Miracle-dz/UniFAR-FTUs huggingface dataset:
The Transcriptome Signature of the Receptive Bovine Uterus Determined at Early Gestation

Pregnancy success is critical to the profitability of cattle operations. However, the molecular events driving the uterine tissue towards embryo receptivity are poorly understood. This study aimed to characterize the uterine transcriptome profiles of pregnant (P) versus non-pregnant (NP) cows during early pregnancy and attempted to define a potential set of marker genes that can be valuable for predicting pregnancy outcome. Therefore, beef cows were synchronized (n=51) and artificially inseminated (n=36) at detected estrus. Six days after AI (D6), jugular blood samples and a biopsy from the uterine horn contralateral to the ovary containing the corpus luteum were collected. Based on pregnancy outcome on D30, samples were retrospectively allocated to the following groups: P (n=6) and NP (n=5). Both groups had similar plasma progesterone concentrations on D6. Uterine biopsies were submitted to RNA-Seq analysis in a Illumina platform. The 272,685,768 million filtered reads were mapped to the Bos Taurus reference genome and 14,654 genes were analyzed for differential expression between groups. Transcriptome data showed that 216 genes are differently expressed when comparing NP versus P uterine tissue (Padj≤0.1). More specifically, 36 genes were up-regulated in P cows and 180 are up-regulated in NP cows. Functional enrichment and pathway analyses revealed enriched expression of genes associated with extracellular matrix remodeling in the NP cows and nucleotide binding, microsome and vesicular fraction in the P cows. From the 40 top-ranked genes, the transcript levels of nine genes were re-evaluated using qRT-PCR. In conclusion, this study characterized a unique set of genes, expressed in the uterus 6 days after insemination, that indicate a receptive state leading to pregnancy success. Furthermore, expression of such genes can be used as potential markers to efficiently predict pregnancy success.
A TolC-Like Protein of Actinobacillus pleuropneumoniae Is Involved in Antibiotic Resistance and Biofilm Formation

Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a significant disease that causes serious economic losses to the swine industry worldwide. Persistent infections caused by bacterial biofilms are recalcitrant to treat because of the particular drug resistance of biofilm-dwelling cells. TolC, a key component of multidrug eﬄux pumps, are responsible for multidrug resistance (MDR) in many Gram-negative bacteria. In this study, we identified two TolC-like proteins, TolC1 and TolC2, in A. pleuropneumoniae. Deletion of tolC1, but not tolC2, caused a significant reduction in biofilm formation, as well as increased drug sensitivity of both planktonic and biofilm cells. The genetic-complementation of the tolC1 mutation restored the competent biofilm and drug resistance. Besides, biofilm formation was inhibited and drug sensitivity was increased by the addition of phenylalanine-arginine beta-naphthylamide (PAβN), a well-known eﬄux pump inhibitor (EPI), suggesting a role for EPI in antibacterial strategies toward drug tolerance of A. pleuropneumoniae. Taken together, TolC1 is required for biofilm formation and is a part of the MDR machinery of both planktonic and biofilm cells, which could supplement therapeutic strategies for resistant bacteria and biofilm-related infections of A. pleuropneumoniae clinical isolate SC1516.
Seasonal variations of hydrological cycle components in the Mississippi River basin from a MAPS version with snow and frozen soil physics

A coupled atmospheric/land-surface model covering the conterminous United States with an associated 1-hour atmospheric data assimilation cycle, the Mesoscale Analysis and Prediction System (MAPS), has been improved to include snow and frozen soil physics. The new aspects of the land-surface model are described in this paper, along with detailed one-dimensional (1-D) tests. These tests show that the MAPS 1-D soil/vegetation/snow model is capable of providing accurate simulations over multi-year periods at locations with significant snow and frozen soil processes. The performance of the full 3-D model/assimilation system running at a 40-km resolution over a 9-month period from November 1997 through July 1998 is then examined. Soil moisture and temperature at multiple levels have been cycled in MAPS since April 1996 and snow water equivalent depth and snow temperature since March 1997. Cycling of these fields gives estimates that are physically consistent with the evolution of atmospheric fields over this fairly long period and are vastly improved over climatological estimates. Precipitation and surface temperature fields show good agreement with monthly analyses from the National Climatic Data Center (NCDC) in the 9-month comparison. Soil moisture fields and hydrological cycle components such as precipitation-minus-evaporation, snow accumulation, snow melt, and surface runoff are also examined from the MAPS cycle and are qualitatively reasonable and mutually consistent. Some needed improvements for MAPS are indicated by these experiments, including reducing moderate spin-up in 0-1 hour precipitation forecasts by improving initial cloud/moisture fields and eliminating biases in convec-tive precipitation over warm oceans and nearby land areas. Overall, the results indicate a system with continuous cycling of soil and snow fields and frequent data assimilation, accurate model physics, and good overall model performance, can provide good seasonal as well as short-range estimates of unobserved components of the hydrological cycle.
Synthesis of High-Level Decision Diagrams for functional test pattern generation

In this paper we present two methods for synthesis of High-Level Decision Diagrams (HLDD) for representing digital systems at higher behavior, functional or register-transfer levels. The first method is based on symbolic execution of procedural descriptions, which corresponds to functional representation of systems on the behavioral level. The second one is based on iterative superposition of HLDDs, and the created model corresponds to the high-level structural representation of the system. The second method can be regarded as the generalization of the superposition of BDDs as the basis for generation of Structurally Synthesized BDDs (SSBDD). Experimental data show the advantages of HLDDs)
Nutritional evaluation in cirrhosis: Emphasis on the phase angle

Protein-calorie malnutrition (PCM) is a common condition in cirrhotic patients, leading to a worse prognosis, complications, poor quality of life and lower survival rates. Among ways of assessing nutritional status, there are anthropometric methods such as the evaluation of the triceps skinfold, the arm circumference, the arm muscle circumference and the body mass index, and non-anthropometric methods such as the subjective global assessment, the handgrip strength of non-dominant hand, and the bioelectrical impedance analysis (BIA). PCM is frequently under-diagnosed in clinical settings in patients with cirrhosis due to the limitations of nutritional evaluation methods in this population. BIA is a useful method, but cannot be indicated in patients with abnormal body composition. In these situations, the phase angle (PA) has been used, and can become an important tool in assessing nutritional status in any situation. The PA is superior to anthropometric methods and might be considered as a nutritional indicator in cirrhosis. The early characterization of the nutritional status in patients with cirrhosis means an early nutritional intervention, with a positive impact on patients’ overall prognosis. Among the usually accepted methods for nutritional diagnosis, the PA provides information in a quick and objective manner.
Investigation of Social Skill Levels of Students in Physical Education and Sport Department

The purpose of this research is to compare physical education and sports teaching department students’ social skill levels according to their grade levels in a university. 192 volunteer students from two different universities (male = 110, female = 82; 39 1st grade, 47 2nd grade, 52 3rd grade and 54 4th grade) participated. Developed by Kocayörük (2000), the Social Skills Scale was used for collecting the data. For data analysis, exploratory factor analysis, descriptive statistics and one-way analysis of variance (ANOVA) was performed. Statistical anaysis showed mean differences among grades levels but these differences were not statistically meaningful [F (3,189) = 2:46; p = . 064)]. Looking mean differences among grade levels (for 1st grade X = 3.43, SD = .44; for 2nd grade X = 3.40, SD = .25; for 3rd grade X = 3.33, SD = .34 and for 4th grade X = 3.50, SD = .38), it was found high social skill mean scores of physical educatşon and sport department students. One of the reasons can be sports’ positive contribution on the social skills of individuals. In future research, therefore, can be proformed to examine social skill differences between students who are active, regularly engaged in sports and inactive students. In addition, different scales of social skills can be used in future studies.
Two Subsets of Large Vessel Vasculitis Characterized by the Absence or Presence of Spondyloarthritis or its Associated Diseases

Background: Whilst large vessel vasculitis (LVV) predominantly occurs in isolation, associations with other infectious and non-infectious diseases have been reported. Limited data describing associations with various autoimmune diseases (AI), including spondyloarthritis exists. The aim of this study was to characterize the association of LVV and spondyloarthritis or its associated diseases (SpAD). Methods: A single centre, retrospective study of patients ≥50yrs with first presentation LVV between 01.06. 2008-01.06. 2015 was performed. Patients were categorized according to SpA or associated disease, other AI or idiopathic LVV (iLVV). Clinical, laboratory and imaging findings were compared. Kaplan-Meyer survival analysis, with relapse taken as the primary end-point, was performed. Results: LVV was confirmed in 62 pts, of who 16/62 (26%) had SpA or associated disease. In these patients, LVV presented earlier (59.2 SpAD vs. 68.1 AI and 70.3yrs iLVV; p=0.01) and occurred predominantly in spring compared to autumn and winter in non-SpA patients, was associated with more centralised pattern of distribution (p=0.05) and was more likely to exhibit a refractory course (p=0.05). Overall relapse rates were similar across groups. Smoking-status influenced age of onset in all groups, being associated with earlier onset. Conclusion: A clear association between LVV and SpAD exists. LVV associated with SpAD has a particular phenotype characterised by earlier onset, thorax-limited disease and increased risk of a refractory course. Given on-going LVV treatment trials further genetic and pathophysiological characterization appears warranted, to evaluate potential variation in treatment response and optimize future care.
Macroecology of Caribbean Bats: Effects of Area, Elevation, Latitude, and Hurricane-Induced Disturbance

Understanding the geographic and environmental characteristics of islands that affect aspects of biodiversity is a major theme in ecology (Begon et al. 2006; Krebs 2001) and biogeography (Cox and Moore 2000; Drakare et al. 2006; Lomolino et al. 2006). Such understanding has become particularly relevant over the past century because human activities on continents have fragmented natural landscapes, often creating islands of isolated habitat dispersed within a sea of land uses that include agriculture, forestry, and various degrees of urban and suburban development. The increasingly fragmented or islandlike structure of mainland habitats has critical ramifications to conservation biology, as it provides insights regarding the mechanisms leading to species persistence and loss. Consequently, the study of patterns and mechanisms associated with island biodiversity is of interest in its own right (Whittaker 1998; Williamson 1981), and may provide critical insights into mainland phenomena that otherwise could not be studied because of ethical, financial, or logistical considerations involved with the execution of large-scale manipulative experiments.
Naive Bayes vs. Decision Trees vs. Neural Networks in the Classification of Training Web Pages

Web classification has been attempted through many different technologies. In this study we concentrate on the comparison of Neural Networks (NN), Naive Bayes (NB) and Decision Tree (DT) classifiers for the automatic analysis and classification of attribute data from training course web pages. We introduce an enhanced NB classifier and run the same data sample through the DT and NN classifiers to determine the success rate of our classifier in the training courses domain. This research shows that our enhanced NB classifier not only outperforms the traditional NB classifier, but also performs similarly as good, if not better, than some more popular, rival techniques. This paper also shows that, overall, our NB classifier is the best choice for the training courses domain, achieving an impressive F-Measure value of over 97%, despite it being trained with fewer samples than any of the classification systems we have encountered.
Quantitative analysis of synaptic distribution along thalamocortical axons in adult mouse barrels

Quantitative data on thalamocortical synapses in adult mouse barrels have been obtained largely by using lesion‐nduced degeneration to label thalamic afferents. By the time degenerating axons can be identified with the electron microscope, they have broken up into many separate pieces, making it impossible to assess the distribution of synapses along unbroken lengths of afferent. Here, this deficiency is rectified by examining intact lengths of axon labeled by the injection of biotinylated dextran amine into ipsilateral thalamus. Serial thin section reconstructions were analyzed to determine the numbers of synapses per axon length made with dendritic spines vs. shafts and the locations of synapses with respect to axonal varicosities. Results for seven axonal segments from six mice showed an average of 0.2 synapses/μm; 80% were made with spines and 20% with dendritic shafts. Just over two‐thirds of axonal varicosities formed one synapse; most of the remainder formed two and rarely three, whereas 8% formed none. Although most synapses occurred at varicosities (88%), more than 12% were made at cylindrically shaped regions of the reconstructed axonal segments. These results serve as a caveat for the use of light microscopy to quantify synapses, wherein the usual approach is to equate one varicosity with one synapse. For thalamocortical afferents to mouse barrels, equating one varicosity with one synapse would prove to be incorrect more than 30% of the time and would exclude the roughly 12% of synaptic connections made at cylindrical regions of thalamocortical afferents. J. Comp. Neurol. 479:56–69, 2004. © 2004 Wiley‐Liss, Inc.
OUTSOURCING XBRL FINANCIAL STATEMENT FILING: A CASE STUDY OF PRACTICES IN TWO PUBLIC FIRMS

Publicly-held companies in the U.S. are now being required by the Securities Exchange Commission (SEC) to file their financial reports using the tagging standard of Extensible Business Reporting Language (XBRL). This interactive data requirement requires all U.S. traded firms to comply by 2011. Our case study examines two accelerated filers to gain insight into their decision whether to in-source or outsource implementation of XBRL filing based on the eight characteristics of the XBRL Client-Vendor Outsourcing Relationship [5]. The eight characteristics are (1) client-vendor relationship, (2) company size, (3) outsourcing contract, (4) intellectual property, (5) communication, (6) custom functionality, (7) task complexity, and (8) vendor’s skills.
Extensible and realistic modeling of resource contention in resource-constrained nodes

In the past, network performance has been strongly determined by the capacity of the wired or wireless links. In future, however, we can expect that with the emergence of resource-constrained nodes (e.g. software routers) and high-speed links (e.g. optical fiber), the network nodes themselves will be the bottleneck. To increase the packet processing of resource-constrained nodes, parallel processing with multi-core processors is required. Intra-node resource contention can have a strong negative impact on the corresponding network node and, therefore, also on the overall performance of the network. However, several commonly used network simulators only offer a rather simplistic node model and do not take into account intra-node resource contention. In particular, latencies and input queueing behavior of resource-constrained nodes are typically not modeled in current simulators. We propose a unified and extensible approach to model intra-node resource contention which enables us to identify and predict performance bottlenecks in current and future networks. We implemented our model as an extension to the network simulator ns-3. The simulation results show that our approach significantly outperforms the original ns-3 in terms of realistic modeling. This claim has been validated successfully by means of real testbed measurements.
Learning to be researchers in physical education and sport pedagogy: the perspectives of doctoral students and early career researchers

Numerous academics have argued that if a field is to progress, attention needs to be paid to how future generations of researchers are being prepared. To date, data generated on research training in physical education and sport pedagogy (PESP) have primarily focused on students undertaking doctoral programmes with a formal coursework component, which is the model predominantly used in the USA. The traditional master-apprentice model is still, however, the dominant model in many countries, including Australia, and there is a dearth of research on this model of research preparation. Hence, this study was an effort to capture the perspectives and experiences of doctoral students (DSs) and early career researchers (ECRs) who are/were engaged in programmes employing the apprentice model of training. The question we sought to examine was ‘what do PESP doctoral students and early career researchers perceive as the facilitators and challenges associated with learning to be researchers? ’. The participants in this study included eight DSs and seven ECRs who were based in Australian and New Zealand institutions. Data were generated through a questionnaire that sought to identify participants’ various research training experiences, a workshop that brought participants together to discuss their research training, and follow-up individual semi-structured interviews. While much of the data generated through this study related to the importance of developing such generic research skills as writing, grant writing and presenting at conferences, participants also discussed PESP-specific skills and dispositions, including particular orientations towards research impact, and the development of research culture. Findings are discussed in reference to the neoliberalisation of education and questions are raised about the forms of research training developing researchers in PESP might need if they are to thrive as researchers within and beyond the field.
Improving the effects of psychotherapy: The use of early identification of treatment and problem-solving strategies in routine practice.

Client-focused research systems have been developed to monitor and provide feedback information about clients' progress in psychotherapy as a method of enhancing outcome for those who are predicted to be treatment failures. In the current study, the authors examined whether feedback regarding client progress and the use of clinical support tools (CSTs) affected client outcome and number of sessions attended. Results showed that clients in the feedback plus CST group stayed in therapy longer and had superior outcomes. Nearly twice as many clients in the feedback plus CST group achieved clinically significant or reliable change, and fewer were classified as deteriorated by the time treatment ended.
Dopaminergic involvement in stimulus selection : a behavioural study

Author: Colm O Tuathaigh Title : Dopaminergic inyolvement in stimulus selection: A behavioural study People with schizophrenia show deficits in the inhibitory processes controlling stimulus selection. Overshadowing and the Kamin blocking effect provide examples of stimulus selection. Overshadowing refers to the phenomenon whereby greater learning accrues to the more salient stimulus of a compound presentation. Kamin blocking occurs when prior learning to a single stimulus in stage 1 disrupts learning to an added stimulus in stage 2, when both stimuli are presented in compound. Both paradigms measure the ability to select relevant and deselect irrelevant information from the stimulus environment, and are dependent upon cognitive processes hypothesised to be disrupted in schizophrenic patients. The study of the neural basis of such stimulus selection phenomena provides a putative model with construct validity for the information processing deficits seen in schizophrenia. A disturbance in central dopaminergic activity is thought to underlie the cognitive deficits of schizophrenia. In die present study, the effect of dopaminergic manipulations on Kamin blocking and overshadowing was assessed in the rat. The indirect dopamine agonist d-amphetamine (1.0 mg/kg, i.p.) disrupted Kamin blocking when administered at stage 2 conditioning. Amphetamine also abolished overshadowing when given at conditioning. It was concluded that amphetamine effects in both paradigms may consist of a selective increase in learning to the less salient stimulus. The DA antagonist haloperidol (0.2 mg/kg, i.p.) failed to reverse the attenuating effects of amphetamine (1.0 mg/kg, i.p.) on overshadowing. However, haloperidol (0.2 mg/kg & 0.5 mg/kg, i.p.) successfully reversed amphetamine-induced hyperlocomotion. Neither the selective D2 receptor antagonist raclopride (0.5 mg/kg, i.p.) nor the selective D2 receptor antagonist sulpiride (50 & 100 mg/kg, i.p.) restored overshadowing in amphetamine treated animals. SCH23390 (0.05 mg/kg, i.p.), the selective D1 receptor antagonist, restored overshadowing in amphetamine treated rats. The D1 receptor agonist SKF 38393 (5 mg/kg, i.p.) disrupted overshadowing in a manner similar to that observed following amphetamine treatment.
An evaluation of wearable activity monitoring devices

This paper examines an increasingly relevant topic in the multimedia community of wearable devices that record the physical activity of a user throughout a day. While activity and other accelerometry-based data has been shown effective in various multimedia applications -- from context-aware music retrieval to approximating carbon footprint -- the most promising role of these target application for healthcare and personal fitness. Recently, several low-cost devices have become available to consumers. In this paper, we perform an evaluation on the most popular devices available on the market (in particular Fitbit and Nike+) and report our findings in terms of accuracy, type of data provided, available APIs, and user experience. This information is useful for researchers considering incorporating these activity-based data streams into their research and for getting a better idea of the reliability and accuracy for use in life-logging and other multimedia applications.