bluuebunny/crossref_metadata_2025 huggingface dataset:
DNS of the spatiotemporal evolution of the vorticity in (pure) mode B of a circular cylinder’s wake
Authors: Lin L M , Tan Z R
Published: January 2022

In the present paper, the spatio-temporal evolution of the vorticity field in the second wake instability, i.e. (pure) mode B is investigated to understand the wake vortex dynamics and sign relationships among the three vorticity components. Direct numerical simulation of the flow past a circular cylinder in the three-dimensional (3D) wake transition is performed, typically at a Reynolds number of 300. According to the time histories of fluid forces and frequency analysis, three different stages are identified. In the fully developed wake (FDW), the spanwise vortex core is almost two-dimensional, while the vortex braid is 3D due to the dominant streamwise interaction. However, streamwise and vertical vorticities owing to the intrinsic 3D instability are already generated first on cylinder surfaces early in the computational transition (CT). The evolution of additional vorticities with the same features as mode B shows that (pure) mode B could already be formed in the late CT. In the FDW, a special sign symmetry of these additional vorticities on the rear surface is observed, which is exactly opposite to that in (pure) mode B. Similarly, the two sign laws found in (pure) mode A are also verified in three typical regions, independent of the Reynolds number, for (pure) mode B. Particularly, the mechanism for the physical origin of streamwise and vertical vortices in the shear layers is the vortex generation on the wall first and then dominant vortex induction just near the wall. The entire process of the formation and shedding of vortices with three components of vorticity is first and completely illustrated. Other characteristics of the evolution of mode B are presented in detail.
Study on anisotropic behavior of 7075 Al alloy after extrusion
Authors: Zhang Yi , Ma Jin , Wang Qiang , Yang Yongbiao , Zhu Mingjie , Jia Penglai , Duan Yuhao , Zhang Zhimin
Published: January 2022

For an extrusion process of 7075 Al alloy, the extrusion direction of the initial blank is changed to study the mechanical properties of the formed plates and characterize their microstructure. The as-received bar is extruded 7075 Al alloy. The secondary extrusion deformation is along and perpendicular to the initial extrusion direction. The results show that the anisotropy of mechanical properties of the two samples decreases obviously after secondary deformation. The anisotropy of yield strength and ultimate tensile strength of ED90 sample is lower than that of ED0 sample, but the plastic anisotropy is slightly higher than that of ED0 sample. In addition, the recrystallized grain proportion of ED90 sample is high and the texture strength is low, so the Schmid factor in the three directions is similar. The tensile fracture mode of the two samples belongs to ductile fracture, but the morphology of dimple and the size of cleavage plane are slightly different.
Improving the stability of nanofluids via surface-modified titanium dioxide nanoparticles for wettability alteration of oil-wet carbonate reservoirs
Authors: Hosseini Marzieh Sadat , Khazaei Masoud , Misaghi Majid , Koosheshi Mohammad Hossein
Published: January 2022

The main challenge of the application of nanofluids for enhanced oil recovery (EOR) in oil-wet carbonate reservoirs is maintaining their stability under high-temperature and high-salinity which is normally seen in reservoir conditions. In this work, surface-modified TiO2 nanoparticles were synthesized by N-(2-Aminoethyl)−3-Aminopropyltrimethoxysilane (AEAPTMS) as a coupling agent for surface modification of nanoparticles. Zeta potential and dynamic light scattering analyses were used to evaluate the stability of the prepared nanofluids. Results indicated that nanofluids had high stability in 90 °C and 20 wt% salinity. The influence of nanofluids on wettability alteration of carbonate rocks was studied by measuring the contact angle value. Untreated rock samples were strongly oil-wet, with water advancing and receding contact angles of 165.1° and 166.2°, respectively. After treatment with 3wt% concentration of surface-modified TiO2 nanoparticles, the rock plate wettability changed to a water-wet state, with water advancing and receding contact angles of 37.6° and 48.2°, respectively. Suggested surface-modified TiO2 nanoparticles were more effective in wettability alteration of the rock surfaces compared to the un-modified TiO2 nanoparticles. Furthermore, higher concentration of nanoparticles, higher the ability of the nanoparticles on changing the rock wettability.
Safety evaluation of a beverage containing mulberry leaf extract
Authors: Yasumoto Keisuke , Hoshiko Hiroyuki , Sekiguchi Noriko , Obata Hidenori , Takara Tsuyoshi
Published: January 2022

Mulberry leaf extract (MLE) has known as inhibits elevated postprandial blood glucose level in human. Then, we conducted a randomized, double-blind placebo-controlled parallel-group trial to evaluate safety when a green tea containing MLE is consumed 3 times a day, every day for 4 weeks. The participants (n = 48) were randomly allocated into 2 groups, an MLE beverage group and a control beverage group. The subjects were instructed to drink either a 500 mL green tea containing 550 mg MLE or a 500 mL green tea not containing MLE, 3 times a day, every day, for 4 weeks. No adverse reactions were observed over the 4 weeks trial, and no difference in the incidence of adverse events between the groups. These findings demonstrate that the consumption of a green tea containing 550 mg MLE 3 times a day for 4 weeks is safe for healthy adults.
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem
Authors: Cameron Daniel L , Dong Ruining , Papenfuss Anthony T
Published: January 2022

StructuralVariantAnnotation is an R/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the three different notations supported by VCF into a breakpoint GRanges data structure suitable for use by the wider Bioconductor ecosystem. It handles both transitive breakpoints and duplication/insertion notational differences of identical variants—both common scenarios when comparing short/long read-based call sets that confound downstream analysis. StructuralVariantAnnotation provides the caller-agnostic foundation needed for a R/Bioconductor ecosystem of structural variant annotation, classification and interpretation tools able to handle both simple and complex genomic rearrangements.

Availability and implementation

StructuralVariantAnnotation is implemented in R and available for download as the Bioconductor StructuralVariantAnnotation package. Details can be found at https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.html. It has been released under a GPL license.
Vivarium: an interface and engine for integrative multiscale modeling in computational biology
Authors: Agmon Eran , Spangler Ryan K , Skalnik Christopher J , Poole William , Peirce Shayn M , Morrison Jerry H , Covert Markus W
Published: January 2022

Motivation

This article introduces Vivarium—software born of the idea that it should be as easy as possible for computational biologists to define any imaginable mechanistic model, combine it with existing models and execute them together as an integrated multiscale model. Integrative multiscale modeling confronts the complexity of biology by combining heterogeneous datasets and diverse modeling strategies into unified representations. These integrated models are then run to simulate how the hypothesized mechanisms operate as a whole. But building such models has been a labor-intensive process that requires many contributors, and they are still primarily developed on a case-by-case basis with each project starting anew. New software tools that streamline the integrative modeling effort and facilitate collaboration are therefore essential for future computational biologists.

Results

Vivarium is a software tool for building integrative multiscale models. It provides an interface that makes individual models into modules that can be wired together in large composite models, parallelized across multiple CPUs and run with Vivarium’s discrete-event simulation engine. Vivarium’s utility is demonstrated by building composite models that combine several modeling frameworks: agent-based models, ordinary differential equations, stochastic reaction systems, constraint-based models, solid-body physics and spatial diffusion. This demonstrates just the beginning of what is possible—Vivarium will be able to support future efforts that integrate many more types of models and at many more biological scales.

Availability and implementation

The specific models, simulation pipelines and notebooks developed for this article are all available at the vivarium-notebooks repository: https://github.com/vivarium-collective/vivarium-notebooks. Vivarium-core is available at https://github.com/vivarium-collective/vivarium-core, and has been released on Python Package Index. The Vivarium Collective (https://vivarium-collective.github.io) is a repository of freely available Vivarium processes and composites, including the processes used in Section 3. Supplementary Materials provide with an extensive methodology section, with several code listings that demonstrate the basic interfaces.

Supplementary information

Supplementary data are available at Bioinformatics online.
Wild-type p53 suppresses formin-binding protein-17 (FBP17) to reduce invasion
Authors: Suman Prabhat , Mehta Vikrant , Craig Andrew W B , Chander Harish
Published: January 2022

Invading tumor cells develop membrane protruding structures called invadopodia to invade and metastasize. Previously, we have reported the role of formin-binding protein-17 (FBP17) in extracellular matrix degradation and invadopodia formation in breast cancer cells. Here, we report a novel axis between tumor-suppressor p53 and FBP17. We observed that cell lines with mutant p53 express FBP17 to a higher level. The expression of FBP17 was reduced upon stabilizing wild-type p53. Furthermore, the immunohistochemistry analysis of breast cancer tissue microarrays demonstrated the correlation between the accumulation of p53 and enhanced FBP17 staining in invasive ductal carcinomas. The double knockdown of p53 and FBP17 showed the contribution of FBP17 in the invasion of cancer cells where p53 lost the regulatory control over FBP17. Taken together, these studies indicate that FBP17 may be a marker to understand the invasion propensity of breast cancer.
Whole-brain connectivity during encoding: age-related differences and associations with cognitive and brain structural decline
Authors: Capogna Elettra , Sneve Markus H , Raud Liisa , Folvik Line , Ness Hedda T , Walhovd Kristine B , Fjell Anders M , Vidal-Piñeiro Didac
Published: January 2022

There is a limited understanding of age differences in functional connectivity during memory encoding. In the present study, a sample of cognitively healthy adult participants (n = 488, 18–81 years), a subsample of whom had longitudinal cognitive and brain structural data spanning on average 8 years back, underwent functional magnetic resonance imaging while performing an associative memory encoding task. We investigated (1) age-related differences in whole-brain connectivity during memory encoding; (2) whether encoding connectivity patterns overlapped with the activity signatures of specific cognitive processes, and (3) whether connectivity associated with memory encoding related to longitudinal brain structural and cognitive changes. Age was associated with lower intranetwork connectivity among cortical networks and higher internetwork connectivity between networks supporting higher level cognitive functions and unimodal and attentional areas during encoding. Task-connectivity between mediotemporal and posterior parietal regions—which overlapped with areas involved in mental imagery—was related to better memory performance only in older age. The connectivity patterns supporting memory performance in older age reflected preservation of thickness of the medial temporal cortex. The results are more in accordance with a maintenance rather than a compensation account.
A neural network account of memory replay and knowledge consolidation
Authors: Barry Daniel N , Love Bradley C
Published: January 2022

Replay can consolidate memories through offline neural reactivation related to past experiences. Category knowledge is learned across multiple experiences, and its subsequent generalization is promoted by consolidation and replay during rest and sleep. However, aspects of replay are difficult to determine from neuroimaging studies. We provided insights into category knowledge replay by simulating these processes in a neural network which approximated the roles of the human ventral visual stream and hippocampus. Generative replay, akin to imagining new category instances, facilitated generalization to new experiences. Consolidation-related replay may therefore help to prepare us for the future as much as remember the past. Generative replay was more effective in later network layers functionally similar to the lateral occipital cortex than layers corresponding to early visual cortex, drawing a distinction between neural replay and its relevance to consolidation. Category replay was most beneficial for newly acquired knowledge, suggesting replay helps us adapt to changes in our environment. Finally, we present a novel mechanism for the observation that the brain selectively consolidates weaker information, namely a reinforcement learning process in which categories were replayed according to their contribution to network performance. This reinforces the idea of consolidation-related replay as an active rather than passive process.
Digital Strategy and Social Media for Infectious Diseases
Authors: Marcelin Jasmine R , del Rio Carlos , Spec Andrej , Swartz Talia H
Published: January 2022

This supplement demonstrates the profound reach of social media across several domains: improved clinical care and advocacy, data analysis, broad reach to diverse patient populations, educational access, best practices in medical education, peer review, digital strategy for individuals and institutions, and combating misinformation.
Predicting the Risk of Human Immunodeficiency Virus Type 1 (HIV-1) Acquisition in Rural South Africa Using Geospatial Data
Authors: Roberts D Allen , Cuadros Diego , Vandormael Alain , Gareta Dickman , Barnabas Ruanne V , Herbst Kobus , Tanser Frank , Akullian Adam
Published: January 2022

Background

Accurate human immunodeficiency virus (HIV) risk assessment can guide optimal HIV prevention. We evaluated the performance of risk prediction models incorporating geospatial measures.

Methods

We developed and validated HIV risk prediction models in a population-based cohort in South Africa. Individual-level covariates included demographic and sexual behavior measures, and geospatial covariates included community HIV prevalence and viral load estimates. We trained models on 2012–2015 data using LASSO Cox models and validated predictions in 2016–2019 data. We compared full models to simpler models restricted to only individual-level covariates or only age and geospatial covariates. We compared the spatial distribution of predicted risk to that of high incidence areas (≥ 3/100 person-years).

Results

Our analysis included 19 556 individuals contributing 44 871 person-years and 1308 seroconversions. Incidence among the highest predicted risk quintile using the full model was 6.6/100 person-years (women) and 2.8/100 person-years (men). Models using only age group and geospatial covariates had similar performance (women: AUROC = 0.65, men: AUROC = 0.71) to the full models (women: AUROC = 0.68, men: AUROC = 0.72). Geospatial models more accurately identified high incidence regions than individual-level models; 20% of the study area with the highest predicted risk accounted for 60% of the high incidence areas when using geospatial models but only 13% using models with only individual-level covariates.

Conclusions

Geospatial models with no individual measures other than age group predicted HIV risk nearly as well as models that included detailed behavioral data. Geospatial models may help guide HIV prevention efforts to individuals and geographic areas at highest risk.
Relating In Vitro Neutralization Level and Protection in the CVnCoV (CUREVAC) Trial
Authors: Cromer Deborah , Reynaldi Arnold , Steain Megan , Triccas James A , Davenport Miles P , Khoury David S
Published: January 2022

The vaccine candidate CVnCoV (CUREVAC) showed surprisingly low efficacy in a recent phase 3 trial compared with other messenger RNA (mRNA) vaccines. Here we show that the low efficacy follows from the dose used and the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and is predicted by the neutralizing antibody response induced by the vaccine.
The impact of a cause–effect elaboration procedure on information security risk perceptions: a construal fit perspective
Authors: Goh Zhang Hao , Hou Minzheng , Cho Hichang
Published: January 2022

Cybersecurity breaches are on the rise. Extant literature in the development of strategies to enhance IT users’ online protective behaviours has neglected users’ cognitive processing of cybersecurity risk information. This study demonstrates a cause–effect elaboration procedure based on the concept of construal fit to influence online users’ cybersecurity risk perceptions. Using online experiments (N = 534), the construal fit between elaboration of causes vs effects of cybersecurity risks and perceived temporal distance (distant vs near) was manipulated. The results revealed that a construal fit between the elaboration of ‘effects’ (vs ‘causes’) and temporally ‘near’ (vs ‘distant’) cybersecurity risks enhanced users’ risk perceptions, which in turn predicted protective behavioural intentions. Ensuring construal fit is a novel, cognition-based approach to safeguard IT users against online threats. Our findings enrich existing staged theories used to investigate cybersecurity risk perceptions and suggest to practitioners that heightened cyber risk perception can effectively be induced by simultaneously enhancing the concreteness of IT users’ construal of cybersecurity incidents and emphasizing on its negative consequences (vs causes).
Overcoming information-sharing challenges in cyber defence exercises
Authors: Brilingaitė Agnė , Bukauskas Linas , Juozapavičius Aušrius , Kutka Eduardas
Published: January 2022

Active usage of threat intelligence information supports effective prevention, mitigation and defence against cyberattacks by threat actors ranging from individual amateurs to state organizations. However, threat intelligence highly depends on security specialists’ ability to share incident data on threat information-sharing platforms. Unfortunately, business managers and educational institutions undervalue the information-sharing aspect when planning the professional development of cybersecurity-related specialists. Consequently, cybersecurity specialists are insufficiently motivated to correctly communicate and propagate relevant information with team members, superiors, relevant institutions and the global community about the impact of the incident. Literature review reveals many technological, legal and psychological obstacles hindering successful information exchange. This research aims to improve threat information sharing by focusing on the educational aspect of the problem and analysing the attitude of cybersecurity specialists during cyber defence exercises (CDX). Our case study disclosed nine factors obstructing both proper reporting to relevant authorities and adequate communication among teams. By addressing these factors, CDX organizers could substantially improve the development of highly beneficial soft skills of the technical specialists.
An enormous right atrial myxoma highlights the role of echocardiography in heart failure pathways: a case report
Authors: Straw Sam , Sengupta Anshuman , Gantenby V Kate , Schlosshan Dominik , Ferrara Antonella , Witte Klaus K
Published: January 2022

Background

Myxomata are rare, benign, primary tumours of the heart which can present with a variety of symptoms depending on size, location, and mobility. Here, we report a case of enormous right atrial myxoma, obliterating the right atrial and right ventricular cavities presenting with symptoms of heart failure.

Case summary

A 66-year-old Caucasian female presented to primary care with symptoms of right heart failure and was found to have elevated N-terminal pro B-type natriuretic peptide of 2829 ng/L (normal value <125 ng/L). The patient was referred for urgent evaluation to the integrated heart failure service at our institution. Echocardiography revealed an enormous mobile mass attached to the right atrial septum, extending into the right ventricle and inferior vena cava measuring 90 × 42 mm. The patient underwent urgent surgical resection. Perioperative transoesophageal echocardiography demonstrated severe tricuspid regurgitation, which was treated with tricuspid annuloplasty ring. The patient made an uneventful recovery and was discharged. Subsequent imaging showed a reduction in right ventricular dimensions and improved systolic function.

Discussion

This case serves to remind us of the critical role of echocardiography in the diagnosis and management of people with breathlessness and raised natriuretic peptides. Therapies for heart failure are guided by ejection fraction, therefore timely and accurate diagnosis is critical. Moreover, as in this case, echocardiography can also identify other features of critical relevance to patient care.
Progression of aortic valve insufficiency during centrifugal versus axial flow left ventricular assist device support
Authors: Jimenez Contreras Fabian , Mendiola Pla Michelle , Schroder Jacob , Bryner Benjamin , Agarwal Richa , Russell Stuart D , Mirza Jacqueline , Daneshmand Mani A , Milano Carmelo
Published: January 2022

OBJECTIVES

Long-term left ventricular assist device (LVAD) support can cause accelerated progression of aortic insufficiency (AI). The MOMENTUM trial has led to increased use of the HeartMate 3 (HM3) LVAD, due to greater hemocompatibility. However, the differential effect on the rate of progression of AI during HM3 support versus HeartMate 2 (HM2) has not been extensively studied. This analysis compares the rates of progression to moderate or severe AI (MSAI) comparing a cohort of patients supported with the HM2 versus HM3.

METHODS

A retrospective review was performed on all consecutive patients implanted with HM2 or HM3 between May 2005 and June 2020. Follow-up time was limited to the first 6 years after LVAD implantation. Demographics and 4005 echocardiograms were assessed for 536 HM2 and 300 HM3 patients. The primary end point was progression to MSAI. Univariable and multivariable Cox proportional hazard regression and landmark analyses were performed.

RESULTS

Progression to MSAI was greater in the HM2 (17%) versus HM3 (9.9%) cohort. On the univariable analysis, the hazard ratio for HM3 was 0.581 (95% confidence interval 0.370–0.909, P = 0.02) whereas on multivariable analysis hazard ratio was 0.624 (95% confidence interval 0.386–1.008, P = 0.0537). Preoperative AI, female sex and body surface area <2 were significantly associated with progression to MSAI. Landmark analysis suggests that LVAD type has the most significant effect on progression to MSAI between 1 and 2 years post-implantation.

CONCLUSIONS

Current practice strategies achieved low rates of progression to MSAI. Preoperative AI, female sex and body surface area <2 were the most important predictors of progression to MSAI. Pump type appears to be of secondary importance.
Immune cell type and DNA methylation vary with reproductive status in women: possible pathways for costs of reproduction
Authors: Ryan Calen P , Jones Meaghan J , Edgar Rachel D , Lee Nanette R , Kobor Michael S , McDade Thomas W , Kuzawa Christopher W
Published: January 2022

Background

Consistent with evolutionarily theorized costs of reproduction (CoR), reproductive history in women is associated with life expectancy and susceptibility to certain cancers, autoimmune disorders and metabolic disease. Immunological changes originating during reproduction may help explain some of these relationships.

Methodology

To explore the potential role of the immune system in female CoR, we characterized leukocyte composition and regulatory processes using DNA methylation (DNAm) in a cross-sectional cohort of young (20–22 years old) women differing in reproductive status.

Results

Compared to nulliparity, pregnancy was characterized by differential methylation at 828 sites, 96% of which were hypomethylated and enriched for genes associated with T-cell activation, innate immunity, pre-eclampsia and neoplasia. Breastfeeding was associated with differential methylation at 1107 sites (71% hypermethylated), enriched for genes involved in metabolism, immune self-recognition and neurogenesis. There were no significant differences in DNAm between nulliparous and parous women. However, compared to nullipara, pregnant women had lower proportions of B, CD4T, CD8T and natural killer (NK) cells, and higher proportions of granulocytes and monocytes. Monocyte counts were lower and NK counts higher among breastfeeding women, and remained so among parous women.

Implications

Our findings point to widespread differences in DNAm during pregnancy and lactation. These effects appear largely transient, but may accumulate with gravidity become detectable as women age. Nulliparous and parous women differed in leukocyte composition, consistent with more persistent effects of reproduction on cell type. These findings support transient (leukocyte DNAm) and persistent (cell composition) changes associated with reproduction in women, illuminating potential pathways contributing to CoR.

Lay Summary: Evolutionary theory and epidemiology support costs of reproduction (CoR) to women’s health that may involve changes in immune function. We report differences in immune cell composition and gene regulation during pregnancy and breastfeeding. While many of these differences appear transient, immune cell composition may remain, suggesting mechanisms for female CoR.
A Stall Only on the Surface? Working Hours and the Persistence of the Gender Wage Gap in Western Germany 1985–2014
Authors: Schmitt Laila , Auspurg Katrin
Published: January 2022

To what extent has the closing of the gender gap in hourly wages (‘gender wage gap’; GWG) in Western Germany stalled due to an increasing supply of non-standard working hours? We use descriptive trend analyses and Juhn–Murphy–Pierce decompositions of German Socio-Economic Panel data for the last 30 years (1985–2014) to analyse the extent to which the expansion of part-time and marginal work, as well as overwork, may have contributed to the dynamics of the GWG in Western Germany. We find that the large increase in part-time work among women in combination with increasing wage gaps between part-time and full-time work substantially widened the GWG (by about one-sixth). Working hour effects were large enough to offset the equalizing effects of declining gender gaps in human capital, and they existed even in the public sector. In contrast to the United States, trends in overwork did not have a meaningful impact on the GWG. In an add-on, we find a widening of the gender gap in monthly earnings, but also an important closing of the gender earnings gap unconditional on employment due to an increased labour supply of women. Our results suggest that working hours should be given more consideration in research on family–work conflict and gender earnings inequalities.
What makes working together work? A scoping review of the guidance on North–South research partnerships
Authors: Voller Shirine , Schellenberg Joanna , Chi Primus , Thorogood Nicki
Published: January 2022

At their best, research partnerships provide a mechanism to optimize each partner’s strengths, make scientific discoveries and achieve development goals. Each partner stands to gain from the relationship and perceives it to be fair. However, partnerships between institutions in the global North and the global South have been beleaguered by structural inequalities and power imbalances, and Northern stakeholders have been criticized for perpetuating paternalistic or neo-colonial behaviours. As part of efforts to redress imbalances and achieve equity and mutual benefit, various principles, guidelines, frameworks and models for partnership have been developed. This scoping review maps the literature and summarizes key features of the guidelines for North–South research partnerships. The review was conducted between October 2020 and January 2021. Three academic journal databases and Google were searched, and additional resources were identified through a hand search of reference lists and expert recommendation. Twenty-two guidelines were identified published between 1994 and 2021 and originating predominantly in the fields of international development and global health. The themes addressed within the guidelines were aggregated using NVivo qualitative analysis software to code the content of each guideline. Topics featuring most prominently in the guidelines were: partner roles, responsibilities and ways of working; capacity strengthening; motivation and goals; resource contributions; agenda setting and study design; governance structures and institutional agreements; dissemination; respect for affected populations; data handling and ownership; funding and long-term commitments. The current study reinforces many of the themes from two recent scoping reviews specific to the field of global health, but gaps remain, which need to be addressed: Southern stakeholders continue to be under-represented in guideline development, and there is limited evidence of how guidelines are used in practice. Further exploration is needed of Southern stakeholder priorities and whether and how guidelines are operationalized.
Obesity and Cerebral Blood Flow in the Reward Circuitry of Youth With Bipolar Disorder
Authors: Grigorian Anahit , Kennedy Kody G , Luciw Nicholas J , MacIntosh Bradley J , Goldstein Benjamin I
Published: January 2022

Background

Bipolar disorder (BD) is associated with elevated body mass index (BMI) and increased rates of obesity. Obesity among individuals with BD is associated with more severe course of illness. Motivated by previous research on BD and BMI in youth as well as brain findings in the reward circuit, the current study investigates differences in cerebral blood flow (CBF) in youth BD with and without comorbid overweight/obesity (OW/OB).

Methods

Participants consisted of youth, ages 13–20 years, including BD with OW/OB (BDOW/OB; n = 25), BD with normal weight (BDNW; n = 55), and normal-weight healthy controls (HC; n = 61). High-resolution T1-weighted and pseudo-continuous arterial spin labeling images were acquired using 3 Tesla magnetic resonance imaging. CBF differences were assessed using both region of interest and whole-brain voxel-wise approaches.

Results

Voxel-wise analysis revealed significantly higher CBF in reward-associated regions in the BDNW group relative to the HC and BDOW/OB groups. CBF did not differ between the HC and BDOW/OB groups. There were no significant region of interest findings.

Conclusions

The current study identified distinct CBF levels relating to BMI in BD in the reward circuit, which may relate to underlying differences in cerebral metabolism, compensatory effects, and/or BD severity. Future neuroimaging studies are warranted to examine for changes in the CBF-OW/OB link over time and in relation to treatment.
A Separable Universal Homogeneous Banach Lattice
Authors: Angelica Tursi Mary
Published: January 2022

We prove the existence of a separable approximately ultra-homogeneous Banach lattice $\mathfrak {B}\mathfrak {L}$ that is isometrically universal for separable Banach lattices. This is done by showing that that the class of finitely generated Banach lattices has the Amalgamation Property and thus form a metric Fraïssé class. Some additional results about the structural properties of $\mathfrak { BL}$ are also proven.
Serum Vitamin D Levels and Life-Threatening Respiratory Syncytial Virus Infection in Previously Healthy Infants
Authors: Ferolla F Martin , Yfran E Walter , Ballerini M Gabriela , Caratozzolo Ana , Toledano Analía , Giordano Ana C , Acosta Patricio L , Cassinelli Hamilton , Bergada Ignacio , Ropelato M Gabriela , Contrini María M , López Eduardo L ,   GUTI Respiratory Infections Network, Neira Pablo , Carrizo Bárbara , Chiormi Agustina , Visingardi Gabriela , Feldman Florencia , Reyero Mariana , Talarico Laura , Retta Alejandra , Matute Javier , Mascardi Normando
Published: January 2022

Background

25-hydroxyvitamin D (VD) effects on lung function and immune-modulation might affect respiratory syncytial virus (RSV) infection outcomes. We aimed to assess VD levels on admission and their association with life-threatening RSV disease (LTD).

Methods

A prospective cohort study was conducted during 2017–2019. Previously healthy infants aged <12 months, hospitalized with a first episode of RSV infection, were enrolled. LTD was defined by need for intensive care and ventilatory support. Serum VD levels <20 ng/mL were categorized as deficient, and 20–29.9 ng/mL as insufficient.

Results

Of 125 patients studied, 73 (58%) were male. Median age was 4 months. Twenty-two patients developed LTD. No differences in viral load were seen between cases with LTD and controls (P = .94). Patients who developed LTD had significantly lower VD levels: median 18.4 ng/mL (IQR, 15.1–26.9 ng/mL) versus 31.7 ng/mL (IQR, 23.6–42.0 ng/mL), P < .001; 59% of infants with LTD had VD deficiency compared with 12% in those with better outcome. Multivariable regression analysis confirmed VD deficiency as a risk factor (odds ratio, 11.83; 95% confidence interval, 3.89–35.9; P < .001).

Conclusions

These findings provide additional evidence for the development of strategies to prevent severe RSV infections.
Spectrum of Activity of Raltegravir and Dolutegravir Against Novel Treatment-Associated Mutations in HIV-2 Integrase: A Phenotypic Analysis Using an Expanded Panel of Site-Directed Mutants
Authors: Smith Robert A , Wu Vincent H , Song Jennifer , Raugi Dana N , Diallo Mbaye Khardiata , Seydi Moussa , Gottlieb Geoffrey S
Published: January 2022

Background

Integrase inhibitors (INIs) are a key component of antiretroviral therapy for human immunodeficiency virus-1 (HIV-1) and HIV-2 infection. Although INI resistance pathways are well-defined for HIV-1, mutations that emerge in HIV-2 in response to INIs are incompletely characterized.

Methods

We performed systematic searches of GenBank and HIV-2 drug resistance literature to identify treatment-associated mutations for phenotypic evaluation. We then constructed a library of 95 mutants of HIV-2ROD9 that contained single or multiple amino acid changes in the integrase protein. Each variant was tested for susceptibility to raltegravir and dolutegravir using a single-cycle indicator cell assay.

Results

We observed extensive cross-resistance between raltegravir and dolutegravir in HIV-2ROD9. HIV-2–specific integrase mutations Q91R, E92A, A153G, and H157Q/S, which have not been previously characterized, significantly increased the half maximum effective concentration (EC50) for raltegravir when introduced into 1 or more mutational backgrounds; mutations E92A/Q, T97A, and G140A/S conferred similar enhancements of dolutegravir resistance. HIV-2ROD9 variants encoding G118R alone, or insertions of residues SREGK or SREGR at position 231, were resistant to both INIs.

Conclusions

Our analysis demonstrates the contributions of novel INI-associated mutations to raltegravir and dolutegravir resistance in HIV-2. These findings should help to improve algorithms for genotypic drug resistance testing in HIV-2–infected individuals.
Performing Rebellion: Karaoke as a Lens into Political Violence
Authors: Brenner David
Published: January 2022

In explaining political violence, Conflict and Security Studies commonly focuses on the rational decision-making of elites. In contrast, this article considers the everyday aspirations of rebel grassroots. Understanding their lifeworlds is important, as their interaction with rebel elites shapes the collective trajectories of revolutionary movements and, thus, wider dynamics of war and peace. This article analyzes the social practice of revolutionary karaoke music in Myanmar's Kachin rebellion as a window into these hidden social dynamics of political violence. It does so by merging a relational reading of rebel figurations with a visual ethnographic methodology that moves beyond the textual study of propaganda lyrics. Instead, it analyzes the audio-visual aesthetics and social practices of revolutionary karaoke. This critical mode of inquiry reveals the emotional dimension of rebellion, that is, its appeal to affect rather than reason. It also suggests that revolutionary cultural artifacts can be more than just instrumental propaganda vehicles for instilling elite ideologies into un-agential masses. Indeed, the article shows that many young Kachin are not just passive consumers of propaganda. In karaoke bars and music studios, they actively perform rebellion. In so doing, they coproduce their own rebel subjectivities and rebel political culture at large.
“A splendid norm”: Human Plants and the Eugenic Secular, 1906–1926
Authors: McCrary Charles
Published: January 2022

This article analyzes eugenics and the secular in early twentieth-century California through the career of Luther Burbank. Burbank was a famous plant breeder who cultivated a theory of human progress based on his breeding work. For him, humans were part of an always-evolving and immanently spiritual natural world. And it was the task of civilized people to perfect that world, making it more beautiful and more productive. This project rested on an enchanted secularization narrative in which the wondrous natural world is made better through human direction. Late in his life, in the 1920s, Burbank turned his attention to fundamentalists and their “primitive” and “superstitious” beliefs about evolution. With attention to the aesthetics of the secular, this article analyzes secularism as a biopolitical project that racializes religion and its others. In Burbank’s case, this project is the result of a liberal romanticism that sought to unite spirituality and science.
Comparing ascertainment of chronic condition status with problem lists versus encounter diagnoses from electronic health records
Authors: Voss Robert W , Schmidt Teresa D , Weiskopf Nicole , Marino Miguel , Dorr David A , Huguet Nathalie , Warren Nate , Valenzuela Steele , O’Malley Jean , Quiñones Ana R
Published: January 2022

Objective

To assess and compare electronic health record (EHR) documentation of chronic disease in problem lists and encounter diagnosis records among Community Health Center (CHC) patients.

Materials and methods

We assessed patient EHR data in a large clinical research network during 2012–2019. We included CHCs who provided outpatient, older adult primary care to patients age ≥45 years, with ≥2 office visits during the study. Our study sample included 1 180 290 patients from 545 CHCs across 22 states. We used diagnosis codes from 39 Chronic Condition Warehouse algorithms to identify chronic conditions from encounter diagnoses only and compared against problem list records. We measured correspondence including agreement, kappa, prevalence index, bias index, and prevalence-adjusted bias-adjusted kappa.

Results

Overlap of encounter diagnosis and problem list ascertainment was 59.4% among chronic conditions identified, with 12.2% of conditions identified only in encounters and 28.4% identified only in problem lists. Rates of coidentification varied by condition from 7.1% to 84.4%. Greatest agreement was found in diabetes (84.4%), HIV (78.1%), and hypertension (74.7%). Sixteen conditions had <50% agreement, including cancers and substance use disorders. Overlap for mental health conditions ranged from 47.4% for anxiety to 59.8% for depression.

Discussion

Agreement between the 2 sources varied substantially. Conditions requiring regular management in primary care settings may have a higher agreement than those diagnosed and treated in specialty care.

Conclusion

Relying on EHR encounter data to identify chronic conditions without reference to patient problem lists may under-capture conditions among CHC patients in the United States.
Symmetrically partitioned isotropic model for quantitative equivalent simulation of circumferential anisotropy
Authors: Song Yunhong , Chen Hao , Li Chao , Li Wei
Published: January 2022

Simulation wells with known parameters are vital in the study of anisotropic methods and logging equipment development. We propose a symmetrically partitioned isotropic (SPI) model, which can quantitatively control the parameters of equivalent circumferential anisotropy. First, the circumferential anisotropy of the flexural wave dispersion in the SPI model is analysed using a perturbation method, and the azimuth characteristics of the flexural wave and the wave velocity in the model are evaluated using a numerical simulation algorithm. Next, the circumferential anisotropy characteristics of the model are verified. Finally, the linear relationship between the fast and slow shear-wave velocities of the model and the model parameters is obtained through multiple linear regression analyses, and then, the equivalent circumferential anisotropy is predicted. The feasibility of the quantitative equivalent simulation of circumferential anisotropy media using the SPI model is verified.
Zero-offset data estimation using CNN for applying 1D full waveform inversion
Authors: Lee Dawoon , Shin Sungryul , Son Woohyun , Chung Wookeen
Published: January 2022

Full waveform inversion (FWI) in the time domain has limitations due to large computing time and memory requirements. Some studies have addressed this problem by using machine learning techniques. Most FWI studies using machine learning directly estimate the subsurface velocity structure by training the seismic data generated through various synthetic models to obtain the subsurface velocity structure. In this study, we propose a method to convert the common midpoint (CMP) gather to zero-offset data at a CMP location using a convolutional neural network (CNN) to increase the computing efficiency for the FWI. As the training data, we use synthetic data generated by the seismic exploration geometry and the source signature of field data. Since the proposed method performs FWI using the converted zero-offset data, it can be performed more efficiently than FWI using the existing multichannel data. However, it is difficult to apply a seismic exploration geometry and a source signature that has not been used for training. To verify the proposed method, it is applied to a synthetic model not used for learning as well as focused field data. It is confirmed that a proper subsurface velocity structure was obtained.
Intrinsic entropy model for feature selection of scRNA-seq data
Authors: Li Lin , Tang Hui , Xia Rui , Dai Hao , Liu Rui , Chen Luonan
Published: January 2022

Recent advances of single-cell RNA sequencing (scRNA-seq) technologies have led to extensive study of cellular heterogeneity and cell-to-cell variation. However, the high frequency of dropout events and noise in scRNA-seq data confounds the accuracy of the downstream analysis, i.e. clustering analysis, whose accuracy depends heavily on the selected feature genes. Here, by deriving an entropy decomposition formula, we propose a feature selection method, i.e. an intrinsic entropy (IE) model, to identify the informative genes for accurately clustering analysis. Specifically, by eliminating the ‘noisy’ fluctuation or extrinsic entropy (EE), we extract the IE of each gene from the total entropy (TE), i.e. TE = IE + EE. We show that the IE of each gene actually reflects the regulatory fluctuation of this gene in a cellular process, and thus high-IE genes provide rich information on cell type or state analysis. To validate the performance of the high-IE genes, we conduct computational analysis on both simulated datasets and real single-cell datasets by comparing with other representative methods. The results show that our IE model is not only broadly applicable and robust for different clustering and classification methods, but also sensitive for novel cell types. Our results also demonstrate that the intrinsic entropy/fluctuation of a gene serves as information rather than noise in contrast to its total entropy/fluctuation.
Racial and Ethnic Differences in Genomic Profiling of Early Onset Colorectal Cancer
Authors: Hein David M , Deng Weiye , Bleile MaryLena , Kazmi Syed Ali , Rhead Brooke , De La Vega Francisco M , Jones Amy L , Kainthla Radhika , Jiang Wen , Cantarel Brandi , Sanford Nina N
Published: January 2022

The incidence and mortality of early onset colorectal cancer (EOCRC) is rising; outcomes appear to differ by race and ethnicity. We aimed to assess differences in mutational landscape and gene expression of EOCRC by racial and ethnic groups (non-Hispanic Asian, non-Hispanic Black, non-Hispanic White, White Hispanic) using data from the American Association for Cancer Research Project GENIE (10.2) and University of Texas Southwestern, the latter enriched in Hispanic patients. All statistical tests were 2-sided. Of 1752 EOCRC patients, non-Hispanic Black patients had higher rates of KRAS mutations (60.9%; P = .001, q = 0.015), and non-Hispanic White and non-Hispanic Black patients had higher rates of APC mutations (77.1% and 76.6% among non-Hispanic White and non-Hispanic Black patients, respectively; P = .001, q = 0.015) via the Fisher exact test with Benjamini-Hochberg correction. Using R packages DESeq2 and clusterProfiler, we found that White Hispanic patients had increased expression of genes involved in oxidative phosphorylation (P < .001, q = 0.025). Genomic profiling has the potential to identify novel diagnostics and influence individualized treatment options to address the currently limited prognosis of EOCRC.