bluuebunny/crossref_metadata_2025_split huggingface dataset:
An iterative convex relaxation method for proton LET optimization
Authors: Li Wangyao , Lin Yuting , Li Harold , Rotondo Ronny , Gao Hao 
Published: February 2023

Abstract

Objective: A constant relative biological effectiveness of 1.1 in current clinical practice of proton radiotherapy (RT) is a crude approximation and may severely underestimate the biological dose from proton RT to normal tissues, especially near the treatment target at the end of Bragg peaks that exhibits high linear energy transfer (LET). LET optimization can account for biological effectiveness of protons during treatment planning, for minimizing biological proton dose and hot spots to normal tissues. However, the LET optimization is usually nonlinear and nonconvex to solve, for which this work will develop an effective optimization method based on iterative convex relaxation (ICR). Approach: In contrast to the generic nonlinear optimization method, such as Quasi-Newton (QN) method, that does not account for specific characteristics of LET optimization, ICR is tailored to LET modeling and optimization in order to effectively and efficiently solve the LET problem. Specifically, nonlinear dose-averaged LET term is iteratively linearized and becomes convex during ICR, while nonconvex dose-volume constraint and minimum-monitor-unit constraint are also handled by ICR, so that the solution for LET optimization is obtained by solving a sequence of convex and linearized convex subproblems. Since the high LET mostly occurs near the target, a 1 cm normal-tissue expansion of clinical target volume (CTV) (excluding CTV), i.e. CTV1cm, is defined to as an auxiliary structure during treatment planning, where LET is minimized. Main results: ICR was validated in comparison with QN for abdomen, lung, and head-and-neck cases. ICR was effective for LET optimization, as ICR substantially reduced the LET and biological dose in CTV1cm the ring, with preserved dose conformality to CTV. Compared to QN, ICR had smaller LET, physical and biological dose in CTV1cm, and higher conformity index values; ICR was also computationally more efficient, which was about 3 times faster than QN. Significance: A LET-specific optimization method based on ICR has been developed for solving proton LET optimization, which has been shown to be more computationally efficient than generic nonlinear optimizer via QN, with better plan quality in terms of LET, biological and physical dose conformality.
Buckling behavior of fiber reinforced Innegra sandwich beams incorporating carbon nanofiber
Authors: Hosseini Rezvan , Tooski Mehdi Yarmohammad , Khorshidvand Ahmad Reza , Khorsandijou Seyed Mehdi 
Published: February 2023

Abstract
This study examined the effect of carbon nanofiber (CNF) on the buckling behavior of sandwich beams under axial compressive load. Three different configurations of sandwich beams consisting of composite skins with different arrangement of layers and polyvinyl chloride (PVC) foam core were considered. Each composite skin is made of four layers reinforced with different materials consisting of Innegra, carbon and Innegra/carbon (hybrid) and epoxy resin modified by CNF. Because of the difference in the thickness of the samples, the specific critical load parameter (the ratio of the critical buckling load to the thickness of the structure) was used to compare the buckling behavior of sandwich beams. The experimental test results indicated that carbon fiber as a stiffening interface in hybrid samples improved the specific critical load compared to Innegra samples. Also, the addition of 0.3 wt%-CNF increases the specific critical load, while the further increase of CNF led to the decrease of the specific critical loads, which is the main cause of weak interfacial stress between CNF and epoxy resin. In addition, the effect of different percentages of CNF and types of fibers on the increase in toughness and damage mechanisms were investigated.
Hybridized GWO-RUN optimized fractional order control for permanent magnet brush-less dc motor
Authors: Kumari Sweety , Kumar Ramesh 
Published: February 2023

Abstract
The permanent magnet brush-less dc motor is a nonlinear, multivariable structure and magnetic coupled system wherein the load disturbances and the parameter uncertainties adversely affect the dynamic performance. From this, it required that the designed controller for the system must deal with the complexities. The objective of this paper is to introduce a novel fractional order proportional-integral controller for permanent magnet brush-less dc motor dealing with set parameter tracking problem. In this paper, in order to find the needed optimal gain parameters combination of metaheuristic and numerical optimization algorithm called Grey Wolf-Runge–Kutta algorithm is proposed. The efficacy of the proposed technique is demonstrated by comparing it with existing optimization technique viz. particle swarm, grey wolf, and Runge–Kutta algorithm. Furthermore, the stability and robustness analysis for the proposed controller is also studied for different operating conditions such as set speed variations, load disturbances and parameter variations. The simulation is performed using MATLAB toolbox. From the simulation results it is evident that FOPI controller optimized with novel hybrid algorithm guarantee the best set speed tracking and also capable to ameliorate the system robustness for parameter variations as well as external load disturbances.
Supplementing recurrent neural networks with annealing to solve combinatorial optimization problems
Authors: Ahsan Khandoker Shoummo , Munshad Abedin Jawaril , Hibat-Allah Mohamed 
Published: February 2023

Abstract
Combinatorial optimization problems can be solved by heuristic algorithms such as simulated annealing (SA) which aims to find the optimal solution within a large search space through thermal fluctuations. This algorithm generates new solutions through Markov-chain Monte Carlo techniques which can result in severe limitations, such as slow convergence and a tendency to stay within the same local search space at small temperatures. To overcome these shortcomings, we use the variational classical annealing (VCA) framework that combines autoregressive recurrent neural networks (RNNs) with traditional annealing to sample solutions that are uncorrelated. In this paper, we demonstrate the potential of using VCA as an approach to solving real-world optimization problems. We explore VCA’s performance in comparison with SA at solving three popular optimization problems: the maximum cut problem (Max-Cut), the nurse scheduling problem (NSP), and the traveling salesman problem (TSP). For all three problems, we find that VCA outperforms SA on average in the asymptotic limit by one or more orders of magnitude in terms of relative error. Interestingly, we reach large system sizes of up to 256 cities for the TSP. We also conclude that in the best case scenario, VCA can serve as a great alternative when SA fails to find the optimal solution.
Instability of solution-processed perovskite films: origin and mitigation strategies
Authors: Wang Shuo , Li Ming-Hua , Jiang Yan , Hu Jin-Song 
Published: February 2023

Abstract
Perovskite solar cells (PSCs) are promising next-generation photovoltaics due to their unique optoelectronic properties and rapid rise in power conversion efficiency. However, the instability of perovskite materials and devices is a serious obstacle hindering technology commercialization. The quality of perovskite films, which is an important prerequisite for long-term stable PSCs, is determined by the quality of the precursor solution and the post-deposition treatment performed after perovskite formation. Herein, we review the origin of instability of solution-processed PSCs from the perspectives of the precursor solutions and the perovskite films. In addition, we summarize the recent strategies for improving the stability of the perovskite films. Finally, we pinpoint possible approaches to further advance their long-term stability.
Evaluation of Workplace Exposures to Volatile Chemicals During COVID-19 Building Disinfection Activities with Proton Transfer Reaction Mass Spectrometry
Authors: Ding Xiaosu , Jiang Jinglin , Tasoglou Antonios , Huber Heinz , Shah Amisha D , Jung Nusrat 
Published: February 2023

Abstract
We conducted an experimental case study to demonstrate the application of proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) for mobile breathing zone (BZ) monitoring of volatile chemical exposures in workplace environments during COVID-19 disinfection activities. The experiments were conducted in an architectural engineering laboratory—the Purdue zero Energy Design Guidance for Engineers (zEDGE) Tiny House, which served as a simulated workplace environment. Controlled disinfection activities were carried out on impermeable high-touch indoor surfaces, including the entry door, kitchen countertop, toilet bowl, bathroom sink, and shower. Worker inhalation exposure to volatile organic compounds (VOCs) was evaluated by attaching the PTR-TOF-MS sampling line to the researcher’s BZ while the disinfection activity was carried out throughout the entire building. The results demonstrate that significant spatiotemporal variations in VOC concentrations can occur in the worker’s BZ during multi-surface disinfection events. Application of high-resolution monitoring techniques, such as PTR-TOF-MS, are needed to advance characterization of worker exposures towards the development of appropriate mitigation strategies for volatile disinfectant chemicals.
Abdominoplasty in the Presence of a Stoma for Functional and Aesthetic Indications
Authors: Firriolo Joseph M , Truong Ashley K , Charvet Heath J 
Published: February 2023

Abstract

Background
Abdominoplasty is widely available; however, patients with abdominal stomas appear to be relatively undertreated. Apprehension to offer abdominoplasty in the presence of a stoma may be secondary to the fear of surgical site infection and stoma compromise.

Objectives
To demonstrate the feasibility and safety of abdominoplasty in the presence of an abdominal stoma for both functional and aesthetic indications and to define perioperative protocols to reduce the risk of surgical site infection in this patient population.

Methods
The authors present 2 patients with stomas who underwent abdominoplasty. Patient 1 was a 62-year-old female with a history of urostomy formation and weight loss. She had a fold of skin overhanging her ostomy site, making it difficult to maintain a seal on her urostomy bag. She underwent fleur-de-lis abdominoplasty and urostomy revision. Patient 2 was a 43-year-old female with a history of end ileostomy formation, who requested cosmetic abdominoplasty to address postpartum abdominal changes; she had no functional stoma-related complaints. Abdominoplasty, flank liposuction, and ileostomy revision were performed.

Results
Both patients were satisfied with their aesthetic and functional outcomes. There were no complications and no instances of stoma compromise. At follow-up, Patient 1 reported a complete amelioration of her urosotomy appliance issues.

Conclusions
Abdominoplasty may confer both functional and aesthetic benefits to patients with abdominal stomas. The authors present peri- and intraoperative protocols, both to prevent stoma compromise and to reduce the risk of surgical site infection. The presence of a stoma does not appear to be an absolute contraindication to cosmetic abdominoplasty.

Level of Evidence: 5
A unified approach to protein domain parsing with inter-residue distance matrix
Authors: Zhu Kun , Su Hong , Peng Zhenling , Yang Jianyi 
Published: February 2023

Abstract

Motivation
It is fundamental to cut multi-domain proteins into individual domains, for precise domain-based structural and functional studies. In the past, sequence-based and structure-based domain parsing was carried out independently with different methodologies. The recent progress in deep learning-based protein structure prediction provides the opportunity to unify sequence-based and structure-based domain parsing.

Results
Based on the inter-residue distance matrix, which can be either derived from the input structure or predicted by trRosettaX, we can decode the domain boundaries under a unified framework. We name the proposed method UniDoc. The principle of UniDoc is based on the well-accepted physical concept of maximizing intra-domain interaction while minimizing inter-domain interaction. Comprehensive tests on five benchmark datasets indicate that UniDoc outperforms other state-of-the-art methods in terms of both accuracy and speed, for both sequence-based and structure-based domain parsing. The major contribution of UniDoc is providing a unified framework for structure-based and sequence-based domain parsing. We hope that UniDoc would be a convenient tool for protein domain analysis.

Availability and implementation
https://yanglab.nankai.edu.cn/UniDoc/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves:Climacteris)
Authors: Edwards Scott V , Tonini João F R , Mcinerney Nancy , Welch Corey , Beerli Peter 
Published: February 2023

AbstractThe Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.
Interrupted versus continuous suture technique for biliary-enteric anastomosis: randomized clinical trial
Authors: Seifert Lena , von Renesse Janusz , Seifert Adrian M , Sturm Dorothée , Meisterfeld Ronny , Rahbari Nuh N , Kahlert Christoph , Distler Marius , Weitz Jürgen , Reissfelder Christoph 
Published: February 2023

Abstract

Background
Biliary-enteric anastomosis (BEA) can be performed using continuous or interrupted suture techniques, but high-quality evidence regarding superiority of either technique is lacking. The aim of this study was to compare the suture techniques for patients undergoing BEA by evaluating the suture time as well as short- and long-term biliary complications.

Methods
In this single-centre randomized clinical trial, patients scheduled for elective open procedure with a BEA between 21 January 2016 and 20 September 2017 were randomly allocated in a 1:1 ratio to have the BEA performed with continuous suture (CSG) or interrupted suture technique (ISG). The primary outcome was the time required to complete the anastomosis. Secondary outcomes were BEA-associated postoperative complications with and without operative revision of the BEA, including bile leakage, cholestasis, and cholangitis, as well as morbidity and mortality up to day 30 after the intervention and survival.

Results
Altogether, 82 patients were randomized of which 80 patients received the allocated intervention (39 in ISG and 41 in CSG). Suture time was longer in the ISG compared with the CSG (median (interquartile range), 22.4 (15.0–28.0) min versus 12.0 (10.0–17.0) min, OR 1.26, 95 per cent c.i. 1.13 to 1.40; unit of increase of 1 min; P &lt; 0.001). Short-term and long-term biliary complications were similar between groups. The incidence of bile leakage (6 (14.6 per cent) versus 4 (10.3 per cent), P = 0.738) was comparable between groups. No anastomotic stenosis occurred in either group.

Conclusion
Continuous suture of BEA is equally safe, but faster compared with interrupted suture.

Registration number
NCT02658643 (http://www.clinicaltrials.gov).
A morphological analysis of Syzygium, with a focus on fibre bundles and description of a new subgenus
Authors: Hatt Sebastian , Low Yee Wen , Burslem David F R P , Middleton David J , Biffin E D , Maurin Olivier , Lucas Eve J 
Published: February 2023

Abstract
Syzygium is a large genus (1200–1500 species) of Old World tropical trees, currently divided into five subgenera containing widely different numbers of species. Syzygium subgenus Perikion was defined by the presence of fibre bundles in the hypanthium wall, although until now this feature has not been investigated or images published. Furthermore, discovery of fibre bundles in certain species outside Syzygium subgenus Perikion calls for reassessment of the subgenus. In this paper, a morphological analysis is presented for all species previously associated with Syzygium subgenus Perikion or known to have fibre bundles. Results indicate the need for description of a new subgenus, Syzygium subgenus Oborapi, characterized by a distinctly goblet-shaped calyx, presence of fibre bundles in the hypanthium/mesocarp, prominent black lenticels on the abaxial leaf surface, ascending ovule orientation and species diversity centred on the Sunda Shelf. Fibre bundles are photographed and documented for the first time from a range of species and at different magnifications. A preliminary list of species is presented for Syzygium subgenus Perikion and Syzygium subgenus Oborapi, with recommendations for further investigation.
Persistence of the immune response after two doses of ChAdOx1 nCov-19 (AZD1222): 1 year of follow-up of two randomized controlled trials
Authors: Voysey Merryn , Flaxman Amy , Aboagye Jeremy , Aley Parvinder K , Belij-Rammerstorfer Sandra , Bibi Sagida , Bittaye Mustapha , Cappuccini Federica , Charlton Sue , Clutterbuck Elizabeth A , Davies Sophie , Dold Christina , Edwards Nick J , Ewer Katie J , Faust Saul N , Folegatti Pedro M , Fowler Jamie , Gilbride Ciaran , Gilbert Sarah C , Godfrey Leila , Hallis Bassam , Humphries Holly E , Jenkin Daniel , Kerridge Simon , Mujadidi Yama F , Plested Emma , Ramasamy Maheshi N , Robinson Hannah , Sanders Helen , Snape Matthew D , Song Rinn , Thomas Kelly M , Ulaszewska Marta , Woods Danielle , Wright Daniel , Pollard Andrew J , Lambe Teresa 
Published: February 2023

AbstractThe trajectory of immune responses following the primary dose series determines the decline in vaccine effectiveness over time. Here we report on maintenance of immune responses during the year following a two-dose schedule of ChAdOx1 nCoV-19/AZD1222, in the absence of infection, and also explore the decay of antibody after infection. Total spike-specific IgG antibody titres were lower with two low doses of ChAdOx1 nCoV-19 vaccines (two low doses) (P = 0.0006) than with 2 standard doses (the approved dose) or low dose followed by standard dose vaccines regimens. Longer intervals between first and second doses resulted in higher antibody titres (P &lt; 0.0001); however, there was no evidence that the trajectory of antibody decay differed by interval or by vaccine dose, and the decay of IgG antibody titres followed a similar trajectory after a third dose of ChAdOx1 nCoV-19. Trends in post-infection samples were similar with an initial rapid decay in responses but good persistence of measurable responses thereafter. Extrapolation of antibody data, following two doses of ChAdOx1 nCov-19, demonstrates a slow rate of antibody decay with modelling, suggesting that antibody titres are well maintained for at least 2 years. These data suggest a persistent immune response after two doses of ChAdOx1 nCov-19 which will likely have a positive impact against serious disease and hospitalization.
Challenges in the Management of and Biologic Use in Incarcerated Patients With Inflammatory Bowel Disease
Authors: Barbina Sarah , Romano John , Forster Erin 
Published: February 2023

AbstractBackgroundTherapy and management of inflammatory bowel disease (IBD) require commitment from both the provider and patient to ensure optimal disease management. Prior studies show vulnerable patient populations with chronic medical conditions and compromised access to health care, such as incarcerated patients, suffer as a result. After an extensive literature review, there are no studies outlining the unique challenges associated with managing prisoners with IBD.MethodsA detailed retrospective chart review of 3 incarcerated patients cared for at a tertiary referral center with an integrated patient-centered IBD medical home (PCMH) and a review of literature was performed.ResultsAll 3 patients were African American males in their 30s with severe disease phenotypes requiring biologic therapy. All patients had challenges with medication adherence and missed appointments related to inconsistent access to clinic. Two of the 3 cases depicted better patient-reported outcomes through frequent engagement with the PCMH.ConclusionsIt is evident there are care gaps and opportunities to optimize care delivery for this vulnerable population. It is important to further study optimal care delivery techniques such as medication selection, though interstate variation in correctional services poses challenges. Efforts can be made to focus on regular and reliable access to medical care, especially for those who are chronically ill.
Automated categorization of virtual reality studies in cardiology based on the device usage: a bibliometric analysis (2010–2022)
Authors: Higaki Akinori , Watanabe Yuta , Akazawa Yusuke , Miyoshi Toru , Kawakami Hiroshi , Seike Fumiyasu , Higashi Haruhiko , Nagai Takayuki , Nishimura Kazuhisa , Inoue Katsuji , Ikeda Shuntaro , Yamaguchi Osamu 
Published: February 2023

AbstractAimsCurrently, virtual reality (VR) constitutes a vital aspect of digital health, necessitating an overview of study trends. We classified type A studies as those in which health care providers utilized VR devices and type B studies as those in which patients employed the devices. This study aimed to analyse the characteristics of each type of studies using natural language processing (NLP) methods.Methods and resultsLiterature related to VR in cardiovascular research was searched in PubMed between 2010 and 2022. The characteristics of studies were analysed based on their classification as type A or type B. Abstracts of the studies were used as corpus for text mining. A binary logistic regression model was trained to automatically categorize the abstracts into the two study types. Classification performance was evaluated by accuracy, precision, recall, F-1 score, and c-statistics of the receiver operator curve (ROC) analysis. In total, 171 articles met the inclusion criteria, where 120 (70.2%) were type A studies and 51 (29.8%) were type B studies. Type A studies had a higher proportion of case reports than type B studies (18.3% vs. 3.9%, P = 0.01). As for abstract classification, the binary logistic regression model yielded 88% accuracy and an area under the ROC of 0.98. The words ‘training’, ‘3d’, and ‘simulation’ were the most powerful determinants of type A studies, while the words ‘patients’, ‘anxiety’, and ‘rehabilitation’ were more indicative for type B studies.ConclusionsNLP methods revealed the characteristics of the two types of VR-related research in cardiology.