Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Increased Excursion of the Ankle on the Severity of Acute Eccentric Contraction-Induced Strain Injury in the Gastrocnemius

Background Although muscle strain injury models are frequently employed, highly invasive procedures, including surgical intervention, are typically used to produce these models. In this study, a minimally invasive model of acute strain injury was produced with a single eccentric contraction. Hypothesis The authors tested whether the severity of strain injury in the in vivo gastrocnemius depends on the excursion of the ankle. Study Design Controlled laboratory study. Methods Animals were randomly assigned to 2 groups: a small range of motion group (90°-105°, n = 10) and a large range of motion group (90°-125°, n = 10). Tetanically activated gastrocnemius muscles with percutaneous electrical stimulation were simultaneously elongated by forced dorsiflexion of the ankle joint. Results Isometric tetanic force of the large range of motion group was significantly lower than the pretreatment control 1, 2, and 3 days after treatment. Such reduction was not observed in the small range of motion group. Apparent pathologic damage was observed in the large range of motion group throughout the study period of 10 days. Conclusions A larger range of motion causes more damage in eccentric contraction by using the in vivo model. Clinical Relevance This in vivo model is useful to elucidate mechanisms of prevention and recovery of strain injury.
Phenotypic changes in dorsal root ganglion and spinal cord in the collagen antibody‐induced arthritis mouse model

The mechanisms underlying rheumatoid arthritis (RA)‐induced pain are still not fully elucidated, and accumulating data indicate that peripheral inflammation is not the only factor driving pain in these patients. The focus of our work is to investigate the molecular basis for long‐term alterations in nociceptive pathways induced by polyarthritis using the collagen antibody‐induced arthritis (CAIA) mouse model. In this model, mechanical hypersensitivity outlasts the joint inflammation by weeks. Here we examined expression levels of neuropeptides, ion channels, and nerve injury markers associated with neuropathic and/or inflammatory pain in dorsal root ganglia (DRGs) and spinal cord both during the peak of inflammation (day 15) and when the inflammation has resolved but the hypersensitivity persists (days 45–47). No apparent differences were observed in substance P, calcitonin gene‐related peptide, or neuropeptide Y protein expression in DRGs and spinal cord of CAIA mice. However, the neuropeptide galanin, the ATP‐gated ion channel P2X3, and calcium channel subunit α2δ1 were significantly increased in the CAIA DRGs as compared to controls, both 15 and 47 days after induction of arthritis. On day 15 there was an increase in expression of two factors associated with nerve injury and cell stress, activating transcription factor 3 and growth‐associated protein 43 in DRGs, whereby the latter was still dramatically upregulated after 47 days. In conclusion, this study suggests that long‐term joint inflammation has an impact on DRG neurons that resembles both inflammation and nerve injury‐induced pain states. Thus, antibody‐driven inflammation generates a pain state with a unique neurochemical profile. J. Comp. Neurol. 523:1505–1528, 2015. © 2015 Wiley Periodicals, Inc.
Metal Deficiency Increases Aberrant Hydrophobicity of Mutant Superoxide Dismutases That Cause Amyotrophic Lateral Sclerosis*

The mechanisms by which mutant variants of Cu/Zn-superoxide dismutase (SOD1) cause familial amyotrophic lateral sclerosis are not clearly understood. Evidence to date suggests that altered conformations of amyotrophic lateral sclerosis mutant SOD1s trigger perturbations of cellular homeostasis that ultimately cause motor neuron degeneration. In this study we correlated the metal contents and disulfide bond status of purified wild-type (WT) and mutant SOD1 proteins to changes in electrophoretic mobility and surface hydrophobicity as detected by 1-anilinonaphthalene-8-sulfonic acid (ANS) fluorescence. As-isolated WT and mutant SOD1s were copper-deficient and exhibited mobilities that correlated with their expected negative charge. However, upon disulfide reduction and demetallation at physiological pH, both WT and mutant SOD1s underwent a conformational change that produced a slower mobility indicative of partial unfolding. Furthermore, although ANS did not bind appreciably to the WT holoenzyme, incubation of metal-deficient WT or mutant SOD1s with ANS increased the ANS fluorescence and shifted its peak toward shorter wavelengths. This increased interaction with ANS was greater for the mutant SOD1s and could be reversed by the addition of metal ions, especially Cu2+, even for SOD1 variants incapable of forming the disulfide bond. Overall, our findings support the notion that misfolding associated with metal deficiency may facilitate aberrant interactions of SOD1 with itself or with other cellular constituents and may thereby contribute to neuronal toxicity.
Multistage negotiation for distributed constraint satisfaction

A cooperation paradigm and coordination protocol for a distributed planning system consisting of a network of semi-autonomous agents with limited internode communication and no centralized control is presented. A multistage negotiation paradigm for solving distributed constraint satisfaction problems in this kind of system has been developed. The strategies presented enable an agent in a distributed planning system to become aware of the extent to which its own local decisions may have adverse nonlocal impact in planning. An example problem is presented in the context of transmission path restoration for dedicated circuits in a communications network. Multistage negotiation provides an agent with sufficient information about the impact of local decisions on a nonlocal state so that the agent may make local decisions that are correct from a global perspective, without attempting to provide a complete global state to all agents. Through multistage negotiation, an agent is able to recognize when a set of global goals cannot be satisfied, and is able to solve a related problem by finding a way of satisfying a reduced set of goals. >
Cholesterol metabolism in Mycobacterium smegmatis.

The metabolism of cholesterol in Mycobacterium smegmatis mc(2) 155 has been investigated by using a microarray approach. The transcriptome of M. smegmatis growing in cholesterol was compared with that of cells growing in glycerol as the sole carbon and energy sources during the middle exponential phase. Microarray analyses revealed that only 89 genes were upregulated at least threefold during growth on cholesterol compared with growth on glycerol. The upregulated genes are scattered throughout the 7 Mb M. smegmatis genome and likely reflect a general physiological adaptation of the bacterium to grow on this highly hydrophobic polycyclic compound. Nevertheless, 39 of the catabolic genes are organized in three specific clusters. These results not only supported the role of KstR and KstR2 as auto-regulated repressors of cholesterol catabolism, and revealed some metabolic similarities and differences on actinobacteria, but more important, they have facilitated the identification of new catabolic genes, opening a research scenario that might provide important clues on the role of cholesterol in tuberculosis infection.
Critical and Supercritical Spatiotemporal Calcium Dynamics in Beta Cells

A coordinated functioning of beta cells within pancreatic islets is mediated by oscillatory membrane depolarization and subsequent changes in cytoplasmic calcium concentration. While gap junctions allow for intraislet information exchange, beta cells within islets form complex syncytia that are intrinsically nonlinear and highly heterogeneous. To study spatiotemporal calcium dynamics within these syncytia, we make use of computational modeling and confocal high-speed functional multicellular imaging. We show that model predictions are in good agreement with experimental data, especially if a high degree of heterogeneity in the intercellular coupling term is assumed. In particular, during the first few minutes after stimulation, the probability distribution of calcium wave sizes is characterized by a power law, thus indicating critical behavior. After this period, the dynamics changes qualitatively such that the number of global intercellular calcium events increases to the point where the behavior becomes supercritical. To better mimic normal in vivo conditions, we compare the described behavior during supraphysiological non-oscillatory stimulation with the behavior during exposure to a slightly lower and oscillatory glucose challenge. In the case of this protocol, we observe only critical behavior in both experiment and model. Our results indicate that the loss of oscillatory changes, along with the rise in plasma glucose observed in diabetes, could be associated with a switch to supercritical calcium dynamics and loss of beta cell functionality.
Cultural adaptation of a supportive care needs measure for Hispanic men cancer survivors

ABSTRACT Objective. Research with ethnic minority populations requires instrumentation that is cultural and linguistically relevant. The aim of this study was to translate and culturally adapt the Cancer Survivor Unmet Needs measure into Spanish. Methods. We describe the iterative, community-engaged consensus-building approaches used to adapt the instrument for Hispanic male cancer survivors. We used an exploratory sequential mixed method study design. Methods included translation and back-translation, focus groups with cancer survivors (n = 18) and providers (n = 5), use of cognitive interview techniques to evaluate the comprehension and acceptability of the adapted instrument with survivors (n = 12), ongoing input from the project's community advisory board, and preliminary psychometric analysis (n = 84). Results. The process emphasized conceptual, content, semantic, and technical equivalence. Combining qualitative and quantitative approaches offered a rigorous, systematic, and contextual approach to translation alone and supports the cultural adaptation of this measure in a purposeful and relevant manner. Conclusion. Our findings highlight the importance of going beyond translation when adapting measures for cross-cultural populations and illustrate the importance of taking culture, literacy, and language into consideration.
Mother Nature: A History of Mothers, Infants, and Natural Selection

Section two, "Law and Single Parents" considers the legal framework that hinders single parents, notably mothers, from overcoming obstacles that negatively impact on their lives and opportunities for their children. Here, Dowd presents a balanced view of the strengths of the single parent family and the unique resources that single parents can offer to all parents. The laws ofthe United States (and through inference, other industrialized Western countries) foster the negative stigmatization of all single parent families. Dowd, however, recognizes that single parents can be positive role models for children and society. Utilizing the historical, cultural, and situational realities of black single mothers, she describes alternative family structures, not as deviant but as valuable. In the section on "Law Reform," Dowd offers alternative policies for single-parent families and legal strategies to challenge the limitations imposed on single-parent families. Here she writes, "Although we have shified away from this [traditional] model, we have not yet articulated an alternative model. Our notions of equality no longer allow for presumed gender-based assignment of family roles, nor for the limitation of workplace opportunities. " As a family therapist and researcher who examines parental roles, I was hopeful but wary when reading this book. Dowd writes, however, with remarkable precision as she details the realities of the single parent experience. This she does without glamorizing, demonizing, martyring, or vilifying single parents or traditional families. She recognizes that the traditional two-parent family, like society, has changed it is time we looked at our structures, laws, and attitudes that, through omission or commission, have ignored these changes. In Defense of Single-Parent Families is a thoroughly researched work that defends single-parent families. I strongly recommend it.
A novel RAB 7 mutation in a Chinese family with Charcot – Marie – Tooth type 2 B disease

a Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China b Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310009, China c Department of Neurology, Yantai Municipal Laiyang Central Hospital, Laiyang, Shandong 265200,China
On FSM-Based Testing: An Empirical Study: Complete Round-Trip Versus Transition Trees

Finite state machines being intuitively understandable and suitable for modeling in many domains, they are adopted by many software designers. Therefore, testing systems that are modeled with state machines has received genuine attention. Among the studied testing strategies are complete round-trip paths and transition trees that cover round-trip paths in a piece wise manner. We present an empirical study that aims at comparing the effectiveness of the complete round-trip paths test suites to the transition trees test suites in one hand, and comparing the effectiveness of the different techniques used to generate transition trees (breadth first traversal, depth first traversal, and random traversal) on the other hand. We also compare the effectiveness of all the testing trees generated using each single traversal criterion. This is done through conducting an empirical evaluation using four case studies from different domains. Effectiveness is evaluated with mutants. Experimental results are presented and analyzed.
A compact high power T/R module for X-band phased array radar applications using an anodized aluminum substrate

This paper presents a compact high-power X-band transmit/receive (T/R) module based on a multi-chip-module (MCM) structure using a selectively anodized aluminum substrate. The proposed T/R module package used thick anodized aluminum (Al2O3) layers and bare MMICs directly mounted on an aluminum substrate for an effective heat sink and a high electrical isolation. The study demonstrates a 28 × 28 × 0.5 mm3 compact T/R module for X-band phased array applications. The fabricated T/R module has a maximum transmit output power of 39.21 dBm (8.3 W), maximum transmit gain of 39.82 dB, and receive gain of 22.1 dB over the 9–10 GHz frequency band. The RF-signal phase amplitude control is achieved with a six-bit phase shifter with RMS accuracy better than 6° and a gain setting range of 24 dB with RMS accuracy better than 2 dB. The proposed aluminum package has the advantages of reducing the module size, decreasing the cost, and managing thermal problems in X-band high-power T/R module package applications.
AGILE PLANNING METHODOLOGY FOR SOFTWARE PRODUCTION

This paper shows an empirical study for a new agile release planning methodology. The case study includes the application of the methodology by two teams in different software business domains (Game development and medical software development). The suggested methodology showed clear improvements in teams’ productivity, enhanced software quality and better handling of the overall software architecture and technical debt. It allowed software teams to have more predictable release plan with fewer technical uncertainties. Results are showed in comparison with the traditional scrum release planning approach.
Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater

ABSTRACT We report here the draft genome sequence of picalivirus D, a member of picalivirus, a picorna-like superfamily, and likely member of the order Picornavirales, assembled from metagenomic sequencing of organisms in San Francisco wastewater. This virus likely constitutes a novel genus within the picalivirus family.
Classification of PE Files using Static Analysis

Malware is one of the most terrible and major security threats facing the Internet today. Anti-malware vendors are challenged to identify, classify and counter new malwares due to the obfuscation techniques being used by malware authors. In this paper, we present a simple, fast and scalable method of differentiating malwares from cleanwares on the basis of features extracted from Windows PE files. The features used in this work are Suspicious Section Count and Function Call Frequency. After automatically extracting features of executables, we use machine learning algorithms available in WEKA library to classify them into malwares and cleanwares. Our experimental results provide an accuracy of over 98% for a data set of 3,087 executable files including 2,460 malwares and 627 cleanwares. Based on the results obtained, we conclude that the Function Call Frequency feature derived from the static analysis method plays a significant role in distinguishing malware files from benign ones.
Economic effects of bovine mastitis and mastitis management: A review

Summary Several studies have been published since 1990 on the economics of mastitis and mastitis management. However, hardly any of these studies has discussed the consistency of results with other studies. In the present paper, the economic factors associated with mastitis are explained, providing a framework for economic analysis. As a second step calculations of the costs of mastitis and the costs in relation to the benefits of mastitis management published since 1990 in peer‐reviewed journals are extensively reviewed and analysed. The result shows a large variation in the calculated costs and benefits of mastitis and mastitis management between the different studies. Moreover, it is clear that important factors were ignored in some of the studies. The framework provided in this paper can provide a basis for analysis for future studies on the economics of mastitis and mastitis management.
The DNA Damage Response Regulates RAG1/2 Expression in Pre–B Cells through ATM-FOXO1 Signaling

The recombination activating gene (RAG) 1 and RAG2 protein complex introduces DNA breaks at Tcr and Ig gene segments that are required for V(D)J recombination in developing lymphocytes. Proper regulation of RAG1/2 expression safeguards the ordered assembly of Ag receptors and the development of lymphocytes, while minimizing the risk for collateral damage. The ataxia telangiectasia mutated (ATM) kinase is involved in the repair of RAG1/2-mediated DNA breaks and prevents their propagation. The simultaneous occurrence of RAG1/2-dependent and -independent DNA breaks in developing lymphocytes exposed to genotoxic stress increases the risk for aberrant recombinations. In this study, we assessed the effect of genotoxic stress on RAG1/2 expression in pre–B cells and show that activation of the DNA damage response resulted in the rapid ATM-dependent downregulation of RAG1/2 mRNA and protein expression. We show that DNA damage led to the loss of FOXO1 binding to the enhancer region of the RAG1/2 locus (Erag) and provoked FOXO1 cleavage. We also show that DNA damage caused by RAG1/2 activity in pre–B cells was able to downmodulate RAG1/2 expression and activity, confirming the existence of a negative feedback regulatory mechanism. Our data suggest that pre–B cells are endowed with a protective mechanism that reduces the risk for aberrant recombinations and chromosomal translocations when exposed to DNA damage, involving the ATM-dependent regulation of FOXO1 binding to the Erag enhancer region.
New targeted therapies such as anti-adhesion molecules, anti-IL-12/23 and anti-Janus kinases are looking toward a more effective treatment of inflammatory bowel disease

Abstract Antitumor necrosis factor α agents have dramatically changed the management of inflammatory bowel disease (IBD). However, a significant proportion of patients does not respond or lose response over time. Hence, there is an urgent need for new molecules, with different mechanisms of action, and with a targeted and more effective approach. These new drugs include either small molecules or biological agents. We describe the three most promising classes of molecules in the field of IBD: anti-adhesion, anti-interleukin 12/23 and anti-Janus Kinases therapies.
Cloning, expression, and localization of a new member of a Paracentrotus lividus cell surface multigene family

We have isolated and characterized a cDNA clone corresponding to a new member of bep (butanol, extracted, proteins) Paracentrotus lividus multigene family coding for cell surface proteins. The cDNA, called bep3, encodes a 370 amino acid protein and shares the same structural organization in the coding region with other members of the same gene family already characterized. Expression of this clone studied by Northern blot and by whole mount hybridization shows that the bep3 messenger is transcribed during oogenesis and utilized till the gastrula stage, whereas at the prism stage, unlike other members of the same gene family, new synthesis of messenger occurs. By whole mount hybridization spatial distribution of bep3 messenger in egg and embryos is established. This messenger appears located in the animal half of the unfertilized egg and moves to the cortical zone after fertilization; it is not present in the structures derived by the vegetal part of the embryo, such as the micromeres of the 16‐cell stage, the primary mesenchyme cells of the blastula, and the primary intestine of the gastrula. At the prism stage instead, hybridization of bep3 messenger is restricted to the part of the embryo that will give origin to the oral region as successively confirmed by hybridization at the pluteus stage. The result of whole mount hybridization was confirmed by Northern blot hybridization of separated meso‐macromere and micromere RNAs. A Southern blot experiment demonstrates that bep3 is codified by a single copy gene. Conservation of the bep multigene family in several Mediterranean and Japanese sea urchin species has also been analyzed. © 1996 Wiley‐Liss, Inc.
A network of allosterically coupled residues in the bacteriophage T4 Mre11–Rad50 complex

The Mre11–Rad50 (MR) protein complex, made up of a nuclease and ATPase, respectively, is involved in the processing of double‐strand breaks as part of an intricate mechanism for their repair. Although it is clear that the MR complex is subject to allosteric regulation and that there is communication between the nuclease and ATPase active sites, the underlying mechanisms are poorly understood. We performed statistical coupling analysis on Mre11 and Rad50 to predict linked residues based on their evolutionary correlation. This analysis predicted a coevolving sector of six residues that may be allosterically coupled. The prediction was tested using double‐mutant cycle analysis of nuclease and ATPase activity. The results indicate that a tyrosine residue located near the active site of Mre11 is allosterically coupled to several Rad50 residues located over 40 Å away. This allosteric coupling may be the basis for the reciprocal regulation of the ATPase and nuclease activities of the complex.