bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Swiss chiropractic practice-based research network: a population-based cross-sectional study to inform future musculoskeletal research
Authors: Lalji Rahim , Hofstetter Léonie , Kongsted Alice , von Wyl Viktor , Puhan Milo A. , Hincapié Cesar A. 
Published: April 2023

AbstractThe Swiss chiropractic practice-based research network (PBRN) is a nationwide project developed in collaboration with patients, clinicians, and academic stakeholders to advance musculoskeletal epidemiologic research. The aim of this study was to describe the clinician population recruited and representativeness of this PBRN to inform future collaboration. A population-based cross-sectional study was performed. PBRN clinician characteristics were described and factors related to motivation (operationalised as VAS score ≥ 70) to participate in a subsequent patient cohort pilot study were assessed. Among 326 eligible chiropractors, 152 enrolled in the PBRN (47% participation). The PBRN was representative of the larger Swiss chiropractic population with regards to age, language, and geographic distribution. Of those enrolled, 39% were motivated to participate in a nested patient cohort pilot study. Motivation was associated with age 40 years or older versus 39 years or younger (OR 2.3, 95% CI 1.0–5.2), and with a moderate clinic size (OR 2.4, 95% CI 1.1–5.7) or large clinic size (OR 2.8, 95% CI 1.0–7.8) versus solo practice. The Swiss chiropractic PBRN has enrolled almost half of all Swiss chiropractors and has potential to facilitate collaborative practice-based research to improve musculoskeletal health care quality.Trial registration: Swiss chiropractic PBRN (ClinicalTrials.gov identifier: NCT05046249); Swiss chiropractic cohort (Swiss ChiCo) pilot study (ClinicalTrials.gov identifier: NCT05116020).
Counter-gradient variation and the expensive tissue hypothesis explain parallel brain size reductions at high elevation in cricetid and murid rodents
Authors: Nengovhela Aluwani , Ivy Catherine M. , Scott Graham R. , Denys Christiane , Taylor Peter J. 
Published: April 2023

AbstractTo better understand functional morphological adaptations to high elevation (> 3000 m above sea level) life in both North American and African mountain-associated rodents, we used microCT scanning to acquire 3D images and a 3D morphometric approach to calculate endocranial volumes and skull lengths. This was done on 113 crania of low-elevation and high-elevation populations in species of North American cricetid mice (two Peromyscus species, n = 53), and African murid rodents of two tribes, Otomyini (five species, n = 49) and Praomyini (four species, n = 11). We tested two distinct hypotheses for how endocranial volume might vary in high-elevation populations: the expensive tissue hypothesis, which predicts that brain and endocranial volumes will be reduced to lessen the costs of growing and maintaining a large brain; and the brain-swelling hypothesis, which predicts that endocranial volumes will be increased either as a direct phenotypic effect or as an adaptation to accommodate brain swelling and thus minimize pathological symptoms of altitude sickness. After correcting for general allometric variation in cranial size, we found that in both North American Peromyscus mice and African laminate-toothed (Otomys) rats, highland rodents had smaller endocranial volumes than lower-elevation rodents, consistent with the expensive tissue hypothesis. In the former group, Peromyscus mice, crania were obtained not just from wild-caught mice from high and low elevations but also from those bred in common-garden laboratory conditions from parents caught from either high or low elevations. Our results in these mice showed that brain size responses to elevation might have a strong genetic basis, which counters an opposite but weaker environmental effect on brain volume. These results potentially suggest that selection may act to reduce brain volume across small mammals at high elevations but further experiments are needed to assess the generality of this conclusion and the nature of underlying mechanisms.
Inference of transcriptome signatures of Escherichia coli in long-term stationary phase
Authors: Takano Sotaro , Takahashi Hiromi , Yama Yoshie , Miyazaki Ryo , Furusawa Chikara , Tsuru Saburo 
Published: April 2023

Abstract“Non-growing” is a dominant life form of microorganisms in nature, where available nutrients and resources are limited. In laboratory culture systems, Escherichia coli can survive for years under starvation, denoted as long-term stationary phase, where a small fraction of cells manages to survive by recycling resources released from nonviable cells. Although the physiology by which viable cells in long-term stationary phase adapt to prolonged starvation is of great interest, their genome-wide response has not been fully understood. In this study, we analyzed transcriptional profiles of cells exposed to the supernatant of 30-day long-term stationary phase culture and found that their transcriptome profiles displayed several similar responses to those of cells in the 16-h short-term stationary phase. Nevertheless, our results revealed that cells in long-term stationary phase supernatant exhibit higher expressions of stress-response genes such as phage shock proteins (psp), and lower expressions of growth-related genes such as ribosomal proteins than those in the short-term stationary phase. We confirmed that the mutant lacking the psp operon showed lower survival and growth rate in the long-term stationary phase culture. This study identified transcriptional responses for stress-resistant physiology in the long-term stationary phase environment.
Estimating infection fatality risk and ascertainment bias of COVID-19 in Osaka, Japan from February 2020 to January 2022
Authors: Zhang Tong , Nishiura Hiroshi 
Published: April 2023

AbstractThe present study aimed to estimate the infection fatality risk (IFR) and ascertainment bias of SARS-CoV-2 for six epidemic waves in Japan from February 2020 to January 2022. We used two types of datasets: (i) surveillance-based datasets containing the cumulative numbers of confirmed cases and deaths in each epidemic wave and (ii) seroepidemiological datasets conducted in a serial cross-sectional manner. Smoothing spline function was employed to reconstruct the age-specific cumulative incidence of infection. We found that IFR was highest during the first wave, and the second highest during the fourth wave, caused by the Alpha variant. Once vaccination became widespread, IFR decreased considerably among adults aged 40 years plus during the fifth wave caused by the Delta variant, although the epidemic size of fifth wave was the largest before the Omicron variant emerged. We also found that ascertainment bias was relatively high during the first and second waves and, notably, RT-PCR testing capacity during these early periods was limited. Improvements in the ascertainment were seen during the third and fourth waves. Once the Omicron variant began spreading, IFR diminished while ascertainment bias was considerably elevated.
Seasonal changes in photoperiod and temperature lead to changes in cuticular hydrocarbon profiles and affect mating success in Drosophila suzukii
Authors: Kárpáti Zsolt , Deutsch Ferenc , Kiss Balázs , Schmitt Thomas 
Published: April 2023

AbstractSeasonal plasticity in insects is often triggered by temperature and photoperiod changes. When climatic conditions become sub-optimal, insects might undergo reproductive diapause, a form of seasonal plasticity delaying the development of reproductive organs and activities. During the reproductive diapause, the cuticular hydrocarbon (CHC) profile, which covers the insect body surface, might also change to protect insects from desiccation and cold temperature. However, CHCs are often important cues and signals for mate recognition and changes in CHC composition might affect mate recognition. In the present study, we investigated the CHC profile composition and the mating success of Drosophila suzukii in 1- and 5-day-old males and females of summer and winter morphs. CHC compositions differed with age and morphs. However, no significant differences were found between the sexes of the same age and morph. The results of the behavioral assays show that summer morph pairs start to mate earlier in their life, have a shorter mating duration, and have more offspring compared to winter morph pairs. We hypothesize that CHC profiles of winter morphs are adapted to survive winter conditions, potentially at the cost of reduced mate recognition cues.
Changes of the coronal lumbar-pelvic-femoral alignment after conversion total hip arthroplasty in patients with unilateral ankylosed hip
Authors: Kobayashi Takaomi , Morimoto Tadatsugu , Hirata Hirohito , Yoshihara Tomohito , Tsukamoto Masatsugu , Sonohata Motoki , Mawatari Masaaki 
Published: April 2023

AbstractTo elucidate the changes in coronal lumbar-pelvic-femoral alignment after conversion total hip arthroplasty (THA) in patients with unilateral ankylosed hip. A retrospective radiologic study of 48 patients (48 hips) with unilateral hip arthrodesis who underwent conversion THA was conducted. Cobb’s angle of lumbar scoliosis (LS), the pelvic obliquity (PO) angle, and the hip adduction angle (HAA) on standing anterior–posterior spine-pelvis-hip radiographs were measured before and after THA. The differences of LS, PO, and HAA before and after THA were defined as ΔLS, ΔPO, and ΔHAA, respectively. A paired samples t-test or the Wilcoxon signed-rank test were used to compare the absolute values of the LS, PO, and HAA between preoperative and postoperative groups. The Pearson’s correlation coefficient (r) or Spearman’s correlation coefficient (ρ) was calculated to assess the relationship between ΔLS, ΔPO, and ΔHAA and possible associated factors. Significant differences were found in the preoperative LS (mean, 10.8° vs. 8.2°, p = 0.004), PO (median, 6.8° vs. 2.0°, p < 0.001), and HAA (median, 10.0° vs. 6.0°, p = 0.003). ΔLS was correlated with the preoperative LS (ρ =  − 0.621, p < 0.001), PO (ρ =  − 0.580, p < 0.001), and HAA (ρ =  − 0.467, p < 0.001). ΔPO was correlated with the preoperative LS (r =  − 0.596, p < 0.001), PO (ρ =  − 0.892, p < 0.001), and HAA (ρ =  − 0.728, p < 0.001). ΔHAA was correlated with the preoperative LS (r =  − 0.583, p < 0.001), PO (ρ =  − 0.751, p < 0.001), and HAA (ρ =  − 0.824, p < 0.001). LS, PO, and HAA were significantly improved after conversion THA. Greater improvement in LS, PO, and HAA can be expected in patients with larger preoperative LS, PO, and HAA values.
Quantum-resistance in blockchain networks
Authors: Allende Marcos , León Diego López , Cerón Sergio , Pareja Adrián , Pacheco Erick , Leal Antonio , Da Silva Marcelo , Pardo Alejandro , Jones Duncan , Worrall David J. , Merriman Ben , Gilmore Jonathan , Kitchener Nick , Venegas-Andraca Salvador E. 
Published: April 2023

AbstractThe advent of quantum computing threatens blockchain protocols and networks because they utilize non-quantum resistant cryptographic algorithms. When quantum computers become robust enough to run Shor’s algorithm on a large scale, the most used asymmetric algorithms, utilized for digital signatures and message encryption, such as RSA, (EC)DSA, and (EC)DH, will be no longer secure. Quantum computers will be able to break them within a short period of time. Similarly, Grover’s algorithm concedes a quadratic advantage for mining blocks in certain consensus protocols such as proof of work. Today, there are hundreds of billions of dollars denominated in cryptocurrencies and other digital assets that rely on blockchain ledgers as well as thousands of blockchain-based applications storing value in blockchain networks. Cryptocurrencies and blockchain-based applications require solutions that guarantee quantum resistance in order to preserve the integrity of data and assets in these public and immutable ledgers. The quantum threat and some potential solutions are well understood and presented in the literature. However, most proposals are theoretical, require large QKD networks, or propose new quantum-resistant blockchain networks to be built from scratch. Our work, which is presented in this paper, is pioneer in proposing an end-to-end framework for post-quantum blockchain networks that can be applied to existing blockchain to achieve quantum-resistance. We have developed an open-source implementation in an Ethereum-based (i.e., EVM compatible) network that can be extended to other existing blockchains. For the implementation we have (i) used quantum entropy to generate post-quantum key pairs, (ii) established post-quantum TLS connections and X.509 certificates to secure the exchange of information between blockchain nodes over the internet without needing a large QKD network, (iii) introduced a post-quantum second signature in transactions using Falcon-512 post-quantum keys, and (iv) developed the first on-chain verification of post-quantum signatures using three different mechanisms that are compared and analyzed: Solidity smart-contracts run by the validators for each transaction, modified EVM Opcode, and precompiled smart contracts.
Collagen type I alters the proteomic signature of macrophages in a collagen morphology-dependent manner
Authors: Vasse Gwenda F. , Russo Sara , Barcaru Andrei , Oun Asmaa A. A. , Dolga Amalia M. , van Rijn Patrick , Kwiatkowski Marcel , Govorukhina Natalia , Bischoff Rainer , Melgert Barbro N. 
Published: April 2023

AbstractIdiopathic pulmonary fibrosis is a progressive lung disease that causes scarring and loss of lung function. Macrophages play a key role in fibrosis, but their responses to altered morphological and mechanical properties of the extracellular matrix in fibrosis is relatively unexplored. Our previous work showed functional changes in murine fetal liver-derived alveolar macrophages on fibrous or globular collagen morphologies. In this study, we applied differential proteomics to further investigate molecular mechanisms underlying the observed functional changes. Macrophages cultured on uncoated, fibrous, or globular collagen-coated plastic were analyzed by liquid chromatography-mass spectrometry. The presence of collagen affected expression of 77 proteins, while 142 were differentially expressed between macrophages grown on fibrous or globular collagen. Biological process and pathway enrichment analysis revealed that culturing on any type of collagen induced higher expression of enzymes involved in glycolysis. However, this did not lead to a higher rate of glycolysis, probably because of a concomitant decrease in activity of these enzymes. Our data suggest that macrophages sense collagen morphologies and can respond with changes in expression and activity of metabolism-related proteins. These findings suggest intimate interactions between macrophages and their surroundings that may be important in repair or fibrosis of lung tissue.
The GAPDH redox switch safeguards reductive capacity and enables survival of stressed tumour cells
Authors: Talwar Deepti , Miller Colin G. , Grossmann Justus , Szyrwiel Lukasz , Schwecke Torsten , Demichev Vadim , Mikecin Drazic Ana-Matea , Mayakonda Anand , Lutsik Pavlo , Veith Carmen , Milsom Michael D. , Müller-Decker Karin , Mülleder Michael , Ralser Markus , Dick Tobias P. 
Published: April 2023

AbstractGlyceraldehyde 3-phosphate dehydrogenase (GAPDH) is known to contain an active-site cysteine residue undergoing oxidation in response to hydrogen peroxide, leading to rapid inactivation of the enzyme. Here we show that human and mouse cells expressing a GAPDH mutant lacking this redox switch retain catalytic activity but are unable to stimulate the oxidative pentose phosphate pathway and enhance their reductive capacity. Specifically, we find that anchorage-independent growth of cells and spheroids is limited by an elevation of endogenous peroxide levels and is largely dependent on a functional GAPDH redox switch. Likewise, tumour growth in vivo is limited by peroxide stress and suppressed when the GAPDH redox switch is disabled in tumour cells. The induction of additional intratumoural oxidative stress by chemo- or radiotherapy synergized with the deactivation of the GAPDH redox switch. Mice lacking the GAPDH redox switch exhibit altered fatty acid metabolism in kidney and heart, apparently in compensation for the lack of the redox switch. Together, our findings demonstrate the physiological and pathophysiological relevance of oxidative GAPDH inactivation in mammals.
Regression Transformer enables concurrent sequence regression and generation for molecular language modelling
Authors: Born Jannis , Manica Matteo 
Published: April 2023

AbstractDespite tremendous progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a method that abstracts regression as a conditional sequence modelling problem. This introduces a new direction for multitask language models, seamlessly bridging sequence regression and conditional sequence generation. We demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by an alternating training scheme that enables the model to decorate seed sequences on the basis of desired property constraints, for example, to optimize reaction yield. We expect that the RT’s capability to jointly tackle predictive and generative tasks in biochemistry can find applications in property-driven, local exploration of the chemical or protein space. Such multitask approaches will pave the road towards foundation models in materials design.
Protecting Brazilian Amazon Indigenous territories reduces atmospheric particulates and avoids associated health impacts and costs
Authors: Prist Paula R. , Sangermano Florencia , Bailey Allison , Bugni Victoria , Villalobos-Segura María del Carmen , Pimiento-Quiroga Nataly , Daszak Peter , Zambrana-Torrelio Carlos 
Published: April 2023

AbstractIndigenous territories are considered important for conservation, but little is known about their role in maintaining human health. Here we quantified the potential human health and economic benefits of protecting these territories in the Brazilian Amazon, by using cardiovascular and respiratory diseases cases, pollutant and forest cover data. Between 2010 and 2019, 1.68 tons of Particulate Matter of small size (PM2.5) were released every year, with negative effects for human health. A lower number of diseases and infections was also found in municipalities with more forested areas, and with a low level of fragmentation, which probably is related to the potential capacity of the Amazon Forest to absorb PM2.5 (26,376.66 tons year−1, 27% of this absorption capacity in Indigenous territories). Our estimates indicate that by protecting Amazon Indigenous territories, over 15 million of respiratory and cardiovascular cases could be avoided every year, with ~$2 billion USD being saved only in health costs.
Crustose coralline algae can contribute more than corals to coral reef carbonate production
Authors: Cornwall Christopher E. , Carlot Jérémy , Branson Oscar , Courtney Travis A. , Harvey Ben P. , Perry Chris T. , Andersson Andreas J. , Diaz-Pulido Guillermo , Johnson Maggie D. , Kennedy Emma , Krieger Erik C. , Mallela Jennie , McCoy Sophie J. , Nugues Maggy M. , Quinter Evan , Ross Claire L. , Ryan Emma , Saderne Vincent , Comeau Steeve 
Published: April 2023

AbstractUnderstanding the drivers of net coral reef calcium carbonate production is increasingly important as ocean warming, acidification, and other anthropogenic stressors threaten the maintenance of coral reef structures and the services these ecosystems provide. Despite intense research effort on coral reef calcium carbonate production, the inclusion of a key reef forming/accreting calcifying group, the crustose coralline algae, remains challenging both from a theoretical and practical standpoint. While corals are typically the primary reef builders of contemporary reefs, crustose coralline algae can contribute equally. Here, we combine several sets of data with numerical and theoretical modelling to demonstrate that crustose coralline algae carbonate production can match or even exceed the contribution of corals to reef carbonate production. Despite their importance, crustose coralline algae are often inaccurately recorded in benthic surveys or even entirely missing from coral reef carbonate budgets. We outline several recommendations to improve the inclusion of crustose coralline algae into such carbonate budgets under the ongoing climate crisis.
The effect of epigenetic reprogramming using MI192 HDAC inhibitor on enhancing the osteogenesis of human adipose-derived stem cells in vitro
Authors: Lu Wei , Ji Kun , Lawlor Liam , Saha Sushmita , Hempshall Aiden , Jin Yan , Yang Xuebin B. 
Published: April 2023

Abstract
The ability to control stem cell function is the key to stem cell-based therapy and living tissue regeneration. In natural conditions, histone deacetylases (HDAC) are regarded as the important defining epigenetic reprogramming for stem cell differentiation. To date, human adipose-derived stem cells (hADSCs) have been widely utilised for bone tissue engineering applications. The present study aimed to examine the effect of a novel HDAC2&3-selective inhibitor, MI192, on hADSCs epigenetic reprogramming for regulating its osteogenic potential in vitro. The results confirmed that MI192 treatment reduced the hADSCs viability in a time and dose-dependent manner. The optimal concentration and pre-treatment time of MI192 for hADSCs osteogenic induction was 30 μM and 2 days representatively. A quantitative biochemical assay confirmed that the pre-treatment with MI192 (30 μM) for 2 days significantly enhanced hADSCs alkaline phosphatase (ALP) specific activity (P&lt;0.05) compared with that of the valproic acid (VPA) pre-treatment group. Real-time PCR analysis revealed that MI192 pre-treatment up-regulated hADSCs gene expressions of osteogenic markers (e.g., Runx2, Col1, and OCN) under the osteogenic induction. DNA flow cytometric analysis indicated that two days’ pre-treatment with MI192 (30 μM) resulted in G2/M arrest in hADSCs and this G2/M arrest was reversible. Our results suggest that MI192 is capable of epigenetic reprogramming of hADSCs via HDAC inhibition for controlling the cell cycle, resulting in enhancing hADSCs osteogenic differentiation, which indicates the potential of using MI192 for promoting bone tissue regeneration.