bluuebunny/crossref_metadata_2025 huggingface dataset:
TransAC4C—a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution
Authors: Liu Ruijie , Zhang Yuanpeng , Wang Qi , Zhang Xiaoping
Published: May 2024

N4-acetylcytidine (ac4C) is a modification found in ribonucleic acid (RNA) related to diseases. Expensive and labor-intensive methods hindered the exploration of ac4C mechanisms and the development of specific anti-ac4C drugs. Therefore, an advanced prediction model for ac4C in RNA is urgently needed. Despite the construction of various prediction models, several limitations exist: (1) insufficient resolution at base level for ac4C sites; (2) lack of information on species other than Homo sapiens; (3) lack of information on RNA other than mRNA; and (4) lack of interpretation for each prediction. In light of these limitations, we have reconstructed the previous benchmark dataset and introduced a new dataset including balanced RNA sequences from multiple species and RNA types, while also providing base-level resolution for ac4C sites. Additionally, we have proposed a novel transformer-based architecture and pipeline for predicting ac4C sites, allowing for highly accurate predictions, visually interpretable results and no restrictions on the length of input RNA sequences. Statistically, our work has improved the accuracy of predicting specific ac4C sites in multiple species from less than 40% to around 85%, achieving a high AUC > 0.9. These results significantly surpass the performance of all existing models.
scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data
Authors: Huang Yixiang , Jiang Hao , Ching Wai-Ki
Published: May 2024

With the emergence of large amount of single-cell RNA sequencing (scRNA-seq) data, the exploration of computational methods has become critical in revealing biological mechanisms. Clustering is a representative for deciphering cellular heterogeneity embedded in scRNA-seq data. However, due to the diversity of datasets, none of the existing single-cell clustering methods shows overwhelming performance on all datasets. Weighted ensemble methods are proposed to integrate multiple results to improve heterogeneity analysis performance. These methods are usually weighted by considering the reliability of the base clustering results, ignoring the performance difference of the same base clustering on different cells. In this paper, we propose a high-order element-wise weighting strategy based self-representative ensemble learning framework: scEWE. By assigning different base clustering weights to individual cells, we construct and optimize the consensus matrix in a careful and exquisite way. In addition, we extracted the high-order information between cells, which enhanced the ability to represent the similarity relationship between cells. scEWE is experimentally shown to significantly outperform the state-of-the-art methods, which strongly demonstrates the effectiveness of the method and supports the potential applications in complex single-cell data analytical problems.
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys
Authors: Zong Yuxuan , Zhao Hongyu , Wang Tao
Published: May 2024

Potentially pathogenic or probiotic microbes can be identified by comparing their abundance levels between healthy and diseased populations, or more broadly, by linking microbiome composition with clinical phenotypes or environmental factors. However, in microbiome studies, feature tables provide relative rather than absolute abundance of each feature in each sample, as the microbial loads of the samples and the ratios of sequencing depth to microbial load are both unknown and subject to considerable variation. Moreover, microbiome abundance data are count-valued, often over-dispersed and contain a substantial proportion of zeros. To carry out differential abundance analysis while addressing these challenges, we introduce mbDecoda, a model-based approach for debiased analysis of sparse compositions of microbiomes. mbDecoda employs a zero-inflated negative binomial model, linking mean abundance to the variable of interest through a log link function, and it accommodates the adjustment for confounding factors. To efficiently obtain maximum likelihood estimates of model parameters, an Expectation Maximization algorithm is developed. A minimum coverage interval approach is then proposed to rectify compositional bias, enabling accurate and reliable absolute abundance analysis. Through extensive simulation studies and analysis of real-world microbiome datasets, we demonstrate that mbDecoda compares favorably with state-of-the-art methods in terms of effectiveness, robustness and reproducibility.
Colloidal titration: from the perspective of stability constants between oppositely charged polyelectrolytes
Authors: Hattori Toshiaki
Published: May 2024

Colloidal titration is a unique method to measure the concentration of charged groups based on the association between cationic and anionic colloids. Titrimetry must involve a unidirectional reaction with a large formation constant. However, the underlying polyelectrolyte complex (PEC) for colloidal titration lacks sufficient data regarding the stability constants (KI). To date, the stoichiometry of colloidal titration has not been discussed in relation to KI. Thus, in this paper, we reviewed PEC studies by focusing on KI and discuss colloidal titration comprehensively. The topics include the history of its establishment, the method to calculate KI, and the special characteristics of PEC compared with ion association reactions, the practical use of colloid titration, and the condition by which the stability constant can be increased. In terms of analytical reagents, polyelectrolytes are similar to (but positioned as a subspecies of) ion association reagents. Ionic strength strongly affects KIs values. Excluding coaggregation effects, the maximum values of log10  KI obtained from reliable data were found to decrease linearly as ionic strength increases logarithmically. The critical line connected with the maximum KI value at each ionic strength can be used as an empirical reference value and facilitate the analytical design of colloidal titration.
‘You’re speaking my language’: an eczema case complicated by social determinants of health
Authors: Lin Alice J , Le Thomas K , Patton Timothy
Published: May 2024

Social determinants of health (SDOH) have received increasing attention in all aspects of healthcare. However, the role of SDOH in dermatological care is an ongoing area of research. We demonstrate the occupational, language and literacy constraints that complicate the diagnosis and treatment of an immigrant Vietnamese nail salon technician with chronic dyshidrotic eczema. This case serves to illustrate the importance of SDOH considerations in optimizing dermatological care.
A retrospective study of adult patients with Parry–Romberg syndrome
Authors: Sandler Mykayla , Shah Nishi , Fedeles Flavia , Tiao Janice
Published: May 2024

Parry–Romberg syndrome (PRS), also known as progressive hemifacial atrophy, is characterized by atrophy of the skin and subcutaneous tissue, including muscle, bone and cartilage. PRS is a clinical diagnosis, although supportive imaging and histology may be obtained. We present a case series of 10 adult patients with a diagnosis of PRS seen at Massachusetts General Hospital and Brigham and Women’s Hospital from 2000 to 2021. Nine of 10 patients were women, with a mean (SD) age at onset of 27.3 (12.1) years and a mean (SD) of 12.4 (7.8) years between disease onset and diagnosis. Of the 10 patients, 4 had biopsies with supportive histopathology findings and 7 had positive imaging findings. Patients typically received both medical and surgical treatments.
The reliability and quality of YouTube videos about isotretinoin treatment and suicide
Authors: Ünlü Açıkel Sezin , Özdemir Ahmet Kağan , Emre Selma
Published: May 2024

Background

Seeking health information online has drastically increased. Isotretinoin is one of the agents used to treat acne.

Objectives

In this study, we aimed to investigate the reliability and quality of YouTube videos related to acne treatment. There is a misconception that use of isotretinoin increases risk of suicide.

Methods

We used the terms ‘isotretinoin suicide’ and ‘acne treatment suicide’ to search YouTube videos. Videos that were not in English, were irrelevant, or were devoid of audio were not included. The information in the videos was primarily categorized as ‘reliable’ or ‘unreliable’ based on its scientific validation. DISCERN and the Global Quality Score were used to evaluate the videos’ overall quality.

Results

In total, 200 videos were examined and 112 videos were included in the study. Of these, 39 videos (34.8%) were found to be reliable, and 73 videos (65.2%) were found to be unreliable. The DISCERN values of videos uploaded by physicians or professional organizations, and health information websites were found to be significantly higher. There were statistically significant negative correlations between DISCERN score and both video length and the length of time the video was on YouTube, while a positive correlation was observed between DISCERN score and the number of subscribers.

Conclusions

Although videos created by dermatologists have become widespread in recent years, they are still insufficient. Patient experience videos mostly contain information that does not reflect reality, and they emphasize that isotretinoin increases the risk of suicide without evidence. As the number of dermatologists posting videos on YouTube increases, the chances of people accessing correct information will increase.
Auditory change detection and visual selective attention: association between MMN and N2pc
Authors: Kong Yuanjun , Zhao Chenguang , Li Dongwei , Li Bingkun , Hu Yiqing , Liu Hongyu , Woolgar Alexandra , Guo Jialiang , Song Yan
Published: May 2024

While the auditory and visual systems each provide distinct information to our brain, they also work together to process and prioritize input to address ever-changing conditions. Previous studies highlighted the trade-off between auditory change detection and visual selective attention; however, the relationship between them is still unclear. Here, we recorded electroencephalography signals from 106 healthy adults in three experiments. Our findings revealed a positive correlation at the population level between the amplitudes of event-related potential indices associated with auditory change detection (mismatch negativity) and visual selective attention (posterior contralateral N2) when elicited in separate tasks. This correlation persisted even when participants performed a visual task while disregarding simultaneous auditory stimuli. Interestingly, as visual attention demand increased, participants whose posterior contralateral N2 amplitude increased the most exhibited the largest reduction in mismatch negativity, suggesting a within-subject trade-off between the two processes. Taken together, our results suggest an intimate relationship and potential shared mechanism between auditory change detection and visual selective attention. We liken this to a total capacity limit that varies between individuals, which could drive correlated individual differences in auditory change detection and visual selective attention, and also within-subject competition between the two, with task-based modulation of visual attention causing within-participant decrease in auditory change detection sensitivity.
Urbanization does not increase “object curiosity” in vervet monkeys, but semi-urban individuals selectively explore food-related anthropogenic items
Authors: Ellington Lindsey , Mercier Stephanie , Motes-Rodrigo Alba , van de Waal Erica , Forss Sofia
Published: May 2024

Urban environments expose animals to abundant anthropogenic materials and foods that facilitate foraging innovations in species with opportunistic diets and high behavioral flexibility. Neophilia and exploration tendency are believed to be important behavioral traits for animals thriving in urban environments. Vervet monkeys (Chlorocebus pygerythrus) are one of few primate species that have successfully adapted to urban environments, thus making them an ideal species to study these traits. Using a within-species cross-habitat approach, we compared neophilia and exploration of novel objects (jointly referred to as “object curiosity”) between semi-urban, wild, and captive monkeys to shed light on the cognitive traits facilitating urban living. To measure “object curiosity,” we exposed monkeys to various types of novel stimuli and compared their approaches and explorative behavior. Our results revealed differences in the number of approaches and explorative behavior toward novel stimuli between the habitat types considered. Captive vervet monkeys were significantly more explorative than both semi- urban and wild troops, suggesting that positive experiences with humans and lack of predation, rather than exposure to human materials per se, influence object curiosity. Across habitats, juvenile males were the most explorative age-sex class. This is likely due to males being the dispersing sex and juveniles being more motivated to learn about their environment. Additionally, we found that items potentially associated with human food, elicited stronger explorative responses in semi-urban monkeys than non-food related objects, suggesting that their motivation to explore might be driven by “anthrophilia”, that is, their experience of rewarding foraging on similar anthropogenic food sources. We conclude that varying levels of exposure to humans, predation and pre-exposure to human food packaging explain variation in “object curiosity” in our sample of vervet monkeys.
Fibrosis-related Transcriptome Unveils a Distinctive Remodelling Matrix Pattern in Penetrating Ileal Crohn’s Disease
Authors: Tavares de Sousa Helena , Ferreira Marta , Gullo Irene , Rocha Ana Mafalda , Pedro Ana , Leitão Dina , Oliveira Carla , Carneiro Fátima , Magro Fernando
Published: May 2024

Background and Aims

Stricturing [B2] and penetrating [B3] ileal Crohn’s disease have been reported to present similar levels of histopathological transmural fibrosis. This study aimed to compare the fibrosis-related transcriptomic profiles of penetrating and stricturing ileal Crohn’s disease.

Methods

Using Nanostring technology and comparative bioinformatics, we analysed the expression of 787 fibrosis-related genes in 36 ileal surgical specimens, 12 B2 and 24 B3, the latter including 12 cases with associated stricture[s] [B3s] and 12 without [B3o]. Quality control of extracted RNA was performed according to Nanostring parameters and principal component analysis for the distribution analysis. For the selection of the differentially expressed genes, a p-adjusted <0.05 and fold change ≤-1.5 or ≥1.5 were adopted. Quantitative polymerase chain reaction (qPCR) and immunohistochemistry analyses were used to validate selected differentially expressed genes.

Results

We included 34 patients with B2 and B3 phenotypes, balanced for age at diagnosis, age at surgery, gender, Crohn’s disease localisation, perianal disease, and therapy. Inflammation and fibrosis histopathological scoring were similar in all cases. B2 and B3 groups showed a very good clustering regarding 30 significantly differentially expressed genes, all being remarkably upregulated in B3. More than half of these genes were involved in Crohn’s disease fibrogenesis, and eight differentially expressed genes were so in other organs. The most significantly active biological processes and pathways in penetrating disease were response to TGFβ and matrix organisation and degradation, as validated by immunohistochemistry.

Conclusions

Despite the histopathological similarities in fibrosis between stricturing and penetrating ileal Crohn’s disease, their fibrosis-related transcriptomic profiles are distinct. Penetrating disease exhibits a distinctive transcriptomic landscape related to enhanced matrix remodelling.
The Effect of Non-pooled Multidonor Faecal Microbiota Transplantation for Inducing Clinical Remission in Patients with Chronic Pouchitis: Results from a Multicentre, Randomised, Double-blinded, Placebo-controlled Trial [MicroPouch]
Authors: Kousgaard Sabrina Just , Cold Frederik , Halkjær Sofie Ingdam , Petersen Andreas Munk , Kjeldsen Jens , Hansen Jane Møller , Dall Sebastian Mølvang , Albertsen Mads , Nielsen Hans Linde , Kirk Karina Frahm , Duch Kirsten , Sønderkær Mads , Thorlacius-Ussing Ole
Published: May 2024

Background and Aims

To investigate if treatment with non-pooled, multidonor faecal microbiota transplantation [FMT] for 4 weeks was superior to placebo to induce clinical remission in patients with chronic pouchitis.

Methods

The study was a randomised, double-blinded, placebo-controlled study with a 4-week intervention period and 12-month follow-up. Eligible patients with chronic pouchitis were recruited from five Danish hospitals. Participants were randomised to non-pooled, multidonor FMT derived from four faecal donors, or placebo. Treatment was delivered daily by enema for 2 weeks, followed by every second day for 2 weeks. Disease severity was accessed at inclusion and 30-day follow-up, using the Pouchitis Disease Activity Index [PDAI]; PDAI <7 was considered equivalent to clinical remission. Faecal samples from participants and donors were analysed by shotgun metagenomic sequencing.

Results

Inclusion was stopped after inclusion of 30 participants who were randomised 1:1 for treatment with FMT or placebo. There was no difference in participants achieving clinical remission between the two groups at 30-day follow-up, relative risk 1.0 (95% CI [0.55; 1.81]). Treatment with FMT resulted in a clinically relevant increase in adverse events compared with placebo, incidence rate ratio 1.67 (95% CI [1.10; 2.52]); no serious adverse events within either group. Faecal microbiota transplantation statistically significantly increased the similarity of participant faecal microbiome to the faecal donor microbiome at 30-day follow-up [p = 0.01], which was not seen after placebo.

Conclusions

Non-pooled, multidonor FMT was comparable to placebo in inducing clinical remission in patients with chronic pouchitis, but showed a clinically relevant increase in adverse events compared with placebo. ClincialTrials.gov number, NCT04100291.
Accuracy and reliability of magnetic resonance imaging in orthodontic diagnosis and treatment planning—a systematic review and meta-analysis
Authors: Srivastav Sukeshana , Spin-Neto Rubens , Aiyar Akila , Stoustrup Peter Bangsgaard
Published: May 2024

Background

Magnetic resonance imaging (MRI) is a non-ionizing imaging technique. Using MRI in dentistry may potentially lower the general radiation dose of the examined population, provided MRI can replace various radiation-based images. Furthermore, novel MRI imaging modalities for three-dimensional and two-dimensional cephalometrics have recently been developed for orthodontic diagnosis.

Objectives

This systematic review aimed to determine the diagnostic accuracy and reliability of MRI in orthodontic diagnosis and treatment planning.

Search methods

An electronic search was conducted on 20 November 2022 in the following databases: PubMed, LILACS, Web of Science, EMBASE, Scopus, and Cochrane. The search was updated on 30 August 2023. Furthermore, a grey literature search was performed in Google Scholar and Open-Grey.

Selection criteria

This review included descriptive, observational, cohort studies, cross-sectional, case-control studies, and randomized/non-randomized trials related to the research question. The study excluded studies related to patients with syndromes, chronic diseases, craniofacial anomalies, or bone diseases.

Data collection and analysis

The included studies were quality assessed using the “Joanna Brigg’s Critical Appraisal Tool for diagnostic test accuracy”. The GRADE approach for non-randomized studies was used for strength-of-evidence analysis.

Results

Eight of the 10 included studies compared MRI with either cone beam computed tomography or lateral cephalogram and found a high intra- and inter-rater agreement for landmark identification. The risk of bias was high in four studies, moderate in three, and low in three studies. Homogeneity was lacking among the included studies in terms of MRI imaging parameters and sample characteristics. This should be taken into consideration by future studies where uniformity with respect to these parameters may be considered.

Conclusions

Despite dissimilarity and heterogeneity in the sample population and other methodological aspects, all the included studies concluded that MRI enjoyed considerable intra- and inter-examiner reliability and was comparable to current diagnostic standards in orthodontics. Furthermore, the studies agreed on the innovative potential of MRI in radiation-free diagnosis and treatment planning in orthodontics in the future.

Registration

CRD number: CRD420223XXXXX
Septal venous channel perforation during left bundle branch area pacing: a prospective study
Authors: Ghosh Anindya , Sekar Anbarasan , Sriram Chenni S , Sivakumar Kothandam , Upadhyay Gaurav A , Pandurangi Ulhas M
Published: May 2024

Aims

To characterize the diagnosis, frequency, and procedural implications of septal venous channel perforation during left bundle branch area pacing (LBBAP).

Methods and results

All consecutive patients undergoing LBBAP over an 8-month period were prospectively studied. During lead placement, obligatory septal contrast injection was performed twice, at initiation (implant entry zone) and at completion (fixation zone). An intuitive fluoroscopic schema using orthogonal views (left anterior oblique/right anterior oblique) and familiar landmarks is described. Using this, we resolved zonal distribution (I–VI) of lead position on the ventricular septum and its angulation (post-fixation angle θ). Subjects with and without septal venous channel perforation were compared. Sixty-one patients {male 57.3%, median age [interquartile range (IQR)] 69.5 [62.5–74.5] years} were enrolled. Septal venous channel perforation was observed in eight (13.1%) patients [male 28.5%, median age (IQR) 64 (50–75) years]. They had higher frequency of (i) right-sided implant (25% vs. 1.9%, P = 0.04), (ii) fixation in zone III at the mid-superior septum (75% vs. 28.3%, P = 0.04), (iii) steeper angle of fixation—median θ (IQR) [19 (10–30)° vs. 5 (4–19)°, P = 0.01], and (iv) longer median penetrated-lead length (IQR) [13 (10–14.8) vs. 10 (8.5–12.5) mm, P = 0.03]. Coronary sinus drainage of contrast was noted in five (62.5%) patients. Abnormal impedance drops during implantation (12.5% vs. 5.7%, P = NS) were not significantly different.

Conclusion

When evaluated systematically, septal venous channel perforation may be encountered commonly after LBBAP. The fiducial reference framework described using fluoroscopic imaging identified salient associated findings. This may be addressed with lead repositioning to a more inferior location and is not associated with adverse consequence acutely or in early follow-up.
Accounting for subwavelength heterogeneities in full waveform inversion based on wavefield gradient measurements
Authors: Mukumoto Kota , Capdeville Yann , Singh Sneha , Tsuji Takeshi
Published: May 2024

Seismic gradient measurements from distributed acoustic sensors and rotational sensors are becoming increasingly available for field surveys. These measurements provide a wealth of information and are currently being considered for many applications such as earthquake detection and subsurface characterizations. In this work, using a simple 2-D numerical approach, we tackle the implications of such wavefield gradient measurements on full waveform inversion (FWI) techniques using a simple 2-D numerical test. In particular, we study the impact of the wavefield gradient measurement sensitivity to heterogeneities that are much smaller than the minimum wavelength. Indeed, as shown through the homogenization theory, small-scale heterogeneities induce an unexpected coupling of the strain components to the wavefield gradient measurement. We further show that this coupling introduces a potential limitation to the FWI results if it is not taken into account. We demonstrate that a gradient measurement-based FWI can only reach the accuracy of a classical displacement field-based FWI if the coupling coefficients are also inverted. Furthermore, there appears to be no specific gain in using gradient measurements instead of conventional displacement (or velocity, acceleration) measurements to image structures. Nevertheless, the inverted correctors contain fine-scale heterogeneities information that could be exploited to reach an unprecedented resolution, particularly if an array of receivers is used.
Use of artificial intelligence and the future of peer review
Authors: Bauchner Howard , Rivara Frederick P
Published: May 2024

Conducting high-quality peer review of scientific manuscripts has become increasingly challenging. The substantial increase in the number of manuscripts, lack of a sufficient number of peer-reviewers, and questions related to effectiveness, fairness, and efficiency, require a different approach. Large-language models, 1 form of artificial intelligence (AI), have emerged as a new approach to help resolve many of the issues facing contemporary medicine and science. We believe AI should be used to assist in the triaging of manuscripts submitted for peer-review publication.
Pediatric to Adult Transition in Inflammatory Bowel Disease: Consensus Guidelines for Australia and New Zealand
Authors: Vernon-Roberts Angharad , Chan Patrick , Christensen Britt , Havrlant Rachael , Giles Edward , Williams Astrid-Jane
Published: May 2024

Background

The incidence of pediatric inflammatory bowel disease (IBD) is rising, and there is an increasing need to support adolescents when they transition to adult care. Evidence supports the use of a structured transition process but there is great variation across Australasia. The study aim was to develop evidence and expert opinion–based consensus statements to guide transitional care services in IBD.

Methods

A modified UCLA-RAND methodology was employed to develop consensus statements. An IBD expert steering committee was formed and a systematic literature review was conducted to guide the drafting of consensus statements. A multidisciplinary group was formed comprising 16 participants (clinicians, nurses, surgeons, psychologists), who anonymously voted on the appropriateness and necessity of the consensus statements using Likert scales (1 = lowest, 9 = highest) with a median ≥7 required for inclusion. Patient support groups, including direct input from young people with IBD, informed the final recommendations.

Results

Fourteen consensus statements were devised with key recommendations including use of a structured transition program and transition coordinator, mental health and transition readiness assessment, key adolescent discussion topics, allied health involvement, age for transition, and recommendations for clinical communication and handover, with individualized patient considerations. Each statement reached median ≥8 for appropriateness, and ≥7 for necessity, in the first voting round, and the results were discussed in an online meeting to refine statements.

Conclusions

A multidisciplinary group devised consensus statements to optimize pediatric to adult transitional care for adolescents with IBD. These guidelines should support improved and standardized delivery of IBD transitional care within Australasia.
Investigating the Relationships Among HMP, Credibility, and TPP of News Media and Their Links to News Media Policy Support
Authors: Hyun Ki Deuk , Seo Mihye , Kim Yonghwan
Published: May 2024

Prior research has suggested that perceptions of bias, credibility, and influence of news media may relate to one another but there have been relatively few efforts to integrate these concepts under a coherent theoretical framework. Based on social identity theory, we examined whether political identity relates to hostile media perception (HMP), credibility, and third-person perception (TPP) and if such perceptions in tandem predict attitudes toward news media policies—restriction of news media and media literacy education, which may neutralize the influences of seemingly hostile and untrustworthy news media. Findings from two national online surveys showed that strong partisans tend to perceive stronger HMP and less credibility in news media. Additionally, progressives had greater HMP. HMP and TPP were positively associated with media restriction policy support and media literacy education support. Credibility showed negative associations with restrictive media policy support, whereas the opposite pattern was found in the relationship with media education support. Furthermore, the positive associations between HMP and media policy support were mediated by TPP. The negative associations between credibility and restrictive media policy support were also mediated by TPP.
Simultaneous automated ascertainment of prevalent vertebral fracture and abdominal aortic calcification in clinical practice: role in fracture risk assessment
Authors: Schousboe John T , Lewis Joshua R , Monchka Barret A , Reid Siobhan B , Davidson Michael J , Kimelman Douglas , Jozani Mohammad Jafari , Smith Cassandra , Sim Marc , Gilani Syed Zulqarnain , Suter David , Leslie William D
Published: May 2024

Whether simultaneous automated ascertainments of prevalent vertebral fracture (auto-PVFx) and abdominal aortic calcification (auto-AAC) on vertebral fracture assessment (VFA) lateral spine bone density (BMD) images jointly predict incident fractures in routine clinical practice is unclear. We estimated the independent associations of auto-PVFx and auto-AAC primarily with incident major osteoporotic and secondarily with incident hip and any clinical fractures in 11 013 individuals (mean [SD] age 75.8 [6.8] years, 93.3% female) who had a BMD test combined with VFA between March 2010 and December 2017. Auto-PVFx and auto-AAC were ascertained using convolutional neural networks (CNNs). Proportional hazards models were used to estimate the associations of auto-PVFx and auto-AAC with incident fractures over a mean (SD) follow-up of 3.7 (2.2) years, adjusted for each other and other risk factors.

At baseline, 17% (n = 1881) had auto-PVFx and 27% (n = 2974) had a high level of auto-AAC (≥ 6 on scale of 0 to 24). Multivariable-adjusted hazard ratios (HR) for incident major osteoporotic fracture (95% CI) were 1.85 (1.59, 2.15) for those with compared with those without auto-PVFx, and 1.36 (1.14, 1.62) for those with high compared with low auto-AAC. The multivariable-adjusted HRs for incident hip fracture were 1.62 (95% CI, 1.26 to 2.07) for those with compared to those without auto-PVFx, and 1.55 (95% CI, 1.15 to 2.09) for those high auto-AAC compared with low auto-AAC. The 5-year cumulative incidence of major osteoporotic fracture was 7.1% in those with no auto-PVFx and low auto-AAC, 10.1% in those with no auto-PVFx and high auto-AAC, 13.4% in those with auto-PVFx and low auto-AAC, and 18.0% in those with auto-PVFx and high auto-AAC. While physician manual review of images in clinical practice will still be needed to confirm image quality and provide clinical context for interpretation, simultaneous automated ascertainment of auto-PVFx and auto-AAC can aid fracture risk assessment.
The Figure of the Staggering Rat: Reading Colonial Outbreak Narratives Against the Grain of “Virus Hunting”
Authors: Lynteris Christos
Published: May 2024

The image of dazed, plague-infected rats coming out of their nests and performing a pirouette in front of the surprised eyes of humans before dying is one well-known to us through Albert Camus’s The Plague (1947). This article examines the historical roots of this image and its emergence in French missionary narratives about plague outbreaks in the Chinese province of Yunnan in the 1870s on the eve of the Third Plague Pandemic. Showing that accounts of the “staggering rat” were not meant as naturalist observations of a zoonotic disease, as is generally assumed by historians, but as a cosmological, end-of-the-world narrative with a colonial agenda, the article argues for an approach to historical accounts of epidemics that does not succumb to the current trend of “virus hunting” in the archive, but rather takes colonial outbreak narratives ethnographically seriously.
Preference for hibernacula microclimates varies among 3 bat species susceptible to white-nose syndrome
Authors: Johnson Levi E , Johnson Joseph S
Published: May 2024

North American bat populations have experienced precipitous declines since the introduction of white-nose syndrome (WNS). Evidence that bats have responded to WNS by altering their winter habitat selection has been used to manipulate underground environments and improve winter survival. However, such management practices must be based on local data, which do not exist for all regions. Our goal was to identify determinants of winter habitat use for 3 bat species with varying susceptibility to WNS. To do so, we conducted 188 surveys of 129 potential hibernacula over 3 winters. We found that the range of winter temperatures and presence of water were important for the Little Brown Myotis (Myotis lucifugus) and Tricolored Bat (Perimyotis subflavus), species that are highly susceptible to WNS. Counts of both species were greater in sites with a narrow (<5 °C) temperature range and where streams or water bodies >25 m2 were present. In addition, we found larger groups of Little Brown Myotis in abandoned railroad tunnels than in caves. Winter counts of these species increased over time at 3 railroad tunnels that were surveyed for 3 consecutive winters, whereas populations were extirpated from historically important caves and mines. Counts of Big Brown Bats (Eptesicus fuscus), which are less susceptible to WNS, were also greater in hibernacula with water bodies. However, average winter temperature also helped predict counts of Big Brown Bats. This species had a curvilinear response to temperature, with most bats found at hibernacula with average winter temperatures of 4 to 6 °C, and fewer bats observed at warmer and colder conditions. These data show that focusing solely on historically important hibernacula may fail to achieve conservation goals for the Little Brown Myotis and Tricolored Bat in our region, and suggest that anthropogenic structures can provide habitat for remnant populations of imperiled bat species.
Model-assisted sensitivity analysis for treatment effects under unmeasured confounding via regularized calibrated estimation
Authors: Tan Zhiqiang
Published: May 2024

Consider sensitivity analysis for estimating average treatment effects under unmeasured confounding, assumed to satisfy a marginal sensitivity model. At the population level, we provide new representations for the sharp population bounds and doubly robust estimating functions. We also derive new, relaxed population bounds, depending on weighted linear outcome quantile regression. At the sample level, we develop new methods and theory for obtaining not only doubly robust point estimators for the relaxed population bounds with respect to misspecification of a propensity score model or an outcome mean regression model, but also model-assisted confidence intervals which are valid if the propensity score model is correctly specified, but the outcome quantile and mean regression models may be misspecified. The relaxed population bounds reduce to the sharp bounds if outcome quantile regression is correctly specified. For a linear outcome mean regression model, the confidence intervals are also doubly robust. Our methods involve regularized calibrated estimation, with Lasso penalties but carefully chosen loss functions, for fitting propensity score and outcome mean and quantile regression models. We present a simulation study and an empirical application to an observational study on the effects of right-heart catheterization. The proposed method is implemented in the R package RCALsa.
Wide en-bloc thymectomy and venous axis reconstruction in Masaoka stage IIIB thymoma: a case report and literature review
Authors: Nahas Mohamad A , Samha Raghad , Shbat Mohamad , Ghaddar Sawsane A , Jobran Afnan W M , Msheik Layal , Al nahhas Zaher , Chaban Hussain
Published: May 2024

Thymomas are rare tumors originating from thymic tissue and rarely metastasize. They can be diagnosed either incidentally or symptomatically when compressing or invading nearby structure. A 36-year-old man presented with significant high-grade fever, chest pain that worsens upon lying down, and dyspnea. A chest X-Ray and computed tomography followed by biopsy confirmed the diagnosis of thymoma. The management included chemotherapy cycles, followed by surgery. Pericardiectomy was performed with en-bloc thymectomy and partial resection of the infiltrating lung. Venous drainage was restored by 8/16 mm inverted bifurcated brachiocephalic-superior vena cava Dacron bypass. The pericardium was reconstructed by a synthetic Dacron patch, and the right diaphragm metastasis was resected. Neoadjuvant chemotherapy was initiated. After 3 months of follow-up, no recurrence was evidenced by computed tomography.
Early-onset severe ovarian endometriosis in adolescents with completely obstructed Müllerian anomalies accompanied by ipsilateral renal agenesis: two case reports
Authors: Yu Bo Ram , Chae Hee-Suk , Rheu Chul-Hee
Published: May 2024

Endometriosis is known to occur frequently in adolescents with obstructed Müllerian anomalies. Our cases emphasize that endometriosis can rapidly progress to a severe stage in obstructed hemivagina and ipsilateral renal anomaly syndrome, one of the completely obstructed Müllerian anomalies. The first patient was a 14-year-old girl who complained of cyclic abdominal pain. Imaging revealed a uterine didelphys with unilateral hematocolpos and a left adnexal endometrioma. The second, an 11-year-old girl, visited the hospital complaining of cyclic abdominal pain, had a unicornuate uterus with a functioning horn and left adnexal endometrioma. Also, both patients had unilateral renal agenesis. The surgery in both cases revealed Stage IV endometriosis. Adjuvant hormone therapy was administered for 1 year, and there was no recurrence until 3 years after surgery. We emphasize that patients diagnosed with renal agenesis should be screened to check for gynecological anomalies when menstrual cramps occur after menarche.
Postprocessing Workflow for Laboratory Diffraction Contrast Tomography: A Case Study on Chromite Geomaterials
Authors: Chen Xiao , Godel Belinda , Verrall Michael
Published: May 2024

Texture stands as a fundamental descriptor in the realms of geology and earth and planetary science. Beyond offering insights into the geological processes underlying mineral formation, its characterization plays a pivotal role in advancing engineering applications, notably in mining, mineral processing, and metal extraction, by providing quantitative data for predictive modeling. Laboratory diffraction contrast tomography (LabDCT), a recently developed 3D characterization technique, offers nondestructive measurement of grain phases including their morphology, distribution, and crystal orientation. It has recently shown its potential to assess 3D textures in complex natural rock samples. This study looks at improving on previous work by examining the artifacts and presents a novel postprocessing workflow designed to correct them. The workflow is developed to rectify inaccurate grain boundaries and interpolate partially reconstructed grains to provide more accurate results and is illustrated using multi-scan examples on chromite sands and natural chromitite from the Upper Group 2 Reef layer in South Africa. The postcorrected LabDCT results were validated through qualitative and quantitative assessment using 2D electron back-scattered diffraction on polished sample surfaces. The successful implementation of this postprocessing workflow underscores its substantial potential in achieving precise textural characterization and will provide valuable insights for both earth science and engineering applications.
Quenching massive galaxies across cosmic time with the semi-analytic model shark v2.0
Authors: Lagos Claudia del P , Bravo Matías , Tobar Rodrigo , Obreschkow Danail , Power Chris , Robotham Aaron S G , Proctor Katy L , Hansen Samuel , Chandro-Gómez Ángel , Carrivick Julian
Published: May 2024

We introduce version 2.0 of the shark semi-analytic model of galaxy formation after many improvements to the physics included. The most significant being (i) a model describing the exchange of angular momentum (AM) between the interstellar medium and stars; (ii) a new active galactic nuclei feedback model which has two modes, a wind and a jet mode, with the jet mode tied to the jet energy production; (iii) a model tracking the development of black hole (BH) spins; (iv) more sophisticated modelling of environmental effects on satellite galaxies; and (v) automatic parameter exploration using Particle Swarm Optimization. We focus on two timely research topics: the structural properties of galaxies and the quenching of massive galaxies. For the former, sharkv2.0 is capable of producing a more realistic stellar size–mass relation with a plateau marking the transition from disc- to bulge-dominated galaxies, and scaling relations between specific AM and mass that agree well with observations. For the quenching of massive galaxies, sharkv2.0 produces massive galaxies that are more quenched than the previous version, reproducing well the observed relations between star formation rate (SFR) and stellar mass, and specific SFR and BH mass at z = 0. shark v2.0 produces a number density of massive-quiescent galaxies >1 dex higher than the previous version, in good agreement with JWST observations at z ≤ 5; predicts a stellar mass function of passive galaxies in reasonably good agreement with observations at 0.5 < z < 5; and environmental quenching to already be effective at z = 5.
Decretion disc size in Be/X-ray binaries depends upon the disc aspect ratio
Authors: Martin Rebecca G , Lubow Stephen H , Armitage Philip J , Price Daniel J
Published: May 2024

With three-dimensional hydrodynamical simulations we show that the size of the decretion disc and the structure of the accretion flow on to the neutron star in a Be/X-ray binary strongly depends upon the disc aspect ratio, H/R. We simulate a Be star disc that is coplanar to the orbit of a circularly or moderately eccentric neutron star companion, thereby maximizing the effects of tidal truncation. For low-disc aspect ratio, H/R ≲ 0.1, the disc is efficiently tidally truncated by the neutron star. Most material that escapes the Roche lobe of the Be star is accreted by the neutron star through tidal streams. For larger disc aspect ratio, the outflow rate through the Be star disc is higher, tidal truncation becomes inefficient, the disc fills the Roche lobe and extends to the orbit of the companion. Some material escapes the binary as a gas stream that begins near the L2 point. While the accretion rate on to the neutron star is higher, the fraction of the outflow that is accreted by the neutron star is smaller. Low-density Be star discs are expected to be approximately isothermal, such that H/R increases with radius. Tidal truncation is therefore weaker for larger separation binaries, and lower mass primaries.
The recent star formation histories of nearby galaxies on resolved scales
Authors: Lomaeva Maria , Saintonge Amélie , De Looze Ilse
Published: May 2024

Star formation histories (SFHs) of galaxies are affected by a variety of factors, both external (field versus cluster/group) and internal [presence of a bar and active galactic nucleus (AGN), morphological type]. In this work, we extend our previous study and apply the $\langle \mathrm{SFR}_{\textnormal {5}} \rangle \big / \langle \mathrm{SFR}_{\textnormal {200}} \rangle$ metric to a sample of 11 nearby galaxies with Multi-Unit Spectroscopic Explorer observations. Based on a combination of H α and ultraviolet photometry, $\langle \mathrm{SFR}_{\textnormal {5}} \rangle \big / \langle \mathrm{SFR}_{\textnormal {200}} \rangle$ is sensitive to star formation time-scales of ∼5–200 Myr and therefore measures the present-day rate of change in the star formation rate (SFR), dSFR/dt. Within this limited galaxy sample, we do not observe systematic variations between the global value of $\langle \mathrm{SFR}_{\textnormal {5}} \rangle \big / \langle \mathrm{SFR}_{\textnormal {200}} \rangle$ and the presence of an AGN, stellar bar, or group or cluster membership. Within some of the individual galaxies, we, however, observe significant differences in $\langle \mathrm{SFR}_{\textnormal {5}} \rangle \big / \langle \mathrm{SFR}_{\textnormal {200}} \rangle$ between the arm and interarm regions. In half of the galaxies, the recent SFH of both arm and interarm regions has been very similar. However, in the galaxies with higher bulge-to-total light ratios and earlier morphological type, the SFR is declining more rapidly in the interarm regions. This decline in SFR is not a result of low molecular gas surface density or a decrease in the star formation efficiency, implying that other factors are responsible for this SFR decrease.
The Thousand-Pulsar-Array programme on MeerKAT – XIV. On the high linearly polarized pulsar signals
Authors: Johnston Simon , Mitra Dipanjan , Keith Michael J , Oswald Lucy S , Karastergiou Aris
Published: May 2024

The S-shaped swing of the linear polarization position angle (PPA) observed in many pulsars can be interpreted by the rotating vector model (RVM). However, efforts to fit the RVM for a large sample of pulsars observed with the MeerKAT telescope as a part of the Thousand-Pulsar-Array (TPA) programme, only succeeded for about half the cases. High time-resolution studies suggest that the failed cases arise due to the presence of orthogonal polarization modes, or highly disordered distribution of PPA points. One such example is PSR J1645−0317. Recently it has been shown that the RVM can be recovered in this pulsar by using only time samples which are greater than 80 per cent linearly polarized. In this work, we test this novel approach on the brightest 249 pulsars from the TPA sample, of which 177 yield sufficient highly polarized samples to be amenable to our method. Remarkably, only nine of these pulsars (5 per cent) now fail to fit the RVM as opposed to 59 per cent from the original analysis. This result favours the paradigm that the underlying mechanism is coherent curvature radiation.
The relationship between the turnover frequency and photo-ionization in radio sources
Authors: Curran S J
Published: May 2024

We investigate the connection between the turnover frequency in the radio spectrum, νTO, and the rate of ionizing ultraviolet photons, $Q_{\rm {H{\small I}}}$, in extragalactic sources. From a large, optically selected sample, we find νTO to be correlated with $Q_{\rm {H\,{\small I}}}$ in sources that exhibit a turnover. The significance of the correlation decreases when we include power-law radio sources as limits, by assuming that the turnover frequency occurs below the lowest value observed. However, the power-law fit sources are less well sampled across the band and so these may just be contributing noise to the data. Given that the observed νTO–$Q_{\rm {H{\small I}}}$ correlation is purely empirical, we use the ionizing photon rate to obtain the electron density in a free–free absorption model. For each of the constant, exponential, constant plus exponential (Milky Way), and spherical models of the gas distribution, there is also an increase in the turnover frequency with ionizing photon rate. Furthermore, for a given gas mass, we find that the turnover frequency is anticorrelated with the scale-factor of the gas density. While other mechanisms, such as ageing electrons or synchrotron self-absorption, may be required to reproduce the spectral indices, for an exponential scale-factor similar to the linear size, this simple free–free absorption model reproduces the turnover-size correlation seen in radio sources.