bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of multi-step annealing with different heating rates on magnetic properties of Fe-Si-B-P-Cu nano-crystalline alloy
Authors: Hao Ziyan , Wei Linzhuo , Cai Yuanfei , Wang Yaocen , Xiang Mingliang , Zhao Fang , Zhang Yan , Perov Nikolai S , Cao Chongde
Published: December 2022

The crystallization behaviors of Fe83Si4B8P4.3Cu0.7 amorphous alloy with different heating rates and magnetic softness of annealed alloys have been widely studied. The rapid heating significantly helped with the decrease of coercivity for annealed samples compared with that for slow heating. It is found that the peak temperature (T
p1) of the first crystallization stage in DSC curves is a critical temperature parameter to distinguish the nucleation and growth processes of α-Fe phase. When the temperature at a constant heating rate is beyond the T
p1, the nucleation process should be almost finished. The necessary temperature range of high heating rate (400 K min−1) for the improvement of magnetic softness has been determined from 650 K to 740 K through multi-step annealing with different heating rates. The shortened temperature window of rapid heating and partial rapid heating may simplify and improve the annealing process of high-performance soft magnetic materials in industry. The multi-step annealing with various heating rates also provides a promising strategy for the investigation of crystallization behaviors of amorphous alloys.
Assessing sustainability hotspots in the production of paper-based printed electronics
Authors: Sudheshwar Akshat , Beni Valerio , Malinverno Nadia , Hischier Roland , Nevo Yuval , Dhuiège Benjamin , Borras Mateu , Chbani Aiman , Aucher Christophe , Martinez-Crespiera Sandra , Eibensteiner Friedrich , Kurzhals Steffen , Giebelhauser Lisa , Melnik Eva , Mutinati Giorgio C , Fall Andreas , Aulin Christian , Abitbol Tiffany , Som Claudia
Published: December 2022

Novel printed electronics are projected to grow and be manufactured in the future in large volumes. In many applications, printed electronics are envisaged as sustainable alternatives to conventional (PCB-based) electronics. One such application is in the semi-quantitative drug detection and point-of-care device called ‘GREENSENSE’ that uses paper-based printed electronics. This paper analyses the carbon footprint of GREENSENSE in order to identify and suggest means of mitigating disproportionately high environmental impacts, labeled ‘sustainability hotspots’, from materials and processes used during production which would be relevant in high-volume applications. Firstly, a life cycle model traces the flow of raw materials (such as paper, CNCs, and nanosilver) through the three ‘umbrella’ processes (circuit printing, component mounting, and biofunctionalization) manufacturing different electronic components (the substrate, conductive inks, energy sources, display, etc) that are further assembled into GREENSENSE. Based on the life cycle model, life cycle inventories are modeled that map out the network of material and energy flow throughout the production of GREENSENSE. Finally, from the environmental impact and sustainability hotspot analysis, both crystalline nanocellulose and nanosilver were found to create material hotspots and they should be replaced in favor of lower-impact materials. Process hotspots are created by manual, lab-, and pilot-scale processes with unoptimized material consumption, energy use, and waste generation; automated and industrial-scale manufacturing can mitigate such process hotspots.
Compact, Watt-class 785 nm dual-wavelength master oscillator power amplifiers
Authors: Müller André , Maiwald Martin , Sumpf Bernd
Published: December 2022

785 nm micro-integrated, dual-wavelength master oscillator power amplifiers with a footprint of 5 mm × 25 mm are presented. They are based on Y-branch distributed Bragg reflector ridge waveguide diode lasers and anti-reflection coated tapered amplifiers. In order to reduce the impact of potential optical feedback, devices with master oscillator front facet reflectivities of 5% and 30% as well as with an integrated miniaturized optical isolator have been realized. A comparison up to 1 W shows narrowband dual wavelength laser emission with a spectral distance of 0.6 nm (10 cm−1) and individual spectral widths <20 pm. As expected, a higher front facet reflectivity leads to a significant reduction of feedback related mode hops. Longitudinal modes corresponding to the master oscillator resonator length remain within spectral windows <0.15 nm (3 cm−1), suitable for applications such as Raman spectroscopy and especially shifted excitation Raman difference spectroscopy. Integrating a compact 30 dB optical isolator completely eliminates the observed optical feedback effects. Lateral beam propagation ratios of 1.2 (1/e2) enable easy beam shaping and fiber coupling. Outside of the experimental comparison, the developed MOPAs provide up to 2.7 W of optical output power available for applications.
On the influence of VOCs on new particle growth in a Continental-Mediterranean region
Authors: Gómez-Moreno Francisco Javier , Alonso-Blanco Elisabeth , Díaz Elías , Coz Esther , Molero Francisco , Núñez Lourdes , Palacios Magdalena , Barreiro Marcos , Fernández Javier , Salvador Pedro , Piñeiro-Iglesias María , López-Mahía Purificación , Borrás Esther , Vera Teresa , Muñoz Amalia , Tritscher Torsten , Schmitt Sebastian , Artíñano Begoña
Published: December 2022

A field campaign has been performed in the Madrid region to study the VOC influence in the growth of new particles in ambient air. A number of instruments have been deployed to characterize the main pollutant gases and particle properties and composition. The measurements were performed simultaneously at three sites (rural, urban background and urban traffic influenced) in the period 1–17 July 2019. The sites: Tres Cantos (rural), CIEMAT (urban background) and Leganés (urban traffic) were located within the Madrid airshed. Particle size distributions, mass concentrations at fractions PM10, PM2.5 and PM1, black carbon, VOCs species and gaseous pollutants (NOx and O3) were obtained in the sites. Some supplementary measurements were obtained in at least one of the sites: meteorological parameters, non-refractory submicron aerosol species and vertical profiles of aerosol optical properties. It has been observed that the new particle formation (NPF) events, nucleation and subsequent growth, happened at a regional scale, although differently among the sites. In the rural site, fewer events than expected were observed because of the high temperatures that affected the BVOC emissions. In the urban background site, the highest number of events was reached. In this station, it is common to receive air masses from the nearby forest and from the urban area, producing a mix of conditions with high BVOC and AVOC concentrations. In the urban traffic site, several NPF cases appeared, being a site dominated by AVOCs. Among the BVOCs measured in the three stations, the most common were α-Pinene and Limonene. Among the AVOCs measured, aromatics and linear hydrocarbon compounds for C10 and above were found. The linear group was found to be predominant during the NPF event days in the urban background site. This work provides new insights about the aerosol-forming precursors and growth of new particles in the Madrid region.
No association between age beginning tackle football, or years played and neurocognitive performance later-in-life among older National Football League retirees
Authors: Schaffert Jeff , Didehbani Nyaz , LoBue Christian , Hart John , Wilmoth Kristin , Cullum C Munro
Published: December 2022

Objective

In a retrospective cohort, we evaluated whether age beginning tackle football (ABTF) and more total years of playing football (TYPF) were associated with worse later-in-life neuropsychological change among older retired National Football League (NFL) players.

Method

Participants were 19 older NFL retirees aged 54–79, including 12 who returned for follow-up evaluation 15–51 months later. Mixed-linear models evaluated the association between ABTF/TYFP and baseline neuropsychological composite scores (executive functioning/attention/speed, language, memory), and neuropsychological composites over time.

Results

ABTF and TYPF were not significantly associated with neuropsychological composites at baseline or over time (all p’s > .05). There were no significant differences in neuropsychological performance between those ABTF <12 and ≥ 12 years old (all p’s ≥ .475) or between those with TYPF <19 or ≥ 19 years played (median split; all p’s ≥ .208).

Conclusions

Preliminary findings suggest that ABTF and TYPF does not worsen neurocognitive decline later-in-life among older NFL retirees.
Concordance Between Logical Memory and Craft Story 21 in Community-Dwelling Older Adults: The Role of Demographic Factors And Cognitive Status
Authors: Nester Caroline O , Qin Jiyue , Wang Cuiling , Katz Mindy J , Lipton Richard B , Rabin Laura A
Published: December 2022

Objective

Episodic memory loss, a hallmark symptom of Alzheimer’s Disease, is frequently quantified by story memory performance. The National Alzheimer’s Coordinating Center Uniform Data Set Neuropsychological Battery (UDSNB) replaced Logical Memory with Craft Story 21 in UDSNB Version 3. The concordance between these story memory tasks is poorly characterized in demographically diverse older adults, possibly jeopardizing the integrity of longitudinal data in aging cohorts.

Method

Einstein Aging Study participants (n = 298; Mage = 76.6; Meducation = 15; 66.4% women; 43.3% Non-Hispanic White) completed UDSNB measures, including Craft Story and Logical Memory. Classification as normal cognition (n = 206) or mild cognitive impairment (n = 90) was based on Jak/Bondi criteria. Analyses included correlations, linear regression, and equipercentile equating methods to characterize the relationship between Logical Memory and Craft Story. Multivariate linear mixed effects models explored the association of covariates and practice effects over follow-up, stratified by cognitive status and race/ethnicity.

Results

Immediate (r = 0.54) and delayed (r = 0.56) versions of Logical Memory and Craft Story were moderately correlated. Age, education, depression, and female sex were associated with Logical Memory, while age, education, cognitive status, and male sex were associated with Craft Story. Significant differential effects of sex on story memory were observed.

Conclusions

We demonstrated that Logical Memory and Craft Story may be used largely interchangeably; however, memory may be enhanced for stories with a protagonist of the same sex as the participant. Craft Story was somewhat more associated with mild cognitive impairment in the overall sample, but especially in non-Hispanic Black participants. We discuss how results inform test selection considerations.
Simulation of mass spectrometry-based proteomics data with Synthedia
Authors: Leeming Michael G , Ang Ching-Seng , Nie Shuai , Varshney Swati , Williamson Nicholas A
Published: December 2022

Motivation

A large number of experimental and bioinformatic parameters must be set to identify and quantify peptides in mass spectrometry experiments and each of these will impact the results. An ability to simulate raw data with known contents would allow researchers to rapidly explore the effects of varying experimental parameters and systematically investigate downstream processing software. A range of data simulators are available for established data-dependent acquisition methodologies, but these do not extend to the rapidly developing field of data-independent acquisition (DIA) strategies.

Results

Here, we present Synthedia—a software package to simulate DIA liquid chromatography-mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for the customization of a wide variety of chromatographic and mass spectrometry parameters.

Availability and implementation

Synthedia is freely available via the internet and can be used through a graphical website (https://synthedia.org/) or locally via the command line (https://github.com/mgleeming/synthedia/).

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Integrative chromatin domain annotation through graph embedding of Hi-C data
Authors: Shokraneh Neda , Arab Mariam , Libbrecht Maxwell
Published: December 2022

Motivation

The organization of the genome into domains plays a central role in gene expression and other cellular activities. Researchers identify genomic domains mainly through two views: 1D functional assays such as ChIP-seq, and chromatin conformation assays such as Hi-C. Fully understanding domains requires integrative modeling that combines these two views. However, the predominant form of integrative modeling uses segmentation and genome annotation (SAGA) along with the rigid assumption that loci in contact are more likely to share the same domain type, which is not necessarily true for epigenomic domain types and genome-wide chromatin interactions.

Results

Here, we present an integrative approach that annotates domains using both 1D functional genomic signals and Hi-C measurements of genome-wide 3D interactions without the use of a pairwise prior. We do so by using a graph embedding to learn structural features corresponding to each genomic region, then inputting learned structural features along with functional genomic signals to a SAGA algorithm. We show that our domain types recapitulate well-known subcompartments with an additional granularity that distinguishes a combination of the spatial and functional states of the genomic regions. In particular, we identified a division of the previously identified A2 subcompartment such that the divided domain types have significantly varying expression levels.

Availability and implementation

https://github.com/nedashokraneh/IChDA.

Supplementary information

Supplementary data are available at Bioinformatics online.
A transformation perspective on marginal and conditional models
Authors: Barbanti Luisa , Hothorn Torsten
Published: December 2022

Clustered observations are ubiquitous in controlled and observational studies and arise naturally in multicenter trials or longitudinal surveys. We present a novel model for the analysis of clustered observations where the marginal distributions are described by a linear transformation model and the correlations by a joint multivariate normal distribution. The joint model provides an analytic formula for the marginal distribution. Owing to the richness of transformation models, the techniques are applicable to any type of response variable, including bounded, skewed, binary, ordinal, or survival responses. We demonstrate how the common normal assumption for reaction times can be relaxed in the sleep deprivation benchmark data set and report marginal odds ratios for the notoriously difficult toe nail data. We furthermore discuss the analysis of two clinical trials aiming at the estimation of marginal treatment effects. In the first trial, pain was repeatedly assessed on a bounded visual analog scale and marginal proportional-odds models are presented. The second trial reported disease-free survival in rectal cancer patients, where the marginal hazard ratio from Weibull and Cox models is of special interest. An empirical evaluation compares the performance of the novel approach to general estimation equations for binary responses and to conditional mixed-effects models for continuous responses. An implementation is available in the tram add-on package to the R system and was benchmarked against established models in the literature.
The impact of integrated brain molecular PET measures on DLB cognitive phenotype and clinical course
Authors: Perani Daniela
Published: December 2022

This scientific commentary refers to ‘Interrelation of striatal dopamine, brain metabolism and cognition in dementia with Lewy bodies’ by Yoo et al. (https://doi.org/10.1093/brain/awac084).
Design and implementation of a new portable hybrid solar atmospheric water-generation system
Authors: Shafeian Nafise , Ranjbar A A , Gorji Tahereh B
Published: December 2022

During recent years, atmospheric water generation (AWG) has garnered significant attention among researchers as a viable solution to the water-scarcity problem. Generally, AWG requires dehumidification, which includes two main principles of refrigeration and sorption. Among refrigeration methods, thermoelectric coolers are suitable and, among sorption methods, it is best to utilize desiccant materials with high sorption capacity and low heat generation. In the present study, a portable hybrid/integrated solar AWG system was designed and tested under realistic conditions of Babol, Iran (36.5387°N, 52.6765°E) over four typical summer days between 14 and 31 August 2021. Two models (Models A and B) were designed and evaluated. Temperature, relative humidity, solar irradiance and water-production data were recorded to assess the system performance (i.e. the ratio between the generated water and consumed power in ml/W.hour) and economically analyse the system. Based on the results acquired, the maximum water production in the proposed configuration (acquired from Model B) was 2.12 l/m2.day at an average relative humidity and a temperature of 52% and 36°C, respectively. The desired AWG system had a system performance of 0.19 ml/W.hour, annual water production of 774.4 l/m2, production cost of 0.0246 $/l/m2 and a payback period of 1.19 years.
High-definition trans cranial direct current stimulation and its effects on cognitive function: a systematic review
Authors: Tedla Jaya Shanker , Sangadala Devika Rani , Reddy Ravi Shankar , Gular Kumar , Dixit Snehil
Published: December 2022

High-Definition Transcranial Direct Current Stimulation (HD-tDCS) is focal and improves higher mental functions. Due to the lack of published evidence, we conducted this review on the effect of HD-tDCS on cognitive functions in healthy and diseased individuals. We performed an electronic-data and gray-literature search to obtain the relevant studies for the review. The two distinct literature searches obtained a total of 468 studies. Out of these, a total of 12 studies were conducted on higher mental functions, and of these, two were on disordered consciousness, five were on memory, two were on speech, two were on cognition, and one was on execution. We submitted nine studies with control group to methodological quality assessment using the PEDro Scale. Remaining three studies underwent quality assessment by Quality Assessment Tool for Before-After (Pre-Post) Studies with No Control Group. We found that anodal HD-tDCS stimulation is significantly effective in treating disordered consciousness and improving memory, speech, cognition, and execution.
Reporting of Antimicrobial Resistance from Blood Cultures, an Antibacterial Resistance Leadership Group Survey Summary: Resistance Marker Reporting Practices from Positive Blood Cultures
Authors: Simner Patricia J , Dien Bard Jennifer , Doern Christopher , Kristie Johnson J , Westblade Lars , Yenokyan Gayane , Patel Robin , Hanson Kimberly E ,   for the Antibacterial Resistance Leadership Group
Published: December 2022

Background

We assessed how laboratories use and handle reporting of results of rapid diagnostics performed on positive blood culture broths, with a focus on antimicrobial resistance (AMR) markers.

Methods

A survey assembled by the Antibacterial Resistance Leadership Group Diagnostics Committee was circulated from December 2020 to May 2021. The survey was sent to local hospitals, shared on the ClinMicroNet and Division C listservs, and included in a College of American Pathologists proficiency testing survey.

Results

Ninety-six laboratories of various sizes across the United States (95%) and outside of the United States (5%) participated. Of the laboratories that had at least 1 rapid diagnostic in place (94%), significant heterogeneity in methods used and reporting practices was found across community (52%) and academic (40%) laboratories serving hospitals of various sizes. Respondents had implemented 1 to 6 different panels/platforms for a total of 31 permutations. Methods of reporting rapid organism identification and AMR results varied from listing all targets as “detected”/“not detected” (16–22%) without interpretive guidance, to interpreting results (23–42%), or providing therapeutic guidance comments to patient-facing healthcare teams (3–17%).

Conclusions

Current approaches to reporting molecular AMR test results from positive blood culture vary significantly across clinical laboratories. Providing interpretative comments with therapeutic guidance alongside results reported may assist clinicians who are not well-versed in genetic mechanisms of AMR. However, this is currently not being done in all clinical laboratories. Standardized strategies for AMR gene result reporting are needed.
Moderate-intensity statin with ezetimibe vs. high-intensity statin in patients with diabetes and atherosclerotic cardiovascular disease in the RACING trial
Authors: Lee Yong-Joon , Cho Jae Young , You Seng Chan , Lee Yong-Ho , Yun Kyeong Ho , Cho Yun-Hyeong , Shin Won-Yong , Im Sang Wook , Kang Woong Chol , Park Yongwhi , Lee Sung Yoon , Lee Seung-Jun , Hong Sung-Jin , Ahn Chul-Min , Kim Byeong-Keuk , Ko Young-Guk , Choi Donghoon , Hong Myeong-Ki , Jang Yangsoo , Kim Jung-Sun
Published: December 2022

Aims

This study evaluated the effect of moderate-intensity statin with ezetimibe combination therapy vs. high-intensity statin monotherapy among patients with diabetes mellitus (DM) and atherosclerotic cardiovascular disease (ASCVD).

Methods and results

This was a pre-specified, stratified subgroup analysis of the DM cohort in the RACING trial. The primary outcome was a 3-year composite of cardiovascular death, major cardiovascular events, or non-fatal stroke. Among total patients, 1398 (37.0%) had DM at baseline. The incidence of the primary outcome was 10.0% and 11.3% among patients with DM randomized to ezetimibe combination therapy vs. high-intensity statin monotherapy (hazard ratio: 0.89; 95% confidence interval: 0.64–1.22; P = 0.460). Intolerance-related discontinuation or dose reduction of the study drug was observed in 5.2% and 8.7% of patients in each group, respectively (P = 0.014). LDL cholesterol levels <70 mg/dL at 1, 2, and 3 years were observed in 81.0%, 83.1%, and 79.9% of patients in the ezetimibe combination therapy group, and 64.1%, 70.2%, and 66.8% of patients in the high-intensity statin monotherapy group (all P < 0.001). In the total population, no significant interactions were found between DM status and therapy regarding primary outcome, intolerance-related discontinuation or dose reduction, and the proportion of patients with LDL cholesterol levels <70 mg/dL.

Conclusion

Ezetimibe combination therapy effects observed in the RACING trial population are preserved among patients with DM. This study supports moderate-intensity statin with ezetimibe combination therapy as a suitable alternative to high-intensity statins if the latter cannot be tolerated, or further reduction in LDL cholesterol is required among patients with DM and ASCVD.

Clinical Trial Registration

ClinicalTrials.gov, Identifier:NCT03044665.
Heimat and Nation: Jewish Historians and the Construction of Regional Identities in Posen and Alsace-Lorraine during the German Empire
Authors: Seiter Mathias
Published: December 2022

The late nineteenth and early twentieth centuries saw a wave of interest in history among Jews in Germany. The popularity of the subject extended to those who lived at the geographic margins of the German Empire, in the Prussian Province of Posen and the Reichsland of Alsace-Lorraine. Living in borderlands in which national identities were contested, Jewish historians established and joined regional historical societies that looked to the local and regional past to construct identities. While Jewish historians in the German east worked alongside non-Jewish colleagues to create a German Heimat against the backdrop of ethnic strife between Germans and Poles, their co-religionists in Alsace-Lorraine tried to maintain a regional identity which preserved the cultural and historical uniqueness of the Franco-German borderland. These different visions of regional history and identity surfaced again in the responses to the establishment of a central German-Jewish archive in Berlin. Jews from Posen were instrumental in integrating the local Jewish past into a national German-Jewish narrative. However, in the Franco-German borderland, Jews were opposed to the idea of a national archive, which they saw as a challenge to their Alsace-Lorrainian Jewish identity. This article argues that Jewish historians engaged with and were part of the wider German discourses on Heimat, regionalism and localness. Although Jewish historians in Posen and Alsace-Lorraine differed in their understanding of these concepts, they used them as markers of identity which allowed Jews to define their position towards notions of Germanness and the idea of a German-Jewish community.
Live yeast supplementation altered the bacterial community’s composition and function in rumen and hindgut and alleviated the detrimental effects of heat stress on dairy cows
Authors: Li Zihao , Fan Yang , Bai Hao , Zhang Jiyou , Mao Shengyong , Jin Wei
Published: December 2022

The objective of this study was to investigate the effects of live yeast (LY, Saccharomyces cerevisiae) on the lactation performance, bacterial community, and functions in the rumen and hindgut of dairy cows under heat stress. Thirty-three multiparous (parity 3.9 ± 0.8) Holstein dairy cows (189.1 ± 6.6 d in milk at the beginning of the experiment) were randomly assigned to three groups (11 cows per treatment). Cows in the three groups were fed a diet without yeast (CON), with 10 g yeast/d/head (LY-10), and with 20 g yeast/d/head (LY-20). The yeast product contained 2.0 × 1010 CFU/g. Supplementing LY decreased the rectal temperature and respiratory rate of cows, and increased dry matter intake, milk yield, milk fat yield, milk protein yield, and milk lactose yield (P < 0.001), yet decreased milk urea nitrogen concentration (P = 0.035). Interaction effects of treatment × week were observed for rectal temperature (P < 0.05), respiratory rate (P < 0.05), milk yield (P = 0.015), milk urea nitrogen (P = 0.001), milk protein yield (P = 0.008), and milk lactose yield (P = 0.030). In rumen, LY increased the concentrations of acetate, isobutyrate, isovaterate, valerate, total volatile fatty acids (VFAs), and NH3-N (P < 0.05). Miseq sequencing of the 16S rRNA genes showed that LY increased the relative abundance of Prevotella and Prevotellaceae UCG-003 at the genus level with a series of enriched pathways in the metabolism of carbohydrates and protein. In fecal samples, LY did not affect the profile of VFAs (P > 0.05). Clostridium sensu stricto 1 (P = 0.013) and Actinobacillus (P = 0.011) increased in the relative abundance by LY, whereas Bacteroides (P = 0.016) and Oscillospirales UCG-010 (P = 0.005) decreased with a series of enriched pathways in carbohydrate metabolism, secondary bile acid biosynthesis. In summary, LY supplementation altered the bacterial community’s composition and function in rumen and hindgut, and simultaneously alleviated the detrimental effects of heat stress on dairy cows. These findings provide extended insight into the effects of LY in the rumen and hindgut of dairy cows exposed to heat stress.
Who Supports the Huawei 5G Ban? Advancing a Two-Level Ideational Approach in International Relations
Authors: Lee Yoon Jin
Published: December 2022

The US allies’ decisions to ban or allow Huawei from building fifth-generation (5G) mobile broadband are significant to various actors, but their decisions have not been examined systematically. While related literatures point to relative bargaining power or domestic political constraints, I argue that strengths of pre-existing ideas, across national leader and national security institutional levels of analysis, help explain US allies’ positions. Specifically, I argue that the following three understandings are key: (1) China has aggressive intentions, (2) information and communications technology (ICT) system requires security, and (3) data privacy needs state protection. I argue that when the three key understandings are strong across national leader and national security institutional levels, the leader would likely adopt the Huawei 5G ban. On the other hand, when the three key understandings are weak across two levels, the leader would likely allow Huawei to partake in building 5G networks without tougher controls. I conduct a plausibility probe-based comparison of the decision cases of Australia and South Korea and find support for my hypotheses. The cross-national evidence calls for more attention to specific understandings—particular to action contexts—across at least two levels of analysis in explaining decisions of interest.
How Alive Is the Anti-Death Penalty Norm? Evidence from the British and French Treatment of ISIS Foreign Fighters
Authors: Efrat Asif , Richemond-Barak Daphné
Published: December 2022

This article enhances our understanding of international norms by developing a set of indicators to measure norm robustness at the domestic level. We apply these indicators to assess the robustness of the prohibition on the death penalty: a well-established international norm that terrorism-related cases have put to the test. In the United Kingdom, the government agreed to share information with the United States, possibly leading to the imposition of the death penalty on two ISIS foreign fighters of UK origin. France facilitated the trials of French ISIS fighters in Iraq, where they were sentenced to death. While the UK government, under public and judicial pressure, reversed its decision to cooperate with US authorities, the French government failed to acknowledge its violation of the death-penalty ban. We conclude that the anti-death penalty norm is more robust in the United Kingdom than in France. This case demonstrates how established democracies might break international human rights norms, and it reveals the nuances of the norm-decaying process.
Deep contextual disambiguation of homonyms and polysemants
Authors: Vakulenko Maksym O
Published: December 2022

A new metric method for word sense disambiguation is put forward, being formulated within a phenomenological analogy to the wave function of an observable quantity in quantum mechanics where the actual meaning of a multivalued word (a homonym or a polysemant) is determined by its context. The choice of the actualized sense is determined by the minimal semantic distance between the semantics of possible word senses and that of the context, where the meanings of the word in question and the context follow from their semantic fields based on lexicographic hyperchains. In contrast to the common models, our method accounts for semantic polarity. The formulated method showed good results in disentangling polysemy, which was not possible to achieve within the contextualized embedding approacdh based on bidirectional encoder representations from transformers (BERT).
Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor
Authors: Fukuchi Satoshi , Noguchi Tamotsu , Anbo Hiroto , Homma Keiichi
Published: December 2022

Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer the internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the “small bang” model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them were subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat–mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analyzed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs.
Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis
Authors: Behle Anna , Dietsch Maximilian , Goldschmidt Louis , Murugathas Wandana , Berwanger Lutz C , Burmester Jonas , Yao Lun , Brandt David , Busche Tobias , Kalinowski Jörn , Hudson Elton P , Ebenhöh Oliver , Axmann Ilka M , Machné Rainer
Published: December 2022

In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5’/3’ gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.
RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation
Authors: Tsegay Pawlos S , Hernandez Daniela , Qu Fei , Olatunji Mustapha , Mamun Yasir , Chapagain Prem , Liu Yuan
Published: December 2022

DNA repair is mediated by DNA synthesis guided by a DNA template. Recent studies have shown that DNA repair can also be accomplished by RNA-guided DNA synthesis. However, it remains unknown how RNA can guide DNA synthesis to repair DNA damage. In this study, we revealed the molecular mechanisms underlying RNA-guided DNA synthesis and base damage repair mediated by human repair DNA polymerases. We showed that pol β, pol κ, and pol ι predominantly synthesized one nucleotide, and pol η, pol ν, and pol θ synthesized multi-nucleotides during RNA-guided DNA base damage repair. The steady-state kinetics showed that pol η exhibited more efficient RNA-guided DNA synthesis than pol β. Using molecular dynamics simulation, we further revealed dynamic conformational changes of pol β and pol η and their structural basis to accommodate the RNA template and misoriented triphosphates of an incoming nucleotide. We demonstrated that RNA-guided base damage repair could be accomplished by the RNA-guided DNA strand-displacement synthesis and nick translation leading to nick ligation in a double-strand DNA region. Our study revealed a novel RNA-guided base damage repair pathway during transcription and DNA replication.
Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates
Authors: Morse Michael , Sefcikova Jana , Rouzina Ioulia , Beuning Penny J , Williams Mark C
Published: December 2022

The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into the viral particle. N protein consists of two ordered domains, with the N terminal domain (NTD) primarily associated with RNA binding and the C terminal domain (CTD) primarily associated with dimerization/oligomerization, and three intrinsically disordered regions, an N-arm, a C-tail, and a linker that connects the NTD and CTD. We utilize an optical tweezers system to isolate a long single-stranded nucleic acid substrate to measure directly the binding and packaging function of N protein at a single molecule level in real time. We find that N protein binds the nucleic acid substrate with high affinity before oligomerizing and forming a highly compact structure. By comparing the activities of truncated protein variants missing the NTD, CTD, and/or linker, we attribute specific steps in this process to the structural domains of N protein, with the NTD driving initial binding to the substrate and ensuring high localized protein density that triggers interprotein interactions mediated by the CTD, which forms a compact and stable protein-nucleic acid complex suitable for packaging into the virion.
Voluminous continental growth of the Altaids and its control on metallogeny
Authors: Wang Tao , Huang He , Zhang Jianjun , Wang Chaoyang , Cao Guangyue , Xiao Wenjiao , Yang Qidi , Bao Xuewei
Published: December 2022

The Altaids is generally considered to be the largest Phanerozoic accretionary orogen on Earth, but it is unclear whether it was associated with extensive continental crustal growth and whether there is a link between the crustal growth and ore mineralization. This paper reviews whole-rock Nd and zircon Hf isotope data for felsic–intermediate–mafic igneous rocks in the Altaids and presents Nd + Hf isotopic contour maps for this region. The maps highlight the 3D lithospheric compositional architecture of the Altaids and make it possible to quantitatively evaluate the crustal growth and its relationship with ore deposits. The Altaids hosts ∼4 107 350 km2 and ∼184 830 750 km3 (assuming a crustal thickness of 40–50 km) juvenile crust (ϵNd(t) > 0), accounting for 58% by isotope-mapped area (∼7 010 375 km2) of almost all outcrops of the Altaids (∼8 745 000 km2) and formed during 1000–150 Ma (mainly 600–150 Ma). The juvenile crustal, slightly juvenile-reworked crustal and slightly reworked crustal provinces controlled the Cu–Au, the Pb–Zn–Ag and the Li–Be, Nb–Ta and W–Sn ore deposits. According to the crustal architecture and background of deep compositions, we propose that the ore deposits can be grouped into three types: juvenile crust-related, mixed-source (or slightly juvenile crust)-related and reworked crust-related. This highlights the close relationship between accretion, continental growth and mineralization, and will facilitate exploration for specific ore-deposit types in the Altaids.
Sex and Race Disparities in Mortality and Years of Potential Life Lost Among People With HIV: A 21-Year Observational Cohort Study
Authors: Pellegrino Rachael A , Rebeiro Peter F , Turner Megan , Davidson Amber , Best Noelle , Shaffernocker Chandler , Kheshti Asghar , Kelly Sean , Raffanti Stephen , Sterling Timothy R , Castilho Jessica L
Published: December 2022

Background

Since the availability of antiretroviral therapy, mortality rates among people with HIV (PWH) have decreased; however, this does not quantify premature deaths among PWH, and disparities persist.

Methods

We examined all-cause and premature mortality among PWH receiving care at the Vanderbilt Comprehensive Care Clinic from January 1998 to December 2018. Mortality rates were compared by demographic and clinical factors, and adjusted incidence rate ratios (aIRRs) were calculated using multivariable Poisson regression. For individuals who died, age-adjusted years of potential life lost (aYPLL) per total person-years living with HIV were calculated from US sex-specific life tables, and sex and race differences were examined using multivariable linear regression.

Results

Among 6531 individuals (51% non-Hispanic [NH] White race, 40% NH Black race, 21% cis-gender women, 78% cis-gender men) included, 956 (14.6%) died. In adjusted analysis, PWH alive in the most recent calendar era (2014–2018) had decreased risk of mortality compared with those in the earliest calendar era (1998–2003; aIRR, 0.22; 95% CI, 0.17–0.29), and women had increased risk of death compared with men (aIRR, 1.31; 95% CI, 1.12–1.54). Of those who died, Black women had the highest aYPLL (aIRR, 592.5; 95% CI, 588.4–596.6), followed by Black men (aIRR, 470.7; 95% CI, 468.4–472.9), White women (aIRR, 411.5; 95% CI, 405.6–417.4), then White men (aIRR, 308.6; 95% CI, 308.0–309.2). In adjusted models, higher YPLL remained associated with NH Black race and cis-gender women, regardless of HIV risk factor.

Conclusions

Despite marked improvement over time, sex disparities in mortality as well as sex and race disparities in YPLL remained among PWH in this cohort.
The Social Organization of Black Communities
Authors: Green Dan S.
Published: December 2022

W. E. B. Du Bois began his illustrious career as an academic sociologist dedicated to providing valid data about the status and condition of African Americans as well as their progress since emancipation. His goal was to put science into sociology through empirical studies of Black Americans. From 1898 to 1910 he produced several groundbreaking empirical studies of urban and rural Black communities, focusing primarily on their social organization. These studies were the initial empirical studies in sociology by an American sociologist. His pioneering research also introduced sociology to the importance of social organization and its relevance in human social life. This chapter examines Du Bois’s pioneering analyses of social organization that evolved in Black communities following emancipation.
Sociology of Religion and the Black Church
Authors: Blume Oeur Freeden , Blum Edward J.
Published: December 2022

More than just a topic of inquiry for W. E. B. Du Bois, religion provided a language that the scholar used to convey larger truths concerning racial equity and identity, and the possibility for social change. This chapter first describes how Du Bois’s sociology of religion not only was a careful study of the place of religion in society and history but was also grounded in a philosophical commitment to understanding the dynamic relationship between science and religion. It turns next to Du Bois’s writings on the central place of religion in the history of African and African American peoples. The third section is dedicated to Du Bois’s writings on the Black Church. The fourth section discusses Du Bois’s critique of colonialism and white Christianity. The chapter concludes with observations on how Du Bois, an architect of the sociology of religion, continues today to inspire the study of religion and racial politics.
W. E. B. Du Bois and the Field and Function of Historically Black Colleges and Universities
Authors: Alridge Derrick P.
Published: December 2022

Drawing on W. E. B. Du Bois’s speeches and writings, this chapter examines his assessments of historically black colleges and universities (HBCUs) in the midst of a segregated US society and presents his pragmatic and farsighted vision of these institutions in the twentieth century. The chapter also presents Du Boisian-based principles that address contemporary domestic and global sociopolitical issues faced by HBCUs. The chapter concludes with a set of recommendations of ways for HBCUs to navigate the twenty-first century.
W. E. B. Du Bois and Journalism
Authors: Green Dan S.
Published: December 2022

During his long life, wholly dedicated to fighting racism and social inequality, W. E. B. Du Bois used several strategies. Early in his career, as an academic sociologist, he discovered that his scholarly work promoting social justice was not valued. He turned to public sociology, deciding it was a more effective method of getting his message about social justice to the public. His first magazine, The Moon, was short-lived, lasting only a year. Together with two sympathetic colleagues, he then initiated The Horizon, which lasted three years. In 1910, when he was active in the formation of the NAACP, and known as a journalist, the NAACP hired him as editor of their proposed journal The Crisis, a position he kept for twenty-three years. During this time, and still with the NAACP, he published a children’s magazine, The Brownies’ Book, in 1920–21. He resigned from the NAACP in 1934 because of a long-standing feud with the board over editorial control of The Crisis, returning to Atlanta University, where he initiated his fifth journal, Phylon, a journal of race relations, and edited it from 1940 to 1944.
Du Bois and Women Activists
Authors: Dennie Nneka D.
Published: December 2022

W. E. B. Du Bois’s relationships with women activists and women’s activism—particularly that of Black women—are fraught with tensions. He at times writes with clarity about women’s rights, but at some points in his career, he sidelined Black women contemporaries and minimized the ways they influenced his work. This chapter undertakes a network analysis of how Du Bois worked with women activists in order to identify and reconcile the contradictions in his work. Through examining Du Bois’s relationships with Jessie Fauset, Zora Neale Hurston, Mary White Ovington, Ida B. Wells, and others, it argues that Du Bois often mentored younger Black women and collaborated with White women allies but erased established Black women activists. The chapter contends that Du Bois’s divergent treatment of Black and White women activists stemmed from their differential access to power in early suffrage and reform movements, which influenced the ways he approached potential collaborations with women.
Folk Belief and Religion in Ukraine
Authors: Lesiv Mariya
Published: December 2022

After briefly introducing the current religious landscape in Ukraine, this chapter focuses on the newly emergent folk expressions in the forms of the supernatural apparitions of the Mother of God. The apparitions were identified in small villages that, in turn, developed into pilgrimage sites. Ukrainian village dwellers are often the victims of placism. The apparitions, while drawing on firmly established beliefs and models of religious authority and behavior, become powerful vehicles for creating the charisma of place in localities that are otherwise deeply marginalized. The charisma-building processes are manifested in three overlapping expressive forms, namely, personal narrative, material culture, and ritual. This study is based on the ethnographic methodology of “vernacular” or “lived” religion.