Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional trade‐offs in the limb muscles of dogs selected for running vs. fighting

The physical demands of rapid and economical running differ from those of physical fighting such that functional trade‐offs may prevent simultaneous evolution of optimal performance in both behaviours. Here we test three hypotheses of functional trade‐off by measuring determinants of limb musculoskeletal function in two breeds of domestic dogs that have undergone intense artificial selection for running (Greyhound) or fighting performance (Pit Bull). We found that Greyhounds differ from Pit Bulls in having relatively less muscle mass distally in their limbs, weaker muscles in their forelimbs than their hindlimbs, and a much greater capacity for elastic storage in the in‐series tendons of the extensor muscles of their ankle joints. These observations are consistent with the hypothesis that specialization for rapid or economical running can limit fighting performance and vice versa. We suggest that functional trade‐offs that prevent simultaneous evolution of optimal performance in both locomotor and fighting abilities are widespread taxonomically.
Transactional client-server cache consistency: alternatives and performance

Client-server database systems based on a data shipping model can exploit client memory resources by caching copies of data items across transaction boundaries. Caching reduces the need to obtain data from servers or other sites on the network. In order to ensure that such caching does not result in the violation of transaction semantics, a transactional cache consistency maintenance algorithm is required. Many such algorithms have been proposed in the literature and, as all provide the same functionality, performance is a primary concern in choosing among them. In this article we present a taxonomy that describes the design space for transactional cache consistency maintenance algorithms and show how proposed algorithms relate to one another. We then investigate the performance of six of these algorithms, and use these results to examine the tradeoffs inherent in the design choices identified in the taxonomy. The results show that the interactions among dimensions of the design space impact performance in many ways, and that classifications of algorithms as simply “pessimistic” or “optimistic” do not accurately characterize the similarities and differences among the many possible cache consistency algorithms.
Staging of advanced ovarian cancer: comparison of imaging modalities--report from the Radiological Diagnostic Oncology Group.

PURPOSE To compare ultrasonography (US), magnetic resonance (MR) imaging, and computed tomography (CT) for diagnosing and staging advanced ovarian cancer. MATERIALS AND METHODS US, CT, and MR imaging were performed in 280 patients. Images were read by three radiologists from each of the five hospitals. Image analysis included determination of malignancy within the peritoneum (11 sites), lymph nodes (10 sites), and hepatic parenchyma. The standard of reference was based on surgical and histopathologic findings. Statistical methods used were receiver operating characteristic (ROC) curve analysis, pairwise comparison of areas under the ROC curves (A(z)), analysis of sensitivity and specificity pairs, and assessment of agreement between the degree of suspicion and standard of reference. RESULTS There were 118 patients with malignant tumors; 73 (62%) had stage III or IV disease. Metastases were found in the peritoneum in 70 (59%), nodes in 20 (17%), and liver in seven (6%) cases. In the peritoneum, MR imaging and CT (A(z) = 0.96 for both) were more accurate than US (A(z) = 0.86), especially in the subdiaphragmatic spaces and hepatic surfaces. MR imaging and CT were more sensitive than US (95%, 92%, and 69%, respectively) for peritoneal metastases. MR imaging was more accurate than CT for detection of lymph node metastases (A(z) = 0.76 vs 0.57, P =. 04). In the liver, the A(z) values for the three modalities were 0.77-0.94. CONCLUSION CT and MR imaging are equally accurate, and either modality can be used to stage advanced ovarian cancer.
Platelet-released growth factors enhance the secretion of hyaluronic acid and induce hepatocyte growth factor production by synovial fibroblasts from arthritic patients.

OBJECTIVES Autologous platelet-secreted growth factors (GFs) may have therapeutic effects in osteoarthritis (OA) capsular joints via multiple mechanisms. Our aim was to examine the effect of a platelet-derived preparation rich in growth factors (PRGFs) in OA synovial cell biology. METHODS Synovial cells were isolated from 10 osteoarthritic patients and cultured in serum-free media (basal conditions) and exposed to either a platelet-poor preparation or PRGF for 72 h. Cells activated with interleukin-1beta (IL-1beta) for 48 h were also exposed to PRGF. Changes in several events relevant to joint homeostasis including (i) hyaluronic acid (HA) secretion, (ii) the balance between metalloproteinase-1, -3 and -13 (MMP-1, MMP-3 and MMP-13) and tissue inhibitor-1 (TIMP-1) and (iii) the secretion of transforming growth factor-beta1(TGF-beta1), vascular endothelial growth factor (VEGF) and hepatocyte growth factor (HGF), were all assessed. RESULTS PRGF significantly enhanced HA secretion compared with platelet-poor preparations, P < 0.05; at the same time release of TIMP-1, MMP-1, MMP-3 and MMP-13 were not affected. An increased HGF production was observed (P < 0.05) but VEGF and TGF-beta1 levels remained unchanged. PRGF significantly enhanced the secretion of HA induced by IL-1beta activation, P < 0.05, but it did not modify the IL-1beta-induced rise in MMP-1, MMP-3 and VEGF. In contrast, PRGF-induced HGF production was abolished by the presence of IL-1beta during PRGF treatment, P < 0.05. CONCLUSIONS Intra-articular administration of PRGF might be beneficial in restoring HA concentration and switching angiogenesis to a more balanced status but does not halt the effects of IL-1beta on synovial cells.
GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.
An assessment method of tongue image quality in Traditional Chinese Medicine

In the paper, we present a method for evaluating the quality of tongue images in Traditional Chinese Medicine (TCM). First, we preprocess the original images to segment the tongue images. Second, geometric features, texture features and spectral entropy features and spatial entropy features based on Spatial-Spectral Entropy-based Quality (SSEQ) index of tongue images are extracted respectively to form 17 dimensional feature vector for the tongue image quality assessment. Finally, Support vector machine (SVM) model is used to classify the samples. The experimental result shows that our method has a better effect on the tongue image quality assessment for the objectification of tongue diagnosis.
Evaluation of a national eye care programme: re-survey after 10 years

AIM To re-survey the Gambia after an interval of 10 years to assess the impact of a national eye care programme (NECP) on the prevalence of blindness and low vision. METHOD Comparison of two multistage cluster random sample surveys taking into account the marked increase in population in the Gambia, west Africa. Samples of the whole population in 1986 and 1996 were taken. The definition of blindness is presenting vision less than 3/60 in the better eye, or visual fields constricted to less than 10° from fixation. Low vision is less than 6/18 but 3/60 or better. Causes of blindness were determined clinically by three ophthalmologists. RESULTS The crude prevalence of blindness fell from 0.70% to 0.42%, a relative reduction of 40%. During the same 10 year period, the population increased by 51% from 775 000 to 1 169 000. When the results were standardised for age, a west to east gradient was found for changes in risk of blindness over the 10 year period. This matched the phased west to east introduction of the NECP interventions. There was a modest but significant increase in the risk of low vision across the whole country. CONCLUSIONS The overall reduction in risk of blindness, in those areas where the NECP has been active, appears to justify the programme and the support of donor organisations. The low vision cases due to cataract must now be addressed.
Security and Usability Challenges of Moving-Object CAPTCHAs: Decoding Codewords in Motion

We explore the robustness and usability of moving-image object recognition (video) captchas, designing and implementing automated attacks based on computer vision techniques. Our approach is suitable for broad classes of moving-image captchas involving rigid objects. We first present an attack that defeats instances of such a captcha (NuCaptcha) representing the state-of-the-art, involving dynamic text strings called codewords. We then consider design modifications to mitigate the attacks (e.g., overlapping characters more closely). We implement the modified captchas and test if designs modified for greater robustness maintain usability. Our lab-based studies show that the modified captchas fail to offer viable usability, even when the captcha strength is reduced below acceptable targets--signaling that the modified designs are not viable. We also implement and test another variant of moving text strings using the known emerging images idea. This variant is resilient to our attacks and also offers similar usability to commercially available approaches. We explain why fundamental elements of the emerging images concept resist our current attack where others fails.
A critical role for the autophagy gene Atg5 in T cell survival and proliferation

Macroautophagy (hereafter referred to as autophagy) is a well-conserved intracellular degradation process. Recent studies examining cells lacking the autophagy genes Atg5 and Atg7 have demonstrated that autophagy plays essential roles in cell survival during starvation, in innate cell clearance of microbial pathogens, and in neural cell maintenance. However, the role of autophagy in T lymphocyte development and survival is not known. Here, we demonstrate that autophagosomes form in primary mouse T lymphocytes. By generating Atg5−/− chimeric mice, we found that Atg5-deficient T lymphocytes underwent full maturation. However, the numbers of total thymocytes and peripheral T and B lymphocytes were reduced in Atg5 chimeras. In the periphery, Atg5−/− CD8+ T lymphocytes displayed dramatically increased cell death. Furthermore, Atg5−/− CD4+ and CD8+ T cells failed to undergo efficient proliferation after TCR stimulation. These results demonstrate a critical role for Atg5 in multiple aspects of lymphocyte development and function and suggest that autophagy may be essential for both T lymphocyte survival and proliferation.
Determination and morphogenesis in the sea urchin embryo.

The study of the sea urchin embryo has contributed importantly to our ideas about embryogenesis. This essay re-examines some issues where the concerns of classical experimental embryology and cell and molecular biology converge. The sea urchin egg has an inherent animal-vegetal polarity. An egg fragment that contains both animal and vegetal material will produce a fairly normal larva. However, it is not clear to what extent the oral-aboral axis is specified in embryos developing from meridional fragments. Newly available markers of the oral-aboral axis allow this issue to be settled. When equatorial halves, in which animal and vegetal hemispheres are separated, are allowed to develop, the animal half forms a ciliated hollow ball. The vegetal half, however, often forms a complete embryo. This result is not in accord with the double gradient model of animal and vegetal characteristics that has been used to interpret almost all defect, isolation and transplantation experiments using sea urchin embryos. The effects of agents used to animalize and vegetalize embryos are also due for re-examination. The classical animalizing agent, Zn2+, causes developmental arrest, not expression of animal characters. On the other hand, Li+, a vegetalizing agent, probably changes the determination of animal cells. The stability of these early determinative steps may be examined in dissociation-reaggregation experiments, but this technique has not been exploited extensively. The morphogenetic movements of primary mesenchyme are complex and involve a number of interactions. It is curious that primary mesenchyme is dispensable in skeleton formation since in embryos devoid of primary mesenchyme, the secondary mesenchyme cells will form skeletal elements. It is likely that during its differentiation the primary mesenchyme provides some of its own extracellular microenvironment in the form of collagen and proteoglycans. The detailed form of spicules made by primary mesenchyme is determined by cooperation between the epithelial body wall, the extracellular material and the inherent properties of primary mesenchyme cells. Gastrulation in sea urchins is a two-step process. The first invagination is a buckling, the mechanism of which is not understood. The secondary phase in which the archenteron elongates across the blastocoel is probably driven primarily by active cell repacking. The extracellular matrix is important for this repacking to occur, but the basis of the cellular-environmental interaction is not understood. (ABSTRACT TRUNCATED AT 400 WORDS)
Human Integrin α3β1 Regulates TLR2 Recognition of Lipopeptides from Endosomal Compartments

Background Toll-like receptor (TLR)-2/TLR1 heterodimers recognize bacterial lipopeptides and initiate the production of inflammatory mediators. Adaptors and co-receptors that mediate this process, as well as the mechanisms by which these adaptors and co-receptors function, are still being discovered. Methodology/Principal Findings Using shRNA, blocking antibodies, and fluorescent microscopy, we show that U937 macrophage responses to the TLR2/1 ligand, Pam3CSK4, are dependent upon an integrin, α3β1. The mechanism for integrin α3β1 involvement in TLR2/1 signaling is through its role in endocytosis of lipopeptides. Using inhibitors of endosomal acidification/maturation and physical tethering of the ligand, we show that the endocytosis of Pam3CSK4 is necessary for the complete TLR2/1-mediated pro-inflammatory cytokine response. We also show that TLR2/1 signaling from the endosome results in the induction of different inflammatory mediators than TLR2/1 signaling from the plasma membrane. Conclusion/Significance Here we identify integrin α3β1 as a novel regulator for the recognition of bacterial lipopeptides. We demonstrate that induction of a specific subset of cytokines is dependent upon integrin α3β1-mediated endocytosis of the ligand. In addition, we address an ongoing controversy regarding endosomal recognition of bacterial lipopeptides by demonstrating that TLR2/1 signals from within endosomal compartments as well as the plasma membrane, and that downstream responses may differ depending upon receptor localization. We propose that the regulation of endosomal TLR2/1 signaling by integrin α3β1 serves as a mechanism for modulating inflammatory responses.
Hd28 .m414 Ob^ey Empirical Research on Software Maintenance

Despite its economic importance, the activity of software maintenance is relatively under-studied by researchers. This comprehensive survey documents that only two percent of all articles appearing in three leading journals and two refereed conferences over the past decade were devoted to empirical studies of software maintenance. The primary purpose of this paper is to document "what is known" from this research, and to suggest future avenues of research. The sixty-one articles surveyed are conveniently summarized as to major differences and similarities in a set of detailed tables. The text is used to highlight major findings and differences. Although the emphasis of the paper is on the subject matter, a section discussing appropriate research methodologies is included as a guide to researchers new to this area.
Analysis and control of Boolean networks: A semi-tensor product approach

A Boolean network is a logical dynamic system, which has been used to describe cellular networks. Using a new matrix product, called semi-tensor product of matrices, a logical function can be expressed as an algebraic function. This expression can covert the Boolean networks into discrete-time linear dynamic systems. Similarly, the Boolean control networks can also be converted into discrete time bilinear dynamic systems. Under these forms the standard matrix analysis can be used to consider the structure and the control problems of Boolean (control) networks. After the detailed description of this new approach, the controllability of Boolean control networks is considered in the paper as an application.
Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota

Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.
Estimation of (co)variance components and breeding values for test-day milk production traits of Holstein dairy cattle via Bayesian approach

Genetic parameters of milk, fat, and protein yields were estimated in the first lactation of Holstein dairy cattle. The records were collected during the period 2006 to 2011 and analyzed fitting the random regression model. The data included 41178, 25397 and 18716 test-day records of milk, fat and protein yields, respectively that produced by 4746, 3437 and 2525 cows respectively. Fixed effects in model included herd-year-month of test day and age-season of calving. The fixed and random regressions were modeled with normalized Legendre polynomials and (co)variance components were estimated by Bayesian method and Gibbs sampling was used to obtain posterior distributions. Estimates of heritability for milk, fat and protein yields ranged from 0.18 to 0.26; 0.06 to 0.11 and 0.09 to 0.22, respectively. Heritabilities for 305-d milk, fat and protein yields were 0.36, 0.23 and 0.29, respectively. For milk and protein yields, heritabilities were lower at the early of lactation due to the trends of lower additive genetic variance, higher permanent environmental variance. Genetic correlations for milk, fat and protein yields ranged from 0.14 to 1.00; 0.39 to 1.00 and 0.27 to 1.00, respectively. Ranges of estimated breeding values for 305-d yield of milk, fat and protein yields were from -1194.48 to 1412.44; -210.57 to 271.22 and -194.08 to 203.25, respectively. According to the results of this study, random regression model seems to be a flexible and reliable procedure for the genetic evaluation of milk production traits and it can be useful in the breeding programs for Iranian dairy cattle.
Examination of Relations between the Neo Personality Inventory-Revised and the Temperament and Character Inventory

The present investigation examined the relation of the Five Factor Model of personality as measured by the NEO Personality Inventory-Revised to the seven-factor model of temperament and character as tapped by the Temperament and Character Inventory by testing a sample of 344 undergraduate students. Correlations and regression analyses suggest there is substantial overlap between the NEO-Personality Inventory-Revised domains and Temperament and Character Inventory dimensions as reflected in multiple correlations ranging from . 54 to . 80 for the latter when used as predictors of NEO Personality Inventory-Revised domains and . 46 to . 78 for the former domains when used as predictors of Temperament and Character Inventory dimension scores. Information for constructing the regression equations to allow for the prediction of personality constructs for one model from scores obtained on the other are provided.
Yeast Bim1p Promotes the G1-specific Dynamics of Microtubules

Microtubule dynamics vary during the cell cycle, and microtubules appear to be more dynamic in vivo than in vitro. Proteins that promote dynamic instability are therefore central to microtubule behavior in living cells. Here, we report that a yeast protein of the highly conserved EB1 family, Bim1p, promotes cytoplasmic microtubule dynamics specifically during G1. During G1, microtubules in cells lacking BIM1 showed reduced dynamicity due to a slower shrinkage rate, fewer rescues and catastrophes, and more time spent in an attenuated/paused state. Human EB1 was identified as an interacting partner for the adenomatous polyposis coli (APC) tumor suppressor protein. Like human EB1, Bim1p localizes to dots at the distal ends of cytoplasmic microtubules. This localization, together with data from electron microscopy and a synthetic interaction with the gene encoding the kinesin Kar3p, suggests that Bim1p acts at the microtubule plus end. Our in vivo data provide evidence of a cell cycle–specific microtubule-binding protein that promotes microtubule dynamicity.