Miracle-dz/UniFAR-FTUs huggingface dataset:
An observational study on tail biting in commercial grower- finisher barns

Methods: In two finishing barns, prevalence and severity of tail-biting lesions in docked pigs and association of bitten tails with gender were determined in a cross-sectional study. The associations with space allowance per pig, animal density, and barrow:gilt ratio per pen were examined. A matched case-control study determined the association between length of tail, severity of lesions on bitten tails, and chest girth (a surrogate measure of body weight). Results: In a total of 1895 pigs (58% barrows, 42% gilts), the prevalence of bitten tails was 16.3% (barrows 21%; gilts 9.4%). The odds of being a bitten barrow was 2.6 times higher than being a bitten gilt (P < .001). Approximately 60% of affected pigs of both genders had severe lesions. Neither prevalence nor severity of lesions was associated with space allowance, animal density, or barrow:gilt ratio within pen. The prevalence of bitten barrows was positively correlated with the percentage of gilts in the pen (r = 0.56, P = .001). Severely bitten pigs had significantly smaller chest girth than less affected pigs. No association of the severity of lesions with length of the tail was observed.
PINOCCHIO and the hierarchical build-up of dark matter haloes

ABSTRA C T We study the ability of PINOCCHIO (PINpointing Orbit-Crossing Collapsed HIerarchical Objects) to predict the merging histories of dark matter (DM) haloes, comparing the PINOCCHIO predictions with the results of two large N-body simulations run from the same set of initial conditions. We focus our attention on the quantities most relevant to galaxy formation and large-scale structure studies. PINOCCHIO is able to predict the statistics of merger trees with a typical accuracy of 20 per cent. Its validity extends to higher-order moments of the distribution of progenitors. The agreement is also valid at the object-byobject level, with 70 ‐ 90 per cent of the progenitors cleanly recognized when the parent halo is cleanly recognized itself. Predictions are also presented for quantities that are usually not reproduced by semi-analytic codes, such as the two-point correlation function of the progenitors of massive haloes and the distribution of initial orbital parameters of merging haloes. For the accuracy of the prediction and for the facility with which merger histories are produced, PINOCCHIO provides a means to generate catalogues of DM haloes, which is extremely competitive with large-scale N-body simulations, making it a suitable tool for galaxy formation and large-scale structure studies.
Anti-Bacterial Activity of Recombinant Human β-Defensin-3 Secreted in the Milk of Transgenic Goats Produced by Somatic Cell Nuclear Transfer

The present study was conducted to determine whether recombinant human β-defensin-3 (rHBD3) in the milk of transgenic goats has an anti-bacterial activity against Escherichia coli (E. coli), Staphylococcus aureus (S. aureus) and Streptococcus agalactiae (S. agalactiae) that could cause mastitis. A HBD3 mammary-specific expression vector was transfected by electroporation into goat fetal fibroblasts which were used to produce fourteen healthy transgenic goats by somatic cell nuclear transfer. The expression level of rHBD3 in the milk of the six transgenic goats ranged from 98 to 121 µg/ml at 15 days of lactation, and was maintained at 90–111 µg/ml during the following 2 months. Milk samples from transgenic goats showed an obvious inhibitory activity against E. coli, S. aureus and S. agalactiae in vitro. The minimal inhibitory concentrations of rHBD3 in milk against E. coli, S. aureus and S. agalactiae were 9.5–10.5, 21.8–23.0 and 17.3–18.5 µg/mL, respectively, which was similar to those of the HBD3 standard (P>0.05). The in vivo anti-bacterial activities of rHBD3 in milk were examined by intramammary infusion of viable bacterial inoculums. We observed that 9/10 and 8/10 glands of non-transgenic goats infused with S. aureus and E. coli became infected. The mean numbers of viable bacteria went up to 2.9×103 and 95.4×103 CFU/ml at 48 h after infusion, respectively; the mean somatic cell counts (SCC) in infected glands reached up to 260.4×105 and 622.2×105 cells/ml, which were significantly higher than the SCC in uninfected goat glands. In contrast, no bacteria was presented in glands of transgenic goats and PBS-infused controls, and the SSC did not significantly change throughout the period. Moreover, the compositions and protein profiles of milk from transgenic and non-transgenic goats were identical. The present study demonstrated that HBD3 were an effective anti-bacterial protein to enhance the mastitis resistance of dairy animals.
Association of Hospital Arrival Time with Modified Rankin Scale at Discharge in Patients with Acute Cerebral Infarction

This study evaluated the time interval from the development or recognition of a symptom to hospital arrival and investigated its association with the modified Rankin Scale (mRS) at discharge in patients with acute cerebral infarction. A registry was established with ischemic stroke patients admitted to an academic medical center in Korea from January 2005 to March 2009. The time interval between symptom onset and hospital arrival was recorded for each patient and analyzed along with the patient’s clinical characteristics and mRS at discharge. Regardless of initial severity at admission, mRS was significantly different between two groups of hospital arrival: within 3 h and beyond 3 h. Multiple regression analysis also showed more positive mRS scores for patients within the 3-hour arrival, controlling for other significant factors. The findings provided patients’ initiatives for early hospital arrival.
Public Reporting in Germany: the Content of Physician Rating Websites

Summary Background: Physician rating websites (PRWs) are gaining in popularity among patients seeking quality information about physicians. However, little knowledge is available about the quantity and type of information provided on the websites. Objective: To determine and structure the quantity and type of information about physicians in the outpatient sector provided on German-language physician rating websites. Methods: In a first step, we identified PRWs through a systematic internet search using German keywords from a patient´s perspective in the two search engines Google and Yahoo. Afterwards, information about physicians available on the websites was collected and categorised according to Donabedian´s structure/process/outcome model. Furthermore, we investigated whether the information was related to the physician himself/ herself or to the practice as a whole. Results: In total, eight PRWs were detected. Our analysis turned up 139 different information items on eight websites; 67 are related to the structural quality, 4 to process quality, 5 to outcomes, and 63 to patient satisfaction/experience. In total, 37% of all items focus specifically on the physician and 63% on the physician’s practice. In terms of the total amount of information provided on the PRWs, results range from 61 down to 13.5 items. Conclusions: A broad range of information is available on German PRWs. While structural information can give a detailed overview of the financial, technical and human resources of a practice, other outcome measures have to be interpreted with caution. Specifically, patient satisfaction results are not risk-adjusted, and thus, are not appropriate to represent a provider’s quality of care. Consequently, neither patients nor physicians should yet use the information provided to make their final decision for or against an individual physician.
Distinct Episodic Verbal Memory Profiles in Schizophrenia

According to some authors, episodic memory impairment may be a feature shared by all schizophrenic patients, whereas others argue in favor of the mnesic heterogeneity. Our aims were to determine whether patients can be grouped based on according to their mnesic performances. The California Verbal Learning Test (CVLT), an episodic verbal learning test, was compared in 61 schizophrenic patients and 61 matched healthy subjects. The 32 indices were calculated using CVLT Scoring Software. This process allowed us to describe patients’ episodic processes in detail (encoding, storage, retrieval). We isolated one group with normative data, another showed impairment of both encoding and retrieval processes, and in the last one, only encoding process was impaired. As schizophrenia is heterogeneous with regard to episodic memory, impairments should not be considered as a common core to the various forms of the illness and it would be fruitful to systematically assess episodic processes in detail to take into account individual abilities and challenges.
Evaluation of left renal vein and inferior vena cava variations through routine abdominal multi-slice computed tomography.

BACKGROUND The aim of this study was to evaluate the frequency of left renal vein (LRV) and inferior vena cava (IVC) variations and the effect of gender on this frequency, as well as the presence of associated abdominal pathologies. MATERIALS AND METHODS Multi-slice computed tomography (MSCT) images from 746 patients were evaluated retrospectively. RESULTS Left renal vein variations were identified in 9.8% of cases, while retroaortic LRV (RLRV) and circumaortic LRV (CLRV) were found in 7.4% and 2.4% of cases, respectively. No significant correlation was found between gender and LRV variations (p = 0.797). Of the cases with LRV and IVC variations, 73% had abdominal pathologies, the most common of which were nephrolithiasis, which appeared in 18 (32%) cases, and renal cysts, which appeared in 14 (25.4%) cases. CONCLUSIONS MSCT is a rapid and reliable method of identifying LRV and IVC variations and associated abdominal pathologies.
Twitter gender classification using user unstructured information

This paper describes an approach to automatically detect the gender of Twitter users, based only on clues provided by their profile information in an unstructured form. A number of features that capture phenomena specific of Twitter users is proposed and evaluated on a dataset of about 242K English language users. Different supervised and unsupervised approaches are used to assess the performance of the proposed features, including Naive Bayes variants, Logistic Regression, Support Vector Machines, Fuzzy c-Means clustering, and K-means. An unsupervised approach based on Fuzzy c-Means proved to be very suitable for this task, returning the correct gender for about 96% of the users.
LXY6090 – a novel manassantin A derivative – limits breast cancer growth through hypoxia-inducible factor-1 inhibition

Hypoxia-inducible factor-1 (HIF-1) represents a novel antitumor target owing to its involvement in vital processes considered hallmarks of cancer phenotypes. Manassantin A (MA) derived from Saururus cernuus has been reported as a selective HIF-1 inhibitor. Herein, the structure of MA was optimized to achieve new derivatives with simple chemical properties while retaining its activity. LXY6090 was designed to replace the central tetrahydrofuran moiety of MA with a cyclopentane ring and was identified as a potent HIF-1 inhibitor with an IC50 value of 4.11 nM. It not only inhibited the activity of HIF-1 in breast cancer cells but also downregulated the protein level of HIF-1α, which depended on von Hippel–Lindau for proteasome degradation. The related biological evaluation showed that the activity of HIF-1 target genes, VEGF and IGF-2, was decreased by LXY6090 in breast cancer cell lines. LXY6090 presented potent antitumor activity in vitro. Furthermore, LXY6090 showed in vivo anticancer efficacy by decreasing the HIF-1α expression in nude mice bearing MX-1 tumor xenografts. In conclusion, our data provide a basis for the future development of the novel compound LXY6090 as a potential therapeutic agent for breast cancer.
cis,cis,cis-(Acetato-κ2 O,O′)bis[1,2-bis(diphenylphosphanyl)ethane-κ2 P,P′]ruthenium(II) 0.75-trifluoromethanesulfonate 0.25-chloride

In the title RuII carboxylate compound, [Ru(C2H3O2)(C26H24P2)2](CF3O3S)0.75Cl0. 25, the distorted tris-bidentate octahedral stereochemistry about the RuII atom in the complex cation comprises four P-atom donors from two 1,2-bis(diphenylphosphanyl)ethane ligands [Ru—P = 2.2881 (13)–2.3791 (13) Å] and two O-atom donors from the acetate ligand [Ru—O = 2.191 (3) and 2.202 (3) Å]. The disordered counter-anions are located on the same site in the structure in a 3:1 ratio, the expanded formula comprising four complex cations, three trifluoromethanesulfonate anions and one chloride anion, with two such formula units in the unit cell.
Variational Relevance Vector Machines

The Support Vector Machine (SVM) of Vapnik (1998) has become widely established as one of the leading approaches to pattern recognition and machine learning. It expresses predictions in terms of a linear combination of kernel functions centred on a subset of the training data, known as support vectors. Despite its widespread success, the SVM suffers from some important limitations, one of the most significant being that it makes point predictions rather than generating predictive distributions. Recently Tipping (1999) has formulated the Relevance Vector Machine (RVM), a probabilistic model whose functional form is equivalent to the SVM. It achieves comparable recognition accuracy to the SVM, yet provides a full predictive distribution, and also requires substantially fewer kernel functions. The original treatment of the RVM relied on the use of type II maximum likelihood (the `evidence framework') to provide point estimates of the hyperparameters which govern model sparsity. In this paper we show how the RVM can be formulated and solved within a completely Bayesian paradigm through the use of variational inference, thereby giving a posterior distribution over both parameters and hyperparameters. We demonstrate the practicality and performance of the variational RVM using both synthetic and real world examples.
Fusobacterium and colorectal cancer: causal factor or passenger? Results from a large colorectal cancer screening study

Colorectal cancer is a leading cause of morbidity and mortality worldwide in both men and women. The gut microbiome is increasingly recognized as having an important role in human health and disease. Fusobacterium has been identified in former studies as a leading gut bacterium associated with colorectal cancer, but it is still not clear if it plays an oncogenic role. In the current study, fecal samples were collected prior to bowel preparation from participants of screening colonoscopy in the German BliTz study. Using 16S rRNA gene analysis, we examined the presence and relative abundance of Fusobacterium in fecal samples from 500 participants, including 46, 113, 110 and 231 individuals with colorectal cancer, advanced adenomas, non-advanced adenomas and without any neoplasms, respectively. We found that the abundance of Fusobacterium in feces was strongly associated with the presence of colorectal cancer (P-value < 0.0001). This was confirmed by PCR at the species level for Fusobacterium nucleatum. However, no association was seen with the presence of advanced adenomas (P-value = 0.80) or non-advanced adenomas (P-value = 0.80), nor were there any associations observed with dietary or lifestyle habits. Although a causal role cannot be ruled out, our observations, based on fecal microbiome, support the hypothesis that Fusobacterium is a passenger that multiplies in the more favorable conditions caused by the malignant tumor rather than a causal factor in colorectal cancer development.
Multiple exposure integration with image denoising

We propose a denoising technique for multiple exposure image integration. In our method, noise removal is achieved by the wavelet-shrinkage for multiple exposures, and a novel weighting scheme for the integration. A weighted image is converted to the low and the high frequency elements by the shift invariant wavelet transform, and the wavelet coefficient in the high frequencies are decreased by thresholding based on the wavelet-based hard shrinkage. The weight is designed to reduce sensor noise and quantization noise in the process of the multiple exposure integration. Our method works well especially for noise in shadow areas. We show the validity of the proposed algorithm by simulating the method with some actual noisy images.
Evaluation of the Yale-Brown Obsessive Compulsive Scale (YBOCS-hd) for heavy drinking with mild to moderately dependent alcohol abusers.

BACKGROUND Many similarities have been noted between urges and desires to drink heavily and obsessive-compulsive disorders (OCD). Based on such similarities, Modell et al. (1992) developed the Yale-Brown Obsessive Compulsive Scale for heavy drinking (YBOCS-hd), a modified version of YBOCS, to assess obsessions and compulsions related to heavy drinking. Evaluation of the YBOCS-hd has been limited to more severely dependent alcohol abusers. METHODS The present study used a self-administered version of the YBOCS-hd to evaluate (1) the severity of drinking-related obsessive compulsive symptoms with mild to moderately dependent alcohol abusers (problem drinkers), and (2) whether end-of-treatment changes in YBOCS-hd scores would be related to within-treatment functioning. RESULTS Results indicated that problem drinkers have lower alcohol-related Obsessive and Compulsive subscale scores than did more severely dependent drinkers, but higher scores than did non-problem drinkers, supporting the construct validity of the YBOCS-hd. In addition, at the end of treatment, the YBOCS-hd scores of alcohol abusers who drank at low-risk levels during treatment were significantly lower than the scores of those who drank at high-risk levels. Lastly, exploratory factor analysis did not provide support for the two purported YBOCS-hd subscales (Obsessive, Compulsive). Instead, the analysis yielded a single general factor and a second factor that contained two questions measuring heavy drinking. CONCLUSIONS Despite the fact that total YBOCS-hd scores covaried with drinking, neither the total YBOCS-hd pretreatment score nor the two subscale scores predicted functioning at the end of treatment. The present results call into question the utility of the YBOCS-hd, because a single item measuring the heaviness of drinking was as useful as the total YBOCS-hd and its two subscales in relating changes during treatment to end-of-treatment functioning for problem drinkers. However, although the YBOCS-hd does not predict changes in drinking, it may have value as an indirect measure of drinking in situations where direct measurement of alcohol consumption is undesirable (i.e., direct measurement might be reactive). Because the present findings are derived from problem drinkers, further research is needed to confirm the factor structure of the YBOCS-hd with clients who represent a broader range of alcohol problem severity.
Comparative Analysis of Single-Species and Polybacterial Wound Biofilms Using a Quantitative, In Vivo, Rabbit Ear Model

Introduction The recent literature suggests that chronic wound biofilms often consist of multiple bacterial species. However, without appropriate in vivo, polybacterial biofilm models, our understanding of these complex infections remains limited. We evaluate and compare the effect of single- and mixed-species biofilm infections on host wound healing dynamics using a quantitative, in vivo, rabbit ear model. Methods Six-mm dermal punch wounds in New Zealand rabbit ears were inoculated with Staphylococcus aureus strain UAMS-1, Pseudomonas aeruginosa strain PAO1, or both, totaling 10∧6 colony-forming units/wound. Bacterial proliferation and maintenance in vivo were done using procedures from our previously published model. Wounds were harvested for histological measurement of wound healing, viable bacterial counts using selective media, or inflammatory cytokine (IL-1β, TNF-α) expression via quantitative reverse-transcription PCR. Biofilm structure was studied using scanning electron microscopy (SEM). For comparison, biofilm deficient mutant UAMS-929 replaced strain UAMS-1 in some mixed-species infections. Results Bacterial counts verified the presence of both strains UAMS-1 and PAO1 in polybacterial wounds. Over time, strain PAO1 became predominant (p<0.001). SEM showed colocalization of both species within an extracellular matrix at multiple time-points. Compared to each monospecies infection, polybacterial biofilms impaired all wound healing parameters (p<0.01), and increased expression of IL-1β and TNF-α (p<0.05). In contrast, mixed-species infections using biofilm-deficient mutant UAMS-929 instead of wild-type strain UAMS-1 showed less wound impairment (p<0.01) with decreased host cytokine expression (p<0.01), despite a bacterial burden and distribution comparable to that of mixed-wild-type wounds. Conclusions This study reveals that mixed-species biofilms have a greater impact on wound healing dynamics than their monospecies counterparts. The increased virulence of polybacterial biofilm appears dependent on the combined pathogenicity of each species, verified using a mutant strain. These data suggest that individual bacterial species can interact synergistically within a single biofilm structure.
The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of >50 species known as the “Fusarium solani species complex”. Members of this complex have diverse biological properties including the ability to cause disease on >100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.