bluuebunny/crossref_metadata_2025 huggingface dataset:
Imputation and polygenic score performances of human genotyping arrays in diverse populations
Authors: Nguyen Dat Thanh , Tran Trang , Tran Mai , Tran Khai , Pham Duy , Duong Nguyen Thuy , Nguyen Quan , Vo Nam S.
Published: June 2022

Regardless of the overwhelming use of next-generation sequencing technologies, microarray-based genotyping combined with the imputation of untyped variants remains a cost-effective means to interrogate genetic variations across the human genome. This technology is widely used in genome-wide association studies (GWAS) at bio-bank scales, and more recently, in polygenic score (PGS) analysis to predict and to stratify disease risk. Over the last decade, human genotyping arrays have undergone a tremendous growth in both number, and content making a comprehensive evaluation of their performances became more important. Here, we performed a comprehensive performance assessment for 23 available human genotyping arrays in 6 ancestry groups using diverse public, and in-house datasets. The analyses focus on performance estimation of derived imputation (in terms of accuracy and coverage) and PGS (in term of concordance to PGS estimated from whole genome sequencing data) in three different traits and diseases. We found that the arrays with a higher number of SNPs are not necessarily the ones with higher imputation performance, but the arrays that are well-optimized for the targeted population could provide very good imputation performance. In addition, PGS estimated by imputed SNP array data is highly correlated to PGS estimated by whole genome sequencing data in most of cases. When optimal arrays are used, the correlations of key PGS metrics between two types of data can be higher than 0.97, but interestingly, arrays with high density can result in lower PGS performance. Our results suggest the importance of properly selecting a suitable genotyping array for PGS applications. Finally, we developed a web tool that provide interactive analyses of tag SNP contents and imputation performance based on population and genomic regions of interest. This study would act as a practical guide for researchers to design their genotyping arrays-based studies. The tool is available at: https://genome.vinbigdata.org/tools/saa/
HIV skews the SARS-CoV-2 B cell response toward an extrafollicular maturation pathway
Authors: Krause Robert , Snyman Jumari , Shi-Hsia Hwa , Muema Daniel , Karim Farina , Ganga Yashica , Ngoepe Abigail , Zungu Yenzekile , Gazy Inbal , Bernstein Mallory , Khan Khadija , Mazibuko Matilda , Mthabela Ntombifuthi , Ramjit Dirhona ,   COMMIT-KZN Team, Limbo Oliver , Jardine Joseph , Sok Devin , Wilson Ian , Hanekom Willem , Sigal Alex , Kloverpris Henrik , Ndung’u Thumbi , Leslie Alasdair
Published: June 2022

Background

HIV infection dysregulates the B cell compartment, affecting memory B cell formation and the antibody response to infection and vaccination. Understanding the B cell response to SARS-CoV-2 in people living with HIV (PLWH) may explain the increased morbidity, reduced vaccine efficacy, reduced clearance, and intra-host evolution of SARS-CoV-2 observed in some HIV-1 coinfections.

Methods

We compared B cell responses to COVID-19 in PLWH and HIV negative (HIV-ve) patients in a cohort recruited in Durban, South Africa, during the first pandemic wave in July 2020 using detailed flow cytometry phenotyping of longitudinal samples with markers of B cell maturation, homing and regulatory features.

Results

This revealed a coordinated B cell response to COVID-19 that differed significantly between HIV-ve and PLWH. Memory B cells in PLWH displayed evidence of reduced germinal center (GC) activity, homing capacity and class-switching responses, with increased PD-L1 expression, and decreased Tfh frequency. This was mirrored by increased extrafollicular (EF) activity, with dynamic changes in activated double negative (DN2) and activated naïve B cells, which correlated with anti-RBD-titres in these individuals. An elevated SARS-CoV-2 specific EF response in PLWH was confirmed using viral spike and RBD bait proteins.

Conclusions

Despite similar disease severity, these trends were highest in participants with uncontrolled HIV, implicating HIV in driving these changes. EF B cell responses are rapid but give rise to lower affinity antibodies, less durable long-term memory, and reduced capacity to adapt to new variants. Further work is needed to determine the long-term effects of HIV on SARS-CoV-2 immunity, particularly as new variants emerge.

Funding

This work was supported by a grant from the Wellcome Trust to the Africa Health Research Institute (Wellcome Trust Strategic Core Award [grant number 201433/Z/16/Z]). Additional funding was received from the South African Department of Science and Innovation through the National Research Foundation (South African Research Chairs Initiative, [grant number 64809]), and the Victor Daitz Foundation.
Spatial distribution of bacteria and extracellular polymeric substances impacts nanoparticle penetration in biofilms
Authors: Coppens Bart , Belpaire Tom E. R. , Pešek Jiří , Steenackers Hans P. , Ramon Herman , Smeets Bart
Published: June 2022

Extracellular polymeric substances (EPS) in bacterial biofilms complicate treatment by inactivating drugs and slowing down diffusion. Through enhanced penetration and resistance to degradation in bacterial biofilms, nanoparticle (NP) carriers can help improve biofilm treatment. However, the way in which biofilm architecture influences the diffusive properties and penetration of NPs in biofilms is still poorly understood. In this work, we combined single particle tracking (SPT) and confocal laser scanning microscopy (CLSM) in Salmonella biofilms with simulations of a Brownian dynamics model to quantify how macro- (spatial organization of the bacteria) and micro- (EPS dependent) structure of the biofilm affects NP penetration. In CLSM images we observed immobilization of NPs in the EPS, which allows shielding of bacteria from the NPs, an effect that was more pronounced in dispersed biofilms, grown in nutrient-rich conditions, than in compacted biofilms, grown in nutrient-poor conditions. SPT experiments revealed anomalous diffusion, with an increased probability for small displacements near clusters of bacteria. Simulations of a Brownian dynamics model revealed that EPS reinforces shielding by affecting the pore structure of the biofilm. Finally, in virtual biofilms with varying spatial distribution of bacteria, we found that even for the same number of bacteria, dispersed biofilm structures provide more shielding than biofilms organized in dense, compacted clusters, even when accounting for decreased NP diffusivity.
F-actin regulates polarized secretion of pollen tube attractants inArabidopsissynergid cell
Authors: Susaki Daichi , Izumi Rie , Oi Takao , Takeuchi Hidenori , Shin Ji Min , Sugi Naoya , Kinoshita Tetsu , Higashiyama Tetsuya , Kawashima Tomokazu , Maruyama Daisuke
Published: June 2022

Pollen tube attraction is a key event of sexual reproduction in flowering plants. In the ovule, two synergid cells neighboring the egg cell control pollen tube arrival via the active secretion of attractant peptides such as AtLURE1 and XIUQIU from the filiform apparatus facing toward the micropyle. Distinctive cell polarity together with longitudinal F-actin and microtubules are hallmarks of the synergid cell in various species, though functions of these cellular structures are still unclear. In this study we used genetic and pharmacological approaches to elucidate the roles of cytoskeletal components in filiform apparatus formation and pollen tube guidance inArabidopsis thaliana. Inhibition of microtubule formation reduced invaginations of the plasma membrane but did not abolish micropylar AtLURE1.2 accumulation. In contrast, the expression of a dominant-negative form of ACTIN8 induced disorganization of the filiform apparatus and loss of polar AtLURE1.2 distribution toward the filiform apparatus. Interestingly, after pollen tube reception, F-actin became unclear for a few hours in the persistent synergid cell, which may be involved in pausing and resuming pollen tube attraction during early polytubey block. Our data propose the central role of F-actin in the maintenance of cell polarity and function of male-female communication in the synergid cell.
Cell-type specific transcriptomic signatures of neocortical circuit organization and their relevance to autism
Authors: Moussa Anthony J. , Wester Jason C.
Published: June 2022

A prevailing challenge in neuroscience is understanding how diverse neuronal cell types select their synaptic partners to form circuits. In the neocortex, major classes of excitatory projection neurons and inhibitory interneurons are conserved across functionally distinct regions. There is evidence these classes form canonical circuit motifs that depend primarily on their identity; however, regional cues likely also influence their choice of synaptic partners. We mined the Allen Institute’s single-cell RNA-sequencing database of mouse cortical neurons to study the expression of genes necessary for synaptic connectivity and maintenance in two regions: the anterior lateral motor cortex (ALM) and the primary visual cortex (VISp). We used the Allen’s metadata to parse cells by clusters representing major excitatory and inhibitory classes that are common to both ALM and VISp. We then performed two types of pairwise differential gene expression analysis: 1) between different neuronal classes within the same brain region (ALM or VISp), and 2) between the same neuronal class in ALM and VISp. We filtered our results for differentially expressed circuit connectivity related genes and developed a novel bioinformatic approach to determine the sets uniquely enriched in each neuronal class in ALM, VISp, or both. This analysis provides an organized set of genes that may regulate circuit formation in a cell-type-specific manner. Furthermore, it identifies candidate mechanisms for the formation of circuits that are conserved across functionally distinct cortical regions or that are region dependent. Finally, we used the SFARI Human Gene Module to identify genes from this analysis that are related to risk for autism spectrum disorder (ASD). Our analysis provides clear molecular targets for future studies to understand neocortical circuit organization and abnormalities that underly autistic phenotypes.
A single-component luminescent biosensor for the SARS-CoV-2 spike protein
Authors: Ravalin Matthew , Roh Heegwang , Suryawanshi Rahul , Kumar G. Renuka , Pak John , Ott Melanie , Ting Alice Y.
Published: June 2022

Many existing protein detection strategies depend on highly functionalized antibody reagents. A simpler and easier to produce class of detection reagent is highly desirable. We designed a single-component, recombinant, luminescent biosensor that can be expressed in laboratory strains of E. coli and S. cerevisiae. This biosensor is deployed in multiple homogenous and immobilized assay formats to detect recombinant SARS-CoV-2 spike antigen and cultured virus. The chemiluminescent signal generated facilitates detection by an un-augmented cell phone camera. Binding Activated Tandem split-enzyme (BAT) biosensors may serve as a useful template for diagnostics and reagents that detect SARS-CoV-2 antigens and other proteins of interest.
Effects of magnetic and non-magnetic doping on the vortex lattice in MgB2
Authors: Louden Elizabeth R. , Manni Soham , Zandt Judah E. Van , Leishman Allan W. D. , Taufour Valentin , Bud'ko Sergey L. , DeBeer-Schmitt Lisa , Honecker Dirk , Dewhurst Charles D. , Canfield Paul C. , Eskildsen Morten R.
Published: June 2022

Small-angle neutron scattering has been used to study the vortex lattice in superconducting MgB2 doped with either manganese or carbon to achieve a similar suppression of the critical temperature. Measurements were performed with the magnetic field applied along the c axis, where the vortex lattice in pure MgB2 is known to undergo a field- and temperature-driven 30° rotation transition. For Mn doping, the vortex lattice phase diagram remains qualitatively similar to that of pure MgB2, indicating only a modest effect on the vortex–vortex interaction. In contrast, the vortex lattice rotation transition is completely suppressed in the C-doped case, probably due to a change in the electronic structure which affects the two-band/two-gap nature of superconductivity in MgB2. The vortex lattice longitudinal correlation length shows the opposite behavior, remaining roughly unchanged between pure and C-doped MgB2 while it is significantly reduced in the Mn-doped case. However, the extensive vortex lattice metastability and related activated behavior, observed in conjunction with the vortex lattice transition in pure MgB2, are also seen in the Mn-doped sample. This shows that the vortex lattice disordering is not associated with a substantially increased vortex pinning.
Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously
Authors: Bhatia Indu , Yadav Savita , Biswal Bichitra K.
Published: June 2022

The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 Å resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni2+), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the α3 and α4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.
“I felt goosebumps”: emotional experiences of pre-service English teachers and the critical use of narratives
Authors: Abruzzo Emma , Bartow Jacobs Katrina
Published: June 2022

Purpose

This paper aims to suggest a new way for structuring English teacher preparation within traditional university programs, challenging the age-old use of formal lesson plan reflections and introducing critical narratives as course texts to better understand pre-service teacher experiences. Through this reimagined English methods curriculum, the authors establish increased cohesion between practice and theory, facilitate the development of teacher reflective practice and establish methods for apprehending the emotional experience of pre-service educators.

Design/methodology/approach

This study of 18 pre-service English language arts students considers how teacher education programs could better emphasize socio-emotional elements of teaching by asking students to produce and engage with critical narratives that require more than just an appraisal of learning outcomes of direct instruction, but merge critical inquiry, ethical teaching considerations, self-reflection and perceptions of practice.

Findings

The findings indicate that when compared with traditional lesson plan reflections, critical narrative reflections of field experiences increase student focus on emotional aspects of teaching, provide a more nuanced lens into emotional experiences and establish a more complex conception of the teaching practice.

Originality/value

This curricular design challenges the prevailing ways that English pre-service educators are understood and taught through a reimagined understanding and application of narrative writing as course texts.
Approaching systems change at Fulfilling Lives South East in efforts to improve unsupported temporary accommodation: a qualitative case study
Authors: Cooke Charlotte , Jones Kate , Rieley Rebecca , Sylvester Sandra
Published: June 2022

Purpose

The purpose of this paper is to consider how a South East project approached systems change to improve unsupported temporary accommodation (UTA) and the changes made for people experiencing multiple disadvantage (“multiple and complex needs”). This paper also covers some matters that are hard to change or uncertain, such as housing shortages and financial constraints. The paper focuses on a case study of the East Sussex Temporary Accommodation Action Group (TAAG) – a multi-agency action group.

Design/methodology/approach

A qualitative case study involving a thematic analysis of seven semi-structured interviews, with a review of published literature and internal documentation.

Findings

This example of setting up a TAAG shows us the value of having a dedicated forum to look at a part of the system that requires changing and to identify what works well. Creating a collaborative and democratic space with a common purpose brings different stakeholders and perspectives together and opens discussions to new ways of working. Equalising partners creates an opportunity to create change from the bottom-up within a system traditionally governed by statutory bodies. This study found that the TAAG has facilitated learning around trauma-informed practice and nurtured more sustainable changes towards a Standards Charter and women-only safe UTA.

Originality/value

This is one of the first qualitative case studies of a local systems change approach to improving UTA for people experiencing multiple disadvantage in East Sussex.
Heat transmission in Darcy-Forchheimer flow of Sutterby nanofluid containing gyrotactic microorganisms
Authors: Khan Ambreen A. , Arshad Alina , Ellahi R. , Sait Sadiq M.
Published: June 2022

Purpose

This paper aims to deal with the heat transmission of Sutterby fluid-containing gyrotactic microorganism by incorporating non-Darcy resistance law. The mathematical modeling is based on nanoparticle concentration, energy, momentum and motile microorganism equations.

Design/methodology/approach

The governing nonlinear coupled equations are first rendered into nonlinear ordinary equations using appropriate transformation and are then solved analytically by using the optimal homotopy.

Findings

Graphical illustration of results depict the behavior of flow involved physical parameters on temperature, gyrotactic microorganism, concentration and velocity. Additionally, local Nusselt number and skin friction coefficient are computed numerically and validated through comparison with existing literature as a special case of proposed model. It is found that the temperature profile decreases by increasing values of Brownian-motion parameter and Prandtl number. An increase in thermophoresis parameter and Schmidt number results in decrease in concentration of nanoparticles. Bioconvection Peclet number corresponds to decreasing behavior of nondimensional gyrotactic microorganism field is observed. Finally, a comparison with the existing literature is made, and an excellent agreement is seen.

Originality/value

To the best of the authors’ knowledge, this study is reported for the first time.
Understanding virtual organizational identity through the intersection of information technology and narratives
Authors: Davis Daniel J.
Published: June 2022

Purpose

Virtual organizations present numerous challenges for managers, especially in regards to organizational identity formation. This paper aims to address this gap in the extant literature by exploring how organizational narratives can foster identification with the virtual organization. Moreover, information technology can further catalyze the positive effects of narratives on identity formation.

Design/methodology/approach

Qualitative data from in-depth interviews with 18 members of a nonprofit, virtual organization – DiverseCS – were collected. Participants were asked about their roles in the organization, challenges and collaborative efforts. Grounded theory methodology was used to analyze the data.

Findings

Efforts to instill a sense of identity and community through the adoption of information technology was met with resistance. Rather, senior leaders encouraged and institutionalized the creation of organizational narratives. Novel use of information technology – social media and hyperlinks – became a means to amplify the positive effects of narrative creation and sharing by organizational members.

Originality/value

This study investigates how some members of a virtual organization use information technology in novel ways to further spread organizational narratives to other organizational members and also to external collaboration partners. This research contributes to the extant literature on virtual organizational identity and also proposes a research agenda.
Proposed flood evacuation routes for heritage areas based on spatial configuration analysis: a case study of Penang, Malaysia
Authors: Safizadeh Mina , Hedayati Marzbali Massoomeh , Abdullah Aldrin , Maliki Nor Zarifah
Published: June 2022

Purpose

Because of the global increase of climate change effects, floods are becoming more frequent and severer, especially in urban areas of coastal cities and islands where floodplains have turned into buildings because of rapid urbanisation, leading to a higher risk of damages. Urban heritage areas should be highly considered in the time of evacuation because of the vulnerability of streets and buildings and limitations on taking counteractions. Given these limitations, this study aims to propose a network of potential evacuation routes based on spatial configuration analysis of the heritage areas.

Design/methodology/approach

Penang Island's heritage site, namely, George Town, located on the northwest coast of Malaysia, is chosen as the case study. By using an approach of spatial configuration analysis using space syntax techniques in addition to considering the potential starting points for evacuation and flood risk map of the area, this study analysed the area's street network values for evacuation function during flood crisis time.

Findings

Potential evacuation routes were identified for flood disasters in the George Town heritage area. Furthermore, the proposed evacuation routes were evaluated in terms of time for evacuation by metric step-depth analysis of space syntax.

Originality/value

A few studies have focused on practical guidelines for evacuation routes based on spatial configuration analysis, an important yet neglected approach in this regard, especially concerning urban island areas. This study can contribute to providing strategies to reduce vulnerability and casualties in urban heritage areas.
Virtue or vice? Public policies and Nigerian entrepreneurial venture performance
Authors: Olorunshola Damilola Temitope , Odeyemi Temitayo Isaac
Published: June 2022

Purpose

The purpose of this paper is to explore how inter-agency engagement across levels of government and the agencies' policies impact the development of Micro, Small and Medium Scale Enterprises (MSMEs) in Nigeria, with focus on taxation, business registration and access to finance.

Design/methodology/approach

The empirical study involved data sourced through questionnaire administered to 192 MSMEs owners, semi-structured interviews with key officials, and Focus Group Discussion (FGD) with leading members of the Osun State Chamber of Commerce, Mines, Industry and Agriculture (OSUCCIMA).

Findings

Amidst increasing levels of engagement amongst public agencies, most MSMEs had not benefited from MSMEs' support programmes. Also, although agencies increasingly utilised the mediating roles of OSUCCIMA in policies for MSMEs, gaps remain because of not factoring in OSUCCIMA's inputs into final policy/programme drafts. Again, policies and programmes were tangential to the desired development outcomes amongst MSMEs, irrespective of size.

Research limitations/implications

Considering differences in socio-economic and psycho-social orientations of residents/business owners across the various states, further studies focussing on other parts of Nigeria will help to strengthen the argument on how Nigeria aligns with the developing countries literature on the subject.

Originality/value

Existing literature demonstrates government's recognition of the significance of MSMEs and policy actions taken in setting the right atmosphere for them to thrive, focussing on the national or local governments. This study draws on these but also explores actions at the subnational level and the role of mediating institutions, thereby showing how a multi-level governance approach could influence outcomes.
Narrative forward-looking information disclosure, do ownership concentration, boardroom gender diversity and cultural values matter? A cross country study
Authors: Abdallah Maysa Ali Mohamed , Eltamboly Nayera Adeldayem
Published: June 2022

Purpose

This study aims to identify the main factors that drive the differences in the levels of forward-looking information disclosure (FLID) across four countries. This study goes beyond the firm-specific characteristics to the countries-specific factors to explain the observable differences in the level of FLID among the UK, Italian, Hong Kong and Chinese American Depositary Receipts (ADRs) firms trading in US Exchanges.

Design/methodology/approach

To validate the levels of FLID, corporate financial information environment (CFIE)-final reports structure extractor (FRSE) was conducted on the annual reports of a sample of 353 listed firm observations in 2020 across four different countries. Also, the ordinary least square regression model was used to examine the proposed relationships.

Findings

The empirical results indicate that the level of FLID is highest among the Chinese ADRs firms trading in US Exchanges and UK listed firms. Also, ownership concentration and gender diversity have a positive correlation with the level of FLID. Additionally, long-term orientation positively influences the level of FLID. Considering the moderation effect of power distance and masculinity dimensions, countries with larger power distance tend to have a lower impact of ownership concentration on the level of FLID, whereas countries with higher masculinity tend to have a lesser positive relationship between gender diversity and the level of FLID.

Originality/value

Notwithstanding, this study provides novel and persuasive evidence regarding the effects of firm- and country-specific characteristics as possible determinants of forward-looking disclosures, drawing on evidence from international companies with free floats, boards with female quotas and cultural values including masculinity and long-term orientation. This work offers unique insights from the upper echelons lens, which implies that firms need to obtain a critical mass of gender diversity to achieve a more balanced forward-looking perspective on their annual reports.
Distribution and functional data of fungal families
Authors: Matsuoka Shunsuke , Hatano Yuki , Osono Takashi
Published: June 2022

Fungi have unique ecosystem functions, such as organic matter decomposition, parasitism, and symbiosis with other organisms in terrestrial and aquatic ecosystems. Their taxonomic and functional diversities are essential factors for predicting ecosystem functions and their responses to environmental changes. With the widespread use of high‐throughput sequencing (HTS) in recent years, the detection of fungal DNA sequences in various regions and on different environmental substrates has advanced. HTS‐obtained DNA sequences can be compared with those in databases to identify the taxa of organisms from which they are derived. Therefore, a global DNA database containing taxonomic information has been developed. However, functional data on the distribution and function of individual taxa remain scarce. In this study, the ecological information of each fungal family was compiled from review papers and published books. Specifically, the following information was collected: reported distribution (11 categories including information on the presence of fungi in Japan) and function (38 categories related to ecological functional data, such as guilds and habitats) of 553 families included in the literature. These data will provide information on the ecology of specific fungi detected in the field and help estimate the functional group composition and diversity of fungi from their DNA assemblage data. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-02.1/jalter-en.
Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa
Authors: Xu Xuejie , Yan Yunfang , Huang Jiadai , Zhang Zihao , Wang Zhihan , Wu Min , Liang Haihua
Published: June 2022

The opportunistic pathogen Pseudomonas aeruginosa has evolved several systems to adapt to complex environments. The GntR family proteins play important roles in the regulation of metabolic processes and bacterial pathogenesis. In this study, we uncovered that the gene clusters of PA1513‐PA1518 and PA1498‐PA1502 in P. aeruginosa are required for uric acid and glyoxylate metabolism respectively. We also identified a GntR family regulator UgmR that is involved in regulation of uric acid and glyoxylate metabolism. Promoter activity measurement and biochemical assays revealed that the UgmR directly represses the transcriptional activity of PA1513‐PA1518 and PA1498‐PA1502, and this inhibition was relieved by the addition of uric acid. Importantly, further experiments showed that UgmR also participates in the glyoxylate shunt. Collectively, these findings contribute to a better understanding of the UgmR factor involved in uric acid and glyoxylate metabolism, which provide insights into the complex metabolic pathways in P. aeruginosa.
Evaluation of the close degree of the spatial relationship between natural enemies of tea gardens and Frankliniella intonsa based on variance analysis of cluster samples
Authors: Honghao Cheng , Shiyan Chen , Xiaomeng Wu , Yue Xu , Lin Zhang , Jiazhao Sun , Xiazhi Zhou , Yunding Zou , Shoudong Bi
Published: June 2022

The aim of this paper is to clarify the difference of spatial closeness between natural enemies and Frankliniella intonsa, and to provide a scientific basis for rational protection and utilization of natural enemies. This paper applied the block‐sample square difference analysis method, Gray correlation degree method, the aggregation intensity index method and
index method to study the difference in the closeness of the spatial relationship between F. intonsa and natural enemies when the number of F. intonsa and their natural enemies was the highest and the minimum area occupied by F. intonsa individuals and colonies in five tea plantations in Hefei, Anhui province in 2021 and four tea plantations in 2020. The results were as follows: 1) Tetragnatha squamata Karsch, Xysticus ephippiafus, Erigonidium graminicolum and Theridion Octomaculatum were the top four natural enemies closely related to F. intonsa in 2021. The top three natural enemies closely related to F. intonsa in 2020 were Tetragnatha squamata Karsch, Xysticus ephippiafus and Theridion Octomaculatum. Two years ago, Tetragnatha squamata Karsch and Xysticus ephippiafus were the same. 2) Cluster size did not change the distribution patterns of natural enemies and F. intonsa. 3) The aggregation of F. intonsa was caused by their own causes or some environmental factors, and the aggregation of natural enemies was caused by environmental factors. 4) In 2021, the minimum area occupied by individuals and groups of F. intonsa in tea gardens was 2m2, and in 2020, it was 8 m2.
Peppermint essential oil‐loaded solid lipid nanoparticle in gelatin coating: Characterization and antibacterial activity against foodborne pathogen inoculated on rainbow trout (Oncorhynchus mykiss) fillet during refrigerated storage
Authors: Laein Sara Safaeian , Khanzadi Saeid , Hashemi Mohammad , Gheybi Fatemeh , Azizzadeh Mohammad
Published: June 2022

The present study was conducted to determine the characterization and antibacterial activity of peppermint essential oil‐loaded solid lipid nanoparticle (PEO–SLN) and its impact on the quality of trout fillet stored at 4 ± 1°C for 12 days. The SLNs were prepared through a bath sonication technique. PEO–SLNs contained 0.2% (w/v) PEO in 2% of lipid phase glycerol monostearate (GMS) and tween 80 (1% w/v) used as a surfactant in the aqueous phase. The characterization parameter of PEO–SLN was evaluated, and the antibacterial activity of PEO–SLNs was conducted under in vitro conditions. Trout samples were analyzed for inoculatedPseudomonas aeruginosa, Listeria monocytogenes, andEscherichia coliO157:H7 during refrigerated storage. The mean particle size of PEO–SLNs was 154.83 ± 1.21 nm with a polydispersity index (PDI) of 0.35 ± 0.01 and zeta potential was about −24.16 ± 0.51 mV. The results indicated that PEO–SLN had higher antibacterial activity than the free form of PEO and also when used in combination with gelatin coating (gel + PEO–SLN) had a significant effect on preventing microbial growth in trout fillets (p < 0.05). The most decreasing rate ofP. aeruginosa(1.92 log CFU/g),E. coliO157:H7 (0.71 log CFU/g), andL.monocytogenescount (1.69 log CFU/g) was seen in gel + PEO–SLN. These findings illustrated that PEO–SLNs could potentially be utilized in the food industry to increase the shelf life of fish fillets.
Acceptability of orange corn‐common bean as an alternative to corn–soybean complementary porridge in Malawi
Authors: Gama Aggrey Pemba , Matumba Limbikani , Munthali Justice , Namaumbo Sydney , Chimbaza Monica , Ngoma Theresa , Kammwamba Kondwani , Chisapo Gift , Chilembo Madalitso , Meleke Nyadani , Chirwa Rowland , Fungo Robert
Published: June 2022

This study assessed the acceptability of porridge from a corn‐common bean flour blend to increase the diversity of complementary foods in Malawi. Porridges prepared using commercial corn–soybean flour (C‐CSB), homemade orange corn–soybean flour (H‐CSB), and orange corn‐common bean flour (CCBB) were evaluated by 101 pairs of mothers and their respective children aged from 6 to 24 months. A home use test (HUT) setup was used in this study, and the flours were given sequentially to participating households following a randomized complete block design. Each sample type was evaluated for 3 days in a row followed by a 1‐day break (washout period) between sample types. Based on aggregate mean scores, all the samples were liked by both the children and their mothers. However, clustering results revealed two distinct consumer segments for mothers as well as for children. Most of the mothers (59.4% in cluster 1) liked all the samples, while the minority (cluster 2) were neutral (neither like nor dislike) regarding the H‐CSB porridge. Likewise, most children (66.3% in cluster 2) liked all the samples, while the rest in cluster 1 did not like CCBB porridge. Infants (≤12 months) and those from food‐insecure households, respectively, were 5.42 and 6.75 times more likely to like the CCBB porridge than their counterparts. The study has demonstrated the potential of introducing CCBB complementary porridge in Malawi and possibly in other countries with similar food preferences and socioeconomic stature.

Practical Application

The study provides a solution to the limited diversity of complementary foods in sub‐Saharan Africa and Malawi in particular. The findings can help food scientists, nutritionists, marketers, and policymakers develop strategies for promoting the consumption of orange corn‐common bean porridge. Furthermore, the findings can inform decisions on commercializing orange corn‐common bean flour by flour processors.
Evaluating Soil Conservation Effectiveness: An Investigation of Spatial Targeting, Conservation Adoption, and Financial Incentives
Authors: Fowler Ames F. , Boll Jan , Beall King Allyson
Published: June 2022

Identifying and treating erosion‐prone, critical source areas (CSA) presents the opportunity to effectively address erosion at a watershed scale. Social and financial drivers of conservation adoption, however have buffered implementation. An integrated systems understanding is needed to identify internal feedbacks and potential synergistic conservation policies. We simulate the physical, social, and financial incentive interactions with a high‐level system dynamics model to understand the conservation adoption and subsequent erosion behavior of the system. A Bass diffusion model integrated with physical modeling results enables the simulation of CSA, the diffusion of innovations, and payment for conservation practices. Land retirement and tillage reduction best management practices are assessed for the dryland wheat farming region in the Inland Pacific Northwest of the United States. Model utility was confirmed with quantitative land management data and qualitative local expertise. Historical, voluntary‐based efforts to reduce erosion suffer marginal returns. We conclude that: (1) All targeting of CSA reduces long‐term erosion rates; (2) The most effective use of conservation funds, however, occurs when the diffusion of innovation mechanism is reinforced by broad‐scale payments for tillage reduction; and (3) By identifying and utilizing positive feedback, our simulations suggest large gains in erosion reduction and conservation fund efficiency are possible.
A mixed‐methods approach to improve the measurement of alcohol‐induced blackouts: ABOM‐2
Authors: Boness Cassandra L. , Gatten Natalie , Treece Mc Kenna , Miller Mary Beth
Published: June 2022

Background

Alcohol‐induced blackouts describe memory loss resulting from alcohol consumption. Approximately half of college students report experiencing a blackout in their lifetime. Blackouts are associated with an increased risk for negative consequences, including serious injury. Research has documented two types of blackouts, en bloc (EB) and fragmentary (FB). However, research is limited by the lack of a validated measure that differentiates between these two forms of blackout. This study used a mixed‐methods approach to improve the assessment of FB and EB among young adults. Specifically, we sought to improve the existing Alcohol‐Induced Blackout Measure (ABOM), which was derived from a relatively small pool of items that did not distinguish FB from EB.

Methods

Study 1 used three rounds of cognitive interviewing with U.S. college students (N = 31) to refine existing assessment items. Nineteen refined blackout items were retained for Study 2. Study 2 used face validity, factor analysis, item response theory, and external validation analyses to test the two‐factor blackout model among U.S. heavy‐drinking college students (N = 474) and to develop and validate a new blackout measure (ABOM‐2).

Results

Iterative factor analyses demonstrated that the items were well represented by correlated EB and FB factors, consistent with our hypothesis. External validation analyses demonstrated convergent and discriminant validity. These analyses also provided preliminary evidence for the two factors having differential predictive validity (e.g., FB correlated with enhancement drinking motives, while EB correlated with coping and conformity motives).

Conclusions

The Alcohol‐Induced Blackout Measure‐2 (ABOM‐2) improves the measurement of blackout experiences among college students. Its use could facilitate the examination of EB and FB as differential predictors of alcohol‐related outcomes in future studies.
African agricultural development: How are we contributing?
Authors: Vink Nick
Published: June 2022

A database of journal articles and conference papers that cover the economics of agricultural development in Africa during the period 2016–2020 was compiled. These papers are first described in terms of demographic and bibliometric criteria, followed by a network analysis of the main centers of origin and of influence of this research. Finally, three different processes were used to test the policy relevance of the work. These include a simple enumeration of the policy recommendations in a sample of the papers, a megatrend analysis, and a comparison of their focus with the standard narrative of the role of agriculture in economic development. The results show that a large proportion of the literature is not forward‐looking, and is weak on policy relevance. We ignore a number of issues that engage the attention of those concerned with implementing structural change in agriculture across the many very different but very real natural resource, political, social, economic, and technological environments around the continent.
Observer‐driven pseudoturnover in vegetation monitoring is context‐dependent but does not affect ecological inference
Authors: Boch Steffen , Küchler Helen , Küchler Meinrad , Bedolla Angéline , Ecker Klaus T. , Graf Ulrich H. , Moser Tobias , Holderegger Rolf , Bergamini Ariel
Published: June 2022

Aims

Resurveys of vegetation plots are prone to several errors that can result in misleading conclusions. Minimizing such errors and finding alternative approaches for analyzing resurvey data are therefore important. We focused on inter‐observer error and excluded other sources of variation. Our main questions were: How large is the inter‐observer error (i.e. pseudoturnover) in vegetation surveys, and can it be reduced by simple data aggregation approaches? Which factors are affecting pseudoturnover and does it vary between morphological species groups or change over time? Is ecological inference robust against inter‐observer differences?

Location

Switzerland.

Methods

Over seven years, we double‐surveyed a total of 224 plots that were marked once in the field and then sampled by two observers independently on the same day. Both observers conducted full vegetation surveys, recording all vascular plant species, their cover, and additional plot information. We then calculated mean ecological indicator values and pseudoturnover.

Results

Average pseudoturnover was 29% when raw species lists were compared. However, by applying simple aggregation steps to the species list, pseudoturnover was reduced to 17%. Pseudoturnover further varied among habitat types and declined over the years, indicating a training effect among observers. Most overlooked taxa, responsible for pseudoturnover, had low cover values. Mean ecological indicator values were robust against inter‐observer differences.

Conclusions

To minimize pseudoturnover, we suggest continuous training of observers and species‐list aggregation prior to analysis. As mean ecological indicator values were robust against inter‐observer differences, we conclude that they can provide a reliable estimate of temporal vegetation and ecological changes.
Phase IIb study of pembrolizumab combined with S‐1 + oxaliplatin or S‐1 + cisplatin as first‐line chemotherapy for gastric cancer
Authors: Yamaguchi Kensei , Minashi Keiko , Sakai Daisuke , Nishina Tomohiro , Omuro Yasushi , Tsuda Masahiro , Iwagami Shiroh , Kawakami Hisato , Esaki Taito , Sugimoto Naotoshi , Oshima Takashi , Kato Ken , Amagai Kenji , Hosaka Hisashi , Komine Keigo , Yasui Hisateru , Negoro Yuji , Ishido Kenji , Tsushima Takahiro , Han Shirong , Shiratori Shinichi , Takami Tomoko , Shitara Kohei
Published: June 2022

The KEYNOTE‐659 study evaluated the efficacy and safety of first‐line pembrolizumab plus S‐1 and oxaliplatin (SOX) (cohort 1) or S‐1 and cisplatin (SP) (cohort 2) for advanced gastric/gastroesophageal junction (G/GEJ) cancer in Japan. Herein, we update the results of cohort 1 and describe the results of cohort 2. This open‐label phase IIb study enrolled patients with advanced programmed death‐ligand 1 (PD‐L1)‐positive (combined positive score ≥ 1) human epidermal growth factor receptor 2 (HER2)‐negative G/GEJ adenocarcinoma. The primary end‐point was the objective response rate (ORR). Other end‐points were duration of response (DOR), disease control rate (DCR), progression‐free survival (PFS), overall survival (OS), and safety. One hundred patients were enrolled. In cohorts 1 and 2, median follow‐up time was 16.9 and 17.1 months; ORR (central review), 72.2% and 80.4%; DOR, 10.6 and 9.5 months; DCR (central review), 96.3% and 97.8%; median PFS (central review), 9.4 and 8.3 months; and median OS, 16.9 and 17.1 months, respectively. Treatment‐related adverse events (TRAEs) occurred in all patients, including peripheral sensory neuropathy (94.4%, cohort 1), decreased neutrophil count (82.6%, cohort 2), nausea (59.3% and 60.9% in cohorts 1 and 2), and decreased appetite (61.1% and 60.9% in cohorts 1 and 2). Grade 3 or higher TRAEs were reported by 59.3% (cohort 1) and 78.3% (cohort 2), including decreased platelet count (14.8%, cohort 1) and decreased neutrophil count (52.2%, cohort 2). Pembrolizumab in combination with SOX or SP showed favorable efficacy and safety in patients with PD‐L1‐positive, HER2‐negative G/GEJ adenocarcinoma.
High‐resolution hippocampal diffusion tensor imaging of mesial temporal sclerosis in refractory epilepsy
Authors: Chau Loo Kung Gustavo , Chiu Andrew , Davey Zach , Mouchawar Nicole , Carlson Mackenzie , Moein Taghavi Hossein , Martin Douglas , Graber Kevin , Razavi Babak , McNab Jennifer , Zeineh Michael
Published: June 2022

Objective

We explore the possibility of using diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) to discern microstructural abnormalities in the hippocampus indicative of mesial temporal sclerosis (MTS) at the subfield level.

Methods

We analyzed data from 57 patients with refractory epilepsy who previously underwent 3.0‐T magnetic resonance imaging (MRI) including DTI as a standard part of presurgical workup. We collected information about each subject's seizure semiology, conventional electroencephalography (EEG), high‐density EEG, positron emission tomography reports, surgical outcome, and available histopathological findings to assign a final diagnostic category. We also reviewed the radiology MRI report to determine the radiographic category. DTI‐ and NODDI‐based metrics were obtained in the hippocampal subfields.

Results

By examining diffusion characteristics among subfields in the final diagnostic categories, we found lower orientation dispersion indices and elevated axial diffusivity in the dentate gyrus in MTS compared to no MTS. By similarly examining among subfields in the different radiographic categories, we found all diffusion metrics were abnormal in the dentate gyrus and CA1. We finally examined whether diffusion imaging would better inform a radiographic diagnosis with respect to the final diagnosis, and found that dentate diffusivity suggested subtle changes that may help confirm a positive radiologic diagnosis.

Significance

The results suggest that diffusion metric analysis at the subfield level, especially in dentate gyrus and CA1, maybe useful for clinical confirmation of MTS.