Miracle-dz/UniFAR-FTUs huggingface dataset:
Fragment assembly with double-barreled data

For the last twenty years fragment assembly was dominated by the "overlap - layout - consensus" algorithms that are used in all currently available assembly tools. However, the limits of these algorithms are being tested in the era of genomic sequencing and it is not clear whether they are the best choice for large-scale assemblies. Although the "overlap - layout - consensus" approach proved to be useful in assembling clones, it faces difficulties in genomic assemblies: the existing algorithms make assembly errors even in bacterial genomes. We abandoned the "overlap - layout - consensus" approach in favour of a new Eulerian Superpath approach that outperforms the existing algorithms for genomic fragment assembly (Pevzner et al. 2001 InProceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01), 256-26). In this paper we describe our new EULER-DB algorithm that, similarly to the Celera assembler takes advantage of clone-end sequencing by using the double-barreled data. However, in contrast to the Celera assembler, EULER-DB does not mask repeats but uses them instead as a powerful tool for contig ordering. We also describe a new approach for the Copy Number Problem: "How many times a given repeat is present in the genome? ". For long nearly-perfect repeats this question is notoriously difficult and some copies of such repeats may be "lost" in genomic assemblies. We describe our EULER-CN algorithm for the Copy Number Problem that proved to be successful in difficult sequencing projects.
A Reliability and Validity Study of the Bergen Shift Work Sleep Questionnaire in Nurses Working Three-Shift Rotations

The “Bergen Shift Work Sleep Questionnaire” (BSWSQ) was developed to systematically assess discrete sleep problems related to different work shifts (day, evening, night shifts) and rest days. In this study, we assessed the psychometric properties of the BSWSQ using a sample of 760 nurses, all working in a three-shift rotation schedule: day, evening, and night shifts. BSWSQ measures insomnia symptoms using seven questions: >30-min sleep onset latency, >30-min wake after sleep onset, >30-min premature awakenings, nonrestorative sleep, being tired/sleepy at work, during free time on work days, and when not working/on vacation. Symptoms are assessed separately for each work shift and rest days, as “never,” “rarely,” “sometimes,” “often,” “always,” or “not applicable. ” We investigated the BSWSQ model fit, reliability (test-retest of a subsample, n = 234), and convergent and discriminant validity between the BSWSQ and Epworth Sleepiness Scale, Fatigue Questionnaire, and Hospital Anxiety Depression Scale. We also investigated differences in mean scores between the different insomnia symptoms with respect to different work shifts and rest days. BSWSQ demonstrated an adequate model fit using structural equation modeling: root mean square error of approximation = . 071 (90% confidence interval [CI] = .066–.076), comparative fit index = . 91, and chi-square/degrees of freedom = 4.41. The BSWSQ demonstrated good reliability (test-retest coefficients p < .001). We found good convergent and discriminant validity between BSWSQ and the other scales (all coefficients p < .001). There were significant differences between the overall/composite scores of the various work shifts. Night shift showed the highest score compared to day and evening shifts as well as to rest days (all post hoc comparisons p < .001). Mean scores of different symptoms also varied significantly within the individual work shifts. We conclude that the BSWSQ meets the necessary psychometric standards, enabling systematic study of discrete insomnia symptoms in different work shifts. (Author correspondence: elisabeth.flo@psykp.uib.no)
Disagreement, Short Sale Constraints, and Speculative Trading Before Earnings Announcements

Consistent with theoretical models of speculative trading, we show that abnormal trading activity increases before earnings announcements, especially for stocks with high dispersion of opinions. Moreover, consistent with Miller's (1977) theory and other disagreement models, for stocks that are also short sale constrained this increased speculative pressure is dominated by buyer-initiated trading. As a result, stocks that are already prone to Miller's overpricing (with high dispersion of opinions and binding short sale constraints) have a further price increase before earnings announcements. Finally, these same stocks have a predictable price reversal after the announcement that dominates the pre-announcement run-up, and is related to the abnormal trading activity before the announcement.
Corneal Asphericity and Its Related Factors in 1052 Chinese Subjects

Purpose. To observe and analyze corneal asphericity and its related factors in Chinese subjects. Methods. The corneal asphericity of 1052 right eyes from a Chinese population was determined using the Wavelight-ALLEGRO Topographer. The corneal asphericity coefficient Q describes the rate of curvature variation of the cornea from its center to the periphery and specifies the type of conicoid that best represents its shape. All cases were grouped by age in years (A: ≤9; B: 10 to 19; C: 20 to 29; D: 30 to 39; E: 40 to 49; F: ≥50), and 223 myopic cases were grouped by magnitude in spherical equivalent (SE) refractive error (low myopia, >−3.0 diopters (D); moderate myopia, −6.0 D < SE ≤−3.0 D; high myopia, −8.0 D < SE ≤−6.0 D; and super high myopia, SE≤−8.0 D). In addition, corneal asphericity was analyzed by corneal quadrant (nasal, temporal, superior, and inferior) and two meridians (vertical and horizontal). Results. The mean Q value of 1052 right eyes was −0.30 ± 0.12. Although statistical differences were found between some age groups, no statistical correlation between Q values and age was found in this study (r = −0.58, p = 0.06). Q values of the nasal and superior corneal quadrant were significantly more oblate than that of the temporal and inferior quadrants, respectively (both p < 0.0001). A trend toward more oblate Q values was found as the level of myopia increased (r = 0.166, p = 0.013). There was a negative relationship between Q value and central corneal radius in this entire study population (r = −0.09, p = 0.004). Conclusions. Corneal asphericity in this population is related more to corneal quadrant location than to age. The results from this study suggest that degree of myopia and central corneal radius both have a significant though weak association with corneal asphericity in Chinese eyes.
Fuzzing with Code Fragments

Fuzz testing is an automated technique providing random data as input to a software system in the hope to expose a vulnerability. In order to be effective, the fuzzed input must be common enough to pass elementary consistency checks; a JavaScript interpreter, for instance, would only accept a semantically valid program. On the other hand, the fuzzed input must be uncommon enough to trigger exceptional behavior, such as a crash of the interpreter. The LangFuzz approach resolves this conflict by using a grammar to randomly generate valid programs; the code fragments, however, partially stem from programs known to have caused invalid behavior before. LangFuzz is an effective tool for security testing: Applied on the Mozilla JavaScript interpreter, it discovered a total of 105 new severe vulnerabilities within three months of operation (and thus became one of the top security bug bounty collectors within this period); applied on the PHP interpreter, it discovered 18 new defects causing crashes.
Experimental therapy in myelofibrosis with myeloid metaplasia

Myelofibrosis with myeloid metaplasia (MMM) is a Philadelphia chromosome-negative myeloproliferative disorder that is characterised by constitutional symptoms, progressive anaemia and extramedullary haematopoiesis. There are no curative therapies available for patients with MMM apart from stem cell transplantation, which is associated with significant morbidity and mortality, and for which most patients are not suitable candidates. Traditional pharmacological therapy of MMM has focused on the palliation of symptoms associated with myeloproliferation and correction of cytopoenias. Recently, new findings regarding the molecular basis of MMM and the pathogenesis of the associated bone marrow stromal reaction have provided both basic and clinical researchers with invaluable tools to develop effective targeted therapies for patients with MMM. Several novel treatment strategies are being investigated including antiangiogenic agents, signal transduction inhibitors, inhibitors of fibrogenesis and small-molecule inhibitors of the JAK2V617F mutation. This article reviews the current status of experimental novel therapies for MMM.
[Pulmonary hypertension in patients with ankylosing spondilitis: main factors of development].

AIM To detect factors associated with onset of pulmonary hypertension (PH) in patients with ankylosing spondilitis (AS). MATERIAL AND METHODS 102 patients aged 38.1 +/- 8.9 years (18-58 years) with a documented diagnosis of AS were examined with estimation of clinical idices, smoking status, spinal motility, chest excurtion, AS activity, severity of functional impairment. External respiration function was assessed at spirography, systolic pressure in the pulmonary artery (SPPA) was studied with echocardiography. PH was stated at SPPA > or = 36 mm Hg. Endothelial function was assessed by dopplerography of the brachial artery in the test with reactive hyperemia (endothelium-dependent vasodilation -EDVD) and nitroglycerin (non-endothelium-dependent vasodilation - NEDVD). As a marker of endothelial affection we used the level of circulating endothelial cells (CEC). RESULTS PH patients were characterized by older age, body mass index, longer smoking history, AS duration, more severe functional impairment by BASFI, worse spinal motility. Both subgroups had moderate reduction of respiratory volumes. PH patients had much lower EDVD while CEC was higher. CONCLUSION Some factors were revealed which are associated with PH onset in AS patients irrespective of ERF disorders. Endothelial dysfunction is a pathogenetic link mediating effects of these factors, first of all hypoxia, smoking and persistent systemic inflammation, on blood pressure in the system of pulmonary circulation in AS patients.
The Role of Rossby Wave Breaking in Shaping the Equilibrium Atmospheric Circulation Response to North Atlantic Boundary Forcing

Abstract The role of Rossby wave breaking (RWB) is explored in the transient response of an atmospheric general circulation model to boundary forcing by sea ice anomalies related to the North Atlantic Oscillation (NAO). When the NCAR Community Climate Model, version 3, was forced by an exaggerated sea ice extent anomaly corresponding to one arising from a positive NAO, a localized baroclinic response developed and evolved into a larger-scale equivalent barotropic pattern resembling the negative polarity of the NAO. The initial baroclinic response shifted the phase speeds of the dominant eddies away from a critical value equal to the background zonal flow speed, resulting in significant changes in the spatial distribution of RWB. The forcing of the background zonal flow by the changes in RWB accounts for 88% of the temporal pattern of the response and 80% of the spatial pattern of the zonally averaged response. Although results here focus on one experiment, this “RWB critical line mechanism” appears to be .
Organizing for Mindfulness

An enriched view of mindfulness, jointly informed by Eastern and Western thinking, suggests that attentional processes in organizing have been underspecified. Respecification of attention in the context of classical views of mindfulness results in a perspective that features diminished dependence on concepts, increased focus on sources of distraction, and greater reliance on acts with meditative properties. Enriched mindfulness reveals the reality of impermanence and the necessity for continuous organizing to produce wise action.
The potential for CD4 cell increases in HIV-positive individuals who control viraemia with highly active antiretroviral therapy

Objectives: To study the long-term CD4 cell responses to highly active antiretroviral therapy (HAART) in treatment-naive patients whose viral loads remained below 500 copies/ml for prolonged periods. Design: A total of 237 patients whose viral loads remained below 500 copies/ml for one year or more. Median follow-up was 1.9 years. Methods: CD4 cell counts were analysed to investigate long-term immunological response using mixed-effects models with the slope allowed to change after 1, 12 and 24 months of HAART. Results: The median baseline CD4 cell count was 175 cells/mm3. After an initial rapid increase in the first month after HAART (97.2 cells/mm3 a month), increases in CD4 cell counts continued less rapidly (11.6 cells/mm3 a month). This increase slowed by 2.4 cells/mm3 a month after one year. CD4 cell counts continued increasing after 2 years, but the rate of increase again slowed (estimated slope at 2 years 5.4 cells/mm3 a month; decrease in slope from year 2 compared with years 1–2 3.7 cell/mm3 a month). A total of 198 out of 211 patients (94%) with measurements at baseline and one year experienced an increase in CD4 cell counts in this interval; 81 and 67% had an increasing slope between 1 and 2 and 2 and 3 years, respectively. By the end of follow-up, CD4 cell counts had increased by 319 cells/mm3, and were more than 500 cells/mm3 in 40% of patients. Conclusion: Although the rate of immune recovery slowed after 2 years, CD4 cell counts rose in most and began to return to levels seen in HIV-negative individuals.
Introducing Group Participation Support into P2P Web Caching Systems

In this paper, we introduce group participation support into decentralized peer-to-peer(P2P) web caching systems. The support allows P2P web caching systems to have more participators, and as a result, realizes highly scalable caching systems. An implementation design of systems is described in this paper. Some experimental results show that every node in our system can get better performance by the introduction of group participation support.
The Transformative Power of Travel? Four Social Studies Teachers Reflect on Their International Professional Development

Abstract Common sense thinking on international professional development suggests that the rewards for teachers are automatic. One of the most frequently advertised gains teachers are expected to see from participation includes the likelihood that they will have a transformative experience, whereby aspects of their personal or professional attributes are fundamentally modified in some productive way. This qualitative inquiry is an examination of the stories four teachers told after participating in one international professional development program. Employing interviews and observations while drawing on postcolonial theory, it investigates if and to what degree travel to and study in China constituted a transformative experience. Specifically, this study is concerned with the influence of 1 study tour on the perceptual understandings of 4 in-service social studies teachers, and if their travel alters the way they interpret often underrepresented and misrepresented content of their curricula.
Neurons are the Primary Target Cell for the Brain-Tropic Intracellular Parasite Toxoplasma gondii

Toxoplasma gondii, a common brain-tropic parasite, is capable of infecting most nucleated cells, including astrocytes and neurons, in vitro. Yet, in vivo, Toxoplasma is primarily found in neurons. In vitro data showing that interferon-γ-stimulated astrocytes, but not neurons, clear intracellular parasites suggest that neurons alone are persistently infected in vivo because they lack the ability to clear intracellular parasites. Here we test this theory by using a novel Toxoplasma-mouse model capable of marking and tracking host cells that directly interact with parasites, even if the interaction is transient. Remarkably, we find that Toxoplasma shows a strong predilection for interacting with neurons throughout CNS infection. This predilection remains in the setting of IFN-γ depletion; infection with parasites resistant to the major mechanism by which murine astrocytes clear parasites; or when directly injecting parasites into the brain. These findings, in combination with prior work, strongly suggest that neurons are not incidentally infected, but rather they are Toxoplasma’s primary in vivo target.
Unintended Effects of Emphasizing Disparities in Cancer Communication to African-Americans

Little is known about how minority groups react to public information that highlights racial disparities in cancer. This double-blind randomized study compared emotional and behavioral reactions to four versions of the same colon cancer (CRC) information presented in mock news articles to a community sample of African-American adults (n = 300). Participants read one of four articles that varied in their framing and interpretation of race-specific CRC mortality data, emphasizing impact (CRC is an important problem for African-Americans), two dimensions of disparity (Blacks are doing worse than Whites and Blacks are improving, but less than Whites), or progress (Blacks are improving over time). Participants exposed to disparity articles reported more negative emotional reactions to the information and were less likely to want to be screened for CRC than those in other groups (both P < 0.001). In contrast, progress articles elicited more positive emotional reactions and participants were more likely to want to be screened. Moreover, negative emotional reaction seemed to mediate the influence of message type on individuals wanting to be screened for CRC. Overall, these results suggest that the way in which disparity research is reported in the medium can influence public attitudes and intentions, with reports about progress yielding a more positive effect on intention. This seems especially important among those with high levels of medical mistrust who are least likely to use the health care system and are thus the primary target of health promotion advertising. (Cancer Epidemiol Biomarkers Prev 2008;17(11):2946–53)
Incorporating the Experiential Learning Cycle into Online Classes

Based on a case study built upon an introductory digital media class in a large urban school, this case study explores the relationship between ee-learning, a combination of experiential and e-learning, and technological integration in online higher education classes. By incorporating the experiential learning theory proposed by Kolb (1984), which elaborates upon John Dewey's notion of continuity of experience and interaction, the author contributes to the understanding of the roles of direct media experiences in online learning environments and proposes a useful model for teachers designing online technology courses. The ee-learning theory helps to address the wide variation of technological skills among students that instructors of online classes encounter.
Cognitive therapy v. usual treatment for borderline personality disorder: prospective 6-year follow-up.

BACKGROUND Longer-term follow-up of patients with borderline personality disorder have found favourable clinical outcomes, with long-term reduction in symptoms and diagnosis. AIMS We examined the 6-year outcome of patients with borderline personality disorder who were randomised to 1 year of cognitive-behavioural therapy for personality disorders (CBT-PD) or treatment as usual (TAU) in the BOSCOT trial, in three centres across the UK (trial registration: ISRCTN86177428). METHOD In total, 106 participants met criteria for borderline personality disorder in the original trial. Patients were interviewed at follow-up by research assistants masked to the patient's original treatment group, CBT-PD or TAU, using the same measures as in the original randomised trial. Statistical analyses of data for the group as a whole are based on generalised linear models with repeated measures analysis of variance type models to examine group differences. RESULTS Follow-up data were obtained for 82% of patients at 6 years. Over half the patients meeting criteria for borderline personality disorder at entry into the study no longer did so 6 years later. The gains of CBT-PD over TAU in reduction of suicidal behaviour seen after 1-year follow-up were maintained. Length of hospitalisation and cost of services were lower in the CBT-PD group compared with the TAU group. CONCLUSIONS Although the use of CBT-PD did not demonstrate a statistically significant cost-effective advantage, the findings indicate the potential for continued long-term cost-offsets that accrue following the initial provision of 1 year of CBT-PD. However, the quality of life and affective disturbance remained poor.
Understanding acculturation among second-generation South Asian Muslims in the United States

This article addresses an understudied area in studies of immigration—why patterns of acculturation of second-generation immigrants vary. To address this question, I draw on ethnographic research conducted among second-generation South Asian Muslims in New York City. Sociologists generally assume that acculturation is an inevitable process, and that it proceeds from less to more. I argue that acculturation is a more complex process that varies over time and situation for individuals, and can even go from more to less acculturation. Building on Judith Harris's group socialisation theory and Murray Milner Jr.'s theory of status relations, I propose that acculturation is a dynamic status process, and that we can better understand variations in patterns of acculturation of individuals by looking at their peers—the kinds of intimate associations that individuals make, and the kinds of peer group norms to which individuals conform.
Update on anesthesia for craniotomy

Purpose of review In this review, we present an update on the relationship between anesthesia and intraoperative hemodynamic complications, early postanesthesia recovery, postoperative pain and postoperative nausea and vomiting after craniotomy. We also review latest advances in education and research in neuroanesthesia for brain surgery. Recent findings Insights from clinical reports published from January 2012 to April 2013 on anesthesia for craniotomy will be summarized. Recent findings address the need for a tight intraoperative hemodynamic monitoring – that should include aggressive prevention of arterial hypotension and cardiac arrhythmias – and a careful management of fluids and electrolytes balance. Data on the relationship between anesthesia (selection of anesthetics used intraoperatively) and early recovery demonstrate a limited benefit when ultra-short acting drugs (as remifentanil vs fentanyl) are used. Evidence on postoperative pain and postoperative nausea and vomiting contribute to define how to better prevent and treat these complications. Latest guidelines on training and research in neuroanesthesia define unique end points in this subspecialty. Summary Neuroanesthesia for craniotomy should be aimed to ensure intraoperative loss of consciousness (unless awake craniotomy is the selected anesthesiological approach), pain control and an uneventful postoperative recovery, but should also be addressed to manipulate physiological variables including cerebral blood flow and to obtain optimal surgical exposure.