bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternating Polarity as a Novel Strategy for Cultivating Electro-Methanogenic Microbial Communities Capable of Robust Biogas Production
Authors: Yao Shiyun , Swanson Clifford S , Cheng Zhang , He Qiang , Yuan Heyang 
Published: August 2023

AbstractElectro-methanogenic microbial communities can produce biogas with high efficiency. Extensive efforts have been made to cultivate these communities in engineered systems. Conventional cultivation strategies can select electrotrophic methanogens but not their electron-donating partners, resulting in communities that are sensitive to perturbations. Herein, we developed an alternating polarity strategy to simultaneously select both microbial populations. In two-chamber bioelectrochemical systems amended with activated carbon, the electrode potential was alternated between +0.8 V and -0.4 V vs. standard hydrogen electrode every three days. After eight alternating cycles, cultivated activated carbon was transferred into new bioreactors, and the enrichment procedure was repeated four times. Cumulative biogas production under alternating polarity increased from 45 L/L/kg-activated carbon after start-up to 125 L/L/kg after the 4thenrichment, significantly higher than that under intermittent cathode (-0.4 V/open circuit), continuous cathode (-0.4 V), and open circuit. The communities cultivated under alternating polarity were electroactive and structurally different from those cultivated under other conditions. OneMethanobacteriumpopulation and twoGeobacterpopulations were consistently abundant and active in the communities. Their 16S rRNA was upregulated by electrode potentials. Bayesian networks inferred close associations between these populations. The cultivation strategy can enhance biogas production, and the cultivated communities may serve as a model system for elucidating the mechanisms of extracellular electron uptake.SynopsisAn alternating polarity strategy was developed in this study to cultivate electro-methanogenic microbial communities. The cultivated communities can produce biogas more efficiently and help us understand the ecophysiology of the key microbial populations.
Multi-omics investigation on the prognostic and predictive factors in metastatic breast cancer using data from Phase III ribociclib clinical trials: A statistical and machine learning analysis plan
Authors: Coroller Thibaud , Sahiner Berkman , Amatya Anup , Gossmann Alexej , Karagiannis Konstantinos , Samala Ravi K. , Santana-Quintero Luis , Solovieff Nadia , Wang Craig , Amiri-Kordestani Laleh , Cao Qian , Cha Kenny H. , Orbach Rosane Charlab , Cross Frank H. , Hu Tingting , Huang Ruihao , Kraft Jeffrey , Krusche Peter , Li Yutong , Li Zheng , Mazo Ilya , Moloney Conor , Paul Rahul , Plawinski Jason , Schnakenberg Susan , Serra Paolo , Smith Sean , Song Chi , Su Fei , Subramaniam Sajanth , Tiwari Mohit , Vechery Colin , Xiong Xin , Zarate Juan Pablo , Ziegler Jonathan , Zhu Hao , Chakravartty Arunava , Liu Qi , Ohlssen David , Petrick Nicholas , Schneider Julie A. , Walderhaug Mark , Zuber Emmanuel 
Published: August 2023

AbstractIn 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to find novel radiogenomics-based prognostic and predictive factors for HR+/HER2-metastatic breast cancer under a Research Collaboration Agreement. This manuscript aims to detail the guiding principles and methodology for this study. We include a discussion of internal and external clinical, genomics, imaging datasets, data processing workflows, and machine learning model development strategies. We also prospectively define our success criteria to ensure robust scientific outputs.DisclosureThis publication reflects the views of the authors and should not be construed to represent FDA’s views or policies.
De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments
Authors: Eloff Kevin , Kalogeropoulos Konstantinos , Morell Oliver , Mabona Amandla , Jespersen Jakob Berg , Williams Wesley , van Beljouw Sam P. B. , Skwark Marcin , Laustsen Andreas Hougaard , Brouns Stan J. J. , Ljungers Anne , Schoof Erwin M. , Van Goey Jeroen , auf dem Keller Ulrich , Beguir Karim , Carranza Nicolas Lopez , Jenkins Timothy P. 
Published: August 2023

AbstractBottom-up mass spectrometry-based proteomics is challenged by the task of identifying the peptide that generates a tandem mass spectrum. Traditional methods that rely on known peptide sequence databases are limited and may not be applicable in certain contexts.De novopeptide sequencing, which assigns peptide sequences to the spectra without prior information, is valuable for various biological applications; yet, due to a lack of accuracy, it remains challenging to apply this approach in many situations. Here, we introduce InstaNovo, a transformer neural network with the ability to translate fragment ion peaks into the sequence of amino acids that make up the studied peptide(s). The model was trained on 28 million labelled spectra matched to 742k human peptides from the ProteomeTools project. We demonstrate that InstaNovo outperforms current state-of-the-art methods on benchmark datasets and showcase its utility in several applications. Building upon human intuition, we also introduce InstaNovo+, a multinomial diffusion model that further improves performance by iterative refinement of predicted sequences. Using these models, we couldde novosequence antibody-based therapeutics with unprecedented coverage, discover novel peptides, and detect unreported organisms in different datasets, thereby expanding the scope and detection rate of proteomics searches. Finally, we could experimentally validate tryptic and non-tryptic peptides with targeted proteomics, demonstrating the fidelity of our predictions. Our models unlock a plethora of opportunities across different scientific domains, such as direct protein sequencing, immunopeptidomics, and exploration of the dark proteome.
Immune Evasion and Membrane Fusion of SARS-CoV-2 XBB Subvariants EG.5.1 and XBB.2.3
Authors: Faraone Julia N. , Qu Panke , Goodarzi Negin , Zheng Yi-Min , Carlin Claire , Saif Linda J. , Oltz Eugene M. , Xu Kai , Jones Daniel , Gumina Richard J. , Liu Shan-Lu 
Published: August 2023

AbstractImmune evasion by SARS-CoV-2 paired with immune imprinting from monovalent mRNA vaccines has resulted in attenuated neutralizing antibody responses against Omicron subvariants. In this study, we characterized two new XBB variants rising in circulation — EG.5.1 and XBB.2.3, for their ability of neutralization and syncytia formation. We determined the neutralizing antibody in sera of individuals that received a bivalent mRNA vaccine booster, BA.4/5-wave infection, or XBB.1.5-wave infection. Bivalent vaccination-induced antibodies neutralized efficiently ancestral D614G, but to a much less extent, two new EG.5.1 and XBB.2.3 variants. In fact, the enhanced neutralization escape of EG.5.1 appeared to be driven by its key defining mutation XBB.1.5-F456L. Notably, infection by BA.4/5 or XBB.1.5 afforded little, if any, neutralization against EG.5.1, XBB.2.3 and previous XBB variants — especially in unvaccinated individuals, with average neutralizing antibody titers near the limit of detection. Additionally, we investigated the infectivity, fusion activity, and processing of variant spikes for EG.5.1 and XBB.2.3 in HEK293T-ACE2 and CaLu-3 cells but found no significant differences compared to earlier XBB variants. Overall, our findings highlight the continued immune evasion of new Omicron subvariants and, more importantly, the need to reformulate mRNA vaccines to include XBB spikes for better protection.
Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons
Authors: Yang Xiaoyu , Jones Ian R. , Chen Poshen B. , Yang Han , Ren Xingjie , Zheng Lina , Li Bin , Li Yang Eric , Sun Quan , Wen Jia , Beaman Cooper , Cui Xiekui , Li Yun , Wang Wei , Hu Ming , Ren Bing , Shen Yin 
Published: August 2023

AbstractGenome-wide association studies (GWAS) have identified thousands of non-coding variants that contribute to psychiatric disease risks, likely by perturbingcis-regulatory elements (CREs). However, our ability to interpret and explore their mechanisms of action is hampered by a lack of annotation of functional CREs (fCREs) in neural cell types. Here, through genome-scale CRISPR screens of 22,000 candidate CREs (cCREs) in human induced pluripotent stem cells (iPSCs) undergoing differentiation to excitatory neurons, we identify 2,847 and 5,540 fCREs essential for iPSC fitness and neuronal differentiation, respectively. These fCREs display dynamic epigenomic features and exhibit increased numbers and genomic spans of chromatin interactions following terminal neuronal differentiation. Furthermore, fCREs essential for neuronal differentiation show significantly greater enrichment of genetic heritability for neurodevelopmental diseases including schizophrenia (SCZ), attention deficit hyperactivity disorder (ADHD), and autism spectrum disorders (ASD) than cCREs. Using high-throughput prime editing screens we experimentally confirm 45 SCZ risk variants that act by affecting the function of fCREs. The extensive and in-depth functional annotation of cCREs in neuronal types therefore provides a crucial resource for interpreting non-coding risk variants of neuropsychiatric disorders.
Gene co-expression patterns in Atlantic salmon adipose tissue provide a molecular link among seasonal changes, energy balance and age at maturity
Authors: Ahi Ehsan Pashay , Verta Jukka-Pekka , Kurko Johanna , Ruokolainen Annukka , Singh Pooja , Debes Paul Vincent , Erkinaro Jaakko , Primmer Craig R. 
Published: August 2023

AbstractSexual maturation in many fishes requires a major physiological change that involves a rapid transition between energy storage and usage. In Atlantic salmon, this transition for the initiation of maturation is tightly controlled by seasonality and requires a high-energy status. Lipid metabolism is at the heart of this transition since lipids are the main energy storing molecules. The balance between lipogenesis (lipid accumulation) and lipolysis (lipid use) determines energy status transitions. A genomic region containing a transcription co-factor of the Hippo pathway,vgll3, is the main determinant of maturation timing in Atlantic salmon. Interestingly,vgll3acts as an inhibitor of adipogenesis in mice and its genotypes are potentially associated with seasonal heterochrony in lipid storage and usage in juvenile Atlantic salmon. Here, we explored changes in expression of more than 300 genes directly involved in the processes of adipogenesis, lipogenesis and lipolysis, as well as the Hippo pathway in the adipose tissue of immature and mature Atlantic salmon with distinctvgll3genotypes. We found molecular evidence consistent with a scenario in which immature males exhibitingvgll3genotype specific seasonal direction of change in their lipid profiles. We also identified components of the Hippo signaling pathway as potential major drivers ofvgll3genotype specific differences in adipose tissue gene expression. This study demonstrates the importance of adipose gene expression patterns for directly linking environmental changes with energy balance and age at maturity through genetic factors bridging lipid metabolism, seasonality and sexual maturation.
Exploring literary festivals in Ireland
Authors: McGuckin Mary 
Published: August 2023

PurposeThe purpose of this paper is to explore the origins and management of literary festivals in Ireland from the perspective of their founders or those involved in managing these festivals.Design/methodology/approachThis qualitative research study explores six literary festivals across the island of Ireland. The research and data collection instruments include bibliographic research and a series of in-depth interviews with festival founders, directors and managers.FindingsThe festivals in this study have evolved from a range of origins and are strongly influenced by the artistic vision and strategic approach of their founders and/or directors. Generating adequate revenue remains a constant challenge for these festivals as they rely on three primary sources of funding, i.e. ticket sales, sponsorship and grant support. Volunteering at literary festivals provides an opportunity for increased community involvement, participation and a sense of co-creation. Building strong partnerships and positive stakeholder engagement is fundamental to successful festival support and funding, ensuring that festivals can deliver well-structured programmes that will attract a loyal and engaging audience.Research limitations/implicationsThis exploratory research is limited to six literary festivals in Ireland and there is potential to extend this into a more comprehensive study.Practical implicationsThis study provides insights into this increasingly popular festival sector and identifies practical strategies for developing and managing literary festivals and related events.Originality/valueEven though literary festivals have proliferated in Ireland over the past twenty years, there is a dearth of academic research in this area. The research study focuses on literary festivals, primarily from a “supply” rather than “demand” perspective.
The effect of relational investments on supply chain quality integration: protection or constraint of legal bonds?
Authors: Akhtar Faheem , Wang Qianwen , Huo Baofeng 
Published: August 2023

PurposeThis study examines the effect of relational investments (e.g. supplier involvement and commitment, customer involvement and commitment) on supply chain quality integration (e.g. supplier and customer quality integration), which leads to financial performance. Moreover, the authors explore the moderating effects of legal bonds on the relationship between relational investments and supply chain quality integration.Design/methodology/approachA survey study of manufacturing firms is presented to illustrate the conceptual model. The authors use the data from 213 manufacturing firms to test the hypotheses by structural equation modeling.FindingsThe results show that supplier and customer quality integration are positively related to financial performance. Supplier involvement and commitment are positively related to supplier quality integration. Customer involvement is positively related to customer quality integration, but customer commitment is not significantly related to customer quality integration. Additionally, on the supplier side, legal bonds negatively moderate the relationship between supplier involvement and supplier quality integration but positively moderate the relationship between supplier commitment and supplier quality integration. On the customer side, legal bonds do not moderate the relationship between customer involvement and customer quality integration, but negatively moderate the relationship between customer commitment and customer quality integration.Originality/valueThis study provides novel insights into supply chain quality management from relational perspectives, as well as the contingent role of legal bonds between them.
Effects of brodalumab on psoriasis and depressive symptoms in patients with insufficient response to TNF‐α inhibitors
Authors: Andersch‐Björkman Ylva , Micu Emanuela , Seifert Oliver , Lonne‐Rahm Sol‐Britt , Gillstedt Martin , Osmancevic Amra 
Published: August 2023

AbstractThe objective of this study was to evaluate emotions of depression and anxiety in psoriatic patients that due to insufficient response to tumor necrosis factor‐alpha inhibition (TNF‐α), underwent a treatment switch from TNF‐α to interleukin 17 inhibition using brodalumab. The Self‐rated Montgomery‐Asberg Depression Rating Scale and the Hospital Anxiety and Depression Scale were used to assess depression and anxiety. A total of 20 patients with psoriasis were enrolled in the study. They were monitored for a period of 3 months following the transition to brodalumab treatment. The results showed a significant improvement in both the Psoriasis Area and Severity Index as well as symptoms of depression; anxiety symptoms showed a reduction, though not statistically significant. Perhaps of more interest, the positive effects on depression and anxiety seem to be independent of the reduction in skin related psoriatic lesions. These findings highlight the importance of addressing depressive and anxiety symptoms, together with psoriasis severity and quality of life, when managing patients with psoriasis.
Fit by design: Developing seed–substrate combinations to adapt dike grasslands to microclimatic variation
Authors: Bauer Markus , Huber Jakob K. , Kollmann Johannes 
Published: August 2023

Abstract

Sowing is a well‐established restoration technique to overcome dispersal limitation. Seed mixtures adapted to certain environmental conditions, like substrate or microclimate, are most effective to achieve functional communities. This is especially important if the restored vegetation has to protect critical infrastructure like roadsides and dikes. Here, an improved seed–substrate combination will secure slope stability, make restorations more effective and generate species‐rich grasslands.

A full‐factorial field experiment addressed this topic on a dike at River Danube in SE Germany in 2018–2021. Within 288 plots, we tested three sand admixtures, two substrate depths, two seed densities and two seed mixture types (mesic hay meadow and semidry calcareous grassland) in north and south exposition and measured the recovery completeness by calculating the successional distance to reference sites, the persistence of sown species and the Favourable Conservation Status (FCS) of target species.

Overall, the sown vegetation developed in the desired direction, but a recovery debt remained after 4 years, and some plots still showed similarities to negative references from ruderal sites. In north exposition, hay meadow seed mixtures developed closer to their reference communities than dry grassland mixtures to their reference.

In south exposition, the sown communities established poorly, which might be due to a severe drought during establishment. This initial negative effect remained over the entire observation period.

Sand admixture had a slightly positive effect on target variables, while the tested substrate depths, seed densities and seed mixture types had no effects on species persistence or FCS.

Synthesis and applications: Site‐adapted seed mixtures make restoration more effective, while applying several seed–substrate combinations might foster beta diversity. Furthermore, additional management efforts are recommended, as they might be necessary to reduce the recovery debt, as well as re‐sowing after unfavourable conditions like droughts.
A network meta‐analysis of association between cardiometabolic risk factors and COVID‐19 outcome severity
Authors: Li Alina Binbin , Yang Bo , Li Yufei , Huynh Rachel , Shim Samuel , Lo Kenneth , Li Jie , Zullo Andrew , Wu Wen‐Chih , Liu Simin 
Published: August 2023

AbstractBackgroundCardiometabolic comorbidities have been associated with a higher risk of COVID‐19 severity and mortality, but more investigations are needed to determine which comorbidity is more detrimental.MethodsEmbase, Emcare, and MEDLINE were searched systematically for prospective and retrospective studies assessing the associations of cardiometabolic risk factors and COVID‐19 outcomes of hospitalization, severity, and mortality among COVID‐19‐diagnosed patients. Literature search was performed from first publication to May 19, 2021. Study quality was assessed by the Newcastle‐Ottawa Scale.ResultsFrom the literature search, 301 studies suggested that all included cardiometabolic risk factors were associated with a higher risk of COVID‐19 hospitalization, severity, and mortality, except that overweight was associated with a decreased risk of mortality (relative risk [RR] 0.88; 95% CI, 0.80–0.98). Patients with diabetes (RR 1.46; 95% CI, 1.45–1.47) were most likely to be hospitalized; patients with heart failure had the highest risk for severe COVID‐19 outcomes (RR 1.89; 95% CI, 1.71–2.09); while patients with stroke were most susceptible to overall mortality (RR 1.99; 95% CI, 1.90–2.08). In the network meta‐analysis, cerebrovascular disease had the highest impact (RR 1.69; 95% CI, 1.65–1.73) on COVID‐19 outcomes compared to other cardiometabolic risk factors. For different combinations of risk factors, cardiovascular disease and diabetes combined (RR 6.98; 95% CI, 5.28–9.22) was more detrimental than others.ConclusionsConsidering the high prevalence of cardiometabolic comorbidities and risk of all severe outcomes, patients with cardiometabolic comorbidities should be prioritized in vaccination and treatment development of COVID‐19.
Trust, lies, and inequality
Authors: Du Ninghua , Gui Shan , Houser Daniel 
Published: August 2023

AbstractThe effect of endowment equality on trust may stem from outcome inequality aversion or changes in expected trustworthiness. Here, we measure trust as the expectation of honesty in a sender‐receiver game, where participants must make trust decisions without knowing the outcome. Our design enables us to isolate the effect of initial endowment inequality on trust. Our results show that endowment inequality reduces trust regardless of whether it favors the sender or the receiver. We further find that the frequency of lies is insensitive to endowment inequality. Our results amplify the importance of equal starting positions in promoting trust.
A X‐linked nonsense APOO/MIC26 variant causes a lethal mitochondrial disease with progeria‐like phenotypes
Authors: Peifer‐Weiß Leon , Kurban Mazen , David Céline , Lubeck Melissa , Kondadi Arun Kumar , Nemer Georges , Reichert Andreas S. , Anand Ruchika 
Published: August 2023

AbstractAPOO/MIC26 is a subunit of the MICOS complex required for mitochondrial cristae morphology and function. Here, we report a novel variant of the APOO/MIC26 gene that causes a severe mitochondrial disease with overall progeria‐like phenotypes in two patients. Both patients developed partial agenesis of the corpus callosum, bilateral congenital cataract, hypothyroidism, and severe immune deficiencies. The patients died at an early age of 12 or 18 months. Exome sequencing revealed a mutation (NM_024122.5): c.532G>T (p.E178*) in the APOO/MIC26 gene that causes a nonsense mutation leading to the loss of 20 C‐terminal amino acids. This mutation resulted in a highly unstable and degradation prone MIC26 protein, yet the remaining minute amounts of mutant MIC26 correctly localized to mitochondria and interacted physically with other MICOS subunits. MIC26 KO cells expressing MIC26 harboring the respective APOO/MIC26 mutation showed mitochondria with perturbed cristae architecture and fragmented morphology resembling MIC26 KO cells. We conclude that the novel mutation found in the APOO/MIC26 gene is a loss‐of‐function mutation impairing mitochondrial morphology and cristae morphogenesis.