bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 transmission by asymptomatic healthcare workers positive to screening swab: an Italian study
Authors: Palese Francesca , Arnoldo Luca , Brunelli Laura , Buzancic Silvana , De Giusti Valentina Anna , Ferrazzano Alberto , Gallo Tolinda , Iob Andrea , Mauro Katia , Pipan Corrado , Polonia Marta , Ruscio Edoardo , Treleani Maurizio , Conte Alessandro 
Published: September 2022

Abstract

Background
SARS-CoV-2 spreads primarily through respiratory droplets of symptomatic individuals. With respect to asymptomatic individuals, there are conflicting results in the literature and a lack of studies specifically examining transmission in healthcare settings.

Methods
The aim of this retrospective study, conducted in a northeastern Italian region, was to estimate the contagiousness of asymptomatic healthcare workers (HCWs) who tested positive for SARS-CoV-2. Asymptomatic HCWs who tested positive for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (rRT-PCR) at a regular screening nasopharyngeal or oropharyngeal swab between 1 February 2020 and 15 September 2020 were considered index cases. Contacts who were at high risk of infection and had follow-up swabs were included. Contacts were considered infected if they had a positive follow-up swab and/or symptoms associated with COVID-19 confirmed by a positive test within 14 days of exposure. Information was taken from records previously collected to identify contacts. Infectivity was estimated using the attack rate (AR) with a 95% confidence interval (95% CI).

Results
Thirty-eight asymptomatic HCWs who were positive at the screening swab and 778 contacts were identified. Contacts included 63.8% of colleagues, 25.6% of patients, 7.7% of family members and 3.0% of other contacts. Seven contacts tested positive for SARS-CoV-2 (AR: 0.91%, 95% CI: 0.89–0.93). Five of them were family members (AR: 8.3%), one was a colleague (0.2%) and one was a contact of other type (4.2%).

Conclusions
Viral spread by asymptomatic HCWs was less than in other settings. Identification of risk factors for transmission and reliable indicators of infectivity would be important to prioritize preventive measures.
Emancipation and Constitutional Patriotism: The Centralverein and the Weimar Republican Order
Authors: Rybak Jan 
Published: September 2022

Abstract
The article explores the conceptualization of Jewish emancipation and the republican order of state by activists of the Central Association of German Citizens of the Jewish Faith (Centralverein deutscher Staatsbürger jüdischen Glaubens, CV) in the Weimar years. It argues that activists adopted a liberal conception of constitutional patriotism and involved themselves in a republican nation-building project that went substantially beyond its traditional tasks of defence (Abwehr) and enlightenment (Aufklärung) against antisemitism. This entailed rallying fellow republicans to the defence of the order of state, advocating for the spirit of the constitution and rule of law and actively participating in the development of the republican society. In doing so, the CV rethought what it meant to be ‘German’ and came to understand it in a distinctively republican form, arguing that identification with the constitution and the republican ideals were the truest expression of Germanness. As ‘German’ came to be understood as the free expression of the people’s spirit and will, Jews’ belonging to Germany was seen as the result of a teleological process of the materialization of the ‘German spirit’, manifested in the republic. The article therefore reads the history of the Centralverein during the Weimar Republic not only in regard to its role for the Jewish community but crucially as one of the liberal movements that aimed to develop and defend the German republic.
Multicenter, Multivendor Validation of an FDA-approved Algorithm for Mammography Triage
Authors: Retson Tara A , Watanabe Alyssa T , Vu Hoanh , Chim Chi Yung 
Published: September 2022

Abstract

Objective
Artificial intelligence (AI)–based triage algorithms may improve cancer detection and expedite radiologist workflow. To this end, the performance of a commercial AI-based triage algorithm on screening mammograms was evaluated across breast densities and lesion types.

Methods
This retrospective, IRB-exempt, multicenter, multivendor study examined 1255 screening 4-view mammograms (400 positive and 855 negative studies). Images were anonymized by providing institutions and analyzed by a commercially available AI algorithm (cmTriage, CureMetrix, La Jolla, CA) that performed retrospective triage at the study level by flagging exams as “suspicious” or not. Sensitivities and specificities with confidence intervals were derived from area under the curve (AUC) calculations.

Results
The algorithm demonstrated an AUC of 0.95 (95% CI: 0.94–0.96) for case identification. Area under the curve held across densities (0.95) and lesion types (masses: 0.94 [95% CI: 0.92–0.96] or microcalcifications: 0.97 [95% CI: 0.96–0.99]). The algorithm has a default sensitivity of 93% (95% CI: 95.6%–90.5%) with specificity of 76.3% (95% CI: 79.2%–73.4%). To evaluate real-world performance, a sensitivity of 86.9% (95% CI: 83.6%–90.2%) was tested, as observed for practicing radiologists by the Breast Cancer Surveillance Consortium (BCSC) study. The resulting specificity was 88.5% (95% CI: 86.4%–90.7%), similar to the BCSC specificity of 88.9%, indicating performance comparable to real-world results.

Conclusion
When tested for lesion detection, an AI-based triage software can perform at the level of practicing radiologists. Drawing attention to suspicious exams may improve reader specificity and help streamline radiologist workflow, enabling faster turnaround times and improving care.
Towards an Internet of Energy for smart and distributed generation: applications, strategies, and challenges
Authors: Gu Qifeng , Qu Qiang 
Published: September 2022

AbstractThe global demands for clean and sustainable energy are rapidly increasing because of population and economic growth. The future of energy essentially requires novel thinking and new systems to transform energy generation, distribution, and consumption. The Internet of Energy (IoE), as a new concept, transforms the way of energy production, supply, and consumption to fulfill high-energy demands via a smart network of industrial energy producers and consumers. The main objective of this paper is to address how the Internet of Things (IoT) would meet the requirements of smart and distributed power generation. We did a comprehensive literature review to provide insights into the IoE applications and enlighten the current challenges. Furthermore, the paper provides deep insights into the existing research challenges to address the current limitations of the IoE security issues, and potential directions are also pointed for future work. The findings of this study include identifying the requirements and enabler factors influencing the IoT-based distributed generation that would be useful for policymakers and decision-makers in the field.
Is Your Sample Truly Mediating? Bayesian Analysis of Heterogeneous Mediation (BAHM)
Authors: Dyachenko Tatiana L , Allenby Greg M 
Published: September 2022

Abstract
Mediation analysis is used to study the relationship between stimulus and response in the presence of intermediate, generative variables. The traditional approach to the analysis utilizes the results of an aggregate regression model, which assumes that all respondents go through the same data-generating mechanism. We introduce a new approach that is able to uncover the heterogeneity in mediating mechanisms and provides more informative insights from mediation studies. The proposed approach provides individual-specific probabilities to mediate as well as a new measure of the degree of mediation as the prevalence of mediation in the sample. Covariates in the proposed model help describe the variation in the probability to mediate among respondents. The empirical examination of published studies demonstrates the presence of heterogeneity in mediating processes and supports the need for this new approach. We present evidence that the results of our more flexible heterogeneous mediation analysis do not necessarily agree with the traditional aggregate measures. We find that the conclusions from the aggregate analysis are neither sufficient nor necessary to claim mediation in the presence of heterogeneity. A web-based application allowing researchers to analyze the data with the proposed model in a user-friendly environment is developed.
The single-sample network module biomarkers (sNMB) method reveals the pre-deterioration stage of disease progression
Authors: Zhong Jiayuan , Liu Huisheng , Chen Pei 
Published: September 2022

ABSTRACT
The progression of complex diseases generally involves a pre-deterioration stage that occurs during the transition from a healthy state to disease deterioration, at which a drastic and qualitative shift occurs. The development of an effective approach is urgently needed to identify such a pre-deterioration stage or critical state just before disease deterioration, which allows the timely implementation of appropriate measures to prevent a catastrophic transition. However, identifying the pre-deterioration stage is a challenging task in clinical medicine, especially when only a single sample is available for most patients, which is responsible for the failure of most statistical methods. In this study, a novel computational method, called single-sample network module biomarkers (sNMB), is presented to predict the pre-deterioration stage or critical point using only a single sample. Specifically, the proposed single-sample index effectively quantifies the disturbance caused by a single sample against a group of given reference samples. Our method successfully detected the early warning signal of the critical transitions when applied to both a numerical simulation and four real datasets, including acute lung injury, stomach adenocarcinoma, esophageal carcinoma, and rectum adenocarcinoma. In addition, it provides signaling biomarkers for further practical application, which helps to discover prognostic indicators and reveal the underlying molecular mechanisms of disease progression.
Housing and Cancer Care and Outcomes: A Systematic Review
Authors: Fan Qinjin , Nogueira Leticia , Yabroff K Robin , Hussaini S M Qasim , Pollack Craig E 
Published: September 2022

Abstract

Background
Access to stable and affordable housing is an important social determinant of health in the United States. However, research addressing housing and cancer care, diagnosis, and outcomes has not been synthesized.

Methods
We conducted a systematic review of studies examining associations of housing and cancer care and outcomes using PubMed, Embase, Scopus, and CINAHL. Included studies were conducted in the United States and published in English between 1980 and 2021. Study characteristics and key findings were abstracted and qualitatively synthesized.

Results
A total of 31 studies were identified. Housing-related measures were reported at the individual level in 20 studies (65%) and area level in 11 studies (35%). Study populations and housing measures were heterogeneous. The most common housing measures were area-level housing discrimination (8 studies, 26%), individual-level housing status (8 studies, 26%), and individual-level housing concerns (7 studies, 23%). The most common cancer outcomes were screening (12 studies, 39%) and mortality (9 studies, 29%). Few studies assessed multiple dimensions of housing. Most studies found that exposure to housing insecurity was statistically significantly associated with worse cancer care (11 studies) or outcomes (10 studies).

Conclusions
Housing insecurity is adversely associated with cancer care and outcomes, underscoring the importance of screening for housing needs and supporting systemic changes to advance equitable access to care. Additional research is needed to develop and test provider- and policy-level housing interventions that can effectively address the needs of individuals throughout the cancer care continuum.
Adaptation and Evolution of Pathogens in the Cystic Fibrosis Lung
Authors: Planet Paul J 
Published: September 2022

AbstractAs opposed to acute respiratory infections, the persistent bacterial infections of the lung that characterize cystic fibrosis (CF) provide ample time for bacteria to evolve and adapt. The process of adaptation is recorded in mutations that accumulate over time in the genomes of the infecting bacteria. Some of these mutations lead to obvious phenotypic differences such as antibiotic resistance or the well-known mucoid phenotype of Pseudomonas aeruginosa. Other mutations may be just as important but harder to detect such as increased mutation rates, cell surface changes, and shifts in metabolism and nutrient acquisition. Remarkably, many of the adaptations occur again and again in different patients, signaling that bacteria are adapting to solve specific challenges in the CF respiratory tract. This parallel evolution even extends across distinct bacterial species. This review addresses the bacterial systems that are known to change in long-term CF infections with a special emphasis on cross-species comparisons. Consideration is given to how adaptation may impact health in CF, and the possible evolutionary mechanisms that lead to the repeated parallel adaptations.
Genome editing of SlMYB3R3, a cell cycle transcription factor gene of tomato, induces elongated fruit shape
Authors: Zheng Qingyou , Takei-Hoshi Rie , Okumura Hitomi , Ito Masaki , Kawaguchi Kohei , Otagaki Shungo , Matsumoto Shogo , Luo Zhengrong , Zhang Qinglin , Shiratake Katsuhiro 
Published: September 2022

Abstract
Fruit shape is an important trait that attracts consumers, and the regulation of genes related to cell division is crucial for shaping multicellular organs. In Arabidopsis, MYB3R transcription factors, which harbor three imperfect repeats in the N-terminus, control organ growth by regulating cell division. However, the function of MYB3Rs in tomato remains unknown. Here, we characterized tomato SlMYB3R3, which was preferentially expressed in flowers and placed in a subclade with two Arabidopsis cell cycle suppressors (MYB3R3/5). slmyb3r3 knockout mutants were generated using the CRISPR/Cas9 system. Morphological observation of the slmyb3r3 mutants showed that fruits that were elongated and occasionally peanut-like in shape were formed, which was caused by significantly increased cell numbers in the longitudinal direction. Transcriptome and yeast one-hybrid assay results suggested that SlMYB3R3 acted as a suppressor of cell-cycle-related genes by binding to the mitosis-specific activator (MSA) motifs in their promoters. Taken together, knock out of the suppressor SlMYB3R3 leads to elongated fruit, which results from the altered cell division pattern at the ovary stage, by regulating cell-cycle-related genes in an MSA-dependent manner. Our results suggest that SlMYB3R3 and its orthologs have the potential to change fruit shape as part of the molecular breeding of fruit crops.
A new demethylase gene, OsDML4, is involved in high temperature-increased grain chalkiness in rice
Authors: Yan Yan , Li Chao , Liu Zhen , Zhuang Jun-Jie , Kong Jia-Rui , Yang Zhen-Kun , Yu Jie , Shah Alam Mohammad , Ruan Cheng-Cheng , Zhang Heng-Mu , Xu Jian-Hong 
Published: September 2022

Abstract
High temperature (HT) can affect the accumulation of seed storage materials and cause adverse effects on the yield and quality of rice. DNA methylation plays an important role in plant growth and development. Here, we identified a new demethylase gene OsDML4 and discovered its function in cytosine demethylation to affect endosperm formation. Loss of function of OsDML4 induced chalky endosperm only under HT and dramatically reduced the transcription and accumulation of glutelins and 16 kDa prolamin. The expression of two transcription factor genes RISBZ1 and RPBF was significantly decreased in the osdml4 mutants, which caused adverse effects on the formation of protein bodies (PBs) with greatly decreased PB-II number, and incomplete and abnormally shaped PB-IIs. Whole-genome bisulfite sequencing analysis of seeds at 15 d after pollination revealed much higher global methylation levels of CG, CHG, and CHH contexts in the osdml4 mutants compared with the wild type. Moreover, the RISBZ1 promoter was hypermethylated but the RPBF promoter was almost unchanged under HT. No significant difference was detected between the wild type and osdml4 mutants under normal temperature. Our study demonstrated a novel OsDML4-mediated DNA methylation involved in the formation of chalky endosperm only under HT and provided a new perspective in regulating endosperm development and the accumulation of seed storage proteins in rice.
Limitations of the invertible-map equivalences
Authors: Dawar Anuj , Grädel Erich , Lichter Moritz 
Published: September 2022

Abstract
This note draws conclusions that arise by combining two recent papers, by Anuj Dawar, Erich Grädel and Wied Pakusa, published at ICALP 2019, and by Moritz Lichter, published at LICS 2021. In both papers, the main technical results rely on the combinatorial and algebraic analysis of the invertible-map equivalences ${\equiv ^{\text {IM}}_{k, Q}}$ on certain variants of Cai–Fürer–Immerman structures (CFI-structures for short). These ${\equiv ^{\text {IM}}_{k, Q}}$-equivalences, for a natural number $k$ and a set of primes $Q$, refine the well-known Weisfeiler–Leman equivalences used in algorithms for graph isomorphism. The intuition is that two graphs $G{\equiv ^{\text {IM}}_{k, Q}}H$ cannot be distinguished by iterative refinements of equivalences on $k$-tuples defined via linear operators on vector spaces over fields of characteristic $p \in Q$. In the first paper it has been shown, using considerable algebraic machinery, that for a prime $q \notin Q$, the ${\equiv ^{\text {IM}}_{k, Q}}$ equivalences are not strong enough to distinguish between non-isomorphic CFI-structures over the field $\mathbb {F}_q$. In the second paper, a similar but not identical construction for CFI-structures over the rings $\mathbb {Z}_{2^i}$ has, again by rather involved combinatorial and algebraic arguments, been shown to be indistinguishable with respect to ${\equiv ^{\text {IM}}_{k, \{2\}}}$. Together with an earlier work on rank logic, this second result suffices to separate rank logic from polynomial time. We show here that the two approaches can be unified to prove that CFI-structures over the rings $\mathbb {Z}_{2^i}$ are in fact indistinguishable with respect to ${\equiv ^{\text {IM}}_{k, {\mathbb {P}}}}$, for the set ${\mathbb {P}}$ of all primes. In particular, this implies the following two results. First, there is no fixed $k$ such that the invertible-map equivalence ${\equiv ^{\text {IM}}_{k, {\mathbb {P}}}}$ coincides with isomorphism on all finite graphs. Second, no extension of fixed-point logic by linear-algebraic operators over fields can capture polynomial time.
GRMHD simulations of accreting neutron stars I: Non-rotating dipoles
Authors: Çıkıntoğlu Sercan , Ekşi K Yavuz , Rezzolla Luciano 
Published: September 2022

ABSTRACT
We study the general-relativistic dynamics of matter being accreted on to and ejected by a magnetized and non-rotating neutron star. The dynamics is followed in the framework of fully general relativistic magnetohydrodynamics (GRMHD) within the ideal-MHD limit and in two spatial dimensions. More specifically, making use of the numerical code BHAC, we follow the evolution of a geometrically thick matter torus driven into accretion by the development of a magnetorotational instability. By making use of a number of simulations in which we vary the strength of the stellar dipolar magnetic field, we can determine self-consistently the location of the magnetospheric (or Alfvén) radius rmsph and study how it depends on the magnetic moment μ and on the accretion rate. Overall, we recover the analytic Newtonian scaling relation, i.e. rmsph ∝ B4/7, but also find that the dependence on the accretion rate is very weak. Furthermore, we find that the material torque correlates linearly with the mass-accretion rate, although both of them exhibit rapid fluctuations. Interestingly, the total torque fluctuates drastically in strong magnetic field simulations and these unsteady torques observed in the simulations could be associated with the spin fluctuations observed in X-ray pulsars.
Optical properties of the solar gravity lens
Authors: Engeli Sara , Saha Prasenjit 
Published: September 2022

Abstract
It is well known that the solar gravitational field can be considered as a telescope with a prime focus at locations beyond 550 au. In this work, we present a new derivation of the wave-optical properties of the system by adapting the arrival-time formalism from gravitational lensing. At the diffraction limit, the angular resolution is similar to that of a notional telescope with the diameter of the Sun, and the maximum light amplification is 8π4GM⊙/(c2λ), enough to detect a $1\,$W laser on Proxima Centauri b pointed in the general direction of the Sun. Extended sources, however, would be blurred by the wings of the point spread function into the geometrical-optics regime of gravitational lensing. Broad-band sources would have to further contend with the solar corona. Imaging an exoplanet surface as advocated in the literature, without attempting to reach the diffraction limit, appears achievable. For diffraction-limited imaging (sub-km scales from 100 pc), nearby neutron stars appear to be most plausible targets.
Binary parameters from astrometric and spectroscopic errors – candidate hierarchical triples and massive dark companions in Gaia DR3
Authors: Andrew Shion , Penoyre Zephyr , Belokurov Vasily , Evans N Wyn , Oh Semyeong 
Published: September 2022

ABSTRACT
We show how astrometric and spectroscopic errors introduced by an unresolved binary system can be combined to give estimates of the binary period and mass ratio. This can be performed analytically if we assume we see one or more full orbits over our observational baseline, or numerically for all other cases. We apply this method to Gaia DR3 data, combining the most recent astrometric and spectroscopic data. We compare inferred periods and mass ratios calculated using our method with orbital parameters measured for non-single stars in Gaia DR3 and find good agreement. Finally, we use this method to search the subset of the Gaia DR3 RVS data set with rv_method_used = 1 for compact object candidates. We select sources with significant astrometric and spectroscopic errors (RUWEast &gt; 1.25 and RUWEspec &gt; 2), large inferred mass ratios, and large inferred companion masses (q &gt; 1 and m2 &gt; 3M⊙) giving a catalogue of 4641 candidate hierarchical triples and Main Sequence + Compact Object pairs. We apply more stringent cuts, and impose low levels of photometric variability to remove likely triples (RUWEphot &lt; 2), producing a gold sample of 45 candidates.