Miracle-dz/UniFAR-FTUs huggingface dataset:
A transcriptomic study of grapevine (Vitis vinifera cv. Cabernet-Sauvignon) interaction with the vascular ascomycete fungus Eutypa lata

Eutypa dieback is a vascular disease that may severely affect vineyards throughout the world. In the present work, microarrays were made in order (i) to improve our knowledge of grapevine (Vitis vinifera cv. Cabernet-Sauvignon) responses to Eutypa lata, the causal agent of Eutypa dieback; and (ii) to identify genes that may prevent symptom development. Qiagen/Operon grapevine microarrays comprising 14 500 probes were used to compare, under three experimental conditions (in vitro, in the greenhouse, and in the vineyard), foliar material of infected symptomatic plants (S+R+), infected asymptomatic plants (S–R+), and healthy plants (S–R–). These plants were characterized by symptom notation after natural (vineyard) or experimental (in vitro and greenhouse) infection, re-isolation of the fungus located in the lignified parts, and the formal identification of E. lata mycelium by PCR. Semi-quantitative real-time PCR experiments were run to confirm the expression of some genes of interest in response to E. lata. Their expression profiles were also studied in response to other grapevine pathogens (Erysiphe necator, Plasmopara viticola, and Botrytis cinerea). (i) Five functional categories of genes, that is those involved in metabolism, defence reactions, interaction with the environment, transport, and transcription, were up-regulated in S+R+ plants compared with S–R– plants. These genes, which cannot prevent infection and symptom development, are not specific since they were also up-regulated after infection by powdery mildew, downy mildew, and black rot. (ii) Most of the genes that may prevent symptom development are associated with the light phase of photosynthesis. This finding is discussed in the context of previous data on the mode of action of eutypin and the polypeptide fraction secreted by Eutypa.
Jumps in the Convenience Yield of Crude Oil

Abstract The potential presence of jumps and time-varying volatility in convenience yields can lead to abnormally fat tails, which has implications for investment in storage capacity, leasing and drilling for crude oil. In this paper we evaluate the potential for these features in convenience yields. To that end, we analyze the rate of change in convenience yields for five futures prices time horizons (1, 3-, 6-, 9- and 12-month ahead), allowing for the both jumps and time-varying volatility. We find that both features exert a statistically important effect on convenience yields, for each of the five time horizons. We also calculate the implied probability that at least one jump would occur on any date, which reveals a period of relative calm at the start of the fracking boom, when large stockpiles built up at the trading hub for West Texas Intermediate, and a period of considerable churn, after the ban on exporting crude oil was lifted. Both elements underscore a linkage between inventory holdings and convenience yields.
Nosocomial Candidemia; Risk Factors and Prognosis Revisited; 11 Years Experience from a Norwegian Secondary Hospital

The aim of the study was to review the epidemiology and prognosis of candidemia in a secondary hospital, and to examine the intra-hospital distribution of candidemia patients. Study design is a retrospective cohort study. Trough 2002–2012, 110 cases of candidemia were diagnosed, giving an incidence of 2, 6/100000 citizens/year. Overall prognosis of candidemia was dismal, with a 30 days case fatality rate of 49% and one year case fatality rate of 64%. Candidemia was a terminal event in 55% of 30 days non-survivors, defined as Candida blood cultures reported positive on the day of death or thereafter (39%), or treatment refrained due to hopeless short-term prognosis (16%). In terminal event candidemias, advanced or incurable cancer was present in 29%. Non-survivors at 30 days were 9 years (median) older than survivors. In 30 days survivors, candidemia was not recognised before discharge in 13% of cases. No treatment were given and no deaths or complications were observed in this group. Candidemia patients were grouped into 8 patient categories: Abdominal surgery (35%), urology (13%), other surgery (11%), pneumonia (13%), haematological malignancy (7%), intravenous drug abuse (4%), other medical (15%), and new-borns (3%). Candidemia was diagnosed while admitted in the ICU in 46% of patients. Urology related cases were all diagnosed in the general ward. Multiple surgical procedures were done in 60% of abdominal surgery patients. Antibiotics were administered prior to candidemia in 87% of patients, with median duration 17 (1–108) days. Neutropenia was less common than expected in patients with candidemia (8/105) and closely associated to haematological malignancy (6/8). Compared with previous national figures the epidemiology of invasive candidiasis seems not to have changed over the last decade.
Factors Influencing Adoption of Management and Control Technologies for Prosopis juliflora in Marigat, Baringo County, Kenya

Prosopis juliflora is an invasive woody plant that was introduced to Marigat Sub County of Baringo County in 1970s and over the years its spread has altered the livelihoods of the pastoral communities who are the majority in most of the affected areas. This is because Prosopis juliflora invasion has reduced available dry season grazing fields, chocked river banks and interfered with access roads. To control its spread several management and control technologies were promoted in Marigat Sub-County in early 2004 that included clearing and planting pasture, charcoal production and killing of cut stumps with chemicals among others. However, the interventions have not yielded the desired results for the species has continued to spread into newer areas and intensifying their presence in already invaded areas. A study was initiated in 2017 to determine the factors influenced the local households to adopt the promoted management and control technologies in Marigat Sub-county one of the areas of original introduction and most affected by the infestations. The study was done through socio-ecological survey using questionnaires and checklist administered to 337 households. The factors considered were Socio-economic (education, land size income) and demographic (gender, age, household size). Data collected was then processed and analyzed using descriptive and inferential statistics of SPSS. The inferential tools used were chi-square analysis, regression and correlation analysis and Pearson Moment Correlation analysis. The results showed land size, incomes from Prosopis products, age and household size significantly influenced adoption of management and control technologies for Prosopis in the study area. The adoption rates association direction depended mostly on labour availability and incomes to hire extra labour for undertake the arduous job of Prosopis clearing and control of reinvasions. Level of education of the respondents had no significant effect on the adoption rates of the various control measures. Keywords: Adoption, Prosopis juliflora , Management, Invasion and Household
An Empirical Study on the Physicians' Behavioral Intention with Electronic Medical Record Systems in Taiwan

Currently in healthcare organizations paper-based patient record management faces many challenges. Most countries are promoting the full implementation of electronic medical records in every hospital. Medical environments change frequently and dramatically, which makes full acceptance of electronic medical records (EMR) by physicians an important issue. This empirical study combines the theory on reasoned action (TRA) and information technology acceptance model (TAM) resulted in a modified TAM to find what critical factors influence the acceptance behavior of EMR by physicians. To test these hypotheses, this study administered a cross-sectional mailed questionnaire survey during the period of three months in 2012. The survey was deployed to1000 physicians randomly from the estimated total 2000 physicians of 50 regional acute hospitals (more than 300 beds) in Taiwan currently. From these, 252effective responses were received, resulting in a net response rate of 25%. These research findings indicate that four variables significantly positively impact the intention to adopt EMR. Among these, attitude has the most significant positive impact on adoption intentions. Moreover, it shows that the professional autonomy might play an important role to moderate the attitude with significant statistics. These results maintain enough explanatory power (R2 =78.4%) to help explain the attitudes and intentions of physicians in adopting electronic medical record information systems. Our analysis revealed the importance of the perception usefulness which moderated by professional autonomy and pragmatism by physicians for their adoption electronic medical record systems in clinical practices.
Smart TWAP Trading in Continuous-Time Equilibria

This paper presents a continuous-time equilibrium model of liquidity provision in a market with multiple strategic investors with intraday trading targets. We show analytically that there are infinitely many Nash equilibria. We solve for the welfare-maximizing equilibrium and the competitive equilibrium, and we illustrate that these equilibria are different. The model is easily computed numerically, and we provide a number of numerical illustrations.
A SAR-BASED NWP ERROR WARNING PRODUCT

Verification of numerical weather prediction (NWP) models at sea is complicated by the relative dearth of in situ observations. Aloft, this issue can be addressed in part by using cloud-track winds. Surface verification is equally challenging, with satellite-borne scatterometers such as ASCAT (Figa-Saldaña et al. 2002) and passive techniques offering the primary means of mapping the oceanic surface wind field (herein, surface refers to 10 m above sea level). In both cases the process is somewhat incestuous as these observations are also assimilated into many over-ocean NWP models. Both also suffer from relatively low spatial resolution, limiting verification of mesoscale and sub-mesoscale features. Spaceborne synthetic aperture radar (SAR) offers the potential to address this resolution issue. SAR also offers the advantage of verifying the NWP model against independent data, unlike scatterometer wind observations which are often assimilated into the model. In this study we used RADARSAT-1 and Envisat Wide Swath synthetic aperture radar (SAR) observations to detect surface wind field errors in the NOGAPS global model. The study focused on the Gulf of Alaska and adjacent waters because of the broad range of meteorological phenomena that inhabit this region.
Multiagent Flocking Under General Communication Rule

In this paper, we consider a multiagent system consisting of mobile agents with second-order dynamics. The communication network is determined by a general interaction rule based on the distance between agents. The goal of this paper is to determine practical conditions ensuring that the agents asymptotically agree on a common velocity, i.e., a flocking behavior is achieved. Unlike previous studies on the topic, our results simultaneously satisfy the three following features: 1) our conditions apply to a model, which does not require long distance communication; 2) they only depend on the initial positions and velocities of the agents; and 3) most importantly, our results allow for the disconnection of communication links which are not necessary for flocking. To circumvent the difficulty arising from the state dependent dynamics, a suitable bounding process is used. We apply our result to two cases, where communication takes place either within deterministic or stochastic distance radiuses. Our result is illustrated through simulations.
Compensating for hyperarticulation by modeling articulatory properties

In spoken dialogue systems, hyperarticulation occur as an eﬀect to recover previous recognition errors. It is commonly observed that users of automatic speech recognition systems apply similar recovery strategies as in human-human interactions. Previous studies have shown that current speech recognizers don’t cover hyperarticu-lated speech well. As an eﬀect of higher word error rates at hyperarticulated speech, humans try to reinforce this speaking style which results in even more recognition errors. In this study, we investigate the use of articulatory features to compensate hyperarticulated eﬀects. The underlying idea is, that acoustic models for articulatory features are more robust against variations in the speaking style compared to pure phone models. We present a streaming architecture which integrates articulatory features in a standard HMM based system. Using this approach, we achieved an error reduction of 25 . 1% for hyper-articulated speech and even 8 . 9% for normal speech without any use of hyperarticulated training data.
Optimal Portfolio Choice with Predictability in House Prices and Transaction Costs

We develop and solve a model of optimal portfolio choice with transaction costs and predictability in house prices. We model house prices using a process with a time-varying expected growth rate. Housing adjustments are infrequent and characterized by both the wealth-to-housing ratio and the expected growth in house prices. We find that the housing portfolio share immediately after moving to a more valuable house is higher during periods of high expected growth in house prices. We also find that the share of wealth invested in risky assets is lower during periods of high expected growth in house prices. Finally, the decrease in risky portfolio holdings for households moving to a more valuable house is greater in high-growth periods. These findings are robust to tests using household-level data from the Panel Study of Income Dynamics (PSID) and Survey of Income and Program Participation (SIPP) surveys. The coefficients obtained using model-simulated data are consistent with those obtained in the empirical tests.
Mutation in the Box a Increases the Risk of Hepatocellular Carcinoma in Patients with Chronic Hepatitis B Virus Genotype C Infection

Kiyoaki Ito, Yasuhito Tanaka, Etsuro Orito, Masaya Sugiyama, Kei Fujiwara, Fuminaka Sugauchi, Takanobu Kato, Hajime Tokita, Namiki Izumi, Michio Kato, Man-Fung Yuen, Ching-Lung Lai, Robert G. Gish, Ryuzo Ueda, and Masashi Mizokami Departments of Clinical Molecular Informative Medicine and Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Department of Gastroenterology, National Tokyo Hospital, and Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, and National Hospital Organization Osaka National Hospital, Osaka, Japan; Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong; and Division of Hepatology and Complex Gastroenterology, California Pacific Medical Center, San Francisco
The role of the lymphatic system in cholesterol transport

Reverse cholesterol transport (RCT) is the pathway for removal of peripheral tissue cholesterol and involves transport of cholesterol back to liver for excretion, starting from cellular cholesterol efflux facilitated by lipid-free apolipoprotein A1 (ApoA1) or other lipidated high-density lipoprotein (HDL) particles within the interstitial space. Extracellular cholesterol then is picked up and transported through the lymphatic vasculature before entering into bloodstream. There is increasing evidence supporting a role for enhanced macrophage cholesterol efflux and RCT in ameliorating atherosclerosis, and recent data suggest that these processes may serve as better diagnostic biomarkers than plasma HDL levels. Hence, it is important to better understand the processes governing ApoA1 and HDL influx into peripheral tissues from the bloodstream, modification and facilitation of cellular cholesterol removal within the interstitial space, and transport through the lymphatic vasculature. New findings will complement therapeutic strategies for the treatment of atherosclerotic vascular disease.
Simulation and Optimization in an AGC System after Deregulation

In this paper, the traditional AGC two-area system is modified to take into account the effect of bilateral contracts on the dynamics. The concept of DISCO participation matrix to simulate these bilateral contracts is introduced and reflected in the two-area block diagram. Trajectory sensitivities are used to obtain optimal parameters of the system using a gradient Newton algorithm.
Natural Shocks and Risk Behavior : A Concise Review of Literature

Increasing occurrence of devastating natural shocks has stimulated research interest in the economics of natural disasters. Much of this scholarly work concentrates on effects of shocks on poverty, risk and vulnerability, and very little on understanding the effects of natural shocks on risk behavior. Referring to a 24 year-old disaster, we use unique survey data and experiment results from two disaster affected communities in rural Cameroon to test two hypotheses: (1) Natural shocks affect long term risk behavior; and (2) self-relocation into risk-prone areas is an explicit demonstration of risk taking. The results reveal differentiated risk behavior in self-relocated and stateresettled households, with the former taking higher risks compared to resettled households. Experiments strongly support trends observed in the empirical study, but captured cognitive behavior better than the survey. Results support previous evidence on applying experiments in understanding cognitive risk behavior and confirm our hypotheses.
Targeting algorithms for online social advertising markets

Advertisers in online social networks (OSNs) like Facebook and LinkedIn have some preferred set of users they wish to reach by showing their ads. OSNs offer fine-grained sets of user characteristics - including their career, wealth, education information, etc - that advertisers can specify for targeting their audience, and each of these characteristics requires different amounts of money for targeting. The problem we address is what we call the targeting problem, that is, given a set ST characteristics of interest to an advertiser (that is, the advertiser wishes to reach users who have these characteristics, i.e. U(ST)) and a budget b0 he wishes to spend, how to split the budget among the user characteristics so that they can reach the most number of users in U(ST)? ; OSN-perspective. OSNs have complete knowledge of each user and their characteristics. In this case, we propose a polynomial time algorithm for the targeting problem and prove that it is an 1-1/e approximation to the targeting that gets the optimal number of users. We define the marginal increment and iteratively maximize it. ; Advertiser-perspective. No single advertiser has the mapping of users to their characteristics or the distribution of users over the characteristics, and hence they cannot use the algorithm from above. We show through empirical data analysis that the strategy of targeting subsets U(S) ⊆ U(ST) is their only feasible approach (in other words, targeting U(S) ⊈ U(ST) will be arbitrarily worse than the direct solution). For evaluation, we crawl and analyze more than one million suggested bids from Facebook and LinkedIn. Further, we propose a fast greedy algorithm for the targeting problem based on targeting subsets, that in empirical analysis, increases the number of reached preferred users by nearly 40% over directly targeting the characteristics of interest, and for a moderate budget, it increases the number of reached preferred users by nearly 20%.
Human CD 34 + CD 133 + Hematopoietic Stem Cells Cultured with Growth Factors Including Angptl 5 Efficiently Engraft Adult NOD-SCID Il 2 r # − / − ( NSG ) Mice

Increasing demand for human hematopoietic stem cells (HSCs) in clinical and research applications necessitates expansion of HSCs in vitro. Before these cells can be used they must be carefully evaluated to assess their stem cell activity. Here, we expanded cord blood CD34 CD133 cells in a defined medium containing angiopoietin like 5 and insulin-like growth factor binding protein 2 and evaluated the cells for stem cell activity in NOD-SCID Il2rg (NSG) mice by multi-lineage engraftment, long term reconstitution, limiting dilution and serial reconstitution. The phenotype of expanded cells was characterized by flow cytometry during the course of expansion and following engraftment in mice. We show that the SCID repopulating activity resides in the CD34 CD133 fraction of expanded cells and that CD34 CD133 cell number correlates with SCID repopulating activity before and after culture. The expanded cells mediate long-term hematopoiesis and serial reconstitution in NSG mice. Furthermore, they efficiently reconstitute not only neonate but also adult NSG recipients, generating human blood cell populations similar to those reported in mice reconstituted with uncultured human HSCs. These findings suggest an expansion of long term HSCs in our culture and show that expression of CD34 and CD133 serves as a marker for HSC activity in human cord blood cell cultures. The ability to expand human HSCs in vitro should facilitate clinical use of HSCs and large-scale construction of humanized mice from the same donor for research applications. Citation: Drake AC, Khoury M, Leskov I, Iliopoulou BP, Fragoso M, et al. (2011) Human CD34 CD133 Hematopoietic Stem Cells Cultured with Growth Factors Including Angptl5 Efficiently Engraft Adult NOD-SCID Il2rc (NSG) Mice. PLoS ONE 6(4): e18382. doi:10.1371/journal.pone. 0018382 Editor: John J. Rossi, Beckman Research Institute of the City of Hope, United States of America Received October 20, 2010; Accepted March 3, 2011; Published April 29, 2011 Copyright: 2011 Drake 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. Funding: This work has been supported by the Singapore MIT Alliance for Research and Technology Infectious disease research grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Harvey Lodish has applied for a patent on the culture method used. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials. * E-mail: jchen@mit.edu . These authors contributed equally to this work.
Diurnal availability for peer-to-peer systems

Ensuring content availability in a persistent manner is essential for providing any consistent service over peer-to-peer (P2P) systems. This paper introduces an efficient protocol, called DATA, to design highly available P2P systems irrespective of peer uptime and churn. Our approach utilizes the diurnal pattern of globally dispersed peers to develop a grouping strategy where each group aims to ensure 24 × 7 data availability within the group. Simulation results reveal that our protocol converges fast and ensures high availability for each group with minimal overhead.