bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monoclonal antibodies and amyloid removal as a therapeutic strategy for cardiac amyloidosis
Authors: Emdin Michele , Morfino Paolo , Crosta Lucia , Aimo Alberto , Vergaro Giuseppe , Castiglione Vincenzo 
Published: April 2023

Abstract
Cardiac amyloidosis (CA) is an infiltrative disease caused by progressive deposition of amyloid fibres in the heart. The most common forms include immunoglobulin light-chain and transthyretin amyloidosis. Current therapies for CA either stabilize or block the production of amyloidogenic precursors, preventing further amyloid deposition. This approach, while reducing cell damage and disease progression, does not target pre-existing amyloid deposits. Conversely, amyloid removal might stimulate functional recovery of the affected organ, thus improving quality of life and survival. A therapeutic strategy based on monoclonal antibodies capable of selectively binding amyloid deposits and inducing their removal has recently been tested in various clinical trial, with promising results, and could represent a key treatment for CA in the near future.
Clinical results and mechanism of action of icosapent ethyl
Authors: Borghi Claudio , Bragagni Alessio 
Published: April 2023

Abstract
Serum triglyceride concentration is considered as an additional component that often contributes to residual cardiovascular risk in patients already at high risk; these considerations have led to several clinical studies aimed at evaluating the efficacy of supplements based on omega-3 fatty acids in reducing serum triglyceride levels and consequently cardiovascular risk. Although partially inconclusive and contradictory, these clinical trials laid the foundations for the implementation of the REDUCE-IT and EVAPORATE studies, in which the use of a purified derivative of eicosapentaenoic acid, icosapent ethyl, resulted in a significant reduction both of the composite for cardiovascular death, non-fatal myocardial infarction, and non-fatal stroke and of the reduction in the volumetric progression up to the induction of a real regression of the coronary atheromatous plaques detected by computerized coronary angiography tomography. Surprisingly, these brilliant results seem to be, at least in part, not related to the reduction of triglyceride concentration. The purpose of this article is to examine the latest evidence regarding icosapent ethyl therapy, describing the results of the main clinical trials performed to date and formulating hypotheses on the potential mechanisms of action of this fascinating molecule.
Cardiovascular prevention: Mediterranean or low-fat diet?
Authors: Temporelli Pier Luigi 
Published: April 2023

Abstract
The international scientific community has long agreed on the fact that a low-fat diet is actually able to bring benefits to cardiovascular health and beyond. By low-fat diet, experts mean a diet where the average calories assimilated daily are made up of no more than 30% fat. The Mediterranean Diet, on the other hand, identifies a nutritional model inspired by the traditional eating habits of the countries bordering the Mediterranean Sea. It began to be studied scientifically in the 1950s and it is still today one of the diets that have a positive impact on our health when associated with correct lifestyles. Although epidemiological and mechanistic studies show similar results, there is no evidence from large-scale, long-term clinical trials on the efficacy of the Mediterranean Diet compared with another active group, particularly in secondary prevention. A convincing response has been obtained from the recent CORDIOPREV study (CORonary Diet Intervention with Olive oil and cardiovascular PREVention) which randomized ∼1000 patients with documented coronary artery disease to a Mediterranean Diet or a low-fat dietary intervention. In a 7-year follow-up, the Mediterranean Diet was superior to the low-fat diet in the prevention of major cardiovascular events.
A novelNitrospiralineage isolated from activated sludge using elevated temperatures
Authors: Keuter Sabine , Koch Hanna , Nowka Boris , Lipski André , Kruse Myriam , Lücker Sebastian , Spieck Eva 
Published: April 2023

AbstractThe genus Nitrospira represents the dominant nitrite-oxidizing clade in most wastewater treatment plants (WWTPs) globally, and several Nitrospira strains have been isolated from activated sludge. Using a pre-enrichment strategy with alternating nitrifying and denitrifying conditions, followed by incubation at elevated temperatures, we isolated a novel Nitrospira species, named Nitrospira tepida. This moderately thermophilic species with optimal growth between 37 and 45°C is only distantly related to other Nitrospira and forms a novel lineage VII within the genus, together with few environmental 16S rRNA gene sequences predominantly detected in thermal wastewater or oxygen-limited systems. Genomic and physiological analyses revealed remarkable differences between N. tepida and two other isolates previously obtained from the same WWTP, suggesting niche differentiation between these nitrite oxidizers. N. tepida grows in aggregates, and tolerates nitrite and nitrate concentrations of up to 20 mM and 40 mM, respectively. The Km value for nitrite of N. tepida is 77 ± 26 µM. In summary, this novel Nitrospira lineage seems to be well-adapted for wastewater treatment processes at elevated temperatures and limited aeration, conditions that potentially reduce operational costs of such systems.
Features of disruption mutants of genes encoding for hydrophobin Vmh2 and Vmh3 in mycelial formation and resistance to environmental stress in Pleurotus ostreatus
Authors: Han Junxian , Kawauchi Moriyuki , Schiphof Kim , Terauchi Yuki , Yoshimi Akira , Tanaka Chihiro , Nakazawa Takehito , Honda Yoichi 
Published: April 2023

Abstract
Hydrophobins, which are small-secreted proteins with both hydrophobic and hydrophilic parts, can self-assemble into an amphiphilic film at the air-water interface, helping the fungus to form aerial hyphae. In the agaricomycete Pleurotus ostreatus, more than 20 putative hydrophobin genes have been predicted. Of these, two hydrophobin genes, vmh2 and vmh3, are predominantly expressed in the vegetative mycelium. In this study, we focused on the functions of Vmh2 and Vmh3 in vegetative mycelia. Based on the observation of the mycelial cross-section by transmission electron microscopy and the disappearance time of water droplets on the mycelial surface, Vmh2 and Vmh3 were considered essential for the maintenance of the surface hydrophobicity of the mycelium. The Δvmh3 and Δvmh2Δvmh3 strains exhibited relatively slower aerial mycelia formation on a liquid medium, and no significant alteration was observed in Δvmh2 strains. Only the Δvmh3 and Δvmh2Δvmh3 strains grew slower than the wild-type strain under stress conditions involving SDS and H2O2 on agar plates. This study revealed possible distinct roles for these hydrophobins in stress resistance. These results suggest that Agaricomycetes, including P. ostreatus, have evolved to possess multiple different hydrophobins as a means of adapting to various environments.
In vitro antimicrobial activity of crude propolis extracts and fractions
Authors: Sa-eed Alhassan , Donkor Eric S , Arhin Reuben E , Tetteh-Quarcoo Patience B , Attah Simon K , Kabotso Daniel E K , Kotey Fleischer C N , Dayie Nicholas T K D 
Published: April 2023

Abstract
The search for antimicrobials in propolis presents a new dimension for addressing the problem of antimicrobial drug resistance. The aim of this study was to determine the antimicrobial activity of extracts of crude propolis collected from different regions in Ghana and their active fractions. The antimicrobial activity of the extracts, as well as that of the chloroform, ethyl acetate, and petroleum ether fractions of the active samples were determined using the agar well diffusion method. The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) of the most active fractions were determined. The various crude propolis extracts frequently produced zones of inhibition against Staphylococcus aureus (17/20) than Pseudomonas aeruginosa (16/20), and Escherichia coli (1/20) test isolates. Chloroform and ethyl acetate solvents produced fractions possessing greater antimicrobial activity than the petroleum ether fraction. The mean MIC range of the most active fractions was greatest for S. aureus (76.0 ± 34.8–48.0 ± 33.0 mg/ml) than for P. aeruginosa (40.8 ± 33.3–30.4 ± 6.7 mg/ml) and E. coli, as was the mean MBC. Propolis has antimicrobial potential, and hence should be exploited as an alternative for the treatment of bacterial infections.
Methods for identifying and measuring the diversity of ectomycorrhizal fungi
Authors: Janowski Daniel , Leski Tomasz 
Published: April 2023

Abstract
Mycorrhiza is a mutualistic symbiosis between some plant species and a diverse group of soil fungi. Mycorrhizal symbiosis is categorized into discrete types based on the structural differences and the taxonomic position of involved plants and fungi. The main types of mycorrhiza include arbuscular, ericoid, orchid, monotropoid and ectomycorrhiza, the latter being the main focus of this review. Identifying ectomycorrhizal fungi (EMF) is crucial for understanding the ecology and preservation of rare and endangered plants, fungi and habitats. Thus, since the discovery of ectomycorrhiza, new identification methods have been constantly developed. This review tracks the history of EMF identification methods, presents their limitations and aims to discern the frontier of the field. The early methods were based on the morphology and anatomy of EMF, which allowed ectomycorrhizae formed by different EMF to be distinguished. Recognizing the EMF species that formed them, however, was difficult. The introduction of molecular methods that analysed taxon-specific DNA barcodes was a breakthrough in EMF identification, and the internal transcribed spacer gene was adopted as a routine fungal barcoding sequence. Identifying EMF from randomly sampled roots by morphology or polymerase chain reaction (PCR)-based methods results in rare EMF taxa being missed and underreported. This is addressed by bulk sampling combined with environmental DNA metabarcoding methods, which, in turn, yield a lower resolution of taxonomic identification. Most EMF identification methods incorporate PCR reactions, which are biased against some groups of EMF; developing PCR-free molecular methods would constitute a significant advancement. As the traditional concept of species is challenging for fungi, studying EMF functional rather than taxonomic diversity appears to be promising.
Music Engagement and Episodic Memory Among Middle-Aged and Older Adults: A National Longitudinal Analysis
Authors: Rouse Hillary J , Doyle Cassidy , Hueluer Gizem , Torres Mia D , Peterson Lindsay J , Pan Xi , Dobbs Debra , Du Yan , Conner Kyaien , Meng Hongdao 
Published: April 2023

Abstract

Objectives
The objective of this study was to examine associations between music engagement and episodic memory for more than 12 years in a nationally representative sample of middle- and older-aged adults in the United States.

Methods
This study is based on a secondary analysis of data from a sample (N = 5,021) of cognitively normal adults from the Health and Retirement Study (2006–2018). Episodic memory was measured by immediate and delayed recall tasks. Music engagement was classified as none, passive (i.e., listening to music), active (i.e., singing and/or playing an instrument), or both (i.e., listening to music and singing or playing an instrument).

Results
Compared with those with no music engagement, respondents who reported both passive and active engagement performed 0.258 points better at baseline on episodic memory tasks. This group also performed better across time with scores that declined by 0.043 points fewer per study visit. Additionally, compared to those with no music engagement, participants with passive music engagement had scores that declined by 0.023 points fewer per visit. There were no significant differences in performance at baseline for those with passive or active music engagement, or across time for those with active engagement.

Discussion
The results of this study suggest that engaging in both passive and active music engagement may be superior to engaging with music only passively or actively and that engaging in music both ways may be able to protect against age-related declines in episodic memory. Future research should examine whether community-based music engagement interventions can affect this trajectory of decline.
DivBrowse—interactive visualization and exploratory data analysis of variant call matrices
Authors: König Patrick , Beier Sebastian , Mascher Martin , Stein Nils , Lange Matthias , Scholz Uwe 
Published: April 2023

Abstract

Background
The sequencing of whole genomes is becoming increasingly affordable. In this context, large-scale sequencing projects are generating ever larger datasets of species-specific genomic diversity. As a consequence, more and more genomic data need to be made easily accessible and analyzable to the scientific community.

Findings
We present DivBrowse, a web application for interactive visualization and exploratory analysis of genomic diversity data stored in Variant Call Format (VCF) files of any size. By seamlessly combining BLAST as an entry point together with interactive data analysis features such as principal component analysis in one graphical user interface, DivBrowse provides a novel and unique set of exploratory data analysis capabilities for genomic biodiversity datasets. The capability to integrate DivBrowse into existing web applications supports interoperability between different web applications. Built-in interactive computation of principal component analysis allows users to perform ad hoc analysis of the population structure based on specific genetic elements such as genes and exons. Data interoperability is supported by the ability to export genomic diversity data in VCF and General Feature Format 3 files.

Conclusion
DivBrowse offers a novel approach for interactive visualization and analysis of genomic diversity data and optionally also gene annotation data by including features like interactive calculation of variant frequencies and principal component analysis. The use of established standard file formats for data input supports interoperability and seamless deployment of application instances based on the data output of established bioinformatics pipelines.
BiotechLec: an interactive guide of commercial lectins for glycobiology and biomedical research applications
Authors: Schnider Boris , Escudero Francisco L , Imberty Anne , Lisacek Frédérique 
Published: April 2023

Abstract
For decades, lectins have been used as probes in glycobiology and this usage has gradually spread to other domains of Life Science. Nowadays, researchers investigate glycan recognition with lectins in diverse biotechnology and clinical applications, addressing key questions regarding binding specificity. The latter is documented in scattered and heterogeneous sources, and this situation calls for a centralized and easy-access reference. To address this need, an on-line solution called BiotechLec (https://www.unilectin.eu/biotechlec) is proposed in a new section of UniLectin, a platform dedicated to lectin molecular knowledge.
Substantive Law Aspects of the ‘Design Package’
Authors: Kur Annette , Endrich-Laimböck Tobias , Huckschlag Marc 
Published: April 2023

Abstract
On 28 November 2022, the EU Commission published proposals for amendment of the Community Design Regulation (CDR) and for the recast of the Design Directive (DDir). Both proposals (in the following: PEUDR, PDDir) were preceded by reports and comprehensive consultations with interested circles. The aim of both proposals is to streamline and simplify the proceedings, enhance harmonisation, and improve the functioning of design legislation inter alia regarding novel forms of designs and reproduction technologies, providing a more robust catalogue of limitations, liberalisation of the spare parts market, and clarification of the relationship with copyright. The present article highlights the issues which are considered to be particularly important and deserving of further comments and clarifications.
Novel mRNA Signature for Anti-TNF-α Therapy Primary Response in Patients With Ulcerative Colitis
Authors: Yang Xinhui , Shi Jintong , Wang Gaoyang , Chen Huifang , Ye Youqiong , Zhong Jie , Wang Zhengting 
Published: April 2023

Abstract

Background
Ulcerative colitis (UC), an idiopathic, chronic inflammatory disorder of the colonic mucosa, is commonly treated with antitumor necrosis factor α (anti-TNF-α) agents. However, only approximately two-thirds have an initial response to these therapies.

Methods
We integrated gene expression profiling from 3 independent data sets of 79 UC patients before they began anti-TNF-α therapy and calculated the differentially expressed genes between patient response and nonresponse to anti-TNF-α therapy and developed a de novo response-associated transcription signature score (logOR_Score) to demonstrate the predictive capability of anti-TNF-α therapy for therapeutic efficacy. Furthermore, we performed association analysis of the logOR_Score and clinical features, such as disease activity and immune microenvironment.

Results
A total of 2522 responsive and 1824 nonresponsive genes were identified from the integrated data set. Responsive genes were significantly enriched in metabolism-related pathways, whereas nonresponsive ones were associated with immune response–related pathways. The logOR_Score enabled the accurate prediction of the therapeutic efficacy of anti-TNF-α in 4 independent patient cohorts and outperformed the predictions made based on 6 transcriptome-based signatures. In terms of clinical features, the logOR_Score correlated highly with the activity of UC. From an immune microenvironment perspective, logOR_Scores of CD8+IL-17+ T cells, follicular B cells, and innate lymphoid cells significantly decreased in inflamed UC tissue.

Conclusions
The de novo response-associated transcription signature may provide novel insights into the personalized treatment of patients with UC. Comprehensive analyses of the response-related subtypes and the association between logOR_Score and clinical features and immune microenvironment may provide insights into the underlying UC pathogenesis.
Creation of a structured molecular genomics report for Germany as a local adaption of HL7’s Genomic Reporting Implementation Guide
Authors: Stellmach Caroline , Sass Julian , Auber Bernd , Boeker Martin , Wienker Thomas , Heidel Andrew J , Benary Manuela , Schumacher Simon , Ossowski Stephan , Klauschen Frederick , Möller Yvonne , Schmutzler Rita , Ustjanzew Arsenij , Werner Patrick , Tomczak Aurelie , Hölter Thimo , Thun Sylvia 
Published: April 2023

AbstractObjectiveThe objective was to develop a dataset definition, information model, and FHIR® specification for key data elements contained in a German molecular genomics (MolGen) report to facilitate genomic and phenotype integration in electronic health records.Materials and MethodsA dedicated expert group participating in the German Medical Informatics Initiative reviewed information contained in MolGen reports, determined the key elements, and formulated a dataset definition. HL7’s Genomics Reporting Implementation Guide (IG) was adopted as a basis for the FHIR® specification which was subjected to a public ballot. In addition, elements in the MolGen dataset were mapped to the fields defined in ISO/TS 20428:2017 standard to evaluate compliance.ResultsA core dataset of 76 data elements, clustered into 6 categories was created to represent all key information of German MolGen reports. Based on this, a FHIR specification with 16 profiles, 14 derived from HL7®’s Genomics Reporting IG and 2 additional profiles (of the FamilyMemberHistory and RiskAssessment resources), was developed. Five example resource bundles show how our adaptation of an international standard can be used to model MolGen report data that was requested following oncological or rare disease indications. Furthermore, the map of the MolGen report data elements to the fields defined by the ISO/TC 20428:2017 standard, confirmed the presence of the majority of required fields.ConclusionsOur report serves as a template for other research initiatives attempting to create a standard format for unstructured genomic report data. Use of standard formats facilitates integration of genomic data into electronic health records for clinical decision support.
Comparative studies of ovipositional preference, larval feeding selectivity, and nutritional indices of Spodoptera frugiperda (Lepidoptera: Noctuidae) on 6 crops
Authors: Wang Wen-Wen , He Peng-Yang , Liu Tong-Xian , Jing Xiang-Feng , Zhang Shi-Ze 
Published: April 2023

Abstract
The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), is a significant invasive pest identified as a serious threat to global agricultural production and food security. However, its ovipositional preference, larval feeding selectivity, and nutritional indices are less studied. Here, we investigated these traits of FAW when fed on maize, wheat, soybean, tomato, cotton, and Chinese cabbage, and analyzed the correlation between its nutritional indices and the nutritional contents of crops. The results showed that the highest number of eggs were laid on maize and the lowest number were laid on tomato. The highest feeding choice rate of third instar larvae was on maize, and the lowest was on Chinese cabbage. The fifth instar larvae showed the highest feeding choice rate on maize, but no significant differences were found among other crop species. The food consumption (FC), the relative growth rate (RGR), and the approximate digestibility (AD) were significantly higher on maize and wheat, while the efficiency of conversion of ingested food (ECI) and the efficiency of conversion of digested food (ECD) were significantly higher when fed on cotton and Chinese cabbage. The FC, the relative consumption rate (RCR), RGR, and AD were significantly and positively correlated with soluble sugar and protein contents of host plants, while the ECI and ECD were significantly and negatively correlated with the soluble sugar content. The present study indicates that FAW may cause potential economic losses to these crops besides maize, and these findings are valuable in managing and controlling this pest.
Exploring the effects of caffeine on Aedes albopictus (Diptera: Culicidae) survival and fecundity
Authors: Abernathy Haley A , Boyce Ross M , Reiskind Michael H 
Published: April 2023

Abstract
Investigating new avenues of mosquito control is an important area of entomological research. Examining the effects of various compounds on mosquito biology contributes to the foundation of knowledge from which novel control methods can be built. Caffeine, in particular, is a commonly consumed compound that has not been thoroughly studied for its potential in disrupting the natural life cycle of mosquitoes. In this exploratory study, we analyzed caffeine’s effect on the blood-feeding behavior, survival, and fecundity of Aedes albopictus Skuse (Diptera: Culicidae) mosquitoes. Two outcomes, blood-feeding behavior and fecundity, were analyzed in the first experiment in which mosquitoes were exposed to caffeine doses ranging from 0.2 to 2.4 mg/ml. We found a negative linear relationship between dose and fecundity, but no significant impact on blood-feeding behavior. Adjustments were made to the experimental design in which mosquitoes were exposed to doses ranging from 2.5 to 20 mg/ml. From this experiment, we found that caffeine negatively affected blood-feeding behavior, survival, and fecundity especially at higher concentrations. These results suggest that caffeine could be a potential target for future mosquito control research.