bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational method of the cardiovascular diseases classification based on a generalized nonlinear canonical decomposition of random sequences
Authors: Atamanyuk Igor , Kondratenko Yuriy , Havrysh Valerii , Volosyuk Yuriy 
Published: January 2023

AbstractDecision support systems can seriously help medical doctors in the diagnosis of different diseases, especially in complicated cases. This article is devoted to recognizing and diagnosing heart disease based on automatic computer processing of the electrocardiograms (ECG) of patients. In the general case, the change of the ECG parameters can be presented as a random sequence of the signals under processing. Developing new computational methods for such signal processing is an important research problem in creating efficient medical decision support systems. Authors consider the possibility of increasing the diagnostic accuracy of cardiovascular diseases by implementing of the new proposed computational method of information processing. This method is based on the generalized nonlinear canonical decomposition of a random sequence of the change of cardiogram parameters. The use of a nonlinear canonical model makes it possible to significantly simplify the maximum likelihood criterion for classifying diseases. This simplification is provided by the transition from a multi-dimensional distribution density of cardiogram parameters to a product of one-dimensional distribution densities of independent random coefficients of a nonlinear canonical decomposition. The absence of any restrictions on the class of random sequences under study makes it possible to achieve maximum accuracy in diagnosing cardiovascular diseases. Functional diagrams for implementing the proposed method reflecting the features of its application are presented. The quantitative parameters of the core of the computational diagnostic procedure can be determined in advance based on the preliminary statistical data of the ECGs for different heart diseases. That is why the developed method is quite simple in terms of computation (computing complexity, accuracy, computing time, etc.) and can be implemented in medical computer decision systems for monitoring cardiovascular diseases and for their diagnosis in real time. The results of the numerical experiment confirm the high accuracy of the developed method for classifying cardiovascular diseases.
A nomogram risk assessment model to predict the possibility of type II endoleak-related re-intervention after endovascular aneurysm repair (EVAR)
Authors: Liu Zongwei , Chen Yonghui , Qin Yafei , Bi Jiaxue , Wang Jiaxin , Niu Fang , Dai Xiangchen 
Published: January 2023

AbstractThis study aimed to develop and validate a novel nomogram risk assessment model to predict the possibility of type II endoleak (T2EL)-related re-intervention. The data of 455 patients with abdominal aortic aneurysms who underwent elective endovascular aneurysm repair (EVAR) procedures between January 2018 and December 2021 at our single center were retrospectively reviewed. Following the implementation of exclusion criteria, 283 patients were finally included and divided into T2EL-related re-intervention (n = 42) and non-T2EL (n = 241) groups. The overall T2EL-related re-intervention rate for 283 patients was 14.8% (42/283). Using multivariate analysis, significant risk factors for re-intervention included age (OR, 1.172; 95% CI, 1.051–1.307; P = 0.004), smoking (OR, 13.418; 95% CI, 2.362–76.215; P = 0.003), diameter of inferior mesenteric artery (IMA) (OR, 21.380; 95% CI, 3.060–149.390; P = 0.002), and number of patent lumbar arteries (OR, 9.736; 95% CI, 3.175–29.857; P < 0.001). The discrimination ability of this risk-predictive model was reasonable (concordance index [C-index] = 0.921; 95% CI, 0.878–0.964). The Hosmer–Lemeshow goodness of fit test was performed on the model, and the chi-square value was 3.210 (P = 0.920), presenting an excellent agreement between the model-predicted and observed values. The receiver operating characteristic (ROC) curve identified that the risk thresholds of re-intervention were a diameter of > 2.77 mm for the diameter of the inferior mesenteric artery and a proportion of < 45.5% for thrombus volume in the aneurysm sac. This novel nomogram risk assessment model for predicting the possibility of patients’ T2EL-related re-interventions after EVAR should be helpful in discriminating high-risk patients. Two novel risk thresholds may imply a higher possibility of T2EL-related re-intervention after EVAR.
Efficacy and safety of repeated endoscopic radial incision and cutting procedure for benign esophageal stricture
Authors: Kano Yuki , Kadota Tomohiro , Inaba Atsushi , Sunakawa Hironori , Takashima Kenji , Nakajo Keiichiro , Murano Tatsuro , Shinmura Kensuke , Yoda Yusuke , Ikematsu Hiroaki , Akimoto Tetsuo , Yano Tomonori 
Published: January 2023

Abstract
Background and study aims: Radial incision and cutting (RIC) is indicated for refractory benign esophageal strictures after curative treatment for esophageal cancer and has shown favorable short-term outcomes. However, re-stricture after RIC may occur in the long term, and RIC is performed repeatedly in such cases, but the efficacy and safety of repeated RIC are unclear. Therefore, we aimed to demonstrate the efficacy and safety of the repeated RIC for refractory benign esophageal strictures after surgical and non-surgical treatment.
Patients and methods: Between April 2008 and September 2019, we enrolled patients who were treated with the first RIC for benign esophageal strictures. The RIC was indicated for the refractory stricture and repeatedly performed for re-refractory esophageal stricture after RIC. We retrospectively evaluated the 6-month refractory stricture-free rate, and adverse events (AEs) in the first RIC and repeated RICs.
Results: Forty-six patients (39 men, 7 women; median age, 71 years, range 49–85) were included. RIC was performed once in 24 patients (non-repeated RIC group) and two or more times in 22 patients (repeated RIC group). In all patients, the 6-month refractory stricture-free rate after the first RIC were 42.3 %. In the repeated RIC group, the 6-month refractory stricture-free rate after the first and repeated RICs were 18.2 % vs 18.2 %, respectively. No AEs were noted.
Conclusions: Repeated RIC could be effective in the short-term and safe even for patients with refractory benign esophageal stricture after the first RIC. However, it cannot be considered curative treatment for refractory stricture because of poor long-term results.
Gender Parity in Healthcare: A Chronicle of Escalating Success Rate of Female Radiation Oncologists in India
Authors: Sarkar Biplab , Pradhan Anirudh 
Published: January 2023

Objectives This editorial describes the growth pattern of female radiation oncologists (FRO) in India and the prediction of gender equality through a mathematical formulation.
Materials and Methods Among the countries in South Asia, India has the largest population of radiation oncologists (RO), a total of 3,763: 1,286 female and 2,477 male radiation oncologists (MROs), and they are registered with the Association of Radiation Oncologists of India (AROI). The data were analyzed to find the differential and cumulative growth pattern of the FROs and MROs and predict gender equality in radiation oncology. The cumulative growth rate indicates the total number of FROs and MROs by end of every year. Differential growth rate indicates the differential increase in the number of FROs and MROs for a particular year. Annual cumulative and differential growth patterns were plotted as a function of the time, and an analytical functional form was fitted to predict the future growth pattern and achievement of gender equality.
Results AROI registration of FROs and MROs for 2013–2020 were as follows: FRO: MRO 2013-54: 102, 2014-99: 162, 2015-77: 148; 2016-86: 143, 2017-110: 110, 2018-116: 151, 2019-121: 152, 2020 (October)-129: 110. Differential growth pattern between 2013 and 2020 with the average incremental growth rate for FROs and MROs were 12.7 ± 14.8% and 2.1 ± 32.0%. Differential growth rate FRO fits in a power-law exponent 58.6 ×(Power0.3695), where MRO growth pattern showed a saturation [4.7ln(×) + 128.5] . Gender parity among Indian radiation oncologists is likely to be achieved by end of 2027.
Conclusions The present density of FRO in India 34.1% is high compared to developed countries such as the United States (≈26%). It is a big leap for the Indian radiation oncology society tending toward gender parity.
Patellar Proximo-Distal Displacement following Modified Maquet Technique Is Not Predictive of Patellar Luxation
Authors: Giansetto Thomas Elie , Pierrot Emilie , Picavet Pierre P. , Lefebvre Michael , Rives Albane , Farnir Frédéric , Claeys Stéphanie , Balligand Marc 
Published: January 2023

Abstract
Objective The aim of this study was to test the low sensitivity of the Allberg and Miles index to the stifle opening angle, evaluate the displacement of the patella after a Modified Maquet Technique using this index and assess the incidence of patellar luxation post-Modified Maquet Technique in dogs.
Study Design Medical records were reviewed from 2012 to 2017. Allberg Miles index were determined for each stifle pre- and postoperatively, as well as the stifle joint opening of each case. Occurrence of patellar luxation was recorded.
Results 137 stifles on 116 dogs were reviewed. The stifle opening angle did not influence the Allberg Miles index. Pre- and postoperative index showed a distal displacement of the patella after a Modified Maquet Procedure, especially at 135° of stifle opening angle. Only 1/137 cases demonstrated patellar luxation after the surgery.
Conclusion Based on our statistical analysis, we were able to conclude that within the maximum stifle opening angle range recorded in our series of cases; the Allberg Miles index variation was not significant. While patellar baja is clearly induced by the Modified Maquet Technique, the latter did not seem to predispose patients to post-operative patellar luxation in our study population.
Venous Thromboembolism Associated with Assisted Reproductive Technology: A Systematic Review and Meta-analysis
Authors: Goualou Marianne , Noumegni Steve , de Moreuil Claire , Le Guillou Mathilde , De Coninck Gabrielle , Hoffmann Clément , Robin Sara , Morcel Karine , Le Moigne Emmanuelle , Tremouilhac Christophe , Merviel Philippe , Le Mao Raphael , Leroyer Christophe , Bouée Sarah , Couturaud Francis , Tromeur Cécile 
Published: January 2023

Background Hormonal exposure leads to an increased risk of venous thromboembolism (VTE) but the risk of VTE associated with assisted reproductive technology (ART) is not clearly determined.
Methods We searched in PubMed, EMBASE, Web of Science, and the Cochrane Library databases and identified all relevant articles published up to February 1, 2021. The primary objective was to determine the frequency of VTE associated with ART. Secondary objectives were to determine (1) the risk of VTE associated with ART as compared to pregnancy without ART; (2) the risk of VTE associated with ovarian hyperstimulation syndrome (OHSS); and (3) to determine potential risk factors of VTE related to ART.
Results Fourteen studies were included. The overall frequency of VTE associated with ART was 0.23% (95% confidence interval [CI]: 0.07–0.46). Women undergoing ART had a two- to threefold increased risk of VTE as compared to spontaneous pregnancy (relative risk [RR]: 2.66; 95% CI: 1.60–4.43). The overall frequency of VTE specifically related to OHSS was <0.001%. The risk of VTE after ART complicated by OHSS, as compared to ART without OHSS, was higher but not statistically significant (RR: 14.83; 95% CI: 0.86–255.62). Risk factors of VTE associated with ART were in vitro fertilization procedure (RR, odds ratio [OR], and hazard ratio varying from 1.77, 95% CI: 1.41–2.23 to 4.99, 95% CI: 1.24–20.05), hyperhomocysteinemia (OR: 15.2; 95% CI: 2.0–115.0), polycystic ovarian syndrome (PCOS) (RR: 4.8; 95% CI: 1.7–13.4), successful ART leading to pregnancy (OR: 13.94; 95% CI: 1.41–137.45).
Conclusion Further large prospective studies on risk factors of VTE in women undergoing ART are needed in order to optimize thromboprophylaxis in this context.
Inference of 3D genome architecture by modeling overdispersion of Hi-C data
Authors: Varoquaux Nelle , Noble William S , Vert Jean-Philippe 
Published: January 2023

Abstract

Motivation
We address the challenge of inferring a consensus 3D model of genome architecture from Hi-C data. Existing approaches most often rely on a two-step algorithm: first, convert the contact counts into distances, then optimize an objective function akin to multidimensional scaling (MDS) to infer a 3D model. Other approaches use a maximum likelihood approach, modeling the contact counts between two loci as a Poisson random variable whose intensity is a decreasing function of the distance between them. However, a Poisson model of contact counts implies that the variance of the data is equal to the mean, a relationship that is often too restrictive to properly model count data.

Results
We first confirm the presence of overdispersion in several real Hi-C datasets, and we show that the overdispersion arises even in simulated datasets. We then propose a new model, called Pastis-NB, where we replace the Poisson model of contact counts by a negative binomial one, which is parametrized by a mean and a separate dispersion parameter. The dispersion parameter allows the variance to be adjusted independently from the mean, thus better modeling overdispersed data. We compare the results of Pastis-NB to those of several previously published algorithms, both MDS-based and statistical methods. We show that the negative binomial inference yields more accurate structures on simulated data, and more robust structures than other models across real Hi-C replicates and across different resolutions.

Availability and implementation
A Python implementation of Pastis-NB is available at https://github.com/hiclib/pastis under the BSD license.

Supplementary information
Supplementary data are available at Bioinformatics online.
The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates
Authors: Vandelli Andrea , Arnal Segura Magdalena , Monti Michele , Fiorentino Jonathan , Broglia Laura , Colantoni Alessio , Sanchez de Groot Natalia , Torrent Burgas Marc , Armaos Alexandros , Tartaglia Gian Gaetano 
Published: January 2023

Abstract

Summary
Biological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here, we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress granules, processing bodies and other assemblies including droplets and amyloids. PRALINE provides information about the predicted and experimentally validated protein–protein, protein–RNA and RNA–RNA interactions. For proteins, it reports the liquid–liquid phase separation and liquid–solid phase separation propensities. For RNAs, it provides information on predicted secondary structure content. PRALINE shows detailed information on human single-nucleotide variants, their clinical significance and presence in protein and RNA binding sites, and how they can affect condensates’ physical properties.

Availability and implementation
PRALINE is freely accessible on the web at http://praline.tartaglialab.com.
Brain microdialysate tau dynamics predict functional and neurocognitive recovery after poor-grade subarachnoid haemorrhage
Authors: Heilig Marina , Rass Verena , Lindner Anna , Kofler Mario , Ianosi Bogdan-Andrei , Gaasch Maxime , Putnina Lauma , Humpel Christian , Scherfler Christoph , Zamarian Laura , Bodner Thomas , Djamshidian Atbin , Schiefecker Alois , Thomé Claudius , Beer Ronny , Pfausler Bettina , Helbok Raimund 
Published: January 2023

Abstract
Subarachnoid haemorrhage is a devastating disease that results in neurocognitive deficits and a poor functional outcome in a considerable proportion of patients. In this study, we investigated the prognostic value of microtubule-associated tau protein measured in the cerebral microdialysate for long-term functional and neuropsychological outcomes in poor-grade subarachnoid haemorrhage patients. We recruited 55 consecutive non-traumatic subarachnoid haemorrhage patients who underwent multimodal neuromonitoring, including cerebral microdialysis. Mitochondrial dysfunction was defined as lactate-to-pyruvate ratio &gt;30 together with pyruvate &gt;70 mmol/L and metabolic distress as lactate-to-pyruvate ratio &gt;40. The multidimensional 12-month outcome was assessed by means of the modified Rankin scale (poor outcome: modified Rankin scale ≥4) and a standardized neuropsychological test battery. We used multivariable generalized estimating equation models to assess associations between total microdialysate-tau levels of the first 10 days after admission and hospital complications and outcomes. Patients were 56 ± 12 years old and presented with a median Hunt & Hess score of 5 (interquartile range: 3–5). Overall mean total microdialysate-tau concentrations were highest within the first 24 h (5585 ± 6291 pg/mL), decreased to a minimum of 2347 ± 4175 pg/mL on Day 4 (P &lt; 0.001) and remained stable thereafter (P = 0.613). Higher total microdialysate-tau levels were associated with the occurrence of delayed cerebral ischaemia (P = 0.001), episodes of metabolic distress (P = 0.002) and mitochondrial dysfunction (P = 0.034). Patients with higher tau levels had higher odds for a poor 12-month functional outcome (adjusted odds ratio: 2.61; 95% confidence interval: 1.32–5.17; P = 0.006) and impaired results in the trail making test-B (adjusted odds ratio: 3.35; 95% confidence interval: 1.16–9.68; P = 0.026) indicative of cognitive flexibility. Total microdialysate-tau levels significantly decreased over the first 10 days (P &lt; 0.05) in patients without delayed cerebral ischaemia or good functional outcomes and remained high in those with delayed cerebral ischaemia and poor 12-month outcomes, respectively. Dynamic changes of total tau in the cerebral microdialysate may be a useful biomarker for axonal damage associated with functional and neurocognitive recovery in poor-grade subarachnoid haemorrhage patients. In contrast, ongoing axonal damage beyond Day 3 after bleeding indicates a higher risk for delayed cerebral ischaemia as well as a poor functional outcome.
Unemployment persistence among second-generation immigrants
Authors: Aradhya Siddartha , Grotti Raffaele , Härkönen Juho 
Published: January 2023

Abstract
Many immigrant groups disproportionately experience unemployment and this disadvantage often extends to their children—the second generation. This paper contributes to this stream of research by studying unemployment dynamics of the ancestral population and second-generation immigrants in Sweden. In particular, we ask: does unemployment persistence differ between ancestral Swedes and 10 second-generation immigrant groups? We answer this question using correlated dynamic random-effects logit models to study the effect of past on current unemployment—also known as genuine state dependence. We use Swedish register data to follow individuals over their early working careers. The results indicate that although past unemployment has a similar relative effect on current unemployment across the ancestry groups, past unemployment increases the probability of current unemployment (absolute effect) more among second-generation Middle-Eastern, Turkish, and Southern European immigrants. Because of higher baseline levels of unemployment, the labour market consequences of similar relative effects are more pronounced among the second generation as compared to ancestral Swedes. The paper concludes by elaborating on the reasons behind these contrasting results while highlighting the importance of examining heterogeneous effects on both the relative and absolute scales.
Members ofEnsiferandRhizobiumgenera are new bacterial endosymbionts nodulatingPisum sativum(L.)
Authors: Mahdhi A , Mars M , Rejili M 
Published: January 2023

AbstractA total of 84 Pisum sativum legume nodulating bacteria (LNB) were isolated from seven geographical sites from southern Tunisia. Phylogenetic analyses based on partial sequences of 16S rRNA gene and the housekeeping genes glnII, and recA grouped strains into six clusters, four of which belonged to the genus Rhizobium and two to the Ensifer genus. Among Rhizobium clusters, 41 strains were affiliated to Rhizobium leguminosarum, two strains to R. pisi, two strains to R. etli, and interestingly two strains belonged to previously undescribed Rhizobium species. The remaining two strains were closely related to Ensifer medicae (two strains) and Ensifer meliloti (two strains). A symbiotic nodC gene-based phylogeny and host specificity test showed that all Rhizobium strains nodulating pea belonged to the symbiovar viciae, whereas the Ensifer strains were associated with the symbiovar meliloti never described to date. All strains under investigation differed in the number of induced root nodules and the effectiveness of atmospheric nitrogen fixation. The R. leguminosarum PsZA23, R. leguminosarum PsGBL42, and E. medicae PsTA22a, forming the most effective symbiosis with the plant host, are potential candidates for inoculation programs.
The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes
Authors: Fletcher Kyle , Martin Frank , Isakeit Thomas , Cavanaugh Keri , Magill Clint , Michelmore Richard 
Published: January 2023

Abstract
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.