Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasma Amino Acids vs Conventional Predictors of Insulin Resistance Measured by the Hyperinsulinemic Clamp

Context: Specific plasma amino acid (AA) profiles including elevated postabsorptive branched-chain amino acids (BCAAs) have been associated with insulin resistance (IR), mostly estimated by homeostatic model assessment. This study assessed the associations of postabsorptive AAs with IR directly measured by insulin-mediated glucose disposal and determined the quantitative value of AAs and conventional IR predictors. Design: Fifty-one healthy, 31 overweight or obese (Ow/Ob), and 52 men and women with type 2 diabetes (T2D) were studied retrospectively. The main outcome measures were the glucose disposal (M/I) index (using 3-[3H]-glucose) during a hyperinsulinemic–euglycemic clamp and whole-body protein turnover (using 1-[13C]-leucine). Results: Compared with healthy participants, M/I was lower in Ow/Ob participants and lowest in those with T2D. BCAAs, glutamate, and lysine were higher in the Ow/Ob and T2D groups than in healthy participants; glycine and threonine were lower. Most AAs were higher in men. Principal component analysis identified component 1 (C1: BCAAs, methionine) and C3 (glycine, threonine, serine). Glutamate, C1, ornithine, lysine, methionine, and tyrosine correlated negatively with M/I; C3 and glycine correlated positively. Waist circumference and sex strongly influenced AA–IR relationships; only glutamate correlated after these factors were controlled for. From regression analysis, waist circumference, fasting glucose, insulin, and free fatty acids (FFAs) negatively predicted 64% of the M/I variance; glutamate added 2% more. In nondiabetic participants, IR was predicted by waist circumference, insulin, and FFAs, without contribution from AAs. Conclusion: Several postabsorptive AAs correlated with IR but added limited predictive value to conventional markers because levels were determined largely by abdominal adiposity. Data suggest a sex-specific regulation of AA metabolism by excess adiposity, particularly the BCAAs, warranting investigation.
Line Art Rendering via a Coverage of Isoparametric Curves

A line art nonphotorealistic rendering scheme of scenes composed of freeform surfaces is presented. A freeform surface coverage is constructed using a set of isoparametric curves. The density of the isoparametric curves is set to be a function of the illumination of the surface determined using a simple shading model, or of regions of special importance such as silhouettes. The outcome is one way of achieving an aesthetic and attractive line art rendering that employs isoparametric curve based drawings that is suitable for printing publication. >
Etiology of Aseptic Meningitis, Peripheral Facial Nerve Palsy, and a Combination of Both in Children

Background: A variety of microorganisms have been shown to cause peripheral facial nerve palsy (PFNP) and/or aseptic meningitis in children. Clinical findings and history may help to predict the specific etiology of these entities. Method: Children ≥12 months old hospitalized at the University Children's Hospital Basel, Switzerland, from 2000 to 2005 with clinical signs of PFNP and/or aseptic meningitis were studied retrospectively. History, clinical, and laboratory findings were evaluated using analysis of variance with Bonferroni (Dunn) correction. Results: Of 181 patients, 123 (68%) had aseptic meningitis, 28 (15%) had PFNP, and 30 (17%) had a combination of both. PFNP with aseptic meningitis was associated with Borrelia burgdorferi (Bb) infection in the majority of patients (73%) compared with 11% and 9% of patients with PFNP or aseptic meningitis, respectively. The majority of patients with aseptic meningitis without PFNP had enterovirus infection (63%). In patients with aseptic meningitis, mean leukocyte counts in cerebrospinal fluid (CSF) were higher with enterovirus (565/&mgr;L) compared with Bb infection (191/&mgr;L; P < 0.01) or unknown causes (258/&mgr;L; P < 0.01). Further, CSF mean mononuclear cell proportion was higher in patients with Bb (89%) than in those with enterovirus infection (51%; P < 0.01) or unknown causes (60%; P < 0.01). Mean time interval between onset of disease and admission to hospital showed significant differences between Bb (7.6 days) and enterovirus infection (2.8 days; P < 0.01) or unknown causes (2.0 days; P < 0.01). Conclusions: Time interval between onset of disease and hospital admission and CSF characteristics can contribute to distinguishing the etiology of aseptic meningitis with or without PFNP. As expected, the most common etiology for aseptic meningitis with PFNP was Bb infection whereas enterovirus infection was the predominant cause for aseptic meningitis alone.
Extended Adjuvant Tamoxifen for Early Breast Cancer: A Meta-Analysis

Background Hormone receptor positive breast cancer is characterized by the potential for disease recurrence many years after initial diagnosis. Endocrine therapy has been shown to reduce the risk of such recurrence, but the optimal duration of endocrine therapy remains unclear. Methods We conducted a systematic review and meta-analysis to quantify the benefits and harms of extended adjuvant tamoxifen (>5 years of therapy) compared with adjuvant tamoxifen (5 years of therapy). Odds ratios (ORs) and 95% confidence intervals (CIs) were computed for disease recurrence, death and adverse events. Subgroup analyses by timing of recurrence and baseline lymph node and menopause status were carried. Results Five trials comprising 21,554 patients were included. Extended adjuvant tamoxifen was not associated with a significant reduction in the risk of recurrence (OR:0.89, 95% CI 0.76–1.05, p = 0.17). There was no association between extended adjuvant tamoxifen and all-cause death (OR:0.99, 95% CI 0.84–1.16, p = 0.88). There was an apparent reduction in risk of recurrence occurring after completion of extended adjuvant tamoxifen with little evidence of effect during therapy, however, this difference was not significant (p for difference 0.10). Subgroup analysis suggested that a greater effect size among lymph node positive patients compared with those who are lymph node negative (NNT: 25 vs. 49). There was no apparent difference in the effect between pre- and post-menopausal patients. Endometrial carcinoma was substantially more frequent with extended adjuvant tamoxifen (OR:2.06, 95% CI 1.65–2.58, p<0.001, number needed to harm:89). Conclusion In unselected patients, extended adjuvant tamoxifen is not associated with a significant reduction in recurrence, or a reduction in all-cause death. Patients with lymph node positive breast cancer may derive some benefit. Reduction in the risk of recurrence appears to occur only after completion of extended adjuvant therapy.
From Molecular Classification to Targeted Therapeutics: The Changing Face of Systemic Therapy in Metastatic Gastroesophageal Cancer

Histological classification of adenocarcinoma or squamous cell carcinoma for esophageal cancer or using the Lauren classification for intestinal and diffuse type gastric cancer has limited clinical utility in the management of advanced disease. Germline mutations in E-cadherin (CDH1) or mismatch repair genes (Lynch syndrome) were identified many years ago but given their rarity, the identification of these molecular alterations does not substantially impact treatment in the advanced setting. Recent molecular profiling studies of upper GI tumors have added to our knowledge of the underlying biology but have not led to an alternative classification system which can guide clinician's therapeutic decisions. Recently the Cancer Genome Atlas Research Network has proposed four subtypes of gastric cancer dividing tumors into those positive for Epstein-Barr virus, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. Unfortunately to date, many phase III clinical trials involving molecularly targeted agents have failed to meet their survival endpoints due to their use in unselected populations. Future clinical trials should utilize molecular profiling of individual tumors in order to determine the optimal use of targeted therapies in preselected patients.
Oral clefts and maternal biomarkers of folate-dependent one-carbon metabolism in Utah.

BACKGROUND Maternal folate intake and related biomarkers have been inconsistently associated with a risk of oral clefts. METHODS Maternal concentrations of plasma folate (PF) and erythrocyte folate (EF), plasma pyridoxal-5'-phosphate (PLP; active vitamin B(6) ) and total plasma homocysteine (tHcy) were measured in a Utah study with 347 cases and 469 controls. RESULTS Risk of all clefts combined, including cleft lip with or without cleft palate (CL/P) and cleft palate only (CP), was 65% lower in the highest versus lowest PF quartile (odds ratio [OR], 0.35; 95% confidence interval [CI], 0.23-0.53; p-trend < 0.001). Results remained significant in the subgroups with isolated CL/P and CP (p-trend < 0.001 in each). EF results were similar. In the highest versus lowest PLP quartile, risk of CP with other malformations was lower (OR, 0.25; 95% CI, 0.07-0.95); however, no other associations were significant for PLP or tHcy. Differences in mean biomarker levels between cases and controls widened with an increasing interval between delivery and maternal blood collection. Decreased cleft risk with increasing quartiles of PF, EF, and PLP and decreasing tHcy was more apparent in mothers with a longer versus shorter interval between the index child delivery and blood collection. CONCLUSION Low maternal blood folate concentration was associated with an increased risk of clefts, and the differences in mean case and control PF, EF, PLP, and tHcy concentrations widened over time. Additional mechanistic studies are warranted to elucidate whether an acquired or inherited disorder of folate metabolism plays a role in the etiology of clefts.
The Bile Acid Sensor FXR Is Required for Immune-Regulatory Activities of TLR-9 in Intestinal Inflammation

Background Toll like receptors (TLRs) sense the intestinal microbiota and regulate the innate immune response. A dysregulation of TLRs function participates into intestinal inflammation. Farnesoid X Receptor (FXR) is a nuclear receptor and bile acid sensor highly expressed in entero-hepatic tissues. FXR regulates lipid metabolism and innate immunity. Methodology/Principal Findings In this study we have investigated whether FXR gene expression/function in the intestine is modulated by TLRs. We found that in human monocytes activation of membrane TLRs (i.e. TLR2, 4, 5 and 6) downregulates, while activation of intracellular TLRs (i.e. TLR3, 7, 8 and 9) upregulates the expression of FXR and its target gene SHP, small heterodimer partner. This effect was TLR9-dependent and TNFα independent. Intestinal inflammation induced in mice by TNBS downregulates the intestinal expression of FXR in a TLR9-dependent manner. Protection against TNBS colitis by CpG, a TLR-9 ligand, was lost in FXR−/− mice. In contrast, activation of FXR rescued TLR9−/− and MyD88−/− mice from colitis. A putative IRF7 response element was detected in the FXR promoter and its functional characterization revealed that IRF7 is recruited on the FXR promoter under TLR9 stimulation. Conclusions/Significance Intestinal expression of FXR is selectively modulated by TLR9. In addition to its role in regulating type-I interferons and innate antiviral immunity, IRF-7 a TLR9-dependent factor, regulates the expression of FXR, linking microbiota-sensing receptors to host's immune and metabolic signaling.
Effects of a Low Dose of Melatonin on Sleep in Children with Angelman Syndrome

The effects of low dose melatonin therapy on sleep behavior and serum melatonin levels were studied in Angelman syndrome (AS) children suffering from insomnia. 24-hour motor activity was monitored in 13 AS children (age 2-10 yr) in their home environments for 7 days prior to melatonin treatment and for 5 days during which a 0.3 mg dose of melatonin was administered daily 0.5-1 hour before the patient's habitual bedtime. Blood samples were with-drawn at hourly intervals over two 21-hour periods in order to measure individual endogenous serum melatonin levels and the levels induced by melatonin treatment. Actigraphic recording of motor activity, confirmed by parents' reports, showed a significant improvement in the patients' nocturnal sleep pattern as a result of melatonin treatment. Analysis of the group data revealed a significant decrease in motor activity during the total sleep period following melatonin treatment, and an increase in the duration of the total sleep period. Endogenous peak nocturnal melatonin values ranged from 19 to 177 pg/ml. The administration of melatonin elevated peak serum hormone levels to 128-2800 pg/ml in children of different ages and body mass. These data suggest that a moderate increase in circulating melatonin levels significantly reduces motor activity during the sleep period in Angelman syndrome children, and promotes sleep.
Visualization of streaming data: Observing change and context in information visualization techniques

Visualizing data streams poses numerous challenges in the data, image and user space. In the era of big data, we need incremental visualization methods that will allow the analysts to explore data faster and help them make important decisions on time. In this paper, we have reviewed several well-known information visualization methods that are commonly used to visualize static datasets and analyzed their degrees of freedom. By observing which independent visual variables can change in each method, we described how these changes are related to the attribute and structure changes that can occur in the data stream. Most of the changes in the data stream lead to potential loss of temporal and relational context between the new data and the past data. We present potential directions for measuring the amount of change and loss of context by reviewing related work and identify open issues for future work in this domain.
6q25.1 (TAB2) microdeletion syndrome: Congenital heart defects and cardiomyopathy

Congenital heart defects (CHD) are the most frequent type of congenital anomaly and are often associated with genetic and chromosomal syndromes. Haploinsufficiency of TAB2 (TGF‐beta activated kinase 1/MAP3K7 binding protein 2) has been proposed to cause valvular and cardiac outflow tract structural abnormalities. In this study, we describe 13 newly identified individuals with microdeletions of chromosome 6q25.1 that involve TAB2. One of the patients in our study cohort has the smallest deletion yet reported, affecting only TAB2. These were compared to 27 other patients reported in the published literature or DECIPHER to have similar microdeletions, for a total study group of 40 patients. Our study shows that individuals with TAB2 deletions are predisposed to developing a primary cardiomyopathy with reduced systolic function, even in the absence of CHD. Our study cohort also shares a number of non‐cardiac phenotypic findings: characteristic dysmorphic facial features, intrauterine growth restriction and/or postnatal proportionate short stature, hypotonia, developmental delay and/or intellectual disability, and connective tissue abnormalities. We conclude that a microdeletion of 6q25.1 that includes TAB2 causes a distinctive, multi‐systemic syndrome. The 6q25.1 microdeletion syndrome should be considered in a patient with cardiomyopathy or a CHD, especially valve and/or atrial or ventricular septal abnormalities, and with phenotypic features described in this study. We recommend that patients with a TAB2 deletion be screened longitudinally for systolic heart failure, even if an initial echocardiogram is normal.
GEOMETRIC CORROBORATION OF THE EARLIEST LENSED GALAXY AT z ≃ 10.8 FROM ROBUST FREE-FORM MODELLING

A multiply lensed galaxy, MACS0647-JD, with a probable photometric redshift of is claimed to constitute one of the very earliest known galaxies, formed well before reionization was completed. However, spectral evidence that MACS0647-JD lies at high redshift has proven infeasible and so here we seek an independent-lensing-based “geometric redshift” derived from the angles between the three lensed images of MACS0647-JD, using our free-form mass model (WSLAP+) for the lensing cluster MACSJ0647.7+7015 (at z = 0.591). Our lens model uses the nine sets of multiple images, including those of MACS0647-JD, identified by the CLASH survey toward this cluster. We convincingly exclude the low-redshift regime of z < 3, for which convoluted critical curves are generated by our method, as the solution bends to accommodate the wide angles of MACS0647-JD for this low redshift. Instead, a best fit to all sets of lensed galaxy positions and redshifts provides a geometric redshift of for MACS0647-JD, strongly supporting the higher photometric redshift solution. Importantly, we find a tight linear relation between the relative brightnesses of all nine sets of multiply lensed images and their relative magnifications as predicted by our model. This agreement provides a benchmark for the quality of the lens model, and establishes the robustness of our free-form lensing method for measuring model-independent geometric source distances and for deriving objective central cluster mass distributions. After correcting for its magnification the luminosity of MACS0647-JD remains relatively high at MUV = −19.4, which is within a factor of a few in flux of some surprisingly luminous z ≃ 10–11 candidates discovered recently in Hubble blank field surveys.
Tumor Necrosis Factor Promotes Phosphorylation and Binding of Insulin Receptor Substrate 1 to Phosphatidylinositol 3-Kinase in 3T3-L1 Adipocytes (*)

Chronic incubation of 3T3-L1 adipocytes with tumor necrosis factor (TNF) induces a state of insulin resistance characterized by a diminished ability of insulin to induce phosphorylation of the β subunit of its own receptor and insulin receptor substrate 1 (IRS-1). When adipocytes are briefly pretreated with TNF and then stimulated with insulin, tyrosine phosphorylation of IRS-1 increases above the level induced by insulin alone. By itself, TNF induces the time-dependent tyrosine phosphorylation of proteins in 3T3-L1 adipocytes. Among these is IRS-1, a docking protein with tyrosine phosphorylation sites that bind cytoplasmic signaling molecules that contain Src homology 2 (SH2) domains. TNF stimulation of 3T3-L1 adipocytes also promotes the association of the p85 regulatory subunit of phosphatidylinositol 3-kinase (PI 3-kinase) with IRS-1 and also its tyrosine phosphorylation. In murine 3T3-L1 adipocytes, IRS-1 and PI 3-kinase phosphorylation and the association of these proteins are promoted by murine TNF, which interacts with the type 1 and type 2 TNF receptors. Human TNF, which binds to the murine type 1 TNF receptor selectively, also promotes IRS-1 phosphorylation and binding of IRS-1 to PI 3-kinase. This is the first demonstration that a member of the TNF/nerve growth factor receptor superfamily can use an IRS-1 signaling system as a component of its cellular response and provides a mechanism through which TNF receptors may engage downstream elements in signaling pathways.
Systematic Review and Adjusted Indirect Comparison Meta-Analysis of Oral Anticoagulants in Atrial Fibrillation

Background—Oral anticoagulants such as apixaban, dabigatran, and rivaroxaban are alternatives to warfarin for preventing events in patients with atrial fibrillation. Direct comparative studies between agents are unavailable. Our objective was to conduct an adjusted indirect comparison meta-analysis between new oral agents in atrial fibrillation. Methods and Results—We searched MEDLINE and Cochrane Central through February 2012 for randomized, controlled trials in patients with atrial fibrillation evaluating apixaban, dabigatran, or rivaroxaban versus warfarin. For dabigatran, only data from the Food and Drug Administration–approved dose were included. Outcomes included the composite of stroke or systemic embolism, any stroke, and major bleeding among, others. Outcomes were initially pooled using standard random-effects methods, producing risk ratio and 95% confidence intervals. Adjusted indirect comparisons using these pooled estimates were then performed. A total of 44 733 patients from 4 studies were analyzed. Most analyses yielded no differences between agents. Dabigatran lowered risk of composite outcome (risk ratio, 0.75; 95% confidence interval, 0.57–1.00), ischemic stroke (0.67; 0.48–0.93), and hemorrhagic stroke (0.45; 0.45–0.99) versus rivaroxaban. No differences in all strokes or mortality were seen. Apixaban lowered the risk of major bleeding (0.74; 0.60–0.91) and gastrointestinal bleeding (0.58; 0.41–0.82) versus dabigatran and major bleeding versus rivaroxaban (0.68; 0.55–0.83), but increased systemic emboli versus rivaroxaban (3.86; 1.17–12.75). Conclusions—Significant differences in efficacy and safety parameters may exist between oral anticoagulant agents in patients with atrial fibrillation. Apixaban lowers the risk of major and gastrointestinal bleeding versus dabigatran and rivaroxaban. Dabigatran lowers the composite of stroke or systemic emboli, and ischemic stroke versus rivaroxaban. Head-to-head clinical trials are required to confirm these findings.
Transient performance of an incremental combination of LMS filters

Incremental combinations were first introduced as a solution to the convergence stagnation issue of parallel-independent combinations, both convex and affine. Since then, this topology has been shown to enhance performance to the point of allowing a combination of LMS filters to outperform the APA with lower complexity. In order to better understand and improve this structure, the present work develops mean and mean square transient models for the incremental combination of two LMS filters, that is shown to be a generalization of the data reuse LMS (DR-LMS). By formulating the optimal supervisor and deriving its constraints, the previously proposed adaptive combiner is redesigned to improve the combination's overall performance, as shown by simulations and analysis.
The State of the Art of Service Description Languages

The service-oriented computing paradigm has gained more and more attention in research and practice over the last couple of years. Today, the idea of composing services in a loosely and flexible way in order to support the rapid and low-cost development of applications has been widely accepted. Along with the increasing success of the service-oriented computing paradigm came a variety of languages, which aim at documenting service properties in order to support the selection and binding of services. Amongst them are approaches like the Web Service Description Language or the Web Ontology Language for services. However, until today no approach was able to establish itself as a sufficient standard for a complete description of all relevant service properties. In this paper, we aim at classifying current web service description languages to identify the different properties that a service description language can cover. We furthermore debate on the characteristics of the analyzed approaches and highlight areas where further research is required.