bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raman spectroscopy of colloidal semiconductor nanocrystals
Authors: Boldt Klaus 
Published: January 2022

Abstract
Raman spectroscopy is a powerful method that gives insight into the atomic structure and composition of nanomaterials, but also allows to draw conclusions about their electronic properties. It is based on the inelastic scattering of light, which is able to excite phonons in the material. In the field of semiconductor nanocrystals, Raman spectroscopy has been employed to make significant contributions to the analysis of lattice distortion, interfaces, phase mixing, and defect formation. Yet, there is no clear consensus on how the electronic and crystal structure of the material interacts with the incident light to yield the observed spectra. This review gives a brief overview over the method. It then reviews the most important findings, current developments, and discusses the efforts to formulate a consistent model that allows to establish the method as a tool for structural analysis.
Financiers' perceptions of risk in relation to large hydropower projects
Authors: Braeckman Judith Plummer , Markkanen Sanna , Seega Nina 
Published: January 2022

Abstract
More renewable electricity generation capacity will be needed to support progress towards Sustainable Development Goals and the Paris Agreement objective in lower income and lower-middle income countries (LICs and L-MICs). In the context of declining availability of public sector finance for energy generation, there is a widespread expectation that much of the new generation capacity will need to be financed entirely by the private sector or through public-private-partnerships (PPPs). Sustainably developed large hydropower could play a vital role in a future electricity mix dominated by intermittent renewables. In addition to generating low-cost, low-carbon electricity at a large scale, hydropower is capable of delivering ancillary services that are needed to facilitate greater penetration of intermittent renewable electricity. However, concerns over social and environmental outcomes, uncertain financial returns and thus a widespread perception of large hydropower as a ‘high risk’ investment has so far made it difficult to attract private sector investment for such projects, especially in many LICs and L-MICs. This paper addresses the gap in the existing knowledge base by developing a conceptual analytical framework for public and private sector actors. The framework provides a structured approach to the analysis of risk which can aid governments, developers, lenders and investors in maximising the likelihood of a project obtaining sustainable finance. The findings suggest that many of the greatest risks associated with large PPP hydropower projects in LICs and L-MICs are those that can cause reputational damage to the involved parties, such as social and environmental risks. The results presented in this paper will enable governments and developers to take targeted action to reduce risk and thus facilitate more effective use of the PPP financing model for large renewable energy infrastructure projects in LICs and L-MICs where additional large-scale sustainable electricity generation capacity is most needed.
Effectiveness of a multicomponent exercise program to reverse pre-frailty in community-dwelling Chinese older adults: a randomised controlled trial
Authors: Dun Yaoshan , Hu Peng , Ripley-Gonzalez Jeffrey W , Zhou Nanjiang , Li Hui , Zhang Wenliang , Chen Meijuan , Zheng Qingsong , Cui Ni , Wu Shaoping , Liu Suixin 
Published: January 2022

Abstract

Background
the Xiangya Hospital circuit training (X-CircuiT), was developed to reverse pre-frailty in Chinese older adults and determine potential mechanisms through which pre-frailty is reversed.

Methods
this randomised controlled trial was performed at Xiangya Hospital, Changsha, China from September 2020 to May 2021. Forty-eight pre-frail older adults were enrolled. Participants were randomly assigned (1:1) to X-CircuiT (46 min/session, three supervised sessions/week for 3 months at a community health centre) or control (1-time advice on physical activity without supervised exercise). The primary outcome was the proportion of participants with pre-frailty after 3-month intervention. The secondary outcomes included absolute risk reduction (ARR), number needed to treat (NNT), and the changes in senior fitness, body composition and clinical measures.

Results
among 48 participants (mean age, 72 years; women [65%]), 22 participants in the X-CircuiT (92%) and 21 participants in the control (88%) completed the study. After 3 months, the proportion of pre-frailty was significantly lower in the X-CircuiT group than the control (14% versus 95%, P &lt; 0.001). The ARR and NNT were 82% [95% CI, 65–99] and 1 [1–2], respectively. X-CircuiT was associated with significant improvements in senior fitness indicators and body composition. No significant difference in blood chemistry, carotid ultrasound and echocardiography parameters was found between groups. No significant interaction was detected between sex, BMI, baseline peak oxygen consumption and study groups.

Conclusion
this study demonstrates that X-CircuiT could significantly reverse pre-frailty in Chinese older adults. The underlying mechanisms may involve X-CircuiT-induced improvements in body composition and senior fitness.
The trial is registered at Chictr.org.cn. Number: ChiCTR2100048125.
The impact of an exercise intervention on frailty levels in hospitalised older adults: secondary analysis of a randomised controlled trial
Authors: Pérez-Zepeda Mario Ulises , Martínez-Velilla Nicolás , Kehler Dustin Scott , Izquierdo Mikel , Rockwood Kenneth , Theou Olga 
Published: January 2022

Abstract

Background
physical activity reduces frailty in community-dwelling older adults. How exercise influences frailty in hospitalised older adults requires additional investigation.

Objectives
(i) to examine the impact of an exercise intervention on frailty in older adults admitted to an acute care ward, and (ii) to determine the impact of baseline frailty on the effectiveness of this intervention.

Setting/participants
this is a secondary analysis of a randomised controlled clinical trial that tested an intensive exercise intervention in ≥75-year-old adults admitted to an acute care ward.

Methods
the intervention included two daily sessions of moderate-intensity exercises (control received usual care). A 63-item Frailty Index (FI) was constructed, and three groups were formed: &lt;0.2, 0.2–0.29 and ≥0.3. Other outcomes included Short Physical Performance Battery (SPPB) and Barthel Index (BI).

Results
a total of 323 individuals were included. The mean age was 87.1 years (± 4.8 standard deviation [SD]) and 56.3% were females. The intervention group improved FI from 0.26 (± 0.10 SD) to 0.20 (± 0.10 SD), whereas the control group FI worsened from 0.25 (± 0.1 SD) to 0.27 (± 0.10 SD). After stratifying by baseline FI, SPPB and depression improved in the intervention group across all levels of frailty; FI, BI and quality of life only improved in individuals with a baseline FI ≥ 0.2.

Conclusions
frailty improves with an intensive individualised exercise intervention, especially in those with high baseline levels of frailty. In addition, frailty is a useful outcome when examining the impact of an intervention of hospitalised older adults.
Prediction of potential miRNA–disease associations based on stacked autoencoder
Authors: Wang Chun-Chun , Li Tian-Hao , Huang Li , Chen Xing 
Published: January 2022

Abstract
In recent years, increasing biological experiments and scientific studies have demonstrated that microRNA (miRNA) plays an important role in the development of human complex diseases. Therefore, discovering miRNA–disease associations can contribute to accurate diagnosis and effective treatment of diseases. Identifying miRNA–disease associations through computational methods based on biological data has been proven to be low-cost and high-efficiency. In this study, we proposed a computational model named Stacked Autoencoder for potential MiRNA–Disease Association prediction (SAEMDA). In SAEMDA, all the miRNA–disease samples were used to pretrain a Stacked Autoencoder (SAE) in an unsupervised manner. Then, the positive samples and the same number of selected negative samples were utilized to fine-tune SAE in a supervised manner after adding an output layer with softmax classifier to the SAE. SAEMDA can make full use of the feature information of all unlabeled miRNA–disease pairs. Therefore, SAEMDA is suitable for our dataset containing small labeled samples and large unlabeled samples. As a result, SAEMDA achieved AUCs of 0.9210 and 0.8343 in global and local leave-one-out cross validation. Besides, SAEMDA obtained an average AUC and standard deviation of 0.9102 ± /−0.0029 in 100 times of 5-fold cross validation. These results were better than those of previous models. Moreover, we carried out three case studies to further demonstrate the predictive accuracy of SAEMDA. As a result, 82% (breast neoplasms), 100% (lung neoplasms) and 90% (esophageal neoplasms) of the top 50 predicted miRNAs were verified by databases. Thus, SAEMDA could be a useful and reliable model to predict potential miRNA–disease associations.
ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants
Authors: Cherif Emira , Thiam Fatou Seck , Salma Mohammad , Rivera-Ingraham Georgina , Justy Fabienne , Deremarque Theo , Breugnot Damien , Doudou Jean-Claude , Gozlan Rodolphe Elie , Combe Marine 
Published: January 2022

Abstract

Motivation
Amplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. ZIKA, EBOLA) or pandemics (e.g. SARS-CoV-2). However, there is still a lack of versatile and easy-to-use tools that allow users with minimal bioinformatics skills to perform the main steps of downstream analysis, from quality testing to SNPs effect to phylogenetic analysis.

Results
Here, we present ONTdeCIPHER, an amplicon-based Oxford Nanopore Technology sequencing pipeline to analyze the genetic diversity of SARS-CoV-2 and other pathogens. Our pipeline integrates 13 bioinformatics tools. With a single command line and a simple configuration file, users can pre-process their data and obtain the sequencing statistics, reconstruct the consensus genome, identify variants and their effects for each viral isolate, infer lineage and, finally perform multi-sequence alignments and phylogenetic analyses.

Availability and implementation
ONTdeCIPHER is available at https://github.com/emiracherif/ONTdeCIPHER.

Supplementary information
Supplementary data are available at Bioinformatics online.
Distribution-on-distribution regression via optimal transport maps
Authors: Ghodrati Laya , Panaretos Victor M 
Published: January 2022

Summary
We present a framework for performing regression when both covariate and response are probability distributions on a compact interval. Our regression model is based on the theory of optimal transportation, and links the conditional Fréchet mean of the response to the covariate via an optimal transport map. We define a Fréchet-least-squares estimator of this regression map, and establish its consistency and rate of convergence to the true map, under both full and partial observations of the regression pairs. Computation of the estimator is shown to reduce to a standard convex optimization problem, and thus our regression model can be implemented with ease. We illustrate our methodology using real and simulated data.
Violent Conflict in Contemporary Europe: Specifying the Relationship Between War Exposure and Interpersonal Violence in a War-Weary Country
Authors: Timmer Anastasiia , Antonaccio Olena , Botchkovar Ekaterina V , Johnson Robert J , Hughes Lorine A 
Published: January 2022

Abstract
This study uses survey data from multi-stage stratified random samples of adults from two large Ukrainian cities to examine and specify associations between war exposure and the likelihood of committing violent acts against another person. Findings from regression models reveal that both direct and vicarious war exposure predict projected interpersonal violence by civilians, and mediation analyses show that daily strains and, in some instances, negative affect serve as links in the relationship between vicarious war exposure and the likelihood of violent behaviour. Daily strains also emerge as a significant and robust moderator of this relationship. The study demonstrates dangerous effects of war-related events on civilians and highlights the need for interventions aimed at reducing violence in war-weary countries around the world.
Neonatal amygdala resting-state functional connectivity and socio-emotional development in very preterm children
Authors: Kanel Dana , Vanes Lucy D. , Ball Gareth , Hadaya Laila , Falconer Shona , Counsell Serena J. , Edwards A. David , Nosarti Chiara 
Published: January 2022

Abstract
Very preterm children are more likely to exhibit difficulties in socio-emotional processing than their term-born peers. Emerging socio-emotional problems may be partly due to alterations in limbic system development associated with infants’ early transition to extrauterine life. The amygdala is a key structure in this system and plays a critical role in various aspects of socio-emotional development, including emotion regulation. The current study tested the hypothesis that amygdala resting-state functional connectivity at term-equivalent age would be associated with socio-emotional outcomes in childhood. Participants were 129 very preterm infants (&lt;33 weeks' gestation) who underwent resting-state functional MRI at term and received a neurodevelopmental assessment at 4–7 years (median = 4.64). Using the left and right amygdalae as seed regions, we investigated associations between whole-brain seed-based functional connectivity and three socio-emotional outcome factors which were derived using exploratory factor analysis (Emotion Moderation, Social Function and Empathy), controlling for sex, neonatal sickness, post-menstrual age at scan and social risk. Childhood Emotion Moderation scores were significantly associated with neonatal resting-state functional connectivity of the right amygdala with right parahippocampal gyrus and right middle occipital gyrus, as well as with functional connectivity of the left amygdala with the right thalamus. No significant associations were found between amygdalar resting-state functional connectivity and either Social Function or Empathy scores. The current findings show that amygdalar functional connectivity assessed at term is associated with later socio-emotional outcomes in very preterm children.
Characterization of resting functional MRI activity alterations across epileptic foci and networks
Authors: Sainburg Lucas E , Little Aubrey A , Johnson Graham W , Janson Andrew P , Levine Kaela K , González Hernán F J , Rogers Baxter P , Chang Catie , Englot Dario J , Morgan Victoria L 
Published: January 2022

Abstract
Brain network alterations have been studied extensively in patients with mesial temporal lobe epilepsy (mTLE) and other focal epilepsies using resting-state functional magnetic resonance imaging (fMRI). However, little has been done to characterize the basic fMRI signal alterations caused by focal epilepsy. Here, we characterize how mTLE affects the fMRI signal in epileptic foci and networks. Resting-state fMRI and diffusion MRI were collected from 47 unilateral mTLE patients and 96 healthy controls. FMRI activity, quantified by amplitude of low-frequency fluctuations, was increased in the epileptic focus and connected regions in mTLE. Evidence for spread of this epileptic fMRI activity was found through linear relationships of regional activity across subjects, the association of these relationships with functional connectivity, and increased activity along white matter tracts. These fMRI activity increases were found to be dependent on the epileptic focus, where the activity was related to disease severity, suggesting the focus to be the origin of these pathological alterations. Furthermore, we found fMRI activity decreases in the default mode network of right mTLE patients with different properties than the activity increases found in the epileptic focus. This work provides insights into basic fMRI signal alterations and their potential spread across networks in focal epilepsy.
Cortical thickness of contralesional cortices positively relates to future outcome after severe stroke
Authors: Rojas Albert Alina , Backhaus Winifried , Graterol Pérez José A , Braaβ Hanna , Schön Gerhard , Choe Chi-un , Feldheim Jan , Bönstrup Marlene , Cheng Bastian , Thomalla Götz , Gerloff Christian , Schulz Robert 
Published: January 2022

Abstract
Imaging studies have evidenced that contralesional cortices are involved in recovery after motor stroke. Cortical thickness (CT) analysis has proven its potential to capture the changes of cortical anatomy, which have been related to recovery and treatment gains under therapy. An open question is whether CT obtained in the acute phase after stroke might inform correlational models to explain outcome variability. Data of 38 severely impaired (median NIH Stroke Scale 9, interquartile range: 6–13) acute stroke patients of 2 independent cohorts were reanalyzed. Structural imaging data were processed via the FreeSurfer pipeline to quantify regional CT of the contralesional hemisphere. Ordinal logistic regression models were fit to relate CT to modified Rankin Scale as an established measure of global disability after 3–6 months, adjusted for the initial deficit, lesion volume, and age. The data show that CT of contralesional cortices, such as the precentral gyrus, the superior frontal sulcus, and temporal and cingulate cortices, positively relates to the outcome after stroke. This work shows that the baseline cortical anatomy of selected contralesional cortices can explain the outcome variability after severe stroke, which further contributes to the concept of structural brain reserve with respect to contralesional cortices to promote recovery.
Long-Term Accuracy of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Interferon-γ Release Assay and Its Application in Household Investigation
Authors: Murugesan Kanagavel , Jagannathan Prasanna , Altamirano Jonathan , Maldonado Yvonne A , Bonilla Hector F , Jacobson Karen B , Parsonnet Julie , Andrews Jason R , Shi Run Zhang , Boyd Scott , Pinsky Benjamin A , Singh Upinder , Banaei Niaz 
Published: January 2022

Abstract

Background
An immunodiagnostic assay that sensitively detects a cell-mediated immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is needed for epidemiological investigation and for clinical assessment of T- cell-mediated immune response to vaccines, particularly in the context of emerging variants that might escape antibody responses.

Methods
The performance of a whole blood interferon-gamma (IFN-γ) release assay (IGRA) for the detection of SARS-CoV-2 antigen-specific T cells was evaluated in coronavirus disease 2019 (COVID-19) convalescents tested serially up to 10 months post-infection and in healthy blood donors. SARS-CoV-2 IGRA was applied in contacts of households with index cases. Freshly collected blood in the lithium heparin tube was left unstimulated, stimulated with a SARS-CoV-2 peptide pool, and stimulated with mitogen.

Results
The overall sensitivity and specificity of IGRA were 84.5% (153/181; 95% confidence interval [CI]: 79.0–89.0) and 86.6% (123/142; 95% CI: 80.0–91.2), respectively. The sensitivity declined from 100% (16/16; 95% CI: 80.6–100) at 0.5-month post-infection to 79.5% (31/39; 95% CI: 64.4–89.2) at 10 months post-infection (P &lt; .01). The IFN-γ response remained relatively robust at 10 months post-infection (3.8 vs 1.3 IU/mL, respectively). In 14 households, IGRA showed a positivity rate of 100% (12/12) and 65.2% (15/23), and IgG of 50.0% (6/12) and 43.5% (10/23) in index cases and contacts, respectively, exhibiting a difference of + 50% (95% CI: +25.4 to +74.6) and +21.7% (95% CI: +9.23 to +42.3), respectively. Either IGRA or IgG was positive in 100% (12/12) of index cases and 73.9% (17/23) of contacts.

Conclusions
The SARS-CoV-2 IGRA is a useful clinical diagnostic tool for assessing cell-mediated immune response to SARS-CoV-2.
Severe Acute Respiratory Syndrome Coronavirus 2 Vaccination Boosts Neutralizing Activity Against Seasonal Human Coronaviruses
Authors: Lawrenz Jan , Xie Qinya , Zech Fabian , Weil Tatjana , Seidel Alina , Krnavek Daniela , van der Hoek Lia , Münch Jan , Müller Janis A , Kirchhoff Frank 
Published: January 2022

Abstract

Background
Most of the millions of people that are vaccinated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), have previously been infected by related circulating human coronaviruses (hCoVs) causing common colds and will experience further encounters with these viruses in the future. Whether COVID-19 vaccinations impact neutralization of seasonal coronaviruses is largely unknown.

Methods
We analyzed the capacity of sera derived from 24 individuals before and after heterologous ChAdOx1 nCoV-19 BNT162b2 prime-boost vaccination to neutralize genuine OC43, NL63, and 229E hCoVs, as well as viral pseudoparticles carrying the SARS-CoV-1, SARS-CoV-2, Middle East Respiratory Syndrome (MERS)-CoV, and hCoV-OC43, hCoV-NL63, and hCoV-229E spike proteins. Genuine hCoVs or spike containing pseudovirions were incubated with different concentrations of sera and neutralization efficiencies were determined by measuring viral RNA yields, intracellular viral nucleocapsid expression, or reporter gene expression in Huh-7 cells.

Results
All individuals showed strong preexisting immunity against hCoV-OC43. Neutralization of hCoV-NL63 was more variable and all sera showed only modest inhibitory activity against genuine hCoV-229E. SARS-CoV-2 vaccination resulted in efficient cross-neutralization of SARS-CoV-1 but not of MERS-CoV. On average, vaccination significantly increased the neutralizing activity against genuine hCoV-OC43, hCoV-NL63, and hCoV-229E.

Conclusions
Heterologous COVID-19 vaccination may confer some cross-protection against endemic seasonal coronaviruses.