Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Spectroscopic study of plasma nitrocarburizing processes with an industrial-scale carbon active screen

The active screen plasma nitrocarburizing technology is an improvement of conventional plasma nitrocarburizing by providing a homogeneous temperature distribution within the workload and reducing soot formation. In this study, an industrial-scale active screen (AS) made of carbon-fibre-reinforced carbon serves as the cathode as well as the carbon source for the plasma-chemical processes taking place. The pulsed dc discharge was maintained at a few mbar of pressure while simultaneously being fed with a mixed gas flow of hydrogen and nitrogen ranging from 10 to 100 slh. Using in situ infrared laser absorption spectroscopy with lead salt tuneable diode lasers and external-cavity quantum cascade lasers, the temperatures and concentrations of HCN, NH3, CH4, C2H2, and CO have been monitored as a function of pressure and total gas flow. To simulate industrial treatment conditions the temperature of the sample workload in the centre of the reactor volume was kept at 773 K by varying the plasma power at the AS between 6 and 8.5 kW. The resulting spectroscopically measured temperatures in the plasma agreed well with this value. Concentrations of the various species ranged from 6 × 1013 to 1 × 1016 cm−3 with HCN being the most abundant species

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

УРОЖАЙНОСТЬ САЛАТНОЙ ЛИНИИ ПРИ ИСПОЛЬЗОВАНИИ СВЕТОДИОДНЫХ СВЕТИЛЬНИКОВ В ЗИМНИХ ТЕПЛИЦАХ НА CЕВЕРЕ

The lettuce (Lactuca sativa L.) is widely known and favorite vegetable crop among people. In Europe the main production of lettuce is performed on protected ground with application of  artificial  light  sources. The artificially-lighted  culture  of salad became very actually acquired in the north. Previously, on the basis of multi-year studies on yield registration and experiments with different regimes of lighting we have defined the appropriate parameters of supplementary lighting for lettuce with sodium high-pressure lamps that provided the production in different seasons per year. The aim was to study the accumulation of biomass and yield quality in lettuce ‘Aphytsion’ being grown in winter rotation under light-emitting diodes lamps. The accumulation of biomass and yield quality was studied in ‘Aphytsion’,  grown in winter rotation under lightemitting diodes lamps ECOLED-BIO-112-185WD120 UniversaLED (ООО ‘GK’  ‘CET’), Perm, in  industrial greenhouse OOO ‘Prigorodniy’  at Syktyvkar city. The commodity  output  was obtained  for  two  cycle  of  cultivation, November-December  and  December-January.  Yield  of foliage biomass was 2.4 kg/m2 with flow density PAR (Photosynthetically active radiation) about 90 μmole quantum/m2  s. at 20 W/m2 with total light energy 54 MJ/m2  supplied to plants from LED lamps. The plants produced about 0.5 g. of dry weight calculated on one mole of spent light energy. Energy efficiency of PAR was 3% that corresponded with data observed earlier with sodium high-pressure lamps. The conclusion was made about the suitableness of this type of light-emitting diode lamps for lettuce cultivation in winter rotation in first photic zone. It was recommended to increase duration of supplemental lighting up to 22-24 hours in December and up to 20-22 hours in January to improve the productivity and biological value of plant output. It enables to raise RAP income in plants by 35 %, on average for one cycle of cultivation.Исследовали  накопление биомассы и качество урожая листового салата сорта Афицион,  культивируемого в зимнем  обороте под  светодиодными светильниками «ECOLED-BIO-112-185W-D120  UniversaLED» (ООО  «ГК «СЭТ», г.  Пермь)  в  производственной теплице ООО «Пригородный»  (г. Сыктывкар). В двух циклах выращивания (ноябрь-декабрь и декабрьянварь) получена товарная продукция. Урожайность надземной биомассы составила  2.4  кг/м2   при  плотности  потока ФАР  около  90 мкмоль квантов/м2 с (20 Вт/м2) и суммарном поступлении к растениям 54 МДж/м2   световой энергии от  LED-светильников. В  расчете на  моль  потраченной световой энергии  растения синтезировали около  0.5  г  сухой массы. КПД ФАР составил 3%, что сопоставимо с данными, полученными ранее с использованием натриевых ламп высокого давления (ДНАЗ). Сделано заключение о пригодности данного типа  светодиодных светильников для культивирования  салата в зимнем обороте в условиях первой световой зоны. Для повышения продуктивности и биологической ценности продукции рекомендовано  увеличить продолжительности  досвечивания  в декабре до 22-24 ч, в январе – до 20-22 ч, что позволит повысить поступление ФАР к растениям за цикл выращивания в среднем на 35%

Recommendations for measuring whisker movements and locomotion in mice with sensory, motor and cognitive deficits.

BACKGROUND: Previous studies have measured whisker movements and locomotion to characterise mouse models of neurodegenerative disease. However, these studies have always been completed in isolation, and do not involve standardized procedures for comparisons across multiple mouse models and background strains. NEW METHOD: We present a standard method for conducting whisker movement and locomotion studies, by carrying out qualitative scoring and quantitative measurement of whisker movements from high-speed video footage of mouse models of Amyotrophic Lateral Sclerosis, Huntington's disease, Parkinson's disease, Alzheimer's disease, Cerebellar Ataxia, Somatosensory Cortex Development and Ischemic stroke. RESULTS: Sex, background strain, source breeder and genotype all affected whisker movements. All mouse models, apart from Parkinson's disease, revealed differences in whisker movements during locomotion. R6/2 CAG250 Huntington's disease mice had the strongest behavioural phenotype. Robo3R3-5-CKO and RIM-DKOSert mouse models have abnormal somatosensory cortex development and revealed significant changes in whisker movements during object exploration. COMPARISON WITH EXISTING METHOD(S): Our results have good agreement with past studies, which indicates the robustness and reliability of measuring whisking. We recommend that differences in whisker movements of mice with motor deficits can be captured in open field arenas, but that mice with impairments to sensory or cognitive functioning should also be filmed investigating objects. Scoring clips qualitatively before tracking will help to structure later analyses. CONCLUSIONS: Studying whisker movements provides a quantitative measure of sensing, motor control and exploration. However, the effect of background strain, sex and age on whisker movements needs to be better understood

Standards of Care for the Health of Transgender and Gender Diverse People, Version 8

Background: Transgender healthcare is a rapidly evolving interdisciplinary field. In the last decade, there has been an unprecedented increase in the number and visibility of transgender and gender diverse (TGD) people seeking support and gender-affirming medical treatment in parallel with a significant rise in the scientific literature in this area. The World Professional Association for Transgender Health (WPATH) is an international, multidisciplinary, professional association whose mission is to promote evidence-based care, education, research, public policy, and respect in transgender health. One of the main functions of WPATH is to promote the highest standards of health care for TGD people through the Standards of Care (SOC). The SOC was initially developed in 1979 and the last version (SOC-7) was published in 2012. In view of the increasing scientific evidence, WPATH commissioned a new version of the Standards of Care, the SOC-8. Aim: The overall goal of SOC-8 is to provide health care professionals (HCPs) with clinical guidance to assist TGD people in accessing safe and effective pathways to achieving lasting personal comfort with their gendered selves with the aim of optimizing their overall physical health, psychological well-being, and self-fulfillment. Methods: The SOC-8 is based on the best available science and expert professional consensus in transgender health. International professionals and stakeholders were selected to serve on the SOC-8 committee. Recommendation statements were developed based on data derived from independent systematic literature reviews, where available, background reviews and expert opinions. Grading of recommendations was based on the available evidence supporting interventions, a discussion of risks and harms, as well as the feasibility and acceptability within different contexts and country settings. Results: A total of 18 chapters were developed as part of the SOC-8. They contain recommendations for health care professionals who provide care and treatment for TGD people. Each of the recommendations is followed by explanatory text with relevant references. General areas related to transgender health are covered in the chapters Terminology, Global Applicability, Population Estimates, and Education. The chapters developed for the diverse population of TGD people include Assessment of Adults, Adolescents, Children, Nonbinary, Eunuchs, and Intersex Individuals, and people living in Institutional Environments. Finally, the chapters related to gender-affirming treatment are Hormone Therapy, Surgery and Postoperative Care, Voice and Communication, Primary Care, Reproductive Health, Sexual Health, and Mental Health. Conclusions: The SOC-8 guidelines are intended to be flexible to meet the diverse health care needs of TGD people globally. While adaptable, they offer standards for promoting optimal health care and guidance for the treatment of people experiencing gender incongruence. As in all previous versions of the SOC, the criteria set forth in this document for gender-affirming medical interventions are clinical guidelines; individual health care professionals and programs may modify these in consultation with the TGD person

TRY plant trait database - enhanced coverage and open access

This article has 730 authors, of which I have only listed the lead author and myself as a representative of University of HelsinkiPlant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.Peer reviewe

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives