Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing the Success of Different Prediction Software in Sequence Analysis: A Review

The abundance of computer software for different types of prediction in DNA and protein sequence analyses raises the problem of adequate ranking of prediction program quality. A single measure of success of predictor software, which adequately ranks the predictors, does not exist. A typical example of such an incomplete measure is the so-called correlation coefficient. This paper provides an overview and short analysis of several different measures of prediction quality. Frequently, some of these measures give results contradictory to each other even when they relate to the same prediction scores. This may lead to confusion. In order to overcome some of the problems, a few new measures are proposed including some variants of a 'generalised distance from the ideal predictor score'; these are based on topological properties, rather than on statistics. In order to provide a sort of a balanced ranking, the averaged score measure (ASM) is introduced. The ASM provides a possibility for the selection of the predictor that probably has the best overall performance. The method presented in the paper applies to the ranking problem of any prediction software whose results can be properly represented in a true positive-false positive framework, thus providing a natural set-up for linear biological sequence analysis.
Post-traumatic stress, anxiety and depression following miscarriage or ectopic pregnancy: a prospective cohort study

Objectives This is a pilot study to investigate the type and severity of emotional distress in women after early pregnancy loss (EPL), compared with a control group with ongoing pregnancies. The secondary aim was to assess whether miscarriage or ectopic pregnancy impacted differently on the type and severity of psychological morbidity. Design This was a prospective survey study. Consecutive women were recruited between January 2012 and July 2013. We emailed women a link to a survey 1, 3 and 9 months after a diagnosis of EPL, and 1 month after the diagnosis of a viable ongoing pregnancy. Setting The Early Pregnancy Assessment Unit (EPAU) of a central London teaching hospital. Participants We recruited 186 women. 128 had a diagnosis of EPL, and 58 of ongoing pregnancies. 11 withdrew consent, and 11 provided an illegible or invalid email address. Main outcome measures Post-traumatic stress disorder (PTSD) was measured using the Post-traumatic Diagnostic Scale (PDS), and anxiety and depression using the Hospital Anxiety and Depression Scale (HADS). Results Response rates were 69/114 at 1 month and 44/68 at 3 months in the EPL group, and 20/50 in controls. Psychological morbidity was higher in the EPL group with 28% meeting the criteria for probable PTSD, 32% for anxiety and 16% for depression at 1 month and 38%, 20% and 5%, respectively, at 3 months. In the control group, no women met criteria for PTSD and 10% met criteria for anxiety and depression. There was little difference in type or severity of distress following ectopic pregnancy or miscarriage. Conclusions We have shown a large number of women having experienced a miscarriage or ectopic pregnancy fulfil the diagnostic criteria for probable PTSD. Many suffer from moderate-to-severe anxiety, and a lesser number depression. Psychological morbidity, and in particular PTSD symptoms, persists at least 3 months following pregnancy loss.
Detection by broad-range real-time PCR assay of Chlamydia species infecting human and animals

Background: Tests available for molecular diagnosis of chlamydial infections detect Chlamydiatrachomatis, but do not find other Chlamydia species associated with genital, ophthalmic, cardiovascular, respiratory or neurological diseases. The routine detection of all Chlamydia species would improve the prognosis of infected people and guide therapeutic choices. Aim: To design and validate a sensitive, specific, reproducible, inexpensive and easy-to-perform assay to quantify most Chlamydia species. Methods: Primers and probe were selected using the gene coding for the 16S rRNA. The detection limits were assessed for suspensions of Chlamydia trachomatis, Chlamydia psittaci and Chlamydia pneumoniae. The performance of this test was compared with that of two commercial kits (Amplicor-Roche and Artus) on 100 samples obtained from children with trachoma. Results: The detection capacities for Chlamydia trachomatis of the broad-range real-time polymerase chain reaction (PCR) were similar or slightly better than those obtained with commercial kits (0.2 copies of DNA/μl). Only the broad-range PCR identified specimens containing Chlamydia psittaci and Chlamydia pneumoniae. The commercial kits and the broad-range assay detected Chlamydia species in 5% and in 11%, respectively, of samples from children with trachoma. Conclusions: This new real-time PCR offers a sensitive, reproducible assay that produces results in <3 h. With panels of quantified Chlamydia species, this real-time PCR can be run with all real-time PCR equipment. Larger trials are needed to confirm the utility of this test in diagnosis and for therapeutic follow-up.
Serum Lycopene, Other Carotenoids, and Prostate Cancer Risk: a Nested Case-Control Study in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial

Background: Reports from several studies have suggested that carotenoids, and in particular lycopene, could be prostate cancer–preventive agents. This has stimulated extensive laboratory and clinical research, as well as much commercial and public enthusiasm. However, the epidemiologic evidence remains inconclusive. Materials and Methods: We investigated the association between prediagnostic serum carotenoids (lycopene, α-carotene, β-carotene, β-cryptoxanthin, lutein, and zeaxanthin) and risk of prostate cancer in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial, a multicenter study designed to examine methods of early detection and risk factors for cancer. The study included 692 incident prostate cancer cases, diagnosed 1 to 8 years after study entry, including 270 aggressive cases, with regional or distant stage (n = 90) or Gleason score ≥7 (n = 235), and 844 randomly selected, matched controls. As study participants were selected from those who were assigned to annual standardized screening for prostate cancer, results are unlikely to be biased by differential screening, a circumstance that is difficult to attain under non–trial conditions. Results: No association was observed between serum lycopene and total prostate cancer [odds ratios (OR), 1.14; 95% confidence intervals (95% CI), 0.82-1.58 for highest versus lowest quintile; P for trend, 0.28] or aggressive prostate cancer (OR, 0.99; 95% CI, 0.62-1.57 for highest versus lowest quintile; P for trend, 0.433). β-Carotene was associated with an increased risk of aggressive prostate cancer (OR, 1.67; 95% CI, 1.03-2.72 for highest versus lowest quintile; P for trend, 0.13); in particular, regional or distant stage disease (OR, 3.16; 95% CI, 1.37-7.31 for highest versus lowest quintile; P for trend, 0.02); other carotenoids were not associated with risk. Conclusion: In this large prospective study, high serum β-carotene concentrations were associated with increased risk for aggressive, clinically relevant prostate cancer. Lycopene and other carotenoids were unrelated to prostate cancer. Consistent with other recent publications, these results suggest that lycopene or tomato-based regimens will not be effective for prostate cancer prevention. (Cancer Epidemiol Biomarkers Prev 2007;16(5):962–8)
The Effect of Gender and Status on the Apology Strategies Used by American Native Speakers of English and Iraqi EFL University Students

In fact, apology varies from one language to another. Thus, teachers and EFL learners must discern the similarities and the differences between their native language and the target one because what is deemed right in one language may not be considered right in the other. No study is conducted to compare apology strategies of Iraqi EFL university students along with that of the American native speakers of English in terms of gender and status. Therefore, the present study will explore these issues in order to clarify them. As such, a discourse completion test has been designed and applied to Iraqi EFL university students and Americans native speakers of English. The results show that Iraqi EFL male leaners use more strategies with people of higher level, while the American males use more strategies with people of lower position. Moreover, unlike the Americans, Iraqi females use more apology strategies than Iraqi males.
MEASUREMENT OF HEAD IMPACTS IN COLLEGIATE FOOTBALL PLAYERS: AN INVESTIGATION OF POSITIONAL AND EVENT‐TYPE DIFFERENCES

OBJECTIVEThere exists a need to better understand the biomechanical forces associated with head impacts in American football. The purpose of this study was to investigate whether or not differences in head accelerations existed between different player positions and different event types in collegiate football. We also sought to identify whether or not any associations existed between high-magnitude impacts and location of head impacts. METHODSWe conducted a prospective field study in which accelerometers were embedded in the football helmets of 72 collegiate football players. Linear accelerations of all head impacts sustained over the course of the 2005 and 2006 National Collegiate Athletic Association football seasons were collected. One-way analyses of variance and χ2 tests of association assessed positional, event type, and location of head impact differences. RESULTSFootball players consistently sustained head impacts between 21 and 23 g. Positional differences were identified within our sample. Impacts sustained during helmets-only practices were greater than those sustained in games or scrimmages. There was an association between position and high-magnitude impacts, as well as between high-magnitude impacts and location of head impact, with the likelihood of impacts to the top of the head much higher than those to the front, back, left, and right sides. CONCLUSIONLess than 0.35% of impacts exceeding theoretical injury thresholds resulted in concussion. More injury data are required before any theoretical thresholds for injury can be confirmed. Coaches and sports medicine professionals should recognize that head impacts sustained in helmets-only practices are as severe as games or scrimmages; there seem to be no “light” days for football players.
The influence of early science experience in kindergarten on children's immediate and later science achievement: Evidence from the early childhood longitudinal study†

This study explores the impacts of selected early science experiences in kindergarten (frequency and duration of teachers' teaching of science, availability of sand/water table and science areas, and children's participation in cooking and science equipment activities) on children's science achievement in kindergarten and third grade using data for 8,642 children from the Early Childhood Longitudinal Study-Kindergarten cohort (ECLS-K). A theoretical model that depicts the relationships between the study variables was developed and tested using structural equation modeling. Results demonstrated that availability of science materials in kindergarten classrooms facilitated teachers' teaching of science and children's participation in science activities. Likewise, the frequency and the duration of kindergarten science teaching was a significant predictor of children's science activities but not of the children's end of kindergarten science achievement scores. Children's engagement with science activities that involved using science equipment also was not a significant predictor of their end of kindergarten science achievement. However, children's participation in cooking activities was. Children's prior knowledge, motivation, socio-economic status, and gender were all statistically significant predictors of their science achievement at the end of kindergarten and end of third grade. Results of this study indicate that early science experiences provided in kindergarten are not strong predictors of children's immediate and later science achievement. Findings of the study suggest that the limited time and nature of science instruction might be related to the limited effect of the science experiences. Implications for teacher education programs and educational policy development are discussed. © 2010 Wiley Periodicals, Inc. J Res Sci Teach 48: 217–235, 2011
Effects of reclamation and natural changes on coastal wetlands bordering China's Yellow Sea from 1984 to 2015

Coastal wetlands are rapidly disappearing worldwide, which is posing a substantial threat to the integrity of coastal ecosystems. In addition to the direct area reduction caused by reclamation, coastal wetlands experience natural changes due to sediment transport in coastal regions. Arguably, the reclamation rates must be less than the net accretion rate to guarantee the restoration of coastal wetlands. By applying an automatic and replicable shoreline algorithm to all available Landsat imagery from 1984 to 2015 using the Google Earth Engine Cloud Platform, we developed distribution maps of coastal wetlands and reclamation in China's Yellow Sea (CYS) at 4‐ or 5‐year intervals. In addition, we divided coastal wetlands into saltmarshes and mudflats and analysed their trends separately. Over the past 30 years, the area of coastal wetlands decreased by 53% (from 6,463 to 3,036 km2), including a 67% decrease in saltmarshes (from 1,471 to 489 km2) and a 49% decrease in mudflats (from 4,992 to 2,547 km2). Meanwhile, the reclaimed area was 7,696 km2 (including 1,276 km2 of saltmarshes and 3,002 km2 of mudflats), which exceeded the area of newly formed coastal wetlands (852 km2). The natural state of mudflats gradually changed from accretion to erosion, but without considering the natural state of coastal wetlands, reclamation will continue at a high rate in CYS according to China's national marine functional zoning (MFZ) for 2010–2020. In view of their important ecological services, there is an urgent need to revise the national MFZ to achieve ‘no net loss’ of coastal wetlands.
End-of-Kindergarten Spelling Outcomes: How Can Spelling Error Analysis Data Inform Beginning Reading Instruction?

ABSTRACT In this study, we examined the spelling performance of 430 kindergartners, which included a high-risk sample, to determine the relations between end-of-kindergarten reading and spelling in a high-quality language arts setting. We described, analyzed, and compared spelling outcomes, including spelling errors, between good and poor readers. The findings suggest that not all of the children achieved the desired standard as outlined by the Common Core State Standards. In addition, not every good reader was a good speller, and not every poor speller was a poor reader. The study shows that spelling tasks that are accompanied by spelling error analysis provide a powerful window for making instructional sense of children’s spelling errors and for individualizing spelling instructional strategies.
High‐Performance Hydrogen Evolution from MoS2(1–x)P
x Solid Solution

A MoS2(1-x) P(x) solid solution (x = 0 to 1) is formed by thermally annealing mixtures of MoS2 and red phosphorus. The effective and stable electrocatalyst for hydrogen evolution in acidic solution holds promise for replacing scarce and expensive platinum that is used in present catalyst systems. The high performance originates from the increased surface area and roughness of the solid solution.
Probiotic treatment of vancomycin‐resistant enterococci: a randomised controlled trial

Australians enjoy a life expectancy that ranks in the top five in the world and a health system that also rates highly, and yet consistent public disquiet about our hospitals persists. Among the root causes for this alarm is the federal–state political divide, which is shackled by the “blame game”, inevitable inefficiencies, duplication of effort, cost shifting, and poorly supervised programs — and all this costs Australians $9 billion to $20 billion a year. Despite a flurry of reports and proposals that the Commonwealth take over state hospitals, this notion has not gained widespread support or moved beyond threats of intervention. Recently, the Prime Minister lobbed a grenade into the political arena, with a promise that the federal government would take over the Mersey Hospital near Devonport in Tasmania to the tune of $45 million a year. The hospital had been earmarked for downsizing by the Tasmanian Government. Call it political opportunism, savvy electioneering, or policy making on-the-run — in a single swoop Howard had created a people’s hospital. This development drew a barrage of salvos from Labor state premiers and from health experts. However, others have backed Howard’s proposal, presumably in the hope this small leak in the dam of the federal–state divide might grow into a torrent that will sweep the whole edifice aside. Labor’s recent health proposal for all hospitals offers some hope that this may eventually occur. It has been claimed that most people in the community are not really interested in who runs their hospitals — “What they’re interested in is the quality of their treatment and being able to walk out of that hospital whole and well in a way that they weren’t when they came in to that hospital”* — surely, another example of belief in the notion of people’s hospitals! But as long as hospital funding continues to be the spoils in the dogfight that is federal and state politics, hospitals will never be the province of people but will remain the preserve of politicians.
Isolation, characterization, and nucleotide sequence of the Streptococcus mutans mannitol-phosphate dehydrogenase gene and the mannitol-specific factor III gene of the phosphoenolpyruvate phosphotransferase system

Streptococcus mutans, the causative agent of dental caries, utilizes carbohydrates by means of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). The PTS facilitates vectorial translocation of metabolizable carbohydrates to form the corresponding sugar-phosphates, which are subsequently converted to glycolytic intermediates. The PTS consists of both sugar-specific and sugar-independent components. Complementation of an Escherichia coli mtlD mutation with a streptococcal recombinant DNA library allowed isolation of the mannitol-1-phosphate dehydrogenase gene (mtlD) and the adjacent sugar-specific mannitol factor III gene (mtlF) from S. mutans. Subsequent transposon mutagenesis of the complementing DNA fragment with Tn5seq1 defined the region that encodes the mtlD-complementing activity, the streptococcal mtlD gene. Nucleotide sequence analysis of this region revealed two complete open reading frames (ORFs) from within the streptococcal mannitol PTS operon. One ORF encodes the mtlD gene product, a 43.0-kDa protein which exhibits similarity to the E. coli and Enterococcus faecalis mannitol-1-phosphate dehydrogenases. The second ORF encodes a 15.8-kDa protein which exhibits similarity to mannitol factor III proteins from several bacterial species. In vitro transcription-translation assays were used to produce proteins of the sizes predicted by the streptococcal ORFs. These data indicate that the S. mutans mannitol PTS utilizes an enzyme II-factor III complex similar to the mannitol system found in other gram-positive organisms, as opposed to that of E. coli, which utilizes an independent enzyme II system.
Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e–H2 vibrational cross section controversy

We commence a fundamental re-examination of the kinetic theory of charged particle swarms in molecular gases, focusing on collisional excitation of molecular rotational and ro-vibrational states by electrons. Modern day analysis of electron swarms has been based upon the kinetic equation of Wang-Chang et al, which simply treats all processes as scalar energy excitations, and ignores angular momentum conservation and the vector dynamics associated with rotational excitation. It is pointed out that there is no alternative, more exact kinetic equation readily available for electrons which enables one to directly ascertain the degree of error introduced by this approximation. Thus in this preliminary study, we approach the problem indirectly, from the standpoint of the neutral molecules, using the Waldmann–Snider quantum kinetic equation, and insist that an electron–molecule collision must look the same from the perspective of both electron and molecule. We give a formula for quantitatively assessing the importance of scalar versus vectorial treatments of rotational excitation by looking at the post-collisional ‘echo’ produced by an electron swarm as it passes through the gas. It is then pointed out that in order to remedy any deficiency, it will be necessary to introduce a kinetic collisional operator non-local in space to properly account for angular momentum conservation, as has long been established in the literature. This is a major exercise and given the preliminary nature of this study, we consider the inclusion of such effects from a formal point of view only. In particular we show how non-local effects lead to a spatially dependent ‘source’ term in the equation of continuity, and hence to corrections for both drift velocity and diffusion coefficients. The magnitude of these corrections has yet to be established.
Development of a DNA Microarray for Enterococcal Species, Virulence, and Antibiotic Resistance Gene Determinations among Isolates from Poultry

ABSTRACT A DNA microarray (Enteroarray) was designed with probes targeting four species-specific taxonomic identifiers to discriminate among 18 different enterococcal species, while other probes were designed to identify 18 virulence factors and 174 antibiotic resistance genes. In total, 262 genes were utilized for rapid species identification of enterococcal isolates, while characterizing their virulence potential through the simultaneous identification of endogenous antibiotic resistance and virulence genes. Enterococcal isolates from broiler chicken farms were initially identified by using the API 20 Strep system, and the results were compared to those obtained with the taxonomic genes atpA, recA, pheS, and ddl represented on our microarray. Among the 171 isolates studied, five different enterococcal species were identified by using the API 20 Strep system: Enterococcus faecium, E. faecalis, E. durans, E. gallinarum, and E. avium. The Enteroarray detected the same species as API 20 Strep, as well as two more: E. casseliflavus and E. hirae. Species comparisons resulted in 15% (27 isolates) disagreement between the two methods among the five API 20 Strep identifiable species and 24% (42 isolates) disagreement when considering the seven Enteroarray identified species. The species specificity of key antibiotic and virulence genes identified by the Enteroarray were consistent with the literature adding further robustness to the redundant taxonomic probe data. Sequencing of the cpn60 gene further confirmed the complete accuracy of the microarray results. The new Enteroarray should prove to be a useful tool to accurately genotype strains of enterococci and assess their virulence potential.
Student Eligibility for a Free Lunch as an SES Measure in Education Research

The use of eligibility for a free lunch as a measure of a student’s socioeconomic status continues to be a fixture of quantitative education research. Despite its popularity, it is unclear that education researchers are familiar with what student eligibility for a free lunch does (and does not) represent. The authors examine the National School Lunch Program, which is responsible for certifying students as eligible for a free lunch, and conclude that free lunch eligibility is a poor measure of socioeconomic status, which suffers from important deficiencies that can bias inferences. A table characterizing key strengths and weaknesses of variables used as measures of socioeconomic status is provided to facilitate comparisons.