bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of fluorescent logic gates for the detection of mercury(II) and ciprofloxacin based on phycocyanin
Authors: Dong Han , Girmatsion Mogos , Wang Ruoyu , Lu Gang , Xie Yunfei , Guo Yahui , Qian He , Yao Weirong 
Published: May 2022

Abstract
Chemical pollutants such as heavy metals and antibiotics in the environment pose a huge threat to humans and animals. Our studies have demonstrated that the fluorescence of phycocyanin showed quenching responses towards both mercury (Hg2+) and ciprofloxacin (CIP), which acted in accordance with the ‘OR’ molecular logic gate. In order to discriminate Hg2+ and CIP in application scenarios, cysteine (Cys) was utilized to design another ‘INHIBIT’ logic gate, in which Hg2+ and Cys were the two inputs. Thus, an intelligent biosensor with dual-target identification capacity was successfully developed by using a fluorescent natural protein in an ingenious logic gate system.
Experimental realization of nonlinear demagnification in plasma-based charged particle optics
Authors: Barman Sushanta , Kumar Maurya Sanjeev , Bhattacharjee Sudeep 
Published: May 2022

Abstract
We experimentally demonstrate nonlinear demagnification (DM) in plasma-based charged particle optics. The nonlinearity originates from the non-uniform penetration of electric fields through the plasma sheath region, when the object beam size (d

P
) is reduced to below the Debye length (λ

d
). The strength of nonlinearity depends upon d

P
and λ

d
, as confirmed from experimental results and a theoretical model. Nonlinear DM is unique to optics of classical Maxwell-Boltzmann systems and unrealized in conventional liquid metal sources where the Fermi Debye length ≪d

P
. The realization of plasma sheaths being able to control DM can greatly enhance the performance of charged particle optical systems.
Effects of Adolescent-Focused Integrated Social Protection on Depression: A Pragmatic Cluster-Randomized Controlled Trial of Tanzania’s Cash Plus Intervention
Authors: Prencipe Leah , Houweling Tanja A J , van Lenthe Frank J , Kajula Lusajo , Palermo Tia ,   on behalf of the Tanzania Adolescent Cash Plus Evaluation Team
Published: May 2022

Abstract
We assessed the impacts of Tanzania’s adolescent-focused Cash Plus intervention on depression. In this pragmatic cluster-randomized controlled trial, 130 villages were randomly allocated to an intervention or control arm (1:1). Youth aged 14–19 years living in households receiving governmental cash transfers were invited to participate. The intervention included an intensive period (a 12-session course) and an aftercare period (9 months of mentoring, productive grants, and strengthened health services). We examined intervention impacts on a depressive symptoms scale (10-item Center for Epidemiologic Studies Depression Scale score (range, 0–30)) and rates of depressive symptomatology (score ≥10 points on the scale), recorded at study baseline (April–June 2017), midline (May–July 2018), and endline (June–August 2019). Using intention-to-treat methodology, we employed logistic and generalized linear models to estimate effects for binary and continuous outcomes, respectively. Quantile regression was used to estimate effects across the scale. From 2,458 baseline participants, 941 intervention and 992 control adolescents were reinterviewed at both follow-ups. At endline, the intervention reduced the odds of depressive symptomatology (adjusted odds ratio = 0.67, 95% confidence interval: 0.52, 0.86), with an undetectable mean scale difference (risk difference = −0.36, 95% confidence interval: –0.84, 0.11). Quantile regression results demonstrated an intervention effect along the upper distribution of the scale. Integration of multisectoral initiatives within existing social protection systems shows potential to improve mental health among youth in low-resource settings.
Protective effect of UV-irradiated red perilla (Perilla frutescens (L.) Britton) on carbon tetrachloride-induced liver injury in mice
Authors: Kurniati Dian , Umeda Ryohei , Kagawa Natsuko , Goto Eiji , Wakabayashi Ryo , Shimada Kanae , Hirai Shizuka , Egashira Yukari 
Published: May 2022

Abstract
UV-irradiated red perilla demonstrated promising protective effects against carbon tetrachloride-induced liver injury in mice. UV exposure significantly enhanced the accumulation of rosmarinic acid, malonylshisonin and shisonin in red perilla, and increased DPPH radical scavenging capacity. The hepatoprotective effect of UV-irradiated red perilla may be attributed to the high level of its polyphenolic compounds, which exhibit antioxidant activity.
AutoDC: an automatic machine learning framework for disease classification
Authors: Bai Yang , Li Yang , Shen Yu , Yang Mingyu , Zhang Wentao , Cui Bin 
Published: May 2022

AbstractMotivationThe emergence of next-generation sequencing techniques opens up tremendous opportunities for researchers to uncover the basic mechanisms of disease at the molecular level. Recently, automatic machine learning (AutoML) frameworks have been employed for genomic and epigenomic data analysis. However, to analyze those high-dimensional data, existing AutoML frameworks suffer from the following issues: (i) they could not effectively filter out the redundant features from the original data, and (ii) they usually obey the rule of feature engineering first and algorithm hyper-parameter tuning later to build the machine learning pipeline, which could lead to sub-optimal outcomes. Thus, it is an urgent need to design a new AutoML framework for high-dimensional omics data analysis.ResultsWe introduce a new method: AutoDC, a tailored AutoML framework, for different disease classification based on gene expression data. AutoDC designs two novel optimization strategies to improve the performance. One is that AutoDC designs a novel two-stage feature selection method to select the features with high gene contribution scores. The other is that AutoDC proposes a novel optimization method, based on a two-layer Multi-Armed Bandit framework, to jointly optimize the feature engineering, algorithm selection and algorithm hyper-parameter tuning. We apply our framework to two public gene expression datasets. Compared with three state-of-the-art AutoML frameworks, AutoDC could effectively classify diseases with higher predictive accuracy.Availability and implementationThe data and codes of AutoDC are available at https://github.com/dingdian110/AutoDC. The data underlying this article are available in the article and in its online supplementary material.Supplementary informationSupplementary data are available at Bioinformatics online.
Stimulation of the cuneiform nucleus enables training and boosts recovery after spinal cord injury
Authors: Hofer Anna-Sophie , Scheuber Myriam I , Sartori Andrea M , Good Nicolas , Stalder Stephanie A , Hammer Nicole , Fricke Kai , Schalbetter Sina M , Engmann Anne K , Weber Rebecca Z , Rust Ruslan , Schneider Marc P , Russi Natalie , Favre Giacomin , Schwab Martin E 
Published: May 2022

Abstract
Severe spinal cord injuries result in permanent paraparesis in spite of the frequent sparing of small portions of white matter. Spared fibre tracts are often incapable of maintaining and modulating the activity of lower spinal motor centres. Effects of rehabilitative training thus remain limited.
Here, we activated spared descending brainstem fibres by electrical deep brain stimulation of the cuneiform nucleus of the mesencephalic locomotor region, the main control centre for locomotion in the brainstem, in adult female Lewis rats.
We show that deep brain stimulation of the cuneiform nucleus enhances the weak remaining motor drive in highly paraparetic rats with severe, incomplete spinal cord injuries and enables high-intensity locomotor training. Stimulation of the cuneiform nucleus during rehabilitative aquatraining after subchronic (n = 8 stimulated versus n = 7 unstimulated versus n = 7 untrained rats) and chronic (n = 14 stimulated versus n = 9 unstimulated versus n = 9 untrained rats) spinal cord injury re-established substantial locomotion and improved long-term recovery of motor function. We additionally identified a safety window of stimulation parameters ensuring context-specific locomotor control in intact rats (n = 18) and illustrate the importance of timing of treatment initiation after spinal cord injury (n = 14).
This study highlights stimulation of the cuneiform nucleus as a highly promising therapeutic strategy to enhance motor recovery after subchronic and chronic incomplete spinal cord injury with direct clinical applicability.
Midlife omega-3 fatty acid intake predicts later life white matter microstructure in an age- andAPOE-dependent manner
Authors: Tsiknia Amaryllis A , Bergstrom Jaclyn , Reas Emilie T 
Published: May 2022

AbstractOmega-3 intake has been positively associated with healthy brain aging, yet it remains unclear whether high omega-3 intake beginning early in life may optimize its protective effects against brain aging. We examined whether omega-3 intake is associated with brain microstructure over 2 decades later among dementia-free older adults. The 128 participants (62% women; age at magnetic resonance imaging: 76.6 ± 7.9) from the Rancho Bernardo Study of Healthy Aging completed at least 1 dietary assessment between 1984 and 1996 and underwent restriction spectrum imaging (RSI) 22.8 ± 3.1 years later. We evaluated associations between prior omega-3 intake and RSI metrics of gray and white matter (WM) microstructure. Higher prior omega-3 intake was associated with greater restricted diffusion in the superior cortico-striatal fasciculus. A correlation between higher prior omega-3 intake and greater cingulum restricted diffusion was stronger among participants &gt;80 years old. Higher omega-3 intake correlated with greater restricted diffusion in the inferior longitudinal and inferior fronto-occipital fasciculus more strongly for apolipoprotein E (APOE) ε4 carriers than noncarriers. Associations were not modified by adjustment for dietary pattern, health, or lifestyle. High omega-3 intake in midlife may help to maintain WM integrity into older age, particularly in the latest decades of life and among APOE ε4 carriers.
Associations between medical therapy after surgical aortic valve replacement for aortic stenosis and long-term mortality: a report from the SWEDEHEART registry
Authors: Baranowska Julia , Törngren Charlotta , Nielsen Susanne J , Lindgren Martin , Björklund Erik , Ravn-Fischer Annica , Skoglund Kristofer , Jeppsson Anders , Martinsson Andreas 
Published: May 2022

Abstract

Aims
The association between the use of statins, renin–angiotensin system (RAS) inhibitors, and/or β-blockers and long-term mortality in patients with aortic stenosis (AS) who underwent surgical aortic valve replacement (SAVR) is unknown.

Methods and results
All patients with AS who underwent isolated first-time SAVR in Sweden from 2006 to 2017 and survived 6 months after discharge were included. Individual patient data from four mandatory nationwide registries were merged. Cox proportional hazards models, with time-updated data on medication status and adjusted for age, sex, comorbidities, type of prosthesis, and year of surgery, were used to investigate associations between dispensed statins, RAS inhibitors, and β-blockers and all-cause mortality. In total, 9553 patients were included, and the median follow-up time was 4.9 years (range 0–11); 1738 patients (18.2%) died during follow-up. Statins were dispensed to 49.1% and 49.0% of the patients within 6 months of discharge from the hospital and after 10 years, respectively. Corresponding figures were 51.4% and 53.9% for RAS inhibitors and 79.3% and 60.7% for β-blockers. Ongoing treatment was associated with lower mortality risk for statins {adjusted hazard ratio (aHR) 0.67 [95% confidence interval (95% CI) 0.60–0.74]; P &lt; 0.001} and RAS inhibitors [aHR 0.84 (0.76–0.93); P &lt; 0.001] but not for β-blockers [aHR 1.17 (1.05–1.30); P = 0.004]. The associations were robust in subgroups based on age, sex, and comorbidities (P for interactions &gt;0.05).

Conclusions
The results of this large population-based real-world study support the use of statins and RAS inhibitors for patients who underwent SAVR due to AS.
Developing a Medication Self-Management Program to Enhance Medication Adherence Among Older Adults With Multimorbidity Using Intervention Mapping
Authors: Yang Chen , Lee Diana Tze Fan , Wang Xiuhua , Chair Sek Ying 
Published: May 2022

Abstract

Background and Objectives
Suboptimal medication adherence is prevalent in older adults with multimorbidity. However, intervention programs for enhancing adherence in this population are limited. This study describes the development process of a medication self-management program for older adults with multimorbidity.

Research Design and Methods
We adopted the first 4 steps of the intervention mapping to develop the program: (1) needs assessment, including a literature review, a systematic review, and a cross-sectional study; (2) development of program outcomes and objectives; (3) selection of theory-based intervention methods and practical applications; and (4) development of the program.

Results
We conducted a needs assessment to identify factors affecting medication adherence among older adults with multimorbidity and created a logic model of the adherence problem in Step 1. In Step 2, we developed the specific program outcomes and objectives and then selected adherence information, personal motivation, social motivation, behavioral skills, and treatment experiences as modifiable and important targets that needed to change in this program. In Step 3, we chose several theory-based methods and strategies for practical applications. We finally created a nurse-led medication self-management program in Step 4. Feedback from relevant stakeholders refined the intervention protocol and materials.

Discussion and Implications
The newly developed medication self-management program incorporated theory and evidence from literature and empirical studies with the engagement of multiple stakeholders, making it a contextually and culturally appropriate intervention. This study provides insights into strategies for geriatrics health care professionals to support medication self-management among older adults with multimorbidity.
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data
Authors: Marini Simone , Oliva Marco , Slizovskiy Ilya B , Das Rishabh A , Noyes Noelle Robertson , Kahveci Tamer , Boucher Christina , Prosperi Mattia 
Published: May 2022

Abstract

Background
Antimicrobial resistance (AMR) is a global health concern. High-throughput metagenomic sequencing of microbial samples enables profiling of AMR genes through comparison with curated AMR databases. However, the performance of current methods is often hampered by database incompleteness and the presence of homology/homoplasy with other non-AMR genes in sequenced samples.

Results
We present AMR-meta, a database-free and alignment-free approach, based on k-mers, which combines algebraic matrix factorization into metafeatures with regularized regression. Metafeatures capture multi-level gene diversity across the main antibiotic classes. AMR-meta takes in reads from metagenomic shotgun sequencing and outputs predictions about whether those reads contribute to resistance against specific classes of antibiotics. In addition, AMR-meta uses an augmented training strategy that joins an AMR gene database with non-AMR genes (used as negative examples). We compare AMR-meta with AMRPlusPlus, DeepARG, and Meta-MARC, further testing their ensemble via a voting system. In cross-validation, AMR-meta has a median f-score of 0.7 (interquartile range, 0.2–0.9). On semi-synthetic metagenomic data—external test—on average AMR-meta yields a 1.3-fold hit rate increase over existing methods. In terms of run-time, AMR-meta is 3 times faster than DeepARG, 30 times faster than Meta-MARC, and as fast as AMRPlusPlus. Finally, we note that differences in AMR ontologies and observed variance of all tools in classification outputs call for further development on standardization of benchmarking data and protocols.

Conclusions
AMR-meta is a fast, accurate classifier that exploits non-AMR negative sets to improve sensitivity and specificity. The differences in AMR ontologies and the high variance of all tools in classification outputs call for the deployment of standard benchmarking data and protocols, to fairly compare AMR prediction tools.
The assembled and annotated genome of the masked palm civet (Paguma larvata)
Authors: Liu Ping , Jiang Hai-Ying , Li Lin-Miao , Zhou Jia-Bin , Huang Wen-Zhong , Chen Jin-Ping 
Published: May 2022

Abstract

Background
The masked palm civet (Paguma larvata) acts as an intermediate host of severe acute respiratory syndrome coronavirus (SARS-CoV), which caused SARS, and transfered this virus from bats to humans. Additionally, P. larvata has the potential to carry a variety of zoonotic viruses that may threaten human health. However, genome resources for P. larvata have not been reported to date.

Findings
A chromosome-level genome assembly of P. larvata was generated using PacBio sequencing, Illumina sequencing, and Hi-C technology. The genome assembly was 2.44 Gb in size, of which 95.32% could be grouped into 22 pseudochromosomes, with contig N50 and scaffold N50 values of 12.97 Mb and 111.81 Mb, respectively. A total of 21,582 protein-coding genes were predicted, and 95.20% of the predicted genes were functionally annotated. Phylogenetic analysis of 19 animal species confirmed the close genetic relationship between P. larvata and species belonging to the Felidae family. Gene family clustering revealed 119 unique, 243 significantly expanded, and 58 significantly contracted genes in the P. larvata genome. We identified 971 positively selected genes in P. larvata, and one known human viral receptor gene PDGFRA is positively selected in P. larvata, which is required for human cytomegalovirus infection.

Conclusions
This high-quality genome assembly provides a valuable genomic resource for exploring virus–host interactions. It will also provide a reliable reference for studying the genetic bases of the morphologic characteristics, adaptive evolution, and evolutionary history of this species.
The Death of the Democratic Advantage?
Authors: Drezner Daniel W 
Published: May 2022

AbstractInternational relations scholarship has posited multiple pathways through which democracies accrue advantages in world politics. These range from enhanced warfighting capabilities to sovereign borrowing capacity to more constructive cooperation with like-minded regimes. A series of crises over the past generation, however, have called these advantages into question. This paper re-examines the key conceptual pillars underlying the democratic advantage in world politics. Scholars have posited that democracies possess inherent advantages in credible commitment mechanisms and public goods provision. The rise of populism has eroded these underlying advantages. Furthermore, the rise of China threatens to hamper the network effects that enhance democratic flourishing at the global level. Whether the democratic advantage is real and sustainable should be one of the defining political science research programs of this century.
Clinical Benefit Scales and Trial Design: Some Statistical Issues
Authors: Korn Edward L , Allegra Carmen J , Freidlin Boris 
Published: May 2022

Abstract
Recently developed clinical-benefit outcome scales by the European Society for Medical Oncology and the American Society of Clinical Oncology allow standardized objective evaluation of outcomes of randomized clinical trials. However, incorporation of clinical-benefit outcome scales into trial designs highlights a number of statistical issues: the relationship between minimal clinical benefit and the target treatment-effect alternative used in the trial design, designing trials to assess long-term benefit, potential problems with using a trial endpoint that is not overall survival, and how to incorporate subgroup analyses into the trial design. Using the European Society for Medical Oncology Magnitude of Clinical Benefit Scale as a basis for discussion, we review what these issues are and how they can guide the choice of trial-design target effects, appropriate endpoints, and prespecified subgroup analyses to increase the chances that the resulting trial outcomes can be appropriately evaluated for clinical benefit.
The Molecular Landscape of Pancreatobiliary Cancers for Novel Targeted Therapies From Real-World Genomic Profiling
Authors: Umemoto Kumiko , Yamamoto Hiroyuki , Oikawa Ritsuko , Takeda Hiroyuki , Doi Ayako , Horie Yoshiki , Arai Hiroyuki , Ogura Takashi , Mizukami Takuro , Izawa Naoki , Moore Jay A , Sokol Ethan S , Sunakawa Yu 
Published: May 2022

Abstract

Background
Chemotherapies have limited efficacy in pancreatic cancer (PC) and biliary tract cancer (BTC), underscoring the need for new regimens. Recently, tumor-agnostic approaches have been developed for some targeted therapies in advanced solid tumors; however, the frequency of alterations by clinical and genomic background is unclear in PC and BTC.

Methods
To assess the frequencies of druggable gene alterations and investigate new potential therapeutic targetable genomic alterations, advanced PC and BTC patients were tested with comprehensive genomic profiling at Foundation Medicine during the course of clinical care.

Results
A total of 16 913 PC patients and 3031 BTC patients were available for analyses, and frequencies of genomic alterations were stratified by age (≥40 years or &lt;40 years), microsatellite instability status, tumor mutational burden status (high ≥10 or low &lt;10 Muts/Mb), and select genomic alterations. Alterations in BRCA2, BRAF, ERBB2, CDK12, PIK3CA, FGFR2, EGFR, and other potential targets were seen across cohorts, with enrichment observed within particular subsets such as in PC patients lacking a KRAS mutation. In BTC patients, the rate of ERBB2 amplification was statistically significantly higher in the tumor mutational burden–high population (23.3% vs 13.7%). Interestingly, CDK12 rearrangement was observed in BTC patients with ERBB2 amplification tumors. In patients younger than 40 years, FGFR2 rearrangement (4%) was observed in PC: GATA6 amplification (11.1%) and rearrangement of BRAF (2.8%)FGFR2 (5.6%) was observed in BTC patients.

Conclusions
We identified an appreciable frequency of immunotherapy biomarkers and targetable gene alterations in both PC and BTC, with notable frequencies in PC samples lacking KRAS mutations and children or adolescent and young adult populations, that should encourage comprehensive genomic profiling testing.