bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating causal effects for binary outcomes using per-decision inverse probability weighting
Authors: Bao Yihan , Bell Lauren , Williamson Elizabeth , Garnett Claire , Qian Tianchen 
Published: July 2024

SUMMARY
Micro-randomized trials are commonly conducted for optimizing mobile health interventions such as push notifications for behavior change. In analyzing such trials, causal excursion effects are often of primary interest, and their estimation typically involves inverse probability weighting (IPW). However, in a micro-randomized trial, additional treatments can often occur during the time window over which an outcome is defined, and this can greatly inflate the variance of the causal effect estimator because IPW would involve a product of numerous weights. To reduce variance and improve estimation efficiency, we propose two new estimators using a modified version of IPW, which we call “per-decision IPW.” The second estimator further improves efficiency using the projection idea from the semiparametric efficiency theory. These estimators are applicable when the outcome is binary and can be expressed as the maximum of a series of sub-outcomes defined over sub-intervals of time. We establish the estimators’ consistency and asymptotic normality. Through simulation studies and real data applications, we demonstrate substantial efficiency improvement of the proposed estimator over existing estimators. The new estimators can be used to improve the precision of primary and secondary analyses for micro-randomized trials with binary outcomes.
Multiparameter cortical surface morphology in former amateur contact sport athletes
Authors: Recht Grace , Hou Jiancheng , Buddenbaum Claire , Cheng Hu , Newman Sharlene D , Saykin Andrew J , Kawata Keisuke 
Published: July 2024

Abstract
The lifetime effects of repetitive head impacts have captured considerable public and scientific interest over the past decade, yet a knowledge gap persists in our understanding of midlife neurological well-being, particularly in amateur level athletes. This study aimed to identify the effects of lifetime exposure to sports-related head impacts on brain morphology in retired, amateur athletes. This cross-sectional study comprised of 37 former amateur contact sports athletes and 21 age- and sex-matched noncontact athletes. High-resolution anatomical, T1 scans were analyzed for the cortical morphology, including cortical thickness, sulcal depth, and sulcal curvature, and cognitive function was assessed using the Dementia Rating Scale-2. Despite no group differences in cognitive functions, the contact group exhibited significant cortical thinning particularly in the bilateral frontotemporal regions and medial brain regions, such as the cingulate cortex and precuneus, compared to the noncontact group. Deepened sulcal depth and increased sulcal curvature across all four lobes of the brain were also notable in the contact group. These data suggest that brain morphology of middle-aged former amateur contact athletes differs from that of noncontact athletes and that lifetime exposure to repetitive head impacts may be associated with neuroanatomical changes.
Two case reports of coronary spastic angina accompanied by the menstrual cycle
Authors: Aoyama Rie , Sudo Hironao , Okino Shinichi , Fukuzawa Shigeru 
Published: July 2024

Abstract

Background
Coronary spastic angina (CSA) in premenopausal women is not frequent but has also been suggested to be associated with oestrogen decline during the menstrual cycle and sometimes becomes refractory and difficult to control. We experienced two premenopausal women with CSA that showed the involvement of the menstrual cycle.

Case summary
Case 1: 41-year-old-woman had ST-segment elevation and chest pain during urosepsis, just 2 days after the onset of menstruation. The acetylcholine stress test was performed according to the menstrual cycle, and multiple coronary spasms were induced. Case 2: 40-year-old-woman had refractory chest pain as a symptom of premenstrual syndrome (PMS). Coronary angiography on drugs at the maximum dose revealed spontaneous multiple coronary spasms. Blood levels of oestrogen were normal, suggesting that hormonal change may be involved, and the introduction of low-dose pills made free from angina and the reduction of drug dose.

Discussion
In premenopausal female angina pectoris, oestrogen may play a role; it is important to ask about the menstrual cycle and history of PMS. Besides, the timing of catheterization in premenopausal women with suspected CSA should be considered. Low-dose pills may be effective in some cases, and active medical collaboration with other departments such as gynaecology is desirable.
Impact of COVID-19 on Drug Positivity Rates in the Emergency Departments in Boston and Surrounding Areas
Authors: Tolan Nicole V , Kang Phillip , Chai Peter R , Erickson Timothy B , Hayes Bryan D , Uljon Sacha N , Demetriou Christiana A , Melanson Stacy E F 
Published: July 2024

Abstract

Background
The COVID-19 pandemic reportedly had a significant impact on drug and alcohol use. In this article, we determine positivity rates for urine drugs of abuse and blood alcohol in 5 emergency departments (ED) in the greater Boston metropolitan area over a 4-year period (pre-, during, and post-COVID-19 pandemic).

Methods
Positivity rates for the urine drug screening (UDS) panel and blood alcohol concentration (&gt;80 mg/dL; over the legal limit in MA) were calculated in patients presenting to one of the 5 ED (2 academic hospitals in Boston, MA and 3 community hospitals outside Boston, MA) during each of the 4 different time periods: pre-COVID (January 1, 2019 to December 31, 2019), stay-at-home (March 24, 2020 to May 18, 2020), during COVID (May 19, 2020 to March 28, 2021), and post-COVID (May 12, 2023 to August 31, 2023). Trend analysis was performed. Additionally, positivity rates during and post-COVID were compared to pre-COVID to determine any significant changes in drug positivity.

Results
Stimulant (amphetamines and cocaine), cannabinoid, and methadone positivity increased during the pandemic and cocaine, cannabinoid, and methadone positivity remains elevated. By contrast, benzodiazepine and opioid (opiates, fentanyl, oxycodone) positivity decreased and remains lower post-COVID compared to pre-COVID. Patients in the ED with blood alcohol over the legal limit decreased both during and post-COVID.

Conclusion
Our study showed that the COVID-19 pandemic significantly affected drug and alcohol positivity rates in patients presenting to the ED in greater Boston area. We encourage other institutions to perform similar analyses to help determine local drug use patterns and appropriate composition of UDS panels.
Impact of overhead evaporative cooling, canopy location, sunlight exposure, inoculation level, region, and growing season on the survival of generic Escherichia coli on in-field Fuji apples
Authors: Murphy Claire M , Mendoza Manoella , Walter Lauren , Jeong Kyu Ho , Liao Andy , Green Tonia , Killinger Karen , Hanrahan Ines , Zhu Mei-Jun 
Published: July 2024

Abstract

Aims
The survival of inoculated Escherichia coli on Fuji apples in Washington State orchards was studied, considering evaporative cooling, canopy location, year, and region, with the examination of sunlight exposure and inoculation levels in year 2.

Methods and results
Rifampicin-resistant E. coli was applied to Fuji apples. Initial concentrations for the high-inoculation study were 7.4 ± 0.3 log10 CFU per apple and 3.4 ± 0.3 log10 CFU per apple for the low-inoculation study. Enumeration of E. coli was conducted at 0, 2, 10, 18, 34, 42, 58, 82, 106, and 154 h after inoculation. Results were analyzed using Tukey’s honest significance difference test and a log-linear model. Log-linear, Weibull, and biphasic models characterized E. coli die-off patterns for high and low inoculations. The application of evaporative overhead cooling water did not significantly influence E. coli survival on Fuji apples; inoculation level and sunlight exposure were significant factors in a log-linear model. Escherichia coli decreased by 5.5 ± 1.3 and 3.3 ± 0.4 log10 CFU per apple for high and low-inoculated apples, respectively, by 154 h. The biphasic model best explained the die-off pattern for high and low-inoculated Fuji apples.

Conclusions
Overhead evaporative cooling, a useful fruit quality practice, did not impact the survival of generic E. coli on Fuji apple surfaces. The significant impact of sunlight exposure and inoculation levels on die-off highlights the importance of ultraviolet radiation in risk reduction and the need for various inoculum concentrations in preharvest field studies
Adapting arepo-rt for exascale computing: GPU acceleration and efficient communication
Authors: Zier Oliver , Kannan Rahul , Smith Aaron , Vogelsberger Mark , Verbeek Erkin 
Published: July 2024

ABSTRACT
Radiative transfer (RT) is a crucial ingredient for self-consistent modelling of numerous astrophysical phenomena across cosmic history. However, on-the-fly integration into radiation hydrodynamics (RHD) simulations is computationally demanding, particularly due to the stringent time-stepping conditions and increased dimensionality inherent in multifrequency collisionless Boltzmann physics. The emergence of exascale supercomputers, equipped with extensive CPU cores and GPU accelerators, offers new opportunities for enhancing RHD simulations. We present the first steps towards optimizing arepo-rt for such high-performance computing environments. We implement a novel node-to-node (n-to-n) communication strategy that utilizes shared memory to substitute intranode communication with direct memory access. Furthermore, combining multiple internode messages into a single message substantially enhances network bandwidth utilization and performance for large-scale simulations on modern supercomputers. The single-message n-to-n approach also improves performance on smaller scale machines with less optimized networks. Furthermore, by transitioning all RT-related calculations to GPUs, we achieve a significant computational speedup of around 15 for standard benchmarks compared to the original CPU implementation. As a case study, we perform cosmological RHD simulations of the Epoch of Reionization, employing a similar setup as the THESAN project. In this context, RT becomes sub-dominant such that even without modifying the core arepo codebase, there is an overall threefold improvement in efficiency. The advancements presented here have broad implications, potentially transforming the complexity and scalability of future simulations for a wide variety of astrophysical studies. Our work serves as a blueprint for porting similar simulation codes based on unstructured resolution elements to GPU-centric architectures.
ASKAP reveals the radio tail structure of the Corkscrew Galaxy shaped by its passage through the Abell 3627 cluster
Authors: Koribalski Bärbel S , Duchesne Stefan W , Lenc Emil , Venturi Tiziana , Botteon Andrea , Shabala Stanislav S , Vernstrom Tessa , Carretti Ettore , Norris Ray P , Anderson Craig , Hopkins Andrew M , Riseley C J , Gupta Nikhel , Velović Velibor 
Published: July 2024

ABSTRACT
Among the bent-tail radio galaxies common in galaxy clusters are some with long, collimated tails (so-called head-tail galaxies) shaped by their interactions with the intracluster medium (ICM). Here, we report the discovery of intricate filamentary structure in and beyond the ∼28 arcmin (570 kpc) long, helical radio tail of the Corkscrew Galaxy (1610–60.5, ESO 137-G007), which resides in the X-ray bright cluster Abell 3627 (D = 70 Mpc). Deep radio continuum data were obtained with wide-field phased array feeds on the Australian Square Kilometer Array Pathfinder (ASKAP) at 944 MHz and 1.4 GHz. While the bright (young) part of the Corkscrew Galaxy tail is highly collimated, the faint (old) part shows increasing oscillation amplitudes, break-ups, and filaments. We find a stunning set of arc-shaped radio filaments beyond and mostly orthogonal to the collimated Corkscrew tail end, forming a partial bubble. This may be the first detection of a ‘proto-lobe’ previously seen in 3D MHD simulations, formed by the face-on impact of the Corkscrew Galaxy with a shock front in the cluster outskirts. Interactions of the radio galaxy tail with the ICM are likely responsible for the tail collimation and shear forces within the ICM for its increasingly filamentary structure. We also report the discovery of small (∼20–30 kpc) ram-pressure stripped radio tails in four Abell 3627 cluster galaxies, located between the Corkscrew Galaxy and its prominent neighbour, the wide-angle tail (WAT) radio galaxy 1610–60.8 (ESO 137-G006).
High ionic strength vector formulations enhance gene transfer to airway epithelia
Authors: Cooney Ashley L , Loza Laura Marquez , Najdawi Kenan , Brommel Christian M , McCray Paul B , Sinn Patrick L 
Published: July 2024

Abstract
A fundamental challenge for cystic fibrosis (CF) gene therapy is ensuring sufficient transduction of airway epithelia to achieve therapeutic correction. Hypertonic saline (HTS) is frequently administered to people with CF to enhance mucus clearance. HTS transiently disrupts epithelial cell tight junctions, but its ability to improve gene transfer has not been investigated. Here, we asked if increasing the concentration of NaCl enhances the transduction efficiency of three gene therapy vectors: adenovirus, AAV, and lentiviral vectors. Vectors formulated with 3–7% NaCl exhibited markedly increased transduction for all three platforms, leading to anion channel correction in primary cultures of human CF epithelial cells and enhanced gene transfer in mouse and pig airways in vivo. The mechanism of transduction enhancement involved tonicity but not osmolarity or pH. Formulating vectors with a high ionic strength solution is a simple strategy to greatly enhance efficacy and immediately improve preclinical or clinical applications.
Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea
Authors: Lin Min-Guan , Yen Cheng-Yi , Shen Yo-You , Huang Yu-Sung , Ng Irene W , Barillà Daniela , Sun Yuh-Ju , Hsiao Chwan-Deng 
Published: July 2024

Abstract
Genome segregation is a fundamental process that preserves the genetic integrity of all organisms, but the mechanisms driving genome segregation in archaea remain enigmatic. This study delved into the unknown function of SegC (SSO0033), a novel protein thought to be involved in chromosome segregation in archaea. Using fluorescence polarization DNA binding assays, we discovered the ability of SegC to bind DNA without any sequence preference. Furthermore, we determined the crystal structure of SegC at 2.8 Å resolution, revealing the multimeric configuration and forming a large positively charged surface that can bind DNA. SegC has a tertiary structure folding similar to those of the ThDP-binding fold superfamily, but SegC shares only 5–15% sequence identity with those proteins. Unexpectedly, we found that SegC has nucleotide triphosphatase (NTPase) activity. We also determined the SegC-ADP complex structure, identifying the NTP binding pocket and relative SegC residues involved in the interaction. Interestingly, images from negative-stain electron microscopy revealed that SegC forms filamentous structures in the presence of DNA and NTPs. Further, more uniform and larger SegC-filaments are observed, when SegA-ATP was added. Notably, the introduction of SegB disrupts these oligomers, with ATP being essential for regulating filament formation. These findings provide insights into the functional and structural role of SegC in archaeal chromosome segregation.
Related type 2C protein phosphatases Pic3 and Pic12 negatively regulate immunity in tomato to Pseudomonas syringae
Authors: Xia Fan , Zhang Ning , Smith Renee E , Chakraborty Joydeep , Sobol Guy , Tang Xuemei , Fei Zhangjun , Sessa Guido , Martin Gregory B 
Published: July 2024

Abstract
Type 2C protein phosphatases (PP2Cs) constitute a large family in most plant species, but relatively few of them have been implicated in immunity. To identify and characterize PP2C phosphatases that affect tomato (Solanum lycopersicum) immunity, we generated loss-of-function mutations in 11 PP2C-encoding genes whose expression is altered in response to immune elicitors or pathogens. We report that 2 closely related PP2C phosphatases, PP2C immunity-associated candidate 3 (Pic3) and Pic12, are involved in regulating resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Loss-of-function mutations in Pic3 led to enhanced resistance to Pst in older but not younger leaves, whereas such mutations in Pic12 resulted in enhanced resistance in both older and younger leaves. Overexpression of Pic3 and Pic12 proteins in leaves of Nicotiana benthamiana inhibited resistance to Pst, and this effect was dependent on Pic3/12 phosphatase activity and an N-terminal palmitoylation motif associated with localization to the cell periphery. Pic3, but not Pic12, had a slight negative effect on flagellin-associated reactive oxygen species generation, although their involvement in the response to Pst appeared independent of flagellin. RNA-sequencing analysis of Rio Grande (RG)-PtoR wild-type plants and 2 independent RG-pic3 mutants revealed that the enhanced disease resistance in RG-pic3 older leaves is associated with increased transcript abundance of multiple defense-related genes. RG-pic3/RG-pic12 double-mutant plants exhibited stronger disease resistance than RG-pic3 or RG-pic12 single mutants. Together, our results reveal that Pic3 and Pic12 negatively regulate tomato immunity in an additive manner through flagellin-independent pathways.
Engineered skin microbiome reduces mosquito attraction to mice
Authors: Liu Feng , Coutinho-Abreu Iliano V , Raban Robyn , Nguyen Tam Thuy Dan , Dimas Alejandra R , Merriman Joseph A , Akbari Omar S 
Published: July 2024

Abstract
The skin microbiome plays a pivotal role in the production of attractive cues detected by mosquitoes. Here, we leveraged recent advances in genetic engineering to significantly reduce the production of L-(+)-lactic acid as a strategy to reduce mosquito attraction to the highly prominent skin commensals Staphylococcus epidermidis and Corynebacterium amycolatum. Engraftment of these engineered bacteria onto the skin of mice reduced mosquito attraction and feeding for up to 11 uninterrupted days, which is considerably longer than the several hours of protection conferred by the leading chemical repellent N,N-diethyl-meta-toluamide. Taken together, our findings demonstrate engineering the skin microbiome to reduce attractive volatiles represents an innovative untapped strategy to reduce vector attraction, preventing bites, and pathogen transmission. These findings set the stage for new classes of long-lasting microbiome-based repellent products.
Commensal microbiome dysbiosis elicits interleukin-8 signaling to drive fibrotic skin disease
Authors: Zhang Wenyu , Peng Qili , Huang Xian , Huang Qing , Zhang Zhiliang , Li Fuli , Zheng Naisheng , Shi Binsheng , Fan Zhihong , Maj Tomasz , Chen Rui 
Published: July 2024

Abstract
Wound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that is related to commensal microbiota and skin fibrosis remains mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterizes microbial composition and divergence between the pathological and normal skin tissues. Moreover, the data show elevation of interleukin-8 (IL-8) in both the circulation and keloid tissue, which elicited the collagen accumulation and migratory program of dermal fibroblasts via CXCR1/2 receptor. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease.
Interaction between alimentary surgery and risk of dementia: a nationwide population-based case–control study
Authors: Tseng Chu-Chiao , Chen Ssu-Yu , Lin Ting-An , Chang Renin , Yip Hei-Tung , Hung Yao-Min 
Published: July 2024

Abstract

Background
Based on current research, it is known that the gastrointestinal tract microbiota and its genome play a crucial role in mental illnesses. Studies indicate a direct correlation between gastrointestinal tract microbiota and the onset of dementia, mediated by metabolic diseases and low-grade inflammation. The association between various gastrointestinal symptoms and neurodegenerative diseases has been recently discussed. However, there is a lack of research regarding the comparative effects of different surgical procedures on neurodegenerative diseases. Therefore, this study primarily focuses on comparing the association between various gastrointestinal surgeries and dementia, aiming to provide guidance for future clinical practice.

Method
A nationwide study using the Taiwanese National Health Insurance Research Database included 26 059 patients diagnosed with dementia or Alzheimer’s disease and 104 236 controls without diseases. Primary exposures were defined as alimentary surgeries, encompassing cholecystectomy, gastrectomy, bowel resection, and appendectomy. Conditional logistic regression was used to examine the odds ratio and 95% confidence interval for prior alimentary surgery between cases and controls.

Results
The results showed that individuals with dementia had a higher rate of gastrectomy. Additionally, individuals with dementia seemed to exhibit a reduced rate of cholecystectomy and appendectomy. Regarding Alzheimer’s disease, all four alimentary surgeries showed comparable trends to those observed with dementia. No significant interaction was observed between alimentary surgery and dementia among the four types of surgery evaluated.

Conclusion
Our study demonstrates that gastrectomy is associated with an elevated risk of dementia. We aim to uncover more direct evidence in future experiments.