bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus
Authors: Planta Jose , Liang Yu-Ya , Xin Haoyang , Chansler Matthew T , Prather L Alan , Jiang Ning , Jiang Jiming , Childs Kevin L 
Published: August 2022

Abstract
The majority of sequenced genomes in the monocots are from species belonging to Poaceae, which include many commercially important crops. Here, we expand the number of sequenced genomes from the monocots to include the genomes of 4 related cyperids: Carex cristatella and Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from Juncaceae. The high-quality, chromosome-scale genome sequences from these 4 cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Some members of the Cyperaceae and Juncaceae are known to possess holocentric chromosomes. We examined the repeat landscapes in our sequenced genomes to search for potential repeats associated with centromeres. Several large satellite repeat families, comprising 3.2–9.5% of our sequenced genomes, showed dispersed distribution of large satellite repeat clusters across all Carex chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large Juncus satellite repeats were clustered in a single location on each chromosome, with sporadic instances of large satellite repeats throughout the Juncus genomes. Recognizable transposable elements account for about 20% of each of the 4 genome assemblies, with the Carex genomes containing more DNA transposons than retrotransposons while the converse is true for the Juncus genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots.
In search of a Drosophila core cellular network with single-cell transcriptome data
Authors: Yang Ming , Harrison Benjamin R , Promislow Daniel E L 
Published: August 2022

Abstract
Along with specialized functions, cells of multicellular organisms also perform essential functions common to most if not all cells. Whether diverse cells do this by using the same set of genes, interacting in a fixed coordinated fashion to execute essential functions, or a subset of genes specific to certain cells, remains a central question in biology. Here, we focus on gene coexpression to search for a core cellular network across a whole organism. Single-cell RNA-sequencing measures gene expression of individual cells, enabling researchers to discover gene expression patterns that contribute to the diversity of cell functions. Current efforts to study cellular functions focus primarily on identifying differentially expressed genes across cells. However, patterns of coexpression between genes are probably more indicative of biological processes than are the expression of individual genes. We constructed cell-type-specific gene coexpression networks using single-cell transcriptome datasets covering diverse cell types from the fruit fly, Drosophila melanogaster. We detected a set of highly coordinated genes preserved across cell types and present this as the best estimate of a core cellular network. This core is very small compared with cell-type-specific gene coexpression networks and shows dense connectivity. Gene members of this core tend to be ancient genes and are enriched for those encoding ribosomal proteins. Overall, we find evidence for a core cellular network in diverse cell types of the fruit fly. The topological, structural, functional, and evolutionary properties of this core indicate that it accounts for only a minority of essential functions.
Idiosyncratic Purifying Selection on Metabolic Enzymes in the Long-Term Evolution Experiment with Escherichia coli
Authors: Maddamsetti Rohan 
Published: August 2022

Abstract
Bacteria, Archaea, and Eukarya all share a common set of metabolic reactions. This implies that the function and topology of central metabolism has been evolving under purifying selection over deep time. Central metabolism may similarly evolve under purifying selection during long-term evolution experiments, although it is unclear how long such experiments would have to run (decades, centuries, millennia) before signs of purifying selection on metabolism appear. I hypothesized that central and superessential metabolic enzymes would show evidence of purifying selection in the long-term evolution experiment with Escherichia coli (LTEE). I also hypothesized that enzymes that specialize on single substrates would show stronger evidence of purifying selection in the LTEE than generalist enzymes that catalyze multiple reactions. I tested these hypotheses by analyzing metagenomic time series covering 62,750 generations of the LTEE. I find mixed support for these hypotheses, because the observed patterns of purifying selection are idiosyncratic and population-specific. To explain this finding, I propose the Jenga hypothesis, named after a children’s game in which blocks are removed from a tower until it falls. The Jenga hypothesis postulates that loss-of-function mutations degrade costly, redundant, and non-essential metabolic functions. Replicate populations can therefore follow idiosyncratic trajectories of lost redundancies, despite purifying selection on overall function. I tested the Jenga hypothesis by simulating the evolution of 1,000 minimal genomes under strong purifying selection. As predicted, the minimal genomes converge to different metabolic networks. Strikingly, the core genes common to all 1,000 minimal genomes show consistent signatures of purifying selection in the LTEE.
How Skin Tone Influences Relationships Between Discrimination, Psychological Distress, and Self-Rated Mental Health Among Older African Americans
Authors: Hamler Tyrone C , Nguyen Ann W , Keith Verna , Qin Weidi , Wang Fei 
Published: August 2022

Abstract

Objectives
As within-group differences have emerged as a key area of inquiry for health disparities among African Americans, skin tone has been identified as an important factor. This study aims to examine: (a) the moderating role of skin tone in the relationship between discrimination, self-rated mental health, and serious psychological distress (SPD) and (b) whether this moderating effect differs across genders in a nationally representative sample of older African Americans.

Methods
Analyses were conducted on a subsample of African Americans aged 55+ (N = 837) from the National Survey of American Life. The mental health outcomes were SPD and self-rated mental health. Discrimination was assessed with the Everyday Discrimination Scale. Skin tone was self-reported. Multiple linear regressions tested the study aims.

Results
Discrimination was associated with worse self-rated mental health and SPD in the total sample and among women. Skin tone moderated the association between discrimination and SPD in the total sample and among men and women. The associations between discrimination and mental health outcomes were stronger among darker-skinned respondents than lighter respondents. Gender-stratified analyses indicated skin tone moderated the association between discrimination and self-rated mental health for men but not women.

Discussion
This study contributes to the emerging body of literature on skin tone, discrimination, and mental health. Uncovering mechanisms behind the “why” is an important next step in understanding how skin tone influences the relationship between discrimination and mental health. The negative psychological effects associated with darker complexion provide several areas to be examined.
Approximate reflection and transmission coefficients at an interface between two contrasting viscoelastic anisotropic half-spaces
Authors: Wu Jianlu , Zhou Bing , Greenhalgh Stewart , Bouzidi Youcef , Zhang Zhiming 
Published: August 2022

SUMMARY
We present and compare two new methods to calculate the reflection and transmission coefficients of qP, qSV and qSH waves at a flat interface between two contrasting viscoelastic anisotropic half-spaces. The first method is a new version of the real ray tracing method that extends the traditional real ray tracing method to tackle the triplications of the qSV wave. This new version is valid for computing the reflection and transmission coefficients of the qP and qSV waves for all pre- and post-critical angles of incidence, which cannot be handled by the previous approach. The second method employs the real slowness direction and Snell's law to provide approximate reflection and transmission coefficients for such wave modes. This approximate method has attractive advantages which are not only the avoidance of the searching process inherent in the real ray tracing method but also offers competitive economical solutions to the first method. Many viscoelastic VTI models are utilized to validate the two methods. The numerical results show that (1) the ray angles, ray velocities, ray Q-factors, and the magnitudes of the reflection and transmission coefficients obtained by the two methods closely agree with each other, except in the vicinity of the critical angles and (2) the phase angles of the reflected and transmitted waves exhibit complexities due to the existence of some reverse phenomena between the approximate and the real ray tracing solutions. However, such phase discrepancies do not affect the magnitudes of the reflection and transmission coefficients. Moreover, the energy ratios of the different wave modes satisfy the energy conservation criterion at the interface.
Active tectonics and fault evolution in the Western Balkans
Authors: D’Agostino N , Copley A , Jackson J , Koçi R , Hajrullai A , Duni L , Kuka N 
Published: August 2022

SUMMARY
The western Balkans occupy a region influenced by two major active tectonic processes: the collision between the Adriatic Region and the Dinarides in the west, and the extension of the Aegean Region and its surroundings as they move towards the Hellenic Trench. An understanding of the kinematics and dynamics of the western Balkans has significance for our understanding of continental tectonics in general, and is the object of this paper. The region is rich in observational data, with many well-studied earthquakes, good geodetic coverage by GNSS (Global Navigation Satellite System) and abundant exposure of active faulting and its associated geomorphology, especially within the Mesozoic carbonates that cover large sectors of the extensional areas. We first use such observations to establish the regional kinematic patterns, by which we mean a clarification of how active faulting achieves the motions observed in the deforming velocity field obtained from GNSS measurements. We then use geomorphological observations on the evolution of drainage systems to establish how kinematic and faulting patterns have changed and migrated during the Late Neogene-Quaternary. The kinematics, and its evolution, can then be used to infer characteristics of the dynamics, by which we mean the origin and effect of the forces that control the overall deformation. The principal influences are: (i) the distribution and evolution of gravitational potential energy (GPE) contrasts arising from crustal thickness variations and elevation, in particular the growth of topography by shortening in the Albanides–Hellenides mountain ranges and the high elevation of mainland Greece relative to the Mediterranean seafloor and (ii) the ability of the boundaries of the region, along the Adriatic coast and in the Hellenic Trench, to support the forces arising from those GPE contrasts. The evolution in space and time indicates an interaction between the anisotropic strength fabric of the upper crust associated with faulting, and the more distributed and smoother patterns of flow that are likely to characterize the ductile deformation of the lower, aseismic part of the lithosphere—both of which influence the deformation on the scale of 100–200 km. The persistent argument about whether continental deformation is best described by a continuum or by rigid-block motions is largely a matter of scale and particular location: both are influential in establishing the patterns we see.
Magnetic resonance sounding signal extraction using the shaping-regularized Prony method
Authors: Lin Tingting , Li Yue , Lin Yusheng , Chen Jian , Wan Ling 
Published: August 2022

SUMMARY
Magnetic resonance sounding (MRS) can be used to implement groundwater detection non-invasively because of the direct relationship between the signal parameters and aquifer properties. Most current approaches to extracting MRS parameters need to use prior knowledge of the precise Larmor frequency to detect the signal envelope, and are vulnerable to the residual noise after de-noising. In this paper, we use a shaping-regularized Prony method to extract MRS signals from high-frequency oscillating data instead of from envelopes of data. Only an approximate Larmor frequency is required in advance. Besides, irrelevant noise components can be dropped during the extraction process. We investigate the selection of an appropriate decomposition quantity for the SRP method and present an intuitive regularization method to control the shape of the estimated coefficients. Impact of different types and magnitudes of noise on the proposed method are analysed. The extraction results obtained from numerical simulations and field surveys reveal that the SRP method yields accurate and reliable parameters estimation and preserves complete signal information. The tolerance to the interference in signal extraction of the proposed method is obviously better than that of the SD method.
Spectral induced polarization monitoring of induced calcite precipitation in subsurface sediments
Authors: Placencia-Gόmez Edmundo , Robinson Judith , Slater Lee , Qafoku Nikolla P 
Published: August 2022

SUMMARY
Co-precipitation of contaminants within the crystalline structure of calcite is a promising natural attenuation or remedial technology being considered at contaminated sites. We explore the sensitivity of the spectral induced polarization (SIP) method to induced calcite precipitation in natural sediments as a path forward to non-invasively monitor these sites. We performed time-lapse column experiments using phased (I–IV) injections over 40 d on natural sediments from the Hanford Site (WA, USA). In the phased injections, abiotic calcite precipitation was induced and confirmed to have occurred. Previous work on glass beads and homogeneous sand was limited to high frequency detection of calcite, however in this work we observed the development of two polarization mechanisms, one at high frequency (&gt;100 Hz) and one at low frequency (&lt;100 Hz). Based on the characteristic frequencies from the SIP high and low frequency regimes, characteristic length scales (L) were computed where the adsorption mode of Na+ versus Ca2+ was compared by using diffusion coefficients corresponding to Na+ versus an arithmetically averaged value for Na+ and Ca2+. Using the diffusion coefficient of Na+, the high frequency L was found to correlate well with the size of the calcite crystals. The low frequency L correlated well with the individual natural sediment grain sizes within the columns. During late experimental times (day 36 and 40), the characteristic low frequency in two of the experimental columns shifted to lower frequencies (&lt;0.001 Hz) which may signify SIP sensitivity of the formed calcite with the sediment grains. In field applications, the development of a low frequency polarization length scale to monitor calcite precipitation is promising for field monitoring applications, however further laboratory work needs to be performed to examine the SIP sensitivity of calcite formation in the presence of natural sediments.
Fatal Intoxications from a Combination of 4-Fluoroamphetamine and 25C-NBOMe
Authors: Gerostamoulos Dimitri , Glowacki Linda , Pricone Maria , Crump Kerryn , Di Rago Matthew , Joubert Samantha , Lynch Matthew J , Woodford Noel W , Drummer Olaf H 
Published: August 2022

AbstractSix fatalities have occurred from the ingestion of a combination of new psychoactive substances (NPSs), 4-fluoroamphetamine (4FA) and 2-(4-chloro-2,5-dimethoxyphenyl)-N-[(2-methoxyphenyl)methyl]ethanamine (25C-NBOMe) over a 9-month period. Four of these fatalities (one older female and three young males) were from direct adverse effects of drugs, and one each from a fall while being intoxicated and during restraint. All cases were subject to full postmortem examinations that included collection of femoral blood. The four drug-caused fatalities had postmortem blood concentrations for 4FA and 25C-NBOMe of 330–682 ng/L (median 417) and 1.4–12 ng/mL (median 4.3), respectively. The other two cases (both young males) where death was considered to have been caused indirectly by drug intoxication had 4FA and 25C-NBOMe postmortem concentrations of 21 and 123 ng/mL, and 1.8 and 4.5 ng/mL, respectively. None of these cases showed concentrations of drugs that suggested use of high recreational doses. In one drug-caused death, capsules and a brown powder obtained from the scene were found to contain a mixture of these two NPSs. With the exception of one drug-caused death, other drugs were detected; however, the effects of the two NPSs together were regarded as the primary triggers for the deaths. There were no consistent symptoms or pathology in these cases; however, agitation/aggression was observed in two cases prior to their collapse, with seizures in possibly three cases. Pulmonary and/or cerebral edema was noted in three cases. Potentially significant natural disease (a mildly enlarged heart) was only observed in one drug-caused case. These cases illustrate a possible increased risk of sudden death with this combination of drugs, both of which can elevate serotonin concentrations as well as act as strong stimulants. These cases also illustrate the difficulty in detecting NPS in cases where no prior information is available that might suggest their use.
A New Chapter in China’s Stance on Labour Protection? An Assessment of the China–EU CAI
Authors: Yan Yueming 
Published: August 2022

ABSTRACT
China overhauled its pre-existing image of being insufficiently friendly to sustainable development in international investment agreements (IIAs) with its sweeping, specific, and strong commitments to labour rights protection in the Comprehensive Agreement on Investment (CAI) recently concluded with the European Union. This article provides an assessment of these labour provisions and examines their impact on China’s national, regional, and global stances on labour protection. Firstly, it analyses the features and purposes of different types of labour provision and the integrated mechanism for settling disputes on labour issues. This article then identifies the gap between China’s commitments under the CAI and its actual practices and presents a wish list for China to enhance labour protection, including efforts to ratify fundamental International Labour Organization conventions, improve domestic legislation on core labour principles, and enhance corporate social responsibility among Chinese investors. Further, this article assesses the macro-level impacts of these labour provisions. It argues that the CAI presents an opportunity to strengthen sustainable development and labour rights protection within China, along the Belt and Road Initiative, and globally. China is advised to continue incorporating modernized labour standards into its future IIAs.
Quantitative Trait Locus Determining the Time of Blood Feeding in Culex pipiens (Diptera: Culicidae)
Authors: Hickner Paul V , Mori Akio , Rund Samuel S C , Severson David W 
Published: August 2022

Abstract
Mosquitoes and other blood feeding arthropods are vectors of pathogens causing serious human diseases, such as Plasmodium spp. (malaria), Wuchereria bancrofti (lymphatic filariasis), Borrelia burgdorferi (Lyme disease), and viruses causing dengue, Zika, West Nile, chikungunya, and yellow fever. Among the most effective strategies for the prevention of vector-borne diseases are those aimed at reducing human–vector interactions, such as insecticide applications and insecticide-treated bed nets (ITNs). In some areas where ITNs are widely used, behavioral adaptations have resulted in mosquitoes shifting their time of blood feeding to earlier or later in the night when the bed nets are not being employed. Little is known about the genetic basis of these behavioral shifts. We conducted quantitative trait locus (QTL) analysis using two strains of Culex pipiens sensu lato with contrasting blood feeding behaviors, wherein the lab adapted Shasta strain blood feeds at any time of the day or night, while the newly established Trinidad strain feeds only at night. We identified a single locus on chromosome 2 associated with the observed variation in feeding times. None of the core clock genes period, timeless, clock, cycle, PAR-domain protein 1, vrille, discs overgrown, cryptochrome 1, or cryptochrome 2 were located within the QTL region. We then monitored locomotor behavior to determine if they differed in their flight activity. The highly nocturnal Trinidad strain showed little daytime activity while the day-feeding Shasta strain was active during the day, suggesting blood feeding behavior and flight activity are physiologically linked.
Pourbiax Diagrams as an Aid to Understanding the Impact of Acid/Base Disturbance on Blood Glucose Point-of-Care Testing
Authors: McPherson Peter A C , McClements Owen S , Johnston Ben M 
Published: August 2022

Abstract

Objective
Assays based on redox reactions that involve proton transfer are vulnerable to artifactual findings in metabolic acidosis/alkalosis. We evaluated the impact of pH on the measurement of blood glucose by the glucose dehydrogenase/pyrroloquinoline quinone system used in point-of-care-testing.

Methods
We applied a series of thermodynamic equations to adjust the Gibbs energy for the pyrroloquinoline quinone couple. This adjusts values taken under standard conditions to those more closely resembling the physiological state.

Results
Under standard conditions, the pyrroloquinoline quinone couple has Eo = −0.125 V whereas adjustment to the physiological state (pH 7.40, ionic strength 0.15 mol/L, and temperature 310.15°K) yields Eo′ = −0.166 V. This corresponds to an uncertainty in blood glucose determination of approximately 0.13 mmol/L.

Conclusion
We have demonstrated that the impact of pH on blood glucose determination by the glucose dehydrogenase/pyrroloquinoline quinone system (under physiologically relevant conditions of ionic strength and temperature) is not clinically significant.