Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian analysis of energy balance data from growing cattle using parametric and non-parametric modelling

Linear and non-linear models have been extensively utilised for the estimation of net and metabolisable energy requirements and for the estimation of the efficiencies of utilising dietary energy for maintenance and tissue gain. In growing animals, biological principles imply that energy retention rate is non-linearly related to the energy intake level because successive increments in energy intake above maintenance result in diminishing returns for tissue energy accretion. Heat production in growing cattle has been traditionally described by logarithmic regression and exponential models. The objective of the present study was to develop Bayesian models of energy retention and heat production in growing cattle using parametric and non-parametric techniques. Parametric models were used to represent models traditionally employed to describe energy use in growing steers and heifers whereas the non-parametric approach was introduced to describe energy utilisation while accounting for non-linearities without specifying a particular functional form. The Bayesian framework was used to incorporate prior knowledge of bioenergetics on tissue retention and heat production and to estimate net and metabolisable energy requirements (NEM and MEM, respectively), and the partial efficiencies of utilising dietary metabolisable energy for maintenance (km) and tissue energy gain (kg). The database used for the study consisted of 719 records of indirect calorimetry on steers and non-pregnant, non-lactating heifers. The NEM was substantially larger in energy retention models (ranged from 0.40 to 0.50 MJ/kg BW0.75.day) than were NEM estimates from heat-production models (ranged from 0.29 to 0.49 MJ/kg BW0.75.day). Similarly, km was also larger in energy retention models than in heat production models. These differences are explained by the nature of y-intercepts (NEM) in these two models. Energy retention models estimate fasting catabolism as the y-intercept, while heat production models estimate fasting heat production. Conversely, MEM was virtually identical in all models and approximately equal to 0.53 MJ/kg BW0.75. day in this database.
TEMHEAD: a single-arm multicentre phase II study of temsirolimus in platin- and cetuximab refractory recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) of the German SCCHN Group (AIO).

BACKGROUND Squamous cell carcinoma of the head and neck (SCCHN) is a common disease, which has a poor prognosis after failure of therapy. Activation of the PI3K-AKT-mTOR axis is commonly detected in recurrent or metastatic SCCHN, and provided the rationale for the clinical phase II trial in pretreated SCCHN. PATIENTS AND METHODS The primary end point was the progression-free survival rate (PFR) at 12 weeks. Forty eligible patients have been recruited after failure of platinum chemotherapy and cetuximab. A preplanned futility analysis was successfully passed after ≥1 success was detected in 20 patients. Secondary objectives consisted of progression-free survival (PFS), disease control rate (DCR), overall survival (OS), safety and tolerability, and predictive biomarkers for KRAS, BRAF, PIK3CA mutations, and HPV status. Archived tumor tissue was analyzed for DNA sequence. RESULTS A total of 40 patients were eligible. The PFR at 12 weeks was 40% (95% CI 25.0-54.6). The median PFS and OS were 56 days (95% CI 36-113 days) and 152 days (76-256 days), respectively. In 33 assessable patients, disease stabilization occurred in 57.6%, with tumor shrinkage in 13 patients (39.4%). Overall, the treatment was well tolerated. Fatigue (47.5%), anemia (25.0%), nausea (20.0%), and pneumonia (20.0%) were the most common adverse events. Neither PIK3CA mutations, nor HPV status were predictive for success with temsirolimus treatment. No mutations were found for KRAS or BRAF. CONCLUSION Tumor shrinkage and efficacy parameter indicate that inhibition of the PI3K-AKT-mTOR axis was a putative novel treatment paradigm for SCCHN. We could not identify parameters predictive for treatment success of temsirolimus, which underscores the need for refinement of the molecular analysis in future studies. CLINICAL TRIALS NUMBER NCT01172769.
Embedding k-outerplanar graphs into ℓ1

We show that the shortest-path metric of any k-outerplanar graph, for any fixed k, can be approximated by a probability distribution over tree metrics with constant distortion, and hence also embedded into l1 with constant distortion. These graphs play a central role in polynomial time approximation schemes for many NP-hard optimization problems on general planar graphs, and include the family of weighted k × n planar grids.This result implies a constant upper bound on the ratio between the sparsest cut and the maximum concurrent flow in multicommodity networks for k-outerplanar graphs, thus extending a classical theorem of Okamura and Seymour [26] for outerplanar graphs, and of Gupta et al. [17] for treewidth-2 graphs. In addition, we obtain improved approximation ratios for k-outerplanar graphs on various problems for which approximation algorithms are based on probabilistic tree embeddings. We also conjecture that our random tree embeddings for k-outerplanar graphs can serve as a building block for more powerful l1 embeddings in future.
Phonetics in Second Language Acquisition: An Acoustic Study of Fluency in Adult Learners of Spanish

Une definition phonetique de l'aisance en discours naturel rend possible le developpement de procedures permettant une mesure empirique de la fluidite. Une analyse des changements de competence en communication orale chez cinq adultes americains apprenant l'espagnol illustrent la maniere par laquelle ces procedures se mettent en œuvre
Gluten sensitivity as a neurological illness

From gut to brain It has taken nearly 2000 years to appreciate that a common dietary protein introduced to the human diet relatively late in evolutionary terms (some 10 000 years ago), can produce human disease not only of the gut but also the skin and the nervous system. The protean neurological manifestations of gluten sensitivity can occur without gut involvement and neurologists must therefore become familiar with the common neurological presentations and means of diagnosis of this disease. ” . the stomach being the digestive organ, labours in digestion, when diarrhoea seizes the patient . and if in addition, the patient's general system be debilitated by atrophy of the body, the coeliac disease of a chronic nature is formed”. 1 This extract is from the book on chronic diseases by Aretaeus the Cappadocian, one of the most distinguished ancient Greek doctors of the first century AD. This chapter, entitled “on the coeliac diathesis”, was the first description of coeliac disease (from the greek word κ⊝ιλιακη meaning abdominal). Aretaeus' books were first published in Latin in 1500 and the new Latin word coeliac was used to translate κ⊝ιλιακη. Coeliac disease (CD) remained obscure until 1887 when Samuel Gee gave a lecture entitled On the coeliac affection 2 at the Hospital for Sick Children, Great Ormond Street, London. In it he acknowledged Areteaus' contribution and went on to give an accurate description of CD based on his own clinical observations. With clinical manifestations primarily confined to the gastrointestinal tract or attributable to malabsorption, it was logical to assume that the target organ and hence the key to the pathogenesis of this disease was the gut. The first report of neurological manifestations associated with CD was by Carnegie Brown in 1908.3 In his book entitled Sprue and its treatment …
Widely Distributed Magnetoencephalography Spikes Related to the Planning and Execution of Human Saccades

With sufficiently fast data sampling, ubiquitous sharp transients appear in magnetoencephalography (MEG) data. Initially, no known collective neuronal activity could explain MEG signal generation well above 100 Hz, so it was assumed that these transients were entirely composed of background electronic noise that could be eliminated by filtering and averaging. Recent studies at the cellular level provided evidence for synchronous synaptic input to dendrites and volleys of near-simultaneous action potentials. MEG studies have also identified high-frequency oscillations well above 200 Hz after averaging large number of somatosensory evoked responses. In this study, we searched for evidence of high-frequency neuronal activity in the raw MEG signal using the highest sampling rate available with our hardware. Two human subjects participated in three experiments using visual cues to define planning, preparation, and execution or inhibition of saccades. Tomographic analysis identified “MEG spikes” that were widely distributed across the cortex, cerebellum, and brainstem during cue presentations and saccades. Here we demonstrate how these MEG spikes can be recorded and localized in real time and show that task demands influence their properties. The MEG spikes were organized into feedforward and corollary discharge sequences that could, when combined with the slower activity-linked processing in discrete brain areas over long periods, lasting hundreds of milliseconds. Preparation for impending saccade began as soon as relevant information became available. Cues providing partial information initiated competing motor programs for as yet undecided future actions that were maintained until cues with new information resolved the uncertainty.
A Survey and Performance Evaluation of Scalable Tree-based Application Layer Multicast Protocols

Application layer multicast (ALM) enables rapid deployment of multicast applications in the Internet. In ALM, application hosts organise themselves into an overlay topology on top of the underlying unicast network. Application data is multicast over the overlay network. In general, ALM protocols can be classified as either tree-first or mesh-first approach. In this paper, we provide a survey and simulation study for the class of tree-first ALM protocols. We investigate the efficiency of HMTP, TBCP, NICE and several variants of transformation-based protocols in terms of tree cost and delay optimisation. To the best of our knowledge, this paper provides the first head-to-head comparison of various tree-first protocols in a single simulation environment. Results show that depth-first searching technique in HMTP can achieve the lowest cost trees. On the other hand, a transformation-based technique that involves only local region nodes is able to construct low latency trees. In addition, we propose an enhancement to TBCP to improve its performance in producing low delay trees.
Increased Basement Membrane Components in Adipose Tissue During Obesity: Links With TGFβ and Metabolic Phenotypes.

CONTEXT Collagen accumulation around adipocytes and vessels (ie, pericellular fibrosis) is a hallmark of obese adipose tissue associated with altered metabolism. OBJECTIVE Our objective was to evaluate components of basement membrane (BM) in adipose tissue, including collagen IV, a major BM component, and its relationships with metabolic parameters and TGFβ isoforms. DESIGN AND SETTING We used immuno-techniques and gene expression approaches to detect BM components in subcutaneous and visceral adipose tissue samples. Adipocytes and endothelial cells were isolated from lean and obese adipose tissue. We also focused on the expression of COL4A1 correlated to metabolic variables in moderate obesity and, in severe obesity before and after bariatric surgery. Using in vitro analysis, we explored the impact of TGFβ isoforms on the expression of inflammatory and extracellular matrix genes in adipocytes and endothelial cells. RESULTS BM components were detected around adipocytes and endothelial cells, and were increased in obese adipocytes. COL4A1 expression was positively correlated with insulin-resistance indices in obese subjects and showed less reduction in severely obese subjects with poorer insulin-resistance outcomes 6 months after gastric bypass. COL4A1 expression also correlated with TGFβ1 and TGFβ3 gene expressions in subcutaneous adipose tissue. Stimulating isolated adipocytes and endothelial cells in vitro with these TGFβ isoforms showed an inflammatory and pro-fibrotic phenotype. However, TGFβ1 and TGFβ3 exposure only provoked COL4A1 overexpression in endothelial cells and not in adipocytes. CONCLUSION The disorganization of several BM components, including collagen IV, could contribute to pathological alterations of obese adipose tissue and cells.
MicroRNA-9 as Potential Biomarker for Breast Cancer Local Recurrence and Tumor Estrogen Receptor Status

MicroRNAs (miRs) are small, non-protein coding transcripts involved in many cellular functions. Many miRs have emerged as important cancer biomarkers. In the present study, we investigated whether miR levels in breast tumors are predictive of breast cancer local recurrence (LR). Sixty-eight women who were diagnosed with breast cancer at the Lombardi Comprehensive Cancer Center were included in this study. Breast cancer patients with LR and those without LR were matched on year of surgery, age at diagnosis, and type of surgery. Candidate miRs were identified by screening the expression levels of 754 human miRs using miR arrays in 16 breast tumor samples from 8 cases with LR and 8 cases without LR. Eight candidate miRs that showed significant differences between tumors with and without LR were further verified in 52 tumor samples using real-time PCR. Higher expression of miR-9 was significantly associated with breast cancer LR in all cases as well as the subset of estrogen receptor (ER) positive cases (p = 0.02). The AUCs (Area Under Curve) of receiver operating characteristic (ROC) curves of miR-9 for all tumors and ER positive tumors are 0.68 (p = 0.02) and 0.69 (p = 0.02), respectively. In ER positive cases, Kaplan-Meier analysis showed that patients with lower miR-9 levels had significantly better 10-year LR-free survival (67.9% vs 30.8%, p = 0.02). Expression levels of miR-9 and another miR candidate, miR-375, were also strongly associated with ER status (p<0.001 for both). The potential of miR-9 as a biomarker for LR warrants further investigation with larger sample size.
The development of similarity: Testing the prediction of a computational model of metaphor comprehension

An empirical study is presented that tests a novel prediction generated by the Metaphor-by-Pattern-Completion (MPC) connectionist model of metaphor comprehension (Thomas & Mareschal, 2001). The MPC model predicts a developmental progression in the way that children process metaphors, from a preference for basic-level metaphors to a preference for subordinate-level metaphors. Preference for different kinds of verbal similarity statements was assessed for 73 children, aged 4–10, along with justifications. The prediction of the model was confirmed, providing evidence for the attendant assumption of the model, specifically that metaphorical comprehension is intimately linked to the emerging structure of semantic representations in children.
African Caribbeans have greater subclinical cerebrovascular disease than Europeans: this is associated with both their elevated resting and ambulatory blood pressure and their hyperglycaemia

Objectives: Stroke is elevated in people of black African descent, but evidence for excess subclinical cerebrovascular disease is conflicting, and the role of risk factors in determining any ethnic differences observed unexplored. Methods: We compared prevalence of brain infarcts, and severe white matter hyperintensities (WMHs) on cerebral MRI, in a community-based sample of men and women aged 58–86 of African Caribbean (214) and European (605) descent, in London, UK. Resting, central and ambulatory blood pressure (BP) were measured; diabetes was assessed by blood testing and questionnaire. Results: Mean age was 70. Multiple (≥4) brain infarcts and severe WMH occurred more frequently in African Caribbeans (18/43%), than Europeans (7/33%, P = 0.05/0.008). Separately, clinic and night-time ambulatory BP were significantly associated with severe WMH in both ethnic groups; when both were entered into the model, the association for clinic SBP was attenuated and lost statistical significance [1.00 (0.98–1.02) P = 0.9 in Europeans, 1.00 (0.97–1.04) P = 0.9 in African Caribbeans], whereas the association for night-time SBP was retained [1.04 (1.02–1.07) P <0.001 in Europeans, 1.08 (1.03–1.12), P = 0.001 in African Caribbeans]. The greater age-adjusted and sex-adjusted risk of severe WMH in African Caribbeans compared with Europeans [2.08 (1.15–3.76) P = 0.02], was attenuated to 1.45 [(0.74–2.83) P = 0.3] on adjustment for clinic and night-time systolic pressure, antihypertensive medication use and glycated haemoglobin. Conclusion: African Caribbeans have a greater burden of subclinical cerebrovascular disease than Europeans. This excess is related to elevated clinic and ambulatory BP, and to hyperglycaemia.
Patterns of individual differences in the perception of missing-fundamental tones.

Recent experimental findings suggest stable individual differences in the perception of auditory stimuli lacking energy at the fundamental frequency (F0), here called missing fundamental (MF) tones. Specifically, some individuals readily identify the pitch of such tones with the missing F0 ("F0 listeners"), and some base their judgment on the frequency of the partials that make up the tones ("spectral listeners"). However, the diversity of goals and methods in recent research makes it difficult to draw clear conclusions about individual differences. The first purpose of this article is to discuss the influence of methodological choices on listeners' responses. The second goal is to report findings on individual differences in our own studies of the MF phenomenon. In several experiments, participants judged the direction of pitch change in stimuli composed of two MF tones, constructed so as to reveal whether the pitch percept was based on the MF or the partials. The reported difference between F0 listeners and spectral listeners was replicated, but other stable patterns of responses were also observed. Test-retest reliability is high. We conclude that there are genuine, stable individual differences underlying the diverse findings, but also that there are more than two general types of listeners, and that stimulus variables strongly affect some listeners' responses. This suggests that it is generally misleading to classify individuals as "F0 listeners" or "spectral listeners. " It may be more accurate to speak of two modes of perception ("F0 listening" and "spectral listening"), both of which are available to many listeners. The individual differences lie in what conditions the choice between the two modes.
Molecular Dynamics Simulations of GABA Binding to the GABAC Receptor: The Role of Arg104

GABA is the major inhibitory neurotransmitter in the nervous system and acts at a variety of receptors including GABAC receptors, which are a subclass of GABAA receptors. Here we have used molecular dynamics simulations of GABA docked into the extracellular domain of the GABAC receptor to explain the molecular interactions of the neurotransmitter with the residues that contribute to the binding site; in particular, we have explored the interaction of GABA with Arg104. The simulations suggest that the amine group of GABA forms cation-π interactions with Tyr102 and Tyr198, and hydrogen-bonds with Gln83, Glu220, Ser243, and Ser168, and, most prominently, with Arg104. Substituting Arg104 with Ala, Glu, or Lys, which experimentally disrupt GABAC receptor function, and repeating the simulation revealed fewer and different bonding patterns with GABA, or the rapid exit of GABA from the binding pocket. The simulations therefore unveil interactions of GABA within the binding pocket, and explain experimental data, which indicate that Arg104 is critical for the efficient functioning of the receptor.
What's in Your Tweets? I Know Who You Supported in the UK 2010 General Election

Nowadays, the use of social media such as Twitter is necessary to monitor trends of people on political issues. As a case study, we collected the main stream of Twitter related to the 2010 UK general election during the associated period. We analyse the characteristics of the three main parties in the election. Also, we propose a simple and practical algorithm to identify the political leaning of users using the amount of Twitter messages which seem related to political parties. The experimental results showed that the best-performing classification method -- which uses the number of Twitter messages referring to a particular political party -- achieved about 86% classification accuracy without any training phase.
Peer-Initiated Motivational Climate and Group Cohesion in Youth Sport

The purpose of the present study was to examine the reciprocal relationship between peer-initiated motivational climate and group cohesion. Measures of peer climate and cohesion were completed across the first half of a competitive season. Controlling for early season perceptions of the dependent variables, hierarchical regression results from 189 participants revealed that early season ego-related climate negatively predicted task cohesion near midseason (p <.01), and task cohesion at early season positively predicted task-related climate at midseason (p <.01). The current study offers preliminary insight into the direction of the relationships between the two constructs in competitive youth sport.
How well do line drawings depict shape?

This paper investigates the ability of sparse line drawings to depict 3D shape. We perform a study in which people are shown an image of one of twelve 3D objects depicted with one of six styles and asked to orient a gauge to coincide with the surface normal at many positions on the object's surface. The normal estimates are compared with each other and with ground truth data provided by a registered 3D surface model to analyze accuracy and precision. The paper describes the design decisions made in collecting a large data set (275,000 gauge measurements) and provides analysis to answer questions about how well people interpret shapes from drawings. Our findings suggest that people interpret certain shapes almost as well from a line drawing as from a shaded image, that current computer graphics line drawing techniques can effectively depict shape and even match the effectiveness of artist's drawings, and that errors in depiction are often localized and can be traced to particular properties of the lines used. The data collected for this study will become a publicly available resource for further studies of this type.