bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel techniques for in situ estimation of shear-wave velocity and damping ratio through MASW testing – I: a beamforming procedure for extracting Rayleigh-wave phase velocity and phase attenuation
Authors: Aimar Mauro , Foti Sebastiano , Cox Brady R 
Published: February 2024

SUMMARY
A robust, in situ estimate of shear-wave velocity VS and the small-strain damping ratio DS (or equivalently, the quality factor QS) is crucial for the design of buildings and geotechnical systems subjected to vibrations or earthquake ground shaking. A promising technique for simultaneously obtaining both VS and DS relies on the Multichannel Analysis of Surface Waves (MASW) method. MASW can be used to extract the Rayleigh wave phase velocity and phase attenuation data from active-source seismic traces recorded along linear arrays. Then, these data can be inverted to obtain VS and DS profiles. This paper introduces two novel methodologies for extracting the phase velocity and attenuation data. These new approaches are based on an extension of the beamforming technique which can be combined with a modal filter to isolate different Rayleigh propagation modes. Thus, the techniques return reliable phase velocity and attenuation estimates even in the presence of a multimode wavefield, which is typical of complex stratigraphic conditions. The reliability and effectiveness of the proposed approaches are assessed on a suite of synthetic wavefields and on experimental data collected at the Garner Valley Downhole Array and Mirandola sites. The results reveal that, under proper modelling of wavefield conditions, accurate estimates of Rayleigh wave phase velocity and attenuation can be extracted from active-source MASW wavefields over a broad frequency range. Eventually, the estimation of soil mechanical parameters also requires a robust inversion procedure to map the experimental Rayleigh wave parameters into soil models describing VS and DS with depth. The simultaneous inversion of phase velocity and attenuation data is discussed in detail in the companion paper.
TCRosetta: An Integrated Analysis and Annotation Platform for T-cell Receptor Sequences
Authors: Yue Tao , Chen Si-Yi , Shen Wen-Kang , Zhang Zhan-Ye , Cheng Liming , Guo An-Yuan 
Published: February 2024

Abstract
T cells and T-cell receptors (TCRs) are essential components of the adaptive immune system. Characterization of the TCR repertoire offers a promising and highly informative source for understanding the functions of T cells in the immune response and immunotherapy. Although TCR repertoire studies have attracted much attention, there are few online servers available for TCR repertoire analysis, especially for TCR sequence annotation or advanced analyses. Therefore, we developed TCRosetta, a comprehensive online server that integrates analytical methods for TCR repertoire analysis and visualization. TCRosetta combines general feature analysis, large-scale sequence clustering, network construction, peptide–TCR binding prediction, generation probability calculation, and k-mer motif analysis for TCR sequences, making TCR data analysis as simple as possible. The TCRosetta server accepts multiple input data formats and can analyze ∼ 20,000 TCR sequences in less than 3 min. TCRosetta is the most comprehensive web server available for TCR repertoire analysis and is freely available at https://guolab.wchscu.cn/TCRosetta/.
The effect of gradually lifting the two-child policy on demographic changes in China
Authors: Lin Yidie , Zhang Baiyang , Hu Meijing , Yao Qiang , Jiang Min , Zhu Cairong 
Published: February 2024

Abstract
Low-fertility rate has been a common problem in many industrialized countries. To reverse the declining trend of new births, Chinese government gradually lifted its restrictions on the number of births per family, allowing for a household to have no more than two children. Little is known about the additional births or population increase contributed by the gradual relaxation of birth restrictions. To fill this gap, this quasi-experimental design study including data from 124 regions used the synthetic control method and controlled interrupted time series analysis to evaluate the differences in birth rates and rates of natural population increase between China and its synthetic control following implementation of the two-child policy from 2011 to 2020. A total of 123 regions were included in the control pool. Data collected during 1990–2010 were used to identify the synthetic China for each study outcome. The mean rate differences of birth rates and rates of natural increase between China and synthetic China after two-child policy implementation were 1.16 per 1000 population and 1.02 per 1000, respectively. These rate differences were distinguished from variation due to chance (one-sided pseudo-P-values: P for birth rates = 0.047, P for rates of natural increase = 0.020). However, there were statistically significant annual reductions in the pre–post trend of birth rates and rates of natural increase compared with those of controls of &lt;0.340 per 1000 population per year [P = 0.007, 95% CI = (−0.584, −0.096)] and &lt;0.274 per 1000 per year [P = 0.028, 95% CI = (−0.518, −0.031)]. The results suggested that lifting birth restrictions had a short-term effect on the increase in birth rates and rates of natural population increase. However, birth policy with lifting birth restrictions alone may not have sustained impact on population growth in the long run.
Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification
Authors: Tian Xue-Chan , Chen Zhao-Yang , Nie Shuai , Shi Tian-Le , Yan Xue-Mei , Bao Yu-Tao , Li Zhi-Chao , Ma Hai-Yao , Jia Kai-Hua , Zhao Wei , Mao Jian-Feng 
Published: February 2024

Abstract
Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.
Impact of cryoablation on operative outcomes in thoracotomy patients
Authors: Pourak Kian , Kubiak Rachel , Arivoli Kumaran , Lagisetty Kiran , Lynch William , Lin Jules , Chang Andrew , Reddy Rishindra M 
Published: February 2024

Abstract

OBJECTIVES
Cryoablation is increasingly being utilized as an alternative to epidurals for patients undergoing thoracotomies. Current evidence suggests cryoablation may decrease postoperative analgesia utilization, but could increase operative times. We hypothesized that the adoption of intraoperative cryoablation to manage post-thoracotomy pain would result in reduced length of stay and reduced perioperative analgesia compared to routine epidural use.

METHODS
A retrospective analysis was performed from a single, quaternary referral centre, prospective database on patients receiving thoracotomies between January 2020 and March 2022. Patients undergoing transthoracic hiatal hernia repair, lung resection or double-lung transplant were divided between epidural and cryoablation cohorts. Primary outcomes were length of stay, intraoperative procedure time, crossover pain management and oral narcotic usage the day before discharge.

RESULTS
During the study period, 186 patients underwent a transthoracic hiatal hernia repair, lung resection or double-lung transplant with 94 receiving a preoperative epidural and 92 undergoing cryoablation. Subgroup analysis demonstrated no significant differences in demographics, operative length, length of stay or perioperative narcotic use. Notably, over a third of patients in each cryoablation subgroup received a postoperative epidural (45.5% transthoracic hiatal hernia repair, 38.5% lung resection and 45.0% double-lung transplant) for further pain management during their admission.

CONCLUSIONS
Cryoablation use was not associated with an increase in procedure time, a decrease in narcotic use or length of stay. Surprisingly, many cryoablation patients received epidurals in the postoperative period for further pain control. Additional analysis is needed to fully understand the benefits and costs of epidural versus cryoablation strategies.
Effects of sequential vs single pneumococcal vaccination on cardiovascular diseases among older adults: a population-based cohort study
Authors: Tong Xinning , Gao Le , Wong Ian C K , Chan Vivien K Y , Wong Angel Y S , Mak Judith C W , Yuen Jacqueline K Y , Jit Mark , Hung Ivan F N , Yiu Kai Hang , Li Xue 
Published: February 2024

Abstract

Background
Recommendations around the use of 23-valent pneumococcal polysaccharide vaccine (PPSV23) and 13-valent pneumococcal conjugate vaccine (PCV13) seldom focus on potential benefits of vaccine on comorbidities. We aimed to investigate whether sequential vaccination with PCV13 and PPSV23 among older adults would provide protection against cardiovascular diseases (CVD) compared with using a single pneumococcal vaccine.

Methods
We conducted a Hong Kong-wide retrospective cohort study between 2012 and 2020. Adults aged ≥65 years were identified as receiving either a single or sequential dual vaccination and followed up until the earliest CVD occurrence, death or study end. To minimize confounding, we matched each person receiving a single vaccination to a person receiving sequential vaccination according to their propensity scores. We estimated the hazard ratio (HR) of CVD risk using Cox regression and applied structural equation modelling to test whether the effect of sequential dual vaccination on CVD was mediated via the reduction in pneumonia.

Results
After matching, 69 390 people remained in each group and the median (interquartile range) follow-up time was 1.89 (1.55) years. Compared with those receiving a single vaccine, those receiving sequential dual vaccination had a lower risk of CVD [HR (95% CI): 0.75 (0.71, 0.80), P &lt; 0.001]. Post-hoc mediation analysis showed strong evidence that the decreased CVD risk was mediated by the reduction in all-cause pneumonia.

Conclusions
Sequential dual pneumococcal vaccination was associated with lower risk of CVD compared with single-dose PCV13 or PPSV23 in older adults. Such additional CVD benefits should be considered when making decisions about pneumococcal vaccination.
New Window Into Hepatitis B in Africa: Liver Sampling Combined With Single-Cell Omics Enables Deep and Longitudinal Assessment of Intrahepatic Immunity in Zambia
Authors: Musonda Taonga , Wallace Michael S , Patel Hailey , Martin Owen P , Oetheimer Christopher , Mwakamui Simutanyi , Sinkala Edford , Nsokolo Bright , Kanunga Annie , Lauer Georg , Chung Raymond T , Wandeler Gilles , Bhattacharya Debika , Kelly Paul , Alatrakchi Nadia , Vinikoor Michael J 
Published: February 2024

Abstract
In Lusaka, Zambia, we introduced liver fine-needle aspiration biopsy (FNAB) into a research cohort of adults with treatment-naive chronic hepatitis B virus (HBV) infection, with and without human immunodeficiency virus (HIV) coinfection, as well as with acute HBV infection. From 117 enrollment and 47 longitudinal FNABs (at 1-year follow-up), we established participant acceptability and safety. We also demonstrated the quality of the material through single-cell RNA sequencing of selected enrollment FNAs, which revealed a range of immune cells. This approach can drive new insights into HBV immunology, informing cure strategies, and can improve our understanding of HBV natural history in Africa.
Effect of different strategies for excluding duplicate cultures on the correlation between hospital resistance rates and antibiotic consumption
Authors: Reyes Barros Tomás , Gutiérrez Torres Waldo , García Cañete Patricia , Cerda Lorca Jaime 
Published: February 2024

Abstract

Introduction
Studies may underestimate the impact of antibiotics on bacterial resistance when correlating hospital antibiotic use with resistance rates (RRs) that exclude duplicate cultures as duplicates usually include more resistant isolates. Comparing correlations between antibiotic consumption and RRs resulting from different strategies for excluding duplicates could help explore how their exclusion affects such correlations.

Methods
We obtained antibiotics consumption and Pseudomonas aeruginosa susceptibility data from 2017 to 2021 for seven antibiotics and for carbapenems as a group in a university hospital. We calculated RRs using seven different time criteria for excluding duplicates. We assessed the correlations of antibiotic consumption to the same-year and next-year RR rates for the three most distinct rates.

Results
Duplicate cultures represented 53.45% of total cultures. RRs were higher when duplicates were included. We compared RRs resulting from excluding all duplicates, excluding duplicates monthly or admitting one culture per day. All antibiotics except meropenem showed a correlation with same-year RRs, either positive or negative, whereas all antibiotics showed a positive correlation with next-year RRs. For same-year and next-year correlations, the criteria with fewer duplicates (and therefore fewer resistant strains) found more correlations. However, the inclusion of duplicates taken at least 1 month apart found the most correlations. Admitting one culture per day found the fewest correlations.

Conclusions
Excluding duplicates from RRs affects the correlation of antibiotics consumption with RRs in P. aeruginosa. Including at least some duplicate cultures in correlation analyses, such as those taken 1 month apart, should be considered.
Carriage of methicillin-resistant Staphylococcus aureus in children &lt;6 years old: a retrospective follow-up study of the natural course and effectiveness of decolonization treatment
Authors: Helbo Thomas , Boel Jonas Bredtoft , Bartels Mette Damkjær , Ahlström Magnus Glindvad , Holzknecht Barbara Juliane , Eriksen Helle Brander 
Published: February 2024

Abstract

Background
Decolonization treatment of MRSA carriers is recommended in Denmark, except in households with MRSA-positive children &lt;2 years old (wait-and-see approach).

Objectives
To investigate a wait-and-see approach in children 2–5 years old, and the effect of decolonization treatment of MRSA carriage in all children &lt;6 years old.

Patients and methods
In this retrospective follow-up study, we included MRSA carriers &lt;6 years old in the Capital Region of Denmark from 2007 to 2021. Data were collected from laboratory information systems and electronic patient records. We divided children into age groups of &lt;2 years or 2–5 years and decolonization treatment versus no treatment. Treatment was chlorhexidine body washes and nasal mupirocin, sometimes supplemented with systemic antibiotics. Children were followed until becoming MRSA free, or censoring. The probability of becoming MRSA free was investigated with Cox regression (higher HRs indicate faster decolonization).

Results
Of 348 included children, 226 were &lt;2 years old [56/226 (25%) received treatment] and 122 were 2–5 years old [90/122 (74%) received treatment]. Multivariable analyses did not show a larger effect of decolonization treatment versus no treatment in &lt;2-year-olds (HR 0.92, 95% CI 0.52–1.65) or 2–5-year-olds (HR 0.54, 95% CI 0.26–1.12). Without treatment, 2–5-year-olds tended to clear MRSA faster than &lt;2-year-olds (HR 1.81, 95% CI 0.98–3.37).

Conclusions
We did not find a larger effect of decolonization treatment versus no treatment in children &lt;6 years old, and 2–5-year-olds tended to become MRSA free faster than &lt;2-year-olds. These results support a wait-and-see approach for all children &lt;6 years old, but further studies are needed.
Improving phage therapy by evasion of phage resistance mechanisms
Authors: Bleriot Inés , Pacios Olga , Blasco Lucia , Fernández-García Laura , López María , Ortiz-Cartagena Concha , Barrio-Pujante Antonio , García-Contreras Rodolfo , Pirnay Jean-Paul , Wood Thomas K , Tomás María 
Published: February 2024

Abstract
Antibiotic failure is one of the most worrisome threats to global health. Among the new therapeutic efforts that are being explored, the use of bacteriophages (viruses that kill bacteria), also known as ‘phages’, is being extensively studied as a strategy to target bacterial pathogens. However, one of the main drawbacks of phage therapy is the plethora of defence mechanisms that bacteria use to defend themselves against phages. This review aims to summarize the therapeutic approaches that are being evaluated to overcome the bacterial defence systems, including the most innovative therapeutic approaches applied: circumvention of phage receptor mutations; modification of prophages; targeting of CRISPR-Cas systems and the biofilm matrix; engineering of safer and more efficacious phages; and inhibition of the anti-persister strategies used by bacteria.
Neutrality, non-belligerency, and permanent neutrality according to recent practice and doctrinal views
Authors: Ronzitti Natalino 
Published: February 2024

Abstract
The conflict between the Russian Federation and Ukraine has again raised the problem of neutrality in the light of the massive shipment by Western States of military assets to Ukraine and the restrictive measures (sanctions) against the Russian Federation. The resolutions by the UN General Assembly and the qualification of the Russian Federation as an aggressor have induced to consider the relationship between neutrality and the UN Charter. This article examines the problem of neutrality according to recent practice and argues that neutrality is still alive, notwithstanding its transformation from its origin. The notion of non-belligerency is also in conformity with international law. Neutrality is no longer an institution of jus in bello but belongs to jus ad bellum and the principle of equality of belligerents should not be applied, except for those rules that have purely humanitarian nature. Permanent neutrality is still a valid institution as the practice shows. Lastly, this article deals with neutrality and non-international conflicts, concluding that the recognition of belligerency, that is the mechanism allowing the application of neutrality to this category of conflict, is almost obsolete.
A comprehensively prognostic and immunological analysis of PARP11 in pan-cancer
Authors: Wang Shengli , Zhang Mingyue , Li Tao , Chen Xinru , Wu Qinhan , Tian Dan , Granot Zvi , Xu Hongbiao , Hao Jianlei , Zhang Hongru 
Published: February 2024

Abstract
Poly (ADP-ribose) polymerase family member 11 (PARP11) has important immune regulatory functions in viral infection and tumor immune response. Particularly, PARP11 showed protumor activities in multiple preclinical murine models. However, no systematic pan-cancer analysis has been conducted to explore PARP11 function. In this study, we used multiple databases to assess PARP11 expression, which is associated with clinical outcomes, immune checkpoint factors, prognostic significance, genomic characteristics, and immunological aspects. The analysis revealed varying expression levels of PARP11 across different cancer types and a significant correlation between its expression and immune cell infiltration. Insights from the CellMiner database suggest a strong link between PARP11 expression and sensitivity to anticancer drugs, highlighting its potential as a therapeutic target. Moreover, PARP11 expression correlates with patient survival during anti-PD1 and anti-CTLA4 treatments, suggesting that PARP11 would be a predictor of immune checkpoint inhibitor treatment. In summary, PARP11 would be a potential immunoregulatory target and a diagnosis and prognosis marker for certain types of cancers. The detailed mechanisms of PARP11 in tumor immune responses need to be further investigated.
Geriatric assessment and quality of life for 2 years in older patients with head and neck cancer
Authors: Lafont Charlotte , Paillaud Elena , Bertolus Chloe , Baron Melany , Caillet Philippe , Bouvard Eric , Laurent Marie , Salvan Didier , Chaumette Laurence , de Decker Laure , Piot Benoit , Barry Beatrix , Raynaud-Simon Agathe , Sauvaget Elisabeth , Minard Aurélien , Anota Amélie , Panjo Henri , Brugel Lydia , Canouï-Poitrine Florence 
Published: February 2024

Abstract

Due to the location and toxicity of treatments, head and neck cancer (HNC) has a major impact on quality of life (QoL). Objective: to assess the effects of geriatric-assessment (GA)-driven interventions on QoL over 2 years in older adults with HNC.
EGeSOR was a randomized study of HNC patients aged ≥65, receiving a pretreatment GA, a geriatric intervention and follow-up (intervention) or standard of care (control). The primary endpoint was QoL score using the European Organisation for Research and Treatment of Cancer’s (EORTC QLQ-C30) and HNC (QLQ-HN35) QoL questionnaires over 24 months.
In total, 475 patients were included (median age: 75.3; women: 31%; oral cancer: 44%). QoL scores improved over 24 months with various trajectories, without significant differences between the groups. A total of 74% of patients (interventional group) did not receive the complete intervention. Cancer characteristics, functional status, and risk of frailty were associated with change in the Global Health Status QoL score.
There is a need to develop an alternative model of implementation such as patient-centered health-care pathways.

Trial registration
NCT02025062.
Better to Trust in the Lord? Religious Salience, Regime Religiosity, and Interstate Dispute Resolution
Authors: Zellman Ariel , Justwan Florian , Fox Jonathan 
Published: February 2024

Abstract
How do religiously salient issues influence the peaceful resolution of interstate territorial disputes? Conflict scholars tend to represent “religious” disputes as uniquely resistant to compromise owing to their supposed symbolic indivisibility and the ideological inflexibility of the actors who pursue them. Rather, we argue that religious regimes’ preferred forums to advance peaceful resolution depend upon interactions between the breadth of a dispute’s religious salience and a claimant regime’s domestic religious legitimacy. Secular regimes lack both religious legitimacy and political motivation to engage. Thus, their dispute resolution forum preferences are unrelated to religious salience. Highly religious regimes command significant religious legitimacy and are therefore empowered to directly negotiate over broadly salient religious issues. Yet their political dependence upon religious constituencies causes them to strictly avoid legally binding conflict management over narrowly salient religious issues. By contrast, moderately religious regimes lack sufficient religious legitimacy to directly negotiate over both broadly and narrowly salient issues, rendering them particularly dispute-resolution avoidant. We test and generally confirm these propositions, utilizing new data measuring the religious salience of interstate territorial disputes in the post-Cold War era.