bluuebunny/crossref_metadata_2025 huggingface dataset:
Is stochastic thermodynamics the key to understanding the energy costs of computation?
Authors: Wolpert David H. , Korbel Jan , Lynn Christopher W. , Tasnim Farita , Grochow Joshua A. , Kardeş Gülce , Aimone James B. , Balasubramanian Vijay , De Giuli Eric , Doty David , Freitas Nahuel , Marsili Matteo , Ouldridge Thomas E. , Richa Andréa W. , Riechers Paul , Roldán Édgar , Rubenstein Brenda , Toroczkai Zoltan , Paradiso Joseph
Published: October 2024

The relationship between the thermodynamic and computational properties of physical systems has been a major theoretical interest since at least the 19th century. It has also become of increasing practical importance over the last half-century as the energetic cost of digital devices has exploded. Importantly, real-world computers obey multiple physical constraints on how they work, which affects their thermodynamic properties. Moreover, many of these constraints apply to both naturally occurring computers, like brains or Eukaryotic cells, and digital systems. Most obviously, all such systems must finish their computation quickly, using as few degrees of freedom as possible. This means that they operate far from thermal equilibrium. Furthermore, many computers, both digital and biological, are modular, hierarchical systems with strong constraints on the connectivity among their subsystems. Yet another example is that to simplify their design, digital computers are required to be periodic processes governed by a global clock. None of these constraints were considered in 20th-century analyses of the thermodynamics of computation. The new field of stochastic thermodynamics provides formal tools for analyzing systems subject to all of these constraints. We argue here that these tools may help us understand at a far deeper level just how the fundamental thermodynamic properties of physical systems are related to the computation they perform.
COX15
deficiency causes oocyte ferroptosis
Authors: Zhang Zhihua , Yu Ran , Shi Qiuwen , Wu Zhi-Jing , Li Qingchun , Mu Jian , Chen Biaobang , Shi Juanzi , Ni Renmin , Wu Ling , Li Qiaoli , Fu Jing , Li Rong , Sun Xiaoxi , Wang Jiucun , He Lin , Kuang Yanping , Sang Qing , Wang Lei
Published: October 2024

Mitochondria play diverse roles in mammalian physiology. The architecture, activity, and physiological functions of mitochondria in oocytes are largely different from those in somatic cells, but the mitochondrial proteins related to oocyte quality and reproductive longevity remain largely unknown. Here, using whole-exome sequencing data from 1,024 women (characterized by oocyte maturation arrest and degenerated or morphologically abnormal oocytes) and 2,868 healthy controls, we performed a population and gene–based burden test for mitochondrial genes and identified a candidate gene, cytochrome c oxidase assembly protein 15 (
COX15).
We report that biallelic
COX15
pathogenic variants cause human oocyte ferroptosis and female infertility in a recessive inheritance pattern.
COX15
variants impaired mitochondrial respiration in
Saccharomyces cerevisiae
and led to reduced protein levels in HeLa cells. Oocyte-specific deletion of
Cox15
led to impaired Fe
2+
and reactive oxygen species homeostasis that caused mitochondrial dysfunction and ultimately sensitized oocytes to ferroptosis. In addition, ferrostatin-1 (an inhibitor of ferroptosis) could rescue the oocyte ferroptosis phenotype in vitro and ex vivo. Our findings not only provide a genetic diagnostic marker for oocyte development defects but also expand the spectrum of mitochondrial disorders to female infertility and contribute to unique insights into the role of ferroptosis in human oocyte defects.
Bee pollination and bee decline: A study about university students’ Knowledge and its educational implication
Authors: Daza Paula , Arista Montserrat , Berjano Regina , Ortiz Pedro , Morón-Monge Hortensia , Antonini Yasmine
Published: October 2024

Science education plays a crucial role in addressing the pollinator crisis by enhancing knowledge and fostering changes in attitudes toward this environmental challenge. Previous research has been focused on validating a specific instrument related to this subject, although its use for assessing students’ knowledge has been little explored. In the present study, we have evaluated the level of awareness regarding the significance of bees as primary pollinators among students of various disciplines at the Universities of Sevilla, in Spain, and Ouro Preto, in Brazil, emphasizing the importance of the plant–bee interaction. 753 students from the fields of biology, agriculture, and education were invited to complete a questionnaire focused on bee biology. The results indicate that knowledge on the subject is closely linked to professional career choice and that the training program for the future teachers effectively increased comprehension of the crucial role played by bees as main supporters of the ecosystem service of pollination.
Satisfactory clinical response to erlotinib in a patient with Olmsted syndrome
Authors: Oktem Ayse , Ongun Feride , Sanli Hatice , Karabulut Halil , Leblebici Can
Published: October 2024

Olmsted syndrome is a rare congenital keratinization disorder characterized by mutilating palmoplantar keratoderma, often accompanied by flexion deformity, periorificial keratotic plaques and hair abnormalities. The majority of Olmsted syndrome cases are attributed to mutations in TRPV3. We report a patient with a sporadic case of Olmsted syndrome with a recurrent c.1717G>T p.Gly573Cys variant in TRPV3, who demonstrated clinical improvement when treated with the epidermal growth factor inhibitor erlotinib.
A resource-aware workload scheduling method for unbalanced GEMMs on GPUs
Authors: Liu Hangda , Diao Boyu , Chen Wenxin , Xu Yongjun
Published: October 2024

GEMM (General Matrix Multiplication) serves as a fundamental operator for deep learning computations. Especially in attention-based deep learning models, such as Bert, GPT, and SAM, the sizes of matrices involved in GEMMs exhibit an unbalanced distribution due to the variable input, resulting in the low utilization of hardware resources. To address the issue, this paper proposes inserting a novel GEMM processing layer into the deep learning inference stack and using an adaptive load balancing method to partition and schedule GEMM computation tasks. The method is implemented with hardware runtime resource information, such as the occupancy of computing units, etc. Experiment results show the remarkable performance of our method in unbalanced input GEMM scenarios, achieving an average performance improvement of 2.3x. The method also performs well in attention-based models (GPT-2 and SAM), achieving an average inference speed improvement of 1.1x. These findings highlight the effectiveness of resource-aware algorithm optimization, especially for computation task scheduling.
Zebrafish arterial valve development occurs through direct differentiation of second heart field progenitors
Authors: Derrick Christopher J , Eley Lorraine , Alqahtani Ahlam , Henderson Deborah J , Chaudhry Bill
Published: October 2024

Aims

Bicuspid aortic valve (BAV) is the most common congenital heart defect, affecting at least 2% of the population. The embryonic origins of BAV remain poorly understood, with few assays for validating patient variants, limiting the identification of causative genes for BAV. In both human and mouse, the left and right leaflets of the arterial valves arise from the outflow tract cushions, with interstitial cells originating from neural crest cells and the overlying endocardium through endothelial-to-mesenchymal transition (EndoMT). In contrast, an EndoMT-independent mechanism of direct differentiation of cardiac progenitors from the second heart field (SHF) is responsible for the formation of the anterior and posterior leaflets. Defects in either of these developmental mechanisms can result in BAV. Although zebrafish have been suggested as a model for human variant testing, their naturally bicuspid arterial valve has not been considered suitable for understanding human arterial valve development. Here, we have set out to investigate to what extent the processes involved in arterial valve development are conserved in zebrafish and, ultimately, whether functional testing of BAV variants could be carried out.

Methods and results

Using a combination of live imaging, immunohistochemistry, and Cre-mediated lineage tracing, we show that the zebrafish arterial valve primordia develop directly from SHF progenitors with no contribution from EndoMT or neural crest, in keeping with the human and mouse anterior and posterior leaflets. Moreover, once formed, these primordia share common subsequent developmental events with all three aortic valve leaflets.

Conclusion

Our work highlights a conserved ancestral mechanism of arterial valve leaflet formation from the SHF and identifies that development of the arterial valve is distinct from that of the atrioventricular valve in zebrafish. Crucially, this confirms the utility of zebrafish for understanding the development of specific BAV subtypes and arterial valve dysplasia, offering potential for high-throughput variant testing.
The burst of satellite DNA in Leptidea wood white butterflies and their putative role in karyotype evolution
Authors: Cabral-de-Mello Diogo Cavalcanti , Yoshido Atsuo , Milani Diogo , Šíchová Jindra , Sahara Ken , Marec František
Published: October 2024

Satellite DNAs (satDNAs) are abundant components of eukaryotic genomes, playing pivotal roles in chromosomal organization, genome stability, and evolution. Here, we combined cytogenetic and genomic methods to characterize the satDNAs in the genomes of Leptidea butterflies. Leptidea is characterized by the presence of a high heterochromatin content, large genomes, and extensive chromosomal reshuffling as well as the occurrence of cryptic species. We show that, in contrast to other Lepidoptera, satDNAs constitute a considerable proportion of Leptidea genomes, ranging between 4.11% and 11.05%. This amplification of satDNAs, together with the hyperactivity of transposable elements, contributes to the substantial genome expansion in Leptidea. Using chromosomal mapping, we show that, particularly LepSat01-100 and LepSat03-167 satDNAs, are preferentially localized in heterochromatin exhibiting variable distribution that may have contributed to the highly diverse karyotypes within the genus. The satDNAs also exhibit W-chromosome accumulation, suggesting their involvement in sex chromosome evolution. Our results provide insights into the dynamics of satDNAs in Lepidoptera genomes and highlight their role in genome expansion and chromosomal organization, which could influence the speciation process. The high proportion of repetitive DNAs in the genomes of Leptidea underscores the complex evolutionary dynamics revealing the interplay between repetitive DNAs and genomic architecture in the genus.
Luminal shape and aortic remodelling after total arch replacement for type A aortic dissection: conventional and frozen elephant trunks
Authors: Sato Hiroshi , Iba Yutaka , Mikami Takuma , Tsushima Shingo , Uchiyama Hiroki , Hosaka Itaru , Mukawa Kei , Iwashiro Yu , Arihara Ayaka , Miura Shuhei , Shibata Tsuyoshi , Nakazawa Jyunji , Nakajima Tomohiro , Komatsu Shigeki , Kawaharada Nobuyoshi , Fukada Joji
Published: October 2024

OBJECTIVES

This study was performed to assess postoperative aortic remodelling (AR) after total arch replacement for acute type A aortic dissection (AAD) with a frozen elephant trunk (FET) or conventional elephant trunk (cET). Furthermore, the shape of the residual true lumen was analysed based on elliptical Fourier analysis and evaluated as a predictor of AR.

METHODS

This study involved patients who underwent total arch replacement with a cET or FET for AAD from December 2006 to January 2023 at five institutions. AR was assessed at the levels of the 4th thoracic vertebra (Th4), Th7, Th10, and above the coeliac trunk. The shape of the residual true lumen at all four levels was analysed based on elliptical Fourier analysis to calculate shape patterns as principal component (PC) values. Inverse probability of treatment weighting was performed for adjustment between the groups.

RESULTS

In total, 180 patients (88 with cET and 92 with FET) were enrolled. The complete AR rate, defined as false lumen remodelling throughout the entire descending thoracic aorta, was significantly higher in the FET than cET group (63.4% vs 32.0%, P = 0.0013). The inverse probability of treatment weighting-adjusted Fine–Gray regression model revealed that the mean PC2 (hazard ratio, 0.22; P < 0.001) and PC3 (hazard ratio, 0.24; P = 0.009) of the four levels were independent predictors of complete AR.

CONCLUSIONS

In AAD repair, the AR rate was significantly higher with use of the FET than cET. The shape patterns of the residual true lumen can be an important reference for predicting postoperative AR.
Concomitant gut dysbiosis and defective gut barrier serve as the bridges between hypercortisolism and chronic systemic inflammation in Cushing’s disease
Authors: Lin Ben , Melnikov Vladimir , Guo Sichen , Cao Zhan , Ye Zhao , Ye Zhen , Ji Chenxing , Chen Jiajun , Wang Jianxin , Zhang Hanwen , Jiang Yiming , Shi Chengzhang , Chen Zhengyuan , Zhang Qilin , Ma Zengyi , Qiao Nidan , Chen Long , Wang Meng , Wang Yongfei , Zhang Zhaoyun , Ye Hongying , Li Yiming , Zhang Yichao , Gao Renyuan , Yu Yifei
Published: October 2024

Objective

The aim of this study was to investigate the gut microbial signatures and related pathophysiological implications in patients with Cushing's disease (CD).

Design and methods

Twenty-seven patients with CD and 45 healthy controls were enrolled. Based on obtained metagenomics data, we performed correlation, network study, and genome interaction group (GIG) analysis. Fecal metabolomics and serum enzyme linked immunosorbent assay (ELISA) analysis were conducted in dichotomized CD patients. Caco-2 cells were incubated with gradient concentrations of cortisol for subsequent transepithelial electrical resistance (TEER) measurement, FITC-dextran transwell permeability assay, qPCR, and western blot analysis.

Results

Gut microbial composition in patients with CD was notably different from that in healthy controls. Network analysis revealed that Eubacterium siraeum might serve as the core specie in the gut microbial system of CD patients. Subsequent GIG analysis identified the positive correlations between GIG9 and UFC. Further serum ELISA and fecal metabolomics uncovered that CD patients with elevated UFC levels were characterized with increased lipopolysaccharide binding protein (LBP). Moreover, remarkable positive association was found between LBP level and relative abundance of E. siraeum. TEER and FITC-dextran transwell assays demonstrated that hypercortisolism induced increased gut permeability. Further qPCR and western blot analysis suggested that dysregulated AhR/Claudin 2 axis might be involved in the development of hypercortisolism-induced defective gut barrier function

Conclusions

Disease activity associated dysbiosis and defective gut barrier might jointly facilitate the development of systemic inflammation in patients with CD.
Parenthood and poverty risk within couples: individual and household poverty risks by gender and education in four European countries
Authors: Siegert Christina
Published: October 2024

This study examines how the presence of children is associated with poverty risk within different-sex couples across welfare state regimes, using no- and full-income pooling scenarios. It focuses on whether partners can achieve an adequate living standard without relying on family ties, and how the costs of children shape poverty risk within these scenarios. Using cross-sectional EU-SILC data (2016–2019) on 30,150 coresidential couples from Austria, France, Spain, and Sweden, I use linear probability models (LPM) to estimate household and individual poverty risks among partners with/out children, by education, gender and country. The results indicate that poverty risks vary by gender, income pooling scenario and country. While partners bear household poverty risks together, there is a pronounced gender gap in individual poverty risk across countries. Men, regardless of their education and fatherhood status, have a relatively low individual poverty risk, with little difference between income pooling scenarios. Conversely, women, especially low-educated mothers, have a higher individual than household poverty risk. Observed cross-country variations highlight that the relationship between motherhood and poverty risk is context-specific. Although education is often promoted as a shield against poverty, in some countries, such as Austria, highly educated mothers also face a high individual poverty risk.
Is There a Link Between Older Adults’ Frequency of (Face-to-Face and Remote) Contact With Grandchildren and Cognitive Functioning Over 12 Years?
Authors: Chereches Flavia S , Ballhausen Nicola , Olaru Gabriel , Laukka Erika J , Brehmer Yvonne
Published: October 2024

Objectives

Past research has linked more frequent social contacts with better cognition and slower cognitive decline in older adults. An open question is whether face-to-face and remote contact with one’s grandchildren can be beneficial.

Methods

We analyzed data from the Swedish National Study on Aging and Care in Kungsholmen covering a span of 12 years and 2 age cohorts (young–old <78, N = 1100; old–old ≥78 years, N = 705). We used latent growth curve models to examine whether frequency of face-to-face or remote grandchild contact was associated with cognitive levels and decline and applied (random intercept) cross-lagged models to investigate if these associations were reciprocal.

Results

Face-to-face contact with grandchildren was positively linked to levels of cognition in young–old adults only. We found no associations with cognitive decline. Results of cross-lagged models suggested that grandparents with better cognition had more face-to-face (for young–old adults only) or remote (for old–old adults only) grandchild contact at subsequent waves. However, more grandchild contact was not associated with later cognition.

Discussion

Our findings suggest that grandparents with better cognition engage more with their grandchildren, but that frequency of grandchild contact is not a protective factor against later cognitive decline in older adults.
Risk factors for wrong-patient medication orders in the emergency department
Authors: Krummrey Gert , Sauter Thomas C , Hautz Wolf E , Müller Martin , Schwappach David L B
Published: October 2024

Objectives

This paper investigates the risk factors for wrong-patient medication orders in an emergency department (ED) by studying intercepted ordering errors identified by the “retract-and-reorder” (RaR) metric (orders that were retracted and reordered for a different patient by the same provider within 10 min).

Materials and Methods

Medication ordering data of an academic ED were analyzed to identify RaR events. The association of RaR events with similarity of patient names and birthdates, matching sex, age difference, the month, weekday, and hour of the RaR event, the elapsed hours since ED shift start, and the proximity of exam rooms in the electronic medical record (EMR) dashboard’s layout was evaluated.

Results

Over 5 years (2017-2021), 1031 RaR events were identified among a total of 561 099 medication orders leading to a proportional incidence of 184 per 100 000 ED orders (95% CI: 172; 195). RaR orders were less likely to be performed by nurses compared to physicians (OR 0.54 [0.47; 0.61], P < .001). Furthermore, RaR pairs were more likely to have the same sex (OR 1.26 [95% CI 1.10; 1.43], P = .001) and the proximity of the exam rooms was closer (−0.62 [95% CI −0.77; −0.47], P = .001) compared to control pairs. Patients’ names, birthdates, age, and the other factors showed no significant association (P > .005).

Discussion and Conclusion

This study found no significant influence from factors such as similarity of patient names, age, or birthdates. However, the proximity of exam rooms in the user interface of the EMR as well as patients’ same sex emerged as risk factors.
Predation on eggs and larvae of the Japanese brown frog Rana japonica Boulenger, 1879 by the invasive crayfish Procambarus clarkii (Girard, 1852) (Decapoda: Astacidea: Cambaridae) under laboratory conditions
Authors: Luong Quang-Tuong , Katsuhara Koki R , Nakata Kazuyoshi
Published: October 2024

We hypothesized that the North American invasive crayfish Procambarus clarkii (Girard, 1852) can negatively affect the populations of native frog species through predation. We conducted three laboratory experiments to examine whether P. clarkii can prey on eggs or larvae of the Japanese native frog Rana japonicaBoulenger, 1879: Experiment I crayfish + frog egg in an aquarium without a substrate or aquatic plants, Experiment II crayfish + frog larva in an aquarium without a substrate or aquatic plants, and Experiment III crayfish + frog larva in an aquarium with a substrate and aquatic plants as shelter for the larva. We used three experimental groups of crayfish individuals (small, intermediate, and large size), each of 10 individuals, and simultaneously placed one crayfish individual and one egg or frog larva in the same aquarium for 24 h and checked for predation by the crayfish. We found that 88.9% and 86.7% of eggs and larvae used in Experiments I and II were preyed upon, respectively. Predation rate of frog larvae was still high (77.8%) in Experiment III, suggesting that crayfish can potentially find and prey on frog larvae in nature. Predation on frog eggs or larvae was high regardless of the crayfish body size. Our results indicate that P. clarkii can potentially have a marked effect on the population of R. japonica by preying on eggs and larvae.
How the Materials of Objects Shape Consumption: An Affordance Theory Perspective
Authors: Pavlyuchenko Roman , Dion Delphine
Published: October 2024

Glasses and stones, metals and textiles, leathers and plastics … . The materials of objects can shape consumption in a variety of ways. Drawing on affordance theory, the authors conceptualize materials as prominent drivers of object affordances, that is, action (im)possibilities with and around objects. The authors explain when, how, and what materials drive object affordances. And, they explain how consumers actualize (or put to use) materials-driven object affordances. This research makes three contributions. First, the authors propose post-hylomorphism as a novel principle of understanding materiality that recognizes matter as a prominent driver of object affordances. Second, the authors explicate how the matter-ness of objects increases object agency and reduces consumer agency. Third, the authors introduce the concept of object affordance management as a novel way to understand how consumers manage object affordances by increasing action possibilities while reducing action impossibilities via a range of processes and micro-practices.
Utopia of Safe Air: How Soviet Research Challenged Western Air Quality Norms, 1950s-1960s
Authors: Mäkiranta Janne
Published: October 2024

During the mid-twentieth century, the Soviet Union developed ambitious hygiene standards for clean air that were grounded in extremely sensitive methods of physiological research. As Western experts sought to develop universal standards for environmental regulation, Soviet hygiene research posed a challenge. This article examines the discussions surrounding the Soviet approach at international conferences on air pollution and industrial hygiene during the mid-twentieth century. The article shows that although the Soviet approach was rejected especially by United States experts, many of its qualities resonated with the ongoing discussions about environmental health in the US. The sensitive and holistic methods of the Soviets were compelling in the effort to reveal the most subtle effects environments had on human health. This article shows how the rejection of Soviet standards stemmed not from different scientific methods but from the differences in the overall ideals of environmental regulation. I argue that Soviet hygiene can be seen as an extreme version of technocratic expertise, and its failure highlights the limits of scientific expertise in managing environmental pollution.
Resolution improvement of differential phase-contrast microscopy via tilt-series acquisition for environmental cell application
Authors: Mitsuishi Kazutaka , Ichihashi Fumiaki , Takahashi Yoshio , Nakazawa Katsuaki , Takeguchi Masaki , Hashimoto Ayako , Tanigaki Toshiaki
Published: October 2024

A simple method that improves the resolution of phase measurement in differential phase-contrast scanning transmission electron microscopy for closed-type environmental cell applications was developed and tested using a model sample simulating environmental cell observations. Because the top and bottom membranes of an environmental cell are typically far apart, the images from these membranes are shifted widely by tilt-series acquisition, and averaging the images after alignment can effectively eliminate undesired signals from the membranes while improving the signal from the object of interest. It was demonstrated that a phase precision of 2π/100 rad is well achievable using the proposed method for the sample in an environmental cell.
Adjuvant modified FOLFIRINOX for resected pancreatic adenocarcinoma: clinical insights and genomic features from a large contemporary cohort
Authors: Keane Fergus , O’Connor Catherine , Moss Drew , Chou Joanne F , Perry Maria A , Crowley Fionnuala , Saxena Parima , Chan Amelia , Schoenfeld Joshua D , Singhal Anupriya , Park Wungki , Cowzer Darren , Harrold Emily , Varghese Anna M , El Dika Imane , Crane Christopher , Harding James J , Abou-Alfa Ghassan K , Kingham T Peter , Wei Alice C , Yu Kenneth H , D’Angelica Michael I , Balachandran Vinod P , Drebin Jeffrey , Jarnagin William R , Bandlamudi Chaitanya , Kelsen David , Capanu Marinela , Soares Kevin C , Balogun Fiyinfolu , O’Reilly Eileen M
Published: October 2024

Background

Adjuvant modified leucovorin calcium, fluorouracil, irinotecan hydrochloride, and oxaliplatin (FOLFIRINOX) is standard of care for fit individuals with resected pancreatic ductal adenocarcinoma (PDAC). Data are limited on adjuvant modified FOLFIRINOX outcomes outside clinical trials.

Methods

We queried institutional databases to identify patients with resected PDAC who received 1 or more doses of adjuvant modified FOLFIRINOX. Primary endpoints were recurrence-free survival (RFS) and overall survival. Secondary endpoints were clinical factors and genomic features associated with outcomes. We estimated RFS and overall survival by using the Kaplan-Meier method. A Cox proportional hazards regression model was used to associate clinicogenomic features with survival outcomes.

Results

A search revealed 147 individuals with PDAC between January 2015 and January 2023. Median patient age was 67 years, with 57 (39%) patients older than 70 years. Unfavorable prognostic features included 52 (36%) patients with N2 nodal status, 115 (78%) patients with lymphovascular invasion, and 133 (90%) patients with perineural invasion. Median time from surgery to initiation of modified FOLFIRINOX was 1.78 months (IQR = 1.45-2.12). In total, 124 (84%) patients completed 12 doses; 98 (67%) patients stopped oxaliplatin early because of neuropathy (median = 10 doses, range = 4-12 doses). Further dosing characteristics are summarized in Table S3, with a median follow-up of 35.1 months, a median RFS of 26 months (95% confidence interval [CI] = 19 to 39), and a median overall survival not reached. For the cohort older than 70 years of age, the median RFS was 23 months (95% CI = 14 to not reached) and the median overall survival was 51 months (95% CI = 37 to not reached). Modified FOLFIRINOX started sooner than 8 weeks from resection was associated with improved RFS (hazard ratio = 0.62, 95% CI = 0.41 to 0.96; P = .033) and overall survival (hazard ratio = 0.53, 95% CI = 0.3 to 0.94; P = .030). KRAS variation and whole-genome doubling trended to shorter RFS and overall survival. Homologous recombination deficiency status did not confer improved survival outcomes.

Conclusions

Adjuvant modified FOLFIRINOX was effective and tolerated in patients with resected PDAC in a nontrial setting, including for patients older than 70 years of age.
Internal migration and multidimensional wellbeing: a case study of North-South migration in Ghana
Authors: Darko Francis Diawuo , Schech Susanne , Saikia Udoy
Published: October 2024

Migration is widely regarded as a principal form of activity available to many of the world’s poor to improve their household’s standard of living. This paper investigates whether and in what ways internal migrants benefit from moving within Ghana’s North-South migration context. This research uses an innovative multidimensional wellbeing framework to assess the effects of migration on migrants’ wellbeing based on six domains: living standards, health, education, community vitality, environmental resilience, and governance. The wellbeing survey of 251 northern Ghanaian migrants working in the informal economic sector within the Sunyani municipality discovered that although most migrants reported improved living standards, a majority could not attain overall wellbeing due to low health and education wellbeing scores. Exploring the relationship between income and wellbeing across domains, the study found a weak positive association, and the complex interplay of factors beyond income was evident. This study challenges the conventional perspective that equates income with the attainment of wellbeing and argues that a multidimensional wellbeing framework permits a more nuanced understanding of the impacts of migration. It highlights the need for the government to actively monitor and address the wellbeing of internal migrants within the Ghanaian context.
SLICK: Strong Lensing Identification of Candidates Kindred in gravitational wave data
Authors: Magare Sourabh , More Anupreeta , Choudhary Sunil
Published: October 2024

By the end of the next decade, we hope to have detected strongly lensed gravitational waves by galaxies or clusters. Although there exist optimal methods for identifying lensed signal, it is shown that machine learning (ML) algorithms can give comparable performance but are orders of magnitude faster than non-ML methods. We present the SLICK pipeline which comprises a parallel network based on deep learning. We analyse the Q-transform maps (QT maps) and the Sine-Gaussian projection (SGP) maps generated for the binary black hole signals injected in Gaussian as well as real noise. We compare our network performance with the previous work and find that the efficiency of our model is higher by a factor of 5 at a false positive rate of 0.001. Further, we show that including SGP maps with QT maps data result in a better performance than analysing QT maps alone. When combined with sky localization constraints, we hope to get unprecedented accuracy in the predictions than previously possible. We also evaluate our model on the real events detected by the LIGO–Virgo collaboration and find that, at a threshold of 0.75 our network correctly classifies all of them, consistent with non-detection of lensing.
Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages
Authors: Wen Jiejie , Zhang Haobo , Chu Dongliang , Chen Xiaoke , Feng Jingru , Wang Yucen , Liu Guanxi , Zhang Yuhao , Li Yuxue , Ning Kang
Published: October 2024

Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.
Impact of antidepressant use on survival outcomes in glioma patients: A systematic review and meta-analysis
Authors: Ge Yulu , Cao Yaning , Wang Qi , Wang Yu , Ma Wenbin
Published: October 2024

Background

Depression is common among glioma patients, and antidepressants are frequently prescribed to manage symptoms. Understanding the impact of antidepressants on glioma patient survival is crucial for informing treatment strategies.

Methods

A systematic search was conducted in PubMed and EMBASE databases for studies published from January 1994 to March 2024. The search strategy included terms related to overall survival, prognosis, antidepressants, and gliomas. A manual search was performed in the reference lists. According to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guideline, 2 authors independently extracted data. Statistical analysis was performed using Review Manager (version 5.4.1) software, employing a random effects model based on study heterogeneity. The primary outcome was overall survival (OS). Hazard ratios (HRs) were used to present survival differences between the 2 arms. HRs after correcting for confounders were prioritized for extraction.

Results

Seven retrospective cohort studies involving 5579 patients were analyzed. Selective serotonin reuptake inhibitors (SSRIs) showed no significant survival difference in all glioma patients (HR = 1.34, 95% confidence interval [CI]: 0.66–2.70) and in GBM patients (HR = 1.05, 95% CI: 0.45–2.46), while non-SSRIs had an unfavorable impact on OS in GBMs (HR = 3.54, 95% CI: 2.51–4.99). When considering LGG, both SSRIs and non-SSRIs usage demonstrated associations with poorer survival outcomes (SSRIs: HR = 3.26, 95%CI: 2.19–4.85; Non-SSRIs: HR = 7.71, 95% CI: 4.25–14.00).

Conclusions

Antidepressant use was not significantly associated with better survival outcomes, emphasizing the need for reconsidering the real effects of antidepressant medication. Future clinical research should address patient heterogeneity to better clarify the effects of antidepressants on glioma survival.
Origin of sulfate in post-snowball-Earth oceans: river inputs vs. shelf-derived H2S
Authors: Bao Huiming , Peng Yongbo , Cao Xiaobin
Published: October 2024

A synthesis of global barite sulfate isotope data from approximately 635 million years ago, at the end of a global glaciation, undermines the hypothesis that river sulfate was the primary carrier of the distinctive 17O-depleted atmospheric O2 signature of the time. Instead, an aqueous H2S oxidation model on the shelf emerges as a compelling alternative, though it demands extensive validation across multiple fronts by the scientific community.
A Content Analysis of Illicit Tobacco-Related Crimes Reported in Australian Media
Authors: Meciar Isabel , Puljević Cheneal , Holland Alice , Gartner Coral
Published: October 2024

Introduction

Australian survey and seizure data suggest a growing illicit tobacco market. As an illicit product, accurately tracking trends in illicit tobacco growing, manufacture, and sales is challenging. We examined trends in Australian illicit tobacco-related crimes using a content analysis of news articles.

Aims and Methods

We analyzed Australian news articles identified in the Factiva database and government press releases describing Australian illicit tobacco-related crimes reported between January 2000 and December 2023. Sources were coded for crime type, location, product type, dollar value of seized products, methods of distribution or storage, agencies involved, and other crimes involved.

Results

We identified 447 crimes reported in 389 sources. The number of illicit tobacco-related crimes reported increased between 2000 and 2023. The most common crimes were possession of illicit tobacco (n = 196/43.7%) and smuggling (n = 187/41.8%), and the most common product type was “illicit cigarettes” (n = 197/44.1%). The most common distribution/storage method reported was via residential premises (n = 98/21.9%). One-hundred and twenty incidents involved other crimes such as financial crimes involving money laundering (n = 59/13.2%). Across all included news articles, the quantity of seized products totaled 827 529 307 cigarette sticks, 76 185 cartons, 668 687 packs, 239 hectares (of land growing tobacco plants), and 2 149 000 plants of illicit tobacco between 2000 and 2023. The median value (worth; AUD) of each seizure was $1 500 000 (range $43 to $67 000 000).

Conclusions

Australian media reporting on illicit tobacco-related crimes increased over the past two decades, particularly since 2018. These findings highlight a need for improved border detection measures, investment in enforcement, and other deterrent activities.

Implications

This media analysis complements trends identified in national survey data that indicate a growing illicit tobacco market in Australia since 2013 with a marked increase since 2018. While survey data suggests that the Australian tobacco tax policy, which has included regular large tax increases since 2010, has decreased consumer demand for tobacco overall, it may have also incentivized criminal networks to supply illicit tobacco products due to it being a “low risk” and “high reward” activity. Controlling the Australian illicit tobacco market should be a policy priority.
Vitamin D as a Modifiable Risk Factor for Juvenile Idiopathic Arthritis: A Systematic Review and Meta-analysis of Observational Studies Comparing Baseline Vitamin D in Children with JIA to Individuals Without
Authors: Zang Kathleen , Bhatia Resham , Xue Elizabeth , Bennett Kalia J , Luo Katherine H , Malvankar-Mehta Monali S
Published: October 2024

Context

The varying interactions contributing to the development of juvenile idiopathic arthritis (JIA) drive the struggle to understand its etiology. Among the environmental risk factors, vitamin D has been posited to have a component in disease progression, acting as an inflammatory mediator.

Objective

To investigate the correlation between serum 25-hydroxyvitamin D [25(OH)D] levels, indicative of vitamin D, among patients diagnosed with JIA compared with control participants. The aim was to elucidate potential therapeutic implications of vitamin D in the management of JIA.

Data Sources

A systematic search of 6 electronic databases (MEDLINE, Embase, Scopus, CINAHL, Web of Science, and Cochrane Library) was performed until February 2023. Inclusion criteria required participants to be <16 years old (either clinically diagnosed with JIA or a matched control participant), with vitamin D levels measured through serum laboratory methods. Exclusion criteria omitted studies in which participants used vitamin D supplementation or medications affecting vitamin D levels without corresponding statistical analyses on their association with vitamin D levels.

Data Extraction

Each article was reviewed by at least 2 independent reviewers to assess eligibility for analysis.

Data Analysis

Data were qualitatively analyzed to compare means of serum 25(OH)D levels (ng/mL) between patients with JIA and control participants, followed by a meta-analysis to obtain effect size.

Results

Ten eligible studies were included qualitatively, and eight were included in the meta-analysis. Seven studies found a statistically significant difference in vitamin D levels between control participants and patients with JIA, with five of these reporting a lower mean vitamin D level in patients with JIA. A random-effects model using standardized mean difference found a statistically significant difference in vitamin D levels between control participants and patients with JIA (–0.49; 95% CI, –0.92 to –0.06).

Conclusions

The findings from the analysis indicate vitamin D levels were lower in patients with JIA as compared with healthy control participants at baseline. It is recommended that research into vitamin D supplementation and JIA should be conducted.
Characterization of the Calmodulin-Like Protein Family in Chara braunii and their Conserved Interaction with the Calmodulin-Binding Transcription Activator Family
Authors: Symonds Kyle , Wali Udo , Duff Liam , Snedden Wayne A
Published: October 2024

Calcium sensor proteins play important roles by detecting changes in intracellular calcium and relaying that information onto downstream targets through protein–protein interaction. Very little is known about calcium sensors from plant species that predate land colonization and the evolution of embryophytes. Here, we examined the genome of the multicellular algae, Chara braunii, for orthologs to the evolutionarily conserved calcium sensor calmodulin (CaM) and for CaM-like (CML) proteins. We identified one CaM and eight CML isoforms that range in size from 16.4 to 21.3 kDa and are predicted to have between two to four calcium-binding (EF-hand) domains. Using recombinant protein, we tested whether CbCaM and CbCML1–CbCML7 possess biochemical properties of typical calcium sensors. CbCaM and the CbCMLs all displayed high-affinity calcium binding with estimated global KD,app values in the physiological µM range. In response to calcium binding, CbCaM and the CbCMLs exhibited varying degrees of increase in exposed hydrophobicity, suggesting that different calcium-induced conformational changes occur among isoforms. We found many examples of putative CaM targets encoded in the C. braunii genome and explored the ability of CbCaM and CbCMLs to interact in planta with a representative putative target, a C. braunii CaM-binding transcription factor (CbCAMTA1). CbCaM, CbCML2 and CbCML4 each associated with the C-terminal region of CbCAMTA1. Collectively, our data support the hypothesis that complex calcium signaling and sensing networks involving CaM and CMLs evolved early in the green lineage. Similarly, it seems likely that calcium-mediated regulation of transcription occurs in C. braunii via CAMTAs and is an ancient trait predating embryophytic emergence.
College Educated Religious Conservatives’ Support for Capital Punishment
Authors: Schwadel Philip , Anderson Amy L
Published: October 2024

Higher education is associated with reduced support for capital punishment among white Americans. Conservative religion, however, is associated with moral foundations and schemas that lead to greater support for capital punishment, which we expect moderate the association between education and views of capital punishment. Using nationally representative survey data, we found that the negative association between higher education and support for the death penalty was attenuated for white religious conservatives. This finding did not apply to nonwhite Americans. We conclude with a discussion of how the moral worldview associated with conservative religion may affect the future of capital punishment, by addressing how the association between higher education and views of capital punishment is contingent on other individual and contextual factors, and by situating the results within the contemporary American context that is characterized by political polarization and the decline of religion.
USP13 overexpression in BMSCs enhances anti-apoptotic ability and guards against methylprednisolone-induced osteonecrosis in rats
Authors: Jiang Yixin , Fan Xiaoli , Yu Yaling , Ge Hongfan , Liu Chengyin , Zhang Yanyan , Yu Lingyun , Yin Wen , Zhou Zhenlei
Published: October 2024

Methylprednisolone (MPS) use is linked to increased cases of osteonecrosis of the femoral head (ONFH). Bone marrow mesenchymal stem cells (BMSCs) have shown potential for treating MPS-induced ONFH, but their effectiveness is limited by high apoptosis rates post-transplantation. We developed a pretreatment strategy for BMSCs to improve their viability. In a rat model of MPS-induced ONFH, we evaluated the effects of USP13 overexpression in BMSCs through micro-CT, HE staining, and TUNEL staining. USP13-overexpressing BMSCs significantly reduced ONFH severity compared to plain BMSCs and direct lentivirus injection. USP13 also protected BMSCs from MPS-induced apoptosis by modulating PTEN and reducing AKT phosphorylation. This led to decreased expression of apoptotic genes and proteins in USP13-overexpressing BMSCs. Our findings highlight USP13 as a promising target for enhancing BMSC survival and efficacy in treating MPS-induced ONFH.
Adaptation of an evidence-based, preventive intervention to promote mental health in Hispanic adolescents: eHealth Familias Unidas Mental Health
Authors: Perrino Tatiana , Lozano Alyssa , Estrada Yannine , Tapia Maria I , Brown C Hendricks , Horigian Viviana E , Beardslee William R , Prado Guillermo
Published: October 2024

Youth internalizing symptoms (i.e., depression and anxiety), suicide ideation and attempts have been rising in recent years, including among Hispanics. Disparities in mental healthcare are concerning and require intervention, ideally prevention or early intervention. Familias Unidas is a culturally-syntonic, family-centered intervention effective in reducing youth drug use and sexual risk, with evidence of unanticipated effects on internalizing symptoms. This paper describes the systematic process used to adapt the eHealth version of the Familias Unidas intervention to more directly address internalizing symptoms and suicide risk in preparation for an effectiveness-implementation hybrid trial for youth with elevated internalizing symptoms, a history of suicide ideation/attempts, or poor parent-youth communication. The resulting eHealth Familias Unidas Mental Health intervention is described. Guided by a 4-phase framework, the steps in the adaptation process involved: assessment of the community and intervention delivery setting (pediatric primary care clinics); integration of previous intervention research, including intervention mechanisms of action; and expert and community consultation via focus groups. Focus group analyses showed that youth and parents perceived that the intervention was helpful. Their feedback was categorized into themes that were used to directly target mental health by addressing technology use, parent mental health, and social support. Effective and scalable preventive interventions are needed to address mental health disparities. The systematic adaptation process described in this paper is an efficient approach to expanding interventions while maintaining known, empirical and theoretical mechanisms of action. Findings from the ongoing effectiveness-implementation trial will be critical.