bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing islet transplantation using a biocompatible collagen-PDMS bioscaffold enriched with dexamethasone-microplates
Authors: Primavera Rosita , Razavi Mehdi , Kevadiya Bhavesh D , Wang Jing , Vykunta Akshara , Di Mascolo Daniele , Decuzzi Paolo , Thakor Avnesh S 
Published: January 2021

Abstract
Islet transplantation is a promising approach to enable type 1 diabetic patients to attain glycemic control independent of insulin injections. However, up to 60% of islets are lost immediately following transplantation. To improve this outcome, islets can be transplanted within bioscaffolds, however, synthetic bioscaffolds induce an intense inflammatory reaction which can have detrimental effects on islet function and survival. In the present study, we first improved the biocompatibility of polydimethylsiloxane (PDMS) bioscaffolds by coating them with collagen. To reduce the inflammatory response to PDMS bioscaffolds, we then enriched the bioscaffolds with dexamethasone-loaded microplates (DEX-μScaffolds). These DEX-microplates have the ability to release DEX in a sustained manner over 7 weeks within a therapeutic range that does not affect the glucose responsiveness of the islets but which minimizes inflammation in the surrounding microenvironment. The bioscaffold showed excellent mechanical properties that enabled it to resist pore collapse thereby helping to facilitate islet seeding and its handling for implantation, and subsequent engraftment, within the epididymal fat pad (EFP). Following the transplantation of islets into the EFP of diabetic mice using DEX-μScaffolds there was a return in basal blood glucose to normal values by day 4, with normoglycemia maintained for 30 d. Furthermore, these animals demonstrated a normal dynamic response to glucose challenges with histological evidence showing reduced pro-inflammatory cytokines and fibrotic tissue surrounding DEX-μScaffolds at the transplantation site. In contrast, diabetic animals transplanted with either islets alone or islets in bioscaffolds without DEX microplates were not able to regain glycemic control during basal conditions with overall poor islet function. Taken together, our data show that coating PDMS bioscaffolds with collagen, and enriching them with DEX-microplates, significantly prolongs and enhances islet function and survival.
Minimizing 4DCBCT imaging dose and scan time with Respiratory Motion Guided 4DCBCT: a pre-clinical investigation
Authors: Reynolds Tess , Lim Praise , Keall Paul J , O’Brien Ricky 
Published: January 2021

Abstract
Current conventional 4D Cone Beam Computed Tomography (4DCBCT) imaging is hampered by inconsistent patient breathing that leads to long scan times, reduced image quality and high imaging dose. To address these limitations, Respiratory Motion Guided 4D cone beam computed tomography (RMG-4DCBCT) uses mathematical optimization to adapt the gantry rotation speed and projection acquisition rate in real-time in response to changes in the patient’s breathing rate. Here, RMG-4DCBCT is implemented on an Elekta Synergy linear accelerator to determine the minimum achievable imaging dose. 8 patient-measured breathing traces were programmed into a 1D motion stage supporting a 3D-printed anthropomorphic thorax phantom. The respiratory phase and current gantry position were calculated in real-time with the RMG-4DCBCT software, which in turn modulated the gantry rotation speed and suppressed projection acquisition. Specifically, the effect of acquiring 20, 25, 30, 35 and 40 projections/respiratory phase bin RMG scans on scan time and image quality was assessed. Reconstructed image quality was assessed via the contrast-to-noise ratio (CNR) and the Edge Response Width (ERW) metrics. The performance of the system in terms of gantry control accuracy was also assessed via an analysis of the angular separation between adjacent projections. The median CNR increased linearly from 5.90 (20 projections/bin) to 8.39 (40 projections/bin). The ERW did not significantly change from 1.08 mm (20 projections/bin) to 1.07 mm (40 projections/bin), indicating the sharpness is not dependent on the total number of projections acquired. Scan times increased with increasing total projections and slower breathing rates. Across all 40 RMG-4DCBCT scans performed, the average difference in the acquired and desired angular separation between projections was 0.64°. RMG-4DCBCT provides the opportunity to enable fast low-dose 4DCBCT (∼70 s, 200 projections), without compromising on current clinical image quality.
Alcohol Consumption, HDL-Cholesterol and Incidence of Colon and Rectal Cancer: A Prospective Cohort Study Including 250,010 Participants
Authors: Tverdal Aage , Høiseth Gudrun , Magnus Per , Næss Øyvind , Selmer Randi , Knudsen Gun Peggy , Mørland Jørg 
Published: January 2021

Abstract

Aims
Alcohol consumption has been linked to colorectal cancer (CRC) and also to the high-density lipoprotein cholesterol level (HDL-C). HDL-C has been associated with the incidence of CRC. The aim of this study was to investigate the association between self-reported alcohol consumption, HDL-C and incidence of CRC, separately for the two sites.

Methods
Altogether, 250,010 participants in Norwegian surveys have been followed-up for an average of 18 years with respect to a first-time outcome of colon or rectal cancer. During follow-up, 3023 and 1439 colon and rectal cancers were registered.

Results
For men, the HR per 1 drink per day was 1.05 with 95% confidence interval (0.98–1.12) for colon and 1.08 (1.02–1.15) for rectal cancer. The corresponding figures for women were 1.03 (0.97–1.10) and 1.05 (1.00–1.10). There was a positive association between alcohol consumption and HDL-C. HDL-C was inversely associated with colon cancer in men (0.74 (0.62–0.89) per 1 mmol/l) and positively associated with rectal cancer, although not statistically significant (1.15 (0.92–1.44). A robust regression that assigned weights to each observation and exclusion of weights ≤ 0.1 increased the HRs per 1 drink per day and decreased the HR per 1 mmol/l for colon cancer. The associations with rectal cancer remained unchanged.

Conclusion
Our results support a positive association between alcohol consumption and colon and rectal cancer, most pronounced for rectal cancer. Considering the positive relation between alcohol consumption and HDL-C, the inverse association between HDL-C and colon cancer in men remains unsettled.
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
Authors: Huang Shien , He Xinyu , Wang Guohua , Bao Ergude 
Published: January 2021

Abstract
Contigs assembled from the third-generation sequencing long reads are usually more complete than the second-generation short reads. However, the current algorithms still have difficulty in assembling the long reads into the ideal complete and accurate genome, or the theoretical best result [1]. To improve the long read contigs and with more and more fully sequenced genomes available, it could still be possible to use the similar genome-assisted reassembly method [2], which was initially proposed for the short reads making use of a closely related genome (similar genome) to the sequencing genome (target genome). The method aligns the contigs and reads to the similar genome, and then extends and refines the aligned contigs with the aligned reads. Here, we introduce AlignGraph2, a similar genome-assisted reassembly pipeline for the PacBio long reads. The AlignGraph2 pipeline is the second version of AlignGraph algorithm proposed by us but completely redesigned, can be inputted with either error-prone or HiFi long reads, and contains four novel algorithms: similarity-aware alignment algorithm and alignment filtration algorithm for alignment of the long reads and preassembled contigs to the similar genome, and reassembly algorithm and weight-adjusted consensus algorithm for extension and refinement of the preassembled contigs. In our performance tests on both error-prone and HiFi long reads, AlignGraph2 can align 5.7–27.2% more long reads and 7.3–56.0% more bases than some current alignment algorithm and is more efficient or comparable to the others. For contigs assembled with various de novo algorithms and aligned to similar genomes (aligned contigs), AlignGraph2 can extend 8.7–94.7% of them (extendable contigs), and obtain contigs of 7.0–249.6% larger N50 value and 5.2–87.7% smaller number of indels per 100 kbp (extended contigs). With genomes of decreased similarities, AlignGraph2 also has relatively stable performance. The AlignGraph2 software can be downloaded for free from this site: https://github.com/huangs001/AlignGraph2.
Metabolomic differences in blastocoel and uterine fluids collected in vivo by ultrasound biomicroscopy on rabbit embryos†
Authors: Calderari Sophie , Daniel Nathalie , Mourier Eve , Richard Christophe , Dahirel Michele , Lager Franck , Marchiol Carmen , Renault Gilles , Gatien Julie , Nadal-Desbarats Lydie , Chavatte-Palmer Pascale , Duranthon Véronique 
Published: January 2021

AbstractThe success of embryo development and implantation depends in part on the environment in which the embryo evolves. However, the composition of the uterine fluid surrounding the embryo in the peri-implantation period remains poorly studied. In this work, we aimed to develop a new strategy to visualize, collect, and analyze both blastocoelic liquid and juxta-embryonic uterine fluid from in vivo peri-implantation rabbit embryos. Using high-resolution ultrasound biomicroscopy, embryos were observed as fluid-filled anechoic vesicles, some of which were surrounded by a thin layer of uterine fluid. Ultrasound-guided puncture and aspiration of both the blastocoelic fluid contained in the embryo and the uterine fluid in the vicinity of the embryo were performed. Using nuclear magnetic resonance spectroscopy, altogether 24 metabolites were identified and quantified, of which 21 were detected in both fluids with a higher concentration in the uterus compared to the blastocoel. In contrast, pyruvate was detected at a higher concentration in blastocoelic compared to uterine fluid. Two acidic amino acids, glutamate and aspartate, were not detected in uterine fluid in contrast to blastocoelic fluid, suggesting a local regulation of uterine fluid composition. To our knowledge, this is the first report of simultaneous analysis of blastocoelic and uterine fluids collected in vivo at the time of implantation in mammals, shedding new insight for understanding the relationship between the embryo and its local environment at this critical period of development.
Significant decline in the prevalence of Barrett’s esophagus among patients with gastroesophageal reflux disease
Authors: Hamade Nour , Weng Gong , Desai Madhav , Chandrasekar Viveksandeep Thoguluva , Dasari Chandrashekhar , Kennedy Kevin , Sharma Prateek 
Published: January 2021

Summary
Barrett’s esophagus (BE), a premalignant condition for the development of esophageal adenocarcinoma (EAC), is a consequence of chronic gastroesophageal reflux disease (GERD). Although the incidence of EAC is increasing, a similar trend for BE is not clear. We aimed to evaluate the prevalence of newly diagnosed BE over time in a cohort of patients presenting with GERD symptoms.
Information was prospectively collected between 1998 and 2015 for patients presenting to the endoscopy unit at a tertiary referral center for their index upper endoscopy for evaluation of GERD symptoms. Patients were asked to complete a validated GERD questionnaire that documents the onset of GERD symptoms (heartburn and acid regurgitation) and grades the frequency and severity of symptoms experienced. Demographic information, body mass index (BMI), and use of aspirin, nonsteroidal anti-inflammatory drugs, acid suppression therapy if any, smoking, family history, and endoscopic findings: erosive esophagitis, BE, and hiatal hernia were recorded. Patients evaluated during 1998–2003 (control) were compared with those presented in subsequent years (3-year cohorts) using chi-square test, and a multivariable logistic regression model was used to evaluate independent predictors.
A total of 1109 patients were included in the analysis: mean age 56.9 years (standard deviation [SD] 12.8), 83% Caucasian, 93% male, and mean BMI 29.8 (SD 5.5). Overall, 226 (20.3%) patients were diagnosed with BE, with a mean BE length of 2.1 cm (SD 2.6). There was a significant decrease in the prevalence of BE over time from 24.3% in 1998–2003 to 13.5% in 2013–2015 (P = 0.002). During the same time period, a significant increasing trend in proton pump inhibitor (PPI) (41.7%; 1998–2003 vs. 80.2%; 2013–2015) (P &lt; 0.001) and aspirin (ASA) use (23.7%; 1998–2003 vs. 25.9%; 2013–2015) (P = 0.034) was noted. There was also a significant reduction in cigarette smoking. In a multivariable logistic regression model for predicting the presence of newly diagnosed BE, there was a significant effect of timeframe even after adjusting for confounding variables.
The results of our study indicate that there has been a steady and significant decline in the prevalence of BE in GERD patients over the last 2 decades. During this same time period, there has been an accompanying increase in the use of PPI, aspirin therapy, and a reduction in smoking, all modifiable risk factors potentially contributing to the decreasing prevalence of BE. Whether this decreasing prevalence of BE will lead to a reduction in EAC remains to be seen.
Social networks, adoption of improved variety and household welfare: evidence from Ghana
Authors: Abdul Mumin Yazeed , Abdulai Awudu 
Published: January 2021

Abstract
In this study, we examine the effects of own and peer adoption of improved soybean variety on household yields and food and nutrient consumption, using observational data from Ghana. We employ the marginal treatment effect approach to account for treatment effect heterogeneity across households and a number of identification strategies to capture social network effects. Our empirical results show that households with higher unobserved gains are more likely to adopt because of their worse outcomes when not adopting. We also find strong peer adoption effect on own yield, only when the household is also adopting, and on food and nutrient consumption when not adopting. However, the peer adoption effect on consumption attenuates when the household adopts the improved variety. Furthermore, our findings reveal that adoption tends to equalise households in terms of observed and unobserved gains on consumption and can thus serve as a mechanism for promoting food security and nutrition in this area.
Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera)
Authors: Olsen Lindsey K , Heckenhauer Jacqueline , Sproul John S , Dikow Rebecca B , Gonzalez Vanessa L , Kweskin Matthew P , Taylor Adam M , Wilson Seth B , Stewart Russell J , Zhou Xin , Holzenthal Ralph , Pauls Steffen U , Frandsen Paul B 
Published: January 2021

Abstract
Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. Although Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving ∼275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least 3-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages.
Shallow seismic structure beneath the continental China revealed byP-wave polarization, Rayleigh wave ellipticity and receiver function
Authors: Xiao Xiao , Cheng Shihua , Wu Jianping , Wang Weilai , Sun Li , Wang Xiaoxin , Wen Lianxing 
Published: January 2021

SUMMARYWe construct a high-resolution shallow 3-D seismic model in the top 10 km of the upper crust in the continental China, with constraints of P polarization, Rayleigh wave ellipticity and receiver function obtained from records of 3848 seismic stations. Our 3-D seismic model has a spatial resolution of 0.6–1.2° in the north–south seismic belt and the trans-north China orogen, and 1–2° in the rest of the continental China (except the Tarim basin and the southwest Tibet). The seismic model exhibits low velocity anomalies of deposits in major sedimentary basins and high velocity anomalies of crustal bedrocks in young orogenic belts and old tectonic blocks. The inferred sediment thickness maps display thick deposits in major sedimentary basins, some compacted sediments in the intermontane basins in young orogenic belts and little sediments in old tectonic blocks. We also discuss compaction effects of the sediments and implications of tectonic history and geological evolution of the major basins in the continental China based on the inferred seismic models. This study provides an effective mean of seismic imaging through joint inversion of various seismic constraints and establishes a framework of seismic data sharing for future studies in the seismological community in a first step of developing a China Seismological Reference Model.
What is the optimal level of suction on digital chest drainage devices following pulmonary lobectomy?
Authors: Sørensen Marlene Fromm , Holbek Bo Laksáfoss , Petersen René Horsleben , Christensen Thomas Decker 
Published: January 2021

Summary
A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was: what is the optimal level of suction on digital chest drainage devices following pulmonary lobectomy? Altogether 367 papers were found using the reported search, of which 4 randomized controlled trials using digital chest drainage devices represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. The new digital drainage systems enhance early mobilization as recommended in the enhanced recovery after surgery programme. There is, however, no consensus on the optimal level of suction to apply after pulmonary lobectomy. This is especially the case for digital drainage devices. Surgeon preference will likely continue to guide practice, until the evidence gives clear-cut recommendations. According to the current data, a low suction reduces total fluid drainage and perhaps air leak duration compared to higher suction levels in both video-assisted thoracoscopic surgery and open pulmonary lobectomies using digital drainage devices, although the evidence is not overwhelming.
Union Freedoms in the Armed Forces: Still a Taboo?
Authors: Falsone Maurizio 
Published: January 2021

Abstract
This article addresses unionisation in the armed forces, an issue which has recently attracted the attention of the courts, most prominently in Europe. First, the article focuses on the organisational profiles of military structure, discussing the relationships between the exercise of union freedoms and the necessity of preserving the chain of command, the readiness of troops and their political neutrality. It concludes that some recent evolutions in military organisation have contributed to the pressure to unionise the military. Therefore, this article focuses on the legal perspective to clarify the role of international law in this issue. To this end, international treaties and courts’ or authoritative bodies’ interpretations of them are collected, analysed and compared. The article then confirms that several arguments developed in the European judicial context can be reasonably applied outside Europe, in accordance with similar or identical clauses enshrined in all international treaties addressing the issue of military unionisation. International law thus leaves room for interpretations whereby restrictions on military unionisation should not go so far as to ban union freedoms altogether. Finally, this article considers the risks inherent in military unionisation and suggests possible approaches that will facilitate a homogeneous balance between union rights and the general interests at stake.
Measurement and monitoring patient safety in prehospital care: a systematic review
Authors: O’connor Paul , O’malley Roisin , Oglesby Anne-Marie , Lambe Kathryn , Lydon Sinéad 
Published: January 2021

Abstract

Background
Prehospital care is potentially hazardous with the possibility for patients to experience an adverse event. However, as compared to secondary care, little is known about how patient safety is managed in prehospital care settings.

Objectives
The objectives of this systematic review were to identify and classify the methods of measuring and monitoring patient safety that have been used in prehospital care using the five dimensions of the Measuring and Monitoring Safety (MMS) framework and use this classification to identify where there are safety ‘blind spots’ and make recommendations for how these deficits could be addressed.

Methods
Searches were conducted in January 2020, with no limit on publication year, using Medline, PsycInfo, CINAHL, Web of Science and Academic Search. Reference lists of included studies and existing related reviews were also screened. English-language, peer-reviewed studies concerned with measuring and monitoring safety in prehospital care were included. Two researchers independently extracted data from studies and applied a quality appraisal tool (the Quality Assessment Tool for Studies with Diverse Designs).

Results
A total of 5301 studies were screened, with 52 included in the review. A total of 73% (38/52) of the studies assessed past harm, 25% (13/52) the reliability of safety critical processes, 1.9% (1/52) sensitivity to operations, 38.5% (20/52) anticipation and preparedness and 5.8% (3/52) integration and learning. A total of 67 methods for measuring and monitoring safety were used across the included studies. Of these methods, 38.8% (26/67) were surveys, 29.9% (20/67) were patient records reviews, 14.9% (10/67) were incident reporting systems, 11.9% (8/67) were interviews or focus groups and 4.5% (3/67) were checklists.

Conclusions
There is no single method of measuring and monitoring safety in prehospital care. Arguably, most safety monitoring systems have evolved, rather than been designed. This leads to safety blind spots in which information is lacking, as well as to redundancy and duplication of effort. It is suggested that the findings from this systematic review, informed by the MMS framework, can provide a structure for critically thinking about how safety is being measured and monitored in prehospital care. This will support the design of a safety surveillance system that provides a comprehensive understanding of what is being done well, where improvements should be made and whether safety interventions have had the desired effect.