bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low genetic divergence and variation in coastal dune populations of the widespread terrestrial orchidEpipactis helleborine
Authors: Jacquemyn Hans , De Kort Hanne , Vanden Broeck An , Brys Rein 
Published: February 2020

AbstractReconstructing the early history of species divergence and quantifying the level of standing genetic variation in diverging populations are central to our understanding of ecotype formation and ultimately speciation. In this study, we used single nucleotide polymorphisms to reconstruct the evolutionary history of species divergence in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine and to investigate the level of standing genetic variation in 29 coastal dune populations in a fragmented dune landscape along the Belgian and French coast. Additionally, we used seed introduction experiments to assess the potential for gene flow into existing populations after long-distance seed dispersal and the ability to colonize vacant sites. Our results showed that coastal dune populations diverged only recently from inland populations, went through a significant bottleneck and were most probably the result of a single colonization event. Current levels of population genetic diversity are low and not related to population size or spatial isolation. The sampled dune populations also showed little genetic differentiation, and no apparent spatial genetic structure was observed. Seed introduction experiments showed that seeds of coastal dune populations germinated easily in both occupied and unoccupied sites in dune habitat, indicating that the availability of suitable mycorrhizal fungi is not limiting the distribution of coastal dune populations and that gene flow through seeds has probably contributed to the observed low levels of genetic differentiation. Overall, these results are consistent with a process of genetic divergence after a single, recent colonization event, followed by extensive gene flow among populations.
Electrographic predictors of successful weaning from anaesthetics in refractory status epilepticus
Authors: Rubin Daniel B , Angelini Brigid , Shoukat Maryum , Chu Catherine J , Zafar Sahar F , Westover M Brandon , Cash Sydney S , Rosenthal Eric S 
Published: February 2020

AbstractIntravenous third-line anaesthetic agents are typically titrated in refractory status epilepticus to achieve either seizure suppression or burst suppression on continuous EEG. However, the optimum treatment paradigm is unknown and little data exist to guide the withdrawal of anaesthetics in refractory status epilepticus. Premature withdrawal of anaesthetics risks the recurrence of seizures, whereas the prolonged use of anaesthetics increases the risk of treatment-associated adverse effects. This study sought to measure the accuracy of features of EEG activity during anaesthetic weaning in refractory status epilepticus as predictors of successful weaning from intravenous anaesthetics. We prespecified a successful anaesthetic wean as the discontinuation of intravenous anaesthesia without developing recurrent status epilepticus, and a wean failure as either recurrent status epilepticus or the resumption of anaesthesia for the purpose of treating an EEG pattern concerning for incipient status epilepticus. We evaluated two types of features as predictors of successful weaning: spectral components of the EEG signal, and spatial-correlation-based measures of functional connectivity. The results of these analyses were used to train a classifier to predict wean outcome. Forty-seven consecutive anaesthetic weans (23 successes, 24 failures) were identified from a single-centre cohort of patients admitted with refractory status epilepticus from 2016 to 2019. Spectral components of the EEG revealed no significant differences between successful and unsuccessful weans. Analysis of functional connectivity measures revealed that successful anaesthetic weans were characterized by the emergence of larger, more densely connected, and more highly clustered spatial functional networks, yielding 75.5% (95% confidence interval: 73.1–77.8%) testing accuracy in a bootstrap analysis using a hold-out sample of 20% of data for testing and 74.6% (95% confidence interval 73.2–75.9%) testing accuracy in a secondary external validation cohort, with an area under the curve of 83.3%. Distinct signatures in the spatial networks of functional connectivity emerge during successful anaesthetic liberation in status epilepticus; these findings are absent in patients with anaesthetic wean failure. Identifying features that emerge during successful anaesthetic weaning may allow faster and more successful anaesthetic liberation after refractory status epilepticus.
Connectivity Gradient in the Human Left Inferior Frontal Gyrus: Intraoperative Cortico-Cortical Evoked Potential Study
Authors: Nakae Takuro , Matsumoto Riki , Kunieda Takeharu , Arakawa Yoshiki , Kobayashi Katsuya , Shimotake Akihiro , Yamao Yukihiro , Kikuchi Takayuki , Aso Toshihiko , Matsuhashi Masao , Yoshida Kazumichi , Ikeda Akio , Takahashi Ryosuke , Lambon Ralph Matthew A , Miyamoto Susumu 
Published: February 2020

Abstract
In the dual-stream model of language processing, the exact connectivity of the ventral stream to the anterior temporal lobe remains elusive. To investigate the connectivity between the inferior frontal gyrus (IFG) and the lateral part of the temporal and parietal lobes, we integrated spatiotemporal profiles of cortico-cortical evoked potentials (CCEPs) recorded intraoperatively in 14 patients who had undergone surgical resection for a brain tumor or epileptic focus. Four-dimensional visualization of the combined CCEP data showed that the pars opercularis (Broca’s area) is connected to the posterior temporal cortices and the supramarginal gyrus, whereas the pars orbitalis is connected to the anterior lateral temporal cortices and angular gyrus. Quantitative topographical analysis of CCEP connectivity confirmed an anterior–posterior gradient of connectivity from IFG stimulus sites to the temporal response sites. Reciprocality analysis indicated that the anterior part of the IFG is bidirectionally connected to the temporal or parietal area. This study shows that each IFG subdivision has different connectivity to the temporal lobe with an anterior–posterior gradient and supports the classical connectivity concept of Dejerine; that is, the frontal lobe is connected to the temporal lobe through the arcuate fasciculus and also a double fan-shaped structure anchored at the limen insulae.
An Atypical Sulcal Pattern in Children with Disorders of the Corpus Callosum and Its Relation to Behavioral Outcomes
Authors: Vasung Lana , Yun Hyuk Jin , Feldman Henry A , Grant Patricia Ellen , Im Kiho 
Published: February 2020

Abstract
Hypogenesis (hCC) and dysgenesis (dCC) of the corpus callosum (CC) are characterized by its smaller size or absence. The outcomes of these patients vary considerably and are unrelated to the size of the CC abnormality. The aim of the current study was to characterize the sulcal pattern in children with hCC and dCC and to explore its relation to clinical outcome. We used quantitative sulcal pattern analysis that measures deviation (similarity index, SI) of the composite or individual sulcal features (position, depth, area, and graph topology) compared to the control group. We calculated SI for each hemisphere and lobe in 11 children with CC disorder (hCC = 4, dCC = 7) and 15 controls. hCC and dCC had smaller hemispheric SI compared to controls. dCC subjects had smaller regional SI in the frontal and occipital lobes, which were driven by a smaller SI in a position or a graph topology. The significantly decreased SI gradient was found across groups only in the sulcal graph topology of the temporal lobes (controls &gt; hCC &gt; dCC) and was related to clinical outcome. Our results suggest that careful examination of sulcal pattern in hCC and dCC patients could be a useful biomarker of outcome.
Molecular and Direct Detection Tests for Treponema pallidum Subspecies pallidum: A Review of the Literature, 1964–2017
Authors: Theel Elitza S , Katz Samantha S , Pillay Allan 
Published: February 2020

AbstractDirect detection methods for Treponema pallidum include dark-field microscopy (DFM), direct fluorescence antibody (DFA) testing, immunohistochemistry (IHC), and nucleic acid amplification tests (NAATs). Here, we reviewed the relevant syphilis diagnostic literature to address 2 main questions with respect to T. pallidum direct detection techniques: “What are the performance characteristics for each direct detection test for T. pallidum and what are the optimal specimen types for each test?” and “What options are available for T. pallidum molecular epidemiology?” To answer these questions, we searched 5 electronic databases (OVID Medline, OVID Embase, CINAHL, Cochrane Library, and Scopus) from 1964 to 2017 using relevant search terms and identified 1928 articles, of which 37 met our inclusion criteria. DFM and DFA sensitivities ranged from 73% to 100% in cases of primary syphilis; and while sensitivity using silver stain histopathology for T. pallidum was generally low (0%–41%), higher performance characteristics were observed for T. pallidum–specific IHC (49–92%). Different genes have been targeted by T. pallidum–specific NAATs, with the majority of studies indicating that sensitivity is primarily dependent on the type of collected biological sample, with highest sensitivity observed in primary lesion exudate (75–95%). Given the rising incidence of syphilis, the development of direct, Food and Drug Administration–cleared T. pallidum NAATs should be considered an immediate priority.
Kidney Transplantation From Hepatitis B Surface Antigen (HBsAg)–Positive Living Donors to HBsAg-Negative Recipients: Clinical Outcomes at a High-Volume Center in China
Authors: Wang Xian-ding , Liu Jin-peng , Song Tu-run , Huang Zhong-li , Fan Yu , Shi Yun-ying , Chen Li-yu , Lv Yuan-hang , Xu Zi-lin , Li Xiao-hong , Wang Li , Lin Tao 
Published: February 2020

Abstract

Background
Data on kidney transplantation (KTx) from hepatitis B surface antigen (HBsAg)–positive (HBsAg+) donors to HBsAg-negative (HBsAg−) recipients [D(HBsAg+)/R(HBsAg-)] are limited. We aimed to report the outcomes of D(HBsAg+)/R(HBsAg−) KTx in recipients with or without hepatitis B surface antibody (HBsAb).

Methods
Eighty-three D(HBsAg+)/R(HBsAg−) living KTx cases were retrospectively identified. The 384 cases of KTx from hepatitis B core antibody–positive (HBcAb+) living donors to HBcAb-negative (HBcAb−) recipients [D(HBcAb+)/R(HBcAb−)] were used as the control group. The primary endpoint was posttransplant HBsAg status change from negative to postive (-− →+).

Results
Before KTx, 24 donors (28.9%) in the D(HBsAg+)/R(HBsAg−) group were hepatitis B virus (HBV) DNA positive, and 20 recipients were HBsAb−. All 83 D(HBsAg+)/R(HBsAg−) recipients received HBV prophylaxis, while no D(HBcAb+)/R(HBcAb−) recipients received prophylaxis. After a median follow-up of 36 months (range, 6–106) and 36 months (range, 4–107) for the D(HBsAg+)/R(HBsAg−) and D(HBcAb+)/R(HBcAb−) groups, respectively, 2 of 83 (2.41%) D(HBsAg+)/R(HBsAg−) recipients and 1 of 384 (0.26%) D(HBcAb+)/R(HBcAb−) became HBsAg+, accompanied by HBV DNA-positive (P = .083). The 3 recipients with HBsAg−→+ were exclusively HBsAb−/HBcAb− before KTx. Recipient deaths were more frequent in the D(HBsAg+)/R(HBsAg−) group (6.02% vs 1.04%, P = .011), while liver and graft function, rejection, infection, and graft loss were not significantly different. In univariate analyses, pretransplant HBsAb−/HBcAb− combination in the D(HBsAg+)/R(HBsAg−) recipients carried a significantly higher risk of HBsAg−→+, HBV DNA−→+, and death.

Conclusions
Living D(HBsAg+)/R(HBsAg−) KTx in HBsAb+ recipients provides excellent graft and patient survivals without HBV transmission. HBV transmission risks should be more balanced with respect to benefits of D(HBsAg+)/R(HBsAg−) KTx in HBsAb-/HBcAb− candidates.
Prevalence of Self-reported Neurologic and Ocular Symptoms in Early Syphilis Cases
Authors: Quilter Laura A S , de Voux Alex , Amiya Rachel M , Davies Erin , Hennessy Robin R , Kerani Roxanne P , Madera Robbie , Matthias James , Pearson Victoria M , Walters Jaime K , Wilson Craig , Kidd Sarah , Torrone Elizabeth 
Published: February 2020

Abstract

Background
Neurosyphilis, a complication of syphilis, can occur at any stage of infection. Measuring the prevalence of neurosyphilis is challenging, and there are limited data on the prevalence of neurologic or ocular symptoms among patients with syphilis. We sought to describe the prevalence of neurologic and/or ocular symptoms among early syphilis (ES) cases and the clinical management of symptomatic cases enrolled in the STD Surveillance Network (SSuN) Neuro/Ocular Syphilis Surveillance project.

Methods
Persons diagnosed with ES were selected for interviews based on current health department protocols in 5 participating SSuN jurisdictions from November 2016 through October 2017. All interviewed ES cases were screened for self-reported neurologic and/or ocular symptoms. Additional clinical information on diagnostic testing and treatment for cases concerning for neurosyphilis/ocular syphilis was obtained from providers.

Results
Among 9123 patients with ES who were interviewed, 151 (1.7%; 95% confidence interval [CI], 1.4%–1.9%) reported ≥ 1 neurologic or ocular symptom. Of the 53 (35%) who underwent lumbar puncture, 22 (42%) had documented abnormal cerebrospinal fluid, of which 21 (95%) were treated for neurosyphilis/ocular syphilis. Among the remaining 98 symptomatic patients with no documented lumbar puncture (65%), 12 (12%) were treated for and/or clinically diagnosed with neurosyphilis/ocular syphilis.

Conclusions
We observed a low prevalence of self-reported neurologic and/or ocular symptoms in interviewed ES cases. Approximately one-third of ES cases who self-reported symptoms underwent further recommended diagnostic evaluation. Understanding barriers to appropriate clinical evaluation is important to ensuring appropriate management of patients with possible neurologic and/or ocular manifestations of syphilis.
Inflammatory Phenotypes Predict Changes in Arterial Stiffness Following Antiretroviral Therapy Initiation
Authors: Kelly Christine , Tinago Willard , Alber Dagmar , Hunter Patricia , Luckhurst Natasha , Connolly Jake , Arrigoni Francesca , Abner Alejandro Garcia , Kamngona Ralph , Sheha Irene , Chammudzi Mishek , Jambo Kondwani , Mallewa Jane , Rapala Alicja , Heyderman Robert S , Mallon Patrick W G , Mwandumba Henry , Walker A Sarah , Klein Nigel , Khoo Saye 
Published: February 2020

Abstract

Background
Inflammation drives vascular dysfunction in HIV, but in low-income settings causes of inflammation are multiple, and include infectious and environmental factors. We hypothesized that patients with advanced immunosuppression could be stratified into inflammatory phenotypes that predicted changes in vascular dysfunction on ART.

Methods
We recruited Malawian adults with CD4 &lt;100 cells/μL 2 weeks after starting ART in the REALITY trial (NCT01825031). Carotid femoral pulse-wave velocity (cfPWV) measured arterial stiffness 2, 12, 24, and 42 weeks post–ART initiation. Plasma inflammation markers were measured by electrochemiluminescence at weeks 2 and 42. Hierarchical clustering on principal components identified inflammatory clusters.

Results
211 participants with HIV grouped into 3 inflammatory clusters representing 51 (24%; cluster-1), 153 (73%; cluster-2), and 7 (3%; cluster-3) individuals. Cluster-1 showed markedly higher CD4 and CD8 T-cell expression of HLADR and PD-1 versus cluster-2 and cluster-3 (all P &lt; .0001). Although small, cluster-3 had significantly higher levels of cytokines reflecting inflammation (IL-6, IFN-γ, IP-10, IL-1RA, IL-10), chemotaxis (IL-8), systemic and vascular inflammation (CRP, ICAM-1, VCAM-1), and SAA (all P &lt; .001). In mixed-effects models, cfPWV changes over time were similar for cluster-2 versus cluster-1 (relative fold-change, 0.99; 95% CI, .86–1.14; P = .91), but greater in cluster-3 versus cluster-1 (relative fold-change, 1.45; 95% CI, 1.01–2.09; P = .045).

Conclusions
Two inflammatory clusters were identified: one defined by high T-cell PD-1 expression and another by a hyperinflamed profile and increases in cfPWV on ART. Further clinical characterization of inflammatory phenotypes could help target vascular dysfunction interventions to those at highest risk.

Clinical Trials Network
NCT01825031.
Penicillin Allergy Testing Is Cost-Saving: An Economic Evaluation Study
Authors: Sousa-Pinto Bernardo , Blumenthal Kimberly G , Macy Eric , Pereira Ana Margarida , Azevedo Luís Filipe , Delgado Luís , Fonseca João Almeida 
Published: February 2020

AbstractBackgroundHaving a penicillin allergy label is associated with the use of less appropriate and more expensive antibiotics and increased healthcare utilization. Penicillin allergy testing results in delabeling most allergy claimants and may be cost-saving. This study aimed to project whether penicillin allergy testing in patients reporting a penicillin allergy is cost-saving.MethodsIn this economic evaluation study, we built decision models to project the economic impact of 2 strategies for a patient with a penicillin allergy label: (1) perform diagnostic testing (drug challenges, with or without skin tests); and (2) do not perform diagnostic testing. The health service perspective was adopted, considering costs with penicillin allergy tests, and with hospital bed-days/outpatient visits, antibiotic use, and diagnostic testing. Twenty-four base case decision models were built, accounting for differences in the diagnostic workup, setting (inpatient vs outpatient) and geographic region. Uncertainty was explored via probabilistic sensitivity analyses.ResultsPenicillin allergy testing was cost-saving in all decision models built. For models assessing the performance of both skin tests and drug challenges, allergy testing resulted in average savings (in United States [US] dollars) of $657 for inpatients (US: $1444; Europe: $489) and $2746 for outpatients (US: $256; Europe: $6045). 75% of simulations obtained through probabilistic sensitivity analysis identified testing as the less costly option.ConclusionsPenicillin allergy testing was projected to be cost-saving across different scenarios. These results are devised to inform guidelines, supporting the adoption of policies promoting widespread testing of patients with a penicillin allergy label.
Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019
Authors: Shen Zijie , Xiao Yan , Kang Lu , Ma Wentai , Shi Leisheng , Zhang Li , Zhou Zhuo , Yang Jing , Zhong Jiaxin , Yang Donghong , Guo Li , Zhang Guoliang , Li Hongru , Xu Yu , Chen Mingwei , Gao Zhancheng , Wang Jianwei , Ren Lili , Li Mingkun 
Published: February 2020

Abstract

Background
A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)–CoV-2, has infected &gt;75 000 individuals and spread to &gt;20 countries. It is still unclear how fast the virus evolved and how it interacts with other microorganisms in the lung.

Methods
We have conducted metatranscriptome sequencing for bronchoalveolar lavage fluid samples from 8 patients with SARS–CoV-2, and also analyzed data from 25 patients with community-acquired pneumonia (CAP), and 20 healthy controls for comparison.

Results
The median number of intrahost variants was 1–4 in SARS–CoV-2–infected patients, ranged from 0 to 51 in different samples. The distribution of variants on genes was similar to those observed in the population data. However, very few intrahost variants were observed in the population as polymorphisms, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. Although current evidence did not support the transmission of intrahost variants in a possible person-to-person spread, the risk should not be overlooked. Microbiotas in SARS–CoV-2–infected patients were similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria.

Conclusion
SARS–CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intrahost variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.
Circad: a comprehensive manually curated resource of circular RNA associated with diseases
Authors: Rophina Mercy , Sharma Disha , Poojary Mukta , Scaria Vinod 
Published: February 2020

Abstract

Circular RNAs (circRNAs) are unique transcript isoforms characterized by back splicing of exon ends to form a covalently closed loop or circular conformation. These transcript isoforms are now known to be expressed in a variety of organisms across the kingdoms of life. Recent studies have shown the role of circRNAs in a number of diseases and increasing evidence points to their potential application as biomarkers in these diseases. We have created a comprehensive manually curated database of circular RNAs associated with diseases. This database is available at URL http://clingen.igib.res.in/circad/. The Database lists more than 1300 circRNAs associated with 150 diseases and mapping to 113 International Statistical Classification of Diseases (ICD) codes with evidence of association linked to published literature. The database is unique in many ways. Firstly, it provides ready-to-use primers to work with, in order to use circRNAs as biomarkers or to perform functional studies. It additionally lists the assay and PCR primer details including experimentally validated ones as a ready reference to researchers along with fold change and statistical significance. It also provides standard disease nomenclature as per the ICD codes. To the best of our knowledge, circad is the most comprehensive and updated database of disease associated circular RNAs.

Availability: http://clingen.igib.res.in/circad/
Biodiversity Survey of Flower-Visiting Spiders Based on Literature Review and Field Study
Authors: Su Qichen , Qi Lin , Zhang Wei , Yun Yueli , Zhao Yao , Peng Yu 
Published: February 2020

Abstract
Many arthropods exhibit flower-visiting behavior, including a variety of spider species. However, as spiders are assumed to be strictly predatory, flower-visiting spiders are an often neglected group. We conducted a systematic biodiversity study of flower-visiting spiders based on published papers and field surveys. Most previous studies have focused on the herbivorous behavior of flower-visiting spiders (nectivory or pollinivory) and their effects on host flowers (tritrophic interactions with flower-visiting insects). In our field survey, we utilized standard transect walks (active sampling) and colored pan traps (passive sampling) to investigate species occurrence, diurnal and seasonal variation, and flower color preference of flower-visiting spiders. From the transect walks, crab spider species were found to be the dominant flower-visiting spiders and, based on all spider species, juvenile visitors were significantly more common than adults. Furthermore, in terms of spider number and species richness, tulips were the preferred flower to visit. For the pan traps, wolf spiders were found to be the dominant spider species. No significant differences were observed in the number of spiders caught in different colored pans, suggesting that color may not be an important flower trait in regard to spider preference. To the best of our knowledge, this study is the first to propose the term ‘flower-visiting spiders’ and conduct a systematic investigation of their diversity. However, this is preliminary research and further studies are required, especially as biodiversity is often closely linked to survey sites and ecotopes.