bluuebunny/crossref_metadata_2025_split huggingface dataset:
nanoNIPT: Short‐fragment nanopore sequencing of cell‐free DNA for non‐invasive prenatal testing of fetal aneuploidies and sex chromosome aberrations
Authors: Jørgensen Maria Winther , Miceikaitė Ieva , Larsen Martin J. 
Published: February 2023

Key pointsWhat's already known about this topic?

Non‐invasive prenatal testing (NIPT) is a sensitive and risk‐free prenatal screening test for common aneuploidies.

Until now, NIPT has required access to expensive next generation sequencing (NGS) sequencers, making it only accessible to large laboratories.

What does this study add?

This proof‐of‐concept study demonstrates that Oxford Nanopore platform, originally developed for long‐reads, can be used to sequence and analyze short cell‐free DNA (cfDNA) fragments with high efficiency and accuracy.

We developed nanoNIPT for non‐invasive detection of fetal aneuploidies and sex chromosome aberrations, which enables NIPT testing without large upfront investments making it accessible in all the clinical labs around the world.
Psychological distress and decision‐making factors for prophylactic bilateral mastectomy in cancer‐unaffected BRCA1/2 pathogenic variant carriers
Authors: Isselhard Anna , Tüchler Anja , Dick Julia , Scherer Anne , Aue Viktoria , Schmutzler Rita K. , Rhiem Kerstin 
Published: February 2023

AbstractObjectiveWomen carrying a BRCA1/2 pathogenic variant have an increased risk for breast cancer and may opt for risk‐reducing bilateral mastectomy. In this study, we examine which demographic, psychosocial, and personality factors are associated with their decision to undergo risk‐reducing bilateral mastectomy.MethodsCancer‐unaffected women with a pathogenic variant in BRCA1 or BRCA2 were recruited before receiving their genetic test result and completed follow‐up including decision to undergo mastectomy over 6–8 months after genetic test result disclosure. Anxiety, depression, breast cancer worry, personality and sociodemographic data were assessed.ResultsA total of 125 cancer‐unaffected women were included in the analysis. Participants were found to have higher anxiety levels than the general female population regardless of mastectomy decision. Breast cancer worry was higher among women who opted for risk‐reducing mastectomy and did not decrease over time. By contrast, women who did not opt for surgery experienced decreasing levels of breast cancer worry. Regression analysis found that women with a pathogenic variant in BRCA1, younger women and women with higher breast cancer worry were more likely to opt for surgery.ConclusionsOur study provides valuable insights into the factors that influence women with a BRCA1/2 pathogenic variant to undergo risk‐reducing mastectomy. These findings may be helpful in understanding individual differences in decision‐making concerning preventive options and show the need to address negative anticipatory feelings associated with carrying a pathogenic variant in a high breast cancer risk gene in clinical care.
Evidential network‐based system reliability assessment by fusing multi‐source evidential information
Authors: Li Xiaopeng 
Published: February 2023

AbstractExpert knowledge is an important information source for reliability assessment of those systems with limited time‐to‐failure data. For a better understanding of the degradation profiles of systems, multiple experts are oftentimes invited to express their judgments and the associated uncertainties on the reliability‐related measures of the system. Evidential variables, as an alternative of uncertainty quantification, have been extensively used in expert systems to quantify the epistemic uncertainty of the elicited expertise. When eliciting the reliability‐related information by evidential variables, experts only need to express the possible ranges of reliability‐related measures and their associated probabilities. Such a type of information well caters to the experts’ elicitation process. In this article, an evidential network (EN)‐based reliability assessment method is put forth by fusing multi‐source evidential information. The proposed method mainly contains three steps. In the first place, the multi‐source evidential information related to all components is elicited from experts in the form of evidential variables. Next, the evidential variable of the component reliability is assessed via a constrained optimization model by treating all pieces of multi‐source evidential information as constraints. The component reliability results are transformed into pieces of mass functions of the components’ states under the theory of belief functions. The system reliability‐box and the reliability‐box over time are, therefore, calculated by the EN model by inputting all mass functions of components’ states. A pipeline system and a chip cutting system are exemplified to examine the effectiveness of the proposed method.
Discrimination between accelerated life models via Approximate Bayesian Computation
Authors: Rabhi Mohamed , Abdessalem Anis Ben , Saintis Laurent , Castanier Bruno , Sohoin Rodrigue 
Published: February 2023

AbstractAccelerated life testing (ALT) is widely used in high‐reliability product estimation to get relevant information about an item's performance and its failure mechanisms. To analyse the observed ALT data, reliability practitioners need to select a suitable accelerated life model based on the nature of the stress and the physics involved. A statistical model consists of (i) a lifetime distribution that represents the scatter in product life and (ii) a relationship between life and stress. In practice, several accelerated life models could be used for the same failure mode and the choice of the best model is far from trivial. For this reason, an efficient selection procedure to discriminate between a set of competing accelerated life models is of great importance for practitioners. In this paper, accelerated life model selection is approached by using the Approximate Bayesian Computation (ABC) method and a likelihood‐based approach for comparison purposes. To demonstrate the efficiency of the ABC method in calibrating and selecting accelerated life model, an extensive Monte Carlo simulation study is carried out using different distances to measure the discrepancy between the empirical and simulated times of failure data. Then, the ABC algorithm is applied to real accelerated fatigue life data in order to select the most likely model among five plausible models. It has been demonstrated that the ABC method outperforms the likelihood‐based approach in terms of reliability predictions mainly at lower percentiles particularly useful in reliability engineering and risk assessment applications. Moreover, it has shown that ABC could mitigate the effects of model misspecification through an appropriate choice of the distance function.
The exploration of thin liquid film flow under the influences of various physical parameters by a new analytical innovation
Authors: Ali Liaqat , Ali Rohail , Humayun Muhammad , Ali Ishtiaq 
Published: February 2023

AbstractA new analytical innovation is utilized to explore the thin liquid film flow of magnetohydrodynamic (MHD) fluid over an unsteady porous stretching surface. Here magnetic field, thermal radiation, and variable viscosity are taken. The self‐similarity variables have been used to transform the modeled partial differential equations into a set of non‐linear coupled differential equations. These non‐linear differential equations for the velocity and temperature profiles have been tackled through an innovation containing homotopy, auxiliary functions, and convergence control parameters. This method is called the second configuration of the Optimal Homotopy Asymptotic Method and is denoted by (OHAM‐2). Galerkin's process is chosen for the optimizations of parameters. The achieved coupled equations are also solved numerically (ND‐Solve Method), and the obtained outcomes are compared with the results elaborated by the suggested algorithm. Here the utmost attention is on the rapid convergence of the proposed algorithm and the consequences of various tangible variables on the velocity and temperature profiles. This straightforward algorithm consists of a few steps but gives better outcomes. The technique can be applied to solve partial differential equations and their systems forming in various disciplines. This technique can also solve Integro differential equations. The residuals achieved by the proposed method for the velocity and temperature fields are shown graphically. The errors and residuals are also taught in Table 1 and Table 2. The effects of parameters are inculcated in Table 3 and Table 4. The results are validated with the published work as shown in Table 5. Nomenclature is indicated in the text below.
An XGBoost-Based Knowledge Tracing Model
Authors: Su Wei , Jiang Fan , Shi Chunyan , Wu Dongqing , Liu Lei , Li Shihua , Yuan Yongna , Shi Juntai 
Published: February 2023

AbstractThe knowledge tracing (KT) model is an effective means to realize the personalization of online education using artificial intelligence methods. It can accurately evaluate the learning state of students and conduct personalized instruction according to the characteristics of different students. However, the current knowledge tracing models still have problems of inaccurate prediction results and poor features utilization. The study applies XGBoost algorithm to knowledge tracing model to improve the prediction performance. In addition, the model also effectively handles the multi-skill problem in the knowledge tracing model by adding the features of problem and knowledge skills. Experimental results show that the best AUC value of the XGBoost-based knowledge tracing model can reach 0.9855 using multiple features. Furthermore, compared with previous knowledge tracing models used deep learning, the model saves more training time.
Unilateral Magma Emplacement of the Telimbela Batholith in the Central Ecuadorian Arc: Implications for Kinematics of Oblique Subduction of the Farallon‐Nazca Plate
Authors: Liu Hongsheng , Liu Liangming , Zhang Dexian , Huang Fangfang , Zhang Xin 
Published: February 2023

AbstractThe N‐S elongated granodioritic Telimbela batholith (TB, ∼220 km2) was emplaced at the restraining bend of the dextral strike‐slip Calacalí‐Pujilí‐Pallatanga Fault (CPPF) developed at the ca. 120 km wide Tertiary Ecuadorian arc. Our and previous zircon U‐Pb ages indicate that the batholith has a westward younging trend, with the oldest and youngest ages of 25.5 ± 0.5 and 17.5 ± 0.3 Ma, respectively, and a minimum duration of 8 ± 0.6 Ma was acquired. The Al‐in‐hornblende geobarometer results show that the TB was emplaced in the upper crust (∼4.7–5.3 km). The anisotropy of magnetic susceptibility (AMS) results of TB show three distinct groups of magnetic foliations, with a mean orientation of (64°/SE ∠ 39°) (0°/E ∠ 83°), and (16°/NW ∠ 83°) in the eastern, central and western parts of TB, respectively. As the TB was syntectonically emplaced with the evolution of CPPF, the vorticity numbers (Wn) of eastern, central, and western parts are determined by the angle between CPPF and mean orientation of AMS with Wn values of 0.79, 0, and 0.53, respectively. According to previous geodynamic studies on Northern Andes, the early and late kinematic transitions recorded in the TB may correspond to the change of plate subduction direction and the decrease in subduction angle, respectively. Comparing the estimated growth rate of TB to the tempo of Tertiary Ecuadorian arc magmatism revealed by detrital zircon ages and previous plate convergence velocity models, the good consistency among them will help to restore a detailed kinematic evolution of the Ecuadorian arc.
Dissolved Lead (Pb) Concentrations and Pb Isotope Ratios Along the East China Sea and Kuroshio Transect—Evidence for Isopycnal Transport and Particle Exchange
Authors: Chen Mengli , Boyle Edward A. , Jiang Shuo , Liu Qian , Zhang Jing , Wang Xianfeng , Zhou Kuanbo 
Published: February 2023

AbstractLead (Pb) isotopes are widely used in tracing processes that transport Pb within the environment due to the globally spread Pb pollution. In today’s ocean, Pb is mainly sourced from anthropogenic emissions and is removed by particle scavenging. However, recent efforts involving Pb isotopes have started to indicate that sediments at ocean boundary, either suspended or benthic, are a previously underestimated source and sink of Pb to the seawater dissolved pool. To assess the contributions of Pb from seawater‐sediment boundary, we measured the dissolved Pb concentrations and isotopic compositions in seawater from the outer East China Sea (ECS) and along the Kuroshio. Along the Kuroshio, depth profiles exhibit highly similar Pb concentrations across constant density planes, suggesting isopycnal transport. Pb isotope ratios in most of the samples show strong contributions of aerosol Pb, except for seawaters from the ECS and deep Okinawa Trough (>800 m), which show evidences of crustal Pb contribution. The Okinawa Trough deep water has overlapping Pb isotope ratios with ECS water, where the suspended particulate matter is abundant. Our data on Pb isotopes in the ECS and the Okinawa Trough deep water, together with data from previous studies at other continental margins suggest that the seawater‐sediment boundary along the continental shelves may be an important source and sink in marine Pb cycling.
An efficient hyperspectral image classification method for limited training data
Authors: Ren Yitao , Jin Peiyang , Li Yiyang , Mao Keming 
Published: February 2023

AbstractHyperspectral image classification has gained great progress in recent years based on deep learning model and massive training data. However, it is expensive and unpractical to label hyperspectral image data and implement model in constrained environment. To address this problem, this paper proposes an effective ghost module based spectral network for hyperspectral image classification. First, Ghost3D module is adopted to reduce the size of model parameter dramatically by redundant feature maps generation with linear transformation. Then Ghost2D module with channel‐wise attention is used to explore informative spectral feature representation. For large field covering, the non‐local operation is utilized to promote self‐attention. Compared with the state‐of‐the‐art hyperspectral image classification methods, the proposed approach achieves superior performance on three hyperspectral image data sets with fewer sample labelling and less resource consumption.
Combining acoustic localisation and high-resolution land cover classification to study predator vocalisation behaviour
Authors: Bru Elisabeth , Smith Bethany R. , Butkiewicz Hannah , Fontaine Amy C. , Dassow Angela , Owens Jessica L. , Root-Gutteridge Holly , Schindler Loretta , Kershenbaum Arik 
Published: February 2023

Context The ecology of cryptic animals is difficult to study without invasive tagging approaches or labour-intensive field surveys. Acoustic localisation provides an effective way to locate vocalising animals using acoustic recorders. Combining this with land cover classification gives new insight into wild animal behaviour using non-invasive tools. Aims This study aims to demonstrate how acoustic localisation – combined with high-resolution land cover classification – permits the study of the ecology of vocalising animals in the wild. We illustrate this technique by investigating the effect of land cover and distances to anthropogenic features on coyote and wolf vocal behaviour. Methods We collected recordings over 13 days in Wisconsin, USA, and triangulated vocalising animals’ locations using acoustic localisation. We then mapped these locations onto land cover using a high-resolution land cover map we produced for the area. Key results Neither coyotes nor wolves vocalised more in one habitat type over another. Coyotes vocalised significantly closer to all human features than expected by chance, whereas wolves vocalised significantly further away. When vocalising closer to human features, coyotes selected forests but wolves showed no habitat preference. Conclusions This novel combination of two sophisticated, autonomous sensing-driven tools permits us to examine animal land use and behavioural ecology using passive sensors, with the aim of drawing ecologically important conclusions. Implications We envisage that this method can be used at larger scales to aid monitoring of vocally active animals across landscapes. Firstly, it permits us to characterise habitat use while vocalising, which is an essential behaviour for many species. Furthermore, if combined with additional knowledge of how a species’ habitat selection while vocalising relates to its general habitat use, this method could permit the derivation of future conclusions on prevailing landscape use. In summary, this study demonstrates the potential of integrating acoustic localisation with land cover classification in ecological research.
Infection-Induced Immunity Is Associated With Protection Against Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Decreased Infectivity
Authors: Frutos Aaron M , Kuan Guillermina , Lopez Roger , Ojeda Sergio , Shotwell Abigail , Sanchez Nery , Saborio Saira , Plazaola Miguel , Barilla Carlos , Kenah Eben , Balmaseda Angel , Gordon Aubree 
Published: February 2023

AbstractBackgroundThe impact of infection-induced immunity on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has not been well established. Here we estimate the effects of prior infection induced immunity in adults and children on SARS-CoV-2 transmission in households.MethodsWe conducted a household cohort study from March 2020-November 2022 in Managua, Nicaragua; following a housheold SARS-CoV-2 infection, household members are closely monitored for infection. We estimate the association of time period, age, symptoms, and prior infection with secondary attack risk.ResultsOverall, transmission occurred in 70.2% of households, 40.9% of household contacts were infected, and the secondary attack risk ranged from 8.1% to 13.9% depending on the time period. Symptomatic infected individuals were more infectious (rate ratio [RR] 21.2, 95% confidence interval [CI]: 7.4–60.7) and participants with a prior infection were half as likely to be infected compared to naïve individuals (RR 0.52, 95% CI:.38–.70). In models stratified by age, prior infection was associated with decreased infectivity in adults and adolescents (secondary attack risk [SAR] 12.3, 95% CI: 10.3, 14.8 vs 17.5, 95% CI: 14.8, 20.7). However, although young children were less likely to transmit, neither prior infection nor symptom presentation was associated with infectivity. During the Omicron era, infection-induced immunity remained protective against infection.ConclusionsInfection-induced immunity is associated with decreased infectivity for adults and adolescents. Although young children are less infectious, prior infection and asymptomatic presentation did not reduce their infectivity as was seen in adults. As SARS-CoV-2 transitions to endemicity, children may become more important in transmission dynamics.
Adherence to Antimicrobial Prophylaxis Guidelines for Elective Surgeries Across 825 US Hospitals, 2019–2020
Authors: Cabral Stephanie M , Harris Anthony D , Cosgrove Sara E , Magder Laurence S , Tamma Pranita D , Goodman Katherine E 
Published: February 2023

Abstract

Background
There are limited US data assessing adherence to surgical antimicrobial prophylaxis guidelines, particularly across a large, nationwide sample. Moreover, commonly prescribed inappropriate antimicrobial prophylaxis regimens remain unknown, hindering improvement initiatives.

Methods
We conducted a retrospective cohort study of adults who underwent elective craniotomy, hip replacement, knee replacement, spinal procedure, or hernia repair in 2019–2020 at hospitals in the PINC AI (Premier) Healthcare Database. We evaluated adherence of prophylaxis regimens, with respect to antimicrobial agents endorsed in the American Society of Health-System Pharmacist guidelines, accounting for patient antibiotic allergy and methicillin-resistant Staphylococcus aureus colonization status. We used multivariable logistic regression with random effects by hospital to evaluate associations between patient, procedural, and hospital characteristics and guideline adherence.

Results
Across 825 hospitals and 521 091 inpatient elective surgeries, 308 760 (59%) were adherent to prophylaxis guidelines. In adjusted analysis, adherence varied significantly by US Census division (adjusted OR [aOR] range: .61–1.61) and was significantly lower in 2020 compared with 2019 (aOR: .92; 95% CI: .91–.94; P &lt; .001). The most common reason for nonadherence was unnecessary vancomycin use. In a post hoc analysis, controlling for patient age, comorbidities, other nephrotoxic agent use, and patient and procedure characteristics, patients receiving cefazolin plus vancomycin had 19% higher odds of acute kidney injury (AKI) compared with patients receiving cefazolin alone (aOR: 1.19; 95% CI: 1.11–1.27; P &lt; .001).

Conclusions
Adherence to antimicrobial prophylaxis guidelines remains suboptimal, largely driven by unnecessary vancomycin use, which may increase the risk of AKI. Adherence decreased in the first year of the COVID-19 pandemic.
The genetic structure within a single tree is determined by the behavior of the stem cells in the meristem
Authors: Iwasa Yoh , Tomimoto Sou , Satake Akiko 
Published: February 2023

Abstract
Genomic sequencing revealed that somatic mutations cause a genetic differentiation of the cells in a single tree. We studied a mathematical model for stem cell proliferation in the shoot apical meristem (SAM). We evaluated the phylogenetic distance between cells sampled from different portions of a shoot, indicating their genetic difference due to mutations accumulated during shoot elongation. The plant tissue has cell walls that suppress the exchange of location between cells. This leads to the genetic differentiation of cells according to the angle around the shoot and a larger genetic variance among cells in the body. The assumptions are as follows: stem cells in the SAM normally undergo asymmetric cell division, producing successor stem cells and differentiated cells. Occasionally, a stem cell fails to leave its successor stem cell and the vacancy is filled by the duplication of one of the nearest neighbor stem cells. A mathematical analysis revealed the following: the genetic diversity of cells sampled at the same position along the shoot increases with the distance from the base of the shoot. Stem cells hold a larger variation if they are replaced only by the nearest neighbors. The coalescent length between two cells increases not only with the difference in the position along the shoot but also in the angle around the shoot axis. The dynamics of stem cells at the SAM determine the genetic pattern of the entire shoot.