Miracle-dz/UniFAR-FTUs huggingface dataset:
Transmission dynamics of foot and mouth disease in selected outbreak areas of northwest Ethiopia

Abstract Foot and mouth disease (FMD) is a highly contagious and economically important disease of cloven-hoofed animals, which is endemic in Ethiopia. An outbreak follow-up study was undertaken to quantify the transmission parameters of FMD in the crop–livestock mixed (CLM) system and commercial dairy farms in selected areas of northwest Ethiopia. The transmission parameters were quantified using a generalised linear model (GLM) based on a susceptible–infectious–recovered (SIR) epidemic model. The per day average transmission rate between animals was 0.26 (95% CI 0.22–0.32) and 0.33 (95% CI 0.21–0.57) in the CLM system and in the commercial dairy farms, respectively. The average basic reproduction ratio of FMD was 1.68 (95% CI 1.42–2.07) in the CLM system and 1.98 (95% CI 1.26–3.42) in the commercial dairy farms. The medium per day transmission rate and moderate basic reproduction ratio observed in this study indicated that a vaccination coverage needed to stop transmission of the disease in these populations might not be very high.
The clinical course of DSM-5 alcohol use disorders in young adult native and Mexican Americans.

BACKGROUND AND OBJECTIVES To determine if the clinical course of DSM-5 alcohol use disorders (AUD) in select populations of young adults (18-30 years) differed based on gender, diagnostic severity (mild, moderate, severe), and ethnicity. METHODS Native Americans (NA) and Mexican Americans (MA) (n = 1,129) were recruited from the community and completed a structured diagnostic interview. Participants with DSM-5 AUDs were compared based on gender, severity of the disorder (mild, moderate, severe), and ethnicity for differences in drinking levels, as well as the clinical course of AUD as defined by the occurrence and sequence of 36 alcohol-related life events. RESULTS Seventy percent of the NA men, 64% of the NA women, 56% of the MA men, and 42% of the MA women met lifetime diagnostic criteria for a DSM-5 AUD. NA reported more alcohol-related life events and at an earlier age than MA. A high degree of similarity in the clinical course was found between men and women and between those with severe or moderate disorder, but not with those with mild disorder. CONCLUSIONS NA had higher drinking levels and more alcohol problems at an earlier age than MA. A similar clinical course was seen based on gender and ethnicity in these young adults, but not based on diagnostic severity. SCIENTIFIC SIGNIFICANCE The DSM-5 mild AUD category differs from the moderate and severe categories on drinking history, clinical course, gender, and ethnic distribution. Mild AUD may not be in the same clinical continuum as moderate and severe AUD in these populations.
Dopamine levels modulate the updating of tastant values

To survive, animals must constantly update the internal value of stimuli they encounter; a process referred to as incentive learning. Although there have been many studies investigating whether dopamine is necessary for reward, or for the association between stimuli and actions with rewards, less is known about the role of dopamine in the updating of the internal value of stimuli per se. We used a single‐bottle forced‐choice task to investigate the role of dopamine in learning the value of tastants. We show that dopamine transporter knock‐out mice (DAT‐KO), which have constitutively elevated dopamine levels, develop a more positive bias towards a hedonically positive tastant (sucrose 400 mM) than their wild‐type littermates. Furthermore, when compared to wild‐type littermates, DAT‐KO mice develop a less negative bias towards a hedonically negative tastant (quinine HCl 10 mM). Importantly, these effects develop with training, because at the onset of training DAT‐KO and wild‐type mice display similar biases towards sucrose and quinine. These data suggest that dopamine levels can modulate the updating of tastant values, a finding with implications for understanding sensory‐specific motivation and reward seeking.
Probe-Free Digital PCR Quantitative Methodology to Measure Donor-Specific Cell-Free DNA after Solid-Organ Transplantation.

BACKGROUND Donor-specific cell-free DNA (dscfDNA) is increasingly being considered as a noninvasive biomarker to monitor graft health and diagnose graft rejection after solid-organ transplantation. However, current approaches used to measure dscfDNA can be costly and/or laborious. A probe-free droplet digital PCR (ddPCR) methodology using small deletion/insertion polymorphisms (DIPs) was developed to circumvent these limitations without compromising the quantification of dscfDNA. This method was called PHABRE-PCR (Primer to Hybridize across an Allelic BREakpoint-PCR). The strategic placement of one primer to hybridize across an allelic breakpoint ensured highly specific PCR amplification, which then enabled the absolute quantification of donor-specific alleles by probe-free ddPCR. METHODS dscfDNA was serially measured in 3 liver transplant recipients. Donor and recipient genomic DNA was first genotyped against a panel of DIPs to identify donor-specific alleles. Alleles that differentiated donor-specific from recipient-specific DNA were then selected to quantify dscfDNA in the recipient plasma. RESULTS Lack of amplification of nontargeted alleles confirmed that PHABRE-PCR was highly specific. In recipients who underwent transplantation, dscfDNA was increased at day 3, but decreased and plateaued at a low concentration by 2 weeks in the 2 recipients who did not develop any complications. In the third transplant recipient, a marked increase of dscfDNA coincided with an episode of graft rejection. CONCLUSIONS PHABRE-PCR was able to quantify dscfDNA with high analytical specificity and sensitivity. The implementation of a DIP-based approach permits surveillance of dscfDNA as a potential measure of graft health after solid-organ transplantation.
Chronic helminth infection and helminth‐derived egg antigens promote adipose tissue M2 macrophages and improve insulin sensitivity in obese mice

Chronic low‐grade inflammation associated with obesity contributes to insulin resistance and type 2 diabetes. Helminth parasites are the strongest natural inducers of type 2 immune responses, and short‐lived infection with rodent nematodes was reported to improve glucose tolerance in obese mice. Here, we investigated the effects of chronic infection (12 weeks) with Schistosoma mansoni, a helminth that infects millions of humans worldwide, on whole‐body metabolic homeostasis and white adipose tissue (WAT) immune cell composition in high‐fat diet‐induced obese C57BL/6 male mice. Our data indicate that chronic helminth infection reduced body weight gain (‐62%), fat mass gain (‐89%), and adipocyte size; lowered whole‐body insulin resistance (‐23%) and glucose intolerance (‐16%); and improved peripheral glucose uptake (+25%) and WAT insulin sensitivity. Analysis of immune cell composition by flow cytometry and quantitative PCR (qPCR) revealed that S. mansoni promoted strong increases in WAT eosinophils and alternatively activated (M2) macrophages. Importantly, injections with S. mansonir‐soluble egg antigens (SEA) recapitulated the beneficial effect of parasite infection on whole‐body metabolic homeostasis and induced type 2 immune responses in WAT and liver. Taken together, we provide novel data suggesting that chronic helminth infection and helminth‐derived molecules protect against metabolic disorders by promoting a T helper 2 (Th2) response, eosinophilia, and WAT M2 polarization. —Hussaarts, L. , García‐Tardón, N. , van Beek, L. , Heemskerk, M. M. , Haeberlein, S. , van der Zon, G. C. , Ozir‐Fazalalikhan, A. , Berbée, J. F. P., Willems van Dijk, K. , van Harmelen, V. , Yazdanbakhsh, M. , Guigas, B. Chronic helminth infection and helminth‐derived egg antigens promote adipose tissue M2 macrophages and improve insulin sensitivity in obese mice. FASEB J. 29, 3027‐3039 (2015). www.fasebj. org
An efficient lapped orthogonal transform image coding technique

A fast and computationally less complex coding technique is described which uses partial-lapped orthogonal transform (LOT) computation algorithm and efficiently discards perceptually insignificant high frequency transform coefficients. The coding process involves activity class energy classification, human visual system weighted normalization and quantization. The values of normalization factors are image independent and governed only by the bit-rate and activity index of the image blocks. Zones of various shapes and sizes are chosen for each activity class to perform zonal sampling which efficiently discards high frequency coefficients having zero values. A progressive transmission version of the proposed technique is also given. This technique gives better performance at comparable bit-rate than that obtained by using LOT/CVQ and LOT/VQ schemes.
Impact of authentic leadership practices of principals and the associated levels of teachers’ trust

The purpose of this comparative case analysis was to examine the authentic leadership practices of school leaders and the associated levels of teachers’ trust within the school setting. The level of trust between teachers and school administrators affects the school as a whole. “Without trust,” as Blase and Blase (2001) write, “a school cannot improve and grow into the rich, nurturing micro-society needed by children and adults alike” (p.25). Empirical qualitative literature that focuses on the leadership practices of school leaders and its effect on trust of teachers warrants further investigation. The comparative analysis addressed the following: an examination of authentic leadership, leadership practices in the public school system, the leadership practices that build trust among teachers and implications for administrators and building leaders. The findings suggest that when a principal was open, influential, articulate and credible, trust was created.
Cochlear Implantation in Children With Congenital and Noncongenital Unilateral Deafness: A Case Series

Objectives Cochlear implantation is rapidly gaining acceptance as the most effective treatment for adult patients with unilateral deafness. The benefits for the pediatric population remain to be investigated. This study aimed to investigate the implications of cochlear implantation in children with congenital and noncongenital unilateral deafness. Design Four children, three with congenital and one with a sudden unilateral deafness, were studied after implantation. The children were aged 17 months, 4.5 years, 6.8 years, and 9 years at the time of implantation. Speech perception in noise and sound localization ability were evaluated using age-appropriate materials. Results The child with postlingual unilateral deafness rapidly integrated the normal acoustic hearing with the electrical signal from the cochlear implant and showed binaural benefits, as indicated by the localization ability and the improvement of speech perception in noise scores. The younger child with congenital unilateral deafness showed some clinical evidence of binaural integration and the two older children with congenital deafness have not yet indicated signs of binaural benefits. Conclusion It seems that cochlear implantation in children with congenital unilateral deafness may provide some of the benefits of binaural hearing if implantation occurs within the critical period for bilateral auditory development.
BopA has no major role in the adhesion of Bifidobacterium bifidum to 1 intestinal epithelial cells , extracellular matrix proteins and mucus 2

28 The ability of bifidobacteria to adhere to the intestine of human host is considered to be 29 important for efficient colonization and achieving probiotic effects. Bifidobacterium 30 bifidum strains DSM20456 and MIMBb75 adhere well to human intestinal cell lines, 31 Caco-2 and HT-29. Surface lipoprotein BopA has previously been described to be 32 involved in mediating adherence of B. bifidum to epithelial cells, but experiments with 33 thioacylated, purified BopA inhibited the adhesion of B. bifidum to epithelial cells in 34 competitive adhesion assays only in very high concentrations indicating an unspecific 35 effect. In this study, the role of BopA in the adhesion of B. bifidum was re-addressed. 36 The gene encoding BopA was cloned and expressed without its lipobox and hydrophobic 37 signal peptide in Escherichia coli, and an antiserum against the recombinant BopA was 38 produced. The antiserum was used to demonstrate the abundant localization of BopA 39 on the cell surface of B. bifidum. However, blocking of B. bifidum BopA with specific 40 antiserum did not reduce adhesion of bacteria to epithelial cell lines arguing that BopA 41 is not an adhesin. Also adhesion of B. bifidum to human colonic mucin and fibronectin 42 was found to be BopA independent. The recombinant BopA was bound only moderately 43 to human epithelial cells and colonic mucus and it failed to bind to fibronectin. Thus, 44 our results contrast the earlier findings on the major role of BopA in adhesion, 45 indicating that the strong adhesion of B. bifidum to epithelial cell lines is BopA 46 independent. 47
Vehicle Miles Traveled, Fuel Economy Efficiency And Costs of Corporate Average Fuel Economy Standard

This paper investigates how fuel economy efficiency affects household vehicle mileage traveled and its distribution. Using a detailed micro-level data of National Household Travel Survey 2001 and 2008, we estimated a recursive structural model for joint determination of vehicle fuel efficiency choice and vehicle mileage traveled each year. We further studied the distributional effects on vehicle miles of fuel efficiency using quantile regression. Comparison on results and tests of weak instruments between our method with literature suggest that using choice probabilities as instruments is not valid and our model and choice of instruments gives consistent estimates. Based on estimation results, we compared the mean effects and distributional effect of vehicle fuel efficiency over time andsimulate the effect of raising CAFE standard.
An introduction to function rank

This paper gives a simple introduction to the concepts of Function Rank and the Rank Operator as they are defined in SHARP APL, and presents examples of their use. It shows the benefits, both in language design and in practice, of these concepts. Comparisons are made with other APL implementations, which do not use these concepts.
Homogenization of Linear Transport Equations in a Stationary Ergodic Setting

We study the homogenization of a linear kinetic equation which models the evolution of the density of charged particles submitted to a highly oscillating electric field. The electric field and the initial density are assumed to be random and stationary. We identify the asymptotic microscopic and macroscopic profiles of the density, and we derive formulas for these profiles when the space dimension is equal to one.
Complex formation by positive and negative translational regulators of GCN4

GCN4 is a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae whose expression is regulated by amino-acid availability at the translational level. GCD1 and GCD2 are negative regulators required for the repression of GCN4 translation under nonstarvation conditions that is mediated by upstream open reading frames (uORFs) in the leader of GCN4 mRNA. GCD factors are thought to be antagonized by the positive regulators GCN1, GCN2 and GCN3 in amino acid-starved cells to allow for increased GCN4 protein synthesis. Previous genetic studies suggested that GCD1, GCD2, and GCN3 have closely related functions in the regulation of GCN4 expression that involve translation initiation factor 2 (eIF-2). In agreement with these predictions, we show that GCD1, GCD2, and GCN3 are integral components of a high-molecular-weight complex of approximately 600,000 Da. The three proteins copurified through several biochemical fractionation steps and could be coimmunoprecipitated by using antibodies against GCD1 or GCD2. Interestingly, a portion of the eIF-2 present in cell extracts also cofractionated and coimmunoprecipitated with these regulatory proteins but was dissociated from the GCD1/GCD2/GCN3 complex by 0.5 M KCl. Incubation of a temperature-sensitive gcdl-101 mutant at the restrictive temperature led to a rapid reduction in the average size and quantity of polysomes, plus an accumulation of inactive 80S ribosomal couples; in addition, excess amounts of eIF-2 alpha, GCD1, GCD2, and GCN3 were found comigrating with free 40S ribosomal subunits. These results suggest that GCD1 is required for an essential function involving eIF-2 at a late step in the translation initiation cycle. We propose that lowering the function of this high-molecular-weight complex, or of eIF-2 itself, in amino acid-starved cells leads to reduced ribosomal recognition of the uORFs and increased translation initiation at the GCN4 start codon. Our results provide new insights into how general initiation factors can be regulated to affect gene-specific translational control.
Dynamic force spectroscopy of single DNA molecules.

To explore the analytic relevance of unbinding force measurements between complementary DNA strands with an atomic force microscope, we measured the forces to mechanically separate a single DNA duplex under physiological conditions by pulling at the opposite 5'-ends as a function of the loading rate (dynamic force spectroscopy). We investigated DNA duplexes with 10, 20, and 30 base pairs with loading rates in the range of 16-4,000 pN/s. Depending on the loading rate and sequence length, the unbinding forces of single duplexes varied from 20 to 50 pN. These unbinding forces are found to scale with the logarithm of the loading rate, which is interpreted in terms of a single energy barrier along the mechanical separation path. The parameters describing the energy landscape, i.e. , the distance of the energy barrier to the minimum energy along the separation path and the logarithm of the thermal dissociation rate, are found to be proportional to the number of base pairs of the DNA duplex. These single molecule results allow a quantitative comparison with data from thermodynamic ensemble measurements and a discussion of the analytic applications of unbinding force measurements for DNA.
Language model adaptation based on correction information for interactive speech transcription

Aiming at language model (LM) adaptation for interactive speech transcription, this paper proposes a topic-based adaptation method using users' correction information. To infer the topic for each utterance in continuous speech, this method uses the correction information of history utterances adjacent to the current one. Perplexity is calculated for topic inference. Topic-related LMs are interpolated with background LM to obtain adapted LMs. Each utterance is transcribed using the adapted model. This method is a supervised adaptation method which is believed to outperform the unsupervised approaches widely used in current speech recognition applications, since it uses the history of user correction. And this method is an online adaptation method for it adapts models before transcribing each utterance. Besides, utterance-level adaptation makes the adapted model much more precise for each utterance. Experimental results have shown that this method raises the average recognition accuracy rates by 2–6 percentage points.
Development of Hardware In-the-Loop Simulation System for Testing Operation and Control Functions of Microgrid

This paper proposes a hardware in-the-loop simulation (HILS) system as a new method to develop and test control algorithms and operation strategies for a microgrid. The HILS system is composed of a real-time digital simulator (RTDS) for real-time simulation of the microgrid, a prototype microgrid management system (MMS) under test, and a communication emulator for interface between the prototype MMS and the RTDS. The prototype MMS is designed to operate microsources of microgrid and to control power flow at the point of common coupling (PCC) in the grid-connected mode, and voltages and frequency in the islanded mode of the microgrid. The MMS is tested in the grid-connected mode and in the islanded mode, respectively, to show the validation of the proposed HILS system.
Nonselective and efficient fluorescent labeling of glycans using 2-amino benzamide and anthranilic acid.

Reaction conditions for conjugation of two fluorescent ortho-substituted aniline derivatives, 2-amino benzamide (2-AB) and 2-anthranilic acid (2-AA), to N- and O-glycans have been investigated. Conjugation conditions for attaching 2-AB and 2-AA to core-fucosylated and non-fucosylated glycans were developed using complex N-glycans radiolabeled at the nonreducing terminus with [3H]C6-galactose. Optimal conditions for each of the following reaction parameters were experimentally defined: [glycans], [2-AB] or [2-AA], solvent and acid composition, temperature and time of Schiff's base formation, nature of reductant, and temperature and time of reduction. Using the optimized reaction conditions it has been shown with several standard glycans and glycoprotein-derived glycan libraries that (i) molar labeling efficiencies are high and essentially independent of the amount of glycans; (ii) negligible (< 2 mol%) desialylation occurs during conjugation; (iii) glycan labeling is nonselective, i.e., independent of glycan structure; and (iv) insignificant fluorescent or chemical "blank" is recovered during the glycan-labeling and purification protocol. Labeling glycan pools with 2-AB or 2-AA therefore allows representative glycan profiles to be obtained and also allows relative molar quantitation of individual glycans in a pool. The 2-AB label is compatible with several chromatographic means for separation of carbohydrates including Bio Gel P4 gel permeation, high-performance anion-exchange chromatography with fluorescence detection, and a variety of HPLC procedures, as well as with mass spectrometric methods including matrix-assisted laser desorption-mass spectrometry and electrospray-mass spectrometry. The 2-AA label is particularly well-suited for electrophoretic separations by polyacrylamide gel electrophoresis. These fluorophores show high intrinsic sensitivity and thus facilitate very sensitive analysis of protein glycosylation.
Microbiological quality of organic vegetables produced in soil treated with different types of manure and mineral fertilizer

An attempt was made to evaluate microbiological quality of horticultural crops grown organically. Three species of vegetables were used, lettuce (Lactuva sativa), radish (Raphanus sativus) and spinach (Tetragonia expansa), grown organically, in fertile soil. Six different treatments were applied: mineral fertilizer, chicken, cow, and pig manure, chicken litter and cow manure, in association with a liquid foliar biofertilizer. These crops were handled according to correct agronomic practices for growing crops organically for commercial purposes. Samples were examined for the Most Probable Number (MPN/g/mL) of total and fecal coliforms and to detect the presence of Escherichia coli and Salmonella spp. All analyzed samples were considered acceptable for consumption, as Salmonella spp. was not detected. However, 63.3%, 50.0%, and 23.3% of the samples of lettuce, radish and spinach, respectively, contained >102 total coliforms/g of product. None of the samples of spinach or radish presented >102 fecal coliforms/g, and only 6.6% of lettuce samples contained >102 fecal coliforms/g. The presence of E. coli was confirmed in one sample of spinach, cultivated with cow manure.