bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dominance Can Increase Genetic Variance After a Population Bottleneck: A Synthesis of the Theoretical and Empirical Evidence
Authors: Mularo Andrew J , Bernal Ximena E , DeWoody J Andrew 
Published: February 2022

AbstractDrastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on 2 theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.
Archives of the Disappeared: Conceptualizing the Personal Collections of Families of Disappeared Persons
Authors: Bermúdez Qvortrup Natalia 
Published: February 2022

Abstract
In the search for their loved ones, the families of the disappeared create, gather, and share records. The Colombian 2016 peace agreement opened spaces for memory practices that help promote a record-keeping culture at the grassroots among families. These personal collections are private spaces of struggle for memory, resistance, and justice. This article aims to make visible this documentation process undertaken by families, by giving these collections a name—archives of the disappeared—contextualizing their creation, purposes, and uses. By focusing on the case of Colombia, I follow a general chronology of a search for the disappeared to understand who the creators are, and trace the creation, accumulation, and uses of these archives based on existing literature, testimonies and interviews with family members, family organizations and NGOs. I argue that these archives are foundational to societies that have undergone human rights violations as they eventually form the basis of much of the NGO and transitional justice documentation, and provide counter narratives that offer an insight into the search process. The concept I propose, archives of the disappeared, is a starting concept to open up reflection and engagement regarding these archives, which although written about in the literature have yet to be conceptualized separately from NGO archives, transitional justice archives or human rights archives in general.
An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes
Authors: Fernandez-Pozo Noe , Haas Fabian B , Gould Sven B , Rensing Stefan A 
Published: February 2022

Abstract
Bryophytes are useful models for the study of plant evolution, development, plant–fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools.
Clinical analysis of gender and pre-existing diabetes mellitus in patients with polymyalgia rheumatica: A retrospective study in a Japanese population
Authors: Horai Yoshiro , Otsuka Mizuna , Kawahara Chieko , Iwanaga Nozomi , Yamasaki Yusuke , Watanobe Taro , Yasui Junichi , Saishoji Yusuke , Torisu Yuichi , Mori Takahiro , Mori Hideki , Izumi Yasumori , Kawakami Atsushi 
Published: February 2022

ABSTRACT

Objective
This study clarifies the involvement of gender and pre-existing diabetes mellitus (DM) in the clinical characteristics of polymyalgia rheumatica (PMR).

Methods
The clinical records of patients diagnosed with PMR in our department between January 2011 and June 2021, especially in terms of gender and DM were retrospectively analysed.

Results
We identified 89 patients with the median age of 75.37 cases were men and 52 cases were women. Pre-existing DM was found in 21 patients (23.6%). Male PMR patients exhibited a higher complication rate of pre-existing DM and C-reactive protein (CRP) levels at diagnosis (p = .04 and p &lt; .01, respectively) than female patients, and men were more common in the patient group with pre-existing DM (p = .04). The CRP levels of male PMR patients without pre-existing DM were higher than female PMR patients without pre-existing DM.

Conclusion
Male PMR patients might have a varying pathophysiology from female patients in terms of high inflammation levels accompanied by a high prevalence rate of pre-existing DM and need a gender-specific approach.
Pregnancy-induced alterations of 1-carbon metabolism and significance for maternal nutrition requirements
Authors: Cochrane Kelsey M , Williams Brock A , Elango Rajavel , Barr Susan I , Karakochuk Crystal D 
Published: February 2022

Abstract

Objectives
The pregnancy-induced alterations in 1-carbon (1C) metabolism, effects of advancing gestation on maternal plasma concentrations of methyl nutrients, and potential implications for maternal dietary intake and infant clinical outcomes are summarized in this narrative review.

Background
1C metabolism encompasses a series of pathways where 1C units are transferred among nutrients such as B vitamins, choline, and amino acids (the methyl nutrients). Use of isotopic tracers and measuring methyl nutrients in maternal plasma and infant cord blood has advanced the understanding of 1C flux in pregnancy and kinetics of maternal-placental-fetal transfer. Methyl nutrients are supplied from maternal plasma to the placenta and fetus to support growth and 1C metabolism in these compartments.

Methods
A literature review was completed in MEDLINE and Google Scholar using search terms related to 1C metabolism, methyl nutrients, and nutrition requirements in pregnancy. English-language articles were reviewed in which 1C metabolism in pregnancy, maternal-placental-fetal transfer of methyl nutrients, and determinants of maternal plasma concentrations of methyl nutrients among healthy pregnant women were assessed.

Discussion
Adaptations in 1C metabolism occur throughout a healthy pregnancy to support this unique period of accelerated growth. Studies report similar temporal changes in plasma concentrations of many methyl nutrients, including B vitamins, choline, betaine, methionine, and cysteine, among healthy pregnant women from diverse geographic regions. Other key findings discussed in this review include an apparent high degree of B vitamin transfer to the placenta and fetus, influence of choline supplementation on 1C flux and possible benefit of supplementation for infant cognitive development, and that glycine may be conditionally essential in pregnancy.

Conclusion
Understanding the flux of 1C metabolism in pregnancy and methyl nutrient transfer from maternal plasma is needed to establish appropriate plasma references ranges and, ultimately, dietary recommendations that aim to prevent deficiency and associated adverse health outcomes for mother and baby.
Integrated transcriptome and amino acid profile analyses reveal novel insights into differential accumulation of theanine in green and yellow tea cultivars
Authors: Xu Yan-Xia , Yang Long , Lei Yun-Sheng , Ju Rui-Na , Miao Shu-Gang , Jin Song-Heng 
Published: February 2022

Abstract
Tea cultivars with yellow- or white-leaf variations have a high economic value due to their high amino acid (especially theanine) concentration. However, the dynamic changes of amino acid components (especially theanine) and related gene expression during new shoot development in these cultivars are still unclear. In this study, 264 tea samples from four representative varieties picked during the harvest period in spring were analyzed for their amino acid profiles. The dynamic change rules of ethylamine and 19 amino acids were summarized in normal green and yellow cultivars during new shoot development. Interestingly, the theanine concentration in the yellow cultivar was significantly higher than that in the green cultivar, and increased gradually as the leaves matured until they reached a maximum in the one bud and three leaves stage. The amino acid concentration in the leaves of the yellow cultivar increased significantly with leaf position, which was generally in contrast to the normal green cultivar. Transcriptome and correlation analyses revealed that CsGS1, CsPDX2, CsGGP5, CsHEMA3 and CsCLH4 might be the key genes potentially responsible for the differential accumulation of theanine in green and yellow tea cultivars. These results provide further information for the utilization and improvement of tea plants.
Diversity and systematics ofTrichomycterusValenciennes 1832 (Siluriformes: Trichomycteridae) in the Rio Doce Basin: iterating DNA, phylogeny and classical taxonomy
Authors: Reis Vinícius , de Pinna Mário 
Published: February 2022

AbstractThe catfish genus Trichomycterus is a recognized taxonomic bottleneck in Neotropical ichthyology. The hitherto poorly-known diversity of Trichomycterus in the Rio Doce Basin, Brazil, is here investigated using an iterative approach based on morphology and cytochrome oxidase subunit I (COI) sequence data. Specimens from the entire Rio Doce Drainage and adjacent basins are analysed, including from type localities. Iteration of different sources of data, dense sampling and taxonomic representation, plus information on relevant type specimens allows a clear view of the diversity, relationships and nomenclature of Trichomycterus in the Rio Doce Basin. Results indicate the presence of at least 14 species in the basin, seven of which are new. A lectotype is designated for Trichomycterus immaculatus and the type locality is accordingly restricted to the Rio São Mateus, a satellite basin north of the Rio Doce. Geographic distributions are mapped for all recognized species. The wide distributions of some species (e.g. Trichomycterus alternatus, T. immaculatus) are explained against information on geomorphological processes and comparative information on their biology. A Bayesian phylogenetic analysis shows that a large portion of the assemblage of Trichomycterus in the Rio Doce forms a clade, a pattern relevant to understanding the evolution of the genus in eastern South America.
Oxathiapiprolin Alone or Mixed with Metalaxyl Seed Treatment for Management of Soybean Seedling Diseases Caused by Species of Phytophthora, Phytopythium, and Pythium
Authors: Vargas Amilcar , Paul Pierce A. , Winger Jonell , Balk Christine Susan , Eyre Meredith , Clevinger Bruce , Noggle Sarah , Dorrance Anne E. 
Published: February 2022

Species of Phytophthora, Phytopythium, and Pythium affect soybean seed and seedlings each year, primarily through reduced plant populations and yield. Oxathiapiprolin is effective at managing several foliar diseases caused by some oomycetes. The objectives of these studies were to evaluate oxathiapiprolin in a discriminatory dose assay in vitro; evaluate oxathiapiprolin as a soybean seed treatment on a moderately susceptible cultivar in 10 environments; compare the impact of seed treatment on plant populations and yields in environments with low and high precipitation; and compare a seed treatment mixture on cultivars with different levels of resistance in four environments. There was no reduction in growth in vitro among 13 species of Pythium at 0.1 µg ml−1. Soybean seed treated with the base fungicide plus oxathiapiprolin (12 and 24 µg a.i. seed−1) alone, oxathiapiprolin (12 µg a.i. seed−1) plus mefenoxam (6 µg a.i. seed−1), or oxathiapiprolin (24 µg a.i. seed−1) plus ethaboxam (12.1 µg a.i. seed−1) had greater yields in environments that received ≥50 mm of precipitation within 14 days after planting compared with those that received less. Early plant population and yield were significantly higher for seed treated with oxathiapiprolin (24 µg a.i. seed−1) + metalaxyl (13.2 µg a.i. seed−1) compared with nontreated for six of seven cultivars in at least one of four environments. Oxathiapiprolin combined with another Oomycota fungicide applied to seed has the potential to be used to protect soybean plant establishment and yield in regions prone to poor drainage after high levels of precipitation.
Adverse Events Associated With 10-kHz Dorsal Column Spinal Cord Stimulation
Authors: D’Souza Ryan S. , Olatoye Oludare O. , Butler Casey S. , Barman Ross A. , Ashmore Zachary M. , Hagedorn Jonathan M. 
Published: February 2022

Background:
High-frequency (10-kHz) spinal cord stimulation (SCS) continues to be an emerging therapy in chronic pain management. The same complications that plagued earlier SCS systems may affect newer stimulation technologies, although there is limited data on the type of complications and surgical management of these complications.

Objective:
The aim of this study was to systematically examine real-world complications associated with 10-kHz SCS reported on the Manufacturer and User Facility Device Experience (MAUDE) database.

Materials and Methods:
The MAUDE database was queried for entries reported between January 1, 2016 and December 31, 2020. Entries were classified into procedural complications, device-related complications, patient complaints, surgically managed complications, serious adverse events, and/or other complications. Primary outcomes included type and frequency of complications, and surgical management of complications.

Results:
A total of 1651 entries were analyzed. Most entries were categorized as procedural complications (72.6%), followed by serious adverse events (10.5%), device-related complications (10.5%), and patient complaints (9.9%). Most complications were managed surgically with explant (50.9%) rather than revision (5.0%) or incision/drainage (6.6%). Of procedural complications, the most common entries included non-neuraxial infection (52.9%), new neurological symptoms (14.7%), and dural puncture (9.5%). Of device-related complications, the most common entries included lead damage (41.6%), erosion (18.5%), and difficult insertion (11.5%).

Conclusion:
This retrospective 5-year analysis of complications from10-kHz SCS provides a real-world assessment of safety data unique for this stimulation modality. This analysis may help inform future clinical decisions, lead to device enhancement and optimization, and improve mitigation of risks to provide safe and efficacious use of 10-kHz SCS.
Lung Ultrasound and Electrical Impedance Tomography During Ventilator-Induced Lung Injury*
Authors: Steinberg Irene , Pasticci Iacopo , Busana Mattia , Costamagna Andrea , Hahn Günter , Gattarello Simone , Palermo Paola , Lazzari Stefano , Romitti Federica , Herrmann Peter , Moerer Onnen , Saager Leif , Meissner Konrad , Quintel Michael , Gattinoni Luciano 
Published: February 2022

OBJECTIVES:
Lung damage during mechanical ventilation involves lung volume and alveolar water content, and lung ultrasound (LUS) and electrical impedance tomography changes are related to these variables. We investigated whether these techniques may detect any signal modification during the development of ventilator-induced lung injury (VILI).

DESIGN:
Experimental animal study.

SETTING:
Experimental Department of a University Hospital.

Subjects:
Forty-two female pigs (24.2 ± 2.0 kg).

INTERVENTIONS:
The animals were randomized into three groups (n = 14): high tidal volume (TV) (mean TV, 803.0 ± 121.7 mL), high respiratory rate (RR) (mean RR, 40.3 ± 1.1 beats/min), and high positive-end-expiratory pressure (PEEP) (mean PEEP, 24.0 ± 1.1 cm H2O). The study lasted 48 hours. At baseline and at 30 minutes, and subsequently every 6 hours, we recorded extravascular lung water, end-expiratory lung volume, lung strain, respiratory mechanics, hemodynamics, and gas exchange. At the same time-point, end-expiratory impedance was recorded relatively to the baseline. LUS was assessed every 12 hours in 12 fields, each scoring from 0 (presence of A-lines) to 3 (consolidation).

MEASUREMENTS AND MAIN RESULTS:
In a multiple regression model, the ratio between extravascular lung water and end-expiratory lung volume was significantly associated with the LUS total score (p < 0.002; adjusted R
2, 0.21). The variables independently associated with the end-expiratory difference in lung impedance were lung strain (p < 0.001; adjusted R
2, 0.18) and extravascular lung water (p < 0.001; adjusted R
2, 0.11).

CONCLUSIONS:
Data suggest as follows. First, what determines the LUS score is the ratio between water and gas and not water alone. Therefore, caution is needed when an improvement of LUS score follows a variation of the lung gas content, as after a PEEP increase. Second, what determines the end-expiratory difference in lung impedance is the strain level that may disrupt the intercellular junction, therefore altering lung impedance. In addition, the increase in extravascular lung water during VILI development contributed to the observed decrease in impedance.
Increased mortality with intensive control in patients with higher baseline SBP and lower Framingham risk
Authors: Pan Heng-Yu , Lin Hung-Ju , Chen Wen-Jone , Wang Tzung-Dau 
Published: February 2022

Objective:
In the Systolic Blood Pressure Intervention Trial (SPRINT), the relative reduction in primary outcome with intensive blood pressure (BP) control was numerically smallest in the highest baseline SBP tertile. In this post hoc analysis of SPRINT, the goal was to explore whether the effects of intensive BP treatment varied among patients with different baseline SBP and cardiovascular risks.

Methods:
Patient-level data from 9361 randomized participants in SPRINT were used. Heterogeneity between treatment and patient characteristics were examined stratified by different baseline SBP levels. Cumulative incidences of primary outcome and all-cause death were compared between treatment groups for patients with baseline SBP at least 160 mmHg and lower Framingham risk.

Results:
For participants with a baseline SBP of at least 160 mmHg, intensive treatment was associated with a higher rate of all-cause death as compared with standard treatment (1.86 vs. 1.62% per year). After adjustment for age and sex, intensive treatment was associated with significantly increased all-cause death compared with standard treatment [hazard ratio (95% CI) for intensive group: 3.12 (1.00–9.69); P = 0.049] in participants with an SBP of at least 160 mmHg and a Framingham risk score of 31.3% or less (average of median and geometric mean). Patient outcomes were otherwise similar regarding age, use of antihypertensive therapy, cardiovascular disease or chronic kidney disease.

Conclusion:
Among the SPRINT participants with a baseline SBP of at least 160 mmHg and a lower Framingham risk score, targeting an SBP of less than 120mmHg compared with less than 140mmHg resulted in a significantly higher rate of all-cause death.
Gut microbiome and retinal diseases: an updated review
Authors: Nadeem Urooba , Boachie-Mensah Michael , Zhang Jason , Skondra Dimitra 
Published: February 2022

Purpose of review
The gut microbiome, trillions of microorganisms residing in our digestive tract, is now believed to play a significant role in retinal diseases. Breakthroughs in computational biology and specialized animal models have allowed researchers not only to characterize microbes associated with retinal diseases, but also to provide early insights into the function of the microbiome in relation to biological processes in the retinal microenvironment. This review aims to provide an update on recent advances in the current knowledge on the relationship between the gut microbiome and retinal disorders.

Recent findings
Recent work demonstrates distinct gut microbial compositions associated with retinal diseases such as agerelated macular degeneration and retinopathy of prematurity. Currently, it is believed that gut dysbiosis leads to increased gut permeability, elevated circulation of bacterial products, microbial metabolites and inflammatory mediators that result in immune dysregulation at distant anatomic sites including the retina.

Summary
Emerging evidence for the gut-retina axis can elucidate previously unknown pathways involved in retinal diseases and also presents an exciting potential therapeutic avenue. Further preclinical and clinical studies are necessary to establish causation and delineate the precise relationship of the gut microbiome with retinal disorders.
Early Results of Irrigating Goniectomy With TrabEx+: A Novel Device for the Treatment of Open-angle Glaucoma
Authors: Gosling Daniel , Wang Haoyu , Auger Graham 
Published: February 2022

Précis:
Irrigating goniectomy with the TrabEx+ device can lower intraocular pressure (IOP) in patients with glaucoma, as a standalone procedure or combined with cataract surgery.

Purpose:
The aim was to describe the efficacy and safety of irrigating goniectomy performed using the TrabEx+ device, either as a standalone procedure or combined with cataract surgery, in eyes with medically treated open-angle glaucoma.

Methods:
A retrospective case series of eyes treated by a single surgeon at a single UK teaching hospital. Data was collected at follow-up visits at 1 week, 3, 6, 12, 18, and 24 months postoperatively. Primary outcomes included IOP and glaucoma medication reduction after surgery. Proportion of eyes achieving >20% IOP reduction, IOP <21 mm Hg, and no reoperation were classified as surgical success.

Results:
Seventy-three consecutive eyes of 64 patients (mean age 68.4±13.7 y) were enrolled. 62% were treated as combined procedures with cataract surgery. Overall, mean IOP decreased from 31.3±7.3 to 20.9±10.4 mm Hg at the latest follow-up (34% reduction) (P<0.001) at the latest follow-up (16.1±10.3 mo) with mean preoperative medications decreased from 2.9±1.2 to 1.9±1.3 (P<0.001). 73% met the definition of success at latest follow-up. Postoperative complications were recorded including hyphaema (17%), uveitis (3%), hypotony (1%), and persistent vitreous hemorrhage (1%). Eighteen percent required reoperation because of treatment failure.

Conclusion:
TrabEx+ appears to be effective in lowering IOP and medication with or without cataract surgery. However, long-term safety and efficacy will be better understood in a prospective study with longer follow-up.