Miracle-dz/UniFAR-FTUs huggingface dataset:
Dysmaturation of the default mode network in autism

Two hypotheses of autism spectrum disorder (ASD) propose that this condition is characterized by deficits in Theory of Mind and by hypoconnectivity between remote cortical regions with hyperconnectivity locally. The default mode network (DMN) is a set of remote, functionally connected cortical nodes less active during executive tasks than at rest and is implicated in Theory of Mind, episodic memory, and other self‐reflective processes. We show that children with ASD have reduced connectivity between DMN nodes and increased local connectivity within DMN nodes and the visual and motor resting‐state networks. We show that, like the trajectory of synaptogenesis, internodal DMN functional connectivity increased as a quadratic function of age in typically developing children, peaking between, 11 and 13 years. In children with ASD, these long‐distance connections fail to develop during adolescence. These findings support the “developmental disconnection model” of ASD, provide a possible mechanistic explanation for the Theory‐of‐Mind hypothesis of ASD, and show that the window for effectively treating ASD could be wider than previously thought. Hum Brain Mapp 35:1284–1296, 2014. © 2013 Wiley Periodicals, Inc.
Conservative Extensions in Expressive Description Logics

The notion of a conservative extension plays a central role in ontology design and integration: it can be used to formalize ontology refinements, safe mergings of two ontologies, and independent modules inside an ontology. Regarding reasoning support, the most basic task is to decide whether one ontology is a conservative extension of another. It has recently been proved that this problem is decidable and 2ExpTime-complete if ontologies are formulated in the basic description logic ALC. We consider more expressive description logics and begin to map out the boundary between logics for which conservativity is decidable and those for which it is not. We prove that conservative extensions are 2ExpTime-complete in ALCQI, but undecidable in ALCQIO. We also show that if conservative extensions are defined model-theoretically rather than in terms of the consequence relation, they are undecidable already in ALC.
Prediction and prevention of musculoskeletal injury: a paradigm shift in methodology

Traditional methods employed to study musculoskeletal injury mechanisms and joint biomechanics utilise in vivo or in vitro techniques. The advent of new technology and improved methods has also given rise to in silico (computer modelling) techniques. Under the current research paradigm, in vivo, in vitro and in silico methods independently provide information regarding the mechanisms and prevention of musculoskeletal injury. However, individually, each of these methods has multiple, inherent limitations and is likely to provide incomplete answers about multifactorial, complex injury conditions. The purpose of this treatise is to review current methods used to study, understand, and prevent musculoskeletal injury and to develop new conceptual-methodological frameworks that may help create a paradigm shift in musculoskeletal injury prevention research. We term the fusion of these three techniques in simulacra amalgama, or simply in sim, meaning a “union of models done on the likeness of phenomena. ” Anterior cruciate ligament (ACL) injury will be employed as a model example for the utility and applicability of the proposed, synthesised approach. Shifting the current experimental paradigm to incorporate a multifaceted, multidisciplinary, integration of in vivo, in vitro and in silico methods into the proposed in sim approaches may provide a platform for a more comprehensive understanding of the relationships between complex joint biomechanics and observed injury mechanisms.
Semi-automatic Domain Ontology Construction from Spoken Corpus in Tunisian Dialect: Railway Request Information

In this paper, we present a hybrid method for semi-automatic building of domain ontology from spoken dialogue corpus in Tunisian Dialect for the railway request information domain. The proposed method is based on a statistical method for term and concept extraction and a linguistic method for semantic relation extraction. This method consists of three fundamental phases, namely the corpus construction and treatment, the ontology construction and the ontology evaluation. The proposed method is implemented through the ABDO system to generate the RIO ontology that contains 14 concepts, 25 semantic relations and 387 concepts instances. The generated domain ontology is used to semantically label Tunisian dialect utterances in spoken dialogue.
Pertussis Across the Globe: Recent Epidemiologic Trends From 2000-2013.

Pertussis has reemerged as a problem across the world. To better understand the nature of the resurgence, we reviewed recent epidemiologic data and we report disease trends from across the world. Published epidemiologic data from January 2000 to July 2013 were obtained via PubMed searches and open-access websites. Data on vaccine coverage and reported pertussis cases from 2000 through 2012 from the 6 World Health Organization (WHO) regions were also reviewed. Findings are confounded by the lack of systematic and comparable observations in many areas of the world, but also by the cyclic nature of pertussis with peaks occurring every 3 to 5 years. It appears that pertussis incidence has increased in school-age children in North America and western Europe, where acellular pertussis vaccines are used, but an increase has also occurred in some countries that use whole-cell vaccines. Worldwide, pertussis remains a serious health concern, especially for infants, who bear the greatest disease burden. Factors that may contribute to the resurgence include lack of booster immunizations, low vaccine coverage, improved diagnostic methods, and genetic changes in the organism. To better understand the epidemiology of pertussis and optimize disease control, it is important to improve surveillance worldwide, irrespective of pertussis vaccine types and schedules used in each country.
Taste Neurons Consist of Both a Large TrkB-Receptor-Dependent and a Small TrkB-Receptor-Independent Subpopulation

Brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT-4) are two neurotrophins that play distinct roles in geniculate (taste) neuron survival, target innervation, and taste bud formation. These two neurotrophins both activate the tropomyosin-related kinase B (TrkB) receptor and the pan-neurotrophin receptor p75. Although the roles of these neurotrophins have been well studied, the degree to which BDNF and NT-4 act via TrkB to regulate taste development in vivo remains unclear. In this study, we compared taste development in TrkB−/− and Bdnf−/−/Ntf4−/− mice to determine if these deficits were similar. If so, this would indicate that the functions of both BDNF and NT-4 can be accounted for by TrkB-signaling. We found that TrkB−/− and Bdnf−/−/Ntf4−/− mice lose a similar number of geniculate neurons by E13.5, which indicates that both BDNF and NT-4 act primarily via TrkB to regulate geniculate neuron survival. Surprisingly, the few geniculate neurons that remain in TrkB−/− mice are more successful at innervating the tongue and taste buds compared with those neurons that remain in Bdnf−/−/Ntf4−/− mice. The remaining neurons in TrkB−/− mice support a significant number of taste buds. In addition, these remaining neurons do not express the TrkB receptor, which indicates that either BDNF or NT-4 must act via additional receptors to influence tongue innervation and/or targeting.
Evaluation of balloon and satellite water vapour measurements in the Southern tropical UTLS during the HIBISCUS campaign

Balloon water vapour in situ and remote measurements in the tropical upper troposphere and lower stratosphere (UTLS) obtained during the HIBISCUS campaign around 20° S in Brazil in February–March 2004 using a tunable diode laser (μSDLA), a surface acoustic wave (SAW) and a Vis-NIR solar occultation spectrometer (SAOZ) on a long duration balloon, have been used for evaluating the performances of satellite borne remote water vapour instruments available at the same latitude and measurement period. In the stratosphere, HALOE displays the best precision (2.5%), followed by SAGE II (7%), MIPAS (10%), SAOZ (20–25%) and SCIAMACHY (35%), all of which show approximately constant H2O mixing ratios between 20–25 km. Compared to HALOE of ±10% accuracy between 0.1–100 hPa, SAGE II and SAOZ show insignificant biases, MIPAS is wetter by 10% and SCIAMACHY dryer by 20%. The currently available GOMOS profiles of 25% precision show a positive vertical gradient in error for identified reasons. Compared to these, the water vapour of the Reprobus Chemistry Transport Model, forced at pressures higher than 95 hPa by the ECMWF analyses, is dryer by about 1 ppmv (20%). In the lower stratosphere between 16–20 km, most notable features are the steep degradation of MIPAS precision below 18 km, and the appearance of biases between instruments far larger than their quoted total uncertainty. HALOE and SAGE II (after spectral adjustment for reducing the bias with HALOE at northern mid-latitudes) both show decreases of water vapour with a minimum at the tropopause not seen by other instruments or the model, possibly attributable to an increasing error in the HALOE altitude registration. Between 16–18 km where the water vapour concentration shows little horizontal variability, and where the μSDLA balloon measurements are not perturbed by outgassing, the average mixing ratios reported by the remote sensing instruments are substantially lower than the 4–5 ppmv observed by the μSDLA. Differences between μSDLA and HALOE and SAGE II (of the order of −2 ppmv), SCIAMACHY, MIPAS and GOMOS (−1 ppmv) and SAOZ (−0.5 ppmv), exceed the 10% uncertainty of μSDLA, implying larger systematic errors than estimated for the various instruments. In the upper troposphere, where the water vapour concentration is highly variable, AIRS v5 appears to be the most consistent within its 25% uncertainty with balloon in-situ measurements as well as ECMWF. Most of the remote measurements show less reliability in the upper troposphere, losing sensitivity possibly because of absorption line saturation in their spectral ranges (HALOE, SAGE II and SCIAMACHY), instrument noise exceeding 100% (MIPAS) or imperfect refraction correction (GOMOS). An exception is the SAOZ-balloon, employing smaller H2O absorption bands in the troposphere.
Early Word Recognition in Sentence Context: French and English 24-Month-Olds' Sensitivity to Sentence-Medial Mispronunciations and Assimilations

Recent work has shown that young children can use fine phonetic detail during the recognition of isolated and sentence-final words from early in lexical development. The present study investigates 24-month-olds' word recognition in sentence-medial position in two experiments using an Intermodal Preferential Looking paradigm. In Experiment 1, French toddlers detect word-final voicing mispronunciations (e.g., buz [byz] for bus [bys] “bus”), and they compensate for native voicing assimilations (e.g., buz devant toi [buzdəvɑtwa] “bus in front of you”) in the middle of sentences. Similarly, English toddlers detect word-final voicing mispronunciations (e.g., sheeb for sheep) in Experiment 2, but they do not compensate for illicit voicing assimilations (e.g., sheeb there). Thus, French and English 24-month-olds can take into account fine phonetic detail even if words are presented in the middle of sentences, and French toddlers show language-specific compensation abilities for pronunciation variation caused by native voicing assimilation.
SERO-PREVALENCE OF FOOT-AND-MOUTH DISEASE IN SMALL RUMINANTS OF PAKISTAN

Foot-and-mouth disease (FMD) is a contagious viral disease of cloven-footed animals. It is endemic in Pakistan with huge economic losses. The aim of the study was to estimate the sero-prevalence of FMD in small ruminants (sheep and goats) kept in proximity to large ruminants with a recent history of FMD outbreak. The study was conducted in seven purposively selected districts of Pakistan. A total of 1478 sera were collected from small ruminants during 2010-2012. Serum samples were tested for the presence of antibodies against non-structural protein (3ABC) of FMD virus using CHEKIT FMD-3ABC bo-ov kit (IDEXX laboratories, USA). The data were analyzed using χ2 test and multiple logistic regression methods. The sero-prevalence of FMD in small ruminants was 22.8% (337/1478). The FMD sero-prevalence in goats (282/1094; 25.8%) was significantly higher (χ2=21.18; p<0.001) than that in sheep (55/384; 14.3%). After adjusting for other factors, the risk of FMD in sheep was 0.56 times of that in goats (CI; 0.4-0.78, p=0.001). The seropositivity in male animals was higher 17.8% (76/428) than female animals 24.9% (261/1050). Female animals were more likely to be positive for FMD infection compared to male animals (χ2=8.71; p<0.003). The sero-prevalence in district Islamabad (11.8%) was significantly lower than other districts (p<0.001). The findings indicate that FMD is endemic in small ruminants kept in close contact with large ruminants and these animals may serve as reservoirs of FMD virus and possible sources of infection in susceptible livestock.
Serum levels of appetite-regulating hormones and pro-inflammatory cytokines are ameliorated by a CLA diet and endurance exercise in rats fed a high-fat diet

[Purpose] This study examined whether conjugated linoleic acid (CLA) supplementation and endurance exercise affect appetite-regulating hormones and pro-inflammatory cytokines in rats. [Methods] Seven-week-old male Sprague-Dawley rats were divided randomly into the high-fat diet sedentary group (HS, n=8), the 1.0% CLA supplemented high-fat diet sedentary group (CS, n=8), and the 1.0% CLA supplemented high-fat diet exercise group (CE, n=8). Rats in the CE group swam 60 min/day, 5 days/week for 4 weeks. [Results] Leptin and insulin levels in the CS and CE groups were significantly lower than those in the HS group (p<0.001), whereas leptin (p<0.01) and insulin (p<0.05) levels decreased significantly in the CE compared to those in the CS group. Interleukin (IL)-1β (p<0.001) and IL-6 (p<0.01) levels in the CS and CE groups decreased significantly compared to those in the HS group. Leptin (IL-1β: r=0.835, p<0.001), IL-6 (r=0.607, p<0.05), insulin (IL-1β: r=0.797, p<0.01), and IL-6 (r=0.827, p<0.01) levels were positively related with pro-inflammatory cytokine levels. [Conclusion] Endurance exercise may play an important role during CLA supplementation of rats on a high-fat diet.
TECHNICAL AND ECONOMICAL ASSESSMENT OF THERMO-MECHANICAL EXTRUSION PRETREATMENT FOR CELLULOSIC ETHANOL PRODUCTION

The Renewable Fuel Standard (RFS) in the Energy Independence and Security Act of 2007 has set the goal of 36 billion gallons of annual ethanol production in the U.S. by 2022, which is equivalent to 17.5% of the current gasoline consumption in the U.S. However, corn ethanol is expected to plateau at a level of 7.3% of current gasoline consumption on an energyequivalent basis. Thus, it is essential to utilize a variety of substrates including lignocellulosic biomass from perennial energy crops such as switch grass, crop residues such as corn and sorghum stover, and agri-industrial co-products such as soybean hulls and wheat bran. Lignocellulosic substrates have a recalcitrant nature and require a pretreatment step that is critical for efficient enzymatic hydrolysis of cellulose and hemicellulose to fermentable sugars. In this study, soybean hulls were used as a model substrate for cellulosic ethanol. A novel thermo-mechanical pretreatment process using extrusion was investigated and compared with two traditional pretreatment methods, dilute acid and alkali hydrolysis, with regard to structural changes in the lignocellulosic substrate, and glucose and ethanol yields. The effect of extrusion parameters, such as barrel temperature, in-barrel moisture and screw speed, on glucose yield from soybean hulls was determined. Optimum processing conditions were screw speed of 350 rpm, maximum barrel temperature of 80C and 40% in-barrel moisture content, resulting in 95% cellulose conversion to glucose. Compared with untreated soybean hulls, the cellulose to glucose conversion of soybean hulls increased by 69.5, 128.4 and 132.2% for dilute acid, alkali and thermo-mechanical pretreatments, respectively. Glucose and other hexose sugars such as mannose and galactose were effectively fermented by Saccharomyces cerevisiae, resulting in ethanol yields of 13.04–15.44 g/L. Fermentation inhibitors glycerol, furfural, 5-(hydroxymethyl)2-furaldehyde (HMF) and acetic acid were found in the thermo-mechanically pretreated substrate, ranging in concentrations from 0.072–0.431, 0–0.049, 0–0.023 and 0.181–0.278 g/L, respectively, which were lower than those reported from acid hydrolyzed substrates. The economic feasibility of commercial cellulosic ethanol production processes employing dilute acid hydrolysis and thermo-mechanical pretreatment were compared using a system dynamics modeling approach. It was concluded that low feedstock cost and high sugar conversion are important factors that can make cellulosic ethanol production commercially viable. Thermomechanical pretreatment was a more promising technology as compared to dilute acid hydrolysis because of the lower capital and operating costs, and higher sugar conversion. TECHNICAL AND ECONOMICAL ASSESSMENT OF THERMO-MECHANICAL EXTRUSION PRETREATMENT FOR CELLULOSIC ETHANOL PRODUCTION
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

Protein–small molecule docking algorithms provide a means to model the structure of protein–small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side‐chain flexibility for an accurate prediction of the protein–small molecule interfaces has become apparent, and an increasing number of docking algorithms probe different approaches to include protein flexibility. Here we describe a new method for docking small molecules into protein binding sites employing a Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side‐chain conformations are optimized simultaneously. The energy function comprises van der Waals (VDW) interactions, an implicit solvation model, an explicit orientation hydrogen bonding potential, and an electrostatics model. In an evaluation of the scoring function the computed energy correlated with experimental small molecule binding energy with a correlation coefficient of 0.63 across a diverse set of 229 protein– small molecule complexes. The docking method produced lowest energy models with a root mean square deviation (RMSD) smaller than 2 Å in 71 out of 100 protein–small molecule crystal structure complexes (self‐docking). In cross‐docking calculations in which both protein side‐chain and small molecule internal degrees of freedom were varied the lowest energy predictions had RMSDs less than 2 Å in 14 of 20 test cases. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Sensitivity to radiation-induced chromosome damage may be a marker of genetic predisposition in young head and neck cancer patients

We previously showed that levels of chromosome damage induced by ionizing radiation were, on average, higher in G2and G0lymphocytes of breast cancer patients than of normal healthy controls, but that there was no correlation between the results in the two assays. We proposed that enhanced sensitivity to G2or G0irradiation was a marker of low-penetrance predisposition to breast cancer, and have recently demonstrated heritability of sensitivity in families of breast cancer cases. We have now applied these assays to patients with head and neck cancers, for whom there is epidemiological evidence of inherited predisposition in addition to environmental causes. The mean frequency of radiation-induced G2aberrations was higher in the 42 patients than in 27 normal controls, but not significantly so. However, cases less than 45 years old were significantly more sensitive than normals of the same age range (P = 0.046), whereas there was no difference between patients and normals of less than 45 years. Also, there was an inverse correlation between G2sensitivity and age for patients but not for normals. Radiation-induced micronuclei in G0cells were more frequent in 49 patients than in 31 normals (P = 0.056) but, as with the G2assay, the greatest difference was seen between early-onset patients and young normals. Again there was an inverse correlation with age for patients but not for normals. Six patients with enhanced toxicity to radiotherapy were G2tested and four other such patients were G0tested; levels of chromosome damage were not significantly greater than in patients with normal reactions. Both assays were used on 64 individuals (39 patients, 25 normals) and there was no significant correlation between the results. We suggest that a proportion of early-onset head and neck cancer patients are genetically predisposed and that each of the two assays detects a different subset of these cases. © 2001 Cancer Research Campaign
A new approach to the long-term reconstruction of the solar irradiance leads to large historical solar forcing

Context. The variable Sun is the most likely candidate for the natural forcing of past climate changes on time scales of 50 to 1000 years. Evidence for this understanding is that the terrestrial climate correlates positively with the solar activity. During the past 10 000 years, the Sun has experienced the substantial variations in activity and there have been numerous attempts to reconstruct solar irradiance. While there is general agreement on how solar forcing varied during the last several hundred years – all reconstructions are proportional to the solar activity – there is scientific controversy on the magnitude of solar forcing. Aims. We present a reconstruction of the total and spectral solar irradiance covering 130 nm–10 μ m from 1610 to the present with an annual resolution and for the Holocene with a 22-year resolution. Methods. We assume that the minimum state of the quiet Sun in time corresponds to the observed quietest area on the present Sun. Then we use available long-term proxies of the solar activity, which are 10 Be isotope concentrations in ice cores and 22-year smoothed neutron monitor data, to interpolate between the present quiet Sun and the minimum state of the quiet Sun. This determines the long-term trend in the solar variability, which is then superposed with the 11-year activity cycle calculated from the sunspot number. The time-dependent solar spectral irradiance from about 7000 BC to the present is then derived using a state-of-the-art radiation code. Results. We derive a total and spectral solar irradiance that was substantially lower during the Maunder minimum than the one observed today. The difference is remarkably larger than other estimations published in the recent literature. The magnitude of the solar UV variability, which indirectly affects the climate, is also found to exceed previous estimates.We discuss in detail the assumptions that lead us to this conclusion.
WeSearch: supporting collaborative search and sensemaking on a tabletop display

Groups of users often have shared information needs -- for example, business colleagues need to conduct research relating to joint projects and students must work together on group homework assignments. In this paper, we introduce WeSearch, a collaborative Web search system designed to leverage the benefits of tabletop displays for face-to-face collaboration and organization tasks. We describe the design of WeSearch and explain the interactions it affords. We then describe an evaluation in which eleven groups used WeSearch to conduct real collaborative search tasks. Based on our study's findings, we analyze the effectiveness of the features introduced by WeSearch.