bluuebunny/crossref_metadata_2025 huggingface dataset:
Composite Gaussian pulsed waveform for robust resonance radar signal
Authors: Aldhubaib Faisal
Published: November 2022

The paper assesses the feasibility of forming a composite excitation pulse with a high potential to combat the noise and onset ambiguity when estimating the target resonance behaviour in a radar target signal. The assessment investigates four composite pulse configurations of unified or adaptive setups for the fractional bandwidth and peak weight to find the best setup to enhance the resonance signature robustness. The assessment uses the method pencil function to extract the resonance parameters of the composite time data (coherent) and then to determine the degree of robustness over‐extraction onset and range of noise level. Determining the robustness rate requires finding the error between the original excitation frequencies and the extractable resonant frequencies and, second, the similarity between the original and reconstructed pulse waveforms. The qualitative assessments of the robustness merit concluded that the adaptive configuration of peak weight and small adaptive fractional bandwidth outperforms the other arrangements in enhancing the resonance return in radar signature.
Maternal Serum Gasdermin D Concentrations in Pregnancies Complicated
by Isolated Intrauterine Growth Restriction
Authors: Kobal Berna Buse , Kale İbrahim , Pektaş Ahmet Murat , Ozel Aysegul , Muhcu Murat
Published: November 2022

Objective We aimed to investigate the relationship between the isolated
intrauterine growth restriction (IUGR) and maternal serum gasdermin D (GSDMD)
concentration.

Materials and methods This cross-sectional study was conducted with 80
pregnant women who applied to the Umraniye Training and Research Hospital
Gynecology and Obstetrics Clinic between January 2022 and May 2022. The IUGR
group consisted of 40 pregnant women diagnosed with IUGR in the third trimester,
and the control group consisted of 40 healthy pregnant women matched with the
IUGR group in terms of age and BMI. Demographic characteristics, ultrasound
findings, and neonatal outcomes were noted. The two groups were compared in
terms of maternal serum GSDMD concentrations.

Results Both groups were similar in terms of demographic characteristics.
Fetal biometric measurements were found to be significantly lower in the IUGR
group compared to the control group, and umbilical artery Doppler PI and SD were
found to be higher. Gestational age, newborn birth weight, birth height, and
Apgar scores were significantly lower and NICU admission rate was higher in the
IUGR group. Gestational age at blood sampling for GSDMD was similar in both
groups (p=0.805). While maternal serum GSDMD concentration was
11.14 ng/ml in the IUGR group, it was 6.66 ng/ml
in the control group (p=0.000). ROC analysis was performed to determine
the value of GSDMD concentration in terms of IUGR estimation. AUC analysis of
GSDMD for IUGR estimation was 0.88 (p<.001, 95%
CI=0.80–0.95). The optimal cutoff value for GSDMD concentration
was determined as 8.84 ng/ml with 80% sensitivity and
75% specificity.

Conclusion Maternal serum GSDMD concentrations were found to be higher in
pregnant women whose pregnancy was complicated by isolated IUGR. We think that
high GSDMD concentrations may be a reflection of increased GSDMD-mediated
pyroptosis in placental tissue in isolated IUGR cases.
Physiomimetic In Vitro Human Models for Viral Infection in the Liver
Authors: McDuffie Dennis , Barr David , Helm Madeline , Baumert Thomas , Agarwal Ashutosh , Thomas Emmanuel
Published: November 2022

Viral hepatitis is a leading cause of liver morbidity and mortality globally. The mechanisms underlying acute infection and clearance, versus the development of chronic infection, are poorly understood. In vitro models of viral hepatitis circumvent the high costs and ethical considerations of animal models, which also translate poorly to studying the human-specific hepatitis viruses. However, significant challenges are associated with modeling long-term infection in vitro. Differentiated hepatocytes are best able to sustain chronic viral hepatitis infection, but standard two-dimensional models are limited because they fail to mimic the architecture and cellular microenvironment of the liver, and cannot maintain a differentiated hepatocyte phenotype over extended periods. Alternatively, physiomimetic models facilitate important interactions between hepatocytes and their microenvironment by incorporating liver-specific environmental factors such as three-dimensional ECM interactions and co-culture with non-parenchymal cells. These physiologically relevant interactions help maintain a functional hepatocyte phenotype that is critical for sustaining viral hepatitis infection. In this review, we provide an overview of distinct, novel, and innovative in vitro liver models and discuss their functionality and relevance in modeling viral hepatitis. These platforms may provide novel insight into mechanisms that regulate viral clearance versus progression to chronic infections that can drive subsequent liver disease.
Palladium-Catalyzed C(sp2)–H Silylation via a Native-Amine-Directed Strategy
Authors: Yan Yintao , Wang Xuan , Li Jianhua , Jiang Chao
Published: November 2022

A palladium-catalyzed C(sp2)–H silylation of morpholinones to afford silyl morpholinones is reported. The native secondary amine, which is tolerated in the reaction, is able to promote the C–H activation and silylation of the aryl group. The substrates are monosilylated selectively and tolerate various functional groups. The resulting silyl morpholinone derivatives are potentially useful in pharmaceuticals and agrochemicals.
Role of GPR56 in Platelet Activation and Arterial Thrombosis
Authors: Liu Dongsheng , Zhang Peng , Zhang Kandi , Bi Changlong , Li Li , Xu Yanyan , Zhang Tiantian , Zhang Junfeng
Published: November 2022

The adhesion G protein-coupled receptor GPR56 mediates cell–cell and cell–extracellular matrix interactions. To examine the function of GPR56 in platelet activation and arterial thrombosis, we generated GPR56-knockout mice and evaluated GPR56 expression in human and mouse platelets. The results revealed that the levels of the GPR56 N-terminal fragment were significantly higher on the first day after myocardial infarction than on the seventh day in the plasma of patients with ST-segment-elevation myocardial infarction. Next, we investigated the effects of GPR56 on platelet function in vitro and in vivo. We observed that collagen-induced aggregation and adenosine triphosphate release were reduced in Gpr56
−/− platelets. Furthermore, P-selectin expression on the Gpr56
−/− platelet surface was also reduced, and the spreading area on immobilized collagen was decreased in Gpr56
−/− platelets. Furthermore, collagen-induced platelet activation in human platelets was inhibited by an anti-GPR56 antibody. Gpr56
−/− mice showed an extended time to the first occlusion in models with cremaster arteriole laser injury and FeCl3-induced carotid artery injury. GPR56 activated the G protein 13 signaling pathway following collagen stimulation, which promoted platelet adhesion and thrombus formation at the site of vascular injury. Thus, our study confirmed that GPR56 regulated the formation of arterial thrombosis. Inhibition of the initial response of GPR56 to collagen could significantly inhibit platelet activation and thrombus formation. Our results provide new insights for research into antiplatelet drugs.
Impact of ABO Blood Group on Thromboembolic and Bleeding Complications in Patients with Left Ventricular Assist Devices
Authors: Tscharre Maximilian , Wittmann Franziska , Kitzmantl Daniela , Schlöglhofer Thomas , Cichra Philip , Lee Silvia , Eichelberger Beate , Wadowski Patricia P. , Laufer Günther , Wiedemann Dominik , Panzer Simon , Zimpfer Daniel , Gremmel Thomas
Published: November 2022

Background The ABO blood group system is linked to hemostasis via its relationship with von Willebrand factor (VWF) and factor VIII (FVIII). In the current study, we investigated the association of the ABO system with clinical outcomes as well as VWF and platelet function in patients with left ventricular assist devices (LVADs).

Methods Bleeding and thromboembolic complications were assessed in 111 patients during 1 year after LVAD implantation. In 67 LVAD patients, VWF antigen, VWF activity, VWF ristocetin cofactor, VWF collagen-binding, and FVIII activity were assessed. Platelet surface P-selectin and activated glycoprotein IIb/IIIa were determined by flow cytometry, and soluble P-selectin was measured with an enzyme-linked immunoassay. Platelet aggregation was assessed by light transmission and impedance aggregometry.

Results Thirty-six patients (32.4%) experienced a bleeding and 22 patients (19.8%) a thromboembolic event. In univariate analyses, patients with blood group O had numerically more bleeding complications and less thromboembolic events as compared to patients with blood group non-O (both p ≥ 0.05). After multivariable adjustment, blood group O was significantly associated with a higher risk of bleeding (hazard ratio 2.42 [95% confidence interval 1.03–5.70], p = 0.044) but not linked to thromboembolic complications.

Conclusion Patients with blood group O had significantly lower levels of VWF and FVIII (all p < 0.05), whereas P-selectin expression in response to thrombin-receptor activating peptide and soluble P-selectin were higher as compared to patients with blood group non-O (both p < 0.05). LVAD patients with blood group O are at an increased bleeding risk, potentially due to lower VWF and FVIII levels.
Association of Chronic Periodontitis with Helicobacter pylori Infection in Stomach or Mouth: A Systematic Review and Meta-Analysis
Authors: Tsimpiris Athanasios , Tsolianos Ioannis , Grigoriadis Andreas , Moschos Ioannis , Goulis Dimitrios G. , Kouklakis Georgios
Published: November 2022

Helicobacter pylori (H. pylori) infection and periodontitis are both inflammatory conditions associated with systemic diseases. Researchers have attempted to investigate the correlation between them. This systematic review and meta-analyses were conducted to investigate the association of H. pylori infection in the stomach and/or in subgingival plaque and gingival crevicular fluid with chronic periodontitis. The protocol was created according to the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P) statement. The study was designed according to the Cochrane criteria. A comprehensive literature search was performed in MEDLINE, Scopus, and CENTRAL, combined with hand-searching and assessment of gray literature. The meta-analysis of the included studies was made by the Review Manager (RevMan) 5.4 software. The effect measure of the outcome was odds ratios with 95% confidence intervals. Heterogeneity was assessed by chi-square and I2. Four observational studies involving 818 subjects were included in this meta-analysis. The odds of oral H. pylori presence were higher in patients with chronic periodontitis, compared to healthy controls, with an odds ratio of 1.87 (95% confidence interval 0.85–4.10; p = 0.12). The odds of the presence of H. pylori in the stomach also were higher in patients with chronic periodontitis, with an odds ratio of 1.80 (95% confidence interval 0.82–3.95; p = 0.15). There is no evidence for an association between chronic periodontitis and the prevalence of H. pylori, detected either in subgingival plaque and gingival crevicular fluid or in the stomach.
Free-androgen Index in Women with Polycystic Ovarian Syndrome: A Meta-Analysis
Authors: Patil Prakash , D'Souza Neevan , Ghate Sudeep D. , Nagendra Lakshmi , Girijashankar Harish B.
Published: November 2022

Objectives Hyperandrogenism, a key feature of polycystic ovarian syndrome (PCOS), is caused by excess androgen secretion, most commonly of ovarian origin. Although the serum total testosterone (TT) levels have long been used as a traditional measure of hyperandrogenemia in women with PCOS, it is associated with many fallacies due to the fact that a component of TT is linked to sex hormone-binding globulin (SHBG). Recent research has discovered that measuring free testosterone levels and computing the free androgen index (FAI), which is a ratio of TT and SHBG, are better predictors of androgen excess in PCOS. The aim of this meta-analysis is to determine the association of FAI in diagnosing hyperandrogenism and its ability to discriminate PCOS from controls.

Materials and Methods The publicly available databases PubMed, Scopus and Web of Science were searched using MeSH terms, ‘Polycystic Ovarian Syndrome’ OR ‘PCOS’ OR ‘PCOD’ AND ‘Testosterone’ AND ‘Sex Hormone Binding Globulin’ OR ‘SHBG’ to collect the full-text articles for the retrieval of related data of case–control and cross-sectional studies. The studies quality was assessed using the Newcastle–Ottawa scale, and a sub-group analysis and publication bias between the studies was evaluated by funnel plot.

Statistical Analysis The R program (v4.0.3) and R packages ‘metafor’ and ‘dmetar’ were used for statistical analyses of quantitative data and the plots were generated using ‘ggplot2’ package through a comparison of pooled SMD by Egger's linear regression and Beggs-Mazumdar tests.

Results Twenty-four studies involving 7,847 participants including 3,290 controls and 4,557 PCOS were included in the meta-analysis. The pooled data analysis of the included studies showed that the PCOS women had higher FAI than controls, with SMD of 1.56 (95%CI 1.08–2.04; p < 0.01). The publication bias was tested using a funnel plot and Egger's regression asymmetry test, which revealed no risk of publishing bias (p = 0.1727). Additionally, the sub-group meta-analysis of geographic region revealed that FAI levels were more significant in PCOS subjects of Asia and Europe, compared with the American region.

Conclusion Overall, this meta-analysis indicates that FAI could be a reliable marker to differentiate PCOS patients from controls in Asian and European ethnicities.
A Bibliometric Analysis of Ophthalmology Resident Research Productivity in the United States
Authors: Huang Austin , Kim Sarah , Zhu Harrison , Pathare Nihar , Ooi Xin Yee , Kirby R. Parker , Yoon Stephen P. , Al-Mohtaseb Zaina
Published: November 2022

Background The extent and impact of ophthalmology resident scholarly output is not well known. The authors aim to quantify scholarly activity of ophthalmology residents during residency and assess what factors may be associated with greater research productivity of these residents.

Material and Methods Ophthalmology residents who graduated in 2021 were identified from their respective program Web sites. Bibliometric data published by these residents between the beginning of their postgraduate year 2 (July 1, 2018) until 3 months after graduation (September 30, 2021) were captured through searches via PubMed, Scopus, and Google Scholar. The association of the following factors with greater research productivity numbers was analyzed: residency tier, medical school rank, sex, doctorate degree, type of medical degree, and international medical graduate status.

Results We found 418 ophthalmology residents from 98 residency programs. These residents published a mean (±standard deviation [SD]) number of 2.68 ± 3.81 peer-reviewed publications, 2.39 ± 3.40 ophthalmology-related publications, and 1.18 ± 1.96 first-author publications each. The mean (±SD) Hirsch index (h-index) for this cohort was 0.79 ± 1.17. Upon multivariate analysis, we discovered significant correlations between both residency tier and medical school rank and all bibliometric variables assessed. Pairwise comparisons revealed that residents from higher tier programs had greater research productivity numbers than those from lower tier programs.

Conclusion We obtained bibliometric standards for ophthalmology residents on a national scale. Residents who graduated from higher-ranked residency programs and medical schools possessed higher h-indices and published more peer-reviewed publications, ophthalmology-related articles, and first-author publications.
Epistemologies of ignorance in far right studies: the invisibilisation of racism and whiteness in times of populist hype
Authors: Mondon Aurelien
Published: November 2022

Research on the far right has been a booming field for decades now, with far-right parties generally being much more researched than their right, centre and left counterparts, even when they are marginal in terms of politics or electoral support. Yet, for a field that is notorious for its lively definitional debates and tendency to evolve and reinvent itself terminologically, it has appeared unwilling to engage with the concepts of race, racism and whiteness, or with its very positioning in political structures. Through a mixed-methods discursive approach, this article analyses the titles and abstracts of all articles published in peer-reviewed journal in the sub-field of far right studies between 2016 and 2021 (n= 2543) to highlight which terms and concepts are primed and which are obscured. This article highlights a tendency to prime euphemising terms and concepts such as ‘populism’ and avoid those which engage with systemic and structural forms of oppression such as racism and whiteness. This article thus aims to both map and make sense of the absence of whiteness and racism in the corpus by arguing that it is a symbol of the ongoing presence of colourblind approaches and a lack of reckoning with the scale and pervasion of systemic racism in contemporary societies.
Study on the heat transfer enhancement of self-excited oscillating pulsating flow by the boundary vortex group
Authors: Sun Xiao , Wang Zhaohui , Cheng Ziqiang , Wang Dongdong , Gao Quanjie
Published: November 2022

In this work, the self-excited oscillating pulsating circular pipe is the object of study. Based on the flow evolution characteristics of the boundary layer and vortex, the mechanism of enhanced heat transfer by self-excited oscillating pulsating flow is investigated. Moreover, a vital flow structure, the boundary vortex ring (BVR for short), is proposed. The study results show that the vortex evolution within the shear layer inside the self-excited oscillating pulsating chamber has an important influence on the formation of the downstream boundary vortex ring. Both have the same period but different phases. The boundary vortex group formed by the BVR is distributed at intervals in the pipe, and its role in promoting fluid flow increases first and then decreases. At the same time, the strength of the central mainstream area is gradually strengthened. The boundary vortex group's flow state determines the downstream pipe's heat transfer characteristics. The low-velocity zone on both sides determines the position of the heat transfer coefficient enhancement, and the central vorticity determines the amplitude of the enhancement. The boundary vortex group with a complete structure can effectively promote heat transfer, while the boundary vortex group with an incomplete structure can suppress heat transfer. The time-averaged boundary layer thickness increase ratio δ′ and the time-averaged equal diameter circular tube performance evaluation index ηT provide the fundamental indexes for designing and optimizing variable cross section heat transfer circular tubes. Furthermore, the heat transfer coefficient of the tube wall varies synchronously with the thickness of the boundary layer.
Eliminating flooding by phase separation in condenser tube
Authors: Li Yixuan , Li Wenxiao , Xie Jian , Xu Jinliang , Miao Zheng
Published: November 2022

Flooding may take place for in-tube condensation, causing unstable flow and deteriorated heat transfer. Here, the phase separation principle is proposed to eliminate flooding. Comparative experiments of condensation were performed in both bare tube (BT) and modulated heat transfer tube (MHTT) with a mesh membrane tube (MMT) insert. The working fluid is water-steam under a sub-atmospheric pressure. It was observed that slug flow exists at small mass fluxes and vapor mass qualities in BT. Due to the periodic formation of liquid column over the tube cross section, flooding indeed takes place, causing unstable flow, deteriorated heat transfer, and large pressure drop. The MHTT completely eliminated flooding, converting the unstable flow into a stable flow. Heat transfer coefficients are 7.47 times of those in BT, maximally, accompanying reduced pressure drops. High-speed visualization and theoretical analysis indicated that smaller pore size provides larger capability to prevent the vapor phase penetrating the mesh screen, resulting in larger driving force for liquid suction toward the MMT inside. The MMT provided a tunnel for liquid transportation in the upward direction, which is the mechanism to eliminate flooding. The modulation of the annular flow pattern was also performed and analyzed by using the phase separation principle, and the results indicated the effectiveness of MMT in the annular flow regime. This work is benefit for applications, such as air-cooled condenser, whose performance is important to influence the whole system performance for power generation.
Ceramic hydroxyapatite chromatography plays a critical role in bispecific antibody purification process for impurity removal
Authors: Waller Jessica A , Zheng Ji , Dyer Rachel , Slaney Thomas , Wu Wei , Tao Li , Ghose Sanchayita
Published: November 2022

Background

Significant challenges exist in downstream purification of bispecific antibodies (BsAbs) due to the complexity of BsAb architecture. A unique panel of mispaired species can result in a higher level of product-related impurities. In addition to process-related impurities such as host cell proteins (HCPs) and residual DNA (resDNA), these product-related impurities must be separated from the targeted BsAb product to achieve high purity. Therefore, development of an efficient and robust chromatography purification process is essential to ensure the safety, quality, purity and efficacy of BsAb products that consequently meet regulatory requirements for clinical trials and commercialization.

Methods

We have developed a robust downstream BsAb process consisting of a mixed-mode ceramic hydroxyapatite (CHT) chromatography step, which offers unique separation capabilities tailored to BsAbs, and assessed impurity clearance.

Results

We demonstrate that the CHT chromatography column provides additional clearance of low molecular weight (LMW) and high molecular weight (HMW) species that cannot be separated by other chromatography columns such as ion exchange for a particular BsAb, resulting in ≥98% CE-SDS (non-reduced) purity. Moreover, through Polysorbate-80 (PS-80) spiking and LC–MS HCP assessments, we reveal complete clearance of potential PS-80-degrading HCP populations in the CHT eluate product pool.

Conclusions

In summary, these results demonstrate that CHT mixed-mode chromatography plays an important role in separation of product- and process-related impurities in the BsAb downstream process.
Temporality of ovarian steroids and LH/FSH pulse profiles encompassing selection of the dominant follicle in heifers
Authors: Gomez-Leon Victor E , Ginther O J , Domingues Rafael R , Sanglard Leticia P , Wiltbank Milo C
Published: November 2022

The tested hypotheses were (1) LH/FSH pulses and F2 diameter are diminished by P4 and, (2) E2 increases during the transition to deviation and alters LH/FSH pulses. On Day 5 (Day 0 = ovulation), heifers were randomized into an untreated group (HiP4, n = 11), and a prostaglandin analog treated group (NoP4, n = 10). On Day 6, a follicular wave was induced by follicle ablation. Ultrasound and blood collections were performed every 12 h from Days 7 to 11. Blood was collected every 15 min for 10 h on Day 9 (largest follicle expected to be ~7.5 mm). Estradiol was ~75% greater (0.36 ± 0.14 vs 0.63 ± 0.19 pg/mL) in heifers with F1 ≥ 7.2 mm than in heifers with F1 < 7.2 mm. The HiP4 had smaller second largest follicle (F2) diameter, lower estradiol (P = 0.06), LH pulse baseline and peak concentrations (P < 0.007), in addition to half the frequency of LH/FSH pulses (4.1 ± 0.3 vs 9.6 ± 0.7 in 10 h) than the NoP4. Within HiP4, heifers with F1 ≥ 7.2 mm had ~25% fewer (P = 0.03) LH pulses compared to heifers with F1 < 7.2 mm. In contrast, within the NoP4, heifers with F1 ≥ 7.2 mm had ~75% greater LH (P = 0.05) and FSH (P = 0.08) pulse amplitude. We propose that greater F2 diameter at deviation in low P4 is related to greater LH baseline and peak concentrations, and greater frequency of LH/FSH pulses. A greater increase in E2 after F1 reaches ~7.2 mm results in further stimulation of LH/FSH pulse amplitude. Elevated P4 not only diminished frequency of LH/FSH pulses but also converted an E2 increase into a negative feedback effect on LH/FSH pulse frequency leading to smaller F2 at deviation.
Dynamic cellular and molecular characteristics of spermatogenesis in the viviparous marine teleostSebastes schlegelii
Authors: Wang Xueying , Liu Qinghua , Li Jun , Zhou Li , Wang Tao , Zhao Ning
Published: November 2022

Spermatogenesis is a dynamic cell developmental process that is essential for reproductive success. Vertebrates utilize a variety of reproductive strategies, including sperm diversity, and internal and external fertilization. Research on the cellular and molecular dynamic changes involved in viviparous teleost spermatogenesis, however, is currently lacking. Here, we combined cytohistology, 10 × genomic single-cell RNA-seq, and transcriptome technology to determine the dynamic development characteristics of the spermatogenesis of Sebastes schlegelii. The expressions of lhcgr (Luteinizing hormone/Choriogonadotropin receptor), fshr (follicle-stimulating hormone receptor), ar (androgen receptor), pgr (progesterone receptor), and cox (cyclo-oxygen-ase), as well as the prostaglandin E and F levels peaked during the maturation period, indicating that they were important for sperm maturation and mating. Fifteen clusters were identified based on the 10 × genomic single-cell results. The cell markers of the sub-cluster were identified by their upregulation; piwil, dazl, and dmrt1 were upregulated and identified as spermatogonium markers, and sycp1/3 and spo11 were identified as spermatocyte markers. For S. schlegelii, the sperm head nucleus was elongated (spherical to streamlined in shape), which is a typical characteristic for sperm involved in internal fertilization. We also identified a series of crucial genes associated with spermiogenesis, such as spata6, spag16, kif20a, trip10, and klf10, while kif2c, kifap3, fez2, and spaca6 were found to be involved in nucleus elongation. The results of this study will enrich our cellular and molecular knowledge of spermatogenesis and spermiogenesis in fish that undergo internal fertilization.
The low dimensionality of post-stroke cognitive deficits: it’s the lesion anatomy!
Authors: Sperber Christoph , Gallucci Laura , Umarova Roza
Published: November 2022

For years, dissociation studies on neurological single-case patients with brain lesions were the dominant method to infer fundamental cognitive functions in neuropsychology. In contrast, the association between deficits was considered to be of less epistemological value. Still, associational computational methods for dimensionality reduction—such as principal component analysis or factor analysis—became popular for the identification of fundamental cognitive functions and to understand human cognitive brain architecture from post-stroke neuropsychological profiles. In the present in silico study with lesion imaging of 300 stroke patients, we investigated the dimensionality of artificial simulated neuropsychological profiles that exclusively contained independent fundamental cognitive functions without any underlying low-dimensional cognitive architecture. Still, the anatomy of stroke lesions alone was sufficient to create a dependence between variables that allowed a low-dimensional description of the data with principal component analysis. All criteria that we used to estimate the dimensionality of data, including the Kaiser criterion, were strongly affected by lesion anatomy, while the Joliffe criterion provided the least affected estimates. The dimensionality of profiles was reduced by 62–70% for the Kaiser criterion, up to the degree that is commonly found in neuropsychological studies on actual cognitive measures. The interpretability of such low-dimensional factors as deficits of fundamental cognitive functions and their provided insights into human cognitive architecture thus seem to be severely limited, and the heavy focus of current cognitive neuroscience on group studies and associations calls for improvements. We suggest that qualitative criteria and dissociation patterns could be used to refine estimates for the dimensionality of the cognitive architecture behind post-stroke deficits. Further, given the strong impact of lesion anatomy on the associational structure of data, we see the need for further optimization of interpretation strategies of computational factors in post-stroke lesion studies of cognitive deficits.
Association of Upper Respiratory Streptococcus pneumoniae Colonization With Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Adults
Authors: Parker Anna M , Jackson Nicole , Awasthi Shevya , Kim Hanna , Alwan Tess , Wyllie Anne L , Baldwin Alisha B , Brennick Nicole B , Moehle Erica A , Giannikopoulos Petros , Kogut Katherine , Holland Nina , Mora Ana M , Eskenazi Brenda , Riley Lee W , Lewnard Joseph A
Published: November 2022

Background

Streptococcus pneumoniae interacts with numerous viral respiratory pathogens in the upper airway. It is unclear whether similar interactions occur with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods

We collected saliva specimens from working-age adults undergoing SARS-CoV-2 molecular testing at outpatient clinics and via mobile community-outreach testing between July and November 2020 in Monterey County, California. After bacterial culture enrichment, we tested for pneumococci by means of quantitative polymerase chain reaction targeting the lytA and piaB genes, and we measured associations with SARS-CoV-2 infection using conditional logistic regression.

Results

Analyses included 1278 participants, with 564 enrolled in clinics and 714 enrolled through outreach-based testing. The prevalence of pneumococcal carriage was 9.2% (117 of 1278) among all participants (11.2% [63 of 564] in clinic-based testing and 7.6% [54 of 714] in outreach-based testing). The prevalence of SARS-CoV-2 infection was 27.4% (32 of 117) among pneumococcal carriers and 9.6% (112 of 1161) among noncarriers (adjusted odds ratio [aOR], 2.73 [95% confidence interval (CI): 1.58–4.69). Associations between SARS-CoV-2 infection and pneumococcal carriage were enhanced in the clinic-based sample (aOR, 4.01 [95% CI: 2.08–7.75]) and among symptomatic participants (3.38 [1.35–8.40]), compared with findings within the outreach-based sample and among asymptomatic participants. The adjusted odds of SARS-CoV-2 coinfection increased 1.24-fold (95% CI: 1.00–1.55-fold) for each 1-unit decrease in piaB quantitative polymerase chain reaction cycle threshold value among pneumococcal carriers. Finally, pneumococcal carriage modified the association of SARS-CoV-2 infection with recent exposure to a suspected coronavirus disease 2019 case (aOR, 7.64 [95% CI: 1.91–30.7] and 3.29 [1.94–5.59]) among pneumococcal carriers and noncarriers, respectively).

Conclusions

Associations of pneumococcal carriage detection and density with SARS-CoV-2 suggest a synergistic relationship in the upper airway. Longitudinal studies are needed to determine interaction mechanisms between pneumococci and SARS-CoV-2.
Key Node Identification Method Integrating Information Transmission Probability and Path Diversity in Complex Network
Authors: Liu Xiaoyang , Gao Luyuan , Fiumara Giacomo , De Meo Pasquale
Published: November 2022

Previous key node identification approaches assume that the transmission of information on a path always ends positively, which is not necessarily true. In this paper, we propose a new centrality index called Information Rank (IR for short) that associates each path with a score specifying the probability that such path successfully conveys a message. The IR method generates all the shortest paths of any arbitrary length coming out from a node $u$ and defines the centrality of u as the sum of the scores of all the shortest paths exiting $u$. The IR algorithm is more robust than other centrality indexes based on shortest paths because it uses alternative paths in its computation, and it is computationally efficient because it relies on a Beadth First Search-BFS to generate all shortest paths. We validated the IR algorithm on nine real networks and compared its ability to identify super-spreaders (i.e. nodes capable of spreading an infection in a real network better than others) with five popular centrality indices such as Degree, Betweenness, K-Shell, DynamicRank and PageRank. Experimental results highlight the clear superiority of IR over all considered competitors.
Paternal transmission of behavioural and metabolic traits induced by postnatal stress to the 5th generation in mice
Authors: Boscardin Chiara , Manuella Francesca , Mansuy Isabelle M
Published: November 2022

Life experiences and environmental conditions in childhood can change the physiology and behaviour of exposed individuals and, in some cases, of their offspring. In rodent models, stress/trauma, poor diet, and endocrine disruptors in a parent have been shown to cause phenotypes in the direct progeny, suggesting intergenerational inheritance. A few models also examined transmission to further offspring and suggested transgenerational inheritance, but such multigenerational inheritance is not well characterized. Our previous work on a mouse model of early postnatal stress showed that behaviour and metabolism are altered in the offspring of exposed males up to the 4th generation in the patriline and up to the 2nd generation in the matriline. The present study examined if symptoms can be transmitted beyond the 4th generation in the patriline. Analyses of the 5th and 6th generations of mice revealed that altered risk-taking and glucose regulation caused by postnatal stress are still manifested in the 5th generation but are attenuated in the 6th generation. Some of the symptoms are expressed in both males and females, but some are sex-dependent and sometimes opposite. These results indicate that postnatal trauma can affect behaviour and metabolism over many generations, suggesting epigenetic mechanisms of transmission.
Proton Pump Inhibitor Use and Cognitive Function in the Boston Puerto Rican Health Study
Authors: Dinesh Deepika , Lee Jong Soo , Scott Tammy M , Tucker Katherine L , Palacios Natalia
Published: November 2022

Background

There is a lack of consensus among studies on the association between proton pump inhibitor (PPI) use and cognitive impairment. This association is not well studied among minority populations, including among Puerto Ricans. Therefore, we sought to examine this association among Boston-area Puerto Ricans.

Methods

The Boston Puerto Rican Health Study is an ongoing longitudinal cohort that enrolled 1499 Boston-area Puerto Rican adults, aged 45–75 years at baseline. Complete outcome and exposure data was available for 1290 baseline participants. Covariate-adjusted linear regression and linear mixed effects models were used to examine the association between PPI use, and global cognition, executive function, and memory cross-sectionally and longitudinally over ~12.7 years of follow-up. Furthermore, we examined the cross-sectional association between long-term PPI use (continuous use of ~6.2 years) and global cognition, executive function, and memory.

Results

Among 1 290 participants at baseline, 313 (24.3%) self-reported PPI use. Baseline PPI use was not associated with baseline global cognition, executive function, or memory. Baseline PPI use also did not alter the trajectory of global cognition, executive function, or memory over ~12.7 years of follow-up. Long-term PPI use was not associated with global cognition, executive function, or memory over ~12.7 years of follow-up.

Conclusion

In this study of Boston-area Puerto Ricans, we did not observe an association between PPI use and global cognition, executive function, or memory either cross-sectionally or over 12.7 years of follow-up.
Immunogenicity of an Additional mRNA-1273 SARS-CoV-2 Vaccination in People With HIV With Hyporesponse After Primary Vaccination
Authors: Jongkees Marlou J , Geers Daryl , Hensley Kathryn S , Huisman Wesley , GeurtsvanKessel Corine H , Bogers Susanne , Gommers Lennert , Papageorgiou Grigorios , Jochems Simon P , den Hollander Jan G , Schippers Emile F , Ammerlaan Heidi S M , Bierman Wouter F W , van der Valk Marc , Berrevoets Marvin A H , Soetekouw Robert , Langebeek Nienke , Bruns Anke H W , Leyten Eliane M S , Sigaloff Kim C E , van Vonderen Marit G A , Delsing Corine E , Branger Judith , Katsikis Peter D , Mueller Yvonne M , de Vries Rory D , Rijnders Bart J A , Brinkman Kees , Rokx Casper , Roukens Anna H E
Published: November 2022

Background

The COVIH study is a prospective coronavirus disease 2019 (COVID-19) vaccination study in 1154 people with HIV (PWH), of whom 14% showed reduced antibody levels after primary vaccination. We evaluated whether an additional vaccination boosts immune responses in these hyporesponders.

Methods

The primary end point was the increase in antibodies 28 days after additional mRNA-1273 vaccination. Secondary end points included neutralizing antibodies, S-specific T-cell and B-cell responses, and reactogenicity.

Results

Of the 66 participants, 40 previously received 2 doses ChAdOx1-S, 22 received 2 doses BNT162b2, and 4 received a single dose Ad26.COV2.S. The median age was 63 years (interquartile range [IQR], 60–66), 86% were male, and median CD4+ T-cell count was 650/μL (IQR, 423–941). The mean S1-specific antibody level increased from 35 binding antibody units (BAU)/mL (95% confidence interval [CI], 24–46) to 4317 BAU/mL (95% CI, 3275–5360) (P < .0001). Of all participants, 97% showed an adequate response and the 45 antibody-negative participants all seroconverted. A significant increase in the proportion of PWH with ancestral S-specific CD4+ T cells (P = .04) and S-specific B cells (P = .02) was observed.

Conclusions

An additional mRNA-1273 vaccination induced a robust serological response in 97% of PWH with a hyporesponse after primary vaccination.

Clinical Trials Registration. EUCTR2021-001054-57-N.
Environmental Concern Leads to Trade Skepticism on the Political Left and Right
Authors: Rudolph Lukas , Quoß Franziska , Buchs Romain , Bernauer Thomas
Published: November 2022

The environmental implications of international trade appear to be associated with public backlash against trade liberalization and efforts at greening international trade. Because public support is essential to environmental and trade policy-making alike, we examine the trade–environment nexus from a public opinion perspective. We investigate whether negative attitudes toward trade are in fact fueled by concern over its environmental consequences. We argue that environmental concern affects how citizens evaluate the costs and benefits of trade, and that such evaluation is moderated by political ideology. The empirical analysis relies on a large representative survey and a population-based survey experiment in Switzerland, a small open economy. We show that environmental concern leads to decreasing appreciation of and support for international trade, with different manifestations of trade skepticism on the political left and right. This suggests (i) that policy-makers should focus more on greening global supply chains, and thus trade, if they wish to sustain public support for liberal international trade policy; and (ii) that the public follows informational cues on the environmental impacts of trade.
X-ray from outflow-cloud interaction and its application in tidal disruption events
Authors: Chen Jiashi , Wang Wei
Published: November 2022

Tidal disruption events (TDEs) may occur in supermassive black holes (SMBHs) surrounded by clouds. TDEs can generate ultrafast and large opening-angle outflow with a velocity of ∼0.01–0.2 c, which will collide with clouds with time lags depending on outflow velocity and cloud distances. Since the fraction of the outflow energy transferred into cloud’s radiation is anticorrelated with the cloud density, high-density clouds was thought to be inefficient in generating radiation. In this work, we studied the radiation from the outflow-cloud interactions for high-density clouds, and found that thermal conduction plays crucial roles in increasing the cloud’s radiation. Up to 10 per cent of the bow shock energy can be transferred into clouds and gives rise to X-ray emission with equivalent temperature of 105–6 K due to the cooling catastrophe. The inverse Compton scattering of TDE UV/optical photons by relativistic electrons at bow shock generates power-law X-ray spectra with photon indices Γ ∼ 2–3. This mechanism may account for some TDE candidates with delayed X-ray emission, and can be examined by delayed radio and gamma-ray emissions.
LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2
Authors: Zhang He , Li Sizhen , Zhang Liang , Mathews David H , Huang Liang
Published: November 2022

Many RNAs fold into multiple structures at equilibrium, and there is a need to sample these structures according to their probabilities in the ensemble. The conventional sampling algorithm suffers from two limitations: (i) the sampling phase is slow due to many repeated calculations; and (ii) the end-to-end runtime scales cubically with the sequence length. These issues make it difficult to be applied to long RNAs, such as the full genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address these problems, we devise a new sampling algorithm, LazySampling, which eliminates redundant work via on-demand caching. Based on LazySampling, we further derive LinearSampling, an end-to-end linear time sampling algorithm. Benchmarking on nine diverse RNA families, the sampled structures from LinearSampling correlate better with the well-established secondary structures than Vienna RNAsubopt and RNAplfold. More importantly, LinearSampling is orders of magnitude faster than standard tools, being 428× faster (72 s versus 8.6 h) than RNAsubopt on the full genome of SARS-CoV-2 (29 903 nt). The resulting sample landscape correlates well with the experimentally guided secondary structure models, and is closer to the alternative conformations revealed by experimentally driven analysis. Finally, LinearSampling finds 23 regions of 15 nt with high accessibilities in the SARS-CoV-2 genome, which are potential targets for COVID-19 diagnostics and therapeutics.
TOXRIC: a comprehensive database of toxicological data and benchmarks
Authors: Wu Lianlian , Yan Bowei , Han Junshan , Li Ruijiang , Xiao Jian , He Song , Bo Xiaochen
Published: November 2022

The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.
Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase
Authors: Li Zhuo , Kaur Parminder , Lo Chen-Yu , Chopra Neil , Smith Jamie , Wang Hong , Gao Yang
Published: November 2022

Twinkle is a mitochondrial replicative helicase which can self-load onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the important role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain directly contacts the C-terminal helicase domain, and the contact interface is a hotspot for disease-related mutations. Mutations at the interface destabilize Twinkle hexamer and reduce helicase activity. With HS-AFM, we observed that a highly dynamic Twinkle domain, which is likely to be the N-terminal domain, can protrude ∼5 nm to transiently capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which is distinct from related helicases from bacteriophages.