bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socio-ecological Risk Mitigation in the Construction of the Sicincin-Padang Toll Road, West Sumatra
Authors: Putri Nora Eka , Helmi  , Noer Melinda , Yossyafra  
Published: November 2022

Abstract
Although infrastructure development aims to improve the welfare of the whole society, it poses adverse environmental effects in practice. One of such developments carried out by the Indonesian government is the trans-Sumatra toll road, which created social and environmental problems, particularly on the Sicincin-Padang toll road in West Sumatra. The affected communities in this province lost their homes, agricultural land and livelihoods to lifestyle changes. One of the villages experienced significant flooding due to large water discharge after clearing the land. Therefore, this research aims to explain the mitigation of socio-ecological risks in developing toll road infrastructure in West Sumatra. This research was carried out using the multi-method approach with qualitative and quantitative data analyzed by CATWOE analysis. The results explained that the construction of toll roads in West Sumatra has social and environmental impacts. Social and ecological risk mitigation is carried out by formulating policies through a soft system methodology (SSM) by involving many parties, especially affected communities, in decision-making.
Creating Green Industries through Circular Economy
Authors: Hadi Sudharto P. 
Published: November 2022

Abstract
The role of industrial sector is very important aligned with a program of economic transformation heading to competitive manufacture. However, industrial activities also cause adverse environmental and social impacts such as air and water pollution, odour, vibration, noise, traffic jam, land subsidence, flood, in turn, deteriorating people’s health. One policy to deal with this problem is by encouraging industries to participate on business performance rating on environmental management called proper. To achieve the environmental excellent, companies must adopt life cycle assessment (LCA) and corporate social innovation. This paper observes the companies adopting LCA and practicing circular economy based on LCA. The type of research is a descriptive analysis. The data collection techniques consist of literature review, informal interview with relevant persons and webinar. The study showed that the companies adopting LCA benefit from reducing emission, energy used, the volume of water consumed and the waste being generated, in turn, reducing the cost of production. The benefit of practicing corporate social innovation includes reduction of waste heading to zero waste, consumer’s loyalty and good relation with community. It is recommended for industries to formulate corporate social innovation at the initial stage of the program through social mapping.
Computational analysis in underexpanded jets simulations
Authors: Martins J R , Barbosa J V , Santos F P , Silva L F L R 
Published: November 2022

Abstract
Flammable gases leaks at high pressures are hazardous, especially the free underexpanded jets. Therefore, understanding their behavior is fundamental to guarantee a safe environment. Due to the difficulty to obtain experimental data from free under expanded jets, related to the great speeds and gradients, computational fluid dynamics (CFD) has become an essential tool. Simulations for free underexpanded jets to identify algorithms that better represent this problem were performed in this work. The analysis involved different algorithms for fluid flow solution and a local time stepping approach using both OpenFOAM and ANSYS Fluent CFD packages. Our study concluded that all algorithms and software studied had a satisfactory result compared to experimental data. However, we observed that Fluent had a considerable advantage because the simulation was faster compared with other solvers in OpenFOAM, for instance.
Preparation, AIE and ESIPT behaviour, controllable solid-state fluorescence and application of Co2+ probe based on α-cyanostilbene
Authors: Chen Meihui , Huang Wenheng , Li Yangping , Chen Yongchun , Ji Dan , Zhu Mingguang 
Published: November 2022

Abstract
A simple α-cyanostilbene-functioned salicylaldehyde-based Schiff-base probe, which exhibited outstanding ‘aggregation-induced emission and excited state intramolecular proton transfer (AIE + ESIPT)’ emission in solution, aggregation and solid states, was synthesized in high yield of 87%. Its solid-states with different morphologies emitted different fluorescence after crystallization in EtOH/H2O (1/2, v/v) mixtures or pure EtOH solvent. Besides, it exhibited an obvious spectro-photometrical fluorescence quenching for highly selective sensing of Co2+ in THF/water system (ƒw = 60%, pH = 7.4), accompanied by an intense green fluorescence turn-off behavior under UV365nm illumination. The binding stochiometry between the ligand and Co2+ was found to be 2:1, and the detection limit (DL) was calculated to be 0.41 × 10−8 M. In addition, it could be applied to detect Co2+ in real water samples and on silica gel testing strip.
rGREAT: an R/bioconductor package for functional enrichment on genomic regions
Authors: Gu Zuguang , Hübschmann Daniel 
Published: November 2022

Abstract

Summary
GREAT (Genomic Regions Enrichment of Annotations Tool) is a widely used tool for functional enrichment on genomic regions. However, as an online tool, it has limitations of outdated annotation data, small numbers of supported organisms and gene set collections, and not being extensible for users. Here, we developed a new R/Bioconductorpackage named rGREAT which implements the GREAT algorithm locally. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

Availability and implementation
The package rGREAT is freely available from the Bioconductor project: https://bioconductor.org/packages/rGREAT/. The development version is available at https://github.com/jokergoo/rGREAT. Gene Ontology gene sets for more than 600 organisms retrieved from Ensembl BioMart are presented in an R package BioMartGOGeneSets which is available at https://github.com/jokergoo/BioMartGOGeneSets.

Supplementary information
Supplementary data are available at Bioinformatics online.
scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data
Authors: Faure Louis , Soldatov Ruslan , Kharchenko Peter V , Adameyko Igor 
Published: November 2022

Abstract

Summary
scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a focus on cell biasing and fate splits at the level of bifurcations. It is meant to be fully integrated into the scanpy ecosystem for seamless analysis of trajectories from single-cell data of various modalities (e.g. RNA and ATAC).

Availability and implementation
scFates is released as open-source software under the BSD 3-Clause ‘New’ License and is available from the Python Package Index at https://pypi.org/project/scFates/. The source code is available on GitHub at https://github.com/LouisFaure/scFates/. Code reproduction and tutorials on published datasets are available on GitHub at https://github.com/LouisFaure/scFates_notebooks.

Supplementary information
Supplementary data are available at Bioinformatics online.
A close-up on the expanding landscape of CD21–/low B cells in humans
Authors: Gjertsson Inger , McGrath Sarah , Grimstad Kristoffer , Jonsson Charlotte A , Camponeschi Alessandro , Thorarinsdottir Katrin , Mårtensson Inga-Lill 
Published: November 2022

SummaryMemory B cells (MBCs) are an essential part of our immunological memory. They respond fast upon re-encountering pathogens and can differentiate into plasma cells that secrete protective antibodies. The focus of this review is on MBCs that lack, or express low levels of, CD21, hereafter referred to as CD21–/low. These cells are expanded in peripheral blood with age and during chronic inflammatory conditions such as viral infections, malaria, common variable immunodeficiency, and autoimmune diseases. CD21–/low MBCs have gained significant attention; they produce disease-specific antibodies/autoantibodies and associate with key disease manifestations in some conditions. These cells can be divided into subsets based on classical B-cell and other markers, e.g. CD11c, FcRL4, and Tbet which, over the years, have become hallmarks to identify these cells. This has resulted in different names including age-associated, autoimmune-associated, atypical, tissue-like, tissue-resident, tissue-restricted, exhausted, or simply CD21–/low B cells. It is however unclear whether the expanded ‘CD21–/low’ cells in one condition are equivalent to those in another, whether they express an identical gene signature and whether they have a similar function. Here, we will discuss these issues with the goal to understand whether the CD21–/low B cells are comparable in different conditions.
Human Immunodeficiency Virus (HIV) Care Continuum Outcomes After Transition to Adult Care Among a Prospective Cohort of Youth With HIV in Atlanta, Georgia
Authors: Hussen Sophia A , Doraivelu Kamini , Goldstein Madeleine H , Shenvi Neeta , Easley Kirk A , Zanoni Brian C , Camacho-González Andrés , del Río Carlos 
Published: November 2022

Abstract

Background
Healthcare transition from pediatric to adult-oriented clinical settings is often viewed as a high-risk time for care disengagement. However, there is a paucity of prospective, longitudinal research documenting human immunodeficiency virus (HIV) care outcomes after healthcare transition.

Methods
We conducted a prospective, observational cohort study of healthcare transition among youth enrolled at an HIV care center in Atlanta, Georgia. Pediatric clinic patients (average age, 24 years) were enrolled up to 3 months before the expected transition and were followed up to determine linkage, retention, and viral suppression in adult care through electronic medical record abstractions at the baseline and at 6, 12, 18, and 24 months.

Results
The majority of our cohort (n = 70) was male (88.6%) and black (92.9%) and acquired HIV horizontally (80%). Most of our cohort was linked to adult care by 12 months (84%) after enrollment. Of those who linked to adult care by 12 months, retention rates were 86% (95% confidence interval, 78%–94%) at 6 months, 76% (66%–86%) at 12 months, and 66% (55%–78%) at 18 and 24 months. Once in adult care, the proportion with viral suppression was stable (73% at baseline and 74%, 77%, 67%, and 78% at 6, 12, 18, and 24 months, respectively).

Conclusions
Although most youth successfully linked to adult care, retention rates decreased over the 24-month follow-up period. Rates of viral suppression were stable for those who remained in care. Strategies to support retention in adult care will be critical to optimizing this transition for youth with HIV.
Endoscopic Recurrence or Anastomotic Wound Healing Phenomenon after Ileocolic Resection for Crohn’s Disease: The Challenges of Accurate Endoscopic Scoring
Authors: van der Does de Willebois Eline M L , Duijvestein Marjolijn , Wasmann Karin A , D’Haens Geert R A M , van der Bilt Jarmila D W , Mundt Marco W , Hompes Roel , van der Vlugt Manon , Buskens Christianne J , Bemelman Willem A 
Published: November 2022

Abstract

Background and Aims
Adequate endoscopic scoring in Crohn’s disease [CD] is crucial, as it dictates the need for initiating postoperative medical therapy and is utilized as an outcome parameter in clinical trials. Here we aimed to observe anastomotic wound healing in relation to endoscopic scoring of both inverted and everted stapled lines in side-to-side anastomoses.

Methods
Two prospective patient cohorts were included: ileocolic resection [ICR] for CD, and right-sided colon resection for colorectal cancer [CRC]. Videos taken during colonoscopy 6 months postoperatively were evaluated. The Simplified Endoscopic Activity Score for Crohn’s Disease and modified Rutgeerts score were determined. The primary outcome was the presence of ulcerations in CD patients on both the inverted and the everted stapled lines. Secondary outcomes were the presence of anastomotic ulcerations in CRC patients and the number of cases having ulcerations exclusively at the inverted stapled line.

Results
Of the 82 patients included in the CD cohort, ulcerations were present in 63/82 [76.8%] at the inverted- vs 1/71 [1.4%] at the everted stapled line. Likewise in the CRC cohort, ulcerations were present in 4/6 [67.7%] at the inverted vs 0/6 [0%] at the everted stapled line. In total, 27% of the 63 patients in the CD cohort had ulcerations exclusively on the inverted stapled line.

Conclusion
Inverted stapled lines heal with ulcerations, whereas everted stapled lines heal without any ulcerations, in both CD and non-CD patients. The abnormalities at the inverted stapled line might interfere with endoscopic scoring of recurrence, with potentially an impact on patients’ quality of life and on healthcare costs if postoperative treatment is initiated incorrectly.
Long-term outcomes of mini-sternotomy versus conventional sternotomy for aortic valve replacement: a randomized controlled trial
Authors: Telyuk Pyotr , Hancock Helen , Maier Rebecca , Batty Jonathan A , Goodwin Andrew , Owens W Andrew , Ogundimu Emmanuel , Akowuah Enoch 
Published: November 2022

Abstract

OBJECTIVES
Aortic valve replacement (AVR) for severe symptomatic aortic stenosis is one of the most common cardiac surgical procedures with excellent long-term outcomes. Multiple previous studies have compared short-term outcomes of AVR with mini-sternotomy versus AVR with conventional sternotomy. We have previously reported the results of the randomized MAVRIC trial, which aimed to evaluate early postoperative morbidity among patients undergoing mini-sternotomy and conventional sternotomy AVR. We now report the long-term all-cause mortality, reoperation, MACE outcomes and echocardiographic data from this trial.

METHODS
The prospective, randomized, single-centre, single-blind MAVRIC (manubrium-limited mini-sternotomy versus conventional sternotomy for aortic valve replacement) trial compared manubrium-limited mini-sternotomy and conventional median sternotomy for the treatment of patients with severe aortic stenosis. The previously reported primary outcome was the proportion of patients receiving red cell transfusion postoperatively and within 7 days of the index procedure. Currently reported exploratory analyses of a combined long-term all-cause mortality and reoperation were compared between groups via the log-rank test. Sensitivity analyses reviewed individual components of the combined end point. The primary analysis and long-term exploratory analyses were based on an intention-to-treat principle.

RESULTS
Between March 2014 and June 2016, 270 patients were enrolled and randomized in a 1:1 fashion to undergo mini-sternotomy AVR (n = 135) or conventional median sternotomy AVR (n = 135). At the median follow-up of 6.1 years, the composite outcome of all-cause mortality and reoperation occurred in 18.5% (25/135) of patients in the conventional sternotomy group and in 17% (23/135) of patients in the mini-sternotomy group. The incidence of chronic kidney disease, cerebrovascular accident and myocardial infarction was not significantly different between 2 groups. Follow-up echocardiographic data suggested no difference in peak and mean gradients or incidence of aortic regurgitation between 2 approaches.

CONCLUSIONS
This exploratory long-term analysis demonstrated that, in patients with severe aortic stenosis undergoing isolated AVR, there was no significant difference between manubrium-limited mini-sternotomy and conventional sternotomy with respect to all-cause mortality, rate of reoperation, MACE events and echocardiographic data at the median of 6.1-year follow-up.
Bone morphogenetic protein 10: a novel risk marker of ischaemic stroke in patients with atrial fibrillation
Authors: Hijazi Ziad , Benz Alexander P , Lindbäck Johan , Alexander John H , Connolly Stuart J , Eikelboom John W , Granger Christopher B , Kastner Peter , Lopes Renato D , Ziegler André , Oldgren Jonas , Siegbahn Agneta , Wallentin Lars 
Published: November 2022

Abstract

Aims
Biomarkers specifically related to atrial tissue may increase the understanding of the pathophysiology of atrial fibrillation (AF) and further improve risk prediction in this setting. Bone morphogenetic protein 10 (BMP10) is a protein expressed in the atrial myocardium. We evaluated the association between BMP10 and the risk of ischaemic stroke and other cardiovascular events in large cohorts of patients with AF, treated with and without oral anticoagulation (OAC).

Methods and results
BMP10 was measured in plasma samples collected at randomisation in patients with AF without OAC in the ACTIVE A and AVERROES trials (n = 2974), and with OAC in the ARISTOTLE trial (n = 13 079). BMP10 was analysed with a prototype Elecsys immunoassay. Associations with outcomes were evaluated by Cox-regression models adjusted for clinical characteristics, kidney function, and N-terminal pro-B-type natriuretic peptide (NT-proBNP). Median concentrations of BMP10 were 2.47 and 2.44 ng/mL, in the non-OAC and OAC cohort, respectively. Increasing BMP10 was associated with lower body mass index, older age, female sex, kidney dysfunction, and AF rhythm. BMP10 was consistently associated with ischaemic stroke. In the non-OAC cohort, BMP10 increased the concordance index of the multivariable model from 0.713 to 0.733 (P = 0.004) and in the OAC cohort from 0.673 to 0.694 (P &lt; 0.001). Additionally, BMP10 maintained a significant prognostic value after additionally adjusting for NT-proBNP. BMP10 was not independently associated with bleeding or with death.

Conclusion
The novel atrial biomarker BMP10 was independently associated with ischaemic stroke in patients with AF irrespective of OAC treatment. BMP10 seems to be more specifically related to the risk of ischaemic stroke in AF.

One-sentence Summary
In this study, BMP10 may be a novel specific biomarker of ischaemic stroke in patients with atrial fibrillation, irrespective of oral anticoagulation.
Different calcification patterns of tricuspid and bicuspid aortic valves and their clinical impact
Authors: Gollmann-Tepeköylü Can , Nägele Felix , Engler Clemens , Stoessel Leon , Zellmer Berit , Graber Michael , Hirsch Jakob , Pölzl Leo , Ruttmann Elfriede , Tancevski Ivan , Tiller Christina , Barbieri Fabian , Stastny Lukas , Reinstadler Sebastian J , Oezpeker Ulvi Cenk , Semsroth Severin , Bonaros Nikolaos , Grimm Michael , Feuchtner Gudrun , Holfeld Johannes 
Published: November 2022

Abstract

OBJECTIVES
Mechanical strain plays a major role in the development of aortic calcification. We hypothesized that (i) valvular calcifications are most pronounced at the localizations subjected to the highest mechanical strain and (ii) calcification patterns are different in patients with bicuspid and tricuspid aortic valves.

METHODS
Multislice computed tomography scans of 101 patients with severe aortic stenosis were analysed using a 3-dimensional post-processing software to quantify calcification of tricuspid aortic valves (n = 51) and bicuspid aortic valves (n = 50) after matching.

RESULTS
Bicuspid aortic valves exhibited higher calcification volumes and increased calcification of the non-coronary cusp with significantly higher calcification of the free leaflet edge. The non-coronary cusp showed the highest calcium load compared to the other leaflets. Patients with annular calcification above the median had an impaired survival compared to patients with low annular calcification, whereas patients with calcification of the free leaflet edge above the median did not (P = 0.53).

CONCLUSIONS
Calcification patterns are different in patients with aortic stenosis with bicuspid and tricuspid aortic valves. Patients with high annular calcification might have an impaired prognosis.
On Fourier Coefficients and Hecke Eigenvalues of Siegel Cusp Forms of Degree 2
Authors: Paul Biplab , Saha Abhishek 
Published: November 2022

Abstract
We investigate some key analytic properties of Fourier coefficients and Hecke eigenvalues attached to scalar-valued Siegel cusp forms $F$ of degree 2, weight $k,$ and level $N$. First, assuming that $F$ is a Hecke eigenform that is not of Saito–Kurokawa type, we prove an improved bound in the $k$-aspect for the smallest prime at which its Hecke eigenvalue is negative. Secondly, we show that there are infinitely many sign changes among the Hecke eigenvalues of $F$ at primes lying in an arithmetic progression. Third, we show that there are infinitely many positive as well as infinitely many negative Fourier coefficients in any “radial” sequence comprising of prime multiples of a fixed fundamental matrix. Finally, we consider the case when $F$ is of Saito–Kurokawa type, and in this case we prove the (essentially sharp) bound $| a(T) | ~\ll _{F, \epsilon }~ \big ( \det T \big )^{\frac {k-1}{2}+\epsilon }$ for the Fourier coefficients of $F$ whenever $\gcd (4 \det (T), N)$ is squarefree, confirming a conjecture made (in the case $N=1$) by Das and Kohnen.
Wave Function for GL(n,ℝ) Hyperbolic Sutherland Model II. Dual Hamiltonians
Authors: Kharchev S , Khoroshkin S 
Published: November 2022

Abstract
Recently, we found Mellin–Barnes integrals, representing the wave function for $GL(n,{\mathbb {R}})$ hyperbolic Sutherland model. In present paper, we establish bispectral properties of this wave function with respect to dual Ruijesenaars–Macdonald operators.
Short Communication: changes in gait after 12 wk of shoeing in previously barefoot horses
Authors: Panos Katelyn E , Morgan Kristin , Gately Rachael , Wilkinson Julia , Uden Alexandra , Reed Sarah A 
Published: November 2022

Abstract
Farriery can impact gait symmetry and lameness outcomes, but there is limited scientific data documenting these effects. We hypothesized that shoeing previously barefoot horses with plain stamp shoes on the hind hooves would increase gait symmetry, alter hock angles and increase range of motion, and improve lameness scores more than shoeing with traditional fullered shoes. At the start of the study, gait symmetry via wireless inertial motion sensors (IMS), kinematic gait analysis (hock angle and range of motion), and American Association for Equine Practitioner’s (AAEP) lameness scoring were completed for 14 barefoot horses. Horses were then trimmed and hind hooves were shod (wk 0) in three-quarter fullered shoes or plain stamp style shoes. Horses were trimmed and re-shod at week 6. At the end of 12 wk, the IMS analysis, kinematic gait analysis, and lameness scoring were repeated. Differences between shod and barefoot values were calculated for each horse, and impact of shoe type was analyzed via t-test. Significance was determined at P ≤ 0.05. No differences were observed in the IMS scores, hock angles or range of motion, or AAEP lameness scores between horses shod in fullered or plain stamp shoes (P ≥ 0.08). As no variables were determined to be significantly different between the two shoe types, data from all horses were combined to analyze the differences between the barefoot and shod state. Shoeing increased the maximum angle of the right and left hocks (P ≤ 0.03) and the minimum angle of the left (P = 0.02) but not right hock (P = 0.23) relative to barefoot conditions. No differences in hock range of motion were observed in either hock. Lower AAEP lameness scores were observed in horses when shod compared with barefoot (P = 0.001). In conclusion, shoeing previously barefoot horses improved AAEP lameness scores and increased hock angles, regardless of the type of shoe.