bluuebunny/crossref_metadata_2025 huggingface dataset:
Strategies to address non-communicable diseases in the Commonwealth of Independent States countries: a scoping review
Authors: Muratalieva Elvira , Nendaz Mathieu , Beran David
Published: November 2022

Aim:

The aim of this study is to review the literature in Commonwealth of Independent States (CIS) countries with regard to their response to non-communicable diseases (NCDs) and the implementation of the World Health Organization (WHO) Package of Essential Non-communicable (PEN) disease interventions for primary health care.

Background:

NCDs are estimated to account from 62% to 92% of total deaths in CIS countries. Current management of NCDs in CIS countries is focused on specialists and hospital care versus primary health care (PHC) as recommended by the WHO.

Methods:

This paper uses a scoping review of published and grey literature focusing on diabetes and hypertension in CIS countries. These two conditions are chosen as they represent a large burden in CIS countries and are included in the responses proposed by the WHO PEN.

Findings:

A total of 96 documents were identified and analysed with the results presented using the WHO Health System Building Blocks. Most of the publications identified focused on the service delivery (41) and human resources (20) components, while few addressed information and research (17), and only one publication was related to medical products. As for their disease of focus, most studies focused on hypertension (14) and much less on diabetes (3). The most studies came from Russia (18), followed by Ukraine (21) and then Kazakhstan (12). Only two countries Moldova and Kyrgyzstan have piloted the WHO PEN. Overall, the studies identified highlight the importance of the PHC system to better control and manage NCDs in CIS countries. However, these present only strategies versus concrete interventions. One of the main challenges is that NCD care at PHC in CIS countries continues to be predominantly provided by specialists in addition to focusing on treatment versus preventative services.
Broadband Dynamic Rupture Modeling With Fractal Fault Roughness, Frictional Heterogeneity, Viscoelasticity and Topography: The 2016 Mw 6.2 Amatrice, Italy Earthquake
Authors: Taufiqurrahman T. , Gabriel A.‐A. , Ulrich T. , Valentová L. , Gallovič F.
Published: November 2022

Advances in physics‐based earthquake simulations, utilizing high‐performance computing, have been exploited to better understand the generation and characteristics of the high‐frequency seismic wavefield. However, direct comparison to ground motion observations of a specific earthquake is challenging. We here propose a new approach to simulate data‐fused broadband ground motion synthetics using 3D dynamic rupture modeling of the 2016 Mw 6.2 Amatrice, Italy earthquake. We augment a smooth, best‐fitting model from Bayesian dynamic rupture source inversion of strong‐motion data (<1 Hz) with fractal fault roughness, frictional heterogeneities, viscoelastic attenuation, and topography. The required consistency to match long periods allows us to quantify the role of small‐scale dynamic source heterogeneities, such as the 3D roughness drag, from observational broadband seismic waveforms. We demonstrate that 3D data‐constrained fully dynamic rupture synthetics show good agreement with various observed ground‐motion metrics up to ∼5 Hz and are an important avenue toward non‐ergodic, physics‐based seismic hazard assessment.
Volume Estimation From Planform Characteristics of Washover Morphology
Authors: Lazarus Eli D. , Williams Hannah E. , Goldstein Evan B.
Published: November 2022

Overwash is the cross‐shore transport of water and sediment from a waterbody over the crest of a sand or gravel barrier beach, and washover is the resulting sedimentary deposit. Washover volume, and alongshore patterns of washover distribution, are fundamental components of sediment budgets for low‐lying coastal barrier systems. Accurate sediment budgets are essential to forecasting barrier system sustainability under future climate‐driven forcing. However, comprehensive surveys of three‐dimensional washover morphology are challenging to deliver. Here, we use the results of a physical experiment, analysis of lidar data, and examples of washover characteristics reported in the literature to develop scaling relationships for washover morphometry that demonstrate volume can be reasonably inferred from planform measurements, for washover in natural (non‐built) and built barrier settings. Gaining three‐dimensional insight into washover deposits from two‐dimensional information unlocks the ability to analyze past aerial imagery and estimate contributions from washover flux to sediment budgets for past storms.
Increasing Drought Risks Over the Past Four Centuries Amidst Projected Flood Intensification in the Kabul River Basin (Afghanistan and Pakistan)—Evidence From Tree Rings
Authors: Khan Nasrullah , Nguyen Hung T. T. , Galelli Stefano , Cherubini Paolo
Published: November 2022

Increased flood risks have been projected, but with large uncertainties, in the Kabul River Basin (Afghanistan and Pakistan). To place future changes in a long‐term perspective, we produce a 382‐year precipitation reconstruction for the basin using seven tree‐ring chronologies of old‐growth conifers from the Hindu Kush Mountains, a monsoon‐shadow area. The reconstruction proves robust over rigorous cross‐validations (R2 = 0.60, RE = 0.60, CE = 0.53). The full reconstruction (1637–2018) reveals a steady decline in the low end of the precipitation distribution, implying increasing drought risks. We show that droughts are getting more severe, shorter, and more frequent, interspersed with more frequent pluvials in the past century. Drought risks, compounded with projected flood intensification, pose significant threats for this transboundary river. Therefore, future water management needs to account for both flood and drought risks and be informed by long‐term hydroclimatic variability.
Ecosystem Metabolism and Gradients of Temperature, Oxygen and Dissolved Inorganic Carbon in the Littoral Zone of a Macrophyte‐Dominated Lake
Authors: Martinsen Kenneth Thorø , Zak Nathalie Brandt , Baastrup‐Spohr Lars , Kragh Theis , Sand‐Jensen Kaj
Published: November 2022

Dense submerged macrophyte stands in lakes may promote alternating daytime stratification and nighttime convective mixing, driving extensive spatiotemporal variations in water temperature, oxygen, pH, and inorganic carbon (DIC). We set out to investigate environmental conditions and ecosystem metabolism in the macrophyte‐dominated littoral zone (0.6 m depth) of a shallow, mesotrophic lake and compared this with the pelagic zone (3.0 m deep). We found that, during summer, vertical water column gradients only occasionally occurred and were weak in the pelagic zone, while dense littoral macrophyte stands of charophytes exhibited strong diel changes and steep daytime temperature and oxygen depth gradients. Oxygen showed daytime surface supersaturation and bottom anoxia, alternating with nighttime mixing. In spring, before charophytes appeared, the vertical gradients were largely absent. Ecosystem metabolism was primarily positive in spring, but areal rates of daily gross primary production (GPP) and closely related respiration increased 6‐fold in summer. Ecosystem metabolism calculated based on oxygen or DIC was very similar, with a 1:1 M basis. Daytime DIC loss by CaCO3precipitation on charophyte surfaces averaged 6.3% of total DIC loss, and this loss was restored during nighttime. The contribution of shallow littoral macrophyte communities to whole‐lake summer GPP exceeded that estimated for phytoplankton. Environmental conditions in the macrophyte‐covered littoral zone differed markedly from pelagic waters with steep vertical gradients in temperature and chemistry during daytime including anoxic micro‐habitats in stark contrast to deep pelagic waters. The study highlights the significant influence of the littoral zone and macrophytes on whole‐lake ecosystem processes.
A Semi‐Analytical Solution for Heat Transport in Rock With Parallel Fractures and a Heat Source in Both Fracture and Matrix
Authors: Wu Xiao‐Long , Novakowski Kent , Kueper Bernard H.
Published: November 2022

In recent decades, numerous analytical solutions have been developed to quantify temperature perturbations in fractured rock having mobile and immobile fluid phases. The assumption of one‐dimensional heat conduction in the matrix, or neglecting heat dispersion and storage in fractures, however, are typical simplifications adopted to overcome the difficulties in mathematically representing the problem. In this study, we propose a two‐dimensional semi‐analytical solution framework based on Green's function approach for a flexible heat source definition, including source dimensions, energy delivery strength and duration, and the presence of a heat source in the matrix and/or fracture. The solution fully accounts for heat conduction, advection, dispersion, and transient heat exchange between the fracture fluid and rock matrix in a system of parallel fractures. The solution having a strip heat source extending from a fracture into the matrix indicates that one‐dimensional heat conduction in the matrix underestimates and overestimates temperature responses at early and later times, respectively. Additionally, the temperature peak arrival time is also substantially delayed by simplification. The fracture temperature grows slower near the heat source area as the fracture aperture increases. The fracture temperature growth is enhanced via the overlapped heating areas between the parallel fractures. The transient temperature analyses imply that the spatial temperature variation is strongly associated with heat delivery strength. The early time temperature variances are closely related to the heat source configurations, and the later time temperatures in the domain are mainly determined by the total energy being delivered into the domain.
The Impact of Climate Change on Operational Probable Maximum Precipitation Estimates
Authors: Visser J. B. , Kim S. , Wasko C. , Nathan R. , Sharma A.
Published: November 2022

The safety of high‐risk water infrastructure, such as dams and nuclear power plants, is often assessed by reference to their ability to accommodate floods derived from the Probable Maximum Precipitation (PMP). However, a key shortcoming of traditional PMP estimates is the assumption of a stationary climate, with evidence indicating that key meteorological conditions related to the magnitudes of extreme storms, such as atmospheric moisture, are changing in a warming climate. Due to the pragmatic nature of PMP methods derived for design purposes, inferring potential changes in PMP estimates based solely on trends or projections of atmospheric variables can ignore PMP method complexities and constraints. Here we explore how different traditional PMP methods will respond to a potential increase in atmospheric moisture. We find that increases in persisting dewpoint will lead to increases in PMP estimates, and the nature of this impact depends on whether the moisture maximization step is based on local or transposed regional information. An historical trend analysis reveals annual maximum persisting dewpoint temperatures have increased continuously over Australia over the past 60 years, with further increases predicted over the coming decades for all Shared Socioeconomic Pathways (SSPs). PMP estimates across Australia are predicated to increase by an average value of 13% by 2100 based on the conservative SSP1‐2.6, compared to 33% for SSP5‐8.5. We conclude PMP methods will require regular updating to account for changing persisting dewpoints and likely progressive increases in PMP, and the ensuing flood estimates.
A Hybrid Framework for Rapidly Locating Transition Zones: A Comparison of Event‐ and Response‐Based Return Water Levels in the Suwannee River FL
Authors: Jane R. A. , Malagón‐Santos V. , Rashid M. M. , Doebele L. , Wahl T. , Timmers S. R. , Serafin K. A. , Schmied L. , Lindemer C.
Published: November 2022

Flood risk assessments commonly use event‐based approaches to reduce the number of scenarios required to be run through computationally intensive physical process models. Often the return period of the response variable (e.g., a fluvial water level or overtopping discharge) generated by an event (e.g., upstream/downstream water level or set of sea state variables) does not match that of the event itself; a limitation of event‐based approaches which can lead to the misspecification of flood risk. We present a transferable hybrid statistical‐hydraulic modeling framework for rapidly locating transition zones; river reaches where extreme water levels are driven by both upstream riverine discharge and downstream sea level. Instead of an event‐based approach the framework utilizes a surrogate model to reduce computational expense of the hydraulic model. The surrogate‐based approach allows the empirical estimation of response‐based along‐river return levels from a large number of plausible discharge–coastal still water level events simulated from the statistical model. We assess the robustness of the event‐based approach by comparing the associated return levels with the response‐based return levels. The framework is applied to the Suwannee River in Florida (United States). Three surrogate models are evaluated, highlighting the enhanced ability of non‐linear models to accurately capture discharge‐sea level interactions along the river. The along‐river return levels of the “most‐likely” design event are found to lie within the range of variability of the response‐based return levels for most of the transition zone.
Large Wood in Small Channels: A 20‐Year Study of Budgets and Piece Mobility in Two Redwood Streams
Authors: Lininger K. B. , Hilton S.
Published: November 2022

Large wood (LW) influences geomorphic and ecological processes. However, most field data sets describing LW dynamics are conducted over the span of only a few years. We present a unique long‐term data set from northern California, USA of LW volumes, inputs, and transport in two small headwater streams, the North Fork (NF) and South Fork (SF) of Caspar Creek. We used data collected approximately every 2 years from 1998 to 2018 to assess how LW budgets change over time between catchments, what factors influence inputs from standing trees to the streams, and controls on LW piece mobility. We find that the SF, which experienced stream‐side logging and instream wood removal in the 1970s, continued to have lower LW volumes (range of 101–153 m3 km−1 over the 20‐year period) compared to the NF (range of 297–313 m3 km−1), which experienced logging in the 1980s but with buffer strips left near the channel. If current trends continue, it will likely take ∼100–200 years from the time of logging for the SF to reach NF instream wood volumes. We show that windstorms combined with precipitation events, very high winds, and hillslope steepness are strongly associated with LW piece inputs from standing trees. LW moves infrequently in the channel, with piece characteristics, the number of wood pieces per meter surrounding an LW piece, and discharge metrics influencing LW entrainment and displacement lengths. Our data set provides strong support to previously identified controls on LW dynamics in streams while also capturing variability over a 20‐year period.
Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy
Authors: Cheung Laurence C. , Aya-Bonilla Carlos , Cruickshank Mark N. , Chiu Sung K. , Kuek Vincent , Anderson Denise , Chua Grace-Alyssa , Singh Sajla , Oommen Joyce , Ferrari Emanuela , Hughes Anastasia M. , Ford Jette , Kunold Elena , Hesselman Maria C. , Post Frederik , Faulk Kelly E. , Breese Erin H. , Guest Erin M. , Brown Patrick A. , Loh Mignon L. , Lock Richard B. , Kees Ursula R. , Jafari Rozbeh , Malinge Sébastien , Kotecha Rishi S.
Published: November 2022

Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.
Mitochondria play an essential role in the trajectory of adolescent neurodevelopment and behavior in adulthood: evidence from a schizophrenia rat model
Authors: Ene Hila M. , Karry Rachel , Farfara Dorit , Ben-Shachar Dorit
Published: November 2022

Ample evidence implicate mitochondria in early brain development. However, to the best of our knowledge, there is only circumstantial data for mitochondria involvement in late brain development occurring through adolescence, a critical period in the pathogenesis of various psychiatric disorders, specifically schizophrenia. In schizophrenia, neurodevelopmental abnormalities and mitochondrial dysfunction has been repeatedly reported. Here we show a causal link between mitochondrial transplantation in adolescence and brain functioning in adulthood. We show that transplantation of allogenic healthy mitochondria into the medial prefrontal cortex of adolescent rats was beneficial in a rat model of schizophrenia, while detrimental in healthy control rats. Specifically, disparate initial changes in mitochondrial function and inflammatory response were associated with opposite long-lasting changes in proteome, neurotransmitter turnover, neuronal sprouting and behavior in adulthood. A similar inverse shift in mitochondrial function was also observed in human lymphoblastoid cells deived from schizophrenia patients and healthy subjects due to the interference of the transplanted mitochondria with their intrinsic mitochondrial state. This study provides fundamental insights into the essential role of adolescent mitochondrial homeostasis in the development of normal functioning adult brain. In addition, it supports a therapeutic potential for mitochondria manipulation in adolescence in disorders with neurodevelopmental and bioenergetic deficits, such as schizophrenia, yet emphasizes the need to monitor individuals’ state including their mitochondrial function and immune response, prior to intervention.
A micropeptide JunBP regulated by TGF-β promotes hepatocellular carcinoma metastasis
Authors: Zhang Hongwei , Liao Zhibin , Wang Weijian , Liu Yachong , Zhu He , Liang Huifang , Zhang Bixiang , Chen Xiaoping
Published: November 2022

Transforming growth factor beta (TGF-β) signaling pathway plays important roles in hepatocellular carcinoma (HCC) progression. Long intergenic non-protein coding RNAs (lincRNAs) are important components of TGF-β signaling pathway and perform their functions through different mechanisms. Here, we found that LINC02551 was activated by TGF-β transcriptionally and identified a 174-amino-acid peptide, Jun binding micropeptide (JunBP), encoded by LINC02551 in HCC tissues and HCC cell lines. Functional study showed that JunBP promotes HCC metastasis through binding to c-Jun and subsequent promotion of its phosphorylated activation. Activated c-Jun has higher binding affinity to SMAD3, which in turn leads to more SMAD3 recruited to the promoter region of LINC02551. We find a positive feedback among them, and this mechanism provides a novel potential prognostic biomarker and therapeutic target in HCC.
Meta-analysis of genome-wide association studies of hoarding symptoms in 27,651 individuals
Authors: Strom Nora I. , Smit Dirk J. A. , Silzer Talisa , Iyegbe Conrad , Burton Christie L. , Pool René , Lemire Mathieu , Crowley James J. , Hottenga Jouke-Jan , Ivanov Volen Z. , Larsson Henrik , Lichtenstein Paul , Magnusson Patrik , Rück Christian , Schachar Russell J. , Wu Hei Man , Meier Sandra M. , Crosbie Jennifer , Arnold Paul D. , Mattheisen Manuel , Boomsma Dorret I. , Mataix-Cols David , Cath Danielle
Published: November 2022

Hoarding Disorder (HD) is a mental disorder characterized by persistent difficulties discarding or parting with possessions, often resulting in cluttered living spaces, distress, and impairment. Its etiology is largely unknown, but twin studies suggest that it is moderately heritable. In this study, we pooled phenotypic and genomic data from seven international cohorts (N = 27,651 individuals) and conducted a genome wide association study (GWAS) meta-analysis of parent- or self-reported hoarding symptoms (HS). We followed up the results with gene-based and gene-set analyses, as well as leave-one-out HS polygenic risk score (PRS) analyses. To examine a possible genetic association between hoarding symptoms and other phenotypes we conducted cross-trait PRS analyses. Though we did not report any genome-wide significant SNPs, we report heritability estimates for the twin-cohorts between 26–48%, and a SNP-heritability of 11% for an unrelated sub-cohort. Cross-trait PRS analyses showed that the genetic risk for schizophrenia and autism spectrum disorder were significantly associated with hoarding symptoms. We also found suggestive evidence for an association with educational attainment. There were no significant associations with other phenotypes previously linked to HD, such as obsessive-compulsive disorder, depression, anxiety, or attention-deficit hyperactivity disorder. To conclude, we found that HS are heritable, confirming and extending previous twin studies but we had limited power to detect any genome-wide significant loci. Much larger samples will be needed to further extend these findings and reach a “gene discovery zone”. To move the field forward, future research should not only include genetic analyses of quantitative hoarding traits in larger samples, but also in samples of individuals meeting strict diagnostic criteria for HD, and more ethnically diverse samples.
A nationwide survey of hydroxychloroquine retinopathy presenting to the hospital eye service in the United Kingdom
Authors: Yusuf Imran H. , Han Ruofan C. , Downes Susan M. , Sharma Srilakshmi M.
Published: November 2022

Background

The risk of developing hydroxychloroquine retinopathy is considered sufficient to justify national monitoring programmes. There are an estimated 71,144–77,170 long-term hydroxychloroquine users in the UK. However, the number of patients diagnosed with retinopathy is unknown. This study aimed to identify the number of cases and clinical characteristics of hydroxychloroquine retinopathy diagnosed annually in hospital eye services across the UK.

Methods

A nationwide, prospective case ascertainment study was undertaken using the British Ophthalmological Surveillance Unit, which sends approximately 1420 reporting cards to UK Ophthalmologists monthly. The case definition was two abnormal tests suggestive of hydroxychloroquine retinopathy. Demographic and clinical data relating to hydroxychloroquine use and retinopathy were collected from identified cases using a standardised questionnaire over a 1-year period (2018–2019).

Results

Sixty-six cases of hydroxychloroquine retinopathy were reported, and 46 questionnaires were received (73% response rate). Twenty-four incident cases of hydroxychloroquine retinopathy were identified (24-43 cases following adjustment). The median duration of drug therapy was 19 years (range: 4–50 years, IQR: 14.5–23 years). Fourteen patients were asymptomatic, and 9 symptomatic at diagnosis. A trend towards a lower mean deviation on visual field testing was observed in the symptomatic group (−11.55 dB versus −6.9 dB; P = 0.15).

Conclusion

Between 1 in 1655 and 3215 (0.03–0.06%) long-term hydroxychloroquine users were diagnosed with retinopathy over the study period. We estimate that monitoring was available for 1.9–3.8% of long-term users, accounting for a lower than expected incidence. The high proportion of symptomatic retinopathy at diagnosis underlines the importance of monitoring to detect pre-symptomatic disease.
General invariance and equilibrium conditions for lattice dynamics in 1D, 2D, and 3D materials
Authors: Lin Changpeng , Poncé Samuel , Marzari Nicola
Published: November 2022

The long-wavelength behavior of vibrational modes plays a central role in carrier transport, phonon-assisted optical properties, superconductivity, and thermomechanical and thermoelectric properties of materials. Here, we present general invariance and equilibrium conditions of the lattice potential; these allow to recover the quadratic dispersions of flexural phonons in low-dimensional materials, in agreement with the phenomenological model for long-wavelength bending modes. We also prove that for any low-dimensional material the bending modes can have a purely out-of-plane polarization in the vacuum direction and a quadratic dispersion in the long-wavelength limit. In addition, we propose an effective approach to treat invariance conditions in crystals with non-vanishing Born effective charges where the long-range dipole-dipole interactions induce a contribution to the lattice potential and stress tensor. Our approach is successfully applied to the phonon dispersions of 158 two-dimensional materials, highlighting its critical relevance in the study of phonon-mediated properties of low-dimensional materials.
A population-based cohort study on the risk of obstructive lung disease after bilateral oophorectomy
Authors: Nguyen Trinh T. , Smith Carin Y. , Gazzuola Rocca Liliana , Rocca Walter A. , Vassallo Robert , Dulohery Scrodin Megan M.
Published: November 2022

There is increasing evidence that sex hormones may impact the development of obstructive lung disease (OLD). Therefore, we studied the effect of bilateral oophorectomy (oophorectomy) on the development of OLD. Women were identified from the Mayo Clinic Cohort Study of Oophorectomy and Aging-2. Data were collected using the Rochester Epidemiology Project records-linkage system. A total of 1653 women who underwent oophorectomy and 1653 referent women of similar age were assessed for OLD using diagnostic codes and medical record abstraction. Women who underwent oophorectomy had an overall higher risk of all OLD, all chronic obstructive pulmonary disease (COPD), emphysema, and chronic bronchitis but not of all asthma, confirmed asthma, or confirmed COPD. The association with all OLD was stronger in women who were age ≤45 years at oophorectomy, never smokers, non-obese, and in women with benign indications; however, the interactions were not statistically significant. There was an increased risk of all asthma in women age ≤45 years at oophorectomy who took estrogen therapy. Never smokers of all ages had a stronger association of oophorectomy with all asthma and all COPD, whereas smokers had a stronger association of oophorectomy with emphysema and chronic bronchitis. Non-obese women of all ages had a stronger association of oophorectomy with all COPD, emphysema, and chronic bronchitis. The results of this study combined with the increased risk of several chronic diseases reported in previous studies suggest that oophorectomy in premenopausal women should be avoided unless there is clear evidence of a high genetic risk of ovarian cancer.
Stronger gut microbiome modulatory effects by postbiotics than probiotics in a mouse colitis model
Authors: Zhang Tao , Zhang Weiqin , Feng Cuijiao , Kwok Lai-Yu , He Qiuwen , Sun Zhihong
Published: November 2022

Probiotics are increasingly used as adjunctive therapy to manage gastrointestinal diseases, such as ulcerative colitis. However, probiotic use has posed some safety concerns. Thus, postbiotics are proposed as alternatives to probiotics in clinical applications. However, no study has directly compared the clinical benefits of probiotics and postbiotics. This study compared the beneficial effect of postbiotics and probiotics derived from the strain, Bifidobacterium adolescentis B8589, in a dextran sulfate sodium (DSS)-induced experimental colitis mouse model. Four groups of mice (n = 7 per group) were included in this work: Control (received water plus saline), DSS (received DSS without postbiotic/probiotic), Postbiotic (received DSS plus postbiotic), and Probiotic (received DSS plus probiotic). Our results showed that intragastric administration of both probiotic and postbiotic ameliorated colitis, reflected by decreased histology scores in Postbiotic and Probiotic groups compared with DSS group (P < 0.05). The fecal microbiota alpha diversity was not significantly affected by DSS-, postbiotic, or probiotic treatment. However, the postbiotic treatment showed stronger effects on modulating the fecal microbiota beta diversity, composition, and metagenomic potential than the probiotic treatment. Overall, our findings suggested that probiotics and postbiotics had similar ability to improve disease phenotype but had distinct ability to regulate the gut microbiota and metabolic pathways in the context of ulcerative colitis. In view of the smaller safety concern of postbiotics compared with probiotics and its stronger modulatory effect on the host gut microbiota, we propose that postbiotics are to be considered for use as next-generation biotherapeutics in managing ulcerative colitis or even other diseases.
Systematic review of primary and booster COVID-19 sera neutralizing ability against SARS-CoV-2 omicron variant
Authors: Sitaras Ioannis , Jacobsen Henning , Higdon Melissa M. , Dowling William E. , Bar-Zeev Naor , Deloria Knoll Maria
Published: November 2022

Virus neutralization data using post-vaccination sera are an important tool in informing vaccine use policy decisions, however, they often pose interpretive challenges. We systematically reviewed the pre-print and published literature for neutralization studies against Omicron using sera collected after both primary and booster vaccination. We found a high proportion of post-primary vaccination sera were not responding against Omicron but boosting increased both neutralizing activity and percent of responding sera. We recommend reporting percent of responders alongside neutralization data to portray vaccine neutralization ability more accurately.
Sequential use of Ad26-based vaccine regimens in NHP to induce immunity against different disease targets
Authors: Khan Selina , Salisch Nadine C. , Gil Ana Izquierdo , Boedhoe Satish , Boer Karin Feddes-de , Serroyen Jan , Schuitemaker Hanneke , Zahn Roland C.
Published: November 2022

The adenovirus (Ad)26 serotype–based vector vaccine Ad26.COV2.S has been used in millions of subjects for the prevention of COVID-19, but potentially elicits persistent anti-vector immunity. We investigated if vaccine-elicited immunity to Ad26 vector–based vaccines significantly influences antigen-specific immune responses induced by a subsequent vaccination with Ad26 vector–based vaccine regimens against different disease targets in non-human primates. A homologous Ad26 vector–based vaccination regimen or heterologous regimens (Ad26/Ad35 or Ad26/Modified Vaccinia Ankara [MVA]) induced target pathogen–specific immunity in animals, but also persistent neutralizing antibodies and T-cell responses against the vectors. However, subsequent vaccination (interval, 26–57 weeks) with homologous and heterologous Ad26 vector–based vaccine regimens encoding different target pathogen immunogens did not reveal consistent differences in humoral or cellular immune responses against the target pathogen, as compared to responses in naïve animals. These results support the sequential use of Ad26 vector–based vaccine regimens targeting different diseases.
Proteomic genotyping of SNP of Complement Factor H (CFH) Y402H and I62V using multiple reaction monitoring (MRM) assays
Authors: Kim Kyoung Lae , Kim Hyerim , Lee Youngju , Lee Cheolju , Joo Kwangsic , Park Sang Jun , Park Kyu Hyung , Park Seong-Jun , Woo Se Joon
Published: November 2022

The single nucleotide polymorphisms (SNPs) of complement factor H (CFH) gene are well-known genetic risk factors for age-related macular degeneration (AMD). To identify whether the measurement of plasma protein concentrations of CFH variants using the multiple reaction monitoring (MRM) assay can determine the genotypes of CFH SNP rs1061170 and rs800292, 120 patients with AMD and 26 controls were included in this study. The number of cases were TT:TC:CC = 121:24:1 in CFH SNP Y402H and GG:AG:AA = 72:57:17 in CFH SNP I62V. Plasma concentrations of tryptic peptides were measured using the MRM assay, and tyrosine/histidine (Y/H) and valine/isoleucine (V/I) CFH variant protein ratios were obtained. To discriminate the genotypes by the plasma protein ratios, cut-off values were set for Y/H ratios (TT: > 4.428; TC: 1.00–4.428; CC: < 1.00) and V/I ratios (GG: > 1.09; AG: 0.0089–1.08; AA: < 0.0089). Correlation analysis revealed that the plasma CFH variant protein ratios and genotypes of CFH were exactly matched (100%) without overlap in the total patients and controls. The measurement of plasma protein CFH variants using the MRM assay can accurately identify the genotypes of CFH SNPs of Y402H and I62V.
Impact of γ-irradiation and SBR content in the compatibility of aminated (PVC/LLDPE)/ZnO for improving their AC conductivity and oil removal
Authors: Sharshir A. I. , Fayek S. A. , El-Gawad Amal F. Abd , Farahat M. A. , Ismail M. I. , Ghobashy Mohamed Mohamady
Published: November 2022

In some cases, blends containing PVC and LLDPE show low compatibility. Adding styrene-butadiene rubber to the PVC/LLDPE mixtures leads to a noticeable increase in tensile strength and compatibility of the blends. Also, an improvement in tensile strength is observed after incorporating SBR compatibilizer resulting in entirely different gamma irradiation doses. Without a compatibilizer, the mixture exhibits a distributed PVC and LLDPE phase with variable sizes and shapes; even a sizable portion of the domains resemble droplets. Styrene butadiene rubber (SBR) and gamma radiation make mixtures of (PVC/LLDPE) more compatible. The SEM study of the blends demonstrated that adding the compatibilizer resulted in finer blend morphologies with less roughness. At the same time, gamma irradiation reduced this droplet and gave a more smooth surface. Poly(vinyl chloride) (PVC) was chemically modified with four different amino compounds, including ethylene diamine (EDA), aniline (An), p-anisidine (pA) and dimethyl aniline (DMA) for improving the electric conductivity and oil removal capability of the blend polymer. All ionomers were prepared by nucleophilic substitution in a solvent/non-solvent system under mild conditions. This work novelty shows a sustainable route for producing oil adsorption materials by recycling plastic waste. After the amination process of poly(vinyl chloride) the oil adsorption was significantly enhanced.
Rapid pathogen identification and phenotypic antimicrobial susceptibility directly from urine specimens
Authors: Burg Larry , Crewe Gretel , DiMeo James , Guo Xin , Li Carmen G. , Mayol Melissa , Tempesta Andrew , Lauzier William , Markham Rachelle , Crissy Katarzyna , Barry Colleen , Walsh Bruce , Kirby James E. , Straus Don
Published: November 2022

Implementing effective antimicrobial therapy close to the onset of infection lowers morbidity and mortality and attenuates the spread of antimicrobial resistance. Current antimicrobial susceptibility testing (AST) methods, however, require several days to determine optimal therapies. We present technology and an automated platform that identify (ID) Urinary Tract Infection pathogens in 45 min and provide phenotypic AST results in less than 5 h from urine specimens without colony isolation. The ID and AST tests count cells fluorescently labeled with specific rRNA probes using non-magnified digital imaging. The ID test detected five pathogens at ≤ 7,000 CFU/mL and had a linear range of ~ 4 orders of magnitude. For contrived specimens, AST tests gave 93.1% categorical agreement with 1.3% Very Major Errors (VME), 0.3% Major Errors (ME), and 6.3% minor Errors (mE) compared to the broth microdilution (BMD) reference method. For clinical specimens, the ID test had 98.6% agreement and the AST test had 92.3% categorical agreement with 4.2% mE, 3.4% ME and 4.0% VME compared to BMD. Data presented demonstrates that direct-from-specimen AST tests can accurately determine antimicrobial susceptibility/resistance for each pathogen in a specimen containing two pathogens. The method is robust to urine matrix effects and off-target commensal and contaminating bacteria.
Evaluation of radiomics feature stability in abdominal monoenergetic photon counting CT reconstructions
Authors: Tharmaseelan Hishan , Rotkopf Lukas T. , Ayx Isabelle , Hertel Alexander , Nörenberg Dominik , Schoenberg Stefan O. , Froelich Matthias F.
Published: November 2022

Feature stability and standardization remain challenges that impede the clinical implementation of radiomics. This study investigates the potential of spectral reconstructions from photon-counting computed tomography (PCCT) regarding organ-specific radiomics feature stability. Abdominal portal-venous phase PCCT scans of 10 patients in virtual monoenergetic (VM) (keV 40–120 in steps of 10), polyenergetic, virtual non-contrast (VNC), and iodine maps were acquired. Two 2D and 3D segmentations measuring 1 and 2 cm in diameter of the liver, lung, spleen, psoas muscle, subcutaneous fat, and air were obtained for spectral reconstructions. Radiomics features were extracted with pyradiomics. The calculation of feature-specific intraclass correlation coefficients (ICC) was performed by comparing all segmentation approaches and organs. Feature-wise and organ-wise correlations were evaluated. Segmentation-resegmentation stability was evaluated by concordance correlation coefficient (CCC). Compared to non-VM, VM-reconstruction features tended to be more stable. For VM reconstructions, 3D 2 cm segmentation showed the highest average ICC with 0.63. Based on a criterion of ≥ 3 stable organs and an ICC of ≥ 0.75, 12—mainly non-first-order features—are shown to be stable between the VM reconstructions. In a segmentation-resegmentation analysis in 3D 2 cm, three features were identified as stable based on a CCC of > 0.6 in ≥ 3 organs in ≥ 6 VM reconstructions. Certain radiomics features vary between monoenergetic reconstructions and depend on the ROI size. Feature stability was also shown to differ between different organs. Yet, glcm_JointEntropy, gldm_GrayLevelNonUniformity, and firstorder_Entropy could be identified as features that could be interpreted as energy-independent and segmentation-resegmentation stable in this PCCT collective. PCCT may support radiomics feature standardization and comparability between sites.
Manatee calf call contour and acoustic structure varies by species and body size
Authors: Brady Beth , Ramos Eric Angel , May-Collado Laura , Landrau-Giovannetti Nelmarie , Lace Natalija , Arreola Maria Renee , Santos Gabriel Melo , da Silva Vera Maria Ferreira , Sousa-Lima Renata S.
Published: November 2022

Vocal activity and signal characteristics of mammals are driven by several factors that result in both stability and plasticity over multiple time scales. All three extant species of manatee communicate with several calls that are especially important for maintaining contact between cows and calves. Determining if calf calls differ across manatee species will provide insights into the evolution of species-specific acoustic communication traits. We investigated the interspecific differences in the vocalizations of calves of Amazonian manatees (Trichechus inunguis) and the two subspecies of the West Indian manatee (T. manatus). Vocalizations of individual calves were recorded in rehabilitation centers in Brazil, Puerto Rico, the United States, and Mexico. The acoustic structure of calls produced by manatee calves varied between species and with body size. Amazonian manatee calves produced shorter calls with multiple notes at higher frequency while West Indian calves produced modulated calls that were lower in frequency and longer in duration. Smaller West Indian calves produced frequency modulated, hill-shaped calls that flattened with an increase in body length. Our results provide evidence for divergence in the ontogeny of vocalizations acrossT. manatusandT. inunguisand suggest variation in body size contributed to the evolution of differences in the characteristics of their calls.
Interaction preferences between protein side chains and key epigenetic modifications 5-methylcytosine, 5-hydroxymethycytosine and N6-methyladenine
Authors: Hajnic Matea , Alonso-Gil Santiago , Polyansky Anton A. , de Ruiter Anita , Zagrovic Bojan
Published: November 2022

Covalent modifications of standard DNA/RNA nucleobases affect epigenetic regulation of gene expression by modulating interactions between nucleic acids and protein readers. We derive here the absolute binding free energies and analyze the binding modalities between key modified nucleobases 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (m6A) and all non-prolyl/non-glycyl protein side chains using molecular dynamics simulations and umbrella sampling in both water and methanol, the latter mimicking the low dielectric environment at the dehydrated nucleic-acid/protein interfaces. We verify the derived affinities by comparing against a comprehensive set of high-resolution structures of nucleic-protein complexes involving 5mC. Our analysis identifies protein side chains that are highly tuned for detecting cytosine methylation as a function of the environment and can thus serve as microscopic readers of epigenetic marks. Conversely, we show that the relative ordering of sidechain affinities for 5hmC and m6A does not differ significantly from those for their precursor bases, cytosine and adenine, respectively, especially in the low dielectric environment. For those two modified bases, the effect is more nuanced and manifests itself primarily at the level of absolute changes in the binding free energy. Our results contribute towards establishing a quantitative foundation for understanding, predicting and modulating the interactions between modified nucleic acids and proteins at the atomistic level.
Combining deep learning and crowd-sourcing images to predict housing quality in rural China
Authors: Xu Weipan , Gu Yu , Chen Yifan , Wang Yongtian , Chen Luan , Deng Weihuan , Li Xun
Published: November 2022

Housing quality is essential to human well-being, security and health. Monitoring the housing quality is crucial for unveiling the socioeconomic development status and providing political proposals. However, depicting the nationwide housing quality in large-scale and fine detail is exceedingly rare in remote rural areas owing to the high cost of canonical survey methods. Taking rural China as an example, we collect massive rural house images for housing quality assessment by various volunteers and further build up a deep learning model based on the assessed images to realize an automatic prediction for huge raw house images. As a result, the model performance achieves a high R2 of 0.76. Afterward, the housing qualities of 10,000 Chinese villages are estimated based on 50,000 unlabeled geo-images, and an apparent spatial heterogeneity is discovered. Specifically, divided by Qinling Mountains-Huaihe River Line, housing quality in southern China is much better than in northern China. Our method provides high-resolution predictions of housing quality across the extensive rural area, which could be a complementary tool for automatical monitoring of housing change and supporting house-related policymaking.
QTL associated with resistance to Stagonosporopsis citrulli in Citrullus amarus
Authors: Adams Lincoln , McGregor Cecilia
Published: November 2022

Gummy stem blight (GSB) is a fungal disease affecting cucurbit crops, including watermelon (Citrullus lanatus), leading to significant yield losses. The disease is caused by three Stagonosporopsis species, of which Stagonosporopsis citrulli is the most common in the southeastern United States. Currently no gummy stem blight-resistant watermelon cultivars are available to growers. In this study, QTL-seq in an interspecific population developed from Sugar Baby × PI 189225 (Citrullus amarus) identified QTL on chromosomes 2, 5, 9 and 11. A novel QTL on chromosome 5 (Qgsb5.2) associated with resistance to S. citrulli (PVE = 13.3%) was confirmed by genetic mapping. KASP marker assays were developed for selection of Qgsb5.2 to allow breeders to track the allele contributing resistance to GSB, reducing the need for laborious phenotyping. Pyramiding different GSB resistance QTL could be a useful strategy to develop GSB resistant watermelon cultivars.
Impacts of breast cancer and chemotherapy on gut microbiome, cognitive functioning, and mood relative to healthy controls
Authors: Bilenduke Emily , Sterrett John D. , Ranby Krista W. , Borges Virginia F. , Grigsby Jim , Carr Alaina L. , Kilbourn Kristin , Lowry Christopher A.
Published: November 2022

Women diagnosed with breast cancer undergoing chemotherapy experience cognitive impairment, symptoms of anxiety and depression, and physical side effects including disruption in the diversity and community composition of the gut microbiome. To date, there is limited research exploring the associations among these specific challenges. The present cross-sectional study explored the associations of self-reported cognitive functioning, depression, and anxiety symptoms, and gut microbiome diversity and community composition in women who were diagnosed with and undergoing chemotherapy treatment for breast cancer (BC) compared to cancer-free healthy controls (HC). The BC group displayed higher rates of cognitive dysfunction (p < 0.001) and depressive symptoms (p < 0.05) relative to HC. There was a significant difference in microbiome community composition between BC and HC, particularly characterized by a decreased relative abundance of the mucin-degrading genus Akkermansia in BC compared to HC (p < 0.05). Association models identified significant associations among group, cognitive, depression, and microbiome variables (p < 0.001). Overall, the study identified that BC participants experienced significant differences in self-reported cognitive functioning, self-reported depression symptoms, microbiome community composition, and mucin-degrading bacteria of the gut-mucosal barrier, relative to HC. The present study is consistent with the hypothesis that gut microbiome community composition impacts a woman’s experience with breast cancer and treatment suggesting that microbiome-based interventions have potential for improving quality of life outcomes in individuals with breast cancer.