bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire
Authors: Rodriguez Oscar L. , Safonova Yana , Silver Catherine A. , Shields Kaitlyn , Gibson William S. , Kos Justin T. , Tieri David , Ke Hanzhong , Jackson Katherine J. L. , Boyd Scott D. , Smith Melissa L. , Marasco Wayne A. , Watson Corey T.
Published: July 2022

Variation in the antibody response has been linked to differential outcomes in disease, and suboptimal vaccine and therapeutic responsiveness, the determinants of which have not been fully elucidated. Countering models that presume antibodies are generated largely by stochastic processes, we demonstrate that polymorphisms within the immunoglobulin heavy chain locus (IGH) significantly impact the naive and antigen-experienced antibody repertoire, indicating that genetics predisposes individuals to mount qualitatively and quantitatively different antibody responses. We pair recently developed long-read genomic sequencing methods with antibody repertoire profiling to comprehensively resolve IGH genetic variation, including novel structural variants, single nucleotide variants, and genes and alleles. We show that IGH germline variants determine the presence and frequency of antibody genes in the expressed repertoire, including those enriched in functional elements linked to V(D)J recombination, and overlapping disease-associated variants. These results illuminate the power of leveraging IGH genetics to better understand the regulation, function and dynamics of the antibody response in disease.
Studies on the interaction of three lytic bacteriophages with a wide collection of Escherichia coli strains implicated in swine enteric colibacillosis
Authors: Ferreira Alice , Almeida Carina , Silva Daniela , García-Meniño Isidro , Mora Azucena , Oliveira Hugo , Oliveira Ana
Published: July 2022

Abstract

The misuse of antibiotics in the swine industry and their on-going restriction requires alternatives to control enterotoxigenic and shiga toxin-producing Escherichia coli (ETEC and STEC, respectively). This study evaluates the potential of three coliphages, vB_EcoM_FJ1, vB_EcoM_FN and vB_EcoM_SP1 against 104 ETEC, STEC and ETEC/STEC strains isolated from pig colibacillosis in Portuguese (2018-2020) and Spanish farms (2006-2016), encompassing 71.2% mcr-positive strains (33.7% with mcr-1, 1.9% mcr-2, 35.6% mcr-4 and 2.9% mcr-5) and 18.3% positive strains for TEM (1%), SHV (6.7%), and CTX-M (11.5%) extended-spectrum beta-lactamase-encoding genes. In general, all bacteriophages presented a narrow lytic spectrum (up to 2.9%) against the 104 ETEC, STEC and ETEC/STEC. Bacteriophages shared >80% overall nucleotide identity with E. coli phage T4 (Tevenvirinae subfamily), but a particular look at the distal part of the long tail fiber (gp38) revealed no homology. All bacteriophages recognize lipopolysaccharides as receptors, and additionally, FN binds to an outer membrane protein A. Bacteriophage-insensitive mutants of vB_EcoM_FJ1 (90%) and vB_EcoM_FN (100%) were shown to be more susceptible to pig serum inactivation comparatively to the parental strain and furthermore, their adhesion capacity to porcine intestinal cells was diminished by, approximately, 90%. Contrariwise, vB_EcoM_SP1 insensitive variants did not display phenotypic differences comparing to the wild-type strain. This study demonstrates that besides being T4-like, these bacteriophages revealed a narrow lytic spectrum against diarrhoeagenic E. coli strains and that the acquisition of novel bacteriophage-encoded adhesins (gp38) seems to be determinant for such results.
Kelpwatch: A new visualization and analysis tool to explore kelp canopy dynamics reveals variable response to and recovery from marine heatwaves
Authors: Bell Tom W. , Cavanaugh Kyle C. , Saccomanno Vienna R. , Cavanaugh Katherine C. , Houskeeper Henry F. , Eddy Norah , Schuetzenmeister Falk , Rindlaub Nathaniel , Gleason Mary
Published: July 2022

Giant kelp and bull kelp forests are increasingly at risk from marine heatwave events, herbivore outbreaks, and the loss or alterations in the behavior of key herbivore predators. The dynamic floating canopy of these kelps is well-suited to study via satellite imagery, which provides high temporal and spatial resolution data of floating kelp canopy across the western United States and Mexico. However, the size and complexity of the satellite image dataset has made ecological analysis difficult for scientists and managers. To increase accessibility of this rich dataset, we created Kelpwatch, a web-based visualization and analysis tool. This tool allows researchers and managers to quantify kelp forest change in response to disturbances, assess historical trends, and allow for effective and actionable kelp forest management. Here, we demonstrate how Kelpwatch can be used to analyze long-term trends in kelp canopy across regions, quantify spatial variability in the response to and recovery from the 2014 to 2016 marine heatwave events, and provide a local analysis of kelp canopy status around the Monterey Peninsula, California. We found that 18.6% of regional sites displayed a significant trend in kelp canopy area over the past 38 years and that there was a latitudinal response to heatwave events for each kelp species. The recovery from heatwave events was more variable across space, with some local areas like Bahía Tortugas in Baja California Sur showing high recovery while kelp canopies around the Monterey Peninsula continued a slow decline and patchy recovery compared to the rest of the Central California region. Kelpwatch provides near real time spatial data and analysis support and makes complex earth observation data actionable for scientists and managers, which can help identify areas for research, monitoring, and management efforts.
Adapting to visuomotor rotations in stepped increments increases implicit motor learning
Authors: Modchalingam Shanaathanan , Ciccone Marco , D’Amario Sebastian , ’t Hart Bernard Marius , Henriques Denise Y.P.
Published: July 2022

Human motor adaptation relies on both explicit conscious strategies and implicit unconscious updating of internal models to correct motor errors. Implicit adaptation is powerful, requiring less preparation time before executing adapted movements, but recent work suggests it is limited to some absolute magnitude regardless of the size of a visuomotor perturbation when the perturbation is introduced abruptly. It is commonly assumed that gradually introducing a perturbation should lead to improved implicit learning beyond this limit, but outcomes are conflicting. We tested whether introducing a perturbation in two distinct gradual methods can overcome the apparent limit and explain past conflicting findings. We found that gradually introducing a perturbation in a stepped manner, where participants were given time to adapt to each partial step before being introduced to a larger partial step, led to ∼80% higher implicit aftereffects of learning, but introducing it in a ramped manner, where participants adapted larger rotations on each subsequent reach, did not. Our results clearly show that gradual introduction of a perturbation can lead to substantially larger implicit adaptation, as well as identify the type of introduction that is necessary to do so.
Genome-wide analysis resolves the radiation of New Zealand’s freshwaterGalaxias vulgariscomplex and reveals a candidate species obscured by mitochondrial capture
Authors: Campbell Ciaran S.M. , Dutoit Ludovic , King Tania M. , Craw Dave , Burridge Christopher P. , Wallis Graham P. , Waters Jonathan M.
Published: July 2022

Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species diversity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand’s stream-residentGalaxias vulgariscomplex have yielded conflicting phylogenies. We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187Galaxiasspecimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations. In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species (G. ‘Pomahaka’), apparently obscured by introgressive mitochondrial capture. We identify additional examples of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries. Our study highlights the need for genome-wide approaches for delimiting freshwater biodiversity. Genetic data also reveal the influence of drainage history on freshwater biodiversity, including the rapid divergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.
Electron-counting MicroED data with the K2 and K3 direct electron detectors
Authors: Clabbers Max T.B. , Martynowycz Michael W. , Hattne Johan , Nannenga Brent L. , Gonen Tamir
Published: July 2022

Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances in hardware as well as methods development, the data quality has continuously improved over the past decade, to the point where even macromolecular structures can be determined ab initio. Detectors suitable for electron diffraction should ideally have fast readout to record data in movie mode, and high sensitivity at low exposure rates to accurately report the intensities. Direct electron detectors are commonly used in cryo-EM imaging for their sensitivity and speed, but despite their availability are generally not used in diffraction. Primary concerns with diffraction experiments are the dynamic range and coincidence loss, which will corrupt the measurement if the flux exceeds the count rate of the detector. Here, we describe instrument setup and low-exposure MicroED data collection in electron-counting mode using K2 and K3 direct electron detectors and show that the integrated intensities can be effectively used to solve structures of two macromolecules between 1.2 Å and 2.8 Å. Even though a beam stop was not used in these studies we did not observe damage to the camera. As these cameras are already available in many cryo-EM facilities, this provides opportunities for users who do not have access to dedicated facilities for MicroED.
Mapping the Spatial Dynamics of the Human Oral Mucosa in Chronic Inflammatory Disease
Authors: Caetano Ana J. , Redhead Yushi , Karim Farah , Dhami Pawan , Kannambath Shichina , Nuamah Rosamond , Volponi Ana A. , Nibali Luigi , Booth Veronica , D’Agostino Eleanor M. , Sharpe Paul T.
Published: July 2022

The interplay among different cells in a tissue is essential for maintaining homeostasis. Although, disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary role of multicellular functions to understand health and disease, opening new avenues to understand pathogenesis and develop new treatment strategies. We recently described the cellular composition and dynamics of the human oral mucosa; however, the spatial arrangement of cells is needed to better understand a morphologically complex tissue. Here, we link single-cell RNA sequencing, spatial transcriptomics, and high-resolution multiplex fluorescence in situ hybridisation to characterise human oral mucosa in health and oral chronic inflammatory disease. We deconvolved expression for resolution enhancement of spatial transcriptomic data and defined highly specialised epithelial and stromal compartments describing location-specific immune programs. Furthermore, we spatially mapped a rare pathogenic fibroblast population localised in a highly immunogenic region, responsible for lymphocyte recruitment through CXCL8 and CXCL10 and with a possible role in pathological angiogenesis through ALOX5AP. Collectively, our study provides a comprehensive reference for the study of oral chronic disease pathogenesis.
EXORIBONUCLEASE4 integrates metabolic signals induced by osmotic stress into the circadian system
Authors: Prasetyaningrum Putri , Litthauer Suzanne , Vegliani Franco , Wood Matthew William , Battle Martin William , Dickson Cathryn , Jones Matthew Alan
Published: July 2022

The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3’-Phospho-Adenosine 5’-Phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of EXORIBONUCLEASEs (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that degradation of specific circadian clock transcripts is modulated by osmotic stress, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms, withLWD1, LWD2, andPRR7identified as specific XRN4 targets that are post-transcriptionally regulated to delay circadian progression.

One Sentence Summary

Post-transcriptional regulation of specific transcripts enables the circadian system to respond to osmotic stress.
Even if suboptimal, novelty drives human exploration
Authors: Modirshanechi Alireza , Lin Wei-Hsiang , Xu He A. , Herzog Michael H. , Gerstner Wulfram
Published: July 2022

Humans successfully explore their environment to find ‘extrinsic’ rewards, even when exploration requires several intermediatereward-freedecisions. It has been hypothesized that ‘intrinsic’ rewards such as novelty guide this reward-free exploration. However, different intrinsic rewards lead to different exploration strategies, some prone to suboptimal attraction to irrelevant stochastic stimuli, sometimes called the ‘noisy TV problem.’ Here, we ask whether humans show a similar attraction to reward-free stochasticity and, if so, which type of intrinsic reward guides their exploration. We design a multi-step decision-making paradigm where human participants search for rewarding states in an environment with a highly stochastic but reward-free sub-region. We show that (i) participants persistently explore the stochastic sub-region and (ii) their decisions are best explained by algorithms driven by novelty but not by ‘optimal’ algorithms driven by information gain. Our results suggest that humans use suboptimal but computationally cheap strategies for exploration in complex environments.
Multivariate versus traditional quantitative phase analysis of X-ray powder diffraction and fluorescence data of mixtures showing preferred orientation and microabsorption
Authors: Lopresti Mattia , Mangolini Beatrice , Milanesio Marco , Caliandro Rocco , Palin Luca
Published: July 2022

In materials and earth science, but also in chemistry, pharmaceutics and engineering, the quantification of elements and crystal phases in solid samples is often essential for a full characterization of materials. The most frequently used techniques for this purpose are X-ray fluorescence (XRF) for elemental analysis and X-ray powder diffraction (XRPD) for phase analysis. In both methods, relations between signal and quantity do exist but they are expressed in terms of complex equations including many parameters related to both sample and instruments, and the dependence on the active element or phase amounts to be determined is convoluted among those parameters. Often real-life samples hold relations not suitable for a direct quantification and, therefore, estimations based only on the values of the relative intensities are affected by large errors. Preferred orientation (PO) and microabsorption (MA) in XRPD cannot usually be avoided, and traditional corrections in Rietveld refinement, such as the Brindley MA correction, are not able, in general, to restore the correct phase quantification. In this work, a multivariate approach, where principal component analysis is exploited alone or combined with regression methods, is used on XRPD profiles collected on ad hoc designed mixtures to face and overcome the typical problems of traditional approaches. Moreover, the partial or no known crystal structure (PONKCS) method was tested on XRPD data, as an example of a hybrid approach between Rietveld and multivariate approaches, to correct for the MA effect. Particular attention is given to the comparison and selection of both method and pre-process, the two key steps for good performance when applying multivariate methods to obtain reliable quantitative estimations from XRPD data, especially when MA and PO are present. A similar approach was tested on XRF data to deal with matrix effects and compared with the more classical fundamental-parameter approach. Finally, useful indications to overcome the difficulties of the general user in managing the parameters for a successful application of multivariate approaches for XRPD and XRF data analysis are given.
Combination of an inject-and-transfer system for serial femtosecond crystallography
Authors: Lee Keondo , Kim Jihan , Baek Sangwon , Park Jaehyun , Park Sehan , Lee Jong-Lam , Chung Wan Kyun , Cho Yunje , Nam Ki Hyun
Published: July 2022

Serial femtosecond crystallography (SFX) enables the determination of room-temperature crystal structures of macromolecules with minimized radiation damage and provides time-resolved molecular dynamics by pump–probe or mix-and-inject experiments. In SFX, a variety of sample delivery methods with unique advantages have been developed and applied. The combination of existing sample delivery methods can enable a new approach to SFX data collection that combines the advantages of the individual methods. This study introduces a combined inject-and-transfer system (BITS) method for sample delivery in SFX experiments: a hybrid injection and fixed-target scanning method. BITS allows for solution samples to be reliably deposited on ultraviolet ozone (UVO)-treated polyimide films, at a minimum flow rate of 0.5 nl min−1, in both vertical and horizontal scanning modes. To utilize BITS in SFX experiments, lysozyme crystal samples were embedded in a viscous lard medium and injected at flow rates of 50–100 nl min−1 through a syringe needle onto a UVO-treated polyimide film, which was mounted on a fixed-target scan stage. The crystal samples deposited on the film were raster scanned with an X-ray free electron laser using a motion stage in both horizontal and vertical directions. Using the BITS method, the room-temperature structure of lysozyme was successfully determined at a resolution of 2.1 Å, and thus BITS could be utilized in future SFX experiments.
Dynamic network analysis of stakeholder-associated social risks of megaprojects: a case study in China
Authors: Xia Xin , Xiang Pengcheng
Published: July 2022

Purpose

Managers of megaprojects face social risk management challenges throughout the various design, construction, and operation stages, owing to the various conflicts of interest among stakeholders, public skepticism, and opposition. However, most existing studies have not focused on the dynamic analysis of integrating social risks in these stages. This study developed a dynamic analysis approach to explore the dynamics of critical social risk factors and related stakeholders of megaprojects and built the managerial maps for various stakeholders.

Design/methodology/approach

Based on the social analysis network (SNA), a dynamic network analysis approach for understanding the dynamics of social risk and related stakeholders has been developed by literature and case analysis. The approach comprises the following steps: (1) generating social risk–stakeholder networks in different stages; (2) analysis of the critical stakeholders and social risk factors; (3) dynamic analysis of social risk factors; and (4) developing social risk management maps for various stakeholders. To verify the feasibility and effectiveness of the approach, 40 megaprojects from China were analyzed.

Findings

According to the results, the local government is a critical stakeholder during all stages, inadequate information promotion (IIP) and imperfect communication and coordination mechanism (ICCM) are key social risk sources throughout the megaproject life cycle. Furthermore, the management maps for government organizations, project implementation groups, and external stakeholders were constructed.

Originality/value

This research has three contributions. First, a dynamic analysis approach of stakeholder-associated social risks in megaprojects is developed, which enriches the social risk management theory of megaprojects and provides inspiration for future research focus. Second, the social risk–stakeholder networks and critical social risks in different stages are confirmed to provide a more valid and accurate picture of social risk management in megaprojects. Third, the social risk managerial maps for different stakeholders built in this research will be beneficial for governments, project implementation groups, and external stakeholders to optimize management strategies.
Feeling torn? The conflicting effects of market and entrepreneurial orientations on manufacturing SMEs' innovation performance
Authors: Kim Hyojin , Hur Daesik
Published: July 2022

Purpose

This study focuses on how a small and medium-sized enterprise's (SME's) main strategic orientation can affect SMEs' approach to innovation. The authors aim to answer the following simple yet important questions: how do SMEs with market orientation (MO) and those with entrepreneurial orientation (EO) differ in terms of innovation performance? Do MO and EO have conflicting effects on the process of innovation at SMEs? If so, how does this conflict affect the innovation performance of SMEs?

Design/methodology/approach

This study explores the effects of MO and EO on different types of technological innovation among SMEs using data collected from 124 INNOBIZ-certified manufacturing SMEs in South Korea. Logistic regression analysis and moderated regression analysis were conducted to test the hypotheses.

Findings

The empirical results demonstrate that MO and EO engender different kinds of technological innovations. MO stimulates “new-to-the-firm” product innovation, while EO drives “new-to-the-industry” innovation in processes and products. Furthermore, SMEs' overall innovation performance will suffer from the conflicting interplay between MO and EO.

Originality/value

The findings of this study encourage SMEs to concentrate SMEs' resources and learning efforts on one specific innovation orientation and only then to develop SMEs' ambidextrous managerial capabilities. This study offers academic contributions in that the study overcomes the limitations of past studies on the strategic orientation of SMEs by empirically confirming the dilemmas faced by SMEs and expands the theoretical understanding of the relationship between MO and EO.
Training students for complex sustainability issues: a literature review on the design of inter- and transdisciplinary higher education
Authors: Horn Annemarie , Scheffelaar Aukelien , Urias Eduardo , Zweekhorst Marjolein B.M.
Published: July 2022

Purpose

To prepare students to address complex sustainability issues, they need to be trained in inter- and transdisciplinarity. This paper aims to contribute to better understanding how to do this, by providing insight into design elements and strategies deployed in inter- and transdisciplinary sustainability education.

Design/methodology/approach

A systematic literature search was conducted to select inter- and transdisciplinary sustainability programmes. Through deductive and inductive qualitative analysis, design elements and strategies were identified and defined.

Findings

Eleven inter- and transdisciplinary programmes were identified. A comprehensive overview of their design elements and strategies is provided. Moreover, three patterns emerged: students were often only involved in the execution, but not in the preparation and evaluation stages of projects, and thus not trained in these; many programmes relied on diverse student representation for interdisciplinary learning and did not explicitly train interdisciplinary integration; and the societal value of transdisciplinary collaboration received little attention in the evaluation of outcomes and impacts.

Research limitations/implications

Follow-up research into the effectiveness of design elements and strategies for inter- and transdisciplinary sustainability education is needed, because the field seems to be understudied.

Practical implications

The comprehensive overview of design elements and strategies for inter- and transdisciplinary sustainability education holds the promise to inform design of novel programmes with similar ambitions. Moreover, the findings urge additional attention for explicitly training interdisciplinary integration and safeguarding the societal value of transdisciplinarity.

Originality/value

This review presents new insights into strategies and design elements for inter- and transdisciplinary sustainability education.
Alkem Laboratories: managing employee motivation during pandemics
Authors: Sarangi Subrat , Priyadarshi Ashok , Chalil Gloryson R.B. , Panda Rasananda
Published: July 2022

Theoretical basis

The case dwells with the following theoretical concepts: Appreciate the different need dimensions required to motivate different employee types based on need theory (Alderfer, 1969). Identify the functional needs as per Maslow’s need hierarchy (Hall & Naougaim, 1968) for the permanent and contractual workers. Outline why only hygiene factors are insufficient to arrest worker absenteeism during a pandemic like COVID-19. Apply need theory and “Herzberg’s two-factor theory” (Herzberg, 1966; Herzberg et al., 1957) to enumerate the measures that need to be implemented to build supply chain resilience by reducing absenteeism by motivating employees.

Research methodology

The case is based on primary research carried out by the authors at Alkem Laboratories Ltd., Sikkim unit in India, during the COVID-19 pandemic that hit the company leading to high absenteeism of contractual workers.

Case overview/Synopsis

Alkem Laboratories Ltd. is a leading pharma major from India with a global footprint. At the break of COVID-19 pandemic, the manufacturing unit of the company at Sikkim is facing the scare of mass absenteeism, especially among the contractual workers who account for 60% of the workforce of the unit. Ashok Priyadarshi (Vice President, Human Resources) and his team along with the think tank of the unit have to find a solution to the problem at hand. What shall be the measures that the think tank will propose? The team sets out to find an answer to these questions so that Alkem could seize the business opportunity at the wake of the COVID-19 pandemic.

Complexity academic level

The case is suitable for undergraduate- and graduate-level courses in organizational behavior, organizational change and development and supply chain risk management. The case can also be positioned for executive education and training modules in companies on employee motivation and commitment.
Thermoregulatory opportunity and competition act independently on life‐history traits in aquatic ectotherms
Authors: Gvoždík Lumír
Published: July 2022

Many ectothermic species use behavioural thermoregulation to reduce their exposure to climate change. The buffering effect of behavioural thermoregulation will depend on the time available for an ectotherm to attain a body temperature within the target range, that is, the ‘opportunity for thermoregulation’. Behavioural thermoregulation can be further altered by the presence of competitors. Spatiotemporal dynamics in opportunity for thermoregulation and competition intensity should affect variation in ectotherm life history and fitness; however, experimental support for their joint influence is missing.

I tested this prediction in a mesocosm experiment using larvae of two sympatric amphibians, the alpine newt Ichthyosaura alpestris and the common newt Lissotriton vulgaris. Thermoregulatory opportunities and competition intensities were manipulated by exposing larvae to warmer temperatures and altering densities of con‐ and heterospecifics. Life‐history traits were monitored until metamorphic emergence from the water.

Thermoregulatory opportunity accelerated differentiation rate and time to metamorphic emergence, while both intra‐ and interspecific competition affected growth rate and mass at emergence. The impact of competition on survival and injury rates varied between taxa.

Thermoregulatory opportunity and competition impacted larval life‐history traits in an additive fashion. Suitable conditions for thermoregulation allowed larvae to shorten their developmental period, and thus escape from the aquatic environment earlier than in thermoregulatory challenging environment. Competition was a primary determinant of mass at emergence, which is an important fitness correlate in amphibians. Species‐specific survival under competition may contribute to variation in habitat requirements between sympatric taxa.

To sum up, predictions on the impact of climate change on ectotherm life histories require information not only about environmental temperatures, but also about species thermoregulatory opportunities and competitive abilities. Thermoregulatory opportunity is an ecologically relevant habitat property not only for basking ectotherms but also for taxa using less conspicuous thermoregulatory adjustments. The influence of thermoregulatory opportunity and competitive interactions on life histories varies among traits, indicating the need for a multi‐trait approach for understanding the complex influences of environmental change on ectotherm population dynamics and species interactions.

Read the free Plain Language Summary for this article on the Journal blog.
Improving electrodialysis separation efficiency of minerals from acid whey by nano‐filtration pre‐processing
Authors: Nielsen Emilie N , Skibsted Leif H , Yazdi Saeed R , Merkel Arthur , Ahrné Lilia M
Published: July 2022

Acid whey (AW) contains valuable minerals, such as calcium and magnesium. Electrodialysis (ED) is an efficient technology to recover these minerals; however, the less nutritional sodium will also be recovered during ED. AW was processed by nanofiltration prior to ED in order to change the ratio between the monovalent and divalent ions. The nano‐filtration increased the efficiency of the ED process regarding recovery of Ca2+ and Mg2+ ions by 70% and 67%, respectively, while it did not affect the K+, Na+, phosphates and lactate. The spent energy was more effectively used to recover Ca2+ in the nano‐filtrated AW.
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity
Authors: Yu Xiang‐Qin , Jiang Yin‐Zi , Folk Ryan A. , Zhao Jian‐Li , Fu Chao‐Nan , Fang Liang , Peng Hua , Yang Jun‐Bo , Yang Shi‐Xiong
Published: July 2022

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as “super‐barcodes,” might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super‐barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super‐barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH‐psbA, nrITS) and super‐barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned data sets—the lowest estimated rate of super‐barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super‐barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multilocus nuclear markers for species discrimination in plant groups.
Non‐invasive prediction of histologic chorioamnionitis using maternal serum markers in women with preterm prelabour rupture of membranes
Authors: Shi Haoning , Sun Lingling , Wang Zhenjie , Zhang Aimei , Cao Huaiming , Zhao Wanying , Wang Hongyu , Yang Xiao , Li Jing
Published: July 2022

Problem

This study aimed to evaluate and compare the predictive accuracy of serum markers for histological chorioamnionitis (HCA) among women with preterm prelabour rupture of membranes (PPROM), and to develop a nomogram prediction model to minimize the damage of the disease.

Method of Study

This case‐control study included 153 pregnant women with PPROM with a gestational age of 20+0∼36+6 weeks. The subjects were assigned into two groups: PPROM with and without HCA. According to the results of logistic regression analysis, the predictive equation and nomogram were generated using key parameters, and the discrimination and consistency of the model were evaluated by receiver operating characteristic (ROC) curves and calibration curves.

Results

From 153 subjects with PPROM, 77 developed HCA. Compared with the PPROM without HCA group, the CRP, PCT and NLR were significantly higher in HCA group (P < 0.001), and the CRP had the highest predictive value. The area under the curve (AUC) of the prediction model was 0.873, and the sensitivity and specificity of predicting HCA were 68.8% and 92.1%, respectively. And the calibration curves fitted well with the realistic situation.

Conclusion

Maternal serum CRP and NLR could be used as predictive biomarkers for HCA in women with PPROM, while PCT needs to be further explored due to its slightly lower predictive value. Our serum markers and gestational age at PPROM could be used as a non‐invasive and convenient method to predict HCA in women with PPROM.
Impact of thiopurines and tumour necrosis factor antagonists on primary sclerosing cholangitis outcomes in patients with inflammatory bowel disease
Authors: Biron Amélie , Beaugerie Laurent , Chazouillères Olivier , Kirchgesner Julien
Published: July 2022

Background

Patients with primary sclerosing cholangitis (PSC) and inflammatory bowel disease (IBD) are at risk of biliary tract cancer and liver damage (possibly leading to liver transplantation), and are often treated for IBD with thiopurines and/or tumour necrosis factor antagonists (anti‐TNF) on a long‐term basis.

Aims

To assess the risk of biliary tract cancer and liver transplantation in patients exposed to thiopurines and/or anti TNF agents in a French nationwide cohort.

Methods

We performed a population‐based study of patients aged 18 years or older with PSC and IBD in the French national health insurance database. Patients were followed from 1 January 2009 to 31 December 2018. The risks of biliary tract cancer and liver transplantation associated with thiopurines and anti‐TNF exposure were assessed with marginal structural Cox proportional hazard models, adjusting for baseline demographics and comorbidities, and time‐varying medications and PSC activity.

Results

Among the 1929 patients with PSC and IBD included, 37 biliary tract cancers and 83 liver transplantations occurred. Compared with patients not exposed to thiopurines or anti‐TNF agents, patients exposed to thiopurines (hazard ratio [HR], 1.05; 95% confidence interval [CI], 0.39–2.82) or anti‐TNF agents (HR, 0.59; 95% CI, 0.13–2.80) had no excess risk of biliary tract cancer. Similarly, patients exposed to thiopurines (HR, 0.67; 95% CI, 0.30–1.48) or anti‐TNF agents (HR, 0.68; CI, 0.22–2.09) had no excess risk of liver transplantation.

Conclusions

Patients with PSC and IBD who are exposed to thiopurines or anti‐TNF agents are not at excess risk of biliary tract cancer or liver transplantation.
Infinite Hidden Markov Models for Multiple Multivariate Time Series with Missing Data
Authors: Hoskovec Lauren , Koslovsky Matthew D. , Koehler Kirsten , Good Nicholas , Peel Jennifer L. , Volckens John , Wilson Ander
Published: July 2022

Exposure to air pollution is associated with increased morbidity and mortality. Recent technological advancements permit the collection of time-resolved personal exposure data. Such data are often incomplete with missing observations and exposures below the limit of detection, which limit their use in health effects studies. In this paper, we develop an infinite hidden Markov model for multiple asynchronous multivariate time series with missing data. Our model is designed to include covariates that can inform transitions among hidden states. We implement beam sampling, a combination of slice sampling and dynamic programming, to sample the hidden states, and a Bayesian multiple imputation algorithm to impute missing data. In simulation studies, our model excels in estimating hidden states and state-specific means and imputing observations that are missing at random or below the limit of detection. We validate our imputation approach on data from the Fort Collins Commuter Study. We show that the estimated hidden states improve imputations for data that are missing at random compared to existing approaches. In a case study of the Fort Collins Commuter Study, we describe the inferential gains obtained from our model including improved imputation of missing data and the ability to identify shared patterns in activity and exposure among repeated sampling days for individuals and among distinct individuals.
Bread loaf sections provide useful information on more than 0·5% of surgical margins
Authors: Warne Melissa M. , Klawonn Matthew M. , Brodell Robert T.
Published: July 2022

It is often quoted that classic bread-loaf sectioning of excisional specimens assesses 0.5% of the margin, but careful mathematical analysis reveals that bread-loaf sectioning appraises far more than that and is an effective and economical means to check margins.
Low‐temperature thermal history of the McArthur Basin: Influence of the Cambrian Kalkarindji Large Igneous Province on hydrocarbon maturation
Authors: Nixon Angus L. , Glorie Stijn , Hasterok Derrick , Collins Alan S. , Fernie Nicholas , Fraser Geoffrey
Published: July 2022

The McArthur Basin of the North Australian Craton is one of the very few places on Earth where extensive hydrocarbons are preserved that were generated from Mesoproterozoic source rocks, prior to the development of extensive multicellular life. It is, however, unclear precisely when hydrocarbons from these source rocks matured, and if this occurred as a singular event or multiple phases. In this study, we present new apatite fission track data from a combination of outcrop and sub‐surface samples from the McArthur Basin to investigate the post‐depositional thermal history of the basin, and to explore the timing of hydrocarbon maturation. Apatite fission track data and thermal modelling suggest that the McArthur Basin experienced a basin‐wide reheating event contemporaneous with the eruption of the Cambrian Kalkarindji Large Igneous Province in the North and West Australian cratons, during which thick (>500 m) basaltic flows blanketed the basin surface. Reheating at ca. 510 Ma coinciding with Kalkarindji volcanism is consistent with a proposed timing of elevated hydrocarbon maturation, particularly in the Beetaloo Sub‐basin, and provides a mechanism for petroleum generation throughout the basin. Subsequent regional cooling was slow and gradual, most likely facilitated by gentle erosion (ca. 0.01–0.006 km/Ma) of overlying Georgina Basin sediments in the Devonian–Carboniferous with little structural reactivation. This model provides a framework in which hydrocarbons, sourced from Mesoproterozoic carbon‐rich rocks, may have experienced thermal maturation much later in the Cambrian. Preservation of these hydrocarbons was aided by a lack of widespread structural exhumation following this event.
A Thousand Days—A programme for vulnerable early childhood in Argentina: Targeting, dropout risk factors and correlates of time to graduation
Authors: Gonzalez Maria Sol , Santos Maria Emma
Published: July 2022

Background

Mil Días (A Thousand Days) is a programme for the first thousand days of life, from gestation to 2 years of age, targeted at highly vulnerable children and/or mothers and pregnant women. The programme was implemented in August 2015 in the municipality of San Miguel, in Argentina. Mil Días is designed in a holistic and intersectoral way. The main form of intervention is through home visits, but other benefits are available depending on the 51 vulnerability criteria by which participants are admitted to the programme, most of which are related to health issues. Exits of the programme occur when the mother and/or child have reversed the deprivation/s of the entrance‐criteria.

Methods

This paper provides an analysis of the programme's primary data between August 2015 and May 2019, with a total of 1,111 programme participants. First, we perform a statistical analysis of the targeted population of the programme. Second, using a logistic regression, we study factors associated to the withdrawal from the programme. Third, using survival analysis, we study the correlates of time to graduation from the programme.

Results

We find that the programme is well‐targeted, as participants exhibit higher deprivation levels than those exhibited by beneficiaries of social programmes in general in the same municipality. We also find that programme participants in situations of most extreme vulnerability are more likely to abandon the programme and that successful exits from the programme take longer for more complex cases.

Conclusions

Mil Días–San Miguel is a programme for early childhood development in Argentina, which was pioneer when it was first introduced. It is well targeted and exhibits encouraging results despite complex cases taking longer to sucessfully exit the programme. In addition, the poorest poor participants are more likely to abandon the programme and so additional actions could be taken to retain them, as intended by the ‘Leave No One Behind’ 2030 commitment.
Iodine status in Danish pregnant women after an increase in iodine fortification
Authors: Knøsgaard Louise , Andersen Stig , Hansen Annebirthe Bo , Sørensen Anne , Vestergaard Peter , Andersen Stine Linding
Published: July 2022

Objective

Iodine fortification programmes are implemented in many countries and often associated with an increase in population iodine intake. However, the initial attempt may not be sufficient and in Denmark the level of iodine added to salt was increased in 2019. Sparse evidence is available on the impact of such modification in iodine fortification. The aim of this study was to evaluate iodine status in Danish pregnant women in 2021 after this increase in iodine fortification and compare to iodine status in 2012.

Design

Cross‐sectional study.

Patients

Pregnant women in the North Denmark Region referred for routine obstetric ultrasound in 2021.

Measurements

Participants filled out a questionnaire and delivered a spot urine. Median urinary iodine concentration (UIC) was calculated and assessed according to the recommended range in pregnancy (150–249 µg/L).

Results

Altogether 147 pregnant women were included and 88% used iodine‐containing supplements. Median UIC was overall 77 µg/L [95% confidence interval (CI): 61–96 µg/L], which was lower than in 2012 (101 µg/L [95% CI: 89–111 µg/L]) (p < 0.001). Considering sources of iodine intake in pregnancy, lower daily intake of dairy products (p = 0.008) and bread (p < 0.001) and a lower content of iodine in the supplement used (p < 0.001) was seen in 2021 compared to 2012.

Conclusion

Despite an increase in iodine fortification and frequent use of iodine‐containing supplements, iodine status in pregnant women in the North Denmark Region was insufficient. Results call for continued monitoring and attention to ensure adequate iodine status during pregnancy in Denmark.
Diabetes self‐management during the COVID‐19 pandemic and its associations with COVID‐19 anxiety syndrome, depression and health anxiety
Authors: Distaso Walter , Malik Mohammad M.A.H. , Semere Saba , AlHakami Amal , Alexander Emma C. , Hirani Dhruti , Shah Ronak J. , Suba Kinga , McKechnie Vicky , Nikčević Ana , Oliver Nick , Spada Marcantonio , Salem Victoria
Published: July 2022

Introduction

The effects of the COVID‐19 pandemic on mental health have been profound. Mental health and diabetes self‐care are inter‐related. We examined whether COVID‐19 anxiety, depressive symptoms and health anxiety were associated with domains of diabetes self‐management and investigated whether greater COVID‐19 anxiety syndrome would independently contribute to suboptimal diabetes self‐care.

Research design and methods

Surveys were sent to people attending diabetes clinics of three London hospitals. Participants completed the Diabetes Self‐Management Questionnaire (DSMQ), the COVID‐19 Anxiety Syndrome Scale (C‐19 ASS), which measures perseveration and avoidant maladaptive coping behaviour, assessed with measures of co‐existent depressive symptoms and anxiety, controlling for age, gender and social deprivation. Clinical data, including pre‐ and post‐lockdown HbA1c measures, were obtained from hospital records for 369 respondents, a response rate of 12.8%.

Results

Depressive symptom scores were high. Both pre‐existing health anxiety and depressive symptoms were independently linked to improvable measures of diabetes care, as was lower socio‐economic rank. However, avoidant COVID‐19 anxiety responses were independently associated with higher diabetes self‐care scores. HbA1c levels improved modestly over the year of UK lockdown in this cohort.

Conclusion

During the height of lockdown, avoidant coping behaviours characteristic of the COVID‐19 anxiety syndrome may in fact work to improve diabetes self‐care, at least in the short term. We recommend screening for depressive symptoms and being aware of the significant minority of people with COVID‐19 anxiety syndrome who may now find it difficult to re‐engage with face‐to‐face clinic opportunities.
Banting memorial lecture 2022: ‘Type 2 diabetes and nonalcoholic fatty liver disease: Partners in crime’
Authors: Byrne Christopher D.
Published: July 2022

Nonalcoholic fatty liver disease (NAFLD) was first described in the 1980s, but in the 21st century, NAFLD has become a very common condition. The explanation for this relatively recent problem is in large part due to the recent epidemic of obesity and type 2 diabetes (T2DM) increasing the risk of NAFLD. NAFLD is a silent condition that may not become manifest until severe liver damage (fibrosis or cirrhosis) has occurred. Consequently, NAFLD and its complications often remain undiagnosed. Research evidence shows that NAFLD is extremely common and some estimates suggest that it occurs in up to 70% of people with T2DM. In the last 5 years, it has become evident that NAFLD not only increases the risk of cirrhosis, primary liver cancer and end‐stage liver disease, but NAFLD is also an important multisystem disease that has major implications beyond the liver. NAFLD increases the risk of incident T2DM, cardiovascular disease, chronic kidney disease and certain extra‐hepatic cancers, and NAFLD and T2DM form part of a vicious spiral of worsening diseases, where one condition affects the other and vice versa. Diabetes markedly increases the risk of liver fibrosis and liver fibrosis is the most important risk factor for hepatocellular carcinoma. It is now possible to diagnose liver fibrosis with non‐invasive tools and therefore it is important to have clear care pathways for the management of NAFLD in patients with T2DM. This review summarises key recent research that was discussed as part of the Banting lecture at the annual scientific conference in 2022.