bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding Hybrid Incompatibilities Using Genome Sequences from Hybrid Populations
Authors: Blanckaert Alexandre , Payseur Bret A 
Published: June 2021

Abstract
Natural hybrid zones offer a powerful framework for understanding the genetic basis of speciation in progress because ongoing hybridization continually creates unfavorable gene combinations. Evidence indicates that postzygotic reproductive isolation is often caused by epistatic interactions between mutations in different genes that evolved independently of one another (hybrid incompatibilities). We examined the potential to detect epistatic selection against incompatibilities from genome sequence data using the site frequency spectrum (SFS) of polymorphisms by conducting individual-based simulations in SLiM. We found that the genome-wide SFS in hybrid populations assumes a diagnostic shape, with the continual input of fixed differences between source populations via migration inducing a mass at intermediate allele frequency. Epistatic selection locally distorts the SFS as non-incompatibility alleles rise in frequency in a manner analogous to a selective sweep. Building on these results, we present a statistical method to identify genomic regions containing incompatibility loci that locates departures in the local SFS compared with the genome-wide SFS. Cross-validation studies demonstrate that our method detects recessive and codominant incompatibilities across a range of scenarios varying in the strength of epistatic selection, migration rate, and hybrid zone age. Our approach takes advantage of whole genome sequence data, does not require knowledge of demographic history, and can be applied to any pair of nascent species that forms a hybrid zone.
Constraints on ultra-low-frequency gravitational waves with statistics of pulsar spin-down rates. II. Mann–Whitney U test
Authors: Kumamoto Hiroki , Hisano Shinnosuke , Takahashi Keitaro 
Published: June 2021

Abstract
We investigate gravitational waves with sub-nHz frequencies (10−11 Hz ≲ fGW ≲ 10−9 Hz) from the spatial distribution of the spin-down rates of millisecond pulsars. As we suggested in Yonemaru et al. (2018, MNRAS, 478, 1670), gravitational waves from a single source induce a bias in the observed spin-down rates of pulsars depending on the relative direction between the source and the pulsar. To improve the constraints on the time derivative of gravitational wave amplitude obtained in our previous work (Kumamoto et al. 2019, MNRAS, 489, 3547), we adopt a more sophisticated statistical method called the Mann–Whitney U test. Applying our method to the ATNF pulsar catalogue, we first find that the current data set is consistent with no gravitational wave signal from any direction in the sky. Then, we estimate the effective angular resolution of our method to be 66 deg2 by studying the probability distribution of the test statistic. Finally, we investigate gravitational wave signals from the Galactic Center (GC) and M 87 and, comparing simulated mock data sets with the real pulsar data, we obtain upper bounds on the time derivative as $\dot{h}_{\rm GC} &lt; 8.9 \times 10^{-19}$ s−1 for the GC and $\dot{h}_{\rm M87} &lt; 3.3 \times 10^{-19}$ s−1 for M 87, which are stronger than those obtained in Kumamoto et al. (2019, MNRAS, 489, 3547) by factors of 7 and 25, respectively.
SIRIUS project. III. Star-by-star simulations of star cluster formation using a direct
N
-body integrator with stellar feedback
Authors: Fujii Michiko S , Saitoh Takayuki R , Hirai Yutaka , Wang Long 
Published: June 2021

Abstract
One of the computational challenges of cluster formation simulations is resolving individual stars and simulating massive clusters with masses of more than 104 M⊙ without gravitational softening. Combining a direct N-body code with smoothed-particle hydrodynamics (SPH) code, we have developed a new code, ASURA+BRIDGE, in which we can integrate stellar particles without softening. We add a feedback model for H ii regions into this code, in which thermal and momentum feedback is given within the Strömgren radius. We perform N-body/SPH simulations of star cluster formation. Without softening, a portion of massive stars are ejected from the forming clusters. As a result, the stellar feedback works outside the clusters. This enhances/suppresses the star formation in initially sub-virial/super-virial clouds. We find that the formed star clusters are denser than currently observed open clusters, but the mass–density relation is consistent with or even higher than that which is estimated as an initial cluster density. We also find that some clusters have multiple peaks in their stellar age distribution as a consequence of their hierarchical formation. Irrespective of the virial ratio of molecular clouds, approximately one-third of stars remain in the star clusters after gas expulsion.
An analytical density profile of dense circumstellar medium in Type II supernovae
Authors: Tsuna Daichi , Takei Yuki , Kuriyama Naoto , Shigeyama Toshikazu 
Published: June 2021

Abstract
Observations of Type II supernovae imply that a large fraction of their progenitors experience enhanced mass loss years to decades before core collapse, creating a dense circumstellar medium (CSM). Assuming that the CSM is produced by a single mass eruption event, we analytically model its density profile. We find that a double power-law profile, where the inner (outer) power-law index has a characteristic value of −1.5 (−10 to −12), gives a good fit to the CSM profile obtained using radiation hydrodynamical simulations. With our profile the CSM is well described by just two parameters, the transition radius r* and density at r = r* (alternatively r* and the total CSM mass). We encourage future studies to include this profile, if possible, when modelling emission from interaction-powered transients.
Improving implementation of school-based healthy eating and physical activity policies, practices, and programs: a systematic review
Authors: Barnes Courtney , McCrabb Sam , Stacey Fiona , Nathan Nicole , Yoong Sze Lin , Grady Alice , Sutherland Rachel , Hodder Rebecca , Innes-Hughes Christine , Davies Marc , Wolfenden Luke 
Published: June 2021

Abstract
Although best practice recommendations exist regarding school-based healthy eating and physical activity policies, practices, and programs, research indicates that implementation is poor. As the field of implementation science is rapidly evolving, an update of the recent review of strategies to improve the implementation of healthy eating and physical activity interventions in schools published in the Cochrane Library in 2017 was required. The primary aim of this review was to examine the effectiveness of strategies that aim to improve the implementation of school-based policies, practices, or programs to address child diet, physical activity, or obesity. A systematic review of articles published between August 31, 2016 and April 10, 2019 utilizing Cochrane methodology was conducted. In addition to the 22 studies included in the original review, eight further studies were identified as eligible. The 30 studies sought to improve the implementation of healthy eating (n = 16), physical activity (n = 11), or both healthy eating and physical activity (n = 3). The narrative synthesis indicated that effect sizes of strategies to improve implementation were highly variable across studies. For example, among 10 studies reporting the proportion of schools implementing a targeted policy, practice, or program versus a minimal or usual practice control, the median unadjusted effect size was 16.2%, ranging from –0.2% to 66.6%. Findings provide some evidence to support the effectiveness of strategies in enhancing the nutritional quality of foods served at schools, the implementation of canteen policies, and the time scheduled for physical education.
Cypermethrin induces Sertoli cell apoptosis through mitochondrial pathway associated with calcium
Authors: Wang Heng-Xue , Zhang Rui , Li Zheng , Wang Lu-Shan , Yu Yue , Wang Qi , Ding Zhen , Zhang Jin-Peng , Zhang Mei-Rong , Xu Li-Chun 
Published: June 2021

Abstract
Cypermethrin, one kind of pyrethroid pesticides, has been shown to act as endocrine-disrupting chemicals (EDCs). The purpose of this study was to explore the roles of Sertoli cell apoptosis through mitochondrial pathway associated with calcium (Ca2+) in cypermethrin-induced male reproductive toxicology. The mouse Sertoli cells TM4 were cultured with 0 μM, 10 μM, 20 μM, 40 μM and 80 μM of cypermethrin. We used flow cytometry, Fluo-4 AM, western blot and JC-1 Assay Kit to examine apoptosis, intracellular Ca2+, expressions of mitochondrial apoptotic pathway-related proteins and mitochondrial membrane potential. We found cypermethrin increased apoptosis rate of TM4 cells significantly and with a significant increase in intracellular Ca2+ concentration. Cypermethrin significantly decreased the protein expressions of cytosolic B-cell lymphoma-2 (Bcl-2) and mitochondrial cytochrome c (Cyt-c). The protein expressions of cytosolic Bcl-2-associated x (Bax), Cyt-c, cleaved caspase-3, calmodulin (CaM), Ca2+/CaM-dependent protein kinases II (CaMKII) and phosphorylated CaMKII were increased significantly in cypermethrin-exposed TM4 cells. Cypermethrin decreased mitochondrial membrane potential significantly. Then, Bcl-2 family and Ca2+/CaM/CaMKII pathway participate in cypermethrin-induced homeostasis. Ca2+ overload activates mitochondrial pathway by increasing permeability of mitochondrial membrane and decreasing mitochondrial membrane potential. We suggest cypermethrin induces Sertoli cell apoptosis involving mitochondrial pathway associated with Ca2+ regulated by Bcl-2 family and Ca2+/CaM/CaMKII pathway. The study provides a new insight into mechanisms involved in cypermethrin-induced male reproductive toxicology.
Analytical and Omics-Based Advances in the Study of Drug-Induced Liver Injury
Authors: Kralj Thomas , Brouwer Kim L R , Creek Darren J 
Published: June 2021

Abstract
Drug-induced liver injury (DILI) is a significant clinical issue, affecting 1–1.5 million patients annually, and remains a major challenge during drug development—toxicity and safety concerns are the second-highest reason for drug candidate failure. The future prevalence of DILI can be minimized by developing a greater understanding of the biological mechanisms behind DILI. Both qualitative and quantitative analytical techniques are vital to characterizing and investigating DILI. In vitro assays are capable of characterizing specific aspects of a drug’s hepatotoxic nature and multiplexed assays are capable of characterizing and scoring a drug’s association with DILI. However, an even deeper insight into the perturbations to biological pathways involved in the mechanisms of DILI can be gained through the use of omics-based analytical techniques: genomics, transcriptomics, proteomics, and metabolomics. These omics analytical techniques can offer qualitative and quantitative insight into genetic susceptibilities to DILI, the impact of drug treatment on gene expression, and the effect on protein and metabolite abundance. This review will discuss the analytical techniques that can be applied to characterize and investigate the biological mechanisms of DILI and potential predictive biomarkers.
Imaging correlates of serum enzyme-linked immunoelectrotransfer blot (EITB) positivity in patients with parenchymal neurocysticercosis: results from 521 patients
Authors: Vasudevan Prabhakaran , Moorthy Ranjith K , Rebekah Grace , Jackson Ellen , Pamela Betcy Evangeline , Thamizhmaran Subashini , Manoj Josephin , Thanigachalam Anupriya , Drevets Douglas , Carabin Hélène , Rajshekhar Vedantam 
Published: June 2021

Abstract

Background
The presence of perilesional edema among patients with parenchymal neurocysticercosis (pNCC) of various lesion subtypes has not been correlated with results of serum enzyme-linked immunotransfer blot (EITB) for cysticercal antibodies.

Methods
In total, 521 patients with pNCC were classified into solitary cysticercus granuloma (SCG), multiple lesions, at least one of which was an enhancing granuloma (GMNCC), solitary calcified cysticercal lesion (SCC) and multiple calcified cysticercal lesions (CMNCC). The proportion of EITB positivity among each lesion subtype and its association with perilesional edema were determined.

Results
There were significantly higher positive EITB results in patients with GMNCC (90/111, 81.1%) compared with other lesion types. Perilesional edema was associated with positive EITB in patients with CMNCC. On univariate analysis, perilesional edema and GMNCC were associated with EITB positivity. On multivariate analysis, only GMNCC (OR 7.5; 95% CI 3.5 to 16.2) was significantly associated with EITB positivity.

Conclusions
In patients with pNCC, the presence of perilesional edema is associated with a higher probability of a positive EITB result in patients with CMNCC, suggesting a synchronicity in the mechanisms associated with formation of perilesional edema and the antibody response in this subtype. In patients with enhancing granulomas, edema is not an independent predictor of a positive EITB, suggesting that the enhancement itself is associated with a strong antibody response.
A Novel Signaling Pathway Connects Thiamine Biosynthesis, Bacterial Respiration, and Production of the Exopolysaccharide Amylovoran inErwinia amylovora
Authors: Yuan Xiaochen , McGhee Gayle C. , Slack Suzanne M. , Sundin George W. 
Published: June 2021

Erwinia amylovora is a plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. This bacterium colonizes host vascular tissues via the production of exopolysaccharides (EPSs) including amylovoran. It is well-established that the nearly ubiquitous plasmid pEA29 of E. amylovora is an essential virulence factor, but the underlying mechanism remains uncharacterized. Here, we demonstrated that pEA29 was required for E. amylovora to produce amylovoran and to form a biofilm, and this regulation was dependent on the thiamine biosynthesis operon thiOSGF. We then conducted carbohydrate and genetic analyses demonstrating that the thiamine-mediated effect on amylovoran production was indirect, as cells lacking thiOSGF produced an EPS that did not contain glucuronic acid, one of the key components of amylovoran, whereas the transcriptional activity and RNA levels of the amylovoran biosynthesis genes were not altered. Alternatively, addition of exogenous thiamine restored amylovoran production in the pEA29-cured strain of E. amylovora and positively impacted amylovoran production in a dose-dependent manner. Individual deletion of several chromosomal thiamine biosynthesis genes also affected amylovoran production, implying that a complete thiamine biosynthesis pathway is required for the thiamine-mediated effect on amylovoran production in E. amylovora. Finally, we determined that an imbalanced tricarboxylic acid cycle negatively affected amylovoran production, which was restored by addition of exogenous thiamine or overexpression of the thiOSGF operon. In summary, our report revealed a novel signaling pathway that impacts E. amylovora virulence in which thiamine biosynthesis enhances bacterial respiration that provides energetic requirements for the biosynthesis of EPS amylovoran.[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 .
Risk of Immune-related Adverse Events in Melanoma Patients With Preexisting Autoimmune Disease Treated With Immune Checkpoint Inhibitors
Authors: Tully Karl H. , Cone Eugene B. , Cole Alexander P. , Sun Maxine , Chen Xi , Marchese Maya , Roghmann Florian , Kilbridge Kerry L. , Trinh Quoc-Dien 
Published: June 2021

Objective:
The objective of this study was to examine the risk of immune-related adverse events (irAEs) in patients with a preexisting autoimmune disease (pAID) presenting with a cutaneous melanoma receiving an immune checkpoint inhibitor (ICI) therapy.

Methods:
Data from the Surveillance, Epidemiology, and End Results cancer registries and linked Medicare claims between January 2010 and December 2015 was used to identify patients diagnosed with cutaneous melanoma who had pAID or received ICI or both. Patients were then stratified into 3 groups: ICI+pAID, non-ICI+pAID, and ICI+non-pAID. Inverse probability of treatment weighted Cox proportional hazards regression models were fitted to assess the risk of cardiac, pulmonary, endocrine, and neurological irAE.

Results:
In total, 3704 individuals were included in the analysis. The majority of patients consisted of non-ICI+pAID patients (N=2706/73.1%), while 106 (2.9%) patients and 892 (24.1%) were classified as ICI+pAID and ICI+non-pAID, respectively. The risk of irAE was higher in the ICI+pAID group compared with the non-ICI+pAID and ICI+non-pAID, respectively (non-ICI: cardiac: hazard ratio [HR]=3.59, 95% confidence interval [CI]: 2.83-4.55; pulmonary: HR=3.94, 95% CI: 3.23-4.81; endocrine: HR=1.72, 95% CI: 1.53-1.93; neurological: HR=3.88, 95% CI: 2.30-6.57/non-pAID: cardiac: HR=3.83, 95% CI: 3.39-4.32; pulmonary: HR=2.08, 95% CI: 1.87-2.32; endocrine: HR=1.23, 95% CI: 1.14-1.32; neurological: HR=3.77, 95% CI: 2.75-5.18).

Conclusions:
Patients with a pAID face a significantly higher risk of irAEs. Further research examining the clinical impact of these events on the patients’ oncological outcome and quality of life is urgently needed given our findings of significantly worse rates of adverse events.
Sluggish Cognitive Tempo and Daytime Sleepiness Mediate Relationships Between Sleep and Academic Performance
Authors: O'Hare Kirstie , White Naomi , Harding Rebecca , Galland Barbara , Sellbom Martin , Shine Ben , Schaughency Elizabeth 
Published: June 2021

ABSTRACT:

Objective:
Sleep difficulties, daytime sleepiness, and sluggish cognitive tempo (SCT) are associated with impairments in academic performance. SCT refers to symptoms of sluggishness, tiredness/lethargy, and slowed thinking/processing, but despite symptom overlap with sleepiness, research examining interrelations of SCT with sleep and daytime sleepiness is limited. The aims of this study were to evaluate the relationship between SCT and daytime sleepiness and to examine pathways between sleep, daytime sleepiness, SCT, and academic performance.

Method:
Participants were a community sample of 1628 parents/caregivers of children aged between 6 and 10 years who completed questionnaires about their child's behavior, sleep, and academic performance. Confirmatory factor analysis was used to examine whether SCT was distinct from daytime sleepiness. Then, structural equation modeling was used to examine direct and indirect pathways between sleep (sleep-disordered breathing [SDB] symptoms, sleep duration, and latency), daytime sleepiness, SCT, and academic performance in reading, writing, and math.

Results:
SCT and daytime sleepiness were distinct but moderately correlated (r = 0.33, p ≤ 0.001). Sleep, in particular SDB symptoms, predicted increased SCT and daytime sleepiness. SCT was directly and negatively associated with all domains of academic performance, daytime sleepiness was associated with poorer reading performance, and longer sleep duration was directly associated with poorer math performance. SCT and, to a lesser extent, daytime sleepiness mediated effects of sleep on academic performance.

Conclusion:
SCT symptoms are important for understanding how sleep difficulties affect academic performance in children. Sleep, daytime sleepiness, and SCT are interrelated but distinct factors that affect children's academic performance.
Novel Technique for 27-Gauge Forceps–Assisted Transscleral Refixation of the Dislocated CZ70BD Intraocular Lens
Authors: Yip Lai Ting , Fong Angie , Tsang Chi Wai 
Published: June 2021

Purpose:
To report a novel technique for refixation of the dislocated CZ70BD intraocular lens.

Methods:
Posterior vitrectomy is performed with a 23-gauge or 25-gauge pars plana vitrectomy system with chandelier illumination. One needle of a double-arm 9-0 prolene needle is passed through the sclera 1.5 mm postlimbus. The needle is retrieved through the corneal paracentesis using a 27-G needle, and the suture is then cut. The suture end is passed through the eyelet of the dislocated CZ70BD intraocular lens inside the vitreous cavity. This is aided with a pair of 27-G MaxGrip forceps, which is inserted through a 27-G sclerostomy site at the intended scleral outlet. After passing the suture through the eyelet, the suture is pulled out at the 27-G sclerostomy site and a knot is tied and rotated. Similar procedure is performed for the second haptic if necessary.

Results:
Seven eyes were successfully operated on using this technique with a mean follow-up of 12.4 months. There was significant improvement in the best-corrected visual acuity after the operation (P = 0.016). Postoperative intraocular lens centration and alignment were satisfactory. One patient developed macula-on retinal detachment 1 month after the operation, which was successfully repaired without loss in the best-corrected visual acuity.

Conclusion:
The described novel technique is effective for refixation of dislocated CZ70BD intraocular lens.
LESSONS LEARNED FROM PACORES IN PROLIFERATIVE DIABETIC RETINOPATHY MANAGEMENT, DATA FROM LATIN AMERICA AND SPAIN
Authors: Arevalo J. Fernando , Beatson Bradley ,   for the Pan-American Collaborative Retina Study Group (PACORES)
Published: June 2021

Purpose:
To review the current literature on the management of proliferative diabetic retinopathy (PDR) and the challenges in the real-world setting.

Methods:
A review of the literature was performed on the therapeutic options for PDR, with a focus on the real-world data presented by the Pan-American Collaborative Retina Study Group.

Results:
Data from clinical trials and previous literature have reported that intravitreal antivascular endothelial growth factor (anti-VEGF) therapy is noninferior to the gold standard panretinal photocoagulation for treating PDR. However, PDR recurs rapidly after cessation of anti-VEGF therapy. This is especially important in the context of the diabetic population that is prone to loss to follow-up. In a real-world, prospective study, patients with prior panretinal photocoagulation followed by anti-VEGF therapy had higher rates of sustained PDR regression relative to anti-VEGF therapy alone.

Conclusion:
Owing to its transient therapeutic effect, anti-VEGF therapy in patients with diabetes can present a risk of recurrent retinal neovascularization and progression of PDR if follow-up cannot be guaranteed. A combined paradigm with less aggressive, immediate panretinal photocoagulation followed by anti-VEGF therapy should be considered in this population.
Association Between the Physical Work Environment and Work Functioning Impairment While Working From Home Under the COVID-19 Pandemic in Japanese Workers
Authors: Okawara Makoto , Ishimaru Tomohiro , Tateishi Seiichiro , Hino Ayako , Tsuji Mayumi , Ikegami Kazunori , Nagata Masako , Matsuda Shinya , Fujino Yoshihisa 
Published: June 2021

Objective:
To examine the relationship between the physical work environment and work function while working from home (WFH).

Methods:
A cross-sectional study was conducted. Data from 5760 workers who worked from home at least 1 day a month were analyzed. The physical work environment while WFH was used as an exposure factor. The presence of work functioning impairment was measured using Work Functioning impairment Scale (WFun). Mixed-effects logistic regression was used with the prefecture of residence as a random effect.

Results:
Work functioning impairment was significantly associated with a “No” response to recommended environments. The highest odds ratio (OR) of work functioning impairment was associated with a “No” response to “There is enough light to do my work” (adjusted odds ratio [aOR]: 2.02, 95% confidence interval [CI]: 1.73 to 2.35, P < 0.01).

Conclusions:
Improving work environments may prevent negative health effects and improve productivity while WFH.