bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type 2 Diabetes–Prevention Diet and All-Cause and Cause-Specific Mortality: A Prospective Study
Authors: Wang Chun-Rui , Hu Tian-Yang , Hao Fa-Bao , Chen Nan , Peng Yang , Wu Jing-Jing , Yang Peng-Fei , Zhong Guo-Chao 
Published: October 2021

AbstractWe aimed to examine whether type 2 diabetes–prevention diet, a dietary pattern previously developed for reducing type 2 diabetes risk, was associated with mortality in a US population. A population-based cohort of 86,633 subjects was identified from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (1993–2015). Dietary information was collected with a food frequency questionnaire. A dietary diabetes risk-reduction score was calculated to reflect adherence to this dietary pattern, with higher scores representing better adherence. Hazard ratios (HRs) and absolute risk differences (ARDs) in mortality rates per 10,000 person-years were calculated. After a mean follow-up of 13.6 years, 17,532 all-cause deaths were observed. Participants with the highest versus the lowest quintiles of dietary diabetes risk-reduction score were observed to have decreased risks of death from all causes (HR = 0.76, 95% CI: 0.72, 0.80; ARD: −81.94, 95% CI: −93.76, −71.12), cardiovascular disease (HR = 0.73, 95% CI: 0.66, 0.81; ARD: −17.82, 95% CI: −24.81, −11.30), and cancer (HR = 0.85, 95% CI: 0.78, 0.94; ARD: −9.92, 95% CI: −15.86, −3.59), which were modified by sex, smoking status, or alcohol consumption in subgroup analyses (P for interaction &lt; 0.05 for all). In conclusion, a type 2 diabetes–prevention diet confers reduced risks of death from all causes, cardiovascular disease, and cancer in this US population.
The Romance of Consequentiality
Authors: James David 
Published: October 2021

Abstract
Criticism has had a long-standing love affair with the prospect of its own real-world impact. An enchantment with the notion that literary-critical acts might not only change minds but also challenge political structures unites professional readers of all dispositions and allegiances, despite the climate of ideological friction and internecine dispute that has emerged from vociferous method debates in the past decade. Enduring, seductive, deeply consoling—this romance of consequentiality both supplies and reinforces criticism’s ongoing sense of self-importance, becoming a rich resource for sustaining our field’s dreams of social agency. This essay reflects on how that romance is at once instantiated and contested across this special issue, identifying its principal registers in critics’ defiance, longing, and self-conscious aggrandizement. Literary studies’ desire to leave some sort of material footprint has only been intensified by current pressures on the humanities to withstand institutional disinvestment and populist ridicule, on the one hand, while also interpreting and opposing systemically magnified forms of injustice, on the other. A certain baseline level of disciplinary faith is therefore impossible to ignore in these essays—including a faith in the possibility that criticism could still influence constituencies beyond those with whom, in solidarity, it already comfortably converses.
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools
Authors: Pockrandt Christopher , Steinegger Martin , Salzberg Steven L 
Published: October 2021

AbstractSummaryPhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments (MSAs). It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF/GTF files using precomputed tracks or computes and scores MSAs on the fly with MMseqs2.Availability and implementationPhyloCSF++ is released under the AGPLv3 license. Binaries and source code are available at https://github.com/cpockrandt/PhyloCSFpp. The software can be installed through bioconda. A variety of tracks can be accessed through ftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/.
Deepfakes and Digitally Altered Imagery Abuse: A Cross-Country Exploration of an Emerging form of Image-Based Sexual Abuse
Authors: Flynn Asher , Powell Anastasia , Scott Adrian J , Cama Elena 
Published: October 2021

AbstractDeepfake and digitally altered nude and sexual imagery is a serious and harmful emerging form of image-based sexual abuse (IBSA). This article reports on a multi-methods and cross-country study of IBSA across the United Kingdom, New Zealand and Australia, with a specific focus on the creation, distribution and threat to distribute deepfake and digitally altered imagery. Our findings suggest this abuse involves poly-victimization and poly-perpetration, and is disproportionately experienced and engaged in by those with mobility and/or communication assistance needs, members of the LGB+ community, males, young people and racial minorities (perpetration only). In this article, we discuss the pervasiveness and harms of deepfake and digitally altered imagery abuse, as well as challenges in legal responses, policing and prevention.
Minimising carbon and financial costs of steam sterilisation and packaging of reusable surgical instruments
Authors: Rizan Chantelle , Lillywhite Rob , Reed Malcolm , Bhutta Mahmood F 
Published: October 2021

Abstract

Background
The aim of this study was to estimate the carbon footprint and financial cost of decontaminating (steam sterilization) and packaging reusable surgical instruments, indicating how that burden might be reduced, enabling surgeons to drive action towards net-zero-carbon surgery.

Methods
Carbon footprints were estimated using activity data and prospective machine-loading audit data at a typical UK in-hospital sterilization unit, with instruments wrapped individually in flexible pouches, or prepared as sets housed in single-use tray wraps or reusable rigid containers. Modelling was used to determine the impact of alternative machine loading, opening instruments during the operation, streamlining sets, use of alternative energy sources for decontamination, and alternative waste streams.

Results
The carbon footprint of decontaminating and packaging instruments was lowest when instruments were part of sets (66–77 g CO2e per instrument), with a two- to three-fold increase when instruments were wrapped individually (189 g CO2e per instrument). Where 10 or fewer instruments were required for the operation, obtaining individually wrapped items was preferable to opening another set. The carbon footprint was determined significantly by machine loading and the number of instruments per machine slot. Carbon and financial costs increased with streamlining sets. High-temperature incineration of waste increased the carbon footprint of single-use packaging by 33–55 per cent, whereas recycling reduced this by 6–10 per cent. The absolute carbon footprint was dependent on the energy source used, but this did not alter the optimal processes to minimize that footprint.

Conclusion
Carbon and financial savings can be made by preparing instruments as part of sets, integrating individually wrapped instruments into sets rather than streamlining them, efficient machine loading, and using low-carbon energy sources alongside recycling.
Leveraging machine learning predictive biomarkers to augment the statistical power of clinical trials with baseline magnetic resonance imaging
Authors: Lou Carolyn , Habes Mohamad , Illenberger Nicholas A , Ezzati Ali , Lipton Richard B , Shaw Pamela A , Stephens-Shields Alisa J , Akbari Hamed , Doshi Jimit , Davatzikos Christos , Shinohara Russell T 
Published: October 2021

Abstract
A key factor in designing randomized clinical trials is the sample size required to achieve a particular level of power to detect the benefit of a treatment. Sample size calculations depend upon the expected benefits of a treatment (effect size), the accuracy of measurement of the primary outcome, and the level of power specified by the investigators. In this study, we show that radiomic models, which leverage complex brain MRI patterns and machine learning, can be utilized in clinical trials with protocols that incorporate baseline MR imaging to significantly increase statistical power to detect treatment effects. Akin to the historical control paradigm, we propose to utilize a radiomic prediction model to generate a pseudo-control sample for each individual in the trial of interest. Because the variability of expected outcome across patients can mask our ability to detect treatment effects, we can increase the power to detect a treatment effect in a clinical trial by reducing that variability through using radiomic predictors as surrogates. We illustrate this method with simulations based on data from two cohorts in different neurologic diseases, Alzheimer’s disease and glioblastoma multiforme. We present sample size requirements across a range of effect sizes using conventional analysis and models that include a radiomic predictor. For our Alzheimer’s disease cohort, at an effect size of 0.35, total sample size requirements for 80% power declined from 246 to 212 for the endpoint cognitive decline. For our glioblastoma multiforme cohort, at an effect size of 1.65 with the endpoint survival time, total sample size requirements declined from 128 to 74. This methodology can decrease the required sample sizes by as much as 50%, depending on the strength of the radiomic predictor. The power of this method grows with increased accuracy of radiomic prediction, and furthermore, this method is most helpful when treatment effect sizes are small. Neuroimaging biomarkers are a powerful and increasingly common suite of tools that are, in many cases, highly predictive of disease outcomes. Here, we explore the possibility of using MRI-based radiomic biomarkers for the purpose of improving statistical power in clinical trials in the contexts of brain cancer and prodromal Alzheimer’s disease. These methods can be applied to a broad range of neurologic diseases using a broad range of predictors of outcome to make clinical trials more efficient.
The molecular makeup of peripheral and central baroreceptors: stretching a role for Transient Receptor Potential (TRP), Epithelial Sodium Channel (ENaC), Acid Sensing Ion Channel (ASIC), and Piezo channels
Authors: Yang Hannah , Tenorio Lopes Luana , Barioni Nicole O , Roeske Jamie , Incognito Anthony V , Baker Jacquie , Raj Satish R , Wilson Richard J A 
Published: October 2021

Abstract
The autonomic nervous system maintains homeostasis of cardiovascular, respiratory, gastrointestinal, urinary, immune, and thermoregulatory function. Homeostasis involves a variety of feedback mechanisms involving peripheral afferents, many of which contain molecular receptors sensitive to mechanical deformation, termed mechanosensors. Here, we focus on the molecular identity of mechanosensors involved in the baroreflex control of the cardiovascular system. Located within the walls of the aortic arch and carotid sinuses, and/or astrocytes in the brain, these mechanosensors are essential for the rapid moment-to-moment feedback regulation of blood pressure (BP). Growing evidence suggests that these mechanosensors form a co-existing system of peripheral and central baroreflexes. Despite the importance of these molecules in cardiovascular disease and decades of research, their precise molecular identity remains elusive. The uncertainty surrounding the identity of these mechanosensors presents a major challenge in understanding basic baroreceptor function and has hindered the development of novel therapeutic targets for conditions with known arterial baroreflex impairments. Therefore, the purpose of this review is to (i) provide a brief overview of arterial and central baroreflex control of BP, (ii) review classes of ion channels currently proposed as the baroreflex mechanosensor, namely Transient Receptor Potential (TRP), Epithelial Sodium Channel (ENaC), Acid Sensing Ion Channel (ASIC), and Piezo, along with additional molecular candidates that serve mechanotransduction in other organ systems, and (iii) summarize the potential clinical implications of impaired baroreceptor function in the pathophysiology of cardiovascular disease.
Cryoballoon vs. radiofrequency catheter ablation: insights from NOrwegian randomized study of PERSistent Atrial Fibrillation (NO-PERSAF study)
Authors: Shi Li-Bin , Rossvoll Ole , Tande Pål , Schuster Peter , Solheim Eivind , Chen Jian 
Published: October 2021

Abstract

Aims
Pulmonary vein isolation (PVI) is still regarded as a cornerstone for treatment of persistent atrial fibrillation (AF). This study evaluated the effectiveness of PVI performed with cryoballoon ablation (CBA) in comparison with radiofrequency ablation (RFA) in patients with persistent AF.

Methods and results
A total of 101 patients with symptomatic persistent AF were enrolled and randomized (1:1) to CBA or RFA groups and followed up for 12 months. The primary endpoint was any documented recurrent atrial tachyarrhythmia (ATA) lasting longer than 30 s following a 3-month blanking period. Secondary endpoints were procedure-related complications, procedure and ablation duration, and fluoroscopy time. The ATA-free survival curves were estimated by Kaplan–Meier method and analysed by the log-rank test. According to intention-to-treat analysis, freedom from ATA was achieved in 36 out of 52 patients in the CBA group and 30 out of 49 patients in the RFA group (69.2% vs. 61.2%, P = 0.393). No difference in AF recurrence was found between the two groups (27.5% in CBA vs. 38.0% in RFA, P = 0.258), and less atrial flutter recurrence was documented in the CBA group compared with the RFA group (3.9% vs. 18.0%, P = 0.020). The procedure and ablation duration were significantly shorter in the CBA group (160 ± 31 vs. 197 ± 38 min, P &lt; 0.0001; 36.7 ± 9.5 vs. 55.3 ± 16.7 min, P &lt; 0.0001). There was no difference regarding fluoroscopy time (21.5 ± 7.8 vs. 23.4 ± 11.2 min, P &gt; 0.05).

Conclusion
Compared with RFA, PVI performed by CBA led to shorter procedure and ablation duration, with less atrial flutter recurrence and similar freedom from ATA at 12-month follow-up.
1588, the first ministerial revolution in France or the King in check
Authors: Fontvieille Damien 
Published: October 2021

Abstract
In 1588, Henri III dismissed his secrétaires d’État, chancelier, surintendant des finances and intendants. This first ministerial revolution provoked much surprise in France as the men who occupied these offices had been in power for a long time, were very experienced and seemed, to many, to have the king’s favour. This fall from grace raised many questions, the event being seen, for example, as an expression of the king’s desire to retake control of his kingdom or as the result of political differences between the monarch and his ministers. This article reconsiders the causes of this loss of favour from the point of view of the secrétaires d’État in order to show how this event revealed the new position they had acquired within the monarchical government. As the secrétaires foiled the king’s projects, examining their new role is, indeed, a way to put the impact of this fall from grace into perspective.
Bacterial adaptation by a transposition burst of an invading IS element
Authors: Miller Scott R , Abresch Heidi E , Ulrich Nikea J , Sano Emiko B , Demaree Andrew H , Oman Andrew R , Garber Arkadiy I 
Published: October 2021

Abstract
The general importance of transposable elements (TEs) for adaptive evolution remains unclear. This in part reflects a poor understanding of the role of TEs for adaptation in non-model systems. Here, we investigated whether insertion sequence (IS) elements are a major source of beneficial mutations during 400 generations of laboratory evolution of the cyanobacterium Acaryochloris marina strain CCMEE 5410, which has experienced a recent or on-going IS element expansion and has among the highest transposase gene contents for a bacterial genome. Most mutations detected in the eight independent experimental populations were IS transposition events. Surprisingly, however, the majority of these involved the copy-and-paste activity of only a single copy of an unclassified element (ISAm1) that has recently invaded the strain CCMEE 5410 genome. ISAm1 transposition was largely responsible for the highly repeatable evolutionary dynamics observed among populations. Notably, this included mutations in multiple targets involved in the acquisition of inorganic carbon for photosynthesis that were exclusively due to ISAm1 activity. These mutations were associated with an increase in linear growth rate under conditions of reduced carbon availability but did not appear to impact fitness when carbon was readily available. Our study reveals that the activity of a single transposase can fuel adaptation for at least several hundred generations but may also potentially limit the rate of adaptation through clonal interference.
Azimuthal anisotropy from eikonal tomography: example from ambient-noise measurements in the AlpArray network
Authors: Kästle E D , Molinari I , Boschi L , Kissling E ,   and the AlpArray Working Group
Published: October 2021

SUMMARY
Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150 000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wave fronts that affect the phase traveltime measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the traveltime field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at mid-crustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E–W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
A large animal model of RDH5-associated retinopathy recapitulates important features of the human phenotype
Authors: Occelli Laurence M , Daruwalla Anahita , De Silva Samantha R , Winkler Paige A , Sun Kelian , Pasmanter Nathaniel , Minella Andrea , Querubin Janice , Lyons Leslie A ,   99 Lives Consortium, Robson Anthony G , Heon Elise , Michaelides Michel , Webster Andrew R , Palczewski Krzysztof , Vincent Ajoy , Mahroo Omar A , Kiser Philip D , Petersen-Jones Simon M 
Published: October 2021

Abstract
Pathogenic variants in retinol dehydrogenase 5 (RDH5) attenuate supply of 11-cis-retinal to photoreceptors leading to a range of clinical phenotypes including night blindness because of markedly slowed rod dark adaptation and in some patients, macular atrophy. Current animal models (such as Rdh5−/− mice) fail to recapitulate the functional or degenerative phenotype. Addressing this need for a relevant animal model we present a new domestic cat model with a loss-of-function missense mutation in RDH5 (c.542G &gt; T; p.Gly181Val). As with patients, affected cats have a marked delay in recovery of dark adaptation. In addition, the cats develop a degeneration of the area centralis (equivalent to the human macula). This recapitulates the development of macular atrophy that is reported in a subset of patients with RDH5 mutations and is shown in this paper in seven patients with biallelic RDH5 mutations. There is notable variability in the age at onset of the area centralis changes in the cat, with most developing changes as juveniles but some not showing changes over the first few years of age. There is similar variability in development of macular atrophy in patients and while age is a risk factor, it is hypothesized that genetic modifying loci influence disease severity, and we suspect the same is true in the cat model. This novel cat model provides opportunities to improve molecular understanding of macular atrophy and test therapeutic interventions for RDH5-associated retinopathies.
Cwc27, associated with retinal degeneration, functions as a splicing factorin vivo
Authors: Bertrand Renae Elaine , Wang Jun , Li Yumei , Cheng Xuesen , Wang Keqing , Stoilov Peter , Chen Rui 
Published: October 2021

AbstractPrevious in vitro studies indicate that CWC27 functions as a splicing factor in the Bact spliceosome complex, interacting with CWC22 to form a landing platform for eIF4A3, a core component of the exon junction complex. However, the function of CWC27 as a splicing factor has not been validated in any in vivo systems. CWC27 variants have been shown to cause autosomal recessive retinal degeneration, in both syndromic and non-syndromic forms. The Cwc27K338fs/K338fs mouse model was shown to have significant retinal dysfunction and degeneration by 6 months of age. In this report, we have taken advantage of the Cwc27K338fs/K338fs mouse model to show that Cwc27 is involved in splicing in vivo in the context of the retina. Bulk RNA and single cell RNA-sequencing of the mouse retina showed that there were gene expression and splicing pattern changes, including alternative splice site usage and intron retention. Positive staining for CHOP suggests that ER stress may be activated in response to the splicing pattern changes and is a likely contributor to the disease mechanism. Our results provide the first evidence that CWC27 functions as a splicing factor in an in vivo context. The splicing defects and gene expression changes observed in the Cwc27K338fs/K338fs mouse retina provide insight to the potential disease mechanisms, paving the way for targeted therapeutic development.
A deterministic model for non-monotone relationship between translation of upstream and downstream open reading frames
Authors: Andreev D E , Baranov P V , Milogorodskii A , Rachinskii D 
Published: October 2021

Abstract
Totally asymmetric simple exclusion process (TASEP) modelling was shown to offer a parsimonious explanation for the experimentally confirmed ability of a single upstream open reading frames (uORFs) to upregulate downstream translation during the integrated stress response. As revealed by numerical simulations, the model predicts that reducing the density of scanning ribosomes upstream of certain uORFs increases the flow of ribosomes downstream. To gain a better insight into the mechanism which ensures the non-monotone relation between the upstream and downstream flows, in this work, we propose a phenomenological deterministic model approximating the TASEP model of the translation process. We establish the existence of a stationary solution featuring the decreasing density along the uORF for the deterministic model. Further, we find an explicit non-monotone relation between the upstream ribosome density and the downstream flow for the stationary solution in the limit of increasing uORF length and increasingly leaky initiation. The stationary distribution of the TASEP model, the stationary solution of the deterministic model and the explicit limit are compared numerically.