Miracle-dz/UniFAR-FTUs huggingface dataset:
TRV – GFP : a modified Tobacco rattle virus vector for efficient and visualizable analysis of gene function

Virus-induced gene silencing (VIGS) is a useful tool for functional characterization of genes in plants. Unfortunately, the efficiency of infection by Tobacco rattle virus (TRV) is relatively low for some non-Solanaceae plants, which are economically important, such as rose (Rosa sp.). Here, to generate an easy traceable TRV vector, a green fluorescent protein (GFP) gene was tagged to the 3’ terminus of the coat protein gene in the original TRV2 vector, and the silencing efficiency of the modified TRV–GFP vector was tested in several plants, including Nicotiana benthamiana, Arabidopsis thaliana, rose, strawberry (Fragaria ananassa), and chrysanthemum (Dendranthema grandiflorum). The results showed that the efficiency of infection by TRV–GFP was equal to that of the original TRV vector in each tested plant. Spread of the modified TRV virus was easy to monitor by using fluorescent microscopy and a hand-held UV lamp. When TRV–GFP was used to silence the endogenous phytoene desaturase (PDS) gene in rose cuttings and seedlings, the typical photobleached phenotype was observed in 75–80% plants which were identified as GFP positive by UV lamp. In addition, the abundance of GFP protein, which represented the concentration of TRV virus, was proved to correlate negatively with the level of the PDS gene, suggesting that GFP could be used as an indicator of the degree of silencing of a target gene. Taken together, this work provides a visualizable and efficient tool to predict positive gene silencing plants, which is valuable for research into gene function in plants, especially for nonSolanaceae plants.
Evaluation of Volta-based DGX-1 System Using DNN Workloads

Multi-GPU systems are being widely used to train deep neural networks (DNNs) as GPUs can significantly reduce the training time. Data parallelism is a popular choice to train DNNs on a multi-GPU system. GPUs in a multi-GPU system repeatedly perform Forward Propagation (FP), Backward Propagation (BP) and, Weight Update (WU) to train a DNN. During the WU stage, GPUs communicate with each other. To improve communication time, different data transfer mechanisms and libraries have been introduced by NVIDIA, and adopted by high-level frameworks to train DNNs. We evaluate the use of two of the most popular communication methods (peer-to-peer (P2P) data transfer and NCCL library-based communication) for training DNNs on a DGX-1 multi-GPU system. We profile and analyze the training of five DNNs using 1, 2, 4 and 8 GPUs. Our analyses provide insights into the software– and hardware–level limiting factors for training DNNs on a multi-GPU system.
Distribution of Objects to Bins : Generating All Distributions

In this paper we give an elegant algorithm to generate all distributions of n identical objects to m bins without repetition. Our algorithm generates each distribution in constant time. To the best of our knowledge, our algorithm is the first algorithm which generates each solution in O(1) time in ordinary sense. By modifying our algorithm, we can generate the distributions in anti-lexicographic order. Finally, we extend our algorithm for the case when the bins have priorities associated with them. Overall space complexity of our algorithm is O(m), where m is the number of bins.
Feature Meeting Highlights : Genome Informatics 4 – 8 September 2002 , Wellcome Trust Genome Campus , Hinxton , Cambridge , UK

We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust ‘Genome Informatics’ Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later. Copyright  2003 John Wiley & Sons, Ltd.
Passive UHF RFID tag design for mounting on cylindrical metallic surfaces

Esta pesquisa propoe uma etiqueta passiva exivel que opera na faixa de 902-928 MHz de Ultra Alta Frequencia (UHF) para aplicacoes de Radio Frequency Identication (RFID). A antena pequena tem uma dimensao de 13 mm x 28 mm x 0.4 mm e esta composta de um substrato comercial exivel com facilidade de obtencao, para ser colada sobre superficies cilindricas metalicas com diferentes tamanhos. A geometria da antena foi otimizada, usando o algoritmo genetico, para maximizar sua distância de leitura. O desempenho da antena foi avaliado sobre superficies planas e curvas, atraves de simulacoes da impedância de entrada, ganho, coeciente de reexao e distância de leitura. Alem disso, medicoes do coeciente de reexao da etiqueta foram desenvolvidos. Os resultados da etiqueta RFID provam que a antena proposta pode ser utilizada sobre superficies metalicas cilindricas com uma distância de leitura superior a um metro para aplicacoes relacionadas com gestao de ativos industriais, controle de acesso, equipamentos medicos e da construcao, identicacao de pecas metalicas pequenas como ferramentas, instrumentos de cozinha, recipientes metalicos e sprays. Adicionalmente, neste trabalho foi estudado o comportamento eletromagnetico da antena sobre cilindros fabricados com materiais de polyethylene terephthalate (PET) para garrafas plasticas. Baseado no processo de otimizacao, que tem como objetivo maximizar o raio de cobertura da etiqueta, uma distância de leitura de um metro foi conseguida. Os resultados mostram que a antena tem um comportamento conavel e util sobre cilindros com pequeno raio. Alem disso, a adicao de liquidos dentro do material PET, dependendo de sua permissividade, pode incrementar a distância de leitura da etiqueta RFID.
Definition of terms for applications of respiratory sounds

Computerized lung sound analysis is a multidiscipli-nary ﬁeld. Work in this ﬁeld would be easier if the terms tobe used were clearly deﬁned. This chapter is meant fordoctors, engineers and other persons who are workingwith respiratory sound analysis.The terms collected in this paper of the ComputerizedRespiratory Sound Analysis (CORSA) guidelines includeterms of respiratory diseases, pulmonary physiology,acoustics, automatic data handling and instrumentation.The list includes terms that have not yet been deﬁnedclearly in the literature, or deﬁned in a controversial way.Some terms included have been deﬁned elsewhere, e.g . the terms of lung function variables, but were regardeduseful to be included in this selection in order to improvethe readability. Some general terms have also beenincluded in cases where the common sense meaning ofthat term is different from the speciﬁc meaning in the dis-cipline of respiratory sound research.Each deﬁnition of a term includes, as a rule, a short for-mal deﬁnition, some additional characteristics and refer-ences if available. Ofﬁcial guidelines (European Respir atorySociety Guidelines for Lung Function Studies, AmericanThoracic Society publications) position papers, statementsand reports of international societies as well as originalpapers and review articles in scientiﬁc international jour-nals have been used as references. Handbooks have alsobeen used.The terms deﬁned are listed in alphabetical order, andhave been used systematically in the CORSA guidelines.For the deﬁnition of different kinds of sounds, anattempt has been made to make clear distinctions betweenadjectives indicating locations (like lung, trachea, etc.),
Involvement of ST 6 Gal I in the biosynthesis of a unique human colon cancer biomarker candidate , a 2 , 6-sialylated blood group type 2 H ( ST 2 H ) antigen

Department of Disease Glycomics (Seikagaku Corporation), The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047; Department of Immunology, Osaka Medical Center for Cancer and Cardiovascular Diseases, 1-3-2 Nakamichi, Higashinari-ku, Osaka 537-8511; and Systems Glycobiology Research Group, Advanced Science Institute, Chemical Biology Department, RIKEN, 21-1 Hirosawa Wako, Saitama 351-0198, Japan
Reflections The inheritance of acquired epigenetic variations †

There is evidence that the functional history of a gene in one generation can influence its expression in the next. In somatic cells, changes in gene activity are frequently associated with changes in the pattern of methylation of the cytosines in DNA; these methylation patterns are stably inherited. Recent work suggests that information about patterns of methylation and other epigenetic states can also be transmitted from parents to offspring. This evidence is the basis of a model for the inheritance of acquired epigenetic variations. According to the model, an environmental stimulus can induce heritable chromatin modifications which are very specific and predictable, and might result in an adaptive response to the stimulus. This type of response probably has most significance for adaptive evolution in organisms such as fungi and plants, which lack distinct segregation of the soma and germ line. However, in all organisms, the accumulation of specific and random chromatin modifications in the germ line may be important in speciation, because these modifications could lead to reproductive isolation between populations. Heritable chromatin variations may also alter the frequency and distribution of classical mutations and meiotic recombination. Therefore, inherited epigenetic changes in the structure of chromatin can influence neo-Darwinian evolution as well as cause a type of “Lamarckian” inheritance.
Is unsupervised exercise following breast cancer safe for all women

One in eight women living in developed countries will be diagnosed with breast cancer before the age of 85, with the mean age at first diagnosis approximately 60 years. Stage I represents just under 50% of diagnoses, while 45% of cases are diagnosed at later stages (stages II to IV; the remainder being unknown stage). Breast cancer continues to be the most common cause of cancer-related deaths in women , and although survival for women with stage I disease is high (98% 5-year relative survival), survival is significantly lower for those diagnosed with more advanced disease stage (i.e., stages II to IV, 83%; an unknown stage, 50%) .
UvA-DARE ( Digital Academic Repository ) Some affixes are roots , others are heads

A recent debate in the morphological literature concerns the status of derivational affixes. While some linguists (Marantz 1997, 2001; Marvin 2003) consider derivational affixes a type of functional morpheme that realizes a categorial head, others (Lowenstamm 2015; De Belder 2011) argue that derivational affixes are roots. Our proposal, which finds its empirical basis in a study of Dutch derivational affixes, takes a middle position. We argue that there are two types of derivational affixes: some that are roots (i.e. lexical morphemes) and others that are categorial heads (i.e. functional morphemes). Affixes that are roots show ‘flexible’ categorial behavior, are subject to ‘lexical’ phonological rules, and may trigger idiosyncratic meanings. Affixes that realize categorial heads, on the other hand, are categorially rigid, do not trigger ‘lexical’ phonological rules nor allow for idiosyncrasies in their interpretation.
Levels of vasoactive intestinal peptide, cholecystokinin and calcitonin gene-related peptide in plasma and jejunum of rats following traumatic brain injury and underlying significance in gastrointestinal dysfunction

AIM:To study the alterations of brain-gut peptides following traumatic brain injury (TBI) and to explore the underlying significance of these peptides in the complicated gastrointestinal dysfunction.METHODS:Rat models of focal traumatic brain injury were established by impact insult method,and divided into 6 groups (6 rats each group) including control group with sham operation and TBI groups at postinjury 3,12,24,72h,and d 7.Blood and proximal jejunum samples were taken at time point of each group and gross observations of gastrointestinal pathology were recorded simultaneously.The levels of vasoactive intestinal peptide (VIP) in plasma,calcitonin gene-related peptide (CGRP) and cholecystokinin (CCK) in both plasma and jejunum were measured by enzyme immunoassay (EIA). Radioimmunoassay (RIA) was used to determine the levels of VIP in jejunum.RESULTS:Gastric distension,delayed gastric emptying and intestinal dilatation with a large amount of yellowish effusion and thin edematous wall were found in TBI rats through 12h and 72h, which peaked at postinjury 72h. As compared with that of control group (247.8±29.5ng/L), plasma VIP levels were significantly decreased at postinjury 3,12 and 24h (106.7±34.1ng/L, 148.7±22.8ng/L,132.8±21.6ng/L,respectively),but significantly increased at 72h (405.0±29.8ng/L) and markedly declined on d 7 (130.7±19.3ng/L). However,Plasma levels CCK and CGRP were significantly increased through 3h and 7d following TBI (126-691% increases),with the peak at 72 h.Compared with control (VIP, 13.6±1.4ng/g;CGRP,70.6±17.7ng/g);VIP and CGRP levels in jejunum were significantly increased at 3h after TBI (VIP,35.4±5.0ng/g;CGRP,103.8±22.1ng/g),and declined gradually at 12 h and 2d h (VIP,16.5±1.8ng/g,5.5±1.4ng/g;CGRP,34.9±9.7ng/g, 18.5±7.7ng/g),but were significantly increased again at 72 h (VIP, 48.7±9.5ng/g; CGRP,142.1±24.3ng/g),then declined in various degrees on d 7 (VIP, 3.8±1.1ng/g; CGRP, 102.5±18.1ng/g). The CCK levels in jejunum were found to change in a similar trend as that in p
Pulmonary and Renal Pathology 7 Nicotinic Acetylcholine Receptor Regulates Airway Epithelium Differentiation by Controlling Basal Cell Proliferation

Airway epithelial basal cells are known to be critical for regenerating injured epithelium and maintaining tissue homeostasis. Recent evidence suggests that the 7 nicotinic acetylcholine receptor (nAChR), which is highly permeable to Ca , is involved in lung morphogenesis. Here, we have investigated the potential role of the 7 nAChR in the regulation of airway epithelial basal cell proliferation and the differentiation of the human airway epithelium. In vivo during fetal development and in vitro during the regeneration of the human airway epithelium, 7 nAChR expression coincides with epithelium differentiation. Inactivating 7 nAChR function in vitro increases cell proliferation during the initial steps of the epithelium regeneration, leading to epithelial alterations such as basal cell hyperplasia and squamous metaplasia, remodeling observed in many bronchopulmonary diseases. The regeneration of the airway epithelium after injury in 7 / mice is delayed and characterized by a transient hyperplasia of basal cells. Moreover, 1-year-old 7 / mice more frequently present basal cells hyperplasia. Modulating nAChR function or expression shows that only 7 nAChR, as opposed to heteropentameric x y nAChRs, controls the proliferation of human airway epithelial basal cells. These findings suggest that 7 nAChR is a key regulator of the plasticity of the human airway epithelium by controlling basal cell proliferation and differentiation pathway and is involved in airway remodeling during bronchopulmonary diseases. (Am J Pathol 2009, 175:1868–1882; DOI: 10.2353/ajpath.2009.090212)
Sense in Pb 2 + Sensing

It is generally acknowledged that Pb2+, which is sequestered by live cells from their direct environment, affects a large number of cellular processes at picomolar to micromolar concentrations. However, resolving the specific molecular targets and mechanisms responsible for the neurotoxic effects of this xenobiotic metal is hampered by the lack of suitable tools to investigate the intracel­ lular dynamics of Pb2+ at low concentrations. Fluorescent Ca2+ indicators have been used as Pb2+ sensors and have proven useful to detect cellular Pb2+ entry and to estimate the overall intracellu­ lar free Pb2+ concentration associated with adverse cellular effects. Despite the high affinity of these Ca2+ indicators for Pb2+, their utility for more advanced studies is limited. This is merely due to their moderate metal selectivity and uncertainties about the sub­ cellular (co)localization of the indicators and the targets. Novel Pb2+ sensors, specifically developed for this purpose, still lack affinity to sense toxicologically relevant intracellular concentra­ tions of Pb2+. Nonetheless, the development of genetically encoded protein sensors for Ca2+, Zn2+, and, recently, also for Pb2+ opens a new and promising perspective to resolve spatiotemporal changes in intracellular Pb2+ in relation to cellular signaling and intracell­ ular divalent metal homeostasis. Such a development is required for enabling more systematic studies of the intracellular dynamics of Pb2+, which are essential for progress in mechanistic knowledge and will ultimately reveal the critical toxic targets of Pb2+ at the subcellular and molecular level.
Presentation preference : Either Topic : Chemical Sensors , Sensor Arrays and Data Analysis Development of Metal-Organic Framework ( MOF ) Coated Bulk Acoustic Sensors for Carbon Dioxide and Methane Detection

In this study, a quartz crystal microbalance (QCM) sensor coated with a thin layer of the metal-organic framework (MOF) ZIF-8 was fabricated and tested for detection of N2/CO2/CH4 with a comparison to a computational analysis. We analyzed the mass uptake of mixtures of N2, CO2, and CH4 in ZIF-8 in atmospheric conditions, using all mixtures with varying each component from 0 to 100 percent by 20 percent increments. Experiments used a ZIF-8 film of 500 nm thickness and resulted in mass uptake of the gases showing a positive linear relationship with CO2. Similarly, the adsorption of all mixtures in the MOF were obtained computationally via grand canonical Monte Carlo (GCMC) simulations, reported also as the total mass uptake of the MOF. We directly compare our experimental and computational results, showing that similar trends exist in the affinity of ZIF-8 towards CO2. We show that computational methods may be used to model the output of a chemical sensor, specifically in this work for a MOF on QCM device.
New fossils of paraceratheres ( Perissodactyla , Mammalia ) from the Early Oligocene of the Lanzhou Basin , Gansu Province , China

New fossils of paraceratheres (Perissodactyla, Mammalia) from the Early Oligocene of the Lanzhou Basin, Gansu Province, China LI Yong-Xiang ZHANG Yun-Xiang LI Ji LI Zhi-Chao XIE Kun (1 State Key Laboratory of Continental Dynamics, Department of Geology, Institute of Cenozoic Geology and Environment, Northwest University Xi’an 710069 * Corresponding author: yxzhang@nwu.edu.cn) (2 Institute of Silk Road Studies, Northwest University Xi’an 710069) (3 Northwest Institute of Historical Environment and Socio-Economic Development, Shaanxi Normal University Xi’an 710119)
Flexible Audio Source Separation Toolbox ( FASST ) Version 1 . 0 User Guide

This user guide describes how to use FASST, an implementation of the general flexible source separation framework presented in [1]. Before reading the user guide you are strongly encouraged to read [1], at least the two first sections. This guide is organized as follows. Some notations and abbreviations used throughout this document are listed in section 2. Section 3 gives a detailed specification of the mixture structure (a Matlab structure), used to define the available prior information. The main functions the user should know about are listed in section 4 and an example of usage is given in section 5.
Q-learning Supplemented Crowdsensing Framework for Resource Constrained Devices

In mobile crowdsensing the most significant challenge is to motivate smart devices to perform various sensing tasks for diverse goal oriented applications. This can be realized by the interaction between task owner with smart devices via a specific platform (application interface) to influence their acceptance for the task completion; employing various incentive schemes and techniques mentioned in existing literatures. However, it becomes a critical issue to handle distinct energy restrictions of participating devices, and appropriately assigning task loads based upon their capabilities that has been overlooked mostly, and even more in an unknown interaction environment. In this paper we address this issue at first by evaluating an optimal task load assignment that maximizes participating resource constraint node’s utility at a resourceful node (broker), and then model a distributed Q-learning framework of crowdsensing to improve cumulative reward for participating nodes. Simulation results show the proposed algorithm converges quickly for the designed framework, and is very efficient to employ.
Jawa Timur Menggunakan Polymerase Chain Reaction ( DETECTION OF ORGANOPHOSPHATE INSECTICIDES RESISTANT GENES IN AEDES AEGYPTI IN BANYUWANGI DISTRICT , EAST JAVA USING POLYMERASE CHAIN REACTION )

Banyuwangi is still listed as areas not completely free from hemorrhagic dengue fever outbreak. Changes in the genome of Aedes aegypti mosquito as the main vector of dengue virus is estimated to be the cause of difficulty in controlling the disease. Expression of Voltage Gated Sodium Channel (VGSC) genes can be used as an important indication of Aedes aegypti mosquitoes resistancy to certain groups insecticides. The purpose of this study was to detect the Voltage Gated Sodium Channel (VGSC) genes coding in Aedes aegypti using Polymerase Chain Reaction (PCR); as it is related to the mechanism of resistance to organophosphate insecticides groups. Results of resistency by susceptibility test showed that Aedes aegypti mosquito samples from three district ie. Tegaldlimo, Purwoharjo, and Banyuwangi were resistant to malathion 0.8% insecticide (organophosphates group). PCR results detected gen band with 250 bp length, which confirmed that insecticide resistance gene has been detected in the tested samples. Based on this study results, it is recommended to use alternative insecticides apart from organophosphate group for dengue vector control in Banyuwangi.
' s response to reviews Title : Association between legume Intake and self-reported Diabetes among adult men and women in India

We thank you very much for providing us an opportunity to revise and resubmit our paper. We are grateful for the detailed editorial and reviewer comments which we found very helpful in revising our paper. Please find a point wise response to the reviewer’s comments (written below the comments). We have also incorporated all the comments and suggestions by the two reviewers in the revised version of the manuscript. The revision is marked red all throughout the revised manuscript. We hope that the responses and revisions in the paper address all the concerns and are now acceptable for publication. Please do get in touch with me if you have any further comments or questions about our paper. I am looking forward to hearing from you.