bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species-specific basecallers improve actual accuracy of nanopore sequencing in plants
Authors: Ferguson Scott , McLay Todd , Andrew Rose L. , Bruhl Jeremy J. , Schwessinger Benjamin , Borevitz Justin , Jones Ashley 
Published: December 2022

Abstract
Background
Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specific basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specific basecaller models. We also evaluate accuracy gains from ONT’s improved flowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads.

Results
Basecalling with ONT Guppy 5 and 6 super-accurate gave almost identical results, attaining read accuracies of 91.96% and 94.15%. Guppy’s plant-specific model gave highly mixed results, attaining read accuracies of 91.47% and 96.18%. Species-specific basecalling models improved read accuracy, attaining 93.24% and 95.16% read accuracies. R10.4 sequencing kits also improve sequencing accuracy, attaining read accuracies of 95.46% (super-accurate) and 96.87% (species-specific).

Conclusions
The use of a single mixed-species basecaller model, such as ONT Guppy super-accurate, may be reducing the accuracy of nanopore sequencing, due to conflicting genome biology within the training dataset and study species. Training of single-species and genome-specific basecaller models improves read accuracy. Studies that aim to do large-scale long-read genotyping would primarily benefit from training their own basecalling models. Such studies could use sequencing accuracy gains and improving bioinformatics tools to improve study outcomes.
Transcoronary sinus repair of a severely dilated and tortuous right coronary artery fistulized to coronary sinus complicated with tricuspid valve insufficiency
Authors: Li Xuebiao , Qian Jianfang , Shen Zhonghua , Dong Aiqiang 
Published: December 2022

Abstract
Background
Right coronary artery (RCA) fistulized to the coronary sinus is rare condition in adult cardiac anomalies, and the management and operative indication are controversial.

Case presentation
We describe the case of a 45-year female patient who presented with exertional dyspnea, accompanied by intermitted lower limbs and facial edema. She was diagnosed with severe tricuspid regurgitation second to a severely dilated RCA fistulized to the coronary sinus. After multidisciplinary discussion, she underwent surgery through routine medium sternotomy, the right atrium was opened under cardiopulmonary bypass. The coronary arteriovenous fistula from the distal portion of RC to a severely enlarged coronary sinus was found. Trans-coronary sinus closure of the fistula was performed with continuous stitching and a tricuspid ring annuloplasty was done. The patient recovered uneventful post operation.

Conclusion
According to current literatures, surgical treatment was adopted for this case, instead of endovascular intervention. The optimal approach for these cases should consider the heart’s anatomical characteristics. But we need to be aware of the occurrence of myocardial infarction and tricuspid regurgitation in the early and late stage after operation.
Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries
Authors: dos Santos Vieira Bruna , Bernabé César H. , Zhang Shuxin , Abaza Haitham , Benis Nirupama , Cámara Alberto , Cornet Ronald , Le Cornec Clémence M. A. , ’t Hoen Peter A. C. , Schaefer Franz , van der Velde K. Joeri , Swertz Morris A. , Wilkinson Mark D. , Jacobsen Annika , Roos Marco 
Published: December 2022

Abstract
Introduction
Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data Findable, Accessible, Interoperable, and Reusable (FAIR) for humans and machines at source enables federated discovery and analysis across data custodians. This facilitates accurate diagnosis, optimal clinical management, and personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The process and the implementation choices for making data FAIR (‘FAIRification’) differ among ERN registries. For example, registries use different software systems and are subject to different legal regulations. To support the ERNs in making informed decisions and to harmonise FAIRification, the FAIRification steward team was established to work as liaisons between ERNs and researchers from the European Joint Programme on Rare Diseases.

Results
The FAIRification steward team inventoried the FAIRification challenges of the ERN registries and proposed solutions collectively with involved stakeholders to address them. Ninety-eight FAIRification challenges from 24 ERNs’ registries were collected and categorised into “training” (31), “community” (9), “modelling” (12), “implementation” (26), and “legal” (20). After curating and aggregating highly similar challenges, 41 unique FAIRification challenges remained. The two categories with the most challenges were “training” (15) and “implementation” (9), followed by “community” (7), and then “modelling” (5) and “legal” (5). To address all challenges, eleven types of solutions were proposed. Among them, the provision of guidelines and the organisation of training activities resolved the “training” challenges, which ranged from less-technical “coffee-rounds” to technical workshops, from informal FAIR Games to formal hackathons. Obtaining implementation support from technical experts was the solution type for tackling the “implementation” challenges.

Conclusion
This work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of the ERNs. Finally, the lessons learned from the experience of the FAIRification steward team described in this paper may help to increase FAIR awareness and provide insights into FAIRification challenges and solutions of rare disease registries.
Fathers and mothers’ parenting stress and adolescent depressive symptoms: the mediating roles of overt and covert coparenting conflict behaviors
Authors: Ren Yizhen , Zou Shengqi , Wang Hui , Ying Jiefeng , Wang Xinyi , Wu Xinchun 
Published: December 2022

Abstract
Background
It is yet to be clarified if and how parenting stress was linked to adolescent depressive symptoms during the pandemic.

Objectives
This study adopted an interdependent approach to examine the relationship between parenting stress and adolescent depressive symptoms in Chinese families. It then examined the mediating effects of overt and covert coparenting conflict behaviors.

Methods
As a national survey, data were obtained from different regions in China. Fathers, mothers, and adolescents from 1031 families participated in this study. The fathers and mothers reported parenting stress; the adolescents rated their fathers and mothers’ overt and covert coparenting conflict behaviors and their own depressive symptoms.

Results
Maternal parenting stress was related to adolescent depressive symptoms through the mediating effects of paternal overt and maternal covert coparenting conflict behaviors. Both paternal and maternal parenting stress were directly related to adolescent depressive symptoms. However, maternal parenting stress had a more substantial effect on adolescent depressive symptoms than paternal parenting stress.

Conclusions
The findings support the effects of parenting stress on adolescent depressive symptoms. The study also highlights the mediating roles of paternal overt and maternal covert coparenting conflict behaviors in relationships.
STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci
Authors: Dashnow Harriet , Pedersen Brent S. , Hiatt Laurel , Brown Joe , Beecroft Sarah J. , Ravenscroft Gianina , LaCroix Amy J. , Lamont Phillipa , Roxburgh Richard H. , Rodrigues Miriam J. , Davis Mark , Mefford Heather C. , Laing Nigel G. , Quinlan Aaron R. 
Published: December 2022

AbstractExpansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for “novel” STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at:github.com/quinlan-lab/STRling.
Somatostatin receptor saturation after administration of high peptide amounts of [177Lu]Lu-HA-DOTATATE: when enough is enough
Authors: Siebinga Hinke , Veerman Chayenne H. A. M. , de Wit-van der Veen Linda , Stokkel Marcel P. M. , Hendrikx Jeroen J. M. A. , Aalbersberg Else A. 
Published: December 2022

Abstract
Background
Receptor saturation during peptide receptor radionuclide therapy (PRRT) could result in altered [177Lu]Lu-HA-DOTATATE uptake in tumors and organs. Therefore, receptor expression status and effects of different (unlabeled) administered peptide amounts during PRRT need to be evaluated. The aim of this study was to assess potential receptor saturation during PRRT by comparing organ and tumor uptake after administration of [177Lu]Lu-HA-DOTATATE with low, standard and high administered peptide amounts in patients with advanced metastatic neuroendocrine tumors (NETs).

Methods
Data of NET patients that received 7.4 GBq 177-Lutetium labeled to a low or high amount of HA-DOTATATE were retrospectively included. From included patients other PRRT cycles, containing standard administered peptide amounts, were included for intra-patient comparison. Uptake quantification was performed for spleen, liver, kidney, bone marrow, blood pool and tumor lesions on post-treatment SPECT/CT scans. A paired Wilcoxon signed-rank test was performed to determine uptake differences between two adjacent cycles for each patient.

Results
Thirteen patients received [177Lu]Lu-HA-DOTATATE with a high administered peptide amount (mean 346 µg vs 178 µg standard peptide amount). Low peptide amounts were administered to fifteen patients (mean 109 µg vs 202 µg standard peptide amount). High administered peptide amount resulted in significantly lower [177Lu]Lu-HA-DOTATATE uptake in the spleen (p = 0.00012), kidney (p = 0.013) and tumor lesions (p < 0.0001) versus standard peptide amounts. For low administered peptide amount, uptake was increased in the spleen (p = 0.015), while tumor uptake was significantly reduced (p = 0.015) compared to uptake after administration of standard peptide amounts.

Conclusions
These findings confirmed a peptide amount-dependent organ and tumor accumulation for [177Lu]Lu-HA-DOTATATE, with receptor saturation in spleen for high and standard peptide amounts, while tumor and kidney receptor saturation occur only with high administered peptide amounts. A high peptide amount (~ 350 µg) is not recommended for standard-dose PRRT and standard amounts (~ 200 µg) seem more suitable to achieve optimal tumor accumulation with limited organ uptake.
Enabling real time big data solutions for manufacturing at scale
Authors: Cakir Altan , Akın Özgün , Deniz Halil Faruk , Yılmaz Ali 
Published: December 2022

AbstractToday we create and collect more data than we have in the past. All this data comes from different sources, including social media platforms, our phones and computers, healthcare gadgets and wearable technology, scientific instruments, financial institutions, the manufacturing industry, news channels, and more. When these data are analyzed in a real-time nature, it offers businesses the opportunity to take quick action in business-development processes (B2B, B2C), gain a different perspective, and better understand applications, creating new opportunities. While changing their sales and marketing strategies, businesses are now able to manage the data they collect in real-time to transform themselves, to record them in a healthy way, to analyze and evaluate data-based processes, and to determine their digital transformation roadmaps, their interactions with their customers, sectoral diffraction, application, and analysis. They want to accelerate the transformation processes within the technology triangle. Thus, big data, recently called as small and wide data, is at the center of everything and becomes an important application for digital transformation. Digital transformation helps companies embrace change and stay competitive in an increasingly digital world. The value of big data in manufacturing, independent from sectoral variations, comes from its ability to combine both in an organization’s efforts to both digitize and automate its end-to-end business operations. In this study, the current digitalization and automation applications of one of the plastic injection-based manufacturing companies at scale will be discussed. Presented open-source-based big data analytics platform, DataCone, that increases data processing efficiency, storage optimization, encourages innovation for real time monitorization and analytics, and support new business models in different industry segments will be demonstrated and discussed. Thus, development and applied ML solutions will be discussed providing important prospects for the future.
Image quality assessment along the one metre axial field-of-view of the total-body Biograph Vision Quadra PET/CT system for 18F-FDG
Authors: Rausch Ivo , Mannheim Julia G. , Kupferschläger Jürgen , la Fougère Christian , Schmidt Fabian P. 
Published: December 2022

Abstract
Aim
Recently, total-body PET/CT systems with an extended axial field-of-view (aFOV) became commercially available which allow acquiring physiologic information of multiple organs simultaneously. However, the nominal aFOV may clinically not be used effectively due to the inherently reduced sensitivity at the distal ends of the aFOV. The aim of this study was to assess the extent of the useful aFOV of the Biograph Vision Quadra PET/CT system.

Methods
A NEMA image quality (IQ) phantom mimicking a standard [18F]FDG examination was used. Image contrast and noise were assessed across the 106 cm aFOV of the Biograph Vision Quadra PET/CT system (Siemens Healthineers). Phantom acquisitions were performed at different axial positions. PET data were rebinned to simulate different acquisition times for a standard injected activity and reconstructed using different filter settings to evaluate the noise and images along the axial direction.

Results
Image noise and contrast were stable within the central 80 cm of the aFOV. Outside this central area, image contrast variability as well as image noise increased. This degradation of IQ was in particular evident for short acquisition times of less than 30 s. At 10 min acquisition time and in the absence of post-reconstruction filtering, the useful aFOV was 100 cm. For a 2 min acquisition time, a useful aFOV with image noise below 15% was only achievable using Gaussian filtering with axial extents of between 83 and 103 cm when going from 2 to 6 mm full-width-half-maximum, respectively.

Conclusion
Image noise increases substantially towards the ends of the aFOV. However, good IQ in compliance with generally accepted benchmarks is achievable for an aFOV of > 90 cm. When accepting higher image noise or using dedicated protocol settings such as stronger filtering a useful aFOV of around 1 m can be achieved for a 2 min acquisition time.
Nitrous oxide intoxication: systematic literature review and proposal of new diagnostic possibilities
Authors: Luigi Cipolloni , Stefania De Simone 
Published: December 2022

Abstract
Background
Nitrous oxide (N2O), also called “laughing gas,” is the most commonly used inhalation anesthetic in dentistry. The N2O is no longer used, because of the long-term neurologic and cardiovascular sequelae. Due to its sedative and euphoric properties, N2O is often used for recreational use or in some erotic activities. Accidental deaths are mainly associated with the uses of N2O: death can occur from sudden cardiac arrhythmia or, most commonly, acute asphyxiation due to hypoxia. This paper aims to study the literature concerning deaths due to N2O intoxication and highlight pathological findings useful for diagnosis when the crime scene investigation does not reveal any evidence.

Materials and methods
The authors conducted the literature search by PubMed and Scopus databases, searching for articles from 1 January 1970 to 1 March 2020 using the key terms: “Nitrous oxide,” “Laughing gas,” “Hypoxic damage,” “Nitrous oxide anesthesia,” and “Nitrous oxide death.”

Results and discussion
A total of 244 articles were collected. Only 26 articles were included in the systematic review. Most of the deaths from intoxication are due to asphyxiation; the diagnosis is often difficult and immunohistochemistry could be helpful. Nitrous oxide increases the intracellular adhesion molecule expression, E- and P-Selectin (markers of the early inflammatory response), and HIF-1 α (indicative of oxidative stress during ischemia-reperfusion).

Conclusion
The macroscopic and microscopic signs of N2O intoxication are non-specific, but N2O has been proven to cause hypoxic damage to the brain. The suspicion of the presence of the gas in the environment should guide the pathologist. Tissue analyzes provide important information; immunohistochemical stains can confirm hypoxic damage through the use of markers such as HIF-1 α, E-Selectin, and P-Selectin.
Choking together with aspiration of gastric contents: rare form of maternal death
Authors: Vadysinghe Amal Nishantha , Nayakarathne Tharanga Bandara , Banda Ilangarathne , Perera Ranasinghe Arachchilage Erandathi I 
Published: December 2022

Abstract
Background
The common causes of early postpartum maternal deaths are cardiomyopathies, obstetric hemorrhage, hypertensive disorders, and sepsis. However, a maternal death from choking together with aspiration of gastric contents is a rare occurrence to be diagnosed at the autopsy examination.

Case presentation
A 27-year-old previously healthy lady developed breathlessness 48 h after delivery, while on supine position, 1 h after meals, and pronounced death on admission. Autopsy was insignificant except for large amount of gastric contents in the air ways. Microscopic examination revealed bronchioles filled with eosinophilic materials and a significant number of neutrophil infiltrations at the margin. Alveoli were free from edema fluid and inflammatory cells. Some alveoli were expanded with broken septae. Cause of death was airway obstruction due to choking together with aspiration of gastric contents.

Conclusions
Aspiration of gastric contents can cause sudden unexpected death at postpartum, and it is recommended to educate immediate and early postpartum mothers regarding the risk of aspiration.
Association of the ANGPTL3 gene polymorphisms and haplotypes with cardiovascular diseases in Birjand longitudinal aging study (BLAS)
Authors: Poursalehi Forough , Aghasizadeh Malihe , Ghorbanzadeh Somaye , heydari Farzaneh , Kazemi Tooba , Sharifi Farshad , Moodi Mitra , Fakrzadeh Hossen , Miri-Moghaddam Ebrahim 
Published: December 2022

Abstract
Subject
Cardiovascular disease is now well established as an interaction between genetic and environmental components. Newly identified single nucleotide polymorphisms of angiopoietin-like 3 (ANGPTL3) influence lipid concentrations and risk of coronary artery disease. The current study aimed to determine the association between ANGPTL3 gene variants with incident CVDs in elderly population of the Birjand longitudinal aging study (BLAS).

Method
Totally, 360 individuals were recruited in baseline of BLAS including 128 patients with CVD and 153 control subjects. DNA extraction of samples and genotyping were performed by Tetra-ARMS PCR (amplification refractory mutation system polymerase chain reaction). The association between three polymorphisms of ANGPTL3 gene (rs1748195, rs11207997, and rs10789117 variants) with CVD and its risk factors were evaluated using multivariate analysis.

Results
Univariate and multiple analyses showed that individuals carrying the GG genotype of rs1748195 and those carrying the TT genotype of rs11207997 directly increased the risk of CVD. CC genotype of rs1748195 and rs11207997 polymorphisms had a significant negative relationship with the disease. In addition, the findings of this study indicate a significant difference in LDL, HDL, cholesterol levels between different genotypes of the rs1748195 and rs10789117 in the healthy group. Individuals with haplotypes CAC, CCC and CCT showed a significant positive relationship with CVD, CVA, AMI and CHD. As well as haplotype was associated with a 1.7-fold increase in risk of CVA, AMI, and CHD.

Conclusion
We found that polymorphism of ANGPTL3 gene might support to identify individuals with a cardiometabolic and genetic disorders susceptibility. Three haplotypes CAC, CCC and CCT associated with CVD, CVA, AMI and CHD were reported.