Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonalcoholic fatty liver disease: diagnostic and fat-grading accuracy of low-flip-angle multiecho gradient-recalled-echo MR imaging at 1.5 T.

PURPOSE To assess the accuracy of four fat quantification methods at low-flip-angle multiecho gradient-recalled-echo (GRE) magnetic resonance (MR) imaging in nonalcoholic fatty liver disease (NAFLD) by using MR spectroscopy as the reference standard. MATERIALS AND METHODS In this institutional review board-approved, HIPAA-compliant prospective study, 110 subjects (29 with biopsy-confirmed NAFLD, 50 overweight and at risk for NAFLD, and 31 healthy volunteers) (mean age, 32.6 years +/- 15.6 [standard deviation]; range, 8-66 years) gave informed consent and underwent MR spectroscopy and GRE MR imaging of the liver. Spectroscopy involved a long repetition time (to suppress T1 effects) and multiple echo times (to estimate T2 effects); the reference fat fraction (FF) was calculated from T2-corrected fat and water spectral peak areas. Imaging involved a low flip angle (to suppress T1 effects) and multiple echo times (to estimate T2* effects); imaging FF was calculated by using four analysis methods of progressive complexity: dual echo, triple echo, multiecho, and multiinterference. All methods except dual echo corrected for T2* effects. The multiinterference method corrected for multiple spectral interference effects of fat. For each method, the accuracy for diagnosis of fatty liver, as defined with a spectroscopic threshold, was assessed by estimating sensitivity and specificity; fat-grading accuracy was assessed by comparing imaging and spectroscopic FF values by using linear regression. RESULTS Dual-echo, triple-echo, multiecho, and multiinterference methods had a sensitivity of 0.817, 0.967, 0.950, and 0.983 and a specificity of 1.000, 0.880, 1.000, and 0.880, respectively. On the basis of regression slope and intercept, the multiinterference (slope, 0.98; intercept, 0.91%) method had high fat-grading accuracy without statistically significant error (P > .05). Dual-echo (slope, 0.98; intercept, -2.90%), triple-echo (slope, 0.94; intercept, 1.42%), and multiecho (slope, 0.85; intercept, -0.15%) methods had statistically significant error (P < .05). CONCLUSION Relaxation- and interference-corrected fat quantification at low-flip-angle multiecho GRE MR imaging provides high diagnostic and fat-grading accuracy in NAFLD.
Fertilization rate and embryo quality in superovulated Holstein heifers artificially inseminated with X-sorted or unsorted sperm

Although studies have demonstrated reasonable pregnancy rates in single-ovulating heifers inseminated with sexed sperm, it is not yet clear if sexed sperm can be successfully used in superovulated females. Therefore, the objective of this trial was to determine fertilization rate and embryo quality in superovulated heifers inseminated with frozen-thawed Xchromosome bearing sperm at 2 different dosages versus unsorted sperm. Nulliparous Holstein heifers (n = 23; 12 to 16 mo) were superovulated with FSH and observed for estrus twice a day. Following detection of estrus, bilateral deep uterine horn AI was performed once (1X) or twice (2X) in each heifer, according to the treatments: S20-1X: AI with 20 million X-sorted sperm 12 h after the onset of estrus; S10-2X: AI with 10 million X-sorted sperm 12 and 24 h after the onset of estrus; and U10-2X: AI with 10 million unsorted sperm 12 and 24 h after the onset of estrus. Embryos/ova were collected 7 d after estrus and evaluated. Ten d later, heifers were resynchronized for a second superovulatory treatment and assigned to a second treatment group. Data were compared using mixed effects models. When sexed sperm were used, number and percentage of fertilized and viable embryos recovered per flush was similar between the S20-1X and S10-2X group (63.5% and 61.9%), but lower (P < 0.01) than in the U10-2X group (90.9%). In addition, heifers bred with X-sorted sperm had an increase (P < 0.05) in the percentage of degenerate embryos when only fertilized structures were included in the analysis (S20-1X = 58.6%, S10-2X = 53.1%, U10-2X = 24.2%). In conclusion, it seems likely that the sorting process may have caused damage in the sperm that compromised fertilization as well as subsequent embryonic development in superovulated heifers.
Learning to Count with Back-propagated Information

Error back-propagation is one of the principled learning strategies widely used in pattern recognition and machine learning, e.g. neural networks. The existing frameworks employed back-propagated error as a performance criteria (or termed, object function) aiming for supervising model-learning. Inspired by the recent success achieved by learning with the privileged information (LPI), we propose a novel regression-based framework by extending the concept of back-propagation in supervised learning methods to high-level guiding the model learning, so the proposed model is able to mine the importance of samples contributed to the fitting performance, which is missed in the existing regression techniques. To verify the effectiveness of the proposed learning paradigm, both low-level imagery features and intermediary semantic attributes are adopted in this paper. Extensive evaluations on pedestrian counting with public UCSD and Mall benchmarks demonstrate that the effectiveness of the proposed framework.
Blood-Brain Barrier Impairment in an Animal Model of MPS III

Background: Sanfilippo syndrome type B (MPS III B) is caused by a deficiency of a-N-acetylglucosaminidase enzyme, leading to accumulation of heparan sulfate within lysosomes and eventual progressive cerebral and systemic multiple organ abnormalities. However, little is known about the competence of the blood-brain barrier (BBB) in MPS III B. BBB dysfunction in this devastating disorder could contribute to neuropathological disease manifestations. Methodology/Principal Findings: In the present study, we investigated structural (electron microscope) and functional (vascular leakage) integrity of the BBB in a mouse model of MPS III B at different stages of disease, focusing on brain structures known to experience neuropathological changes. Major findings of our study were: (1) endothelial cell damage in capillary ultrastructure, compromising the BBB and resulting in vascular leakage, (2) formation of numerous large vacuoles in endothelial cells and perivascular cells (pericytes and perivascular macrophages) in the large majority of vessels, (3) edematous space around microvessels, (4) microaneurysm adjacent to a ruptured endothelium, (6) Evans Blue and albumin microvascular leakage in various brain structures, (7) GM3 ganglioside accumulation in endothelium of the brain microvasculature. Conclusions/Significance: These new findings of BBB structural and function impairment in MPS III B mice even at early disease stage may have implications for disease pathogenesis and should be considered in current and future development of treatments for MPS III B. Citation: Garbuzova-Davis S, Louis MK, Haller EM, Derasari HM, Rawls AE, et al. (2011) Blood-Brain Barrier Impairment in an Animal Model of MPS III B. PLoS ONE 6(3): e16601. doi:10.1371/journal.pone. 0016601 Editor: Eric Kremer, French National Centre for Scientific Research, France Received September 13, 2010; Accepted January 4, 2011; Published March 7, 2011 Copyright: 2011 Garbuzova-Davis 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 study was supported by the Children’s Medical Research Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: sgarbuzo@health.usf. edu
664 CARDIOVASCULAR RISK FACTORS IN MIDDLE-AGED AND ELDERLY RESIDENTS IN SOUTH-EAST NIGERIA - THE INFLUENCE OF URBANIZATION

Background: Cardiovascular diseases (CVD) were previously considered to be a problem of the developed nations only. Emerging facts show that CVD and their risk factors are now prevalent in both low-income and middle-income countries1. The burden is dramatically increasing globally, and several African nations are not left out of this global phenomenon2–4. Design: We carried out a cross-sectional, population-based survey to determine if there is any association between place of residence (rural or urban) and the burden of CVD risk factors in South East Nigeria. Results: The mean and 95% CI for mean of the characteristics of subjects showed that they were in the middle-age group with apparently normal mean cardiovascular risk indices except for systolic and diastolic blood pressure indices which suggested pre-hypertension. The subjects residing in the rural area were older than those residing in the urban area but cardiovascular risk factors had higher mean values in urban residents except systolic blood pressure (SBP). These observations did not differ when the subjects were compared gender-wise and by place of residence. However, the significant differences in SBP and fasting blood glucose were lost. The most prevalent cardiovascular risk factors in the study group were hypertension (Systolic > diastolic) and obesity. Conclusion: Urban residence was associated with higher prevalence of the risk factors especially obesity and diastolic hypertension.
Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases

Background: Deep learning (DL) is a representation learning approach ideally suited for image analysis challenges in digital pathology (DP). The variety of image analysis tasks in the context of DP includes detection and counting (e.g., mitotic events), segmentation (e.g., nuclei), and tissue classification (e.g., cancerous vs. non-cancerous). Unfortunately, issues with slide preparation, variations in staining and scanning across sites, and vendor platforms, as well as biological variance, such as the presentation of different grades of disease, make these image analysis tasks particularly challenging. Traditional approaches, wherein domain-specific cues are manually identified and developed into task-specific "handcrafted" features, can require extensive tuning to accommodate these variances. However, DL takes a more domain agnostic approach combining both feature discovery and implementation to maximally discriminate between the classes of interest. While DL approaches have performed well in a few DP related image analysis tasks, such as detection and tissue classification, the currently available open source tools and tutorials do not provide guidance on challenges such as (a) selecting appropriate magnification, (b) managing errors in annotations in the training (or learning) dataset, and (c) identifying a suitable training set containing information rich exemplars. These foundational concepts, which are needed to successfully translate the DL paradigm to DP tasks, are non-trivial for (i) DL experts with minimal digital histology experience, and (ii) DP and image processing experts with minimal DL experience, to derive on their own, thus meriting a dedicated tutorial. Aims: This paper investigates these concepts through seven unique DP tasks as use cases to elucidate techniques needed to produce comparable, and in many cases, superior to results from the state-of-the-art hand-crafted feature-based classification approaches. Results : Specifically, in this tutorial on DL for DP image analysis, we show how an open source framework (Caffe), with a singular network architecture, can be used to address: (a) nuclei segmentation (F-score of 0.83 across 12,000 nuclei), (b) epithelium segmentation (F-score of 0.84 across 1735 regions), (c) tubule segmentation (F-score of 0.83 from 795 tubules), (d) lymphocyte detection (F-score of 0.90 across 3064 lymphocytes), (e) mitosis detection (F-score of 0.53 across 550 mitotic events), (f) invasive ductal carcinoma detection (F-score of 0.7648 on 50 k testing patches), and (g) lymphoma classification (classification accuracy of 0.97 across 374 images). Conclusion: This paper represents the largest comprehensive study of DL approaches in DP to date, with over 1200 DP images used during evaluation. The supplemental online material that accompanies this paper consists of step-by-step instructions for the usage of the supplied source code, trained models, and input data.
Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

Genome-wide association studies identified noncoding SNPs associated with type 2 diabetes and obesity in linkage disequilibrium (LD) blocks encompassing HHEX-IDE and introns of CDKAL1 and FTO [Sladek R, et al. (2007) Nature 445:881–885; Steinthorsdottir V, et al. (2007) Nat. Genet 39:770–775; Frayling TM, et al. (2007) Science 316:889–894]. We show that these LD blocks contain highly conserved noncoding elements and overlap with the genomic regulatory blocks of the transcription factor genes HHEX, SOX4, and IRX3. We report that human highly conserved noncoding elements in LD with the risk SNPs drive expression in endoderm or pancreas in transgenic mice and zebrafish. Both HHEX and SOX4 have recently been implicated in pancreas development and the regulation of insulin secretion, but IRX3 had no prior association with pancreatic function or development. Knockdown of its orthologue in zebrafish, irx3a, increased the number of pancreatic ghrelin-producing epsilon cells and decreased the number of insulin-producing β-cells and glucagon-producing α-cells, thereby suggesting a direct link of pancreatic IRX3 function to both obesity and type 2 diabetes.
Disentangling disease and environmental effects in body weight and blood parameters 4 in Iberian ibex affected by sarcoptic mange 5 6

RUNNING HEADING: PÉREZ ET AL. – WEIGHT, HEMATOLOGY AND 1 BIOCHEMISTRY OF SCABIETIC MALE IBERIAN IBEX 2 3 Disentangling disease and environmental effects in body weight and blood parameters 4 in Iberian ibex affected by sarcoptic mange 5 6 Jesús M. Pérez 1,* , Emmanuel Serrano 2 , Ramón C. Soriguer 3 , Francisco J. González 4 , 7 Mathieu Sarasa 1 , José E. Granados 5 , Francisco J. Cano-Manuel 5 , Rafaela Cuenca 2 , 8 and Paulino Fandos 6 9 10
Chondrosarcoma arising in osteochondroma

Secondary chondrosarcomas are rare. An analysis of 75 cases of chondrosarcomas secondary to osteochondroma (42 lesions were from the Mayo Clinic files and 33 were from consultation files) revealed that 40 of the patients had single exostosis and 35 had multiple lesions. More males than females were affected, and most of the patients were age 20 to 40 years. The tumors involved various bones. Malignant change was manifested radiologically by fuzzy margins of the cartilage cap and by the presence of lucent zones within the lesion. Grossly, the surface of the thickened cartilage cap was irregular. Microscopically, most of the tumors were well‐differentiated (Grade 1). Treatment was surgical. Simple excision of the tumor resulted in a large recurrence rate. Resection and amputation were generally curative. Only 12 of the patients have died of their tumor. Most patients died of local recurrence. Only two of the 75 patients had definite evidence of metastatic disease.
Validity of the World Health Organization Adult ADHD Self‐Report Scale (ASRS) Screener in a representative sample of health plan members

The validity of the six‐question World Health Organization Adult ADHD Self‐Report Scale (ASRS) Screener was assessed in a sample of subscribers to a large health plan in the US. A convenience subsample of 668 subscribers was administered the ASRS Screener twice to assess test‐retest reliability and then a third time in conjunction with a clinical interviewer for DSM‐IV adult ADHD. The data were weighted to adjust for discrepancies between the sample and the population on socio‐demographics and past medical claims. Internal consistency reliability of the continuous ASRS Screener was in the range 0.63–0.72 and test‐retest reliability (Pearson correlations) in the range 0.58–0.77. A four‐category version The ASRS Screener had strong concordance with clinician diagnoses, with an area under the receiver operating characteristic curve (AUC) of 0.90. The brevity and ability to discriminate DSM‐IV cases from non‐cases make the six‐question ASRS Screener attractive for use both in community epidemiological surveys and in clinical outreach and case‐finding initiatives. Copyright © 2007 John Wiley & Sons, Ltd.
A Laughing Matter: Patterns of Laughter and the Effectiveness of Working Dyads

Poor communication in teams has been found to result in disappointing team performance. Integrating research on team communication and laughter, we tested hypotheses about the relationship between working dyads’ patterns of laughter and their open communication and effectiveness. We examined two patterns of laughter: shared laughter occurs when both individuals laugh frequently in a dyad, and unshared laughter occurs when one individual in a dyad laughs frequently, but the other does not. Using data collected from 93 flight simulations in two aviation courses, we found that dyads engage in more open communication and are more effective when one member laughs frequently, but the other member does not. In addition, we found that the agreeableness of a dyad member reduces team effectiveness by increasing the likelihood of shared laughter. These results highlight the important role of laughter in team interactions and expand the growing literature on the role of emotions in teams.
Argumentation Quality Assessment: Theory vs. Practice

Argumentation quality is viewed differently in argumentation theory and in practical assessment approaches. This paper studies to what extent the views match empirically. We find that most observations on quality phrased spontaneously are in fact adequately represented by theory. Even more, relative comparisons of arguments in practice correlate with absolute quality ratings based on theory. Our results clarify how the two views can learn from each other.
Evidence that the gonococcal porA pseudogene is present in a broad range of Neisseria gonorrhoeae strains; suitability as a diagnostic target

Aims: The primary aim of the study was to determine if the gonococcal porA pseudogene is a stable sequence target for the detection of Neisseria gonorrhoeae by PCR. Methods: A total of 240 gonococcal strains from various geographic locations were tested by porA pseudogene PCR. In addition, porA pseudogene PCR positivity rates were compared with established gonococcal assays in three Australian states. Results: All N. gonorrhoeae isolates provided positive results in the porA pseudogene PCR. Positivity rates compared favourably with established gonococcal assays, with increased N. gonorrhoeae detection in the Northern Territory and Western Australia. Conclusions: The results of this multicentre study provide further evidence that the porA pseudogene is highly conserved across a diverse range N. gonorrhoeae strains and is a suitable PCR target for routine detection of N. gonorrhoeae.
Production and Characterization of Bacteriocin Produced by Lactobacillus Viridescence(NICM 2167)

The present study focused on the production optimization of bacteriocin by Lactobacillus viridescence NICM 2167 followed by its purification and characterization. The bacteriocins are antimicrobial peptides produced by many Gram positive and Gram negative bacteria.The bacteriocin produced by LAB (lactic acid bacteria) received attention in recent years due to their potential application as natural preservatives in food. Bacteriocinproduced by Lactobacillus viridescence showed broad range of antimicrobial activity against food borne pathogens. Production parameters were optimized showing highest production of bacteriocinin MRS broth with pH= 7.0 incubated at 37°C for 48 h. Bacteriocin was purified in two steps involving ammonium sulphate precipitation followed by gel filtration using Sephadex G-100. Purified bacteriocin with single band on SDS-PAGE showed molecular weight of 8.3 kDa. This purified bacteriocin was stable over wide range of pH (4-10) as well as temperatures (4°C-121°C) suggesting it as a potent candidate for preservation of various foods.
Las variables temporales en el español de Costa Rica y de España: Un estudio comparativo

El objetivo de esta investigacion es describir las variables temporales en dos variantes del espanol: una de Costa Rica (San Jose) y la otra de Espana (Barcelona). De manera mas especifica, se examinan, con una perspectiva comparativa, la velocidad de elocucion, el numero de pausas, su duracion y la velocidad de articulacion en una tarea de lectura en voz alta. Tambien se estudia el efecto de la edad y del sexo del locutor en la velocidad de articulacion, asi como el efecto de la longitud del enunciado, ya que se ha demostrado que estos factores afectan a la velocidad de articulacion en otras lenguas como el frances, el ingles o el neerlandes. Los resultados principales del presente trabajo indican, por una parte, que los locutores costarricenses realizan pausas mas largas que los locutores espanoles y, por otra parte, que los locutores de las dos variantes presentan una velocidad de articulacion similar, que se ve afectada por factores tanto extralinguisticos (i.e. la edad o la profesion de los locutores) como linguisticos (i.e. longitud del enunciado).
Antiretroviral treatment of men infected with human immunodeficiency virus type 1 reduces the incidence of heterosexual transmission. Italian Study Group on HIV Heterosexual Transmission.

OBJECTIVE To determine the incidence of heterosexual human immunodeficiency virus type 1 disease transmission and the effect of zidovudine therapy on this risk of transmission. DESIGN A cohort of 436 monogamous seronegative female sexual partners of human immunodeficiency virus type 1-infected males was followed up for 740 person-years with regular structured interviews and laboratory tests. PATIENTS At enrollment of the women, 50% of their infected partners had one or more signs of disease progression (symptoms of acquired immunodeficiency syndrome, p24 antigen positivity, or CD4+ cell counts lower than 0.4 x 10(9)/L) and 15% were treated with zidovudine. MAIN OUTCOME MEASURE Incidence rates of seroconversion were calculated and relative risks were estimated as incidence rate ratios. RESULTS Twenty-seven women seroconverted during follow-up, and the incidence of seroconversion was 3.7 per 100 person-years. Seroconversion was about six times more frequent (relative risk, 5.8; 95% confidence interval, 2.2 to 15.3) in couples not using condoms. Men with signs of disease progression transmitted infection to their partners more frequently and were more frequently treated with zidovudine. When the risk of transmission was estimated accounting for disease progression, the rate of transmission in zidovudine-treated men was lower than in untreated men (relative risk, 0.5; 95% confidence interval, 0.1 to 0.9). CONCLUSION Treatment of human immunodeficiency virus type-1 infected men with zidovudine reduces, but does not eliminate, heterosexual transmission of infection. Behavioral counseling that encourages sexual practices with a lower risk of transmission remains the most important method of prevention.