bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical simulations and optimization of perovskite/CI(G)S tandem solar cells using the transfer matrix method
Authors: Bojar Aleksandra , Micha Daniel , Giteau Maxime , Ruiz-Preciado Marco A , Paetzold Ulrich W , Simor Marcel , Gevaerts Veronique S , Carron Romain , Medjoubi Karim , Collin Stéphane , Naghavi Negar , Guillemoles Jean-François , Schulz Philip
Published: April 2023

In this work we employ the transfer matrix method for the analysis of optical materials properties to simulate and optimize monolithic tandem solar cell devices based on CuIn1−x
Ga
x
Se2, CI(G)S, and perovskite (PVK) absorbers. By finding models that fit well the experimental data of the CI(G)S solar cell, the semitransparent perovskite solar cell (PSC) and the PVK/CI(G)S monolithic tandem solar cell, we were able to perform a detailed optical loss analysis that allowed us to determine sources of parasitic absorption. We found better substitute materials for the transport layers to increase the power conversion efficiency and, in case of semitransparent PSCs, sub-bandgap transmittance. Our results set guidelines for the monolithic PVK/CI(G)S tandem solar cells development, predicting an achievable efficiency of 30%.
Simulation of new thin film Zn(O,S)/CIGS solar cell with bandgap grading
Authors: Elhady Fady , M Abdolkader Tarek , Fedawy Mostafa
Published: April 2023

Copper-Indium-Gallium-diSelenide (CIGS) thin film solar cell is a promising candidate for energy harvesting because of its high absorption coefficient and low cost compared to silicon-based solar cells. Absorber layer bandgap grading is a suitable method to improve CIGS thin film solar cell performance. Bandgap grading leads to a decrease in the recombination rate at the rear surface, which increases the open circuit voltage. Furthermore, bandgap grading improves the short circuit current due to the enhancement of collection probability. This paper introduces various routes for improving the performance of thin film CIGS solar cells by using bandgap grading. As a first step, both the bandgap energy and the thickness of the CIGS absorber layer of a uniform bandgap profile are optimized to get the best performance. Simulation is performed using SCAPS software and optimization results show that CIGS absorber layer with a bandgap of 1.2 eV and a thickness of 0.7 μm achieves a 22.48% efficiency. Then, bandgap grading with a parabolic distribution of various profiles is investigated and compared. It is found that with a parabolic double bandgap grading profile, which is a combination of front and back grading, an efficiency of up to 24.16% is achieved. This improvement is obtained using a gallium composition ratio of 0.1 for the minimal bandgap at 0.1 μm and 0.13 μm from the back contact and front contact, respectively. This result represents a 7.47% improvement compared to the baseline structure of a CIGS solar cell.
Policy approaches to mitigate in-use methane emissions from natural gas use as a marine fuel
Authors: Laskar Imranul I , Giang Amanda
Published: April 2023

Unregulated in-use methane emissions (or methane slip) can reduce or even eliminate the overall climate benefits of using liquefied natural gas as a marine fuel. We conduct critical review and expert interviews to identify methane slip mitigation measures, and then identify and evaluate potential policy instruments that could incentivize their uptake while considering the shipping sector’s climate targets. We find that regulatory instruments are expected to perform the best across a range of criteria when they are at the global level, include methane on a CO2-equivalent and lifecycle basis, promote polycentric approaches to climate governance, and allow flexibility in how the industry incorporates decarbonization measures. Market-based approaches and informational governance policies complement regulatory instruments by improving cost-effectiveness and increasing the availability of relevant information on emissions mitigation. The urgency and scale of shipping climate targets underscore the need for policy approaches that support planning for long-term decarbonization pathways and that can avoid locking into fossil-carbon intensive systems.
Escalation to intensive care for the older patient. An exploratory qualitative study of patients aged 65 years and older and their next of kin during the COVID-19 pandemic: the ESCALATE study
Authors: Warner Bronwen E , Harry Alice , Wells Mary , Brett Stephen J , Antcliffe David B
Published: April 2023

Background

older people comprise the majority of hospital medical inpatients so decision-making regarding admission of this cohort to the intensive care unit (ICU) is important. ICU can be perceived by clinicians as overly burdensome for patients and loved ones, and long-term impact on quality of life considered unacceptable, effecting potential bias against admitting older people to ICU. The COVID-19 pandemic highlighted the challenge of selecting those who could most benefit from ICU.

Objective

this qualitative study aimed to explore the views and recollections of escalation to ICU from older patients (aged ≥ 65 years) and next of kin (NoK) who experienced a COVID-19 ICU admission.

Setting

the main site was a large NHS Trust in London, which experienced a high burden of COVID-19 cases.

Subjects

30 participants, comprising 12 patients, 7 NoK of survivor and 11 NoK of deceased.

Methods

semi-structured interviews with thematic analysis using a framework approach.

Results

there were five major themes: inevitability, disconnect, acceptance, implications for future decision-making and unique impact of the COVID-19 pandemic. Life was highly valued and ICU perceived to be the only option. Prior understanding of ICU and admission decision-making explanations were limited. Despite benefit of hindsight, having experienced an ICU admission and its consequences, most could not conceptualise thresholds for future acceptable treatment outcomes.

Conclusions

in this study of patients ≥65 years and their NoK experiencing an acute ICU admission, survival was prioritised. Despite the ordeal of an ICU stay and its aftermath, the decision to admit and sequelae were considered acceptable.
A Mixture Model for Estimating SARS-CoV-2 Seroprevalence in Chennai, India
Authors: Hitchings Matt D T , Patel Eshan U , Khan Rifa , Srikrishnan Aylur K , Anderson Mark , Kumar K S , Wesolowski Amy P , Iqbal Syed H , Rodgers Mary A , Mehta Shruti H , Cloherty Gavin , Cummings Derek A T , Solomon Sunil S
Published: April 2023

Serological assays used to estimate the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) often rely on manufacturers’ cutoffs established on the basis of severe cases. We conducted a household-based serosurvey of 4,677 individuals in Chennai, India, from January to May 2021. Samples were tested for SARS-CoV-2 immunoglobulin G (IgG) antibodies to the spike (S) and nucleocapsid (N) proteins. We calculated seroprevalence, defining seropositivity using manufacturer cutoffs and using a mixture model based on measured IgG level. Using manufacturer cutoffs, there was a 5-fold difference in seroprevalence estimated by each assay. This difference was largely reconciled using the mixture model, with estimated anti-S and anti-N IgG seroprevalence of 64.9% (95% credible interval (CrI): 63.8, 66.0) and 51.5% (95% CrI: 50.2, 52.9), respectively. Age and socioeconomic factors showed inconsistent relationships with anti-S and anti-N IgG seropositivity using manufacturer cutoffs. In the mixture model, age was not associated with seropositivity, and improved household ventilation was associated with lower seropositivity odds. With global vaccine scale-up, the utility of the more stable anti-S IgG assay may be limited due to the inclusion of the S protein in several vaccines. Estimates of SARS-CoV-2 seroprevalence using alternative targets must consider heterogeneity in seroresponse to ensure that seroprevalence is not underestimated and correlates are not misinterpreted.
CREPE: a Shiny app for transcription factor cataloguing
Authors: Rosado-Tristani Diego A , Rodríguez-Martínez José A
Published: April 2023

Transcription factors (TFs) are proteins that directly interpret the genome to regulate gene expression and determine cellular phenotypes. TF identification is a common first step in unraveling gene regulatory networks. We present CREPE, an R Shiny app to catalogue and annotate TFs. CREPE was benchmarked against curated human TF datasets. Next, we use CREPE to explore the TF repertoires of Heliconius erato and Heliconius melpomene butterflies.

Availability and implementation

CREPE is available as a Shiny app package available at GitHub (github.com/dirostri/CREPE).

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Deciphering associations between gut microbiota and clinical factors using microbial modules
Authors: Wang Ran , Zheng Xubin , Song Fangda , Wong Man Hon , Leung Kwong Sak , Cheng Lixin
Published: April 2023

Motivation

Human gut microbiota plays a vital role in maintaining body health. The dysbiosis of gut microbiota is associated with a variety of diseases. It is critical to uncover the associations between gut microbiota and disease states as well as other intrinsic or environmental factors. However, inferring alterations of individual microbial taxa based on relative abundance data likely leads to false associations and conflicting discoveries in different studies. Moreover, the effects of underlying factors and microbe–microbe interactions could lead to the alteration of larger sets of taxa. It might be more robust to investigate gut microbiota using groups of related taxa instead of the composition of individual taxa.

Results

We proposed a novel method to identify underlying microbial modules, i.e. groups of taxa with similar abundance patterns affected by a common latent factor, from longitudinal gut microbiota and applied it to inflammatory bowel disease (IBD). The identified modules demonstrated closer intragroup relationships, indicating potential microbe–microbe interactions and influences of underlying factors. Associations between the modules and several clinical factors were investigated, especially disease states. The IBD-associated modules performed better in stratifying the subjects compared with the relative abundance of individual taxa. The modules were further validated in external cohorts, demonstrating the efficacy of the proposed method in identifying general and robust microbial modules. The study reveals the benefit of considering the ecological effects in gut microbiota analysis and the great promise of linking clinical factors with underlying microbial modules.

Availability and implementation

https://github.com/rwang-z/microbial_module.git.
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape
Authors: Boniolo Fabio , Hoffmann Markus , Roggendorf Norman , Tercan Bahar , Baumbach Jan , Castro Mauro A A , Robertson A Gordon , Saur Dieter , List Markus
Published: April 2023

Motivation

Cancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene–miRNA gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity.

Results

We show how spongEffects can be used for downstream interpretation and machine learning tasks such as tumor classification and for identifying subtype-specific regulatory interactions. In a concrete example of breast cancer subtype classification, we prioritize modules impacting the biology of the different subtypes. In summary, spongEffects prioritizes ceRNA modules as biomarkers and offers insights into the miRNA regulatory landscape. Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking.

Availability and implementation

https://bioconductor.org/packages/devel/bioc/html/SPONGE.html.
Effective design and inference for cell sorting and sequencing based massively parallel reporter assays
Authors: Gilliot Pierre-Aurélien , Gorochowski Thomas E
Published: April 2023

Motivation

The ability to measure the phenotype of millions of different genetic designs using Massively Parallel Reporter Assays (MPRAs) has revolutionized our understanding of genotype-to-phenotype relationships and opened avenues for data-centric approaches to biological design. However, our knowledge of how best to design these costly experiments and the effect that our choices have on the quality of the data produced is lacking.

Results

In this article, we tackle the issues of data quality and experimental design by developing FORECAST, a Python package that supports the accurate simulation of cell-sorting and sequencing-based MPRAs and robust maximum likelihood-based inference of genetic design function from MPRA data. We use FORECAST’s capabilities to reveal rules for MPRA experimental design that help ensure accurate genotype-to-phenotype links and show how the simulation of MPRA experiments can help us better understand the limits of prediction accuracy when this data are used for training deep learning-based classifiers. As the scale and scope of MPRAs grows, tools like FORECAST will help ensure we make informed decisions during their development and the most of the data produced.

Availability and implementation

The FORECAST package is available at: https://gitlab.com/Pierre-Aurelien/forecast. Code for the deep learning analysis performed in this study is available at: https://gitlab.com/Pierre-Aurelien/rebeca.
Cortical microstructural gradients capture memory network reorganization in temporal lobe epilepsy
Authors: Royer Jessica , Larivière Sara , Rodriguez-Cruces Raul , Cabalo Donna Gift , Tavakol Shahin , Auer Hans , Ngo Alexander , Park Bo-yong , Paquola Casey , Smallwood Jonathan , Jefferies Elizabeth , Caciagli Lorenzo , Bernasconi Andrea , Bernasconi Neda , Frauscher Birgit , Bernhardt Boris C
Published: April 2023

Temporal lobe epilepsy (TLE), one of the most common pharmaco-resistant epilepsies, is associated with pathology of paralimbic brain regions, particularly in the mesiotemporal lobe. Cognitive dysfunction in TLE is frequent, and particularly affects episodic memory. Crucially, these difficulties challenge the quality of life of patients, sometimes more than seizures, underscoring the need to assess neural processes of cognitive dysfunction in TLE to improve patient management.

Our work harnessed a novel conceptual and analytical approach to assess spatial gradients of microstructural differentiation between cortical areas based on high-resolution MRI analysis. Gradients track region-to-region variations in intracortical lamination and myeloarchitecture, serving as a system-level measure of structural and functional reorganization.

Comparing cortex-wide microstructural gradients between 21 patients and 35 healthy controls, we observed a reorganization of this gradient in TLE driven by reduced microstructural differentiation between paralimbic cortices and the remaining cortex with marked abnormalities in ipsilateral temporopolar and dorsolateral prefrontal regions. Findings were replicated in an independent cohort. Using an independent post-mortem dataset, we observed that in vivo findings reflected topographical variations in cortical cytoarchitecture. We indeed found that macroscale changes in microstructural differentiation in TLE reflected increased similarity of paralimbic and primary sensory/motor regions. Disease-related transcriptomics could furthermore show specificity of our findings to TLE over other common epilepsy syndromes. Finally, microstructural dedifferentiation was associated with cognitive network reorganization seen during an episodic memory functional MRI paradigm and correlated with interindividual differences in task accuracy.

Collectively, our findings showing a pattern of reduced microarchitectural differentiation between paralimbic regions and the remaining cortex provide a structurally-grounded explanation for large-scale functional network reorganization and cognitive dysfunction characteristic of TLE.
Why people engage in corrupt collaboration: an observation at the multi-brain level
Authors: Zhang Dandan , Zhang Shen , Lei Zhen , Li Yiwei , Li Xianchun , Gu Ruolei
Published: April 2023

Recent studies suggest that corrupt collaboration (i.e. acquiring private benefits with joint immoral acts) represents a dilemma between the honesty and reciprocity norms. In this study, we asked pairs of participants (labeled as A and B) to individually toss a coin and report their outcomes; their collective benefit could be maximized by dishonestly reporting (a corrupt behavior). As expected, the likelihood of corrupt behavior was high; this probability was negatively correlated with player A’s moral judgment ability but positively correlated with player B’s empathic concern (EC). Functional near-infrared spectroscopy data revealed that the brain-to-brain synchronization in the right dorsolateral prefrontal cortex was associated with fewer corrupt behaviors, and that it mediated the relationship between player A’s moral judgment ability and corrupt collaboration. Meanwhile, the right temporal–parietal junction synchronization was associated with more corrupt behaviors, and that it mediated the relationship between player B’s EC and corrupt collaboration. The roles of these 2 regions are interpreted according to the influence of the honesty and reciprocity norms on corrupt collaboration. In our opinion, these findings provide insight into the underlying mechanisms and modulating factors of corrupt collaboration.
A multidisciplinary approach to re-intervention in an Ebstein patient: a case report
Authors: Pius Charlene , Aggarwal Suneil , Rao Archana , Ashrafi Reza
Published: April 2023

Background

Ebstein’s anomaly is a rare condition due to incomplete delamination of the tricuspid valve (TV) leaflets with downward displacement of the proximal leaflet attachments. It is associated with a smaller functional right ventricle (RV) and tricuspid regurgitation (TR) that is typically treated with TV replacement or repair. However, future re-intervention poses challenges. We describe a multidisciplinary team approach to re-intervention in a pacing-dependant Ebstein patient with severe bioprosthetic TV regurgitation.

Case summary

A 49-year-old female patient underwent bioprosthetic TV replacement for severe TR in Ebstein’s. Post-operatively, she developed complete atrioventricular (AV) block necessitating the implantation of a permanent pacemaker which included a coronary sinus (CS) lead as the ventricular lead. Five years later, she presented with syncope due to a failing ventricular pacing lead, and a new RV lead was positioned across the TV bioprosthesis due to the lack of CS options. Two years later, she presented with breathlessness and lethargy with severe TR identified on transthoracic echocardiography. She successfully underwent a percutaneous leadless pacemaker implant, extraction of existing pacing system, and implantation of valve-in-valve TV.

Discussion

Patients with Ebstein’s anomaly typically undergo TV repair or replacement. Following surgical intervention, owing to the anatomical location, patients can develop AV block requiring a pacemaker. Pacemaker implantation may involve a CS lead to avoid placing a lead across the new TV in efforts to avoid lead induced TR. Over time, these patients not uncommonly require re-intervention that can be challenging especially in pacing-dependant patients with leads across the TV.
Rapid virtual fractional flow reserve using 3D computational fluid dynamics
Authors: Newman Thomas , Borker Raunak , Aubiniere-Robb Louise , Hendrickson Justin , Choudhury Dipankar , Halliday Ian , Fenner John , Narracott Andrew , Hose D Rodney , Gosling Rebecca , Gunn Julian P , Morris Paul D
Published: April 2023

Aims

Over the last ten years, virtual Fractional Flow Reserve (vFFR) has improved the utility of Fractional Flow Reserve (FFR), a globally recommended assessment to guide coronary interventions. Although the speed of vFFR computation has accelerated, techniques utilising full 3D computational fluid dynamics (CFD) solutions rather than simplified analytical solutions still require significant time to compute.

Methods and results

This study investigated the speed, accuracy and cost of a novel 3D-CFD software method based upon a graphic processing unit (GPU) computation, compared with the existing fastest central processing unit (CPU)-based 3D-CFD technique, on 40 angiographic cases. The novel GPU simulation was significantly faster than the CPU method (median 31.7 s (Interquartile Range (IQR) 24.0–44.4s) vs. 607.5 s (490–964 s), P < 0.0001). The novel GPU technique was 99.6% (IQR 99.3–99.9) accurate relative to the CPU method. The initial cost of the GPU hardware was greater than the CPU (£4080 vs. £2876), but the median energy consumption per case was significantly less using the GPU method (8.44 (6.80–13.39) Wh vs. 2.60 (2.16–3.12) Wh, P < 0.0001).

Conclusion

This study demonstrates that vFFR can be computed using 3D-CFD with up to 28-fold acceleration than previous techniques with no clinically significant sacrifice in accuracy.
A machine learning approach to predicting 30-day mortality following paediatric cardiac surgery: findings from the Australia New Zealand Congenital Outcomes Registry for Surgery (ANZCORS)
Authors: Betts Kim S , Marathe Supreet P , Chai Kevin , Konstantinov Igor , Iyengar Ajay , Suna Jessica ,   ANZCORS Collaborative, Andrews David , Brink Johann , Brizard Christian , Finucane Kirsten , d’Udekem Yves , Karl Tom R , Liava’a Matt , Orr Yishay , Venugopal Prem , Alphonso Nelson
Published: April 2023

OBJECTIVES

We aim to develop the first risk prediction model for 30-day mortality for the Australian and New Zealand patient populations and examine whether machine learning (ML) algorithms outperform traditional statistical approaches.

METHODS

Data from the Australia New Zealand Congenital Outcomes Registry for Surgery, which contains information on every paediatric cardiac surgical encounter in Australian and New Zealand for patients aged <18 years between January 2013 and December 2021, were analysed (n = 14 343). The outcome was mortality within the 30-day period following a surgical encounter, with ∼30% of the observations randomly selected to be used for validation of the final model. Three different ML methods were used, all of which employed five-fold cross-validation to prevent overfitting, with model performance judged primarily by the area under the receiver operating curve (AUC).

RESULTS

Among the 14 343 30-day periods, there were 188 deaths (1.3%). In the validation data, the gradient-boosted tree obtained the best performance [AUC = 0.87, 95% confidence interval = (0.82, 0.92); calibration = 0.97, 95% confidence interval = (0.72, 1.27)], outperforming penalized logistic regression and artificial neural networks (AUC of 0.82 and 0.81, respectively). The strongest predictors of mortality in the gradient boosting trees were patient weight, STAT score, age and gender.

CONCLUSIONS

Our risk prediction model outperformed logistic regression and achieved a level of discrimination comparable to the PRAiS2 and Society of Thoracic Surgery Congenital Heart Surgery Database mortality risk models (both which obtained AUC = 0.86). Non-linear ML methods can be used to construct accurate clinical risk prediction tools.
Harmonious relations: quality transmission among composers in the very long run
Authors: Borowiecki Karol Jan , Ford Nicholas Martin , Marchenko Maria
Published: April 2023

Most creative professionals develop and refine their talents by learning from others. In most empirical settings, estimating how this learning process fosters quality is challenging. This paper explores the transmission of quality among music composers over more than seven centuries. How does a composer’s quality influence the quality of the composers they teach? Using a unique dataset of 17,433 composers, we show a strong relationship between student and teacher quality. Moreover, this quality transmission persists across multiple generations. Our results provide new insights on drivers of creativity, as well as the influence of teachers on students’ achievements.
Treatment of multiple valve disease: surgery, structural intervention, or both?
Authors: Berti Sergio , Bonanni Michela , D’agostino Andreina , Celi Simona , Mariani Massimiliano
Published: April 2023

Multiple valve heart disease refers to the simultaneous presence of several valvular anomalies, while mixed valvular heart disease refers to the combination of stenotic lesions or regurgitation affecting the same valve. The pathophysiology of multiple and mixed valvular heart disease depends on the combination of affected valves and the severity of the individual valvular defects. Imaging is essential for diagnosis and assessment of disease severity. The treatment of combined valvular defects currently represents a challenge for both cardiac surgeons and interventional cardiologists since only few data in the literature address the clinical and therapeutic decision-making process related to these complex lesions. These are heterogeneous conditions, which differ from each other in the combination of the valves involved, in the pathogenesis with which they develop, in the severity of the individual lesions, in the associated surgical risk, in the possibility of being repaired, and in the undergoing transcatheter treatments. In addition to the severity of the individual valve defects, the choice of treatment also depends on the ventricular function and the general condition of the patient. This work aims to provide a review of the state of the art regarding the possible management strategies of the most common multiple valve diseases in clinical practice.
Predicting left ventricular functional recovery in ischaemic cardiomyopathy: needs and challenges
Authors: Radesich Cinzia , Cappelletto Chiara , Indennidate Carla , Perotto Maria , Di Lenarda Andrea
Published: April 2023

Left ventricular (LV) systolic function is an essential parameter for the evaluation of patients with ischaemic heart disease, and therapeutic choices are significantly driven by LV ejection fraction (LVEF) in the early stage of the disease and during follow-up. After an acute coronary syndrome, ventricular dysfunction may be reversible when caused by transient myocardial stunning. Therefore, the identification of clinical, laboratory, and instrumental predictors of improvement in LV systolic function (in addition to LVEF) is essential for an adequate prognostic stratification. In the setting of chronic ischaemic heart disease, there is no evidence that an improvement in LV systolic function is invariably associated with a better prognosis and LVEF is only one of many parameters that should be considered for the risk stratification. This state-of-the-art review will critically analyse the scientific evidence regarding known predictors of LVEF recovery, trying to elucidate their pathophysiological principles and clinical value.
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

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

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

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

The 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

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

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

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

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

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

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

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

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

Objective

The 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 Methods

A 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.

Results

A 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.

Conclusions

Our 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.