cycles at 50% strain. The mechanical stretchability and optical stability of our ACEL fiber device provides new possibilities towards next-generation stretchable displays, electronic textiles, advanced biomedical imaging and lighting, conformable visual readouts in arbitrary shapes, and novel health-monitoring devices.
Classification of respiratory disturbances in Rett Syndrome patients using Restricted Boltzmann Machine

Rett syndrome (RTT) is a severe neurodevelopmental disorder that can cause pervasive wakeful respiratory disturbances that include tachypnea, breath-holding, and central apnea. Quantitative analysis of these respiratory disturbances in RTT is considered a promising outcome measure for clinical trials. Currently, machine learning methodologies have not been employed to automate the classification of RTT respiratory disturbances. In this paper, we propose using temporal, flow, and autocorrelation features taken from the respiratory inductance plethsymography chest signal. We tested the performance of six classifiers including: Support Vector Machine, Restricted-Boltzmann-Machine, Back-propagation, Levenberg-Marquardt, and Decision-Fusion. We evaluate this classification in two modalities: (1) a subject-independent modality (leave-one-subject-out) obtaining the best F1 score in 93.67%, and (2) a trial-independent modality (leave-one-trial-out per subject) obtaining the best F1 score in 78.21%.
Genetic diversity and promising crosses indication in lima bean (Phaseolus lunatus) accessions

O feijao-fava e uma alternativa de renda para a populacao rural do Nordeste do Brasil, que consome seus graos verdes ou maduros. Nessa regiao, todo germoplasma utilizado pelos agricultores e originario de seus proprios cultivos havendo intercâmbio de sementes entre comunidades rurais. O conhecimento sobre a diversidade genetica tem proporcionado importantes contribuicoes no gerenciamento de bancos de germoplasmas e na conservacao de recursos geneticos. Neste trabalho, objetivou-se estimar a diversidade genetica entre vinte quatro acessos de feijao-fava do Banco Ativo de Germoplasma (BAG) da Universidade Federal do Piaui (UFPI), com base em descritores morfoagronomicos. O experimento foi conduzido em condicoes de campo, em latice com quatro repeticoes e dez plantas por parcela, no periodo de fevereiro a agosto de 2009, sendo utilizados sete descritores qualitativos e seis quantitativos. Para os caracteres quantitativos foram formados quatro grupos pelos metodos de Tocher e UPGMA, enquanto que para os qualitativos formaram-se tres grupos pelo metodo de Tocher e seis pelo UPGMA. O carater que mais contribuiu para divergencia genetica (35,23%) foi largura da vagem. UFPI-220 produziu grande numero de vagens por planta, caracteristica importante na identificacao de acessos potencialmente produtivos. Ha expectativa de combinacao promissora entre UFPI-220 x UFPI-468, em virtude da maior dissimilaridade observada e do melhor desempenho medio desses acessos.
TRAIL/TRAIL Receptor System and Susceptibility to Multiple Sclerosis

The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation. It is able to inhibit proliferation and activation of T cells and to induce apoptosis of neurons and oligodendrocytes, and seems to be implicated in autoimmune diseases. Thus, TRAIL and TRAIL receptor genes are potential candidates for involvement in susceptibility to multiple sclerosis (MS). To test whether single-nucleotide polymorphisms (SNPs) in the human genes encoding TRAIL, TRAILR-1, TRAILR-2, TRAILR-3 and TRAILR-4 are associated with MS susceptibility, we performed a candidate gene case-control study in the Spanish population. 59 SNPs in the TRAIL and TRAIL receptor genes were analysed in 628 MS patients and 660 controls, and validated in an additional cohort of 295 MS patients and 233 controls. Despite none of the SNPs withstood the highly conservative Bonferroni correction, three SNPs showing uncorrected p values<0.05 were successfully replicated: rs4894559 in TRAIL gene, p = 9.8×10−4, OR = 1.34; rs4872077, in TRAILR-1 gene, p = 0.005, OR = 1.72; and rs1001793 in TRAILR-2 gene, p = 0.012, OR = 0.84. The combination of the alleles G/T/A in these SNPs appears to be associated with a reduced risk of developing MS (p = 2.12×10−5, OR = 0.59). These results suggest that genes of the TRAIL/TRAIL receptor system exerts a genetic influence on MS.