bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between Mid-Upper Arm Circumference and Body Mass Index in the assessment of adults’ nutritional status in Malawi
Authors: Mzumara Thokozani , Lubanga Adriano Focus , Afonne Joseph , Munthali George , Kaonga Byenala , Harawa Gracian , Bwanali Akim Nelson
Published: July 2024

Background

Body Mass Index (BMI) is a widely used and accepted indicator of nutritional status in adults. Mid-Upper-Arm-Circumference (MUAC) is another anthropometric measure used primarily among children. While BMI remains the best indicator of nutritional status, it can sometimes be impractical because of logistical requirements for weight and height measurement, especially for large population-based studies and bed-ridden patients. Therefore, we analyzed anthropometric data collected from the Malawi Epidemiology and Intervention Research Unit (MEIRU) Non-Communicable Disease (NCD) survey to determine the correlation between BMI and MUAC in the assessment of adult nutritional status in Malawi.

Methods

A secondary data analysis utilizing descriptive and correlational statistical research methods was used to determine the relationship between BMI and MUAC in the assessment of adults’ nutritional status in Malawi. The data was analyzed using SPSS version 27. The independent t test and Chi-square were employed. Furthermore, the study included the Pearson correlation test to assess the relationship between variables. A p-value of <0.05 was considered statistically significant.

Results

The study assessed 30,575 participants, of whom the majority (61.8%) were females. The mean MUAC was 27.2 (SD = 3.300), and the mean BMI was 23.5 (SD = 4.55). The study found a strong positive statistically significant correlation between MUAC and BMI among Malawians (r = 0.836, CI = (0.832-0.839) such that for each additional centimeter increase in MUAC, BMI is expected to increase by approximately 1.153 units (BMI = -7.797 + 1.153 (MUAC)). There was a significant positive correlation between BMI and MUAC in both males and females and in rural and urban residents (P<0.01). The ROC curve was excellent for BMI in the overweight range (AUC = 0.87), and the findings were superior in the obese range (AUC = 0.956).

Conclusion

The correlation between MUAC and BMI is positive regardless of sex or rural/urban residence. Therefore, the MUAC can be used as a clinical test to predict BMI.
Machine-Learning based Prediction Models for Healthcare Outcomes in Patients Participating in Cardiac Rehabilitation: A Systematic Review
Authors: Tieliwaerdi Xiarepati , Manalo Kathryn , Abuduweili Abulikemu , Khan Sana , Appiah-kubi Edmund , Oehler Andrew
Published: July 2024

Purpose

CR has been proven to reduce mortality and morbidity in patients with CVD. ML techniques are increasingly used to predict healthcare outcomes in various fields of medicine including CR. This systemic review aims to perform critical appraisal of existing ML based prognosis predictive model within CR and identify key research gaps in this area.

Review methods

A systematic literature search was conducted in Scopus, PubMed, Web of Science and Google Scholar from the inception of each database to 28th January 2024. The data extracted included clinical features, predicted outcomes, model development and validation as well as model performance metrics. Included studies underwent quality assessments using the IJMEDI.

22 ML-based clinical models from 7 studies across multiple phases of CR were included. Most models were developed using smaller patient cohorts from 41 to 227, with one exception involving 2280 patients. The prediction objectives ranged from patient intention to initiate CR to graduate from outpatient CR along with interval physiological and psychological response to CR. The best-performing ML models reported AUC between 0.82 and 0.91, sensitivity from 0.77 to 0.95, indicating good prediction capabilities. However, none of them underwent calibration or external validation. Most studies raised concerns for bias. Readiness of these models for implement into practice is questionable. External validation of existing models and development of new models with robust methodology based on larger populations and targeting diverse clinical overcomes in CR are needed.
Developing a natural language processing system using transformer-based models for adverse drug event detection in electronic health records
Authors: Wu Jingyuan , Ruan Xiaodi , McNeer Elizabeth , Rossow Katelyn M. , Choi Leena
Published: July 2024

Objective

To develop a transformer-based natural language processing (NLP) system for detecting adverse drug events (ADEs) from clinical notes in electronic health records (EHRs).

Materials and Methods

We fine-tuned BERT Short-Formers and Clinical-Longformer using the processed dataset of the 2018 National NLP Clinical Challenges (n2c2) shared task Track 2. We investigated two data processing methods, window-based and split-based approaches, to find an optimal processing method. We evaluated the generalization capabilities on a dataset extracted from Vanderbilt University Medical Center (VUMC) EHRs.

Results

On the n2c2 dataset, the best average macro F-scores of 0.832 and 0.868 were achieved using a 15-word window with PubMedBERT and a 10-chunk split with Clinical-Longformer. On the VUMC dataset, the best average macro F-scores of 0.720 and 0.786 were achieved using a 4-chunk split with PubMedBERT and Clinical-Longformer.

Discussion

Our study provided a comparative analysis of data processing methods. The fine-tuned transformer models showed good performance for ADE-related tasks. Especially, Clinical-Longformer model with split-based approach had a great potential for practical implementation of ADE detection. While the token limit was crucial, the chunk size also significantly influenced model performance, even when the text length was within the token limit.

Conclusion

We provided guidance on model development, including data processing methods for ADE detection from clinical notes using transformer-based models. Our results on two datasets indicated that data processing methods and models should be carefully selected based on the type of clinical notes and the allocation trade-offs of human and computational power in annotation and model fine-tuning.
High incidence and geographic distribution of cleft palate cases in Finland are associated with a regulatory variant inIRF6
Authors: Rahimov Fedik , Nieminen Pekka , Kumari Priyanka , Juuri Emma , Nikopensius Tiit , Paraiso Kitt , German Jakob , Karvanen Antti , Kals Mart , Elnahas Abdelrahman G. , Karjalainen Juha , Kurki Mitja , Palotie Aarno ,   FinnGen, Estonian Biobank Research Team, Heliövaara Arja , Esko Tõnu , Jukarainen Sakari , Palta Priit , Ganna Andrea , Patni Anjali P. , Mar Daniel , Bomsztyk Karol , Mathieu Julie , Ruohola-Baker Hannele , Visel Axel , Fakhouri Walid D. , Schutte Brian C. , Cornell Robert A. , Rice David P.
Published: July 2024

In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip with or without cleft palate (CL/P). This trend contrasts to that in other European countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial clefts, which include CL/P and CP, in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is highly enriched in Finns and Estonians, as being strongly associated with CP (P= 5.25 × 10−34, OR = 8.65, 95% CI 6.11–12.25), but not with CL/P (P= 7.2 × 10−5), with genome-wide significance. The risk allele frequency of rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in independent cohorts of CP cases from Finland (P= 8.82 × 10−28) and Estonia (P= 1.25 × 10−5). The risk allele of rs570516915 disrupts a conserved binding site for the transcription factor IRF6 within a previously characterized enhancer upstream of theIRF6gene. Through reporter assay experiments we found that the risk allele of rs570516915 diminishes the enhancer activity. Oral epithelial cells derived from CRISPR-Cas9 edited induced pluripotent stem cells demonstrate that the CP-associated allele of rs570516915 concomitantly decreases the binding of IRF6 and the expression level ofIRF6, suggesting impairedIRF6autoregulation as a molecular mechanism underlying the risk for CP.
Rapid loss of genetic variation and increased inbreeding in small and isolated populations of Norwegian wild reindeer
Authors: Hansen Brage B. , Peeters Bart , Flagstad Øystein , Røed Knut , Martin Michael D. , Jensen Henrik , Burnett Hamish A. , Bieker Vanessa C. , Mysterud Atle , Sun Xin , Côté Steeve D. , Robert Claude , Rolandsen Christer M. , Strand Olav
Published: July 2024

Wildlife responses to habitat loss and fragmentation are a central concern in the management and conservation of biodiversity. Small and isolated populations are vulnerable, both due to demographic and genetic mechanisms, which are often linked. Thus, understanding how (changes in) genetic diversity, effective population sizes, and levels of inbreeding relate to population size and degree of isolation is key for developing effective conservation strategies. High-density Single Nucleotide Polymorphism (SNP) arrays represent an increasingly cost-efficient tool to achieve the data needed for such analysis. Here, we present the development of a novel 625k SNP array for reindeerRangifer tarandusand apply this array to assess conservation genetic issues across thirteen Norwegian wild reindeer populations of varying size, isolation, and genetic origin (i.e., semi-domesticated reindeer origin or a mix of wild reindeer and semi-domesticated reindeer origins). Many of these populations are currently completely isolated, with no gene flow from other populations. We genotyped n = 510 individuals sampled by hunters and found that variation in population size across the populations largely predicted their (recent loss of) genetic variation (observed heterozygosity, Ho), as well as effective population size (Ne) and (change in) level of recent inbreeding. For the smallest and most isolated populations, with total population sizes of <50-100 individuals and a high and increasing level of recent inbreeding, estimated loss of genetic variation was as high as 3-10% over the time span of a generation or less, and estimated Newas as low as six individuals. With the current level of isolation and associated lack of gene flow, and considering their already low genetic diversity, these populations are hardly viable – neither demographically nor genetically – in the long term. These results have direct relevance for the management of Norwegian wild reindeer, recently red-listed as ‘Near Threatened’. Yet, these genetic challenges, characterizing many of the small ‘wild reindeer’ populations in Norway, have been largely ignored by management thus far. Mitigation efforts such as reducing barriers would introduce substantial conservation dilemma due to the aim of avoiding further spread of chronic wasting disease (CWD), as well as potential further domestic introgression into populations with genetically wild reindeer (or mixed) origin. Nevertheless, our cost-efficient and high-density SNP array especially designed for reindeer and caribou offers a powerful genetic tool to include in future monitoring, providing important contributions to management and conservation decisions.
Spatial transcriptomics unveils landscape of resistance to concurrent chemo-radiotherapy in hypopharyngeal squamous cell carcinoma: the role ofSPP1+macrophages
Authors: Ohn Jungyoon , Bae Sungwoo , Choi Hongyoon , Kim In Gul , Na Kwon Joong , Chung Eun-Jae
Published: July 2024

Hypopharyngeal squamous cell carcinoma (SCC) is a highly aggressive cancer with a poor prognosis, particularly in advanced stages where concurrent chemoradiotherapy (CCRT) is used for treatment. However, resistance to CCRT poses a significant challenge, often leading to treatment failure and disease progression. This study explores the tumor microenvironment (TME) of hypopharyngeal SCC to understand the molecular mechanisms underlying CCRT resistance. Using spatial transcriptomics (ST), we analyzed tissue samples from patients with locally advanced hypopharyngeal SCC, distinguishing between those who were CCRT-resistant and those who were CCRT-naive. The analysis revealed six distinct cellular clusters within the TME, including a prominent epithelio-immune cellular area in CCRT-resistant tissues. SPP1 was identified as a key gene with significantly higher expression in CCRT-resistant samples, specifically within macrophages. Further investigation showed that SPP1+ macrophages interacted with malignant epithelial cells through SPP1-CD44 and SPP1-ITGB1 ligand-receptor pairs. These interactions were primarily localized in the peri-tumoral and intra-tumoral regions, highlighting their potential role in driving CCRT resistance. Our findings suggest that SPP1+ macrophages contribute to the resistant phenotype in hypopharyngeal SCC by modulating the TME and interacting with cancer cells. Understanding these interactions offers valuable insights into the mechanisms of CCRT resistance and may inform the development of targeted therapies to improve patient outcomes.
Age-dependent predictors of effective reinforcement motor learning across childhood
Authors: Hill Nayo M. , Tripp Haley M. , Wolpert Daniel M. , Malone Laura A. , Bastian Amy J.
Published: July 2024

Across development, children must learn motor skills such as eating with a spoon and drawing with a crayon. Reinforcement learning, driven by success and failure, is fundamental to such sensorimotor learning. It typically requires a child to explore movement options along a continuum (grip location on a crayon) and learn from probabilistic rewards (whether the crayon draws or breaks). Here, we studied the development of reinforcement motor learning using online motor tasks to engage children aged 3 to 17 and adults (cross-sectional sample, N=385). Participants moved a cartoon penguin across a scene and were rewarded (animated cartoon clip) based on their final movement position. Learning followed a clear developmental trajectory when participants could choose to move anywhere along a continuum and the reward probability depended on final movement position. Learning was incomplete or absent in 3 to 8-year-olds and gradually improved to adult-like levels by adolescence. A reinforcement learning model fit to each participant identified three age-dependent factors underlying improvement: amount of exploration after a failed movement, learning rate, and level of motor noise. We predicted, and confirmed, that switching to discrete targets and deterministic reward would improve 3 to 8-year-olds’ learning to adult-like levels by increasing exploration after failed movements. Overall, we show a robust developmental trajectory of reinforcement motor learning abilities under ecologically relevant conditions i.e., continuous movement options mapped to probabilistic reward. This learning appears to be limited by immature spatial processing and probabilistic reasoning abilities in young children and can be rescued by reducing the demands in these domains.
Lacticaseibacillus rhamnosusP118 enhances host tolerance toSalmonellainfection by promoting microbe-derived indole metabolites
Authors: Wang Baikui , Peng Xianqi , Zhou Xiao , Jin Xiuyan , Siddique Abubakar , Yao Jiayun , Zhang Haiqi , Li Weifen , Li Yan , Yue Min
Published: July 2024

Salmonellais one of the most common foodborne pathogens, resulting in inflammatory gastroenteritis and frequently accompanied by dysbiosis. Gut commensals, such asLactobacillusspecies, have been proven to exhibit broad anti-bacterial activities and protect hosts against pathogenic infections. Here,Lacticaseibacillus rhamnosusstrain P118, screened from 290 isolates recovered from fermented yoghurts and healthy piglet intestines using traditional andC. elegans-infection screening strategies, exerts great probiotic properties. Notably, P118 and its supernatant exhibited great antibacterial activities and attenuatedCaenorhabditis eleganssusceptibility toSalmonellainfection. We found that P118 protected mice againstSalmonellalethal infections by enhancing colonization resistance, reducing pathogen invasion, alleviating intestinal pro-inflammatory response, and improving microbial dysbiosis and fecal metabolite changes. Microbiota and fecal metabolome analyses suggested P118 administration significantly decreased the relative abundances of potentially harmful microbes (e.g.,Salmonella,Anaeroplasma,Klebsiella) and increased the fecal levels of tryptophan and its derivatives (indole, indole-3-acrylic acid, 5-hydroxytryptophan, 5-methoxyindoleacetate). Deterministic processes determined the gut microbial community assembly of P118-pretreated mice. Integrated omics further demonstrated that P118 probiotic activities in enhancing host tolerance toSalmonellainfection were mediated by microbe-derived tryptophan/indole metabolites (e.g., indole-3-acrylic acid, indole, tryptophan, 5-methoxyindoleacetic acid, and 5-hydroxytryptophan). Collective results demonstrate thatL. rhamnosusP118 could enhance host tolerance toSalmonellainfections via various pathways, including direct antibacterial actions, inhibitingSalmonellacolonization and invasion, attenuating pro-inflammatory responses of intestinal macrophages, and modulating gut microbiota mediated by microbe-derived indole metabolites.
Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing
Authors: Nguyen Long T. , Rakestraw Noah R. , Pizzano Brianna L.M. , Young Cullen B. , Huang Yujia , Beerensson Kate T. , Fang Anne , Antal Sydney G. , Anamisis Katerina V. , Peggs Coleen M.D. , Yan Jun , Jing Yangwode , Burdine Rebecca D. , Adamson Britt , Toettcher Jared E. , Myhrvold Cameron , Jain Piyush K.
Published: July 2024

Prime editing has emerged as a precise and powerful genome editing tool, offering a favorable gene editing profile compared to other Cas9-based approaches. Here we report new nCas9-DNA polymerase fusion proteins to create chimeric oligonucleotide-directed editing (CODE) systems for search-and-replace genome editing. Through successive rounds of engineering, we developed CODEMax and CODEMax(exo+) editors that achieve efficient genome modifications in human cells with low unintended edits. CODEMax and CODEMax(exo+) contain an engineered Bst DNA polymerase derivative known for its robust strand displacement ability. Additionally, CODEMax(exo+) features a 5’ to 3’ exonuclease activity that promotes effective strand invasion and repair outcomes favoring the incorporation of the desired edit. We demonstrate CODEs can perform small insertions, deletions, and substitutions with improved efficiency compared to PEMax at many loci. Overall, CODEs complement existing prime editors to expand the toolbox for genome manipulations without double-stranded breaks.
Transcription Factors DksA and PsrA are synergistic contributors toL. pneumophilavirulence inAcanthamoeba castellaniiprotozoa
Authors: Graham Christopher I. , Gierys Andrew J. , MacMartin Teassa L. , Penner Tiffany V. , Beck Jordan C. , Prehna Gerd , de Kievit Teresa R. , Brassinga Ann Karen C.
Published: July 2024

The environmental bacteriumLegionella pneumophila, an intracellular parasite of free-living freshwater protozoa as well as an opportunistic human pathogen, has a biphasic lifestyle. The switch from the vegetative replicative form to the environmentally resilient transmissive phase form is governed by a complex stringent response-based regulatory network that includes RNA polymerase co-factor DksA. Here we report that, through a dysfunctional DksA mutation (DksA1), a synergistic interplay was discovered between DksA and transcription regulator PsrA using theAcanthamoeba castellaniiprotozoan infection model. Surprisingly,in transexpression of PsrA partially rescued the growth defect of adksA1strain. Whilein transexpression of DksA expectantly could fully rescued the growth defect of thedksA1strain, it could also surprisingly rescue the growth defect of a ΔpsrAstrain. Conversely, the severe intracellular growth defect of a ΔdksAstrain could be rescued byin transexpression of DksA and DksA1, but not PsrA.In vitrophenotypic assays show that either DksA or DksA1 were required for extended culturability of bacterial cells, but normal cell morphology and pigmentation required DksA only.

Comparative structural modeling predicts that the DksA1 mutation affects coordination of Mg2+into the active site of RNAP compromising transcription efficiency. Taken together, we propose that PsrA transcriptionally assists DksA in the expression of select transmissive phase traits.

Additionally,in vitroevidence suggests that the long chain fatty chain metabolic response is mediated by PsrA together with DksA inferring a novel regulatory link to the stringent response pathway.
Optogenetic control of a horizontally acquired region in yeast prevent stuck fermentations
Authors: Figueroa David , Ruiz Diego , Tellini Nicolò , De Chiara Matteo , Kessi-Pérez Eduardo I. , Martínez Claudio , Liti Gianni , Querol Amparo , Guillamón José M. , Salinas Francisco
Published: July 2024

Nitrogen limitations in the grape must is the main cause of stuck fermentations during the winemaking process. InSaccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain known as ‘ALL’ using long-read sequencing and determined that region A is present in a single copy with two possible subtelomeric locations. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene inside this region, generating a collection of 12 strains that allow for light- activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.

IMPORTANCE

Stuck fermentations due to limited nitrogen availability in grape must represents one of the main problems in the winemaking industry. Nitrogen limitation in grape musts reduce yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results support the idea that region A is a genetic signature for wine yeast strains adapted to low nitrogen conditions.
Developmental, regenerative, and behavioral dynamics in acoel reproduction
Authors: Chandra Vikram , Tseng Samantha E. , Kann Allison P. , Bolaños D. Marcela , Srivastava Mansi
Published: July 2024

Acoel worms belong to an enigmatic and understudied animal lineage in the phylum Xenacoelomorpha. Sparse taxonomic and histological work suggests that these worms exhibit a diversity of reproductive anatomies and likely a corresponding diversity in reproductive behavior. Here, we study the reproductive life history of the three-banded panther wormHofstenia miamia, an acoel that is emerging as a lab-tractable model system. Using confocal microscopy and histology, we describeH. miamia’s reproductive organs, identifying structures previously unknown in acoels. Following a cohort of worms from zygote to adulthood, we quantify the developmental dynamics of their reproductive organs, and find that these organs emerge in a stereotyped sequence as a function of increasing body size. Studying the dynamics of organ growth and de-growth during regeneration and in starvation, we show that reproductive organs follow similar growth rules in these contexts, suggesting that they are regulated by a size-associated program in all growth contexts. Finally, we study egg-laying behavior, finding thatH. miamialay their eggs through their mouths after loading them into their pharynges. Worms lay eggs for multiple months after a single mating, suggesting long-term sperm storage despite lacking a storage organ; we also find that worms can lay viable eggs without mating, indicating a capacity for self-fertilization. Further, we show that worms assess their environment to make decisions about when and where to lay their eggs, and sometimes lay eggs in communal clutches. Together, our work establishes foundational knowledge to enable the experimental study of reproductive anatomy, physiology, and behavior in acoels.
Single-cell analysis of pediatric acute myeloid leukemia samples uncovers treatment-resistant stem and mast cells
Authors: Ohlstrom Denis , Bakhtia Mojtaba , Mumme Hope , Michaud Marina , Chien Frank , Pilcher William , Satpathy Sarthak , Jordan Sean , Bhasin Swati , Bhasin Manoj
Published: July 2024

Pediatric acute myeloid leukemia (pAML) is a heterogeneous malignancy driven by diverse cytogenetic mutations. While risk stratification improved by identifying cytogenetic lesions, prognostication remains inadequate with 30% of standard-risk patients experiencing relapse within 5 years. Single-cell RNA sequencing (scRNAseq) enabled the interrogation of malignant cell heterogeneity in pAML and characterization of the immune microenvironment. Herein we report the largest pAML scRNAseq analysis to date with 708,285 cells from 164 bone marrow biopsies of 95 patients and 11 healthy controls. We uncovered treatment-resistant (TR) subtypes of pAML specific to RUNX1-RUNX1T1, FLT3-ITD, and CBFB-MYH11 patients. The enrichment of TR subtype gene signatures on the TARGET pAML data supported an association with significantly poor outcomes. Intriguingly, in addition to leukemic stem cells, we identified mast cell-like pAML associated with treatment resistance and poor outcomes. Together, immature and mature pAML subtypes are promising biomarkers for identifying patients at increased risk of relapse within cytogenetic categories.
DEAD box RNA helicases are pervasive protein kinase interactors and activators
Authors: Hirth Alexander , Fatti Edoardo , Netz Eugen , Acebron Sergio P. , Papageorgiou Dimitris , Švorinić Andrea , Cruciat Cristina-Maria , Karaulanov Emil , Gopanenko Alexandr , Zhu Tianheng , Sinning Irmgard , Krijgsveld Jeroen , Kohlbacher Oliver , Niehrs Christof
Published: July 2024

DEAD box (DDX) RNA helicases are a large family of ATPases, many of which have unknown functions. There is emerging evidence that besides their role in RNA biology, DDX proteins may stimulate protein kinases. To investigate if protein kinase–DDX interaction is a more widespread phenomenon, we conducted three orthogonal large-scale screens, including proteomics analysis with 32 RNA helicases, protein array profiling, and kinome-wide in vitro kinase assays. We retrieved Ser/Thr protein kinases as prominent interactors of RNA helicases and report hundreds of binary interactions. We identified members of ten protein kinase families, which bind to, and are stimulated by, DDX proteins, including CDK, CK1, CK2, DYRK, MARK, NEK, PRKC, SRPK, STE7/MAP2K, and STE20/PAK family members. We identified MARK1 in all screens and validated that DDX proteins accelerate the MARK1 catalytic rate. These findings indicate pervasive interactions between protein kinases and DEAD box RNA helicases, and provide a rich resource to explore their regulatory relationships.
Accurate allocation of multimapped reads enables regulatory element analysis at repeats
Authors: Morrissey Alexis , Shi Jeffrey , James Daniela Q. , Mahony Shaun
Published: July 2024

Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. However, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard “multimapped” reads that align equally well to multiple genomic locations. Because multimapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address this shortcoming, we developed Allo, a new approach to allocate multimapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multimapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multimapping read assignment. Allo also provides read-level output in the form of a corrected alignment file, making it compatible with existing regulatory genomics analysis pipelines and downstream peak-finders. In a demonstration application on CTCF ChIP-seq data, we show that Allo results in the discovery of thousands of new CTCF peaks. Many of these peaks contain the expected cognate motif and/or serve as TAD boundaries. We additionally apply Allo to a diverse collection of ENCODE ChIP-seq data sets, resulting in multiple previously unidentified interactions between transcription factors and repetitive element families. Finally, we show that Allo may be particularly beneficial in identifying ChIP-seq peaks at centromeres, near segmentally duplicated genes, and in younger TEs, enabling new regulatory analyses in these regions.
Measurement of the sodium and iodine scintillation quenching factors across multiple NaI(Tl) detectors to identify systematics
Authors: Cintas D. , Hedges S. , Thompson W. G. , An P. , Awe C. , Barbeau P. S. , Barbosa de Souza E. , Jo J. H. , Li L. , Martínez M. , Maruyama R. H. , Rich G. C. , Runge J. , Sarsa M. L.
Published: July 2024

The amount of light produced by nuclear recoils in scintillating targets is strongly quenched compared to that produced by electrons. A precise understanding of the quenching factor is particularly interesting for weakly interacting massive particles (WIMP) searches and coherent elastic neutrino-nucleus scattering (CEνNS) measurements since both rely on nuclear recoils, whereas energy calibrations are more readily accessible from electron recoils. There is a wide variation among the current measurements of the quenching factor in sodium iodide (NaI) crystals, especially below 10 keV, the energy region of interest for dark matter and CEνNS studies. A better understanding of the quenching factor in NaI(Tl) is of particular interest for resolving the decades-old puzzle in the field of dark matter between the null results of most WIMP searches and the claim for dark matter detection by the DAMA/LIBRA collaboration. In this work, we measured sodium and iodine quenching factors for five small NaI(Tl) crystals grown with similar thallium concentrations and growth procedures. Unlike previous experiments, multiple crystals were tested, with measurements made in the same experimental setup to control systematic effects. The quenching factors agree in all crystals we investigated, and both sodium and iodine quenching factors are smaller than those reported by DAMA/LIBRA. The dominant systematic effect was due to the electron equivalent energy calibration originating from the nonproportional behavior of the NaI(Tl) light yield at lower energies, potentially the cause for the discrepancies among the previous measurements.

Published by the American Physical Society
2024
“Effing Awful!”: developing audio representation as a medium for conveying people’s experiences of flooded homes
Authors: Angel David , Chmutina Ksenia , Haines Victoria , Del Pinto Monia
Published: July 2024

Purpose

Disaster research is often geared towards logocentrism and has relatively few outputs that explore alternative forms of representation, particularly those using an artistic medium. This paper explores how the creative use of audio representation can enhance understanding of flooding experiences, challenging the predominant text-based approach within qualitative study.

Design/methodology/approach

During a series of visits to people who had been flooded in 2019 in the UK, interviews and ambient sounds were recorded, analysed and then intertwined with musical elements composed by the lead author. The result is a phonographic representation of the synthesised data. The process explores a tripartite, creative, sonic approach that comingles thematic spoken excerpts with local sounds and musical compositions.

Findings

This article presents three sonic vignettes that illustrate the use of audio as a medium for academic research outputs. It contributes to the current consensus that the interpretation, representation and dissemination of research findings should be broadened beyond the dominance of the written word to align with the ethos of the Disaster Studies Manifesto.

Research limitations/implications

The research contributes to disaster scholarship by developing a transdisciplinary approach to explore people’s experiences. By retaining the participants’ voices at its core, it makes use of in-depth, rich data to illustrate individuality, rather than aiming to generalise.

Originality/value

Very little disaster research has focussed on pushing the boundaries of investigation by using the arts as a lens for both the researcher and their audience. Such work may connect with a wider range of people compared to a text-based “traditional” academic output. It can offer new opportunities for practical uses within Disaster Risk Reduction, for example as a communicative and educational tool.

Contribution to impact

This paper contributes to understanding the impact of developing audio representation as a medium for conveying people’s experiences of flooded homes.
The role of macro institutional factors in determining types of entrepreneurial start-ups: a longitudinal panel study
Authors: Li Tianchen
Published: July 2024

Purpose

What shapes entrepreneurs’ intention to allocate entrepreneurial effort towards different types of entrepreneurial start-ups? Grounded in a “national business systems” approach, the purpose of this paper is to examine the impacts of institutional dimensions on Schumpeterian and Kirznerian entrepreneurship.

Design/methodology/approach

Drawing upon a global context comprising 82 countries over the period between 2007 and 2018, this research applies a dynamic panel modelling approach, namely, the dynamic panel generalised method of moments estimator. This estimator allows to account for unobserved country-specific heterogeneity and to address endogeneity constraints that might occur between institutions and entrepreneurship.

Findings

The findings reveal that there are positive relationships between financial capital and both Schumpeterian and Kirznerian entrepreneurship. Educational capital positively affects the allocation of entrepreneurial efforts towards opportunity-based entrepreneurial activities. Moreover, institutional regulatory conditions could hinder the allocation of entrepreneurs’ resources into a Schumpeterian while facilitating the allocation of resources into a Kirznerian type of venture. Finally, a higher level of corruption promotes innovative entrepreneurial activities (i.e. a Schumpeterian type of venture) and leads to constraints on Kirznerian entrepreneurship.

Practical implications

The research findings demonstrate the significance of the macro environment for enacting and implementing policies to reap the benefits of different types of start-ups. It suggests different political actions are needed to motivate highly qualified individuals to engage in Schumpeterian and Kirznerian entrepreneurship, rather than focusing purely on enhancing a country’s overall start-up rates.

Originality/value

By acknowledging the multidimensional nature of entrepreneurship, this research provides greater theoretical exposition and empirical support for the role played by macro-level institutions in determining types of entrepreneurship. It reveals the important role played by macro institutional conditions in influencing choices about different types of start-ups and gives rise to the multidimensional nature of entrepreneurship.
Mentorship as a tool for improving construction artisan's skills to achieve sustainable development Goal 8 via qualitative approach
Authors: Ebekozien Andrew , Aigbavboa Clinton Ohis , Samsurijan Mohamad Shaharudin , Aliu John , Nwaole Angeline Ngozika Chibuike
Published: July 2024

Purpose

The paucity of artisans in some construction trades and the transitioning of the experience of the few for sustainability calls for concern. Mentorship programmes offer a promising mechanism to support construction artisans through those transitions. Mentorship may enhance artisan decent work and economic growth, like increased income for artisans. This is part of Sustainable Development Goal 8 (Goal 8). Hence, this study aims to investigate issues hindering construction artisan skills growth and suggest measures to improve construction artisan skills through mentorship mechanisms to achieve Goal 8.

Design/methodology/approach

The study adopted a qualitative approach and collected data via oral interviews with knowledgeable participants. The participants were consultant experts in mentorship and Sustainable Development Goals (SDGs) matters, construction organisation management staffers and construction artisans in the Nigerian construction industry. The study covered Lagos and Abuja and achieved saturation at the 30th interviewee. Also, the research utilised a thematic method to analyse the collated data.

Findings

Enhanced knowledge sharing accelerates junior artisans’ learning skills quickly, improving artisans’ performance, ensuring sustainability of the skills learned (knowledge retention), encouraging collaboration, building the next generation of leaders and transitioning of experience to mentees emerged as mentorship’s role in developing construction artisans’ skills. Findings show that mentorship mechanisms to develop construction artisan skills face encumbrances. The perceived 32 encumbrances were re-clustered into mentee, mentor and government-related encumbrances. Also, achieving Goal 8 regarding construction artisans may be threatened if these issues are not checked. Thus, the study recommended measures improving construction artisan skills through mentorship mechanisms to achieve Goal 8.

Originality/value

Identifying the major encumbrances facing construction artisan skills improvement through mentorship would be useful to advocate measures to improve construction artisan’s skills to achieve Goal 8.
Non-profit and hybrid organizations as multi-sided platforms: insights from the analysis of sustainability models
Authors: Landoni Paolo , Trabucchi Daniel
Published: July 2024

Purpose

This study investigates the sustainability models of non-profit and hybrid organizations, which aim to balance economic, social and environmental objectives. The research introduces the Sustainability Model Canvas to analyze these organizations and identify common patterns, unique characteristics and managerial insights to balance the triple bottom line.

Design/methodology/approach

The research utilizes the Sustainability Model Canvas to examine the sustainability models of 200 non-profit and hybrid organizations. Data were collected from secondary sources, including articles, reports and websites. The analysis was conducted using the activity system theoretical framework, which helped to identify design elements and themes within the business models of the studied organizations.

Findings

The study reveals four primary sustainability model patterns: donated income, earned income, public income and auto-generated income. An additional mixed approach pattern is identified, combining elements from the four primary patterns. The research highlights the parallels between these sustainability models and multi-sided platform business models, offering managerial suggestions for leveraging these patterns to achieve sustainability.

Research limitations/implications

The study is based on secondary data, which may limit the depth of insights compared to primary data collection. At the same time, the chance to consider hybrid organization through multi-sided platform lenses provides relevant contributions to both the literature streams.

Practical implications

The identified sustainability model patterns and managerial suggestions can serve as blueprints for non-profit and hybrid organizations aiming to design or innovate their sustainability models. The Sustainability Model Canvas offers a practical tool for organizations to visualize and balance their triple bottom line objectives.

Social implications

The research underscores the importance of integrating social and environmental considerations into business models, promoting a holistic approach to sustainability that can lead to broader social and environmental benefits.

Originality/value

This research contributes to the business model literature by extending the focus beyond traditional profit-oriented organizations to include non-profit and hybrid organizations. The introduction of the Sustainability Model Canvas provides a new tool for designing and analyzing sustainability-oriented business models. The study also suggests considering sustainability models as multi-sided platforms, offering new insights for both academic and practical applications.
Analysing the dropout patterns of individual children in Nepal: relationship between school dropout and grade repetition/entrance age
Authors: Ezaki Naruho
Published: July 2024

Purpose

Using longitudinal data of children in Nepal, this study examines the relationships between dropouts, grade repetition and the causes of dropout, such as entrance age, to derive concrete recommendations to improve the basic education completion rates in Nepal, one of the targets of Sustainable Development Goal 4 (SDG4).

Design/methodology/approach

The data for this study were drawn from school records kept in the target schools, home visit surveys and interviews with principals and teachers. After comparing the repetition experience and the frequency of repetitions between graduates and dropouts, the study analysed the dropout patterns of individual children. The study then examined the effects of repetition and entrance age on children’s schooling.

Findings

The results identified a large group of children who dropped out of school without any repetition, with only 15.9% of the children repeating a grade immediately before dropping out. The findings indicated that harsh family environments, being overage and low educational expectations were factors in sudden dropout.

Originality/value

Collecting longitudinal data is difficult in developing countries, and few studies use such data. The question of access to education has been re-ignited by the COVID-19 pandemic; this study used longitudinal data to thoroughly analyse children’s dropout patterns and provide specific recommendations that will contribute to the achievement of SDG4.
Mechanoreception of pneumatic soft robotic finger without tactile sensor based on dual-position feature
Authors: Shi Kai , Li Jun , Bao Gang
Published: July 2024

Purpose

Mechanoreception is crucial for robotic planning and control applications, and for robotic fingers, mechanoreception is generally obtained through tactile sensors. As a new type of robotic finger, the soft finger also requires mechanoreception, like contact force and object stiffness. Unlike rigid fingers, soft fingers have elastic structures, meaning there is a connection between force and deformation of the soft fingers. It allows soft fingers to achieve mechanoreception without using tactile sensors. This study aims to provide a mechanoreception sensing scheme of the soft finger without any tactile sensors.

Design/methodology/approach

This research uses bending sensors to measure the actual bending state under force and calculates the virtual bending state under assumed no-load conditions using pressure sensors and statics model. The difference between the virtual and actual finger states is the finger deformation under load, and its product with the finger stiffness can be used to calculate the contact force. There are distinctions between the virtual and actual finger state change rates in the pressing process. The difference caused by the stiffness of different objects is different, which can be used to identify the object stiffness.

Findings

Contact force perception can achieve a detection accuracy of 0.117 N root mean square error within the range of 0–6 N contact force. The contact object stiffness perception has a detection average deviation of about 15%, and the detection standard deviation is 10% for low-stiffness objects and 20% for high-stiffness objects. It performs better at detecting the stiffness of low-stiffness objects, which is consistent with the sensory ability of human fingers.

Originality/value

This paper proposes a universal mechanoreception method for soft fingers that only uses indispensable bending and pressure sensors without tactile sensors. It helps to reduce the hardware complexity of soft robots. Meanwhile, the soft finger no longer needs to deploy the tactile sensor at the fingertip, which can benefit the optimization design of the fingertip structure without considering the complex sensor installation. On the other hand, this approach is no longer confined to adding components needed. It can fully use the soft robot body’s physical elasticity to convert sensor signals. Essentially, It treats the soft actuators as soft sensors.
Mapping the path to sustainable accounting: a DEMATEL-based analysis of key factors influencing effective extended producer responsibility in the circular economy
Authors: Sahu Manabhanjan , Jee Kishan , Uddin Furquan , Sani Alamgir , Tiwari Satish Chandra
Published: July 2024

Purpose

This study aims to assess the factors influencing the effective implementation of extended producer responsibility (EPR) practices within the context of sustainable accounting goals and circular economy principles. It seeks to provide insights into the significance of EPR policies for manufacturing industries striving to enhance their environmental, social and governance performance while ensuring sustainable accounting of their business operations.

Design/methodology/approach

The methodology proposed in this article is based on the decision-making trial and evaluation laboratory (DEMATEL) technique. This approach formulates a structural framework for evaluating influential elements among critical recognized factors. By using DEMATEL, the study examines the interconnectedness between assessed factors through a cause-and-effect diagram, facilitating the integration of EPR into sustainable accounting practices.

Findings

The research findings reveal that the most impactful contributors to sustainable accounting practices of EPR within the framework of sustainable development goals and circular economy are producers, consumers, eco-design, public awareness and the support of local authorities. These findings underscore the importance of considering these factors in implementing EPR and advancing sustainable accounting practices.

Originality/value

This paper contributes to the literature by proposing a DEMATEL-based model for evaluating the factors affecting the implementation of EPR within the context of sustainable accounting goals and circular economy principles.