bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host range, transmissibility and antigenicity of a pangolin coronavirus
Authors: Hou Yixuan J. , Chiba Shiho , Leist Sarah R. , Meganck Rita M. , Martinez David R. , Schäfer Alexandra , Catanzaro Nicholas J. , Sontake Vishwaraj , West Ande , Edwards Catlin E. , Yount Boyd , Lee Rhianna E. , Gallant Samuel C. , Zost Seth J. , Powers John , Adams Lily , Kong Edgar F. , Mattocks Melissa , Tata Aleksandra , Randell Scott H. , Tata Purushothama R. , Halfmann Peter , Crowe James E. , Kawaoka Yoshihiro , Baric Ralph S. 
Published: September 2023

AbstractThe pathogenic and cross-species transmission potential of SARS-CoV-2-related coronaviruses (CoVs) remain poorly characterized. Here we recovered a wild-type pangolin (Pg) CoV GD strain including derivatives encoding reporter genes using reverse genetics. In primary human cells, PgCoV replicated efficiently but with reduced fitness and showed less efficient transmission via airborne route compared with SARS-CoV-2 in hamsters. PgCoV was potently inhibited by US Food and Drug Administration approved drugs, and neutralized by COVID-19 patient sera and SARS-CoV-2 therapeutic antibodies in vitro. A pan-Sarbecovirus antibody and SARS-CoV-2 S2P recombinant protein vaccine protected BALB/c mice from PgCoV infection. In K18-hACE2 mice, PgCoV infection caused severe clinical disease, but mice were protected by a SARS-CoV-2 human antibody. Efficient PgCoV replication in primary human cells and hACE2 mice, coupled with a capacity for airborne spread, highlights an emergence potential. However, low competitive fitness, pre-immune humans and the benefit of COVID-19 countermeasures should impede its ability to spread globally in human populations.
A computational framework for the inference of protein complex remodeling from whole-proteome measurements
Authors: Buljan Marija , Banaei-Esfahani Amir , Blattmann Peter , Meier-Abt Fabienne , Shao Wenguang , Vitek Olga , Tang Hua , Aebersold Ruedi 
Published: September 2023

AbstractProtein complexes are responsible for the enactment of most cellular functions. For the protein complex to form and function, its subunits often need to be present at defined quantitative ratios. Typically, global changes in protein complex composition are assessed with experimental approaches that tend to be time consuming. Here, we have developed a computational algorithm for the detection of altered protein complexes based on the systematic assessment of subunit ratios from quantitative proteomic measurements. We applied it to measurements from breast cancer cell lines and patient biopsies and were able to identify strong remodeling of HDAC2 epigenetic complexes in more aggressive forms of cancer. The presented algorithm is available as an R package and enables the inference of changes in protein complex states by extracting functionally relevant information from bottom-up proteomic datasets.
Relative attitude stability analysis of double satellite formation for gravity field exploration in space debris environment
Authors: Pan Baocai , Meng Yunhe 
Published: September 2023

AbstractSpacecraft operating in low orbit are at risk of being hit by space debris. In the debris environment, the impact of debris is likely to cause the double satellite formation to exit science mode or even lead to the divergence of the control system, thus affecting the scientific exploration mission. In this paper, the attitude stability of the double satellite formation for gravity field in the near circular and polar orbit in the space debris environment is studied. Firstly, based on Lyapunov control and LQR, two sets of control models of stochastic collision for two satellites aligned with each other were proposed, and the actuators were modelled and assigned. Secondly, models of collision probability and momentum are developed. The distribution law of space debris is obtained according to the international common debris software. Meanwhile, probability density function of two independent collisions is gained. Finally, through Monte Carlo simulation and statistics, the changes of relative attitude and thrust torque are simulated when the satellite obtains the angular momentum for a short period of time due to being impacted by space debris. During the 10-year mission period, the number of times that the space debris impact makes the satellite attitude out of the science mode and the number of times that the control system diverges are obtained, which provides a reference for the normal manner of the double satellite formation for gravity field exploration.
Genomic characterization of rare earth binding by Shewanella oneidensis
Authors: Medin Sean , Schmitz Alexa M. , Pian Brooke , Mini Kuunemuebari , Reid Matthew C. , Holycross Megan , Gazel Esteban , Wu Mingming , Barstow Buz 
Published: September 2023

AbstractRare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We identified 18 gene ontologies and 13 gene operons that make up key systems that affect biosorption. We found, among other things, that disruptions of a key regulatory component of the arc system (hptA), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes (wbpQ, wbnJ, SO_3183) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685, a capsular polysaccharide (CPS) synthesis gene, disruption of which results in an up to 79% increase in biosorption; and nusA, a transcriptional termination/anti-termination protein, disruption of which results in an up to 35% decrease in biosorption. Knockouts of glnA, pyrD, and SO_3183 produce small but significant increases (≈ 1%) in relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Modeling suggests that while these changes to lanthanide biosorption selectivity are small, they could already reduce the length of repeated enrichment process by up to 27%. This broad exploratory study begins to elucidate how genetics affect REE-biosorption by S. oneidensis, suggests new areas of investigation for better mechanistic understanding of the membrane chemistry involved in REE binding, and offer potential targets for improving biosorption and separation of REE by genetic engineering.
Modeling transformational policy pathways on low growth and negative growth scenarios to assess impacts on socioeconomic development and carbon emissions
Authors: Moyer Jonathan D. 
Published: September 2023

AbstractDegrowth advocates argue for structural transformations in how economies and societies prioritize material wealth accumulation to reduce the negative effects of future anthropogenic climate change. Degrowth proponents argue that human economic activity could be lessened, and societies transformed to prioritize improved wellbeing, reducing the threat of climate change. This paper explores implications of alternative patterns of economic growth with transformational policy pathways (i.e., redistribution) to assess what effects economic growth and broader policies have on changing patterns of human development across both the Global North and South. Using the International Futures model, this article shows that negative growth and societal transformations in the Global North are possible without dramatically damaging long-term global socioeconomic development, though these interventions do not solve the global climate crisis, reducing future cumulative carbon emissions by 10.5% through 2100. On the other hand, a global negative growth scenario will significantly reduce future cumulative carbon emissions (45%) but also dramatically undermines the pursuit of global development goals, like the elimination of poverty. Even with global policies that significantly increase cash transfers to the poor and retired, dramatically improve income inequality, and eliminate military spending, the Global Negative Growth Big Push scenario leads to an increase of 15 percentage points in global extreme poverty by 2100.
Effects of iron-based phosphate binders on mortality and cardiovascular events in patients receiving maintenance dialysis
Authors: Tanaka Akihito , Sasaki Sho , Noma Hisashi , Wang Jui , Onishi Yoshihiro , Inaguma Daijo 
Published: September 2023

AbstractPhosphate binders are the main treatment for hyperphosphatemia in patients with chronic kidney disease, and iron-based phosphate binders have been used with increasing frequency in recent years. This study examined the association of the use of iron-based, rather than non-iron-based, phosphate binders with the incidence of cardiovascular events, in a real-world setting. We used data from a cohort comprising representative adult patients on maintenance hemodialysis in Japan. The exposure of interest was the time-varying use of phosphate binders, classified into “iron-based”, “only non-iron-based”, and “no use”. The primary outcome was a composite of cardiovascular events and all-cause deaths. A marginal structural Cox regression model was used to deal with possible time-dependent confounding. Of the 2247 patients from 58 hemodialysis facilities, iron-based and only non-iron-based phosphate binders were used in 328 (15%) and 1360 (61%), respectively, at baseline. Hazard ratios (95% confidence intervals) for iron-based and non-iron-based phosphate binders versus no use of phosphate binders were 0.35 (0.24, 0.52) and 0.44 (0.33, 0.58), respectively. The hazard ratio for iron-based relative to non-iron-based phosphate binders was 0.81 (0.58, 1.13), which was not statistically significant. Further studies are warranted to elucidate whether the use of iron-based phosphate binders reduces the event rate.
Glucagon-like peptide-1 and glucagon-like peptide-2 regulation during human liver regeneration
Authors: Ammann Markus , Santol Jonas , Pereyra David , Kalchbrenner Tamara , Wuerger Tanja , Laengle Johannes , Smoot Rory L. , Hulla Wolfgang , Laengle Friedrich , Starlinger Patrick 
Published: September 2023

AbstractAccumulating evidence suggests that metabolic demands of the regenerating liver are met via lipid metabolism and critical regulators of this process. As such, glucagon-like peptide-1 (GLP-1) and glucagon-like peptide-2 (GLP-2) critically affect hepatic regeneration in rodent models. The present study aimed to evaluate potential alterations and dynamics of circulating GLP-1 and GLP-2 in patients undergoing liver resections, focusing on post-hepatectomy liver failure (PHLF). GLP-1, GLP-2, Interleukin-6 (IL-6) and parameters of lipid metabolism were determined perioperatively in fasting plasma of 46 patients, who underwent liver resection. GLP-1 and GLP-2 demonstrated a rapid and consistently inverse time course during hepatic regeneration with a significant decrease of GLP-1 and increase of GLP-2 on POD1. Importantly, these postoperative dynamics were significantly more pronounced when PHLF occurred. Of note, the extent of resection or development of complications were not associated with these alterations. IL-6 mirrored the time course of GLP-2. Assessing the main degradation protein dipeptidyl peptidase 4 (DPP4) no significant association with either GLP-1 or -2 could be found. Additionally, in PHLF distinct postoperative declines in plasma lipid parameters were present and correlated with GLP-2 dynamics. Our data suggest dynamic inverse regulation of GLP-1 and GLP-2 during liver regeneration, rather caused by an increase in expression/release than by changes in degradation capacity and might be associated with inflammatory responses. Their close association with circulating markers of lipid metabolism and insufficient hepatic regeneration after liver surgery suggest a critical involvement during these processes in humans.
Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast
Authors: Akter Salma , Rahman M. Shaminur , Ali Hazrat , Minch Benjamin , Mehzabin Kaniz , Siddique Md. Moradul , Galib Syed Md. , Yesmin Farida , Azmuda Nafisa , Adnan Nihad , Hasan Nur A. , Rahman Sabita Rezwana , Moniruzzaman Mohammad , Ahmed Md Firoz 
Published: September 2023

AbstractThe Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB’s eastern coast, viz., Saint Martin and Cox’s Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox’s Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox’s Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox’s Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.
Impact of beta-tricalcium phosphate on preventing tooth extraction-triggered bisphosphonate-related osteonecrosis of the jaw in rats
Authors: Funayama Naoki , Yagyuu Takahiro , Imada Mitsuhiko , Ueyama Yoshihiro , Nakagawa Yosuke , Kirita Tadaaki 
Published: September 2023

AbstractAntiresorptive or antiangiogenic drugs can cause medication-related osteonecrosis of the jaw that is refractory. Bisphosphonate-related osteonecrosis of the jaw (BRONJ) may be caused by procedures such as tooth extraction damage the alveolar bone, release bisphosphonates (BPs) and impede healing. This study investigated strategies for BRONJ prevention and molecular mechanisms of its onset. We assessed the effectiveness of filling extraction sockets with beta-tricalcium phosphate (β-TCP). Rats were administered zoledronic acid (ZA) 1.2 mg/kg once per week for 2 weeks, and a molar was extracted. They were randomly assigned to the β-TCP group (bone defects filled with 0.01 g of β-TCP) or control group. Tissue content measurements indicated 2.2 ng of ZA per socket in the β-TCP group and 4.9 ng in the control group, confirming BP distribution and BP adsorption by β-TCP in vivo. At 4 weeks after extraction, the β-TCP group had normal mucosal coverage without inflammation. Moreover, at 8 weeks after extraction, enhanced bone healing, socket coverage, and new bone formation were observed in the β-TCP group. Connective tissue in the extraction sockets suggested that local increases in BP concentrations may suppress the local autophagy mechanisms involved in BRONJ. Filling extraction sockets with β-TCP may prevent BRONJ.
Intradiscal cement leakage (ICL) increases the stress on adjacent vertebrae after kyphoplasty for osteoporotic vertebra compression fracture (OVCF): a finite-element study
Authors: Meng Hai , Li Qiujun , Lin Jisheng , Yang Yong , Fei Qi 
Published: September 2023

AbstractThis study aimed to explore the biomechanical effects on adjacent vertebra of thoracolumbar Osteoporotic Vertebra Compression Fracture (OVCF) after Percutaneous Kyphoplasty (PKP) with intraoperative intradiscal cement leakage (ICL) by applying a Finite-Element Analysis. We collected pre- and post-operative computer tomography (CT) images of a 71-year-old female patient with single T12 OVCF, who underwent an intraoperative cement leakage into the T12–L1 disc. Three-dimensional finite element models of thoracolumbar spine (T10–L2) were built with the support of Materialise Interactive Medical Image Control System (MIMICS) and ABAQUS software. The stress on adjacent vertebrae and endplates under the uniform compressive pressure (0.3 MPa) and during different loading moments were analyzed. The three-dimensional finite element models reveal an asymmetrical distribution of von Mises stresses on the adjacent endplate unaffected by the surgical intervention. The maximum von Mises stress on adjacent vertebral bodies increased during different loading conditions, especially for lateral bending and rotation loading conditions, whereas the maximum von Mises stress on distal non-treated vertebrae decreased on anteflexion and backward extension loading conditions. Post-operative adjacent vertebra compression fractures after PKP with intraoperative intradiscal cement leakage (ICL) may be closely related to the biomechanical changes of adjacent vertebrae of thoracolumbar OVCF, and it may increase the risk of postoperative fracture.
Collaborative Intelligence to catalyze the digital transformation of healthcare
Authors: Bhatt Ami B. , Bae Jennifer 
Published: September 2023

AbstractCollaborative intelligence reflects the promise and limits of leveraging artificial intelligence (AI) technologies in clinical care. It involves the use of advanced analytics and computing power with an understanding that humans bear responsibility for the accuracy, completeness and any inherent bias found in the training data. Clinicians benefit from using this technology to address increased complexity and information overload, support continuous care and optimized resource allocation, and to enact efforts to eradicate disparities in health care access and quality. This requires active clinician engagement with the technology, a general understanding of how the machine produced its insight, the limitations of the algorithms, and the need to screen datasets for bias. Importantly, by interacting, the clinician and the analytics will create trust based on the clinician’s critical thinking skills leveraged to discern value of machine outputs within clinical context. Utilization of collaborative intelligence should be staged with the level of understanding and evidence. It is particularly well suited to low-complexity non-urgent care and to identifying individuals at rising risk within a population. Clinician involvement in algorithm development and the amassing of evidence to support safety and efficacy will propel adoption. Utilization of collaborative intelligence represents the natural progression of health care innovation, and if thoughtfully constructed and equitably deployed, holds the promise to decrease clinician burden and improve access to care.
Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance
Authors: Mukesh Sumit , Mukherjee Goutam , Singh Ridhima , Steenbuck Nathan , Demidova Carolina , Joshi Prachi , Sangamwar Abhay T. , Wade Rebecca C. 
Published: September 2023

AbstractThe propensity of poorly water-soluble drugs to aggregate at supersaturation impedes their bioavailability. Supersaturated amorphous drug-salt-polymer systems provide an emergent approach to this problem. However, the effects of polymers on drug-drug interactions in aqueous phase are largely unexplored and it is unclear how to choose an optimal salt-polymer combination for a particular drug. Here, we describe a comparative experimental and computational characterization of amorphous solid dispersions containing the drug celecoxib, and a polymer, polyvinylpyrrolidone vinyl acetate (PVP-VA) or hydroxypropyl methylcellulose acetate succinate, with or without Na+/K+ salts. Classical models for drug-polymer interactions fail to identify the best drug-salt-polymer combination. In contrast, more stable drug-polymer interaction energies computed from molecular dynamics simulations correlate with prolonged stability of supersaturated amorphous drug-salt-polymer systems, along with better dissolution and pharmacokinetic profiles. The celecoxib-salt-PVP-VA formulations exhibit excellent biopharmaceutical performance, offering the prospect of a low-dosage regimen for this widely used anti-inflammatory, thereby increasing cost-effectiveness, and reducing side-effects.
The effect of environment on depressive symptoms in late adolescence and early adulthood: an exposome-wide association study and twin modeling
Authors: Wang Zhiyang , Zellers Stephanie , Whipp Alyce M. , Heinonen-Guzejev Marja , Foraster Maria , Júlvez Jordi , van Kamp Irene , Kaprio Jaakko 
Published: September 2023

AbstractThe exposome represents the totality of environmental effects, but systematic evaluation between it and depressive symptoms is scant. Here we sought to comprehensively identify the association of the exposome with depressive symptoms in late adolescence and early adulthood and determine genetic and environmental covariances between them. Based on the FinnTwin12 cohort (3,025 participants in young adulthood and 4,127 at age 17), the exposome-wide association study (ExWAS) design was used to identify significant exposures from 12 domains. Bivariate Cholesky twin models were fitted to an exposome score and depressive symptoms. In ExWASes, 29 and 46 exposures were significantly associated with depressive symptoms in young adulthood and at age 17, respectively, and familial exposures were the most influential. Twin models indicated considerable genetic and environmental covariances between the exposome score and depressive symptoms with sex differences. The findings underscore the systematic approach of the exposome and the consideration of relevant genetic effects.