bluuebunny/crossref_metadata_2025_split huggingface dataset:
Open Access Redefined: Survey Data and Literature Study on the Impact of Sci-Hub in Orthopaedic Research
Authors: Gathen Martin , Cucchi Davide , Kabir Koroush , Welle Kristian , Jaenisch Max , Jansen Tom Rainer , Randau Thomas Martin 
Published: March 2022

Abstract
Background Since Alexandra Elbanyan founded Sci-Hub in 2011, the website has been used by a growing number of researchers worldwide. Sci-Hub is a so-called shadow library or
guerrilla open access format bypassing publishers’ paywalls, giving everyone free access to scientific papers. Until today, there have been no publications about usage by orthopaedic and
trauma surgeons of Sci-Hub or other “pirate sites” and how it may influence their work.
Materials and Methods Orthopaedic and trauma surgeons of four university hospitals in Germany and Europe were consulted using a standardised questionnaire containing multiple items
about the use and evaluation of Sci-Hub. In addition, the Medline and Cochrane databases were screened for all studies related to Sci-Hub. Two reviewers independently reviewed all articles
and the references of these articles.
Results Of all orthopaedic surgeons consulted, 69% knew of Sci-Hub and 66.7% used it on a regular basis. Of the younger participants (< 45 years old), 77% knew the webpage, while
only 25% of older participants (> 45 years old) knew the webpage. Ninety percent found the quality of their citation and research had been enhanced since using Sci-Hub. On a scale of 1 to
10, user-friendliness was rated with a mean rating of 7.58 (95% CI: 7.262–7.891). Ethical or legal concerns among users seem mixed. On a scale of 1 (no concerns) to 5 (many concerns), the
mean score was 2.39 (95% CI: 2.154–2.615). Of doctors using Sci-Hub, 89% would recommend it to other colleagues.
Conclusion The quality and number of articles in Sci-Hub is outstanding, and the rate of young researchers using the website is high. The most important shift in literature research
for decades is a phenomenon mostly used by young researchers and is not the subject of current research itself. Sci-Hub may have already changed how orthopaedic research works.
Public health implications of opening National Football League stadiums during the COVID-19 pandemic
Authors: García Bulle Bernardo , Shen Dennis , Shah Devavrat , Hosoi Anette E. 
Published: March 2022

Significance
Using data from 2020, we measure the public health impact of allowing fans into sports stadiums during the COVID-19 pandemic; these results may inform future policy decisions regarding large outdoor gatherings during public health crises. Second, we demonstrate the utility of robust synthetic control in this context. Synthetic control and other statistical approaches may be used to exploit the underlying low-dimensional structure of the COVID-19 data and serve as useful instruments in analyzing the impact of mitigation strategies adopted by different communities. As with all statistical methods, reliable outcomes depend on proper implementation strategies and well-established robustness tests; in the absence of these safeguards, these statistical methods are likely to produce specious or misleading conclusions.
In dialogue with non-humans or how women are silenced in incels’ discourse
Authors: Prażmo Ewelina 
Published: March 2022

AbstractDialogue plays a most important role in interpersonal relations creating and strengthening social cohesion. Conversely, the lack of dialogue – and more tellingly a deliberate resistance to it – leads to social friction and animosity. In this paper I focus on a strategy used to intentionally disable a possibility of a meaningful dialogue and to deny any voice to the “other”. Dehumanising the “other” by linguistically representing them as animals or machines exempts the perpetrator from any obligation towards the “other”, including the obligation to respect their rights. I adopt Haslam’s model of dehumanisation (2006) which shows how, by means of metaphorical language, women are dehumanised and denied the possibility to participate in a meaningful dialogue in the so called manosphere.
Screen printing strategy for fabricating flexible crystallized perovskite nanocomposite patterns with high photoluminescence
Authors: Shan Chengwei , Wang Zhuang , Wang Zhaojin , Wang Teng , Luo Dou , Wang Kai , Sun Xiao Wei , Kyaw Aung Ko Ko 
Published: March 2022

Abstract
Organohalide perovskites have been witnessed as an emerging class of solution processable semiconductor with huge potential for applications in optoelectronic devices. However, a low-cost and high-yield patterning of these materials needs to be further improved. Herein, we demonstrated a facile approach to pattern perovskite nanocrystals embedded in polymer matrix by screen printing strategy. Importantly, this strategy achieves a champion photoluminescence quantum yield up to 96.5% and exhibited an intense green emission band centered at 517 nm with narrow full width at half-maximum of 20 nm. In addition, the composite films show an extraordinary stability in various environments, such as air, water, high temperature (80 °C), and Ultraviolet -radiation. The photoluminescence intensity of composite films decreases only 1.4% after being stored in air with 85% relative humidity for 3 months and remains 81.6% of initial values after being submerged in water for 3 months. Finally, we printed high-resolution patterns of 175 µm, demonstrating that the screen printing is very promising for patterning perovskite composite microarrays.
Multifunctional energy storage and piezoelectric properties of 0.65Pb(Mg1/3Nb2/3)O3–0.35PbTiO3 thick films on stainless-steel substrates
Authors: Sadl Matej , Nadaud Kevin , Bah Micka , Levassort Franck , Eckstein Udo , Khansur Neamul H , Webber Kyle G , Ursic Hana 
Published: March 2022

Abstract
The miniaturization of electronic devices and power systems requires the fabrication of functional components in the form of micrometer-sized thick films. A major challenge is the integration of functional ceramics with metals, which are considered incompatible with high-temperature ceramic processing. To overcome the integration barrier, an aerosol deposition (AD) spray-coating method based on room temperature deposition can be used. By employing the AD method, we were able to deposit relaxor-ferroelectric 0.65Pb(Mg1/3Nb2/3)O3–0.35PbTiO3 ceramic thick films on low-cost stainless-steel substrates. The as-deposited films were dense, with ∼97% of the theoretical density. Moreover, the post-deposition annealing at 500 °C did not result in any microstructural changes. Compared to the as-deposited films, the annealed films exhibit improved energy storage and electromechanical properties. The annealed thick films achieve a recoverable energy density of 15.1 J⋅cm−3 at an electric field of 1350 kV⋅cm−1 and an electric-field cycling stability of 5 million cycles. A piezoelectric response was detected through the entire film thickness by piezoelectric force microscopy. Macroscopic displacement measurements revealed a maximum relative strain of 0.38% at 1000 kV⋅cm−1, corresponding to inverse effective piezoelectric coefficient of ∼40 pm⋅V−1. In this study, we overcame the integration challenges and demonstrated the multifunctionalization of future ceramic-metal structures, as the deposited thick films on stainless steel exhibit energy storage capability and piezoelectric properties.
Magnetic phase diagram of the austenitic Mn-rich Ni–Mn–(In, Sn) Heusler alloys
Authors: Bonfà P , Chicco S , Cugini F , Sharma S , Dewhurst J K , Allodi G 
Published: March 2022

Abstract
Heusler compounds have been intensively studied owing to the important technological advancements that they provide in the fields of shape memory, thermomagnetic energy conversion and spintronics. Many of their intriguing properties are ultimately governed by their magnetic states and understanding and possibly tuning them is evidently of utmost importance. In this work we examine the

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alloys with density functional theory simulations and 55Mn nuclear magnetic resonance and combine these two methods to carefully describe their ground state magnetic order. In addition, we compare the results obtained with the conventional generalized gradient approximation with the ones collected using the strongly constrained and appropriately normed (SCAN) semilocal functional for exchange and correlation. Experimental results eventually allow to discriminate between two different scenarios identified by ab initio simulations.
Latent demand for electricity in sub-Saharan Africa: a review
Authors: Van-Hein Sackey Charles , Levin Todd , Nock Destenie 
Published: March 2022

Abstract
Universal access to electricity is an essential part of sub-Saharan Africa’s path to development. With the United Nations setting Goal 7 of its sustainable development goals to be universal access to clean, reliable and affordable electricity, substantial research efforts have been made to optimize electricity supply based on projected demand in sub-Saharan African (SSA) countries. Our study reviews the literature on electricity demand, with a specific focus on latent demand (i.e., electricity demand that would exist if the necessary techno-economic conditions were met) in SSA. We found that out of 57 electricity demand papers reviewed, only 3 (5%) incorporated latent demand in their electricity demand projections. Furthermore, majority of the literature on electricity consumption and demand estimation in SSA use econometric models to identify determinants of electricity consumption and project future demand. We find that population density, urbanization, household income, electricity price, market value of crops and availability of natural resources to be significant determinants of electricity consumption in SSA. We conclude the review by proposing a methodology, and providing an initial proof of concept, for more accurately projecting latent demand in sub-Saharan Africa. Incorporating latent demand in electrification models would help inform energy sector stakeholders (e.g., investors and policymakers) about which sectors and geographic locations hold potential for wealth creation via electricity access.
FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data
Authors: Leonard Simon , Lardenois Aurélie , Tarte Karin , Rolland Antoine D , Chalmel Frédéric 
Published: March 2022

Abstract

Motivation
Dot plots are heatmap-like charts that provide a compact way to simultaneously display two quantitative information by means of dots of different sizes and colors. Despite the popularity of this visualization method, particularly in single-cell RNA-sequencing (scRNA-seq) studies, existing tools used to make dot plots are limited in terms of functionality and usability.

Results
We developed FlexDotPlot, an R package for generating dot plots from multifaceted data, including scRNA-seq data. It provides a universal and easy-to-use solution with a high versatility. An interactive R Shiny application is also available allowing non-R users to easily generate dot plots with several tunable parameters.

Availability and implementation
Source code and detailed manual are available on CRAN (stable version) and at https://github.com/Simon-Leonard/FlexDotPlot (development version). Code to reproduce figures is available at https://github.com/Simon-Leonard/FlexDotPlot_paper. A Shiny app is available as a stand-alone application within the package.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation
Authors: Almodaresi Fatemeh , Khan Jamshed , Madaminov Sergey , Ferdman Michael , Johnson Rob , Pandey Prashant , Patro Rob 
Published: March 2022

AbstractMotivationIn the past few years, researchers have proposed numerous indexing schemes for searching large datasets of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes—Mantis, VariMerge and Bifrost—that can serve as colored de Bruijn graph representations in addition to serving as k-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data.ResultsIn this paper, we show how to build a scalable and updatable exact raw sequence-search index. Specifically, we extend Mantis using the Bentley–Saxe transformation to support efficient updates, called Dynamic Mantis. We demonstrate Dynamic Mantis’s scalability by constructing an index of ≈40K samples from SRA by adding samples one at a time to an initial index of 10K samples. Compared to VariMerge and Bifrost, Dynamic Mantis is more efficient in terms of index-construction time and memory, query time and memory and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Dynamic Mantis scaled to more than 39K samples. Queries were over 24× faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Dynamic Mantis indexes were about 2.5× smaller than Bifrost’s indexes and about half as big as VariMerge’s indexes.Availability and implementationDynamic Mantis implementation is available at https://github.com/splatlab/mantis/tree/mergeMSTs.Supplementary informationSupplementary data are available at Bioinformatics online.
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
Authors: Liao Chun-Chieh , Fu Po-Ying , Huang Chih-Wei , Chuang Chia-Hsien , Yen Yun , Lin Chung-Yen , Chen Shu-Hwa 
Published: March 2022

Abstract

Motivation
Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have limitations on either the sequence redundancy or the delay on new sequence recruitment. To improve the 16S rRNA gene-based taxonomic classification, we merged these widely used databases and a collection of novel sequences systemically into an integrated resource.

Results
MetaSquare version 1.0 is an integrated 16S rRNA sequence database. It is composed of more than 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods.

Availability and implementation
Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare

Supplementary information
Supplementary data are available at Bioinformatics online.
Study on the Correlation Between the Appearance Traits and Intrinsic Chemical Quality of Bitter Almonds Based on Fingerprint-Chemometrics
Authors: Zhang Guoqin , Li Huanhuan , Sun Lili , Liu Yi , Cao Ying , Ren Xiaoliang , Liu Yanan 
Published: March 2022

Abstract
Bitter almond is a well-known and commonly used traditional Chinese medicine (TCM) for relieving coughs and asthma. However, the bioactive chemical composition of bitter almonds, especially their amygdalin content, which determines their quality for TCM use, is variable and this can cause problems with formulating and prescribing TCMs based on bitter almonds. Therefore, a simple method was developed to evaluate the compositional quality of bitter almonds from their appearance traits, based on a combination of chromatographic fingerprinting and chemometrics. Bitter almonds were analyzed by high-performance liquid chromatography (HPLC). Hierarchical cluster analysis (HCA) and principal components analysis (PCA) were applied to classify bitter almonds, which split the samples into two independent clusters. Three chemical markers (amygdalin, prunasin, and one unidentified component) were found by partial least squares-discriminant analysis (PLS-DA). What’s more, a new PLS-DA model was reconstructed to confirm the obtained chemical markers from PLS-DA. Additionally, the appearance trait indices and amygdalin content of bitter almond were determined and the classification was confirmed by one-way analysis of variance. This method can easily determine the quality of bitter almonds from their appearance alone, high quality correlated closely with kernels that were larger, oblong in shape and heavier.
Comparison of Mold Active Triazoles as Primary Antifungal Prophylaxis in Patients With Newly Diagnosed Acute Myeloid Leukemia in the Era of Molecularly Targeted Therapies
Authors: Rausch Caitlin R , DiPippo Adam J , Jiang Ying , DiNardo Courtney D , Kadia Tapan , Maiti Abhishek , Montalban-Bravo Guillermo , Ravandi Farhad , Kontoyiannis Dimitrios P 
Published: March 2022

AbstractBackgroundMultiple factors influence the choice of primary antifungal prophylaxis (PAP) in patients with acute myeloid leukemia (AML) undergoing remission induction chemotherapy (RIC) given the recent incorporation of targeted leukemia therapies into these regimens.MethodsWe evaluated the incidence and characteristics of breakthrough invasive fungal infections (bIFI) in 277 adult patients with newly diagnosed AML undergoing RIC with high-intensity, or low-intensity venetoclax-containing therapy. Patients receiving posaconazole (PCZ), voriconazole (VCZ), or isavuconazole (ISA) for &gt; 5 days as PAP during RIC were included. Echinocandin use prior to, but not concomitantly with, the PAP azole was allowed. IFI (modified EORTC/MSG criteria) occurring after &gt; 5 days of continuous azole exposure or within 14 days of discontinuation were considered bIFI.ResultsProven or probable bIFI were observed in 11 patients (4%). The incidence of bIFI was 2.9% for PCZ, 4.8% for VCZ, and 5.7% for ISA (P = .55). In total, 161 patients (58%) received echinocandin prophylaxis prior to azole initiation. Neither echinocandin exposure nor chemotherapy intensity impacted bIFI rate. Patients with bIFI had a lower rate of absolute neutrophil count recovery &gt; 1000 cells/µL (64% vs 90%, P = .021) or complete remission (CR; 18% vs 66%, P = .002) after RIC. Thirty-eight patients (14%) discontinued PAP due to toxicity, most often hepatotoxicity. Discontinuation due to hepatotoxicity was similar among azoles (PCZ: 13%; VCZ: 15%; ISA: 13%).ConclusionsThe rate of bIFI is low during RIC in patients with newly diagnosed AML receiving any of the mold-active triazoles as PAP. Neutrophil recovery and achievement of CR are important for bIFI risk.
5-Year results from the prospective European multi-centre study on decellularized homografts for pulmonary valve replacement ESPOIR Trial and ESPOIR Registry data
Authors: Bobylev Dmitry , Horke Alexander , Boethig Dietmar , Hazekamp Mark , Meyns Bart , Rega Filip , Dave Hitendu , Schmiady Martin , Ciubotaru Anatol , Cheptanaru Eduard , Vida Vladimiro , Padalino Massimo , Tsang Victor , Jashari Ramadan , Laufer Günther , Andreas Martin , Andreeva Alexandra , Tudorache Igor , Cebotari Serghei , Haverich Axel , Sarikouch Samir 
Published: March 2022

Abstract

OBJECTIVES
Early results from the prospective ESPOIR Trial have indicated excellent results for pulmonary valve replacement using decellularized pulmonary homografts (DPH).

METHODS
A 5-year analysis of ESPOIR Trial patients was performed to provide an insight into the midterm DPH performance. ESPOIR Trial and Registry patients were matched with cryopreserved homografts (CH) patients considering patient age, type of heart defect and previous procedures to present the overall experience with DPH.

RESULTS
A total of 121 patients (59 female) were prospectively enrolled (8/2014–12/2016), median age 16.5 years (interquartile range 11.2–29.8), and median DPH diameter 24 mm. One death (73 year-old) occurred during a median follow-up of 5.9 years (5.4–6.4), in addition to 2 perioperative deaths resulting in an overall mortality rate of 2.5%. One case of endocarditis in 637 patient-years was noticed, resulting in an incidence of 0.15% per patient-year. At 5 years, the mean peak gradient was 19.9 mmHg (9.9), mean regurgitation 0.9 (0.6, grade 0–3) and freedom from explantation/any reintervention 97.5% (1.5). The combined DPH cohort, n = 319, comprising both Trial and Registry data, showed significantly better freedom from explantation for DPH 95.5% (standard deviation 1.7) than CH 83.0% (2.8) (P &lt; 0.001) and less structural valve degeneration at 10 years when matched to 319 CH patients [DPH 65.5% (standard deviation 4.4) and CH 47.3% (3.7), P = 0.11].

CONCLUSIONS
The 5-year data of the prospective ESPOIR Trial show excellent performance for DPH and low rates of adverse events. ESPOIR Registry data up to 15 years, including a matched comparison with CH, demonstrated statistically significant better freedom from explantation.
Feature selection algorithm based on density and distance for fault diagnosis applied to a roll-to-roll manufacturing system
Authors: Oh Hyogeun , Lee Yoonjae , Lee Jongsu , Joo Changbeom , Lee Changwoo 
Published: March 2022

Abstract
Roll-to-roll systems that include rotary components such as driven rolls and idle rollers have significant potential for application in fabrication of flexible functional devices. They are inexpensive, mass producible, and environmentally friendly; however, even minor defects in their component bearings can render them susceptible to severe damage, which necessitates accurate diagnoses of bearing quality. The main steps in machine learning for fault diagnosis include feature extraction and selection. In the case of high-dimensional feature data, critical study is required to identify the best feature combination for proper diagnosis. Thus, this study aims to develop a method that extracts fault characteristics of a bearing from the measured signal and qualify the bearing according to the Mahalanobis distances and differences in density between normal and faulty data groups. Features extracted from vibration data collected from industry-scale roll-to-roll systems and CWRU data were trained with principal component analysis, other modern feature selection techniques, and the proposed algorithm-based eight classifiers. Compared with the existing algorithm, the accuracy increased by up to 9.24%, the training time decreased by up to 34.46%, and the number of features to obtain the maximum accuracy decreased by up to 59.92%. Thus, the proposed algorithm provides an effective and time-efficient approach to improve the accuracy of fault diagnosis of rotary components.
Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria
Authors: Cao Sha , Brandis Gerrit , Huseby Douglas L. , Hughes Diarmaid 
Published: March 2022

Abstract
Analysis of bacterial genomes shows that, whereas diverse species share many genes in common, their linear order on the chromosome is often not conserved. Whereas rearrangements in gene order could occur by genetic drift, an alternative hypothesis is rearrangement driven by positive selection during niche adaptation (SNAP). Here, we provide the first experimental support for the SNAP hypothesis. We evolved Salmonella to adapt to growth on malate as the sole carbon source and followed the evolutionary trajectories. The initial adaptation to growth in the new environment involved the duplication of 1.66 Mb, corresponding to one-third of the Salmonella chromosome. This duplication is selected to increase the copy number of a single gene, dctA, involved in the uptake of malate. Continuing selection led to the rapid loss or mutation of duplicate genes from either copy of the duplicated region. After 2000 generations, only 31% of the originally duplicated genes remained intact and the gene order within the Salmonella chromosome has been significantly and irreversibly altered. These results experientially validate predictions made by the SNAP hypothesis and show that SNAP can be a strong driving force for rearrangements in chromosomal gene order.