bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Salivary Alpha-Amylase, Sialic Acid, and pH in Pregnant and Nonpregnant Subjects
Authors: Shirzaiy Masoomeh , Dalirsani Zohreh
Published: August 2021

Objectives During pregnancy, systemic physiological alterations lead to some changes in the oral cavity, which could prepare the mouth environment for oral and dental problems. This study was aimed to investigate salivary α-amylase, sialic acid levels, and pH levels in pregnant and nonpregnant females.

Materials and Methods In this analytical, case–control study, unstimulated saliva samples were collected with spiting method from 35 pregnant women (case group) and 35 nonpregnant women (control group) and transferred to the laboratory to assess salivary α-amylase, sialic acid, and pH levels. Data were analyzed by SPSS (version: 19) software through statistical methods of independent t-test and analysis of variance.

Results The mean sialic acid levels were 2.285 ± 1.230 mg/dL in pregnant and 2.744 ± 1.326 in nonpregnant women without any significant difference (p = 0.138). The mean salivary α-amylase concentrations were 2.461 ± 1.869 U/L and 2.439 ± 2.058 U/L, respectively, in pregnant and nonpregnant women, with no significant difference (p = 0.963).

The mean salivary pH in nonpregnant women was significantly more than that in pregnant women (7.845 ± 0.430 and 6.868 ± 0.413, respectively) (p < 0.001). Also, the mean salivary pH levels in pregnant women were 7.474 ± 0.420 in the first trimester, 6.868 ± 0.413 in the second trimester, and 6.568 ± 0.387 in the third trimester, which were significantly different (p < 0.001).

Conclusion Salivary sialic acid and α-amylase levels among pregnant women were no different from those of other subjects. During pregnancy, the salivary pH significantly reduced, and the mean salivary pH during pregnancy had a decreasing trend from the first trimester to the third trimester.
Measuring Electronic Health Record Use in the Pediatric ICU Using Audit-Logs and Screen Recordings
Authors: Sinha Amrita , Stevens Lindsay A. , Su Felice , Pageler Natalie M. , Tawfik Daniel S.
Published: August 2021

Background Time spent in the electronic health record (EHR) has been identified as an important unit of measure for health care provider clinical activity. The lack of validation of audit-log based inpatient EHR time may have resulted in underuse of this data in studies focusing on inpatient patient outcomes, provider efficiency, provider satisfaction, etc. This has also led to a dearth of clinically relevant EHR usage metrics consistent with inpatient provider clinical activity.

Objective The aim of our study was to validate audit-log based EHR times using observed EHR-times extracted from screen recordings of EHR usage in the inpatient setting.

Methods This study was conducted in a 36-bed pediatric intensive care unit (PICU) at Lucile Packard Children's Hospital Stanford between June 11 and July 14, 2020. Attending physicians, fellow physicians, hospitalists, and advanced practice providers with ≥0.5 full-time equivalent (FTE) for the prior four consecutive weeks and at least one EHR session recording were included in the study. Citrix session recording player was used to retrospectively review EHR session recordings that were captured as the provider interacted with the EHR.

Results EHR use patterns varied by provider type. Audit-log based total EHR time correlated strongly with both observed total EHR time (r = 0.98, p < 0.001) and observed active EHR time (r = 0.95, p < 0.001). Each minute of audit-log based total EHR time corresponded to 0.95 (0.87–1.02) minutes of observed total EHR time and 0.75 (0.67–0.83) minutes of observed active EHR time. Results were similar when stratified by provider role.

Conclusion Our study found inpatient audit-log based EHR time to correlate strongly with observed EHR time among pediatric critical care providers. These findings support the use of audit-log based EHR-time as a surrogate measure for inpatient provider EHR use, providing an opportunity for researchers and other stakeholders to leverage EHR audit-log data in measuring clinical activity and tracking outcomes of workflow improvement efforts longitudinally and across provider groups.
A novel taxonomy of smart sustainable city indicators
Authors: Pira Milad
Published: August 2021

Building a smart city that follows sustainability goals enhances the quality of life and preserves environmental, human, and social capital. Yet, existing smart sustainable city projects have concentrated on the technological dimensions of smart cities such as using big data or smart devices to follow sustainability goals. Currently, there is no comprehensive category of smart sustainable city indicators in the literature. This paper aims to discover these indicators by considering the common features of sustainability and smart city concepts. Two rounds of the content analysis technique were employed to investigate semantic, lexical, and conceptual relationships between smart city and sustainability indicators. This paper employed the Sustainable Development Indicators suggested by OECD and the Smart City Index Master by Cohen as the two main groups of indicators. The findings offer a novel set of indicators that enables policymakers and researchers to consider the smartness and sustainability of their projects simultaneously. This includes socio-cultural, economic, environmental, and governance categories with 28 associated indicators. The outcome of this paper offers a unique combined category of smart sustainable city indicators by considering the key elements of sustainability and smart city concepts. Academics and policymakers can also employ this set of indicators as a guideline to build a smart sustainable community.
Proof-of-concept of a reinforcement learning framework for wind farm energy capture maximization in time-varying wind
Authors: Stanfel P. , Johnson K. , Bay C. J. , King J.
Published: August 2021

In this paper, we present a proof-of-concept distributed reinforcement learning framework for wind farm energy capture maximization. The algorithm we propose uses Q-Learning in a wake-delayed wind farm environment and considers time-varying, though not yet fully turbulent, wind inflow conditions. These algorithm modifications are used to create the Gradient Approximation with Reinforcement Learning and Incremental Comparison (GARLIC) framework for optimizing wind farm energy capture in time-varying conditions, which is then compared to the FLOw Redirection and Induction in Steady State (FLORIS) static lookup table wind farm controller baseline.
Silicon-nitride nanosensors toward room temperature quantum optomechanics
Authors: Serra Enrico , Borrielli Antonio , Marin Francesco , Marino Francesco , Malossi Nicola , Morana Bruno , Piergentili Paolo , Prodi Giovanni Andrea , Sarro Pasqualina Maria , Vezio Paolo , Vitali David , Bonaldi Michele
Published: August 2021

Micro- and nanomechanical resonators play a prominent part in many sensing and signal processing platforms due to their capability to pervasively couple with a wide variety of physical systems. Particularly relevant is their embedding in advanced optomechanical setups, which has recently pioneered optically cooled mechanical oscillators toward the quantum regime. A frequently adopted experimental scheme exploits a thin, highly tensioned Si3N4 nanomembrane where the membrane’s vibrations are dispersively coupled to the optical mode of a Fabry–Pérot cavity. A significant effort has been done into realizing high-quality factor membranes, considering that low mechanical loss represents a benchmark to operate in the elusive quantum regime. In this article, we compare two state-of-the-art SiN resonators, realized exploiting the dilution of the material’s intrinsic dissipation and efficient solutions to fully isolate the membrane from the substrate. In particular, we examine and discuss the interplay between the edge and distributed dissipation and propose an analytical approach to evaluate the total intrinsic loss. Also, our analysis delves into the sensitivity of the devices to a point-like force and a uniform-density force field. These results provide meaningful guidelines for designing new ultra-coherent resonating devices.
Anharmonic lattice dynamics of SnS across phase transition: A study using high-dimensional neural network potential
Authors: Ouyang Niuchang , Wang Chen , Zeng Zezhu , Chen Yue
Published: August 2021

SnS that exhibits strong lattice anharmonicity and a structural phase transition between the Pnma and Cmcm phases has emerged as a high-performance thermoelectric material. Herein, the lattice dynamics of SnS have been investigated by molecular dynamics to reveal the soft mode mechanisms across the phase transition. We construct a first-principles-based machine-learning potential, which is capable of reproducing the dynamical nature of the structural phase transition of SnS. We reproduce an explicit softening of the zone-center phonon mode and unveil a similar behavior at the zone boundary U = (0.5, 0.0, 0.5) of SnS, which are attributed to the large anharmonicity induced by the phase transition. Our results reveal a non-monotonic temperature dependence of the linewidth of the soft modes beyond the perturbative regime. The zone-center optical soft mode collapses across the structural phase transition, corresponding to a second-order nature. These results pave the way for further phonon engineering of SnS and the related IV–VI thermoelectrics.
Epitaxial Zn3N2 thin films by molecular beam epitaxy: Structural, electrical, and optical properties
Authors: John P. , Al Khalfioui M. , Deparis C. , Welk A. , Lichtensteiger C. , Bachelet R. , Saint-Girons G. , Rotella H. , Hugues M. , Grundmann M. , Zúñiga-Pérez J.
Published: August 2021

Single-crystalline Zn3N2 thin films have been grown on MgO (100) and YSZ (100) substrates by plasma-assisted molecular beam epitaxy. Depending on growth conditions, the film orientation can be tuned from (100) to (111). For each orientation, x-ray diffraction and reflection high-energy electron diffraction are used to determine the epitaxial relationships and to quantify the structural quality. Using high-temperature x-ray diffraction, the Zn3N2 linear thermal expansion coefficient is measured with an average of (1.5 ± 0.1) × 10−5 K−1 in the range of 300–700 K. The Zn3N2 films are found to be systematically n-type and degenerate, with carrier concentrations of 1019–1021 cm−3 and electron mobilities ranging from 4 to 388 cm2 V−1 s−1. Low-temperature Hall effect measurements show that ionized impurity scattering is the main mechanism limiting the mobility. The large carrier densities lead to measured optical bandgaps in the range of 1.05–1.37 eV due to Moss–Burstein band filling, with an extrapolated value of 0.99 eV for actual bandgap energy.
Quantum-electrodynamical time-dependent density functional theory within Gaussian atomic basis
Authors: Yang Junjie , Ou Qi , Pei Zheng , Wang Hua , Weng Binbin , Shuai Zhigang , Mullen Kieran , Shao Yihan
Published: August 2021

Inspired by the formulation of quantum-electrodynamical time-dependent density functional theory (QED-TDDFT) by Rubio and co-workers [Flick et al., ACS Photonics 6, 2757-2778 (2019)], we propose an implementation that uses dimensionless amplitudes for describing the photonic contributions to QED-TDDFT electron–photon eigenstates. This leads to a Hermitian QED-TDDFT coupling matrix that is expected to facilitate the future development of analytic derivatives. Through a Gaussian atomic basis implementation of the QED-TDDFT method, we examined the effect of dipole self-energy, rotating-wave approximation, and the Tamm–Dancoff approximation on the QED-TDDFT eigenstates of model compounds (ethene, formaldehyde, and benzaldehyde) in an optical cavity. We highlight, in the strong coupling regime, the role of higher-energy and off-resonance excited states with large transition dipole moments in the direction of the photonic field, which are automatically accounted for in our QED-TDDFT calculations and might substantially affect the energies and compositions of polaritons associated with lower-energy electronic states.
Photon management with superlattice for image sensor pixels
Authors: Cao Yuqing , Zhang Zijian , Wang Ken Xingze
Published: August 2021

It is important to increase light absorption and quantum efficiency in image sensor pixels, especially for wavelength ranges in which material absorption is weak. Surface textures, including nanostructure lattices, have been invented for significant improvement in light absorption. Those nanostructures typically support a number of physical processes for which the optimal geometries are different. We design a class of nanostructure superlattices to enable the co-optimization of different physical processes for further enhancement in light absorption.
High thermoelectric figure of merit predicted in Cu26V2Sn6Se32 colusite induced by vacancy defects and glassy-like vibrational modes
Authors: Gupta Raveena , Bera Chandan
Published: August 2021

High-performance thermoelectric (TE) properties of pristine Sn-based colusites are investigated theoretically. A recent experimental article [Bourgès et al., J. Am. Chem. Soc. 140, 2186 (2018)] showed how structural disordering reduced the lattice thermal conductivity in Cu26V2Sn6S32 and improved the TE figure of merit (ZT). In this article, it is observed that low energy soft optical phonons and the vacancy defect play a crucial role in reducing thermal conductivity. An ultra-low lattice thermal conductivity 0.35Wm−1K−1 is observed in Cu26V2Sn6Se32. It is seen that mass variance perturbation and number of vacancies are important to tune the thermal and electrical properties. Though the electrical conductivity decreases with the number of vacant sites, the Seebeck coefficient enhances due to the reduction in carrier concentration. The detailed study of thermoelectric properties of Cu26V2Sn6Se32 with Se vacancies points to enhanced ZT values of 0.34 at 300 K, which is ∼15 times greater than ZT of Cu26V2Sn6S32. A maximum ZT of 1.68 at 755 K is predicted for Cu26V2Sn6Se32 with Se vacancies, which is the highest to date reported for Sn-based colusites.
Success factors for a Mandarin bilingual program
Authors: Liu Wei
Published: August 2021

Immersion-style bilingual school programs have proven to be effective ways for children’s acquisition of additional languages. However, such programs seem to be scarce across the world in comparison to the value people attach to bilingual skills and bilingual education. Through a case study of a successful Mandarin bilingual program in western Canada, the study hopes to explore the factors that contribute to the success of such programs in North America. The study points to the importance of government language policy environments, the attitude of local school boards, the commitment and active involvement of parents, and the availability and recruitment of quality teachers as key factors for the success of a bilingual school program.
Food safety and methods to ensure food security in the face of climate change
Authors: Tripathi Jyoti , Variyar Prasad S.
Published: August 2021

Serious social, economic, and ecological consequences of climate change due to the high levels of greenhouse gases (GHGs) in our atmosphere resulting from a wide range of human activities including the burning of fossil fuels and land use have impacted weather events world over. Extreme weather events and warmer global temperatures are likely to be more frequent with an adverse overall effect on agricultural production unless there is an urgent reduction in GHG emissions. There is thus an immediate need for increasing adaptive capacity in agriculture to long-term climatic trends and increasing variability in weather patterns. Climate change also poses significant challenges to global food safety due to the emergence of new pathogens, insect pests, and toxicants. Food safety threats cause an enormous burden on economies due to disruptions or restrictions in global and regional agrifood trade, food loss, and associated income. Food safety thus plays a critical role across the four pillars of food security—availability, access, utilization, and stability. Climate change is likely to create new safety issues entailing reassessing our tolerance to risk and safety limits presently established for the human food chain. The present review focuses on the factors affecting food security and safety as a consequence of climate change and the pre- and postharvest strategies that need to be adopted to mitigate these effects for enhancing food safety and global food sufficiency in future.
Electric trapping and circuit cooling of charged nanorotors
Authors: Martinetz Lukas , Hornberger Klaus , Stickler Benjamin A
Published: August 2021

The motion of charged particles can be interfaced with electric circuitry via the current induced in nearby pick-up electrodes. Here we show how the rotational and translational dynamics of levitated objects with arbitrary charge distributions can be coupled to a circuit and how the latter acts back on the particle motion. The ensuing cooling rates in series and parallel RLC circuits are determined, demonstrating that quadrupole ion traps are well suited for implementing all-electric cooling. We derive the effective macromotion potential for general trap geometries and illustrate how consecutive rotational and translational resistive cooling of a microscale particle can be achieved in linear Paul traps.
Bio-3D printing iPSC-derived human chondrocytes for articular cartilage regeneration
Authors: Nakamura Anna , Murata Daiki , Fujimoto Ryota , Tamaki Sakura , Nagata Sanae , Ikeya Makoto , Toguchida Junya , Nakayama Koichi
Published: August 2021

Osteoarthritis is a leading cause of pain and joint immobility, the incidence of which is increasing worldwide. Currently, total joint replacement is the only treatment for end-stage disease. Scaffold-based tissue engineering is a promising alternative approach for joint repair but is subject to limitations such as poor cytocompatibility and degradation-associated toxicity. To overcome these limitations, a completely scaffold-free Kenzan method for bio-3D printing was used to fabricate cartilage constructs feasible for repairing large chondral defects. Human induced pluripotent stem cell (iPSC)-derived neural crest cells with high potential to undergo chondrogenesis through mesenchymal stem cell differentiation were used to fabricate the cartilage. Unified, self-sufficient, and functional cartilaginous constructs up to 6 cm2 in size were assembled by optimizing fabrication time during chondrogenic induction. Maturation for 3 weeks facilitated the self-organisation of the cells, which improved the construct’s mechanical strength (compressive and tensile properties) and induced changes in glycosaminoglycan and type II collagen expression, resulting in improved tissue function. The compressive modulus of the construct reached the native cartilage range of 0.88 MPa in the 5th week of maturation. This paper reports the fabrication of anatomically sized and shaped cartilage constructs, achieved by combining novel iPSCs and bio-3D printers using a Kenzan needle array technology, which may facilitate chondral resurfacing of articular cartilage defects.
Study of bleaching of old newsprint recycled paper: reproduction of newspaper material
Authors: Zeb Hassan , Hussain Muhammad Asif , Ahmed Iftikhar , Akram Muhammad Sarfraz , Haider Bilal , Haider Rizwan , Babar Zaeem Bin , Saleem Rana Mujahid , Ahsan Abuzar , Aziz Iqra , Arif Muhammad
Published: August 2021

With the utilization of used newspaper into the paper making industry, bleaching has been an area of concern to obtain a balance between desired brightness and the amount of treatment it requires. Motivation of this study was to optimize bleaching of recycled newsprint fibers in terms of five variables namely hydrogen peroxide charge, amount of sodium hydroxide employed, pulp consistency, bleaching temperature, and bleaching time. Experimental work was conducted in the laboratory to simulate bleaching plant and it was found that higher peroxide charge is better for improvement in brightness, but it is uneconomical to increase peroxide charge indefinitely. The amount of hydrogen peroxide is added so that the residual peroxide at the end of the reaction is not less than 10% of the initially added peroxide. Sodium hydroxide provides alkalinity which is very important for making the fibers flexible and softening of ink particles but it also contributes to pulp yellowing if residual hydrogen peroxide contents are lesser than the minimum required value. So, for 16 kg t−1 of hydrogen peroxide, 6 kg t−1 of sodium hydroxide prevented the brightness reversion in this study. Higher pulp consistency is better but unavailability of very high consistency pulp mixer in the industry is a limiting factor for higher than 30% pulp consistency. Temperature and time are quite interrelated and, with the given bleaching conditions, a temperature of 95 °C with 10 min residence time was found to be optimum for this study. It was also observed that multiple pre-washings increase brightness and save bleaching chemicals.
Preparation and in vitro release of total alkaloids from alstonia scholaris leaf-loaded mPEG-PMA microspheres
Authors: Jiang Nianfeng , Zheng Xiangyu , Feng Yan , Wu Hongtao , Yuan Mingwei , He Yi , Li Hongli , Yuan Minglong
Published: August 2021

The total alkaloids extracted from the leaves of Alstonia scholaris (ASAs) have been reported to reduce fever, remove phlegm, and relieve coughs. However, their drug half-lives are short. Thus, to obtain sustained-release preparations of total alkaloids from ASAs, mandelic acid oxyanhydride (mandelic acid OCA) was synthesized by the reaction of L-mandelic acid (MA) with triphosgene, and subsequent copolymerization with polyethylene glycol monomethyl ether (mPEG) of different molecular weights yielded the corresponding mPEG poly-MA (mPEG-PMA) copolymers. ASAs-loaded microspheres were then prepared using the double emulsion method, and their in vitro release (15 d, 37 °C) and in vitro degradation behaviors were studied. The morphology, size, embedding efficiency, and drug loading efficiency were investigated for the prepared microspheres, and screening was carried out using the mPEG10K-PMA drug-loaded microspheres to analyze their biological characteristics. Anti-inflammatory experiments using Kunming mice and Sprague Dawley rats showed that the microspheres exhibited good anti-inflammatory properties. Moreover, the ASAs-loaded microspheres exhibited a good biocompatibility, and the hemolysis rate was <5%.
Hyaluronic acid-based supramolecular hydrogels for biomedical applications
Authors: Mihajlovic Marko , Fermin Liline , Ito Keita , van Nostrum Cornelus F , Vermonden Tina
Published: August 2021

Soft materials, such as hydrogels, are used as scaffolds in tissue engineering and regenerative medicine to help tissues regenerate and heal. Recently, supramolecular hydrogels, based on non-covalent interactions, have grown in popularity, especially in the development of materials for biomedical use. Their potential lies in the dynamic, reversible and temporary nature of their crosslinks, which can make them responsive to stimuli, injectable and suitable for 3D printing. Such versatility and processability is important when developing new biomaterials for drug delivery or as implantable scaffolds. The behavior and properties of such hydrogels are different compared to those of chemically crosslinked hydrogels. In this review, we give an overview on supramolecular hydrogels which contain hyaluronic acid (HA) as one of the building blocks. HA is particularly interesting, due to its hydrophilicity, biofunctionality and ease of chemical modification. Specifically, we focus on HA-based hydrogels that make use of hydrogen bonding, hydrophobic interactions, electrostatic interactions, metal–ion coordination and guest–host interactions, and are intended for applications in the biomedical field, with potential for clinical translation.
Impaired Cx43 gap junction endocytosis causes morphological and functional defects in zebrafish
Authors: Hyland Caitlin , Mfarej Michael , Hiotis Giorgos , Lancaster Sabrina , Novak Noelle , Iovine M. Kathryn , Falk Matthias M.
Published: August 2021

It is shown for the first time that impaired gap junction turnover achieved by CRISPR/Cas9-mediated deletion of critical amino acid residues (256-289) in zebrafish causes a suite of developmental defects that include pronounced cardiovascular morphology and function.
A Tale of Two Approaches
Authors: Ghayad Jean Pierre E , Barakett-Hamadé Vanda P
Published: August 2021

Objectives

To summarize and assess the literature on the performances of methods beyond the Friedewald formula (FF) used in routine practice to determine low-density lipoprotein cholesterol (LDL-C).

Methods

A literature review was performed by searching the PubMed database. Many peer-reviewed articles were assessed.

Results

The examined methods included direct homogeneous LDL-C assays, the FF, mathematical equations derived from the FF, the Martin-Hopkins equation (MHE), and the Sampson equation. Direct homogeneous assays perform inconsistently across manufacturers and disease status, whereas most FF-derived methods exhibit variable levels of performance across populations. The MHE consistently outperforms the FF but cannot be applied in the setting of severe hypertriglyceridemia. The Sampson equation shows promise against both the FF and MHE, especially in severe hypertriglyceridemia, but data are still limited on its validation in various settings, including disease and therapeutic states.

Conclusions

There is still no consensus on a universal best method to estimate LDL-C in routine practice. Further studies are needed to assess the performance of the Sampson equation.
The influence of maternal glucocorticoids on offspring phenotype in high- and low-risk environments
Authors: MacLeod Kirsty J , Langkilde Tracy , Venable Cameron P , Ensminger David C , Sheriff Michael J
Published: August 2021

Elevated maternal glucocorticoid levels during gestation can lead to phenotypic changes in offspring via maternal effects. Although such effects have traditionally been considered maladaptive, maternally derived glucocorticoids may adaptively prepare offspring for their future environment depending upon the correlation between maternal and offspring environments. Nevertheless, relatively few studies test the effects of prenatal glucocorticoid exposure across multiple environments. We tested the potential for ecologically relevant increases in maternal glucocorticoids in the eastern fence lizard (Sceloporus undulatus) to induce adaptive phenotypic changes in offspring exposed to high or low densities of an invasive fire ant predator. Maternal treatment had limited effects on offspring morphology and behavior at hatching, but by 10 days of age, we found maternal treatment interacted with offspring environment to alter anti-predator behaviors. We did not detect differences in early-life survival based on maternal treatment or offspring environment. Opposing selection on anti-predator behaviors from historic and novel invasive predators may confound the potential of maternal glucocorticoids to adaptively influence offspring behavior. Our test of the phenotypic outcomes of transgenerational glucocorticoid effects across risk environments provides important insight into the context-specific nature of this phenomenon and the importance of understanding both current and historic evolutionary pressures.
Co-evolutionary distance predictions contain flexibility information
Authors: Schwarz Dominik , Georges Guy , Kelm Sebastian , Shi Jiye , Vangone Anna , Deane Charlotte M
Published: August 2021

Motivation

Co-evolution analysis can be used to accurately predict residue–residue contacts from multiple sequence alignments. The introduction of machine-learning techniques has enabled substantial improvements in precision and a shift from predicting binary contacts to predict distances between pairs of residues. These developments have significantly improved the accuracy of de novo prediction of static protein structures. With AlphaFold2 lifting the accuracy of some predicted protein models close to experimental levels, structure prediction research will move on to other challenges. One of those areas is the prediction of more than one conformation of a protein. Here, we examine the potential of residue–residue distance predictions to be informative of protein flexibility rather than simply static structure.

Results

We used DMPfold to predict distance distributions for every residue pair in a set of proteins that showed both rigid and flexible behaviour. Residue pairs that were in contact in at least one reference structure were classified as rigid, flexible or neither. The predicted distance distribution of each residue pair was analysed for local maxima of probability indicating the most likely distance or distances between a pair of residues. We found that rigid residue pairs tended to have only a single local maximum in their predicted distance distributions while flexible residue pairs more often had multiple local maxima. These results suggest that the shape of predicted distance distributions contains information on the rigidity or flexibility of a protein and its constituent residues.

Supplementary information

Supplementary data are available at Bioinformatics online.
ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions
Authors: Nikolaienko Oleksii , Lønning Per Eystein , Knappskog Stian
Published: August 2021

Motivation

With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyze such events.

Results

We have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs). ramr can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of ramr and confirmed its applicability for analysis of large public datasets. Using ramr we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages.

Availability and implementation

The R package is freely available at https://github.com/BBCG/ramr and https://bioconductor.org/packages/ramr.

Supplementary information

Supplementary data are available at Bioinformatics online.
Inflection across Categories: Tracking Abstract Morphological Processing in Language Production with MEG
Authors: Hauptman Miriam , Blanco-Elorrieta Esti , Pylkkänen Liina
Published: August 2021

Coherent language production requires that speakers adapt words to their grammatical contexts. A fundamental challenge in establishing a functional delineation of this process in the brain is that each linguistic process tends to correlate with numerous others. Our work investigated the neural basis of morphological inflection by measuring magnetoencephalography during the planning of inflected and uninflected utterances that varied across several linguistic dimensions. Results reveal increased activity in the left lateral frontotemporal cortex when inflection is planned, irrespective of phonological specification, syntactic context, or semantic type. Additional findings from univariate and connectivity analyses suggest that the brain distinguishes between different types of inflection. Specifically, planning noun and verb utterances requiring the addition of the suffix -s elicited increased activity in the ventral prefrontal cortex. A broadly distributed effect of syntactic context (verb vs. noun) was also identified. Results from representational similarity analysis indicate that this effect cannot be explained in terms of word meaning. Together, these results 1) offer evidence for a neural representation of abstract inflection that separates from other stimulus properties and 2) challenge theories that emphasize semantic content as a source of verb/noun processing differences.
Sublamina-Specific Dynamics and Ultrastructural Heterogeneity of Layer 6 Excitatory Synaptic Boutons in the Adult Human Temporal Lobe Neocortex
Authors: Schmuhl-Giesen Sandra , Rollenhagen Astrid , Walkenfort Bernd , Yakoubi Rachida , Sätzler Kurt , Miller Dorothea , von Lehe Marec , Hasenberg Mike , Lübke Joachim H R
Published: August 2021

Synapses “govern” the computational properties of any given network in the brain. However, their detailed quantitative morphology is still rather unknown, particularly in humans. Quantitative 3D-models of synaptic boutons (SBs) in layer (L)6a and L6b of the temporal lobe neocortex (TLN) were generated from biopsy samples after epilepsy surgery using fine-scale transmission electron microscopy, 3D-volume reconstructions and electron microscopic tomography. Beside the overall geometry of SBs, the size of active zones (AZs) and that of the three pools of synaptic vesicles (SVs) were quantified. SBs in L6 of the TLN were middle-sized (~5 μm2), the majority contained only a single but comparatively large AZ (~0.20 μm2). SBs had a total pool of ~1100 SVs with comparatively large readily releasable (RRP, ~10 SVs L6a), (RRP, ~15 SVs L6b), recycling (RP, ~150 SVs), and resting (~900 SVs) pools. All pools showed a remarkably large variability suggesting a strong modulation of short-term synaptic plasticity. In conclusion, L6 SBs are highly reliable in synaptic transmission within the L6 network in the TLN and may act as “amplifiers,” “integrators” but also as “discriminators” for columnar specific, long-range extracortical and cortico-thalamic signals from the sensory periphery.
Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in the United States: Living Density, Viral Load, and Disproportionate Impact on Communities of Color
Authors: Cerami Carla , Popkin-Hall Zachary R , Rapp Tyler , Tompkins Kathleen , Zhang Haoming , Muller Meredith S , Basham Christopher , Whittelsey Maureen , Chhetri Srijana B , Smith Judy , Litel Christy , Lin Kelly D , Churiwal Mehal , Khan Salman , Rubinstein Rebecca , Claman Faith , Mollan Katie , Wohl David , Premkumar Lakshmanane , Powers Kimberly A , Juliano Jonathan J , Lin Feng-Chang , Lin Jessica T
Published: August 2021

Background

Households are hot spots for severe acute respiratory syndrome coronavirus 2 transmission.

Methods

This prospective study enrolled 100 coronavirus disease 2019 (COVID-19) cases and 208 of their household members in North Carolina though October 2020, including 44% who identified as Hispanic or non-White. Households were enrolled a median of 6 days from symptom onset in the index case. Incident secondary cases within the household were detected using quantitative polymerase chain reaction of weekly nasal swabs (days 7, 14, 21) or by seroconversion at day 28.

Results

Excluding 73 household contacts who were PCR-positive at baseline, the secondary attack rate (SAR) among household contacts was 32% (33 of 103; 95% confidence interval [CI], 22%–44%). The majority of cases occurred by day 7, with later cases confirmed as household-acquired by viral sequencing. Infected persons in the same household had similar nasopharyngeal viral loads (intraclass correlation coefficient = 0.45; 95% CI, .23–.62). Households with secondary transmission had index cases with a median viral load that was 1.4 log10 higher than those without transmission (P = .03), as well as higher living density (more than 3 persons occupying fewer than 6 rooms; odds ratio, 3.3; 95% CI, 1.02–10.9). Minority households were more likely to experience high living density and had a higher risk of incident infection than did White households (SAR, 51% vs 19%; P = .01).

Conclusions

Household crowding in the context of high-inoculum infections may amplify the spread of COVID-19, potentially contributing to disproportionate impact on communities of color.
On the Security of the Stream Ciphers RCR-64 and RCR-32
Authors: Joseph Mabin , Sekar Gautham , Balasubramanian R , Venkiteswaran G
Published: August 2021

The stream ciphers RCR-64 and RCR-32 designed by Sekar et al. are the most recent additions to the Py-family of stream ciphers, originally designed by Biham et al. The ciphers are among the fastest stream ciphers on software. To the best of our knowledge, the only reported attacks on the ciphers are due to Ding et al., published in the Journal of Universal Computer Science. In this paper, we review these alleged attacks on the RCR ciphers and show that they are based on non-existent keystream biases stemming from flawed probability calculations.
Impact of SMART Pass filter in patients with ajmaline-induced Brugada syndrome and subcutaneous implantable cardioverter-defibrillator eligibility failure: results from a prospective multicentre study
Authors: Conte Giulio , Cattaneo Fabio , de Asmundis Carlo , Berne Paola , Vicentini Alessandro , Namdar Mehdi , Scalone Antonio , Klersy Catherine , Caputo Maria Luce , Demarchi Andrea , Özkartal Tardu , Salghetti Francesca , Casu Gavino , Passarelli Ilaria , Mameli Stefano , Shah Dipen , Burri Haran , De Ferrari Gaetano , Brugada Pedro , Auricchio Angelo
Published: August 2021

Aims

Ajmaline challenge can unmask subcutaneous implantable cardioverter-defibrillator (S-ICD) screening failure in patients with Brugada syndrome (BrS) and non-diagnostic baseline electrocardiogram (ECG). The efficacy of the SMART Pass (SP) filter, a high-pass filter designed to reduce cardiac oversensing (while maintaining an appropriate sensing margin), has not yet been assessed in patients with BrS. The aim of this prospective multicentre study was to investigate the effect of the SP filter on dynamic Brugada ECG changes evoked by ajmaline and to assess its value in reducing S-ICD screening failure in patients with drug-induced Brugada ECGs.

Methods and results

The S-ICD screening with conventional automated screening tool (AST) was performed during ajmaline challenge in subjects with suspected BrS. The S-ICD recordings were obtained before, during and after ajmaline administration and evaluated by the means of a simulation model that emulates the AST behaviour with and without SP filter. A patient was considered suitable for S-ICD if at least one sensing vector was acceptable in all tested postures. A sensing vector was considered acceptable in the presence of QRS amplitude >0.5 mV, QRS/T-wave ratio >3.5, and sense vector score >100. Of the 126 subjects (mean age: 42 ± 14 years, males: 61%, sensing vectors: 6786), 46 (36%) presented with an ajmaline-induced Brugada type 1 ECG. Up to 30% of subjects and 40% of vectors failed the screening during the appearance of Brugada type 1 ECG evoked by ajmaline. The S-ICD screening failure rate was not significantly reduced in patients with Brugada ECGs when SP filter was enabled (30% vs. 24%). Similarly, there was only a trend in reduction of vector-failure rate attributable to the SP filter (from 40% to 36%). The most frequent reason for screening failure was low QRS amplitude or low QRS/T-wave ratio. None of these patients was implanted with an S-ICD.

Conclusion

Patients who pass the sensing screening during ajmaline can be considered good candidates for S-ICD implantation, while those who fail might be susceptible to sensing issues. Although there was a trend towards reduction of vector sensing failure rate when SP filter was enabled, the reduction in S-ICD screening failure in patients with Brugada ECGs did not reach statistical significance.

Clinical trial registration

https://clinicaltrials.gov Unique Identifier NCT04504591.
Frequency dependence of attenuation components including mantle leakage in Garhwal Himalaya based on a modified MLTWA method
Authors: Padhy Simanchal , Subhadra Nampally
Published: August 2021

Attenuation mechanism of seismic waves derived with an appropriate scattering model is a mandate for high-frequency earthquake ground-motion modelling. The assumption of uniform half-space is not always realistic and can have significant implications on the results obtained. We tested this assumption for the case of Garhwal Himalaya using a two-layered half-space model. To this end, we analysed the 1999 Chamoli earthquake aftershock sequence in Garhwal Himalaya based on the MLTWA method assuming both the uniform and layered models. The data set consists of 384 seismograms from 72 aftershocks recorded by a temporary seismic network of twelve stations. The uniform model cannot fully describe the energy loss by intrinsic and scattering attenuation, expecting bias in the corresponding attenuation estimates which are constrained by comparing results of numerical simulations with analytical solutions. By comparing the coda envelopes of both the analytical and numerical experiments for a suite of models that include the varying degree of scattering and intrinsic attenuation of crust and mantle (half-space), we could obtain improved attenuation estimates. Monte Carlo method was used to numerically solve the radiative transfer equation to deal with multiple isotropic scattering of seismic waves in 3-D heterogeneous acoustic media. The coda envelopes for the uniform model could reasonably fit those for the layered ones. The envelope fits suggest that the intrinsic and scattering coefficients for the uniform model are overestimated, by a factor that is frequency-dependent, as compared to those for the layered earth model. The factor lies in the range 4.0–7.5 (5.75 ± 1.75) below ∼3 Hz and 2.8–4.0 (3.4 ± 0.6) above 3 Hz for intrinsic, and the range 1.1–2.5 (1.8 ± 0.7) for scattering coefficient at 1–12 Hz. Under the assumption of a layered model, we could further reinterpret the apparent frequency-dependent energy loss as a sum of frequency-dependent mantle leakage and frequency-independent intrinsic attenuation. The results in the assumption of a layered model suggest strong scattering in the upper crust and weak mantle leakage in the frequency range 1.5–24 Hz. The small-scale random heterogeneities responsible for the observed scattering likely represent the fluid-filled fractured-crust, as evidenced from seismic tomography in the source area of the 1999 event.
Charcot–Marie–tooth disease causing mutation (p.R158H) in pyruvate dehydrogenase kinase 3 (PDK3) affects synaptic transmission, ATP production and causes neurodegeneration in a CMTX6C. elegansmodel
Authors: Narayanan Ramesh K , Brewer Megan H , Perez-Siles Gonzalo , Ellis Melina , Ly Carolyn , Burgess Andrew , Neumann Brent , Nicholson Garth A , Vucic Steve , Kennerson Marina L
Published: August 2021

Charcot–Marie-Tooth (CMT) is a commonly inherited, non-fatal neurodegenerative disorder that affects sensory and motor neurons in patients. More than 90 genes are known to cause axonal and demyelinating forms of CMT. The p.R158H mutation in the pyruvate dehydrogenase kinase 3 (PDK3) gene is the genetic cause for an X linked form of axonal CMT (CMTX6). In vitro studies using patient fibroblasts and iPSC-derived motor neurons have shown that this mutation causes deficits in energy metabolism and mitochondrial function. Animal models that recapitulate pathogenic in vivo events in patients are crucial for investigating mechanisms of axonal degeneration and developing therapies for CMT. We have developed a C. elegans model of CMTX6 by knocking-in the p.R158H mutation in pdhk-2, the ortholog of PDK3. In addition, we have developed animal models overexpressing the wild type and mutant form of human PDK3 specifically in the GABAergic motor neurons of C. elegans. CMTX6 mutants generated in this study exhibit synaptic transmission deficits, locomotion defects and show signs of progressive neurodegeneration. Furthermore, the CMTX6 in vivo models display energy deficits that recapitulate the phenotype observed in patient fibroblasts and iPSC-derived motor neurons. Our CMTX6 animals represent the first in vivo model for this form of CMT and have provided novel insights into the cellular function and metabolic pathways perturbed by the p.R158H mutation, all the while closely replicating the clinical presentation observed in CMTX6 patients.
A new approach to minimize carbon emission rate in turning processes
Authors: Cakir Ali Kemal
Published: August 2021

This paper aims to analyze the correlation between CNC machine turning properties and the CO2 output, so that a minimum value is obtained and an optimal process is created. The need to find an optimal process is to help in reducing carbon emissions during the ongoing climate change. In this study, the total carbon emission values in turning have been investigated by calculating the carbon emission values of the features used in turning processes, which are work piece, cutting tool, machine electrical system, cutting tool features, cutting parameters, chip removal, etc. The actions to be taken in experimental study are decided. In the first stage, the equations required to calculate the carbon emission values are determined. Then, carbon emission values were calculated. An experimental design was created in the Taguchi method in order to use the carbon emission values obtained. In the experimental design, the cutting parameters were chosen as the factor, while the cutting time and carbon emission values were chosen as the response. Next, optimum conditions were determined in minimizing the carbon emission value. Later, the most effective cutting parameter with minimum carbon emission value was found in an analysis of variance. Unlike the studies on carbon emission in the machining sector in the literature, the effect of cutting parameters on cutting time and thus on carbon emission was also investigated. Again, in the study, unlike the studies in the literature, a numerical value is given in determining the lowest carbon emission.
Knowledge Acquisition in Times of the 2020 Coronavirus Pandemic: Evidence from a Four-Wave Panel Study
Authors: Damstra Alyt , Hameleers Michael
Published: August 2021

This paper focuses on the accuracy of COVID-19-related knowledge during the 2020 pandemic. We look at the effects of traditional vs. digital news use and distinguish between positive (number of recoveries) and negative (number of casualties) knowledge. Importantly, the moderating role of crisis context is examined when tracing media effects on knowledge. Relying on a four-wave panel survey fielded in the Netherlands, we find that people’s knowledge became more accurate over the course of the crisis. News exposure did not lead to more accuracy, in fact, a negative relation was found. The impact of digital news use weakened as the crisis continued.