bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solent oyster enhancement reef concrete colonisation trials
Authors: Collins K J , Hauton C , Jensen A C , Mallinson J J 
Published: August 2022

Abstract
The Interreg funded project RECIF (2012-2015) developed waste shell concrete formulations specifically for artificial reefs. Its successor MARINEFF continues these evaluating further formulations to maximise both physical performance and endurance with biological attractiveness. Four formulations were produced by ESITC Caen for trials based on combinations of two cement types (CEM II and CEM IV) with either coarse aggregate or crushed oyster shells replacing 20% of the aggregate. The most extensive colonisation trials were carried out with 5x5x2cm blocks by both UK and French partners. These test blocks also had smooth and rough faces. This paper describes the results of Southampton biological colonisation trials. Four blocks, one of each formulation along with an oyster shell cut to the same area were secured in a framework and pairs of these were suspended vertically at 6 fully saline sites around the Solent region (Calshot, Beaulieu River, Hamble River, Itchen River, Portsmouth and Langstone Harbours) from May to August 2019. On recovery these were analysed for Total Biomass, Algae (PAM & %cover), Anemones (n), Ascidians (%cover), Barnacles (n & % cover), Bryozoans (%cover), Hydroids (%cover), Mytilus edulis (n), Pomatoceros sp. (n), Sponges (%), Spirorbis sp (n). There were considerable differences in colonisation between the sites which are described in detail, but overall in terms of overall biomass the formulation using CEM V and 20% oyster shell performed as well as the oyster shell. Given that it is accepted that oysters are attracted to natural shell substrate, this concrete was promising for the choice mix of the final oyster reef modules deployed at Calshot, September 2020.
In-situ mineralized homogeneous collagen-based scaffolds for potential guided bone regeneration
Authors: Li Zhengwei , Du Tianming , Gao Chongjian , Tang Lan , Chen Kinon , Liu Juan , Yang Jirong , Zhao Xiaoli , Niu Xufeng , Ruan Changshun 
Published: August 2022

Abstract
For guided bone regeneration (GBR) in clinical orthopedics, the importance of a suitable scaffold which can provide the space needed for bone regeneration and simultaneously promotes the new bone formation cannot be overemphasized. Due to its excellent biocompatibility, mechanical strength, and similarity in structure and composition to natural bone, the mineralized collagen-based scaffolds have been increasingly considered as promising GBR scaffolds. Herein, we propose a novel method to fabricate an in-situ mineralized homogeneous collagen-based scaffold (IMHCS) with excellent osteogenic capability for GBR by electrospinning the collagen solution in combination with essential mineral ions. The IMHCS exhibited homogeneous distribution of apatite crystals in electrospun fibers, which helped to achieve a significantly higher tensile strength than the pure collagen scaffold (CS) and the scaffold with directly added nano-hydroxyapatite particles (HAS). Furthermore, the IMHCS had significantly better cell compatibility, cell migration ratio, and osteogenic differentiation property than the HAS and CS. Therefore, the IMHCS not only retains traditional function of inhibiting fibroblast invasion, but also possesses excellent osteogenic differentiation property, indicating a robust alternative for GBR applications.
Xeno-free bioengineered human skeletal muscle tissue using human platelet lysate-based hydrogels
Authors: Fernández-Garibay Xiomara , Gómez-Florit Manuel , Domingues Rui M A , Gomes Manuela E , Fernández-Costa Juan M , Ramón-Azcón Javier 
Published: August 2022

Abstract
Bioengineered human skeletal muscle tissues have emerged in the last years as new in vitro systems for disease modeling. These bioartificial muscles are classically fabricated by encapsulating human myogenic precursor cells in a hydrogel scaffold that resembles the extracellular matrix. However, most of these hydrogels are derived from xenogenic sources, and the culture media is supplemented with animal serum, which could interfere in drug testing assays. On the contrary, xeno-free biomaterials and culture conditions in tissue engineering offer increased relevance for developing human disease models. In this work, we used human platelet lysate (PL)-based nanocomposite hydrogels (HUgel) as scaffolds for human skeletal muscle tissue engineering. These hydrogels consist of human PL reinforced with aldehyde-cellulose nanocrystals (a-CNC) that allow tunable mechanical, structural, and biochemical properties for the 3D culture of stem cells. Here, we developed hydrogel casting platforms to encapsulate human muscle satellite stem cells in HUgel. The a-CNC content was modulated to enhance matrix remodeling, uniaxial tension, and self-organization of the cells, resulting in the formation of highly aligned, long myotubes expressing sarcomeric proteins. Moreover, the bioengineered human muscles were subjected to electrical stimulation, and the exerted contractile forces were measured in a non-invasive manner. Overall, our results demonstrated that the bioengineered human skeletal muscles could be built in xeno-free cell culture platforms to assess tissue functionality, which is promising for drug development applications.
Efficient combination and enhancement of high-power mid-infrared pulses in plasmas
Authors: ZHU Xinglong 
Published: August 2022

Abstract
High-power intense optical sources in the mid-to-long wavelength infrared region are very attractive for a wide range of fields from fundamental research to materials science and biology applications. However, there are still significant challenges in extending long-wavelength infrared pulses into the relativistic regime using conventional optical techniques. Here, based upon a new type of plasma-based optical method, we present an efficient scheme capable of combining several high-power long-wavelength infrared laser pulses into one single, more intense pulse, thus bringing the intensity of the output pulse to the relativistic regime. Such intense infrared pulses will open up new possibilities for strong-field physics and ultrafast applications. Furthermore, this is beneficial to understand the underlying physics and nonlinear processes of modulation, propagation and energy transfer of high-power intense laser pulses in plasmas.
Social Genomics of Methamphetamine Use, HIV Viral Load, and Social Adversity
Authors: Li Michael J , Richter Emily I , Okafor Chukwuemeka N , Kalmin Mariah M , Dalvie Shareefa , Takada Sae , Gorbach Pamina M , Shoptaw Steven J , Cole Steven W 
Published: August 2022

Abstract

Background
Social genomics has demonstrated altered inflammatory and type I interferon (IFN) gene expression among people experiencing chronic social adversity. Adverse social experiences such as discrimination and violence are linked to stimulant misuse and HIV, conditions that dysregulate inflammatory and innate antiviral responses, leading to increased HIV viral replication and risk of chronic diseases.

Purpose
We aimed to determine whether methamphetamine (MA) use, unsuppressed HIV viral load (VL) (≥200 c/mL), and experienced intimate partner violence (IPV) (past 12 months) predicted inflammatory and type I IFN gene expression in HIV-positive Black and Latinx men who have sex with men (MSM).

Methods
Participants were 147 HIV-positive Black and Latinx MSM recruited from the mSTUDY, a cohort of 561 MSM aged 18–45 in Los Angeles, CA, of whom half are HIV-positive and substance-using. Transcriptomic measures of inflammatory and type I IFN activity were derived from RNA sequencing of peripheral blood mononuclear cells and matched to urine drug tests, VL, and survey data across two time points 12 months apart. Analysis used linear random intercept modeling of MA use, unsuppressed VL, and experienced IPV on inflammatory and type I IFN expression.

Results
In adjusted models, MA use predicted 27% upregulated inflammatory and 31% upregulated type I IFN expression; unsuppressed VL predicted 84% upregulated type I IFN but not inflammatory expression; and experienced IPV predicted 31% upregulated inflammatory and 26% upregulated type I IFN expression.

Conclusions
In Black and Latinx MSM with HIV, MA use, unsuppressed VL, and experienced IPV predicted upregulated social genomic markers of immune functioning.
Development of Noun Phrase Complexity Across Genres in Children’s Writing
Authors: Durrant Philip , Brenchley Mark 
Published: August 2022

AbstractComplex noun phrases (NP) are central to mature academic writing and often a focus of explicit teaching. The National Curriculum in England, for example, requires specific components of NP complexity to be taught at specific educational stages. However, the evidence base for such practices is unclear. Research on the emergence of NP components is both limited and dated. Moreover, some work has suggested that NP development is late-occurring and genre-specific, calling into question curricular guidance which specifies teaching from the earliest years and which makes no mention of genre. Analysing 240 texts written by children in England aged six to 16, this study shows that overall complexity develops at a roughly constant rate from primary school onwards. Increases are principally driven by postmodification, especially relative clauses and proposition phrases. By the end of their mandatory education, children make some use of genre distinctions evident in adult writing. However, there are also clear patterns of overuse and underuse of particular NP components. Key distinctive features are examined in context to understand the roles NP components play in writing development.
pcnaDeep: a fast and robust single-cell tracking method using deep-learning mediated cell cycle profiling
Authors: Gui Yifan , Xie Shuangshuang , Wang Yanan , Wang Ping , Yao Renzhi , Gao Xukai , Dong Yutian , Wang Gaoang , Chan Kuan Yoow 
Published: August 2022

Abstract

Summary
Computational methods that track single cells and quantify fluorescent biosensors in time-lapse microscopy images have revolutionized our approach in studying the molecular control of cellular decisions. One barrier that limits the adoption of single-cell analysis in biomedical research is the lack of efficient methods to robustly track single cells over cell division events. Here, we developed an application that automatically tracks and assigns mother–daughter relationships of single cells. By incorporating cell cycle information from a well-established fluorescent cell cycle reporter, we associate mitosis relationships enabling high fidelity long-term single-cell tracking. This was achieved by integrating a deep-learning-based fluorescent proliferative cell nuclear antigen signal instance segmentation module with a cell tracking and cell cycle resolving pipeline. The application offers a user-friendly interface and extensible APIs for customized cell cycle analysis and manual correction for various imaging configurations.

Availability and implementation
pcnaDeep is an open-source Python application under the Apache 2.0 licence. The source code, documentation and tutorials are available at https://github.com/chan-labsite/PCNAdeep.

Supplementary information
Supplementary data are available at Bioinformatics online.
Rifapentine With and Without Moxifloxacin for Pulmonary Tuberculosis in People With Human Immunodeficiency Virus (S31/A5349)
Authors: Pettit April C , Phillips Patrick P J , Kurbatova Ekaterina , Vernon Andrew , Nahid Payam , Dawson Rodney , Dooley Kelly E , Sanne Ian , Waja Ziyaad , Mohapi Lerato , Podany Anthony T , Samaneka Wadzanai , Savic Rada M , Johnson John L , Muzanyi Grace , Lalloo Umesh G , Bryant Kia , Sizemore Erin , Scott Nigel , Dorman Susan E , Chaisson Richard E , Swindells Susan ,   for the Tuberculosis Trials Consortium (TBTC) Study 31/AIDS Clinical Trials Group (ACTG) A5349 study team
Published: August 2022

Abstract

Background
Tuberculosis (TB) Trials Consortium Study 31/AIDS Clinical Trials Group A5349, an international randomized open-label phase 3 noninferiority trial showed that a 4-month daily regimen substituting rifapentine for rifampin and moxifloxacin for ethambutol had noninferior efficacy and was safe for the treatment of drug-susceptible pulmonary TB (DS-PTB) compared with the standard 6-month regimen. We explored results among the prespecified subgroup of people with human immunodeficiency virus (HIV) (PWH).

Methods
PWH and CD4+ counts ≥100 cells/μL were eligible if they were receiving or about to initiate efavirenz-based antiretroviral therapy (ART). Primary endpoints of TB disease-free survival 12 months after randomization (efficacy) and ≥ grade 3 adverse events (AEs) on treatment (safety) were compared, using a 6.6% noninferiority margin for efficacy. Randomization was stratified by site, pulmonary cavitation, and HIV status. PWH were enrolled in a staged fashion to support cautious evaluation of drug–drug interactions between rifapentine and efavirenz.

Results
A total of 2516 participants from 13 countries in sub-Saharan Africa, Asia, and the Americas were enrolled. Among 194 (8%) microbiologically eligible PWH, the median CD4+ count was 344 cells/μL (interquartile range: 223–455). The rifapentine-moxifloxacin regimen was noninferior to control (absolute difference in unfavorable outcomes −7.4%; 95% confidence interval [CI] −20.8% to 6.0%); the rifapentine regimen was not noninferior to control (+7.5% [95% CI, −7.3% to +22.4%]). Fewer AEs were reported in rifapentine-based regimens (15%) than the control regimen (21%).

Conclusions
In people with HIV-associated DS-PTB with CD4+ counts ≥100 cells/μL on efavirenz-based ART, the 4-month daily rifapentine-moxifloxacin regimen was noninferior to the 6-month control regimen and was safe.

Clinical Trials Registration
NCT02410772.
Rethinking the Blackstone Ratio with Global Public Opinion: Crime Control and Due Process
Authors: Xiong Moulin 
Published: August 2022

Abstract
Both the Blackstone ratio and due process are cornerstones of classical philosophy in criminal law and justice around the world. However, less consideration has been paid to contemporary society and whether the public shares this theoretical approach. Using data from four waves of the International Social Survey Programme, examining public attitudes towards controlling habitual criminals and suspected terrorists across countries, I offer evidence for how preference towards authorities’ reactions (a proxy of fear of crime) affects preferences about judicial errors. My analysis shows that (i) the public supports the authorities in taking action against criminals and terrorists without a court order, though in different proportions depending on the specific means at hand; (ii) the apparent paradox of public support for the elegance of due process and fear of crime can be explained by the difficult reality of controlling criminals; (iii) absolute proponents consider type one errors to be worse and thus will not support any measures being taken, while absolute proponents consider type two errors to be worse and steps therefore need to be taken to prevent communities from the risk from crime or terrorist attacks; (iv) members of the public who favour proactive policing are significantly less likely to consider type one errors to be worse than type two; and (v) citizens across countries share the above features in a longitudinal survey. Legislators, law professors, and criminologists in transitional risk societies around the world should reconsider their justification of anti-Blackstonian theory and the crime control model.
Regulating the Role of Religion in Society in an Era of Change and Secularist Self-doubt: Why European Courts Have Been Right to Adopt a Hands-Off Approach
Authors: McCrea Ronan 
Published: August 2022

Abstract
Why have the European Court of Human Rights and Court of Justice of the European Union adopted such a hands-off approach in relation to the steady stream of national measures that have intensified limits on religious expression in, and influence over, the public realm? This article argues that the intensifying of these limits can be seen, in part, as reflective of a justified loss of confidence in previously dominant, deterministic narratives that saw secularization of society as inevitable. In response, many states are attempting to harness the power of the law to push a secularization process that they previously regarded as inevitable. The article suggests that, while these laws are sometimes troubling, given the scale, pace and unprecedented nature of the religious change Europe is undergoing, how coexistence and freedom of and from religion can best be preserved cannot but be an open question. It concludes that in these circumstances, judges in pan-European courts have been correct to avoid attempting to identify ideal solutions and to impose them across the board.
Preoperative percutaneous needle indigo carmine and lipiodol mixture marking in lung segmentectomy
Authors: Matsui Takuya , Takahashi Yusuke , Nakada Takeo , Sakakura Noriaki , Hasegawa Takaaki , Sato Yozo , Inaba Yoshitaka , Haneda Hiroshi , Okuda Katsuhiro , Nakanishi Ryoichi , Kuroda Hiroaki 
Published: August 2022

Abstract

OBJECTIVES
For successful nodule localization and appropriate surgical margin distances in pulmonary segmentectomy for patients with lung malignancies, the effectiveness and feasibility of preoperative marking using an indigo carmine and lipiodol mixture remain unclear.

METHODS
Patients who underwent thoracoscopic pulmonary segmentectomy with (marking group, n = 69) and without (non-marking group, n = 265) preoperative marking at our institution from January 2013 to March 2020 were retrospectively reviewed and compared in terms of surgical outcomes. All markings were performed using a fine needle to percutaneously inject an indigo carmine and lipiodol mixture under the guidance of computed tomography fluoroscopy.

RESULTS
Successful localization was achieved in 66 (96%) patients, of whom 62 (94%) underwent dye pigmentation and 4 (6%) underwent intraoperative fluoroscopy. On images, the marking group showed a significantly longer distance between the lung surface and tumour [mm, 9 (1–17) vs 0 (0–10); P &lt; 0.01] and smaller maximum tumour size [mm, 16 (11–21) vs 17 (13–23); P = 0.03] and consolidation tumour ratio [0.4 (0.3–1) vs 0.8 (0.4–1); P &lt; 0.01] than the non-marking group. Both groups had comparable operative outcomes, perioperative complications, pulmonary function changes and surgical margin distances [mm, 20 (15–21) vs 20 (15–20); P = 0.96] without any local recurrence on the surgical margin. Propensity score-matching analysis also showed similar findings for both groups.

CONCLUSIONS
Thoracoscopic pulmonary segmentectomy with preoperative marking using an indigo carmine and lipiodol mixture may be an acceptable therapeutic option for small malignancies located in deep lung parenchyma.
Government finance and imposition of serfdom after the Black Death
Authors: Peters Margaret E 
Published: August 2022

AbstractAfter the Black Death, serfdom disappeared in Western Europe while making a resurgence in Eastern Europe. What explains this difference? I argue that serfdom was against the interests of the sovereign and was only imposed when the nobility, who needed serfdom to maintain their economic and political standing, had leverage to impose their will. The nobility gained this power through financing the state. Using data from the fourteenth through the eighteenth centuries, I show that serfdom was imposed and strengthened in areas where sovereigns had few other resources to finance the state.
Lost individual income due to severe health events: life-course perspective in the Northern Finland Birth Cohort 1966
Authors: Rissanen Ina , Nerg Iiro , Ala-Mursula Leena , Korhonen Marko 
Published: August 2022

Abstract

Background
Severe health events may lead to reduced income among survivors. Importantly, individuals’ risks for both severe health events and for lower income are shaped by early life course. Our aim was to consider early-life factors in determining lost individual income after stroke, heart attack and cancer between ages 18 and 50.

Methods
A population-based Northern Finland Birth Cohort 1966 (N = 12 058) was used. Early-life factors were collected since mid-pregnancy until age 16 years and used to match all persons with stroke, heart attack, or cancer (n = 995) with four controls. Registered annual individual income development 15 years before and after the event was compared between cases and propensity score matched controls using time-to-event mixed models, stratified for sex.

Results
Compared to controls, a new decreasing income trend emerged among women after stroke (logarithmic income per time −0.54; 95% CI −0.88 to −0.20), whereas men getting stroke showed declining earnings already by the time of the event, further declining after stroke (−1.00, −1.37 to −0.63). Getting heart attack was associated with a new declining trend both in women (−0.68; −1.28 to −0.09) and men (−0.69, −1.05 to −0.32). Income declined also among control men (−0.24, −0.34 to −0.14), who had higher income but were less educated than control women.

Conclusions
Stroke and heart attack but not cancer have exogenous deleterious effects on individual economy, independently of early-life factors. The effects accelerate by time. Negative income trend in control men shows that severe health events do not explain all decrease in income.
Limited microbiome differences in captive and semi-wild primate populations consuming similar diets
Authors: Kuthyar Sahana , Watson Karli , Huang Shi , Brent Lauren J N , Platt Michael , Horvath Julie , Gonzalez-Martinez Janis , Martínez Melween , Godoy-Vitorino Filipa , Knight Rob , Dominguez-Bello Maria Gloria , Amato Katherine R 
Published: August 2022

Abstract
Gut microbial communities are shaped by a myriad of extrinsic factors, including diet and the environment. Although distinct human populations consistently exhibit different gut microbiome compositions, variation in diet and environmental factors are almost always coupled, making it difficult to disentangle their relative contributions to shaping the gut microbiota. Data from discrete animal populations with similar diets can help reduce confounds. Here, we assessed the gut microbiota of free-ranging and captive rhesus macaques with at least 80% diet similarity to test the hypothesis that hosts in difference environments will have different gut microbiomes despite a shared diet. Although we found that location was a significant predictor of gut microbial composition, the magnitude of observed differences was relatively small. These patterns suggest that a shared diet may limit the typical influence of environmental microbial exposure on the gut microbiota.