bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variovorax durovernum nov. sp., a novel species isolated from an infected prosthetic aortic graft in a human
Authors: Alcolea-Medina Adela , Payne Lara , Snell Luke B , Alder Chris , Turnbull Jake D. , Charalampous Themoula , Bryan Lisa , Klein John L , Edgeworth Jonathan D , Batra Rahul , Goodman Anna L 
Published: October 2022

Abstract
Variovorax durovernum nov. sp.was isolated from an infected, prosthetic endovascular graft explanted from a shepherd. Variovorax durovernum nov.sp. was isolated from blood agar, chocolate and MacConkey agar incubated at 37°C in an aerobic environment after 48h of incubation. Variovorax durovernum nov sp. is an aerobic, Gram-negative, motile, curved rod. Whole genome sequence (WGS) and targeted 16S sequencing was performed to retrieve nucleotide sequences representing the 16S rRNA gene of the isolate. The 16S gene were compared with all available Variovorax species.The 16S rRNA gene of Variovorax isolates differed by a minimum of 6 SNPs (99.6% identity) for V. paradoxus and 7 SNPs for V. boronicumulans (99.5%). The phylogeny of 16S gene placed Variovorax durovernum nov.sp. in a monophyletic cluster with closest relative being V. boronicumulans. The fatty acid profile consisted of 10:0 3OH (9.90%), Sum In Feature 3 (16:1 ω7c/16:1 ω6c - 16.36%), 16:0 (24.23%), 17:0 cyclo (13,35%), and Sum in Feature 8 (18:1 ω7c, 18:1 ω6c).In silico DNA-DNA hybridisation between the isolate and other Variovorax species was estimated at 32.1% for V. boronicumulans and 31.9% for V. paradoxus. Based on these results, Variovorax durovernum nov. sp. was designated as a novel species within the Variovorax genus, identified as the first case of human pathology caused by any Variovorax sp.
Investigation of Expression Levels of Transcription Factor Genes in Native Sheep Breeds of Turkey
Authors: ARSLAN Korhan , Daldaban Fadime , Bayram Davut , Sohel Mahmodul Hasan , Akyüz Bilal , Çınar Mehmet Ulaş 
Published: October 2022

Abstract
This study, it was aimed to investigate the expression levels of transcription factor (TF) genes (MYF6, MYOD1, MYF5, MYOG) and proteins associated with muscle growth in the longissimus dorsi (LD) and gluteal (GL) muscles in sheep. For this purpose, two fat-tailed sheep breeds (Akkaraman (n = 10), İvesi (n = 10)) and two thin-tailed sheep breeds (Kivircik (n = 10) and Karayaka (n = 10)) from Turkey's native sheep breeds were examined. The expression level of RNAs and proteins isolated from fresh tissues and MYF6, MYOD1, MYF5, MYOG proteins were analyzed. As a result of the statistical analysis, in the LD tissue, respectively, MYOG and MYF5 genes in the Karayaka sheep breed; MYOD1 gene in Akkaraman sheep breed; MYF5 gene in Awassi sheep breed were found to be statistically significant (P < 0.05). In GL tissue, respectively, MYOG and MYF6 genes in Akkaraman sheep breed; MYOD1 gene in Karayaka sheep breed; MYF6 gene in Akkaraman and Awassi sheep breed were found to be statistically significant (P < 0.05). In the present study, it was found that the MYOG (fold change 6.87) and MYOD1 (fold change 15.41) genes were upregulated in the GL muscle of the fat-tailed Akkaraman sheep breed. In addition, in the thin-tailed Karayaka sheep breed, down-regulation of MYOD1 (fold change − 0.22) gene in LD muscle and up-regulation of MYOD1 (fold change 6.67) gene in GL muscle was found. As a result, it can be considered that MYOG and MYOD1 genes as candidate genes in molecular selection studies for our fat-tailed and thin-tailed indigenous breeds in terms of muscle development.
Modeling minimum miscibility pressure using multiple mixing cells: Comparison of injection of gases enriched with Naphta, LPG, and NGL
Authors: Rashidi Mohammad Amin , Khademahmadi Mohammad Reza , Kazemzadeh Yousef , Riazi Masoud 
Published: October 2022

Abstract
The increase in oil production from hydrocarbon reservoirs has always been of interest due to the increase in global oil consumption. One of the effective and useful methods for enhancing oil recovery from hydrocarbon reservoirs is gas injection. Injectable gas can be injected into two modes of miscible and immiscible, but in order to inject more efficiently and efficiently, different factors, including Minimum Miscibility Pressure (MMP) in the gas near-miscible injection mode should be investigated and determined. In order to investigate the minimum miscible pressure, different laboratory and simulation methods have been prepared and developed. In this method, the theory of multiple mixing cells is used to simulate, calculate and compare the minimum miscible pressure in gas injection enriched with Naptha, LPG, and NGL. Also vaporizing and condensing process is also considered in the simulation. The constructed model is presented with a new algorithm. This modeling has been validated and compared with laboratory results. The results showed that dry gas enriched by NAFTA due to having more intermediate compounds at lower pressure (16 MPa) is miscible. In addition, dry gas, due to very light compounds needs higher pressures (20 MPa) than all enriched gases for miscibility. Therefore, to enrich gas, Naptha can be a good option for injecting rich gas into oil reservoirs.
Multinuclear 1D &amp; 2D NMR with 19F-Photo-CIDNP hyperpolarization in a microfluidic chip with broadband microcoil
Authors: Gomez M. Victoria , Baas Sander , Velders Aldrik H 
Published: October 2022

Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful molecular characterization and quantification techniques available today, yet two major persistent factors limit more wide-spread applications of NMR: the poor sensitivity, and the intricate complex and expensive hardware required for sophisticated NMR experiments. We present a microfluidic NMR-chip in which the 25 nL detection volume can be efficiently illuminated with laser-diode light that enhances the sensitivity by orders of magnitude via the photo-CIDNP hyperpolarization principle, allowing rapid detection of samples in the lower picomole range. The chip is further equipped with a single planar microcoil operating in broadband mode that allows different Larmor frequencies to be addressed simultaneously, permitting advanced hetero-, di- and trinuclear, 1D and 2D NMR experiments. The NMR chips with photo CIDNP and broadband capabilities address two of the major limiting factors of NMR, by enhancing sensitivity as well as reducing cost and hardware complexity, and the performance is compared to state-of-the-art instruments.
Estimating household contact matrices structure from easily collectable metadata
Authors: Dall'Amico Lorenzo , Kleynhans Jackie , Gauvin Laetitia , Tizzoni Michele , Makhasi Mvuyo , Wolter Nicole , Language Brigitte , Wagner Ryan , Cohen Cheryl , Tempia Stefano , Cattuto Ciro 
Published: October 2022

Abstract
The ability of developing accurate models plays a pivotal role in understanding infectious diseases dynamics and designing effective measures for epidemic mitigation. Contact matrices are of crucial importance to quantify the interaction between age groups, but their estimation is a rather time and effort consuming task. In this article we show that they can reliably be estimated combining a context-independent model with easily collectable data, such as co-presence and an age activity parameter. The proposed model is tested on high resolution proximity data collected in a rural and an urban village in South Africa. Given its simplicity and interpretability, we expect our method to be easily applied to other contexts as well and we identify relevant questions that need to be addressed during the data collection procedure.
Designing Planar Frequency Diverse Arrays in Space-Frequency Domain
Authors: Hasheminasab Maryam , Cheldavi Ahmed , Kishk Ahmed 
Published: October 2022

Abstract
Antenna arrays benefit from spatial diversity, which allows controlling the pattern specifications in space. Adding frequency diversity to the arrays initiates opportunity to control the beams in the Space-Time domain. Frequency Diverse Array (FDA) has a Range-Angle dependent pattern; therefore, the array's spatial and time behavior should be designed simultaneously for optimum performance. Due to the lack of simple array factor formulations for non-regular configurations, array geometry design has not been the primary concern in many current studies. Due to coherency between frequency and spatial distribution in FDAs, the spatial and time behavior of the pattern is correlated. Frequency diversity of the FDA leads to time-variant beam in steering and auto-scanning beam in CW applications. The present study in addition of SLL discusses two important scanning array parameters; the pattern periodicity and stability in each scan round. In this study using some symmetry rules, a straightforward formulation for the array factor is obtained and used to achieve a stable and periodic scanning beam, suggesting a novel joint space-frequency allocation scheme for the FDA. The approach allows the location and frequency of elements to be designed in the frequency-space plane that minimizes the error function, which is defined based on the time and spatial behavior of the array. Using these concepts, two arrays are designed, and their results are compared with other planar configurations. This study paves the way for a new approach to design FDAs.
Goodness-of-fit two-phase sampling designs for time-to-event outcomes: a simulation study based on New York University Women’s Health Study for breast cancer
Authors: Lee Myeonggyun , Chen Jinbo , Zeleniuch-Jacquotte Anne , Liu Mengling 
Published: October 2022

Abstract
Background
Sub-cohort sampling designs such as a case-cohort study play a key role in studying biomarker-disease associations due to their cost effectiveness. Time-to-event outcome is often the focus in cohort studies, and the research goal is to assess the association between the event risk and risk factors. In this paper, we propose a novel goodness-of-fit two-phase sampling design for time-to-event outcomes when some covariates (e.g., biomarkers) can only be measured on a subgroup of study subjects.
Methods
Assuming that an external model, which can be the well-established risk models such as the Gail model for breast cancer, Gleason score for prostate cancer, and Framingham risk models for heart diseases, or built from preliminary data, is available to relate the outcome and complete covariates, we propose to oversample subjects with worse goodness-of-fit based on an external survival model and time-to-event. With the oversampled cases and controls, the inverse sampling probability weighting method is used to estimate the log hazard ratio of both incomplete and complete covariates. Based on real data, we conducted extensive simulations to evaluate the efficiency gain of our proposed GOF two-phase sampling designs over case-cohort study designs.
Results
Through extensive simulations based on a dataset from the New York University Women’s Health Study, we showed that the proposed GOF two-phase sampling designs were unbiased and generally had higher efficiency compared to the standard case-cohort study designs.
Conclusion
In cohort studies with rare outcomes, an important design question is how to select informative subjects to reduce sampling costs while maintaining statistical efficiency. Our proposed goodness-of-fit two-phase design provides efficient alternatives to standard case-cohort designs for assessing the association between time-to-event outcome and risk factors. This method is conveniently implemented in standard software.
Effects of living patterns on duration sleep and mental health status of elderly people
Authors: xian xiaobing , Ye Mengliang 
Published: October 2022

Abstract
Background
As the global population is aging, China has also entered an aging society at this stage. Numerous studies have shown that sleep disorders and mental health problems are more serious in the elderly compared to adults. This study aims to explore the effects of living patterns on the sleep duration and mental health status of older adults in China.
Methods
A total of 5,899 participants from the China Health and Retirement Longitudinal Study 2018 baseline study were included in this study. Data were statistically analyzed using SPSS version 25.0, and logistic regression models were used to analyze the effects of two living patterns, living with and without children, on sleep duration, and mental health of older adults.
Results
This study shows not living with children were significant for napping 31–60 min/day and > 60 min/day (OR = 1.137,P < 0.05; OR = 1.185,P < 0.05), indicating that most older adults can get longer naps without living with children. The findings of short sleep (< 7h/day) were significant when not living with children (OR = 0.896, P < 0.05). Different living patterns were positively correlated with depressive symptoms (OR = 1.139, P < 0.05), indicating that compared with "not living with children", "living with children" had a lower depression score and was less likely to acquire depressive symptoms; Not significant in happiness, life satisfaction, no correlation can be drawn.
Conclusions
Living patterns were significantly associated with sleep duration, mental health status of Chinese older adults.
Equivalent running leg lengths require prosthetic legs to be longer than biological legs during standing
Authors: Zhang-Lea Janet H. , Tacca Joshua R. , Beck Owen N. , Taboga Paolo , Grabowski Alena 
Published: October 2022

Abstract
We aimed to determine a method for prescribing a standing prosthetic leg length (ProsL) that results in an equivalent running biological leg length (BioL) for athletes with unilateral and bilateral transtibial amputations (UTTA and BTTA, respectively). We measured standing leg length of ten non-amputee (NA) athletes, ten athletes with UTTA, and five athletes with BTTA. All athletes performed treadmill running trials from 3 m/s to their maximum speed. We calculated standing and running BioL and ProsL lengths and assessed the running-to-standing leg length ratio (Lratio) at three instances during ground contact: touchdown, mid-stance, and take-off. Athletes with UTTA had 2.4 cm longer standing ProsL than BioL length (p = 0.030), but up to 3.3 cm and 4.1 cm shorter ProsL than BioL length at touchdown and mid-stance, respectively, at speed 3-11.5 m/s. At touchdown, mid-stance, and take-off, athletes with BTTA had 0.01–0.05 lower Lratio at 3 m/s (p < 0.001) and 0.03–0.07 lower Lratio at 10 m/s (p < 0.001) in their ProsL compared to the BioL of NA athletes. During running, ProsL were consistently shorter than BioL. To achieve equivalent running leg lengths at touchdown and take-off, athletes with UTTA should set their running-specific prosthesis height so that their standing ProsL length is 2.8–4.5% longer than their BioL length, and athletes with BTTA should set their running-specific prosthesis height so that their standing ProsL lengths are at least 2.1–3.9% longer than their presumed BioL length. Setting ProsL length to match presumed biological dimensions during standing results in shorter legs during running.
Symplectic Encoders for Physics-Constrained Variational Dynamics Inference
Authors: Bacsa Kiran , Lai Zhilu , Liu Wei , Chatzi Eleni , Todd Michael 
Published: October 2022

Abstract
We propose a new variational autoencoder (VAE) with physical constraints capable of learning the dynamics of Multiple Degreeof Freedom (MDOF) dynamic systems. Standard variational autoencoders place greater emphasis on compression thaninterpretability regarding the learned latent space. We propose a new type of encoder, based on the recently developedHamiltonian Neural Networks, to impose symplectic constraints on the inferred a posteriori distribution. In addition to deliveringrobust trajectory predictions under noisy conditions, our model is capable of learning an energy-preserving latent representationof the system. This offers new perspectives for the application of physics-informed neural networks on engineering problemslinked to dynamics.
Inhibition of proliferation of human osteosarcoma cell line (MG63) by ajwain (Trachyspermum ammi L.) plant extract
Authors: Anusha Bande , Darshan V. M Datta , Andallu Bondada 
Published: October 2022

Abstract
Trachyspermum ammi L. (TA), popularly called ajwain, is a well-known spice plant, fruit pods that are used in Indian traditional medicine. Fruits of this plant were scientifically investigated for medicinal properties, but no studies are reported on the vegetative parts of the plant. Hence, the present investigation is aimed to evaluate the aerial parts of TA plant for anti-proliferative and antioxidant effects. Methanolic extract (Me) of TA was subjected to sequential fractionation using the solvents in the increasing order of polarity viz. hexane (He), dichloromethane (Dcm), ethyl acetate (Ea), n-butanol (n-Bu), and water (Aq). Phytochemical analyses, DPPH radical scavenging assay, and in vitro antiproliferative activity on the MG63 osteosarcoma cell line (MTT assay) were performed. Preliminary phytochemical analyses revealed the presence of reducing, non-reducing sugars, amino acids, tannins, phenols, terpenoids, and saponins. Ethyl acetate fraction showed the highest amount of total phenolics (367.9 ± 0.02), followed by n-Bu (287.5 ± 0.04), Dcm (193.56 ± 0.07), Me extract (190.14 ± 0.07), Aq (142.2 ± 0.02) and He (80.74 ± 0.01) fractions. Ethyl acetate fraction exhibited higher DPPH radical scavenging activity (IC50 = 116.74 µg/ml) followed by n-Bu (IC50 = 133.81 µg/ml) fraction with a significant correlation to the higher amount of phenolics and flavonoids. However, maximum antiproliferative activity was exhibited by hexane fraction on MG 63 human osteosarcoma cell line which can be attributed to the presence of thymol, a monoterpenoid phenol present in ajwain. The current study indicates that the aerial parts of Trachyspermum ammi Linn. can be considered as potential antioxidants and therapeutic against osteosarcoma.
Across their range, Common Ravens (Corvus corax) are quite precise when replying contact calls
Authors: Keegan Mark 
Published: October 2022

Abstract
An essential signal for social animals is to establish presence or absence of conspecifics. This investigation looked for instances of the Common Raven contact call "aww" [ɒ:] being answered by one or more other ravens at a distance. The data was gleaned from the entirety of raven recordings -- 5435 recordings, mostly audio, but also audio with video -- held by the Cornell Lab of Ornithology’s Macaulay Library, from 1954 Manitoba to 2022 Morocco. The main finding was ravens sent from 1 to 6 “aww”, and replying ravens tended, to a statistically significant degree, to match this number. This precision suggests not only a strong awareness of quantity of sounds, but the raven's awareness of the minds of its fellow ravens.
The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis
Authors: Huo Chunmao , Bao Fengyun , Long Hong , Qin Tingyang , Zhang Shibin 
Published: October 2022

Abstract
Wellcomia compar (Spirurina: Oxyuridae) is a pinworm which parasitizes in the caecum and colon of animals, and it`s host is mainly porcupines. Despite the importance of pinworms as a pathogen, there is still little knowledge about this pinworm. Parasitic diseases are one of the main diseases that affect the growth and health of animals. Clarifying the species of parasites that animals are infected with is an important reference value for the control of parasitic diseases. This study sequenced for the first time the complete mitochondrial (mt) genome of the pinworm Wellcomia compar that had been sampled from Chinese porcupines, then conducted phylogenetic analyses based on concatenated coding sequences (CDS) of 12 protein-coding genes (PCGs) by maximum likelihood (ML) and MrBayes inference (BI), to ascertain the taxonomic and phylogenetic information of W. compar. The complete mt genome (GenBank no. MW059037) is 14,373 bp in size and contains 36 genes, including 12 PCGs, 2 ribosomal RNA, and 22 transfer RNA genes. In addition to the 28 intergenic regions, there was only one non-coding region (NCR) and one overlapping region. The mt genes of Oxyuridomorpha were compared and found to be more similarly characterized in W. compar and Wellcomia siamensis. Furthermore, the phylogenetic tree indicated that W. comparformed a sister group with W. siamensis. This study reports from Chinese porcupine the first complete W. compar mt genome sequence, and provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts, and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.
The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells
Authors: Fernández Ignacio , Dynesen Lasse Toftdal , Coquin Youna , Pederzoli Riccardo , Brun Delphine , Haouz Ahmed , Gessain Antoine , Rey Félix , Buseyne Florence , Backovic Marija 
Published: October 2022

Abstract
The surface envelope glycoprotein (Env) of all retroviruses mediates virus binding to cells and fusion of the viral and cellular membranes. A structure-function relationship for the HIV Env that belongs to the Orthoretrovirus subfamily has been well established. Structural information is however largely missing for the Env of Foamy viruses (FVs), the second retroviral subfamily. FV Envs lack sequence similarity with their HIV counterpart. We present the X-ray structure of the receptor binding domain (RBD) of a simian FV Env at 2.6 Å resolution, revealing two subdomains and an unprecedented fold. We have generated a model for the organization of the RBDs within the trimeric Env which indicates that the upper subdomain is important for stabilization of the full-length Env, and have demonstrated that residues K342, R343, R359 and R369 in the lower subdomain play key roles in the interaction of the RBD and viral particles with heparan sulfate.
Evaluation of the efficacy of aspirin combined with low doses of clopidogrel in the treatment of symptomatic intracranial artery stenosis in the elderly
Authors: Song Haixia , Zhang Bin , Liu Shan , Shi Zhichao , Wang Ziyun , Lu Haili , Yao Jie , Chen Juan 
Published: October 2022

Abstract
Background
Symptomatic intracranial artery stenosis (ICAS) is a significant worldwide economic and great threat to public health. Currently, little is known about the accurate status of the efficient and tolerable dose of dual antiplatelet therapy (DAPT) as the mainstay treatment for ICAS. The aim of this study is to evaluate the efficacy and safety of aspirin plus clopidogrel in small doses for the treatment of symptomatic ICAS in the elderly.
Methods
This research included 142 older adults with symptomatic ICAS who were enrolled between April 2013 and April 2018. They were split into two groups: 73 patients in the lower dose group who received 75 mg of aspirin daily and 50 mg of clopidogrel daily, and 69 patients in the usual group who received 100 mg of aspirin daily and 75 mg of clopidogrel daily.
Results
Ages of 142 patients ranged from 60 to 81, with a mean of 70.9 ± 6.4. 58 participants were with IS and 84 were with TIA. A total of 132 patients were followed up. The low-dose group had a lower recurrence risk of ischemic stroke (IS) or transient ischaemic attack (TIA) than the conventional group at 1-year and 2-year follow-up, as well as a reduced frequency of adverse events and gastrointestinal injury (P < 0.05). Furthermore, after the 1-year follow-up, patients with severe symptomatic ICAS had a greater recurrence risk of IS and TIA than patients with mild symptomatic ICAS in both groups (P > 0.05).
Conclusion
The efficacy and safety of low-dose aspirin combined with clopidogrel were significantly better than those of ordinary dose within 24 months in elderly patients with symptomatic ICAS. However, the small size of this study limits the validity of the results.