Miracle-dz/UniFAR-FTUs huggingface dataset:
Nutritional status in non-alcoholic sub-clinical porto-systemic encephalopathy.

AIM:To understand the role of nutritional status in cirrhotic patients without clinical porto-systemic encephalopathy (PSE). METHODS:Fifty-one non-alcoholic patients with cirrhosis without PSE were studied prospectively and compared with 20 healthy volunteers. The nutritional evaluation included serum prealbumin, albumin, transferrin, body mass index (BMI), mid-arm muscle circumference (MAMC), and grip power. The occurrence of subclinical PSE (SPSE) was defined when N20-N65 inter-peak latencies of median nerve-stimulated somatosensory evoked potentials were > 2.5 standard deviations of control means. Blood chemistries were tested within 12h of somatosensory evoked potentials test and nutritional evaluation.RESULTS:Twenty-five, 17 and 9 cirrhotic patients were graded as Child-Pugh class A, B, and C, respectively. Twenty-four (47.1%) patients developed SPSE. Cirrhotic patients with SPSE had lower serum albumin (2.8g/dL ± 0.5g/dL vs 3.1g/dL ± 0.7g/dL, P < 0.001) levels than those without SPSE. Prealbumin (10.6mg/dL ± 5.7mg/dL vs 12.5mg/dL ± 5.8mg/dL), transferrin (164mg/dL ± 46mg/dL vs 178mg/dL ± 58mg/dL), BMI (23.7kg/m(2) ± 2.7kg/m(2) vs 25.3kg/m(2) ± 3.6kg/m(2)), MAMC (22.2cm ± 2.6cm vs 22.7cm ± 3.5cm), and grip power (26.3kg ± 6.4kg vs 26.9kg ± 6.8kg) were not different between cirrhotic patients with and without SPSE. N20-N65 inter-peak latencies were correlated with serum albumin levels (P =0.01) but not with prealbumin, transferrin, BMI, MAMC,or grip power. Serum albumin, prealbumin and transferrin levels were different among cirrhotic patients with Child-Pugh classes A, B, and C (P < 0.05). BMI, MAMC, and grip power were not different among Child-Pugh classes A, B and C.CONCLUSION:Our data suggest that serum albumin level is a simple test in the evaluation of nutritional status in patients with cirrhosis.
Selective integration of multiple biological data for supervised network inference

MOTIVATION Inferring networks of proteins from biological data is a central issue of computational biology. Most network inference methods, including Bayesian networks, take unsupervised approaches in which the network is totally unknown in the beginning, and all the edges have to be predicted. A more realistic supervised framework, proposed recently, assumes that a substantial part of the network is known. We propose a new kernel-based method for supervised graph inference based on multiple types of biological datasets such as gene expression, phylogenetic profiles and amino acid sequences. Notably, our method assigns a weight to each type of dataset and thereby selects informative ones. Data selection is useful for reducing data collection costs. For example, when a similar network inference problem must be solved for other organisms, the dataset excluded by our algorithm need not be collected. RESULTS First, we formulate supervised network inference as a kernel matrix completion problem, where the inference of edges boils down to estimation of missing entries of a kernel matrix. Then, an expectation-maximization algorithm is proposed to simultaneously infer the missing entries of the kernel matrix and the weights of multiple datasets. By introducing the weights, we can integrate multiple datasets selectively and thereby exclude irrelevant and noisy datasets. Our approach is favorably tested in two biological networks: a metabolic network and a protein interaction network. AVAILABILITY Software is available on request.
The Non-linear Relationship between Muscle Voluntary Activation Level and Voluntary Force Measured by the Interpolated Twitch Technique

Interpolated twitch technique (ITT) is a non-invasive method for assessing the completeness of muscle activation in clinical settings. Voluntary activation level (VA), measured by ITT and estimated by a conventional linear model, was reported to have a non-linear relationship with true voluntary contraction force at higher activation levels. The relationship needs to be further clarified for the correct use by clinicians and researchers. This study was to established a modified voluntary activation (modified VA) and define a valid range by fitting a non-linear logistic growth model. Eight healthy male adults participated in this study. Each subject performed three sets of voluntary isometric ankle plantar flexions at 20, 40, 60, 80 and 100% maximal voluntary contraction (MVC) with real-time feedback on a computer screen. A supramaximal electrical stimulation was applied on tibia nerve at rest and during contractions. The estimated VA was calculated for each contraction. The relationship between the estimated VA and the actual voluntary contraction force was fitted by a logistic growth model. The result showed that according to the upper and lower limit points of the logistic curve, the valid range was between the 95.16% and 10.55% MVC. The modified VA estimated by this logistic growth model demonstrated less error than the conventional model. This study provided a transfer function for the voluntary activation level and defined the valid range which would provide useful information in clinical applications.
Infant B Cell Memory Differentiation and Early Gut Bacterial Colonization

Germ-free animal models have demonstrated that commensal bacterial colonization of the intestine induces B cell differentiation and activation. Whether colonization with particular bacterial species or groups is associated with B cell development during early childhood is not known. In a prospective newborn/infant cohort including 65 Swedish children, we examined the numbers and proportions of CD20+, CD5+, and CD27+ B cells in blood samples obtained at several time points during the first 3 y of life using flow cytometry. Fecal samples were collected and cultured quantitatively for major facultative and anaerobic bacteria at 1, 2, 4, and 8 wk of life. We found that the numbers of CD20+ B cells and CD5+CD20+ B cells reached their highest levels at 4 mo, whereas CD20+ B cells expressing the memory marker CD27 were most numerous at 18 and 36 mo of age. Using multivariate analysis, we show that early colonization with Escherichia coli and bifidobacteria were associated with higher numbers of CD20+ B cells that expressed the memory marker CD27 at 4 and 18 mo of age. In contrast, we were unable to demonstrate any relation between bacterial colonization pattern and numbers of CD20+ or CD5+CD20+ B cells. These results suggest that the intestinal bacterial colonization pattern may affect the B cell maturation also in humans, and that an early gut microbiota including E. coli and bifidobacteria might promote this maturation.
The untold story of the clones: content-agnostic factors that impact YouTube video popularity

Video dissemination through sites such as YouTube can have widespread impacts on opinions, thoughts, and cultures. Not all videos will reach the same popularity and have the same impact. Popularity differences arise not only because of differences in video content, but also because of other "content-agnostic" factors. The latter factors are of considerable interest but it has been difficult to accurately study them. For example, videos uploaded by users with large social networks may tend to be more popular because they tend to have more interesting content, not because social network size has a substantial direct impact on popularity. In this paper, we develop and apply a methodology that is able to accurately assess, both qualitatively and quantitatively, the impacts of various content-agnostic factors on video popularity. When controlling for video content, we observe a strong linear "rich-get-richer" behavior, with the total number of previous views as the most important factor except for very young videos. The second most important factor is found to be video age. We analyze a number of phenomena that may contribute to rich-get-richer, including the first-mover advantage, and search bias towards popular videos. For young videos we find that factors other than the total number of previous views, such as uploader characteristics and number of keywords, become relatively more important. Our findings also confirm that inaccurate conclusions can be reached when not controlling for content.
Incorporating virtualization awareness in service monitoring systems

Traditional service monitoring systems (e.g., Nagios and Cacti) have been conceived to monitor services hosted in physical computers. With the recent popularization of server virtualization platforms (e.g., Xen and VMware), monitored services can migrate from a physical computer to another, invalidating the original monitoring logic. In this paper, we investigate which strategies should be used to modify traditional service monitoring systems so that they can still provide accurate status information even for monitored services that are constantly moving on top of a set of servers with virtualization support.
A Generalized Steered Response Power Method for Computationally Viable Source Localization

The process of locating an acoustic source given measurements of the sound field at multiple microphones is of significant interest as both a classical array signal processing problem, and more recently, as a solution to the problems of automatic camera steering, teleconferencing, hands-free processing, and others. Despite the proven efficacy of steered-beamformer approaches to localization in harsh conditions, their practical application to real-time settings is hindered by undesirably high computational demands. This paper presents a computationally viable implementation of the steered response power (SRP) source localization method. The conventional approach is generalized by introducing an inverse mapping that maps relative delays to sets of candidate locations. Instead of traversing the three-dimensional location space, the one-dimensional relative delay space is traversed; at each lag, all locations which are inverse mapped by that delay are updated. This means that the computation of the SRP map is no longer performed sequentially in space. Most importantly, by subsetting the space of relative delays to only those that achieve a high level of cross-correlation, the required number of algorithm updates is drastically reduced without compromising localization accuracy. The generalization is scalable in the sense that the level of subsetting is an algorithm parameter. It is shown that this generalization may be viewed as a spatial decomposition of the SRP energy map into weighted basis functions-in this context, it becomes evident that the full SRP search considers all basis functions (even the ones with very low weighting). On the other hand, it is shown that by only including a few basis functions per microphone pair, the SRP map is quite accurately represented. As a result, in a real environment, the proposed generalization achieves virtually the same anomaly rate as the full SRP search while only performing 10% the amount of algorithm updates as the full search.
Why Foreign Ownership May Be Good for You

We develop a general equilibrium two-country model with heterogeneous producers and rent sharing at the firm level due to fairness preferences of workers. We identify two sources of a multinational wage premium. On the one hand, there is a pure composition effect because multinational firms are more productive, make higher profits, and therefore pay higher wages. On the other hand, there is a firm-level wage effect: A multinational firm pays higher wages in its home market than an otherwise identical national firm since it has higher global profits. We analyse how these two sources interact in determining the multinational wage premium in a setting with two identical countries, and show that in this case the wage premium is fully explained by firm characteristics. We then allow for technology differences between countries and find that a residual wage premium exists in the technologically backward country, but not in the advanced country.
Experimental effects of injunctive norms on simulated risky driving among teenage males.

OBJECTIVE Teenage passengers affect teenage driving performance, possibly by social influence. To examine the effect of social norms on driving behavior, male teenagers were randomly assigned to drive in a simulator with a peer-aged confederate to whom participants were primed to attribute either risk-accepting or risk-averse social norms. It was hypothesized that teenage drivers would engage in more risky driving behavior in the presence of peer passengers than no passengers, and with a risk-accepting compared with a risk-averse passenger. METHOD 66 male participants aged 16 to 18 years holding a provisional driver license were randomized to drive with a risk-accepting or risk-averse passenger in a simulator. Failure to Stop at a red light and percent Time in Red (light) were measured as primary risk-relevant outcomes of interest at 18 intersections, while driving once alone and once with their assigned passenger. RESULTS The effect of passenger presence on risky driving was moderated by passenger type for Failed to Stop in a generalized linear mixed model (OR = 1.84, 95% CI [1.19, 2.86], p < .001), and percent Time in Red in a mixed model (B = 7.71, 95% CI [1.54, 13.87], p < .05). CONCLUSIONS Exposure of teenage males to a risk-accepting confederate peer increased teenage males' risky simulated driving behavior compared with exposure to a risk-averse confederate peer. These results indicate that variability in teenage risky driving could be partially explained by social norms.
Tuning of Alternative Splicing - Switch From Proto-Oncogene to Tumor Suppressor

STAT5B, a specific member of the STAT family, is intimately associated with prostate tumor progression. While the full form of STAT5B is thought to promote tumor progression, a naturally occurring truncated isoform acts as a tumor suppressor. We previously demonstrated that truncated STAT5 is generated by insertion of an alternatively spliced exon and results in the introduction of an early termination codon. Present approaches targeting STAT proteins based on inhibition of functional domains of STAT's, such as DNA-binding, cooperative binding (protein-protein interaction), dimerization and phosphorylation will halt the action of the entire gene, both the proto-oncogenic and tumor suppressor functions of Stat5B. In this report we develop a new approach aimed at inhibiting the expression of full-length STAT5B (a proto-oncogene) while simultaneously enhancing the expression of STAT5∆B (a tumor suppressor). We have demonstrated the feasibility of using steric-blocking splice-switching oligonucleotides (SSOs) with a complimentary sequence to the targeted exon-intron boundary to enhance alternative intron/exon retention (up to 10%). The functional effect of the intron/exon proportional tuning was validated by cell proliferation and clonogenic assays. The new scheme applies specific steric-blocking splice-switching oligonucleotides and opens an opportunity for anti-tumor treatment as well as for the alteration of functional abilities of other STAT proteins.
Specificity of Conditional Associative-Learning Deficits in Obsessive-Compulsive Disorder (OCD) and Non-OCD Anxiety Disorders

The acquisition of conditional associations using neutral and disease-related nouns was studied in 15 inpatients with obsessive-compulsive disorder (OCD), 15 inpatients with non-OCD anxiety disorders and 15 chronic pain inpatients. Patients were comparable with respect to age, sex, depression, intelligence, executive functions, verbal and spatial memory, visuoconstructive functions, and handedness. The investigation took place in the diagnostic phase prior to the patient's beginning a standardized behavioral treatment program. It was hypothesized that anxiety patients acquired disease-related material faster than pain patients but that only OCD patients show inferior performance with respect to neutral stimuli. Results show that the three patient groups were widely comparable concerning neuropsychological background measures and showed equivalent results with respect to disease-related stimuli. But OCD patients yielded an inferior degree of performance when neutral stimuli were used whereas non-OCD anxiety disorder and pain patients displayed an equivalent degree of performance both for neutral and disease-related material, respectively. Results are discussed within the framework of obsessive-compulsive spectrum disorders.
Brain growth rate abnormalities visualized in adolescents with autism

Autism spectrum disorder is a heterogeneous disorder of brain development with wide ranging cognitive deficits. Typically diagnosed before age 3, autism spectrum disorder is behaviorally defined but patients are thought to have protracted alterations in brain maturation. With longitudinal magnetic resonance imaging (MRI), we mapped an anomalous developmental trajectory of the brains of autistic compared with those of typically developing children and adolescents. Using tensor‐based morphometry, we created 3D maps visualizing regional tissue growth rates based on longitudinal brain MRI scans of 13 autistic and seven typically developing boys (mean age/interscan interval: autism 12.0 ± 2.3 years/2.9 ± 0.9 years; control 12.3 ± 2.4/2.8 ± 0.8). The typically developing boys demonstrated strong whole brain white matter growth during this period, but the autistic boys showed abnormally slowed white matter development (P = 0.03, corrected), especially in the parietal (P = 0.008), temporal (P = 0.03), and occipital lobes (P = 0.02). We also visualized abnormal overgrowth in autism in gray matter structures such as the putamen and anterior cingulate cortex. Our findings reveal aberrant growth rates in brain regions implicated in social impairment, communication deficits and repetitive behaviors in autism, suggesting that growth rate abnormalities persist into adolescence. Tensor‐based morphometry revealed persisting growth rate anomalies long after diagnosis, which has implications for evaluation of therapeutic effects. Hum Brain Mapp, 2013. © 2011 Wiley Periodicals, Inc.
Predictors of improvement in renal function after calcineurin inhibitor withdrawal for post‐liver transplant renal dysfunction

Abstract: Background: Renal dysfunction after liver transplantation is a major management problem. Predictors of improvement in renal dysfunction after calcineurin inhibitor therapy (CNI) withdrawal and replacement with either mycophenolate mofetil (MMF) or azathioprine (AZA) have not previously been examined.
The Effects of Agave fourcroydes Powder as a Dietary Supplement on Growth Performance, Gut Morphology, Concentration of IgG, and Hematology Parameters in Broiler Rabbits

This study was conducted to determine the effects of Agave fourcroydes powder as a dietary supplement on the growth performance, gut morphology, serum concentration of IgG, and the hematology parameters of broiler rabbits. A total of 32 rabbits [New Zealand × Californian] were weaned at 35 days. They were randomly selected for two dietary treatments (eight repetitions per treatment), which consisted of a basal diet and a basal diet supplemented with 1.5% dried-stem powder of A. fourcroydes. On day 60 from the initiation of treatment, gut histomorphology (duodenum and cecum), serum concentration of IgG, and hematology parameters were all measured. The results showed that A. fourcroydes powder supplementation improved (P < 0.05) the ADFI, ADG, and final BW. Correspondingly, this treatment increased (P < 0.05) the muscle and mucosa thickness and height and width of villi. However, duodenum crypts depth was lower (P < 0.05) when rabbits were fed with this natural product, compared with the basal diet treatment. Results also indicated that the A. fourcroydes powder increased (P < 0.05) the serum concentration of IgG but did not change the hematology parameters. This data indicates that A. fourcroydes powder, as a supplement, had beneficial effects on increasing the growth performance and serum concentration of IgG, as well as improving the gut morphology without affecting the hematology parameters in broiler rabbits.
Identification of Two Distinct Human Immunodeficiency Virus Type 1 Vif Determinants Critical for Interactions with Human APOBEC3G and APOBEC3F

ABSTRACT Human cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) inhibit replication of Vif-deficient human immunodeficiency virus type 1 (HIV-1). HIV-1 Vif overcomes these host restriction factors by binding to them and inducing their proteasomal degradation. The Vif-A3G and Vif-A3F interactions are attractive targets for antiviral drug development because inhibiting the interactions could allow the host defense mechanism to control HIV-1 replication. It was recently reported that the Vif amino acids D14RMR17 are important for functional interaction and degradation of the previously identified Vif-resistant mutant of A3G (D128K-A3G). However, the Vif determinants important for functional interaction with A3G and A3F have not been fully characterized. To identify these determinants, we performed an extensive mutational analysis of HIV-1 Vif. Our analysis revealed two distinct Vif determinants, amino acids Y40RHHY44 and D14RMR17, which are essential for binding to A3G and A3F, respectively. Interestingly, mutation of the A3G-binding region increased Vif's ability to suppress A3F. Vif binding to D128K-A3G was also dependent on the Y40RHHY44 region but not the D14RMR17 region. Consistent with previous observations, subsequent neutralization of the D128K-A3G antiviral activity required substitution of Vif determinant D14RMR17 with SEMQ, similar to the SERQ amino acids in simian immunodeficiency virus SIVAGM Vif, which is capable of neutralizing D128K-A3G. These studies are the first to clearly identify two distinct regions of Vif that are critical for independent interactions with A3G and A3F. Pharmacological interference with the Vif-A3G or Vif-A3F interactions could result in potent inhibition of HIV-1 replication by the APOBEC3 proteins.
Involvement of glial fibrillary acidic protein (GFAP) expressed in astroglial cells in circadian rhythm under constant lighting conditions in mice

To clarify the role of glial fibrillary acidic protein (GFAP)‐expressed glial cells in the circadian clock, we examined GFAP expression in the suprachiasmatic nucleus (SCN) and the intergeniculate leaflet (IGL) under various lighting conditions in mice. We demonstrated that GFAP expression did not show daily change in the SCN under a light‐dark cycle; however, long‐term housing under constant lighting conditions led to dramatic changes in GFAP expression, i.e., a decrease in the SCN and an increase in the IGL. Furthermore, mice that had a targeted deletion in the GFAP gene (GFAP mutant mice) showed longer and more arrhythmic circadian activity rhythms in constant lighting conditions than wild‐type mice, while GFAP mutant mice exhibited stable circadian rhythms both in a light‐dark cycle and constant darkness, and showed normal entrainment to environmental light stimuli. These results suggest that the GFAP‐expressed astroglial cells in the SCN and the IGL may have some role in circadian oscillation under constant lighting conditions. J. Neurosci. Res. 60:212–218, 2000 © 2000 Wiley‐Liss, Inc.
Advanced flamelet modelling of turbulent non-premixed and partially premixed combustion

Current work focuses on the development and performance evaluation of advanced flamelet models for turbulent non-premixed and partially premixed combustion in RANS and large eddy simulation (LES) based modelling. A RANS-based combustion modelling strategy which has the ability to capture the detailed structure of turbulent non-premixed flames, including the pollutant NO, and account for the effects of radiation heat loss and transient evolution of NO, has been developed and incorporated into the in-house RANS code. The strategy employs an 'enthalpy defect'-based non-adiabatic flamelet model in conjunction with steady or unsteady nonadiabatic flamelets based NO submodels. [Continues. ]