bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability analysis of monthly precipitation vector time series in Australia by a new spatiotemporal entropy statistic
Authors: Hines Benjamin , Qian Guoqi , Chu Tingjin , Tordesillas Antoinette 
Published: January 2023

Abstract
Changing climate in Australia has significant impacts on the country’s economy, environment and social well-being. Addressing such impacts, particularly that of precipitation change, entails immediate action due to the more frequent occurrence of extreme dry or wet events in Australia in recent decades. In this paper we investigate the intra-annual Australian precipitation variability and how it changes over space and time. We quantify this variability using information entropy—a statistical tool for measuring the uncertainty of a random variable over its sample space, and propose a compositional data model to compute optimal spatiotemporal estimators of this entropy using 1/1979-to-3/2022 monthly satellite precipitation estimates from the National Oceanic and Atmospheric Administration. The results enable us to identify those locations/times where/when extreme intra-annual precipitation variation or unevenness occurred. We find this variability has been changing over time in large regions of southeastern Queensland and on the coast of South Australia, which would be difficult to find without using the proposed approach. We uncover the development of extreme entropy in the months leading up to, and in the location of, four extreme precipitation events in Australia where inter-annual precipitation amounts and/or trends proved insignificant. In marked contrast to annual precipitation, we found entropy has a weak association with the El Niño Southern Oscillation cycle.
How does increasing temperature affect the sub-annual distribution of monthly rainfall?
Authors: Tie Jiahao , Kim Seokhyeon , Sharma Ashish 
Published: January 2023

Abstract
This paper investigates the relationship between temperature and sub-annual rainfall patterns using long-term monthly rainfall and temperature data from 1920 to 2018 in Australia. A parameter (τ) is used to measure the evenness of temporal rainfall distribution within each year, with τ = 0 indicating a uniform pattern. The study examines the relationship between τ and temperature for each year, considering whether it was warmer or cooler than average across five climate zones (CZs) in Australia, including tropical, arid, and three temperate climate classes. This study discovered a considerable association between annual maximum temperature and the distribution of monthly rainfall, with high temperatures resulting in greater variation (as represented by larger τ values) in the sub-annual distribution of monthly rainfall throughout all CZs, particularly in arid regions with τ values ranging from 0.27 to 0.52. In contrast, regions with temperate climates without dry seasons had a lower and narrower range of τ, from 0.15 to 0.26. This variability in rainfall distribution makes managing water resources more challenging in arid regions in Australia.
NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration
Authors: Abid Dhoha , Brent Michael R 
Published: January 2023

Abstract

Motivation
Many methods have been proposed for mapping the targets of transcription factors (TFs) from gene expression data. It is known that combining outputs from multiple methods can improve performance. To date, outputs have been combined by using either simplistic formulae, such as geometric mean, or carefully hand-tuned formulae that may not generalize well to new inputs. Finally, the evaluation of accuracy has been challenging due to the lack of genome-scale, ground-truth networks.

Results
We developed NetProphet3, which combines scores from multiple analyses automatically, using a tree boosting algorithm trained on TF binding location data. We also developed three independent, genome-scale evaluation metrics. By these metrics, NetProphet3 is more accurate than other commonly used packages, including NetProphet 2.0, when gene expression data from direct TF perturbations are available. Furthermore, its integration mode can forge a consensus network from gene expression data and TF binding location data.

Availability and implementation
All data and code are available at https://zenodo.org/record/7504131#.Y7Wu3i-B2x8.

Supplementary information
Supplementary data are available at Bioinformatics online.
How to optimally sample a sequence for rapid analysis
Authors: Frith Martin C , Shaw Jim , Spouge John L 
Published: January 2023

Abstract

Motivation
We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such as minimizers, syncmers and minimally overlapping words, were developed by heuristic intuition, and are not optimal.

Results
We present a sequence-sampling approach that provably optimizes sensitivity for a whole class of sequence comparison methods, for randomly evolving sequences. It is likely near-optimal for a wide range of alignment-based and alignment-free analyses. For real biological DNA, it increases specificity by avoiding simple repeats. Our approach generalizes universal hitting sets (which guarantee to sample a sequence at least once) and polar sets (which guarantee to sample a sequence at most once). This helps us understand how to do rapid sequence analysis as accurately as possible.

Availability and implementation
Source code is freely available at https://gitlab.com/mcfrith/noverlap.

Supplementary information
Supplementary data are available at Bioinformatics online.
Android Malware Detection in Bytecode Level Using TF-IDF and XGBoost
Authors: Ozogur Gokhan , Erturk Mehmet Ali , Gurkas Aydin Zeynep , Aydin Muhammed Ali 
Published: January 2023

Abstract
Android is the dominant operating system in the smartphone market and there exists millions of applications in various application stores. The increase in the number of applications has necessitated the detection of malicious applications in a short time. As opposed to dynamic analysis, it is possible to obtain results in a shorter time in static analysis as there is no need to run the applications. However, obtaining various information from application packages using reverse engineering techniques still requires a substantial amount of processing power. Although some attempts have been made to solve this problem by analyzing binary files without decoding the source code, there is still more work to be done in this area. In this study, we analyzed the applications in bytecode level without decoding the binary source files. We proposed a model using Term Frequency - Inverse Document Frequency (TF-IDF) word representation for feature extraction and Extreme Gradient Boosting (XGBoost) method for classification. The experimental results show that our model classifies a given application package as a malware or benign in 2.75 s with 99.05% F1-score on a balanced dataset, and in 3.30 s with 99.35% F1-score on an imbalanced dataset containing obfuscated malwares.
Connecting the Young: High School Graduates’ Matching to First Jobs in Booms and Great Recessions
Authors: Hensvik Lena , Müller Dagmar , Skans Oskar Nordström 
Published: January 2023

Abstract
Using Swedish economy-wide data, we examine the relationship between business-cycle conditions and the use of social contacts in the process where young workers are matched to their first real jobs. We measure social contacts acquired during paid work during high school, and we rely on interacted class-establishment fixed-effect models to isolate the effects of interest. One-third of post-graduation matches are formed at establishments where youths worked during their studies. Graduates are much more likely to match with sites to which adult co-workers from these jobs have relocated. The importance of these job-finding channels is strongly counter-cyclical for young labour market entrants.
Routine use of percutaneous femoral cannulation in minimally invasive cardiac surgery
Authors: Ma Kristina , Kastengren Mikael , Svenarud Peter , Green Ram , Dalén Magnus 
Published: January 2023

AbstractOBJECTIVESLarge series of percutaneous femoral access for extracorporeal circulation in minimally invasive cardiac surgery (MICS) are scarcely reported.METHODSThis is a single-centre study describing the use of percutaneous femoral access in patients undergoing MICS via minithoracotomy. Femoral artery closure was performed with a plug-based closure device. To reduce the risk for vascular complications, intraoperative ultrasound assessment of correct deployment of the arterial closure device was done during the later period of the study.RESULTSDuring a 5-year period, 650 patients underwent percutaneous femoral cannulation and decannulation with device closure of the femoral artery puncture. Two hundred and seven patients (31.8%) were operated in the early phase of the experience (August 2017–August 2019), without the use of intraoperative ultrasound assessment of closure device deployment. During the later period of our experience (August 2019–September 2022), 443 patients (68.2%) were operated, of whom all underwent intraoperative ultrasound assessment of closure device deployment. Of the patients operated without intraoperative ultrasound assessment, 6 patients (2.9%) experienced vascular complications compared with none of the patients in whom intraoperative ultrasound-assessment was used (P &lt; 0.001). In total, 15 patients (2.3%) underwent conversion to surgical cutdown owing to incomplete haemostasis or femoral artery stenosis/occlusion and the mechanism was intravascular deployment of the closure device in all 15 cases.CONCLUSIONSPercutaneous femoral access in MICS is safe and the need for surgical cutdown was infrequent. The risk for vascular complications is minimized with the use of intraoperative ultrasound assessment of the correct positioning of the vascular closure device.CLINICAL TRIAL REGISTRATION NUMBERhttp://www.clinicaltrials.gov; Unique identifier: NCT05462769.
Outcomes of the modified Yacoub aortocoronary flap technique for ‘non-separable’ single sinus coronary arteries with intramural course in the neonatal arterial switch operation
Authors: Van den Eynde Jef , van der Palen Roel L F , Knobbe Ingmar , Straver Bart , Stöger Lauran , Ricciardi Gabriella , Konings Thelma C , Jongbloed Monique R M , Hazekamp Mark G 
Published: January 2023

Abstract

OBJECTIVES
Coronary transfer remains the most crucial part of the arterial switch operation (ASO); yet, certain coronary anatomies prohibit the use of button or trap-door transfer techniques. In the rare setting of ‘non-separable’ single sinus coronary arteries with intramural course, the modified Yacoub aortocoronary flap technique is a viable option. The aim of this study is to describe this operative technique and review its early- and mid-term outcomes.

METHODS
This retrospective analysis included all cases with ‘non-separable’ single sinus coronary arteries with intramural course where the modified Yacoub aortocoronary flap technique served as a bail-out option.

RESULTS
Of 516 patients who underwent ASO at our institution between January 1977 and April 2022, 14 underwent the modified Yacoub aortocoronary flap technique. The median age at ASO was 10 (interquartile range 7–19) days. Hospital mortality occurred in 3 patients (21.4%), all being related to coronary complications. All hospital survivors were still alive at a median of 9.1 (interquartile range 4.2–18.3) years after the ASO. None of them developed complaints of ischaemia, ventricular arrhythmias, ventricular dysfunction or exercise intolerance. Surveillance computed tomography angiography showed stable aortocoronary relationships free from stenosis, compression and kinking. No reoperations for coronary artery problems and/or neoaortic valve or root problems were needed.

CONCLUSIONS
Although close monitoring of early coronary events seems crucial to prevent perioperative mortality, the modified Yacoub aortocoronary flap technique may serve as a viable bail-out option in patients with ‘non-separable’ single sinus coronary anatomy with intramural course, with excellent results among hospital survivors.
Temporal trends in the incidence of malignancy in heart failure: a nationwide Danish study
Authors: Bruhn Jonas , Malmborg Morten , Garred Caroline H , Ravn Pauline , Zahir Deewa , Andersson Charlotte , Gislason Gunnar , Torp-Pedersen Christian , Kragholm Kristian , Fosbol Emil , Butt Jawad H , Lang Ninian N , Petrie Mark C , McMurray John , Kober Lars , Schou Morten 
Published: January 2023

AbstractAimsCancer and heart failure (HF) share risk factors, pathophysiological mechanisms, and possibly genetics. Improved HF survival may increase the risk of cancer due to a competing risk. Whether the incidence of cancer has increased over time in patients with HF as survival has improved is unclear. Therefore, temporal trends of new onset cancer in HF patients between 1997 and 2016 were investigated.Methods and resultsUsing Danish nationwide registers, 103 711 individuals alive, free of cancer, and aged 30–80 years 1 year after HF diagnosis (index date) were included between 1 January 1997 and 31 December 2016. A five-year incidence rate of cancer for each year after index date was calculated. The median age and proportion of women at the index date decreased with advancing calendar time [1997–2001: 70.3 interquartile range (Q1–Q3 62.5–75.7), 60.9% men; 2012–16: 67.6 (59.2–73.8), 67.5% men]. The five-year incidence rate of cancer was 20.9 and 20.2 per 1,000 person-years in 1997 and 2016, respectively. In a multivariable Cox regression model, the hazard rates between index years 1997 (reference) and 2016 were not significantly different [hazard ratio 1.09 (0.97–1.23)]. The five-year absolute risk of cancer did not change with advancing calendar year, going from 9.0% (1997–2001) to 9.0% (2012–16). Five-year cumulative incidence of survival for HF patients increased with advancing calendar year, going from 55.9% (1997–2001) to 74.3% (2012–2016).ConclusionAlthough cancer rates during 1997–2016 have remained stable within 1–6 years after the HF diagnosis, long-term survival following a HF diagnosis has increased significantly.
Combination of current and new electrocardiographic-based criteria: a novel score for the discrimination of left bundle branch capture
Authors: Briongos-Figuero Sem , Estévez-Paniagua Álvaro , Sánchez-Hernández Ana , Muñoz-Aguilera Roberto 
Published: January 2023

AbstractAimsMost of the criteria used to diagnose direct capture of the left bundle branch (LBB) have never been validated in an external sample. We hypothesized that lead aVL might add relevant information, and the combination of several electrocardiograph (ECG)-based criteria might discriminate better LBB capture from left ventricular septal (LVS) capture, than each criterion separately.Methods and resultsSingle-centre study involving all consecutive patients who received LBB area pacing. LBB capture was defined according to QRS morphology transition criteria during decremental pacing. Multivariate logistic regression analysis was performed to develop a predictive score for LBB capture. A total of 71 patients with confirmed LBB capture were analysed. The optimal cut-off values of R wave peak time (RWPT) in lead V6 (V6-RWPT) and V6-V1 interpeak interval for the discrimination of LBB capture were &lt;83 ms and ≥33 ms, respectively. The RWPT in lead aVL (aVL-RWPT) showed a good discrimination power for the differential diagnosis of LBB capture and LVS capture. The optimal value for aVL-RWPT was 79 ms [sensitivity (SN) and specificity (SP) of 71.2% and 88.4%, respectively]. A new score, with a good diagnostic performance (area under the curve of 0.976), was constructed gathering the information from V6-RWPT, aVL-RWPT, and V6-V1 interpeak interval. The optimal score of 3 points showed a SN and SP of 89.2% and 100%, respectively for the differentiation of LBB capture.ConclusionsECG-based criteria are useful to confirm the capture of the LBB. The combination of V6-RWPT, aVL-RWPT, and V6-V1 interpeak interval values demonstrated better diagnostic performance than isolated measurements.
Cost-effectiveness analysis of cardiac implantable electronic devices with reactive atrial-based antitachycardia pacing
Authors: Noda Takashi , Ueda Nobuhiko , Tanaka Yuji , Ishiguro Yoko , Matsumoto Tomoko , Uenishi Tatsuhiro , Yamaguchi Hiroko , Shoji Ayako , Myung Jae-Eun , Kusano Kengo 
Published: January 2023

AbstractAimsReactive atrial-based anti-tachycardia pacing (rATP) in pacemakers (PMs) and cardiac resynchronization therapy defibrillators (CRT-Ds) has been reported to prevent progression of atrial fibrillation, and this reduced progression is expected to decrease the risk of complications such as stroke and heart failure (HF). This study aimed to assess the cost-effectiveness of rATP in PMs and CRT-Ds in the Japanese public health insurance system.Methods and resultsWe developed a Markov model comprising five states: bradycardia, post-stroke, mild HF, severe HF, and death. For devices with rATP and control devices without rATP, we compared the incremental cost-effectiveness ratio (ICER) from the payer's perspective. Costs were estimated from healthcare resource utilisation data in a Japanese claims database. We evaluated model uncertainty by analysing two scenarios for each device. The ICER was 763 729 JPY/QALY (5616 EUR/QALY) for PMs and 1,393 280 JPY/QALY (10 245 EUR/QALY) for CRT-Ds. In all scenarios, ICERs were below 5 million JPY/QALY (36 765 EUR/QALY), supporting robustness of the results.ConclusionAccording to a willingness to pay threshold of 5 million JPY/QALY, the devices with rATP were cost-effective compared with control devices without rATP, showing that the higher reimbursement price of the functional categories with rATP is justified from a healthcare economic perspective.
Induction and sustenance of antibacterial activities distinguishes response of mice toSalmonellaTyphi from response toSalmonellaTyphimurium
Authors: Yadav Jitender , Qadri Ayub 
Published: January 2023

AbstractSalmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid in humans, shares a high degree of homology with a closely related serovar, S. Typhimurium. Yet, unlike S. Typhimurium, S. Typhi does not establish infection in mice, the reasons for which are not well understood. Here, we present evidence that the response of mice to infection with S. Typhi is marked by early antibacterial activities. Cell-free peritoneal fluids from S. Typhi but not S. Typhimurium—infected mice inhibited the replication of Salmonella ex vivo. The production of this activity was reduced in the presence of the serine protease inhibitor, phenylmethylsulfonlyl fluoride (PMSF). PMSF also inhibited the generation of antibacterial activity released from in vitro S. Typhi—infected peritoneal macrophages in a cell death—dependent manner. Infection with S. Typhimurium but not S. Typhi was associated with reduction in the mRNA levels of iron-regulating molecules, ferroportin and lipocalin. These results suggest that early induction and sustenance of antibacterial activities may contribute to the nonestablishment of infection with S. Typhi in mice.
A functional spectrum of PROKR2 mutations identified in isolated hypogonadotropic hypogonadism
Authors: Wang Xinying , Chen Danna , Zhao Yaguang , Men Meichao , Chen Zhiheng , Jiang Fang , Zheng Ruizhi , Stamou Maria I , Plummer Lacey , Balasubramanian Ravikumar , Li Jia-Da 
Published: January 2023

Abstract
Isolated hypogonadotropic hypogonadism (IHH) is a rare disease with hypogonadism and infertility caused by the defects in embryonic migration of hypothalamic gonadotropin-releasing hormone (GnRH) neurons, hypothalamic GnRH secretion or GnRH signal transduction. PROKR2 gene, encoding a G-protein coupled receptor PROKR2, is one of the most frequently mutated genes identified in IHH patients. However, the functional consequences of several PROKR2 mutants remain elusive. In this study, we systematically analyzed the Gαq, Gαs and ERK1/2 signaling of 23 IHH-associated PROKR2 mutations which are yet to be functionally characterized. We demonstrate that blockage of Gαq, instead of MAPK/ERK pathway, inhibited PROK2-induced migration of PROKR2-expressing cells, implying that PROKR2-related IHH results primarily due to Gαq signaling pathway disruption. Combined with previous reports, we categorized a total of 63 IHH-associated PROKR2 mutations into four distinct groups according Gαq pathway functionality: (i) neutral (N, &gt;80% activity); (ii) low pathogenicity (L, 50–80% activity); (iii) medium pathogenicity (M, 20–50% activity) and (iv) high pathogenicity (H, &lt;20% activity). We further compared the cell-based functional results with in silico mutational prediction programs. Our results indicated that while Sorting Intolerant from Tolerant predictions were accurate for transmembrane region mutations, mutations localized in the intracellular and extracellular domains were accurately predicted by the Combined Annotation Dependent Depletion prediction tool. Our results thus provide a functional database that can be used to guide diagnosis and appropriate genetic counseling in IHH patients with PROKR2 mutations.
Routine double-ovarian-stimulation (DuoStim) in poor responders lacks rationale, evidence, and follow-up
Authors: Tocci Angelo , Barad David , Łukaszuk Krzysztof , Orvieto Raoul 
Published: January 2023

AbstractDouble ovarian stimulation (DuoStim), initially only suggested for fertility preservation in cancer patients, is now increasingly also used in routine clinical IVF, especially in poor responders. The claimed rational for this is the alleged existence of multiple follicular waves in a single intermenstrual interval, allowing for retrieval of more oocytes in a single IVF cycle. This commentary argues that this expansion of purpose lacks rationale, evidence, and follow-up. Consequently, we suggest that, unless valid clinical indications have been established, DuoStim be only subject of controlled clinical trials with appropriate experimental consents.