Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Responses of Vanilla Accessions to Root Rot and Colonization by [i]Fusarium oxysporum[/i] f. sp [i]radicis-vanillae[/i]

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Differential Responses of Vanilla Accessions to Root Rot and Colonization by [i]Fusarium oxysporum[/i] f. sp [i]radicis-vanillae[/i] Sayuj Koyyappurath, Geneviève Conejero, Jean Bernard Dijoux, Fabienne Lapeyre-Montes, Katia Jade, Frédéric Chiroleu, Frederic Gatineau, Jean-Luc Verdeil, Pascale Besse, Michel Grisoni
A finite element model of the urinary bladder

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Immunogenicity and therapeutic effects of Ag85A/B chimeric DNA vaccine in mice infected with Mycobacterium tuberculosis.

The situation of tuberculosis (TB) is very severe in China. New therapeutic agents or regimens to treat TB are urgently needed. In this study, Mycobacterium tuberculosis-infected mice were given immunotherapy intramuscularly with Ag85A/B chimeric DNA or saline, plasmid vector pVAX1, or Mycobacterium vaccae vaccine. The mice treated with Ag85A/B chimeric DNA showed significantly higher numbers of T cells secreting interferon-gamma (IFN-γ), more IFN-γ in splenocyte culture supernatant, more Th1 and Tc1 cells, and higher ratios of Th1/Th2 and Tc1/Tc2 cells in whole blood, indicating a predominant Th1 immune response to treatment. Infected mice treated with doses of 100 μg Ag85A/B chimeric DNA had an extended time until death of 50% of the animals that was markedly longer than the saline and vector control groups, and the death rate at 1 month after the last dose was lower than that in the other groups. Compared with the saline group, 100 μg Ag85A/B chimeric DNA and 100 μg Ag85A DNA reduced the pulmonary bacterial loads by 0.79 and 0.45 logs, and the liver bacterial loads by 0.52 and 0.50 logs, respectively. Pathological changes in the lungs were less, and the lesions were more limited. These results show that Ag85A/B chimeric DNA was effective for the treatment of TB, significantly increasing the cellular immune response and inhibiting the growth of M. tuberculosis.
Genome-wide investigation of an ID cohort reveals de novo 3′UTR variants affecting gene expression

Intellectual disability (ID) is a severe neurodevelopmental disorder with genetically heterogeneous causes. Large-scale sequencing has led to the identification of many gene-disrupting mutations; however, a substantial proportion of cases lack a molecular diagnosis. As such, there remains much to uncover for a complete understanding of the genetic underpinnings of ID. Genetic variants present in non-coding regions of the genome have been highlighted as potential contributors to neurodevelopmental disorders given their role in regulating gene expression. Nevertheless the functional characterization of non-coding variants remains challenging. We describe the identification and characterization of de novo non-coding variation in 3′UTR regulatory regions within an ID cohort of 50 patients. This cohort was previously screened for structural and coding pathogenic variants via CNV, whole exome and whole genome analysis. We identified 44 high-confidence single nucleotide non-coding variants within the 3′UTR regions of these 50 genomes. Four of these variants were located within predicted miRNA binding sites and were thus hypothesised to have regulatory consequences. Functional testing showed that two of the variants interfered with miRNA-mediated regulation of their target genes, AMD1 and FAIM. Both these variants were found in the same individual and their functional consequences may point to a potential role for such variants in intellectual disability.
A Spectrum of Student Success: Identifying Factors Affecting Access, Experiences, and Outcomes for Students on the Autism Spectrum

Purpose One of every 68 children in the United States has autism (Autism Spectrum Disorder, or ASD for short) (Christenson, Baio, Braun, et al., 2016) a rate of diagnosis that has more than doubled during the last 10 years (Baio, 2014; Christenson, Baio, Braun, et al., 2016). With recent increases in public awareness, early interventions, and K-12 educational support, an increasing number of these students ready and able to pursue higher education (Camarena & Sarigiani, 2009; Chiang, Cheung, Hickson, Xiang, & Tsai, 2012). But statistics about college access and outcomes for this population are disheartening, especially considering that many individuals with ASD achieve academically at the same or higher levels than their typical peers, and would likely succeed at the college level with appropriate support (VanBergeijk, Klin, & Volkmar, 2008). Data from a national sample of teenagers with autism indicate that only 34.7% of these students attend a 2or 4-year college (Shattuck et al., 2012), and fewer than 39% of those who enter earn any form of credential within 6 years (Newman et al., 2011). As more and more students with autism show up on college campuses, it has become increasingly important for college educators to understand these students’ experiences and actively address the underlying challenges that have heretofore contributed to the relatively poor college outcomes for this population. Although a small, but growing, number of studies have begun to explore the experiences and outcomes of college students with autism, the current body of literature is limited in three significant ways. First, a disproportionate number of these studies draw from a narrowly constructed, single dataset (the NLTS-2) that has not been updated since 2009. Second, the vast majority of studies not using NLTS-2 are based on data collected from people other than the students with autism themselves (e.g., parents, instructors, college disability service office administrators). Third, although these studies have generated myriad statistical comparisons, they have yet to yield a comprehensive conceptual model that could be used to help students or their institutions anticipate, address, and overcome challenges that heretofore might undermine the chances of college success for autistic students. The current study addresses all three of these limitations by building a conceptual model based on evidence generated through direct interviews with a diverse group of individuals with autism who had experiences with a wide range of postsecondary educational institutions.
Session Introduction

The concept that an unfolded protein could have biological function was proposed by Linus Pauling in 1940. The first experimental evidence for the existence of unfolded proteins, which are now often called intrinsically disordered proteins and regions (IDPs and IDRs), was published in the 1950s. From the 1950s to the 1990s, many additional articles describing IDPs or IDRs were published, and even several Nobel Prizes have been awarded for research on these proteins. The first computational biology/bioinformatics papers on these proteins were reported between 1998 and 2002, and these computational efforts rapidly increased shortly thereafter. In the late 1980s and mid-1990s, a few IDPs and IDRs involved with signaling and regulation were structurally characterized by nuclear magnet resonance (NMR), and these studies demonstrated a likely involvement of IDPs or IDRs in the associated biological regulation. Altogether, the computational biology/bioinformatics and NMR investigations were synergistic in stimulating the rapid increase in the research on IDPs and IDRs. Herein, we describe this history and recent developments in the IDP research arena. We also highlight a recent collection of papers on IDPs and IDRs that are driven by computational biology and bioinformatics efforts.
TRANSPARENCY , FLEXIBILITY , SIMPLICITY : FROM BUZZWORDS TO STRATEGIES FOR REAL PSS IMPROVEMENT

There is a growing body of academic literature that deals with the gap between Planning Support Systems (PSS) and daily urban planning practices. In response to the identified bottlenecks for implementation and insights from knowledge management, a new approach for improving PSS implementation was recently proposed. This Mediated Planning Support (MPS) approach is grounded in several theoretical schools, such as knowledge management and cognitive science. This article discusses the testing of this approach in three cases of land use and transport strategy-making in the Netherlands, with the aim to increase the understanding of the added value of the mechanisms that underlie the MPS framework. Methodologically speaking, it utilised workshop specific surveys, a general ex-post survey and participatory observation. Although small-N, the results seem to indicate that MPS does improve several of the bottlenecks of PSS implementation defined in other studies: it provided a better fit between the PSS characteristics and the strategy-making processes, it increased understanding of the possibilities (and limitations) of PSS, it fostered acceptance and improved use (awareness and transparency were not significantly influenced). Important mechanisms for promoting these outcomes include an open constructive critical attitude of both PSS developers and planners, a prototyping process, and placing emphasis on externalisation and internalisation of knowledge. The paper closes with a discussion on the implications for PSS development and planning and will provide directions for further research.
Lymphatic mapping and sentinel lymph node biopsy in patients with melanoma: a meta-analysis.

PURPOSE To perform a meta-analysis of all published studies of sentinel lymph node (SLN) biopsy for staging patients with melanoma. METHODS Published literature in all languages between 1990 and 2009 was critically appraised. Primary outcomes evaluated included the proportion successfully mapped (PSM) and test performance including false-negative rate (FNR), post-test probability negative (PTPN), and positive predictive value in the same nodal basin recurrence. RESULTS A total of 71 studies including 25,240 patients met full eligibility criteria. The average PSM was 98.1% (95% CI, 97.3% to 98.6%) and increased with the year of publication, female sex, ulceration, age, and the quality score of the studies. The FNR ranged from 0.0% to 34.0%, averaging 12.5% overall (95% CI, 11% to 14.2%). FNR increased with the length of follow-up (P = .002) but decreased with greater PSM (P = .001). PTPN averaged 3.4% (95% CI, 3.0% to 3.8%), which also increased in studies with longer follow-up, younger age, female sex, deeper Breslow thickness, and with tumor ulceration while decreasing with greater PSM (P < .001). Approximately 20% of the patients with a positive SLN had additional lymph nodes in the complete lymph node dissection and 7.5% of the patients with positive SLN developed recurrence in the same nodal basin which was greater in studies that also reported higher FNR (P = .01). CONCLUSION The estimated risk of nodal recurrence after a negative SLN biopsy was ≤ 5% supporting the use of this technology for staging patients with melanoma.
Residual heart rate variability measures can better differentiate patients with acute myocardial infarction from patients with patent coronary artery

Purpose: It has been shown that the power spectral density (PSD) of heart rate variability (HRV) can be decomposed into a power-law function and a residual PSD (rPSD) with a more prominent high-frequency component than that in traditional PSD. This study investigated whether the residual HRV (rHRV) measures can better discriminate patients with acute myocardial infarction (AMI) from patients with patent coronary artery (PCA) than traditional HRV measures. Materials and methods: The rHRV and HRV measures of 48 patients with AMI and 69 patients with PCA were compared. Results: The high-frequency power of rHRV spectrum was significantly enhanced while the low-frequency and very low-frequency powers of rHRV spectrum were significantly suppressed, as compared to their corresponding traditional HRV spectrum in both groups of patients. The normalized residual high-frequency power (nrHFP = residual high-frequency power/residual total power) was significantly greater than the corresponding normalized high-frequency power in both groups of patients. Between-groups comparison showed that the nrHFP in AMI patients was significantly smaller than that in PCA patients. Receiver operating characteristic curve analysis showed that the nrHFP or nrHFP + normalized residual very low-frequency power (residual very low-frequency power/rTP) had better discrimination capability than the corresponding HRV measures for predicting AMI. Conclusions: Compared with traditional HRV measures, the rHRV measures can slightly better differentiate AMI patients from PCA patients, especially the nrHFP or nrHFP + normalized residual very low-frequency power.
Forecasting of Apricot Production of Turkey by Using Box-Jenkins Method

Turkey is the first largest apricot producer in the world. In 2016, Turkey was responsible for 9,21% of world apricot production with 730 thousand tons. Turkey also generated 11,31% of world apricot exports in 2016. The main aim of this research was to forecast apricot production of Turkey for the period of 2017-2022. The data of this study was obtained from the database of the Food and Agriculture Organization and the time series covered the period of 1961-2016. Box-Jenkins Model was used to forecast apricot production. In the study, it was determined that the time series were not stationary and the series became stationary after the first difference was taken. Moving Average Model ARIMA (2, 1, 1) was determined as the most appropriate model for the stationary data type. The research results show that apricot production quantities of Turkey in 2017 was forecasted as minimum 383.206 tons, maximum 920.409 tons and, average 651.808 tons. However, Turkey’s the apricot production amount in 2022 was forecasted as minimum 271.734 tons, maximum 1.193. 113 tones and average 732.423 tons. Considering the increase in demand, it is thought that apricot production will not be sufficient for the country. To protect the current leading position of the country, it is recommended that the government should give enough support to increase apricot production in Turkey.
Climate Change and ProteCted PlaCes: AdApting to new ReAlities

Climate change has caused deserts, already defined by climatic extremes, to warm and dry more rapidly than other ecoregions in the contiguous United States over the last 50 years. Desert birds persist near the edge of their physiological limits, and climate change could cause lethal dehydration and hyperthermia, leading to decline or extirpation of some species. We evaluated how desert birds have responded to climate and habitat change by resurveying historic sites throughout the Mojave Desert that were originally surveyed for avian diversity during the early 20th century by Joseph Grinnell and colleagues. We found strong evidence of an avian community in collapse. Sites lost on average 43% of their species, and occupancy probability declined significantly for 39 of 135 breeding birds. The common raven was the only native species to substantially increase across survey sites. Climate change, particularly decline in precipitation, was the most important driver of site-level persistence, while habitat change had a secondary influence. Habitat preference and diet were the two most important species traits associated with occupancy change. The presence of surface water reduced the loss of site-level richness, creating refugia. The collapse of the avian community over the past century may in-dicate a larger imbalance in the Mojave and provide an early warning of future ecosystem disintegration, given climate models unanimously predict an increasingly dry and hot future.
Fueling for Performance

Context: Proper nutrition is crucial for an athlete to optimize his or her performance for training and competition. Athletes should be able to meet their dietary needs through eating a wide variety of whole food sources. Evidence Acquisition: PubMed was searched for relevant articles published from 1980 to 2016. Study Design: Clinical review. Level of Evidence: Level 4. Results: An athlete should have both daily and activity-specific goals for obtaining the fuel necessary for successful training. Depending on the timing of their season, athletes may be either trying to gain lean muscle mass, lose fat, or maintain their current weight. Conclusion: An athlete will have different macronutrient goals depending on sport, timing of exercise, and season status. There are no specific athletic micronutrient guidelines, but testing should be considered for athletes with deficiency or injury. Also, some athletes who eliminate certain whole food groups (eg, vegetarian) may need to supplement their diet to avoid deficiencies.
Use of whole genome sequencing to investigate an outbreak of gonorrhoea 1 among females in urban New South Wales , Australia , 2012 to 2014 . 2

5 1 The University of Queensland, UQ Centre for Clinical Research, Herston, 6 Queensland 4029, Australia. 7 2 Australian Infectious Diseases Research Centre, The University of Queensland, 8 Brisbane, Queensland 4072, Australia. 9 3 Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 10 Queensland 4072, Australia. 11 4 School of Chemistry and Molecular Biosciences, The University of Queensland, 12 Brisbane, Queensland, 4072 Australia. 13 5 WHO Collaborating Centre for STD, Microbiology Department, New South Wales 14 Health Pathology East, Prince of Wales Hospital, Sydney, New South Wales 2031, 15 Australia. 16 6 School of Medical Sciences, The University of New South Wales, Sydney, New 17 South Wales 2052, Australia. 18 7 Pathology Queensland, Microbiology Department, Herston, Queensland 4029, 19 Australia. 20
Total Pancreatectomy and Islet Auto-Transplantation in Children with Chronic Pancreatitis

C l i n M e d International Library Citation: Berger M, Bellin M, Schwarzenberg SJ, Srinath Chinnakotla S (2015) Total Pancreatectomy and Islet Auto-Transplantation in Children with Chronic Pancreatitis. Int J Transplant Res Med 1:015 Received: November 06, 2015: Accepted: December 17, 2015: Published: December 19, 2015 Copyright: © 2015 Berger M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Berger et al. Int J Transplant Res Med 2015, 1:2
Adenosine 5 (cid:1) -Monophosphate-Activated Protein Kinase and p38 Mitogen-Activated Protein Kinase Participate in the Stimulation of Glucose Uptake by Dinitrophenol in Adult Cardiomyocytes

During metabolic stress, such as ischemia or hypoxia, glucose becomes the principal energy source for the heart. It has been shown that increased cardiac glucose uptake during meta- bolic stress has a protective effect on cell survival and heart function. Despite its physiological importance, only limited data are available on the molecular mechanisms regulating glucose uptake under these conditions. We used 2,4-dinitro- phenol (DNP), an uncoupler of oxidative phosphorylation, as a model to mimic hypoxia and gain insight into the signaling pathway underlying metabolic stress-induced glucose uptake in primary cultures of rat adult cardiomyocytes. The results demonstratethat0.1m M DNPinduces2.2-and9-foldincreases in AMP-activated protein kinase (AMPK) and p38 MAPK phos- phorylation, respectively. This is associated with a 2.3-fold increase in glucose uptake in these cells. To further delineate the role of AMPK in the regulation of glucose uptake, we used two complementary approaches: pharmacological inhibition of the enzyme with adenine 9- (cid:1) -D arabinofuranoside and adenoviral infection with a dominant-negative AMPK (DN-AMPK) mutant. Our results show that overexpression of DN-AMPK completely suppressed DNP-mediated phosphorylation of acetyl coenzyme A carboxylase, a downstream target of AMPK. Inhibition of AMPK with either 9- (cid:1) -D arabinofuranoside phosphorylation. decreased DNP-stimulated glucose uptake in omyocytes. Inhibition of p38 MAPK with the pharmacological
Weekly Report

To see the effect of spacer length on the shape of p53, We applied our constraint program to p53 by implimenting distance constrant between any 2 p atoms of the selected nucleotide. 3kmd’s sequence contains 20 base pairs with 0 spacer, while bax’s sequence contains 21 base pairs with 1 spacer. Preliminary results is shown in Figure 2, which is the minor groove width from the average of cycles 400,000∼500,000. We can see that the distance constraints have some effect on the shape.
Systematic Review for Phonocardiography Classification Based on Machine Learning

—Phonocardiography, the recording and analysis of heart sounds, has become an essential tool in diagnosing cardiovascular diseases (CVDs). In recent years, machine learning and deep learning techniques have dramatically improved the automation of phonocardiogram classification, making it possible to delve deeper into intricate patterns that were previously difficult to discern. Deep learning, in particular, leverages layered neural networks to process data in complex ways, mimicking how the human brain works. This has contributed to more accurate and efficient diagnoses. This systematic review aims to examine the existing literature on phonocardiography classification based on machine learning, focusing on algorithms, datasets, feature extraction methods, and classification models utilized. The materials and methods used in the study involve a comprehensive search of relevant literature and a critical evaluation of the selected studies. The review also discusses the challenges encountered in this field, especially when incorporating deep learning techniques, and suggests future research directions. Key findings indicate the potential of machine and deep learning in enhancing the accuracy of phonocardiography classification, thereby improving cardiovascular disease diagnosis and patient care. The study concludes by summarizing the overall implications and recommendations for further advancements in this area.
Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn2+-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM. DOI: http://dx.doi. org/10.7554/eLife.15910. 001