bluuebunny/crossref_metadata_2025 huggingface dataset:
Eukaryotic cell walls
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter describes plant cell walls as the best studied of the eukaryotic types, which consist of three basic layers: middle lamella, primary cell wall, and secondary cell wall. It clarifies that plant cells are glued together by a middle lamella, which separates their walls, and within the middle lamella is a primary cell wall. It also examines cellulose, which is the major carbohydrate of most plant cell walls and is the most abundant carbohydrate on earth. The chapter discusses algal cell walls that display an incredibly diverse composition and contain cellulose microfibrils and mannose or xylan-rich carbohydrates. It refers to filamentous fungal cell walls which are composed mainly of the polysaccharides glucans, chitin, and glycoproteins.
Extracellular matrix and connective tissues
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter highlights the extracellular matrix (ECM), which is the ground substance or connective tissue surrounding animal cells. Its thickness varies from being very thin between hepatocytes to the much thicker areolar connective tissue. The chapter describes fibroblasts, Macrophages and mast cells, adipose cells, and mesenchymal stem cells as the resident cell population of the ECM. It also covers major glycoproteins and proteins present in ECM, such as proteoglycans, collagens, elastins, fibronectins, and laminins. The chapter illustrates the proportion of the different components of the ECM and states that this varies enormously between distinct types of connective tissues, which connect other tissues and organs together. It cites two major groups of connective tissues which arise from the mesoderm of the embryo: general connective tissues and specialized connective tissues.
The Analyst’s Toolbox
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter emphasizes the importance of knowing and appreciating the various strengths and limitations of various techniques used for analysis. It focuses on instrumental methods which stem from endeavours to extend the human senses, describing a fairly large range of instruments and the methods associated with each. It also profiles five important types of techniques and instruments that are applied to the majority of problems or applications in chemistry. The chapter introduces ultraviolet-visible (UV-vis) spectroscopy, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance spectrometry (NMR), mass spectrometry (MS), and chromatography (liquid chromatography [LC] and gas chromatography [GC]). It explains how spectrometric methods extend one's ability to see molecules and detect molecular interactions that are outside normal human senses, while chromatography deals with the efficient separation of components of a mixture.
An Introduction to Optics
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter reviews the claim that diffraction grating is the most important optical component used in optical spectrophotometers as it gives the chemist the ability to discriminate among the different energies of light. It describes an instrument wherein the incident light on the grating may be the signal from a spectrophotometer, causing the diffraction grating to select a specific energy of light to send onto a detector. It also determines important “workhorse” instrumental techniques and specialized techniques that involve the interaction of matter and electromagnetic radiation or light. The chapter looks at optical components used to control the direction, power, and wavelength of electromagnetic radiation. It highlights how different optical processes may lead to a decrease or an increase in the level of an optical signal.
An Introduction to Instrumental Electronics
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter states that the core of every instrumental technique is the measurement of either voltage or current. It examines basic electronic components typically found in modern scientific instrumentation and provides a launch point for those who wish to learn more about instrumental electronics. It also examines the importance of understanding electronics as that helps us to diagnose instrument problems and also fosters innovative instrument design. Examples of this include electronics associated with chemical instrumentation. The chapter refers to basic passive electrical components: the resistor, capacitor, and inductor. These do not add energy to the electronic system. The chapter covers other components of instrumentation, such as diodes, transistors, operational amplifiers, and integrated circuits (ICs).
Atomic Absorption Spectroscopy
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter reviews atomic absorption spectroscopy (AAS), which is an elemental analysis technique used to identify and quantify the elements present in a sample matrix. It states that AAS is fundamentally a form of ultraviolet-visible (UV-vis) absorption spectroscopy that requires the analyte to be first converted to atomic vapour prior to analysis. It also explains how AAS is used to quantify the elemental contents of a sample matrix rather than a tool used to probe the molecular nature of a pure analyte. The chapter highlights the utility of AAS in its capacity for elemental determination within complex matrices such as soil, water, petroleum, plastics, paint, and plant and animal tissue without the need to isolate or purify the analyte from the matrix. The chapter determines a basic block schematic of an AAS that looks similar to a basic block schematic of a UV-vis spectrometer.
Infrared Spectroscopy
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter focuses on infrared (IR) spectroscopy, which is used to probe molecular vibrational modes and gives substantive insight into the molecular structure of the analyte. It explains that a vibrational mode is a unique vibration within a molecule in which all atoms involved in the vibration have a sinusoidal motion and the motion of all of the atoms shares the same phase. It also considers the determination of the types of bonds that exist within a molecule as one of the main uses of IR spectroscopy. The chapter highlights the three regions of the IR spectrum: near-IR, mid-IR, and far-IR, which are named based on their anthropocentric relationship to the human eye's lower detection limit. It draws attention to mid-IR radiation, which is used to probe the primary vibrational modes associated with the bonds within a molecule.
Liquid Chromatography
Authors: Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D. , Granger Robert M. , Yochum Hank M. , Granger Jill N. , Sienerth Karl D.
Published: September 2023

This chapter examines liquid chromatography (LC) and lays out the fundamental theory involved. It describes a sample in LC, which is dissolved in a solvent called the mobile phase. Then the solvent carries the sample into the stationary phase. It also details how the mobile phase flows through the stationary phase, noting the various components of the sample that are distributed between the immobile stationary phase and the flowing mobile phase. The chapter covers instrumental considerations that provide for high performance, high resolution, and the automation of modern LC. It looks at ways in which LC separations can be accomplished and determines how to take advantage of various physical and chemical characteristics to distinguish one component from another.
Herpetology
Authors: Pough F. Harvey , Andrews Robin M. , Crump Martha L. , Savitzky Alan H. , Wells Kentwood D. , Brandley Matthew C.
Published: September 2023

Herpetology explains why amphibians and reptiles, which are distantly related evolutionary lineages, are grouped in the discipline known as herpetology, and describes the position of amphibians and reptiles within the evolution of vertebrates. Part I asks, what are amphibians and reptiles? It considers the origins, systematics, and diversity of amphibians and reptiles. Part II looks at the way that amphibians and reptiles actually function. It looks at reproduction and feeding. The third part questions what amphibians and reptiles do? It looks at how they communicate, mate, and at their diets. The last part looks to the future, considering the conservation of amphibians and reptiles and their prospects for survival.
Methods and Principles of Biological Systematics
Authors: Judd Walter S. , Campbell Christopher S. , Kellogg Elizabeth A. , Stevens Peter F. , Donoghue Michael J.
Published: September 2023

This chapter provides a background on biological systematics which focuses on the discovery of phylogeny and how phylogenies can be used to understand the processes underlying diversification. The chapter outlines how to determine the history of a group and discusses how this history can be used to uncover patterns of diversification and to construct a form of classification. Phylogeny can be understood as the history of DNA molecules: DNA replicates in a semi-conservative fashion to produce two daughter molecules that replicate again to produce their own two daughter molecules — a process that goes back to the beginning of life on Earth. This DNA replication process is diagrammed in phylogenetic trees to show ancestor-descendant relationships and trace the history of life. This chapter introduces these trees and analyzes the shape or topology of the trees that is determined by the connections between the branches that can be rotated around the nodes.
Lycophytes, Ferns, and Gymnosperms
Authors: Judd Walter S. , Campbell Christopher S. , Kellogg Elizabeth A. , Stevens Peter F. , Donoghue Michael J.
Published: September 2023

This chapter surveys the diversity of living tracheophytes, clarifying the term tracheo. This term refers to the presence of tracheids, and the Greek root part of the word phyte means plant. The chapter also explains how tracheophytes form a well-supported monophyletic group of generally large plants with branched sporophyte axes and well-developed tissues for the transport of water and carbohydrates within the plant. It also talks about a major clade within embryophytes. These are formed by tracheophytes, and are nested within the paraphyletic “bryophytes.” The chapter examines two major lineages within tracheophytes: lycophytes and euphyllophytes. It refers to the gymnosperm, in which seeds are not enclosed in a protective structure but may sometimes be enclosed at maturity by fused cone scales or bracts.
Plants in Human Nutrition, Diet, and Health
Authors: Chrispeels Maarten J.
Published: September 2023

This chapter looks at food not from a production standpoint, but from the point of view of human nutrition. It describes nutritional biochemistry in terms of some familiar molecules: carbohydrates, fats, proteins, and vitamins. In addition to being the ultimate source of all our food, plants also contain non-nutritive molecules that affect other organisms by defending the plants against herbivory or attracting pollinators. The chapter then considers the consequences of nutritional deficiencies, before exploring organically grown plants. Although humans are omnivores, millions of vegetarians and vegans attest to the fact that animal foods are not essential to our health. The chapter also studies how the intestinal microbiome significantly influences human health.
Plant Propagationby Seeds and Vegetative Processes
Authors: Bradford Kent J. , Chrispeels Maarten J.
Published: September 2023

This chapter describes plant propagation by seeds and vegetative processes. Plants propagate both sexually and asexually (vegetatively) and people exploit both types for plant propagation. The chapter looks at seed germination, seedling establishment, and seed treatments. Seedling establishment in the field is an important agronomic variable for crop-production; sowing healthy seeds at the right time ensures a good stand of the crop. To improve seed germination and crop growth, seeds are coated with chemicals to prevent diseases. The chapter then considers the role of seed banks in preserving the genetic diversity of crops, before studying micropropagation, grafting, and apomixis. Understanding the genetic control of apomixis could result in significant breakthroughs in crop improvement.
Plant Diseases and Strategies for Their Control
Authors: Bent Andrew F.
Published: September 2023

This chapter discusses plant diseases caused by viruses, bacteria, fungi, and oomycetes, and explains how understanding the mechanisms of these diseases can be used to breed more durable resistance into crops. Genetic diversity of a crop species can minimize the threat of severe disease epidemics. Disease problems can be reduced by plant cultivation practices such as crop rotation or altered irrigation, by use of fungicides and other chemicals, and especially by planting disease-resistant plant varieties. The chapter then looks at how plants have a sensitive pathogen-detection system — the innate immune system — that allows early and strong activation of defenses. It also considers how molecular biologists use genetic engineering to protect plants from pathogens. A particularly effective method is called HIGS or host-induced gene silencing.
Challenges and Solutions for Subsistence Farmers
Authors: Raizada Manish N.
Published: September 2023

This chapter studies the challenges and solutions for subsistence farmers. Subsistence farmers in the subtropics suffer from low food production and malnutrition in the dry season. In order to increase their resiliency, subsistence farmers often cultivate a diversity of crops. Opportunities exist to improve crop yields through breeding and agronomic improvements to the cropping system, leading to agricultural intensification. Other crucial constraints on smallhold farmers include lack of precipitation, infertile or degraded soils, and soil erosion. The chapter then looks at weed and pest control, as well as postharvest food processing. Ultimately, lessons may be learned from the success of agriculture in developed nations which transformed from subsistence farming to wealth through a partnership between the private sector that sold a menu of innovative products and publicly funded agricultural extension to train farmers on a menu of best practices.
Photosynthesis and Light
Authors: Gurevitch Jessica , Scheiner Samuel M. , Fox Gordon A.
Published: September 2023

This chapter begins by looking at the interactions plants make with their environment by considering the process by which plants acquire energy and carbon: photosynthesis. It examines how plants capture the energy of sunlight and incorporate carbon from the atmosphere in photosynthesis, their adaptations to the light environment, their water relations, and the mineral nutrients they get from the soil. These processes in turn can play out at the larger scope of ecosystem processes. The chapter also takes a look at the structures in which some of these processes take place and some of the biochemistry involved. It focuses first on processes occurring at the small scale of a cell, a leaf, or an individual plant. Finally, the chapter considers the importance of the forest, where plants have evolved and live in an ecological context. It studies the physical conditions that a plant experiences, determined by the physical features of the environment and by other living organisms in that habitat.
Successful treatment with belimumab for immune thrombocytopenia associated with systemic lupus erythematosus: A report of two cases
Authors: Nakayama Kyohei , Tamimoto Yasuhiro , Nakayama Tsuyoshi
Published: September 2023

Immune thrombocytopenia (ITP) is a common complication of systemic lupus erythematosus (SLE). Glucocorticoids (GCs) and hydroxychloroquine are first-line therapy for SLE-associated ITP (SLE-ITP). SLE-ITP in most of patients is less severe and well controlled with GCs, but some of the patients are GC resistant and require additional immunosuppressants including calcineurin inhibitors, azathioprine, and rituximab. We present two cases of SLE-ITP patients treated with belimumab who were resistant to GCs and achieved remission. For severe SLE-ITP, belimumab has emerged as a novel induction therapeutic option.
An approach for determining the reliability of manual and digital scoring of sleep stages
Authors: Gerardy Bethany , Kuna Samuel T , Pack Allan , Kushida Clete A , Walsh James K , Staley Bethany , Pien Grace W , Younes Magdy
Published: September 2023

Study Objectives

Inter-scorer variability in sleep staging is largely due to equivocal epochs that contain features of more than one stage. We propose an approach that recognizes the existence of equivocal epochs and evaluates scorers accordingly.

Methods

Epoch-by-epoch staging was performed on 70 polysomnograms by six qualified technologists and by a digital system (Michele Sleep Scoring [MSS]). Probability that epochs assigned the same stage by only two of the six technologists (minority score) resulted from random occurrence of two errors was calculated and found to be <5%, thereby indicating that the stage assigned is an acceptable variant for the epoch. Acceptable stages were identified in each epoch as stages assigned by at least two technologists. Percent agreement between each technologist and the other five technologists, acting as judges, was determined. Agreement was considered to exist if the stage assigned by the tested scorer was one of the acceptable stages for the epoch. Stage assigned by MSS was likewise considered in agreement if included in the acceptable stages made by the technologists.

Results

Agreement of technologists tested against five qualified judges increased from 80.8% (range 70.5%–86.4% among technologists) when using the majority rule, to 96.1 (89.8%–98.5%) by the proposed approach. Agreement between unedited MSS and same judges was 90.0% and increased to 92.1% after brief editing.

Conclusions

Accounting for equivocal epochs provides a more accurate estimate of a scorer’s (human or digital) competence in scoring sleep stages and reduces inter-scorer disagreements. The proposed approach can be implemented in sleep-scoring training and accreditation programs.
Management of Retinitis Pigmentosa Via Wharton’s Jelly-Derived Mesenchymal Stem Cells or Combination With Magnovision: 3-Year Prospective Results
Authors: Ozmert Emin , Arslan Umut
Published: September 2023

To investigate whether the natural progression rate of retinitis pigmentosa (RP) can be decreased with subtenon Wharton’s jelly-derived mesenchymal stem cell (WJ-MSC) application alone or combination with Magnovision.

The study included prospective analysis of 130 eyes of 80 retinitis pigmentosa patients with a 36-month follow-up duration. Patients constitute 4 groups with similar demographic characteristics. The subtenon WJ-MSC-only group consisted of 34 eyes of 32 RP patients as Group 1; the Magnovision-only group consisted of 32 eyes of 16 RP patients as Group 2; the combined management group consisted of 32 eyes of 16 RP patients who received combined WJ-MSC and Magnovision as Group 3; the natural course (control) group consisted of 32 eyes of 16 RP patients who did not receive any treatment were classified as Group 4. Fundus autofluorescence surface area (FAF-field), horizontal and vertical ellipsoid zone width (EZW), fundus perimetry deviation index (FPDI), full-field electroretinography magnitude (ERG-m), and best corrected visual acuity (BCVA) changes were compared within and between groups after 36 months follow up period.

FAF-field delta changes were detected 0.39 mm2 in Group 1, 1.50 mm2 in Group 2, 0.07 mm2 in Group 3 and 12.04 mm2 in Group 4 (Δp 4 > 2 > 1 > 3). Horizontal EZW, Vertical EZW, BCVA, and FPDI delta changes were detected Δp 4 > 1,2 > 3. ERG-m delta changes were detected Δp 3 > 1,2,4.

Retinitis pigmentosa characterized by progressive loss of photoreceptors eventually leading to total blindness. The combination of WJ-MSC and Magnovision can significantly slow the progression of the disease in comparison to natural progression rate for 3 years in appropriate cases.

Trial Registration: ClinicalTrials.gov, NCT05800301.
Examining associations between school-level determinants and the implementation of physical activity opportunities
Authors: Craig Derek W , Walker Timothy J , Sharma Shreela V , Cuccaro Paula , Heredia Natalia I , Pavlovic Andjelka , DeFina Laura F , Kohl Harold W , Fernandez Maria E
Published: September 2023

School-based physical activity (PA) opportunities can help students engage in greater amounts of daily PA, meet PA guidelines, and lead to improved health and educational outcomes. However, we do not completely understand the organizational challenges to implementing these opportunities successfully. This exploratory study examined associations between school-level determinants and the implementation of school-based PA opportunities. We analyzed cross-sectional survey data from schools (n = 46) participating in the Healthy Zone School Program (HZSP) (Dallas, Texas, USA) during 2019–2020. Respondents completed an electronic survey that included measures of school-level determinants (e.g. culture, leadership, priority) and the implementation of school-based PA opportunities. We used linear regression models to examine associations between determinants and implementation outcomes (number of PA opportunities delivered, perceived overall success of each PA program/activity used). After adjusting for campus type (i.e. elementary, middle, high, K-12), student race/ethnicity, and percentage of economically disadvantaged students, no constructs were associated with the number of PA opportunities implemented. Linear regression models suggest access to knowledge and information (β = 0.39, P = .012, 95% CI = 0.24–1.44) and implementation climate (β = 0.34, P = .045, 95% CI = 0.02–1.59) were positively associated with the success of school-based PA opportunities. Our findings provide suggestive evidence that access to knowledge and information and a supportive school climate may improve the overall success of PA opportunities provided to students. Future research should examine additional school-level determinants to understand their importance to implementation and inform the development of strategies to improve schools’ capacity for implementing PA opportunities successfully.
Discovery medicine – the HVTN's iterative approach to developing an HIV-1 broadly neutralizing vaccine
Authors: Martin Troy M. , Robinson Sam T. , Huang Yunda
Published: September 2023

Purpose of review

In the past two decades, there has been an explosion in the discovery of HIV-1 broadly neutralizing antibodies (bnAbs) and associated vaccine strategies to induce them. This abundance of approaches necessitates a system that accurately and expeditiously identifies the most promising regimens. We herein briefly review the background science of bnAbs, provide a description of the first round of phase 1 discovery medicine studies, and suggest an approach to integrate these into a comprehensive HIV-1-neutralizing vaccine.

Recent findings

With recent preclinical success including induction of early stage bnAbs in mouse knockin models and rhesus macaques, successful priming of VRC01-class bnAbs with eOD-GT8 in a recent study in humans, and proof-of-concept that intravenous infusion of VRC01 prevents sexual transmission of virus in humans, the stage is set for a broad and comprehensive bnAb vaccine program. Leveraging significant advances in protein nanoparticle science, mRNA technology, adjuvant development, and B-cell and antibody analyses, the HVTN has reconfigured its HIV-1 vaccine strategy by developing the Discovery Medicine Program to test promising vaccine candidates targeting six key epitopes.

The HVTN Discovery Medicine program is testing multiple HIV-1-neutralizing vaccine candidates.
Prevalence and Correlates of Dry Eye in a German Population Sample
Authors: Münch Kathrin , Nöhre Mariel , Westenberger Adrian , Akkus Dilek , Morfeld Matthias , Brähler Elmar , Framme Carsten , de Zwaan Martina
Published: September 2023

Purpose:

In this cross-sectional survey, we assessed the prevalence of dry eye disease (DED) in a representative German population sample. In addition, we examined the associations between DED, health-related quality of life (HRQoL), and level of fatigue. Finally, we further validated the German version of the Standard Patient Evaluation of Eye Dryness (SPEED) questionnaire and present norm data of the German population.

Methods:

A random sample of German residents aged 16 years and older was recruited between October and December 2021. All participants completed the SPEED, Short Form 36, and Multidimensional Fatigue Inventory 20 questionnaires.

Results:

Of the 2495 participants who completed the survey, 450 (21.6%; 95% confidence intervals 20.0–23.1) reported a SPEED total score of ≥4, indicating a positive screening for DED. DED was significantly more common in women and older age. Participants who screened positive for DED reported significantly higher levels of fatigue and lower values in all domains of HRQoL. A receiver operating characteristic curve of the SPEED was generated using an ophthalmologist's diagnosis. The area under the curve was estimated to be 0.886 (95% confidence intervals 0.858–0.913). A cutoff score ≥4 seemed to be appropriate as an indicator of DED. Cronbach's α was excellent (0.95).

Conclusions:

DED is common in the German population. We confirmed associations with sex, age, HRQoL, and fatigue level, indicating a high burden of DED. The German version of the SPEED is a valid instrument for the assessment of DED symptoms.
Using a Cone-Shaped Glass Funnel Adapter Reduces Endothelial Cell Loss Caused by Preloading Descemet Membrane Endothelial Keratoplasty Tissue
Authors: Kigin Matthew , Schmidt Gregory , Revis Benjamin , Vigmostad Sarah , Sales Christopher S.
Published: September 2023

Purpose:

The aims of this study were (1) to compare “front” and “rear” methods for loading Descemet membrane endothelial keratoplasty (DMEK) tissue into both micro-Jones and standard-Jones tubes and (2) to evaluate the efficacy of a cone-shaped glass funnel adapter designed to make loading DMEK tissue safer for corneal endothelial cells.

Methods:

The corneal endothelium was stained with 0.06% trypan blue to confirm equivalence between mate corneas. The tissues were then processed using the Iowa Lions Eye Bank standard DMEK protocol. In comparison 1, one mate was loaded into the rear of a micro-Jones or standard-Jones tube and the other was loaded into the front of the same tube. In comparison 2, one mate was loaded into the front of the micro-Jones tube and the other was loaded through the cone-shaped funnel adapter into the rear. All tissues were ejected through the front of the modified Jones tubes and assessed for endothelial cell loss (ECL) with calcein AM staining, FIJI, and Trainable Weka Segmentation; scroll widths were measured digitally.

Results:

There were no statistically significant differences in ECL between front and rear loading [micro (N = 6 pairs): front 15.74% vs. rear 17.95%; standard (N = 6 pairs): front 19.58% vs. rear 19.17%; all P > 0.05]. DMEK scrolls loaded with the funnel adapter exhibited lower ECL compared with scrolls loaded through the front [micro (N = 8 pairs): front 13.53% vs. loading funnel 2.40%; P < 0.001]. Loading with the adapter was not faster (front 6.66 seconds vs. loading funnel 5.52 seconds; P = 0.24).

Conclusions:

Using a cone-shaped DMEK loading funnel may reduce ECL sustained during preloading.
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019
Authors: Xiaoli Lingzi , Peng Yanhui , Williams Margaret M. , Lawrence Marlon , Cassiday Pamela K. , Aneke Janessa S. , Pawloski Lucia C. , Shil Sadhona Rani , Rashid Mamun Or , Bhowmik Proshanta , Weil Lauren M. , Acosta Anna M. , Shirin Tahmina , Habib Zakir Hossain , Tondella M. Lucia , Weigand Michael R.
Published: September 2023

Respiratory diphtheria is a serious infection caused by toxigenic

Corynebacterium diphtheriae

, and disease transmission mainly occurs through respiratory droplets. Between 2017 and 2019, a large diphtheria outbreak among forcibly displaced Myanmar nationals densely settled in Bangladesh was investigated. Here we utilized whole-genome sequencing (WGS) to characterize recovered isolates of

C. diphtheriae

and two co-circulating non-diphtheritic

Corynebacterium

(NDC) species –

C. pseudodiphtheriticum

and C. propinquum. C. diphtheriae isolates recovered from all 53 positive cases in this study were identified as toxigenic biovar mitis, exhibiting intermediate resistance to penicillin, and formed four phylogenetic clusters circulating among multiple refugee camps. Additional sequenced isolates collected from two patients showed co-colonization with non-toxigenic

C. diphtheriae

biovar gravis, one of which exhibited decreased susceptibility to the first-line antibiotics and harboured a novel 23-kb multidrug resistance plasmid. Results of phylogenetic reconstruction and virulence-related gene contents of the recovered NDC isolates indicated they were likely commensal organisms, though 80.4 %(45/56) were not susceptible to erythromycin, and most showed high minimum inhibition concentrations against azithromycin. These results demonstrate the high resolution with which WGS can aid molecular investigation of diphtheria outbreaks, through the quantification of bacterial genetic relatedness, as well as the detection of virulence factors and antibiotic resistance markers among case isolates.
Virtual biomarkers: predicting immune status using label-free holotomography of individual human monocytes and machine learning analysis
Authors: Lee Mahn Jae , Kim Geon , Lee Moo Sung , Shin Jeong Won , Lee Joong Ho , Ryu Dong Hun , Kim Young Seo , Chung YoonJae , Kim Kyu Seok , Park YongKeun
Published: September 2023

Sepsis is an abnormally dysregulated immune response against infection in which the human immune system ranges from a hyper-inflammatory phase to an immune-suppressive phase. Current assessment methods are limiting owing to time-consuming and laborious sample preparation protocols. We propose a rapid label-free imaging-based technique to assess the immune status of individual human monocytes. High-resolution intracellular compositions of individual monocytes are quantitatively measured in terms of the three-dimensional distribution of refractive index values using holotomography, which are then analyzed using machine-learning algorithms to train for the classification into three distinct immune states: normal, hyper-inflammation, and immune suppression. The immune status prediction accuracy of the machine-learning holotomography classifier was 83.7% and 99.9% for one and six cell measurements, respectively. Our results suggested that this technique can provide a rapid deterministic method for the real-time evaluation of the immune status of an individual.
Enhanced production of eicosanoids in plasma and activation of DNA damage pathways in PBMCs are correlated with the severity of ancestral COVID-19 infection
Authors: Tomalka Jeffrey A. , Owings Anna , Galeas-Pena Michelle , Ziegler Carly G.K. , Robinson Tanya O. , Wichman Thomas G. , Laird Hannah , Williams Haley B. , Dhaliwal Neha S. , Everman Steven , Zafar Yousaf , Shalek Alex K. , Horwitz Bruce H. , Ordovas-Montanes Jose , Glover Sarah C. , Gibert Yann
Published: September 2023

Background

Many questions remain unanswered regarding the implication of lipid metabolites in severe SARS-CoV-2 infections. By re-analyzed sequencing data from the nasopharynx of a previously published cohort, we found thataloxgenes, involved in eicosanoid synthesis, were up-regulated in high WHO score patients, especially in goblet cells. Herein, we aimed to further understand the roles played by eicosanoids during severe SARS-CoV-2 infection.

Methods and findings

We performed a total fatty acid panel on plasma and bulk RNA-seq analysis on peripheral blood mononuclear cells (PBMCs) collected from 10 infected and 10 uninfected patients. Univariate comparison of lipid metabolites revealed that lipid metabolites were increased in SARS-CoV-2 patients including the lipid mediators Arachidonic Acid (AA) and Eicosapentaenoic Acid (EPA). AA, EPA and the fatty acids Docosahexaenoic acid (DHA) and Docosapentaenoic acid (DPA), were positively correlated to WHO disease severity score. Transcriptomic analysis demonstrated that COVID-19 patients can be segregated based on WHO scores. Ontology, KEGG and Reactome analysis identified pathways enriched for genes related to innate immunity, interactions between lymphoid and nonlymphoid cells, interleukin signaling and, cell cycling pathways.

Conclusions

Our study offers an association between nasopharynx mucosa eicosanoid genes expression, specific serum inflammatory lipids and, subsequent DNA damage pathways activation in PBMCs to severity of COVID-19 infection.
Fusarium graminearumSte2 and Ste3 Receptors Undergo Peroxidase Induced Heterodimerization
Authors: Sharma Tanya , Jomphe Robert Y. , Zhang Dongling , Magalhaes Ana C. , Loewen Michele C.
Published: September 2023

F. graminearum FgSte2 andFgSte3 are G-protein coupled receptors (GPCRs) recently shown to play roles in mediating fungal hyphal chemotropism and plant pathogenesis in response to activity arising from host-released peroxidases. Here, we follow up on the previous observation that chemotropism is dependent on bothFgSte2 andFgSte3 being present at the same time; testing the possibility that this effect might be due to formation of anFgSte2-FgSte3 heterodimer. Initially the recombinant cell-surface expression of theF. graminearumGPCRs was validated inS. cerevisiaeby confocal immunofluorescence microscopy. Bioluminescence resonance energy transfer analyses were subsequently conducted, where the addition of horse radish peroxidase (HRP) was found to increase the transfer of energy from the inducibly-expressedFgSte3-Nano luciferase (FgSte3-NLuc) donor, to the constitutively-expressedFgSte2-yellow fluorescent protein (FgSte2-YFP) acceptor, compared to controls. A partial response was also detected when an HRP-derived ligand-containing extract was enriched fromF. graminearumspores and applied to theS. cerevisiaeBRET system directly. The selectivity of the interaction was demonstrated by comparison to treatment with pheromones as well as an unrelated bovine GPCR, rhodopsin, fused to YFP as acceptor, that yielded no response when co-expressed withFgSte3-NLuc. Finally, the peroxidase-stimulated heterodimerization was validated by affinity pulldown. Taken together these findings demonstrate the formation of HRP and HRP-derived ligand stimulated heterodimers betweenFgSte2 andFgSte3. Outcomes are discussed from the context of the roles of ligands and reactive oxygen species in GPCR dimerization.
X-ray structure of the metastable SEPT14–SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization
Authors: Cavini Italo A. , Winter Ashley J. , D'Muniz Pereira Humberto , Woolfson Derek N. , Crump Matthew P. , Garratt Richard C.
Published: September 2023

Septins are membrane-associated, GTP-binding proteins that are present in most eukaryotes. They polymerize to play important roles as scaffolds and/or diffusion barriers as part of the cytoskeleton. α-Helical coiled-coil domains are believed to contribute to septin assembly, and those observed in both human SEPT6 and SEPT8 form antiparallel homodimers. These are not compatible with their parallel heterodimeric organization expected from the current model for protofilament assembly, but they could explain the interfilament cross-bridges observed by microscopy. Here, the first structure of a heterodimeric septin coiled coil is presented, that between SEPT14 and SEPT7; the former is a SEPT6/SEPT8 homolog. This new structure is parallel, with two long helices that are axially shifted by a full helical turn with reference to their sequence alignment. The structure also has unusual knobs-into-holes packing of side chains. Both standard seven-residue (heptad) and the less common 11-residue (hendecad) repeats are present, creating two distinct regions with opposite supercoiling, which gives rise to an overall straight coiled coil. Part of the hendecad region is required for heterodimerization and therefore may be crucial for selective septin recognition. These unconventional sequences and structural features produce a metastable heterocomplex that nonetheless has enough specificity to promote correct protofilament assembly. For instance, the lack of supercoiling may facilitate unzipping and transitioning to the antiparallel homodimeric state.
Increasing the bulk of the 1TEL–target linker and retaining the 10×His tag in a 1TEL–CMG2-vWa construct improves crystal order and diffraction limits
Authors: Gajjar Parag L. , Pedroza Romo Maria J. , Litchfield Celeste M. , Callahan Miles , Redd Nathan , Nawarathnage Supeshala , Soleimani Sara , Averett Jacob , Wilson Elijah , Lewis Andrew , Stewart Cameron , Tseng Yi-Jie , Doukov Tzanko , Lebedev Andrey , Moody James D.
Published: September 2023

TELSAM-fusion crystallization has the potential to become a revolutionary tool for the facile crystallization of proteins. TELSAM fusion can increase the crystallization rate and enable crystallization at low protein concentrations, in some cases with minimal crystal contacts [Nawarathnage et al. (2022), Open Biol.
12, 210271]. Here, requirements for the linker composition between 1TEL and a fused CMG2 vWa domain were investigated. Ala-Ala, Ala-Val, Thr-Val and Thr-Thr linkers were evaluated, comparing metrics for crystallization propensity and crystal order. The effect on crystallization of removing or retaining the purification tag was then tested. It was discovered that increasing the linker bulk and retaining the 10×His purification tag improved the diffraction resolution, likely by decreasing the number of possible vWa-domain orientations in the crystal. Additionally, it was discovered that some vWa-domain binding modes are correlated with scrambling of the 1TEL polymer orientation in crystals and an effective mitigation strategy for this pathology is presented.
Estimating US farmers' speed of climate change adaptation: the case of subsurface tile drainage
Authors: Comstock Haden , DeLay Nathan
Published: September 2023

Purpose

Climate change is expected to cause larger and more frequent precipitation events in key agricultural regions of the United States, damaging crops and soils. Subsurface tile drainage is an important technology for mitigating the risks of a wetter climate in crop production. In this study, the authors examine how quickly farmers adapt to increased precipitation by investing in drainage technology.

Design/methodology/approach

Using farm-level data from the 2018 Agricultural Resource Management Survey (ARMS) of soybean producers, the authors construct a drainage adoption timeline based on when the operator began farming their land and when tile drainage was installed, if at all. The authors examine both the initial investment decision and the speed with which drainage is installed by adopters. A Heckman-style Poisson regression is used to model the count nature of adoption speed (measured in years taken to install tile drainage) and to correct for potential sample-selection bias.

Findings

The authors find that local precipitation is not a significant determinant of the drainage investment decision but may be highly influential in the timing of adoption among drainage users. Farms exposed to crop-damaging levels of precipitation install tile drainage faster than those with low to moderate levels of rainfall. Estimates of farm adaptation speeds are heterogeneous across farm and operator characteristics, most notably land tenure status.

Originality/value

Understanding how US farmers adapt to extreme weather through technology adoption is key to predicting the long-term impacts of climate change on America's food system. This study extends the existing climate adaptation literature by focusing on the speed of adoption of an important and increasingly common climate-mitigating technology – subsurface tile drainage.
Deleterious food socialization: the negative impacts of the school environment on children's food well-being
Authors: Rocha Rodolfo Rodrigues , Chaim Daniel Faria , Veloso Andres Rodriguez , Costa Murilo Lima Araújo , Falcão Roberto Flores
Published: September 2023

Purpose

Food socialization is the process of influences that forms children's eating habits and preferences, affecting their well-being for life. The authors' study explores what children and adolescents eat and how they obtain food at school, aiming to describe the deleterious food socialization phenomenon. The authors focused on understanding how deleterious food socialization influences children's food well-being within the school environment.

Design/methodology/approach

The authors developed a mixed methodology using structured questionnaires with open and closed questions. The authors also took pictures of the schools' canteens, which allowed deepening the understanding of the school environment. The data collection occurred in two Brazilian private schools. The schools' teachers were responsible for collecting 388 useful questionnaires from students between 10 and 14 years old.

Findings

The authors found statistically significant differences between food originating at home and school. The amount of ultra-processed foods and beverages consumed at home and taken by children and adolescents from home to school is smaller than what they buy in the school canteen or get from their colleagues. Thus, the authors suggest that the school environment tends to be more harmful to infant feeding than the domestic one.

Originality/value

This study coins the concept of deleterious food socialization: situations or environments in which the food socialization process negatively impacts one's well-being. The authors' results illustrate the deleterious food socialization phenomenon in the school environment.
MetaWOM – toward a sensory word-of-mouth (WOM) in the metaverse
Authors: Mladenović Dušan , Ismagilova Elvira , Filieri Raffaele , Dwivedi Yogesh K.
Published: September 2023

Purpose

Based on the key dimensions of the Metaverse environment (immersiveness, fidelity and sociability), this paper aims to develop the concept of sensory word-of-mouth (WOM) in Metaverse – the metaWOM. It attempts to upgrade the Reviewchain model and suggests the utilization of non-transferable tokens (NTTs) in curbing the explosion of fake WOM.

Design/methodology/approach

Following Macinnis’ (2011) approach to conceptual contributions, the authors browsed the currently available literature on WOM, Metaverse and NTT to portray the emergence of metaWOM.

Findings

By relying on Metaverse’s three building blocks, the authors map out the persuasiveness of metaWOM in the Metaverse-like environment. By incorporating NTT in the Reviewchain model, the authors upgraded it to provide a transparent, safe and trusted review ecosystem. An array of emerging research directions and research questions is presented.

Research limitations/implications

This paper comprehensively analyzes the implications of a Metaverse-like environment on WOM and debates on technologies that can enhance the metaWOM persuasiveness. The proposed model in this paper can assist various stakeholders in understanding the complex nature of virtual information-seeking and giving.

Originality/value

This is the original attempt to delineate the sensory aspect of WOM in the Metaverse based on three crucial aspects of the Metaverse environment: immersiveness, fidelity and sociability. This paper extends the discussion on the issue of fake reviews and offers viable suggestions to curb the ever-growing number of fraudulent WOM.
The role of local institutions in the technological trajectory of the Brazilian rice industry
Authors: Tello-Gamarra Jorge , Fitz-Oliveira Mônica
Published: September 2023

Purpose

Despite the growing interest regarding the Brazilian rice industry, there is not much literature focusing on the role of the institutions in the process of technological capability accumulation and in the formation of the technological trajectories within this industry. This paper aims to discover the role of local institutions in the generation and dissemination of knowledge for creating the technological capability that can define different technological trajectories, using the Brazilian rice industry as an empirical field.

Design/methodology/approach

To achieve said objective, this paper uses secondary data (documental research) and a multiple case study design based on primary empirical evidence (content analysis and direct observation) about the Brazilian rice industry.

Findings

The paper’s main contribution is the empirical application of a framework that allows us to evaluate the institutions’ roles and activities and how these capabilities evolve as the firms’ technological levels progress and the technological trajectory is formed. Regarding aspects related to public policy, the authors found some implications that are mainly related to the need to consolidate this type of institution in developing countries with the goal of strengthening its technological capabilities, allowing these countries to operate on the technological boundary and to compete with developed countries.

Originality/value

There are few attempts to relate the technological capability, technological trajectories and institutions in the Brazilian rice industry. Therefore, to the best of the authors’ knowledge, the novelty of this study lies in the analysis of these theoretical approaches in this industrial sector, more specifically, in the Brazilian rice industry.
Guided tours and tourist attractions in the postpandemic world: thematic evolutions and spatial changes
Authors: Bassols i Gardella Narcís
Published: September 2023

Purpose

The purpose of this paper is to widen the understanding of the shifts the tourism industry experienced as it went though the Covid-19 pandemic. To contribute to this question, an empirical comparison is made between the supply of guided tours and sights at an urban destination in the pre- and postpandemic eras, thus gauging the changes in the guiding tours industry after the pandemic.

Design/methodology/approach

By conducting a convenience data gathering and a double-level analysis (tours analysis and sights analysis) on the tours and attractions supply at an urban destination, underlying trends come to light, related to the changes in the postpandemic era. This empirical comparison (2019 vs 2022) allows the authors to assess what has and has not changed in the postpandemic context.

Findings

Guided tours and attractions supply are evolving in the researched destination, but at a slow pace. Therefore, we conclude that long-term processes in destinations prevail over short-term disruptions, no matter how strong these disturbances are.

Practical implications

The results are of interest to practitioners as they facilitate a better assessment of the impacts of a crisis and greater awareness of the evolution of attractions in urban tourism. While the “staple tours” in a destination are always there, practitioners should keep an eye on new spaces in the city which the sector is opening up and also new touring trends.

Originality/value

This study is one of the few to empirically compare a pre- and postpandemic situation, as far as city-guided tours are concerned. It helps practitioners and authorities in urban destinations to assess the new trends that have emerged in the postpandemic era, and offers a two-level tool for tour analysis that could be applied to any urban destination.