bluuebunny/crossref_metadata_2025 huggingface dataset:
Local Health Departments' Characteristics and Their Performance Scores in PHAB Accreditation Standards
Authors: Dada Oluwatosin Omolara , Bekemeier Betty , Flaxman Abraham , de Castro Butch
Published: January 2022

Context:

Local health departments (LHDs) function to promote and protect population health by executing programs and activities through the 10 essential public health (PH) services in their operationalization of the core functions of PH systems—assessment, policy development, and assurance. PH accreditation supports LHDs by assessing their ability to promote community well-being through a set of standards and measures based on the 10 essential PH services. Prior studies show variation in LHD characteristics relative to their likelihood of participating in accreditation, but no studies have examined the variation in LHD accreditation scores to understand how LHD characteristics relate to performance improvement.

Objective:

This work examines variation in LHD accreditation scores relative to their organizational and jurisdiction characteristics.

Design:

Cross-sectional data were obtained from 250 LHDs from 38 states that underwent Public Health Accreditation Board (PHAB) accreditation review.

Analysis:

We used exploratory cluster analysis to identify and group LHDs with similar performance scores in PHAB accreditation standards. Descriptive analyses were undertaken to characterize each LHD cluster group's organizational structure, jurisdiction characteristics, and core PH function activity levels. We then employed multivariate regression analysis to confirm the cluster analysis results.

Results:

The analysis showed 3 clusters of PHAB accreditation performance scores (cluster 1 = 0.95; cluster 2 = 0.87; and cluster 3 = 0.71). Subtle differences in organizational and jurisdiction characteristics across clusters, notably in population size of the jurisdictions served, were observed. LHDs in cluster 3 tended to have jurisdictions with less than 250000 population size and serve more than 1 county.

Conclusions:

Performance scores in PHAB accreditation can be a useful standardized metric for assessing LHD ability to promote community well-being. LHDs serving less than 20000 population size, which exhibit relatively lower performance than other LHDs, may require more targeted supports to close the gap in their performance score.
COVID-19 Case Investigation and Contact Tracing Programs and Practice: Snapshots From the Field
Authors: Harper-Hardy Paris , Ruebush Elizabeth , Allen Meredith , Carlin Maggie , Plescia Marcus , Blumenstock James S.
Published: January 2022

Between Fall 2020 and Spring 2021, the Association of State and Territorial Health Officials conducted 2 rapid queries to collect information from the field regarding the status of COVID-19 case investigation and contact tracing (CI/CT) programs and practice. These short surveys were distributed to senior deputies in state and territorial health agencies, yielding a response rate of 45.8% (November 2020) and 40.7% (April 2021). Findings indicated that CI/CT staff roles and assigned functions varied across jurisdictions, as did staffing levels/capacity, approaches for linking individuals to social supports, and program changes that were planned or underway. Agency-reported staffing levels/capacity and programmatic challenges changed over time, highlighting the dynamic nature of CI/CT program practice and implementation. While findings from the surveys cannot be generalized to the national level, they provide critical insights from the field on CI/CT program implementation, challenges, and changes in response to the evolving COVID-19 epidemic in the United States.
Brief Report: Blood and Genital Fluid Viral Load Trajectories Among Treated and Untreated Persons With Acute HIV Infection in Malawi
Authors: Chen Jane S. , Pettifor Audrey E. , Nelson Julie A.E. , Phiri Sam , Pasquale Dana K. , Kumwenda Wiza , Kamanga Gift , Cottrell Mackenzie L. , Sykes Craig , Kashuba Angela D.M. , Tegha Gerald , Krysiak Robert , Thengolose Isaac , Cohen Myron S. , Hoffman Irving F. , Miller William C. , Rutstein Sarah E.
Published: January 2022

Background:

Persons with acute HIV infection (AHI) are highly infectious and responsible for a disproportionate share of incident infections. Immediate antiretroviral therapy (ART) rapidly reduces blood viral loads (VLs), but genital VLs after ART initiation during AHI are less well described.

Setting:

Lilongwe, Malawi, 2012–2014.

Methods:

HIV-seronegative and HIV-serodiscordant persons aged ≥18 years were screened for AHI (RNA positive) and randomized to standard of care, behavioral intervention, or behavioral intervention plus short-term ART (raltegravir/emtricitabine/tenofovir) (1:2:2). Persons who were ART eligible under Malawi guidelines could receive first-line therapy. Blood and genital VLs were assessed at weeks 1, 4, 8, and 12. Fisher's Exact test was used to compare viral suppression by ART status.

Results:

Overall, 46 persons with AHI were enrolled; of whom, 17 started ART within 12 weeks. Median blood VL at AHI diagnosis was 836,115 copies/mL. At week 12, 7% (1/14) of those who initiated ART had a blood VL of ≥400 copies/mL, compared with 100% (23/23; P < 0.0001) of those who did not initiate ART (median VL: 61,605 copies/mL). Median genital VL at week 1 was 772 copies/mL, with 13 of 22 (59%) having VL of ≥400 copies/mL. At week 12, 0 of 10 (0%) of those who initiated ART had genital VL of ≥400 copies/mL, compared with 7 of 15 (47%) of those who did not initiate ART (P = 0.02).

Conclusion:

Although highly correlated, VLs in blood and genital fluids occupy discrete biological compartments with distinct virologic dynamics. Our results corroborate the dramatic reduction in both compartments after ART initiation. Increasing AHI screening and rapidly initiating treatment is key to interrupting transmission.
How common is ventilator-associated pneumonia after coronavirus disease 2019?
Authors: Wicky Paul-Henri , d’Humières Camille , Timsit Jean-François
Published: January 2022

Purpose of review

The first studies on COVID-19 patients with acute respiratory distress syndrome (ARDS) described a high rate of secondary bacterial ventilator-associated pneumonia (VAP). The specificity of VAP diagnoses in these patients are reviewed, including their actual rate.

Recent findings

Published studies described high rates of bacterial VAP among COVID-19 patients with ARDS, and these VAP episodes are usually severe and of specifically poor prognosis with high mortality. Indeed, Severe acute respiratory syndrome - coronavirus disease 19 (SARS-CoV2) infection elicits alterations that may explain a high risk of VAP. In addition, breaches in the aseptic management of patients might have occurred when the burden of care was heavy. In addition, VAP in these patients is more frequently suspected, and more often investigated with diagnostic tools based on molecular techniques.

VAP is frequented and of particularly poor prognosis in COVID-19 patients with ARDS. It can be explained by SARS-CoV-2 pathophysiology, and also breaches in the aseptic procedures. In addition, tools based on molecular techniques allow an early diagnosis and unmask VAP usually underdiagnosed by traditional culture-based methods. The impact of molecular technique-based diagnostics in improving antibacterial therapy and COVID-19 prognosis remain to be evaluated.
Benchmarking Feature Selection Methods in Radiomics
Authors: Demircioğlu Aydin
Published: January 2022

Objectives

A critical problem in radiomic studies is the high dimensionality of the datasets, which stems from small sample sizes and many generic features extracted from the volume of interest. Therefore, feature selection methods are used, which aim to remove redundant as well as irrelevant features. Because there are many feature selection algorithms, it is key to understand their performance in the context of radiomics.

Materials and Methods

A total of 29 feature selection algorithms and 10 classifiers were evaluated on 10 publicly available radiomic datasets. Feature selection methods were compared for training times, for the stability of the selected features, and for ranking, which measures the pairwise similarity of the methods. In addition, the predictive performance of the algorithms was measured by utilizing the area under the receiver operating characteristic curve of the best-performing classifier.

Results

Feature selections differed largely in training times as well as stability and similarity. No single method was able to outperform another one consistently in predictive performance.

Conclusion

Our results indicated that simpler methods are more stable than complex ones and do not perform worse in terms of area under the receiver operating characteristic curve. Analysis of variance, least absolute shrinkage and selection operator, and minimum redundancy, maximum relevance ensemble appear to be good choices for radiomic studies in terms of predictive performance, as they outperformed most other feature selection methods.
Pituitary Metastasis of Renal Cell Carcinoma Characterized by 18F–Prostate-Specific Membrane Antigen–1007 PET/CT
Authors: Tariq Arsalan , Raman Vignesh , Alexander Hamish , Roberts Matthew J. , Thomas Paul
Published: January 2022

Renal cell carcinoma (RCC) is one of the most common oncological diagnoses worldwide. Accurate staging and restaging imaging continue to be a priority in clinical practice as 20% to 30% of patients present with advanced metastatic disease at diagnosis, and 20% to 30% develop recurrence after surgical resection. We present a case of a 71-year-old man presenting with an isolated pituitary RCC metastasis accurately defined on 18F–prostate-specific membrane antigen–1007 masquerading as a macroadenoma on conventional imaging (CT and MRI). This demonstrates the potential utility of 18F–prostate-specific membrane antigen–1007 in characterizing RCC brain metastasis.
To Explore Ideas From the Altered Metabolites: The Metabolomics of Pathological Scar
Authors: Yang Jinxiu , Chen Minliang , He Leren
Published: January 2022

Background:

Pathological scars are dermal fibroproliferative disorders due to rapid inflammatory response after dermal injury. The altered metabolites could reflect pathophysiological changes directly. However, it has not cleared how the metabolites change scars.

Objective:

To explore new ideas of pathological scars from the altered metabolites by using ultra-performance liquid chromatography coupled to tandem mass spectrometry and identifying the key genes.

Methods:

Keloid (KS, n = 10), hypertrophic scar (HS, n = 10), and normal skin (NS, n = 10) were collected. Ultra-performance liquid chromatography coupled to tandem mass spectrometry was used to identify and characterize metabolites. Differential metabolites were analyzed by orthogonal partial least square discriminant analysis and Student t test. The key pathways were analyzed via Kyoto Encyclopedia of Genes and Genomes, and the related enzymes were verified by real-time Polymerase Chain Reaction, both in tissues and their dermal fibroblasts.

Results:

Two hundred fourteen metabolites were detected in total, mostly were fatty acids and amino acids. In the KS and NS groups, 65 different metabolites were screened (P < 0.05), and the polyunsaturated fatty acids (PUFAs) metabolism and butyric acid in keloid should be concerned. The messenger Ribonucleic Acid expression of fatty acid desaturase 1 and fatty acid desaturase 2, which are the key enzyme of PUFA metabolism, were lower in KS and keloid-derived fibroblasts, P < 0.05. In HS group, 17 metabolites were significantly different and branched chain amino acids degradation was the key pathway. Moreover, branched chain keto acid dehydrogenase E1 subunit alpha was lower expressed in HS and their fibroblasts compared with NS, P < 0.05.

Conclusions:

Polyunsaturated fatty acids and butyric acid may be associated with the generation of keloids. The pathogenesis of hypertrophic scars may be involved in branched chain amino acids degradation, which is worth paying attention to.
A Skill Trainer for Balloon/Stent Exchange in Percutaneous Coronary Intervention—Concept and Evaluation
Authors: Petri Nils , Weber Christian , Maniuc Octavian , Oder Daniel , Lengenfelder Björn , Voelker Wolfram
Published: January 2022

Background

To prevent complications, uncontrolled movement of the guidewire during a coronary intervention should be avoided. Unintentional withdrawal of the wire can result in the inability to recross a lesion with the risk of myocardial infarction. On the other hand, unintended forward pushing can lead to a coronary perforation. Thus, interventionalists in training should practice keeping the coronary guidewire in a stable position to prevent complications. For this purpose, a skill trainer has been developed, which provides the possibility of unlimited practice outside of the cath lab.

The purpose of this study was to assess the effectiveness and the validity of this skills trainer.

Methods

Ten novices and 10 participants with experience in diagnostic catheterization underwent training on the skills trainer consisting of 25 procedures. To assess the efficacy of the training module, the mean score of the first 3 procedures was compared with the final 3 procedures in the novice and the advanced group. To determine the construct validity of the simulator, a group of experts (E; performed >1000 percutaneous coronary interventions) also underwent evaluation on the skills trainer. For each procedure, the change in position of the guidewire as well as the time was determined and combined into a skills score with a maximum of 15 points.

Results

The novice and the advanced group improved significantly throughout the training on the simulator (N: 7.1 ± 2.6 to 12.2 ± 2.0, P = 0.007; A: 8.3 ± 2.0 to 13.2 ± 1.0, P = 0.005, Wilcoxon).

The experts scored significantly higher than novices or the advanced participants during their first 3 procedures (E: 12.9 ± 1.0; N: 7.1 ± 2.6, P = 0.001; A: 8.3 ± 2.0, P = 0.001; Mann-Whitney U).

Conclusions

This low-cost task trainer is a valid and effective tool to train adequate balloon/stent exchange while keeping the guidewire in a stable position. Whether the skills acquired on the task trainer can be transferred to procedures performed on patients needs further investigation.
Operative trauma volume is not related to risk-adjusted mortality rates among Pennsylvania trauma centers
Authors: Hornor Melissa A. , Xiong Aria , Imran Jonathan B. , Jacovides Christina L. , Hatchimonji Justin , Scantling Dane , Kaufman Elinore , Cannon Jeremy W. , Holena Daniel N.
Published: January 2022

BACKGROUND

Higher center-level operative volume is associated with lower mortality after complex elective surgeries, but this relationship has not been robustly demonstrated for operative trauma. We hypothesized that trauma centers in Pennsylvania with higher operative trauma volumes would have lower risk-adjusted mortality rates than lower volume institutions.

METHODS

We queried the Pennsylvania Trauma Outcomes Study database (2017–2019) for injured patients 18 years or older at Level I and II trauma centers who underwent an International Classification of Diseases, Tenth Revision (ICD-10), procedure code–defined operative procedure within 6 hours of admission. The primary exposure was tertile of center-level operative volume. The primary outcome of interest was inpatient mortality. We entered factors associated with mortality in univariate analysis (age, injury severity, mechanism, physiology) into multivariable logistic regression models with tertiles of volume accounting for center-level clustering. We conducted secondary analyses varying the form of the association between the volume and mortality to including dichotomous and fractional polynomial models.

RESULTS

We identified 3,650 patients at 29 centers meeting the inclusion criteria. Overall mortality was 15.9% (center-level range, 6.7–34.2%). Operative procedure types were cardiopulmonary (7.3%), vascular (20.1%), abdominopelvic (24.3%), and multiple (48.3%). The mean annual operative volume over the 3 years of data was 10 to 21 operations for low-volume centers, 22 to 47 for medium-volume centers, and 47 to 158 for high-volume centers. After controlling for patient demographics, physiology, and injury characteristics, there was no significant difference in mortality between highest and lowest tertile centers (odds ratio, 0.92; confidence interval, 0.57–1.49). Secondary analyses similarly demonstrated no relationship between center operative volume and mortality in key procedure subgroups.

CONCLUSION

In a mature trauma system, we found no association between center-level operative volume and mortality for patients who required early operative intervention for trauma. Efforts to standardize the care of seriously injured patients in Pennsylvania may ensure that even lower-volume centers are prepared to generate satisfactory outcomes.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level III.
An ERP study on the influence of mental abacus calculation on subthreshold arithmetic priming in children
Authors: Wang Cong-Cong , Sun Yan-Chao , Zhang Yu , Xin Yan-Wei , Gao Wei-Xing , Jia Li-Ping , Liu Xiao-Qin
Published: January 2022

Objective

The objective of this study was to investigate the influence of mental abacus calculation training (MACT) on subliminal cognitive processes.

Methods

Twenty children with intensive MACT (MACT group) and 20 children without MACT (non-MACT group) were selected. The two groups of children were matched in age, sex, handedness and academic grade. The participants were tested with subthreshold arithmetic priming task while their neural activities were recorded with a 32-channel electroencephalogram system.

Results

We found that MACT changed the subliminal cognitive mechanism of computational processing, speeding up the computation. MACT affected the computational processing mode. Specifically, in the identification stage, both groups of children adopted the visual space processing mode, while in the computing stage, the MACT group adopted a visual space processing mode, but the non-MACT group adopted a semantic processing mode. Moreover, MACT improved children’s executive functions.

Conclusion

These results yielded insights into the effect of early abacus training on children’s cognitive processing, providing a theoretical basis for the development and promotion of abacus training.
Trade-offs between foraging reward and mortality risk drive sex-specific foraging strategies in sexually dimorphic northern elephant seals
Authors: Kienle Sarah S. , Friedlaender Ari S. , Crocker Daniel E. , Mehta Rita S. , Costa Daniel P.
Published: January 2022

Sex-specific phenotypic differences are widespread throughout the animal kingdom. Reproductive advantages provided by trait differences come at a cost. Here, we link sex-specific foraging strategies to trade-offs between foraging reward and mortality risk in sexually dimorphic northern elephant seals (
Mirounga angustirostris
). We analyse a decadal dataset on movement patterns, dive behaviour, foraging success and mortality rates. Females are deep-diving predators in open ocean habitats. Males are shallow-diving benthic predators in continental shelf habitats. Males gain six times more mass and acquire energy 4.1 times faster than females. High foraging success comes with a high mortality rate. Males are six times more likely to die than females. These foraging strategies and trade-offs are related to different energy demands and life-history strategies. Males use a foraging strategy with a high mortality risk to attain large body sizes necessary to compete for females, as only a fraction of the largest males ever mate. Females use a foraging strategy with a lower mortality risk, maximizing reproductive success by pupping annually over a long lifespan. Our results highlight how sex-specific traits can drive disparity in mortality rates and expand species' niche space. Further, trade-offs between foraging rewards and mortality risk can differentially affect each sex's ability to maximize fitness.
Dynamics of cumulative advantage and threats to equity in open science: a scoping review
Authors: Ross-Hellauer Tony , Reichmann Stefan , Cole Nicki Lisa , Fessl Angela , Klebel Thomas , Pontika Nancy
Published: January 2022

Open Science holds the promise to make scientific endeavours more inclusive, participatory, understandable, accessible and re-usable for large audiences. However, making processes open will notper sedrive wide reuse or participation unless also accompanied by the capacity (in terms of knowledge, skills, financial resources, technological readiness and motivation) to do so. These capacities vary considerably across regions, institutions and demographics. Those advantaged by such factors will remain potentially privileged, putting Open Science's agenda of inclusivity at risk of propagating conditions of ‘cumulative advantage’. With this paper, we systematically scope existing research addressing the question: ‘What evidence and discourse exists in the literature about the ways in which dynamics and structures of inequality could persist or be exacerbated in the transition to Open Science, across disciplines, regions and demographics?’ Aiming to synthesize findings, identify gaps in the literature and inform future research and policy, our results identify threats to equity associated with all aspects of Open Science, including Open Access, Open and FAIR Data, Open Methods, Open Evaluation, Citizen Science, as well as its interfaces with society, industry and policy. Key threats include: stratifications of publishing due to the exclusionary nature of the author-pays model of Open Access; potential widening of the digital divide due to the infrastructure-dependent, highly situated nature of open data practices; risks of diminishing qualitative methodologies as ‘reproducibility’ becomes synonymous with quality; new risks of bias and exclusion in means of transparent evaluation; and crucial asymmetries in the Open Science relationships with industry and the public, which privileges the former and fails to fully include the latter.
Low-temperature open-air synthesis of PVP-coated NaYF
4
:Yb,Er,Mn upconversion nanoparticles with strong red emission
Authors: MacKenzie Lewis E. , Alvarez-Ruiz Diana , Pal Robert
Published: January 2022

Cubic (α-phase) NaYF
4
:Yb,Er upconversion nanoparticles (UCNPs) are uniquely suited to biophotonics and biosensing applications due to their near-infrared excitation and visible red emission (
λ
ex
approx. 660 nm), enabling detection via thick overlying tissue with no bio-autofluorescence. However, UCNP synthesis typically requires high temperatures in combination with either high pressure reaction vessels or an inert atmosphere. Here, we report synthesis of α-phase NaYF
4
:Yb,Er,Mn UCNPs via the considerably more convenient PVP40-mediated route; a strategy that requires modest temperatures and relatively short reaction time (160°C, 2 h) in open air, with Mn
2+
co-doping serving to greatly enhance red emission. The optimal Mn
2+
co-doping level was found to be 35 mol %, which decreased the average maximum UCNP Feret diameter from 42 ± 11 to 36 ± 15 nm; reduced the crystal lattice parameter,
a
, from 5.52 to 5.45 Å; and greatly enhanced UCNP red/green emission ratio in EtOH by a factor of 5.6. The PVP40 coating enabled dispersal in water and organic solvents and can be exploited for further surface modification (e.g. silica shell formation). We anticipate that this straightforward UCNP synthesis method for producing strongly red-emitting UCNPs will be particularly beneficial for deep tissue biophotonics and biosensing applications.
Interactions between breeding system and ploidy affect niche breadth in
Solanum
Authors: Fumia Nathan , Rubinoff Daniel , Zenil-Ferguson Rosana , Khoury Colin K. , Pironon Samuel , Gore Michael A. , Kantar Michael B.
Published: January 2022

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for agricultural sustainability. The geography of crop wild relatives, including wild potatoes (
Solanum
section
Petota
), have received attention; however, such information has not been analysed in combination with phylogenetic histories, genomic composition and reproductive systems to identify potential species for use in breeding for abiotic stress tolerance. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that make up the climate niche that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate classes within a climate niche inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche breadth through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.
Extraordinarily precise nematode sex ratios: adaptive responses to vanishingly rare mating opportunities
Authors: Van Goor Justin , Herre Edward Allen , Gómez Adalberto , Nason John D.
Published: January 2022

Sex ratio theory predicts both mean sex ratio and variance under a range of population structures. Here, we compare two genera of phoretic nematodes (
Parasitodiplogaster
and
Ficophagus
spp.) associated with 12 fig pollinating wasp species in Panama. The host wasps exhibit classic local mate competition: only inseminated females disperse from natal figs, and their offspring form mating pools that consist of scores of the adult offspring contributed by one or a few foundress mothers. By contrast, in both nematode genera, only sexually undifferentiated juveniles disperse and their mating pools routinely consist of 10 or fewer adults. Across all mating pool sizes, the sex ratios observed in both nematode genera are consistently female-biased (approx. 0.34 males), but markedly less female-biased than is often observed in the host wasps (approx. 0.10 males). In further contrast with their hosts, variances in nematode sex ratios are also consistently precise (significantly less than binomial). The constraints associated with predictably small mating pools within highly subdivided populations appear to select for precise sex ratios that contribute both to the reproductive success of individual nematodes, and to the evolutionary persistence of nematode species. We suggest that some form of environmental sex determination underlies these precise sex ratios.
Southeast Alaskan kelp forests: inferences of process from large-scale patterns of variation in space and time
Authors: Gorra Torrey R. , Garcia Sabrina C. R. , Langhans Michael R. , Hoshijima Umihiko , Estes James A. , Raimondi Pete T. , Tinker M. Tim , Kenner Michael C. , Kroeker Kristy J.
Published: January 2022

Humans were considered external drivers in much foundational ecological research. A recognition that humans are embedded in the complex interaction networks we study can provide new insight into our ecological paradigms. Here, we use time-series data spanning three decades to explore the effects of human harvesting on otter–urchin–kelp trophic cascades in southeast Alaska. These effects were inferred from variation in sea urchin and kelp abundance following the post fur trade repatriation of otters and a subsequent localized reduction of otters by human harvest in one location. In an example of a classic trophic cascade, otter repatriation was followed by a 99% reduction in urchin biomass density and a greater than 99% increase in kelp density region wide. Recent spatially concentrated harvesting of otters was associated with a localized 70% decline in otter abundance in one location, with urchins increasing and kelps declining in accordance with the spatial pattern of otter occupancy within that region. While the otter–urchin–kelp trophic cascade has been associated with alternative community states at the regional scale, this research highlights how small-scale variability in otter occupancy, ostensibly due to spatial variability in harvesting or the risk landscape for otters, can result in within-region patchiness in these community states.
Socio-cultural similarity with host population rather than ecological similarity predicts success and failure of human migrations
Authors: Lynch R. , Loehr J. , Lummaa V. , Honkola T. , Pettay J. , Vesakoski O.
Published: January 2022

Demographers argue that human migration patterns are shaped by people moving to better environments. More recently, however, evolutionary theorists have argued that people move to similar environments to which they are culturally adapted. While previous studies analysing which factors affect migration patterns have focused almost exclusively on successful migrations, here we take advantage of a natural experiment during World War II in which an entire population was forcibly displaced but were then allowed to return home to compare successful with unsuccessful migrations. We test two competing hypotheses: (1) individuals who relocate to environments that are superior to their place of origin will be more likely to remain—The Better Environment Hypothesisor (2) individuals who relocate to environments that are similar to their place of origin will be more likely to remain—The Similar Environment Hypothesis. Using detailed records recording the social, cultural, linguistic and ecological conditions of the origin and destination locations, we find that cultural similarity (e.g. linguistic similarity and marrying within one’s own minority ethnic group)—rather than ecological differences—are the best predictors of successful migrations. These results suggest that social relationships, empowered by cultural similarity with the host population, play a critical role in successful migrations and provide limited support for the similar environment hypothesis. Overall, these results demonstrate the importance of comparing unsuccessful with successful migrations in efforts understand the engines of human dispersal and suggest that the primary obstacles to human migrations and successful range expansion are sociocultural rather than ecological.
The pre-eminent role of directional selection in generating extreme morphological change in glyptodonts (Cingulata; Xenarthra)
Authors: Machado Fabio A. , Marroig Gabriel , Hubbe Alex
Published: January 2022

The prevalence of stasis on macroevolution has been classically taken as evidence of the strong role of stabilizing selection in constraining morphological change. Rates of evolution calculated over longer timescales tend to fall below the expected under genetic drift, suggesting that directional selection signals are erased at longer timescales. Here, we investigated the rates of morphological evolution of the skull in a fossil lineage that underwent extreme morphological modification, the glyptodonts. Contrary to what was expected, we show here that directional selection was the primary process during the evolution of glyptodonts. Furthermore, the reconstruction of selection patterns shows that traits selected to generate a glyptodont morphology are markedly different from those operating on extant armadillos. Changes in both direction and magnitude of selection are probably tied to glyptodonts' invasion of a specialist-herbivore adaptive zone. These results suggest that directional selection might have played a more critical role in the evolution of extreme morphologies than previously imagined.
Fulvivirga lutea sp. nov., a marine bacterium isolated from seawater
Authors: Bae Seung Seob , Jung Yoon-Hee , Kwon Yong Min , Chung Dawoon , Choi Grace , Cho Kichul , Yu Woon-Jong , Baek Kyunghwa
Published: January 2022

A strictly aerobic, Gram-stain-negative, gliding, rod-shaped bacteria, designated strain S481T, was isolated from a surface seawater sample collected at Gunsan marina, in the West Sea of the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S481T formed a monophyletic clade with members of the genus

Fulvivirga

, showing 93.7–95.8% sequence similarity to the type strains. Strain S481T has a single circular chromosome of 4.13 Mbp with a DNA G+C content of 37.3 mol%. The values of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization between strain S481T and all genome-sequenced species of the genus

Fulvivirga

were below 71.2%, 68.6% and 18.9%, respectively, indicating lower values than the standard cut-offs for species delineation. Growth was observed at 20–42 °C (optimum, 37 °C), at pH 6–8 (optimum, pH 7) and with 0 – 6 % NaCl (optimum, 1–2 %). The major fatty acids (>10%) were iso-C15:0, iso-C15:1 G and C16:1ω5c. The respiratory quinone was MK-7. The major polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids and five unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome-based comparison, strain S481T represents a novel species in the genus

Fulvivirga

, for which we propose the name Fulvivirga lutea sp. nov. The type strain is S481T (=KCTC 82209T=JCM 34505T).
CaPTrends: A global database of Carnivoran Population Trends
Authors: Johnson Thomas F. , Cruz Paula , Isaac Nick J. B. , Paviolo Agustin , González-Suárez Manuela
Published: January 2022

Motivation

Population trend information is an ‘Essential Biodiversity Variable’ for monitoring change in biodiversity over time. Here, we present a global dataset of 1122 population trends describing changes in abundance over time in large mammals from the Order Carnivora – some of the world’s most charismatic and functionally important fauna.

Main types of variables included

Key data fields for each record: species, coordinates, trend timeframe, methods of data collection and analysis, and population timeseries or summarised trend value. Population trend values are reported using quantitative metrics in 75% of records that collectively represent more than 6500 population estimates. The remaining records qualitatively describe population change (e.g. increase).

Spatial location and grain

Records represent locations across the globe (latitude: -51.0 to 80.0; longitude: -166.0 to 166.0) with more trends found within the northern temperate zone.

Time period and grain

Records span from 1726 to 2017, with 92% of trends starting after 1950.

Major taxa and level of measurement

We conducted a semi-systematic search for population trend data in 87 species from four families in the order Carnivora: Canidae, Felidae, Hyaenidae and Ursidae. We compiled data for 50 of the 87 species.

Software format

.csv
Dogma and belief: the primary lesion in age-related hearing loss is old news
Authors: McAlpine David , Hernandez-Perez Heivet , Seeto Mark , Edwards Brent
Published: January 2022

Presbycusis, or age-related hearing loss, is the most common sensory deficit globally, and the biggest modifiable risk factor for a later dementia diagnosis. Despite its ubiquity, however, the primary pathology contributing to presbycusis is reportedly contentious, particularly the relative role of damage to the sensory outer hair cells compared to the stria vascularis, an important inner ear structure that maintains the ionic concentration of inner ear fluids that surround it. To determine what might be the “dogma” of the field regarding the primary pathology in presbycusis, we conducted an online Google survey (https://forms.gle/GPreoePmRxBBkchc7) asking relevant respondents in the field their opinions on the matter. In Question (Q1), respondents were asked to rate ‘in your opinion’ from ‘least likely’ to ‘most likely’ (on a scale 1 to 4 [being ‘most likely’]) ‘what is the primary pathology contributing to presbycusis?’ in terms of ‘damage to’: i) the inner hair cells, ii) outer hair cells (OHCs), iii) spiral ganglion, iv) stria vascularis. The term ‘dogma’ suggests that the proportion of people in the field who believe that the main cause of presbycusis is damage to the stria vascularis is at least 50%. The results of our survey estimated this proportion to be 19/101 = 0.188 (95% CI [0.124 0.275]) and a two-sided test of the null hypothesis that this proportion is at least 0.5 was rejected (p < 10−10). When it came to opining what ‘other professionals in the field consider to be the primary pathology contributing to presbycusis’ (Q2), the tendency to rank ‘damage to OHCs’ as being the primary pathology was 45%. Stria vascularis was least likely to be ranked 4 (11%) by professionals in the field opining about the beliefs of others. Even when ‘noise damage was excluded’ as a factor (Q3), the ‘most likely’ contributing factor to presbycusis was stated to be damage to the OHCs (42%). Our data suggest the dogma of the field is that damage to outer hair cells is the primary pathology in presbycusis.
Re-use of labware reduces CO2 equivalent footprint and running costs in laboratories
Authors: Farley Martin , Nicolet Benoit P.
Published: January 2022

Laboratory-based research is resource intensive in terms of financial costs and its carbon footprint. Research laboratories require immense amounts of energy to power equipment, as well as large volumes of materials, particularly of single-use item consumption. In fact, many laboratories have essentially become reliant on single-use plastics. Understanding the full carbon footprint of consumable usage is increasingly important as many research institutes commit to carbon neutrality. To date, no carbon footprint assessment has been conducted to detail the differences between single-use plastics, and reusable glass in a laboratory setting. Here, we analyse the CO2 equivalent (CO2e) footprint of utilising single-use plastics, and re-use of glass or plastic items within laboratory environments. We focused our assessment on four commonly utilised consumables for mammalian cell and bacterial culture, and found that re-use scenarios resulted in substantial reduction in CO2e footprint up to 11-fold. In addition, we estimated the long-term financial costs of re-use and single-use scenarios, and found that re-use had either similar or much lower running costs even when including technical staff wage. We concluded that research facilities must foster re-use in laboratory consumables, while reserving single-use items for select, defined cases. Our study highlights the need to account for indirect CO2e footprint in designing a carbon-neutral lab.
Effectiveness of mRNA COVID-19 Booster Vaccines against Omicron and Delta Variants among US Veterans
Authors: Young-Xu Yinong , Zwain Gabrielle M. , Izurieta Hector S. , Korves Caroline , Powell Ethan I. , Smith Jeremy , Balajee Abirami S. , Holodniy Mark , Beenhouwer David O. , Rodriguez-Barradas Maria C. , Brown Sheldon T. , Marconi Vincent C.
Published: January 2022

Background

We estimated vaccine effectiveness (VE) of mRNA vaccines among US Veterans during periods of Delta and Omicron variant dominance. Patients included in this study were largely 65 years or older (62,834, 55%), male (101,259, 88%), and non-Hispanic white (66,986, 58%).

Methods

We used SARS-CoV-2 laboratory test results to conduct a matched test-negative case-control study to estimate VE of three and two doses of mRNA vaccines against infection (regardless of symptoms), and a matched case-control study to estimate VE against COVID-19-related hospitalization and death. We estimated VE as (1-odds ratio) x 100%. Severity of disease was measured using hospital length of stay (LOS) and admission to an intensive care unit (ICU).

Results

Against infection, booster doses had 7-times higher VE - 59% (95% confidence interval [CI], 57 to 61) - than 2-dose VE (7%; 95% CI, 3 to 10) during the Omicron period. For the Delta period, estimated VE against infection was 90% (95% CI, 88 to 92) among boosted vaccinees, 64% higher than VE among 2-dose vaccinees [55% (95% CI, 51 to 58)]. Against hospitalization, booster dose VE was 87% (95% CI, 80 to 91) during Omicron and 95% (95% CI, 91 to 97) during Delta; the 2-dose VE was 44% (95% CI, 26 to 58) during Omicron and 75% (95% CI, 70 to 80) during Delta. Against death, estimated VE with a booster dose was 94% (95% CI, 85 to 98) during Omicron and 96% (95% CI, 88 to 99) during Delta, while the 2-dose VE was 75% (95% CI, 52 to 87) during Omicron and 93% (95% CI, 85 to 97) during Delta. During the Omicron period, average hospital LOS was 4 days shorter [3 days (95%CI, 3 to 4 days)] than during the Delta period.

Conclusions

A mRNA vaccine booster is more effective against infection, hospitalization, and death than 2-dose vaccination among an older male population with comorbidities.
Double blind placebo-controlled trial for the prevention of ulcerative colitis relapses by β-fructan prebiotics: efficacy and metabolomic analysis
Authors: Valcheva Rosica , Armstrong Heather , Kovic Ognjen , Bording-Jorgensen Michael , Veniamin Simona , Pérez-Muñoz María Elisa , Haskey Natasha , Silva Melissa , Peerani Farhad , Wong Karen , Kao Dina H. , Van Zanten Sander Veldhuyzen , Kroeker Karen I. , Gibson Deanna L. , Wine Eytan , Gänzle Michael , Walter Jens , Dieleman Levinus A.
Published: January 2022

Background

Ulcerative colitis (UC) is associated with altered intestinal microbiome (‘dysbiosis’), most significantly, reduced strict butyrate-producing anaerobes and increased facultative anaerobes. Inulin-type prebiotics appear to reduce and prevent colitis in preclinical studies and small clinical trials. However, these results need to be validated in randomized controlled clinical trial (RCT) studies.

Aims

The aim of this RCT study was to assess the efficacy of β-fructans (oligofructose and inulin) in preventing relapses in UC patients in clinical remission as well as identify potential mechanisms of activity.

Methods

Adult UC patients in clinical remission (total Mayo score ≤ 2) were randomized to supplement their diet with 15g/d of either β-fructans (oligofructose and inulin; Synergy1/Prebiotin) or placebo (maltodextrin) for 6 months. Partial Mayo scores, medications, adverse events and intervention compliance were monitored monthly. Fecal specimens were collected throughout the study to measure fecal calprotectin (FCP), along with stool metabolites.

Results

Eighty-nine UC patients in clinical remission were randomized to β-fructans (n=43) or placebo (n=46). Of those, 11 participants never started, 2 were withdrawn, and 76 were included in the study population (β-fructans n=35; placebo n=41). Although there was no difference in symptomatic clinical flare (β-fructans n=11 flare; placebo n=10 flare, P=0.60), patients randomized to oligofructose and inulin showed only a 3-fold median FCP increase versus 17-fold in the placebo group (P=0.038). Interestingly, antibiotics and serotonin reuptake inhibitors significantly increased the relative risk (RR) of flare (RR 3.321, 95% Cl 2.005 to 5.344, P < 0.0001). β-Fructan intake significantly increased anti-inflammatory fecal metabolites (arabinose, L-arabitol, 5-oxo-D-proline).

Conclusions

Although oligofructose and inulin did not prevent symptomatic relapses in UC patients, their oral administration significantly reduced the severity of biochemical relapse compared to placebo which was further associated with increased anti-inflammatory metabolites.
Increased risk of death immediately after discharge from compulsory care for substance abuse
Authors: Ledberg Anders , Reitan Therese
Published: January 2022

Background

In Sweden, approximately 1000 persons per year are committed to compulsory care for substance abuse for a maximum duration of six months. People admitted to compulsory care are known to suffer high mortality risks, but whether the risk of dying is further heightened immediately after discharge is not known.

Methods

Individual data from Swedish national registers were used to follow all persons discharged from a six months compulsory care episode in the period 2000–2017 (N = 7, 929). Based on a competing risks framework including re-admissions to compulsory care or imprisonment, hazard rates were estimated in five non-overlapping time windows covering the first year after discharge.

Results

In total, 494 persons died during follow-up, corresponding to an overall yearly risk of 6.2 percent (95% confidence interval: 5.7, 6.8). The risk was higher for men than for women and increased with age. The risk of dying during the first two weeks after discharge was higher than during the remaining follow-up period – hazard ratios comparing the first two weeks with subsequent time windows were between 2.6 (1.3, 5.0) and 3.7 (2.4, 5.9). This heightened risk in close proximity to discharge was only observed for deaths due to external causes, and only for people below the median age of 36 years.

Conclusions

The risk of dying immediately after discharge from compulsory care is very high, especially for younger clients, and more efforts should be made to prevent these deaths.
Mucociliary Transport Deficiency and Disease Progression in Syrian Hamsters with SARS-CoV-2 Infection
Authors: Li Qian , Vijaykumar Kadambari , Philips Scott E , Hussain Shah S , Huynh Van N , Fernandez-Petty Courtney M , Lever Jacelyn E Peabody , Foote Jeremy B , Ren Janna , Campos-Gómez Javier , Daya Farah Abou , Hubbs Nathaniel W , Kim Harrison , Onuoha Ezinwanne , Boitet Evan R , Fu Lianwu , Leung Hui Min , Yu Linhui , Detchemendy Thomas W , Schaefers Levi T , Tipper Jennifer L , Edwards Lloyd J , Leal Sixto M , Harrod Kevin S , Tearney Guillermo J , Rowe Steven M
Published: January 2022

Substantial clinical evidence supports the notion that ciliary function in the airways plays an important role in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, consequent impaired mucociliary transport (MCT) remains unknown for the intact MCT apparatus from an in vivo model of disease. Using golden Syrian hamsters, a common animal model that recapitulates human COVID-19, we quantitatively followed the time course of physiological, virological, and pathological changes upon SARS-CoV-2 infection, as well as the deficiency of the MCT apparatus using micro-optical coherence tomography, a novel method to visualize and simultaneously quantitate multiple aspects of the functional microanatomy of intact airways. Corresponding to progressive weight loss up to 7 days post-infection (dpi), viral detection and histopathological analysis in both the trachea and lung revealed steadily descending infection from the upper airways, as the main target of viral invasion, to lower airways and parenchymal lung, which are likely injured through indirect mechanisms. SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 dpi, largely due to diminished motile ciliation coverage, but not airway surface liquid depth, periciliary liquid depth, or cilia beat frequency of residual motile cilia. Further analysis indicated that the fewer motile cilia combined with abnormal ciliary motion of residual cilia contributed to the delayed MCT. The time course of physiological, virological, and pathological progression suggest that functional deficits of the MCT apparatus predispose to COVID-19 pathogenesis by extending viral retention and may be a risk factor for secondary infection. As a consequence, therapies directed towards the MCT apparatus deserve further investigation as a treatment modality.