Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for a One-Allele Assortative Mating Locus

Theoretical models have shown that speciation with gene flow can occur readily via a “one-allele mechanism,” where the spread of the same allele within both of two diverging species reduces their subsequent hybridization. Here we present direct genetic evidence for such an allele in Drosophila pseudoobscura. Alleles conferring high or low assortative mating in D. pseudoobscura produce the same effects when inserted into D. persimilis. This observation suggests that the type of genetic variation that is most conducive to controversial modes of speciation with gene flow, such as reinforcement or sympatric speciation, is present in nature.
The Effect of Singing Intervention for Women Elderly with Dysphagia Risk

Purpose: This study was conducted to describe the risk of dysphagia and to evaluate the effects of a singing intervention for women elderly in community. Methods: One-group pre test-post test design was used. The subjects were 29 women over the age of sixty and residing in a local area. A singing intervention consisted of breathing, vowel production and singing. The one hour intervention occurred once a week for eight weeks. The variables of dysphagia risk, a swallowing test, and nutritional status were measured. Analysis was done by paired t-test. Results: There was a significant decrease in the score of dysphagia risk (p<.001). There were significant increases in the swallowing test scores [modified water swallowing test (p=.032), food test (p=.001)]. There were no significant differences in nutritional status (triceps skin fold thickness, mid arm muscle circumference). Conclusion: The findings support that a singing intervention can be helpful in reducing the risk of dysphagia may improve deglutition for the women elderly. These results suggest that this study may contribute to the use of a singing intervention for women elders with dysphagia risk.
Risk Factors and Early Extracoronary Atherosclerotic Plaques Detected by Three-Site Ultrasound Imaging in Hypercholesterolemic Men

Ultrasonic detection of atherosclerotic plaque of carotid abdominal aortic and femoral arteries and evaluation of risk factors were performed in 208 hypercholesterolemic men without cardiovascular disease. Twenty-six percent of them had no plaque. Plaque at the carotid, aortic, and femoral sites was found in 37%, 48%, and 53% of subjects, respectively. Plaque was associated (1) in carotid arteries with increased total and low-density lipoprotein cholesterol; (2) in the aorta with increased age, pressure, glycemia, and smoking; and (3) in femoral arteries with increased age, systolic pressure, low-density lipoprotein cholesterol, and smoking. Multiple regression analysis showed correlations between carotid plaque and low-density lipoprotein cholesterol; aortic plaque and age, smoking, glycemia, and pressure; femoral plaque and age, smoking, and pressure. This suggests that multiple risk factors influence lesions, and risk profile differs according to atherosis site. ( Arch Intern Med . 1991;151:950-956)
Autoreactive B Cell Responses to RNA-Related Antigens Due to TLR7 Gene Duplication

Antibodies against nuclear self-antigens are characteristic of systemic autoimmunity, although mechanisms promoting their generation and selection are unclear. Here, we report that B cells containing the Y-linked autoimmune accelerator (Yaa) locus are intrinsically biased toward nucleolar antigens because of increased expression of TLR7, a single-stranded RNA-binding innate immune receptor. The TLR7 gene is duplicated in Yaa mice because of a 4-Megabase expansion of the pseudoautosomal region. These results reveal high divergence in mouse Y chromosomes and represent a good example of gene copy number qualitatively altering a polygenic disease manifestation.
ARE FORCE ASYMMETRIES MEASURED IN JUMP TESTS ASSOCIATED WITH PREVIOUS INJURY IN PROFESSIONAL FOOTBALLERS?

Background In female athletes, bilateral aysmmetry in peak landing forces during the drop jump is associated with anterior cruciate ligament (ACL) injury risk and is proposed as a marker of rehabilitation progression following ACL rupture. Less is known regarding the value of the assessment of these asymmetry in jump tasks in relation to recovery from other lower extremity injuries, particularly in male athletes. Objective To evaluate the association between previous injury and bilateral limb asymmetry in peak ground reaction forces during a countermovement jump (CMJ) and a drop jump (DJ). Design Retrospective study. Setting Professional football club. Participants 24 first team players. Risk factor assessment CMJ and DJ performed on two force platforms placed side by side with one foot on each platform. Main outcome measurements Asymmetry in peak force during the take-off and landing phases of a CMJ countermovement jump in healthy players who either had (INJ) or had not (N-INJ) sustained a non-contact lower extremity injury in the preceding season. Results Compared to N-INJ, P-INJ mean asymmetry in P-INJ was CMJ takeoff force was 8% higher (CMT-a), in landing force (CML-a) 57% higher, in DJ first landing (DJ1-a) and second landing (DJ2-a) 11% and 31% higher, respectively. None of these differences were significant, but based on Cohen's d, the difference between INJ and N-INJ in CML-a was large (d=0.65), in DJ2-a was moderate (d=0.39) and in CMT-a and DJ1-a was small (d=0.13 and d=0.28, respectively). Conclusions Our findings suggest that in pro footballers jump landing force asymmetry both in CMJ and DJ may be a marker of residual deficits associated with previous lower extremity injury. Larger studies are needed to confirm these findings and to determine whether these asymmetries may also be a marker of future injury risk.
Comment on "Transitions to Asexuality Result in Excess Amino Acid Substitutions"

Paland and Lynch (Reports, 17 February 2006, p. 990) showed that in Daphnia pulex, the ratio of amino acid replacement to silent substitution in mitochondrial genes is higher in asexual lineages than in sexual lineages. If this base-composition bias is maintained by selection, it too should alter following transitions in reproductive mode. Analysis reveals no such change in the genomes of D. pulex.
Distribution of Borna Disease Virus Antigen and RNA in Tissues of Naturally Infected Bicolored White-Toothed Shrews, Crocidura leucodon, Supporting Their Role as Reservoir Host Species

Borna disease is a severe viral-induced disorder of the central nervous system of horses, sheep, and a few other animal species, occurring in certain areas of central Europe. Pathogenesis and epidemiology of natural Borna disease virus (BDV) infections are still not fully understood; several unique epidemiologic features, however, point toward the existence of BDV reservoir populations other than the final hosts. In this study, 69 mice and 12 shrews were trapped and examined. The virus distribution was investigated in detail in 2 BDV-positive bicolored white-toothed shrews, Crocidura leucodon, by immunohistochemistry and TaqMan real-time reverse transcription polymerase chain reaction (RT-PCR). RT-PCR amplification products were sequenced, and the sequences were compared. These shrews had been collected in a BDV-endemic geographical region using live traps and did not show obvious clinical or pathological disease signs. BDV antigen and nucleic acid were identified in several organs, including the brain, mainly in nerve tissue and neurons, respectively, but also in parenchymal cells (eg, hepatocytes, Leydig cells) and epithelial cells, particularly of the respiratory and urogenital tract.
Genes Required for Mitotic Spindle Assembly in Drosophila S2 Cells

The formation of a metaphase spindle, a bipolar microtubule array with centrally aligned chromosomes, is a prerequisite for the faithful segregation of a cell's genetic material. Using a full-genome RNA interference screen of Drosophila S2 cells, we identified about 200 genes that contribute to spindle assembly, more than half of which were unexpected. The screen, in combination with a variety of secondary assays, led to new insights into how spindle microtubules are generated; how centrosomes are positioned; and how centrioles, centrosomes, and kinetochores are assembled.
Longitudinal Study of Clinicopathological Features of Johne’s Disease in Sheep Naturally Exposed to Mycobacterium avium Subspecies Paratuberculosis

The objective of this study was to describe chronological changes in infection status and enteric lesions of sheep naturally exposed to Mycobacterium avium subspecies paratubercuolosis. Samples of terminal ileum (TI) and mesenteric lymph node (MLN) were collected from 77 Merino sheep via surgical biopsy at 12, 18, and 24 months of age and necropsy at 36 months of age. Infection status at each sampling period was determined by fecal, TI, and MLN culture. Quantitative grading schemes were used to gauge the severity of granulomatous inflammation and degree of mycobacterial colonization affecting TI and MLN sections. Incidences of infection and disease were steady throughout the study; 46 of the 77 (59.7%) sheep became infected, and 30 of the 77 (39.0%) developed Johne’s disease. Infection was first detected after 18 months of age in many sheep, and age when infection was first detected was not associated with clinical outcome. Culture of MLN detected 44 of the 46 (95.6%) infected sheep and initial lesions always involved MLN. Sheep typically developed lesions within 6–12 months following detection of infection by culture. The severity of enteritis and mycobacterial colonization progressed at variable rates among sheep. Severe multibacillary enteritis never regressed, and affected sheep expressed clinical signs within the following 12 months. Lymphocyte-rich paucibacillary enteritis was observed in 3 sheep, causing clinical signs in one and progressing to severe multibacillary enteritis in another. Six of the 46 (8.7%) biopsy-culture–positive sheep later had negative cultures at necropsy, suggesting recovery from infection. Further study is needed to identify factors associated with clearance of infection or progression of disease.
Malignant Lymphoma in African Lions (Panthera Leo)

Malignant lymphoma has become an increasingly recognized problem in African lions (Panthera leo). Eleven African lions (9 male and 2 female) with clinical signs and gross and microscopic lesions of malignant lymphoma were evaluated in this study. All animals were older adults, ranging in age from 14 to 19 years. Immunohistochemically, 10 of the 11 lions had T-cell lymphomas (CD3+, CD79a–), and 1 lion was diagnosed with a B-cell lymphoma (CD3–, CD79a+). The spleen appeared to be the primary site of neoplastic growth in all T-cell lymphomas, with involvement of the liver (6/11) and regional lymph nodes (5/11) also commonly observed. The B-cell lymphoma affected the peripheral lymph nodes, liver, and spleen. According to the current veterinary and human World Health Organization classification of hematopoietic neoplasms, T-cell lymphoma subtypes included peripheral T-cell lymphoma (4/11), precursor (acute) T-cell lymphoblastic lymphoma/leukemia (2/11), chronic T-cell lymphocytic lymphoma/leukemia (3/11), and T-zone lymphoma (1/11). The single B-cell lymphoma subtype was consistent with diffuse large B-cell lymphoma. Feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) testing by immunohistochemistry on sections of malignant lymphoma was negative for all 11 lions. One lion was seropositive for FeLV. In contrast to domestic and exotic cats, in which B-cell lymphomas are more common than T-cell lymphomas, African lions in this study had malignant lymphomas that were primarily of T-cell origin. Neither FeLV nor FIV, important causes of malignant lymphoma in domestic cats, seems to be significant in the pathogenesis of malignant lymphoma in African lions.
Replication of Genome-Wide Association Signals in UK Samples Reveals Risk Loci for Type 2 Diabetes

The molecular mechanisms involved in the development of type 2 diabetes are poorly understood. Starting from genome-wide genotype data for 1924 diabetic cases and 2938 population controls generated by the Wellcome Trust Case Control Consortium, we set out to detect replicated diabetes association signals through analysis of 3757 additional cases and 5346 controls and by integration of our findings with equivalent data from other international consortia. We detected diabetes susceptibility loci in and around the genes CDKAL1, CDKN2A/CDKN2B, and IGF2BP2 and confirmed the recently described associations at HHEX/IDE and SLC30A8. Our findings provide insight into the genetic architecture of type 2 diabetes, emphasizing the contribution of multiple variants of modest effect. The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes.
Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis

The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein—the ∼450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. “Permissive” mutations—substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes—played a major role in determining GR's evolutionary trajectory.
Literature Review of the Challenges of Developing Secure Software Using the Agile Approach

A set of challenges of developing secure software using the agile development approach and methods are reported in the literature. This paper reports about a systematic literature review to identify these challenges and evaluates the causes of each of these challenges, with respect to the agile values, the agile principles, and the security assurance practices. We identified in this study 20 challenges, which are reported in 10 publications. We found that 14 of these challenges are valid and 6 are neither caused by the agile values and principles, nor by the security assurance practices. We also found that 2 of the the valid challenges are related to the software development life-cycle, 4are related to incremental development, 4 are related to security assurance, 2 are related to awareness and collaboration, and 2 are related to security management. These results justify the need for research to make developing secure software smooth.
Towards Black Box Testing of Android Apps

Many state-of-art mobile application testing frameworks (e.g., Dynodroid [1], EvoDroid [2]) enjoy Emma [3] or other code coverage libraries to measure the coverage achieved. The underlying assumption for these frameworks is availability of the app source code. Yet, application markets and security researchers face the need to test third-party mobile applications in the absence of the source code. There exists a number of frameworks both for manual and automated test generation that address this challenge. However, these frameworks often do not provide any statistics on the code coverage achieved, or provide coarse-grained ones like a number of activities or methods covered. At the same time, given two test reports generated by different frameworks, there is no way to understand which one achieved better coverage if the reported metrics were different (or no coverage results were provided). To address these issues we designed a framework called BBOXTESTER that is able to generate code coverage reports and produce uniform coverage metrics in testing without the source code. Security researchers can automatically execute applications exploiting current state-of-art tools, and use the results of our framework to assess if the security-critical code was covered by the tests. In this paper we report on design and implementation of BBOXTESTER and assess its efficiency and effectiveness.
RISKS OF INTENSE, SPECIALIZED TRAINING AND GROWTH FOR INJURY IN YOUNG ATHLETES: A CLINICAL EVALUATION

Background There is little data evaluating the risk for serious overuse injury in young athletes focusing on a single-sport or during growth spurts, in a clinical-based population. Objective To determine whether sports specialization, weekly training volumes, and growth rates are associated with increased risk for injury and serious overuse injury in young athletes. Design Case-control study. Setting Injured young athletes ages (7–18yr) were recruited from sports medicine clinics and compared to healthy controls from primary care clinics presenting for sports physicals in 2 medical centers. Participants There were 1206 participants (50.7% male) who were evaluated at baseline while longitudinal follow up data collection for up to 3 years is ongoing at time of submission. Risk factor assessment Independent variables included hours/week of organized sports, free play, gym, sports specialization, and growth rate. Main outcome measurements Dependent variables included total injuries, acute injuries, overuse injuries, and serious overuse injuries. Results Injured athletes were older than uninjured athletes (14.1 +/−2.1 vs. 12.9 y/o +/−2.6, P<.001) and reported a higher avg. hrs/wk playing organized sports (11.3+/−6.9 vs. 9.4 +/−8.2 hr, P<.001). Picking a main sport to focus on one sport was an independent risk factor for injury even after adjusting for hrs/week in total sports activity and age (OR 1.48 P<.05). Young athletes participating in more sports hrs/wk than their age (P<.05) and participating in>2 times organized sports:free play were more likely to have a serious overuse injury (P=.001). Annual calculated growth rates did not impact injury status (4.76 vs 4.79 cm/yr,injured vs. uninjured respectively). Conclusions Injured young athletes are older, spend more time in organized sports, and specialize. Our data support the need for counseling young specialized athletes as to the risks for overuse injury.
Ransomware Inside Out

Android is currently the most widely used mobile environment. This trend encourages malware writers to develop specific attacks targeting this platform with threats designed to covertly collect data or financially extort victims, the so-called ransomware. In this paper we use formal methods, in particular model checking, to automatically dissect ransomware samples. Starting from manual inspection of few samples, we define a set of rule in order to check whether the behaviours we find are representative of ransomware functionalities.
Nuclear Coupling and Polarization in Molecular Transport Junctions: Beyond Tunneling to Function

Much current experimental research on transport in molecular junctions focuses on finite voltages, where substantial polarization-induced nonlinearities may result in technologically relevant device-type responses. Because molecules have strong polarization responses to changing charge state or external field, molecules isolated between electrodes can show strongly nonlinear current-voltage responses. For small applied voltages (up to ∼0.3 volt), weak interaction between transporting electrons and molecular vibrations provides the basis for inelastic electron tunneling spectroscopy. At higher voltages and for certain time scale regimes, strong coupling effects occur, including Coulomb blockade, negative differential resistance, dynamical switching and switching noise, current hysteresis, heating, and chemical reactions. We discuss a general picture for such phenomena that arise from charging, strong correlation, and polarization (electronic and vibrational) effects in the molecule and at the interface.
FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis

Precise timing of CONSTANS (CO) gene expression is necessary for day-length discrimination for photoperiodic flowering. The FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1), and GIGANTEA (GI) proteins regulate CO transcription in Arabidopsis. We demonstrate that FKF1 and GI proteins form a complex in a blue-light–dependent manner. The timing of this interaction regulates the timing of daytime CO expression. FKF1 function is dependent on GI, which interacts with a CO repressor, CYCLING DOF FACTOR 1 (CDF1), and controls CDF1 stability. GI, FKF1, and CDF1 proteins associate with CO chromatin. Thus, the FKF1-GI complex forms on the CO promoter in late afternoon to regulate CO expression, providing a mechanistic view of how the coincidence of light with circadian timing regulates photoperiodic flowering.
Correlation of Clinical Tests with Microscopic Pathology of the Dental Pulp

While a great amount of effort has been devoted to the microscopic study of pulp conditions and a good deal written about pulp testing methods few combined studies have been made. In this study, by correlating clinical tests with microscopic examination of a series of teeth with vital pulps, in various states of health and disease, it is hoped that a more exact evaluation of present diagnostic methods can be made. Raper states that the electric pulp tester is of great value in determining whether a pulp is vital or necrotic but that crowned teeth, and some teeth with large fillings, cannot be tested; that in a multirooted tooth with part of the pulp vital and part necrotic the reaction is the same as if all were vital; and that it is not practical to attempt to determine any particular pathologic state of a vital pulp with the electric tester. Prinz, on the other hand, states that a normal pulp responds to the faradic current at a specific "irritation point"; hyperemic pulps respond below; acutely inflamed pulps (simple pulpitis) far below; suppurating pulps (acute or chronic suppurative pulpitis) above the normal irritation point; and dead pulps not at all. Mead is in agreement with Prinz. Reiss and Fuerdi, on the other hand, found that pulps that reacted to a normal index (irritation point) included 63.5 percent that were normal and 36.5 pathological; those with moderately high indices, 69 per cent normal and 31 pathological; those with very high indices, 90 per cent pathological. Of the negative responses all were pathological and 87.5 per cent definitely necrotic. Of those that responded severely to a low index, 50 per