bluuebunny/crossref_metadata_2025 huggingface dataset:
On the singularity structure of a discrete modified-Korteweg–deVries equation
Authors: Grammaticos Basil , Tamizhmani Thamizharasi , Willox Ralph
Published: May 2022

We study the singularities of a modified lattice Korteweg–deVries (KdV) equation and show that it admits three families of singularities, with analogous properties to those found in the lattice KdV equation. The first family consists of localised singularities which can occupy an arbitrarily large domain but which are, nevertheless, always confined. The second family consists of one or more lines extending all the way from the South-West to the North-East on the plane, involving a single finite value that depends on the parameter that appears in the equation. We argue that the infinite extent of this singularity is not incompatible with the confinement property or with the integrability of the equation. The third family consists of horizontal strips in which the product of values on vertically adjacent lattice sites is equal to 1. In the case of the lattice KdV equation this type of singularity was dubbed ‘taishi’. The taishi for the modified lattice KdV equation can interact with singularities of the other two families, giving rise to very rich and quite intricate singularity structures. Nonetheless, these interactions can be described in a compact way through the formulation of a symbolic representation of the dynamics that is similar to, but in a sense, simpler than that for the KdV case. We give an interpretation of this symbolic representation in terms of a box & ball system related to the ultradiscrete modified KdV equation. These results show that taishi-type singularities are not limited to the lattice KdV equation, but might very well be a general feature of integrable lattice equations with deep connections to other facets of their integrability.
The need for multicomponent gas standards for breath biomarker analysis
Authors: Jeerage Kavita M , Berry Jennifer L , Murray Jacolin A , Goodman Cassie A , Piotrowski Paulina K , Jones Christina M , Cecelski Christina E , Carney Jennifer , Lippa Katrice A , Lovestead Tara M
Published: May 2022

Exhaled breath is a non-invasive, information-rich matrix with the potential to diagnose or monitor disease, including infectious disease. Despite significant effort dedicated to biomarker identification in case control studies, very few breath tests are established in practice. In this topical review, we identify how gas standards support breath analysis today and what is needed to support further expansion and translation to practice. We examine forensic and clinical breath tests and discuss how confidence has been built through unambiguous biomarker identification and quantitation supported by gas calibration standards. Based on this discussion, we identify a need for multicomponent gas standards with part-per-trillion to part-per-million concentrations. We highlight National Institute of Standards and Technology gas standards developed for atmospheric measurements that are also relevant to breath analysis and describe investigations of long-term stability, chemical reactions, and interactions with gas cylinder wall treatments. An overview of emerging online instruments and their need for gas standards is also presented. This review concludes with a discussion of our ongoing research to examine the feasibility of producing multicomponent gas standards at breath-relevant concentrations. Such standards could be used to investigate interference from ubiquitous endogenous compounds and as a starting point for standards tailored to specific breath tests.
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

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

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.
Non-torsion Brauer groups in positive characteristic
Authors: Esser Louis
Published: May 2022

Unlike the classical Brauer group of a field, the Brauer-Grothendieck group of a singular scheme need not be torsion. We show that there exist integral normal projective surfaces over a large field of positive characteristic with non-torsion Brauer group. In contrast, we demonstrate that such examples cannot exist over the algebraic closure of a finite field.
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

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

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

Motivation

The 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.

Results

We 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 implementation

The 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 information

Supplementary 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

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

Omega-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 >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

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 < 0.001} and RAS inhibitors [aHR 0.84 (0.76–0.93); P < 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 >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

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

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

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

International 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

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

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 <40 years), microsatellite instability status, tumor mutational burden status (high ≥10 or low <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.
Motives for and Barriers to Research Participation Among Racially and Ethnically Diverse Veterans
Authors: Miller Mary Beth , Flores Lisa Y , Dorimé-Williams Marjorie L , Williams Michael S , Martinez Leticia D , Freeman Lindsey K , Everson Adam T , Hall Nicole A , Monk J Kale , McCrae Christina S , Borsari Brian
Published: May 2022

Introduction

Veterans in general—and especially those who identify as Veterans of color—are underrepresented in health-related treatment research. This contributes to health inequity by hindering the development of evidence-based treatment recommendations for people of color. This project utilized culturally centered research procedures to identify health-related research priorities and examine motives for and barriers to research participation in a diverse sample of Veterans.

Materials and Methods

Veterans (N = 330, 32% female; 36% Black, 28% White, 15% Latinx, 12% Asian, 4% Multiracial) reported their experiences with and perspectives on health-related research online from remote locations. Linear regression was used to test associations between discrimination and motives/barriers for research. All procedures were approved by the Institutional Review Board (#2033562).

Results

Participants identified psychological concerns, particularly PTSD, as research priorities for Veterans in their communities, but also prioritized physical problems (e.g., brain injury) and social concerns (e.g., homelessness, access to care). Perceptions of, motives for, and barriers to research were similar across racial/ethnic groups. The most common motive was contributing to research that seems important, and the most common barrier was not knowing about research opportunities. Every-day experiences with discrimination (e.g., people acting as if they are afraid of you because of your race/ethnicity) were associated with more barriers to research among Black participants.

Conclusions

Experiences of racial/ethnic discrimination are associated with different research-related outcomes across racial/ethnic groups. Efforts to engage diverse populations should prioritize access to (not willingness to participate in) health-related research.
High luminescent polymers for stretchable displays
Authors: Zhang Zhitao , Bao Zhenan
Published: May 2022

This perspective summarizes the main approaches to realize stretchable displays with high performance as well as future directions.
Direct and green repairing of degraded LiCoO2 for reuse in lithium-ion batteries
Authors: Wang Junxiong , Zhang Qi , Sheng Jinzhi , Liang Zheng , Ma Jun , Chen Yuanmao , Zhou Guangmin , Cheng Hui-Ming
Published: May 2022

Traditional recycling processes of LiCoO2 rely on destructive decomposition, requiring high-temperature roasting or acid leaching to extract valuable Li and Co, which have significant environmental and economic concerns. Herein, a direct repairing method for degraded LiCoO2 using a LiCl–CH4N2O deep eutectic solvent (DES) was established. The DES is not used to dissolve LiCoO2 but directly serves as a carrier for the selective replenishment of lithium and cobalt. Replenishment of lithium restores LiCoO2 at different states of charge to a capacity of 130 mAh/g (at 0.1 C rate), while replenishing the cobalt increases the capacity retention rate of 90% after 100 cycles, which is comparable to pristine LiCoO2. The DES is collected and reused multiple times with a high repair efficiency. This process reduces energy consumption by 37.1% and greenhouse gas emissions by 34.8% compared with the current production process of LiCoO2, demonstrating excellent environmental and economic viability.
Am I Positive? Improving Human Immunodeficiency Virus Testing in the Era of Preexposure Prophylaxis and Immediate Antiretroviral Therapy Using Machine Learning
Authors: Zucker Jason , Carnevale Caroline , Gordon Peter , Sobieszczyk Magdalena E , Rai Alex J
Published: May 2022

Background

Human immunodeficiency virus (HIV) testing is the first step in the HIV prevention cascade. The Centers for Disease Control and Prevention HIV laboratory diagnostic testing algorithm was developed before preexposure prophylaxis (PrEP) and immediate antiretroviral therapy (iART) became standards of care. PrEP and iART have been shown to delay antibody development and affect the performance of screening HIV assays. Quantitative results from fourth-generation HIV testing may be helpful to disambiguate HIV testing.

Methods

We retrospectively reviewed 38 850 results obtained at an urban, academic medical center. We assessed signal-to-cutoff (s/co) distribution among positive and negative tests, in patients engaged and not engaged in an HIV prevention program, and evaluated changes in patients with multiple results. Classification and regression tree (CART) analysis was used to determine a threshold cutoff, and logistic regression was used to identify predictors of true positive tests.

Results

Ninety-seven percent of patients with a negative HIV test had a result that was ≤0.2 s/co. For patients tested more than once, we found differences in s/co values did not exceed 0.2 s/co for 99.2% of results. CART identified an s/co value, 38.78, that in logistic regression on a unique validation cohort remained associated with the likelihood of a true-positive HIV result (odds ratio, 2.49).

Conclusions

Machine-learning methods may be used to improve HIV screening by automating and improving interpretations, incorporating them into robust algorithms, and improving disease prediction. Further investigation is warranted to confirm if s/co values combined with a patient's risk profile will allow for better clinical decision making for individuals on PrEP or eligible for iART.
ACPA-negative and ACPA-positive RA patients achieving disease resolution demonstrate distinct patterns of MRI-detected joint-inflammation
Authors: Verstappen Marloes , Matthijssen Xanthe M E , Connolly Sean E , Maldonado Michael A , Huizinga Tom W J , van der Helm-van Mil Annette H M
Published: May 2022

Objectives

Although sustained DMARD-free remission (SDFR; sustained absence of clinical-synovitis after DMARD-discontinuation) is increasingly achievable in RA, prevalence differs between ACPA-negative (40%) and ACPA-positive RA (5–10%). Additionally, early DAS remission (DAS4months<1.6) is associated with achieving SDFR in ACPA-negative, but not in ACPA-positive RA. Based on these differences, we hypothesized that longitudinal patterns of local tissue inflammation (synovitis/tenosynovitis/osteitis) also differ between ACPA-negative and ACPA-positive RA patients achieving SDFR. With the ultimate aim being to increase understanding of disease resolution in RA, we studied MRI-detected joint inflammation over time in relation to SDFR development in ACPA-positive RA and ACPA-negative RA.

Methods

A total of 198 RA patients (94 ACPA-negative, 104 ACPA-positive) underwent repeated MRIs (0/4/12/24 months) and were followed on SDFR development. The course of MRI-detected total inflammation, and synovitis/tenosynovitis/osteitis individually were compared between RA patients who did and did not achieve SDFR, using Poisson mixed models. In total, 174 ACPA-positive RA patients from the AVERT-1 were studied as ACPA-positive validation population.

Results

In ACPA-negative RA, baseline MRI-detected inflammation levels of patients achieving SDFR were similar to patients without SDFR but declined 2.0 times stronger in the first year of DMARD treatment [IRR 0.50 (95% CI; 0.32, 0.77); P < 0.01]. This stronger decline was seen in tenosynovitis/synovitis/osteitis. In contrast, ACPA-positive RA-patients achieving SDFR, had already lower inflammation levels (especially synovitis/osteitis) at disease presentation [IRR 0.45 (95% CI; 0.24, 0.86); P = 0.02] compared with patients without SDFR, and remained lower during subsequent follow-up (P = 0.02). Similar results were found in the ACPA-positive validation population.

Conclusion

Compared with RA patients without disease resolution, ACPA-positive RA patients achieving SDFR have less severe joint inflammation from diagnosis onwards, while ACPA-negative RA patients present with similar inflammation levels but demonstrate a stronger decline in the first year of DMARD therapy. These different trajectories suggest different mechanisms underlying resolution of RA chronicity in both RA subsets.
Pharmacological treatment patterns in patients with juvenile idiopathic arthritis in the Netherlands: a real-world data analysis
Authors: Kip Michelle M A , de Roock Sytze , Currie Gillian , Marshall Deborah A , Grazziotin Luiza R , Twilt Marinka , Yeung Rae S M , Benseler Susanne M , Vastert Sebastiaan J , Wulffraat Nico , Swart Joost F , IJzerman Maarten J
Published: May 2022

Objective

To investigate medication prescription patterns among children with JIA, including duration, sequence and reasons for medication discontinuation.

Methods

This study is a single-centre, retrospective analysis of prospective data from the electronic medical records of JIA patients receiving systemic therapy aged 0–18 years between 1 April 2011 and 31 March 2019. Patient characteristics (age, gender, JIA subtype) and medication prescriptions were extracted and analysed using descriptive statistics, Sankey diagrams and Kaplan–Meier survival methods.

Results

Over a median of 4.2 years follow-up, the 20 different medicines analysed were prescribed as monotherapy (n = 15) or combination therapy (n = 48 unique combinations) among 236 patients. In non-systemic JIA, synthetic DMARDs were prescribed to almost all patients (99.5%), and always included MTX. In contrast, 43.9% of non-systemic JIA patients received a biologic DMARD (mostly adalimumab or etanercept), ranging from 30.9% for oligoarticular persistent ANA-positive JIA, to 90.9% for polyarticular RF-positive JIA. Among systemic JIA, 91.7% received a biologic DMARD (always including anakinra). When analysing medication prescriptions according to their class, 32.6% involved combination therapy. In 56.8% of patients, subsequent treatment lines were initiated after unsuccessful first-line treatment, resulting in 68 unique sequences. Remission was the most common reason for DMARD discontinuation (44.7%), followed by adverse events (28.9%) and ineffectiveness (22.1%).

Conclusion

This paper reveals the complexity of pharmacological treatment in JIA, as indicated by: the variety of mono- and combination therapies prescribed, substantial variation in medication prescriptions between subtypes, most patients receiving two or more treatment lines, and the large number of unique treatment sequences.
Carcinoma-Associated Mesenchymal Stem/Stromal Cells: Architects of the Pro-tumorigenic Tumor Microenvironment
Authors: Frisbie Len , Buckanovich Ronald J , Coffman Lan
Published: May 2022

The interaction between tumor cells and non-malignant hosts cells within the tumor microenvironment (TME) is critical to the pathophysiology of cancer. These non-malignant host cells, consisting of a variety of stromal, immune, and endothelial cells, engage in a complex bidirectional crosstalk with the malignant tumor cells. Mesenchymal stem/stromal cells (MSCs) are one of these host cells, and they play a critical role in directing the formation and function of the entire TME. These MSCs are epigenetically reprogrammed by cancer cells to assume a strongly pro-tumorigenic phenotype and are referred to as carcinoma-associated mesenchymal stem/stromal cells (CA-MSCs). Studies over the last decade demonstrate that CA-MSCs not only directly interact with cancer cells to promote tumor growth and metastasis but also orchestrate the formation of the TME. Carcinoma-associated mesenchymal stem/stromal cells can differentiate into virtually all stromal sub-lineages present in the TME, including pro-tumorigenic cancer-associated fibroblasts (CAF), myofibroblasts, and adipocytes. carcinoma-associated mesenchymal stem/stromal cells and the CAFs they produce, secrete much of the extracellular matrix in the TME. Furthermore, CA-MSC secreted factors promote angiogenesis, and recruit immunosuppressive myeloid cells effectively driving tumor immune exclusion. Thus CA-MSCs impact nearly every aspect of the TME. Despite their influence on cancer biology, as CA-MSCs represent a heterogenous population without a single definitive marker, significant confusion remains regarding the origin and proper identification CA-MSCs. This review will focus on the impact of CA-MSCs on cancer progression and metastasis and the ongoing work on CA-MSC identification, nomenclature and mechanism of action.
Estimation of empty body and carcass chemical composition of lactating and growing cattle: comparison of imaging, adipose cellularity, and rib dissection methods
Authors: Xavier Caroline , Driesen Charlotte , Siegenthaler Raphael , Dohme-Meier Frigga , Le Cozler Yannick , Lerch Sylvain
Published: May 2022

The aim of present study was to compare in vivo and post mortem methods for estimating the empty body (EB) and carcass chemical compositions of Simmental lactating and growing cattle. Indirect methods were calibrated against the direct post mortem reference determination of chemical compositions of EB and carcass, determined after grinding and analyzing the water, lipid, protein, mineral masses, and energy content. The indirect methods applied to 12 lactating cows and 10 of their offspring were ultrasound (US), half-carcass and 11th rib dual-energy X-ray absorptiometry (DXA) scans, subcutaneous and perirenal adipose cell size (ACS), and dissection of the 11th rib. Additionally, three-dimensional (3D) images were captured for 8 cows. Multiple linear regressions with leave-one-out-cross-validations were tested between predictive variables derived from the methods tested, and the EB and carcass chemical compositions. Partial least square regressions were used to estimate body composition with morphological traits measured on 3D images. Body weight (BW) alone estimated the EB and carcass composition masses with a root mean squared error of prediction (RMSEP) for the EB from 1 kg for minerals to 12.4 kg for lipids, and for carcass from 0.9 kg for minerals to 7.8 kg for water. Subcutaneous adipose tissue thickness measured by US was the most accurate in vivo predictor when associated with BW to estimate chemical composition, with the EB lipid mass RMSEP = 11 kg and R2 = 0.75; carcass water mass RMSEP = 6 kg and R2 = 0.98; and carcass energy content RMSEP = 236 MJ and R2 = 0.91. Post mortem, carcass lipid mass was best estimated by half-carcass DXA scan (RMSEP = 2 kg, R2 = 0.98), 11th rib DXA scan (RMSEP = 3 kg, R2 = 0.96), 11th rib dissection (RMSEP = 4 kg, R2 = 0.92), and perirenal ACS (RMSEP = 6 kg, R2 = 0.79) in this respective order. The results obtained by 11th rib DXA scan were accurate and close to the half-carcass DXA scan with a reduction in scan time. Morphological traits from 3D images delivered promising estimations of the cow EB and carcass chemical component masses with an error less than 13 kg for the EB lipid mass and than 740 MJ for the EB energy. Future research is required to test the 3D imaging method on a larger number of animals to confirm and quantify its interest in estimating body composition in living animals.
Comparative phylodynamics reveals the evolutionary history of SARS-CoV-2 emerging variants in the Arabian Peninsula
Authors: Alkhamis Moh A , Fountain-Jones Nicholas M , Khajah Mohammad M , Alghounaim Mohammad , Al-Sabah Salman K
Published: May 2022

Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary epidemiology of novel SARS-CoV-2 variants are critical to guide current and future interventions. Here, we utilized a Bayesian phylodynamic pipeline to trace and compare the evolutionary dynamics, spatiotemporal origins, and spread of five variants (Alpha, Beta, Delta, Kappa, and Eta) across the Arabian Peninsula. We found variant-specific signatures of evolution and spread that are likely linked to air travel and disease control interventions in the region. Alpha, Beta, and Delta variants went through sequential periods of growth and decline, whereas we inferred inconclusive population growth patterns for the Kappa and Eta variants due to their sporadic introductions in the region. Non-pharmaceutical interventions imposed between mid-2020 and early 2021 likely played a role in reducing the epidemic progression of the Beta and the Alpha variants. In comparison, the combination of the non-pharmaceutical interventions and the rapid rollout of vaccination might have shaped Delta variant dynamics. We found that the Alpha and Beta variants were frequently introduced into the Arab peninsula between mid-2020 and early 2021 from Europe and Africa, respectively, whereas the Delta variant was frequently introduced between early 2021 and mid-2021 from East Asia. For these three variants, we also revealed significant and intense dispersal routes between the Arab region and Africa, Europe, Asia, and Oceania. In contrast, the restricted spread and stable effective population size of the Kappa and the Eta variants suggest that they no longer need to be targeted in genomic surveillance activities in the region. In contrast, the evolutionary characteristics of the Alpha, Beta, and Delta variants confirm the dominance of these variants in the recent outbreaks. Our study highlights the urgent need to establish regional molecular surveillance programs to ensure effective decision making related to the allocation of intervention activities targeted toward the most relevant variants.
Cool Temperatures Favor Growth of Oregon Isolates of Calonectria pseudonaviculata and Increase Severity of Boxwood Blight on Two Buxus Cultivars
Authors: Weiland Jerry E. , Ohkura Mana , Scagel Carolyn F. , Davis E. Anne , Beck Bryan R.
Published: May 2022

Controlled environment experiments were conducted to evaluate the effects of temperature on Calonectria pseudonaviculata mycelial growth and the effects of temperature and infection period on boxwood blight severity. In experiment 1, 15 Oregon isolates (representing five genotypes) were grown on potato dextrose agar (PDA) and malt extract agar (MEA) at six temperatures from 5 to 30°C. Growth (culture diameter) was measured after 2 weeks. Optimal growth occurred at 25°C on PDA and 20°C on MEA. Isolates of genotype G1 also grew faster than genotype G2, but only on MEA at 25°C. In experiment 2, Buxus cultivars Green Velvet (GV, more susceptible) and Winter Gem (WG, more resistant) were inoculated and incubated in moist chambers for 9 or 24 h at 22°C (infection period), then moved into growth chambers at 15 or 25°C. After 4 weeks, chamber temperatures were switched, and plants were incubated for 4 more weeks. Disease severity was evaluated weekly. During the first 4 weeks, disease was generally more severe on GV than WG, on plants with a 24-h versus a 9-h infection period, and on plants incubated at 15°C versus 25°C. However, disease was just as severe on WG as GV when the 24-h infection period was followed by incubation at 15°C. After the temperatures were switched, disease increased only on WG that were cooled from 25 to 15°C. Results show that Oregon isolates of C. pseudonaviculata are capable of growing faster and causing more severe disease at temperatures cooler than those reported previously.
Long-Term Esca Monitoring Reveals Disease Impacts on Fruit Yield and Wine Quality
Authors: Dewasme Coralie , Mary Séverine , Darrieutort Guillaume , Roby Jean-Philippe , Gambetta Gregory A.
Published: May 2022

Esca is a widespread grapevine trunk disease, and a global increase in esca incidence has been observed in recent decades. Estimates attribute considerable economic losses to esca, and the disease is considered one of the major causes of vine mortality and vineyard dieback. However, accurate quantification of esca incidence is difficult due to symptom inconsistency, and there are very few studies precisely quantifying yield losses and impacts on fruit composition and wine quality. This study carried out an extensive esca surveying program; annually monitoring approximately 57,000 vines across 12 estates in the Bordeaux region for 9 years. In conjunction with this surveying program, we quantified the yield losses of vines with known esca symptom histories and assessed their fruit composition and resulting wine quality. The study revealed that, because of year-to-year variation in symptom expression, accurate rates of esca can only be obtained through monitoring over many years. We found that yield losses in individual vines exhibiting esca can reach up to 50% but they are rarely unproductive, and when scaled to the parcel scale yield losses are low, never exceeding 1 hl/ha. In addition, the quality of the grapes produced is similar to that obtained from vines without symptoms. Finally, the majority of mortality observed in vineyards was not due to esca, with only 40% of dead vines exhibiting an esca history. These results suggest that the impact of esca is likely overestimated and that it is necessary to more broadly investigate other factors contributing to vine mortality and vineyard dieback.

[Formula: see text] Copyright © 2022 The Author(s). This is an open-access article distributed under the CC BY 4.0 International license .