cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Coordinated strategy for a model-based decision support tool for coronavirus disease, Utah, USA
Creators: name: Pettit, J.C
name: Sheets, T
name: Good, M
name: Keegan, L.T
name: Vinik, R.G
name: Frattaroli, S
name: Beams, A
name: Grantz, K.H
name: Barfuss, D
name: Nelson, R.
name: Arehart, E
name: Meredith, H.R
name: McCaffrey, K
name: Lee, E.C
name: Zhang, Y
name: Lessler, J
name: Samore, M.H
name: Dunn, A.C
Publisher: name: Centers for Disease Control and Prevention (CDC)
Year: 2021

description: The coronavirus disease pandemic has highlighted the key role epidemiologic models play in supporting public health decision-making. In particular, these models provide estimates of outbreak potential when data are scarce and decision-making is critical and urgent. We document the integrated modeling response used in the US state of Utah early in the coronavirus disease pandemic, which brought together a diverse set of technical experts and public health and healthcare officials and led to an evidence-based response to the pandemic. We describe how we adapted a standard epidemiologic model; harmonized the outputs across modeling groups; and maintained a constant dialogue with policymakers at multiple levels of government to produce timely, evidence-based, and coordinated public health recommendations and interventions during the first wave of the pandemic. This framework continues to support the state's response to ongoing outbreaks and can be applied in other settings to address unique public health challenges.
Longitudinal patient-reported outcomes on genotype-guided irinotecan dosing: feasibility and clinical relevance
Creators: name: Turk, Anita
name: Deal, Allison M
name: Irvin, William
name: Jonsson, Mattias
name: Basch, Ethan M
name: Sanoff, Hanna K
name: Wood, William A
name: Boles, Jeremiah C
name: Stein, Sophia I
name: Sorah, Jonathan D
name: Innocenti, Federico
Publisher: name: Oxford University Press (OUP)
Year: 2024

description: INTRODUCTION: Standard investigator-based adverse events (AE) assessment is via CTCAE for clinical trials. However, including the patient perspective through PRO (patient-reported outcomes) enhances clinicians' understanding of patient toxicity and fosters early detection of AEs. We assessed longitudinal integration of PRO-CTCAE within clinical workflow in a phase II trial.
MATERIALS AND METHODS: As a sub-study in a phase II trial of genotype-directed irinotecan dosing evaluating efficacy in patients with metastatic colorectal cancer receiving FOLFIRI and bevacizumab, patients reported on 13 AEs generating a PRO-CTCAE form. The primary objective was to estimate forms completed by patients and clinicians at least 80% of time. Secondary objectives were estimating concordance and time to first score of specific symptoms between patient and clinician pairs.
RESULTS: Feasibility of longitudinal PRO-CTCAE integration was met as 96% of patients and clinician-patient pairs completed at least 80% of PRO-CTCAE forms available to them with 79% achieving 100% completion. Concordance between patient and clinician reporting a severe symptom was 73% with 24 disconcordant pairs, 21 involved patients who reported a severe symptom that the clinician did not. Although protocol-mandated dose reductions were guided by CTCAE not PRO-CTCAE responses, the median time to dose reduction of 2.53 months, and the time-to-event curve closely approximated time to patient-reported toxicity.
CONCLUSION: Longitudinal integration of PRO-CTCAE paired CTCAE proved feasible. Compared to clinicians, patients reported severe symptoms more frequently and earlier. Patient-reported toxicity more closely aligned with dose decreases indicating incorporation into routine clinical practice may enhance early detection of toxicity improving patient safety and quality of life.
Quantum-rod sensitized four-dimensional optical data storage
Creators: name: Li, Xiangping
name: Chon, James
name: Evans, Richard A.
name: Gu, Min
Publisher: name: Swinburne
Year: 2024

description: Quantum rods (QRs) are incorporated into polymers that are doped with azo dyes via an energy transfer process. The polarization-dependent refractive-index change allows four-dimensional optical data storage as well as other polarization-controlled photonic applications.
Plectiscidea bistriata
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Plectiscidea
Plectiscidea bistriata

description: Plectiscidea bistriata (THOMSON, 1888)
M a t e r i a l e x a m i n e d: Trap7: 1♀ 19.x.-3.xi.
D i s t r i b u t i o n: Western Palaearctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 118, DOI: 10.5281/zenodo.10788481
Lives saved with vaccination for 10 pathogens across 112 countries in a pre-covid-19 world
Creators: name: Vynnycky, E
name: Clapham, H.E
name: Nayagam, S
name: Ferrari, M
name: Papadopoulos, T
name: Gaythorpe, K.A.M
name: Tam, Y
name: Sweet, S
name: Trotter, C.L
name: Hinsley, W.R
name: Jackson, M.L
name: Carter, E.D
name: Walker, N
name: Lessler, J
name: Jean, K
name: Li, X
name: Karachaliou, A
name: Kraay, A
name: Clark, A
name: Huber, J.H
name: Eilertson, K
name: Gamkrelidze, I
name: Sanderson, C
name: Toor, J
name: Portnoy, A
name: Woodruff, K
name: Abbas, K
name: Minh, Q.T
name: Ferguson, N.M
name: Jit, M
name: Hallett, T.B
name: Echeverria-Londono, S.
name: Metcalf, C.J.E
name: Tanvir, H
name: Perkins, T.A
name: Hogan, D
name: Truelove, S.A.
name: Razavi, H
name: Moore, S.M
name: Resch, S
name: Li, X
name: Mengistu, T
name: Razavi-Shearer, D
name: de Villiers, M.J
name: Winter, A
name: Klepac, P
name: Lopman, B.A
Publisher: name: eLife Sciences Publications Ltd
Year: 2021

description: Background: Vaccination is one of the most effective public health interventions. We investigate the impact of vaccination activities for Haemophilus influenzae type b, hepatitis B, human papillomavirus, Japanese encephalitis, measles, Neisseria meningitidis serogroup A, rotavirus, rubella, Streptococcus pneumoniae, and yellow fever over the years 2000–2030 across 112 countries. Methods: Twenty-one mathematical models estimated disease burden using standardised demographic and immunisation data. Impact was attributed to the year of vaccination through vaccine-activity-stratified impact ratios. Results: We estimate 97 (95%CrI[80, 120]) million deaths would be averted due to vaccination activities over 2000–2030, with 50 (95%CrI[41, 62]) million deaths averted by activities between 2000 and 2019. For children under-5 born between 2000 and 2030, we estimate 52 (95%CrI[41, 69]) million more deaths would occur over their lifetimes without vaccination against these diseases. Conclusions: This study represents the largest assessment of vaccine impact before COVID-19-related disruptions and provides motivation for sustaining and improving global vaccination coverage in the future.
Publications Among Pain Medicine Fellowship-Trained American Board of Anesthesiology Diplomates
Creators: name: Jones, James H
name: Fleming, Neal
Publisher: name: Springer Nature
Year: 2024

description: American Board of Anesthesiology (ABA) diplomates who pursue clinical fellowship training in pain medicine may be better suited to lead scholarly projects and serve as first authors of publications in peer-reviewed journals given their additional training and clinical expertise. The primary aim of this study was to determine whether ABA certification in pain medicine is associated with a greater number of peer-reviewed publications. The secondary aim included assessments of whether pain medicine fellowship training is associated with a higher publication rate (publications per year) or publication in a larger number of peer-reviewed journals. A literature search was conducted in December 2023 using the Scopus database for publications related to anesthesiology and pain medicine in the United States between 2013 and 2023. First authors identified through the search were then individually searched within the ABA physician directory. The following data were collected: author name and identification number, year of publication, publication type (article or review), year of primary anesthesiology certification, and year of fellowship, if applicable. This study identified 9,612 publications and 6,924 unique first authors. Pain medicine fellowship training was associated with a statistically significant increase (p-value < 0.001) in the number of publications (0.546; 95% confidence interval {CI}, 0.386-0.707), publications per year (0.140; 95% CI, 0.121-0.159), and publication in a larger number of peer-reviewed journals (0.256; 95% CI, 0.182-0.330) in regression models adjusted for the number of years from certification. This query of the Scopus database and ABA physician directory indicates that pain medicine fellowship training is associated with statistically significant increases in research productivity, as defined by the number of publications, publications per year, or the number of publications in peer-reviewed journals. However, these increases in research output would not lead to a marked increase in scholarship productivity to justify pursuing a fellowship for this purpose.
Plectiscidea canaliculata
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Plectiscidea
Plectiscidea canaliculata

description: Plectiscidea canaliculata (FÖRSTER, 1871)
M a t e r i a l e x a m i n e d: Trap2: 1♀ 1-15.vi.
D i s t r i b u t i o n: Transpalaearctic, known from Azerbaijan (HUMALA 2003), new record for Georgia.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 118, DOI: 10.5281/zenodo.10788481
Congruences for Hasse-Witt matrices and solutions of p-adic KZ equations
Creators: name: Zudilin, Wadim
name: Varchenko, Alexander
Publisher: name: International Press of Boston
Year: 2024

description: We prove general Dwork-type congruences for Hasse–Witt matrices attached to tuples of Laurent polynomials.We apply this result to establishing arithmetic and p-adic analytic properties of functions originating from polynomial solutions modulo p8 of Knizhnik–Zamolodchikov (KZ) equations, the solutions which come as coefficients of master polynomials and whose coefficients are integers. As an application we show that the p-adic KZ connection associated with the family of hyperelliptic curves (y2 = (t-z1)...(t-z2g+1) has an invariant subbundle of rank g. Notice that the corresponding complex KZ connection has no nontrivial subbundles due to the irreducibility of its monodromy representation.
Plectiscidea moerens
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Plectiscidea
Plectiscidea moerens

description: Plectiscidea moerens (FÖRSTER, 1871)
M a t e r i a l e x a m i n e d: Trap 4: 1♀ 21.ix.-5.x.
D i s t r i b u t i o n: Western Palaearctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on pages 118-119, DOI: 10.5281/zenodo.10788481
Regional sequencing collaboration reveals persistence of the t12 vibrio cholerae o1 lineage in west africa
Creators: name: Wohl, S
name: Melingui, S
name: Boum, Y
name: Ekeng, E
name: Issaka, B.B
name: Akintayo, I
name: Tchatchouang, S
name: Naidoo, D
name: Dano, I.D
name: Akenji, B
name: Azman, A
name: Luquero, F
name: Ahumibe, A
name: Lessler, J
name: Chukwu, C
name: Popoola, M.O
name: Ousmane, S
name: Nzouankeu, A
Publisher: name: eLife Sciences Publications Ltd
Year: 2021

description: Background: Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa—where cholera outbreaks occur every few years—are still poorly understood. Coordinated genomic surveillance of Vibrio cholerae in the areas most affected may reveal transmission patterns important for cholera control. Methods: During a regional sequencing workshop in Nigeria, we sequenced 46 recent V. cholerae isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the V. cholerae bacterium circulating in these three countries. Results: From these isolates, we generated 44 whole Vibrio cholerae O1 sequences and analyzed them in the context of 1280 published V. cholerae O1 genomes. All sequences belonged to the T12 V. cholerae seventh pandemic lineage. Conclusions: Phylogenetic analysis of newly generated and previously published V. cholerae genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts.
African ancestry-derived APOL1 risk genotypes show proximal epigenetic associations
Creators: name: Winkler, Cheryl A.
name: Breeze, Charles E.
name: Lin, Bridget M.
name: Franceschini, Nora
Publisher: name: Springer Nature
Year: 2024

description: Apolipoprotein L1 (APOL1) coding variants, termed G1 and G2, are established genetic risk factors for a growing spectrum of diseases, including kidney disease, in individuals of African ancestry. Evidence suggests that the risk variants, which show a recessive mode of inheritance, lead to toxic gain-of-function changes of the APOL1 protein. Disease occurrence and presentation vary, likely due to modifiers or second hits. To understand the role of the epigenetic landscape in relation to APOL1 risk variants, we performed methylation quantitative trait locus (meQTL) analysis to identify differentially methylated CpGs influenced by APOL1 risk variants in 611 African American individuals. We identified five CpGs that were significantly associated with APOL1 risk alleles in discovery and replication studies, and one CpG-APOL1 association was independent of other genomic variants. Our study highlights proximal DNA methylation alterations  that may help explain the variable disease risk and clinical manifestation of APOL1 variants.
Successive epidemic waves of cholera in South Sudan between 2014 and 2017: a descriptive epidemiological study
Creators: name: Luquero, F.J
name: Jones, F.K
name: Pezzoli, L
name: Wohl, S
name: Azman, A.S
name: Kol, M.T
name: Omar, L.H
name: Lessler, J
name: Wamala, J.F
name: Mawien, P.N
name: Quilici, M.-L
name: Rumunu, J
name: Deng, L
Publisher: name: Elsevier B.V.
Year: 2020

description: Background: Between 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting. Methods: In this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports. Findings: The 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016–17 epidemic (20 438 cases) spread among settlements along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1–2·3) higher attack rates than those where vaccination occurred before the peak. Interpretation: Pandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging. Funding: The Bill & Melinda Gates Foundation.
Gabapentin effects on PKC-ERK1/2 signaling system in the spinal cord of rats with formalin-induced visceral inflammatory pain
Creators: name: Zhang, Yan-Bo
name: Guo, Zheng-Dong
name: Li, Mei-Yi
name: Zhang, Ji-Guo
name: Can-Wen Zhang
name: Yang, Ming-Feng
name: Niu, Jing-Zhong
name: Xun-Ming Ji
name: Lv, Guo-Wei
Publisher: name: figshare
Year: 2015
Subjects: Medicine

description: Statistical analyses were performed with sigmaplot (Systat software inc, San Jose, CA)
Plectiscus agilis
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Plectiscus
Plectiscus agilis

description: Plectiscus agilis (HOLMGREN, 1858)
M a t e r i a l e x a m i n e d: Trap2: 1♀ 7-21.ix.;trap7: 1♀ 27.vii.-20.viii, 1♁ 21.ix.-5.x., 1♀ 5-19.x.
D i s t r i b u t i o n: West Palaearctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 119, DOI: 10.5281/zenodo.10788481
GRAF1 Acts as a Downstream Mediator of Parkin to Regulate Mitophagy in Cardiomyocytes
Creators: name: Bowles, Dawn E.
name: Combs, Matthew E.
name: Zhu, Qiang
name: Pla, Michelle Mendiola
name: Gross, Ryan T.
name: Mack, Christopher P.
name: Taylor, Joan M.
Publisher: name: MDPI
Year: 2024

description: Cardiomyocytes rely on proper mitochondrial homeostasis to maintain contractility and achieve optimal cardiac performance. Mitochondrial homeostasis is controlled by mitochondrial fission, fusion, and mitochondrial autophagy (mitophagy). Mitophagy plays a particularly important role in promoting the degradation of dysfunctional mitochondria in terminally differentiated cells. However, the precise mechanisms by which this is achieved in cardiomyocytes remain opaque. Our study identifies GRAF1 as an important mediator in PINK1-Parkin pathway-dependent mitophagy. Depletion of GRAF1 (Arhgap26) in cardiomyocytes results in actin remodeling defects, suboptimal mitochondria clustering, and clearance. Mechanistically, GRAF1 promotes Parkin-LC3 complex formation and directs autophagosomes to damaged mitochondria. Herein, we found that these functions are regulated, at least in part, by the direct binding of GRAF1 to phosphoinositides (PI(3)P, PI(4)P, and PI(5)P) on autophagosomes. In addition, PINK1-dependent phosphorylation of Parkin promotes Parkin-GRAF1-LC3 complex formation, and PINK1-dependent phosphorylation of GRAF1 (on S668 and S671) facilitates the clustering and clearance of mitochondria. Herein, we developed new phosphor-specific antibodies to these sites and showed that these post-translational modifications are differentially modified in human hypertrophic cardiomyopathy and dilated cardiomyopathy. Furthermore, our metabolic studies using serum collected from isoproterenol-treated WT and GRAF1CKO mice revealed defects in mitophagy-dependent cardiomyocyte fuel flexibility that have widespread impacts on systemic metabolism. In summary, our study reveals that GRAF1 co-regulates actin and membrane dynamics to promote cardiomyocyte mitophagy and that dysregulation of GRAF1 post-translational modifications may underlie cardiac disease pathogenesis.
Stability and convergence analysis of transform-domain LMS adaptive filters with second-order autoregressive process
Creators: name: Zhao, Shengkui
name: Man, Zhihong
name: Khoo, Suiyang
name: Wu, H. R.
Publisher: name: Swinburne
Year: 2024

description: In this paper, the stability and convergence properties of the class of transform-domain least mean square (LMS) adaptive filters with second-order autoregressive (AR) process are investigated. It is well known that this class of adaptive filters improve convergence property of the standard LMS adaptive filters by applying the fixed data-independent orthogonal transforms and power normalization. However, the convergence performance of this class of adaptive filters can be quite different for various input processes, and it has not been fully explored. In this paper, we first discuss the mean-square stability and steady-state performance of this class of adaptive filters. We then analyze the effects of the transforms and power normalization performed in the various adaptive filters for both first-order and second-order AR processes. We derive the input asymptotic eigenvalue distributions and make comparisons on their convergence performance. Finally, computer simulations on AR process as well as moving-average (MA) process and autoregressive-moving-average (ARMA) process are demonstrated for the support of the analytical results.
The development of visual cognition: The emergence of spatial congruency bias
Creators: name: Golomb, Julie D.
name: Sloutsky, Vladimir M.
name: Starks, Maurryce D.
name: Gao, Mengcun
Publisher: name: Wiley
Year: 2024

description: In adults, spatial location plays a special role in visual object processing. People are more likely to judge two sequentially presented objects as being identical when they appear in the same location compared to in different locations (a phenomenon referred to as Spatial Congruency Bias [SCB]). However, no comparable Identity Congruency Bias (ICB) is found, suggesting an asymmetric location-identity relationship in object binding. What gives rise to this asymmetric congruency bias? This paper considered two possible hypotheses. Hypothesis 1 suggests that the asymmetric congruency bias results from an inherently special role of location in the visual system. In contrast, Hypothesis 2 suggests that the asymmetric congruency bias is a product of development, reflecting people's experience with the world. To distinguish the two hypotheses, we tested both adults' and 5-year-old children's SCB and ICB by Identity Judgment Experiments and Spatial Judgment Experiments, respectively. The study found that adults only exhibited a SCB, but no ICB. However, young children exhibited both SCB and ICB, suggesting a symmetric congruency bias and reciprocal influences between location and identity in early development. The results indicate that the asymmetric location-identity relationship develops as object identity's influence on location gets pruned away, while location's influence on identity is preserved, possibly due to people's gained experiences with regularities of the world. RESEARCH HIGHLIGHTS: Adults exhibit Spatial Congruency Bias-an asymmetric location-identity relationship with location biasing their judgment of object identities, but not vice versa. Asymmetric congruency bias may result from an inherently special role of location in visual system (Hypothesis 1) or accumulated experiences with the world (Hypothesis 2). To distinguish the two hypotheses, the study investigated the Spatial Congruency Bias and Identity Congruency Bias in both adults and 5-year-old children. Unlike adults who exhibited only Spatial Congruency Bias, 5-year-old children exhibited both Spatial Congruency Bias and Identity Congruency Bias.
Vibrio cholerae O1 transmission in Bangladesh: insights from a nationally representative serosurvey
Creators: name: Hegde, S.T
name: Salje, H
name: Luquero, F.J
name: Lessler, J
name: Khaton, F
name: Qadri, F
name: Leung, D.T
name: Bhuiyan, T.R
name: Ferdous, J
name: Gurley, E.S
name: Paul, K.K
name: Lauer, S.A
name: Azman, A.S
name: Harris, J.B
Publisher: name: Elsevier Ltd
Year: 2020

description: Background: Pandemic Vibrio cholerae from cholera-endemic countries around the Bay of Bengal regularly seed epidemics globally. Without reducing cholera in these countries, including Bangladesh, global cholera control might never be achieved. Little is known about the geographical distribution and magnitude of V cholerae O1 transmission nationally. We aimed to describe infection risk across Bangladesh, making use of advances in cholera seroepidemiology, therefore overcoming many of the limitations of current clinic-based surveillance. Methods: We tested serum samples from a nationally representative serosurvey in Bangladesh with eight V cholerae-specific assays. Using these data with a machine-learning model previously validated within a cohort of confirmed cholera cases and their household contacts, we estimated the proportion of the population with evidence of infection by V cholerae O1 in the previous year (annual seroincidence) and used Bayesian geostatistical models to create high-resolution national maps of infection risk. Findings: Between Oct 16, 2015, and Jan 24, 2016, we obtained and tested serum samples from 2930 participants (707 households) in 70 communities across Bangladesh. We estimated national annual seroincidence of V cholerae O1 infection of 17·3% (95% CI 10·5–24·1). Our high-resolution maps showed large heterogeneity of infection risk, with community-level annual infection risk within the sampled population ranging from 4·3% to 62·9%. Across Bangladesh, we estimated that 28·1 (95% CI 17·1–39·2) million infections occurred in the year before the survey. Despite having an annual seroincidence of V cholerae O1 infection lower than much of Bangladesh, Dhaka (the capital of Bangladesh and largest city in the country) had 2·0 (95% CI 0·6–3·9) million infections during the same year, primarily because of its large population. Interpretation: Serosurveillance provides an avenue for identifying areas with high V cholerae O1 transmission and investigating key risk factors for infection across geographical scales. Serosurveillance could serve as an important method for countries to plan and monitor progress towards 2030 cholera elimination goals. Funding: The Bill & Melinda Gates Foundation, National Institutes of Health, and US Centers for Disease Control and Prevention.
Data integration via analysis of subspaces (DIVAS)
Creators: name: Ackerman, Andrew
name: Jiang, Meilei
name: Hannig, Jan
name: Tran-Dinh, Quoc
name: Marron, J. S.
name: Prothero, Jack
Publisher: name: Springer Nature
Year: 2024

description: Modern data collection in many data paradigms, including bioinformatics, often incorporates multiple traits derived from different data types (i.e., platforms). We call this data multi-block, multi-view, or multi-omics data. The emergent field of data integration develops and applies new methods for studying multi-block data and identifying how different data types relate and differ. One major frontier in contemporary data integration research is methodology that can identify partially shared structure between sub-collections of data types. This work presents a new approach: Data Integration Via Analysis of Subspaces (DIVAS). DIVAS combines new insights in angular subspace perturbation theory with recent developments in matrix signal processing and convex–concave optimization into one algorithm for exploring partially shared structure. Based on principal angles between subspaces, DIVAS provides built-in inference on the results of the analysis, and is effective even in high-dimension-low-sample-size (HDLSS) situations.
Achieving coordinated national immunity and cholera elimination in Haiti through vaccination: a modelling study
Creators: name: Matrajt, L
name: Ivers, L.C
name: Perez-Saez, J
name: Longini, Jr., I.M
name: Lee, E.C
name: Vissieres, K
name: Lessler, J
name: Finger, F
name: Rinaldo, A
name: Chao, D.L
name: Azman, A.S
name: Sugimoto, J.D
name: Pasetto, D
name: Halloran, M.E
name: Lemaitre, J.C
name: Ternier, R
Publisher: name: Elsevier Ltd
Year: 2020

description: Background: Cholera was introduced into Haiti in 2010. Since then, more than 820 000 cases and nearly 10 000 deaths have been reported. Oral cholera vaccine (OCV) is safe and effective, but has not been seen as a primary tool for cholera elimination due to a limited period of protection and constrained supplies. Regionally, epidemic cholera is contained to the island of Hispaniola, and the lowest numbers of cases since the epidemic began were reported in 2019. Hence, Haiti may represent a unique opportunity to eliminate cholera with OCV. Methods: In this modelling study, we assessed the probability of elimination, time to elimination, and percentage of cases averted with OCV campaign scenarios in Haiti through simulations from four modelling teams. For a 10-year period from January 19, 2019, to Jan 13, 2029, we compared a no vaccination scenario with five OCV campaign scenarios that differed in geographical scope, coverage, and rollout duration. Teams used weekly department-level reports of suspected cholera cases from the Haiti Ministry of Public Health and Population to calibrate the models and used common vaccine-related assumptions, but other model features were determined independently. Findings: Among campaigns with the same vaccination coverage (70% fully vaccinated), the median probability of elimination after 5 years was 0–18% for no vaccination, 0–33% for 2-year campaigns focused in the two departments with the highest historical incidence, 0–72% for three-department campaigns, and 35–100% for nationwide campaigns. Two-department campaigns averted a median of 12–58% of infections, three-department campaigns averted 29–80% of infections, and national campaigns averted 58–95% of infections. Extending the national campaign to a 5-year rollout (compared to a 2-year rollout), reduced the probability of elimination to 0–95% and the proportion of cases averted to 37–86%. Interpretation: Models suggest that the probability of achieving zero transmission of Vibrio cholerae in Haiti with current methods of control is low, and that bolder action is needed to promote elimination of cholera from the region. Large-scale cholera vaccination campaigns in Haiti would offer the opportunity to synchronise nationwide immunity, providing near-term population protection while improvements to water and sanitation promote long-term cholera elimination. Funding: Bill & Melinda Gates Foundation, Global Good Fund, Institute for Disease Modeling, Swiss National Science Foundation, and US National Institutes of Health.
Plectiscus impurator GRAVENHORST 1829
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Plectiscus
Plectiscus impurator

description: Plectiscus impurator GRAVENHORST, 1829
M a t e r i a l e x a m i n e d: Trap 4: 2♀♀ 29.vi.-13.vii., 1♀ 27.vii.-10.viii.; trap 7: 1♀ 27.vii.- 20.viii., 1♀ 21.ix.-5.x.; trap 12: 1♀ 29.vi.-13.vii.; trap 15: 2♀♀ 30.vi.-24.vii.
D i s t r i b u t i o n: West Palaearctic, known from Georgia (RIEDEL & JAPOSHVILI 2021).
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 119, DOI: 10.5281/zenodo.10788481
Life course exposures continually shape antibody profiles and risk of seroconversion to influenza
Creators: name: Guan, Y
name: Jiang, C.Q
name: Yang, B
name: Lessler, J
name: Read, J.M
name: Hay, J.A
name: Zhu, H
name: Kwok, K.O
name: Shen, R
name: Riley, S
name: Cummings, D.A.T
Publisher: name: Public Library of Science
Year: 2020

description: Complex exposure histories and immune mediated interactions between influenza strains contribute to the life course of human immunity to influenza. Antibody profiles can be generated by characterizing immune responses to multiple antigenically variant strains, but how these profiles vary across individuals and determine future responses is unclear. We used hemagglutination inhibition titers from 21 H3N2 strains to construct 777 paired antibody profiles from people aged 2 to 86, and developed novel metrics to capture features of these profiles. Total antibody titer per potential influenza exposure increases in early life, then decreases in middle age. Increased titers to one or more strains were seen in 97.8% of participants during a roughly four-year interval, suggesting widespread influenza exposure. While titer changes were seen to all strains, recently circulating strains exhibited the greatest titer rise. Higher pre-existing, homologous titers at baseline reduced the risk of seroconversion to recent strains. After adjusting for homologous titer, we also found an increased frequency of seroconversion against recent strains among those with higher immunity to older previously exposed strains. Including immunity to previously exposures also improved the deviance explained by the models. Our results suggest that a comprehensive quantitative description of immunity encompassing past exposures could lead to improved correlates of risk of influenza infection.
title: Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT
Creators: name: Neigenfind, Jost
name: Gyetvai, Gabor
name: Basekow, Rico
name: Diehl, Svenja
name: Achenbach, Ute
name: Gebhardt, Christiane
name: Selbig, Joachim
name: Kersten, Birgit
Publisher: name: Universität Potsdam
Year: 2020

description: Background: Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous. Results: Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes. Conclusion: Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at http://www.gabipd.org/projects/satlotyper/. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.
description: Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, 883
Biologically inspired designs for restoring power transmission after an electromagnetic pulse attack
Creators: name: Himmelstein, Daniel
Publisher: name: figshare
Year: 2015
Subjects: Structural Biology

description: Several Congressional Commissions have highlighted the dangers of an electromagnetic pulse (EMP) attack on the American homeland. Recent evidence suggests that several adversaries are interested in the potential damage an electromagnetic attack could wreak on critical national infrastructure and are pursuing the necessary capabilities to stage an EMP strike on the United States. A properly executed EMP strike could destroy electronic systems bringing the power grid to a halt. The ability to restore electricity is of crucial important to critical national infrastructure and minimizing the economic and fatality fallout. This study proposes a novel method using slime mold for designing power grid reconstruction efforts in the aftermath of an EMP attack. Using slime mold as the architect for network design holds several advantages to the traditional human planning approach which may be of vital importance in light of the effects from an electromagnetic attack.
Proclitus fulvicornis FORSTER 1871
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Proclitus
Proclitus fulvicornis

description: Proclitus fulvicornis FÖRSTER, 1871
M a t e r i a l e x a m i n e d: Trap 2: 1♀ 7-21.ix.; trap 7: 1♀ 23.iv.-5.v., 1♀ 27.vii.-10.viii., 1♀ 7-12.ix.; trap 12: 1♀ 20.v.-1.vi., 2♀♀ 21.ix.-5.x.
D i s t r i b u t i o n: Holarctic and Neotropical, known from Georgia (RIEDEL & JAPOSHVILI 2021).
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 119, DOI: 10.5281/zenodo.10788481
Behavioral Health Services Outcomes That Matter Most to Caregivers of Children, Youth, and Young Adults with Mental Health Needs
Creators: name: Sweeney, Millie
name: Kitchens, Katherine
name: Graaf, Genevieve
name: Thomas, Kathleen C.
Publisher: name: MDPI
Year: 2024

description: This project documents the service outcomes that caregivers value most. A diverse group of caregivers, representing six regions of the United States, participated in two rounds of virtual one-hour focus groups. In round 1, participants identified what they hoped to gain from using behavioral health services for themselves, their families, and their child and discussed what made services a positive experience for them. They then reported their top-three most-hoped-for outcomes. In round 2, groups validated and refined summary findings from round 1. Caregivers prioritized service quality outcomes, primarily. They expressed a desire for an accessible, respectful, and supportive treatment environment, underpinned by well-trained and culturally responsive professionals. Caregivers also desire seamless cross-sector provider collaboration and care transitions, which integrate the insights and preferences of families and children themselves to craft a customized care plan. Priority outcomes not related to service quality included hoping to gain increased knowledge, resources, and tools and techniques to support the mental health needs of their children, to see their children improve their daily functioning and for their child develop more effective interpersonal communication skills. Caregivers also reported hoping to experience less stigma related to the mental health needs of their children and to achieve personal fulfillment for themselves and their children. Research, policies, and mental health services should prioritize and be designed to address the outcomes that matter to youth and families.
title: The effects of life stress and neural learning signals on fluid intelligence
Creators: name: Friedel, Eva
name: Schlagenhauf, Florian
name: Beck, Anne
name: Dolan, Raymond J.
name: Huys, Quentin J.M.
name: Rapp, Michael A.
name: Heinz, Andreas
Publisher: name: Universität Potsdam
Year: 2020

description: Fluid intelligence (fluid IQ), defined as the capacity for rapid problem solving and behavioral adaptation, is known to be modulated by learning and experience. Both stressful life events (SLES) and neural correlates of learning [specifically, a key mediator of adaptive learning in the brain, namely the ventral striatal representation of prediction errors (PE)] have been shown to be associated with individual differences in fluid IQ. Here, we examine the interaction between adaptive learning signals (using a well-characterized probabilistic reversal learning task in combination with fMRI) and SLES on fluid IQ measures. We find that the correlation between ventral striatal BOLD PE and fluid IQ, which we have previously reported, is quantitatively modulated by the amount of reported SLES. Thus, after experiencing adversity, basic neuronal learning signatures appear to align more closely with a general measure of flexible learning (fluid IQ), a finding complementing studies on the effects of acute stress on learning. The results suggest that an understanding of the neurobiological correlates of trait variables like fluid IQ needs to take socioemotional influences such as chronic stress into account.
description: Postprints der Universität Potsdam : Humanwissenschaftliche Reihe, 621
A framework for reducing water demand in multi-storey and detached dwellings in the united arab emirates
Creators: name: Shanableh, Abdallah
name: Imteaz, Monzur
name: Merabtene, T.
name: Ahsan, Amimul
Publisher: name: Swinburne
Year: 2024

description: The United Arab Emirates (UAE) is highly dependent on desalination for water supply in urban areas, which comes at significant financial and environmental costs. Therefore, reducing the demand for water is a strategic objective of water authorities in the UAE. The concentration of the UAE population in multi-story buildings in urban areas makes residential water conservation, including greywater recycling, a highly attractive option for reducing water demand and wastewater generation. However, the unique composition of the UAE population poses challenge to adopting water conservation policies that are suitable for the UAE national and expatriate sectors of the population. Furthermore, the current water recycling policies and legal framework do not encourage greywater recycling for internal use in residential buildings. In this study, a framework for assessing the potential and feasibility of water conservation, including greywater recycling, in multi-storey and detached dwellings in the UAE was developed and discussed. The results confirmed that significant potential existed for reducing the residential water demand in the UAE through adopting simple water conservation measures and greywater recycling in multi-story buildings. The discussion was extended to proposing greywater recycling systems suitable for multi-story buildings in the UAE. Such systems involve partial greywater recycling from the higher floors of multi-storey buildings to serve the toilet flushing needs of the whole building and locating greywater treatment systems on the roofs of buildings.
Tax Planning Knowledge Diffusion via the Labor Market
Creators: name: Gallemore, John
name: Barrios, John M.
Publisher: name: Institute for Operations Research and the Management Sciences (INFORMS)
Year: 2024

description: We examine the extent to which the labor market facilitates the diffusion of tax-planning knowledge across firms. Using a novel data set of tax department employee movements between S&P 1500 firms, we find that firms experience an increase in their tax planning after hiring a tax employee from a tax-aggressive firm. This finding is robust to various research designs and specifications. Consistent with tax-planning knowledge driving the result, we find that the tax-planning benefits are more substantial when the employee is involved in a director-level role and has more experience. Further tests suggest that tax-planning knowledge is highly specific in nature: the increase in tax avoidance is larger when the hiring and former firms are similar (i.e., operating in the same sector or having similar foreign operations), and firms are more likely to hire tax department employees from firms with similar characteristics. Finally, we do not find that the prior firm’s tax planning changes after the employee leaves the firm, suggesting that the tax-planning knowledge simply spreads to the hiring firm and does not leave the prior firm. Our study documents the first order role of the labor market in the diffusion of tax-planning knowledge across firms, and our findings suggest that tax department human capital is a central determinant of tax-planning outcomes. This paper was accepted by Suraj Srinivasan, accounting. Supplemental Material: The online appendix and data are available at https://doi.org/10.1287/mnsc.2023.4741 .
PRAME Expression in Melanocytic Proliferations in Special Sites.
Creators: name: Raghavan, Shyam S
name: Maniaci, Joseph L
Publisher: name: Frontline Medical Communications
Year: 2024

description: The subset of nevi occurring at special sites (eg, acral skin, anogeni-tal region, breast, ear, flexural surfaces) have normal histologic variations that preclude the use of routinely used diagnostic criteria for malignancy. Suggested criteria for differentiating malignant special-site lesions from benign lesions have been described, but there is an unmet need for a validated test aiding in the delineation of benign and malignant lesions at special sites. Preferentially expressed antigen of melanoma (PRAME) expression has been characterized as a relatively specific marker of melanoma, but not within the specific population of special-site lesions. This study aimed to determine if PRAME may serve as a specific marker of melanoma within the population of special-sites lesions.