bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of light illumination on the surface structure of two-dimensional Ruddlesden–Popper perovskite in the fabrication process
Authors: Kim Kitae , Park Chanhui , Cha Eunseo , Kang Donghee , Park Jeehong , Cho Sangwan , Yi Yeonjin , Park Soohyung 
Published: March 2023

Abstract
Two-dimensional Ruddlesden–Popper (2DRP) perovskites are promising owing to their excellent environmental stability and competitive efficiency. During the fabrication process, 2DRP perovskites were often unintentionally exposed to light in the laboratory. However, the influence of light illumination on the surface structure of 2DRP during fabrication is unclear. Herein, the photodegradation of 2DRP perovskite (phenethylammonium lead iodide, PEA2PbI4) is comprehensively investigated using x-ray photoelectron spectroscopy, scanning electron microscopy, atomic force microscopy, and photoluminescence spectroscopy. We observed that only high-energy light, including that from a blue laser, air mass 1.5G, and notably, the daily used fluorescent lamp (FL) in the laboratory, significantly degraded PEA2PbI4. However, the red laser and ultraviolet-filtered FL, which had low energies, did not cause photodegradation. From this systematic study, we can explain the discrepancies in the surface morphologies previously studied. For instance, randomly oriented nanorod or rough surface of PEA2PbI4 mostly stems from photodegradation. We observed that photodegradation occurred more strongly when the films were illuminated during annealing than when they were illuminated after all fabrication processes were completed. We suggest that this difference stems from the completeness of the structure and the photodegraded PbI2 passivation effect. Our study provides two key guidelines for the fabrication of PEA2PbI4 films. The daily-use FL in the laboratory must be avoided for high-quality samples, and dark conditions are highly recommended, at least during the annealing process.
Comparative investigation of anisotropic etches for polysilicon nanowire definition in thin film technology
Authors: Hakim M M A 
Published: March 2023

Abstract
We report a low-cost mass manufacturable route for polysilicon nanowire (NW) fabrication through comparative investigations of spacer etch techniques to realize nanowires from amorphous silicon (α-Si) layer. The process uses thin film technology and mature top-down microelectronics (linewidth > 10 μm). Anisotropic deep silicon etch process using the elevated plasma density of high-density low-pressure systems (HDLP) with a simultaneous flow of etchant SF6 and inhibitor C4F8 delivered nanowires with quarter circle shape. The nanowires are also characterised with significant sidewall striations and noticeable aggregation of polymers. HDLP etch system with a sequential flow of etchant SF6 and inhibitor C4F8 delivered a near rectangular nanowire shape. However, the generally good profile is marred with significant sidewall striations and accumulation of polymers at the tip of the etched sidewall. Shallow etch process using low density plasma in a cheap capacitively coupled reactive ion etch (RIE) equipment with a simultaneous flow of etchant SF6 and inhibitor O2 delivered nanowires with ideal rectangular shape. The nanowires have hardly visible sidewall striations and/or polymer. These results indicate that deep silicon HDLP etch processes albeit advanced and costly are not suitable for good quality nanowire definition using spacer etch from a thin film of α-Si layer. Low density plasma process with simultaneous flow of SF6 and O2 gases in relatively cheap RIE system provides high quality nanowires and hence, provides a simple, low cost, wafer scale mass manufacturable route for high quality polysilicon nanowire fabrication.
Realization of mechanical and tribological properties of hybrid banana, sisal, and pineapple fiber epoxy composites using naturally available fillers
Authors: Badyankal Pramod V , Gouda P S Shivakumar , Manjunatha T S , Maruthi Prashanth B H , Shivayogi B H 
Published: March 2023

Abstract
In recent days the use of Natural fiber-reinforced composites in all sorts of consumer goods. A wide variety of technologies necessitate the use of materials with unusual property combinations, such as high strength-to-weight and stiffness ratios. Traditional metal alloys fall short of these quality standards, which has led to a significant increase in the applications of natural fibers. Hence, an effort has been made to investigate the effect of fillers like Coconut shell (CS), Saw dust (SD), Kolam (KP), and Fly ash powder (FA) on the mechanical and wear properties of Epoxy reinforced hybrid Sisal, Banana, and Pineapple fiber composites in this work. The Natural fibers weight percent was taken around 45 wt%, with the same quantity of epoxy blended with 10 wt% Naturally available fillers. The findings revealed that the CS fillers in the composite have a more positive influence on tensile strength and modulus than the composite with other fillers which are used in this study. SEM analysis of tensile-fractured CS specimens also reveals an improved fiber-matrix bonding. Similarly, the CS-filled composite also exhibits better flexural strength, modulus, and Impact strength maximum of up to 18% higher than the BS, SD, KP, and FA-filled Hybrid composites. Further, CS-filled composite has reduced weight loss against wear and friction due to higher lignin content.
Triangular quantum photonic devices with integrated detectors in silicon carbide
Authors: Majety Sridhar , Strohauer Stefan , Saha Pranta , Wietschorke Fabian , Finley Jonathan J , Müller Kai , Radulaski Marina 
Published: March 2023

Abstract
Triangular cross-section silicon carbide (SiC) photonic devices have been studied as an efficient and scalable route for integration of color centers into quantum hardware. In this work, we explore efficient collection and detection of color center emission in a triangular cross-section SiC waveguide by introducing a photonic crystal mirror on its one side and a superconducting nanowire single photon detector (SNSPD) on the other. Our modeled triangular cross-section devices with a randomly positioned emitter have a maximum coupling efficiency of 89% into the desired optical mode and a high coupling efficiency (

>

75%) in more than half of the configurations. For the first time, NbTiN thin films were sputtered on 4H-SiC and the electrical and optical properties of the thin films were measured. We found that the transport properties are similar to the case of NbTiN on SiO2 substrates, while the extinction coefficient is up to 50% higher for 1680 nm wavelength. Finally, we performed finite-difference time-domain simulations of triangular cross-section waveguide integrated with an SNSPD to identify optimal nanowire geometries for efficient detection of light from transverse electric and transverse magnetic polarized modes.
Tumor Microenvironment and Its Clinicopathologic and Prognostic Association in Cutaneous and Noncutaneous Angiosarcomas
Authors: Machado Isidro , Requena Celia , López-Reig Raquel , Fernández-Serra Antonio , Giner Francisco , Cruz Julia , Traves Victor , Lavernia Javier , Claramunt Reyes , Llombart Beatriz , López-Guerrero José Antonio , Llombart-Bosch Antonio 
Published: March 2023

Abstract

Objectives
We explored features of the angiosarcoma (AS) tumor microenvironment to discover subtypes that may respond to immunotherapy.

Methods
Thirty-two ASs were included. Tumors were studied by histology, immunohistochemistry (IHC), and gene expression profile using the HTG EdgeSeq Precision Immuno-Oncology Assay.

Results
Comparing cutaneous and noncutaneous ASs, the second group showed 155 deregulated genes, and unsupervised hierarchical clustering (UHC) delineated two groups: the first mostly cutaneous AS and the second mainly noncutaneous AS. Cutaneous ASs showed a significantly higher proportion of T cells, natural killer cells, and naive B cells. ASs without MYC amplification revealed a higher immunoscore in comparison with ASs with MYC amplification. PD-L1 was significantly overexpressed in ASs without MYC amplification. UHC showed 135 deregulated genes differentially expressed when comparing ASs from the non–head and neck area with patients who had AS in the head and neck area. ASs from the head and neck area showed high immunoscore. PD1/PD-L1 content was significantly more highly expressed in ASs from the head and neck area. IHC and HTG gene expression profiling revealed a significant correlation between PD1, CD8, and CD20 protein expression but not PD-L1.

Conclusions
Our HTG analyses confirmed a high degree of tumor and microenvironment heterogeneity. Cutaneous ASs, ASs without MYC amplification, and ASs located in the head and neck area seem to be the most immunogenic subtypes in our series.
More eyes on the prize: open-source data, software and hardware for advancing plant science through collaboration
Authors: Coleman Guy R Y , Salter William T 
Published: March 2023

Abstract
Automating the analysis of plants using image processing would help remove barriers to phenotyping and large-scale precision agricultural technologies, such as site-specific weed control. The combination of accessible hardware and high-performance deep learning (DL) tools for plant analysis is becoming widely recognised as a path forward for both plant science and applied precision agricultural purposes. Yet, a lack of collaboration in image analysis for plant science, despite the open-source origins of much of the technology, is hindering development. Here, we show how tools developed for specific attributes of phenotyping or weed recognition for precision weed control have substantial overlapping data structure, software/hardware requirements and outputs. An open-source approach to these tools facilitates interdisciplinary collaboration, avoiding unnecessary repetition and allowing research groups in both basic and applied sciences to capitalise on advancements and resolve respective bottlenecks. The approach mimics that of machine learning in its nascence. Three areas of collaboration are identified as critical for improving efficiency, (1) standardized, open-source, annotated dataset development with consistent metadata reporting; (2) establishment of accessible and reliable training and testing platforms for DL algorithms; and (3) sharing of all source code used in the research process. The complexity of imaging plants and cost of annotating image datasets means that collaboration from typically distinct fields will be necessary to capitalize on the benefits of DL for both applied and basic science purposes.
IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data
Authors: Zhang Wei , Ju Jia , Zhou Yong , Xiong Teng , Wang Mengyao , Li Chaohui , Lu Shixin , Lu Zefeng , Lin Liya , Liu Xiao , Li Shuai Cheng 
Published: March 2023

AbstractThe adaptive immune receptor repertoire (AIRR), consisting of T- and B-cell receptors, is the core component of the immune system. The AIRR sequencing is commonly used in cancer immunotherapy and minimal residual disease (MRD) detection of leukemia and lymphoma. The AIRR is captured by primers and sequenced to yield paired-end (PE) reads. The PE reads could be merged into one sequence by the overlapped region between them. However, the wide range of AIRR data raises the difficulty, so a special tool is required. We developed a software package for IMmune PE reads merger of sequencing data, named IMperm. We used the k-mer-and-vote strategy to pin down the overlapped region rapidly. IMperm could handle all types of PE reads, eliminate adapter contamination and successfully merge low-quality and minor/non-overlapping reads. Compared with existing tools, IMperm performed better in both simulated and sequencing data. Notably, IMperm was well suited to processing the data of MRD detection in leukemia and lymphoma and detected 19 novel MRD clones in 14 patients with leukemia from previously published data. Additionally, IMperm can handle PE reads from other sources, and we demonstrated its effectiveness on two genomic and one cell-free deoxyribonucleic acid datasets. IMperm is implemented in the C programming language and consumes little runtime and memory. It is freely available at https://github.com/zhangwei2015/IMperm.
ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides
Authors: Li Zhongshen , Jin Junru , Wang Yu , Long Wentao , Ding Yuanhao , Hu Haiyan , Wei Leyi 
Published: March 2023

AbstractMotivationPlant Small Secreted Peptides (SSPs) play an important role in plant growth, development, and plant–microbe interactions. Therefore, the identification of SSPs is essential for revealing the functional mechanisms. Over the last few decades, machine learning-based methods have been developed, accelerating the discovery of SSPs to some extent. However, existing methods highly depend on handcrafted feature engineering, which easily ignores the latent feature representations and impacts the predictive performance.ResultsHere, we propose ExamPle, a novel deep learning model using Siamese network and multi-view representation for the explainable prediction of the plant SSPs. Benchmarking comparison results show that our ExamPle performs significantly better than existing methods in the prediction of plant SSPs. Also, our model shows excellent feature extraction ability. Importantly, by utilizing in silicomutagenesis experiment, ExamPle can discover sequential characteristics and identify the contribution of each amino acid for the predictions. The key novel principle learned by our model is that the head region of the peptide and some specific sequential patterns are strongly associated with the SSPs’ functions. Thus, ExamPle is expected to be a useful tool for predicting plant SSPs and designing effective plant SSPs.Availability and implementationOur codes and datasets are available at https://github.com/Johnsunnn/ExamPle.
Coverage-preserving sparsification of overlap graphs for long-read assembly
Authors: Jain Chirag 
Published: March 2023

AbstractMotivationRead-overlap-based graph data structures play a central role in computing de novo genome assembly. Most long-read assemblers use Myers’s string graph model to sparsify overlap graphs. Graph sparsification improves assembly contiguity by removing spurious and redundant connections. However, a graph model must be coverage-preserving, i.e. it must ensure that there exist walks in the graph that spell all chromosomes, given sufficient sequencing coverage. This property becomes even more important for diploid genomes, polyploid genomes, and metagenomes where there is a risk of losing haplotype-specific information.ResultsWe develop a novel theoretical framework under which the coverage-preserving properties of a graph model can be analyzed. We first prove that de Bruijn graph and overlap graph models are guaranteed to be coverage-preserving. We next show that the standard string graph model lacks this guarantee. The latter result is consistent with prior work suggesting that removal of contained reads, i.e. the reads that are substrings of other reads, can lead to coverage gaps during string graph construction. Our experiments done using simulated long reads from HG002 human diploid genome show that 50 coverage gaps are introduced on average by ignoring contained reads from nanopore datasets. To remedy this, we propose practical heuristics that are well-supported by our theoretical results and are useful to decide which contained reads should be retained to avoid coverage gaps. Our method retains a small fraction of contained reads (1–2%) and closes majority of the coverage gaps.Availability and implementationSource code is available through GitHub (https://github.com/at-cg/ContainX) and Zenodo with doi: 10.5281/zenodo.7687543.
Quality of life after open versus laparoscopic distal pancreatectomy: long-term results from a randomized clinical trial
Authors: Johansen Karin , Lindhoff Larsson Anna , Lundgren Linda , Gasslander Thomas , Hjalmarsson Claes , Sandström Per , Björnsson Bergthor 
Published: March 2023

Abstract

Background
Pancreatic surgery is rapidly transitioning towards minimally invasive methods. Positive results have been published regarding the safety and efficacy of laparoscopic distal pancreatectomy, but postoperative quality of life after operation remains relatively unexplored. The aim of this study was to assess the long-term quality of life after open versus laparoscopic distal pancreatectomy.

Methods
A long-term analysis of quality-of-life data after laparoscopic and open distal pancreatectomy based on the LAPOP trial (a single-centre, superiority, parallel, open-label, RCT in which patients undergoing distal pancreatectomy were randomized 1 : 1 to either the open or laparoscopic approach). Patients received the quality-of-life questionnaires QLQ-C30 and PAN26 before surgery and at 5–6 weeks, 6 months, 12 months, and 24 months after surgery.

Results
Between September 2015 and February 2019, a total of 60 patients were randomized, and 54 patients (26 in the open group and 28 in the laparoscopic group) were included in the quality-of-life analysis. A significant difference was observed in six domains in the mixed model analysis, with better results among patients who underwent laparoscopic surgery. At the 2-year measurement, a statistically significant difference between groups was seen in three domains, and a clinically relevant difference of 10 or more was seen in 16 domains, with better results among the patients who underwent laparoscopic resection.

Conclusion
Considerable differences were shown in postoperative quality of life after laparoscopic compared with open distal pancreatectomy, with better results among the patients who had undergone laparoscopic resection. Of note, some of these differences persisted up to 2 years after surgery. These results strengthen the ongoing transition from open to minimally invasive pancreatic surgery for distal pancreatectomy. Registration number: ISRCTN26912858 (http://www.controlled-trials.com).
Applying Three Different Horizons to Understand Sibling Experiences When the Brother or Sister Dies for a Drug-related Reason
Authors: Perrin Julie 
Published: March 2023

Abstract
Sibling bereavement is a life-changing event with implications for the individual and family. In a study guided by Gadamer’s philosophical hermeneutics focused on sibling bereavement when the brother or sister dies for a drug-related reason, a critical realisation became apparent; it is possible to understand one person’s story from multiple standpoints. This is directly relevant to social work practice as different viewpoints make it possible to illuminate other aspects of the person’s experience keeping us open to hearing more, reflecting and willing to learn something new. A summary of the literature on the three subject areas is presented, as are the identified gaps that helped refine the research questions. A synopsis of what it means to conduct research underpinned by Gadamer’s philosophy is outlined and then elucidated through application to one participant’s interview. The article serves a dual purpose of presenting information on subject areas relating to drug and alcohol, thanatology and family therapy theory, promoting understanding in these horizons. The primary aim is to focus on one of the participants, Karen, from the larger study to show how different horizons bring different understandings to the fore. The article calls for social workers to expand their horizons of understanding.
Trends in mortality and morbidity in patients with bullous pemphigoid before and after approval of intravenous immunoglobulin in Japan: an interrupted time-series analysis
Authors: Miyachi Hideaki , Konishi Takaaki , Hashimoto Yohei , Matsui Hiroki , Fushimi Kiyohide , Inozume Takashi , Matsue Hiroyuki , Yasunaga Hideo 
Published: March 2023

Abstract

Background
Intravenous immunoglobulin (IVIg) has been reported to be an effective treatment for bullous pemphigoid. However, the impact of IVIg approval on real-world outcomes remains unclear.

Objectives
To investigate the effect of IVIg approval on patients with bullous pemphigoid using a national inpatient database.

Methods
Using the Japanese Diagnosis Procedure Combination database, we identified 14 229 patients admitted to hospital for bullous pemphigoid and treated with systemic corticosteroids between July 2010 and March 2020. We conducted an interrupted time-series analysis to compare in-hospital mortality and morbidity between the patients admitted before and after the approval of reimbursement of IVIg for bullous pemphigoid in the Japanese universal health insurance system in November 2015.

Results
In-hospital mortality was 5.5% before and 4.5% after the approval of IVIg reimbursement. After the IVIg approval, 18% of the patients were treated with IVIg. Based on the interrupted time-series analysis, in-hospital mortality significantly decreased at the time of approval [–1.2%, 95% confidence interval (CI) –2.0 to –0.3, P = 0.009] and a downward trend was observed after the approval (–0.4% annual rate, 95% CI –0.7 to –0.1, P = 0.005). In-hospital morbidity also demonstrated a downward trend after the approval.

Conclusions
IVIg approval is associated with lower in-hospital mortality and morbidity in inpatients with bullous pemphigoid.
Veterans with multiple risk factors for Barrett’s esophagus are infrequently evaluated with upper endoscopy
Authors: Crowe Brooks R , Krigel Anna , Li Tian , Haile Rozina , Al-Ani Firas , Lebwohl Benjamin , Abrams Julian A , Araujo James L 
Published: March 2023

SummaryRecent guidelines recommend screening for patients with chronic gastroesophageal reflux disease who have three or more additional risk factors for Barrett’s esophagus (BE). Failure to screen high-risk individuals represents a missed opportunity in esophageal adenocarcinoma prevention and early detection. We aimed to determine the frequency of upper endoscopy and prevalence of BE and esophageal cancer in a cohort of United States veterans who possessed four or more risk factors for BE. All patients at VA New York Harbor Healthcare System with at least four risk factors for BE between 2012 and 2017 were identified. Procedure records were reviewed for upper endoscopies performed between January 2012 and December 2019. Multivariable logistic regression was used to determine risk factors associated with undergoing endoscopy and factors associated with BE and esophageal cancer. 4505 patients with at least four risk factors for BE were included. 828 patients (18.4%) underwent upper endoscopy, of which 42 (5.1%) were diagnosed with BE and 11 (1.3%) with esophageal cancer (10 adenocarcinoma; 1 squamous cell carcinoma). Among individuals who underwent upper endoscopy, risk factors associated with undergoing endoscopy included obesity (OR, 1.79; 95% CI, 1.41–2.30; P &lt; 0.001) and chronic reflux (OR, 3.86; 95% CI, 3.04–4.90; P &lt; 0.001). There were no individual risk factors associated with BE or BE/esophageal cancer. In this retrospective analysis of patients with 4 or more risk factors for BE, fewer than one-fifth of patients underwent upper endoscopy, supporting the need for efforts aimed at improving BE screening rates.