bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accounting for ingrowth of radioactive progeny in dose assessments: generic weighting factors for dose coefficients
Authors: van Dillen Teun , van Dijk Arjan , Kloosterman Astrid , Russo Federica , Mommaert Chantal 
Published: August 2019

Abstract
In this paper, we describe a practical and convenient method to include the contribution of the ingrowth of radioactive progeny in dose assessments of the corresponding parent nuclides. This method modifies the dose coefficients (DCs) of parent nuclides by adding weighted DCs of the corresponding daughter nuclides to them. Based on the decay kinetics of serial nuclear transformations, the progeny weighting factors, with values between 0 and 1, are derived by analysis of the time-integrated activity of each nuclide in the (branched) decay chain headed by a parent nuclide. Using the electronic, nuclear-decay database of Publication 107 of the International Commission on Radiological Protection (ICRP 2008), DC weighting factors for annual dose assessments are calculated for all daughter radionuclides in the decay chains and are tabulated in this paper. Weighting factors based on integration periods other than one year, ranging from 1 h–70 years, are also provided (see the supplementary material). With a priori established weighting factors, dose assessments become significantly simplified by considering the decay kinetics of only the parent nuclides and by applying the modified DCs. This ensures that the ingrowth of progeny is taken into account realistically. In some cases, one requires a conservative estimate of the dose, for instance when dealing with issues of the clearance of materials under regulatory control. Therefore, we adapted the weighting-factor method to derive conservative DC weighting factors for dose evaluations. These values are calculated for various integration periods and compared with those from an existing method adopted by the Euratom Article 31 Group of Experts and by the International Atomic Energy Agency. Identical progeny weighting factors are obtained for long-lived parent radionuclides, whereas for short-lived parent radionuclides, the new method can yield significantly larger values. For example, the weighting factor of I-131 (daughter of parent Te-131) increases from 0.002 to 1.0 based on an integration period of 1 year. The progeny DC weighting factors, derived based on nuclear transformations in exit-only decay chains, may not always be suitable for use in radiological dose evaluations. For instance, when environmental removal pathways are dominant, the application of these weighting factors may have its limitations. This paper, therefore, provides guidance on the proper selection and application of weighting factors.
New horizons in management of heart failure in older patients
Authors: Stefil Maria , Manzano Luis , Montero-PéRez-Barquero Manuel , Coats Andrew J S , Flather Marcus 
Published: August 2019

Abstract
Heart failure has a high prevalence in older populations, is a common and growing cause for hospital admission and carries a high risk of morbidity and mortality. Important co-morbidities in older patients with heart failure include atrial fibrillation, renal impairment, hypertension and anaemia. Diagnosing and managing heart failure in older patients are complicated due to atypical presentations, co-morbidities and a relative lack of evidence for commonly used treatments in younger patients. The growing epidemic of heart failure is also under-recognised and resourced in most health systems. Despite potential differences, we recommend that the basic approach to manage heart failure patients with an ejection fraction (EF) of &lt;40% should be the same in older and younger. These treatments need to be started at low doses and titrated slowly along with the management of co-morbidities. Older patients with EF 40–49% can be treated in a similar manner to those with &lt;40%, while the treatment of those with EF ≥50% is pragmatic in nature based on symptom control and management of co-morbidities although the evidence base for these recommendations is lacking. Overall management must be holistic and continuous based on the patient’s social circumstances and ongoing needs. Finally, there is an urgent need for more research, evidence and resources directed towards older populations with heart failure to improve their care and the quality of life.
Association of Laboratory Methods, Colonization Density, and Age With Detection of Streptococcus pneumoniae in the Nasopharynx
Authors: Sutcliffe Catherine G , Grant Lindsay R , Cloessner Emily , Klugman Keith P , Vidal Jorge E , Reid Raymond , Colelay Janene , Weatherholtz Robert C , Chochua Sopio , Jacobs Michael R , Santosham Mathuram , O’Brien Katherine L , Hammitt Laura L 
Published: August 2019

Abstract
Culture-based methods for detecting Streptococcus pneumoniae in the nasopharynx lack sensitivity. In this study, we aimed to compare the performance of culture and molecular methods in detecting pneumococcus in the nasopharynx of healthy individuals and to evaluate the associations of age and colonization density with detection. Between 2010 and 2012, nasopharyngeal specimens were collected from healthy individuals living on Navajo Nation and White Mountain Apache Tribal lands in the United States. Pneumococci were detected by means of broth-enrichment culture and autolysin-encoding gene (lytA) quantitative polymerase chain reaction (qPCR). Among 982 persons evaluated (median age, 18.7 years; 47% male), 35% were culture-positive and an additional 27% were qPCR-positive. Agreement between culture and qPCR was 70.9% but was higher among children (age &lt;18 years) (75.9%–84.4%) than among adults (age ≥18 years) (61.0%–74.6%). The mean density of colonization was lower for culture-negative samples (3.14 log10 copies/mL) than for culture-positive samples (5.02 log10 copies/mL), overall and for all age groups. The percent culture-positive increased with increasing density, exceeding 80% at densities of ≥10,000 copies/mL. Mean colonization density decreased with age. Use of qPCR improved detection of pneumococcus in the nasopharynx of healthy individuals. This finding was most notable among adults, probably because of improved detection of low-density colonization.
The role of ultraviolet reflectance and pattern in the pollination system of Hypoxis camerooniana (Hypoxidaceae)
Authors: Klomberg Yannick , Dywou Kouede Raissa , Bartoš Michael , Mertens Jan E J , Tropek Robert , Fokam Eric B , Janeček Štěpán 
Published: August 2019

Abstract
Apart from floral morphology and colours perceived by the human eye, ultraviolet (UV) reflectance acts as an important visual advertisement of numerous flowering plant species for pollinators. However, the effect of UV signalling on attracting pollinators of particular plant species is still insufficiently studied, especially in the Afrotropics. Therefore, we studied the pollination system of Hypoxis camerooniana in montane grasslands of Mount Cameroon, West/Central Africa. We focused mainly on the effects of the flowers’ UV reflectance on its visitors. We experimentally removed UV reflection from petals either completely or partially. Thereafter, flower visitors were recorded and pistils were collected post-flowering to quantify germinated pollen tubes per treatments. The most important visitors were bees, followed by flies. Due to their contacts with reproductive organs bees are considered as the primary pollinators. Visitation rates were lower when UV reflectance was completely removed, whereas the decrease of frequency on half-treated flowers did not differ significantly from control treatments. The complete removal of UV also affected bees’ landing behaviour, but not that of flies. We showed that the presence of UV reflectance is more important than UV pattern for bees visiting flowers of H. camerooniana. We hypothesize that exploiting all flowers irrespective of their pattern can be more efficient for pollinators in the open grasslands of high altitudes to spot these relatively scarce flowers by their UV reflectance. Furthermore, we highlight the necessity of both experimental and natural controls in similar studies to control for additional effects of the used UV manipulations.
Many plants advertise their flowers with UV reflectance visible to their insect visitors. By manipulating the UV reflectance and pattern of Hypoxis camerooniana in the Afromontane grasslands of Mount Cameroon, we have shown how crucial it is for the predominant visitor, bees. Both bees' preferences for flowers and their behaviour during visits are influenced by changes in UV reflectance. However, the presence of some UV signal is more important than the specific pattern. Especially in montane grasslands with higher UV irradiation, the UV floral colours are important for recognition of flowers by potential pollinators.
Linking genetic merit to sparse behavioral data: behavior and genetic effects on lamb growth in Soay sheep
Authors: Regan Charlotte E , Pemberton Josephine M , Pilkington Jill G , Smiseth Per T , Wilson Alastair J 
Published: August 2019

AbstractWild quantitative genetic studies have focused on a subset of traits (largely morphological and life history), with others, such as behaviors, receiving much less attention. This is because it is challenging to obtain sufficient data, particularly for behaviors involving interactions between individuals. Here, we explore an indirect approach for pilot investigations of the role of genetic differences in generating variation in parental care. Variation in parental genetic effects for offspring performance is expected to arise from among-parent genetic variation in parental care. Therefore, we used the animal model to predict maternal breeding values for lamb growth and used these predictions to select females for field observation, where maternal and lamb behaviors were recorded. Higher predicted maternal breeding value for lamb growth was associated with greater suckling success, but not with any other measures of suckling behavior. Though our work cannot explicitly estimate the genetic basis of the specific traits involved, it does provide a strategy for hypothesis generation and refinement that we hope could be used to justify data collection costs needed for confirmatory studies. Here, results suggest that behavioral genetic variation is involved in generating maternal genetic effects on lamb growth in Soay sheep. Though important caveats and cautions apply, our approach may extend the ability to initiate more genetic investigations of difficult-to-study behaviors and social interactions in natural populations.
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API
Authors: Desvignes Thomas , Loher Phillipe , Eilbeck Karen , Ma Jeffery , Urgese Gianvito , Fromm Bastian , Sydes Jason , Aparicio-Puerta Ernesto , Barrera Victor , Espín Roderic , Thibord Florian , Bofill-De Ros Xavier , Londin Eric , Telonis Aristeidis G , Ficarra Elisa , Friedländer Marc R , Postlethwait John H , Rigoutsos Isidore , Hackenberg Michael , Vlachos Ioannis S , Halushka Marc K , Pantano Lorena 
Published: August 2019

Abstract

Motivation
MicroRNAs (miRNAs) are small RNA molecules (∼22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods.

Results
To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification.

Availability and implementation
https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop.

Supplementary information
Supplementary data are available at Bioinformatics online.
breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data
Authors: Porubsky David , Sanders Ashley D , Taudt Aaron , Colomé-Tatché Maria , Lansdorp Peter M , Guryev Victor 
Published: August 2019

Abstract

Motivation
Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data.

Results
Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique.

Availability and implementation
R/Bioconductor package https://bioconductor.org/packages/breakpointR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Gene expression profiles of bovine genital ridges during sex determination and early differentiation of the gonads†
Authors: Planells Benjamín , Gómez-Redondo Isabel , Sánchez José María , McDonald Michael , Cánovas Ángela , Lonergan Patrick , Gutiérrez-Adán Alfonso 
Published: August 2019

AbstractMost current knowledge of sex determination in mammals has emerged from mouse and human studies. To investigate the molecular regulation of the sex determination process in cattle, we used an RNA sequencing strategy to analyze the transcriptome landscape of male and female bovine fetal gonads collected in vivo at key developmental stages: before, during, and after SRY gene activation on fetal days D35 (bipotential gonad formation), D39 (peak SRY expression), and D43 (early gonad differentiation). Differentially expressed genes (DEGs) were identified in male vs. female germinal ridges and among group genes showing similar expression profiles during the three periods. There were 143, 96, and 658 DEG between males and female fetuses at D35, D39, and D43, respectively. On D35, genes upregulated in females were enriched in translation, nuclear export, RNA localization, and mRNA splicing events, whereas those upregulated in males were enriched in cell proliferation regulation and male sex determination terms. In time-course experiments, 767 DEGs in males and 545 DEGs in females were identified between D35 vs. D39, and 3157 DEGs in males and 2008 in females were identified between D39 vs. D43. Results highlight unique aspects of sex determination in cattle, such as the expression of several Y chromosome genes (absent in mice and humans) before SRY expression and an abrupt increase in the nuclear expression of SOX10 (instead of SOX9 expression in the Sertoli cell cytoplasm as observed in mice) during male determination and early differentiation.
Comparative leaf blade anatomy and micromorphology in the systematics and phylogeny of Bambusoideae (Poaceae: Poales)
Authors: Leandro Thales D , Scatena Vera L , Clark Lynn G 
Published: August 2019

AbstractLeaf blade anatomical and micromorphological data have increasingly proved to be useful in the systematics and phylogeny of Bambusoideae. The presence of well-developed, asymmetrically strongly infolded mesophyll cells (arm cells) as seen in cross-section is regarded a synapomorphy for bamboos, whereas many well-known, widely used features for diagnosing groups remain to be formally tested in a comprehensive phylogenetic framework. In this review, we investigate the use of anatomical and micromorphological features in defining and delimiting minor and major groups in Bambusoideae. A general description of the leaf blade as seen in cross-section and surface view is provided for the subfamily, as well as features commonly found in the three currently recognized tribes (Arundinarieae, Bambuseae and Olyreae) and their subtribes. Some features, including midrib vasculature, fusoid cells and stomatal apparatus, are discussed in the light of systematic and phylogenetic perspectives, along with a clarification of terminology. Illustrations of relevant features are also provided. This review allowed us to elucidate anatomical and micromorphological features useful in defining and delimiting lineages but also to highlight some research priorities in Bambusoideae.
The bivariate distribution of amyloid-β and tau: relationship with established neurocognitive clinical syndromes
Authors: Jack Clifford R , Wiste Heather J , Botha Hugo , Weigand Stephen D , Therneau Terry M , Knopman David S , Graff-Radford Jonathan , Jones David T , Ferman Tanis J , Boeve Bradley F , Kantarci Kejal , Lowe Val J , Vemuri Prashanthi , Mielke Michelle M , Fields Julie A , Machulda Mary M , Schwarz Christopher G , Senjem Matthew L , Gunter Jeffrey L , Petersen Ronald C 
Published: August 2019

See Gordon and Tijms (doi:10.1093/brain/awz278) for a scientific commentary on this article.Jack et al. examine relationships between the bivariate distribution of β-amyloid and tau on PET and established neurocognitive clinical syndromes. Amyloidosis appears to be required for high levels of 3R/4R tau deposition. Whereas abnormal amyloid PET is compatible with normal cognition, highly abnormal tau PET is not.
Declines in Lung Function After Antiretroviral Therapy Initiation in Adults With Human Immunodeficiency Virus and Tuberculosis: A Potential Manifestation of Respiratory Immune Reconstitution Inflammatory Syndrome
Authors: Auld Sara C , Maenetje Pholo , Ravimohan Shruthi , Weissman Drew , Ncube Itai , Mlotshwa Mandla , Ratsela Nelly , Chase William , Vangu Mboyo-Di-Tamba , Wallis Robert , Churchyard Gavin , Kornfeld Hardy , Bisson Gregory P 
Published: August 2019

Abstract
End-organ impairment has received relatively little research attention as a possible manifestation of tuberculosis immune reconstitution inflammatory syndrome (TB-IRIS). In this prospective cohort study, one-half of adults with human immunodeficiency virus and pulmonary tuberculosis experienced meaningful declines in lung function on antiretroviral therapy, suggesting a role for lung function in TB-IRIS definitions.
Ceftaroline-associated Encephalopathy in Patients With Severe Renal Impairment
Authors: Martin Thomas C S , Chow Sean , Johns Scott T , Mehta Sanjay R 
Published: August 2019

Abstract
Encephalopathy complicates beta-lactam therapy, particularly with impaired renal function, though no studies have reported ceftaroline-associated encephalopathy. Among 28 patients with estimated glomerular filtration rates &lt;30 mL/min who received ≥5 days of ceftaroline, 3 developed encephalopathy. Ceftaroline, when dosed supra-therapeutically for serious infections, may be a cause of antibiotic-associated encephalopathy.
How Testing Drives Treatment in Asymptomatic Patients: Level of Pyuria Directly Predicts Probability of Antimicrobial Prescribing
Authors: Gupta Kalpana , O’Brien William , Gallegos-Salazar Jaime , Strymish Judith , Branch-Elliman Westyn 
Published: August 2019

Abstract

Background
Urinalysis is a readily available test often used for screening. Pyuria is a common finding in asymptomatic patients; however, it is unknown how often identification of pyuria in the absence of confirmatory cultures leads to antimicrobial prescribing. The objective of this study was to measure the association between pyuria and antimicrobial initiation during the perioperative period and assess harms versus benefits of treatment.

Methods
A retrospective cohort of preoperative patients within the national healthcare system during the period 1 October 2008–30 September 2013 who had a urinalysis performed during the 30-day preoperative period was created; patients with positive urine cultures were excluded. The primary exposure was pyuria on preoperative urinalysis. The primary outcome was antimicrobial initiation. Secondary outcomes included postoperative surgical site (SSI), urinary tract (UTI), and Clostridioides difficile infections. Trend and logistic regression analyses were performed.

Results
Among 41 373 patients, 3617 had pyuria. 887 (24.5%) patients with pyuria received antimicrobials versus 1918 (5.1%) patients without pyuria. As the degree of pyuria increased, the odds of receiving antimicrobials also increased linearly (low, 14.7%; moderate, 24.0%; high pyuria, 37.4%). Preoperative pyuria was associated with postoperative C. difficile infections (aOR, 1.7; 95% CI, 1.2–2.4); risk was higher in patients who received antimicrobials (aOR, 2.4; 1.7–3.4). Pyuria was not associated with SSI but was associated with increases in UTI after orthopedic and vascular procedures; this risk was not mitigated by antimicrobial therapy.

Conclusions
Urine screening during the preoperative period is a low-value intervention that increases antimicrobial exposure but does not improve postoperative outcomes.