bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplotyping pharmacogenes using TLA combined with Illumina or Nanopore sequencing
Authors: Tilleman Laurentijn , Rubben Kaat , Van Criekinge Wim , Deforce Dieter , Van Nieuwerburgh Filip 
Published: October 2022

AbstractThe currently used pharmacogenetic genotyping assays offer limited haplotype information, which can potentially cause specific functional effects to be missed. This study tested if Targeted Locus Amplification (TLA), when using non-patient-specific primers combined with Illumina or Nanopore sequencing, can offer an advantage in terms of accurate phasing. The TLA method selectively amplifies and sequences entire genes based on crosslinking DNA in close physical proximity. This way, DNA fragments that were initially further apart in the genome are ligated into one molecule, making it possible to sequence distant variants within one short read. In this study, four pharmacogenes, CYP2D6, CYP2C19, CYP1A2 and BRCA1, were sequenced after enrichment using different primer pairs. Only 24% or 38% of the nucleotides mapped on target when using Illumina or Nanopore sequencing, respectively. With an average depth of more than 1000X for the regions of interest, none of the genes were entirely covered with either sequencing method. For three of the four genes, less than half of the variants were phased correctly compared to the reference. The Nanopore dataset with the optimized primer pair for CYP2D6 resulted in the correct haplotype, showing that this method can be used for reliable genotyping and phasing of pharmacogenes but does require patient-specific primer design and optimization to be effective.
Effects of different milk feeding levels and frequencies on performance of Holstein heifers during weaning and first lactation
Authors: Ahmadi Fatemeh , Akbarian-Tefaghi Majid , jafari Azam , Ghaffari Morteza Hosseini 
Published: October 2022

AbstractIn the present study, the effects of milk feeding amount and feeding frequency (FF) on performance, blood metabolites, rumen fermentation, and performance of dairy heifers during the first artificial insemination (AI) and first lactation were investigated. The treatment group consisted of 48 female Holstein heifer calves (12/treatment) distributed in a 2 × 2 factorial arrangement with milk feeding [high = 8 L/d, HL or medium = 6 L/d, ML] and feeding frequency [2 × or 3 ×]. All calves were fed on a step-up/step-down method, weaned from milk at 56 d of age, and observed until 70 d of age. Heifer calves were kept uniform from 70 d of age until the first lactation to evaluate the long-term effects of the treatments. We observed no FF effect and no interaction between the level and FF on feed intake, average daily gain (ADG), feed efficiency (FE), body weight (BW), structural growth, blood metabolites, and rumen fermentation parameters. Calves fed HL milk had higher total dry matter intake (DMI), BW, and ADG during the pre- and post-weaning periods. During the preweaning period, HL-fed calves had higher serum insulin (trend) and glucose concentrations compared to ML-fed calves. Lower age at first AI was observed in calves fed HL rather than ML regardless of FF. Weight at first AI, milk yield (305 d), and energy-corrected milk (ECM-305 d) in the first lactation showed a trend toward higher values in HL-fed calves compared to ML-fed calves. Preweaning performance and calf maturity can be positively affected by feeding high amounts of milk at both FF.
Feasibility of the optimal cerebral perfusion pressure value identification without a delay that is too long
Authors: Deimantavicius Mantas , Chaleckas Edvinas , Boere Katherine , Putnynaite Vilma , Tamosuitis Tomas , Tamasauskas Arimantas , Kavaliauskas Mindaugas , Rocka Saulius , Preiksaitis Aidanas , Vosylius Saulius , Krakauskaite Solventa , Berskiene Kristina , Petkus Vytautas , Ragauskas Arminas 
Published: October 2022

AbstractOptimal cerebral perfusion pressure (CPPopt)-targeted treatment of traumatic brain injury (TBI) patients requires 2–8 h multi-modal monitoring data accumulation to identify CPPopt value for individual patient. Minimizing the time required for monitoring data accumulation is needed to improve the efficacy of CPPopt-targeted therapy. A retrospective analysis of multimodal physiological monitoring data from 87 severe TBI patients was performed by separately representing cerebrovascular autoregulation (CA) indices in relation to CPP, arterial blood pressure (ABP), and intracranial pressure (ICP) to improve the existing CPPopt identification algorithms. Machine learning (ML)-based algorithms were developed for automatic identification of informative data segments that were used for reliable CPPopt, ABPopt, ICPopt and the lower/upper limits of CA (LLCA/ULCA) identification. The reference datasets of the informative data segments and, artifact-distorted segments, and the datasets of different clinical situations were used for training the ML-based algorithms, allowing us to choose the appropriate individualized CPP-, ABP- or ICP-guided management for 79% of the full monitoring time for the studied population. The developed ML-based algorithms allow us to recognize informative physiological ABP/ICP variations within 24 min intervals with an accuracy up to 79% (compared to the initial accuracy of 74%) and use these segments for timely optimal value identification or CA limits determination in CPP, ABP or ICP data. Prospective clinical studies are needed to prove the efficiency of the developed algorithms.
On the relations between letter, word, and sentence-level processing during reading
Authors: Brossette Brice , Grainger Jonathan , Lété Bernard , Dufau Stéphane 
Published: October 2022

AbstractMuch prior research on reading has focused on a specific level of processing, with this often being letters, words, or sentences. Here, for the first time in adult readers, we provide a combined investigation of these three key component processes of reading comprehension. We did so by testing the same group of participants in three tasks thought to reflect processing at each of these levels: alphabetic decision, lexical decision, and grammatical decision. Participants also performed a non-reading classification task, with an aim to partial-out common binary decision processes from the correlations across the three main tasks. We examined the pairwise partial correlations for response times (RTs) in the three reading tasks. The results revealed strong significant correlations across adjacent levels of processing (i.e., letter-word; word-sentence) and a non-significant correlation between non-adjacent levels (letter-sentence). The results provide an important new benchmark for evaluating computational models that describe how letters, words, and sentences contribute to reading comprehension.
Realizing high stretch ratio of flexible wavy circuit via laser carving
Authors: Yun Jung-Hoon , Victoria Adebisi Oluwabukola , Cho Maenghyo 
Published: October 2022

AbstractStretchable wavy circuit is an essential component in flexible devices, which have wide applications in various fields. In the industrial field, the stretching ability of the circuit is a crucial factor for flexible devices. Therefore, this study proposes laser carving method to increase both stretch ratio and device resolution of the flexible device. The results obtained from the experiment and finite element analysis verifies that laser carving on the wavy circuit increases the maximum stretch ratio of wavy circuit. The obtained analytic model confirms that laser carving generates tilted section on the wavy circuit, and reduces the bending rigidity of the curvy point of the wavy circuit. The study also verified that laser carved groove induces crack propagation into vertical to the circuit direction, so that the laser carved wavy circuit is less likely to disconnect than uncarved wavy circuit. Due to the reduced bending rigidity and crack induce, the wavy circuit stretches more than the conventional uncarved wavy circuit.
Presence of entry receptors and viral markers suggest a low level of placental replication of hepatitis B virus in a proportion of pregnant women infected with chronic hepatitis B
Authors: Garg Garima , Meenu M. N. , Patel Kajal , Singh Ravinder , Gupta Priyal , Purwar Shashank , Mukhopadhyay Sramana , Mishra Nitu , Gupta Sudheer , Rawat Sumit Kumar , Goel Harsh , Kumar Rahul , Tanwar Pranay , Singh Jitendra , Nema Shashwati , Biswas Debasis , Trehanpati Nirupma , Singh Anirudh K. , Vyas Ashish Kumar 
Published: October 2022

AbstractThe transplacental route of vertical transmission of Hepatitis B Virus (HBV) has been known for over a decade. Here we present evidence which suggest HBV can replicate in placenta. Forty-one HBsAg positive and 10 control pregnant women were enrolled in the study after obtaining informed consent. HBV positives were further divided in the High Viral Load (HVL) Group and Low Viral Load (LVL) Group according to INASL guidelines 2018. The Presence of the HBV DNA and expression of NTCP in the placenta was analyzed by qPCR/RT-qPCR and/or immunohistochemistry (IHC). The presence of cccDNA was assessed using Digital Droplet PCR while the presence of pre-genomic (pg) RNA was assessed through qRT-PCR and sequencing. The presence of HBeAg and HBcAg in the placenta was assessed by IHC. Immunostaining of NTCP, HBeAg and HBcAg on trophoblasts along with the presence of total HBV DNA, cccDNA and pgRNA indicated, that these cells are not only susceptible to HBV infection but may also support viral replication. This is further supported by the finding that trophoblasts of the several HBeAg seronegative samples harbored the HBeAg. Although, we did not find any correlation in NTCP expression and viral markers with viral load indicates placental replication may not aping hepatocytes. The presence of the HBV receptor, NTCP along with the presence of cccDNA, pgRNA, and HBeAg in placenta of HBV infected females without circulating HBeAg suggest that placenta act as a replication host.
Using bioelectrohydrogenesis left-over residues as a future potential fertilizer for soil amendment
Authors: Ndayisenga Fabrice , Yu Zhisheng , Wang Bobo , Yang Jie , Wu Gang , Zhang Hongxun 
Published: October 2022

AbstractIn this current research, the left-over residues collected from the dark fermentation-microbial electrolysis cells (DF-MEC) integrated system solely biocatalyzed by activated sludge during the bioconversion of the agricultural straw wastes into hydrogen energy, was investigated for its feasibility to be used as a potential alternative biofertilizer to the commonly costly inorganic ones. The results revealed that the electrohydrogenesis left-over residues enriched various plant growth-promoting microbial communities including Enterobacter (8.57%), Paenibacillus (1.18%), Mycobacterium (0.77%), Pseudomonas (0.65%), Bradyrhizobium (0.12%), Azospirillum (0.11%), and Mesorhizobium (0.1%) that are generally known for their ability to produce different essential phytohormones such as indole-3-acetic acid/indole acetic acid (IAA) and Gibberellins for plant growth. Moreover, they also contain both phosphate-solubilizing and nitrogen-fixing microbial communities that remarkably provide an adequate amount of assimilable phosphorus and nitrogen required for enhanced plants or crop growth. Furthermore, macro-, and micronutrients (including N, P, K, etc.) were all analyzed from the residues and detected adequate appreciate concentrations required for plant growth promotions. The direct application of MEC-effluent as fertilizer in this current study conspicuously promoted plant growth (Solanum lycopersicum L. (tomato), Capsicum annuum L. (chilli), and Solanum melongena L. (brinjal)) and speeded up flowering and fruit-generating processes. Based on these findings, electrohydrogenesis residues could undoubtedly be considered as a potential biofertilizer. Thus, this technology provides a new approach to agricultural residue control and concomitantly provides a sustainable, cheap, and eco-friendly biofertilizer that could replace the chemical costly fertilizers.
Optimization, purification, and characterization of xylanase production by a newly isolated Trichoderma harzianum strain by a two-step statistical experimental design strategy
Authors: Dhaver Priyashini , Pletschke Brett , Sithole Bruce , Govinden Roshini 
Published: October 2022

AbstractXylanases are hydrolytic enzymes with a wide range of applications in several industries such as biofuels, paper and pulp, food, and feed. The objective of this study was to optimize the culture conditions and medium components for maximal xylanase production from a newly isolated Trichoderma harzianum strain using the Plackett–Burman Design (PBD) and Box Behnken Design (BBD) experimental strategies. Xylanase production was enhanced 4.16-fold to 153.80 U/ml by BBD compared to a preliminary one-factor-at-a-time (OFAT) activity of 37.01 U/ml and 2.24-fold compared to the PBD (68.70 U/ml). The optimal conditions for xylanase production were: 6 days of fermentation, incubation temperature of 70 °C, pH 5.0, agitation of 160 rpm, and 1.2% wheat bran and ammonium sulphate. The experimental design effectively provided conditions for the production of an acidic-thermostable enzyme with exciting potential for application in animal feed improvement. The acidic-thermostable xylanase was purified from the submerged culture and SDS-PAGE analysis revealed a molecular weight of 72 kDa. This protein had maximum xylanolytic activity at pH 6.0 and 65 °C and was stable for 4 h retaining > 70% activity and exhibited substrate specificity for beechwood xylan with a Km of 5.56 mg/ml and Vmax of 1052.63 µmol/min/mg. Enzyme activity was enhanced by Fe2+, Mg2+, and Zn2+. There was an absence of strong inhibitors of xylanase activity. Overall, these characteristics indicate the potential for at least two industrial applications.
Cortical midfrontal theta dynamics following foot strike may index response adaptation during reactive stepping
Authors: Stokkermans Mitchel , Staring Wouter , Cohen Michael X. , Solis-Escalante Teodoro , Weerdesteyn Vivian 
Published: October 2022

AbstractReactive balance recovery often requires stepping responses to regain postural stability following a sudden change in posture. The monitoring of postural stability has been linked to neuroelectrical markers such as the N1 potential and midfrontal theta frequency dynamics. Here, we investigated the role of cortical midfrontal theta dynamics during balance monitoring following foot landing of a reactive stepping response to recover from whole-body balance perturbations. We hypothesized that midfrontal theta dynamics reflect the engagement of a behavioral monitoring system, and therefore that theta would increase time-locked to the moment of foot strike after a stepping response, coinciding with a re-assessment of postural balance to determine if an additional step is necessary. We recorded high-density EEG and kinematic data of 15 healthy young participants while they stood on a platform that delivered multi-directional balance perturbations. Participants were instructed to recover balance with a single step utilizing either their left or right leg (in separate blocks). We used targeted spatial filtering (generalized eigen decomposition) in combination with time–frequency analysis of the EEG data to investigate whether theta dynamics increase following foot strike event. In line with our hypothesis, the results indicate that the foot strike event elicits a midfrontal theta power increase, though only for backward stepping. Counter to our expectations, however, this theta power increase was positively correlated with the margin of stability at foot strike, suggesting a different role of foot strike related theta from monitoring stability. Post-hoc analysis suggests that midfrontal theta dynamics following foot landing may instead facilitate adaptation of stability margins at subsequent stepping responses. We speculate that increase of theta power following foot strikes was not related to stability monitoring but instead may indicate cortical dynamics related to performance monitoring of the balance response.
Natural convection in a porous cavity filled (35%MWCNT-65% Fe3O4)/water hybrid nanofluid with a solid wavy wall via Galerkin finite-element process
Authors: Gumir Fatima Jasim , Al-Farhany Khaled , Jamshed Wasim , Tag El Din El Sayed M. , Abd-Elmonem Assmaa 
Published: October 2022

AbstractA numerical analysis of natural convective heat transfer in a square porous cavity with a solid wavy finite wall filled with (35% MWCNT-65% Fe3O4)/water hybrid nanofluid. The left wavy wall is heated to a constant temperature, the right wall is held at a low temperature, and the top and bottom walls are thermally insulated. Darcy-Brinkman-Forchheimer model is used to model porous medium with hybrid nanofluid. COMSOL Multiphasic Modeling Software via Galerkin finite element method has been used to solve the governing equations. The dimensionless parameters used in this investigation are; modified Rayleigh number (Ra* = 102, 103, 104, and 106), Darcy number (Da = 10–2, 10–4 and 10–6), Solid volume fraction (ϕ = 0.01, 0.03, and 0.05),undulation number (N = 1, 3, 5, and 7), amplitude of the wavy wall (A = 0.1, 0.2, and 0.3), and Prandtl number = 7.2 at constant high porosity. At a high Darcy number (Da = 10–2), the isotherm lines parallel to the vertical cavity walls, which means that conduction is the primary method of heat transport. At the same time, the convection mode is increasingly necessary at a lower Darcy number. The convection flow and the maximum amounts of stream function are reduced when both A = 0.1 and N = 1 increase. The average Nusselt number increases with increasing Ra*, while it decreases with increasing Darcy number and amplitude wave numbers. It has been determined that the largest improvement in heat transfer is at Ra* = 104, Da = 10–6, ϕ = 0.05, A = 0.1, and N = 1.
Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle
Authors: Lovrić Alen , Rassolie Ali , Alam Seher , Mandić Mirko , Saini Amarjit , Altun Mikael , Fernandez-Gonzalo Rodrigo , Gustafsson Thomas , Rullman Eric 
Published: October 2022

AbstractSkeletal muscle adaptations to exercise have been associated with a range of health-related benefits, but cell type-specific adaptations within the muscle are incompletely understood. Here we use single-cell sequencing to determine the effects of exercise on cellular composition and cell type-specific processes in human skeletal muscle before and after intense exercise. Fifteen clusters originating from six different cell populations were identified. Most cell populations remained quantitatively stable after exercise, but a large transcriptional response was observed in mesenchymal, endothelial, and myogenic cells, suggesting that these cells are specifically involved in skeletal muscle remodeling. We found three subpopulations of myogenic cells characterized by different maturation stages based on the expression of markers such asPAX7,MYOD1,TNNI1, andTNNI2. Exercise accelerated the trajectory of myogenic progenitor cells towards maturation by increasing the transcriptional features of fast- and slow-twitch muscle fibers. The transcriptional regulation of these contractile elements upon differentiation was validated in vitro on primary myoblast cells. The cell type-specific adaptive mechanisms induced by exercise presented here contribute to the understanding of the skeletal muscle adaptations triggered by physical activity and may ultimately have implications for physiological and pathological processes affecting skeletal muscle, such as sarcopenia, cachexia, and glucose homeostasis.
Silylium ion migration dominated hydroamidation of siloxy-alkynes
Authors: Wang Heng-Ding , Jiang Ling , Fan Hong-Jun 
Published: October 2022

AbstractThe mechanism of silver-catalyzed hydroamidation of siloxy-alkynes reaction remains controversial. Using density functional theory (DFT), we revealed that the reaction takes place through a silylium ion migration mediated hydroamination (SMH) pathway. The SMH pathway goes through two steps, the first step is Ag+ promoted proton and silylium ion exchange between siloxy-alkynes and amide, leading to ketene and silyl-imines, the second step is Ag+ catalyzed nucleophilic addition between ketene and silyl-imines, following with a silylium ion migration afford the final product. In this reaction, Ag+ activates the siloxy-alkyne into silylium ion (TIPS+) and silver-ketene through thep–πconjugate effect, the silylium ion then catalyzes the reaction. According to our calculation, the scopes of alkynes in this reaction may be extended to silyl-substituted ynamines or silyl-substituted ynamides. The scopes of amide may be extended into thep–πconjugate system such as diazoles, diazepines, etc. Our calculations also reveal a concise way to construct enamides through Ag+ catalyzed nucleophilic addition between substituted-ketenes and silyl-substitutedp–πconjugate system.
Perturbations in stratospheric aerosol evolution due to the water-rich plume of the 2022 Hunga-Tonga eruption
Authors: Zhu Yunqian , Bardeen Charles G. , Tilmes Simone , Mills Michael J. , Wang Xinyue , Harvey V. Lynn , Taha Ghassan , Kinnison Douglas , Portmann Robert W. , Yu Pengfei , Rosenlof Karen H. , Avery Melody , Kloss Corinna , Li Can , Glanville Anne S. , Millán Luis , Deshler Terry , Krotkov Nickolay , Toon Owen B. 
Published: October 2022

AbstractThe January 2022 Hunga Tonga-Hunga Ha’apai volcanic eruption injected a relatively small amount of sulfur dioxide, but significantly more water into the stratosphere than previously seen in the modern satellite record. Here we show that the large amount of water resulted in large perturbations to stratospheric aerosol evolution. Our climate model simulation reproduces the observed enhanced water vapor at pressure levels ~30 hPa for three months. Compared with a simulation without a water injection, this additional source of water vapor increases hydroxide, which halves the sulfur dioxide lifetime. Subsequent coagulation creates larger sulfate particles that double the stratospheric aerosol optical depth. A seasonal forecast of volcanic plume transport in the southern hemisphere indicates this eruption will greatly enhance the aerosol surface area and water vapor near the polar vortex until at least October 2022, suggesting that there will continue to be an impact of this eruption on the climate system.
Diamond nitrogen‐vacancy centres spin‐state‐based quantum sensor using a compact broadband antenna
Authors: Cui Mingming , Shen Fazhong , Qiao Yingying , Du Guanxiang , Zhuo Xiang , Zang Jiawei , Zhang Zhenyuan , Wang Yi , Li Lei , Gao Yang 
Published: October 2022

AbstractThis paper presents a compact broadband antenna that is used in the spin‐state‐based magnetic field quantum sensor. In the diamond nitrogen‐vacancy (NV) centre system, the qubit resonance is excited by the microwave signal, and the frequency shift is proportional to the external magnetic field strength. Conventional narrow‐band antennas or single resonators are not able to match the resonance frequency of the NV centre over a wide bandwidth, resulting in degraded sensitivity and dynamic range of the sensor. Here, the authors designed a compact broadband antenna, which achieves a fractional bandwidth of 71.43% at the Zeeman splitting frequency of 2.87 GHz. With the introduced slot structure on the antenna, a higher microwave near field strength can also be achieved, which improves the magnetic field sensitivity and dynamic range. By applying our design antenna, the experimental results indicate that the NV‐based quantum sensor achieves a sensitivity of 3.07 μT/Hz1/2 and a dynamic range up to 44.9 dB, which are both greatly improved compared to sensor that uses a conventional antenna.