Mapping Studies Research Articles

GENOME-WIDE ASSOCIATION STUDY OF YIELD-RELATED TRAITS IN A NESTED ASSOCIATION MAPPING POPULATION GROWN IN KAZAKHSTAN

This study evaluated 290 recombinant inbred lines (RILs) from the Nested Association Mapping (NAM) population in the UK, consisting of 24 hybrid families. All genotypes were grown in southeastern Kazakhstan (Kazakh Research Institute of Agriculture and Plant Growing, Almaty region, 2021-2022) and northern Kazakhstan (Alexandr Barayev Scientific-Production Center for Grain Farming, Akmola region, 2020). The studied traits included six yield-related characteristics: spike length (SL, cm), number of productive spikes per plant (NPS, pcs), number of kernels per spike (NKS, pcs), weight of kernels per spike (WKS, g), thousand kernel weight (TKW, g), and yield per square meter (YM2, g/m2). The significant phenotypic variability among genotypes was observed, which was suitable for the genome-wide association study of yield-related traits. Pearson's index showed positive correlations among most yield-related traits, although a negative correlation was found between NKS and TKW in southeastern, and no correlation was recorded for northern regions. Top-performing RILs, surpassing local checks, were identified for NKS, TKW, and YM2, suggesting their potential for breeding programs. The application of GWAS allowed the identification of 72 quantitative trait loci (QTLs), including 36 QTLs in the southeastern region, 16 QTLs in the northern region, and 19 in both locations. Eleven QTLs matched those reported in previous QTL mapping studies and GWAS for studied traits. The results can be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity.

Some limitations of the concordance correlation coefficient to characterise model accuracy

Perusal of the environmental modelling literature reveals that the Lin's concordance correlation coefficient is a popular validation statistic to characterise model or map quality. In this communication, we illustrate with synthetic examples three undesirable statistical properties of this coefficient. We argue that ignorance of these properties have led to a frequent misuse of this coefficient in modelling and mapping studies. The stand-alone use of the concordance correlation coefficient is insufficient because i) it does not inform on the relative contribution of bias and correlation, ii) the values cannot be compared across different datasets or studies and iii) it is prone to the same problems as other linear correlation statistics. The concordance coefficient was, in fact, thought initially for evaluating reproducibility studies over repeated trials of the same variable, not for characterising model accuracy. For the validation of models and maps, we recommend calculating statistics that, combined with the concordance correlation coefficient, represent various aspects of the model or map quality, which can be visualised together in a single figure with a Taylor or solar diagram.

The genetics of plant-plant interactions and their cascading effects on agroecosystem - from model plants to application.

Plants are typically surrounded by neighboring individuals in agricultural fields or natural environments. In such circumstances, plant-plant interactions (PPI) are ubiquitous and represent not only important evolutionary forces but also have consequences on (agro-)ecosystem functioning, such as increased productivity and resistance. However, many mechanisms underlying these PPIs remain poorly understood. Recently, new genomic technologies and tools, such as genome-wide association studies, have facilitated genetic approaches to study PPIs, particularly among conspecific individuals. Here, we highlight emerging issues and advances in the field by focusing on three different aspects. First, we overview the current status of genetic mapping studies on PPIs and pinpoint that these studies open a new opportunity that is relevant to agriculture and breeding. Second, we introduce two proof-of-concept studies in Arabidopsis thaliana, in which genetic differences among plants improved the functioning of genotype mixtures. Both studies were able to predict effective mixtures with different experimental designs applied to different outcomes (productivity increase vs. herbivory mitigation). Third, we discuss implications from these case studies about how PPIs have cascading effects that propagate to higher levels of biological organization, such as populations or communities. At the population level, plant yield or resistance can be optimized through breeding that achieves reduced competition or push-pull protection systems, respectively. At the community level, these population-level changes may have further beneficial effects on plant-associated organisms. Overall, we suggest that the increasing availability of genomic resources will improve our understanding of PPIs and thereby contribute to the management of crops or semi-natural ecosystems.

Investigative power of genomic informational field theory relative to genome-wide association studies for genotype-phenotype mapping.

Identifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R. A. Fisher, genome-wide association studies (GWAS) extract information using averages and variances from genotype-phenotype datasets. Averages and variances are legitimated upon creating distribution density functions obtained through the grouping of data into categories. However, as data from within a given category cannot be differentiated, the investigative power of such methodologies is limited. Genomic informational field theory (GIFT) is a method specifically designed to circumvent this issue. The way GIFT proceeds is opposite to that of GWAS. Although GWAS determines the extent to which genes are involved in phenotype formation (bottom-up approach), GIFT determines the degree to which the phenotype can select microstates (genes) for its subsistence (top-down approach). Doing so requires dealing with new genetic concepts, a.k.a. genetic paths, upon which significance levels for genotype-phenotype associations can be determined. By using different datasets obtained in Ovis aries related to bone growth (dataset 1) and to a series of linked metabolic and epigenetic pathways (dataset 2), we demonstrate that removing the informational barrier linked to categories enhances the investigative and discriminative powers of GIFT, namely that GIFT extracts more information than GWAS. We conclude by suggesting that GIFT is an adequate tool to study how phenotypic plasticity and genetic assimilation are linked.NEW & NOTEWORTHY The genetic basis of complex traits remains challenging to investigate using classic genome-wide association studies (GWASs). Given the success of gene editing technologies, this point needs to be addressed urgently since there can only be useful editing technologies whether precise genotype-phenotype mapping information is available initially. Genomic informational field theory (GIFT) is a new mapping method designed to increase the investigative power of biological/medical datasets suggesting, in turn, the need to rethink the conceptual bases of quantitative genetics.

On a family of sparse exponential sums

AbstractWe investigate exponential sums modulo primes whose phase function is a sparse polynomial, with exponents growing with the prime. In particular, such sums model those which appear in the study of the quantum cat map. While they are not amenable to treatment by algebro‐geometric methods such as Weil's bounds, Bourgain gave a nontrivial estimate for these and more general sums. In this work, we obtain explicit bounds with reasonable savings over various types of averaging. We also initiate the study of the value distribution of these sums.

Comparing Apples and Oranges: Advances in Disease Resistance Breeding of Woody Perennial Fruit Crops.

Apple and citrus are perennial tree fruit crops that are vital for nutritional security and agricultural economy and to achieve the Sustainable Development Goals of the United Nations. Apple scab and fire blight, along with Huanglongbing, canker, and tristeza virus, stand out as their most notorious diseases and annually destabilize fruit supply. An environmentally sound approach to managing these diseases is improving tree resistance through breeding and biotechnology. Perennial fruit tree germplasm collections are distributed globally and offer untapped potential as sources of resistance. However, long juvenility, specific pollination and flowering habits, and extensive outcrossing hinder apple and citrus breeding. Advances in breeding approaches include trans- and cis-genesis, genome editing, and rapid-cycle breeding, which, in addition to conventional crossbreeding, can all facilitate accelerated integration of resistance into elite germplasm. In addition, the global pool of available sources of resistance can be characterized by the existing genetic mapping and gene expression studies for accurate discovery of associated loci, genes, and markers to efficiently include these sources in breeding efforts. We discuss and propose a multitude of approaches to overcome the challenges of breeding for resistance in woody perennials and outline a technical path to reduce the time required for the ultimate deployment of disease-resistant cultivars.

Size and Topography of the Brain’s Functional Networks with Psychotic Experiences, Schizophrenia, and Bipolar Disorder

BackgroundExisting functional connectivity studies of psychosis use population-averaged functional network maps, despite highly variable topographies of these networks across the brain surface. We aimed to define the functional network areas and topographies in the general population and the changes associated with psychotic experiences (PEs) and disorders. MethodsMaps of 8 functional networks were generated using an individual-specific template-matching procedure for each participant from the Human Connectome Project Young Adult cohort (n = 1003) and from a matched case cohort (schizophrenia [SCZ], n = 27; bipolar disorder, n = 35) scanned identically with the same Connectom scanner. In the Human Connectome Project Young Adult cohort, PEs were estimated based on scores from the Achenbach Self-Report Scale. The relationship of symptoms to the probability of network representation at each cortical vertex was assessed using logistic regression. ResultsIn Human Connectome Project Young Adult participants, PE severity on the Achenbach thought problems scale was predicted by increased language network (LAN) and dorsal attention network (DAN) areas and decreased cingulo-opercular network area (r < 0.12). Significant effects were found in SCZ, with a larger DAN and LAN and a smaller frontoparietal network. Network pattern analysis in SCZ showed an increased probability of LAN in the posterior region of the left superior temporal gyrus and of the visual network in the left insula. Regression analyses in SCZ found that mood dysregulation was related to increased DAN surface area. ConclusionsThose with PEs and SCZ showed abnormal functional network cortical topographies, particularly involving DAN and LAN. Network findings may predict psychosis progression and guide earlier intervention.

Identification of quantitative trait loci of pod dehiscence in a collection of soybean grown in the southeast of Kazakhstan.

Soybean [Glycine max (L.) Merr.] is one of the important crops that are constantly increasing their cultivation area in Kazakhstan. It is particularly significant in the southeastern regions of the country, which are currently predominant areas for cultivating this crop. One negative trait reducing yield in these dry areas is pod dehiscence (PD). Therefore, it is essential to understand the genetic control of PD to breed new cultivars with high yield potential. In this study, we evaluated 273 soybean accessions from different regions of the world for PD resistance in the conditions of southeastern regions of Kazakhstan in 2019 and 2021. The field data for PD suggested that 12 accessions were susceptible to PD in both studied years, and 32 accessions, in one of the two studied years. The genotyping of the collection using a DNA marker for the Pdh1 gene, a major gene for PD, revealed that 244 accessions had the homozygous R (resistant) allele, 14 had the homozygous S (susceptible) allele, and 15 accessions showed heterozygosity. To identify additional quantitative trait loci (QTLs), we applied an association mapping study using a 6K SNP Illumina iSelect array. The results suggested that in addition to major QTL on chromosome 16, linked to the physical location of Pdh1, two minor QTLs were identified on chromosomes 10 and 13. Both minor QTLs for PD were associated with calmodulin-binding protein, which presumably plays an important role in regulating PD in dry areas. Thus, the current study provided additional insight into PD regulation in soybean. The identified QTLs for PD can be efficiently employed in breeding for high-yield soybean cultivars.

Architecture and anatomy of executive processes: evidence from verbal fluency and Trail Making Test in 2009 stroke patients.

The few voxel-wise lesion-symptom mapping (VLSM) studies aimed at identifying the anatomy of executive function are limited by the absence of a model and by small populations. Using Trail Making Test (TMT) and verbal fluency and a model of their architectures, our objective was to identify the key structures underlying two major executive processes, set-shifting and strategic word search. We applied a validated VLSM analysis to harmonized cognitive and imaging data from 2009 ischemic stroke patients as a part of the Meta VCI Map consortium. All contrast analyses used an adjusted threshold with 2000 Freedman-Lane permutations (p ≤ 0.05). The TMT parts A and B were associated with structures involved in visual-spatial processing, the motor system, the frontal lobes, and their subcortical connections. Set-shifting depended on the left dorsomedial frontal region. Both semantic and phonemic fluency tests depended on verbal output abilities and processing speed with similar slopes in different languages. The strategic search process depended on Broca's area, F2 and related tracts, temporal and deep regions. Lastly, the lesion map of set-shifting did not overlap with those of strategic word search processes. Our results identify the anatomical substrates of two main executive processes, revealing that they represent only a specific subpart of previously reported structures. Finally, our results indicate that executive functions depend on several specific, anatomically separable executive processes mainly operating in various parts of the frontal lobes.

The HAPPY concept mapping study: “to prevent injuries in young handball players it's important to…” – perceptions among stakeholders

Objective: This study aimed to identify facilitators for implementing injury prevention initiatives in youth handball, and to assess stakeholders' perceptions of their importance and feasibility. Method: Four stakeholder groups — coaches, administrators, health staff and players — participated in this mixed-method concept mapping study. Participants (n = 224; 19 % coaches, 22 % health staff, 63 % players, 18 % administrators) first provided statements about facilitators for implementing injury prevention initiatives in youth handball, then thematically grouped them (n = 47), before rating them (n = 57) for importance and feasibility (5-point Likert scales). Stakeholder-specific cluster maps and Go-Zone scatter plots were created. Statements rated above average for both importance and feasibility were considered as prioritized (Go-Zone 1). Results: 87 unique statements were generated during brainstorming. Multidimensional scaling and hierarchical cluster analysis resulted in similar sorting data clustering patterns for coaches, health staff, and administrators, which included federation strategies, club strategies, and coach and athlete education/knowledge. All clusters were rated >3 on average ratings of importance by all stakeholder groups. Six statements were in Go-Zone 1 for all stakeholder groups, including three statements about coach knowledge and education. Players' importance and feasibility ratings had limited overlap with other stakeholder groups' Go-Zone 1 statements. Players' Go-Zone 1 statements mainly addressed individual load management and practical training setup. Conclusion: Coach knowledge and education, alongside collaboration among stakeholder groups, are essential when implementing injury prevention initiatives in youth handball. Stakeholder groups have varying perspectives, underscoring the importance of understanding and addressing these diverse viewpoints when implementing injury prevention initiatives in youth handball.

A Concept Mapping Study on the Challenges of University Life Adjustment for Military Discharged Students

A Concept Mapping Study on the Challenges of University Life Adjustment for Military Discharged Students

Genetic, molecular and physiological crosstalk during drought tolerance in maize (Zea mays): pathways to resilient agriculture.

This review comprehensively elucidates maize drought tolerance mechanisms, vital for global food security. It highlights genetic networks, key genes, CRISPR-Cas applications, and physiological responses, guiding resilient variety development. Maize, a globally significant crop, confronts the pervasive challenge of drought stress, impacting its growth and yield significantly. Drought, an important abiotic stress, triggers a spectrum of alterations encompassing maize's morphological, biochemical, and physiological dimensions. Unraveling and understanding these mechanisms assumes paramount importance for ensuring global food security. Approaches like developing drought-tolerant varieties and harnessing genomic and molecular applications emerge as effective measures to mitigate the negative effects of drought. The multifaceted nature of drought tolerance in maize has been unfolded through complex genetic networks. Additionally, quantitative trait loci mapping and genome-wide association studies pinpoint key genes associated with drought tolerance, influencing morphophysiological traits and yield. Furthermore, transcription factors like ZmHsf28, ZmNAC20, and ZmNF-YA1 play pivotal roles in drought response through hormone signaling, stomatal regulation, and gene expression. Genes, such as ZmSAG39, ZmRAFS, and ZmBSK1, have been reported to be pivotal in enhancing drought tolerance through diverse mechanisms. Integration of CRISPR-Cas9 technology, targeting genes like gl2 and ZmHDT103, emerges as crucial for precise genetic enhancement, highlighting its role in safeguarding global food security amid pervasive drought challenges. Thus, decoding the genetic and molecular underpinnings of drought tolerance in maize sheds light on its resilience and paves the way for cultivating robust and climate-smart varieties, thus safeguarding global food security amid climate challenges. This comprehensive review covers quantitative trait loci mapping, genome-wide association studies, key genes and functions, CRISPR-Cas applications, transcription factors, physiological responses, signaling pathways, offering a nuanced understanding of intricate mechanisms involved in maize drought tolerance.

A debris flow susceptibility mapping study considering sample heterogeneity

A debris flow susceptibility mapping study considering sample heterogeneity

Pengembangan Keuangan Mikro Islam untuk Mengatasi Kemiskinan dan Mencapai Tujuan SDGs: Pendekatan Bibliometrik

This study tries to review research on sustainable microfinance development in Scopus indexed journals. This analysis uses descriptive statistical analysis based on 319 selected papers related to microfinance sustainable development from both national and international journals. All samples of published journals have been published for 27 years from 1996 to 2022. The data is then processed and analyzed using the VOSviewer application program to find out the bibliometric visualization map for sustainable development of microfinance research. The results of this bibliometric mapping study show a map of the development of research in the field of microfinance sustainable development. This study also found a close relationship between microfinance sustainable development and the main goal of the SDGs, namely eradicating poverty to promote prosperity for all people of all ages around the world. This research finds new and interesting keywords for further research.

Identifying and prioritizing recommendations to optimize transitions across the care journey for hip fractures: Results from a mixed-methods concept mapping study.

Individuals who experience a hip fracture have numerous care transitions. Improving the transition process is important for ensuring quality care; however, little is known about the priorities of different key interest groups. Our aim was to gather recommendations from these groups regarding care transitions for hip fracture. We conducted a concept mapping study, inviting persons with lived experience (PWLE) who had a hip fracture, care partners, healthcare providers, and decision-makers to share their thoughts about 'what is needed to improve care transitions for hip fracture'. Individuals were subsequently asked to sort the generated statements into conceptual piles, and then rate by importance and priority using a five-point scale. Participants decided on the final map, rearranged statements, and assigned a name to each conceptual cluster. A total of 35 participants took part in this concept mapping study, with some individuals participating in multiple steps. Participants included 22 healthcare providers, 7 care partners, 4 decision-makers, and 2 PWLE. The final map selected by participants was an 8-cluster map, with the following cluster labels: (1) access to inpatient services and supports across the care continuum (13 statements); (2) informed and collaborative discharge planning (13 statements); (3) access to transitional and outpatient services (3 statements); (4) communication, education and knowledge acquisition (9 statements); (5) support for care partners (2 statements); (6) person-centred care (13 statements); (7) physical, social, and cognitive activities and supports (13 statements); and (8) provider knowledge, skills, roles and behaviours (8 statements). Our study findings highlight the importance of person-centred care, with active involvement of PWLE and their care partners throughout the care journey. Many participant statements included specific ideas related to continuity of care, and clinical knowledge and skills. This study provides insights for future interventions and quality improvement initiatives for enhancing transitions in care among hip fracture populations.

Frictional stability of pumice-reinforced lightweight magnesium composite in ambient and elevated temperature environments

Lightweight materials with better resistance to sliding wear are prominent candidates for automobile brake drums, clutch pads and cylinder block applications to facilitate fuel economy. This attempt is reserved to cater to materials with higher tribological quality needs. Less dense foamy pumice stone particles were involved in three different percentages (5, 10, and 15 wt%) to reinforce lightweight AZ31 Mg alloy. A stir-assisted squeeze casting technique was pursued to process the composite and refine the grain structure. A phase detection, elemental mapping and microstructure study were done through X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), and scanning electron microscopy (SEM), respectively. An experimental dry sliding wear scrutiny was administered using a pin-on-disc apparatus by considering: (i) ambient and elevated temperature environments and (ii) three different levels of loads. The results reveal a significant drop in wear loss and a frictional coefficient for 15% pumice-loaded composite than the base alloy. Post-wear examination acknowledges the fact that the ambient temperature wear is governed by adhesive-abrasive wear and high temperature is by abrasive wear mechanisms. Worn-out scrutiny authenticates the presence of oxide layers and their role in lubrication. A comparative study with previous works upholds the novel magnesium composite is the right candidate for the mentioned automobile applications.

False Discovery Rate Control for Lesion-Symptom Mapping With Heterogeneous Data via Weighted p-Values.

Lesion-symptom mapping studies provide insight into what areas of the brain are involved in different aspects of cognition. This is commonly done via behavioral testing in patients with a naturally occurring brain injury or lesions (e.g., strokes or brain tumors). This results in high-dimensional observational data where lesion status (present/absent) is nonuniformly distributed, with some voxels having lesions in very few (or no) subjects. In this situation, mass univariate hypothesis tests have severe power heterogeneity where many tests are known a priori to have little to no power. Recent advancements in multiple testing methodologies allow researchers to weigh hypotheses according to side information (e.g., information on power heterogeneity). In this paper, we propose the use of p-value weighting for voxel-based lesion-symptom mapping studies. The weights are created using the distribution of lesion status and spatial information to estimate different non-null prior probabilities for each hypothesis test through some common approaches. We provide a monotone minimum weight criterion, which requires minimum a priori power information. Our methods are demonstrated on dependent simulated data and an aphasia study investigating which regions of the brain are associated with the severity of language impairment among stroke survivors. The results demonstrate that the proposed methods have robust error control and can increase power. Further, we showcase how weights can be used to identify regions that are inconclusive due to lack ofpower.

An engineered NKp46 antibody for construction of multi-specific NK cell engagers.

Recent developments in cancer immunotherapy have highlighted the potential of harnessing natural killer (NK) cells in the treatment of neoplastic malignancies. Of these, bispecific antibodies, and NK cell engager (NKCE) protein therapeutics in particular, have been of interest. Here, we used phage display and yeast surface display to engineer RLN131, a unique cross-reactive antibody that binds to human, mouse, and cynomolgus NKp46, an activating receptor found on NK cells. RLN131 induced proliferation and activation of primary NK cells, and was used to create bispecific NKCE constructs of varying configurations and valency. All NKCEs were able to promote greater NK cell cytotoxicity against tumor cells than an unmodified anti-CD20 monoclonal antibody, and activity was observed irrespective of whether the constructs contained a functional Fc domain. Competition binding and fine epitope mapping studies were used to demonstrate that RLN131 binds to a conserved epitope on NKp46, underlying its species cross-reactivity.

On the Pre-Perception of Gamification and Game-Based Learning in Higher Education Students: A Systematic Mapping Study

Background The fields of gamification and game-based learning are growing and changing quickly, with researchers investigating the use of gamification in education using various methods and in numerous case studies, however, no research investigates the significance pre-perception of higher education students has in gamification, game-based learning, and serious games studies. Objective We perform a systematic mapping to identify the gaps in our understanding on the effects of pre-perception in gamification, focusing on the under-researched area of gamification and game-based learning applications for higher education. Results We present three main findings: (1) Current research on the effects of higher education’s students' pre-perception of gamification and game-based learning are limited. (2) The limited available research indicates perception towards gamification and game-based learning in participants may impact on the effectiveness of game-based solutions, but more research is required to better understand the relationship. (3) A significant body of new research work is required to examine how student perception can affect the effectiveness of gamification and game-based learning solutions in higher education. Conclusion Our understanding of the effect pre-perception may have on the results reported by research on gamification applications for higher education is limited. We encourage more, non-empirical research, to be conducted around pre-perception, and more research that considers gamification and game-based learning applications for higher education.

A Systematic Mapping Study about Technologies for Hedonic Aspects Evaluation in Text-based Chatbots

A Systematic Mapping Study about Technologies for Hedonic Aspects Evaluation in Text-based Chatbots