Miracle-dz/UniFAR-FTUs huggingface dataset:
Slow and fast fiber isoform gene expression is systematically altered in skeletal muscle of the Sox6 mutant, p100H

We have previously demonstrated that p100H mutant mice, which lack a functional Sox6 gene, exhibit skeletal and cardiac muscle degeneration and develop cardiac conduction abnormalities soon after birth. To understand the role of Sox6 in skeletal muscle development, we identified muscle‐specific genes differentially expressed between wild‐type and p100H mutant skeletal muscles and investigated their temporal expression in the mutant muscle. We found that, in the mutant skeletal muscle, slow fiber and cardiac isoform genes are expressed at significantly higher levels, whereas fast fiber isoform genes are expressed at significantly lower levels than wild‐type. Onset of this aberrant fiber type‐specific gene expression in the mutant coincides with the beginning of the secondary myotube formation, at embryonic day 15–16 in mice. Together with our earlier report, demonstrating early postnatal muscle defects in the Sox6 null‐p100H mutant, the present results suggest that Sox6 likely plays an important role in muscle development. Developmental Dynamics 234:301–311, 2005. © 2005 Wiley‐Liss, Inc.
Bifid median nerve in carpal tunnel syndrome: Do we need to know?

Introduction: We tested the hypothesis that a bifid median nerve predisposes to development of carpal tunnel syndrome (CTS) and investigated differences in electrophysiological findings and outcome. Methods: A total of 259 consecutive patients with clinically defined CTS were included and investigated clinically, electrophysiologically, and ultrasonographically. Fifty‐four healthy asymptomatic volunteers were investigated ultrasonographically. Results: The prevalence of bifid median nerves is equal in patients with CTS and controls. Electrophysiological and ultrasonographic abnormalities are more pronounced in patients with non‐bifid median nerves. Some outcome data are better in patients with non‐bifid median nerves, but others do not show significant differences. Conclusions: A bifid median nerve is not an independent risk factor for development of CTS. Some of our data suggest outcome after surgical decompression to be different, but others do not. The surgical technique in these patients may therefore have to be reevaluated. Muscle Nerve 50: 835–843, 2014
Cause and Effect in Biology Revisited: Is Mayr’s Proximate-Ultimate Dichotomy Still Useful?

Fifty years ago, Ernst Mayr published a hugely influential paper on the nature of causation in biology, in which he distinguished between proximate and ultimate causes. Mayr equated proximate causation with immediate factors (for example, physiology) and ultimate causation with evolutionary explanations (for example, natural selection). He argued that proximate and ultimate causes addressed different questions and were not alternatives. Mayr’s account of causation remains widely accepted today, with both positive and negative ramifications. Several current debates in biology (for example, over evolution and development, niche construction, cooperation, and the evolution of language) are linked by a common axis of acceptance/rejection of Mayr’s model of causation. We argue that Mayr’s formulation has acted to stabilize the dominant evolutionary paradigm against change but may now hamper progress in the biological sciences.
The number of nuclei in adult rat muscles with special reference to satellite cells

The number and the size of different populations of nuclei were studied in skeletal muscles and in the diaphragm of male Wistar rats of 200‐250 g weight. Nuclei on cross‐sections were counted and classified by electron microscopy, their incidence was corrected for their different lengths, and the number of nuclei per mm3 of muscle was determined by light microscopy. The total number of nuclei per mm3 was 5 · 104 in the superficial part of the anterior tibial muscle, it was 10 · 104 in the soleus, and it was 15 · 104 in the diaphragm. Half of the nuclei were localized inside muscle fibres. The incidence of satellite cell nuclei on cross sections was 4% of muscle nuclei in the anterior tibial muscle, and 8% in soleus and diaphragm. The number of satellite cells per mm3 muscle were 900, 4,900, and 5,300 in these muscles.
Outcomes of Preterm Neonates Transferred Between Tertiary Perinatal Centers

Objective: To verify if preterm neonates transferred between tertiary referral centers have worse outcomes than matched untransferred infants. Design: Cohort study with a historically matched control group. Setting: Two tertiary-level neonatal ICUs. Patients: Seventy-five neonates per group. Interventions: Transfer between tertiary-level neonatal ICUs carried out by a fully equipped transportation team. Measurements and Main Results: We measured in-hospital mortality, frequency of intraventricular hemorrhage greater than 2nd grade, periventricular leukomalacia, necrotizing enterocolitis greater than or equal to grade 2, bronchopulmonary dysplasia, composite outcomes (in-hospital mortality/bronchopulmonary dysplasia, in-hospital mortality/intraventricular hemorrhage > 2nd grade, and bronchopulmonary dysplasia/periventricular leukomalacia/intraventricular hemorrhage > 2nd grade), length of neonatal ICU stay, weight at discharge, and time spent on ventilatory support. Seventy-five similar (except for antenatal steroids administration) neonates were enrolled in each cohort. Cohorts did not differ in mortality, bronchopulmonary dysplasia, intraventricular hemorrhage greater than 2nd grade, periventricular leukomalacia, necrotizing enterocolitis greater than or equal to grade 2, any composite outcomes, neonatal ICU stay, weight at discharge, and duration of respiratory support. Results were unchanged adjusting for antenatal steroids. Conclusions: Neonatal transfer between tertiary-level centers does not impact on clinical outcomes, if performed under optimal conditions.
THE DYNAMICS OF TWO HYBRID ZONES IN APPALACHIAN SALAMANDERS OF THE GENUS PLETHODON

Two zones of intergradation between populations of Plethodon have been studied for 18 and 20 years, respectively. The data consist of systematic scores of colors, made at least twice annually. Near Heintooga Overlook in the Balsam Mountains (Great Smoky Mountains National Park), the salamanders' cheeks are gray. Proceeding north toward the Smokies, there is increasing frequency and intensity of red color at two, four, and six miles. There has been no change in the scores at any location. The width of the zone and our failure to detect any change can be explained by assuming neutrality of the character and random diffusion during the probable time since contact between the two intergrading forms, which most likely took place after the Hypsithermal Interval, 8,000–5,000 BP. At Coweeta Hydrologic Laboratory in the Nantahala Mountains, Plethodon jordani and P. glutinosus hybridize at intermediate elevations. The lateral white spots of glutinosus decrease and the red on the legs of jordani increases with elevation from 685 m to 1,052 m. At the higher elevation, the proportion of animals scored as “pure” jordani declined significantly from 1974 to 1990, an indication that the hybrid zone is spreading upward. The rate of spread is too great to be explained by random diffusion, so selection for glutinosus characters is the best explanation. The rate of spread of the hybrid zone indicates that hybridization began 60–65 years ago, at the end of the time of intense timbering. Such human disturbances have caused hybridization in other organisms.
Effects of Aging on Shape Discrimination

A large number of senior patients manifest eye diseases in addition to normal aging changes in their visual system. Visual tests not affected by age would be very useful in early detection of age-related eye diseases. The purpose of this study was to determine the effects of aging on the detection of contour deformation. Seventy-six normal subjects were divided into three age groups: young adults 15 to 39 years old (N = 26); middle-aged adults 40 to 59 years old (N = 22); and senior adults 60 to 78 years old (N = 28). Stimuli were circular or linear D4 (4th derivative of Gaussian) contours. A spatial two-alternative forced-choice staircase paradigm was used. In each trial, one deformed and one undeformed contour were presented on a screen. Subjects indicated which contour was deformed. Deformation detection thresholds were estimated by a maximum likelihood fitting procedure. We found that at a low modulation frequency (four cycles), the performance of detecting deformation does not change with age, and it does not correlate with either visual acuity or letter contrast sensitivity. At a higher modulation frequency (eight cycles), a significant difference between mean thresholds was found for young and senior adults. For circular D4, the mean threshold was elevated by 18%, from 7.6 sec arc (young adults) to 9.0 sec arc (senior adults). For linear D4, the mean threshold was elevated by 52%, from 5.8 sec arc to 8.8 sec arc. As a comparison, minimum angle of resolution was increased by 33%, and letter contrast threshold was elevated by 81%. The performance for linear D4 at higher modulation frequency was found to be significantly correlated with contrast threshold. These results provide further evidence to support the hypothesis that different mechanisms may be underlying the detection of circular and linear D4 contour deformation. The very small effect of aging on hyperacuity for radial deformation suggests that a global shape discrimination task could be a sensitive test for quantifying the early visual loss caused by eye diseases among seniors.
Evaluation of Nonmotor Symptoms in Diagnosis of Parkinsonism and Tremor

Background. Nonmotor symptoms particularly olfactory dysfunction, RBD, depression, hallucinations, and constipation are currently not included in the typical clinical criteria for diagnosing Lewy body Parkinsonian disorders (LBPD). The aim of this study is to determine the diagnostic value of nonmotor symptoms in patients presenting with Parkinsonism and tremor. Methods. All new patients seen between January 2007 and May 2013 in the Movement Disorders Specialist Clinics of the Royal Melbourne Hospital (RMH), who were referred with a possible neurodegenerative syndrome or concerns of Parkinsonism and/or tremor, were included. Patients underwent routine evaluation with the four-minute “Sniffin Sticks” test, RBD, depression, and constipation. Results. 291 patients were included in the analysis. Conclusion. We found that lower olfaction scores based on “Sniffin Sticks” testing combined with reports of depression and constipation are independent predictors for the diagnosis of the spectrum of Lewy body Parkinsonian disorders (LBPD). Parkinson's disease (PD) cannot be reliably clinically differentiated from other causes of Parkinsonism that share symptomatology and structural abnormalities.
Refinamento da ponta nasal: técnica de sutura minimamente invasiva para a ponta nasal larga

INTRODUCAO: Tecnicas de sutura sao metodos indispensaveis para esculpir as cartilagens nasais. Para obter um melhor contorno em pontas nasais largas ou globosas os autores apresentam uma tecnica de sutura intercrural controlada e minimamente invasiva e os resultados obtidos em 34 pacientes submetidos a rinoplastia. OBJETIVO: Demonstrar a tecnica de sutura intercrural como tratamento para a ponta nasal larga ou globosa em rinoplastia fechada e apresentar os resultados esteticos. METODO: Estudo retrospectivo de documentos clinicos e fotografias de 34 pacientes (5 homens e 29 mulheres), com idade entre 16 e 52 anos, submetidos a rinoplastia com ponta nasal larga ou globosa como elemento anatomico presente no exame fisico. Em todos os casos foi utilizada tecnica de rinoplastia fechada. Uma sutura inabsorvivel e realizada ao longo do processo intermedio. O estudo foi conduzido em 2009 e 2010 no Hospital da Cruz Vermelha Brasileira - Filial do Parana - Brasil e no Hospital Sugisawa. Os pacientes foram operados pelo autor principal e pelos medicos residentes em treinamento. RESULTADOS: A sutura intercrural controlada proporcionou uma refinamento da ponta nasal e uma melhor forma nos ângulos frontal e lateral da ponta nasal. CONCLUSAO: A sutura intercrural controlada e um metodo minimamente invasivo que oferece resultados satisfatorios em refinamento da ponta nasal larga
Neo‐liberalism on crack

Neo‐liberal reform in the Global South has produced a pattern of immiseration that is characterized by what David Harvey has called accumulation by dispossession, a process that destroys the fixed and human capital of the host country while producing huge profits for outside multinational corporations, while producing ‘cities of slums’ that become repositories for severely impoverished economically excluded populations. While this neo‐liberal degradation of host country economies usually takes a decade or longer, the American occupation of Iraq produced the same immiseration in just three years. The American military onslaught, combined with the ‘shock treatment’ of neo‐liberal economic measures, reduced the Iraqi economy, once among the most advanced in the non‐industrial world, to conditions that rival those of the most degraded nations in the Global South. The initial American invasion damaged the already weakened infrastructure in many, but by no means all, Iraqi cities; while the subsequent fighting substantially extended the devastation. Areas which were not war zones were drawn into the widening circle of degradation as the failures in electricity impacted all regions, and as the destroyed upstream sewage system contaminated drinking water, irrigation and fishing throughout the country. Reconstruction budgets were, even by official estimates, incapable of repairing the damage, and they were made more inadequate by the ongoing war, successive reductions (instead of increases) in the allocations and siphoning off of resources for security expenses. In a crystalline example of accumulation by dispossession, US reconstruction policy made the potentially temporary devastation of the war permanent by seeking to impose a free trade market system on a socialist economy. The occupation introduced an extreme version of what has become known as economic ‘shock treatment’, idling state‐owned enterprises that accounted for 35 percent of the economy and contracting with multinational firms to demolish functioning infrastructure and replace it with new systems that were incompatible with existing technologies and local expertise. The new construction was sabotaged by the contractors’ inexperience with the Iraqi physical and economic environment, by widespread corruption, by cost‐plus contracts that incented them to undertake over‐ambitious projects that could not be completed, and by the expenses associated with resolving the incompatibilities with in‐place facilities. Few projects were completed and those that were completed could not be maintained by Iraqi professionals or technicians, and fell into disrepair. With the exhaustion of American reconstruction dollars, the foreign contractors disappeared, leaving a deconstructed Iraq populated by cities of slums.
Effectiveness of Politicians' Soft Campaign on Twitter Versus TV: Cognitive and Experiential Routes

An experiment (N = 183) investigated (a) if individuals respond differently to politicians' Twitter messages and their TV interview, and if so, (b) what cognitive and experiential processes account for such differences. Participants viewed either a segment of a TV talk show, wherein a female politician conversed with the hosts about her personal life and political philosophy, or her Twitter page containing identical messages. Exposure to her TV interview (vs. Twitter page) heightened social presence, inducing stronger parasocial interaction (PSI) and more favorable candidate evaluations among those lower in need for cognition (NFC), but the opposite was true for high NFCs. The candidate's TV interview prompted less source-related thoughts, but more counterarguing among those holding unfavorable attitudes, thereby lowering PSI.
Top quark physics at the Tevatron

The Tevatron proton-antiproton collider at Fermilab with its centre of mass energy of 1.96 TeV is currently the only source for the production of top quarks. Its increased luminosity and centre of mass energy in Run II allow both collider detectors CDF and D0 to study top quarks with unprecedented scrutiny. Recent results on the top quark's pair production cross section and its properties such as mass, electric charge, helicity of the W boson in its decay and branching fraction B(t {yields} Wb) are presented and probe the validity of the Standard Model.
Phase I trial of 177lutetium-labeled J591, a monoclonal antibody to prostate-specific membrane antigen, in patients with androgen-independent prostate cancer.

PURPOSE To determine the maximum tolerated dose (MTD), toxicity, human anti-J591 response, pharmacokinetics (PK), organ dosimetry, targeting, and biologic activity of (177)Lutetium-labeled anti-prostate-specific membrane antigen (PSMA) monoclonal antibody J591 ((177)Lu-J591) in patients with androgen-independent prostate cancer (PC). PATIENTS AND METHODS Thirty-five patients with progressing androgen-independent PC received (177)Lu-J591. All patients underwent (177)Lu-J591 imaging, PK, and biodistribution determinations. Patients were eligible for up to three retreatments. RESULTS Thirty-five patients received (177)Lu-J591, of whom 16 received up to three doses. Myelosuppression was dose limiting at 75 mCi/m(2), and the 70-mCi/m(2) dose level was determined to be the single-dose MTD. Repeat dosing at 45 to 60 mCi/m(2) was associated with dose-limiting myelosuppression; however, up to three doses of 30 mCi/m(2) could be safely administered. Nonhematologic toxicity was not dose limiting. Targeting of all known sites of bone and soft tissue metastases was seen in all 30 patients with positive bone, computed tomography, or magnetic resonance images. No patient developed a human anti-J591 antibody response to deimmunized J591 regardless of number of doses. Biologic activity was seen with four patients experiencing >or= 50% declines in prostate-specific antigen (PSA) levels lasting from 3+ to 8 months. An additional 16 patients (46%) experienced PSA stabilization for a median of 60 days (range, 1 to 21+ months). CONCLUSION The MTD of (177)Lu-J591 is 70 mCi/m(2). Multiple doses of 30 mCi/m(2) are well tolerated. Acceptable toxicity, excellent targeting of known sites of PC metastases, and biologic activity in patients with androgen-independent PC warrant further investigation.
An Eclipse plug-in for Test-to-Code Traceability Recovery

Developers write and maintain unit tests continually in order to reflect changes in the production code and maintain an effective regression test suite. In addition, during refactoring developers must ensure that all unit tests continue to pass, so unit tests often need to be refactored together with the source code. Traceability links between application code and respective unit tests are extremely useful to preserving consistency during refactoring. Unfortunately, support for identifying and maintaining traceability links between unit tests and tested classes in contemporary software engineering environments and tools is not satisfactory. This paper presents SCOTCH (Slicing and COupling based Test to Code trace Hunter), a tool implemented as an Eclipse plug-in that uses dynamic slicing and conceptual coupling to automatically establish the traceability links between unit tests and application code. The evaluation of SCOTCH on several software systems highlights its usefulness as a feature within a software development environment.
Customized answers to summary queries via aggregate views

Statistical users typically require summary tables and want fast and accurate answers to their queries. Usually, the query system keeps materialized aggregate views to speed up the evaluation of summary queries. If the summary table on the variable of interest to a statistical user is not derivable from the set of materialized aggregate views, the answer to his query will consist of an estimate and, if the user is a domain expert, he would like to participate in the estimation process. Therefore, he should be left the possibility of "tuning" the response to an auxiliary variable, for which either there is a materialized aggregate view or aggregate data can be externally provided by the user himself In this framework, we solve the computational problems related to the estimation of summary queries, and propose efficient algorithms which make use of notions and techniques developed in the theory of acyclic database schemes.
Stroke in children and sickle-cell disease

Background/Purpose: The Baltimore-Washington Cooperative Young Stroke Study is the largest biracial urban-suburban population-based study to examine the etiology of strokes in children. Methods: We identified all children aged 1 to 14 years discharged from all 46 hospitals in central Maryland and Washington, DC with a diagnosis of ischemic stroke and intracerebral hemorrhage in the years 1988 and 1991. Each medical record was reviewed by two neurologists for appropriateness of the diagnosis of stroke and for information on the patient's history, clinical presentation, pertinent investigations, hospital stay, and outcome at time of discharge. Results: Eighteen children with ischemic infarction and 17 with intracerebral hemorrhage were identified. The most common cause of ischemic stroke was sickle-cell disease (39%), followed by vasculopathic (33%) and indeterminate(28%) causes. Causes of intracerebral hemorrhages were arteriovenous malformation (29%), hematologic (23%), vasculopathy (18%), surgical complication (12%), coagulopathy (6%), and indeterminate (12%). The overall incidence for childhood stroke was 1.29 per 100,000 per year, with ischemic stroke occurring at a rate of 0.58 per 100,000 and intracerebral hemorrhage occurring at a rate of 0.71 per 100,000. The incidence of stroke among children with sickle-cell disease was estimated to be 0.28% or 285 per 100,000 per year. Conclusion: Sickle-cell disease plays a disproportionately high role in childhood stroke when a biracial population is surveyed.