bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes
Authors: Terradas Gerard , Hermann Anita , James Anthony A , McGinnis William , Bier Ethan 
Published: November 2021

Abstract
Gene drives are programmable genetic elements that can spread beneficial traits into wild populations to aid in vector-borne pathogen control. Two different drives have been developed for population modification of mosquito vectors. The Reckh drive (vasa-Cas9) in Anopheles stephensi displays efficient allelic conversion through males but generates frequent drive-resistant mutant alleles when passed through females. In contrast, the AgNosCd-1 drive (nos-Cas9) in Anopheles gambiae achieves almost complete allelic conversion through both genders. Here, we examined the subcellular localization of RNA transcripts in the mosquito germline. In both transgenic lines, Cas9 is strictly coexpressed with endogenous genes in stem and premeiotic cells of the testes, where both drives display highly efficient conversion. However, we observed distinct colocalization patterns for the two drives in female reproductive tissues. These studies suggest potential determinants underlying efficient drive through the female germline. We also evaluated expression patterns of alternative germline genes for future gene-drive designs.
Diet-induced changes in titer support a discrete response of Wolbachia-associated plastic recombination in Drosophila melanogaster
Authors: Mostoufi Sabrina L , Singh Nadia D 
Published: November 2021

Abstract
Plastic recombination in Drosophila melanogaster has been associated with a variety of extrinsic and intrinsic factors such as temperature, starvation, and parasite infection. The bacterial endosymbiont Wolbachia pipientis has also been associated with plastic recombination in D. melanogaster. Wolbachia infection is pervasive in arthropods and this infection induces a variety of phenotypes in its hosts, the strength of which can depend on bacterial titer. Here, we test the hypothesis that the magnitude of Wolbachia-associated plastic recombination in D. melanogaster depends on titer. To manipulate titer, we raised Wolbachia-infected and uninfected flies on diets that have previously been shown to increase or decrease Wolbachia titer relative to controls. We measured recombination in treated and control individuals using a standard backcrossing scheme with two X-linked visible markers. Our results recapitulate previous findings that Wolbachia infection is associated with increased recombination rate across the yellow-vermillion interval of the X chromosome. Our data show no significant effect of diet or diet by Wolbachia interactions on recombination, suggesting that diet-induced changes in Wolbachia titer have no effect on the magnitude of plastic recombination. These findings represent one of the first steps toward investigating Wolbachia-associated plastic recombination and demonstrate that the phenotype is a discrete response rather than a continuous one.
Identification of condition-specific biomarker systems in uterine cancer
Authors: Hickman Allison R , Hang Yuqing , Pauly Rini , Feltus Frank A 
Published: November 2021

AbstractUterine cancer is the fourth most common cancer among women, projected to affect 66,000 US women in 2021. Uterine cancer often arises in the inner lining of the uterus, known as the endometrium, but can present as several different types of cancer, including endometrioid cancer, serous adenocarcinoma, and uterine carcinosarcoma. Previous studies have analyzed the genetic changes between normal and cancerous uterine tissue to identify specific genes of interest, including TP53 and PTEN. Here we used Gaussian Mixture Models to build condition-specific gene coexpression networks for endometrial cancer, uterine carcinosarcoma, and normal uterine tissue. We then incorporated uterine regulatory edges and investigated potential coregulation relationships. These networks were further validated using differential expression analysis, functional enrichment, and a statistical analysis comparing the expression of transcription factors and their target genes across cancerous and normal uterine samples. These networks allow for a more comprehensive look into the biological networks and pathways affected in uterine cancer compared with previous singular gene analyses. We hope this study can be incorporated into existing knowledge surrounding the genetics of uterine cancer and soon become clinical biomarkers as a tool for better prognosis and treatment.
ABHD5 frameshift deletion in Golden Retrievers with ichthyosis
Authors: Kiener Sarah , Wiener Dominique J , Hopke Kaitlin , Diesel Alison B , Jagannathan Vidhya , Mauldin Elizabeth A , Casal Margret L , Leeb Tosso 
Published: November 2021

Abstract
Ichthyoses are hereditary skin disorders characterized by the formation of scales and defects in the outermost layer of the epidermis. In dogs, at least six different breed-specific ichthyoses including a relatively common PNPLA1-related autosomal recessive ichthyosis in Golden Retrievers are known. In this study, we investigated 14 Golden Retrievers with scales that were not homozygous for the mutant PNPLA1 allele suggesting a genetically distinct new form of ichthyosis. Histopathological examinations showed lamellar, orthokeratotic hyperkeratosis, and mildly hyperplastic epidermis that led to the diagnosis of a nonepidermolytic ichthyosis. Combined linkage and homozygosity mapping in 14 cases and 30 nonaffected family members delimited a critical interval of ∼12.7 Mb on chromosome 23. Whole-genome sequencing of an affected dog revealed a single protein-changing variant within this region that was not present in 795 control genomes. The identified variant is a 14 bp deletion in the ABHD5 gene (c.1006_1019del), leading to a frameshift and altering the last 14 codons p.(Asp336Serfs*6). The genotypes at this variant showed perfect cosegregation with the ichthyosis phenotype in a large family comprising 14 cases and 72 controls. ABHD5 encodes an acyltransferase required for lipid metabolism. In humans, variants in ABHD5 cause Chanarin-Dorfman syndrome, a neutral lipid storage disease with ichthyosis. Our data in dogs together with the knowledge on the effects of ABHD5 variants in humans strongly suggest ABHD5:c.1006_1019del as candidate causative genetic variant for a new canine form of ichthyosis, which we propose to designate as Golden Retriever ichthyosis type 2 (ICH2).
Monitoring the changing seismic site response of a fast-moving rockslide (Brienz/Brinzauls, Switzerland)
Authors: Häusler Mauro , Gischig Valentin , Thöny Reto , Glueer Franziska , Donat Fäh 
Published: November 2021

SUMMARYSeismic measurements on unstable rock slopes are a complementary tool to surface displacement surveys to characterize and monitor landslides. A key parameter is seismic amplification, which tends to scale with the degree of rock mass degradation. Amplification also provides a direct measure of how the wavefield is intensified during seismic loading, eventually leading to coseismic failure. Here we present the dynamic response of the fast-moving Brienz/Brinzauls rock slope instability in Switzerland (10 $ \times $ 106 to 25 $ \times $ 106 m3), which threatens settlements and infrastructure in the area. The rockslide shows strong seismic amplification at two resonant frequencies with factors of up to 11 and wavefield polarization influenced by the local fracture network orientation. We monitored the dynamic response over a period of 30 months using ambient vibrations and regional earthquake recordings. We observed a change in wavefield polarization of up to 50°, coinciding with a rotation of the relative surface displacement vector field measured by geodetic systems, highlighting the linkage between wavefield polarization and stress field (i.e. rock mass kinematics). For the analysis of secondary, relative surface displacements, we propose a singular value filtering of the displacement field to remove the principal component of landslide motion. In addition, we found increased seismic amplification values after periods of strong precipitation, providing empirical field evidence that the local precipitation history is a key parameter for assessing the hazard of earthquake-induced slope failure.
AIM against survey fraud
Authors: Habib Daniel , Jha Nishant 
Published: November 2021

Abstract

Objectives
Although there exists a variety of anonymous survey software, this study aimed to develop an improved system that incentivizes responses and proactively detects fraud attempts while maintaining anonymity.

Materials and Methods
The Anonymous Incentive Method (AIM) was designed to utilize a Secure Hash Algorithm, which deterministically assigned anonymous identifiers to respondents. An anonymous raffle system was established to randomly select participants for a reward. Since the system provided participants with their unique identifiers and passwords upon survey completion, participants were able to return to the survey website, input their passwords, and receive their rewards at a later date. As a case study, the validity of this novel approach was assessed in an ongoing study on vaping in high school friendship networks.

Results
AIM successfully assigned irreversible, deterministic identifiers to survey respondents. Additionally, the particular case study used to assess the efficacy of AIM verified the deterministic aspect of the identifiers.

Discussion
Potential limitations, such as scammers changing the entry used to create the identifier, are acknowledged and given practical mitigation protocols. Although AIM exhibits particular usefulness for network studies, it is compatible with a wide range of applications to help preempt survey fraud and expedite study approval.

Conclusion
The improvements introduced by AIM are 2-fold: (1) duplicate responses can be filtered out while maintaining anonymity and (2) the requirement for the participant to keep their identifier and password for some time before returning to the survey website to claim a reward ensures that rewards only go to actual respondents.
Impact of forage diversity on forage productivity, nutritive value, beef cattle performance, and enteric methane emissions
Authors: Thompson Logan R , Maciel Isabella C F , Rodrigues Patricia D R , Cassida Kim A , Rowntree Jason E 
Published: November 2021

Abstract
Greenhouse gas emissions from the beef industry are largely attributed to the grazing sector, specifically from beef cattle enteric methane emissions. Therefore, the study objective was to examine how forage diversity impacts forage productivity, nutritive value, animal performance, and enteric methane emissions. This study occurred over three consecutive grazing seasons (2018 to 2020) and compared two common Midwest grazing mixtures: 1) a simple, 50:50 alfalfa:orchardgrass mixture (SIMP) and 2) a botanically diverse, cool-season species mixture (COMP). Fifty-six steers and heifers were adapted to an Automated Head Chamber System (AHCS) each year (C-Lock Inc., Rapid City, SD) and stratified into treatment groups based on acclimation visitation. Each treatment consisted of four pastures, three 3.2-ha and one 1.6-ha, with eight and four animals each, respectively. Forage production was measured biweekly in pre- and postgrazed paddocks, and forage nutritive value was analyzed using near-infrared reflectance spectroscopy. Shrunk body weights were taken monthly to determine animal performance. Forage availability did not differ between treatments (P = 0.69) but tended lower in 2018 (P = 0.06; 2.40 t dry matter ha−1) than 2019 (2.92 t dry matter ha−1) and 2020 (P = 0.10; 2.81 t dry matter ha−1). Crude protein was significantly lower for COMP in 2018 compared with SIMP. Forage acid detergent fiber content was significantly lower for the COMP mixture (P = 0.02). The COMP treatment resulted higher dry matter digestibility (IVDMD48) in 2018 and 2019 compared with the SIMP treatment (P &lt; 0.01). Animal performance did not differ between treatments (P &gt; 0.50). There was a tendency for the COMP treatment to have lower enteric CH4 production on a g d−1 basis (P = 0.06), but no difference was observed on an emission intensity basis (g CH4 kg−1 gain; P = 0.56). These results would indicate that adoption of the complex forage mixture would not result in improved forage productivity, animal performance, or reduced emission intensity compared with the simple forage mixture.
Evaluation for Arts-Based Research Performance: Audience Perceptions ofRising from the Ashes
Authors: Viega Michael 
Published: November 2021

AbstractThe purpose of the study is to understand how audiences evaluated an arts-based research performance called Rising from the Ashes. Audience evaluation promises egalitarian and pluralistic perspectives that may assist artist-as-researchers with gaining new insight into out of performative arts-based research results. Rising from the Ashes was performed several times between 2015 and 2019. Evaluations were provided to six different audiences and consisted of rating-scale and open-ended questions based on general criteria for judging arts-based research: incisiveness, concision, generativity, social significance, evocation and illumination, and coherence. Descriptive rating scores and thematic analysis of open-ended questions aided in the artist-as-researcher’s understanding of how audiences responded to the performances. Descriptive scores showed that audiences strongly agreed that the performance was concise, incisive, and evocative and illuminating. The performance was less likely to support audiences’ understanding of the social issues addressed in the study, which implied decreased generativity and social significance. Open-ended questions enhanced and supported rating-scale responses as well as revealed specific elements of the performance that addressed its coherence. The results deepened the artists-as-researcher’s understanding of potential strengths and limitations of Rising from the Ashes based on the audience evaluations. Implications for arts-based research evaluation in music therapy, particularly related to music performance, are discussed.
Critical Appraisal of Paralyzed Veterans of America Guidelines in Spinal Cord Injury: An International Collaborative Study Using the Appraisal of Guidelines for Research and Evaluation II Instrument (AGREE II)
Authors: Liang Ning , Wu Sizhan , Roberts Simon , Makaram Navnit , Ngwayi James Reeves Mbori , Porter Daniel Edward 
Published: November 2021

ABSTRACT

Introduction
Spinal cord injuries (SCI) in military personnel, veterans, and others require an evidence-based, multidisciplinary approach to their care. This appraisal used the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument to evaluate the methodological quality of clinical guidelines for the management of SCI published by the Paralyzed Veterans of America (PVA) organization.

Materials and Methods
We searched clinical guidelines on SCI published by PVA until December 2019. Four appraisers across three international centers independently evaluated the quality of eligible clinical guidelines using AGREE II. Mean AGREE II scores for each domain were calculated. In higher quality domains, scores for individual items were analyzed.

Results
A total of 12 guidelines published by PVA on SCI were assessed. Mean scores for all six domains were as follows: Scope and Purpose (78.8%), Stakeholder Involvement (63.7%), Rigor of Development (68.4%), Clarity of Presentation (80.1%), Applicability (53.0%), and Editorial Independence (28.5%). The mean score for the overall quality of all PVA guidelines was 71.9% (95% CI: 69.7–74.1). No guideline was assessed as “not recommended” by any appraiser. Overall quality was significantly associated with year of publication (rs = 0.754, P = 0.0046). Overall agreement among appraisers was excellent (intraclass correlation coefficients for each guideline ranged from 0.96 to 0.99).

Conclusions
PVA guidelines for the management of SCI demonstrated acceptable or good quality across most domains. We recommend the use of PVA guidelines for the assessment and treatment of SCI and related disorders. The quality of PVA guidelines for the management of SCI have improved over time.
Sex-Specific Physical Performance Adaptive Responses Are Elicited After 10 Weeks of Load Carriage Conditioning
Authors: Wills Jodie A , Saxby David J , Glassbrook Daniel J , Doyle Timothy L A 
Published: November 2021

ABSTRACTIntroductionThe purpose of this study was to identify and characterize sex-specific physical and psychophysical performance adaptations in response to a novel 10-week training program.Materials and MethodsFifteen males and thirteen females completed a standardized load carriage task (5 km at 5.5 km.h−1, wearing a 23 kg torso-borne vest) before and after 10 weeks of resistance and load carriage training. Psychophysical responses (i.e., heart rate and ratings of perceived exertion) were measured throughout the load carriage task. Physical performance (i.e., countermovement and squat jumps, push-ups, sit-ups, and beep test) was measured at before, mid-way, and after the training program (weeks 0, 6, and 11, respectively).ResultsTraining elicited significant improvements in squat jump maximal force, push-ups, and beep test performance (P &lt; .05). Males outperformed females in all performance measures, with interactions (time, sex) for push-ups, sit-ups, and beep test performance. After training, aerobic capacity improved by 5.4% (42.9 mL· kg−1· min−1 to 45.2 mL· kg−1· min−1) in males but did not improve in females. Psychophysical responses decreased for both sexes (P &lt; .05) during the load carriage task post-training.ConclusionWhile 10 weeks of standardized training elicited positive adaptations in both physical and psychophysical performance, sex-specific differences were still evident. To lessen these differences, sex-specific training should be considered to optimize load carriage performance.
The physics of non-ideal general relativistic magnetohydrodynamics
Authors: Andersson N , Hawke I , Celora T , Comer G L 
Published: November 2021

ABSTRACT
We consider a framework for non-ideal magnetohydrodynamics in general relativity, paying particular attention to the physics involved. The discussion highlights the connection between the microphysics (associated with a given equation of state) and the global dynamics (from the point of view of numerical simulations), and includes a careful consideration of the assumptions that lead to ideal and resistive magnetohydrodynamics. We pay particular attention to the issue of local charge neutrality, which tends to be assumed but appears to be more involved than is generally appreciated. While we do not resolve all the involved issues, we highlight how some of the assumptions and simplifications may be tested by simulations. The final formulation prepares the ground for a new generation of models of relevant astrophysical scenarios.
GRB 191016A: a highly collimated gamma-ray burst jet with magnetized energy injection
Authors: Shrestha M , Steele I A , Kobayashi S , Jordana-Mitjans N , Smith R J , Jermak H , Arnold D , Mundell C G , Gomboc A , Guidorzi C 
Published: November 2021

ABSTRACT
Long gamma-ray burst GRB 191016A was a bright and slow rising burst that was detected by the Swift satellite and followed up by ground based Liverpool Telescope (LT). LT follow up started 2411 s after the Swift Burst Alert Telescope (BAT) trigger using imager IO:O around the time of the late optical peak. From 3987–7687 s, we used the LT polarimeter RINGO3 to make polarimetric and photometric observations of the GRB simultaneously in the V, R, and I bands. The combined optical light curve shows an initial late peak followed by a decline until 6147 s, 6087 s, and 5247 s for I, R, and V filters respectively followed by a flattening phase. There is evidence of polarization at all phases including polarization ($P = 14.6 \pm 7.2 {{\ \rm per\ cent}}$) which is coincident with the start of the flattening phase. The combination of the light curve morphology and polarization measurement favours an energy injection scenario where slower magnetized ejecta from the central engine catches up with the decelerating blast wave. We calculate the minimum energy injection to be ΔE/E &gt; 0.36. At a later time, combining the optical light curve from Burst Observer and Optical Transient Exploring System (BOOTES) (reported via GCN) and IO:O we see evidence of a jet break with jet opening angle 2°.
Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference
Authors: Said Iskander , McGurk Michael P , Clark Andrew G , Barbash Daniel A 
Published: November 2021

Abstract
Transposable elements (TEs) are self-replicating “genetic parasites” ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their ancestral forms. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85 Drosophila melanogaster genomes and found that the genetic variation of several TE families shows significant population structure that arises from the population-specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a pattern whereby new TE variants arise by mutation and then increase in copy number, followed by the host producing antisense piRNAs that may be used to silence these emerging variants.
Treatment strategies for elderly-onset rheumatoid arthritis in the new era
Authors: Sugihara Takahiko 
Published: November 2021

ABSTRACTElderly-onset rheumatoid arthritis (EORA) is characterized by acute onset and clinical features of high disease activity. Anti-cyclic citrullinated peptide antibody (ACPA) positivity or the presence of bone erosions predicts a radiological joint destruction of EORA, but ACPA-negative EORA with a polymyalgia rheumatica (PMR) phenotype may also present. Biological disease-modifying antirheumatic drugs (bDMARDs) and Janus kinase inhibitors were beneficial both in older and in younger patients in terms of risk–benefit balance. Implementation of a treat-to-target strategy could improve EORA outcomes, but older patients have more age-related comorbidities and interstitial lung disease than younger patients. Baseline comorbidities, more frequent methotrexate dose-dependent adverse events, serious infections, cardiovascular disease events, and malignancy all influence the choice of treatment and the treatment goals for older patients. Based on articles reviewed here, it is suggested that current treatment strategies for younger patients are also useful for ACPA-positive EORA and for ACPA-negative EORA with bone erosion. Differential diagnosis of ACPA-negative EORA without erosive arthritis and PMR with peripheral manifestations is challenging, and the treatment strategy of patients presenting with this overlap phenotype remained unclear. An appropriate treatment strategy for all patients with EORA still needs to be developed.