bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses
Authors: Park Minkyu , Christin Pascal-Antoine , Bennetzen Jeffrey L 
Published: May 2021

AbstractLimited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.
Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy
Authors: Woodworth Marcus A , Ng Kenneth K H , Halpern Aaron R , Pease Nicholas A , Nguyen Phuc H B , Kueh Hao Yuan , Vaughan Joshua C 
Published: May 2021

Abstract
Proper regulation of genome architecture and activity is essential for the development and function of multicellular organisms. Histone modifications, acting in combination, specify these activity states at individual genomic loci. However, the methods used to study these modifications often require either a large number of cells or are limited to targeting one histone mark at a time. Here, we developed a new method called Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) that uses Expansion Microscopy (ExM) to visualize and quantify multiple histone modifications at non-repetitive genomic regions in single cells at a spatial resolution of ∼75 nm. Using SCEPTRE, we distinguished multiple histone modifications at a single housekeeping gene, quantified histone modification levels at multiple developmentally-regulated genes in individual cells, and evaluated the relationship between histone modifications and RNA polymerase II loading at individual loci. We find extensive variability in epigenetic states between individual gene loci hidden from current population-averaged measurements. These findings establish SCEPTRE as a new technique for multiplexed detection of combinatorial chromatin states at single genomic loci in single cells.
Cooperative DNA looping by PRC2 complexes
Authors: Lin Xingcheng , Leicher Rachel , Liu Shixin , Zhang Bin 
Published: May 2021

Abstract
Polycomb repressive complex 2 (PRC2) is an essential protein complex that silences gene expression via post-translational modifications of chromatin. This paper combined homology modeling, atomistic and coarse-grained molecular dynamics simulations, and single-molecule force spectroscopy experiments to characterize both its full-length structure and PRC2-DNA interactions. Using free energy calculations with a newly parameterized protein-DNA force field, we studied a total of three potential PRC2 conformations and their impact on DNA binding and bending. Consistent with cryo-EM studies, we found that EZH2, a core subunit of PRC2, provides the primary interface for DNA binding, and its curved surface can induce DNA bending. Our simulations also predicted the C2 domain of the SUZ12 subunit to contact DNA. Multiple PRC2 complexes bind with DNA cooperatively via allosteric communication through the DNA, leading to a hairpin-like looped configuration. Single-molecule experiments support PRC2-mediated DNA looping and the role of AEBP2 in regulating such loop formation. The impact of AEBP2 can be partly understood from its association with the C2 domain, blocking C2 from DNA binding. Our study suggests that accessory proteins may regulate the genomic location of PRC2 by interfering with its DNA interactions.
Effects on Smoking Behavior of Switching Menthol Smokers to Non-menthol Cigarettes
Authors: Kotlyar Michael , Shanley Ryan , Dufresne Sheena R , Corcoran Gretchen A , Okuyemi Kolawole S , Mills Anne M , Hatsukami Dorothy K 
Published: May 2021

Abstract

Introduction
Bans of menthol characterizing flavor in cigarettes have been implemented in some localities and have been proposed more broadly. One proposed benefit of such a ban is to increase cessation rates among current menthol smokers. There is currently relatively limited data regarding how smoking behavior changes if menthol smokers switch to non-menthol cigarettes.

Aims and Methods
African American menthol smokers interested in quitting smoking were randomized to either continue smoking menthol (n = 60) or switch to non-menthol cigarettes (n = 62) for 1 month prior to a cessation attempt. Cessation results were reported previously; this analysis reports the results from the pre-cessation visits at which amount smoked, exhaled carbon monoxide (CO) concentration, urinary cotinine concentrations, and subjective measures were assessed.

Results
Over the 4-week study period, those switching to non-menthol (vs. continuing to smoke menthol) cigarettes smoked fewer cigarettes per day (mean ratio: 0.86; 95% confidence interval [CI]: 0.76, 0.98; p = .02), reported lower withdrawal symptom severity (mean difference −1.29; 95% CI: −2.6 to −0.01; p = .05) and higher perceived effectiveness of their skills for quitting smoking (mean difference 0.56; 95% CI: 0.02–1.10; p = .05). No significant differences were found between groups in exhaled CO, urinary cotinine concentrations, or most other subjective effects including support for a ban on menthol characterizing flavor in cigarettes.

Conclusions
These results suggest that were menthol cigarettes no longer available, those that switch to non-menthol cigarettes would not change their smoking behavior in a way that is likely to be more hazardous, with some indicators suggesting that there may be some benefit.
Clinicaltrials.gov # NCT02342327.

Implications
A ban on menthol characterizing flavor in cigarettes has been proposed as a potential means by which to increase smoking cessation rates among current menthol cigarette smokers. This study evaluated how African American menthol cigarette smokers adjusted their smoking behavior after switching to non-menthol cigarettes. Although the overall differences between groups were modest, they were in a direction consistent with decreased smoking suggesting that current smokers would not adjust their behavior in a way that is likely to be more hazardous, with some indicators suggesting that there may be some benefits.
Giant cell reparative granuloma of the phalanx in a violinist
Authors: Ventura-Parellada C , Martínez-Ruiz A , Subirà-i-Álvarez T 
Published: May 2021

Abstract
Giant cell reparative granuloma (GCRG) is a rare, pseudotumoural intraosseous lesion, considered a reactive injury after repeated trauma. Reactive lesions and benign bone tumours may show aggressive clinical and radiographic findings. Differential diagnosis must be performed in order to offer suitable treatment to the patient. Excisional biopsy and curettage of the lesion are the preferred methods of treatment. We present the first case of a GCRG of the distal phalanx of the left little finger in a professional violinist.
Hand–arm vibration and outcomes of surgery for Dupuytren’s contracture
Authors: Stirling P H C , Ng N , Jenkins P J , Clement N D , Duckworth A D , McEachan J E 
Published: May 2021

Abstract

Background
Dupuytren’s contracture was recently designated a prescribed occupational disease when it occurs in patients with previous hand–arm vibration (HAV) exposure.

Aims
The aims of this study were to describe the impact of self-reported HAV exposure on upper limb function and satisfaction following surgery for Dupuytren’s contracture.

Methods
Paired pre- and postoperative Quick version of Disabilities of the Arm, Shoulder and Hand (QuickDASH) and patient satisfaction questionnaires were prospectively collected from all patients undergoing surgery for Dupuytren’s contracture over a 6-year period. Patients self-reported HAV exposure duration.

Results
Results were available for 425 hands (65%) at mean 13 months postoperatively. There were 111 patients (26%) that reported HAV exposure. The prevalence of HAV exposure was significantly greater in male compared with female patients (32% versus 4%; P &lt; 0.001). A statistically significant difference in preoperative (difference 7.47; 95% confidence interval 4.78–10.17; P &lt; 0.001) and postoperative QuickDASH score (difference 6.78; 95% confidence interval 2.69–10.88; P &lt; 0.001) was observed between the two groups, but difference in QuickDASH improvement was not significantly different (difference 1.76; 95% confidence interval −1.58 to 5.10; P &gt; 0.05). No significant difference in satisfaction rate or return to work was observed between the two groups.

Conclusions
Previous HAV exposure influenced the pre and postoperative function in patients undergoing surgery for Dupuytren’s contracture, but had no effect on satisfaction or return to work. Further prospective research will be required to determine whether the introduction of a compensatory framework will have a more profound effect on the functional outcomes of surgery.
Impact of Routine Endoscopic Skull Base Surgery on Subjective Olfaction and Gustation Outcomes
Authors: Hura Nanki , Orlov Cinthia P , Khalafallah Adham M , Mukherjee Debraj , Rowan Nicholas R 
Published: May 2021

Abstract

BACKGROUND
As endoscopic endonasal skull base surgery (EESBS) for sellar pathology has become routine, there is increasing awareness of quality-of-life (QOL) outcomes related to this approach. Similarly, there is a growing interest in postoperative chemosensory function, with notable emphasis on olfaction and the corresponding psychosocial implications of olfactory dysfunction. Meanwhile, there has been minimal direct investigation into gustatory outcomes, and the association between these 2 chemosensory functions remains poorly understood.

OBJECTIVE
To investigate patient-reported chemosensory function and rhinologic-specific QOL following EESBS for routine sellar pathologies.

METHODS
Comprehensive clinical characteristics and sinonasal QOL assessments, measured using Anterior Skull Base Nasal Inventory-12 (ASK Nasal-12), were collected from 46 patients undergoing EESBS for sellar pathology.

RESULTS
Forty-six patients were included: 65.2% female, average age 52.8 yr (range: 27-89). The most common pathology was nonfunctioning pituitary adenoma (n = 28). Preoperative ASK Nasal-12 scores (mean = 0.81) demonstrated postoperative worsening at 2 wk (mean = 2.52, P < .0001) and 1 mo (mean = 1.33, P = .0031), with no difference at 3 mo postoperatively (mean = 0.89, P = .92). Meanwhile, there was significant worsening of preoperative subjective smell (mean = 0.62) and taste function (mean = 0.42) at 2 wk (mean = 3.48, P < .0001; mean = 2.69, P < .0001) and 1 mo (mean = 2.40, P < .0001; mean = 2.03, P < .0001) postoperatively, which persisted at approximately 3 mo postoperatively (mean = 1.26, P = .04; mean = 1.15, P = .0059).

CONCLUSION
Patients undergoing EESBS for sellar pathologies experience anticipated, temporary disruptions in sinonasal QOL but may have longer lasting perturbations in subjective olfaction and gustation. Given the increasing use of the endoscopic endonasal corridor, further investigation in postoperative chemosensory function is essential.
Combined Endovascular and Microsurgical Management of a Tentorial Arteriovenous Malformation in a Hybrid Neurovascular Operating Room: 2-Dimensional Operative Video
Authors: Glauser Gregory , Detchou Donald K E , Arena John , Choudhri Omar 
Published: May 2021

Abstract
Tentorial margin arteriovenous malformations (AVMs) at the cerebello-mesencephalic fissure are deep lesions, which can be safely resected via a lateral supracerebellar infratentorial approach. This video illustrates the case of a patient who presented with hemorrhage from a tentorial AVM. He was managed in the hybrid neurovascular operating room with Onyx (Medtronic) embolization of a superior cerebellar artery feeder followed by resection of the AVM, which included cerebellar relaxation from lumbar cerebrospinal fluid (CSF) drainage and lateral positioning. Wide cisternal arachnoid dissection at the quadrigeminal cistern allowed for a straight trajectory to the AVM without fixed retraction. Intraoperative transradial angiography confirmed complete AVM exclusion. This video was deemed Institutional Review Board (IRB) exempt by the University of Pennsylvania IRB as it is considered a case report, which does not require IRB approval or patient consent.
The patient consented to the procedure.
‘Non-criteria antiphospholipid antibodies’: bridging the gap between seropositive and seronegative antiphospholipid syndrome
Authors: Truglia Simona , Mancuso Silvia , Capozzi Antonella , Recalchi Serena , Riitano Gloria , Longo Agostina , De Carolis Sara , Spinelli Francesca Romana , Alessandri Cristiano , Ceccarelli Fulvia , De Carolis Caterina , Misasi Roberta , Sorice Maurizio , Conti Fabrizio 
Published: May 2021

Abstract

Objective
We aimed to analyse the prevalence of non-criteria anti-phospholipid (aPL) antibodies and their role in the diagnosis, treatment and prognosis in a cohort of patients with clinical features consistent with a diagnosis of antiphospholipid syndrome (APS), but persistently negative for criteria aPL – anti-cardiolipin antibodies (aCL), anti-β2-glycoprotein I antibodies (aβ2-GPI) and lupus anticoagulant (LA) – named seronegative APS (SN-APS).

Methods
Sera from SN-APS patients were tested for aCL by TLC-immunostaining, anti-vimentin/cardiolipin (aVim/CL) and anti-phosphatidylserine/prothrombin (anti-PS/PT) by ELISA. Control groups of our study were APS patients and healthy controls.

Results
We enrolled 114 consecutive SN-APS patients, 69 (60.5%) resulted positive for at least one non-criteria test in two occasions 12 weeks apart. Among the persistently positive patients to these tests, 97% resulted positive for aCL by TLC-immunostaining, 52.3% for aVim/CL and 17.4% for aPS/PT. SN-APS patients with double positivity (aCL by TLC-immunostaining and aVim/CL) showed a likelihood positive ratio of 8 to present mixed thrombotic and obstetrical features. Among SN-APS patients tested positive, after the therapeutic changes, three cases of recurrent thrombosis were observed [median follow-up 41 months (IQR 39.5)]. Twenty pregnancies were recorded in 17 SN-APS patients after the detection of unconventional aPL and 12 of them (60%) experienced a good outcome under conventional treatment for APS.

Conclusions
This is the largest monocentric study demonstrating that aCL tested by TLC-immunostaining and aVim/CL can detect aPL positivity in SN-APS. It may encourage clinicians to monitor and provide adequate targeted therapy, which improve SN-APS prognosis.
Reduced neural responsiveness to looming stimuli is associated with increased aggression
Authors: Blair R James , Zhang R u , Bashford-Largo Johannah , Bajaj Sahil , Mathur Avantika , Ringle Jay , Schwartz Amanda , Elowsky Jaimie , Dobbertin Matthew , Blair Karina S , Tyler Patrick M 
Published: May 2021

Abstract
While neuro-cognitive work examining aggression has examined patients with conditions at increased risk for aggression or individuals self-reporting past aggression, little work has attempted to identify neuro-cognitive markers associated with observed/recorded aggression. The goal of the current study was to determine the extent to which aggression by youth in the first three months of residential care was associated with atypical responsiveness to threat stimuli. This functional MRI study involved 98 (68 male; mean age = 15.96 [sd = 1.52]) adolescents in residential care performing a looming threat task involving images of threatening and neutral human faces or animals that appeared to be either loom or recede. Level of aggression was negatively associated with responding to looming stimuli (irrespective of whether these were threatening or neutral) within regions including bilateral inferior frontal gyrus, right inferior parietal lobule, right superior/middle temporal gyrus and a region of right uncus proximal to the amygdala. These data indicate that aggression level is associated with a decrease in responsiveness to a basic threat cue-looming stimuli. Reduced threat responsiveness likely results in the individual being less able to represent the negative consequences that may result from engaging in aggression, thereby increasing the risk for aggressive episodes.
Sex-specific interaction between cortisol and striato-limbic responses to psychosocial stress
Authors: Henze Gina-Isabelle , Konzok Julian , Kreuzpointner Ludwig , Bärtl Christoph , Giglberger Marina , Peter Hannah , Streit Fabian , Kudielka Brigitte M , Kirsch Peter , Wüst Stefan 
Published: May 2021

Abstract
Although women and men differ in psychological and endocrine stress responses as well as in the prevalence rates of stress-related disorders, knowledge on sex differences regarding stress regulation in the brain is scarce. Therefore, we performed an in-depth analysis of data from 67 healthy participants (31 women, taking oral contraceptives), who were exposed to the ScanSTRESS paradigm in a functional magnetic resonance imaging study. Changes in cortisol, affect, heart rate and neural activation in response to psychosocial stress were examined in women and men as well as potential sex-specific interactions between stress response domains. Stress exposure led to significant cortisol increases, with men exhibiting higher levels than women. Depending on sex, cortisol elevations were differently associated with stress-related responses in striato-limbic structures: higher increases were associated with activations in men but with deactivations in women. Regarding affect or heart rate responses, no sex differences emerged. Although women and men differ in their overall stress reactivity, our findings do not support the idea of distinct neural networks as the base of this difference. Instead, we found differential stress reactions for women and men in identical structures. We propose considering quantitative predictors such as sex-specific cortisol increases when exploring neural response differences of women and men.
OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life
Authors: Mctavish Emily Jane , Sánchez-Reyes Luna Luisa , Holder Mark T 
Published: May 2021

Abstract
The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.[Evolution; open science; phylogenetics; Python; taxonomy.]
Estimation of endogenous intestinal losses of acid hydrolyzed ether extract in growing and finishing pigs using the linear regression method
Authors: Acosta Jesus A , Boyd R Dean , Patience John F 
Published: May 2021

Abstract
The approach of this experiment was to apply the regression method for the estimation of endogenous intestinal losses of ether extract (EEE) when pigs are fed complete diets ad libitum and using dietary levels of fat typical of those employed in commercial situations. A total of 40 gilts (PIC 337 sires × C22 or C29) were allotted to individual pens and randomly assigned to diets (8 pigs per treatment) with 5 different levels of acid hydrolyzed ether extract (AEE). The dietary treatments consisted of a corn-soybean meal diet with no added fat (L1); a corn-soy diet with 6% each of corn distiller’s dried grains with solubles (DDGS), corn germ meal, and wheat middlings (L2); the L2 diet but with 12% each of corn DDGS, corn germ meal, and wheat middlings (L3); the L2 diet plus soybean oil to equalize the NE concentration of the L2 diet with L1 (L4); and the L3 diet plus soybean oil to equalize the NE concentration of the L3 diet with L1 (L5). Pigs received feed and water ad libitum for the growing period (initial BW = 38.5 ± 1.2 kg) and the finishing period (initial BW = 73.82 ± 2.9 kg). A quadratic broken-line model was employed to estimate the response of apparent total tract digestibility (ATTD) of AEE to dietary AEE level. The average true total tract digestibility (TTTD) of AEE and endogenous losses of AEE were estimated using regression analysis of dietary AEE intake (g/kg of DM) against apparent digested AEE (g/kg of DMI). The ATTD of AEE increased in curvilinear fashion as dietary AEE level increased in growing and in finishing pigs (P &lt; 0.001). This suggests an influence of EEE on the ATTD of AEE estimates. The linear regression of apparent digested AEE against dietary AEE intake (L1–L5; P &lt; 0.001, R2 = 0.99 for growing pigs and P &lt; 0.001, R2 = 0.99 for finishing pigs) estimated greater EEE (P &lt; 0.05) and TTTD of AEE (P &lt; 0.05) for growing than finishing pigs. Estimated EEE from growing pigs ranged between 18.1 and 20.2 g/kg of DMI, while TTTD of AEE ranged between 96.40% and 100.70%. In finishing pigs, EEE ranged between 21.6 and 23.8 g/kg of DMI and TTTD of AEE ranged between 91.30% and 95.25%. In conclusion, EEE under practical conditions is estimated to be 19.2 g/kg of DMI in growing and 22.7 g/kg of DMI in finishing pigs.
Effects of Wheat Cultivar Mixtures on Population Genetic Structure of Puccinia striiformis f. sp. tritici
Authors: Chu Bingyao , Yuan Kai , Wang Cuicui , Yang Lujia , Jiang Bingbing , Gu Yilin , Ma Zhanhong 
Published: May 2021

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive wheat diseases worldwide. Understanding the effects of cultivar mixture on disease control and population genetic structure of Pst could promote the effective application of cultivar mixtures. This study designed nine cultivar mixtures composed of different component cultivars with field experiments in Zitong County, Sichuan Province in two seasons from 2016 to 2018. Diseased leaves were collected in each plot of treatment in the spring and, in total, 835 and 568 isolates were obtained and genotyped with 10 pairs of simple sequence repeat markers in the 2 years, respectively. The observed and theoretical values of the area under the disease progress curve (AUDPC), wheat yield, Pst genotypic diversity, and the frequency of Pst dominant genetic groups were compared among cultivar mixtures. With the 2 years’ experiments, there were three and two cultivar mixtures, respectively, showing significant effect on the relative reduction of AUDPC; there were no significant effects on the relative yield increase in all mixtures in the 2 years. There were four and five cultivar mixtures showing positive effects on the relative increase of Pst genotypic diversity in the 2 years, respectively. Moreover, all cultivar mixtures could decrease the frequencies of Pst dominant genetic groups on highly susceptible component cultivar compared with their theoretical frequencies. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .