bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase field crystal model for particles with n-fold rotational symmetry in two dimensions
Authors: Weigel Robert F B , Schmiedeberg Michael
Published: August 2022

We introduce a phase field crystal (PFC) model for particles with n-fold rotational symmetry in two dimensions. Our approach is based on a free energy functional that depends on the reduced one-particle density, the strength of the orientation, and the direction of the orientation, where all these order parameters depend on the position. The functional is constructed such that for particles with axial symmetry (i.e. n = 2) the PFC model for liquid crystals as introduced by Löwen (2010 J. Phys.: Condens. Matter
22 364105) is recovered. We discuss the stability of the functional and explore phases that occur for 1 ⩽ n ⩽ 6. In addition to isotropic, nematic, stripe, and triangular order, we also observe cluster crystals with square, rhombic, honeycomb, and even quasicrystalline symmetry. The n-fold symmetry of the particles corresponds to the one that can be realized for colloids with symmetrically arranged patches. We explain how both, repulsive as well as attractive patches, are described in our model.
The role of Co2+ cation addition in enhancing the AC heat induction power of (CoxMn1–x)Fe2O4 superparamagnetic nanoparticles
Authors: Wang Jie , Kim Hyungsub , Seo HyeongJoo , Ota Satoshi , You Chun-Yeol , Takemura Yasushi , Bae Seongtae
Published: August 2022

The physical role of magnetically semi-hard Co2+ cation addition in enhancing the AC heat induction temperature (T
AC) or specific loss power (SLP) of solid (Co
x
Mn1−x
)Fe2O4 superparamagnetic iron oxide nanoparticles (SPIONPs) was systematically investigated at the biologically safe and physiologically tolerable range of H

AC
(H

AC,safe
= 1.12 × 109 A m−1 s−1, f

appl
= 100 kHz, H
appl = 140 Oe (11.2 A m−1)) to demonstrate which physical parameter would be the most critical and dominant in enhancing the T
AC (SLP) of SPIONPs. According to the experimentally and theoretically analyzed results, it was clearly demonstrated that the enhancement of magnetic anisotropy (K

u
)-dependent AC magnetic softness including the Néel relaxation time constant τ

N
(≈τ

eff
, effective relaxation time constant), and its dependent out-of-phase magnetic susceptibility

χ
″

primarily caused by the Co2+ cation addition is the most dominant parameter to enhance the T
AC (SLP). This clarified result strongly suggests that the development of new design and synthesis methods enabling to significantly enhance the K

u
by improving the crystalline anisotropy, shape anisotropy, stress (magnetoelastic) anisotropy, thermally-induced anisotropy, and exchange anisotropy is the most critical to enhance the T
AC (SLP) of SPIONPs at the H

AC,safe
(particularly at the lower f

appl
< 120 kHz) for clinically safe magnetic nanoparticle hyperthermia.
Validation of SART 3.5D algorithm for cerebrovascular dynamics and artery versus vein classification in presurgical 3D digital subtraction angiographies
Authors: El Hadji Sara , Bonilauri Augusto , De Momi Elena , Castana Laura , Macera Antonio , Berta Luca , Cardinale Francesco , Baselli Giuseppe
Published: August 2022

Classification of arteries and veins in cerebral angiograms can increase the safety of neurosurgical procedures, such as StereoElectroEncephaloGraphy, and aid the diagnosis of vascular pathologies, as arterovenous malformations. We propose a new method for vessel classification using the contrast medium dynamics in rotational digital subtraction angiography (DSA). After 3D DSA and angiogram segmentation, contrast enhanced projections are processed to suppress soft tissue and bone structures attenuation effect and further enhance the CM flow. For each voxel labelled as vessel, a time intensity curve (TIC) is obtained as a linear combination of temporal basis functions whose weights are addressed by simultaneous algebraic reconstruction technique (SART 3.5D), expanded to include dynamics. Each TIC is classified by comparing the areas under the curve in the arterial and venous phases. Clustering is applied to optimize the classification thresholds. On a dataset of 60 patients, a median value of sensitivity (90%), specificity (91%), and accuracy (92%) were obtained with respect to annotated arterial and venous voxels up to branching order 4–5. Qualitative results are also presented about CM arrival time mapping and its distribution in arteries and veins respectively. In conclusion, this study shows a valuable impact, at no protocol extra-cost or invasiveness, concerning surgical planning related to the enhancement of arteries as major organs at risk. Also, it opens a new scope on the pathophysiology of cerebrovascular dynamics and its anatomical relationships.
Surface flattening of 4H-SiC (0001) epitaxial wafers by high temperature oxidation
Authors: Zhao Siqi , Wang Jiulong , Yan Guoguo , Shen Zhanwei , Zhao Wanshun , Wang Lei , Liu Xingfang , Sun Guosheng , Zeng Yiping
Published: August 2022

Due to the special ‘step-controlled epitaxy’ mode of 4H-SiC, it is easy to generate step bunching on the surface. Although the flatness of epitaxial wafers has been greatly improved with the advancement of epitaxy technology, there are still localized steps on the surface of some certain wafers. The presence of localized steps can affect the performance of the subsequently fabricated devices. Therefore, minimizing or even eliminating the local steps of the epitaxial surface to obtain an atomically smooth surface is very important. Here, we utilize a high-temperature oxidation process to reduce the size of the giant steps and obtain a flatter epitaxial surface. We found that oxidation parameters such as temperature, pressure, and time play an important role in the surface planarization, and the degree of planarization can be further improved by multiple oxidation processes. In addition, although the oxidation rate under low pressure is lower than that under atmospheric pressure, a smoother epitaxial surface can be obtained. Our results demonstrate the possibility of obtaining atomically smooth surfaces through a high-temperature oxidation process.
Effect of hydrogen bond on phase transition behavior of polyamides during stretching process
Authors: Li Yufang , Nie Danli , Xiang Zhining , Cai Ziqing , Wang Jintao
Published: August 2022

During the fiber spinning process, the stretching process is the key to improve the mechanical properties of materials. It is very important to study the effect of hydrogen bond density on the aggregation structure evolution of polyamide for the preparation of high-performance fibers. In this paper, three kinds of polyamides (polyamide 6, polyamide 612 and polyamide 1212) were comparatively studied. In these three polyamides, the hydrogen bond density showed a gradient trend. With the increase of hydrogen bond density, the tensile strength and crystallinity of the materials gradually increased. The phase transition process of the three polyamides had significant difference. This was due to the difference of hydrogen bond density which resulted in different thermally stability of crystal blocks. Finally, the phase evolution schematic of polyamides depending on hydrogen bond density and stretching strains was established.
First principles calculations to investigate Li-based quaternary Heusler compounds LiHfCoX (X = Ge, Sn) for thermoelectric applications
Authors: Kaur Tavneet , Singh Jaspal , Goyal Megha , Kaur Kulwinder , Khandy Shakeel Ahmad , Bhat Muzzammil Ahmad , Sharopov Utkir Bahodirovich , Dhiman Shobhna , Wani Aadil Fayaz , Rani Bindu , Sinha M M , Verma S S
Published: August 2022

In the last few decades, varieties of semiconductors have been explored for electronic and thermoelectric applications. As a result of these motivations, the current research work investigates the structural, electronic, vibrational, elastic, mechanical, thermodynamic, and thermoelectric properties of two quaternary Heuslers (QHs), namely LiHfCoGe and LiHfCoSn (both of which are semiconducting in nature), within the computational framework of DensityFunctional Theory (DFT) and Boltzmann transport equations. Both alloys display the p-type semiconductivity, dynamical stability and crystallize in the FCC cubic structure within F-43 m space group. The high Seebeck coefficient values pronounce an excellent and fundamental thermoelectric character. The large melting points expose their scope in the high-temperature regions. However, all of the thermoelectric characteristics are also measured in terms of the estimated relaxation time using deformation potential theory. Even though the figure of merit (ZT) is in the middle of the pack yet better than many compounds of the same sort. The impact of spin–orbit coupling on the thermoelectric characteristics is also examined. The practical utilization of the materials can be evaluated from the elastic and mechanical properties that are favorable in manufacturing efficient and reliable Thermoelectric Modules at high-temperatures.
Bidirectional quantum operation teleportation with a six-qubit composite Bell-GHZ state
Authors: Zhou Jun , Yuan Hao , Kong Min , Zhang Gang
Published: August 2022

A bidirectional quantum operation teleportation scheme is proposed by utilizing a six-qubit composite Bell-GHZ state. In which, two users Anne and Benson can perform their respective concerned single-qubit operations on each other’s target states. Compared with the other existing schemes of quantum operation teleportation (QOT), the present scheme can realize the remote implement of the positive and negative two-way quantum operations, which not only improves the communication capacity, but also expands the application scenarios of QOT. Additionally, it is deterministic and feasible with the present experimental techniques.
Detailed characterization of polycapillary focusing x-ray lenses by a charge-coupled device detector and a pinhole
Authors: Sun Xue-Peng , Shao Shang-Kun , Li Hui-Quan , Yuan Tian-Yu , Sun Tian-Xi
Published: August 2022

A method to measure the detailed performance of polycapillary x-ray optics by a pinhole and charge coupled device (CCD) detector was proposed in this study. The pinhole was located between the x-ray source and the polycapillary x-ray optics to determine the illuminating region of the incident x-ray beam on the input side of the optics. The CCD detector placed downstream of the polycapillary x-ray optics ensured that the incident x-ray beam controlled by the pinhole irradiated a specific region of the input surface of the optics. The intensity of the output beam of the polycapillary x-ray optics was obtained from the far-field image of the output beam of the optics captured by CCD detector. As an application example, the focal spot size, gain in power density, transmission efficiency, and beam divergence of different parts of a polycapillary focusing x-ray lenses (PFXRL) were measured by a pinhole and CCD detector. Three pinholes with diameters of 500, 1000, and 2000 μm were used to adjust the diameter of the incident x-ray beam illuminating the PFXRL from 500 μm to the entire surface of the input side of the PFXRL. The focal spot size of the PFXRL, gain in power density, transmission efficiency, and beam divergence ranged from 27.1 μm to 34.6 μm, 400 to 3460, 26.70% to 5.38%, and 16.8 mrad to 84.86 mrad, respectively.
Statistics of diffusive encounters with a small target: three complementary approaches
Authors: Grebenkov Denis S
Published: August 2022

Diffusive search for a static target is a common problem in statistical physics with numerous applications in chemistry and biology. We look at this problem from a different perspective and investigate the statistics of encounters between the diffusing particle and the target. While an exact solution of this problem was recently derived in the form of a spectral expansion over the eigenbasis of the Dirichlet-to-Neumann operator, the latter is generally difficult to access for an arbitrary target. In this paper, we present three complementary approaches to approximate the probability density of the rescaled number of encounters with a small target in a bounded confining domain. In particular, we derive a simple fully explicit approximation, which depends only on a few geometric characteristics such as the surface area and the harmonic capacity of the target, and the volume of the confining domain. We discuss the advantages and limitations of three approaches and check their accuracy. We also deduce an explicit approximation for the distribution of the first-crossing time, at which the number of encounters exceeds a prescribed threshold. Its relations to common first-passage time problems are discussed.
The coordinate sensitive detector with high space and time resolution based on the MA-20 multianode PMT
Authors: Brekhovskikh V. , Gorin A. , Dyatchenko V. , Medynsky M. , Rykalin V.
Published: August 2022

The work is dedicated to the discussion of the possibility of creating a position-sensitive detector with high coordinate reconstruction. The paper presents the simulation results and the experimentally obtained data for a prototype detector based on the MA-20 multianode PMT [1] and a linear stack of scintillating crystal or plastic strips. The multianode position-sensitive PMT MA-20 has a semitransparent bi-alkaline photocathode with the size of the sensitive area of 10 × 200 mm2, 10 evaporated type bi-alkaline type dynodes of the same length, and 20 separated anodes. This PM is the invention of the authors. The maximum gain of the dynode system is 106. The stack of scintillating strips made of GSO (gadolinium orthosilicate) crystals with an element size of 3 × 10 × 50 mm3, of BGO (bismuth germanate) crystals with an element size of 5 × 15 × 40 mm3, and finally stack of strips made of a plastic scintillator with an element size of 5 × 10 × 200 mm3 were used for experimental measurement of a spatial resolution of the detector prototype. Space resolution was determined by the position of the center of gravity of charges of neighboring anodes [2]. As a source of radiation, the collimated 137Cs (γ 0.662 MeV) and 90Sr (β− 2.283 MeV) were used, the measured number of photoelectrons is 10–20 of one element of the stack, depending on the scintillating strip type. The use of a multi-anode photomultiplier in combination with the stack of crystal or plastic scintillators allows one to get a simple linear detector with high performance in spatial resolution and also with a low level of intrinsic noise in comparison, for example, with silicon PMT. A resolution simulation was performed for a system consisting of a one-dimensional stack of scintillation strips placed on the photocathode of a multi-anode PMT for different values of the strips width and the number of photoelectrons of one strip. The experimental dependences of the signal value versus position of optical fiber with a diameter of 1 mm on the photocathode of the 20 anodes PMT were also measured that allowed to specify the coordinate resolution for the described detector. As a result of processing the collected data, spatial resolution was obtained at the level of 1 mm. The obtained results are in good agreement with the simulation results.
High-power inductive coupler with a high-voltage DC blocker
Authors: Kaizer B. , Zchut T. , Weissman L. , Perry A. , Eizenshtat M. , Gavish I. , Rodnizki J. , Polikarpov I. , Farber E.
Published: August 2022

The authors of this study developed a high-power inductive
coupler with a high-voltage DC blocker that is capable of delivering
up to 100 kW of CW RF power at 176 MHz and 4 kV DC. The
high-power indictive coupler was developed at the Soreq Nuclear
Research Center for the radio-frequency quadrupole of the Soreq
Applied Research Accelerator Facility. The purpose of the DC blocker
is to enable the application of high-voltage DC bias to the inner
conductors of the couplers in order to prevent the multipacting
phenomena. A new, mechanically and thermally improved, version of
the RF coupler is designed and implemented in conjunction with the
DC blocker. The underlying design principles, indigenous
development, and results of tests of the coupler are presented
here.
Reversed and comparable climate impacts from historical anthropogenic aerosol and GHG on global-scale tropical cyclone genesis potential
Authors: Cao Jian , Wang Hao , Zhao Haikun , Wang Bin , Wu Liguang , Wang Chao
Published: August 2022

Emissions of anthropogenic aerosol and greenhouse gases (GHG) have significantly altered various aspects of the climate extremes in recent decades, yet, the observed global tropical cyclone frequency (TCF) shows no significant trend. Untangling this puzzle requires a better understanding of the precise contributions of the individual anthropogenic forcing to global TCF changes. Here, we quantify the relative contributions of anthropogenic aerosol and GHG to global TCF, represented by genesis potential index (GPI), using the single anthropogenic forcing experiments from the 14 Coupled Model Intercomparison Project phase 6 (CMIP6) models. We find that the two forcings have comparable but opposite impacts on GPIs due to their influences on the TC environment, leading to an insignificant change in GPIs in the historical period (1850–2014). Notably, the aerosol radiative forcing’s intensity is only about one-third of that of GHG, suggesting a more effective modulation of aerosol forcing on GPIs. The stable global TC frequency during the past decades could be attributable to the similar pace of the two anthropogenic emissions. The results highlight that a reliable global TC projection depends on both the aerosol and GHG emission policies.
Advancing 3D shaping of vectorial light by counter-propagation of self-healing scalar and vector Bessel–Gaussian beams
Authors: Asché Eric , Otte Eileen , Denz Cornelia
Published: August 2022

It is well known that counter-propagation of structured light fields allows shaping of three-dimensional (3D) structures in amplitude, phase, or polarization. Here, we numerically demonstrate the potential of implementing non-diffracting Bessel–Gaussian (BG) beams for advancing this approach by taking advantage of its characteristic propagation behavior. In this context, we investigate the self-healing property in this counter-propagating configuration, observing a spin angular momentum (SAM) variation and the formation of a continuous orbital angular momentum (OAM) gradient in longitudinal direction. Additionally, by counter-propagation of BG beams of different types, namely, scalar and vector BG beams, we are able to increase the complexity of accessible 3D structured fields, revealing combined amplitude, phase, and polarization modulation in all spatial dimensions. Thereby, the SAM and OAM of the input light fields can be used to design the resulting 3D structure and its angular momenta. The presented light fields open new possibilities for customized optical trapping potentials and allow new insights into fundamental spin–orbit interaction in counter-propagating superpositions of structured fields.
Clustering matrices through optimal permutations
Authors: Morone Flaviano
Published: August 2022

Matrices are two-dimensional data structures allowing one to conceptually organize information. For example, adjacency matrices are useful to store the links of a network; correlation matrices are simple ways to arrange gene co-expression data or correlations of neuronal activities. Clustering matrix entries into geometric patterns that are easy to interpret helps us to understand and explain the functional and structural organization of the system components described by matrix entries. Here we introduce a theoretical framework to cluster a matrix into a desired pattern by performing a similarity transformation obtained by solving an optimization problem named optimal permutation problem. On the numerical side, we present an efficient clustering algorithm that can be applied to any type of matrix, including non-normal and singular matrices.

We apply our algorithm to the neuronal correlation matrix and the synaptic adjacency matrix of the Caenorhabditis elegans nervous system by performing different types of clustering, using block-diagonal, nested, banded, and triangular patterns. Some of these clustering patterns show their biological significance in that they separate matrix entries into groups that match the experimentally known classification of C. elegans neurons into four broad categories made up of interneurons, motor, sensory, and polymodal neurons.
The Grace Note and the Vampire: Adaptation in an Age of Intellectual Property
Authors: Layman Thomas
Published: August 2022

This article attempts to examine in further detail the discourse involved in the difference between adaptation studies and intertextuality. I argue that the field of adaptation studies makes a fundamental but often overlooked assumption in its self-definition: that author and adaptors pre-date the works they are creating. I propose instead that an author doesn’t create a work, but that a work creates an author. This is not universally true, but material in eras and locations in which legal institutions attempt to define authorship. My observation is relevant when considering the modern institution of copyright and the effect IP laws have had on the environment generative of adaptations. The consequences of these effects result in authorship often assigned after the creation of a work and lengthy legal hand-wringing.
Value Pluralism in Restoration Aesthetics
Authors: Hales Steven D
Published: August 2022

In the restoration of art and artifacts there are three salient types of value to consider: relic, aesthetic, and practical. Relic value includes an object’s age, aura, originality, authenticity, and epistemic value. Aesthetic value is connected to how an object looks, sounds, or tastes. Practical value involves whether a thing can be used as designed—whether a book can be read, a building occupied, a car driven. I argue that while these are all legitimate values, it is impossible for a restorer to maximize them all. I conclude that restoration inexorably involves aesthetic choices; there is no supreme value to be maximized and we should be pluralists about the right balance of values. Restoration is like baking a cake; there are many wrong ways to do it, but there are many right ways as well.
Dimensions of end-of-life preferences in the Swiss general population aged 55+
Authors: Borrat-Besson Carmen , Vilpert Sarah , Jox Ralf J , Borasio Gian Domenico , Maurer Jürgen
Published: August 2022

Background

understanding end-of-life preferences in the general population and how they are structured in people’s minds is essential to inform how to better shape healthcare services in accordance with population expectations for their end of life and optimise communication on end-of-life care issues.

Objective

explore key dimensions underlying end-of-life preferences in a nationally representative sample of adults aged 55 and over in Switzerland.

Methods

respondents (n = 2,514) to the Swiss version of the Survey of Health, Ageing and Retirement in Europe assessed the importance of 23 end-of-life items on a 4-point Likert scale. The factorial structure of the underlying end-of-life preferences was examined using exploratory structural equation modelling.

Results

four dimensions underlying end-of-life preferences were identified: a medical dimension including aspects related to pain management and the maintenance of physical and cognitive abilities; a psychosocial dimension encompassing aspects related to social and spiritual support; a control dimension addressing the need to achieve some control and to put things in order before death; and a burden dimension reflecting wishes not to be a burden to others and to feel useful to others.

Conclusion

highlighting the multi-dimensionality of end-of-life preferences, our results reaffirm the importance of a holistic and comprehensive approach to the end of life. Our results also provide a general framework that may guide the development of information and awareness campaigns on end-of-life care issues in the general population, informational materials and guidelines to support healthy individuals in end-of-life thinking and planning, and advance directive templates appropriate for healthy individuals.
Identification of a SGCD × Discrimination Interaction Effect on Systolic Blood Pressure in African American Adults in the Jackson Heart Study
Authors: Hsiao Chu J , Dumeny Leanne , Bress Adam P , Johnson Dayna A , Shimbo Daichi , Cavallari Larisa H , Mulligan Connie J
Published: August 2022

BACKGROUND

In the United States, hypertension disproportionately afflicts over half of African American adults, many of whom also experience racial discrimination. Understanding gene × discrimination effects may help explain racial disparities in hypertension.

METHODS

We tested for the main effects and interactive effects of 5 candidate single nucleotide polymorphisms (SNPs: rs2116737, rs11190458, rs2445762, rs2597955, and rs2416545) and experiences of discrimination on blood pressure (BP) in African Americans not taking antihypertensive medications in the Jackson Heart Study from Mississippi (n = 2,933). Multiple linear regression models assumed an additive genetic model and adjusted for ancestry, age, sex, body mass index, education, and relatedness. We additionally tested recessive and dominant genetic models.

RESULTS

Discrimination was significantly associated with higher diastolic BP (P = 0.003). In contrast, there were no main effects of any SNP on BP. When analyzing SNPs and discrimination together, SGCD (Sarcoglycan Delta; rs2116737) demonstrated a gene × environment interaction. Specifically, an SGCD × Discrimination interaction was associated with systolic BP (β =1.95, P = 0.00028) in a recessive model. Participants carrying a T allele, regardless of discrimination experiences, and participants with a GG genotype and high experiences of discrimination had higher systolic BP than participants with a GG genotype and low experiences of discrimination. This finding suggests the SGCD GG genotype may have a protective effect on systolic BP, but only in a setting of low discrimination.

CONCLUSIONS

The inclusion of culturally relevant stressors, like discrimination, may be important to understand the gene-environment interplay likely underlying complex diseases with racial health inequities.
Harmful Drinking Phenotype in a Large Dutch Community Sample
Authors: Hogenelst Koen , Snippe Almar , Martinic Marjana
Published: August 2022

Aims

Harmful drinking patterns are shaped by a broad complex interaction of factors, societal and individual, psychological and behavioral. Although previous studies have focused on a few variables at a time, the current study simultaneously examines a large number of variables in order to create a comprehensive view (i.e. phenotype) of harmful drinking, and to rank the main predictors of harmful and non-harmful drinking by order of importance.

Methods

We surveyed a large sample of Dutch adults about their habitual drinking characteristics and attitudes, perceptions and motives for drinking. We fed 45 variables into a random forest machine learning model to identify predictors for (1) drinking within and in excess of Dutch guideline recommendations and (2) harmful and non-harmful drinking.

Results

In both models, respondents’ subjective perceptions of ‘responsible drinking’, both per occasion and per week, showed the strongest predictive potential for different drinking phenotypes. The next strongest factors were respondents’ reason for drinking, motives for drinking and age. Other variables, such as drinking location, knowledge about alcohol-related health risks and consumption of different beverage types, were not strong predictors of drinking phenotypes.

Conclusions

Although the direction of the relationship is unclear from the findings, they suggest that interventions and policy measures aimed at individuals and social norms around drinking may offer promise for reducing harmful drinking. Messaging and promotion of drinking guidelines should be tailored with this in mind.
Ballad Poetics in the Era of Black Lives Matter
Authors: Ronda Margaret
Published: August 2022

This essay approaches ballads as a vital cultural form for dramatizing the histories and social meanings of racial conflict in the US, turning to a series of recent poems written alongside the rise of the Black Lives Matter movement. This archive of poems draws attention to recursive racial divisions as they emerge anew in a calamitous event, highlighting themes of anonymity and hypervisibility, motion and arrest, the violent imposition of carceral order, and the insurrectionary prospects of its refusal. Examining the ways a range of Black poets have been drawing on features associated with ballads, this essay considers how these writers recount the stories and scenes of Ferguson and other now-famous locales of anti-Black state violence and community uprising. With their narratives of common persons subjected to surveillance, exposure, and acts of violence, these poems further the social imaginaries and storytelling mode of the ballad to consider continuing forms of racial injustice and new eruptions of protest in the present.The archive of Black poetic works I consider pursues more oppositional orientations, keyed to the insurgent energy of the streets as well as to the layered practices of Black revisionary ballad and the material histories they encode.
Employment Precarity and Increased Risk of Hazardous Occupational Exposures Among Residents of High Socioeconomic Hardship Neighborhoods
Authors: Bonney Tessa , Rospenda Kathleen M , Forst Linda , Conroy Lorraine M , Castañeda Dolores , Avelar Sandra , Castañeda Yvette , Holloway Adlaide , Hebert-Beirne Jeni
Published: August 2022

Background

While there is evidence that workers in nonstandard employment arrangements are disproportionately exposed to recognized occupational hazards, existing studies have not comprehensively examined associations between employment precarity and exposure to occupational hazards for these workers in the USA. The aim of this study was to examine relationships between employment precarity and occupational hazards in two contiguous high socio-economic hardship neighborhoods in Chicago.

Methods

Using a community-based participatory research approach, community researchers administered a community-developed survey to 489 residents of Greater Lawndale who reported current or recent employment in a job that met at least one characteristic of precarious employment (e.g. unpredictable schedule, insecure work, no living wage/benefits). Employment precarity was calculated using a modified version of the Employment Precarity Index (EPI) developed by the Poverty and Employment Precarity in Southern Ontario group. We modeled the association between employment precarity and occupational exposures using logistic regression models.

Results

We identified a high prevalence of precarious employment in this sample, as well as a high prevalence of self-reported exposure to recognized occupational hazards. Increases in relative employment precarity were significantly associated with self-reported exposure to chemical and biological hazards, physical hazards, and slip, trip, strike, fall, trap or crush hazards at work.

Conclusions

Results highlight the importance of using community research approaches and robust measures of employment characteristics, such as the EPI, to evaluate associations between employment precarity and hazardous exposures. These results suggest that variability in employment situations and resultant relative employment precarity are important predictors of exposure to recognized occupational hazards. Findings also suggest that health inequities observed among precariously employed workers may be partly explained by increased risk for exposure to occupational hazards, which has implications for community health and should be investigated in future longitudinal research.
The Causal Relationship between Learner Motivation and Language Achievement: New Dynamic Perspective
Authors: Alamer Abdullah , Alrabai Fakieh
Published: August 2022

It is well known that successful second language (L2) learners are motivated individuals. Accordingly, L2 researchers have tested the predictive power of different motivational constructs on language learning outcomes. However, this perspective appears to neglect the assessment of achievement as a predictor of future motivation. To assess this possibility, we first employed the latent growth curve model (LGCM) to evaluate the initial values and growth rates of the two variables. We further applied a newly developed statistical method, the random-intercept cross-lagged panel model (RI-CLPM), to study the causal relationship. A total of 226 language students were monitored for 17 weeks at three time points. The analysis showed an increasing trend in the association between the growth levels of both variables. However, students’ autonomous motivation at Time 1 appears to affect achievement at Time 2. Further, the second wave of the RI-CLPM illustrated that achievement at Time 2 impacted autonomous motivation at Time 3, while motivation failed to predict scores on achievement at Time 3.
GTFtools: a software package for analyzing various features of gene models
Authors: Li Hong-Dong , Lin Cui-Xiang , Zheng Jiantao
Published: August 2022

Motivation

Gene-centric bioinformatics studies frequently involve the calculation or the extraction of various features of genes such as splice sites, promoters, independent introns and untranslated regions (UTRs) through manipulation of gene models. Gene models are often annotated in gene transfer format (GTF) files. The features are essential for subsequent analysis such as intron retention detection, DNA-binding site identification and computing splicing strength of splice sites. Some features such as independent introns and splice sites are not provided in existing resources including the commonly used BioMart database. A package that implements and integrates functions to analyze various features of genes will greatly ease routine analysis for related bioinformatics studies. However, to the best of our knowledge, such a package is not available yet.

Results

We introduce GTFtools, a stand-alone command-line software that provides a set of functions to calculate various gene features, including splice sites, independent introns, transcription start sites (TSS)-flanking regions, UTRs, isoform coordination and length, different types of gene lengths, etc. It takes the ENSEMBL or GENCODE GTF files as input and can be applied to both human and non-human gene models like the lab mouse. We compare the utilities of GTFtools with those of two related tools: Bedtools and BioMart. GTFtools is implemented in Python and not dependent on any third-party software, making it very easy to install and use.

Availability and implementation

GTFtools is freely available at www.genemine.org/gtftools.php as well as pyPI and Bioconda.
ntHash2: recursive spaced seed hashing for nucleotide sequences
Authors: Kazemi Parham , Wong Johnathan , Nikolić Vladimir , Mohamadi Hamid , Warren René L , Birol Inanç
Published: August 2022

Motivation

Spaced seeds are robust alternatives to k-mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research.

Results

ntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k-mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism.

Availability and implementation

ntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence
Authors: Kuipers Jack , Singer Jochen , Beerenwinkel Niko
Published: August 2022

Motivation

Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patient’s tumour composition and evolutionary history is key for personalized therapies. Single-cell sequencing (SCS) now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the complexity of the underlying evolutionary process.

Results

By modelling the noise processes and allowing mutations to be lost or to reoccur during tumour evolution, we present a method to jointly call mutations in each cell, reconstruct the phylogenetic relationship between cells, and determine the locations of mutational losses and recurrences. Our Bayesian approach allows us to accurately call mutations as well as to quantify our certainty in such predictions. We show the advantages of allowing mutational loss or recurrence with simulated data and present its application to tumour SCS data.

Availability and implementation

SCIΦN is available at https://github.com/cbg-ethz/SCIPhIN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python
Authors: Lubbock Alexander L R , Lopez Carlos F
Published: August 2022

Motivation

Computational systems biology analyses typically make use of multiple software and their dependencies, which are often run across heterogeneous compute environments. This can introduce differences in performance and reproducibility. Capturing metadata (e.g. package versions, GPU model) currently requires repetitious code and is difficult to store centrally for analysis. Even where virtual environments and containers are used, updates over time mean that versioning metadata should still be captured within analysis pipelines to guarantee reproducibility.

Results

Microbench is a simple and extensible Python package to automate metadata capture to a file or Redis database. Captured metadata can include execution time, software package versions, environment variables, hardware information, Python version and more, with plugins. We present three case studies demonstrating Microbench usage to benchmark code execution and examine environment metadata for reproducibility purposes.

Availability and implementation

Install from the Python Package Index using pip install microbench. Source code is available from https://github.com/alubbock/microbench.

Supplementary information

Supplementary data are available at Bioinformatics online.
What is consciousness? Artificial intelligence, real intelligence, quantum mind and qualia
Authors: Kauffman Stuart A , Roli Andrea
Published: August 2022

We approach the question ‘What is consciousness?’ in a new way, not as Descartes’ ‘systematic doubt’, but as how organisms find their way in their world. Finding one’s way involves finding possible uses of features of the world that might be beneficial or avoiding those that might be harmful. ‘Possible uses of X to accomplish Y’ are ‘affordances’. The number of uses of X is indefinite (or unknown), the different uses are unordered, are not listable, and are not deducible from one another. All biological adaptations are either affordances seized by heritable variation and selection or, far faster, by the organism acting in its world finding uses of X to accomplish Y. Based on this, we reach rather astonishing conclusions:

1. Artificial general intelligence based on universal Turing machines (UTMs) is not possible, since UTMs cannot ‘find’ novel affordances.

2. Brain-mind is not purely classical physics for no classical physics system can be an analogue computer whose dynamical behaviour can be isomorphic to ‘possible uses’.

3. Brain-mind must be partly quantum—supported by increasing evidence at 6.0 to 7.3 sigma.

4. Based on Heisenberg’s interpretation of the quantum state as ‘potentia’ converted to ‘actuals’ by measurement, where this interpretation is not a substance dualism, a natural hypothesis is that mind actualizes potentia. This is supported at 5.2 sigma. Then mind’s actualizations of entangled brain-mind-world states are experienced as qualia and allow ‘seeing’ or ‘perceiving’ of uses of X to accomplish Y. We can and do jury-rig. Computers cannot.

5. Beyond familiar quantum computers, we discuss the potentialities of trans-Turing systems.
Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and chromatin structure
Authors: Li Shuang , Shi Yan , Dang Yanna , Hu Bingjie , Xiao Lieying , Zhao Panpan , Wang Shaohua , Zhang Kun
Published: August 2022

Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during preimplantation embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and preimplantation embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in preimplantation embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to a compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in the expression of genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine preimplantation development.
Aqp4 stop codon readthrough facilitates amyloid-β clearance from the brain
Authors: Sapkota Darshan , Florian Colin , Doherty Brookelyn M , White Kelli M , Reardon Kate M , Ge Xia , Garbow Joel R , Yuede Carla M , Cirrito John R , Dougherty Joseph D
Published: August 2022

Alzheimer’s disease is initiated by the toxic aggregation of amyloid-β. Immunotherapeutics aimed at reducing amyloid beta are in clinical trials but with very limited success to date. Identification of orthogonal approaches for clearing amyloid beta may complement these approaches for treating Alzheimer’s disease. In the brain, the astrocytic water channel Aquaporin 4 is involved in clearance of amyloid beta, and the fraction of Aquaporin 4 found perivascularly is decreased in Alzheimer’s disease. Further, an unusual stop codon readthrough event generates a conserved C-terminally elongated variant of Aquaporin 4 (AQP4X), which is exclusively perivascular. However, it is unclear whether the AQP4X variant specifically mediates amyloid beta clearance.

Here, using Aquaporin 4 readthrough-specific knockout mice that still express normal Aquaporin 4, we determine that this isoform indeed mediates amyloid beta clearance. Further, with high-throughput screening and counterscreening, we identify small molecule compounds that enhance readthrough of the Aquaporin 4 sequence and validate a subset on endogenous astrocyte Aquaporin 4. Finally, we demonstrate these compounds enhance brain amyloid-β clearance in vivo, which depends on AQP4X.

This suggests derivatives of these compounds may provide a viable pharmaceutical approach to enhance clearance of amyloid beta and potentially other aggregating proteins in neurodegenerative disease.
A demonstration of cone function plasticity after gene therapy in achromatopsia
Authors: Farahbakhsh Mahtab , Anderson Elaine J , Maimon-Mor Roni O , Rider Andy , Greenwood John A , Hirji Nashila , Zaman Serena , Jones Pete R , Schwarzkopf D Samuel , Rees Geraint , Michaelides Michel , Dekker Tessa M
Published: August 2022

Recent advances in regenerative therapy have placed the treatment of previously incurable eye diseases within arms’ reach. Achromatopsia is a severe monogenic heritable retinal disease that disrupts cone function from birth, leaving patients with complete colour blindness, low acuity, photosensitivity and nystagmus. While successful gene-replacement therapy in non-primate models of achromatopsia has raised widespread hopes for clinical treatment, it was yet to be determined if and how these therapies can induce new cone function in the human brain. Using a novel multimodal approach, we demonstrate for the first time that gene therapy can successfully activate dormant cone-mediated pathways in children with achromatopsia (CNGA3- and CNGB3-associated, 10–15 years). To test this, we combined functional MRI population receptive field mapping and psychophysics with stimuli that selectively measure cone photoreceptor signalling. We measured cortical and visual cone function before and after gene therapy in four paediatric patients, evaluating treatment-related change against benchmark data from untreated patients (n = 9) and normal-sighted participants (n = 28). After treatment, two of the four children displayed strong evidence for novel cone-mediated signals in visual cortex, with a retinotopic pattern that was not present in untreated achromatopsia and which is highly unlikely to emerge by chance. Importantly, this change was paired with a significant improvement in psychophysical measures of cone-mediated visual function. These improvements were specific to the treated eye, and provide strong evidence for successful read-out and use of new cone-mediated information. These data show for the first time that gene replacement therapy in achromatopsia within the plastic period of development can awaken dormant cone-signalling pathways after years of deprivation. This reveals unprecedented neural plasticity in the developing human nervous system and offers great promise for emerging regenerative therapies.
COVID-19 induces CNS cytokine expression and loss of hippocampal neurogenesis
Authors: Soung Allison L , Vanderheiden Abigail , Nordvig Anna S , Sissoko Cheick A , Canoll Peter , Mariani Madeline B , Jiang Xiaoping , Bricker Traci , Rosoklija Gorazd B , Arango Victoria , Underwood Mark , Mann J John , Dwork Andrew J , Goldman James E , Boon Adrianus C M , Boldrini Maura , Klein Robyn S
Published: August 2022

Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with acute and postacute cognitive and neuropsychiatric symptoms including impaired memory, concentration, attention, sleep and affect. Mechanisms underlying these brain symptoms remain understudied. Here we report that SARS-CoV-2-infected hamsters exhibit a lack of viral neuroinvasion despite aberrant blood–brain barrier permeability. Hamsters and patients deceased from coronavirus disease 2019 (COVID-19) also exhibit microglial activation and expression of interleukin (IL)-1β and IL-6, especially within the hippocampus and the medulla oblongata, when compared with non-COVID control hamsters and humans who died from other infections, cardiovascular disease, uraemia or trauma. In the hippocampal dentate gyrus of both COVID-19 hamsters and humans, we observed fewer neuroblasts and immature neurons. Protracted inflammation, blood–brain barrier disruption and microglia activation may result in altered neurotransmission, neurogenesis and neuronal damage, explaining neuropsychiatric presentations of COVID-19. The involvement of the hippocampus may explain learning, memory and executive dysfunctions in COVID-19 patients.