bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domestic chicken omega 3 – a product for promoting human health
Authors: Sefer Dragan , Radulovic Stamen , Peric Dejan , Sefer Matija , Makivic Lazar , Grdovic Svetlana , Markovic Radmila 
Published: November 2021

Abstract
Literature data show that the relationship between two groups of polyunsaturated fatty acids in diet, omega 3 acids, whose basic representative is a-linolenic acid (C18: 3 n-3), and omega 6 acids, whose basic representative is linoleic acid (C18: 2 n-6), has a significant role in development of cardiovascular diseases in humans. The optimal ratio of omega 6 to omega 3 fatty acids is around 4:1. In monogastric animals, the fatty acids in feed are absorbed in the gastrointestinal tract largely unchanged. This means the fatty acid profile of the animal’s diet directly reflects the fatty acid profile of the tissue. The daily intake of unsaturated fatty acids can be increased by an adequate animal nutrition strategy. Flaxseed contains ten times more unsaturated (32.26%) than saturated (3.66%) fatty acids. The largest amount of unsaturated fatty acids (about 70%) is a-linolenic acid (ALA), which is a precursor of the entire omega 3 series of fatty acids, and which makes flaxseed an ideal raw material for the production of a wide range of omega 3 enriched products. In order to obtain chicken meat rich in omega 3, an experiment was organized with a specific diet for broilers at fattening. Thanks to the designed animal feed, it was possible to get products (meat, breast, drumstick, liver, subcutaneous fat) with significantly higher amounts of omega 3 fatty acids compared to the same products obtained from broilers fed with conventional mixtures, or with almost the ideal ratio between omega 6 and omega 3 fatty acids.
Nonlinear thermal vibration of a nanoplate attached to a cavity
Authors: Bai Yuhe , Liu Rumeng , Wang Lifeng 
Published: November 2021

Abstract
Dynamic problems of a nanocircular plate-cavity system are investigated using molecular dynamics (MD) method. A nonlinear plate model considering gas action is developed. The results of the MD simulation show that the helium atoms adsorb on the wall of the cavity at low temperature, resulting in a negative deflection of the molybdenum disulfide (MoS2) plate. As the temperature increases, the pressure in the cavity increases, leading to a gradual rise in the deflection of the plate. A nonlinear phenomenon of stiffness hardening is shown with increasing temperature. The nonlinear plate model can give a relatively good prediction compared with the results of MD simulations. The natural frequency of the plate is affected by temperature and the presence of gas in the cavity. The phenomenon of stiffness hardening and softening can be well simulated by the nonlinear plate model and MD method. The present study provides a reference for vibration experiments of two-dimensional nanostructures.
Additive manufacturing for fused deposition modeling of carbon fiber–polylactic acid composites: the effects of process parameters on tensile and flexural properties
Authors: Mishra Abhay , Srivastava Vivek , Gupta Nitin Kumar 
Published: November 2021

Abstract
In this paper the effect of process parameters on the tensile and flexural properties of carbon fiber–polylactic acid (CF-PLA) composites is analyzed. We used a commercially available fused deposition modeling (FDM) three-dimensional (3D) printer and CF-PLA. When there are a variety of processing parameters, especially when no linear processing parameters are defined, the exact factors required in the design of experiments (DOEs) is hard to research. Furthermore, a large number of samples are needed to discover the optimum processing parameters. The key effects of four processing parameters for the FDM process, i.e. layer height, infill density, printing speed and infill pattern, were examined in this work using the Taguchi DOE. The mechanical characteristics of the fabricated FDM components expressed the power of the processing parameters. We used the Taguchi L9 range of nine runs with three specimens each, so 54 different processes were used to make a total of 54 specimens. In comparison with the 3D computer-aided design model, the measurements of the manufactured specimens were tested according to the standards ASTM D638 and ASTM D790. Variance analysis (ANOVA) was generated using Design Expert tools in order to assess the importance of the variables and their interactions for tensile and flexural strength. After performing ANOVA we obtained the exact parameters for which the mechanical properties are highest.
Religion as a Basic Human Good
Authors: Howes Thomas D 
Published: November 2021

Abstract:
For the sake of defending the political-ethical legitimacy of religious exemptions, this article analyzes what contemporary natural law theorists call the good of religion—harmony with the transcendent source of existence and meaning. This good serves as a principle in practical judgments, not as a premise in a deductive argument, but as an end of action. Practical familiarity and explicit understanding of this good can differ among individuals, and variations of such familiarity and understanding lead to differing practical judgments concerning what constitute reasonable choices in its pursuit. This in turn affects judgments of fairness concerning burdens on that same pursuit. It is optimal for judgments about religious exemptions to presuppose a more paradigmatic understanding of this good so that one can better assess what is really at stake in the minds of religious believers when their religious liberty is burdened. In making a case for a more paradigmatic understanding of religion, this article draws attention to existential data from which practical insight into the good of religion arises.
Positivism’s Implosion
Authors: Köpcke Maris 
Published: November 2021

Abstract:
Kletzer’s recent book The Idea of a Pure Theory illustrates the incoherence of a legal theory’s methodological commitment to “purity,” and hence to independence from moral and empirical concerns. Unlike other self-styled “positivist” accounts that pay mere lip service to this methodological agenda, Kletzer helpfully spells it out and follows it through, to the point of expunging from his account anything bearing the resemblance of an argument from first principles. He associates moral with theological reasoning, and theological reasoning in turn with legal reasoning by appeal to validating criteria. But his account pays a high price for purity. The price is the account’s internal contradiction and inconsistency with a legal theory’s criteria of success. Reflection on Kletzer’s enterprise suggests that we have reason to reject a “pure” method in doing legal theory.
An expectation–maximization approach to quantifying protein stoichiometry with single-molecule imaging
Authors: Boonkird Artittaya , Nino Daniel F , Milstein Joshua N 
Published: November 2021

AbstractMotivationSingle-molecule localization microscopy (SMLM) is a super-resolution technique capable of rendering nanometer scale images of cellular structures. Recently, much effort has gone into developing algorithms for extracting quantitative features from SMLM datasets, such as the abundance and stoichiometry of macromolecular complexes. These algorithms often require knowledge of the complicated photophysical properties of photoswitchable fluorophores.ResultsHere, we develop a calibration-free approach to quantitative SMLM built upon the observation that most photoswitchable fluorophores emit a geometrically distributed number of blinks before photobleaching. From a statistical model of a mixture of monomers, dimers and trimers, the method employs an adapted expectation–maximization algorithm to learn the protomer fractions while simultaneously determining the single-fluorophore blinking distribution. To illustrate the utility of our approach, we benchmark it on both simulated datasets and experimental datasets assembled from SMLM images of fluorescently labeled DNA nanostructures.Availability and implementationAn implementation of our algorithm written in Python is available at: https://www.utm.utoronto.ca/milsteinlab/resources/Software/MMCode/.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
Scalable inference of transcriptional kinetic parameters from MS2 time series data
Authors: Bowles Jonathan R , Hoppe Caroline , Ashe Hilary L , Rattray Magnus 
Published: November 2021

Abstract

Motivation
The MS2-MCP (MS2 coat protein) live imaging system allows for visualization of transcription dynamics through the introduction of hairpin stem-loop sequences into a gene. A fluorescent signal at the site of nascent transcription in the nucleus quantifies mRNA production. Computational modelling can be used to infer the promoter states along with the kinetic parameters governing transcription, such as promoter switching frequency and polymerase loading rate. However, modelling of the fluorescent trace presents a challenge due its persistence; the observed fluorescence at a given time point depends on both current and previous promoter states. A compound state Hidden Markov Model (cpHMM) was recently introduced to allow inference of promoter activity from MS2-MCP data. However, the computational time for inference scales exponentially with gene length and the cpHMM is therefore not currently practical for application to many eukaryotic genes.

Results
We present a scalable implementation of the cpHMM for fast inference of promoter activity and transcriptional kinetic parameters. This new method can model genes of arbitrary length through the use of a time-adaptive truncated compound state space. The truncated state space provides a good approximation to the full state space by retaining the most likely set of states at each time during the forward pass of the algorithm. Testing on MS2-MCP fluorescent data collected from early Drosophila melanogaster embryos indicates that the method provides accurate inference of kinetic parameters within a computationally feasible timeframe. The inferred promoter traces generated by the model can also be used to infer single-cell transcriptional parameters.

Availability and implementation
Python implementation is available at https://github.com/ManchesterBioinference/burstInfer, along with code to reproduce the examples presented here.

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications
Authors: Li Zongren , Zhong Qin , Yang Jing , Duan Yongjie , Wang Wenjun , Wu Chengkun , He Kunlun 
Published: November 2021

Abstract

Summary
DeepKG is an end-to-end deep learning-based workflow that helps researchers automatically mine valuable knowledge in biomedical literature. Users can utilize it to establish customized knowledge graphs in specified domains, thus facilitating in-depth understanding on disease mechanisms and applications on drug repurposing and clinical research. To improve the performance of DeepKG, a cascaded hybrid information extraction framework is developed for training model of 3-tuple extraction, and a novel AutoML-based knowledge representation algorithm (AutoTransX) is proposed for knowledge representation and inference. The system has been deployed in dozens of hospitals and extensive experiments strongly evidence the effectiveness. In the context of 144 900 COVID-19 scholarly full-text literature, DeepKG generates a high-quality knowledge graph with 7980 entities and 43 760 3-tuples, a candidate drug list, and relevant animal experimental studies are being carried out. To accelerate more studies, we make DeepKG publicly available and provide an online tool including the data of 3-tuples, potential drug list, question answering system, visualization platform.

Availability and implementation
All the results are publicly available at the website (http://covidkg.ai/).

Supplementary information
Supplementary data are available at Bioinformatics online.
Catalyzing momentum in male contraceptive development
Authors: Nickels Logan M , Shane Kevin , Vahdat Heather L 
Published: November 2021

Abstract
Globally, nearly half of all pregnancies are unplanned. Male contraceptives offer the potential to decrease unintended pregnancy and introduce contraceptive equity, but decades of research have yet to bring a novel product to market. New funding avenues from the philanthropic sector seek to stimulate research in male contraceptives through investments, grants, and support for trainees alongside other programs that encourage product development and ultimately commercialization. This Forum outlines the purpose of and funding opportunities provided by Male Contraceptive Initiative, a funding agency and non-profit focused on the advancement of non-hormonal, reversible contraceptive technologies for those who produce sperm.
Growth prediction model for abdominal aortic aneurysms
Authors: Ristl Robin , Klopf Johannes , Scheuba Andreas , Wolf Florian , Funovics Martin , Gollackner Bernd , Wanhainen Anders , Neumayer Christoph , Posch Martin , Brostjan Christine , Eilenberg Wolf 
Published: November 2021

Abstract

Background
The most relevant determinant in scheduling monitoring intervals for abdominal aortic aneurysms (AAAs) is maximum diameter. The aim of the study was to develop a statistical model that takes into account specific characteristics of AAA growth distributions such as between-patient variability as well as within-patient variability across time, and allows probabilistic statements to be made regarding expected AAA growth.

Methods
CT angiography (CTA) data from patients monitored at 6-month intervals with maximum AAA diameters at baseline between 30 and 66 mm were used to develop the model. By extending the model of geometric Brownian motion with a log-normal random effect, a stochastic growth model was developed. An additional set of ultrasound-based growth data was used for external validation.

Results
The study data included 363 CTAs from 87 patients, and the external validation set comprised 390 patients. Internal and external cross-validation showed that the stochastic growth model allowed accurate description of the distribution of aneurysm growth. Median relative growth within 1 year was 4.1 (5–95 per cent quantile 0.5–13.3) per cent. Model calculations further resulted in relative 1-year growth of 7.0 (1.0–16.4) per cent for patients with previously observed rapid 1-year growth of 10 per cent, and 2.6 (0.3–8.3) per cent for those with previously observed slow growth of 1 per cent. The probability of exceeding a threshold of 55 mm was calculated to be 1.78 per cent at most when adhering to the current RESCAN guidelines for rescreening intervals. An online calculator based on the fitted model was made available.

Conclusion
The stochastic growth model was found to provide a reliable tool for predicting AAA growth.
Atypical dynamic functional network connectivity state engagement during social–emotional processing in schizophrenia and autism
Authors: Hyatt Christopher J , Wexler Bruce E , Pittman Brian , Nicholson Alycia , Pearlson Godfrey D , Corbera Silvia , Bell Morris D , Pelphrey Kevin , Calhoun Vince D , Assaf Michal 
Published: November 2021

Abstract
Autism spectrum disorder (ASD) and schizophrenia (SZ) are separate clinical entities but share deficits in social–emotional processing and static neural functional connectivity patterns. We compared patients’ dynamic functional network connectivity (dFNC) state engagement with typically developed (TD) individuals during social–emotional processing after initially characterizing such dynamics in TD. Young adults diagnosed with ASD (n = 42), SZ (n = 41), or TD (n = 55) completed three functional MRI runs, viewing social–emotional videos with happy, sad, or neutral content. We examined dFNC of 53 spatially independent networks extracted using independent component analysis and applied k-means clustering to windowed dFNC matrices, identifying four unique whole-brain dFNC states. TD showed differential engagement (fractional time, mean dwell time) in three states as a function of emotion. During Happy videos, patients spent less time than TD in a happy-associated state and instead spent more time in the most weakly connected state. During Sad videos, only ASD spent more time than TD in a sad-associated state. Additionally, only ASD showed a significant relationship between dFNC measures and alexithymia and social–emotional recognition task scores, potentially indicating different neural processing of emotions in ASD and SZ. Our results highlight the importance of examining temporal whole-brain reconfiguration of FNC, indicating engagement in unique emotion-specific dFNC states.
Determination of Tafamidis Plasma Concentrations in Amyloidosis Patients with Glu89Gln Mutation by HPLC-UV Detection
Authors: Smerikarova Miglena , Bozhanov Stanislav , Maslarska Vania , Tournev Ivailo 
Published: November 2021

Abstract
Present study describes a high-performance liquid chromatography method for the determination of the potent kinetic stabilizer—Tafamidis in human plasma. It was approved for medical use in European Union in 2011. Ultra violet (UV) detection mode and isocratic elution of the mobile phase were set and made the analytical procedure fast and widely applicable. Chromatographic determination was performed on a Purospher® RP-18 column. The mobile phase consisted of 0.1% trifluoroacetic acid in water and acetonitrile in the ratio 42:58 v/v and the flow rate was 1.0 ml/min. All analyses were carried at a room temperature and the detector was set at 280 nm. Calibration curve over a range of 1.00–10.00 μM was constructed for the purposes of linearity method validation. The specificity and effectiveness of the developed method made it suitable for observation of patients’ plasma Tafamidis concentration with time and drug therapy monitoring.
The relationship between chronic kidney disease–associated pruritus and health-related quality of life: a systematic review
Authors: Poku Edith , Harnan Sue , Rooney Gill , James Marrissa Martyn-St , Hernández-Alava Mónica , Schaufler Thilo , Thokala Praveen , Fotheringham James 
Published: November 2021

ABSTRACT

Background
Chronic kidney disease–associated pruritus (CKD-aP) is a common and burdensome condition for end-stage kidney disease (ESKD) patients, especially those receiving haemodialysis. High-quality evidence of the relationship between CKD-aP and health-related quality of life (HRQoL) can therefore inform clinicians and policymakers about treatment choice and reimbursement decisions.

Methods
A systematic literature review and narrative synthesis stratified by study design and HRQoL instrument was conducted to evaluate in adult ESKD patients receiving in-centre haemodialysis the relationship between CKD-aP and HRQoL assessed using multi dimensional generic or condition-specific preference- or non-preference-based measures. MEDLINE, Embase, Web of Science, BIOSIS Citation Index, Cochrane Library and PsycINFO from inception to March 2020 were searched, with two reviewers extracting data independently.

Results
Searches identified 2684 unique records, of which 20 papers relating to 18 unique studies [5 randomised controlled trials (RCTs) and 13 observational studies] were included. HRQoL was assessed using four generic and eight disease-specific measures. The impact of CKD-aP was assessed by comparison of means, linear regression and correlation. Observational studies employing comprehensively adjusted multivariable linear regression largely found associations between CKD-aP severities and HRQoL. Analyses suggest this relationship is partially mediated by the sleep disturbance caused by CKD-aP. RCTs showing improvements in CKD-aP severity were associated with clinically meaningful improvements in HRQoL. Compared with generic measures, disease-specific HRQoL instruments reported greater changes with reduced CKD-aP. Heterogeneity in study design and reporting precluded meta-analysis.

Conclusions
CKD-aP severity was found to be associated with a worsening of HRQoL in the majority of observational and RCT studies. Parallel improvements in CKD-aP and HRQoL with interventions may support their use (PROSPERO registration 175035).
On Criticising The Knox Bible
Authors: Horne Andrew J 
Published: November 2021

AbstractRonald Knox’s 1955 translation of the Latin Vulgate met with an overall lackluster reception. Yet critics were never able to agree on what was wrong, or even what the translation was like. Some found Knox modern, others old-fashioned. Some criticised him for departing from the Challoner Douay-Rheims, others for not translating the Hebrew and Greek. Through collation and close reading of reviews, this article traces the clash of expectations that led to the spotty reception of the Knox Bible. Though some took a conservative line, others an aggiornamento line, Knox’s audience largely lacked a way to categorise his readable, rhetorical, designedly atemporal, and unashamedly individualist translation.
Association of baseline and change in global longitudinal strain by computed tomography with post-transcatheter aortic valve replacement outcomes
Authors: Fukui Miho , Hashimoto Go , Lopes Bernardo B C , Stanberry Larissa I , Garcia Santiago , Gössl Mario , Enriquez-Sarano Maurice , Bapat Vinayak N , Sorajja Paul , Lesser John R , Cavalcante João L 
Published: November 2021

Abstract

Aims
Transcatheter aortic valve replacement (TAVR) procedural planning requires computed tomography angiography (CTA) which allows for the assessment of left ventricular global longitudinal strain (CTA-LVGLS). There is, however, limited data on the feasibility of CTA-LVGLS, and its prognostic value. This study sought to evaluate the incremental prognostic value of baseline CTA-LVGLS, change in CTA-LVGLS after TAVR, and their association with post-TAVR outcomes.

Methods and results
A total of 431 patients who underwent multiphasic gated CTA using dual-source system for TAVR planning at baseline and 1-month follow-up were included [median (interquartile range) age, 83 (77–87) years; 44% female, STS-PROM score: 3.3 (2.3–5.1)%, Echo-left ventricular ejection fraction (LVEF): 60 (55–65)%, CTA-LVGLS: −18.0 (−21.6 to −14.2)%, feasible in 97% of patients]. CTA-LVGLS was measured using dedicated feature-tracking software. Over a median follow-up of 19 (13–27) months, 99 endpoints of all-cause death or heart failure hospitalization occurred. The relative hazard of the endpoint increased as baseline CTA-LVGLS worsened with −18.2% as the threshold for higher events (P = 0.005). After adjustment for baseline characteristics, CTA-LVGLS remained associated with the endpoint [hazard ratio (HR) (95% confidence interval, CI), 1.08 (1.03–1.14); P = 0.005] and incrementally improved prognostication (C-index difference, 0.026). Although CTA-LVGLS improved after TAVR [−18.3 (−21.6 to −14.3)% vs. −18.7 (−21.9 to −15.4)%, P &lt; 0.001], patients without CTA-LVGLS improvement had higher risk of the endpoint than those with improvement or preserved baseline global longitudinal strain [HR (95% CI), 1.92 (1.19–3.12); P = 0.008].

Conclusions
In this predominantly low-risk TAVR cohort of patients, mostly with normal LVEF, assessment of CTA-LVGLS is highly feasible improving risk stratification by providing independent and incremental prognostic value over clinical and echocardiographic characteristics.