Miracle-dz/UniFAR-FTUs huggingface dataset:
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of partly or fully sequenced vertebrate genomes, effective tools for performing multiple comparisons are required to accurately and efficiently assist biological discoveries. Here we introduce Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA. Local multiple alignments computed by Mulan ensure reliable representation of short- and large-scale genomic rearrangements in distant organisms. Mulan allows for interactive modification of critical conservation parameters to differentially predict conserved regions in comparisons of both closely and distantly related species. We illustrate the uses and applications of the Mulan tool through multispecies comparisons of the GATA3 gene locus and the identification of elements that are conserved in a different way in avians than in other genomes, allowing speculation on the evolution of birds. Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://www.bx. psu.edu/miller_lab/.
Effects of Nasoalveolar Molding Therapy on Nasal and Alveolar Morphology in Unilateral Cleft Lip and Palate

Objective: The objective of this study was to evaluate the effects of presurgical nasoalveolar molding (PNAM) therapy on nasal and alveolar tissues in patients with unilateral cleft lip and palate. Patients and Methods: Twenty-two patients with a mean age of 23 days, having complete unilateral cleft lip and palate, were included in this prospective study. After the impressions were taken of the palatal and nasolabial regions separately, the maxillary and nasal plaster models were scanned for linear, angular, and area measurements before and after PNAM therapy. The distances between the identified landmarks were measured in the maxillary casts, and the distance and area measurements were performed for the nasal casts with the specified software called Image J developed by the National Institutes of Health. All subjects have undergone PNAM therapy for 6 months. The nasal and maxillary casts are scanned, and the images were evaluated using the software Image J. The alveolar segments should be approximated, and the cleft width and alar base of the affected side after PNAM should be reduced, and the nostril area of the cleft side should be increased. The columella deviation should be decreased. Results: The decrease of the cleft width, arch length, and alar base width on the cleft side and the deviation of the columella were significant, in addition to the significant increase of the arch circumference and nostril area on the affected side (P < 0.001). Conclusions: Presurgical nasoalveolar molding therapy is a significantly helpful treatment for patients with unilateral cleft lip and palate. The reduction in the alveolar cleft region and the nasal reshaping are favorable.
Motor Vehicle Accidents and IDDM

A case-control study examining the 1-yr motor vehicle accident experiences of 158 insulin-dependent diabetes mellitus (IDDM) cases and 158 nondiabetic siblings was undertaken to evaluate the risk of motor vehicle accidents among drivers with IDDM. In multivariate analyses the overall accident risk of the cases and control subjects did not differ significantly. Female diabetic drivers, however, showed a marked increased risk for motor vehicle accidents. The accident risk among female cases was five times higher than among the female control subjects (P < .05). Age and marital status were also significantly associated with accident probability in the multivariate model. The results suggest that IDDM could have an effect on the accident rate of diabetic drivers, particularly women. However, the traditional risk factors for automobile accidents, i.e., age and marital status, appear to have an equally strong influence on accident occurrence. Further studies are needed to 1) document the role of IDDM in accidents among representative samples of the IDDM population and 2) properly evaluate the licensing restrictions recommended for diabetic drivers.
Project Taking Charge: An Evaluation of an Adolescent Pregnancy Prevention Program.

Project Taking Charge is a combined sex and vocational education program which distinguishes it from other abstinence-based programs for 7th graders in economically depressed areas of Wilmington Delaware; West Point Mississippi; and Ironton Ohio. Its similarities to other programs include emphasis on self-concept development decision-making skills parent/child communication and ethical values. The American Home Economics Association implemented this demonstration project with funding through the US Office of Adolescent Pregnancy Programs (OAPP). Relevant research literature on the results of OAPP-funded programs and on the sexual behavior and pregnancy-related variables of occupational goals and community support self-development and parent involvement are discussed. The intervention program itself was a 6-week curriculum for 7th grade home economics students and 3 parent/youth sessions for promotion strong family values in 1989. The sites had high rates of adolescent pregnancy low income families no preexisting sex education or vocational awareness and state and local school district support. It was hypothesized that the treatment group compared with the control group would perform better on 12 measures. The pre- and posttesting and evaluation design were set up to compensate for deficiencies identified by e.g. Roosa and Christopher. Students were randomly selected by teachers; the number varied from 14 to 27. Questionnaires were self-administered. The instrument was pilot tested and used some standard demographic items existing scales and indexes and relevant and standardized items from an OAPP question pool. 1-way analyses of variance (ANOVA) and covariance (ANCOVA) were used. The results indicated support for only 3 hypotheses: realization of significant gains in areas of human sexuality sexual development and sexually transmitted diseases (STDs); communicating with their fathers about vocational issues; and parents knowledge of sexuality and STDs improved. There was no significant changes in parent/child communication about sexual issues in adolescent and parent sexual attitudes in adolescent self-esteem and in educational aspiration. There was a trend toward a lower likelihood of sexual activity if subjects were not sexually active prior to the program although there is no accounting for what in the program was responsible. Limitations were that the instrument was short and items unmeasured the subject numbers were small and limited sophisticated analyses and results were modest.
De novo synthesis of adenine nucleotides in different skeletal muscle fiber types.

Management of adenine nucleotide catabolism differs among skeletal muscle fiber types. This study evaluated whether there are corresponding differences in the rates of de novo synthesis of adenine nucleotide among fiber type sections of skeletal muscle using an isolated perfused rat hindquarter preparation. Label incorporation into adenine nucleotides from the [1-14C]glycine precursor was determined and used to calculate synthesis rates based on the intracellular glycine specific radioactivity. Results show that intracellular glycine is closely related to the direct precursor pool. Rates of de novo synthesis were highest in fast-twitch red muscle (57.0 +/- 4.0, 58.2 +/- 4.4 nmol.h-1.g-1; deep red gastrocnemius and vastus lateralis), relatively high in slow-twitch red muscle (47.0 +/- 3.1; soleus), and low in fast-twitch white muscle (26.1 +/- 2.0 and 21.6 +/- 2.3; superficial white gastrocnemius and vastus lateralis). Rates for four mixed muscles were intermediate, ranging between 32.3 and 37.3. Specific de novo synthesis rates exhibited a strong correlation (r = 0.986) with muscle section citrate synthase activity. Turnover rates (de novo synthesis rate/adenine nucleotide pool size) were highest in high oxidative muscle (0.82-1.06%/h), lowest in low oxidative muscle (0.30-0.35%/h), and intermediate in mixed muscle (0.44-0.55%/h). Our results demonstrate that differences in adenine nucleotide management among fiber types extends to the process of de novo adenine nucleotide synthesis.
CARET, the β‐carotene and retinol efficacy trial to prevent lung cancer in asbestos‐exposed workers and in smokers

CARET is a two-armed, double-blind, randomized chemo-prevention trial to test the hypothesis that oral administration of beta-carotene 30 mg/day plus retinyl palmitate 25 000 IU/day will decrease the incidence of lung cancer in high-risk populations: heavy smokers and asbestos-exposed workers who have smoked. The agents combine anti-oxidant and nuclear tumor suppressor mechanisms. Fastidious monitoring for possible side effects is facilitated by inclusion of a Vanguard population. As of 31 December 1990, 6 105 participants of the 18 000 needed have been randomized in the trial. Efficacy results are expected in 1999.
Fracture energy release and size effect in borehole breakout

SUMMARY The paper presents a simple approximate analytical solution of the remote stresses that cause the collapse of a borehole or other circular cylindrical cavity in an infinite elastic space. Regions of parallel equidistant splitting cracks are assumed to form on the sides of the cavity. Their boundary is assumed to be an eIlipse of a growing horizontal axis, the other axis remaining equal to the borehole diameter. The slabs of rock between the splitting cracks are assumed to buckle as slender columns, and their post-critical stress is considered as the residual stress in the cracked rock. The buckling of these slab columns is assumed to be resisted not only by their elastic bending stiffness but also shear stresses produced on rough crack faces by relative shear displacements. The energy release from the infinite medium'-caused by the growth of the eIliptical cracking region is evaluated according to Eschelby's theorem. This release is set equal to the energy dissipated by the formation of alI the splitting cracks, which is calculated under the assumption of constant fracture energy. This yields the collapse stress as a function of the elastic moduli, fracture energy, ratio of the remote principal stresses, crack shear resistance characteristic and borehole diameter. The collapse stress as a function of crack spacing is found to have a minimum, and the correct crack spacing is determined from this minimum. For small enough diameters, the crack spacing increases as the (4/5)-power of the borehole diameter, while for large enough diameters a constant spacing is approached. In contrast to plastic solutions, the breakout stress exhibits a size effect, such that for small enough diameters the breakout stress decreases as the ( - 2/5)-power of the borehole diameter, while for large enough diameters a constant limiting value is approached. Finally, some numerical estimates are given and the validity of various simplifying assumptions made is discussed.
Can’t We Make It Any Shorter?

Psychological constructs are becoming increasingly important in social surveys. Scales for the assessment of these constructs are usually developed primarily for individual assessment and decision-making. Hence, in order to guarantee high levels of reliability, measurement precision, and validity, these scales are in most cases much too long to be applied in surveys. Such settings call for extremely short measures validated for the population as a whole. However, despite the unquestionable demand, appropriate measures are still lacking. There are several reasons for this. In particular, short scales have often been criticized for their potential psychometric shortcomings with regard to reliability and validity. In this article, the authors discuss the advantages of short scales as alternative measures in large-scale surveys. Possible reasons for the assumed limited psychometric qualities of short scales will be highlighted. The authors show that commonly used reliability estimators are not always appropri.
Deconstructing youth transition to adulthood services: Lessons learned from the VISIONS program

Abstract The Health Belief Model and Theory of Reasoned Action were used in evaluating a community-based human development program for youth in foster care – VISIONS. The study examined youth perceptions of the barriers to, and the skills needed to increase independent living skills and the capacity to become productive adults in the community post discharge from care. Participants' perceived self efficacy, perceived benefit associated with the program, barriers to skills development and the role of mentor relationship in youth mastery of life skills, were assessed. Youth mastery of life skills was assessed using Ansell Casey Life Skills Assessment; while FGDs and the Life Skills Questionnaire were used to examine what participants liked most/least about the program. Findings showed participants reported increased skills mastery at follow-up. Relationship with a mentor was a strong predictor of skills mastery. The findings, point to a need for more dynamic and pragmatic strategies to implementing human development training programs for youth in order to improve ILS outcomes. These and other findings are discussed along with their implications for future research on youth human development needs.
Access to What? Creating a Composite Measure of Educational Quantity and Educational Quality for 11 African Countries

The aim of the current study is to create a composite statistic of educational quantity and educational quality by combining household data (Demographic and Health Survey) on grade completion and survey data (Southern and Eastern African Consortium for Monitoring Educational Quality) on cognitive outcomes for 11 African countries: Kenya, Lesotho, Malawi, Mozambique, Namibia, South Africa, Swaziland, Tanzania, Uganda, Zambia, and Zimbabwe. Doing so overcomes the limitations of earlier studies that focused solely on either quantity or quality. We term the new statistic “access to literacy” and “access to numeracy” and report it by gender and wealth. This new measure combines both quantity and quality and consequently places educational outcomes at the center of the discourse.
Attentional Focus and the Dynamics of Dual Identity Integration

Do situational cues to individuals’ social identities shift the way they look at objects? Do such shifts hinge on the structure of individuals’ self-concept? We hypothesized individuals with integrated identities would exhibit attentional biases congruent with identity cues (assimilative response), whereas those with nonintegrated identities would exhibit attentional biases incongruent with identity cues (contrastive response). Dual identity participants (Asian Americans, Study 1; female lawyers, Study 2) were exposed to identity primes and then asked to focus on central, focal objects in a stimulus display. Among participants with high identity integration, American (Study 1) or lawyer priming (Study 2) shifted attention toward focal objects (assimilative response). Among participants with low identity integration, Asian (Study 1) or female priming (Study 2) shifted attention toward focal objects (contrastive response). Dual identity integration moderates responses to identity cues in attentional focus. Implications for identity structure, object perception, and task performance are discussed.
Biodegradability properties of sulfonamides in activated sludge

Twelve different sulfonamides were selected for a biodegradation study using a respirometric screening test and an activated sludge simulation test. A simple bacterial growth inhibition test was applied to show that the sulfonamides did not affect the bacteria at the concentration levels used. None of the compounds were degraded in the screening test, leading to the conclusion that sulfonamides cannot be classified as readily biodegradable. In the simulation test, primary degradation of mixtures of four compounds at concentration levels of 250 to 500 μg/L were tested and analyzed using high‐performance liquid chromatography. Biodegradation occurred after lag phases of 7 to 10 d at 20°C when nonadapted sludge was applied. Test compounds were degraded within a few days. At 6°C, degradation lag phases and degradation rates were three to four times longer. Degradation curves fit well to the logistic growth model, indicating growth of specific degraders in the test system. Sulfonamide adapted bacterial cultures were able to degrade either the same compounds as previously added or four other sulfonamides in a rapid and uniform way (t1/2 from 0.2 to 3 d). This finding shows that if capable of degrading one sulfonamide substance, these bacteria may also degrade many other sulfonamides. In practice, this implies that because the biodegradation rate is found to be identical for several sulfonamides in the sludge, the compounds may be assessed as a group by studying only a few compounds in applications such as environmental fate assessments. The mechanism for inducement of sulfonamide adaptation to the bacteria was not revealed in this study.
Black hole entropy in 3 D gravity with torsion

The role of torsion in three-dimensional quantum gravity is investigated by studying the partition function of the Euclidean theory in Riemann-Cartan spacetime. The entropy of the black hole with torsion is found to differ from the standard Bekenstein-Hawking result, but its form is in complete agreement with the first law of black hole thermodynamics.
Identifying and Understanding the Health Information Experiences and Preferences of Individuals With TBI, SCI, and Burn Injuries

Introduction: Traumatic brain injury, spinal cord injury, and burn injury can cause lifelong disability and changes in quality of life. In order to meet the challenges of postinjury life, various types of health information are needed. We sought to identify preferred sources of health information and services for persons with these injuries and discover how accessibility could be improved. Methods: Thirty-three persons with injury participated in semistructured interviews. Responses to interview questions were coded using NVivo. Results: Participants’ difficulties accessing health information varied by injury type and individually. The majority of respondents found information via the Internet and advocated its use when asked to describe their ideal health information system. Nearly all participants supported the development of a comprehensive care website. When searching for health information, participants sought doctor and support group networks, long-term health outcomes, and treatments specific to their injury. Conclusion: To optimize the quality of health information resources, Internet-based health-care platforms should add or highlight access points to connect patients to medical professionals and support networks while aggregating specialized, injury-specific research and treatment information.
Avoiding Obstacles to Student Comprehension of Test Questions

We present preliminary criteria to consider in the writing of English for academic purposes (EAP) reading comprehension tests. Such criteria are necessary as a frame of reference for a large and diverse teaching staff. The criteria pertain to the test as a whole as well as to the form of individual questions. The choice of items derives from our classroom and test-writing experience and reflects the comprehension problems that students encounter with test questions. These problems may indeed be stumbling blocks for the student because they constitute processing constraints. Pragmatic theory can provide a theoretical framework to explain these processing constraints.
Relationship between soft bottom macrofauna and polycyclic aromatic hydrocarbons (PAH) from smelter discharge in Norwegian fjords and coastal waters

Data from monitoring surveys were used to test the responses of soft bottom fauna in Norwegian fjords and coastal waters affected by effluents from aluminium and manganese alloy smelters to effluent discharges. Generally, polycyclic aromatic hydrocarbons (PAHs) have been considered the main threat to the biota in the receiving waters. Data from a total of 57 quantitative stations, of which 30 were simultaneously sampled for sedimentary PAHs, were analysed. Canonical Correspondence Analysis (CCA) was used to evaluate species patterns in relation to sediment PAH concentrations and natural environmental variables such as depth, sediment characteristics and riverine input. The PAHs varied from very high concentrations (760 pg g.' total PAH) at the most impacted sites to background levels in reference areas. Despite previous reports of little to no effects of the effluent discharges, the analyses identlf~ed significant species changes along PAH gradients, which could be associated with feeding modes. In particular, a number of carnivorous polychaetes had their dlstnbution ophma In the most affected areas. Based on species statistics calculated by CCA, response functions were fitted for the species on PAH and used to establish a generalised expression of trophic community structure in relation to PAH concentrations. At low PAH levels, the carnivores represented 15 to 20% of the specimens in the communities, but the proportion began to increase from about 10 pg g-' and exceeded 50% at 100 pg g-' total PAH. The fauna1 changes were most evident in shallow waters, possibly reflecting the effects of dissolved PAHs to which the species may react more directly than they do to sedlrnentary particle-associated PAHs.