bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the haplotype and spectro-functional traits interactions to explore the intraspecific diversity of common reed in Central Italy
Authors: Castellani Maria Beatrice , Coppi Andrea , Bolpagni Rossano , Gigante Daniela , Lastrucci Lorenzo , Reale Lara , Villa Paolo 
Published: December 2022

AbstractAs reflectance measured via remote sensing is connected to plant light use and morpho-structural features, it can be used to derive spectral proxies of functional traits, or spectro-functional traits. Focusing on disentangling intraspecific trait variability in nature, we evaluated the links between haplotype and spectro-functional traits inPhragmites australispopulations.Haplotypes sequencing and multi-seasonal satellite data were used to evaluate the temporal dynamics of spectro-functional traits for reed stands sampled from seven wetlands in Central Italy, investigating meteo-climatic drivers, the differences across ecological statuses, sites, and haplotypes, and quantifying intraspecific variability due to haplotype or phenotypic plasticity.Five haplotypes were identified, including an unedited one, which explained a substantial portion of intraspecific variability in canopy traits, differing for aquatic and terrestrial stands. We found that meteo-climatic factors impact on aquatic reeds traits (not over terrestrial ones) and a dualism between most and less common haplotypes, pointing to different evolutionary strategies. Dynamics in reed canopy traits were linked to ecological status, site and haplotype, with signs of haplotype-variable effects of dieback on aquatic stands.Evaluating the spectro-functional variability over reed haplotypes may provide a straightforward approach for monitoring the genotype-phenotype relations across scales and assessing their ecological drivers.
A Systematic Review and Meta-analysis on the Transcriptomic Signatures in Alcohol Use Disorder
Authors: Friske Marion M , Torrico Eva C , Haas Maximilian JW , Borruto Anna M , Giannone Francesco , Hade Andreas-Christian , Yu Yun , Gao Lina , Sutherland Greg T , Hitzemann Robert , Philips Mari-Anne , Fei Suzanne S , Mayfield R Dayne , Sommer Wolfgang H , Spanagel Rainer 
Published: December 2022

AbstractAlcohol use disorder (AUD) is a complex mental health condition. Currently available clinical treatments exhibit limited efficacy and new druggable targets are required. One promising approach to discover new molecular treatment targets involves the transcriptomic profiling of brain regions within the addiction neurocircuitry, utilizing animal models and post-mortem brain tissue from deceased AUD patients. Unfortunately, such studies suffer from large heterogeneity and small sample sizes. To address these limitations, we conducted a cross-species meta-analysis on transcriptome-wide data obtained from brain tissue of AUD patients and animal models. We integrated 36 cross-species transcriptome-wide RNA-expression datasets with an alcohol-dependent phenotype vs. controls, following the PRISMA guidelines. In total, we meta-analyzed 1,000 samples – 502 samples for the prefrontal cortex (PFC), 318 nucleus accumbens (NAc) samples, and 180 amygdala (AMY) samples. The PFC had the highest number of differentially expressed genes (DEGs) across rodents, monkeys, and humans. Commonly dysregulated DEGs pointed towards enrichment in inflammatory responses and alterations in BBB-regulatory mechanisms in astrocytes, microglia and endothelial cells. Gene set enrichment analysis further showed that MAPK/ERK-signaling plays a critical role in AUD and especially in monkeysDusp4as a major inhibitor of the MAPK pathway may be a main driver of these pathway alterations. Our data also suggest that the transcriptomic profile in the NAc is less vulnerable to the maintenance of AUD. Finally, we provide a combination of DEGs that are commonly regulated across different brain tissues as potential biomarker for AUD. In summary, we provide a compendium of genes, signaling pathways, and physiological and cellular processes that are altered in AUD and that require future studies for functional validation.
An Amber-Encoding Helper Phage for More Efficient Phage Display of Noncanonical Amino Acids
Authors: Hampton J. Trae , Cho Chia-Chuan Dean , Geng Zhi Zachary , Coleman Demonta D. , Chen Peng-Hsun Chase , Dubey Gopal K. , Sylvain Lauralee D. , Xu Shiqing , Liu Wenshe Ray 
Published: December 2022

ABSTRACTIn the past two decades, phage display has emerged as a powerful technique for the identification of antibodies and peptide ligands for therapeutic targets. Using the amber suppression-based noncanonical amino acid (ncAA) mutagenesis approach, we and others have shown that the chemical space in phage display can be significantly expanded for drug discovery. However, the use of amber codon in phages results in poor phage yields and requires tedious processes to enrich amber codon-containing (amber obligate) phage clones. In this work, we demonstrate the development of a novel helper phage, CMa13ile40, for rapid and continuous enrichment of amber obligate phage clones and efficient production of ncAA-containing phages. CMa13ile40 was constructed by the insertion of aCandidatus Methanomethylophilus alvuspyrrolysyl-tRNA synthetase/PylT gene cassette into a helper phage genome. The afforded novel helper phage allowed for a continuous amber codon enrichment strategy for two different phage display libraries and demonstrated a 100-fold increase in selectivity for packaging of library plasmids in comparison with original helper phage plasmids. To demonstrate the applicability of the system, CMa13ile40 was used to create two phage-displayed peptide libraries containing two separate ncAAs,Nε-tert-butoxycarbonyl-lysine (BocK) andNε-allyloxycarbonyl-lysine (AllocK), respectively. These were then used to identify peptide ligands that bind to the extracellular domain of ZNRF3, a membrane-bound E3 ligase. Each selection showed differential enrichment of unique sequences dependent upon the ncAA used. Using biolayer interferometry, enriched peptides from both selections were confirmed to have low micromolar affinity for ZNRF3 and this affinity is dependent on the presence of the ncAA used for selection. Our results clearly show that ncAAs in phages provide unique interactions for selection of peptides that are different from each other and from canonical amino acids. As an effective tool for phage display, we believe that CMa13ile40 can be broadly applied to a wide variety of applications.
The contribution of maternal oral, vaginal, and gut microbiota to the developing offspring gut
Authors: Russell Amber L. , Donovan Erin , Seilhamer Nicole , Siegrist Melissa , Franklin Craig L. , Ericsson Aaron C. 
Published: December 2022

AbstractThere is limited understanding of how the microbiota colonizing various maternal tissues contribute to the development of the neonatal gut microbiota (GM). To determine the contribution of various maternal microbiotic sites to the offspring microbiota in the upper and lower gastrointestinal tract (GIT) during early life, litters of mice were sacrificed at 7, 9, 10, 11, 12, 14, and 21 days of age, and fecal and ileal samples were collected. Dams were euthanized alongside their pups, and oral, vaginal, ileal, and fecal samples were collected. This was done in parallel using mice with either a low-richness or high-richness microbiota to assess the consistency of findings across multiple microbial compositions. Sample were analyzed using 16S rRNA amplicon sequencing. The similarities between matched pup and dam samples were used to determine the contribution of each maternal source to the pup fecal and ileal composition at each timepoint. As expected, similarity between pup and maternal feces increased significantly over time. During earlier time-points however, the offspring fecal and ileal microbiotas were closer in composition to the maternal oral microbiota than other maternal sites. Prominent taxa contributed by the maternal oral microbiota to the neonatal gut microbiota were supplier-dependent and includedLactobacillusspp.,Streptococcusspp., and a member of thePasteurellaceaefamily. These findings align with the microbial taxa reported in infant microbiotas, highlighting the translatability of mouse models in this regard, as well as the dynamic nature of the gut microbiota during early life.
RBAtools: a programming interface for Resource Balance Analysis modelling
Authors: Bodeit Oliver , Samir Inès Ben , Karr Jonathan R. , Goelzer Anne , Liebermeister Wolfram 
Published: December 2022

MotivationEfficient resource allocation contributes to an organism’s fitness and improves success in competition. The Resource Balance Analysis (RBA) computational framework enables the analysis of an organism’s growth-optimal configurations in various environments, at genome-scale. The existing RBApy software enables the construction of RBA models on genome-scale and the calculation of medium-specific, growth-optimal cell states, including metabolic fluxes and the abundance of macromolecular machines. However, to address the needs of non-expert users, there is a need for a simple programming API, easy to use and interoperable with other software through convenient formats for models and data.ResultsThe RBAtools python package enables the convenient use of RBA models and addresses non-expert users.As a flexible programming interface, it enables the implementation of custom workflows and simplifies the modification of existing genome-scale RBA models and data export to various formats. The features comprise simulation, model fitting, parameter screens, sensitivity analysis, variability analysis, and the construction of Pareto fronts. Models and data are represented as structured tables, in HTML, and common formats for fluxomics and proteomics visualization.AvailabilityDetails about RBA can be found atrba.inrae.fr. RBAtools documentation, installation instructions, and tutorials are available atsysbioinra.github.io/rbatools.Contactwolfram.liebermeister@inrae.fr,anne.goelzer@inrae.fr
Universal chromatin state annotation of the mouse genome
Authors: Vu Ha , Ernst Jason 
Published: December 2022

AbstractGenome-wide chromatin states learned from integrating genome-wide maps of multiple epigenetic marks within the same cell type have been widely used to generate genome annotations of individual cell types. An alternative strategy based on ‘stacked modeling’ can provide a single ‘universal’ chromatin state annotation based jointly on data from many cell types. In human, such an approach was recently demonstrated and the resulting chromatin state annotation, denoted full-stack, was shown to have complementary advantages to per-cell-type annotations. However, an analogous annotation has not been previously available in mouse. Here, we produce a chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 different cell or tissue types. To characterize each chromatin state, we relate the states to other external annotations and compare them to analogously defined states in human. We expect the full-stack chromatin state annotation for mouse will be a useful resource for studying the genome of this key mammalian model organism.
A Double-Blind, Randomized, Controlled Phase III Trial Investigating Efficacy and Safety of Varenicline for Vaping Cessation in Adult Users
Authors: Caponnetto Pasquale , Campagna Davide , Ahluwalia Jasjit S. , Russell Chistopher , Maglia Marilena , Riela Paolo Marco , Longo Carmelo Fabio , Busa’ Barbara , Polosa Riccardo 
Published: December 2022

ABSTRACTBackgroundVaping cessation is virtually unexplored. The efficacy and safety of varenicline for vaping cessation has not been studied and rigorous research is required to advance best practice and outcomes for e-cigarettes users who want to quit.MethodsEligible patients were randomized to either varenicline (1 mg, administered twice daily for 12 weeks) or placebo treatment (administered twice daily, for 12 weeks) combined with vaping cessation counseling. The trial consisted of a 12-week treatment phase followed by a 12-week follow-up, nontreatment phase. The primary efficacy endpoint of the study was biochemically validated continuous abstinence rate (CAR) at weeks 4 to 12. Secondary efficacy end points were the CAR at weeks 4 to 24 and 7-day point prevalence of vaping abstinence at weeks 12 and 24.ResultsCAR was significantly higher for varenicline vs placebo at each interval: weeks 4-12, 40.0% and 20.0%, respectively (OR = 2.67, 95% CI = [1.25 - 5.68], P = 0.011); weeks 4-24, 34.3% for varenicline and 17.2% for placebo (OR = 2.52, 95% CI = [1.14 - 5.58], P = 0.0224). The 7-day point prevalence of vaping abstinence was also higher for the varenicline than placebo at each time point. Serious adverse events were infrequent in both groups and not treatment-related.ConclusionsInclusion of varenicline and counseling in a vaping cessation program for EC users intending to quit may result in prolonged abstinence. These positive findings may also help guiding future recommendations for vaping cessation by health authorities and healthcare providers.
Impact of guidance on trends of steroid prescriptions for COVID-19 inpatients: an analysis of the nation-wide administrative database in Japan
Authors: Higuchi Takuya , Shin Jung-ho , Takada Daisuke , Morishita Tetsuji , Kunisawa Susumu , Imanaka Yuichi 
Published: December 2022

AbstractBackgroundSince the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, guidance (“Japanese Guide”) has been published by a working group of several academic societies and announced by the Ministry of Health, Labour, and Welfare. Steroids as a candidate treatment for COVID-19 were noted in the Japanese Guide. However, the prescription details for steroids, and whether the Japanese Guide changed its clinical practice, were unclear. This study aimed to examine the impact of the Japanese Guide on the trends in the prescription of steroids for COVID-19 inpatients in Japan.MethodsWe selected our study population using Diagnostic Procedure Combination (DPC) data from hospitals participating in the Quality Indicator/Improvement Project (QIP). The inclusion criteria were patients discharged from hospital between January 2020 and December 2020, who had been diagnosed with COVID-19, and were aged 18 years or older. The epidemiological characteristics of cases and the proportion of steroid prescriptions were described on a weekly basis. The same analysis was performed for subgroups classified by disease severity.ResultsThe study population comprised 8603 cases (410 severe cases, 2231 moderate II cases, and 5962 moderate I/mild cases). The maximum proportion of cases prescribed with dexamethasone increased remarkably from 2.5% to 35.2% in the study population before and after week 29 (July 2020), when dexamethasone was included in the guidance. These increases were 7.7% to 58.7% in severe cases, 5.0% to 57.2% in moderate II cases, and 1.1% to 19.2% in moderate I/mild cases. Although the proportion of cases prescribed prednisolone and methylprednisolone decreased in moderate II and moderate I/mild cases, it remained high in severe cases.ConclusionsWe showed the trends of steroid prescriptions in COVID-19 inpatients. The results showed that guidance can influence drug treatment provided during an emerging infectious disease pandemic.
Association of smoking using with ALS risk and prognosis in China
Authors: Liu Wenchao , Li XiaoGang , Jiang JingSi , Deng Shuai , Song Ying , Liu Na , Deng Min 
Published: December 2022

AbstractObjectivesCigarette smoking using have been posited as possible risk factors for amyotrophic lateral sclerosis (ALS), but few epidemiological studies supporting this hypothesis in China. We therefore explored the association between smoking with ALS incidence and prognosis in Chinese patients.DesignPopulation-based case-control study.Setting, participantsWe performed a population-based case-control study in 812 ALS patients and 1500 matched controls. All the objects were recruited from Peking University Third Hospital, from January 2011 to December 2018 throughout China.Outcome measuresDemographic data and information about premorbid cigarette smoking habits were collected at the time of diagnosis. The association of smoking with ALS was investigated using logistic regression analysis. Kaplan-Meier curves were used to compare survival time. Cox proportional hazards function and the hazard ratio were used to identify adjusted prognostic predictors.ResultsCurrent smokers had an increased risk of ALS (odds ratio = 1.66, 95% confidence interval (CI): 1.46, 1.87) compared to never smokers. Current cigarette pack years ≥20 had a significantly shorter median survival (63.89 months, IQR 55.90–71.87) compared with current cigarette pack years<20 (81.09 months, IQR 77.35–84.84) (p<0.001). Smoking habits were retained in Cox multivariable model.ConclusionsOur study has proved current smoking is associated with an increased risk of ALS. Current cigarette pack years ≥20 is an independent negative prognostic factor for survival, with a dose–response gradient. Its influence is irrelevant to the presence ofchronic obstructive pulmonary disease (COPD) or to respiratory status at time of diagnosis. These results can be helpful for understanding and preventing ALS.
Management control matching pattern and company strategic aggressiveness: empirical test based on annual report text information
Authors: Zeng Xiangfei , Zhang Ting , Zu Yafei 
Published: December 2022

Purpose
This paper aims to investigate the law and logic mechanism of management control matching pattern and company strategy aggressiveness under different strategies by textual analysis, based on the empirical data of Chinese A-share listed companies during the period from 2010 to 2018. Additional analyses further investigate the moderating effect of environmental uncertainty and R&D intensity on the relationship between management control matching type and strategy aggressiveness. The conclusion can help relevant departments to develop management control theory and method system with Chinese characteristics and provide theoretical reference for the matching mode of dual control.

Design/methodology/approach
This paper uses the text analysis method. The main explanatory variables are analyzed using the computer SQL Server database software through the relevant text of the board of directors report in the company annual report. Other financial data came from the CSMAR database, excluding ST and PT and companies with missing data, and 16,902 samples were finally obtained. This paper conducted statistical analysis through Stata12.

Findings
This paper shows that the matching pattern between formal and informal control is divided into three types. They have different impacts on strategy aggressiveness. Specifically, consistent matching type II significantly positively influences the aggressiveness of offensive strategy. Consistent matching type I significantly positively influences the aggressiveness of defensive strategy. Complementary matching type I significantly positively influences the aggressiveness of analytical strategy. Additional analyses find that compared with non-high-tech companies, high-tech companies have more significant influence on the relationship between management control matching pattern and company strategic aggressiveness. And compared with other two “strategy-control” matching patterns, both environmental uncertainty and product innovation have more significant influence on the relationship between consistent matching II and offensive strategy aggressiveness.

Originality/value
To the best of the authors’ knowledge, this paper divides the formal and informal control matching patterns of management control into three categories for the first time. It examines the relationship between the formal and informal control matching of management accounting and the degree of strategy aggressiveness. The conclusion provides new empirical evidence to promote the effective implementation of development strategies for companies. It can help relevant departments to develop management control theory and method systems with Chinese characteristics and provide theoretical references for the matching mode of dual control.
Summer of migration: consolidating institutional repositories into a redesigned singular platform
Authors: Symulevich Allison , Boczar Jason 
Published: December 2022

Purpose
The purpose of this paper is to describe a state mandated merger of two institutional repositories from two separate campuses of a university into one new institutional repository. Due to a State Legislature mandate, the University of South Florida was required to merge institutional repositories from two campus into one new institutional repository.

Design/methodology/approach
USF Libraries formed a committee, planned for the migration and executed of the migration.

Findings
The authors discovered many unforeseen issues during the process of the migration such as difficulties with site redirects and hidden collections.

Originality/value
This project was a large-scale migration of institutional repositories, under a tight deadline due to a legislative mandate, that has not been discussed in detail in the literature.
Alternatives to the quality‐adjusted life year: How well do they address common criticisms?
Authors: Rand Leah Z. , Melendez‐Torres G. J. , Kesselheim Aaron S. 
Published: December 2022

AbstractObjectiveTo analyze whether other outcome measures used in health technology assessment (HTA) address the criticisms of quality‐adjusted life years (QALYs).Data Sources and Study SettingHTA methods guidance from 11 US comparator countries (the G10 and Australia) and six value frameworks from US organizations were reviewed to identify health outcome measures currently used to evaluate the benefits of a drug.Study DesignThe study involved a documentary analysis of guidelines to identify outcome measures used by the sampled HTA organizations. Similar outcomes were grouped together into outcome types. Each type was analyzed to determine the extent to which it replicates key advantages and responds to criticisms of QALYs extracted from the literature.Extraction MethodsOutcomes were included if guidance from at least one HTA organization identified the outcome as acceptable for HTA. Outcomes measuring or evaluating the benefit, clinical effect, or impact of a drug or health technology was included; methods of calculating costs were excluded.Principal FindingsSeven types of outcome measures were identified falling into three groups: preference‐based, single‐dimension outcomes, and outcomes using non‐health perspectives. Among the seven QALY alternative outcome measures currently used for HTA by the sampled countries, no one outcome measure addresses all the QALY criticisms while retaining the advantageous features of the QALY.ConclusionsProposals to adopt health technology assessment (HTA) to support value‐based pricing of prescription drugs in the US have faced pushback over the use of the QALY. There is no single “right” outcome measure, and the criticisms of QALYs apply to other outcome measures used to evaluate health. The measures identified have different features and strengths, which may be appropriate for specific decision making goals, but the QALY remains the best option for decision making that requires comparisons of the overall societal value of health gains.