Miracle-dz/UniFAR-FTUs huggingface dataset:
Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes

Background With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows. Methodology/Principal Findings Our algorithm, named Murasaki, makes it possible to identify anchors within multiple large sequences on the scale of several hundred megabases in few minutes using a single CPU. Two advanced features of Murasaki are (1) adaptive hash function generation, which enables efficient use of arbitrary mismatch patterns (spaced seeds) and therefore the comparison of multiple mammalian genomes in a practical amount of computation time, and (2) parallelizable execution that decreases the required wall-clock and CPU times. Murasaki can perform a sensitive anchoring of eight mammalian genomes (human, chimp, rhesus, orangutan, mouse, rat, dog, and cow) in 21 hours CPU time (42 minutes wall time). This is the first single-pass in-core anchoring of multiple mammalian genomes. We evaluated Murasaki by comparing it with the genome alignment programs BLASTZ and TBA. We show that Murasaki can anchor multiple genomes in near linear time, compared to the quadratic time requirements of BLASTZ and TBA, while improving overall accuracy. Conclusions/Significance Murasaki provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency significantly greater than existing methods. Murasaki is available under GPL at http://murasaki.sourceforge. net.
Planned Neck Dissection before Combined Chemoradiation in Organ Preservation Protocol for N2-N3 of Supraglottic or Hypopharyngeal Carcinoma

Objective: To investigate the clinical therapeutic outcomes and neck node control of a pretreatment neck dissection in the chemoradiation protocol of organ preservation for N2-N3 of supraglottic and hypopharyngeal carcinoma. Methods: Forty-six patients (group A) with untreated N2 or N3 squamous cell carcinoma of the supraglottis or hypopharynx underwent pretreatment neck dissection in a chemoradiation protocol, while 39 patients (group B) did not undergo pretreatment neck dissection in a chemoradiation protocol. Salvage surgeries were used for local or cervical node residual tumor or recurrence after chemoradiotherapy. Results: In group A, the mean time between neck dissection and chemoradiation was 21 days (range 15-29). Only 3 patients (6.5%) experienced wound complications. A ‘boost' of radiation of 12 Gy was delivered after 33 neck dissections (64.8%) in patients with extracapsular spread. The Kaplan-Meier 5-year overall survival rate was 42.5%. The 5-year overall survival rate and disease-specific survival rate in group A was 42.5 and 46.4%. The rate of neck node control in group A was better than that in group B (86.3 vs. 65.9%, p = 0.02). Conclusions: Pretreatment neck dissection in a chemoradiation protocol for supraglottic or hypopharyngeal carcinoma showed low complication rates, no delay for radiation, optimal radiation doses, and a high nodal disease control.
Correlations between endoscopy score and quality of life changes after sinus surgery.

OBJECTIVE To assess whether change in endoscopy score correlates with change in health-related quality of life (HRQOL) following endoscopic sinus surgery for chronic rhinosinusitis. DESIGN Prospective open cohort. SETTING Tertiary rhinology clinic. PATIENTS One hundred two adult patients with and without nasal polyposis who elected to undergo endoscopic sinus surgery and were followed up for 12 +/- 2 months postoperatively. INTERVENTION Patient characteristics and Lund-Mackay computed tomography scores were recorded preoperatively. Lund-Kennedy endoscopy scores and 2 HRQOL surveys, the Rhinosinusitis Disability Index and Chronic Sinusitis Survey, were examined before and after surgery. MAIN OUTCOME MEASURES Postoperative changes in endoscopy score and HRQOL were examined using bivariate and multivariate analyses. RESULTS Statistically significant improvements were found in endoscopy score (P < .001) and for all total and subscale HRQOL measures (P < .001). After controlling for baseline status and comorbid factors, improvement in endoscopy score significantly correlated with 12-month improvement on the total Rhinosinusitis Disability Index (P = .01), the physical (P = .01) and functional (P = .02) subscales of the Rhinosinusitis Disability Index, and the symptom subscale of the Chronic Sinusitis Survey (P = .003) but could explain only 25.5% to 36.6% of the linear variation for these HRQOL improvements. CONCLUSIONS For most patients, endoscopy scores and disease-specific HRQOL significantly improve after endoscopic sinus surgery. Changes in endoscopy scores explain a portion of the improvement in HRQOL. For patients with chronic rhinosinusitis, improvements in disease-specific HRQOL outcomes are complex, multidimensional constructs that cannot be entirely explained by surgical changes measured by endoscopic examination. Trial Registration clinicaltrials.gov Identifier: NCT00799097.
Usefulness of Ultrasound Imaging in Detecting Psoriatic Arthritis of Fingers and Toes in Patients with Psoriasis

Background. Given that clinical evaluation may underestimate the joint damage and that early treatment can slow down psoriatic arthritis (PsA) progression, screening psoriasis patients with imaging tools that can depict early PsA changes would entail clear benefits. Objective. To compare the ability of X-ray and ultrasound (US) examination in detecting morphological abnormalities consistent with early PsA in patients with psoriasis, using rheumatological evaluation as the gold standard for diagnosis. Methods. Patients with chronic plaque psoriasis and no previous PsA diagnosis attending our outpatient dermatology clinic and reporting finger/toe joint and/or tendon pain underwent X-ray and US evaluation; they were subsequently referred to a rheumatologist for clinical examination and review of imaging findings. Results. Abnormal US and/or X-ray findings involving at least one finger and/or toe (joints and/or tendons) were seen in 36/52 patients: 11 had one or more X-ray abnormalities, including erosion, joint space narrowing, new bone formation, periarticular soft tissue swelling, and periarticular osteoporosis; 36 had suspicious changes on US. Conclusion. US proved valuable in detecting joint and/or tendon abnormalities in the fingers and toes of patients with suspicious changes. The dermatologist should consider US to obtain an accurate assessment of suspicious findings.
The Role of Configurational Entropy in Amorphous Systems

Configurational entropy is an important parameter in amorphous systems. It is involved in the thermodynamic considerations, plays an important role in the molecular mobility calculations through its appearance in the Adam-Gibbs equation and provides information on the solubility increase of an amorphous form compared to its crystalline counterpart. This paper presents a calorimetric method which enables the scientist to quickly determine the values for the configurational entropy at any temperature and obtain the maximum of information from these measurements.
What are we like?

In what case do you like reading so much? What about the type of the what we like book? The needs to read? Well, everybody has their own reason why should read some books. Mostly, it will relate to their necessity to get knowledge from the book and want to read just to get entertainment. Novels, story book, and other entertaining books become so popular this day. Besides, the scientific books will also be the best reason to choose, especially for the students, teachers, doctors, businessman, and other professions who are fond of reading.
An exploratory analysis of the relationship between absorptive capacity and business strategy

In this study, we argue that a firm's absorptive capacity will vary depending on the strategy it adopts. To examine this, based on the fact that absorptive capacity is developed through the ability to acquire, assimilate, transform and exploit externally-generated knowledge, we look at the importance of each of these dimensions at firms pursuing different business strategies. To reflect business strategy, we draw on Miles and Snow's typology. The information has been obtained based on a sample made up of 81 Spanish small and medium-sized enterprises. Results show that knowledge acquisition capacity is greater at prospectors than at defenders and analysers, and that transformation and exploitation capacities are greater at prospectors than at defenders. No differences in knowledge assimilation capacity are observed.
Current serological possibilities for the diagnosis of arthritis with special focus on proteins and proteoglycans from the extracellular matrix

This review discusses our current understanding of how the expression and turnover of components of the cartilage extracellular matrix (ECM) have been investigated, both as molecular markers of arthritis and as indicators of disease progression. The cartilage ECM proteome is well studied; it contains proteoglycans (aggrecan, perlecan and inter-α-trypsin inhibitor), collagens and glycoproteins (cartilage oligomeric matrix protein, fibronectin and lubricin) that provide the structural and functional changes in arthritis. However, the changes that occur in the carbohydrate structures, including glycosaminoglycans, with disease are less well studied. Investigations of the cartilage ECM proteome have revealed many potential biomarkers of arthritis. However, a clinical diagnostic or multiplex assay is yet to be realized due to issues with specificity to the pathology of arthritis. The future search for clinical biomarkers of arthritis is likely to involve both protein and carbohydrate markers of the ECM through the application of glycoproteomics.
Safeness and Treatment Mitigate the Effect of Loneliness on Satisfaction With Elderly Care

Maximizing satisfaction among the older persons is the goal of modern individualized elderly care and how to best achieve this is of relevance for people involved in planning and providing elderly care services. Purpose of the Study: What predicts satisfaction with care among older persons can be conceived as a function of process (how care is performed) and the older person. Inspired by the long-standing person versus situation debate, the present research investigated the interplay between person- and process-related factors in predicting satisfaction with elderly care. Design and Methods: A nationwide sample was analyzed, based on a questionnaire with 95,000 individuals using elderly care services. Results: The results showed that person-related factors (i.e., anxiety, health, and loneliness) were significant predictors of satisfaction with care, although less strongly than process-related factors (i.e., treatment, safeness, and perceived staff and time availability). Among the person-related factors, loneliness was the strongest predictor of satisfaction among older persons in nursing homes. Interestingly, a path analysis revealed that safeness and treatment function as mediators in linking loneliness to satisfaction. Implications: The results based on a large national sample demonstrate that the individual aging condition to a significant degree can be countered by a well-functioning care process, resulting in higher satisfaction with care among older persons.
Predation selects for increased immune function in male damselflies, Calopteryx splendens

Predation selects for numerous traits in many animal species, with sick or parasitized prey often being at high risk. When challenged by parasites and pathogens, prey with poor immune functions are thus likely to be at a selective disadvantage. We tested the hypothesis that predation by birds selects for increased immune function in a wild population of male damselflies Calopteryx splendens, while controlling for a trait known to be under selection by bird predation, dark wing-spots. We found that selection on both immune function and wing-spot size was significantly positive, and that selection on either trait was independent of selection on the other. We found no evidence of nonlinear quadratic or correlational selection. In contrast to previous studies, we found no phenotypic correlation between immune function and wing-spot size. There was also no difference in immune response between territorial and non-territorial males. Our study suggests that predation may be an important agent of selection on the immune systems of prey, and because the selection we detected was directional, has the potential to cause phenotypic change in populations.
A Threatening Intellectual Environment: Why Females Are Susceptible to Experiencing Problem-Solving Deficits in the Presence of Males

Does placing females in environments in which they have contact with males cause deficits in their problem-solving performance? Is a situational cue, such as gender composition, sufficient for creating a threatening intellectual environment for females—an environment that elicits performance-impinging stereotypes? Two studies explored these questions. Participants completed a difficult math or verbal test in 3-person groups, each of which included 2 additional people of the same sex as the participant (same-sex condition) or of the opposite sex (minority condition). Female participants in the minority condition experienced performance deficits in the math test only, whereas males performed equally well on the math test in the two conditions. Further investigation showed that females' deficits were proportional to the number of males in their group. Even females who were placed in a mixed-sex majority condition (2 females and 1 male) experienced moderate but significant deficits. Findings are discussed in relation to theories of distinctiveness, stereotype threat, and tokenism.
Identification of Minimal Predictors of Avian Pathogenic Escherichia coli Virulence for Use as a Rapid Diagnostic Tool

ABSTRACT To identify traits that predict avian pathogenic Escherichia coli (APEC) virulence, 124 avian E. coli isolates of known pathogenicity and serogroup were subjected to virulence genotyping and phylogenetic typing. The results were analyzed by multiple-correspondence analysis. From this analysis, five genes carried by plasmids were identified as being the most significantly associated with highly pathogenic APEC strains: iutA, hlyF, iss, iroN, and ompT. A multiplex PCR panel targeting these five genes was used to screen a collection of 994 avian E. coli isolates. APEC isolates were clearly distinguished from the avian fecal E. coli isolates by their possession of these genes, suggesting that this pentaplex panel has diagnostic applications and underscoring the close association between avian E. coli virulence and the possession of ColV plasmids. Also, the sharp demarcation between APEC isolates and avian fecal E. coli isolates in their plasmid-associated virulence gene content suggests that APEC isolates are well equipped for a pathogenic lifestyle, which is contrary to the widely held belief that most APEC isolates are opportunistic pathogens. Regardless, APEC isolates remain an important problem for poultry producers and a potential concern for public health professionals, as growing evidence suggests a possible role for APEC in human disease. Thus, the pentaplex panel described here may be useful in detecting APEC-like strains occurring in poultry production, along the food chain, and in human disease. This panel may be helpful toward clarifying potential roles of APEC in human disease, ascertaining the source of APEC in animal outbreaks, and identifying effective targets of avian colibacillosis control.
Genetics of microenvironmental canalization in Arabidopsis thaliana

Canalization is a fundamental feature of many developmental systems, yet the genetic basis for this property remains elusive. We examine the genetic basis of microenvironmental canalization in the model plant Arabidopsis thaliana, focusing on differential developmental stability between genotypes in one fitness and four quantitative morphological traits. We measured developmental stability in genetically identical replicates of two populations of recombinant inbred (RI) lines and one population of geographically widespread accessions of A. thaliana grown in two different photoperiod-controlled environments. We were able to map quantitative trait loci associated with developmental stability. We also identified a candidate gene, ERECTA, that may contribute to microenvironmental canalization in rosette leaf number under long-day photoperiods, and analysis of mutant lines indicates that the er-105 allele results in increased canalization for this trait. ERECTA, which encodes a signaling protein, appears to act as an ecological amplifier by transducing developmental noise (e.g., microenvironmental variation) into phenotypic differentiation. We also measured genotypic selection on four plant architecture traits and find evidence for selection for both increased and decreased canalization at various traits.
Factors associated with clinical decision-making in relation to treatment need for temporomandibular disorders

Abstract Objective. The aim of this study was to analyze dentist’s clinical decision-making related to treatment need for temporomandibular disorders (TMD) in an adult population. Materials and methods. The study population comprised 779 randomly selected 35, 50, 65 and 75 year old individuals living in the county of Västerbotten, Sweden. The participants filled out a questionnaire and were examined clinically according to a structured protocol. The four examiners (two men, two women) were experienced dentists and were calibrated before the start of the study. After examination they individually assessed the need of treatment owing to TMD. Results. In total, 15% of the study population was considered to have a treatment need owing to TMD. The highest estimate was noted for 35 and 50 years old women and the lowest for 65 and 75 years old men. Overall, 21% of the women and 8% of the men were considered to have a treatment need owing to TMD, with statistically significant differences between men and women for the 35 and 50 years old groups. Inter-individual variations in dentists’ decisions were observed. In a multivariate analysis, female gender, signs and symptoms of TMD pain, signs and symptoms of TMD dysfunction and smoking were associated with estimated treatment need. Conclusions. The prevalence of estimated treatment need owing to TMD was fairly high, but the dentists’ clinical decision-making process showed large inter-individual variability. The observation calls for further research on the factors affecting the decision-making process in care providers.
The Effects of Poor Neonatal Health on Children's Cognitive Development

We make use of a new data resource, merged birth and school records for all children born in Florida from 1992 to 2002, to study the effects of birth weight on cognitive development from kindergarten through schooling. Using twin fixed effects models, we find that the effects of birth weight on cognitive development are essentially constant through the school career; that these effects are very similar across a wide range of family backgrounds; and that they are invariant to measures of school quality. We conclude that the effects of poor neonatal health on adult outcomes are therefore set very early. David N. Figlio Institute for Policy Research Northwestern University 2040 Sheridan Road Evanston, IL 60208 and NBER figlio@northwestern.edu Jonathan Guryan Northwestern University Institute for Policy Research 2040 Sheridan Road Evanston, IL 60208 and NBER j-guryan@northwestern.edu Krzysztof Karbownik Department of Economics Uppsala University Kyrkogardsgatan 10B SE-751 20 Uppsala Sweden krzysztof.karbownik@nek.uu. se Jeffrey Roth Department of Pediatrics University of Florida PO Box 100296 Gainesville, FL 32610-0296 jeffroth@ufl.edu
Evaluation of the citation matching algorithms of CWTS and iFQ in comparison to the Web of science

The results of bibliometric studies provided by bibliometric research groups, for example, the Centre for Science and Technology Studies (CWTS) and the Institute for Research Information and Quality Assurance (iFQ), are often used in the process of research assessment. Their databases use Web of Science (WoS) citation data, which they match according to their own matching algorithms—in the case of CWTS for standard usage in their studies and in the case of iFQ on an experimental basis. Because the problem of nonmatched citations in the WoS persists due to inaccuracies in the references or inaccuracies introduced in the data extraction process, it is important to ascertain how well these inaccuracies are rectified in these citation matching algorithms. This article evaluates the algorithms of CWTS and iFQ in comparison to the WoS in a quantitative and a qualitative analysis. The analysis builds upon the method and the manually verified corpus of a previous study. The algorithm of CWTS performs best, closely followed by that of iFQ. The WoS algorithm still performs quite well (F1 score: 96.41%), but shows deficits in matching references containing inaccuracies. An additional problem is posed by incorrectly provided cited reference information in source articles by the WoS.