Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Analysis in Pediatric Thyroid Cancer and Correlations with Age, Ethnicity, and Clinical Presentation

Background: Well-differentiated thyroid cancer (WDTC) incidence in pediatrics is rising, most being papillary thyroid carcinoma (PTC). The objective of the study was to assess the prevalence of different mutations in pediatric WDTC and correlate the genotype with the clinical phenotype. Methods: This is a single-center retrospective study. Thyroid tissue blocks from 42 consecutive pediatric WDTC patients who underwent thyroidectomy between 2001 and 2013 were analyzed at Quest Diagnostics for BRAFV600E, RAS mutations (N,K,H), and RET/PTC and PAX8/PPARγ rearrangements, using validated molecular methods. Thyroid carcinomas included PTC, follicular thyroid carcinoma (FTC), and follicular variant of PTC (FVPTC). Results: Thirty-nine samples (29 females) were genotyped. The mean age at diagnosis was 14.7 years (range 7.9–18.4 years), and most were Hispanic (56.4%) or Caucasian (35.9%). The mean follow-up period was 2.9 years. Mutations were noted in 21/39 (53.8%), with both BRAFV600E (n = 9), and RET/PTC (n = 6) detected only in PTC. Mutations were detected in 2/5 FTC (PAX8/PPARγ and NRAS) and 3/6 FVPTC cases (PAX8/PPARγ). Of 28 PTC patients, 57.1% had mutations: 32.1% with BRAFV600E, 21.4% with RET/PTC, and 3.6% with NRAS. Of patients with BRAFV600E, 77.8% were Hispanic and 88.9% were >15 years, while all RET/PTC-positive patients were ≤15 years (p = 0.003). Tumor size, lymph node involvement, and distant metastasis at diagnosis (or soon after 131I ablation) did not vary significantly based on the mutation. Conclusions: BRAFV600E was the most common mutation, especially in older and Hispanic adolescents. A larger, ethnically diverse pediatric cohort followed long term will enable the genotypic variability, clinical presentation, and response to therapy to be better assessed.
Misspecified Linear Bandits

We consider the problem of online learning in misspecified linear stochastic multi-armed bandit problems. Regret guarantees for state-of-the-art linear bandit algorithms such as Optimism in the Face of Uncertainty Linear bandit (OFUL) hold under the assumption that the arms expected rewards are perfectly linear in their features. It is, however, of interest to investigate the impact of potential misspecification in linear bandit models, where the expected rewards are perturbed away from the linear subspace determined by the arms features. Although OFUL has recently been shown to be robust to relatively small deviations from linearity, we show that any linear bandit algorithm that enjoys optimal regret performance in the perfectly linear setting (e.g., OFUL) must suffer linear regret under a sparse additive perturbation of the linear model. In an attempt to overcome this negative result,we define a natural class of bandit models characterized by a non-sparse deviation from linearity. We argue that the OFUL algorithm can fail to achieve sublinear regret even under models that have non-sparse deviation. We finally develop a novel bandit algorithm, comprising a hypothesis test for linearity followed by a decision to use either the OFUL or Upper Confidence Bound (UCB) algorithm. For perfectly linear bandit models, the algorithm provably exhibits OFULs favorable regret performance, while for misspecified models satisfying the non-sparse deviation property, the algorithm avoids the linear regret phenomenon and falls back on UCBs sublinear regret scaling. Numerical experiments on synthetic data, and on recommendation data from the public Yahoo! Learning toRank Challenge dataset, empirically support our findings.
Secondary hyperparathyroidism: present and future therapeutic implications.

Secondary Hyperparathyroidism: Present and Future Therapeutic Implications was the first programme in a series of clinically oriented Masterclasses in Nephrology which took place in Vienna, Austria in November 2001. Designed to heighten awareness and understanding within specific areas of nephrology, this masterclass examined issues surrounding the pathogenesis, epidemiology, health consequences and medical management of secondary hyperparathyroidism (HPT) in patients with chronic renal failure (CRF). The pathogenesis of secondary HPT in CRF is associated with disturbances of calcium and phosphate metabolism. The three major factors involved in triggering an increase in parathyroid hormone (PTH) secretion appear to be low plasma calcitriol, hypocalcaemia and hyperphosphataemia. A low calcitriol level prevents the inhibition of preproPTH gene transcription. Hypocalcaemia and hyperphosphataemia result in the stabilization of PTH mRNA, leading to an increase in PTH synthesis. Epidemiological studies investigating the incidence of parathyroidectomy (PTx) among uraemic patients have provided conflicting results. The Lombardy epidemiological study [1] found that the prevalence and incidence of PTx in Lombardy was lower than that previously reported for Europe and Italy, probably because of improvements in the monitoring and management of dialysis patients. However, in more recent years as the Lombardy study has continued, no additional decrease in the incidence of PTx has been observed. One major health consequence of secondary HPT is renal osteodystrophy (ROD). ROD includes bone remodelling disorders, where bone quality is altered, and bone loss disorders, where bone mass is reduced; both abnormalities being potentially associated. Adynamic bone disease is now the most common bone remodelling disorder found in patients with end-stage renal disease [2], while osteoporosis is a significant risk factor for both pre-dialysis and dialysis patients. The dose requirements of recombinant human erythropoietin (rHuEpo) in patients with CRF vary considerably, and many patients do not achieve recommended target haemoglobin levels of )11 gudl. Some evidence suggests that HPT may have an inhibitory effect on erythropoiesis. However, other factors, such as inflammation and iron deficiency, might play a more predominant role in rHuEpo hyporesponsiveness. Control of hyperphosphataemia and maintenance of normocalcaemia form the basis of medical management of secondary HPT. Novel approaches include the use of non-calcium-based phosphate binders, different dialysis modalities, new vitamin D metabolites, second-generation calcimimetics and advances in surgical techniques.
Conceptualizing and Testing a Social Cognitive Model of the Digital Divide

The digital divide has loomed as a public policy issue for over a decade. Yet, a theoretical account for the effects of the digital divide is currently lacking. This study examines three levels of the digital divide. The digital access divide (the first-level digital divide) is the inequality of access to information technology (IT) in homes and schools. The digital capability divide (the second-level digital divide) is the inequality of the capability to exploit IT arising from the first-level digital divide and other contextual factors. The digital outcome divide (the third-level digital divide) is the inequality of outcomes (e.g., learning and productivity) of exploiting IT arising from the second-level digital divide and other contextual factors. Drawing on social cognitive theory and computer self-efficacy literature, we developed a model to show how the digital access divide affects the digital capability divide and the digital outcome divide among students. The digital access divide focuses on computer ownership and usage in homes and schools. The digital capability divide and the digital outcome divide focus on computer self-efficacy and learning outcomes, respectively. This model was tested using data collected from over 4,000 students in Singapore. The results generate insights into the relationships among the three levels of the digital divide and provide a theoretical account for the effects of the digital divide. While school computing environments help to increase computer self-efficacy for all students, these factors do not eliminate knowledge the gap between students with and without home computers. Implications for theory and practice are discussed.
The Discussion Goes on: What Is the Role of Euryarchaeota in Humans?

The human body (primarily the intestinal tract, the oral cavity, and the skin) harbours approximately 1,000 different bacterial species. However, the number of archaeal species known to colonize man seems to be confined to a handful of organisms within the class Euryarchaeota (including Methanobrevibacter smithii, M. oralis, and Methanosphaera stadtmanae). In contrast to this conspicuously low diversity of Archaea in humans their unique physiology in conjunction with the growing number of reports regarding their occurrence at sites of infection has made this issue an emerging field of study. While previous review articles in recent years have addressed the putative role of particularly methanogenic archaea for human health and disease, this paper compiles novel experimental data that have been reported since then. The aim of this paper is to inspire the scientific community of “Archaea experts” for those unique archaeal organisms that have successfully participated in the human-microbe coevolution.
Uncovering the diverse cultural bases of social identity: Ingroup ties predict self‐stereotyping among individualists but not among collectivists

On what basis do people form their social identities? To investigate this issue, the present research investigates cross-cultural differences in self-stereotyping, a key outcome of social identification. In particular, the research tests the hypothesis that ingroup ties are a stronger predictor of self-stereotyping among people from individualist cultures than among people from collectivist cultures. In Study 1, university students (N = 117) completed measures of ingroup ties and self-stereotyping with respect to an intimacy group (family and friends). Consistent with predictions, ingroup ties significantly predicted self-stereotyping among individualists but not among collectivists. Study 2 (N = 104) found a similar pattern of results among members of the global internet community who considered either an intimacy group (their friends), a task group (their work group) or a social category (their gender). These results indicate that people in individualist cultures are more likely than those in collectivist cultures to base their social identities on ingroup ties. The implications of these results are discussed in relation to self-categorization theory's depersonalization account of social identification.
Programmed Death 1 Regulates Development of Central Memory CD8 T Cells after Acute Viral Infection

The T cell response possesses a number of inhibitory receptors to regulate the extent of the antiviral response and prevent immune pathology. These receptors are generally transiently upregulated during an effector response and then downregulated during memory. Some inhibitory receptors, such as programmed death 1 (PD-1) and LAG-3, were shown to be aberrantly upregulated during memory to chronic lymphocytic choriomeningitis virus infection, limiting functional capabilities. However, little is known about the impact of inhibitory receptors on memory development during a normal CD8 T cell response to acute virus infection. Our previous data showed that PD-1 is aberrantly upregulated during a secondary response by memory CD8 T cells that were generated without CD4 T cell help. Therefore, we examined the role of PD-1 in memory differentiation during acute vaccinia virus infection in intact mice. In the absence of PD-1, the primary and memory CD8 T cell responses were enhanced. Moreover, there were distinct phenotypic and functional changes in the memory PD-1−/− CD8 T cells. Higher levels of CD62L, CD27, and CCR7 were detected; cells produced more IL-2 and made an enhanced secondary response. These changes indicate a skewing of the memory population toward the central memory phenotype in the absence of PD-1 signaling.
Preventable infections in children with leukodystrophy

Children with inherited leukodystrophies have high hospitalization rates, often associated with infection. We studied whether potentially modifiable risk factors (preexisting indwelling central intravenous access, urinary catheter, hardware, or mechanical ventilation; and influenza vaccine) were associated with infection‐related hospitalization in children with leukodystrophy. Central intravenous access was associated with sepsis (odds ratio [OR] 9.8); urinary catheter was associated with urinary tract infections (OR 9.0); lack of seasonal vaccination was associated with influenza (OR 6.4); and mechanical ventilation was associated with pneumonia (OR 2.7). We conclude that potentially modifiable risk factors are significantly associated with infection and hospitalization in children with leukodystrophies.
Cosmological parameter estimation using Very Small Array data out to ℓ = 1500

We estimate cosmological parameters using data obtained by the Very Small Array (VSA) in its extended configuration, in conjunction with a variety of other cosmic microwave background (CMB) data and external priors. Within the flat A cold dark matter (ACDM) model, we find that the inclusion of high-resolution data from the VSA modifies the limits on the cosmological parameters as compared to those suggested by the Wilkinson Microwave Anisotropy Probe (WMAP) alone, while still remaining compatible with their estimates. We find that Omega(b)h(2) = 0.0234(-0.0014)(+0.0012), Omegadmh2 = 0.111(-0.016)(+0.014), h = 0.73(-0.05)(+0.09), n(S) = 0.97(-0.03)(+0.06), 10(10) A(S) = 23(-3)(+7) and tau = 0.14(-0.07)(+0.14) for WMAP and VSA when no external prior is included. On extending the model to include a running spectral index of density fluctuations, we find that the inclusion of VSA data leads to a negative running at a level of more than 95 per cent confidence (n(run) = -0.069 +/- 0.032), something that is not significantly changed by the inclusion of a stringent prior on the Hubble constant. Inclusion of prior information from the 2dF galaxy redshift survey reduces the significance of the result by constraining the value of Omega(m). We discuss the veracity of this result in the context of various systematic effects and also a broken spectral index model. We also constrain the fraction of neutrinos and find that f(v) < 0.087 at 95 per cent confidence, which corresponds to m(v) <0.32 eV when all neutrino masses are equal. Finally, we consider the global best fit within a general cosmological model with 12 parameters and find consistency with other analyses available in the literature. The evidence for nrun < 0 is only marginal within this model.
Movement Sonification: Effects on Motor Learning beyond Rhythmic Adjustments

Motor learning is based on motor perception and emergent perceptual-motor representations. A lot of behavioral research is related to single perceptual modalities but during last two decades the contribution of multimodal perception on motor behavior was discovered more and more. A growing number of studies indicates an enhanced impact of multimodal stimuli on motor perception, motor control and motor learning in terms of better precision and higher reliability of the related actions. Behavioral research is supported by neurophysiological data, revealing that multisensory integration supports motor control and learning. But the overwhelming part of both research lines is dedicated to basic research. Besides research in the domains of music, dance and motor rehabilitation, there is almost no evidence for enhanced effectiveness of multisensory information on learning of gross motor skills. To reduce this gap, movement sonification is used here in applied research on motor learning in sports. Based on the current knowledge on the multimodal organization of the perceptual system, we generate additional real-time movement information being suitable for integration with perceptual feedback streams of visual and proprioceptive modality. With ongoing training, synchronously processed auditory information should be initially integrated into the emerging internal models, enhancing the efficacy of motor learning. This is achieved by a direct mapping of kinematic and dynamic motion parameters to electronic sounds, resulting in continuous auditory and convergent audiovisual or audio-proprioceptive stimulus arrays. In sharp contrast to other approaches using acoustic information as error-feedback in motor learning settings, we try to generate additional movement information suitable for acceleration and enhancement of adequate sensorimotor representations and processible below the level of consciousness. In the experimental setting, participants were asked to learn a closed motor skill (technique acquisition of indoor rowing). One group was treated with visual information and two groups with audiovisual information (sonification vs. natural sounds). For all three groups learning became evident and remained stable. Participants treated with additional movement sonification showed better performance compared to both other groups. Results indicate that movement sonification enhances motor learning of a complex gross motor skill—even exceeding usually expected acoustic rhythmic effects on motor learning.
Audible Noise Reduction in Eigendomain for Speech Enhancement

A signal subspace scheme based on masking properties is proposed for enhancement of speech degraded by additive noise. Since the masking properties are related to the critical frequency band that is derived from the characteristics of human cochlea, the incorporation of masking threshold into a subspace technique requires the transformation between the frequency and eigen domains. We present and apply an invertible transformation between the frequency and eigen domains. In this paper, we use masking properties of the human auditory system to define the audible noise quantity in the eigendomain. We derive the eigen-decomposition of the estimated speech autocorrelation matrix with the assumption of white noise. Subsequently, an audible noise reduction scheme is developed based on a signal subspace technique, and the implementation of our proposed scheme is outlined. We further extend the scheme to the colored noise case. Simulation results show the superiority of our proposed scheme over other existing subspace methods in terms of segmental signal-to-noise ratio (SNR), perceptual evaluation of speech quality (PESQ), modified Bark spectral distortion (MBSD), spectrogram and informal listening tests.
Training of a Skull-Stripping Neural Network with efficient data augmentation

Skull-stripping methods aim to remove the non-brain tissue from acquisition of brain scans in magnetic resonance (MR) imaging. Although several methods sharing this common purpose have been presented in literature, they all suffer from the great variability of the MR images. In this work we propose a novel approach based on Convolutional Neural Networks to automatically perform the brain extraction obtaining cutting-edge performance in the NFBS public database. Additionally, we focus on the efficient training of the neural network designing an effective data augmentation pipeline. Obtained results are evaluated through Dice metric, obtaining a value of 96.5%, and processing time, with 4.5s per volume.
Genomics of Foam Cells and Nonfoamy Macrophages From Rabbits Identifies Arginase-I as a Differential Regulator of Nitric Oxide Production

Objective—Conversion of macrophages to foam cells is a critical step in the initiation and progression of atherosclerosis. We sought to identify genes differentially regulated in foam cells, since these are likely to include new targets for intervention. Methods and Results—We used suppression subtraction hybridization to compare foam cells and nonfoamy macrophages isolated from subcutaneous granulomas of rabbits fed a cholesterol-rich or normal chow diet and confirmed upregulation of 3 genes, including matrix metalloproteinase-12 (mRNA 2.0-fold, P<0.005; protein 3.9-fold, P<0.03). Arginase-I mRNA showed the biggest decrease among 11 downregulated genes in foam cells (2.7-fold, P<0.001) and was accompanied by significantly reduced arginase enzymatic activity (60-fold, P<0.01). Arginase-I competes for substrate L-arginine with nitric oxide synthase and consequently nitric oxide production was significantly increased (3-fold, P<0.02) in foam cells compared with nonfoamy macrophages despite no difference in nitric oxide synthase isoenzyme expression. We validated upregulation of matrix metalloproteinase-12 and downregulation of arginase-1 in foam cells of rabbit and human atherosclerotic plaques. Conclusions—Our study identified several differentially expressed genes in foam cells and nonfoamy macrophages derived from live rabbits. The altered pattern of gene expression in foam cells is likely to influence atherosclerosis formation and stability.
Synaptotagmins are trafficked to distinct subcellular domains including the postsynaptic compartment

The synaptotagmin family has been implicated in calcium-dependent neurotransmitter release, although Synaptotagmin 1 is the only isoform demonstrated to control synaptic vesicle fusion. Here, we report the characterization of the six remaining synaptotagmin isoforms encoded in the Drosophila genome, including homologues of mammalian Synaptotagmins 4, 7, 12, and 14. Like Synaptotagmin 1, Synaptotagmin 4 is ubiquitously present at synapses, but localizes to the postsynaptic compartment. The remaining isoforms were not found at synapses (Synaptotagmin 7), expressed at very low levels (Synaptotagmins 12 and 14), or in subsets of putative neurosecretory cells (Synaptotagmins α and β). Consistent with their distinct localizations, overexpression of Synaptotagmin 4 or 7 cannot functionally substitute for the loss of Synaptotagmin 1 in synaptic transmission. Our results indicate that synaptotagmins are differentially distributed to unique subcellular compartments. In addition, the identification of a postsynaptic synaptotagmin suggests calcium-dependent membrane-trafficking functions on both sides of the synapse.
Cell-to-cell communication and myogenesis

Cell-to-cell communication was characterized in prefusion chick embryo myoblast cultures, and it was determined that the prefusion myoblasts can interact via gap junctions, ionic coupling, and metabolic coupling. The biological relevance of this communication was supported by the detection of gap junctions between myoblasts in embryonic muscle. Communication was also examined in fusion-arrested cultures to determine its potential relationship to fusion competency. In cultures that were fusion arrested by treatment with either 1.8 mM ethyleneglycolbis-(beta-aminoethyl ether)N,N'-tetraacetic acid (EGTA), 3.3 X 10(-6) M 5-bromodeoxyuridine (BUdR), or 1 microgram/ml cycloheximide (CHX), both gap junctions and ionic coupling were present. Therefore, it is possible to conclude that cell communication is not a sufficient property by itself, to generate fusion between myob- asts. The potential role of communication in myogenesis is discusssed with respect to these observations.