bluuebunny/crossref_metadata_2025 huggingface dataset:
Drivers of beta diversity along a precipitation gradient in tropical forests of the Cauca River Canyon in Colombia
Authors: Idárraga‐Piedrahíta Álvaro , González‐Caro Sebastián , Duque Álvaro J. , Jiménez‐Montoya Jáider , González‐M. Roy , Parra Juan L. , Rivera‐Gutiérrez Héctor F.
Published: January 2022

Aims

Tropical dry forests are among the most threatened ecosystems on Earth, and understanding the effects of climate on their species distributions is critical to mitigate global change impacts. Here, we assessed the impact of precipitation and dispersal limitation by natural and anthropogenic causes on phylogenetic and taxonomic beta diversity of woody‐plant communities.

Location

Cauca River Canyon in the Northwest Andean mountains, Colombia.

Methods

We used inventory data from 160 0.02‐ha plots and a phylogenetic tree to calculate phylogenetic and taxonomic beta diversity and their components (nestedness and replacement) across plots. We used redundancy analysis to assess the effects of precipitation, spatial distance, and connectivity (a proxy of fragmentation) on changes in beta diversity metrics and estimated each variable's relative contribution.

Results

We found that both phylogenetic and taxonomic replacement were highly related to precipitation differences. Spatial distance and connectivity explained only a small proportion of the variance in phylogenetic and taxonomic replacement. None of the predictor variables explained phylogenetic or taxonomic nestedness.

Conclusions

Patterns of phylogenetic and taxonomic replacement across woody‐plant communities suggest that species and clades are highly specialized to particular precipitation regimes with a minor role for dispersal limitation. Both climate change and fragmentation could drastically influence the future community composition of tropical dry forests.
Affine term structure models: A time‐change approach with perfect fit to market curves
Authors: Mbaye Cheikh , Vrins Frédéric
Published: January 2022

We address the so‐called calibration problem, which consists of fitting in a tractable way a given model to a specified term structure such as yield, prepayment or default probability curves. Time‐homogeneous affine jump diffusions (HAJD) are tractable processes but have limited flexibility; they fail to perfectly replicate actual market curves. Applying a deterministic shift to the latter is a simple but efficient solution that is widely used by both academics and practitioners. However, the shift approach may not be appropriate when positivity is required, a common constraint when dealing with credit spreads or default intensities. In this paper, we address this problem by adopting a time‐change technique. Specific attention is paid to the Cox–Ingersoll–Ross model with compound Poisson jumps (JCIR), which remains standard for modeling intensities. Our time‐changed JCIR (TC‐JCIR) is compared to the shifted JCIR (JCIR++) in various credit applications such as credit default swap (CDS), credit default swaption, and credit valuation adjustment (CVA) under wrong‐way risk (WWR). The TC‐JCIR model is able to generate much larger implied volatilities and covariance effects than JCIR++ under positivity constraints and represents an appealing alternative to the latter.
Northwest Africa 6486: Record of large impact events and fluid alteration on the L chondrite asteroid
Authors: Lorenz C. A. , Korochantseva E. V. , Ivanova M. A. , Hopp J. , Franchi I. A. , Humayun M. , Anosova M. O. , Teplyakova S. N. , Trieloff M.
Published: January 2022

We report the results of petrological, geochemical, and geochronological investigations of the unusual K‐rich L chondrite melt rock Northwest Africa 6486 (NWA 6486). The rock has slightly fractionated siderophile elements and a mostly unfractionated L chondrite pattern of lithophile elements with the exceptions of enrichments in K and Rb and chondritic Sr abundance similar to the K‐rich inclusions found in the ordinary chondrites and indicating a fractionation of alkaline elements through the vapor. We suggest that NWA 6486 and related K‐rich chondritic inclusions were formed in situ on the OC parent bodies and that K and Rb enrichment of these rock most probably is a result of the selective impact evaporation of volatile alkali elements followed by the reaction of a vapor with shock melt. NWA 6486 recorded a breakup event of the L chondrite parent asteroid at 470 Ma during which it was formed. Unusual veins, depleted in K, Na, Ca, and Al relative to the host rock were found in NWA 6486. We suggest that NWA 6486 was affected by aqueous fluids that produced alteration zones depleted in a feldspar component on the walls of opened fractures. The melt veins could be formed during a subsequent impact event by in situ melting of the fracture walls or due to decomposition of an injected supercritical aqueous silicate fluid. The aqueous alteration and the second impact event had no detectable effect on Ar and oxygen isotopic systems. Cosmic ray exposure ages indicate that NWA 6486 was ejected from its parent asteroid ~3–4 Ma ago.
Sampling‐based modified ant colony optimization method for high‐speed rail alignment development
Authors: Roy Sandeepan , Maji Avijit
Published: January 2022

High‐speed railway (HSR) alignment development is a complex and tedious problem due to an infinite number of possible solutions, the existence of non‐linear costs and impacts, and complex location and geometric design constraints. In this study, a low‐discrepancy point sampling‐based modified ant colony optimization (SMACO) algorithm for obtaining horizontal alignments with optimized HSR‐specific cost and impact, including noise and vibration impacts, is proposed. The low‐discrepancy sampling approach is used to identify the potential, from which appropriate intermediate s are selected to develop feasible alignments using the SMACO algorithm. It effectively avoids restricted land parcels and satisfies HSR‐related geometric design requirements. A real‐world case study demonstrated that the HSR alignment obtained using the proposed method was marginally better than the path planner method‐based alignment and the constructed alignment. The sensitivity analysis highlighted the impact of two key parameters, that is, the right of way widths and noise and vibration screening distances on the HSR alignment development. This study advances the alignment development automation, particularly the HSR horizontal alignment for design speeds over 180 km/h. It facilitates extensive search space exploration independent of infeasible regions, identifies and selects without being constrained to prespecified locations and a user‐defined number, and proposes a suitably modified ACO algorithm for the HSR alignment development.
Quality of the Situation‐Background‐Assessment‐Recommendation tool during nurse‐physician calls in the ICU: An observational study
Authors: Scolari Emil , Soncini Leda , Ramelet Anne‐Sylvie , Schneider Antoine Guillaume
Published: January 2022

Background

Situation‐Background‐Assessment‐Recommendation (SBAR) is a tool for structuring communication between healthcare professionals. SBAR reduces medical errors, however few studies have evaluated its quality in real practice.

Aims

To describe the quality of SBAR utilization by intensive care unit (ICU) nurses during phone conversations with physicians. To assess the influence of nurses' training, professional experience, and call circumstances on this quality.

Study Design

This observational study was conducted in the adult ICU of a university hospital in French speaking Switzerland. All consecutive telephone calls from nurses to physicians during a calendar month, were recorded. Those related to a change in patients' clinical status were selected and analysed. The quality of SBAR utilization was assessed using a pre‐defined analysis grid. Scores ranged from 0 (worst quality) to 100% (best quality). Nurses' sociodemographics and training record were collected. Multiple regression was used to assess determinants of SBAR quality including nurses characteristics and level of training.

Results

We analysed 290 phone calls, made by 99 nurses. The median SBAR quality score was 41% (interquartile range [IQR] 33–48). Quality scores varied across the four items of SBAR: Situation 88% (81–94), Background 17% (6–27), Assessment 17% (0–33), and Recommendation 33% (17–40). Factors independently associated with higher SBAR quality were age (−0.66%, p = .002, 95% CI [−1.07; −0.25]), primary language other than French (−8.40%, p = .017, 95% CI [−15.29; −1.51]), lack of ICU expertise (−9.25%, p = .013, 95% CI [−16.5;1–1.99]), and SBAR training in pre‐graduate nursing education (+11.53%, p = .028, 95% CI [1.27; 22.79]).

Conclusions

The quality of SBAR utilization remains low in ICU clinical practice. Pre‐ and post‐graduate training seem to improve its quality.

Relevance to Clinical Practice

Pre‐graduate mandatory training associated with multiple repetitions could improve nurses' SBAR utilization. Training using the SBAR tool should be combined with the development of nursing skills in assessment and clinical judgment.
Analysis of metabolomics and transcriptomics data in head and neck squamous cell carcinoma
Authors: Li Wen , Li Yang , Chen Zhuo , Lam Alfred King‐yin , Li Zeping , Liu Xiaoling , Zhu Baoyu , Qiao Bin
Published: January 2022

Objective

Studies have shown that cancer progression of head and neck squamous cell carcinoma (HNSCC) is related with metabolic alterations. The aim of this study is to identify the clinical roles of metabolic alterations in HNSCC.

Materials and methods

Metabolism‐related genes associated with HNSCC were searched in public databases. A predictive and efficacious LASSO model was fabricated to optimize the diagnosis that was based on these genes. Meantime, ultra‐performance liquid chromatography‐quadrupole/orbitrap high resolution mass spectrometry (UHPLC‐Q‐Orbitrap HRMS) was used to compare patients with HNSCC (n = 73) with healthy controls (n = 51) for serum metabolites. Potential biomarkers and alterations in serum metabolites were analysed and evaluated using t test analysis, principal component analysis and orthogonal partial least square‐discrimination analysis.

Results

Overall, 21 differential metabolites were probed in serum, of which eight metabolites had potential for clinical uses. Transcriptome analysis showed that four genes in the constructed LASSO model were found to be associated with seven differential metabolites. Metabolic pathway analysis by MetaboAnalyst showed that the biomarkers that were related with HNSCC were closely related to four metabolism pathways (p < 0.05).

Conclusion

To conclude, future research on HNSCC should be directed towards multi‐omics to provide treatment, intervention or diagnosis of the disease.
Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates
Authors: Nunn Adam , Rodríguez‐Arévalo Isaac , Tandukar Zenith , Frels Katherine , Contreras‐Garrido Adrián , Carbonell‐Bejerano Pablo , Zhang Panpan , Ramos Cruz Daniela , Jandrasits Katharina , Lanz Christa , Brusa Anthony , Mirouze Marie , Dorn Kevin , Galbraith David W , Jarvis Brice A. , Sedbrook John C. , Wyse Donald L. , Otto Christian , Langenberger David , Stadler Peter F. , Weigel Detlef , Marks M. David , Anderson James A. , Becker Claude , Chopra Ratan
Published: January 2022

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field‐based model species for genetics and epigenetics. The availability of a high‐quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome‐level genome assembly of var. MN106‐Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32‐10) that are highly amenable to genetic transformation. We describe non‐coding RNAs, pseudogenes and transposable elements, and highlight tissue‐specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome‐wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
Exposure to different light intensities affects emission of volatiles and accumulations of both pigments and phenolics in Azolla filiculoides
Authors: Brilli Federico , Dani K. G. Srikanta , Pasqualini Stefania , Costarelli Alma , Cannavò Sara , Paolocci Francesco , Zittelli Graziella Chini , Mugnai Gianmarco , Baraldi Rita , Loreto Francesco
Published: January 2022

Many agronomic trials demonstrated the nitrogen‐fixing ability of the ferns Azolla spp. and its obligate cyanobiont Trichormus azollae. In this study, we have screened the emission of volatile organic compounds (VOCs) and analyzed pigments (chlorophylls, carotenoids) as well as phenolic compounds in Azolla filiculoides–T. azollae symbionts exposed to different light intensities. Our results revealed VOC emission mainly comprising isoprene and methanol (~82% and ~13% of the overall blend, respectively). In particular, by dissecting VOC emission from A. filiculoides and T. azollae, we found that the cyanobacterium does not emit isoprene, whereas it relevantly contributes to the methanol flux. Enhanced isoprene emission capacity (15.95 ± 2.95 nmol m−2 s−1), along with increased content of both phenolic compounds and carotenoids, was measured in A. filiculoides grown for long‐term under high (700 μmol m−2 s−1) rather than medium (400 μmol m−2 s−1) and low (100 μmol m−2 s−1) light intensity. Moreover, light‐responses of chlorophyll fluorescence demonstrated that A. filiculoides was able to acclimate to high growth light. However, exposure of A. filiculoides from low (100 μmol m−2 s−1) to very high light (1000 μmol m−2 s−1) did not affect, in the short term, photosynthesis, but slightly decreased isoprene emission and leaf pigment content whereas, at the same time, dramatically raised the accumulation of phenolic compounds (i.e. deoxyanthocyanidins and phlobaphenes). Our results highlight a coordinated photoprotection mechanism consisting of isoprene emission and phenolic compounds accumulation employed by A. filiculoides to cope with increasing light intensities.
Socioeconomic Status and Public Sector Worker Stereotypes: Results from a Representative Survey
Authors: Bertram Isa , Bouwman Robin , Tummers Lars
Published: January 2022

What views do people have of public sector workers? Public sector workers are often portrayed negatively. It is unclear, however, to what extent such negative perceptions are shared among different groups in society. Using a large representative survey in the Netherlands, we study whether people's socioeconomic status is related to having more negative stereotypes about public sector workers. Contrary to expectations, education and income are unrelated to stereotypes. We do find a relation with subjective income: People with low subjective income have more negative stereotypes. Moreover, the sector people work in is highly relevant. People working in core governmental sectors such as central and local government have positive stereotypes. Other groups—such as private sector and non‐profit workers—have a far more negative image of public sector workers. These findings help us to understand people's perceptions of public sector workers and the problems various groups have with the state.
The importance of being apnoeic (on CPAP)
Authors: Naughton Matthew T.
Published: January 2022

See related article
Multigenerational Mobility Among Males in India
Authors: Kundu Anustup , Sen Kunal
Published: January 2022

Most studies of intergenerational mobility focus on adjacent generations, and there is limited knowledge about multigenerational mobility—status transmission across three generations. We examine multigenerational educational and occupational mobility in India, using a nationally representative data set the India Human Development Survey that contains information about education and occupation for three generations. We find that mobility has increased over generations for education, but not for occupation. We also find that there are stark differences across social groups, with individuals belonging to socially disadvantaged communities lagging behind in social progress. Multigenerational mobility for Muslims in education and occupation has decreased in comparison to Hindus over the three generations. While we find that there is an increase in educational mobility for other disadvantaged groups such as Scheduled Castes, Scheduled Tribes, and Other Backward Classes compared to General Castes, we do not find evidence of increased occupational mobility over the three generations.
Consensus‐based sampling
Authors: Carrillo J. A. , Hoffmann F. , Stuart A. M. , Vaes U.
Published: January 2022

We propose a novel method for sampling and optimization tasks based on a stochastic interacting particle system. We explain how this method can be used for the following two goals: (i) generating approximate samples from a given target distribution and (ii) optimizing a given objective function. The approach is derivative‐free and affine invariant, and is therefore well‐suited for solving inverse problems defined by complex forward models: (i) allows generation of samples from the Bayesian posterior and (ii) allows determination of the maximum a posteriori estimator. We investigate the properties of the proposed family of methods in terms of various parameter choices, both analytically and by means of numerical simulations. The analysis and numerical simulation establish that the method has potential for general purpose optimization tasks over Euclidean space; contraction properties of the algorithm are established under suitable conditions, and computational experiments demonstrate wide basins of attraction for various specific problems. The analysis and experiments also demonstrate the potential for the sampling methodology in regimes in which the target distribution is unimodal and close to Gaussian; indeed we prove that the method recovers a Laplace approximation to the measure in certain parametric regimes and provide numerical evidence that this Laplace approximation attracts a large set of initial conditions in a number of examples.
A comparison of obfuscation methods used for privacy protection: Exploring the challenges of polygon data in agricultural research
Authors: Nowbakht Parvaneh , O'Sullivan Lilian , Cawkwell Fiona , Wall David P. , Holloway Paul
Published: January 2022

A major challenge of sharing spatially explicit agricultural and agri‐environmental data is to identify the trade‐off between field parcel confidentiality and spatial pattern preservation. In this work, 27 point‐based obfuscation and evaluation methods were applied on agricultural data, collected by the Irish Nutrient Management Planning Online (NMP Online) platform, which is a high‐density polygon dataset developed to inform precision agriculture through nutrient management based on soil fertility and agronomic targets. Broad categorizations of methods—including N*Rand, Donut, Density, Pinwheel, AHilb, and k‐anonymity—were developed, combined, and modified to achieve the best trade‐off between security and accuracy. To improve geoprivacy and spatial pattern preservation of existing Donut and Density methods, qualitative approaches, including Donut‐k and Density‐k methods, were introduced which identify the optimal values of radii based on a combination of the Donut method and k‐anonymity satisfaction, and subsequently optimal k‐anonymity determination. Modified AHilb and Donut‐AHilb methods were also developed to generate smaller and arbitrary obfuscation areas to improve location security. The Donut‐AHilb method was found to be the best at spatial pattern preservation and satisfying larger k‐anonymity, but the risk of false identification and non‐unique obfuscation was high when considering the polygon nature of agricultural data such as field parcels. Further, we introduce the term “non‐unique obfuscated points,” which is important when obfuscating static objects as two or more points might have the same obfuscated location, which has relevance to the wider GIScience community.
Effect of lactic acid addition to equine whole blood on platelet aggregation measured by impedance aggregometry
Authors: Lanier Christopher J. , Taintor Jennifer S. , Christopherson Peter W. , Spangler Elizabeth A.
Published: January 2022

Background

Acidemia in sick or injured horses is often due to lactic acid accumulation. Alterations in platelet function and hemostasis are among numerous deleterious effects caused by decreased physiologic pH.

Objectives

We aimed to evaluate the effect of hyperlactatemia and resultant acidemia on platelet aggregation in equine whole blood using impedance aggregometry.

Methods

Platelet aggregation was measured using the Multiplate analyzer in whole blood from 34 healthy horses at baseline and after in vitro addition of lactic acid to adjust the pH. Platelet aggregation of each sample was quantified by the area under the curve measurement reported by the Multiplate system. The association between platelet aggregation and pH was analyzed using a linear mixed‐effects model. The association of baseline platelet aggregation with hematocrits (Hcts), white blood cell (WBC) counts, and platelet counts was evaluated using Pearson's correlations.

Results

There was a significant association between acidemia and decreased platelet aggregation. No significant correlations were detected between platelet aggregation and Hct, WBC count, or platelet count. Platelet aggregation measured in healthy horses using the Multiplate analyzer showed substantial variation between animals.

Conclusions

Acidemia caused by the addition of lactic acid to equine whole blood was associated with a mild though statistically significant decrease in platelet aggregation. In conjunction with other factors, this change may contribute to morbidity‐related disorders of hemostasis, although its precise clinical relevance is uncertain.
Outcomes of dogs undergoing surgery for gastric dilatation volvulus after rapid versus prolonged medical stabilization
Authors: Lhuillery Eloïse , Velay Ludivine , Libermann Stéphane , Le Boedec Kevin , Gautherot Audrey , Bonneau Lucie , Mongellas Emilie , Harris Karen , Etchepareborde Sébastien
Published: January 2022

Objective

To compare the outcomes of dogs surgically treated for gastric dilatation volvulus (GDV) after rapid versus prolonged medical stabilization.

Study Design

Prospective cohort study, monoinstitutional.

Sample Population

One hundred and sixty‐two dogs with GDV.

Methods

Dogs presenting with a GDV were allocated to 1 of 2 groups,immediateordelayed. In theimmediategroup, dogs were stabilized for 90 min prior to undergoing surgery. In thedelayedgroup, dogs underwent surgery after at least 5 h of stabilization. Medical stabilization included gastric decompression and placement of an indwelling nasogastric tube to prevent further gastric dilatation in all dogs. Short‐term outcomes were compared between surgical timings by univariate and multivariate analyses.

Results

Dogs (n = 89) in theimmediategroup underwent surgery a median time of 2.1 h after presentation (range 1.9‐2.5 h), whereas those in thedelayedsurgery group (n = 73) were operated a median time of 9.8 h (range 5.4‐13.7 h) after presentation. Survival rates did not differ between dogs undergoing immediate or delayed surgery at discharge (70/89 and 60/73, respectively) or at 1 month postoperatively (68/89 and 55/73, respectively). The degree of gastric torsion was differently distributed between the 2 groups (P = .05). In theimmediategroup, 19, 52, and 9 dogs had a 0°, 180° and 270° gastric torsion respectively, whereas in thedelayedgroup, 27, 32, and 5 dogs had a 0°, 180° and 270° gastric torsion respectively. Hyperlactatemia 24 h after initiation of fluid therapy was associated with an increased in‐hospital mortality risk and at 1 month postoperatively.

Conclusion

No survival benefit was detected as a result of proceeding to surgery after either a rapid or a prolonged medical stabilization.

Clinical Significance

The aggressive stabilization and monitoring protocol described here can be considered as an alternative to stabilize dogs with GDV prior to surgery within 13.7 h of presentation. Further research is required to investigate the potential risks and benefits of prolonged over rapid stabilization and to identify candidates for each approach.
Stachyurus praecox (Stachyuraceae), first report in Korea
Authors: OH Chan-Jin , SHIN Soon-Ho , CHO Ji-Woong , KIM Hyoun-Woo , HAN Sang-Sub , KIM Ji-Won , CHUNG Jae-Min
Published: January 2022

We report a previously unrecorded woody species, Stachyurus praecox Siebold & Zucc. (Stachyuraceae), in Korea. This species is considered to be endemic to Japan. Stachyurus praecox was collected for the first time in an evergreen forest on an uninhabited island of Bongsun-ri, Saengil-myeon, Wando-gun, Jeollanam-do in Korea. The inflorescence of the species was racemose and pendulous on the axils of the previous year’s branches. Flowers bloomed from March to April. They were functionally dioecy but morphologically hermaphrodite. This woody species was named ‘Wan-do-sul-kkot-na-mu’ in Korean based on the shape of its inflorescence. Morphological characteristics and illustrations of this woody species have been provided with a distribution map and photographs of the natural habitat.
Topology Optimization of Lightweight Structures With Application to Bone Scaffolds and 3D Printed Shoes for Diabetics
Authors: Wang Zhujiang , Srinivasa Arun , Reddy J. N. , Dubrowski Adam
Published: January 2022

An automatic complex topology lightweight structure generation method (ACTLSGM) is presented to automatically generate 3D models of lightweight truss structures with a boundary surface of any shape. The core idea of the ACTLSGM is to use the PIMesh, a mesh generation algorithm developed by the authors, to generate node distributions inside the object representing the boundary surface of the target complex topology structures; raw lightweight truss structures are then generated based on the node distributions; the resulting lightweight truss structure is then created by adjusting the radius of the raw truss structures using an optimization algorithm based on finite element truss analysis. The finite element analysis-based optimization algorithm can ensure that the resulting structures satisfy the design requirements on stress distributions or stiffness. Three demos, including a lightweight structure for a cantilever beam, a femur bone scaffold, and a 3D shoe sole model with adaptive stiffness, can be used to adjust foot pressure distributions for patients with diabetic foot problems and are generated to demonstrate the performance of the ACTLSGM. The ACTLSGM is not limited to generating 3D models of medical devices, but can be applied in many other fields, including 3D printing infills and other fields where customized lightweight structures are required.
Capturing the swelling of solid-electrolyte interphase in lithium metal batteries
Authors: Zhang Zewen , Li Yuzhang , Xu Rong , Zhou Weijiang , Li Yanbin , Oyakhire Solomon T. , Wu Yecun , Xu Jinwei , Wang Hansen , Yu Zhiao , Boyle David T. , Huang William , Ye Yusheng , Chen Hao , Wan Jiayu , Bao Zhenan , Chiu Wah , Cui Yi
Published: January 2022

Preservation of cycling behavior

Understanding the changes in interfaces between electrode and electrolyte during battery cycling, including the formation of the solid-electrolyte interphase (SEI), is key to the development of longer lasting batteries. Z. Zhang
et al
. adapt a thin-film vitrification method to ensure the preservation of liquid electrolyte so that the samples taken for analysis using microscopy and spectroscopy better reflect the state of the battery during operation. A key finding is that the SEI is in a swollen state, in contrast to current belief that it only contained solid inorganic species and polymers. The extent of swelling can affect transport through the SEI, which thickens with time, and thus might also decrease the amount of free electrolyte available for battery cycling. —MSL
Smaller fish species in a warm and oxygen-poor Humboldt Current system
Authors: Salvatteci Renato , Schneider Ralph R. , Galbraith Eric , Field David , Blanz Thomas , Bauersachs Thorsten , Crosta Xavier , Martinez Philippe , Echevin Vincent , Scholz Florian , Bertrand Arnaud
Published: January 2022

Species shifts

Our anthropogenically warmed climate will lead to a suite of organismal changes. To predict how some of these may occur, we can look to past warm (interglacial) periods. Salvatteci
et al
. used this approach and looked at a marine sediment record of the Humboldt Current system off the coast of Peru (see the Perspective by Yasuhara and Deutsch). They found that previous warm periods were dominated by small, goby-like fishes, whereas this ecosystem currently is dominated by anchovy-like fishes. Such a shift is not only relevant to ecosystem shifts but also to fisheries because anchovies are heavily fished as a food source and gobies are much less palatable than anchovies. —SNV
Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies
Authors: Mishra Akaash K. , Hellert Jan , Freitas Natalia , Guardado-Calvo Pablo , Haouz Ahmed , Fels J. Maximilian , Maurer Daniel P. , Abelson Dafna M. , Bornholdt Zachary A. , Walker Laura M. , Chandran Kartik , Cosset François-Loïc , McLellan Jason S. , Rey Felix A.
Published: January 2022

A block to viral cell entry

Crimean-Congo hemorrhagic fever virus is a tickborne virus that can cause severe disease and even death in humans. Disease occurrence is linked to the geographic range of the tick vector, and climate change may increase this range. Infection of host cells requires the fusion glycoprotein Gc, which is the main target of neutralizing antibodies. Mishra
et al
. build on previous work that identified a combination of two Gc-targeting antibodies that gave postexposure protection in an animal model. The authors determined the structure of the antigen-binding fragments of the two antibodies bound to a prefusion form of Gc and also the structure of Gc after the conformational change into the trimeric postfusion form. The structures show how the antibodies work together to block membrane fusion. —VV
Structural basis of branch site recognition by the human spliceosome
Authors: Tholen Jonas , Razew Michal , Weis Felix , Galej Wojciech P.
Published: January 2022

Intron recognition in the spotlight

Excision of noncoding introns from pre–messenger RNAs is catalyzed by the spliceosome, a large RNA-protein complex that recognizes specific sequences at the exon-intron boundaries (splice sites). These sequences are highly degenerate in humans, and it has remained elusive how they are recognized by the spliceosome. Tholen
et al
. report a series of high-resolution structures of the human U2 small nucleolar ribonucleoprotein, the component of the spliceosome that recognizes branch sites. The structures explain how SF3B6 helps to stabilize the branch helix in the absence of extensive sequence complementarity. A newly identified spliceosome assembly intermediate suggests a mechanism for fidelity control of branch site recognition. —DJ
Regulation of zeolite particle morphology
Authors: Fan Weibin , Dong Mei
Published: January 2022

Specific particle morphology endows zeolites with improved molecular recognizability
Paleobiology provides glimpses of future ocean
Authors: Yasuhara Moriaki , Deutsch Curtis A.
Published: January 2022

Fossil records from tropical oceans predict biodiversity loss in a warmer world
Omicron threat remains fuzzy as cases explode
Authors: Kupferschmidt Kai , Vogel Gretchen
Published: January 2022

Many countries break infection records; how much severe disease they will see is unclear
Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil
Authors: Sutton John M. , Bushman Timothy J. , Akob Denise M. , Fierst Janna L.
Published: January 2022

We report the genome of
Rhodococcus opacus
strain MoAcy1 (
DSM 44186
), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.
Draft Genome Sequences of
Sulfurovum
spp. TSL1 and TSL6, Two Sulfur-Oxidizing Bacteria Isolated from Marine Sediment
Authors: Guo Yong , Ihara Hideyuki , Aoyagi Tomo , Hori Tomoyuki , Katayama Yoko
Published: January 2022

Sulfurovum
spp. TSL1 and TSL6 are sulfur-oxidizing chemolithoautotrophic bacteria isolated from the tsunami-launched marine sediment in the Great East Japan earthquake. This announcement describes the draft genome sequences of the two isolates that possess the gene sets for the sulfur oxidation pathway.
Long-Read Genome Assembly of Saccharomyces uvarum Strain CBS 7001
Authors: Chen Jingxuan , Garfinkel David J. , Bergman Casey M.
Published: January 2022

Here, we report a long-read genome assembly for
Saccharomyces uvarum
strain CBS 7001 based on PacBio whole-genome shotgun sequence data. Our assembly provides an improved reference genome for an important yeast in the
Saccharomyces sensu stricto
clade.
Draft Genome Sequences of Aeromonas schubertii Strains Isolated from Asian Seabass from Thailand
Authors: Pinpimai Komkiew , Angsujinda Kitipong , Thitiphuree Tongchai , Kitiyodom Sirikorn , Chokmangmeepisarn Putita , Pirarat Nopadon
Published: January 2022

Aeromonas schubertii
is a Gram-negative, rod-shaped bacterium. It is a rare species that has been reported in humans and aquatic animals. Here, we report the genome sequences of
A. schubertii
strains isolated from two mass mortality events in central Thailand that were associated with aquaculture of Asian seabass.
Uncommon pathogens in an immunocompetent host: respiratory isolation ofCunninghamella bertholletiae, Aspergillus niger, Staphylococcus pseudintermediusand adenovirus in a patient with necrotising pneumonia
Authors: Olivo Freites Christian , Sy Hendrik , Miguez Patricia , Salonia James
Published: January 2022

We present the unusual case of a 60-year-old immunocompetent woman with chronic obstructive pulmonary disease who developed a necrotising pneumonia with isolation ofCunninghamella bertholletiae, Aspergillus niger, Staphylococcus pseudintermediusand adenovirus. The patient recovered with antimicrobial therapy and supportive care in the intensive care unit. The current literature on diagnosis and treatment of these pathogens is reviewed.
A 10-year-old child with acute torticollis due to polymicrobial deep neck infection
Authors: Guri Alex , Scheier Eric
Published: January 2022

Torticollis in children can be a sign of a potentially dangerous disease; the correct diagnosis is not always obvious on history and physical examination. The use of point-of-care ultrasound (POCUS) helps to limit the differential diagnosis and direct appropriate further laboratory and radiology-performed evaluation. We present a case of a 10-year-old child whose deep neck infection (DNI) was timely diagnosed in the paediatric emergency department by early use of POCUS and drained under POCUS guidance after admission to the hospital. The culture from the fluid grewEikenella corrodens, Streptococcus constellatus and Prevotella buccae. This case demonstrates that DNIs occur in children with acute acquired torticollis, even without fever and demonstrates the importance of early use of POCUS in cases where DNI is a potential diagnosis. Moreover, this case emphasises the importance of microbiological identification of DNIs that can be the key to successful treatment.
Case of leprosy mimicking preseptal cellulitis: a diagnostic dilemma
Authors: Sarkar Deepayan , Chawla Himani , Singh Priti , Verma Vidhya
Published: January 2022

A 36-year-old Asian man presented with swelling over the left frontal region involving the upper eyelids, with associated erythema and tenderness for 1 month duration. Clinically he was diagnosed as a case of preseptal cellulitis, however, the lesion did not improve on broad-spectrum systemic antibiotics. CT showed superficial soft tissue swelling in the forehead extending till the superior part of orbit. Histopathological assessment of the lesion revealed clusters of epithelioid cells with multinucleate giant cells in the dermis along with perivascular and periadnexal lymphocytic infiltrates, suggestive of leprosy. The patient was started on oral steroids with multidrug therapy, following which the patient showed early resolution of the lesion within 10 days of treatment. Leprosy is endemic in India, leprosy with reactional episodes mimics other inflammatory and infective etiologies making diagnosis difficult. Leprosy should be present in an ophthalmologist’s diagnostic repertoire while dealing with periorbital swellings for early clinical diagnosis and favourable outcomes.
Impact of statin treatment on non-invasive tests based predictions of fibrosis in a referral pathway for NAFLD
Authors: Al-Karaghouli Mustafa , Fuentes Sonia , Davyduke Tracy , Ma Mang , Abraldes Juan G
Published: January 2022

Objective

In non-alcoholic fatty liver disease (NAFLD), fibrosis determines the risk of liver complications. Non-invasive tests (NITs) such as FIB-4, NAFLD Fibrosis Score (NFS) and Hepamet, have been proposed as a tool to triage NAFLD patients in primary care (PC). These NITs include AST±ALT in their calculations. Many patients with NAFLD take statins, which can affect AST/ALT, but it is unknown if statin affects NITs fibrosis prediction.

Methods

We included 856 patients referred through a standardised pathway from PC with a final diagnosis of NAFLD. 832 had reliable vibration controlled transient elastography (VCTE) measurements. We assessed the effects of statins on the association between NITs and VCTE at different fibrosis thresholds.

Results

129 out of 832 patients were taking a statin and 138 additional patients had indication for a statin. For any given FIB-4 value, patients on a statin had higher probabilities of high VCTE than patients not on a statin. Adjusting for body mass index, diabetes and age almost completely abrogated these differences, suggesting that these were related to patient’s profile rather to a specific effect of statins. Negative predictive values (NPVs) of FIB-4 <1.3 for VCTE >8, 10, 12 and 16 were, respectively, 89, 94, 96% and 100% in patients on a statin and 92, 95, 98% and 99% in patients not on a statin. Statins had similar impact on Hepamet predictions but did not modify NFS predictions.

Conclusion

In patients with NAFLD referred from PC, those on statins had higher chances of a high VCTE for a given FIB-4 value, but this had a negligible impact on the NPV of the commonly used FIB-4 threshold (<1.3).
‘Where are the dead flies!’: perceptions of local communities towards the deployment of Tiny Targets to control tsetse in the Democratic Republic of the Congo
Authors: Vander Kelen Catiane , Mpanya Alain , Hasker Epco , Miaka Erick , Nzuzi Ruth , Torr Steve , Perez Dennis , Pulford Justin
Published: January 2022

The National Programme for the control of human African trypanosomiasis in Democratic Republic of Congo includes a large-scale vector control operation using Tiny Targets. These are small panels of insecticide-impregnated cloth that are deployed in riverine habitat where tsetse flies concentrate. The effectiveness of Tiny Targets depends partly on acceptance by local communities. In 2018, we conducted research to explore the perception and acceptability of Tiny Targets in two different village clusters where Tiny Targets had been deployed by the local community or external teams. We conducted fourteen focus group discussions and seven semistructured interviews in three villages from each cluster in the Yasa Bonga health zone. Our findings showed that acceptability was better in the cluster where communities were involved in the deployment of Tiny Targets. Also in this cluster, awareness about Tiny Targets was satisfactory and the project was implemented within local customs, which promoted a positive perception of Tiny Targets and their benefits. In the cluster where external teams deployed Tiny Targets, a lack of information and communication, stereotypes applied by communities towards the deployment teams and the impression of inadequate respect for local customs led to anxiety and a misleading interpretation of the purpose of Tiny Targets and negatively influenced acceptability. This study highlights the importance of involving communities for programme acceptance. Our research underlined how awareness campaigns and communication are essential, but also how working within the scope of community social norms and customs are equally important. Prospects for the successful use of Tiny Targets are greater when communities are involved because the use can be adapted to social norms.
Does adherence to a quality indicator regarding early weaning from invasive ventilation improve economic outcome? A single-centre retrospective study
Authors: Zuber Alexander , Kumpf Oliver , Spies Claudia , Höft Moritz , Deffland Marc , Ahlborn Robert , Kruppa Jochen , Jochem Roland , Balzer Felix
Published: January 2022

Objectives

To measure and assess the economic impact of adherence to a single quality indicator (QI) regarding weaning from invasive ventilation.

Design

Retrospective observational single-centre study, based on electronic medical and administrative records.

Setting

Intensive care unit (ICU) of a German university hospital, reference centre for acute respiratory distress syndrome.

Participants

Records of 3063 consecutive mechanically ventilated patients admitted to the ICU between 2012 and 2017 were extracted, of whom 583 were eligible adults for further analysis. Patients’ weaning protocols were evaluated for daily adherence to quality standards until ICU discharge. Patients with <65% compliance were assigned to the low adherence group (LAG), patients with ≥65% to the high adherence group (HAG).

Primary and secondary outcome measures

Economic healthcare costs, clinical outcomes and patients’ characteristics.

Results

The LAG consisted of 378 patients with a median negative economic results of −€3969, HAG of 205 (−€1030), respectively (p<0.001). Median duration of ventilation was 476 (248; 769) hours in the LAG and 389 (247; 608) hours in the HAG (p<0.001). Length of stay (LOS) in the LAG on ICU was 21 (12; 35) days and 16 (11; 25) days in the HAG (p<0.001). LOS in the hospital was 36 (22; 61) days in the LAG, and within the HAG, respectively, 26 (18; 48) days (p=0.001).

Conclusions

High adherence to this single QI is associated with better clinical outcome and improved economic returns. Therefore, the results support the adherence to QI. However, the examined QI does not influence economic outcome as the decisive factor.
Preoperative sonographic prediction of intra-abdominal adhesions using sliding sign at repeat caesarean section at the University of Maiduguri Teaching Hospital, Nigeria: a prospective observational study
Authors: Bukar Mohammed , Mana Asta Umar , Ikunaiye Nasiru
Published: January 2022

Objective

To determine if the presence or absence of sonographic sliding sign preoperatively is a good predictor of the presence and type of intra-abdominal adhesions; and to determine the time taken to demonstrate this sign.

Design

A prospective, observational, triple-blind study using tests of diagnostic accuracy.

Setting

Single-centre tertiary health institution in north-east Nigeria.

Participants

67 women in the third trimester scheduled for repeat elective caesarean sections (CS) had transabdominal sonography to determine the absence or presence and degree of sliding sign. The time taken to make these decisions were noted. Surgeons blinded to the ultrasound findings graded adhesions intraoperatively and comparison between sonographic and intraoperative findings made. Women who were scheduled for emergency CS were excluded.

Main outcome measures

Accuracy of preoperative ultrasound to determine no/mild, moderate and severe adhesions. Secondary outcomes were interobserver correlations and time taken to determine sliding.

Results

When classified as adhesion and no adhesion, the sliding sign demonstrated a sensitivity of 100.00% (CI95 85.18% to 100.00%), specificity of 100.00% (CI95 92.13% to 100.00%). In predicting presence of moderate intra-abdominal adhesions, a sensitivity of 65.0% (CI95 40.78% to 84.61%) and specificity of 82.98% (CI95 69.19% to 92.35%) was found. For predicting severe intra-abdominal adhesions, it had a sensitivity of 25.00% (CI95 0.63% to 80.59%) and specificity of 98.41 (CI95 91.47 to 99.96). Disease prevalence for mild, moderate and severe adhesions was 33.82% (CI95 22.79% to 46.32%), 29.85% (CI95 19.28% to 42.27%) and 5.97% (CI95 1.65% to 14.59%), respectively. Interobserver Cohen’s kappa coefficient and PPA were 0.58 (CI95 0.39 to 0.76) and 58.82 (CI95 52.82 to 64.82), respectively. The mean duration to determine sliding sign was 7.56±2.86 s.

Conclusion

This study supports the role of transabdominal sliding sign in preoperative prediction of intra-abdominal adhesions in women with previous CS without significant increase in sonography duration. This information can encourage planning for CS by ensuring that surgeons of appropriate seniority are deployed to undertake anticipated complex operations.
Busting contraception myths and misconceptions among youth in Kwale County, Kenya: results of a digital health randomised control trial
Authors: Gichangi Peter , Gonsalves Lianne , Mwaisaka Jefferson , Thiongo Mary , Habib Ndema , Waithaka Michael , Tamrat Tigest , Agwanda Alfred , Sidha Hellen , Temmerman Marleen , Say Lale
Published: January 2022

Objectives

The objective of this randomised controlled trial in Kenya was to assess the effect of delivering sexual and reproductive health (SRH) information via text message to young people on their ability to reject contraception-related myths and misconceptions.

Design and setting

A three-arm, unblinded randomised controlled trial with a ratio of 1:1:1 in Kwale County, Kenya.

Participants and interventions

A total of 740 youth aged 18–24 years were randomised. Intervention arm participants could access informational SRH text messages on-demand. Contact arm participants received once weekly texts instructing them to study on an SRH topic on their own. Control arm participants received standard care. The intervention period was 7 weeks.

Primary outcome

We assessed change myths believed at baseline and endline using an index of 10 contraception-related myths. We assessed change across arms using difference of difference analysis.

Results

Across arms, <5% of participants did not have any formal education, <10% were living alone, about 50% were single and >80% had never given birth. Between baseline and endline, there was a statistically significant drop in the average absolute number of myths and misconceptions believed by intervention arm (11.1%, 95% CI 17.1% to 5.2%), contact arm (14.4%, 95% CI 20.5% to 8.4%) and control arm (11.3%, 95% CI 17.4% to 5.2%) participants. However, we observed no statistically significant difference in the magnitude of change across arms.

Conclusions

We are unable to conclusively state that the text message intervention was better than text message ‘contact’ or no intervention at all. Digital health likely has potential for improving SRH-related outcomes when used as part of multifaceted interventions. Additional studies with physical and geographical separation of different arms is warranted.

Trial registration number

ISRCTN85156148.