bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unravelling theHabenaria repens(Orchidaceae) complex in Brazil: a biosystematic and molecular phylogenetic approach
Authors: Lau Bruna Ladeira , Batista João Aguiar Nogueira , Massensini Junior Antônio , Whitten W Mark , Borba Eduardo Leite 
Published: February 2021

AbstractHabenaria repens (Orchidaceae) represents a species complex distributed from the southern USA to northern Argentina, including several morphological variants, here referred to as morphotypes. To investigate and clarify the morphological and genetic relationships between these morphotypes and resolve the taxonomy of the complex, we applied a biosystematic multi-population approach using molecular phylogenetic, morphometric and population genetics analyses in the group. We sampled 31 (phylogenetic analyses) and 20 (morphometric and microsatellite analyses) populations of Habenaria aranifera and H. repens from Brazil and the USA, including six morphotypes of H. repens. Bayesian and maximum parsimony phylogenetic analyses of nuclear ribosomal (ITS and ETS) and plastid (matK, trnK and rps16-trnK) markers revealed that the complex is polyphyletic, subdivided into three distantly related clades. Population genetic analyses using microsatellites showed a remarkably similar structure to the phylogenetic analyses, but both were different from the morphometric analyses of floral characters, indicating cases of diversification and convergence, probably due to pollination processes. Habenaria aranifera is embedded in a paraphyletic and polymorphic H. repens with a broad geographical distribution and other attributes of an ochlospecies, probably constituting a progenitor–derivative pair. Our results support the recognition of H. aranifera, H. repens and three or four new species.
Medial septal GABAergic neurons reduce seizure duration upon optogenetic closed-loop stimulation
Authors: Hristova Katerina , Martinez-Gonzalez Cristina , Watson Thomas C , Codadu Neela K , Hashemi Kevan , Kind Peter C , Nolan Matthew F , Gonzalez-Sulser Alfredo 
Published: February 2021

Abstract
Seizures can emerge from multiple or large foci in temporal lobe epilepsy, complicating focally targeted strategies such as surgical resection or the modulation of the activity of specific hippocampal neuronal populations through genetic or optogenetic techniques. Here, we evaluate a strategy in which optogenetic activation of medial septal GABAergic neurons, which provide extensive projections throughout the hippocampus, is used to control seizures. We utilized the chronic intrahippocampal kainate mouse model of temporal lobe epilepsy, which results in spontaneous seizures and as is often the case in human patients, presents with hippocampal sclerosis. Medial septal GABAergic neuron populations were immunohistochemically labelled and were not reduced in epileptic conditions. Genetic labelling with mRuby of medial septal GABAergic neuron synaptic puncta and imaging across the rostral to caudal extent of the hippocampus, also indicated an unchanged number of putative synapses in epilepsy. Furthermore, optogenetic stimulation of medial septal GABAergic neurons consistently modulated oscillations across multiple hippocampal locations in control and epileptic conditions. Finally, wireless optogenetic stimulation of medial septal GABAergic neurons, upon electrographic detection of spontaneous hippocampal seizures, resulted in reduced seizure durations. We propose medial septal GABAergic neurons as a novel target for optogenetic control of seizures in temporal lobe epilepsy.
Preparative Isolation and Purification of Calycosin and Formononetin from Astragali Radix using Hydrolytic Extraction Combined with High Speed Countercurrent Chromatography
Authors: Pan Conglei , Wang Hao , Shan Hu , Lü Haitao 
Published: February 2021

Abstract
Calycosin and formononetin were efficiently extracted from Astragali Radix and purified by high-speed countercurrent chromatography. Calycosin and formononetin could be hydrolyzed from calycosin-7-glucoside and ononin, respectively. The best extraction conditions were realized by single factor and orthogonal experiments, which were 100% ethanol, 2.5 mol/L hydrochloric acid, 1:40 ratio of solid to liquid, extracted 2 h and one time. The two-phase solvent system of n-hexane-ethyl acetate-ethanol-water (3:5:3:5, v/v) was selected for the purification of calycosin, and 1.3 mg calycosin (the purity was 95.8% and the recovery was 85.9%) was obtained from 264.9-mg crude extraction. The two-phase solvent system of n-hexane-ethyl acetate-ethanol-water (4:5:4:5, v/v) was selected for the purification of formononetin, and 2.0 mg formononetin (the purity was 98.9% and the recovery was 84.4%) was obtained from 248.9-mg crude extraction. Their structures were identified by HPLC, melting points, UV, FTIR, ESI-MS, 1H NMR and 13C NMR spectrum. According to the antioxidant activity assay, the scavenging abilities of calycosin to 1,1-diphenyl-2-picrylhydrazyl and hydroxyl free radicals (·OH) were stronger. The scavenging effect of formononetin was not demonstrated.
Aspergillus Polymerase Chain Reaction—An Update on Technical Recommendations, Clinical Applications, and Justification for Inclusion in the Second Revision of the EORTC/MSGERC Definitions of Invasive Fungal Disease
Authors: White P Lewis , Bretagne Stephane , Caliendo Angela M , Loeffler Juergen , Patterson Thomas F , Slavin Monica , Wingard John R 
Published: February 2021

Abstract
Aspergillus polymerase chain reaction testing of blood and respiratory samples has recently been included in the second revision of the EORTC/MSGERC definitions for classifying invasive fungal disease. This is a result of considerable efforts to standardize methodology, the availability of commercial assays and external quality control programs, and additional clinical validation. This supporting article provides both clinical and technical justifications for its inclusion while also summarizing recent advances and likely future developments in the molecular diagnosis of invasive aspergillosis.
Assessment of the Role of 1,3-β-d-Glucan Testing for the Diagnosis of Invasive Fungal Infections in Adults
Authors: Lamoth F , Akan H , Andes D , Cruciani M , Marchetti O , Ostrosky-Zeichner L , Racil Z , Clancy C J 
Published: February 2021

Abstract
Detection of 1,3-β-d-glucan (BDG) in serum has been evaluated for its inclusion as a mycological criterion of invasive fungal infections (IFI) according to EORTC and Mycoses Study Group (MSG) definitions. BDG testing may be useful for the diagnosis of both invasive aspergillosis and invasive candidiasis, when interpreted in conjunction with other clinical/radiological signs and microbiological markers of IFI. However, its performance and utility vary according to patient population (hematologic cancer patients, solid-organ transplant recipients, intensive care unit patients) and pretest likelihood of IFI. The objectives of this article are to provide a systematic review of the performance of BDG testing and to assess recommendations for its use and interpretation in different clinical settings.
Understanding metrics of stress in the context of invasion history: the case of the brown treesnake (Boiga irregularis)
Authors: Claunch Natalie , Moore Ignacio , Waye Heather , Schoenle Laura , Oakey Samantha J , Reed Robert N , Romagosa Christina 
Published: February 2021

Abstract
Invasive species can exert rapid depletion of resources after introduction and, in turn, affect their own population density. Additionally, management actions can have direct and indirect effects on demography. Physiological variables can predict demographic change but are often restricted to snapshots-in-time and delayed confirmation of changes in population density reduces their utility. To evaluate the relationships between physiology and demography, we assessed metrics of individual and demographic stress (baseline and 1-h corticosterone (CORT), body condition and bacterial killing ability) in the invasive snake Boiga irregularis on Guam collected in intervals of 10–15 years. We also assessed potential discrepancies between different methods of measuring hormones [radioimmunoassay (RIA) versus enzyme immunoassay (EIA)]. The magnitude of difference between RIA and EIA was negligible and did not change gross interpretation of our results. We found that body condition was higher in recent samples (2003 and 2018) versus older (1992–93) samples. We found corresponding differences in baseline CORT, with higher baseline CORT in older, poorer body condition samples. Hormonal response to acute stress was higher in 2018 relative to 2003. We also found a weak relationship between circulating CORT and bacterial killing ability among 2018 samples, but the biological significance of the relationship is not clear. In an effort to develop hypotheses for future investigation of the links between physiology and demography in this and other systems, we discuss how the changes in CORT and body condition may reflect changes in population dynamics, resource availability or management pressure. Ultimately, we advocate for the synchronization of physiology and management studies to advance the field of applied conservation physiology.
Endpoints for Perianal Crohn’s Disease Trials: Past, Present and Future
Authors: Caron Bénédicte , D’Amico Ferdinando , Danese Silvio , Peyrin-Biroulet Laurent 
Published: February 2021

Abstract

Background and Aims
Since the 1980s, many studies have evaluated the efficacy of therapies to improve the outcomes of patients with perianal Crohn’s disease. We performed a systematic review to describe the evolution of endpoints in perianal fistulizing Crohn’s disease. Efficacy outcomes, definitions and measurement tools were assessed.

Methods
Electronic databases were searched up to November 1, 2020. All published randomized placebo-controlled trials enrolling patients with perianal fistula and Crohn’s disease were eligible for inclusion. Ongoing randomized clinical trials were also described.

Results
Nineteen randomized controlled trials were included. Clinical efficacy endpoints were reported in all trials. Clinical response was the most frequent primary endpoint [6/19 studies, 31.6%], followed by clinical remission in four studies [21%]. Clinical response was defined as closure of at least 50% of fistulas, while remission was defined as closure of all fistulas. A combined clinical and radiological primary endpoint was used to assess fistula healing in four studies [21%]. The Perianal Disease Activity Index was a primary endpoint in only one study [5.5%]. In addition, eight ongoing controlled trials were identified. Combined clinical and radiological remission was the most frequent primary endpoint in these studies [4/8, 50%].

Conclusion
In this systematic review, significant changes in outcomes used in randomized clinical trials of perianal Crohn’s disease were observed. Radiological endpoints are increasingly used in perianal fistulizing Crohn’s disease trials.
Between a hygiene rock and a hygienic hard place
Authors: Parker William , Sarafian Joshua T , Broverman Sherryl A , Laman Jon D 
Published: February 2021

Abstract
Suboptimal understanding of concepts related to hygiene by the general public, clinicians and researchers is a persistent problem in health and medicine. Although hygiene is necessary to slow or prevent deadly pandemics of infectious disease such as coronavirus disease 2019 (COVID-19), hygiene can have unwanted effects. In particular, some aspects of hygiene cause a loss of biodiversity from the human body, characterized by the almost complete removal of intestinal worms (helminths) and protists. Research spanning more than half a century documents that this loss of biodiversity results in an increased propensity for autoimmune disease, allergic disorders, probably neuropsychiatric problems and adverse reactions to infectious agents. The differences in immune function between communities with and communities without helminths have become so pronounced that the reduced lethality of severe acute respiratory syndrome coronavirus 2 in low-income countries compared to high-income countries was predicted early in the COVID-19 pandemic. This prediction, based on the maladaptive immune responses observed in many cases of COVID-19 in high-income countries, is now supported by emerging data from low-income countries. Herein, hygiene is subdivided into components involving personal choice versus components instituted by community wide systems such as sewage treatment facilities and water treatment plants. The different effects of personal hygiene and systems hygiene are described, and appropriate measures to alleviate the adverse effects of hygiene without losing the benefits of hygiene are discussed. Finally, text boxes are provided to function as stand-alone, public-domain handouts with the goal of informing the public about hygiene and suggesting solutions for biomedical researchers and policy makers.
Lay Summary: Hygiene related to sewer systems and other technology can have adverse effects on immune function, and is distinct from personal hygiene practices such as hand washing and social distancing. Dealing with the drawbacks of hygiene must be undertaken without compromising the protection from infectious disease imposed by hygiene.
Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages
Authors: Fontaine Samantha S , Mineo Patrick M , Kohl Kevin D 
Published: February 2021

ABSTRACT
Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each of the newt's three physiologically distinct developmental stages to determine if each hosted a unique community, or if the two stages which share an aquatic habitat (larvae and adults) harbored more similar communities than those of the third stage, the terrestrial juvenile eft. Additionally, we assessed how the contribution of selective processes to gut microbial assembly changed through development. We found that structurally, each life stage harbored a distinct community, which may be attributable to host factors. Further, across development, we found that community assembly processes shifted from a predominance of neutral to selective forces. However, habitat may also be important in determining community membership and diversity due the uniqueness of eft communities based on these metrics. Our results are similar to those in other vertebrate taxa, suggesting that gut microbiota assembly processes may be conserved across diverse lineages.
Modeling Effects of Overstory Density and Competing Vegetation on Tree Height Growth
Authors: Salas Christian , Stage Albert R. , Robinson Andrew P. 
Published: February 2021

Abstract
We developed and evaluated an individual-tree height growth model for Douglas-fir [Pseudotsuga menziesii (Mirbel) Franco] in the Inland Northwest United States. The model predicts growth for all tree sizes continuously, rather than requiring a transition between independent models for juvenile and mature growth phases. The model predicts the effects of overstory and understory vegetative competition on height growth. Our model requires attained height rather than tree age as a predictor variable, thereby avoiding the problems of site index. Site effects are introduced as a function of ecological habitat type, elevation, aspect, and slope. We used six data sets totaling 3,785 trees in 314 plots. The structure of the data and the model indicated the need for a mixed-effects, nonlinear modeling approach using maximum likelihood in a linear differential equation with a power transformation. Behavior of the model was analyzed using a state-space approach. Our results show that both overstory and understory density affect height growth, allowing a manager to make informed decisions about vegetation control.
The Effects of Fertilization on Soil Respiration in 2-Year-Old Pinus taeda L. Clones
Authors: Tyree Michael C. , Seiler John R. , Fox Thomas R. 
Published: February 2021

Abstract
Fertilization is a common, cost-effective method to increase productivity of managed forests in the southeastern United States; however, little is known about how fertilization will affect the processes that drive total soil CO2 efflux (F S) and ultimately net ecosystem productivity (NEP). The objective of this research was to intensively monitor the response of F S, and its respiratory components during the first year after N and P fertilization in Pinus taeda clones. We monitored F S, heterotrophic respiration (R H), and specific root respiration (R R) and found that F S in fertilized plots differed significantly (P &lt; 0.0001) from that in unfertilized plots, but the direction of this effect was dependent on date. Additionally, R H was consistently lower (P = 0.0001) in fertilized plots relative to control plots, but the magnitude was dependent on the sampling date, and R R significantly (P = 0.04) increased in fertilized plots (+20%) when averaged over the study. Increased R R and decreased R H were probably offsetting each other, resulting in no overall difference in F S 1 year after fertilization. If these short-term trends persisted over the rotation of the stand, increased gross primary productivity accompanied by no change or even a decrease in soil C evolution could result in increased NEP.
A Naturally Heteroplasmic Clam Provides Clues about the Effects of Genetic Bottleneck on Paternal mtDNA
Authors: Iannello Mariangela , Bettinazzi Stefano , Breton Sophie , Ghiselli Fabrizio , Milani Liliana 
Published: February 2021

Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies within an organism. Since these copies are not identical, a single individual carries a heterogeneous population of mtDNAs, a condition known as heteroplasmy. Several factors play a role in the dynamics of the within-organism mtDNA population: among them, genetic bottlenecks, selection, and strictly maternal inheritance are known to shape the levels of heteroplasmy across mtDNAs.
In Metazoa, the only evolutionarily stable exception to the strictly maternal inheritance of mitochondria is the doubly uniparental inheritance (DUI), reported in 100+ bivalve species. In DUI species, there are two highly divergent mtDNA lineages, one inherited through oocyte mitochondria (F-type) and the other through sperm mitochondria (M-type). Having both parents contributing to the mtDNA pool of the progeny makes DUI a unique system to study the dynamics of mtDNA populations. Since, in bivalves, the spermatozoon has few mitochondria (4–5), M-type mtDNA faces a tight bottleneck during embryo segregation, one of the narrowest mitochondrial bottlenecks investigated so far.
Here, we analyzed the F- and M-type mtDNA variability within individuals of the DUI species Ruditapes philippinarum and investigated for the first time the effects of such a narrow bottleneck affecting mtDNA populations. As a potential consequence of this narrow bottleneck, the M-type mtDNA shows a large variability in different tissues, a condition so pronounced that it leads to genotypes from different tissues of the same individual not to cluster together. We believe that such results may help understanding the effect of low population size on mtDNA bottleneck.
Chromosome-wide characterization of meiotic noncrossovers (gene conversions) in mouse hybrids
Authors: Gergelits Vaclav , Parvanov Emil , Simecek Petr , Forejt Jiri 
Published: February 2021

Abstract
During meiosis, the recombination-initiating DNA double-strand breaks (DSBs) are repaired by crossovers or noncrossovers (gene conversions). While crossovers are easily detectable, noncrossover identification is hampered by the small size of their converted tracts and the necessity of sequence polymorphism. We report identification and characterization of a mouse chromosome-wide set of noncrossovers by next-generation sequencing of 10 mouse intersubspecific chromosome substitution strains. Based on 94 identified noncrossovers, we determined the mean length of a conversion tract to be 32 bp. The spatial chromosome-wide distribution of noncrossovers and crossovers significantly differed, although both sets overlapped the known hotspots of PRDM9-directed histone methylation and DNA DSBs, thus supporting their origin in the standard DSB repair pathway. A significant deficit of noncrossovers descending from asymmetric DSBs proved their proposed adverse effect on meiotic recombination and pointed to sister chromatids as an alternative template for their repair. The finding has implications for the molecular mechanism of hybrid sterility in mice from crosses between closely related Mus musculus musculus and Mus musculus domesticus subspecies.
Sex-specific variation in the genome-wide recombination rate
Authors: Peterson April L , Payseur Bret A 
Published: February 2021

Abstract
In most species that reproduce sexually, successful gametogenesis requires recombination during meiosis. The number and placement of crossovers (COs) vary among individuals, with females and males often presenting the most striking contrasts. Despite the recognition that the sexes recombine at different rates (heterochiasmy), existing data fail to answer the question of whether patterns of genetic variation in recombination rate are similar in the two sexes. To fill this gap, we measured the genome-wide recombination rate in both sexes from a panel of wild-derived inbred strains from multiple subspecies of house mice (Mus musculus) and from a few additional species of Mus. To directly compare recombination rates in females and males from the same genetic backgrounds, we applied established methods based on immunolocalization of recombination proteins to inbred strains. Our results reveal discordant patterns of genetic variation in the two sexes. Whereas male genome-wide recombination rates vary substantially among strains, female recombination rates measured in the same strains are more static. The direction of heterochiasmy varies within two subspecies, Mus musculus molossinus and Mus musculus musculus. The direction of sex differences in the length of the synaptonemal complex and CO positions is consistent across strains and does not track sex differences in genome-wide recombination rate. In males, contrasts between strains with high recombination rate and strains with low recombination rate suggest more recombination is associated with stronger CO interference and more double-strand breaks. The sex-specific patterns of genetic variation we report underscore the importance of incorporating sex differences into recombination research.