bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of optical wave propagation through turbulent atmosphere using fractional approach for FSO wireless communication
Authors: Khan Abdullah Nafis , Zubair Muhammad , Younis Usman
Published: January 2023

Free space optical (FSO) wireless communication has emerged as a viable alternative to the existing fiber optics and radio frequency (RF) communications due to its ability to operate in unlicensed spectrum, offering huge data handling capacities and being cost effective with easy deployment. The underlying communication mechanism in the FSO link is based upon the laser beam propagation model. The propagating free space optical beam undergoes signal degradation due to refraction and diffraction caused by atmospheric turbulence measured by refractive index structure parameter (C
n

2). In this work, a novel, robust analytical model for propagating Gaussian-beam through atmospheric turbulence is presented, by solving the space-fractional paraxial wave equation. We report analytical expressions for the intensity and long-term beam spreading of a Gaussian beam in terms of space-fractional parameter D, for the range 2 < D ≤ 3. This range of parameter D, defines the effective number of euclidean space corresponding to atmospheric turbulence levels faced by the propagating Gaussian beam in the FSO link. The results of the proposed fractional model and the existing models agreed well, therefore the D-dimensional parameter can be used to effectively express the value of refractive index structure parameter (C
n

2). The classical values of C
n

2 ranges form 10−13 to 10−16 for strong to weak fluctuations respectively. However, in fractional-dimension scale, these fluctuations can be express as D = 2.668 (strong fluctuations) to D = 2.999 (weak fluctuations). The ideal case of free space beam propagation can be expressed as D = 3, with no turbulence. Moreover, we have studied the fractional-dimension model performance for varying wavelengths. Further, based upon a practical example, we proposed a self-sustainable FSO link architecture to efficiently minimize the effect of weak and strong fluctuations on the propagating optical beam, based upon the D-dimension fractional parameter, hence ensuring reliability of FSO link.
Toward Open and Reproducible Epidemiology
Authors: Mathur Maya B , Fox Matthew P
Published: January 2023

Starting in the 2010s, researchers in the experimental social sciences rapidly began to adopt increasingly open and reproducible scientific practices. These practices include publicly sharing deidentified data when possible, sharing analytical code, and preregistering study protocols. Empirical evidence from the social sciences suggests such practices are feasible, can improve analytical reproducibility, and can reduce selective reporting. In academic epidemiology, adoption of open-science practices has been slower than in the social sciences (with some notable exceptions, such as registering clinical trials). Epidemiologic studies are often large, complex, conceived after data have already been collected, and difficult to replicate directly by collecting new data. These characteristics make it especially important to ensure their integrity and analytical reproducibility. Open-science practices can also pay immediate dividends to researchers’ own work by clarifying scientific reasoning and encouraging well-documented, organized workflows. We consider how established epidemiologists and early-career researchers alike can help midwife a culture of open science in epidemiology through their research practices, mentorship, and editorial activities.
ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR
Authors: Denoulet Marie , Brulé Mathilde , Anquez François , Vincent Audrey , Schnipper Julie , Adriaenssens Eric , Toillon Robert-Alain , Le Bourhis Xuefen , Lagadec Chann
Published: January 2023

Motivation

Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the bisulfite sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP. Therefore, the most convenient way to process results from the direct sequencing of PCR products (direct-BSP) is to manually analyze the chromatogram traces, which is a repetitive and prone to error task.

Results

Here, we implement a new R-based tool, called ABSP for analysis of bisulfite sequencing PCR, providing a complete analytic process of both direct-BSP and cloning-BSP data. It uses the raw sequencing trace files (.ab1) as input to compute and compare CpG methylation percentages. It is fully automated and includes a user-friendly interface as a built-in R shiny app, quality control steps and generates publication-ready graphics.

Availability and implementation

The ABSP tool and associated data are available on GitHub at https://github.com/ABSP-methylation-tool/ABSP.

Supplementary information

Supplementary data are available at Bioinformatics online.
EWF: simulating exact paths of the Wright–Fisher diffusion
Authors: Sant Jaromir , Jenkins Paul A , Koskela Jere , Spanò Dario
Published: January 2023

Motivation

The Wright–Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as selection, mutation and genetic drift. Simulating the paths of the process is challenging due to the form of the transition density. We present EWF, a robust and efficient sampler which returns exact draws for the diffusion and diffusion bridge processes, accounting for general models of selection including those with frequency dependence.

Results

Given a configuration of selection, mutation and endpoints, EWF returns draws at the requested sampling times from the law of the corresponding Wright–Fisher process. Output was validated by comparison to approximations of the transition density via the Kolmogorov–Smirnov test and QQ plots.

Availability and implementation

All softwares are available at https://github.com/JaroSant/EWF.

Supplementary information

Supplementary data are available at Bioinformatics online.
Dealing with dimensionality: the application of machine learning to multi-omics data
Authors: Feldner-Busztin Dylan , Firbas Nisantzis Panos , Edmunds Shelley Jane , Boza Gergely , Racimo Fernando , Gopalakrishnan Shyam , Limborg Morten Tønsberg , Lahti Leo , de Polavieja Gonzalo G
Published: January 2023

Motivation

Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.

Results

Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.

Availability and implementation

All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.

Supplementary information

Supplementary data are available at Bioinformatics online.
PANACEA: network-based methods for pharmacotherapy prioritization in personalized oncology
Authors: Ulgen Ege , Ozisik Ozan , Sezerman Osman Ugur
Published: January 2023

Motivation

Identifying appropriate pharmacotherapy options from genomics results is a significant challenge in personalized oncology. However, computational methods for prioritizing drugs are underdeveloped. With the hypothesis that network-based approaches can improve the performance by extending the use of potential drug targets beyond direct interactions, we devised two network-based methods for personalized pharmacotherapy prioritization in cancer.

Results

We developed novel personalized drug prioritization approaches, PANACEA: PersonAlized Network-based Anti-Cancer therapy EvaluAtion. In PANACEA, initially, the protein interaction network is extended with drugs, and a driverness score is assigned to each altered gene. For scoring drugs, either (i) the ‘distance-based’ method, incorporating the shortest distance between drugs and altered genes, and driverness scores, or (ii) the ‘propagation’ method involving the propagation of driverness scores via a random walk with restart framework is performed. We evaluated PANACEA using multiple datasets, and demonstrated that (i) the top-ranking drugs are relevant for cancer pharmacotherapy using TCGA data; (ii) drugs that cancer cell lines are sensitive to are identified using GDSC data; and (iii) PANACEA can perform adequately in the clinical setting using cases with known drug responses. We also illustrate that the proposed methods outperform iCAGES and PanDrugs, two previous personalized drug prioritization approaches.

Availability and implementation

The corresponding R package is available on GitHub. (https://github.com/egeulgen/PANACEA.git).

Supplementary information

Supplementary data are available at Bioinformatics online.
Reconstructive techniques following low anterior resection for carcinoma of the rectum: meta-analysis
Authors: Mathew Anvin , Ramachandra Deepti , Goyal Anuj , Nariampalli Karthyarth Mithun , Joseph Princy , Raj Rakesh Nirjhar , Kaushal Gourav , Agrawal Abhishek , Singh Bhadoria Ajeet , Dhar Puneet
Published: January 2023

Background

Multiple trials have compared reconstruction techniques used following the resection of distal rectal cancers, including straight colorectal anastomosis (SCA), colonic J pouch (CJP), side-to-end anastomosis (SEA), and transverse coloplasty (TCP). The latest meta-analysis on the subject concluded that all the reservoir techniques produce equally good surgical and functional outcomes compared with SCA. Numerous trials have been published in this regard subsequently. Hence, a network analysis (NMA) was performed to rank these techniques.

Methods

A literature search of MEDLINE, Embase, and the Cochrane Library from their inception until April 2021 was conducted to identify randomized trials. Functional and surgical outcome data were pooled. ORs and standardized mean differences (MDs) were used as pooled effect size measures. A frequentist NMA model was used.

Results

Thirty-two trials met the eligibility criteria comprising 3072 patients. CJP showed better functional outcomes, such as low stool frequency and better incontinence score, both in the short term (stool frequency, MD −2.06, P < 0.001; incontinence, MD −1.17, P = 0.007) and intermediate term (stool frequency, MD −0.81, P = 0.021; incontinence MD −0.56, P = 0.083). Patients with an SEA (long-term OR 4.37; P = 0.030) or TCP (long-term OR 5.79; P < 0.001) used more antidiarrheal medications constantly. The urgency and sensation of incomplete evacuation favoured CJP in the short term. TCP was associated with a higher risk of anastomotic leakage (OR 12.85; P < 0.001) and stricture (OR 3.21; P = 0.012).

Conclusion

Because of its better functional outcomes, CJP should be the reconstruction technique of choice. TCP showed increased anastomotic leak and stricture rates, warranting judicious use.
Hotspots within a hotspot: evolutionary measures unveil interesting biogeographic patterns in threatened coastal forests in Chile
Authors: Mardones Daniela , Scherson Rosa A
Published: January 2023

Given the continuous loss of biodiversity, there is an urgent need to study its patterns to generate conservation measures. Complementing traditional biodiversity measures with indices that incorporate evolutionary aspects such as phylogenetic diversity or phylogenetic endemism (PD or PE) allows us to infer possible historical processes that could explain the conformation of current biodiversity. In this study, patterns of richness and endemism were determined and contrasted with the evolutionary indices PD, PE, PDres (residual PD), RPD (relative PD) and RPE (relative PE) for the woody flora in a latitudinal gradient (30°S to 40°S) in the Chilean coastal range. A phylogenetic tree was constructed using three DNA regions to calculate evolutionary indices (PD and PE) and compare them at different taxonomic levels. The results of PD and PE were spatially consistent with those of richness and endemism, but evolutionarily important sites were discovered. PD-derived indices indicate three evolutionary hotspots: a cradle-type site with a predominance of neoendemics (generating recent diversity) at 33°S, three museum-type sites with a predominance of palaeoendemics (maintaining relict diversity) at 30°S, 38°S and 40°S and one with high PD and PE at 37°S. We found evolutionary hotspots within the hotspot of Central Chile with different characteristics. Incorporating measures that consider the evolutionary aspect has important implications for the conservation of highly diverse and endemic areas.
Plasma biomarker profiles in autosomal dominant Alzheimer’s disease
Authors: Johansson Charlotte , Thordardottir Steinunn , Laffita-Mesa José , Rodriguez-Vieitez Elena , Zetterberg Henrik , Blennow Kaj , Graff Caroline
Published: January 2023

Emerging plasma biomarkers of Alzheimer's disease might be non-invasive tools to trace early Alzheimer's disease-related abnormalities such as the accumulation of amyloid-beta peptides, neurofibrillary tau tangles, glial activation and neurodegeneration. It is, however, unclear which pathological processes in the CNS can be adequately detected by peripheral measurements and whether plasma biomarkers are equally applicable in both clinical and preclinical phases. Here we aimed to explore the timing and performance of plasma biomarkers in mutation carriers compared to non-carriers in autosomal dominant Alzheimer's disease.

Samples (n = 164) from mutation carriers (n = 33) and non-carriers (n = 42) in a Swedish cohort of autosomal dominant Alzheimer's disease (APP p.KM670/671NL, APP p.E693G and PSEN1 p.H163Y) were included in explorative longitudinal analyses. Plasma phosphorylated tau (P-tau181), total tau (T-tau), neurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP) concentrations were measured with a single-molecule array method as previously described. Plasma biomarkers were additionally correlated to Alzheimer's disease core biomarkers in the CSF.

Results from the longitudinal analyses confirmed that plasma P-tau181, NfL and GFAP concentrations were higher in mutation carriers compared to non-carriers. This change was observed in the presymptomatic phase and detectable first as an increase in GFAP approximately 10 years before estimated symptom onset, followed by increased levels of P-tau181 and NfL closer to expected onset. Plasma P-tau181 levels were correlated to levels of P-tau181 and T-tau in the CSF.

Altogether, plasma P-tau181, GFAP and NfL seem to be feasible biomarkers to detect different Alzheimer's disease-related pathologies already in presymptomatic individuals. Interestingly, changes in plasma GFAP concentrations were detected prior to P-tau181 and NfL. Our results suggest that plasma GFAP might reflect Alzheimer's disease pathology upstream to accumulation of tangles and neurodegeneration. The implications of these findings need additional validation, in particular because of the limited sample size.
Brain Communications early career researcher paper prize
Authors: Spires-Jones Tara L
Published: January 2023

Our editor introduces an early career researcher prize for the first author of a paper published in Brain Communications in 2022.
Safety and Effectiveness of Ustekinumab for Crohn’s Disease in Japanese Post-marketing Surveillance in Biologic-Naive and -Experienced Conriemed
Authors: Nagano Katsumasa , Hata Erina , Asano Teita , Tsuchiya Hiroaki , Takagishi Masayuki , Yamazaki Hiroshi , Tominaga Sonoko , Matsumoto Takayuki
Published: January 2023

Background

To present the real-world evidence on the safety and effectiveness of ustekinumab (UST) through 52-week treatment for Crohn’s disease (CD) under an analysis of post-market surveillance data in Japan.

Methods

This prospective, post-marketing surveillance study was conducted in 341 patients from 91 medical facilities in Japan. Patients received UST 90 mg injected subcutaneously once every 12 weeks (or every 8 weeks if patients show weak effectiveness) after an induction dose given intravenously. Clinical response (100-point decrease in Crohn’s Disease Activity Index [CDAI] score), clinical remission (CDAI score of <150), steroid-free clinical remission, C-reactive protein, endoscopy, physician global assessment, and adverse drug reactions (ADRs) were evaluated through 52 weeks.

Results

The overall rate of clinical remission was 49.2% at week 8 and 56.0% at week 52. The rate of clinical remission in biologic-naive patients was 75.9% and 66.7% at weeks 8 and 52, respectively, whereas the rate in biologic-experienced patients was 41.4% and 52.6% at weeks 8 and 52, respectively. For 52 weeks, the overall incidence of ADRs and serious adverse drug reactions (SADRs) was 11.7% and 6.7%, respectively. The most frequently reported SADRs was worsening of CD (1.8%). In multivariate analysis, ADRs incidence was significantly lower in patients with ileal involvement of CD (odds ratio = 0.25, 95% CI 0.07–0.85, P = .026), although disease location has no association with effectiveness of UST.

Conclusions

The present study identified no new safety concerns and effectiveness for CD in Japanese patients treated with UST.
Retrograde venography to navigate an occluded subclavian vein to achieve cardiac resynchronization therapy upgrade via His bundle pacing: a case report
Authors: Pavitt Christopher , Luther Vishal , Lefroy David , Tanner Mark
Published: January 2023

Background

Guidelines support upgrade to cardiac resynchronization therapy (CRT) through His-bundle pacing (HBP) in pacing-induced cardiomyopathy and moderate left ventricular systolic dysfunction (LVSD). Lead-related venous occlusion can represent an obstacle to upgrade procedures. We describe a technique to overcome venous occlusion through direct puncture of a collateral vein facilitating upgrade to HBP.

Case summary

An 84-year-old man with a right ventricular (RV) pacemaker was referred with New York Heart Association (NYHA) Class III breathlessness secondary to moderate LVSD (left ventricular ejection fraction [LVEF] 45%). Device interrogation revealed 100% RV pacing and AV-dyssynchrony. To optimize atrioventricular (AV) and interventricular (VV) synchrony a CRT upgrade with HBP was planned. Venography revealed an occluded left subclavian vein which was probed in a retrograde manner using a 6F MPA catheter from right femoral venous access. We were able to direct the catheter distal to the left brachio-cephalic vein and define the occlusion using contrast. A collateral branch was identified, a J-wire was left in this branch and venous access was secured at this medial subclavian site using the Seldinger technique. A right atrial lead was deployed and 69 cm ISI-1 His lead was deployed via a C315 sheath at the His-bundle. The resulted in non-selective HBP (Stim-QRS end 146 ms). There were no procedural complications. Two months later both symptoms and LV function (LVEF 55%) improved.

Discussion

Lead-related venous occlusion occurs frequently and can be probed in a retrograde manner from femoral venous access using contrast, facilitating direct percutaneous puncture of collateral venous branches to allow upgrade to CRT via HBP.
Cardiac sarcoidosis presenting with complex conduction abnormalities as the first manifestation of widespread systemic sarcoidosis: a case report
Authors: Müller Maximilian L , Poller Wolfgang , Skurk Carsten , Poddubnyy Denis , Siegmund Britta , Schneider Thomas , Landmesser Ulf , Heidecker Bettina
Published: January 2023

Background

Sarcoidosis is a granulomatous multi-organ disease of unknown aetiology. Despite being relatively rare, cardiac sarcoidosis constitutes a very important manifestation of sarcoidosis, as its symptoms regularly precede or occur in isolation of more prevalent ones, and as it is the main driver of mortality in systemic sarcoidosis.

Case summary

We present the case of a 37-year-old woman, in which clinically isolated cardiac sarcoidosis revealed widespread systemic sarcoidosis. Apart from constitutional symptoms and strong recurrent dizziness (i.e. near-syncopes), which persisted for multiple years already, our patient initially presented with complex conduction abnormalities, including a right bundle branch block, left anterior hemi-block, and atrioventricular block °1. Following inconclusive endomyocardial biopsies, performed due to detection of focal septal scarring on cardiac magnetic resonance imaging, an 18F-FDG-PET-CT, performed upon admission to our clinic, showed distinct hypermetabolic lesions indicative of active inflammation in various organs and raised suspicion of systemic sarcoidosis. Eventually, histopathological evidence of non-caseating granulomas in affected lymph nodes, extracted by bronchoscopy, confirmed the diagnosis of systemic sarcoidosis after reasonable exclusion of other granulomatous diseases. Immediate initiation of long-term immunosuppressive therapy led to almost complete remission, as monitored by consequential 18F-FDG-PET-CT scans.

Discussion

Unexplained complex conduction abnormalities in young patients may be a sign of sarcoidosis, even in isolation of more prevalent symptoms. Correct interpretation and prompt initiation of a structured interdisciplinary diagnostic workup, including 18F-FDG-PET-CT as the imaging modality of choice, are essential to initiate specific treatment and obviate the major risk of mortality resulting from cardiac sarcoidosis.
Switch to a bicarbonate-based Impella CP™ purge solution in a patient with haemothorax: a case report
Authors: Van Edom Charlotte , Van Puyvelde Tim , Jacobs Steven , Vandenbriele Christophe
Published: January 2023

Background

Percutaneous mechanical circulatory support (pMCS) by an Impella™ device implies the initiation of systemic anticoagulation to prevent systemic thrombotic complications and a purge fluid to prevent device blockage. Traditionally, unfractionated heparin (UFH) was used for both. In April 2022, the use of bicarbonate-based purge solution (BBPS) as an alternative to UFH in dextrose solution was approved by the Food and Drug Administration in case of contraindications for UFH.

Case summary

We present the case of a 73-year-old female that was admitted to the cardiac intensive care unit with cardiogenic shock, requiring upgrade with pMCS by an axillary Impella CP™. When she developed a severe haemothorax, all UFH was stopped and the purge was switched to BBPS-dextrose solution without increase in purge pressures nor development of haemolysis. The bleeding stagnated and the patient could be weaned from the Impella™ after 2 days.

Discussion

Here, we present the first case report of the switch to BBPS in an Impella CP™ supported patient with major bleeding since the FDA approval in April 2022. The switch to BBSP in addition with the administration of platelets and protamine resulted in cessation of the bleeding in this case.
Intramyocardial cell-based therapy with Lomecel-B during bidirectional cavopulmonary anastomosis for hypoplastic left heart syndrome: the ELPIS phase I trial
Authors: Kaushal Sunjay , Hare Joshua M , Hoffman Jessica R , Boyd Riley M , Ramdas Kevin N , Pietris Nicholas , Kutty Shelby , Tweddell James S , Husain S Adil , Menon Shaji C , Lambert Linda M , Danford David A , Kligerman Seth J , Hibino Narutoshi , Korutla Laxminarayana , Vallabhajosyula Prashanth , Campbell Michael J , Khan Aisha , Naioti Eric , Yousefi Keyvan , Mehranfard Danial , McClain-Moss Lisa , Oliva Anthony A , Davis Michael E
Published: January 2023

Aims

Hypoplastic left heart syndrome (HLHS) survival relies on surgical reconstruction of the right ventricle (RV) to provide systemic circulation. This substantially increases the RV load, wall stress, maladaptive remodelling, and dysfunction, which in turn increases the risk of death or transplantation.

Methods and results

We conducted a phase 1 open-label multicentre trial to assess the safety and feasibility of Lomecel-B as an adjunct to second-stage HLHS surgical palliation. Lomecel-B, an investigational cell therapy consisting of allogeneic medicinal signalling cells (MSCs), was delivered via intramyocardial injections. The primary endpoint was safety, and measures of RV function for potential efficacy were obtained. Ten patients were treated. None experienced major adverse cardiac events. All were alive and transplant-free at 1-year post-treatment, and experienced growth comparable to healthy historical data. Cardiac magnetic resonance imaging (CMR) suggested improved tricuspid regurgitant fraction (TR RF) via qualitative rater assessment, and via significant quantitative improvements from baseline at 6 and 12 months post-treatment (P < 0.05). Global longitudinal strain (GLS) and RV ejection fraction (EF) showed no declines. To understand potential mechanisms of action, circulating exosomes from intramyocardially transplanted MSCs were examined. Computational modelling identified 54 MSC-specific exosome ribonucleic acids (RNAs) corresponding to changes in TR RF, including miR-215-3p, miR-374b-3p, and RNAs related to cell metabolism and MAPK signalling.

Conclusion

Intramyocardially delivered Lomecel-B appears safe in HLHS patients and may favourably affect RV performance. Circulating exosomes of transplanted MSC-specific provide novel insight into bioactivity. Conduct of a controlled phase trial is warranted and is underway.

Trial registration number NCT03525418.
Comparison of meta-analytical estimates of outcomes after Alfieri or neochordal repair in isolated anterior mitral prolapse
Authors: Khairallah Sherif , Rahouma Mohamed , Dabsha Anas , Demetres Michelle , Gaudino Mario Fl , Mick Stephanie L
Published: January 2023

OBJECTIVES

Repair of the isolated degenerative anterior mitral leaflet has been considered more challenging and associated with compromised durability compared with isolated posterior leaflet in major series. Implantation of neochordae or Alfieri edge-to-edge is the most employed repair technique for isolated anterior repair currently, but little data exist comparing their relative durability. We sought to investigate this issue with this meta-analysis.

METHODS

A literature search was performed (Ovid MEDLINE, Ovid Embase and The Cochrane Library). The primary outcome was the incidence rate (IR) of reoperation, the secondary outcomes were recurrent moderately severe/severe mitral regurgitation (MR), in-hospital/30-day reoperation and mortality and follow-up mortality. A random-effect model was used. Leave-one-out, subgroup analysis (Alfieri versus neochordae) and meta-regression were done.

RESULTS

Seventeen studies (including 1358 patients) were included. At a weighted mean follow-up of 5.56 ± 3.31 years, the IR for reoperation was 14.45 event per 1000 person-year and significantly lower in Alfieri than neochordae repair (9.40 vs 18.61, P = 0.04) on subgroup analysis. The IR of follow-up moderately severe/severe MR was 19.89 event per 1000 person-year and significantly lower in Alfieri than neochordae repair (10.68 and 28.63, P = 0.01). In a sensitivity analysis comparing homogenous studies, a significant difference in the recurrence of regurgitation in favour of the Alfieri approach remained. There were no differences in operative outcomes or survival. There were significant associations between increased incidence of late reoperation and New York Heart Association class III/IV and associated coronary artery bypass graft procedure for whole cohort.

CONCLUSIONS

Alfieri repair may be associated with a lower incidence of recurrent MR compared with neochordae-based repair in the setting of isolated degenerative anterior mitral pathology. This is the first such meta-analysis and further inquiry into this area is needed.
Elevated sphingosine-1-phosphate lyase leads to increased metabolism and reduced survival in adrenocortical carcinoma
Authors: Williams Jack L , Smith Chris , Hall Charlotte , Khaled Zakaa , Maharaj Avinaash , Kwong Ruth , Pittaway James , Casas Josefina , Parvanta Laila , Abdel-Aziz Tarek Ezzat , Palazzo Fausto , Chung Teng-Teng , Guasti Leonardo , Metherell Lou , Prasad Rathi
Published: January 2023

Objective

Adrenocortical carcinomas (ACCs) are invasive tumours arising in the adrenal cortex, and steroidogenic tumours are associated with worse prognostic outcomes. Loss-of-function mutations in sphingosine-1-phosphate lyase (SGPL1) cause primary adrenal insufficiency and as a key degradative enzyme in the sphingolipid pathway, SGPL1 also influences the balance of pro-proliferative and pro-apoptotic sphingolipids. We, therefore, hypothesized increased SGPL1 may be linked to increased disease severity in ACC.

Design

Analyse SGPL1 expression impact on patient survival and adrenal cancer cell phenotype. We analysed two ACC cohorts with survival and corresponding transcriptomic data, focusing on SGPL1 and sphingolipid pathway genes. In vitro, we generated SGPL1-knockout and overexpressing H295R adrenocortical cells to investigate the role of SGPL1 in cell signalling in ACCs.

Results

We found increased expression of several sphingolipid pathway receptors and enzymes, most notably SGPL1 correlated with reduced patient survival in both cohorts. Overexpression of SGPL1 in the H295R cell line increased proliferation and migration while reducing apoptosis, while SGPL1 knockout had the opposite effect. RNA-seq revealed a global increase in the expression of genes in the electron transport chain in overexpressing cells, correlating with increased aerobic respiration and glycolysis. Furthermore, the opposite phenotype was seen in cells lacking SGPL1. We subsequently found the increased proliferation is linked to metabolic substrate availability and increased capacity to use different fuel sources, but particularly glucose, in overexpressing cells.

Conclusions

We, therefore, propose that SGPL1-overexpressing ACC tumours reduce patient survival by increasing fuel usage for anabolism and energy production to facilitate growth and invasion.
What is the impact of forced displacement on health? A scoping review
Authors: Cuadrado Cristóbal , Libuy Matías , Moreno-Serra Rodrigo
Published: January 2023

While there is a broad literature analysing the effects of migration on health, important knowledge gaps persist particularly on the causal effects of forced displacement on health outcomes. We undertake a scoping review of applied epidemiological, statistical and econometric studies examining causal health impacts of forced displacement, which initially identified 1454 studies from the health and social sciences disciplines published up to May 2021. Our study makes two key contributions. First, we offer a comprehensive overview of the evidence generated, methodologies adopted and analytical challenges faced by current research examining the causal relationship between forced displacement and health. Second, we present concrete examples of how key challenges around study design and estimation approaches influence the strength of the evidence-base on the topic, using as a case study the broad domain of reproductive health. We find that, beyond the increased mortality risk that can be attributed to forced displacement, most of the available empirical evidence for a wide range of health outcomes is prone to substantial bias, making it difficult to draw firm conclusions. Our synthesis of credible studies conducted in different settings indicates that current research practice in the field could be strengthened through selection of valid control groups and application of more appropriate causal inference methods. Our findings are useful to promote the generation of further evidence on the topic that can reliably inform the design of policies to protect the health of displaced populations.
Effect of the biosynthesis of the volatile compound phenylacetaldehyde on chloroplast modifications in tea (Camellia sinensis) plants
Authors: Zeng Lanting , Zhou Xiaochen , Fu Xiumin , Hu Yilong , Gu Dachuan , Hou Xingliang , Dong Fang , Yang Ziyin
Published: January 2023

Plant volatile compounds have important physiological and ecological functions. Phenylacetaldehyde (PAld), a volatile phenylpropanoid/benzenoid, accumulates in the leaves of tea (Camellia sinensis) plants grown under continuous shading. This study was conducted to determine whether PAld production is correlated with light and to elucidate the physiological functions of PAld in tea plants. Specifically, the upstream mechanism modulating PAld biosynthesis in tea plants under different light conditions as well as the effects of PAld on chloroplast/chlorophyll were investigated. The biosynthesis of PAld was inhibited under light, whereas it was induced in darkness. The structural gene encoding aromatic amino acid aminotransferase 1 (CsAAAT1) was expressed at a high level in darkness, consistent with its importance for PAld accumulation. Additionally, the results of a transcriptional activation assay and an electrophoretic mobility shift assay indicated CsAAAT1 expression was slightly activated by phytochrome-interacting factor 3-2 (CsPIF3-2), which is a light-responsive transcription factor. Furthermore, PAld might promote the excitation of chlorophyll in dark-treated chloroplasts and mediate electron energy transfer in cells. However, the accumulated PAld can degrade chloroplasts and chlorophyll, with potentially detrimental effects on photosynthesis. Moreover, PAld biosynthesis is inhibited in tea leaves by red and blue light, thereby decreasing the adverse effects of PAld on chloroplasts during daytime. In conclusion, the regulated biosynthesis of PAld in tea plants under light and in darkness leads to chloroplast modifications. The results of this study have expanded our understanding of the biosynthesis and functions of volatile phenylpropanoids/benzenoids in tea leaves.
A Critical Study on the Potential of Solid-Phase Fluorescence Spectroscopy (SPFS) in Quantitative Analysis: Effect of Solid Diluent and Sampling Method on Signal Quality
Authors: Öztürk Merve , Gezici Orhan
Published: January 2023

Background

Solid-phase fluorescence spectroscopy (SPFS) is a very useful non-destructive technique for directly analyzing samples in solid form without the use of solvents. However, due to the so-called inner-filter effect, it is sometimes necessary to dilute solid samples using non-fluorescent solids as diluents.

Objective

This study aimed to explore the potential of SPFS in the quantitative analysis of fluorescent species based on: (1) the type of solid diluent; and (2) the sampling method used in the SPFS analysis.

Methods

Four different solids were used as solid diluents in the preparation of standard mixtures having different concentrations of rhodamine b and fluorescein as model compounds. Standard mixtures of model compounds were sampled by two different methods called: (1) the powder-cell method; and (2) the adhesive tape method. LOQ and calibration sensitivity calculated from the calibration graphs were used to assess the measurement performance. The usability of SPFS in real-sample analyses was also evaluated in detail.

Results

Among the solid diluents studied, the best results were obtained with sodium carbonate. The powder-cell method yielded a significant advantage over the adhesive tape method. The lowest LOQs for rhodamine b and fluorescein were obtained by sodium carbonate and the powder-cell method as 0.06 and 0.11 mg/kg, respectively. The results of real-sample analyses were verified using conventional liquid-phase fluorescence spectroscopy (LPFS).

Conclusion

Solid-diluent type and sampling method were found to affect the performance of the SPFS technique. A combination of sodium carbonate and the powder-cell method gave the best results. According to the t-test, no difference was observed between the means obtained by SPFS and LPFS techniques in real-sample analyses.

Highlights

In SPFS, toxic organic solvents and difficult sample preparation steps are not required. This makes the method advantageous over conventional fluorescence analyses performed in the liquid phase.
Financial centre primacy around the world: international analysis based on mergers and acquisitions data
Authors: Wójcik Dariusz , Keenan Liam , Pažitka Vladimír , Urban Michael , Wu Wei
Published: January 2023

We analyse mergers and acquisitions in the financial sector between 2000 and 2017 to explore the domestic hierarchies of financial centres. Across a sample of 16 countries, we reveal different levels of financial centre primacy and explain how these levels change over time. These findings are analysed through a theoretical framework which integrates the literatures on urban primacy, global and world cities and comparative political economy. Situating our findings at the intersection of these literatures allows us to remain sensitive to geography, history and institutions in our analysis of financial centre primacy. Overall, our results show uneven levels of financial centre primacy around the world and that primate financial centres do not universally increase their dominance over time.
Cultures as networks of cultural traits: a unifying framework for measuring culture and cultural distances
Authors: De Benedictis Luca , Rondinelli Roberto , Vinciotti Veronica
Published: January 2023

Using data from the sixth wave of the World Value Survey and operationalising a definition of national culture that emphasises both specific cultural traits and the inter-dependence among them, this paper proposes a methodology to reveal the latent network structure of every national culture and to measure the cultural distance associated with every pair of countries as a Jeffreys’ divergence between copula graphical models. The two components of this new measure of cultural distance show different correlations with measures of geographical, historical, economic, and political distance among countries and with the similarity in the topologies of the countries cultural networks.
Responses of key root traits in the genusOryzato soil flooding mimicked by stagnant, deoxygenated nutrient solution
Authors: Tong Shuai , Kjær Johan Emil , Peralta Ogorek Lucas León , Pellegrini Elisa , Song Zhiwei , Pedersen Ole , Herzog Max
Published: January 2023

Excess water can induce flooding stress resulting in yield loss, even in wetland crops such as rice (Oryza). However, traits from species of wild Oryza have already been used to improve tolerance to abiotic stress in cultivated rice. This study aimed to establish root responses to sudden soil flooding among eight wild relatives of rice with different habitat preferences benchmarked against three genotypes of O. sativa. Plants were raised hydroponically, mimicking drained or flooded soils, to assess the plasticity of adventitious roots. Traits included were apparent permeance (PA) to O2 of the outer part of the roots, radial water loss, tissue porosity, apoplastic barriers in the exodermis, and root anatomical traits. These were analysed using a plasticity index and hierarchical clustering based on principal component analysis. For example, O. brachyantha, a wetland species, possessed very low tissue porosity compared with other wetland species, whereas dryland species O. latifolia and O. granulata exhibited significantly lower plasticity compared with wetland species and clustered in their own group. Most species clustered according to growing conditions based on PA, radial water loss, root porosity, and key anatomical traits, indicating strong anatomical and physiological responses to sudden soil flooding.
Slow mode oscillations in curved arcade loops
Authors: Lopin I , Nagorny I
Published: January 2023

In this work we theoretically investigate the effect of curvature on the slow-mode oscillations in coronal loop arcade. A simple model of an arc circle magnetic slab is used to simulate curved coronal magnetic structures. Solving the set of magnetohydrodynamic (MHD) equations for a compressible plasma, we obtain the dispersion relation that governs the compressible MHD modes in the model. A band of slow body modes with phase speeds close to the internal tube speed and a single hybrid slow mode with phase speed close to the external tube speed are found to exist under typical coronal circumstances. The principal slow body and hybrid modes both produce radial kink-like displacements of the slab axis and distort its cross-section. These motions are accompanied with the dominating longitudinal oscillations. Such mode properties may result in Doppler shift and intensity oscillations as well as oscillating spatial displacements, observed in coronal loops. A number of observations of long-period oscillations in arcade loops are interpreted on the basis of the developed theory.
Islamic Architecture (622–1500)
Authors: Ruggles D. Fairchild
Published: January 2023

The premodern Islamic world was vast. Originating in Mecca and Medina in the Arabian peninsula in 622, it grew to extend from Central Asia into the Indian subcontinent and across northern Africa to Morocco and Iberia. This bibliography covers Islamic architecture up to the year 1500, starting in the formative period in the Middle East where Islam began and then progressing from region to region, beginning in the west and moving eastward. It concludes with a bibliography organized by building types and elements. The earliest architecture emerged from a heavily Roman Mediterranean context under the Umayyad dynasty (661–750), whose political center was Damascus. But eastern elements were introduced after the Abbasids toppled the Umayyads and shifted power to Baghdad. The empire expanded quickly, and because of Islamic expansionism and the general tolerance extended to non-Muslims living under Muslim rule, the culture included not only diverse regions but also diversity within those regions. Thus the empire included Christian and Jewish peoples (together known as dhimmis) as well as different ethnic and linguistic groups such as Arabs, Berbers, and Persians. While sectarian differences yielded distinct places of worship—mosques, churches, and synagogues—the architectural form and ornament of the various buildings shared many structural and ornamental features. This was facilitated by the common use of spolia in early Islamic architecture, and by the largely non-figural content of Islamic art, stemming from hadith traditions that rejected figural art for its possible link to idolatry. Mosaics that in Byzantine churches displayed biblical scenes were replaced by abstract ornament and Arabic inscriptions in mosques. Perhaps because of this, the Islamic visual tradition did not favor manuscript illustration until quite late in the medieval period, with the result that builders at one end of the world could not have had much knowledge of what was occurring at the other end, except through the exchange of artisans. More often the artisans were local, working for whatever patron could employ them. Functional types such as the mosque, tomb, caravanserai, and fortress were ubiquitous and might share important elements such as orientation and aniconism, but building technique, plan, and the manner of ornament varied widely and could reflect regional differences. Artistic transmission occurred along known routes, developed for the annual pilgrimage to Mecca, and were facilitated by the relative speed of sailing across bodies of water Mediterranean and Indian Ocean, and the late medieval rise of the land routes collectively known as the Silk Road.
Action Assembly Theory
Authors: Greene John O.
Published: January 2023

Rather than a single theory, “action assembly theory” actually refers to a family of theoretical formulations that have in common the basic idea that message-relevant thoughts (e.g., ideational content, plans) and overt verbal and nonverbal behaviors are produced by the activation (retrieval), and subsequent assembly (integration) of elemental action specifications held in long-term memory (LTM) as components of “procedural records”—modular structures that preserve action-outcome-in-situation relationships. Also common to the various action-assembly theories is the idea that the result of the assembly process is the “output representation,” a constantly evolving configuration of action features that effectively constitutes a person’s thoughts and actions at any moment. A primary focus of the action-assembly perspective is on explicating how it is possible for people to think, say, and do things that they have never thought, heard, or done before. Other concerns are with person and situational factors bearing on speech fluency, communication-skill acquisition, sources of social-performance deficits, message planning and editing processes, cognitive processes underlying the production of deceptive messages, cross-situational consistency in message behavior, the nature of the “self,” and the nature and function of consciousness.