bluuebunny/crossref_metadata_2025 huggingface dataset:
Adverse Childhood Experiences, Depression, Patient Activation, and Medication Adherence Among Patients With Uncontrolled Hypertension
Authors: Alvarez Carmen , Perrin Nancy , Carson Kathryn A , Marsteller Jill A , Cooper Lisa A ,   RICH LIFE Project Investigators
Published: October 2022

Background

Identifying potential pathways through which adverse childhood experiences (ACEs) impact health and health behavior remains important, given ACE survivors’ increased risk for cardiovascular disease and poor cardiovascular health behaviors. This study examines whether modifiable variables—depression and patient activation—explain the relationship between ACEs and medication adherence.

Methods

Using baseline data from a pragmatic trial designed to decrease disparities in hypertension control, we conducted regression analyses to examine whether depression and patient activation mediated the association between ACEs and medication adherence. Data were collected between August 2017 and October 2019 (n = 1,818).

Results

Participants were predominantly female (59.4%) and Black or African American (57%) with uncontrolled blood pressure (mean—152.3/85.5 mm Hg). Most participants reported experiencing at least 1 ACE (71%) and approximately 50% reported being adherent to their blood pressure medication. A significant indirect effect between ACEs and medication adherence was found for depression symptoms (Sobel’s test z = −5.46, P < 0.001). Patient activation was not a mediator in these relationships.

Conclusions

Experiencing more depression symptoms significantly accounted for the association between ACEs and medication adherence in a diverse sample of adults with uncontrolled blood pressure. Addressing depression symptoms, which may result from experiences with ACEs and other current stressors, could translate to better medication adherence and, potentially, better blood pressure control among this high-risk group. Given the serious lifetime health implications of ACEs, continued efforts are needed for primary prevention of childhood adversities.
The relationship between the main leaf traits and photosynthetic physiological characteristics ofPhragmites australisunder different habitats of a salt marsh in Qinwangchuan, China
Authors: Li Qun , Wen Jun , Zhao Cheng-Zhang , Zhao Lian-Chun , Ke Dan
Published: October 2022

Plant leaf morphological and photosynthetic physiological characteristics are key functional traits in the adaptability of plants to heterogeneous environments. Analysis of the correlation between leaf morphological traits and photosynthetic physiological characteristics of salt marsh plants is helpful to deepen our understanding of how salt marsh plants adjust their leaf structure and function to adapt to their environment. However, there have been few studies on the relationship between leaf morphology and photosynthetic physiological characteristics of plants in inland salt marshes under a habitat gradient. A Phragmites australis community was divided into three plots based on differences in the wetland habitat conditions: a remote water area (plot I, 400–550 m from the water margin), a middle water area (plot II, 200–350 m from the water margin) and a near water area (plot III, 0–150 m from the water margin). The relationship between leaf morphological traits and photosynthetic physiological parameters of P. australis in heterogeneous habitats was studied. The results showed that as the habitat conditions changed from plot I to plot III, the soil characteristics, above-ground characteristics of the community and the photosynthetically active radiation changed significantly (P < 0.05). Besides, there was a highly significant positive correlation (P < 0.01) between leaf dry weight (LDW) and net photosynthetic rate (Pn), the effective quantum yield of PSII photochemistry (Y(II), actual photochemical efficiency of PSII) and photochemical quenching (QP); and between leaf area and Pn, Y(II) and QP in the three habitats. Moreover, in plot I, P. australis tended to have small and thick leaves with a low LDW and specific leaf area. In plot III, leaves were large and thin to adapt to the change in habitat conditions. This study provides a scientific theoretical basis for understanding the ecological adaptation strategies of plants in the harsh environment of an inland salt marsh and the conservation and management of wetland plants.
ConsensuSV—from the whole-genome sequencing data to the complete variant list
Authors: Chiliński Mateusz , Plewczynski Dariusz
Published: October 2022

The detection of the structural variants (SVs) using Illumina sequencing of human DNA is not an easy task. Multiple approaches have been proposed; however, all the methods have their limitations. In this article, we present ConsensuSV pipeline that aids the research in complex variant detection. By using consensus meta-approach, eight independent SV callers are being used to identify a uniform set of high-quality SVs. The pipeline works using raw sequencing data and performs all the necessary steps automatically, significantly reducing the researchers’ time required for processing the data. The output files contain SVs, single nucleotide polymorphisms and Indels. The pipeline uses luigi framework, allowing the software to be run efficiently and parallelly using the high-performance computing infrastructure. We strongly believe that the software is useful to the scientific community interested in the germline variant detection.

Availability and implementation

https://github.com/SFGLab/ConsensuSV-pipeline.

Supplementary information

Supplementary data are available at Bioinformatics online.
Mnk1/2 kinases regulate memory and autism-related behaviours via Syngap1
Authors: Chalkiadaki Kleanthi , Hooshmandi Mehdi , Lach Gilliard , Statoulla Elpida , Simbriger Konstanze , Amorim Ines S , Kouloulia Stella , Zafeiri Maria , Pothos Panagiotis , Bonneil Éric , Gantois Ilse , Popic Jelena , Kim Sung-Hoon , Wong Calvin , Cao Ruifeng , Komiyama Noboru H , Atlasi Yaser , Jafarnejad Seyed Mehdi , Khoutorsky Arkady , Gkogkas Christos G
Published: October 2022

MAPK interacting protein kinases 1 and 2 (Mnk1/2) regulate a plethora of functions, presumably via phosphorylation of their best characterized substrate, eukaryotic translation initiation factor 4E (eIF4E) on Ser209. Here, we show that, whereas deletion of Mnk1/2 (Mnk double knockout) impairs synaptic plasticity and memory in mice, ablation of phospho-eIF4E (Ser209) does not affect these processes, suggesting that Mnk1/2 possess additional downstream effectors in the brain. Translational profiling revealed only a small overlap between the Mnk1/2- and phospho-eIF4E(Ser209)-regulated translatome. We identified the synaptic Ras GTPase activating protein 1 (Syngap1), encoded by a syndromic autism gene, as a downstream target of Mnk1 because Syngap1 immunoprecipitated with Mnk1 and showed reduced phosphorylation (S788) in Mnk double knockout mice. Knockdown of Syngap1 reversed memory deficits in Mnk double knockout mice and pharmacological inhibition of Mnks rescued autism-related phenotypes in Syngap1+/− mice. Thus, Syngap1 is a downstream effector of Mnk1, and the Mnks–Syngap1 axis regulates memory formation and autism-related behaviours.
Squid Game and the imagining of Afro-Asian connections through Black Twitter memescapes
Authors: Love Ta’Les , Kim Youngrim
Published: October 2022

The release of Netflix’s Squid Game facilitated a viral pop culture moment, as the show’s critique of capitalism and structural inequality resonated with global audiences. Memes about the series were frequently shared across social media, as users interpolated themselves into the Squid Game universe. We argue that the memes produced by Black Twitter users are a form of meme play that can be read as a significant moment in the shared cultural and activist lineage of Black and Korean communities. Although racial tension is often at the center of the relationship between these two marginalized groups, we suggest that Black Twitter users’ interpolation of themselves into a distinctly Korean cultural product provides us with a chance to imagine how interracial solidarities can be visualized. This is significant in the age of the Black Lives Matter and Stop Asian Hate Movements, which are supported by members of both communities.
Higher Levels of Cerebrospinal Fluid and Plasma Neurofilament Light in Human Immunodeficiency Virus-Associated Distal Sensory Polyneuropathy
Authors: Ellis Ronald J , Chenna Ahmed , Lie Yolanda , Curanovic Dusica , Winslow John , Tang Bin , Marra Christina M , Rubin Leah H , Clifford David B , McCutchan J Allen , Gelman Benjamin B , Robinson-Papp Jessica , Petropoulos Christos J , Letendre Scott L
Published: October 2022

Background

Neurofilament light (NFL) chain concentrations, reflecting axonal damage, are seen in several polyneuropathies but have not been studied in human immunodeficiency virus (HIV) distal sensory polyneuropathy (DSP). We evaluated NFL in cerebrospinal fluid (CSF) and plasma in relation to DSP in people with HIV (PWH) from 2 independent cohorts and in people without HIV (PWoH).

Methods

Cohort 1 consisted of PWH from the CHARTER Study. Cohort 2 consisted of PWH and PWoH from the HIV Neurobehavioral Research Center (HNRC). We evaluated DSP signs and symptoms in both cohorts. Immunoassays measured NFL in CSF for all and for plasma as well in Cohort 2.

Results

Cohort 1 consisted of 111 PWH, mean ± SD age 56.8 ± 8.32 years, 15.3% female, 38.7% Black, 49.6% White, current CD4+ T-cells (median, interquartile range [IQR]) 532/µL (295, 785), 83.5% with plasma HIV RNA ≤50 copies/mL. Cohort 2 consisted of 233 PWH of similar demographics to PWH in Cohort 1 but also 51 PWoH, together age 58.4 ± 6.68 years, 41.2% female, 18.0% Black, Hispanic, non-Hispanic White 52.0%, 6.00% White. In both cohorts of PWH, CSF and plasma NFL were significantly higher in both PWH with DSP signs. Findings were similar, albeit not significant, for PWoH. The observed relationships were not explained by confounds.

Conclusions

Both plasma and CSF NFL were elevated in PWH and PWoH with DSP. The convergence of our findings with others demonstrates that NFL is a reliable biomarker reflecting peripheral nerve injury. Biomarkers such as NFL might provide, validate, and optimize clinical trials of neuroregenerative strategies in HIV DSP.
Effectiveness of Evusheld in Immunocompromised Patients: Propensity Score–Matched Analysis
Authors: Najjar-Debbiny Ronza , Gronich Naomi , Weber Gabriel , Stein Nili , Saliba Walid
Published: October 2022

Background

Tixagevimab and cilgavimab, a combined monoclonal antibody (Evusheld), was granted emergency use authorization for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) preexposure prophylaxis in individuals with immunocompromising conditions. In this study we used population-based real-world data to evaluate the effectiveness of Evusheld in immunocompromised patients.

Methods

Using the computerized database of the largest healthcare provider in Israel, we identified all adult immunocompromised patients who were eligible to receive Evusheld (150 mg tixagevimab and 150 mg cilgavimab) on 15 February 2022. Patients with a documentation of a prior SARS-CoV-2 infection were excluded. A total of 703 patients who received Evusheld were propensity score matched, using a ratio of 1:4, with 2812 patients who had not received Evusheld (control group). Patients were followed through 30 June 2022 for up to 90 days for the first documentation of SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19)–related hospitalization.

Results

Overall, 72 patients in the Evusheld group and 377 patients in the control group had SARS-CoV-2 infection, reflecting an incidence rate of 4.18 and 5.64 per 100 person-months, respectively. The hazard ratios were 0.75 (95% confidence interval [CI]: .58–.96) for SARS-CoV-2 infection and 0.41 (95% CI: .19–.89) for COVID-19–related hospitalization in the Evusheld group compared to the control group. The magnitude of relative risk reduction of each outcome was greater in nonobese patients (P for interaction = .020 and .045, respectively).

Conclusions

This study suggests that Evusheld is effective in reducing the risk of SARS-CoV-2 infection and COVID-19 hospitalization in immunocompromised patients. The effectiveness of this dose appears to be greater in nonobese patients.
Microbial Volatiles as Diagnostic Biomarkers of Bacterial Lung Infection in Mechanically Ventilated Patients
Authors: Ahmed Waqar M , Fenn Dominic , White Iain R , Dixon Breanna , Nijsen Tamara M E , Knobel Hugo H , Brinkman Paul , Van Oort Pouline M P , Schultz Marcus J , Dark Paul , Goodacre Royston , Felton Timothy , Bos Lieuwe D J , Fowler Stephen J ,   for the BreathDx Consortium, Ahmed Waqar M , Raventos Antonio Artigas , Bannard-Smith Jonathan , Bos Lieuwe D J , Camprubi Marta , Coelho Luis , Dark Paul , Davie Alan , Diaz Emili , Goma Gemma , Felton Timothy , Fowler Stephen J , Goodacre Royston , Johnson Craig , Knobel Hugo , Lawal Oluwasola , Leopold Jan-Hendrik , Martin-Loeches Ignacio , Nijsen Tamara M E , van Oort Pouline M P , Povoa Pedro , Rattray Nicholas J W , Rijnders Guus , Schultz Marcus J , Steenwelle Ruud , Sterk Peter J , Valles Jordi , Verhoeckx Fred , Vink Anton , Weda Hans , White Iain R , Winters Tineke , Zakharkina Tetyana
Published: October 2022

Background

Early and accurate recognition of respiratory pathogens is crucial to prevent increased risk of mortality in critically ill patients. Microbial-derived volatile organic compounds (mVOCs) in exhaled breath could be used as noninvasive biomarkers of infection to support clinical diagnosis.

Methods

In this study, we investigated the diagnostic potential of in vitro–confirmed mVOCs in the exhaled breath of patients under mechanical ventilation from the BreathDx study. Samples were analyzed by thermal desorption–gas chromatography–mass spectrometry.

Results

Pathogens from bronchoalveolar lavage (BAL) cultures were identified in 45 of 89 patients and Staphylococcus aureus was the most commonly identified pathogen (n = 15). Of 19 mVOCs detected in the in vitro culture headspace of 4 common respiratory pathogens (S. aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli), 14 were found in exhaled breath samples. Higher concentrations of 2 mVOCs were found in the exhaled breath of patients infected with S. aureus compared to those without (3-methylbutanal: P < .01, area under the receiver operating characteristic curve [AUROC] = 0.81–0.87; and 3-methylbutanoic acid: P = .01, AUROC = 0.79–0.80). In addition, bacteria identified from BAL cultures that are known to metabolize tryptophan (E. coli, Klebsiella oxytoca, and Haemophilus influenzae) were grouped and found to produce higher concentrations of indole compared to breath samples with culture-negative (P = .034) and other pathogen-positive (P = .049) samples.

Conclusions

This study demonstrates the capability of using mVOCs to detect the presence of specific pathogen groups with potential to support clinical diagnosis. Although not all mVOCs were found in patient samples within this small pilot study, further targeted and qualitative investigation is warranted using multicenter clinical studies.
New Perspectives for Prosthetic Valve Endocarditis: Impact of Molecular Imaging by FISHseq Diagnostics
Authors: Hajduczenia Maria M , Klefisch Frank R , Hopf Alexander G M , Grubitzsch Herko , Stegemann Miriam S , Pfäfflin Frieder , Puhlmann Birgit , Ocken Michele , Kretzler Lucie , von Schöning Dinah , Falk Volkmar , Moter Annette , Kikhney Judith
Published: October 2022

Background

The microbial etiology of prosthetic valve infective endocarditis (PVE) can be difficult to identify. Our aim was to investigate the benefit of molecular imaging technique fluorescence in situ hybridization (FISH) combined with 16S rRNA-gene polymerase chain reaction (PCR) and sequencing (FISHseq) for the analysis of infected prosthetic heart valves.

Methods

We retrospectively evaluated the diagnostic outcome of 113 prosthetic valves from 105 patients with suspected PVE, treated in 2003–2013 in the Department of Cardiac Surgery, Charité University Medicine Berlin. Each prosthetic valve underwent cultural diagnostics and was routinely examined by FISH combined with 16S rRNA gene PCR and sequencing. We compared classical microbiological culture outcomes (blood and valve cultures) with FISHseq results and evaluated the diagnostic impact of the molecular imaging technique.

Results

Conventional microbiological diagnostic alone turned out to be insufficient, as 67% of preoperative blood cultures were noninformative (negative, inconclusive, or not obtained) and 67% of valve cultures remained negative. FISHseq improved the conventional cultural diagnostic methods in PVE in 30% of the cases and increased diagnostic accuracy. Of the valve culture–negative PVE cases, FISHseq succeeded in identifying the causative pathogen in 35%.

Conclusions

FISHseq improves PVE diagnostics, complementing conventional cultural methods. In addition to species identification, FISH provides information about the severity of PVE and state of the pathogens (eg, stage of biofilm formation, activity, and localization on and within the prosthetic material). As a molecular imaging technique, FISHseq enables the unambiguous discrimination of skin flora as contaminant or infectious agent.
Modularity of the ABCD random graph model with community structure
Authors: Kamiński Bogumił , Pankratz Bartosz , Prałat Paweł , Théberge François
Published: October 2022

The Artificial Benchmark for Community Detection (ABCD) graph is a random graph model with community structure and power-law distribution for both degrees and community sizes. The model generates graphs with similar properties as the well-known LFR (Lancichinetti, Fortunato, Radicchi) one, and its main parameter $\xi$ can be tuned to mimic its counterpart in the LFR model, the mixing parameter $\mu$. In this article, we investigate various theoretical asymptotic properties of the ABCD model. In particular, we analyse the modularity function, arguably, the most important graph property of networks in the context of community detection. Indeed, the modularity function is often used to measure the presence of community structure in networks. It is also used as a quality function in many community detection algorithms, including the widely used Louvain algorithm.
A Phase IB/IIA Study of Allogeneic, Bone Marrow-derived, Mesenchymal Stem Cells for the Treatment of Refractory Ileal-anal Anastomosis and Peripouch Fistulas in the Setting of Crohn’s Disease of the Pouch
Authors: Lightner Amy L , Reese Jane , Ream Justin , Nachand Douglas , Jia Xue , Pineiro Ana Otero , Dadgar Neda , Steele Scott , Hull Tracy
Published: October 2022

Background and Aims

Mesenchymal stem cells [MSCs] have been used for the treatment of perianal Crohn’s fistulising disease by direction injection. No studies to date have included patients with an ileal pouch-anal anastomosis [IPAA] in situ.

Methods

A phase IB/IIA, randomised, control trial of bone marrow-derived, allogeneic MSCs via direct injection to treat adult patients with a peripouch fistula[s] was conducted; 75 million MSCs were administered with a 22 G needle, with repeat injection at 3 months if complete clinical and radiographic healing was not achieved. Adverse and serious adverse events at post-procedure Day 1, Week 2, Week 6, Month 3, Month 6, and Month 12 were assessed. Clinical healing, radiographic healing per pelvic magnetic resonance imaging [MRI], and patient-reported outcomes were assessed at the same time points.

Results

A total of 22 patients were enrolled and treated; 16 were treated and six were controls. There were no adverse or serious adverse events related to MSC therapy. At 6 months, 31% of the treatment group and 20% of the control had complete clinical and radiographic healing. When stratifying the treatment group into perianal [n = 7] and ano-vaginal [n = 8] fistulas, 6-month healing in the treatment groups was 57% and 0%, respectively. The perianal Crohn’s disease activity index [PCDAI], Wexner incontinence score, and van Assche score all significantly decreased in treatment patients at 6 months; only the PCDAI decreased in the control group.

Conclusion

Bone marrow-derived, allogeneic MSCs offer a safe and effective alternative treatment approach for peripouch fistulas in the setting of a Crohn’s like phenotype of the pouch [ClinicalTrials.gov Identifier: NCT04519684.]
Discrimination Abilities and Parasitism Success of Pupal Parasitoids Towards Spotted-Wing Drosophila Pupae Previously Parasitized by the Larval Parasitoid Ganaspis brasiliensis (Hymenoptera: Figitidae)
Authors: Hougardy Evelyne , Hogg Brian N , Wang Xingeng , Daane Kent M
Published: October 2022

Pachycrepoideus vindemiae (Rondani) (Hymenoptera: Pteromalidae) and Trichopria drosophilae (Perkins) (Hymenoptera: Diapriidae) are two cosmopolitan and generalist pupal parasitoids that are among a few of the resident parasitoids in North America capable of attacking Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), an invasive pest of small and soft fruit crops worldwide. Ganaspis brasiliensis (Ihering) is a specialist larval parasitoid of D. suzukii that was recently approved for biological control introduction against D. suzukii in the USA. As a solitary koinobiont species, G. brasiliensis oviposits in the host larva but emerges as an adult from the host puparium. This study investigated the discrimination ability and parasitism success by the pupal parasitoids towards D. suzukii pupae previously parasitized by G. brasiliensis, to examine whether interactions with resident parasitoids will affect G. brasiliensis after it is released in the USA. We found preliminary evidence that neither pupal parasitoid could discriminate towards D. suzukii pupae parasitized by early instars of G. brasiliensis. Pachycrepoideus vindemiae was able to successfully develop on D. suzukii pupae containing all preimaginal stages of G. brasiliensis, although parasitism success was significantly higher on those bearing later rather than early stages of G. brasiliensis. Trichopria drosophilae was only able to successfully develop on D. suzukii puparia containing early instars of G. brasiliensis. These results suggest that D. suzukii parasitized by the larval parasitoid could be subsequently attacked by the pupal parasitoids, possibly affecting the success of G. brasiliensis releases.
New England in the Royalist Imagination, 1637–89
Authors: Fullerton Samuel
Published: October 2022

This essay examines representations of New England puritanism in royalist print and manuscript polemic during the English Revolution of 1642–1660 and beyond. Royalist attitudes toward the North American godly colonies have been largely overlooked by modern scholars, who continue to privilege New England’s significance in intra-parliamentarian religious debates over its impact on the events of the civil war itself. As a result, they have neglected a substantial canon of hostile anti-puritan royalist literature that identified colonial puritanism, along with other malevolent international godly influences, as a horrifying example of the future awaiting old England if Charles I’s parliamentarian enemies were to triumph. As a pre-eminent puritan sanctuary from which some godly rebels had been recruited to perpetuate the civil war in Britain and to which domestic parliamentarians later allegedly intended to flee once their uprising had succeeded, New England thus occupied an important place in the royalist political imagination. Although royalist attitudes toward the American puritan colonies waxed and waned in significance during the revolutionary decades, and while New Englanders themselves may not have paid considerable attention to hostile royalist commentary, interested English readers and domestic parliamentarian polemicists alike paid a great deal of attention to the anti-colonial thrust of mid-century cavalier print. Moreover, certain aspects of royalist anti-New England rhetoric lived on to provide later anti-puritan commentators with a convenient explanation for the ongoing hostility of colonial puritans toward Stuart rule for decades following the Restoration.
Defining the optimal revascularization strategy during protected high-risk procedures with Impella
Authors: Sinning Jan-Malte , Al-Rashid Fadi , Ibrahim Karim , Aurigemma Cristina , Chieffo Alaide
Published: October 2022

Complete revascularization (CR) in patients with multi-vessel disease improves outcomes. The use of percutaneous left-ventricular assist devices, such as the Impella heart pump, is useful to minimize the risk of haemodynamic compromise in complex higher risk and clinically indicated patients. The recently published data from the PROTECT III trial suggest more CR during Impella-protected percutaneous coronary intervention with more extensive lesion preparation and treatment, resulting in the reduced need for repeat revascularization. To achieve CR and improve survival, procedural guidance by intravascular imaging, extensive lesion preparation, debulking with atherectomy devices, advanced chronic total occlusion revascularization techniques, and post-interventional treatment with modern anti-platelet medication are essential.
Pyp25α is required for male gametocyte exflagellation
Authors: Zhang Chao , Li Deyi , Meng Zhirong , Zhou Jianwei , Min Zhenxiao , Deng Shengqun , Shen Jijia , Liu Miao
Published: October 2022

Malaria, a mosquito-borne infectious disease, is caused by the unicellular apicomplexan protozoa of the genus Plasmodium. For malaria parasite transmission, the essential sexual stage includes production of gametocytes through gametocytogenesis in vertebrate hosts and formation of gametes from gametocytes through gametogenesis in mosquito vectors. Whereas each female gametocyte forms a single immotile macrogamete, a male gametocyte produces eight flagella-like microgametes in a process called exflagellation. We identified a conserved protein named as Py05543 (Pyp25α), required for male gametocyte exflagellation in Plasmodium yoelii, which is the ortholog of PFL1770c (PF3D7_1236600). Interestingly, PF3D7_1236600 was previously phenotypically screened to be gametocyte-essential genes during gametocytogenesis of Plasmodium falciparum, using piggyBac transposon-mediated insertional mutagenesis. In this study, using CRISPR/Cas9-mediated genome editing, the Pyp25α¯ (KO) parasite line was successfully established. We found that the KO parasites proliferated asexually in mouse blood normally. In addition, compared with that of the parental parasites, the KO parasites displayed similar levels of gametocytes formation. Unexpectedly, the KO parasites showed considerable deficiency in exflagellation of male gametes, by observing exflagellation centre formation. Taken together, our data suggested that Pyp25α gene, the ortholog of PF3D7_1236600, was nonessential for the growth of asexual parasites, required for male gametocyte exflagellation in P. yoelii.
Genetic variants in promoter region of TFR2 is associated with the risk of non-alcoholic fatty liver disease in a Chinese Han population: a case–control study
Authors: Pan Xinting , Peng Hewei , Zhang Junchao , Wu Yunli , Hu Zhijian , Peng Xian-E
Published: October 2022

Background

Iron overload is frequently observed in non-alcoholic fatty liver disease (NAFLD). Transferrin receptor 2 (TFR2) is an important key factor in iron regulation. We aimed to investigate whether TFR2 single nucleotide polymorphisms (SNPs) contribute to susceptibility to NAFLD in a Chinese Han population.

Methods

Five tag SNPs (rs10247962, rs4434553, rs2075672, rs1052897, and rs3757859) in the TFR2 gene were selected and genotyped in a case–control study on participants who visited two affiliated hospitals of Fujian Medical University between June 2011 and August 2017. Propensity score matching and inverse probability of treatment weighting analyses were used to verify the risk associated with TFR2 SNPs.

Results

Logistic regression analyses suggested that subjects with the rs4434553 GA or GG genotype had a lower risk of NAFLD than those carrying the AA genotype (odds ratio = 0.630, 95% confidence interval = 0.504–0.788). Moreover, the rs4434553 GA or GG genotype was negatively correlated with body mass index, hepatic steatosis index, and serum ferritin (b = −0.363, P = 0.008; b = −1.040, P = 0.009; b = −35.258, P = 0.015, respectively), and positively associated with serum hepcidin level (b = 35.308, P < 0.001). Moreover, rs10247962 and rs1052897 had multiplicative interactions with age in relation to the risk of NAFLD (P for interactions, 0.041 and 0.034, respectively). The cumulative effects of the rs10247962, rs1052897, and rs4434553 SNPs were positively associated with the risk of NAFLD (adjusted Ptrend = 0.012).

Conclusions

In this Chinese Han population, the rs4434553 polymorphism in TFR2 may be an independent influencing factor associated with the susceptibility to NAFLD. The ageing effect on the development of NAFLD may be inhibited by SNPs rs10247962 and rs1052897.
Function and Constraint in Enhancer Sequences with Multiple Evolutionary Origins
Authors: Fong Sarah L , Capra John A
Published: October 2022

Thousands of human gene regulatory enhancers are composed of sequences with multiple evolutionary origins. These evolutionarily “complex” enhancers consist of older “core” sequences and younger “derived” sequences. However, the functional relationship between the sequences of different evolutionary origins within complex enhancers is poorly understood. We evaluated the function, selective pressures, and sequence variation across core and derived components of human complex enhancers. We find that both components are older than expected from the genomic background, and complex enhancers are enriched for core and derived sequences of similar evolutionary ages. Both components show strong evidence of biochemical activity in massively parallel report assays. However, core and derived sequences have distinct transcription factor (TF)-binding preferences that are largely similar across evolutionary origins. As expected, given these signatures of function, both core and derived sequences have substantial evidence of purifying selection. Nonetheless, derived sequences exhibit weaker purifying selection than adjacent cores. Derived sequences also tolerate more common genetic variation and are enriched compared with cores for expression quantitative trait loci associated with gene expression variability in human populations. In conclusion, both core and derived sequences have strong evidence of gene regulatory function, but derived sequences have distinct constraint profiles, TF-binding preferences, and tolerance to variation compared with cores. We propose that the step-wise integration of younger derived with older core sequences has generated regulatory substrates with robust activity and the potential for functional variation. Our analyses demonstrate that synthesizing study of enhancer evolution and function can aid interpretation of regulatory sequence activity and functional variation across human populations.
Social Isolation, Loneliness, and Depressive Symptoms: A Twelve-Year Population Study of Temporal Dynamics
Authors: Luo Mengsha
Published: October 2022

Objectives

Social isolation and loneliness are two different aspects of social connections. Whether social isolation and loneliness precede depressive symptoms, or depressive symptoms precede feelings of loneliness and social isolation, or both, has not been fully established. This study aims to examine the possible reciprocity in the relationship between the two aspects of social connections and depressive symptoms among middle-aged and older adults.

Method

This study analyzed four waves of data (2008–2016) from the Health and Retirement Study (N = 5,393 individuals) and investigated within-person level cross-lagged associations of social isolation and loneliness with depressive symptoms using random intercept cross-lagged panel models.

Results

This study revealed a unidirectional relationship between social isolation and depressive symptoms and a bidirectional relationship between loneliness and depressive symptoms at the within-person level. Specifically, net of trait levels and prior states, earlier state depressive symptoms predicted future state social isolation. That is, when adults feel depressed more frequently than they usually do, they are more likely to be socially disconnected than usual at a later time. In the reverse direction, earlier state social isolation did not predict future state depressive symptoms. Within-person deviation in prior expected depressive symptoms predicted deviation in expected loneliness 4 years later and vice versa. Moreover, the strength of the two cross-lagged effects did not differ.

Discussion

Social isolation and loneliness are linked to depressive symptoms differently. Though depressive symptoms might be a potential antecedent of social isolation, they might be both a potential antecedent and an outcome of loneliness.
Best genome sequencing strategies for annotation of complex immune gene families in wildlife
Authors: Peel Emma , Silver Luke , Brandies Parice , Zhu Ying , Cheng Yuanyuan , Hogg Carolyn J , Belov Katherine
Published: October 2022

Background

The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation.

Results

Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation.

Conclusions

Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development
Authors: Zhao Hansheng , Hou Yinguang , Wang Jian , Sun Lei , Gan Junwei , Meng Yufei , Li Zhiqiang , Li Shanying , Fan Zeyu , Wang Yu , Fei Benhua
Published: October 2022

Bamboo, the fast-growing grass plant, and rattan, the spiky climbing palm, are both essential forest resources that have been closely linked with human lives, livelihoods and material culture since ancient times. To promote genetic and genomic research in bamboo and rattan, a comprehensive and coordinated international project, the Genome Atlas of Bamboo and Rattan (GABR), was launched in 2017. GABR achieved great success during Phase I (2017-2022). We will focus on investigating and protecting bamboo and rattan germplasm resources in Phase II ( 2022-2027). Here, we briefly review the achievements of Phase I and introduce the goals of Phase II.
Quantifying uncertainty of salt body shapes recovered from gravity data using trans-dimensional Markov chain Monte Carlo sampling
Authors: Wei Xiaolong , Sun Jiajia , Sen Mrinal K
Published: October 2022

Accurate delineation of salt body shapes is critical for hydrocarbon exploration. Various imaging methods based on seismic data have been developed. Due to the density contrast between salt and sedimentary rocks, gravity data have also been used as a de-risking tool to constrain the salt body shapes. However, quantifying uncertainties of the salt body shapes recovered from gravity data remains underexplored. Our goal is to understand and quantify how different constraints affect uncertainties of the salt body shapes reconstructed from gravity data. We adopt a trans-dimensional Markov chain Monte Carlo (MCMC) approach to explore the uncertainties. To address the computational challenges with MCMC sampling, we resort to two methods: sparse geometry parametrization and randomized parallel tempering. The first uses a set of simple geometries (e.g. ellipses) to approximate the complex shapes of salt bodies, greatly reducing the number of parameters to be sampled and making the MCMC approach computationally feasible. The second serves to further improve the acceptance ratio and computational efficiency. To quantify the uncertainties of the recovered salt body shapes, we design several scenarios to simulate different constraints on the top boundary of salt bodies from seismic imaging. We develop a new method to impose structural constraints on the top boundaries of salt bodies. This new method combines a set of fixed ellipses with randomly sampled ellipses through a concave hull. The results from different scenarios are compared to understand how uncertainties are reduced when stronger constraints are imposed. In addition, to make our uncertainty quantification results more relevant for practitioners, we propose to compute the salt probability models which show the spatial distribution of probabilities of salt materials at each cell. Finally, we investigate the effect of an uncertain salt density on the salt body reconstruction and the case of depth-varying densities in the sedimentary background. We apply our methods to the modified 2-D SEG-EAGE and Sigsbee salt models and quantify the uncertainties of the recovered salt body shapes in different scenarios. Our results highlight the importance of properly interpreting the uncertainty estimates in light of prior information and information content in the data.
Integrating controlled-source and ambient noise seismic measures for archaeological prospection: the Scrovegni Chapel case
Authors: Barone I , Cassiani G , Ourabah A , Boaga J , Pavoni M , Deiana R
Published: October 2022

In this paper, we present the results of an analysis of passive seismic noise recorded around the Scrovegni Chapel in Padua (Italy), using a dense 2-D network with nearly 1500 autonomous seismic nodes. Surface wave tomography using the active records allowed the imaging of several structures located at a depth of few metres, while this study focuses on the processing of about 22 hr of continuous passive records. First, the ambient noise is characterized in terms of amplitude, frequency content and azimuthal distribution, in order to ensure the applicability of the interferometric method. Second, a cross-correlation analysis is performed to retrieve virtual source gathers. Third, traveltimes are extracted from virtual source gathers using the same processing sequence applied to active gathers. Fourth, Eikonal tomography is run to retrieve isotropic phase velocity maps and azimuthal anisotropy. We compare and discuss the results obtained from the active and the passive methods, and finally propose a strategy for the integration of passive and active information. The new quasi-3-D shear wave velocity model obtained from the joint active and passive analysis is more accurate at depth, due to the addition of the passive low-frequency information.
Bovine pericardial patch repair for abdominal aortic pseudoaneurysm to preserve lumbar arteries
Authors: Nabeshima Junya , Mizuno Tomohiro , Nagaoka Eiki
Published: October 2022

We describe a case of aortic repair using bovine pericardium for a pseudoaneurysm of a dissecting abdominal aorta. A 71-year-old man had undergone several aortic replacement surgeries for type B aortic dissection. He developed paraparesis after thoraco-abdominal aortic surgery and recovered. After 3 years, the scheduled computed tomography scan showed a pseudoaneurysm of the dissecting abdominal aorta. Because he was at high risk of spinal cord ischaemia, aortic repair using bovine pericardium was performed, and all lumbar arteries were preserved. During the 12-month follow-up, he was asymptomatic, and computed tomography scans showed no dilation of the aorta.
Perturbations in Respiratory Syncytial Virus Activity During the SARS-CoV-2 Pandemic
Authors: Falsey Ann R , Cameron Andrew , Branche Angela R , Walsh Edward E
Published: October 2022

Respiratory syncytial virus (RSV) is a common cause of respiratory disease in all age groups, with young children and older adults experiencing the most severe illness. The coronavirus disease 2019 (COVID-19) pandemic resulted in striking changes in the activity of seasonal respiratory viruses, including RSV. After a period of suppression early in the pandemic, an interseasonal surge of RSV occurred in 2021. Viral activity was detected primarily in children and young adults after relaxation of public health measures, but without the usual proportional increases in infections and hospitalizations in older adults who were likely still adhering to stricter public health measures.
Bioengineered and functionalized silk proteins accelerate wound healing in rat and human dermal fibroblasts
Authors: Manoharan Chitra , Thomas Dyna Susan , Yashwant Rasalkar Sandhya , Mudagal Manjunatha Panduranga , Janadri Suresh , Roy Gourab , Kunjupillai Vijayan , Mishra Rakesh Kumar , Gopalapillai Ravikumar
Published: October 2022

Wound healing is an intrinsic process directed towards the restoration of damaged or lost tissue. The development of a dressing material having the ability to control the multiple aspects of the wound environment would be an ideal strategy to improve wound healing. Though natural silk proteins, fibroin, and sericin have demonstrated tissue regenerative properties, the efficacy of bioengineered silk proteins on wound healing is seldom assessed. Furthermore, silk proteins sans contaminants, having low molecular masses, and combining with other bioactive factors can hasten the wound healing process. Herein, recombinant silk proteins, fibroin and sericin, and their fusions with cecropin B were evaluated for their wound-healing effects using in vivo rat model. The recombinant silk proteins demonstrated accelerated wound closure in comparison to untreated wounds and treatment with Povidone. Among all groups, the treatment with recombinant sericin-cecropin B (RSC) showed significantly faster healing, greater than 90% wound closure by Day 12 followed by recombinant fibroin-cecropin B (RFC) (88.86%). Furthermore, histological analysis and estimation of hydroxyproline showed complete epithelialization, neovascularization, and collagenisation in groups treated with recombinant silk proteins. The wound healing activity was further verified by in vitro scratch assay using HADF cells, where the recombinant silk proteins induced cell proliferation and cell migration to the wound area. Additionally, wound healing-related gene expression showed recombinant silk proteins stimulated the upregulation of EGF and VEGF and regulated the expression of TGF-β1 and TGF-β3. Our results demonstrated the enhanced healing effects of the recombinant silk fusion proteins in facilitating complete tissue regeneration with scar-free healing. Therefore, the recombinant silks and their fusion proteins have great potential to be developed as smart bandages for wound healing.
Morphology-based Phylogenetic Analysis of Membracoidea (Hemiptera: Cicadomorpha) With Placement of Fossil Taxa and Description of a New Subfamily
Authors: Dietrich Christopher H , Dmitriev Dmitry A , Takiya Daniela M , Thomas M Jared , Webb Michael D , Zahniser James N , Zhang Yalin
Published: October 2022

Recently discovered amber-preserved fossil Cicadellidae exhibit combinations of morphological traits not observed in the modern fauna and have the potential to shed new light on the evolution of this highly diverse family. To place the fossils explicitly within a phylogenetic context, representatives of five extinct genera from Cretaceous Myanmar amber, and one from Eocene Baltic amber were incorporated into a matrix comprising 229 discrete morphological characters and representatives of all modern subfamilies. Phylogenetic analyses yielded well resolved and largely congruent estimates that support the monophyly of most previously recognized cicadellid subfamilies and indicate that the treehoppers are derived from a lineage of Cicadellidae. Instability in the morphology-based phylogenies is mainly confined to deep internal splits that received low branch support in one or more analyses and also were not consistently resolved by recent phylogenomic analyses. Placement of fossil taxa is mostly stable across analyses. Three new Cretaceous leafhopper genera, Burmotettix gen. nov., Kachinella gen nov., and Viraktamathus gen. nov., consistently form a monophyletic group distinct from extant leafhopper subfamilies and are placed in Burmotettiginae subfam. nov. Extinct Cretaceous fossils previously placed in Ledrinae and Signoretiinae are recovered as sister to modern representatives of these groups. Eomegophthalmus Dietrich and Gonçalves from Baltic amber consistently groups with a lineage comprising treehoppers, Megophthalminae, Ulopinae, and Eurymelinae but its position is unstable. Overall, the morphology-based phylogenetic estimates agree with recent phylogenies based on molecular data alone suggesting that morphological traits recently used to diagnose subfamilies are generally informative of phylogenetic relationships within this group.
“Yes-Man” Firms: Government Campaign and Policy Positioning of Businesses in China
Authors: Naoi Megumi , Shi Weiyi , Zhu Boliang
Published: October 2022

We demonstrate material origin of strategic preference expression in authoritarian systems, where firms express dissent against or conform to the government's position based on what they seek to obtain from the government: politically powerful firms are more likely to dissent to negotiate policy concessions while politically weak firms are more likely to conform to the government's position to obtain side payments or to avoid punishment. We test this argument using survey experiments with firm executives in China. A treatment that signals the government's commitment to liberalize inward foreign direct investment increases the percentage of firms that report to “benefit” from the policy between 14 and 36 percentage points. Powerful firms (state- and foreign-owned) conform the least to the government and politically vulnerable firms and the recipients of government contracts conform the most. Our results suggest that political standing is a key driver of business position-taking in China.
Why Territorial Disputes Escalate: The Causes of Conquest Attempts since 1945
Authors: Altman Dan , Lee Melissa M
Published: October 2022

Although attempts to conquer entire states became rare after 1945, attempts to conquer small pieces of territory persisted. Why do states so often seize—and even fight wars over—remarkably small areas? We argue that traditional explanations predicated on the material or ethnic value of disputed territories largely cannot explain the escalation of territorial disputes since 1945. Instead, actors more often seize territory to be seen seizing it. We theorize that the roots of these conquest attempts often lie in careerist incentives within militaries. Military officers seize small pieces of disputed territory in pursuit of promotions or political office, especially in states where the military wields greater political power. We test this theory with a statistical analysis of conquest attempts in territorial disputes (1965–2000) using new geospatial and conquest data along with a medium-n process analysis of all conquest attempts since 1945. Our results suggest that careerist self-aggrandizement plays an important role in contemporary territorial conflict.