bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demethylation and tannin-like properties of guaiacyl/syringyl-type and syringyl-type dehydrogenation polymers using iodocyclohexane
Authors: Kobayashi Tokimitsu , Tobimatsu Yuki , Kamitakahara Hiroshi , Takano Toshiyuki 
Published: August 2022

AbstractThe demethylation of guaiacyl/syringyl (G/S)-type (G/S = 1/1) and syringyl (S)-type dehydrogenation polymers (DHPs) using iodocyclohexane (ICH) under reflux in DMF was performed to afford demethylated G/S- and S-DHPs in moderate yields. Along with significant structural changes, such as side-chain cleavage and recondensation, as observed using heteronuclear single quantum coherence (HSQC) NMR spectra, the phenolic-OH content of the demethylated DHPs increased, as expected. The tannin-like properties, such as the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging ability, iron(III) binding ability, and bovine serum albumin (BSA) adsorption ability, of the demethylated DHPs increased with increasing reaction time. In particular, the BSA adsorption ability was significantly enhanced by demethylation of the G/S- and S-DHPs, and was better than that of G-DHP reported previously. These results indicate that hardwood lignin containing both G and S units is more suitable than softwood lignin containing only G units for functionalization through demethylation into a tannin-like polymer, which has applications as a natural oxidant, metal adsorbent, and protein adsorbent.
Evaluation of vicinity-based hidden Markov models for genotype imputation
Authors: Wang Su , Kim Miran , Jiang Xiaoqian , Harmanci Arif Ozgun 
Published: August 2022

AbstractBackgroundThe decreasing cost of DNA sequencing has led to a great increase in our knowledge about genetic variation. While population-scale projects bring important insight into genotype–phenotype relationships, the cost of performing whole-genome sequencing on large samples is still prohibitive. In-silico genotype imputation coupled with genotyping-by-arrays is a cost-effective and accurate alternative for genotyping of common and uncommon variants. Imputation methods compare the genotypes of the typed variants with the large population-specific reference panels and estimate the genotypes of untyped variants by making use of the linkage disequilibrium patterns. Most accurate imputation methods are based on the Li–Stephens hidden Markov model, HMM, that treats the sequence of each chromosome as a mosaic of the haplotypes from the reference panel.ResultsHere we assess the accuracy of vicinity-based HMMs, where each untyped variant is imputed using the typed variants in a small window around itself (as small as 1 centimorgan). Locality-based imputation is used recently by machine learning-based genotype imputation approaches. We assess how the parameters of the vicinity-based HMMs impact the imputation accuracy in a comprehensive set of benchmarks and show that vicinity-based HMMs can accurately impute common and uncommon variants.ConclusionsOur results indicate that locality-based imputation models can be effectively used for genotype imputation. The parameter settings that we identified can be used in future methods and vicinity-based HMMs can be used for re-structuring and parallelizing new imputation methods. The source code for the vicinity-based HMM implementations is publicly available athttps://github.com/harmancilab/LoHaMMer.
Proteome-wide analysis of lysine 2-hydroxyisobutyrylation in Frankliniella occidentalis
Authors: Ding Chengying , Song Liyun , Li Ying , Shen Lili , Liu Dongyang , Wang Fenglong , Lin Zhonglong , Yang Jinguang 
Published: August 2022

Abstract
Background
Lysine 2-hydroxyisobutyrylation (Khib) is a novel and conserved post-translational modification (PTM). Frankliniella occidentalis are economically important agricultural pests globally and also notorious for vectoring destructive plant viruses. To better study the disease transmission mechanism of F. occidentalis, it is necessary to conduct in-depth analysis of it. So far, no Khib modification of insects has been reported.

Results
In this study, a proteome-wide analysis of Khib modifications in F. occidentalis was analyzed for the first time through the combination of high performance liquid chromatography fractionation technology and 2-hydroxyisobutyrylated peptide enrichment and other advanced technologies, 4093 Khib sites were identified on 1125 modified proteins. Bioinformatics and functional enrichment analyses showed that Khib-modified proteins were significantly enriched in many cell compartments and pathways, especially related to various cellular components and biological processes, and were more concentrated in ribosomes and proteasome subunits, involved in energy metabolism, protein synthesis and degradation, compared to the other nine species including Japonica rice, Homo sapiens, P. patens, Botrytis, Ustilaginoidea virens, Saccharomyces cerevisiae, T. gondii, C. albicans, and F. oxysporum. And Khib sites on virus-interacting insect proteins were discovered for the first time, such as cyclophilin and endoCP-GN.

Conclusions
After three repeated experiments, we found a total of 4093 Khib sites on 1125 proteins. These modified proteins are mainly concentrated in ribosomes and proteasome subunits, and are widely involved in a variety of critical biological activities and metabolic processes of F. occidentalis. In addition, for the first time, Khib modification sites are found on the proteome of F. occidentalis, and these sites could be acted as for the virus interaction, including cyclophilin and endoCP-GN. The global map of 2-hydroxyisobutyrylation in thrips is an invaluable resource to better understand the biological processes of thrips and provide new means for disease control and mitigation of pest damage to crops.
Reference values of gait characteristics in community-dwelling older persons with different physical functional levels
Authors: Dapp Ulrike , Vinyard Dominic , Golgert Stefan , Krumpoch Sebastian , Freiberger Ellen 
Published: August 2022

Abstract
Background
Mobility is one major component of healthy ageing of older persons. It includes gait speed, nowadays valued as the sixth vital sign of ageing. Quantitative gait analysis can support clinical diagnostics, monitor progression of diseases and provide information about the efficacy of interventions. Fast gait speed is an additional marker in the area of functional ability. Our aim was to contribute reference values of gait parameters of older persons based on their functional ability.

Methods
We visualised and combined three different established frameworks that assess gait characteristics into a new framework based approach that comprises eight gait parameters: gait speed, stride length, walk ratio, single and double support time, step width, step width CV (coefficient of variance), stride length CV. Gait parameters were stratified by two instruments that indicate levels of functional ability: First, the LUCAS Functional Ability Index (FAI), a self-administered screening tool easy to apply to a public-health orientated approach and second the Short Physical Performance Battery (SPPB), an established performance test widely used in comprehensive geriatric assessments (CGA). Gait parameters of older community-dwelling persons were measured with an objective Gait system (GAITRite) across differing functional ability ranging from robust to transient (postrobust and prefrail) to frail physical status.

Results
Of 642 community-dwelling participants (age 78.5 ± 4.8; n = 233 male, n = 409 female) categorisations by SPPB were 27.1% for robust (11–12 points), 44.2% for transient (8–10 points), 28.7% for frail (0–7 points), and 16.2, 50.3, 33.5% for robust, transient, frail by LUCAS FAI. Overall, our results showed that distinction by functional level only uncovers a wide spectrum of functional decline for all investigated gait parameters. Stratification by functional ability (biological age) revealed a greater range of differentiation than chronological age.

Conclusions
Gait parameters, carefully selected by literature, showed clinically meaningful differences between the functional featuring a gradient declining from robust over transient to frail in most gait parameters. We found discriminative power of stratifications by SPPB to be the highest, closely followed by LUCAS FAI, age groups and dichotomous age making the application of the LUCAS FAI more cost and time effective than conducting SPPB.
Development and psychometric properties of the hospitalized elder abuse questionnaire (HEAQ): a mixed methods study
Authors: Naderi Zeinab , Gholamzadeh Sakineh , Ebadi Abbas , Zarshenas Ladan 
Published: August 2022

Abstract
Background
Older patients are more vulnerable and prone to abuse and neglect in hospitals and acute care settings. The present study aimed to develop and assess the psychometric properties of a questionnaire for screening abuse in hospitalized older adults.

Methods
This study was conducted from October 2017 to September 2019 using the exploratory sequential mixed-methods research design. The participants were selected among those admitted to various wards of six teaching hospitals affiliated with Shiraz University of Medical Sciences, Shiraz, Iran. In the qualitative phase of the study, using the inductive content analysis method, the concept of abuse in hospitalized older adults was extracted through individual in-depth semi-structured interviews with 16 older patients and 11 family caregivers. Based on qualitative findings and a review of existing literature, an initial version of the questionnaire was developed. In the quantitative phase of the study, the psychometric properties (face, content, construct, and convergent validity; internal consistency and stability) of the questionnaire were examined.

Results
Based on qualitative findings and literature review, a pool of 154 candidate items was defined. These items were reduced to 37 after initial refinement, qualitative and quantitative face and content validity, and item analysis. The outcome of principal component analysis further reduced the number of items to 27, which were grouped into 5 components, namely “Shortcomings in management and care facility”, “Neglect of professional commitments”, “Physical and psychological abuse”, “Protracted treatment process”, and “Invasion of privacy”. The explained variance of these 5 components was 50.09% of the overall variability of the questionnaire. The convergent validity of the questionnaire was acceptable (P < 0.00, r = − 0.44). Cronbach’s alpha coefficient and intraclass correlation coefficient for the entire questionnaire were 0.89 and 0.92, respectively; indicating high reliability and stability of the questionnaire.

Conclusion
The hospitalized elder abuse questionnaire (HEAQ) has acceptable psychometric properties. It is recommended to use HEAQ to screen for suspected cases of abuse of hospitalized older adults.
Increased transmissibility of SARS-CoV-2 alpha variant (B.1.1.7) in children: three large primary school outbreaks revealed by whole genome sequencing in the Netherlands
Authors: Gorgels Koen M. F. , van Alphen Lieke B. , van der Veer Brian M. J. W. , Hackert Volker H. , Hensels Audrey Y. J. , Heijer Casper D. J. den , Dingemans Jozef , Savelkoul Paul H. M. , Hoebe Christian J. P. A. 
Published: August 2022

Abstract
Background
Variant of concern (VOC) SARS-CoV-2 alpha variant (B.1.1.7) was the dominant strain in the Netherlands between March 2021–June 2021. We describe three primary school outbreaks due to the alpha variant using whole genome sequencing with evidence of large-scale transmission among children, teachers and their household contacts.

Method
All outbreaks described were investigated by the South Limburg Public Health Service, the Netherlands. A case was defined as an individual with a real-time polymerase chain reaction test or antigen test positive for SARS-CoV-2. Whole genome sequencing was performed on random samples from at least one child and one teacher of each affected class.

Results
Peak attack rates in classes were 53%, 33% and 39%, respectively. Specific genotypes were identified for each school across a majority of affected classes. Attack rates were high among staff members, likely to promote staff-to-children transmission. Cases in some classes were limited to children, indicating child-to-child transmission. At 39%, the secondary attack rate (SAR) in household contacts of infected children was remarkably high, similar to SAR in household contacts of staff members (42%). SAR of household contacts of asymptomatic children was only 9%.

Conclusion
Our findings suggest increased transmissibility of the alpha variant in children compared to preceding non-VOC variants, consistent with a substantial rise in the incidence of cases observed in primary schools and children aged 5–12 since the alpha variant became dominant in March 2021. Lack of mandatory masking, insufficient ventilation and lack of physical distancing also probably contributed to the school outbreaks. The rise of the delta variant (B.1.617.2) since July 2021 which is estimated to be 55% more transmissible than the alpha variant, provides additional urgency to adequate infection prevention in school settings.
Effectiveness and safety of bedaquiline-containing regimens for treatment on patients with refractory RR/MDR/XDR-tuberculosis: a retrospective cohort study in East China
Authors: Zhang Shao-Jun , Yang Yan , Sun Wen-Wen , Zhang Zhong-Shun , Xiao He-Ping , Li Yu-Ping , Zhang Zhe-Min , Fan Lin 
Published: August 2022

AbstractObjectiveRefractory rifampicin-resistant/multidrug resistant/extensively-drug resistant tuberculosis (RR/MDR/XDR-TB) were defined as patients infected withMycobacterium tuberculosis(MTB) resistant to rifampicin(RR-TB), or at least resistant to rifampicin and isoniazid (MDR-TB) or added resistant to fluoroquinolones (FQs) and one of second line injectable agents (XDR-TB), a patient for whom an effective regimen (fewer than 4 effective agents due to adverse events (AEs) or multiple drug resistances) cannot be developed. To compare the effectiveness and safety of bedaquiline (BDQ)-containing and BDQ-free regimens for treatment of patients with refractory RR/MDR/XDR-TB.MethodsPatients with refractory RR/MDR/XDR-TB receiving BDQ-containing regimens (BDQ group, n = 102) and BDQ-free regimens (non-BDQ group, n = 100) satisfied with included criteria were strictly included in this retrospective historical control study across East China. Culture conversion, treatment outcome, cavity closing rate, and AEs were compared between two groups.ResultsThe baseline characteristics involved all possible aspects of patients were well balanced between two groups (p > 0.05). Culture conversion rates in the BDQ group at month 3 (89.2% vs. 66.0%), month 6 (90.2% vs 72.0%), month 9 (91.2% vs. 66.0%), and month 12 (94.1% vs 65.0%) were all significantly higher than those in non-BDQ group (p < 0.001). Similar results were observed in the cavity closing rate at month 9 (19.6% vs 8.0%,p = 0.0) and month 12 (39.2% vs 15.0%,p < 0.001). Patients receiving BDQ-containing regimens had more treatment success than those receiving BDQ-free regimens (p < 0.001; cure rate, 69.6% vs. 45.0%; complete the treatment, 22.5% vs. 18.0%; treatment success, 92.2% vs. 63.0%); the use of BDQ and combined with Linezolid or Clofazimine or Cycloserine were identified as independent predictors of treatment success and no culture reversion (P < 0.05). AEs were similarly reported in 26.5% of patients in the BDQ group and 19.0% in the non-BDQ group (p = 0.2).ConclusionsBDQ-containing regimens resulted in better treatment outcomes and similar safety relative to BDQ-free regimens for patients with refractory pulmonary RR/MDR/XDR-TB.
The Lebanese Regie state-owned tobacco monopoly: lessons to inform monopoly-focused endgame strategies
Authors: Alaouie Hala , Branston J Robert , Bloomfield Michael John 
Published: August 2022

AbstractBackgroundMany countries have started pursuing tobacco ‘endgame’ goals of creating a ‘tobacco-free’ country by a certain date. Researchers have presented models to attain this goal, including shifting the supply of tobacco to a monopoly-oriented endgame model (MOEM), wherein a state-owned entity controls the supply and distribution of tobacco products. Although not designed to end tobacco use, theRegiein Lebanon exhibits some of the key features identified in MOEM and hence can serve as a practical example from which to draw lessons.MethodsWe comprehensively review previous literature exploring tobacco endgame proposals featuring a MOEM. We distil these propositions into core themes shared between them to guide a deductive analysis of the operations and actions of theRegieto investigate how it aligns (or does not) with the features of the MOEM.ResultsAnalysing the endgame proposals featuring MOEM, we generated two main themes: the governance of the organisation; and its operational remit. In line with these themes, the investigation of theRegieled to several reflections on the endgame literature itself, including that it: (i) does not seem to fully appreciate the extent to which the MOEM could end up acting like Transnational Tobacco Companies (TTC); (ii) has only vaguely addressed the implications of political context; and (iii) does not address tobacco growing despite it being an important element of the supply chain.ConclusionThe implementation of tobacco endgame strategies of any type is now closer than ever. Using theRegieas a practical example allows us to effectively revisit both the potential and the pitfalls of endgame strategies aiming to introduce some form of monopoly and requires a focus on: (i) establishing appropriate governance structures for the organisation; and (ii) adjusting the financial incentives to supress any motivation for the organisation to expand its tobacco market.
Socio-economic analysis of short-term trends of COVID-19: modeling and data analytics
Authors: El Jai Mostapha , Zhar Mehdi , Ouazar Driss , Akhrif Iatimad , Saidou Nourddin 
Published: August 2022

AbstractBackgroundCOVID-19 caused a worldwide outbreak leading the majority of human activities to a rough breakdown. Many stakeholders proposed multiple interventions to slow down the disease and number of papers were devoted to the understanding the pandemic, but to a less extend some were oriented socio-economic analysis. In this paper, a socio-economic analysis is proposed to investigate the early-age effect of socio-economic factors on COVID-19 spread.MethodsFifty-two countries were selected for this study. A cascade algorithm was developed to extract the R0 number and the day J*; these latter should decrease as the pandemic flattens. Subsequently, R0 and J* were modeled according to socio-economic factors using multilinear stepwise-regression.ResultsThe findings demonstrated that low values of days before lockdown should flatten the pandemic by reducing J*. Hopefully, DBLD is only parameter to be tuned in the short-term; the other socio-economic parameters cannot easily be handled as they are annually updated. Furthermore, it was highlighted that the elderly is also a major influencing factor especially because it is involved in the interactions terms in R0 model. Simulations proved that the health care system could improve the pandemic damping for low elderly. In contrast, above a given elderly, the reproduction number R0 cannot be reduced even for developed countries (showing high HCI values), meaning that the disease’s severity cannot be smoothed regardless the performance of the corresponding health care system; non-pharmaceutical interventions are then expected to be more efficient than corrective measures.DiscussionThe relationship between the socio-economic factors and the pandemic parameters R0 and J* exhibits complex relations compared to the models that are proposed in the literature. The quadratic regression model proposed here has discriminated the most influencing parameters within the following approximated order, DLBL, HCI, Elderly, Tav, CO2, and WC as first order, interaction, and second order terms.ConclusionsThis modeling allowed the emergence of interaction terms that don’t appear in similar studies; this led to emphasize more complex relationship between the infection spread and the socio-economic factors. Future works will focus on enriching the datasets and the optimization of the controlled parameters to short-term slowdown of similar pandemics.
The extent of violence inflicted on adolescent Aboriginal girls in the Northern Territory
Authors: Moore Susan , Condon John R. , He Vincent YF , Stothers Kylie , Williams Tamika , Guthridge Steven 
Published: August 2022

Abstract
Background
Australian Aboriginal and Torres Strait Islander women are at very high risk of violence but there is little evidence about the age at which their higher exposure to violence commences. The aim of this study was to investigate violence inflicted on Aboriginal girls during childhood and adolescence, relative to Aboriginal boys and non-Aboriginal girls.

Methods
This was a retrospective cohort study using de-identified administrative data for NT residents aged 0-17 years. This study used linked hospital and child protection data to investigate hospitalization for injury caused by assault and substantiated child maltreatment involving violence (physical and sexual abuse).

Results
The incidence of assault hospitalization and substantiated physical/sexual abuse was much higher for Aboriginal than non-Aboriginal adolescents but similar for girls and boys to about age ten, then increased much more for Aboriginal girls than boys. In the 14-17 age-group, assault hospitalization incidence was 125% higher for Aboriginal girls than boys but 56% lower for non-Aboriginal girls than boys. 4.6% of Aboriginal girls were hospitalized (30.9% more than once) for assault between twelfth and eighteenth birthdays, compared to 3.4% of Aboriginal boys and 0.3% of non-Aboriginal girls. The incidence of assault hospitalization during adolescence was over three times higher for Aboriginal children who had substantiated child maltreatment during childhood.

Conclusion
The very high levels of violence suffered by Aboriginal women commence in the pre-teen years. Non-Aboriginal girls are ‘protected’ from the rising levels of violence that boys experience as they progress through adolescence, but Aboriginal girls are not afforded such protection.