bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepCap-Kcr: accurate identification and investigation of protein lysine crotonylation sites based on capsule network
Authors: Khanal Jhabindra , Tayara Hilal , Zou Quan , To Chong Kil 
Published: October 2021

Abstract
Lysine crotonylation (Kcr) is a posttranslational modification widely detected in histone and nonhistone proteins. It plays a vital role in human disease progression and various cellular processes, including cell cycle, cell organization, chromatin remodeling and a key mechanism to increase proteomic diversity. Thus, accurate information on such sites is beneficial for both drug development and basic research. Existing computational methods can be improved to more effectively identify Kcr sites in proteins. In this study, we proposed a deep learning model, DeepCap-Kcr, a capsule network (CapsNet) based on a convolutional neural network (CNN) and long short-term memory (LSTM) for robust prediction of Kcr sites on histone and nonhistone proteins (mammals). The proposed model outperformed the existing CNN architecture Deep-Kcr and other well-established tools in most cases and provided promising outcomes for practical use; in particular, the proposed model characterized the internal hierarchical representation as well as the important features from multiple levels of abstraction automatically learned from a small number of samples. The trained model was well generalized in other species (papaya). Moreover, we showed the features and properties generated by the internal capsule layer that can explore the internal data distribution related to biological significance (as a motif detector). The source code and data are freely available at https://github.com/Jhabindra-bioinfo/DeepCap-Kcr.
Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file
Authors: Schutz Sacha , Monod-Broca Charles , Bourneuf Lucas , Marijon Pierre , Montier Tristan 
Published: October 2021

Abstract

Summary
Cutevariant is a graphical user interface (GUI)-based desktop application designed to filter variations from annotated VCF file. The application imports data into a local SQLite database where complex filter queries can be built either from GUI controllers or using a domain-specific language called Variant Query Language. Cutevariant provides more features than existing applications and is fully customizable thanks to a complete plugins architecture.

Availability and implementation
Cutevariant is distributed as a multiplatform client-side software under an open source license and is available at https://github.com/labsquare/cutevariant.
SigTools: exploratory visualization for genomic signals
Authors: Masoumi Shohre , Libbrecht Maxwell W , Wiese Kay C 
Published: October 2021

Abstract

Motivation
With the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data.

Results
SigTools is an R-based genomic signals visualization package developed with two objectives: (i) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement and development by including distribution and autocorrelation plots; (ii) to enable genomic signals interpretation by including correlation and aggregation plots. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools.

Availability and implementation
SigTools source code, installation guide and manual is freely available on http://github.com/shohre73
CHRAC1 promotes human lung cancer growth through regulating YAP transcriptional activity
Authors: Wang Mingwei , Li Shasha , Guo Wencong , Wang Lulu , Huang Jiaxin , Zhuo Junzhe , Lai Botao , Liao Chenqi , Ge Tianlan , Nie Yuxuan , Jin Su , Wang Manxiang , Zhang Yanggeling , Liu Yimeng , Li Xiaowen , Zhang Huixia 
Published: October 2021

Abstract
ATP-dependent chromatin remodeling complexes regulate chromatin structure and play important roles in gene expression, differentiation, development and cancer progression. Dysregulation in the subunits of the complexes often has been found in different cancers, but how they influence cancer initiation and progression is not fully understood. Here, we show that Chromatin Accessibility Complex Subunit 1 (CHRAC1), the accessory subunit of chromatin remodeling complex, is highly expressed in lung cancer tissues, which correlates with poor prognosis in lung cancer patients. CHRAC1 overexpression promotes lung cancer cell proliferation and migration in vitro and tumor growth in genetically engineered KrasG12D.LSL lung adenocarcinoma mouse model. Consistent with this, CHRAC1 silencing inhibits cell proliferation and migration in lung cancer cells and suppresses tumor growth in xenograft mouse model. Further, CHRAC1 binds to the transcription coactivator Yes-associated protein (YAP), enhances the transcription of downstream target oncogenes in Hippo pathway and thus promotes the tumor growth. Together, our study defines a critical role of CHRAC1 in promoting YAP transcriptional activity and lung cancer tumorigenesis, which makes it a potential target for lung cancer.
A new iteration for the single-access large-bore technique during Impella supported complex and high-risk coronary intervention: a case report
Authors: Araco Marco , Quagliana Angelo , Pedrazzini Giovanni , Valgimigli Marco 
Published: October 2021

Abstract

Background
Complex and high-risk coronary intervention (CHIP-PCI) and PCI in cardiogenic shock complicating acute coronary syndrome (ACS) are increasingly performed under mechanical circulatory support—so-called protected PCI. Among the available options, Impella Cardiac Power (CP) heart pump (Abiomed) is percutaneously inserted over the femoral artery and typically requires a second arterial access to perform PCI, which further enhances the risk of vascular and bleeding complications. The single-access technique allows Impella CP placement and PCI performance through the same vascular access. When a 7 Fr system is desirable, only a long and entirely hydrophilic coated sheath has been previously used, which is not available in Europe.

Case summary
A 85-year-old patient admitted with non ST-elevation - acute coronary syndrome (NSTE-ACS), severely reduced left ventricular function and three-vessel coronary artery disease underwent single-access CHIP-PCI under Impella CP support. After a failed attempt to insert a standard 7 Fr long femoral sheath alongside the Impella catheter, we successfully introduced a 7.5 Fr sheathless guiding catheter and delivered the planned percutaneous treatment with the benefits conferred by a 7 Fr—rather than 6—lumen catheter, without the need for an additional arterial access.

Discussion
This is, to the best of our knowledge, the first case of CHIP-PCI performed under Impella support utilizing the single-access technique with a 7.5 Fr sheathless guiding catheter. Beyond advantages of the single-access technique in sparing time and avoiding vascular complications associated with gaining a second arterial access, the lower outer diameter of the sheathless catheter compared with standard 7 Fr sheaths may allow improved limb perfusion and lower chance of interference with the Impella CP catheter.
Cardiovascular disease in an intensive care unit: patterns of an often fatal omen
Authors: Rocha B , Cunha G , Maltes S , Moura A N N E , Coelho F , Torres J , Santos P , Monteiro F , Monteiro F , Almeida G , Lamas T , Simoes I , Gaspar I , Mendes M , Carmo E 
Published: October 2021

Abstract

Background
Care for the critically ill patient with Cardiovascular Disease (CVD) requires a unique management approach, as the theoretical critical threshold for decompensation is lower and inherent adaptive mechanisms may be compromised. We aimed to characterize the prognostic impact of CVD in patients admitted to an Intensive Care Unit (ICU).

Methods
We performed a cohort study of consecutive patients admitted to an ICU from January to December 2019. Patients were stratified as follows: (1) established CVD – presence of either atrial fibrillation, heart failure, coronary artery disease and/or peripheral artery disease; (2) at higher risk of CVD – known arterial hypertension, dyslipidemia, diabetes mellitus and/or current smoking, in the absence of established CVD; and (3) at lower risk of CVD – i.e. none of the above. The co-primary endpoints were all-cause death in ICU and death during index hospitalization.

Results
During 2019, there were 334 admissions in ICU, comprising a total of 296 patients (mean age 67±15 years, 58.1% male). Overall, 69 (23.3%) and 108 (36.5%) died in ICU and during index hospitalization, respectively. Compared to patients at lower risk of CVD, those at higher CVD risk or with established CVD had markers of more severe disease, as noted by higher risk scores (e.g., SAPS-II 35.0±20.0 vs. 43.5±22.3 vs. 52.6±20.0; p&lt;0.001), higher rates of mechanical ventilation (41.5 vs. 57.3 vs. 63.9%; p=0.020), shock during ICU stay (34.0 vs. 52.7 vs. 66.9%; p&lt;0.001) and acute kidney injury (26.4 vs. 35.5 vs. 57.9%; p&lt;0.001), respectively, as well as higher death rates in ICU (5.7 vs. 21.8 vs. 31.6%; p=0.001) and index hospitalization (9.4 vs. 37.3 vs. 46.6%; p&lt;0.001). In multivariate analysis, adjusted for age and cause of admission, established CVD independently predicted the risk of all-cause death in ICU (HR: 2.084; 95% CI: 1.136–3.823; p=0.018) and during index hospitalization (HR 1.712; CI: 1.009–2.889; p=0.046). The analysis for the group of patients at higher risk of CVD yielded similar results to the abovementioned.

Conclusion
Roughly 4 in every 5 patients admitted in ICU were at risk of or had established CVD. The presence of either of the above independently predicted a two- to three-fold higher risk of death during hospitalization. Our findings emphasize the considerable burden of CVD in ICU and underscore the importance of comprehensive management of the complex critically ill patient.

Funding Acknowledgement
Type of funding sources: None.
Redistribution of garbage codes to underlying causes of death: a systematic analysis on Italy and a comparison with most populous Western European countries based on the Global Burden of Disease Study 2019
Authors: Monasta Lorenzo , Alicandro Gianfranco , Pasovic Maja , Cunningham Matthew , Armocida Benedetta , J L Murray Christopher , Ronfani Luca , Naghavi Mohsen ,   GBD 2019 Italy Causes of Death Collaborators, Monasta Lorenzo , Alicandro Gianfranco , Pasovic Maja , Cunningham Matthew , Armocida Benedetta , Albano Luciana , Beghi Ettore , Beghi Massimiliano , Bosetti Cristina , Bragazzi Nicola Luigi , Carreras Giulia , Castelpietra Giulio , Catapano Alberico L , Cattaruzza Maria Sofia , Collatuzzo Giulia , Conti Sara , Damiani Giovanni , Ferrara Pietro , Fornari Carla , Gallus Silvano , Giampaoli Simona , Golinelli Davide , Isola Gaetano , Lauriola Paolo , La Vecchia Carlo , Leonardi Matilde , Magnani Francesca Giulia , Minelli Giada , Moccia Marcello , Pedersini Paolo , Perico Norberto , Raggi Alberto , Remuzzi Giuseppe , Sanmarchi Francesco , Sattin Davide , Unim Brigid , Villafañe Jorge Hugo , Violante Francesco S , Murray Christopher J L , Ronfani Luca , Naghavi Mohsen 
Published: October 2021

Abstract

Background
The proportion of reported causes of death (CoDs) that are not underlying causes can be relevant even in high-income countries and seriously affect health planning. The Global Burden of Disease (GBD) study identifies these ‘garbage codes’ (GCs) and redistributes them to underlying causes using evidence-based algorithms. Planners relying on vital registration data will find discrepancies with GBD estimates. We analyse these discrepancies, through the analysis of GCs and their redistribution.

Methods
We explored the case of Italy, at national and regional level, and compared it to nine other Western European countries with similar population sizes. We analysed differences between official data and GBD 2019 estimates, for the period 1990–2017 for which we had vital registration data for most select countries.

Results
In Italy, in 2017, 33 000 deaths were attributed to unspecified type of stroke and 15 000 to unspecified type of diabetes, these making a fourth of the overall garbage. Significant heterogeneity exists on the overall proportion of GCs, type (unspecified or impossible underlying causes), and size of specific GCs among regions in Italy, and among the select countries. We found no pattern between level of garbage and relevance of specific GCs. Even locations performing below average show interesting lower levels for certain GCs if compared to better performing countries.

Conclusions
This systematic analysis suggests the heterogeneity in GC levels and causes, paired with a more detailed analysis of local practices, strengths and weaknesses, could be a positive element in a strategy for the reduction of GCs in Italy.
Hsp90 interaction networks in fungi—tools and techniques
Authors: Crunden Julia L , Diezmann Stephanie 
Published: October 2021

ABSTRACT
Heat-shock protein 90 (Hsp90) is a central regulator of cellular proteostasis. It stabilizes numerous proteins that are involved in fundamental processes of life, including cell growth, cell-cycle progression and the environmental response. In addition to stabilizing proteins, Hsp90 governs gene expression and controls the release of cryptic genetic variation. Given its central role in evolution and development, it is important to identify proteins and genes that interact with Hsp90. This requires sophisticated genetic and biochemical tools, including extensive mutant collections, suitable epitope tags, proteomics approaches and Hsp90-specific pharmacological inhibitors for chemogenomic screens. These usually only exist in model organisms, such as the yeast Saccharomyces cerevisiae. Yet, the importance of other fungal species, such as Candida albicans and Cryptococcus neoformans, as serious human pathogens accelerated the development of genetic tools to study their virulence and stress response pathways. These tools can also be exploited to map Hsp90 interaction networks. Here, we review tools and techniques for Hsp90 network mapping available in different fungi and provide a summary of existing mapping efforts. Mapping Hsp90 networks in fungal species spanning &gt;500 million years of evolution provides a unique vantage point, allowing tracking of the evolutionary history of eukaryotic Hsp90 networks.
Sharp stability for finite difference approximations of hyperbolic equations with boundary conditions
Authors: Coulombel Jean-François , Faye Grégory 
Published: October 2021

Abstract
In this article, we consider a class of finite rank perturbations of Toeplitz operators that have simple eigenvalues on the unit circle. Under a suitable assumption on the behavior of the essential spectrum, we show that such operators are power bounded. The problem originates in the approximation of hyperbolic partial differential equations with boundary conditions by means of finite difference schemes. Our result gives a positive answer to a conjecture by Trefethen, Kreiss and Wu that only a weak form of the so-called uniform Kreiss–Lopatinskii condition is sufficient to imply power boundedness.
Factors Associated With Infectious Disease Fellowship Fill Rate: An Analysis of 2019, 2020, and 2021 Match Cycles
Authors: Lanjewar Swapnil , Filipiak Rachel , Osman Fauzia , Tischendorf Jessica S 
Published: October 2021

AbstractHistorically, there has been a relative paucity of applicants to infectious disease fellowships. This leads to a significant number of programs being unfilled in the fellowship match. We sought to identify predictors of a program filling all positions offered in the match through retrospective review of available match and program data for the 2019–2021 match cycles. In the 2021 match, hospital and research rankings were associated with filling, as were offering specialized training tracks and having an active Twitter account. Knowledge of these associations can help programs direct resources to optimize recruitment and enrichment of infectious disease fellows.
Comparison of different antimicrobial use indicators and antimicrobial resistance data in food-producing animals
Authors: Sanders Pim , Mevius Dik , Veldman Kees , van Geijlswijk Inge , Wagenaar Jaap A , Bonten Marc , Heederik Dick 
Published: October 2021

Abstract

Objectives
To explore the effects of using different indicators to quantify antimicrobial usage (AMU) in livestock and compare outcomes with antimicrobial resistance (AMR) data.

Methods
Three indicators were used to quantify AMU, two indicators in which the denominator varied: defined daily doses per average mass of the animals present per year (DDD/AY) and defined daily doses per population correction unit (DDD/PCU) and one in which the numerator varied: milligrams of active ingredient per PCU (mg/PCU). AMU was compared with antimicrobial resistance data from the national monitoring programme from 2013 to 2018 with the proportion of Escherichia coli isolates fully susceptible to a predefined panel of antimicrobials for the broiler, dairy cattle and pig farming livestock sectors in the Netherlands.

Results
The ranking of livestock sectors differs between sectors when using different indicators to express AMU. Dairy cattle rank lowest when expressing AMU in DDD/AY, followed by pigs and broilers corresponding to the rankings of the sectors for AMR. When changing the denominator to PCU, the ranking in AMU is reversed: use ranks highest in dairy cattle and lowest broilers.

Conclusions
Using different denominators in AMU indicators has a major impact on measured use. This might result in misinterpretation of effects of interventions on AMU and the associations of AMU with AMR across animal sectors. From an epidemiological perspective, indicators that take into account time at risk of exposure to antimicrobials are to be preferred and reflect the AMR risk most accurately.
NGLY1: insights from Caenorhabditis elegans
Authors: Lehrbach Nicolas John 
Published: October 2021

Abstract
Peptide:N-glycanase is an evolutionarily conserved deglycosylating enzyme that catalyses the removal of N-linked glycans from cytosolic glycoproteins. Recessive mutations that inactivate this enzyme cause NGLY1 deficiency, a multisystemic disorder with symptoms including developmental delay and defects in cognition and motor control. Developing treatments for NGLY1 deficiency will require an understanding of how failure to deglycosylate NGLY1 substrates perturbs cellular and organismal function. In this review, I highlight insights into peptide:N-glycanase biology gained by studies in the highly tractable genetic model animal Caenorhabditis elegans. I focus on the recent discovery of SKN-1A/Nrf1, an N-glycosylated transcription factor, as a peptide:N-glycanase substrate critical for regulation of the proteasome. I describe the elaborate post-translational mechanism that culminates in activation of SKN-1A/Nrf1 via NGLY1-dependent ‘sequence editing’ and discuss the implications of these findings for our understanding of NGLY1 deficiency.
Are Pesticides Used to Control Thrips Harmonious with Soil-Dwelling Predatory Mite Cosmolaelaps sabelis (Mesostigmata: Laelapidae)?
Authors: Barroso G , Pazini J B , Iost Filho F H , Barbosa D P L , de Paiva A C R , Matioli T F , Yamamoto P T 
Published: October 2021

Abstract
Edaphic predatory mites could be introduced in pest management programs of pests that live, or spend part of their life cycle, in the soil. Some mesostigmatic mites have been widely used for the management of different species of thrips (Thysanoptera), especially in protected cultivation. The edaphic predator Cosmolaelaps sabelis (Mesostigmata: Laelapidae) was a model species in this study, being exposed to the most applied insecticides for the control of thrips in Brazil. After lethal, sublethal and transgenerational effects were evaluated. The pesticides acephate, acetamiprid + etofenprox, azadirachtin, spinetoram, formetanate hydrochloride, and imidacloprid were classified according to the IOBC/WPRS (International Organization for Biological Control-West Paleartic Regional Section) recommendation, considering the acute toxicity and the effects on adult females’ reproduction, in the maternal and first generation. The pesticides acetamiprid + etofenprox and azadirachtin were classified as slightly harmful (Class 2), while spinetoram was classified as moderately harmful (Class 3). Acephate and formetanate hydrochloride were classified as harmful (Class 4). Only imidacloprid didn’t cause negative effects on the females. Regarding effects on the first generation, acetamiprid + etofenprox, azadirachtin, and spinetoram caused reduction in the oviposition rates. Therefore, we suggest that complimentary bioassays should be done under semi-field and field conditions using the pesticides that were considered harmful in this study, to assess their effects on this predator in other environments prior to recommending not to use them in integrated programs to manage soil-based pests using chemical and biological tools.
Creating ‘a palace of art’
Authors: Hilary John 
Published: October 2021

Abstract
Nineteenth-century art collecting in Britain is typically characterized as a rejection of the earlier aristocratic tradition of amassing Old Masters in favour of a bourgeois preference for more relevant contemporary paintings. Inspired by the intellectual ideal of ‘Bildung’, however, German-Jewish collectors settling in fin-de-siècle London brought with them an expectation of high cultural engagement with the most important masterworks of the European tradition. This paper’s reconstruction of the lost collection of Leopold and Mathilde Hirsch reveals a level of sophistication and personal involvement with the art market which dispels any suggestion that these were uncultured parvenus seeking to secure a place in high society by means of conspicuous consumption. It also requires us to distinguish between German-Jewish migrant collectors and their British contemporaries when describing the different models of collecting among those who shared a non-aristocratic family background.