Miracle-dz/UniFAR-FTUs huggingface dataset:
Drawing Links from Transcriptome to Metabolites: The Evolution of Aroma in the Ripening Berry of Moscato Bianco (Vitis vinifera L.)

Monoterpenes confer typical floral notes to “Muscat” grapevine varieties and, to a lesser extent, to other aromatic non-Muscat varieties. Previous studies have led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are largely unknown. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries. In particular, gas chromatography-mass spectrometry analysis of free and bound terpenoid compounds was combined with microarray analysis in the skins of berries collected at five developmental stages from pre-veraison to over-ripening. Differentially expressed metabolites and probes were identified in the pairwise comparison between time points by using the early stage as a reference. Metabolic and transcriptomic data were integrated through pairwise correlation and clustering approaches to discover genes linked with particular metabolites or groups of metabolites. These candidate transcripts were further checked for co-localization with quantitative trait loci (QTLs) affecting aromatic compounds. Our findings provide insights into the biological networks of grapevine secondary metabolism, both at the catalytic and regulatory levels. Examples include a nudix hydrolase as component of a terpene synthase-independent pathway for monoterpene biosynthesis, genes potentially involved in monoterpene metabolism (cytochrome P450 hydroxylases, epoxide hydrolases, glucosyltransferases), transport (vesicle-associated proteins, ABCG transporters, glutathione S-transferases, amino acid permeases), and transcriptional control (transcription factors of the ERF, MYB and NAC families, intermediates in light- and circadian cycle-mediated regulation with supporting evidence from the literature and additional regulatory genes with a previously unreported association to monoterpene accumulation).
Population structure analysis of habanero chili (capsicum chinense Jacq.) with AFLP

The structure of four Habanero Chili pepper populations (C. chinense Jacq.), was estimated with AFLP (Amplified fragment length polymorphisms) markers. Three of the four evaluated populations were selected in Tabasco and one from Campeche, each population consisted of 15 individual plants. The six oligonucleotides combinations used at this research showed products of 34 to 422 pb, and produced 1722 total bands. Combination E-AAG/M-CAG amplified the largest bands number (329) and E-ACA/M-CTG detected the minor bands number (190). The populations of Mucuychacán, Campeche, presented the largest polimorphism (1371 polimorphic bands), with mean of 228.5 bands polimorphic per oligonucleotide, the polimorphic bands minor number was observed at Cucuyulapa, Tabasco with 1216. The AMOVA (Variance Molecular Analysis) showed a genetic differentiation index of FST= 0.13, the variability explained among populations were minor (14.14%), that within populations (85.86%). The populations structure was determined with a value of deltaK=3. The cluster analysis grouped the plants of Santa Cruz Tlacotalpa as an independent population, and some plants of Mucuychacán, Cucuyulapa and Ranchería El Habanero populations were grouped at the cluster I.
Conceptual: Digital Book in the Era of Digital Learning Approaches (DLA)

Nowadays, the advancement of ICT has been reached all over the world with tremendous influences, particularly in an educational world. In this digital age, for instance, there is an innovation of learning resources based on technology. They are electronic books (e-books) or digital books. The features of digital books such as multimodal components (text, audio, animation, and video) become more desirable than the printed books, although the current research often shows the constraint toward the effectiveness of the electronic books in reading comprehension. The digital books provide an interactive aspect of self-regulated learning in the context of distance learning. This article proposes a literature review of the existing studies around digital books in an educational environment. The result of review revealed that the effectiveness of the digital book for learning purposes depends on several factors that are the curriculum development appropriateness, students’ prior knowledge of technology, and adults’ role as facilitators in a learning activity.
Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

Capnocytophaga ochracea (Prévot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically not yet charted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic (CO2-requiring) organism with the ability to grow under anaerobic as well as aerobic conditions (oxygen concentration larger than 15%), here only in the presence of 5% CO2. Strain VPI 2845T, the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the GenomicEncyclopedia ofBacteria andArchaea project.
THE QSM ALGORITHM AND ITS APPLICATION TO SOFTWARE BEHAVIOR MODEL INDUCTION

This article presents a novel application of grammatical inference techniques to the synthesis of behavior models of software systems. This synthesis is used for the elicitation of software requirements. This problem is formulated as a deterministic finite-state automaton induction problem from positive and negative scenarios provided by an end user of the software-to-be. A query-driven state merging (QSM) algorithm is proposed. It extends the Regular Positive and Negative Inference (RPNI) and blue-fringe algorithms by allowing membership queries to be submitted to the end user. State merging operations can be further constrained by some prior domain knowledge formulated as fluents, goals, domain properties, and models of external software components. The incorporation of domain knowledge both reduces the number of queries and guarantees that the induced model is consistent with such knowledge. The proposed techniques are implemented in the ISIS tool and practical evaluations on standard requirements engineering test cases and synthetic data illustrate the interest of this approach.
Müller Cell-Derived VEGF Is Essential for Diabetes-Induced Retinal Inflammation and Vascular Leakage

OBJECTIVE Vascular endothelial growth factor (VEGF-A or VEGF) is a major pathogenic factor and therapeutic target for diabetic retinopathy (DR). Since VEGF has been proposed as a survival factor for retinal neurons, defining the cellular origin of pathogenic VEGF is necessary for the effectiveness and safety of long-term anti-VEGF therapies for DR. To determine the significance of Müller cell-derived VEGF in DR, we disrupted VEGF in Müller cells with an inducible Cre/lox system and examined diabetes-induced retinal inflammation and vascular leakage in these conditional VEGF knockout (KO) mice. RESEARCH DESIGN AND METHODS Leukostasis was determined by counting the number of fluorescently labeled leukocytes inside retinal vasculature. Expression of biomarkers for retinal inflammation was assessed by immunoblotting of TNF-α, ICAM-1, and NF-κB. Vascular leakage was measured by immunoblotting of retinal albumin and fluorescent microscopic analysis of extravascular albumin. Diabetes-induced vascular alterations were examined by immunoblotting and immunohistochemistry for tight junctions, and by trypsin digestion assays for acellular capillaries. Retinal integrity was analyzed with morphologic and morphometric analyses. RESULTS Diabetic conditional VEGF KO mice exhibited significantly reduced leukostasis, expression of inflammatory biomarkers, depletion of tight junction proteins, numbers of acellular capillaries, and vascular leakage compared to diabetic control mice. CONCLUSIONS Müller cell-derived VEGF plays an essential and causative role in retinal inflammation, vascular lesions, and vascular leakage in DR. Therefore, Müller cells are a primary cellular target for proinflammatory signals that mediates retinal inflammation and vascular leakage in DR.
3-Acetyl-4-hydroxyphenyl acrylate

In the title compound, C12H12O4, the hydroxy O and the C and O atoms of the acetyl group are almost coplanar [maximum deviation = 0.0356 (1) Å] with the benzene ring. The dihedral angle between the benzene ring and the plane through the non-H atoms of the methacryloyloxy group is 86.1 (1)°. In the crystal structure, molecules are linked by two C—H⋯O hydrogen bonds, forming dimers with graph-set descriptor R 2 2(16). A strong intramolecular O—H⋯O hydrogen bond is also observed.
Designing Systolic Architecture For Symmetrizing Hessenberg Matrices

In this paper, we describe a systematic method for mapping the problem of symmetrizing Hessenberg matrices onto systolic architectures. The starting point of our method is a graphical abstraction of the system of linear recurrence equations that speciies the problem. Using a procedure called cubization, we transform the dependency graph of the problem into a graph we term the Modiied Dependency Graph. Using the modiied dependency graph, we design systolic programs on a very general architecture referred to as a basic systolic architecture. Next, we map the basic systolic architecture onto a given systolic architecture using a set of semantics-preserving transformations and hence, the correctness of the solution comes for free. Finally, we compare the architectures for symmetrizing Hessenberg matrices obtained by our method with those proposed previously.
Antiretroviral Treatment and Prevention of Peripartum and Postnatal HIV Transmission in West Africa: Evaluation of a Two-Tiered Approach

Background Highly active antiretroviral treatment (HAART) has only been recently recommended for HIV-infected pregnant women requiring treatment for their own health in resource-limited settings. However, there are few documented experiences from African countries. We evaluated the short-term (4 wk) and long-term (12 mo) effectiveness of a two-tiered strategy of prevention of mother-to-child transmission of HIV (PMTCT) in Africa: women meeting the eligibility criteria of the World Health Organization (WHO) received HAART, and women with less advanced HIV disease received short-course antiretroviral (scARV) PMTCT regimens. Methods and Findings The MTCT-Plus Initiative is a multi-country, family-centred HIV care and treatment program for pregnant and postpartum women and their families. Pregnant women enrolled in Abidjan, Côte d'Ivoire received either HAART for their own health or short-course antiretroviral (scARV) PMTCT regimens according to their clinical and immunological status. Plasma HIV-RNA viral load (VL) was measured to diagnose peripartum infection when infants were 4 wk of age, and HIV final status was documented either by rapid antibody testing when infants were aged ≥ 12 mo or by plasma VL earlier. The Kaplan-Meier method was used to estimate the rate of HIV transmission and HIV-free survival. Between August 2003 and June 2005, 107 women began HAART at a median of 30 wk of gestation, 102 of them with zidovudine (ZDV), lamivudine (3TC), and nevirapine (NVP) and they continued treatment postpartum; 143 other women received scARV for PMTCT, 103 of them with sc(ZDV+3TC) with single-dose NVP during labour. Most (75%) of the infants were breast-fed for a median of 5 mo. Overall, the rate of peripartum HIV transmission was 2.2% (95% confidence interval [CI] 0.3%–4.2%) and the cumulative rate at 12 mo was 5.7% (95% CI 2.5%–9.0%). The overall probability of infant death or infection with HIV was 4.3% (95% CI 1.7%–7.0%) at age week 4 wk and 11.7% (95% CI 7.5%–15.9%) at 12 mo. Conclusions This two-tiered strategy appears to be safe and highly effective for short- and long-term PMTCT in resource-constrained settings. These results indicate a further benefit of access to HAART for pregnant women who need treatment for their own health.
A voice activity detector for an echo suppressor and an echo suppressor

A voice action detector suitable for use in the echo suppressor comprising a whitening filter (19) for equalization in the frequency spectrum of the signal in the transmission path rising tone, to provide a balanced signal, further comprising a decision means (20) , the above-mentioned whitening filter coupled to the measurement signal energy balance, thereby detecting speech in the transmit path. Voice whitening filter is a whitening filter, adaptively work (8, 19) in accordance with a speech decoder the speech parameters received in the receive path. On the other hand, the transmission path enters the near-end speech and far end voice echoes generated from different receive paths, a voice on the transmission path is substantially due to the time received from the echo path caused by transmit and receive attenuators (26, 27) according to a first arrangement configured to, when the voice of the transmission line is at least partially caused by near-end speech, arrangements according to the second configuration.
Seasonal Changes in the Home Range of the Antelope Jackrabbit (Lepus alleni)

Abstract. In the face of climate change, more research is needed to understand how animals adjust to dynamic ecosystems. Seasonal environments offer a unique opportunity to observe how animals use the landscape in a fluctuating system. The antelope jackrabbit (Lepus alleni) is an understudied lagomorph found in the Sonoran Desert of Arizona, USA and Mexico. Basic ecological information on this species is lacking beyond historical responses to rangeland conditions. Using radio telemetry, we collected data on home range size and seasonal ranges of antelope jackrabbits on the Buenos Aires National Wildlife Refuge in southcentral Arizona. Male and female antelope jackrabbit mean home range size differed slightly, though not significantly. Within a seasonal landscape of semidesert and Sonoran savanna grasslands, antelope jackrabbits seasonal range size did not change but the home range usage percentage differed across seasons and degree of interseason similarity was low. Antelope jackrabbit home ranges are comparable to range sizes reported for the widespread black-tailed jackrabbit (Lepus californicus) as well as the closely related Tehuantepec jackrabbit (Lepus flavigularis). This study is the first to document antelope jackrabbit home range, and our results permit a better understanding of how these hares use the landscape in a complex arid environment.
An Inductive-bounce Enhanced Output-pad for CMOS UltraWideBand RF Applications

Resonant pad designs that tunes out parasitic pad capacitances is a difficult task in broadband wireless RF applications. This paper reports a novel CMOS output pad design using inductive ground bounce which is found to be suitable for ultrawideband RF applications. As pad parasitic capacitances as small as 0.35 pF becomes a significant ground leakage path for the ultrawideband frequency range of 3.1 GHz-10.6 GHz, inductive bounces from inductors as small as 1-2 nH can provide substantial impedance against this leakage. Simulations using the 0.18 mum TSMC process parameters indicate considerable output pad performance improvement when inductive bounce is used. Also, s- parameter simulations verify the results obtained.
Bayesian analysis of agricultural field experiments

The paper describes Bayesian analysis for agricultural field experiments, a topic that has received very little previous attention, despite a vast frequentist literature. Adoption of the Bayesian paradigm simplifies the interpretation of the results, especially in ranking and selection. Also, complex formulations can be analysed with comparative ease, by using Markov chain Monte Carlo methods. A key ingredient in the approach is the need for spatial representations of the unobserved fertility patterns. This is discussed in detail. Problems caused by outliers and by jumps in fertility are tackled via hierarchical t formulations that may find use in other contexts. The paper includes three analyses of variety trials for yield and one example involving binary data; none is entirely straightforward. Some comparisons with frequentist analyses are made.
Word2Vec is only a special case of Kernel Correspondence Analysis and Kernels for Natural Language Processing

We show Correspondence Analysis (CA) is equivalent to defining Gini-index with appropriate scaled one-hot encoding. Using this relation, we introduce non-linear kernel extension of CA. The extended CA gives well-known analysis for categorical data (CD) and natural language processing by specializing kernels. For example, our formulation can give G-test, skip-gram with negative-sampling (SGNS), and GloVe as a special case. We introduce two kernels for natural language processing based on our formulation. First is a stop word(SW) kernel. Second is word similarity(WS) kernel. The SW kernel is the system introducing appropriate weights for SW. The WS kernel enables to use WS test data as training data for vector space representations of words. We show these kernels enhances accuracy when training data is not sufficiently large.
Characteristic utilities, join policies and efficient incentives in Mobile Crowdsensing Systems

In this paper we identify basic design issues of Mobile Crowdsensing Systems (MCS) and investigate some characteristic challenges. We define the basic components of an MCS - the Task, the Server and the Crowd - and investigate the functions describing/governing their interactions. We identify three qualitatively different types of Tasks; a) those whose added utility is proportional to the size of the Task, b) those whose added utility is proportional to the progress of the Task and c) those whose added utility is reversely proportional to the progress of the Task. For a given type of Task, and a finite Budget, the Server makes offers to the agents of the Crowd based on some Incentive Policy. On the other hand, each agent that receives an offer decides whether it will undertake the Task or not, based on the inferred cost (computed via a Cost function) and some Join Policy. In their policies, the Crowd and the Server take into account several aspects, such as the number and quality of participating agents, the progress of execution of the Task and possible network effects, present in real-life systems. We evaluate the impact and the performance of selected characteristic policies, for both the Crowd and the Server, in terms of Task execution and Budget efficiency of the Crowd. Experimental findings demonstrate key performance features of the various policies and indicate that some policies are more effective in enabling the Server to efficiently manage its Budget while providing satisfactory incentives to the Crowd and effectively executing the system Tasks. Interestingly, incentive policies that take into account the current crowd participation achieve a better trade-off between Task completion and budget expense.
8 Paraquat : An Oxidative Stress Inducer

Paraquat (1,1_-dimethyl-4,4_-bipyridinium dichloride), is a foliar-applied and non selective bipyridinium herbicides, and it is one of the most widely used herbicides in the world, controlling weeds in a huge variety of crops like corn, rice, soybean, wheat, potatoes; major fruits: apples, oranges, bananas; beverages: coffee, tea, cocoa; and processed crops: cotton, oil palm, sugarcane and rubber.
Oral rehabilitation of primary dentition affected by amelogenesis imperfecta: a case report.

AIM The purpose of the case report was to describe the treatment of a 4(1/2)-year-old boy with amelogenesis imperfect (AI) in the primary dentition. BACKGROUND AI is a hereditary condition that affects the development of enamel, causing quantity, structural, and compositional anomalies involving all dentitions. Consequently, the effects can extend to both the primary and secondary dentitions. CASE REPORT A 4(1/2)-year-old boy was brought to the dental clinic complaining of tooth hypersensitivity during meals. The medical history and clinical examination were used to arrive at the diagnosis of amelogenesis imperfecta. The treatment was oral rehabilitation of the primary molars with stainless steel crowns and resin-filled celluloid forms of both maxillary and mandibular primary incisors and canines. Improvements in the patient's psychological behavior and the elimination of tooth sensitiveness were observed, and the reestablishment of a normal occlusion resulted in improved eating habits. The child was monitored in the Pediatric Dentistry Clinic at four-month intervals until the mixed dentition stage. SUMMARY The oral rehabilitation of young children with AI is necessary to reestablish the stomatognathic system function, so important for a child's systemic health. An adequate medical history and a careful clinical examination were essential for a correct diagnosis. Treatment was rendered that was appropriate for the child's age and clinical/psychological characteristics. CLINICAL SIGNIFICANCE Cost-effective restorative techniques involving stainless steel and composite-resin crowns are shown for the restoration of a young patient with amelogensis imperfecta.
Semantic Shot Classification in Sports Video

In this paper, we present a unified framework for semantic shot classification in sports videos. Unlike previous approaches, which focus on clustering by aggregating shots with similar low-level features, the proposed scheme makes use of domain knowledge of a specific sport to perform a top-down video shot classification, including identification of video shot classes for each sport, and supervised learning and classification of the given sports video with low-level and middle-level features extracted from the sports video. It is observed that for each sport we can predefine a small number of semantic shot classes, about 5~10, which covers 90~95% of sports broadcasting video. With the supervised learning method, we can map the low-level features to middle-level semantic video shot attributes such as dominant object motion (a player), camera motion patterns, and court shape, etc. On the basis of the appropriate fusion of those middle-level shot classes, we classify video shots into the predefined video shot classes, each of which has a clear semantic meaning. The proposed method has been tested over 4 types of sports videos: tennis, basketball, volleyball and soccer. Good classification accuracy of 85~95% has been achieved. With correctly classified sports video shots, further structural and temporal analysis, such as event detection, video skimming, table of content, etc, will be greatly facilitated.