bluuebunny/crossref_metadata_2025 huggingface dataset:
HTPN 078: an enhanced case management study to achieve viral suppression among viremic HIV-positive men who have sex with men in the United States
Authors: Remien Robert H. , Dacus Jagadīśa-devaśrī , Farley Jason E. , Hughes James P. , Gamble Theresa , Wang Zhe (Zoe) , Batey D. Scott , Mayer Kenneth H. , del Rio Carlos , Balán Iván C. , Irvin Risha , Mitchell Kate M. , Cummings Vanessa , Eshleman Susan H. , Conserve Donaldson F. , Knox Justin , Yu Kaiyue , Beyrer Chris
Published: December 2022

Objective(s):

After identifying and recruiting men who have sex with men living with HIV and virally unsuppressed, this study attempted to enhance treatment and care via case management to increase the proportion who achieved viral suppression.

Design:

Participants were randomized into one of two study arms: standard of care (SOC) or enhanced case management (CM) intervention. Participants were followed for 12 months with quarterly study assessments, with blood collected for CD4+ cell count testing, HIV viral load testing (primary prespecified outcome), and plasma storage.

Methods:

Participants identified via respondent-driven sampling and direct recruitment and were invited to participate in the randomized controlled trial. The CM intervention provided a wide range of support services including, health education, clinical care coordination, medication adherence support, and social service assistance. The month-12 assessment included questions about healthcare utilization, stigma, substance use, and mental health.

Results:

Among the 144 participants virally unsuppressed at baseline, most had had a previous positive HIV test result; were Black, non-Hispanic, gay and bisexual men, aged 22–50. Among the 128 participants at the last study visit, 68 were virally suppressed, with no statistically significant difference between the CM and SOC arms (viral suppression 42% and 53%, respectively; adjusted odds ratio = 0.62 [P = 0.15; 95% confidence interval: 0.32, 1.2]).

Conclusions:

Reaching targets of at least 90% sustained viral suppression among all people with HIV will likely require more than an individual-level CM approach that addresses barriers to optimal care and treatment at multiple levels.
Prevalence of HIV drug resistance in Nigeria: results from a cross-sectional, population-based survey of Nigerian adults with unsuppressed viral load
Authors: Aliyu Gambo G. , Lawton Jonathan G. , Mitchell Andrew B. , Abimiku Alash’le G. , Jelpe Tapdiyel , Bassey Orji , Riedel David J. , Swaminathan Mahesh , Chang Joy Chih-Wei , DeVos Joshua R. , Patel Hetal , Charurat Man E. , Stafford Kristen A.
Published: December 2022

Background:

HIV drug resistance (HIVDR) surveillance is an important tool to monitor threats to progress towards epidemic control. The characterization of HIVDR in Nigeria at the national level is needed to inform both clinical decisions and population-level HIV policy strategies. This study uses data obtained from the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS) to describe the prevalence and distribution of HIVDR in Nigeria.

Methods:

NAIIS was a cross-sectional, population-based survey of households throughout Nigeria in 2018. NAIIS was designed to provide estimates of HIV prevalence and related health indicators from a nationally representative sample. The study population included participants aged 15–64 years who tested positive for HIV, had a viral load at least 1000 copies/ml, and had available HIV drug resistance genotypes. HIV isolates were genotyped to detect drug resistance mutations. Individual characteristics of study participants associated with HIVDR were identified using a weighted multivariable logistic regression model.

Results:

Of 1355 respondents with available HIV genotypes, 293 (19%) had evidence of drug-resistant mutations (DRMs) that conferred resistance to at least one antiretroviral drug. The majority of DRMs observed conferred resistance to NNRTIs (17.6%) and NRTIs (11.2%). HIVDR was associated with being ART-experienced, longer duration on ART, and lower CD4+ count but not sociodemographic characteristics.

Conclusion:

The population level DRM prevalence in Nigeria was consistent with what would be expected in a mature HIV treatment landscape. The continued roll out of dolutegravir-anchored regimens should mitigate the impact of NNRTI resistance on population viral load suppression and progress towards epidemic control.
The prevalence of mental health disorders in people with HIV and the effects on the HIV care continuum
Authors: Lang Raynell , Hogan Brenna , Zhu Jiafeng , McArthur Kristen , Lee Jennifer , Zandi Peter , Nestadt Paul , Silverberg Michael J. , Parcesepe Angela M. , Cook Judith A. , Gill M. John , Grelotti David , Closson Kalysha , Lima Viviane D. , Goulet Joseph , Horberg Michael A. , Gebo Kelly A. , Camoens Reena M. , Rebeiro Peter F. , Nijhawan Ank E. , McGinnis Kathleen , Eron Joseph , Althoff Keri N.
Published: December 2022

Objective:

To describe the prevalence of diagnosed depression, anxiety, bipolar disorder, and schizophrenia in people with HIV (PWH) and the differences in HIV care continuum outcomes in those with and without mental health disorders (MHDs).

Design:

Observational study of participants in the North American AIDS Cohort Collaboration on Research and Design.

Methods:

PWH (≥18 years) contributed data on prevalent schizophrenia, anxiety, depressive, and bipolar disorders from 2008 to 2018 based on International Classification of Diseases code mapping. Mental health (MH) multimorbidity was defined as having two or more MHD. Log binomial models with generalized estimating equations estimated adjusted prevalence ratios (aPR) and 95% confidence intervals for retention in care (≥1 visit/year) and viral suppression (HIV RNA ≤200 copies/ml) by presence vs. absence of each MHD between 2016 and 2018.

Results:

Among 122 896 PWH, 67 643 (55.1%) were diagnosed with one or more MHD: 39% with depressive disorders, 28% with anxiety disorders, 10% with bipolar disorder, and 5% with schizophrenia. The prevalence of depressive and anxiety disorders increased between 2008 and 2018, whereas bipolar disorder and schizophrenia remained stable. MH multimorbidity affected 24% of PWH. From 2016 to 2018 (N = 64 684), retention in care was marginally lower among PWH with depression or anxiety, however those with MH multimorbidity were more likely to be retained in care. PWH with bipolar disorder had marginally lower prevalence of viral suppression (aPR = 0.98 [0.98–0.99]) as did PWH with MH multimorbidity (aPR = 0.99 [0.99–1.00]) compared with PWH without MHD.

Conclusion:

The prevalence of MHD among PWH was high, including MH multimorbidity. Although retention and viral suppression were similar to people without MHD, viral suppression was lower in those with bipolar disorder and MH multimorbidity.
Persistence of envelopes in different CD4+ T-cell subsets in antiretroviral therapy-suppressed people with HIV
Authors: Gartner Matthew J. , Tumpach Carolin , Dantanarayana Ashanti , Stern Jared , Zerbato Jennifer M. , Chang J. Judy , Angelovich Thomas A. , Anderson Jenny L. , Symons Jori , Deeks Steve G. , Flynn Jacqueline K. , Lewin Sharon R. , Churchill Melissa J. , Gorry Paul R. , Roche Michael
Published: December 2022

Objectives:

Despite suppressive antiretroviral therapy (ART), HIV can persist in a diverse range of CD4+ T-cell subsets. Through longitudinal env sampling from people with HIV (PWH) on ART, we characterized the persistence and phenotypic properties of HIV envs over two time-points (T1 and T2).

Methods:

Longitudinal blood and lymphoid tissue samples were obtained from eight PWH on suppressive ART. Single genome amplification (SGA) was performed on env to understand the genetic diversity and degree of clonal expansions over time. A subset of envs were used to generate pseudovirus particles to assess sensitivity to autologous plasma IgG and broadly neutralizing antibodies (bNAbs).

Results:

Identical env sequences indicating clonal expansion persisted between T1 and T2 and within multiple T-cell subsets. At both time-points, CXCR4-tropic (X4) Envs were more prevalent in naive and central memory cells; the proportion of X4 Envs did not significantly change in each subset between T1 and T2. Autologous purified plasma IgG showed variable neutralization of Envs, with no significant difference in neutralization between R5 and X4 Envs. X4 Envs were more sensitive to neutralization with clinical bNAbs, with CD4-binding site bNAbs demonstrating high breadth and potency against Envs.

Conclusion:

Our data suggest the viral reservoir in PWH on ART was predominantly maintained over time through proliferation and potentially differentiation of infected cells. We found the humoral immune response to Envs within the latent reservoir was variable between PWH. Finally, we identified coreceptor usage can influence bNAb sensitivity and may need to be considered for future bNAb immunotherapy approaches.
Impact of pre-antiretroviral treatment HIV-RNA on time to successful virological suppression and subsequent virological failure – two nationwide, population-based cohort studies
Authors: Sörstedt Erik , Tetens Malte Mose , Nilsson Staffan , Nowak Piotr , Treutiger Carl Johan , Månsson Fredrik , Änghagen Lena , Gisslén Magnus , Obel Niels , Yilmaz Aylin
Published: December 2022

Background:

The impact of pre-antiretroviral treatment (ART) HIV-RNA on time to successful virological suppression and subsequent failure in HIV patients remains poorly investigated.

Methods:

We used the Swedish InfCareHIV database and the Danish HIV Cohort Study to evaluate impact of pre-ART HIV-RNA on primary virological suppression (HIV-RNA < 50 copies/ml) and risk of secondary virological failure (two consecutive HIV-RNA > 200 copies/ml or one >1000 copies/ml). The study included 3366 Swedish and 2050 Danish ART naïve individuals who initiated ART in the period 2000–2018. We used Kaplan–Meier estimates and Cox regression analyses to estimate absolute risks and hazard ratios.

Results:

In both cohorts, more than 95% of patients with a pre-ART HIV-RNA <100 000 copies/ml obtained virological suppression within the first year after ART initiation contrasting 74% (Sweden) and 86% (Denmark) in those with HIV-RNA >1 000 000 copies/ml. Almost all patients obtained virological suppression after four years irrespective of pre-ART HIV-RNA. In contrast, we observed no substantial impact of pre-ART HIV-RNA on risk of virological failure once virological suppression was obtained.

Conclusion:

High pre-ART HIV-RNA is strongly associated with increased time to successful virological suppression, but pre-ART HIV-RNA has no impact on risk of subsequent virological failure.
Cisgender women with HIV in the United States: how have HIV care continuum outcomes changed over time? 2015–2020
Authors: O'Shea Jesse Garrett , Neblett Fanfair Robyn , Dasgupta Sharoda , Tie Yunfeng , Yuan Xin , Beer Linda , Weiser John
Published: December 2022

Objective:

To evaluate HIV care continuum trends over time among women with HIV (WWH).

Design:

The Medical Monitoring Project (MMP) is a complex sample survey of adults with diagnosed HIV in the United States.

Methods:

We used 2015–2019 MMP data collected from 5139 adults with diagnosed HIV infection who identified as cisgender women. We calculated weighted percentages with 95% confidence intervals (CIs) for all characteristics and estimated annual percentage change (EAPC) and the associated 95% CI to assess trends. EAPCs were considered meaningful from a public health perspective if at least 1% with P values less than 0.05.

Results:

Among cisgender women with diagnosed HIV infection during 2015–2019, 58.8% were Black or African American (95% CI 54.4–63.3), 19% were Hispanic/Latina (95% CI 14.7–23.2), and 16% were Non-Hispanic White (95% CI 14.1–17.9) persons. There was a meaningful increase in the percentage who ever had stage 3 HIV disease from 55.8% (95% CI 51.0–60.5) in 2015 to 61.5% (95% CI 58.1–64.8) in 2019 (EAPC 1.7%; CI 1.5–1.9; P < 0.001). There were no meaningful changes over time among women, overall, in retention in care, antiretroviral therapy (ART) prescription, ART adherence, missed appointments, or recent or sustained viral suppression.

Conclusion:

The HIV care continuum outcomes among WWH did not meaningfully improve from 2015 to 2019, raising a concern that Ending the HIV Epidemic in the US (EHE) initiative goals will not be met. To improve health and reduce transmission of HIV among WWH, multifaceted interventions to retain women in care, increase ART adherence, and address social determinants of health are urgently needed.
Association between inflammatory biomarker profiles and cardiovascular risk in individuals with and without HIV
Authors: Sukumaran Luxsena , Kunisaki Ken M. , Bakewell Nicholas , Winston Alan , Mallon Patrick W.G. , Doyle Nicki , Anderson Jane , Boffito Marta , Haddow Lewis , Post Frank A. , Vera Jaime H. , Sachikonye Memory , Sabin Caroline A.
Published: December 2022

Background:

People with HIV have an increased risk for cardiovascular morbidity and mortality. Inflammation and immune activation may contribute to this excess risk.

Methods:

We assessed thirty-one biomarkers in a subset of POPPY participants and identified three distinct inflammatory profiles: ‘gut/immune activation’, ‘neurovascular’, and ‘reference’ (relatively low levels of inflammation). Ten-year cardiovascular disease (CVD) risk predictions were calculated using the QRISK, Framingham Risk Score (FRS) and the Data Collection on Adverse effects of anti-HIV Drugs (D:A:D) algorithms. The distributions of CVD risk scores across the different inflammatory profiles, stratified by HIV status, were compared using median quantile regression.

Results:

Of the 312 participants included [70% living with HIV, median (interquartile range; IQR) age 55 (51–60) years; 82% male; 91% white], 36, 130, and 146 were in the ‘gut/immune activation’, ‘neurovascular’, and ‘reference’ cluster, respectively. The median (IQR) QRISK scores were 9.3% (4.5–14.5) and 10.2% (5.5–16.9) for people with and without HV, respectively, with similar scores obtained with the FRS and D:A:D. We observed statistically significant differences between the distributions of scores in the three clusters among people with HV. In particular, median QRISK [5.8% (1.0–10.7) and 3.1% (0.3–5.8)] scores were higher, respectively, for those in the ‘gut/immune activation’ and ‘neurovascular’ clusters compared to those in the reference cluster.

Conclusions:

People with HIV with increased gut/immune activation have a higher CVD risk compared to those with relatively low inflammation. Our findings highlight that clinically important inflammatory subgroups could be useful to differentiate risk and maximise prediction of CVD among people with HIV.
Impaired immune function accompanies social evolution in spiders
Authors: Bechsgaard Jesper , Jorgensen Tove Hedegaard , Jønsson Anne Katrine , Schou Mads , Bilde Trine
Published: December 2022

An efficient immune system is essential to the survival of many animals. Sociality increases risk of pathogen transmission, which should select for enhanced immune function. However, two hypotheses instead predict a weakened immune function: relaxed selection caused by social immunity/protection, and reduced efficacy of selection due to inbreeding, reproductive skew and female bias in social species that reduce effective population size and accelerate genetic drift. We assessed the effect of social evolution on immune function in a comparative study of two social spider species and their closely related subsocial sister species (genus
Stegodyphus
). The haemolymph of social species was less efficient in inhibiting bacterial growth of the potentially pathogenic bacteria
Bacillus subtilis
than that of subsocial species. Reduced efficacy of selection in social species was supported by comparative genomic analysis showing substantially elevated non-synonymous substitutions in immune genes in one of the social species. We propose that impaired immune function results from reduced efficacy of selection because the evolution of sociality in spiders is accompanied by demographic processes that elevate genetic drift. Positive feedback between pathogen-induced local extinctions and the resulting elevation of genetic drift may further weaken responses to selection by pathogens, and threaten species persistence.
Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons
Authors: Esquerré Damien , Brennan Ian G. , Donnellan Stephen , Keogh J. Scott
Published: December 2022

Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
Lionel Alexander Bethune (Alastair) Pilkington. 7 January 1920—5 May 1995
Authors: Oxley B. W.
Published: December 2022

Alastair Pilkington spent his whole working career in the glass industry, initiating and leading development of the revolutionary float process, which involves floating molten glass on molten tin. This novel glassmaking venture emerged in the small town of St Helens, where the Pilkington Company, founded in 1826, had the strength to see the project through to a successful conclusion, solving a huge number of complex technological problems and investing substantial funds. Almost all the glass one sees today, in myriads of applications worldwide, owes its optically perfect surfaces to the float process. Alastair interfaced so effectively with his engineering team and the Board of Directors of Pilkington Brothers that he rose to become an exemplary chairman of the company, with involvements and influence well beyond the field of glassmaking.
Nigel Oscar Weiss. 16 December 1936—24 June 2020
Authors: Proctor FRS Michael
Published: December 2022

Nigel Weiss was an astrophysicist and applied mathematician, born in South Africa but based in Cambridge for most of his career. He made a number of important contributions to the study of sunspots, where he produced a detailed model of their complex structure. He also made important contributions to theory of the solar 22-year magnetic cycle, using pioneering numerical modelling and drawing attention to the dynamical effects of symmetry breaking and of historic proxy data through observations of radioactive isotopes in tree rings and ice cores. A major part of his work was the numerical and theoretical investigation of many aspects of the interaction of magnetic fields with thermal convection in the Sun and stars. The numerical studies in particular were pioneering in the context of computer resources at that time. He led a talented group of students and postdocs, many of whom have held senior positions in UK and US universities. He combined great physical insight with expertise in numerical computation, nonlinear dynamics and bifurcation theory, and was an inspirational supervisor and mentor, combining high academic standards with an open generous nature. Apart from his work he had a strong interest in twentieth-century art and served on the National Gallery Consultative Group for many years.
Published correlational effect sizes in social and developmental psychology
Authors: Weinerová Josefína , Szűcs Dénes , Ioannidis John P. A.
Published: December 2022

The distribution of effect sizes may offer insights about the research done and reported in a scientific field. We have evaluated 12 412 manually collected correlation effect sizes (Sample 1) and 31 157 computer-extracted correlation effect sizes (Sample 2) published in journals focused on social or developmental psychology. Sample 1 consisted of 243 studies from six journals published in 2010 and 2019. Sample 2 consisted of 5012 papers published in 10 journals between 2010 and 2019. The 25th, 50th and 75th effect size percentiles were 0.08, 0.17 and 0.33, and 0.17, 0.31 and 0.52 in Samples 1 and 2, respectively. Sample 2 percentiles were probably larger because Sample 2 only included effect sizes from the text but not from tables. In text authors may have emphasized larger correlations. Large sample sizes were associated with smaller reported correlations. In Sample 1 about 70% of studies specified a directional hypothesis. In 2010 no papers had power calculations, while in 2019 14% of papers had power calculations. These data offer empirical insights into the distribution of reported correlations and may inform the interpretation of effect sizes. They also demonstrate the importance of computation of statistical power and highlight potential reporting bias.
Tiered social distancing policies and epidemic control
Authors: Bliman Pierre-Alexandre , Carrozzo-Magli Alessio , d’Onofrio Alberto , Manfredi Piero
Published: December 2022

Tiered social distancing policies have been adopted by many governments to mitigate the harmful consequences of COVID-19. Such policies have a number of well-established features, i.e. they are short-term, adaptive (to the changing epidemiological conditions), and based on a multiplicity of indicators of the prevailing epidemic activity. Here, we use ideas from Behavioural Epidemiology to represent tiered policies in an SEIRS model by using a composite information index including multiple indicators of current and past epidemic activity mimicking those used by governments during the COVID-19 pandemic, such as transmission intensity, infection incidence and hospitals’ occupancy. In its turn, the dynamics of the information index is assumed to endogenously inform the governmental social distancing interventions. The resulting model is described by a hereditary system showing a noteworthy property, i.e. a dependency of the endemic levels of epidemiological variables from initial conditions. This is a consequence of the need to normalize the different indicators to pool them into a single index. Simulations suggest a rich spectrum of possible results. These include policy suggestions and identify pitfalls and undesired outcomes, such as a worsening of epidemic control, that can arise following such types of approaches to epidemic responses.
Analytic mode-matching for accurate handling of exceptional points in a lined acoustic waveguide
Authors: Lawrie Jane B. , Nennig B. , Perrey-Debain E.
Published: December 2022

Exceptional points (which occur when two or more modes coalesce) have long been associated with optimal attenuation in lined acoustic waveguides. In recent years, with a view to optimizing sound absorption, some effort has gone into designing liners that generate exceptional points (EPs) at specified frequencies. However, analytic modelling of acoustic scattering in the presence of an EP is not well developed, with most authors relying on standard methods applied close to (but not at) EP conditions. Indeed, exact treatment requires care since the mathematical system under-pinning the scattering process is degenerate. This article presents an analytic mode-matching approach to modelling the scattering of a plane wave travelling towards the junction of a rigid duct with a lined duct at EP conditions. Both EP2 and EP3 (coalescence of two and three modes respectively) are considered. The enhanced mode-matching scheme is shown to be valid and numerically robust, and it is anticipated that it will be straightforward to adapt to a wide range of applications involving complex symmetric operators.
Mixed-species bird flocks re-assemble interspecific associations across an elevational gradient
Authors: Shen Yong , Holyoak Marcel , Goodale Eben , Mammides Christos , Zou Fasheng , Chen Yuxin , Zhang Chaoming , Quan Qing , Zhang Qiang
Published: December 2022

Understanding how non-trophic social systems respond to environmental gradients is still a challenge in animal ecology, particularly in comparing changes in species composition to changes in interspecific interactions. Here, we combined long-term monitoring of mixed-species bird flocks, data on participating species' evolutionary history and traits, to test how elevation affected community assemblages and interspecific interactions in flock social networks. Elevation primarily affected flocks through reassembling interspecific associations rather than modifying community assemblages. Specifically, flock networks at higher elevations (compared to low elevations) had stronger interspecific associations (larger average weighted degree), network connectivity (enhanced network density) and fewer subnetworks. A phylogenetic and functional perspective revealed that associations between similar species weakened, whereas connections between dissimilar and/or random species were unchanged or strengthened with elevation. Likewise, network assortativity for the traits of vertical stratum and breeding period declined with elevation. The overall pattern is a change from modular networks in the lowlands, where species join flocks with other species that have matching traits, to a more open, random system at high elevations. Collectively, this rewiring of interspecific networks across elevational gradients imparts network stability and resiliency and makes mixed-species flocks less sensitive to local extinctions caused by harsh environments.
Taking quantitative genomics into the wild
Authors: Johnston Susan E. , Chen Nancy , Josephs Emily B.
Published: December 2022

We organized this special issue to highlight new work and review recent advances at the cutting edge of ‘wild quantitative genomics’. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
Individual differences and knockout in zebrafish reveal similar cognitive effects of BDNF between teleosts and mammals
Authors: Lucon-Xiccato Tyrone , Montalbano Giulia , Gatto Elia , Frigato Elena , D'Aniello Salvatore , Bertolucci Cristiano
Published: December 2022

The remarkable similarities in cognitive performance between teleosts and mammals suggest that the underlying cognitive mechanisms might also be similar in these two groups. We tested this hypothesis by assessing the effects of the brain-derived neurotrophic factor (BDNF), which is critical for mammalian cognitive functioning, on fish's cognitive abilities. We found that individual differences in zebrafish's learning abilities were positively correlated withbdnfexpression. Moreover, a CRISPR/Cas9 mutant zebrafish line that lacks the BDNF gene (bdnf−/−) showed remarkable learning deficits. Half of the mutants failed a colour discrimination task, whereas the remaining mutants learned the task slowly, taking three times longer than controlbdnf+/+zebrafish. The mutants also took twice as long to acquire a T-maze task compared to control zebrafish and showed difficulties exerting inhibitory control. An analysis of habituation learning revealed that cognitive impairment in mutants emerges early during development, but could be rescued with a synthetic BDNF agonist. Overall, our study indicates that BDNF has a similar activational effect on cognitive performance in zebrafish and in mammals, supporting the idea that its function is conserved in vertebrates.
Adenoviral-Based Vaccine Elicits Robust Systemic and Mucosal Cross-Reactive Responses in African Green Monkeys and Reduces Shedding after SARS-CoV-2 Challenge
Authors: Tedjakusuma Sarah N. , Lester Colin A. , Neuhaus Elena D. , Dora Emery G. , Tucker Sean N. , Flitter Becca A.
Published: December 2022

As new SARS-CoV-2 variants continue to emerge and impact communities worldwide, efforts to develop next generation vaccines that enhance mucosal immunity would be beneficial for protecting individuals and reducing community transmission. We have developed a non-replicating recombinant adenovirus vector (rAd5) vaccine delivered by mucosal administration engineered to express both a protein antigen and a novel molecular adjuvant in the same cell. Here we describe the immunogenicity of three unique SARS-CoV-2 rAd5 vaccine preclinical candidates and their efficacy following viral challenge in African green monkeys. Animals were prime and boost immunized intranasally twenty-nine days apart with rAd5 vaccine candidates containing viral SARS-CoV-2 spike protein alone or in combination with viral nucleocapsid. Mucosal immunization elicited significant increases in antigen-specific serum antibody responses and functional neutralizing activity against multiple variants of concern. Robust antigen specific mucosal IgA responses were observed after a single administration of rAd5 and generated strong cross-reactive neutralizing antibodies against multiple variants including delta. Importantly, all vaccinated animals exhibited a significant reduction in viral loads and infectious particle shedding in both the nasal passages and lower airways compared to unvaccinated controls following challenge with SARS-CoV-2. These findings demonstrate that mucosal immunization using rAd5 is highly immunogenic, confers protective cross-reactive humoral responses in both the circulation and mucosa, and reduces viral loads and shedding upon challenge with multiple SARS-CoV-2 variants.
Polyethylene valorization by combined chemical catalysis with bioconversion by plastic-enriched microbial consortia
Authors: Gregory Gwendolyn J. , Wang Cong , Sadula Sunitha , Koval Sam , Lobo Raul , Vlachos Dionisios G. , Papoutsakis E. Terry
Published: December 2022

There are few reports of microbial deconstruction or functionalization of the recalcitrant backbone of polyolefins. However, microbes can utilize polyolefin deconstruction products, including n-alkanes. Here, we combined chemical catalysis with bioconversion to valorize polyethylene (PE) deconstruction products. High-density PE (HDPE) was deconstructed via hydrogenolysis over a ruthenium on carbon catalyst. The resultingn-alkane mixture (C4-C35) was utilized as a feedstock for microbial consortia derived from soil from local recycling plants. We found two consortia that utilized the PE-deconstruction product mix as a sole carbon source. We adapted the consortia on a commercially-availablen-alkane mix to reduce the number of species present and enrich for enhanced alkane utilization. Both resulting enriched consortia utilized the PE-deconstruction product mix more effectively than the original (parent) consortia. The predominant metabolite produced by both enriched consortia was a C16-C16wax ester. Wax esters have considerable industrial value, with the longer chain lengths (C32-C36) having the highest value. We identified twoRhodococcus aetherivoransstrains that grow well on C24, indicating this species is important for the functionalization of long-chain alkanes. This work demonstrates that enriched consortia from plastic-enriched environments can be combined with chemical catalysis to valorize polyethylene.

Synopsis

Chemical catalysis can be used to deconstruct polyethylene waste material to produce a mixture of alkanes. Enriched environmental microbial consortia can valorize these polyethylene deconstruction products via functionalization that preserves the alkane chain length thus minimizing CO2production.
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution
Authors: Tuffery Pierre , Derreumaux Philippe
Published: December 2022

1

Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.
Effects of nonantibiotic alternative growth promoter combinations on nutrient utilization, digestive enzyme activity, intestinal morphology, and cecal microflora of broilers
Authors: Li Zunyan , Zhang Beibei , Zhu Weimin , Lin Yingting , Chen Jia , Zhu Fenghua , Guo Yixuan
Published: December 2022

Given the ban on antibiotic growth promoters, six nonantibiotic alternative growth promoter combinations (NAGPCs) for broilers were evaluated. All birds were fed pellets of two basal diets—starter (0−21 d) and grower (22−42 d)—with either enramycin (ENR) or NAGPC supplemented. 1) control + 100 mg/kg ENR; 2) control diet (CON, basal diet); 3) control + 2,000 mg/kg mannose oligosaccharide (MOS) + 300 mg/kg mannanase (MAN) + 1,500 mg/kg sodium butyrate (SB) (MMS); 4) control + 2,000 mg/kg MOS + 300 mg/kg MAN + 500 mg/kgBacillus subtilis(BS) (MMB); 5) control + 2,000 mg/kg MOS + 9,000 mg/kg fruit oligosaccharide (FOS) + 1,500 mg/kg SB (MFS); 6) control + 9,000 mg/kg FOS + 500 mg/kg BS (MFS) (MBP). The experiment used a completely random block design with six replicates per group: 50 Ross 308 broilers in the starter phase and 16 in the grower phase. All the NAGPCs significantly improved (P < 0.01) utilization of dry matter (DM), organic matter (OM), crude protein (CP), and crude fat (CF) on d 21, significantly increased DM, OM (P < 0.01), and CP (P < 0.05) on d 42, and significantly increased (P < 0.01) villus height, crypt depth, and the villus height to crypt depth ratio in the jejunum and ileum compared with CON and ENR. On d 21 and 42, trypsin, lipase, and amylase activity of the duodenum significantly increased in the MMS, MMB, MFB, and MFM groups. Compared with ENR and CON, MMS, MMB, and MBP increased the abundance ofFirmicutesat d 21 and ofBacteroidesat d 42 whereas MMB, MFB, and MBP decreased the abundance ofProteobacteriaat d 21 and 42. Overall, the NAGPCs were found to have some beneficial effects and may be used as effective antibiotic replacements in broilers.
DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network
Authors: Wen Jia , Li Gang , Chen Jiawen , Sun Quan , Liu Weifang , Guan Wyliena , Lai Boqiao , Zhou Haibo , Szatkiewicz Jin P , He Xin , Sullivan Patrick F. , Li Yun
Published: December 2022

Genetic dissection of neuropsychiatric disorders can potentially reveal novel therapeutic targets. While genome-wide association studies (GWAS) have tremendously advanced our understanding, we approach a sample size bottleneck (i.e., the number of cases needed to identify >90% of all loci is impractical). Therefore, computationally enhancing GWAS on existing samples may be particularly valuable. Here, we describe DeepGWAS, a deep neural network-based method to enhance GWAS by integrating GWAS results with linkage disequilibrium and brain-related functional annotations. DeepGWAS enhanced schizophrenia (SCZ) loci by ∼3X when applied to the largest European GWAS, and 21.3% enhanced loci were validated by the latest multi-ancestry GWAS. Importantly, DeepGWAS models can be transferred to other neuropsychiatric disorders. Transferring SCZ-trained models to Alzheimer’s disease and major depressive disorder, we observed 1.3-17.6X detected loci compared to standard GWAS, among which 27-40% were validated by other GWAS studies. We anticipate DeepGWAS to be a powerful tool in GWAS studies.
Kinematic scattering by nanocrystals
Authors: Thomas Olivier , Noyan Ismail Cevdet
Published: December 2022

Various formulations are compared which describe diffraction from ultra-thin single-crystal films in the symmetric scattering configuration, showing that, for this thickness range, several implicit assumptions in these formulations are no longer satisfied. Consequently, the position, integrated intensity and integral breadth of a diffraction peak cannot be related to the lattice spacing of the material or the number of unit cells along the diffraction vector using traditional analysis methods. Some simple equations are proposed to obtain the correct values of these parameters for this specific sample/diffraction geometry combination. More generally, the development of rigorous formalisms for analyzing diffraction from nanocrystals is proposed.
Algorithms and programs for the shell decomposition of oscillating functions in space
Authors: Urzhumtseva Ludmila , Lunin Vladimir , Urzhumtsev Alexandre
Published: December 2022

Real-space refinement of atomic models in macromolecular crystallography and cryo-electron microscopy fits a model to a map obtained with experimental data. To do so, the atomic model is converted into a map of limited resolution and then this map is compared quantitatively with the experimental one. For an appropriate comparison, the atomic contributions comprising the model map should reflect the resolution of the experimental map and the atomic displacement parameter (ADP) values. Such contributions are spherically symmetric oscillating functions, different for chemically different kinds of atoms, different ADPs and different resolution values, and their derivatives with respect to atomic parameters rule the model refinement. For given parameter values, every contribution may be calculated numerically using two Fourier transforms, which is highly time consuming and makes calculation of the respective derivatives problematic. Alternatively, for an atom of each required type its contribution can be expressed in an analytical form as a sum of specially designed terms. Each term is different from zero essentially inside a spherical shell, and changing the ADP value does not change its form but rather changes the value of one of its arguments. In general, these terms become a convenient tool for the decomposition of oscillating spherically symmetric functions. This work describes the algorithms and respective software, named dec3D, to carry out such a shell decomposition for density contributions of different kinds of atoms and ions.
Environmental accounting and state power in the Grand Duchy of Tuscany (1537–1621)
Authors: Bigoni Michele , Lazzini Simone , Occhipinti Zeila , Verona Roberto
Published: December 2022

Purpose

The study investigates the use of early forms of environmental accounting in the implementation of environmental strategies in the Grand Duchy of Tuscany between the 16th and 17th centuries.

Design/methodology/approach

The study adopts the Foucauldian concept of raison d’État to shed light on the ways in which environmental accounting practices were used by Tuscan Grand Dukes to form a detailed knowledge of the territory to be governed and act accordingly.

Findings

Financial and non-financial information relating to environmental issues enabled the Grand Dukes to “visualise” the territory to be managed as an enclosed disciplinary space whereby the conduct of people living therein could be decisively influenced. Accounting practices as a tool for the implementation of environmental strategies did not merely aim to protect the environment but were a means to reinforce the power of the State.

Research limitations/implications

The paper can inform future works that investigate the ways in which environmental policies and accounting are used to pursue far-reaching governmental goals. It encourages scholars to examine further the origins of environmental accounting and its early forms.

Social implications

The study documents how environmental strategies and the related use of accounting can have a significant influence on how individuals are allowed to conduct themselves. It also shows that environmental accounting practices can be an important tool in a State’s machinery of power.

Originality/value

The study offers a novel perspective on the use of environmental accounting information as a tool in the exercise of State power. It explores explicitly the interrelations between accounting, sustainability and power. It also adds new evidence to historical research that has engaged with early forms of environmental accounting.
Job demands and technology overload influencing work stress in organizations during the COVID-19 pandemic
Authors: Yen Yung-Shen
Published: December 2022

Purpose

This study is based on the stimulus–organism–response (SOR) model to examine how job demands and technology overload affect work stress for workers using video conferencing apps (VCAs) in organizations during the COVID-19 pandemic. Moreover, the moderating effect of technology self-efficacy was tested in the model on the relationship between technology overload and work stress.

Design/methodology/approach

An online survey was conducted to investigate workers on PTT forums in Taiwan. A sample was obtained of 253 workers, and structural equation modeling was conducted using AMOS to test the hypotheses.

Findings

Job demands positively affect work stress through information overload, communication overload and system feature overload. Moreover, high technology self-efficacy may weaken the relationship between technology overload and work stress.

Research limitations/implications

The study may have sample bias because our sample was obtained from an online survey on social networking sites. Regarding the theoretical implications, this study demonstrated that technology overload, as an internal organism, is a critical mediator influencing the relationship between job demands (stimulus) and work stress (response). Thus, this study extended the applicability of the SOR model in the context of working with VCAs in organizations.

Practical implications

Company managers need to effectively control the information amount, communication interruptions and system features of social media at optimum levels for workers. Moreover, companies should recruit workers with high technology self-efficacy or provide technology training and technology-related consulting to those with low technology self-efficacy.

Originality/value

The extant work stress knowledge is extended to workers using VCAs in organizations.
Family incivility and burnout: a moderated mediation model of life satisfaction and psychological capital
Authors: Maria Tresita Paul V. , Aboobaker Nimitha , Devi Uma N.
Published: December 2022

Purpose

This study investigates the relationship between family incivility (FI) and burnout in line with the conservation of resources theory and work–home resources model. The authors also examine the conditional indirect effects of psychological capital (PsyCap) and life satisfaction (LS) in the aforementioned relationship. The purpose of this paper is to address these issues.

Design/methodology/approach

Data were collected using a time-lagged methodological design by administering a structured questionnaire among 296 rural doctors. The collected data were analyzed using PROCESS macro in Statistical Package for the Social Sciences (SPSS) 23.

Findings

The study indicates that FI is an emotional home demand and influences burnout at the workplace through the depletion of LS. At the same time, PsyCap proves to be a vital resource that mitigates the adverse effects of FI and burnout.

Research limitations/implications

This study adds to the work–family and well-being literature by exploring the underlying mechanism through which FI connects to different outcomes. The implications of these findings for applications and extension of the work–home resources model to the family domain is elaborated in detail.

Originality/value

This study is among the first to empirically substantiate the long-term adverse consequences of FI and its potential for negatively affecting the work domain by inducing long-term psychological disorder “burnout.”
Public user innovation: exploring the support mechanisms and user roles in a public organisation
Authors: Fosstenløkken Siw Marita
Published: December 2022

Purpose

This article expands literature on user innovation by exploring the mechanisms that support user innovations in the context of a public organisation. Research has hitherto documented support mechanisms for user innovation in producer companies, where users contribute in early or temporary innovation phases as external non-employees or lead-users engaged by the producer. Complementarily, this paper explores a lesser known area of support mechanisms, those that support internal user innovations in a public sector setting.

Design/methodology/approach

Employing a qualitative study of a Norwegian public hospital at the interface between users (personnel and patients) and organisational support (facilitators who orchestrate user innovations), this article analyses in-house user innovation based on observations, text documentation and interviews over a four-year period.

Findings

In this public hospital, holistic organisational facilitation of “public user innovators” formed the key support mechanism built on “people” (facilitating co-creation), “process” (facilitating ideas, project realisation and implementation) and “coordination” (facilitating systems and communication). The findings show that public and producer organisational mechanisms both resemble and differ in many respects, as illustrated by the framework developed to describe these characteristics, such as that producers insource users, while the public organisation outsources production.

Originality/value

The originality of the article lies in the identification and description of “public user innovation”, a new term developed from this study of a public organisation in contrast to the dominant literature on producer companies. This article contributes new insights by differentiating the roles of user innovators and the mechanisms that support such innovations. New implications are drawn from the public side of organisational support in user innovation research.