bluuebunny/crossref_metadata_2025 huggingface dataset:
Programmed-DNA Elimination in the free-living nematodes Mesorhabditis
Authors: Rey Carine , Launay Caroline , Wenger Eva , Delattre Marie
Published: March 2022

In most species, elaborate programs exist to protect chromatin and maintain its integrity over cell cycles and generations. However some species systematically undergo excision and elimination of portions of their genome in somatic cells in a process called programmed-DNA elimination (PDE). PDE involves the elimination of mainly repeated elements but also protein-coding genes. PDE has been described in approximately 100 species from very distinct phyla, and more extensively in the parasitic nematodes Ascaris and in the unicellular Ciliates. In Ciliates, where PDE is pervasive, the underlying mechanisms have been studied and involve small RNA-guided heterochromatinization. In striking contrast, chromatin recognition and excision mechanisms remain mysterious in Metazoans, because the study species are not amenable to functional approaches. Above all, the function of such a mechanism, which has emerged repeatedly throughout evolution, is unknown. Answering these questions will provide significant insights into our understanding of chromatin regulation and genome stability.

We fortuitously discovered the phenomenon of PDE in all species of the free-living nematode genus Mesorhabditis. Mesorhabditis, which belong to the same family as C. elegans, have a small ∼150 Mb genome and offer many experimental advantages to start elucidating the elimination mechanisms in Metazoans. In this first study, we have used a combination of cytological observation and genomic approaches to describe PDE in Mesorhabditis. We found that the dynamics of chromosome fragmentation and loss are very similar to those described in Ascaris. Elimination occurs once in development, at the third embryonic cell division in all 5 presomatic blastomeres. Similar to other species, Mesorhabditis eliminate repeated elements but also about a hundred unique sequences. Most of the eliminated unique sequences are either pseudogenes or poorly conserved protein-coding genes. Our results raise the possibility that PDE has not been selected for a gene regulatory function in Mesorhabditis but rather mainly is a mechanism to irreversibly silence repeated elements in the soma.
Thermodynamic coupling between neighboring binding sites in homo-oligomeric ligand sensing proteins from mass resolved ligand dependent population distributions
Authors: Li Weicheng , Norris Andrew S. , Lichtenthal Katie , Kelly Skyler , Ihms Elihu C. , Gollnick Paul , Wysocki Vicki H. , Foster Mark P.
Published: March 2022

Homo-oligomeric ligand-activated proteins are ubiquitous in biology. The functions of such molecules are commonly regulated by allosteric coupling between ligand binding sites. Understanding the basis for this regulation requires both quantifying the free energy ΔG transduced between sites, and the structural basis by which it is transduced. We consider allostery in three variants of the model ring-shaped homo-oligomeric trpRNA binding attenuation protein, TRAP. First, we developed nearest-neighbor statistical thermodynamic binding models comprising microscopic free energies for ligand binding to isolated sites ΔGN0, and for coupling between one or both adjacent sites, ΔGN1 and ΔGN2. Using the resulting partition function (PF) we explored the effects of these parameters on simulated population distributions for the 2N possible liganded states. We then experimentally monitored liganddependent population shifts using conventional spectroscopic and calorimetric methods, and using native mass spectrometry (MS). By resolving species with differing numbers of bound ligands by their mass, native MS revealed striking differences in their ligand-dependent population shifts. Fitting the populations to a binding polynomial derived from the PF yielded coupling free energy terms corresponding to orders of magnitude differences in cooperativity. Uniquely, this approach predicts which of the possible 2N liganded states are populated at different ligand concentrations, providing necessary insights into regulation. The combination of statistical thermodynamic modeling with native MS may provide the thermodynamic foundation for a meaningful understanding of the structure-thermodynamic linkage that drives cooperativity.

TOC Figure (draft)

TOC Figure.

Ligand (Trp) binding to multiple sites on homo-oligomeric ring-shaped proteins like TRAP alters their functional states. Homotropic cooperativity is expected to alter the activation pathway in response to cellular ligand concentration. In the presence of positive nearest-neighbor cooperativity, ligand binding is favored at adjacent sites, whereas in the absence of cooperativity, a random “Normal” distribution is expected.
DNA repair defects in cancer and therapeutic opportunities
Authors: Hopkins Jessica L. , Lan Li , Zou Lee
Published: March 2022

DNA repair and DNA damage signaling pathways are critical for the maintenance of genomic stability. Defects of DNA repair and damage signaling contribute to tumorigenesis, but also render cancer cells vulnerable to DNA damage and reliant on remaining repair and signaling activities. Here, we review the major classes of DNA repair and damage signaling defects in cancer, the genomic instability that they give rise to, and therapeutic strategies to exploit the resulting vulnerabilities. Furthermore, we discuss the impacts of DNA repair defects on both targeted therapy and immunotherapy, and highlight emerging principles for targeting DNA repair defects in cancer therapy.
Survey of young consumer’s attitudes using food sharing attitudes and behaviors model
Authors: Wiśniewska Małgorzata , Czernyszewicz Eugenia
Published: March 2022

Purpose

Given the importance of food wastes in households, the purpose was to identify the attitudes of young consumers towards the food sharing (FS) phenomenon in its cognitive, emotional and behavioral dimensions and to verify the reliability of the FAB (food sharing attitudes and behaviors) model, used as a research tool.

Design/methodology/approach

The study was conducted in 2021 using the computer assisted web interview (CAWI) method. The FAB model was based on the ABC (affect, behavior and cognition) model of attitudes, which includes three components: affect, behavior and cognition. Questions on the phenomenon of FS were scaled on a 5-point Likert scale. A total of 469 correctly completed forms were obtained. To assess the reliability of the FAB model the Cronbach’s alpha was used. In the statistical analysis SPSS Statistics 27 was used.

Findings

Young consumers have a positive attitude towards the idea of FS and the initiative of FS points. Gender is a significant factor in FS attitudes. The FAB model has proven to be a reliable tool for exploring consumer attitudes towards FS. A set of activities was proposed to promote the idea of FS on university campuses and among other potential stakeholders.

Originality/value

To contribute to the body of knowledge on FS, the authors proposed the FAB model. The results of this study are relevant for reducing food wastes; they promote sustainable food consumption and the European Green Deal (EGD).
Conjoint assessment of rural water security and system sustainability in Nagpur, India
Authors: Sukhwani Vibhas , Shaw Rajib
Published: March 2022

Purpose

In spite of the growing usage of “water security” as a policy template, the sustainable delivery of adequate quantity/quality of water remains a major challenge, specifically in the rural areas of developing countries. Focusing on the specific case of Nagpur (India), this study aims to establish a broader understanding of rural water security and (water supply) system sustainability issues at grassroots-level.

Design/methodology/approach

Taking due account of the existing assessment methods and the study context of Nagpur, contextualized indicator-based frameworks have been developed for conjointly assessing both the research subjects. Within the identified eight rural clusters (comprising 72 settlements), focus group discussions (with the residents) and semi-structured interviews [with the members of village water and sanitation committees) (VWSCs)] are then conducted to methodically investigate the local stakeholder perception.

Findings

Through the rural water security (state change) assessment in selected settlements, the water accessibility indicators are consistently reported to have witnessed mostly positive changes, whereas contrasting changes have been reported for various indicators of availability, quality and risks. Superimposing these findings with those of system sustainability assessment (e.g. only 56% VWSCs are reported to be actively functioning), it has been realized that the sustainability of water supply systems is imperative to attain water security goals in the long term.

Originality/value

Through the conjoint assessment of water security and system sustainability issues, this research responds to the growing call for a broader consideration of these concepts. Moreover, it reports practical ground-level challenges based on primary surveys.
Divergence of beliefs and IPO initial return: the quasi-moderating role of investor demand
Authors: Albada Ali , Low Soo-Wah , Toh Moau Yong
Published: March 2022

Purpose

This study aims to investigate the moderating role of investor demand on the relationship between the investors' divergence of beliefs and the first-day initial public offering (IPO) return.

Design/methodology/approach

The study sample covers the period from 2010 to 2019 and consists of 117 IPOs that are priced using the fixed price and listed on the Malaysian stock exchange (Bursa Malaysia). This study employed both the ordinary least square (OLS) and the quantile regression (QR) methods.

Findings

Investor demand, proxied by the over-subscription ratio (OSR), plays a moderating role in increasing the effect of investors' divergence of beliefs on initial return, and the moderation effects vary across the quantile of initial return. Pure moderation effects are observed at the bottom and top quantiles, suggesting that investor demand is necessary for divergence of beliefs to influence IPO initial return. However, at the middle quantile of initial return, investor demand is a quasi-moderator. That is, the OSR not only moderates the relationship between the divergence of beliefs and initial return but also has a positive effect on the initial return.

Practical implications

Investors' excessive demand for an IPO issue exacerbates the IPO under-pricing issue induced by a divergence of beliefs amongst investors, thus rendering greater equity market inefficiency.

Originality/value

To the authors' knowledge, this study is amongst the first to empirically investigate the moderating role of investor demand on the investors' divergence of beliefs and IPO initial return relationship.
Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce
Authors: Redondo Miguel A. , Oliva Jonàs , Elfstrand Malin , Boberg Johanna , Capador‐Barreto Hernán D. , Karlsson Bo , Berlin Anna
Published: March 2022

The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.
The Logic of Policies to Address Income‐Related Health Inequity: A Problem‐Oriented Approach
Authors: BERKOWITZ SETH A.
Published: March 2022

Policy Points

 Income is a fundamental cause of health across the life course. To address income‐related health inequities, we need a set of overlapping and complementary policy approaches rather than focusing on a single policy.

 During their lives, individuals inhabit different roles with regard to their ability to earn wages, and at any given time, only about 50% of the US population are expected to earn wages, while the rest (e.g., children, older adults, those who are disabled, unemployed, students, and/or caregivers) are not.

 Three key “branch points” for designing policy approaches to address income‐related health inequity are (1) should the needed good or service be obtained on the market? (2) do policy beneficiaries currently earn income? and (3) have policy beneficiaries earned income previously? The responses to these questions suggest one of four policy approaches: social services, social enfranchisement, social insurance, or social assistance.
The beginning and ending of a respiratory viral pandemic‐lessons from the Spanish flu
Authors: Brüssow Harald
Published: March 2022

The COVID‐19 pandemic goes into its third year and the world population is longing for an end to the pandemic. Computer simulations of the future development of the pandemic have wide error margins and predictions on the evolution of new viral variants of SARS‐CoV‐2 are uncertain. It is thus tempting to look into the development of historical viral respiratory pandemics for insight into the dynamic of pandemics. The Spanish flu pandemic of 1918 caused by the influenza virus H1N1 can here serve as a potential model case. Epidemiological observations on the shift of influenza mortality from very young and old subjects to high mortality in young adults delimitate the pandemic phase of the Spanish flu from 1918 to 1920. The identification and sequencing of the Spanish flu agent allowed following the H1N1 influenza virus after the acute pandemic phase. During the 1920s H1N1 influenza virus epidemics with substantial mortality were still observed. As late as 1951, H1N1 strains of high virulence evolved but remained geographically limited. Until 1957, the H1N1 virus evolved by accumulation of mutations (‘antigenic drift’) and some intratypic reassortment. H1N1 viruses were then replaced by the pandemic H2N2 influenza virus from 1957, which was in 1968 replaced by the pandemic H3N2 influenza virus; both viruses were descendants from the Spanish flu agent but showed the exchange of entire gene segments (‘antigenic shift’). In 1977, H1N1 reappeared from an unknown source but caused only mild disease. However, H1N1 achieved again circulation in the human population and is now together with the H3N2 influenza virus an agent of seasonal influenza winter epidemics.
Sexually dimorphic organization of open field behavior following moderate prenatal alcohol exposure
Authors: Osterlund Oltmanns Jenna R. , Schaeffer Ericka A. , Goncalves Garcia Monica , Donaldson Tia N. , Acosta Gabriela , Sanchez Lilliana M. , Davies Suzy , Savage Daniel D. , Wallace Douglas G. , Clark Benjamin J.
Published: March 2022

Background

Prenatal alcohol exposure (PAE) can produce deficits in a wide range of cognitive functions but is especially detrimental to behaviors requiring accurate spatial information processing. In open field environments, spatial behavior is organized such that animals establish “home bases” marked by long stops focused around one location. Progressions away from the home base are circuitous and slow, while progressions directed toward the home base are non‐circuitous and fast. The impact of PAE on the organization of open field behavior has not been experimentally investigated.

Methods

In the present study, adult female and male rats with moderate PAE or saccharin exposure locomoted a circular high walled open field for 30 minutes under lighted conditions.

Results

The findings indicate that PAE and sex influence the organization of open field behavior. Consistent with previous literature, PAE rats exhibited greater locomotion in the open field. Novel findings from the current study indicate that PAE and sex also impact open field measures specific to spatial orientation. While all rats established a home base on the periphery of the open field, PAE rats, particularly males, exhibited significantly less clustered home base stopping with smaller changes in heading between stops. PAE also impaired progression measures specific to distance estimation, while sex alone impacted progression measures specific to direction estimation.

Conclusions

These findings support the conclusion that adult male rats have an increased susceptibility to the effects of PAE on the organization of open field behavior.
Longitudinal accounting comparability and bond credit spreads: Evidence from China
Authors: Cao Shijiao , Wang Jianqiong
Published: March 2022

This paper proposes a procedure to measure firms’ longitudinal accounting comparability and investigates whether it affects bond risk premiums. The results provide robust evidence that bonds of firms with more longitudinally comparable accounting information have lower credit spreads. This effect is stronger when the firms’ financial performance is poor and for bonds with speculative credit ratings. Results also reveal that firms with less longitudinally comparable accounting information are more informationally asymmetric and do have a higher expected default probability. Finally, the effects of the longitudinal and the cross‐sectional comparability in reducing bond credit spreads are incremental to each other.
Review article: Lynch Syndrome—a mechanistic and clinical management update
Authors: Curtius Kit , Gupta Samir , Boland C. Richard
Published: March 2022

Background

Lynch syndrome (LS) is an autosomal dominant familial condition caused by a pathogenic variant (PV) in a DNA mismatch repair gene, which then predisposes carriers to various cancers.

Aim

To review the pathogenesis, clinical presentation, differential diagnosis and clinical strategies for detection and management of LS.

Methods

A narrative review synthesising knowledge from published literature, as well as current National Comprehensive Cancer Network guidelines for management of LS was conducted.

Results

LS tumours are characterised by unique pathogenesis, ultimately resulting in hypermutation, microsatellite instability and high immunogenicity that has significant implications for cancer risk, clinical presentation, treatment and surveillance. LS is one of the most common hereditary causes of cancer, and about 1 in 279 individuals carry a PV in an LS gene that predisposes to associated cancers. Individuals with LS have increased risks for colorectal, endometrial and other cancers, with significant variation in lifetime risk by LS‐associated gene.

Conclusions

As genetic testing becomes more widespread, the number of individuals identified with LS is expected to increase in the population. Understanding the pathogenesis of LS informs current strategies for detection and clinical management, and also guides future areas for clinical innovation. Unravelling the mechanisms by which these tumours evolve may help to more precisely tailor management by the gene involved.
Editorial: opposite effects of genetic polymorphisms known to induce NAFLD on hepatic and cardiovascular outcomes in Chinese population—authors' reply
Authors: Xia Mingfeng , Gao Xin
Published: March 2022

LINKED CONTENT

This article is linked to Xia et al papers. To view these articles, visit https://doi.org/10.1111/apt.16772 and https://doi.org/10.1111/apt.16818
Editorial: meal‐induced symptoms in irritable bowel syndrome—“all in the mind”?
Authors: Fox Mark
Published: March 2022

LINKED CONTENT

This article is linked to Wu et al papers. To view these articles, visit https://doi.org/10.1111/apt.16812
Automatic market research of mobile health apps for the self‐management of allergic rhinitis
Authors: Antó Aram , Sousa‐Pinto Bernardo , Czarlewski Wienczyslawa , Pfaar Oliver , Bosnic‐Anticevich Sinthia , Klimek Ludger , Matricardi Paolo , Tripodi Salvatore , Fonseca Joao A. , Antó Josep M. , Bousquet Jean
Published: March 2022

Background

Only a small number of apps addressing allergic rhinitis (AR) patients have been evaluated. This makes their selection difficult. We aimed to introduce a new approach to market research for AR apps, based on the automatic screening of Apple App and Google Play stores.

Methods

A JavaScript programme was devised for automatic app screening, and applied in a market assessment of AR self‐management apps. We searched the Google Play and Apple App stores of three countries (USA, UK and Australia) with the following search terms: "hay fever", "hayfever", "asthma", "rhinitis", "allergic rhinitis". Apps were eligible if symptoms were evaluated. Results obtained with the automatic programme were compared to those of a blinded manual search. As an example, we used the search to assess apps that can be used to design a combined medication score for AR.

Results

The automatic search programme identified 39 potentially eligible apps out of a total of 1593 retrieved apps. Each of the 39 apps was individually checked, with 20 being classified as relevant. The manual search identified 19 relevant apps (out of 6750 screened apps). Combining both methods, a total of 21 relevant apps were identified, pointing to a sensitivity of 95% and a specificity of 99% for the automatic method. Among these 21 apps, only two could be used for the combined symptom‐medication score for AR.

Conclusions

The programmed algorithm presented herein is able to continuously retrieve all relevant AR apps in the Apple App and Google Play stores, with high sensitivity and specificity. This approach has the potential to unveil the gaps and unmet needs of the apps developed so far.
A rural ecosystem of recovery: Lessons from substance users' experiences of accessing services in Western Australia's South West
Authors: Cuesta‐Briand Beatriz , Taran Michael , Coleman Mathew
Published: March 2022

Introduction

Substance use is a public health issue with a greater burden in rural areas. Barriers to accessing services are exacerbated for rural substance users, with confidentiality concerns, longer travel distances, workforce issues and limited availability of services. This paper presents results from a study exploring substance users' experiences of accessing services in Western Australia's South West.

Methods

This qualitative study was informed by phenomenology, and drew from social determinants and socio‐ecological theories. Data were collected through 22 semi‐structured telephone interviews with current and past substance users residing in the South West. Interviews were audio‐recorded and transcripts were subjected to thematic analysis.

Results

Two themes were identified: readiness to engage as a three‐way street; and building an ecosystem of recovery networks. Effective engagement with services required multi‐level readiness. Individual readiness was strongly influenced by the social environment, while service readiness required trustworthiness and responsiveness. A number of local access barriers were identified that hindered broader system readiness. Participants experienced recovery as on‐going and require an ecosystem of support with peer support at the centre and a network of healthy relationships established through meaningful connections.

Discussion and Conclusions

An effective ecosystem of support for alcohol and other drugs users in the South West should include expanded access to health, community and welfare services, with an emphasis on peer‐led support programs, and strong cross‐sector collaboration to mitigate the access barriers operating at the broader community level. Lessons from our study can inform the development of rural ecosystems of support for alcohol and other drugs users.
Captive breeding of odonate larvae: Effects of type of water, handling, and sex
Authors: Palacino‐Rodríguez Fredy , Cordero‐Rivera Adolfo , Palacino Diego Andrés , Penagos Andrea Carolina
Published: March 2022

Basic information on life histories, ecology, and behaviour for aquatic stages in many species of insects is difficult to obtain in the field. Here, a method to breed and monitor individual Odonata larvae in captivity is proposed. In total, 3788 individuals of six Odonata species – Rhionaeschna marchali (Rambur), Erythrodiplax abjecta (Rambur), Sympetrum gilvum (Selys), Ischnura chingaza Realpe, Ischnura cruzi De Marmels, and Mesamphiagrion laterale (Selys) – were reared individually in water‐filled plastic containers, whose size was increased to fit larval growth, at ambient temperature (12–34 °C, 12 h light per day, ca. 300 lux, and ad libitum food). We tested the effects of water type (habitat water, dechlorinated tap water, and drinking water), handling method, and sex on larval developmental time and number of instars. The number of instars was calculated as the mean number of moults for the individuals that successfully emerged as adults. Life cycle length was calculated by averaging the days over individuals that completed their development until emergence. The probability of achieving the adult stage was not significantly affected by the type of water, sex, or handling method. On the other hand, the number of instars was affected by species identity, and type of water, with fewer instars in water from the natural habitat, but not affected by sex or handling method. The duration of the life cycle was bimodal in most species, and was affected by type of water, but in an idiosyncratic, species‐specific way. The methodology proposed here allows monitoring and breeding large numbers of odonate larvae.
Demonstration of local adaptation in maize landraces by reciprocal transplantation
Authors: Janzen Garrett M. , Aguilar‐Rangel María Rocío , Cíntora‐Martínez Carolina , Blöcher‐Juárez Karla Azucena , González‐Segovia Eric , Studer Anthony J. , Runcie Daniel E. , Flint‐Garcia Sherry A. , Rellán‐Álvarez Rubén , Sawers Ruairidh J. H. , Hufford Matthew B.
Published: March 2022

Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland‐adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (QST) was greater than neutral allele frequency differentiation (FST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces’ native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland‐adaptive. These results give substance to the long‐held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.
Fed_ADBN: An efficient intrusion detection framework based on client selection in AMI network
Authors: Xia Zhuoqun , Chen Yaling , Yin Bo , Liang Haolan , Zhou Hongmei , Gu Ke , Yu Fei
Published: March 2022

Data transmission between smart meters and data center is facing network security threats in advanced metering infrastructure of smart grid. The traditional solution is to move the data to the data center to build a centralized attack detection model, or divide the collected data into several independent and identically distributed datasets to build a distributed attack detection model. However, the long‐distance transmission and the centralized storage of data not only increase the communication overhead and time overhead, but also increase the risk of being attacked, causing privacy disclosure during the process of building the model. In this paper, we propose an efficient intrusion detection framework Fed_ADBN based on federated attention deep belief network and client selection. Clients cooperate with the data center to jointly build a horizontal federated learning framework. Under the premise of protecting data security by keeping data on the clients, we design a client selection algorithm based on client computing power, communication quality and security risks, which can improve the operating efficiency of federated learning. We also deploy a deep belief neural network with attention mechanism in each client to accurately detect possible network attacks in AMI network in real time. Experimental results show that compared with state‐of‐the‐art methods, the proposed framework can not only maintain good detection accuracy but also protect privacy.
Atrophic gastritis in Helicobacter pylori‐infected children
Authors: Hsieh Hsuan , Yang Hsiao‐Bai , Sheu Bor‐Shyang , Yang Yao‐Jong
Published: March 2022

Background

Helicobacter pylori infection is the leading cause of peptic ulcer and chronic gastritis and may initiate gastric carcinogenesis following the Correa cascade. Another lineage of metaplasia, spasmolytic peptide‐expressing metaplasia (SPEM) has recently been found to be an alternative precursor to gastric cancer. To date, few reports have investigated gastric precancerous lesions among children with H. pylori infection. This study aimed to evaluate the histopathological pattern of H. pylori atrophic gastritis in children and the extent of precancerous lesions.

Materials and Methods

This study enrolled pediatric patients with H. pylori infection from 1998 to 2019. During esophagogastroduodenoscopy examinations, biopsy fragments were collected from the gastric antrum and corpus for rapid urease test, culture, and histology evaluation. The presence and degree of chronic inflammation, activity of gastritis, H. pylori density, atrophy, and intestinal metaplasia (IM) were assessed according to the modified Updated Sydney System. Trefoil factor 2 (TFF2) immunohistochemistry was also performed to assess SPEM in the gastric tissues collected from each case using rabbit anti‐human TFF2 antibodies.

Results

A total of 92 children with H. pylori infection and adequate gastric mucosa biopsies were enrolled. Esophagogastroduodenoscopy showed that 39 (42.4%) had duodenal ulcers, 11 (12.0%) had gastric ulcers, 41 (44.6%) had gastritis, and 1 (1.1%) had negative findings. Mild‐to‐moderate IM was identified in 4 patients (4.3%). SPEM was found in 8 patients (8.7%) with a significantly higher incidence among female patients (15.8% vs. 8.7%, p = .031). Gastric glandular atrophy presented in 28 patients (30.4%), and high‐grade atrophy was more common in female patients (3.2% vs. 1.9%, p = .031).

Conclusions

The prevalence rates of atrophic gastritis in the children with H. pylori infection were 30.4% for gastric glandular atrophy, 4.3% for IM and 8.7% for SPEM. SPEM and high‐grade atrophy were more common in female patients.
Expression profiles of cdca9 related to ovarian development in loach (Misgurnus anguillicaudatus)
Authors: Huang Yuwei , Zhang Yunbang , Gao Jian , Cao Xiaojuan
Published: March 2022

The function of borealin proteins has been widely reported in the cell division of animals. Nonetheless, there is little research about their only known paralogue (cell division cycle associated 9, cdca9). In this study, cdca9 was investigated in loach (Misgurnus anguillicaudatus) for the first time. cdca9 was highly expressed in the embryo before the gastrula stage, and it was predominantly expressed in the ovary, especially in the oocytes of stage II. In conclusion, this study reveals a potential function of cdca9 in the early embryogenesis and ovarian development of fish.
Prediction of mass‐based process designing parameters of amla fruit using different modeling techniques
Authors: Tomar Mahipal Singh , Pradhan Rama Chandra
Published: March 2022

The machine designing parameters such as size, volume, criteria projected area are important for quality evaluation at the time of packaging, grading, and sorting of fruits. All these designing parameters also depend on mass of the fruit sample. So, the correlation between mass and designing parameters could be useful for automation of the process industry. The research was inducted to predict the dimension, projected area, and volume of fruit as a function of fruit mass. Prediction modeling was done using different models, that is, mathematical model (MM), artificial neural network (ANN), and support vector regression (SVR). The mathematical model (linear, quadratic, and power) showed better prediction results than SVR modeling. In addition, the best results were achieved by neural network‐based prediction modeling. It showed the highest correlation coefficient of .884, .986, .992, .999 and the lowest error of 0.570, 0.241, 8.080, 0.059 for height, diameter, projected area, and volume, respectively. It is observed that the physical properties of fruit can be predicted using ANN‐based modeling which could be useful in automation and efficient designing of post‐harvest equipment.

Practical Application

The machine designing parameters are the essential and fundamental parameters for designing of grading, sorting, packaging, and handling equipments of various horticultural products including amla. Fruits and vegetables are non‐uniform in size and shape. So, minor changes in shape and size of fruits could decrease the efficiency of various processes and its equipment. The design parameters of fruits and vegetables are dependent on the mass of samples. So, accurate knowledge of mass and design parameters could help in designing the automatic grading system. Different models can be used to predict various designing parameter of amla or similar fruits. By using various models, fruit can be separated more accurately based on minor changes in shape and size rather than its mass. The ANN‐based prediction will be beneficial for the automation of the fruits grading system at an industrial scale.
Detection of frequent neutrophil misclassification by the ProCyte Dx in sick dogs and how to avoid it
Authors: Bergstrand E. , Tvedten H. W. , Lilliehöök I.
Published: March 2022

Objectives

A common and severe error in identifying neutrophils in feline blood samples by the IDEXX ProCyte Dx haematology analyser (ProCyte) has been reported. The hypothesis was that the same or similar error would be identified during analysis of canine blood samples and that white blood cell dot plot evaluation would be critical to detect and avoid erroneous results.

Materials and Methods

Eighty‐six canine blood samples collected for clinical diagnosis of hospital patients were evaluated. Differential leukocyte counts were determined by the ProCyte Dx, ADVIA 2120 and manual methods. ProCyte neutrophil percentage results were considered unacceptable if the result was 15% different than percentage results from both ADVIA 2120 and manual counts. ProCyte WBC dot plots and instrument flags were evaluated for correctness.

Results

The ProCyte neutrophil counts were unacceptably lower than the ADVIA 2120 and manual neutrophil counts in 13 samples (15% of 86 samples). Neutrophils misclassified by the instrument were erroneously classified as monocytes and/or lymphocytes. All these samples were from patients with systemic inflammation. The error could be eliminated by rejecting results from samples with incorrect separation of cell clusters in the ProCyte WBC dot plots.

Clinical Significance

The ProCyte neutrophil count error with canine blood samples is common, severe and might affect clinical decisions. Operators of the instrument must evaluate white blood cell dot plots for correctness to avoid the error.
The power of directional predictions in psychology
Authors: Trafimow David
Published: March 2022

The vast majority of empirical hypotheses in psychology, or in the social sciences more generally, are directional whereas in other sciences, such as the physical sciences, there are more point or narrow‐interval empirical hypotheses. Characteristics of theories and auxiliary assumptions play a role in the difference. Given that psychology research strongly features directional predictions, it is important to question the extent to which these provide convincing tests of theories that they are designed to test. The present work aims to provide a nuanced view that considers the complex interaction between the obviousness of directional predictions, the obviousness of the theory from which they derive, and the quality of the auxiliary assumptions that push towards directional predictions. Then, too, there is the related issue of vulnerability of directional predictions to alternative explanations and how to address them.
Quantitative differential analysis of norovirus outbreak samples using RT-ddPCR
Authors: Song Miok , Hwang Youngok , Park Jungeun , Cha Eukyong , Jeong Hyoeon , Kim Minkyeong , Kim Jinseok , Baek Soyune , Kwon Eunyoung , Park Sanghun , Oh Younghee , Shin Yongseoung
Published: March 2022

Noroviruses cause acute gastroenteritis with symptoms of diarrhoea and vomiting, and their high infectivity allows outbreaks to readily occur. Quickly identifying and isolating potential contaminants is an effective method to prevent the spread of outbreaks. A total of 376 samples collected from nine outbreaks were categorized as either patient, asymptomatic individual, cook or environmental samples, according to the source of contamination. Using real-time PCR and sequencing analysis, norovirus GII genotypes were detected in 34·9% of samples from patients, 19·2% from asymptomatic individuals, 2·4% from the environment and 1·4% from cooks. Our findings showed contrasting results in samples categories quantified based on the limit of blank and detection limit by reverse transcription droplet digital PCR, which is a more sensitive testing method than real-time-PCR.
Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species
Authors: Cheek Rebecca G. , Forester Brenna R. , Salerno Patricia E. , Trumbo Daryl R. , Langin Kathryn M. , Chen Nancy , Scott Sillett T. , Morrison Scott A. , Ghalambor Cameron K. , Chris Funk W.
Published: March 2022

We investigated the potential mechanisms driving habitat‐linked genetic divergence within a bird species endemic to a single 250‐km2 island. The island scrub‐jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine–oak ecotones on Santa Cruz Island, California (USA), similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3000 single nucleotide polymorphisms in 123 adult island scrub‐jay males from across Santa Cruz Island using restriction site‐associated DNA sequencing. Neutral landscape genomic analyses revealed that genome‐wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis while controlling for spatial effects. Finally, two genome‐wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
A cytosolic pentatricopeptide repeat protein is essential for tapetal plastid development by regulating OsGLK1 transcript levels in rice
Authors: Zheng Shaoyan , Dong Jingfang , Lu Jingqin , Li Jing , Jiang Dagang , Yu Haopeng , Ye Simiao , Bu Wenli , Liu Zhenlan , Zhou Hai , Ding Yiliang , Zhuang Chuxiong
Published: March 2022

Most plant pentatricopeptide repeat (PPR) proteins localize to and function inside plastids and mitochondria. However, the function of PPRs that only localize to the cytoplasm remains unknown.

Here, we demonstrated that the rice (Oryza sativa) PPR protein CYTOPLASM‐LOCALIZED PPR1 (OsCPPR1) contributes to pollen development and localizes to the cytoplasm.

Knocking down OsCPPR1 led to abnormal plastid development in tapetal cells, prolonged tapetal programmed cell death (PCD) and tapetum degradation, and significantly reduced pollen fertility. Transcriptome analysis revealed that the transcript level of OsGOLDEN‐LIKE1 (OsGLK1), which encodes a transcription factor that regulates plastid development and maintenance, was significantly higher in the OsCPPR1 knockdown plants compared to wild‐type plants. We further determined that OsCPPR1 downregulates OsGLK1 transcription by directly binding to the single‐stranded regions of OsGLK1 mRNAs. Overexpression of OsGLK1 resulted in abnormal tapetum and plastid development, similar to that seen in OsCPPR1 knockdown plants, and suppression of OsGLK1 partially restored pollen fertility in the OsCPPR1 knockdown plants. We therefore conclude that OsCPPR1 suppresses OsGLK1 in the regulation of plastid development and PCD in the tapetum.

Our work revealed novel functions for a cytosolic PPR, demonstrating the diverse roles of PPRs in plants and identifying a new regulatory mechanism for regulating pollen development in rice.
Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism
Authors: Arias Cintia Lucía , Quach Truyen , Huynh Tu , Nguyen Hanh , Moretti Ademar , Shi Yu , Guo Ming , Rasoul Amira , Van Kyujung , McHale Leah , Clemente Tom Elmo , Alonso Ana Paula , Zhang Chi
Published: March 2022

Soybean oil is one of the most consumed vegetable oils worldwide. Genetic improvement of its concentration in seeds has been historically pursued due to its direct association with its market value. Engineering attempts aiming to increase soybean seed oil presented different degrees of success that varied with the genetic design and the specific variety considered. Understanding the embryo’s responses to the genetic modifications introduced, is a critical step to successful approaches. In this work, the metabolic and transcriptional responses to AtWRI1 and AtDGAT1 expression in soybean seeds were evaluated. AtWRI1 is a master regulator of fatty acid (FA) biosynthesis, and AtDGAT1 encodes an enzyme catalysing the final and rate‐limiting step of triacylglycerides biosynthesis. The events expressing these genes in the embryo did not show an increase in total FA content, but they responded with changes in the oil and carbohydrate composition. Transcriptomic studies revealed a down‐regulation of genes putatively encoding for oil body packaging proteins, and a strong induction of genes annotated as lipases and FA biosynthesis inhibitors. Novel putative AtWRI1 targets, presenting an AW‐box in the upstream region of the genes, were identified by comparison with an event that harbours only AtWRI1. Lastly, targeted metabolomics analysis showed that carbon from sugar phosphates could be used for FA competing pathways, such as starch and cell wall polysaccharides, contributing to the restriction in oil accumulation. These results allowed the identification of key cellular processes that need to be considered to break the embryo’s natural restriction to uncontrolled seed lipid increase.
OsHIPL1, a hedgehog‐interacting protein‐like 1 protein, increases seed vigour in rice
Authors: He Ying , Chen Shanshan , Liu Kexin , Chen Yongji , Cheng Yanhao , Zeng Peng , Zhu Peiwen , Xie Ting , Chen Sunlu , Zhang Hongsheng , Cheng Jinping
Published: March 2022

The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog‐interacting protein‐like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA‐seq) revealed that the ABA‐related genes were involved in the OsHIPL1 regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of OsHIPL1 mutants and NIL‐qsv3 line compared to IR26 plants, with two up‐regulated ABA biosynthesis genes (OsZEP and OsNCED4) and one down‐regulated ABA catabolism gene OsABA8ox3. The expression of abscisic acid‐insensitive 3 (OsABI3), OsABI4 and OsABI5 was significantly up‐regulated in germinating seeds of OsHIPL1 mutants and NIL‐qsv3 line compared to IR26 plants. These results indicate that the regulation of seed vigour of OsHIPL1 may be through modulating endogenous ABA levels and altering OsABIs expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of OsHIPL1 that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of OsHIPL1 on seed vigour.