THE FARM LEVEL EFFECTS OF BETTER ACCESS TO INFORMATION: THE CASE OF DART

In this study, two methods of entering and accessing dairy herd records are compared: the traditional mail-in Dairy Herd Improvement (DHI) system and the Direct Access to Records by Telephone (DART) system, which provides more timely and convenient access to records. An evaluation of DART was carried out using mail survey responses from 117 DART users and telephone surveys of 40 randomly selected users. Results indicate that DART users are generally satisfied with the system and feel that it improves their herd management. Variations in use of the DART system by DART users are explained by herd, cost, and management variables. DART users and comparable non-DART, DHI users are compared with respect to gains in herd production efficiency. Results indicate that DART users made somewhat better gains in most efficiency measures but that the differences were generally not statistically significant.Farm Management,

FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

Complex genome evolution in Anopheles coluzzii associated with increased insecticide usage in Mali.

In certain cases, a species may have access to important genetic variation present in a related species via adaptive introgression. These novel alleles may interact with their new genetic background, resulting in unexpected phenotypes. In this study, we describe a selective sweep on standing variation on the X chromosome in the mosquito Anopheles coluzzii, a principal malaria vector in West Africa. This event may have been influenced by the recent adaptive introgression of the insecticide resistance gene known as kdr from the sister species Anopheles gambiae. Individuals carrying both kdr and a nearly fixed X-linked haplotype, encompassing at least four genes including the P450 gene CYP9K1 and the cuticular protein CPR125, have rapidly increased in relative frequency. In parallel, a reproductively isolated insecticide-susceptible A. gambiae population (Bamako form) has been driven to local extinction, likely due to strong selection from increased insecticide-treated bed net usage

Non-inherited maternal human leukocyte antigen alleles in susceptibility to familial rheumatoid arthritis.

OBJECTIVES: Some patients with rheumatoid arthritis (RA) lack RA-associated human leukocyte antigen (HLA) alleles. Prior studies investigated non-inherited maternal HLA alleles (NIMA) in RA risk with conflicting results. METHODS: We examined NIMA in a large cohort of families from the North American Rheumatoid Arthritis Consortium (NARAC). RESULTS: Among 620 patients with 1 or both parents having a HLA genotype, patients with RA informative for analysis included 176 without HLA-DRB1*04 and 86 without the HLA shared epitope (SE). The frequency of NIMA encoding HLA-DR4 or the SE was compared to the non-inherited paternal allele (NIPA). DR4-encoding NIMA vs NIPA revealed no significant difference (27% vs 20%). However, parity is known to modulate RA risk and analyses stratified by sex and age of onset showed significant variation among women. Interestingly, among women with onset or =45 years at onset the reverse was observed (31% vs 16% compared to 10% vs 60%, p = 0.008). DR4 encoding NIMA vs NIPA did not differ in men. The SE did not differ in men or women. CONCLUSIONS: Risk of RA was associated with HLA-DR4 encoding NIMA in younger-onset women but not in older-onset women or men. These observations could help explain conflicting prior results of NIMA in RA

Ice sheets as a significant source of highly reactive nanoparticulate iron to the oceans

The Greenland and Antarctic Ice Sheets cover ~\n10% of global land surface, but are rarely considered as active components of the global iron cycle. The ocean waters around both ice sheets harbour highly productive coastal ecosystems, many of which are iron limited. Measurements of iron concentrations in subglacial runoff from a large Greenland Ice Sheet catchment reveal the potential for globally significant export of labile iron fractions to the near-coastal euphotic zone. We estimate that the flux of bioavailable iron associated with glacial runoff is 0.40–2.54?Tg per year in Greenland and 0.06–0.17?Tg per year in Antarctica. Iron fluxes are dominated by a highly reactive and potentially bioavailable nanoparticulate suspended sediment fraction, similar to that identified in Antarctic icebergs. Estimates of labile iron fluxes in meltwater are comparable with aeolian dust fluxes to the oceans surrounding Greenland and Antarctica, and are similarly expected to increase in a warming climate with enhanced melting

Walks on SPR Neighborhoods

A nearest-neighbor-interchange (NNI) walk is a sequence of unrooted phylogenetic trees, T_0, T_1, T_2,... where each consecutive pair of trees differ by a single NNI move. We give tight bounds on the length of the shortest NNI-walks that visit all trees in an subtree-prune-and-regraft (SPR) neighborhood of a given tree. For any unrooted, binary tree, T, on n leaves, the shortest walk takes {\theta}(n^2) additional steps than the number of trees in the SPR neighborhood. This answers Bryant's Second Combinatorial Conjecture from the Phylogenetics Challenges List, the Isaac Newton Institute, 2011, and the Penny Ante Problem List, 2009

Personality Measurement and Assessment in Large Panel Surveys

Personality tests are being added to large panel studies with increasing regularity, such as the Health and Retirement Study (HRS). To facilitate the inclusion and interpretation of these tests, we provide some general background on personality psychology, personality assessment, and the validity of personality tests. In this review, we provide background on definitions of personality, the strengths and weaknesses of the self-report approaches to personality testing typically used in large panel studies, and the validity of personality tests for three outcomes: genetics, income, and health. We conclude with recommendations on how to improve personality assessment in future panel studies

The Relationship of a Systemic Student Support Intervention to Academic Achievement in Urban Catholic Schools

Much of the achievement gap between rich and poor students can be attributed to out-of-school factors, yet few schools have a comprehensive, coordinated system for addressing students’ nonacademic needs. Within a group of Catholic schools located in one city, this study examines academic achievement on the Stanford Achievement Test battery in mathematics, reading, and language among 2nd through 8th grade students participating in such an intervention, and compares the results with those of similar nonparticipating students in nearby cities. Using hierarchical longitudinal growth modeling and adjusting for demographic characteristics, this study found that students in intervention schools outperformed the comparison group on average in 6th grade mathematics. Intervention students also experienced significantly higher rates of growth in achievement than the comparison group in all three subjects. The results suggest that systemic service provision models have the potential to help urban Catholic schools meet their mission of educating the whole child and serving the poorest families. Keywords Catholic education, longitudinal growth analysis, achievement gap Le lien entre une intervention systémique de soutien aux élèves et la réussite scolaire dans les écoles catholiques en milieu urbain. Une bonne partie de l\u27écart entre les résultats obtenus par les élèves riches et les pauvres peut être attribuée à des facteurs extérieurs à l\u27école, pourtant peu d\u27écoles disposent d\u27un système complet et coordonné pour résoudre les besoins extrascolaires des élèves. Cette étude, qui porte sur un groupe d\u27écoles catholiques situées dans une seule ville, examine la réussite scolaire sut la batterie de tests de réussite de Stanford en mathématiques, lecture et langage parmi des élèves de la 11eà la 3eparticipant à cette intervention et compare les résultats avec ceux d\u27élèves similaires, dans des villes voisines qui n\u27y participaient pas. À l\u27aide d\u27une modélisation longitudinale de croissance, avec un ajustement pour les caractéristiques démographiques, cette étude a trouvé que les élèves des écoles où avait lieu l\u27intervention avaient de meilleurs résultats en moyenne que le groupe de comparaison en mathématiques de classe de 6e. Les élèves bénéficiant de l\u27intervention ont aussi eu des taux de croissance plus élevés que le groupe de comparaison dans les trois matières. Ce résultat indique que des modèles de service systémique fourni aux élèves peuvent potentiellement aider les écoles catholiques urbaines à remplir leur mission d\u27éducation intégrale de l\u27enfant et rendre service aux familles pauvres. Mots-clés : éducation catholique, analyse longitudinale de croissance, écart de réussite Relación entre una intervención sistémica de apoyo al estudiante y los logros académicos en escuelas católicas urbanas La mayor parte de la brecha en los logros entre estudiantes ricos y pobres puede atribuirse a factores extraescolares, sin embargo, pocas escuelas disponen de un sistema comprensivo coordinado que aborde las necesidades no académicas de los estudiantes. Tomando un grupo de escuelas católicas ubicadas en una misma ciudad, este estudio examina los logros académicos en las pruebas de aptitud de Stanford (SAT) en matemáticas, lectura y lengua de estudiantes entre segundo y octavo curso que participan en tales intervenciones; y compara los resultados a los de estudiantes no participantes, con perfiles similares, en ciudades cercanas. Al emplear modelos de crecimiento longitudinal jerárquico y al ajustarlos a las características demográficas, el presente estudio encontró que los estudiantes de escuelas con intervención superaron la media de los resultados del grupo de comparación en 6º curso de matemáticas. Los estudiantes con intervención también experimentaron significativamente mayores tasas de crecimiento que los del grupo de comparación en las tres materias. Los resultados sugieren que los modelos que proveen servicios sistémicos disponen del potencial para ayudar a que las escuelas católicas urbanas cumplan su misión de educar al niño en su totalidad y de servir a las familias pobres. Palabras clave educación católica, análisis de crecimiento longitudinal, brecha de logro

Outcomes of Randomized Clinical Trials of Interventions to Enhance Social, Emotional, and Spiritual Components of Wisdom: A Systematic Review and Meta-analysis.

ImportanceWisdom is a neurobiological personality trait made up of specific components, including prosocial behaviors, emotional regulation, and spirituality. It is associated with greater well-being and happiness.ObjectiveTo evaluate the effectiveness of interventions to enhance individual components of wisdom.Data sourcesMEDLINE and PsycINFO databases were searched for articles published through December 31, 2018.Study eligibility criteriaRandomized clinical trials that sought to enhance a component of wisdom, used published measures to assess that component, were published in English, had a minimum sample size of 40 participants, and presented data that enabled computation of effect sizes were included in this meta-analysis.Data extraction and synthesisRandom-effect models were used to calculate pooled standardized mean differences (SMDs) for each wisdom component and random-effects meta-regression to assess heterogeneity of studies.Main outcomes and measuresImprovement in wisdom component using published measures.ResultsFifty-seven studies (N = 7096 participants) met review criteria: 29 for prosocial behaviors, 13 for emotional regulation, and 15 for spirituality. Study samples included people with psychiatric or physical illnesses and from the community. Of the studies, 27 (47%) reported significant improvement with medium to large effect sizes. Meta-analysis revealed significant pooled SMDs for prosocial behaviors (23 studies; pooled SMD, 0.43 [95% CI, 0.22-0.3]; P = .02), emotional regulation (12 studies; pooled SMD, 0.67 [95% CI, 0.21-1.12]; P = .004), and spirituality (12 studies; pooled SMD, 1.00 [95% CI, 0.41-1.60]; P = .001). Heterogeneity of studies was considerable for all wisdom components. Publication bias was present for prosocial behavior and emotional regulation studies; after adjusting for it, the pooled SMD for prosocial behavior remained significant (SMD, 0.4 [95% CI, 0.16-0.78]; P = .003). Meta-regression analysis found that effect sizes did not vary by wisdom component, although for trials on prosocial behaviors, large effect sizes were associated with older mean participant age (β, 0.08 [SE, 0.04]), and the reverse was true for spirituality trials (β, -0.13 [SE, 0.04]). For spirituality interventions, higher-quality trials had larger effect sizes (β, 4.17 [SE, 1.07]), although the reverse was true for prosocial behavior trials (β, -0.91 [SE 0.44]).Conclusions and relevanceInterventions to enhance spirituality, emotional regulation, and prosocial behaviors are effective in a proportion of people with mental or physical illnesses and from the community. The modern behavioral epidemics of loneliness, suicide, and opioid abuse point to a growing need for wisdom-enhancing interventions to promote individual and societal well-being