bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of telephone and in-person interview modalities: duration, richness, and costs in the context of exploring determinants of equitable access to community health services in Meru, Kenya
Authors: Allen Luke N , Karanja Sarah , Tlhakanelo John , Macleod David , Tlhajoane Malebogo , Bastawrous Andrew 
Published: March 2024

AbstractBackgroundOur research team is conducting phenomenological interviews in Kenya with people who have not been able to access community eye health services, aiming to explore the barriers and ideas for potential service modifications. We conducted an embedded study that compared in-person and telephone interview modalities in terms of time requirements, costs, and data richness.MethodsA team of six interviewers conducted 31 in-person interviews and 31 telephone interviews using the same recruitment strategy, topic guide, and analytic matrix for each interview. We compared the mean duration; mean number of themes reported by each participant; total number of themes reported; interviewer rating of perceived richness; interviewer rating of perceived ease of building rapport; number of days taken by the team to complete all interviews; and all costs associated with conducting the interviews in each modality.FindingsIn-person interviews were 44% more expensive and took 60% longer to complete than our telephone interviews (requiring 5 days and 3 days respectively). The average in-person interview lasted 110 seconds longer than the average telephone interview (p=0.05) and generated more words and themes. However, the full set of interviews from both approaches identified similar numbers of barriers (p=0.14) and the same number of solutions (p=0.03). Interviewers universally felt that the in-person approach was associated with better rapport and higher quality data (p=0.01). Triangulation of themes revealed good agreement, with 88% of all solutions occurring in both sets, and no areas of thematic dissonance.DiscussionThe in-person approach required more time and financial resources, but generated more words and themes per person, and was perceived to afford richer data by interviewers. However, this additional richness did not translate into a greater number of themes that our team can act upon to improve services.
Dietary and Lifestyle Factors of Brain Iron Accumulation and Parkinson’s Disease Risk
Authors: Ahern Jonathan , Boyle Mary ET , Thompson Wesley K. , Fan Chun Chieh , Loughnan Robert 
Published: March 2024

AbstractPurposeIron is an essential nutrient which can only be absorbed through an individual’s diet. Excess iron accumulates in organs throughout the body including the brain. Iron dysregulation in the brain is commonly associated with neurodegenerative diseases like Alzheimer’s disease and Parkinson’s Disease (PD). Our previous research has shown that a pattern of iron accumulation in motor regions of the brain related to a genetic iron-storage disorder called hemochromatosis is associated with an increased risk of PD. To understand how diet and lifestyle factors relate to this brain endophenotype and risk of PD we analyzed the relationship between these measures, estimates of nutrient intake, and diet and lifestyle preference using data from UK Biobank.MethodsUsing distinct imaging and non-imaging samples (20,477 to 28,388 and 132,023 to 150,603 participants, respectively), we performed linear and logistic regression analyses using estimated dietary nutrient intake and food preferences to predict a) brain iron accumulation score (derived from T2-Weighted Magnetic Resonance Imaging) and b) PD risk. In addition, we performed a factor analysis of diet and lifestyle preferences to investigate if latent lifestyle factors explained significant associations. Finally, we performed an instrumental variable regression of our results related to iron accumulation and PD risk to identify if there were common dietary and lifestyle factors that were jointly associated with differences in brain iron accumulation and PD risk.ResultsWe found multiple highly significant associations with measures of brain iron accumulation and preferences for alcohol (factor 7: t=4.02, pFDR=0.0003), exercise (factor 11: t=-4.31, pFDR=0.0001), and high-sugar foods (factor 2: t=-3.73, pFDR=0.0007). Preference for alcohol (factor 7: t=-5.83, pFDR<1×10-8), exercise (factor 11: t=-7.66, pFDR<1×10-13), and high sugar foods (factor 2: t=6.03, pFDR<1×10-8) were also associated with PD risk. Instrumental variable regression of individual preferences revealed a significant relationship in which dietary preferences associated with higher brain iron levels also appeared to be linked to a lower risk for PD (p=0.004). A similar relationship was observed for estimates of nutrient intake (p=0.0006). Voxel-wise analysis of i) high-sugar and ii) alcohol factors confirmed T2-weighted signal differences consistent with iron accumulation patterns in motor regions of the brain including the cerebellum and basal ganglia.ConclusionDietary and lifestyle factors and preferences, especially those related to carbohydrates, alcohol, and exercise, are related to detectable differences in brain iron accumulation and alterations in risk of PD, suggesting a potential avenue for lifestyle interventions that could influence risk.Graphical Abstract
TheGPAT4/6/8clade functions in Arabidopsis root suberization non-redundantly with theGPAT5/7clade required for suberin lamellae
Authors: Gully Kay , Berhin Alice , De Bellis Damien , Herrfurth Cornelia , Feussner Ivo , Nawrath Christiane 
Published: March 2024

SummaryLipid polymers such as cutin and suberin strengthen the diffusion barrier properties of the cell wall in specific cell types and are essential for water relations, mineral nutrition, and stress protection in plants. Land plant–specific glycerol-3-phosphate acyltransferases (GPATs) of different clades are central players in cutin and suberin monomer biosynthesis. Here, we show that theGPAT4/6/8clade inArabidopsis thaliana, which is known to mediate cutin formation, is also required for developmentally regulated root suberization, in addition to the established roles ofGPAT5/7in suberization. TheGPAT5/7clade is mainly required for abscisic acid–regulated suberization. In addition, theGPAT5/7clade is crucial for the formation of the typical lamellated suberin ultrastructure observed by transmission electron microscopy, as distinct amorphous globular polyester structures were deposited in the apoplast of thegpat5 gpat7double mutant, in contrast to the thinner but still lamellated suberin deposition in thegpat4 gpat6 gpat8triple mutant. The intrinsic phosphatase activity of GPAT4, GPAT6, and GPAT8, which leads to monoacylglycerol biosynthesis, may be important for suberin biosynthesis. GPAT5/7 lack an active phosphatase domain. Notably,gpat5 gpat7phenotypes were partially reverted by treatment with a phosphatase inhibitor or the expression of phosphatase-dead variants ofGPAT4/6/8.Thus, GPATs that lack an active phosphatase domain, which are predicted to synthetize lysophosphatidic acids, might be crucial for the formation of the lamellated structure of suberin. GPATs with active and non-active phosphatase domains appear to have non-redundant functions and must cooperate to achieve the efficient biosynthesis of correctly structured suberin.Significance statementThe establishment of proper lamellated suberin in roots plays essential roles in regulating mineral nutrition and water relations in plants. The basis for the macromolecular arrangement determining the ultrastructure and properties of suberin lamellae is unknown. Here, we report that both theGPAT4/6/8andGPAT5/7clades of glycerol-3-phosphate acyltransferases (GPATs) contribute to suberin formation in Arabidopsis roots. In addition, we reveal that theGPAT5/7clade is required for the formation of the lamellated suberin ultrastructure. Several lines of evidence suggest that the loss of phosphatase activity in GPATs might have played a crucial role in the formation of suberin lamellae during evolution.
Joint contribution of adaptation and neuronal population recruitment to response level in visual area MT: a computational model
Authors: Cravo Maria Inês , Bernardes Rui , Castelo-Branco Miguel 
Published: March 2024

AbstractAdaptation is a form of short-term plasticity triggered by prolonged exposure to a stimulus, often resulting in altered perceptual sensitivity to stimulus features through a reduction in neuronal firing rates. Experimental studies have explored adaptation to bistable stimuli, specifically a stimulus comprising inward-moving plaids that can be perceived as either a grating moving coherently downward or two plaids moving incoherently through each other. Functional magnetic resonance imaging (fMRI) recordings have shown higher activity during incoherent perception and lower activity during coherent stimulus perception. There are two potential explanations for the underlying neural mechanisms: a weaker coherent stimulus response may result from stronger adaptation to coherent versus incoherent motion, or a stronger incoherent stimulus response could stem from the involvement of more neural populations to represent motion in more directions. Here, we employ a computational model of visual neurons with and without firing rate adaptation to test these hypotheses. By simulating the mean activity of a network of thirty-two columnar populations of visual area MT, each tuned to one direction of motion, we investigate the impact of firing rate adaptation on the blood-oxygen-level-dependent (BOLD) signal generated by the network in response to coherent and incoherent stimuli. Our results replicate the experimental curves both during and after stimulus presentation only when the model includes adaptation, highlighting the importance of this mechanism. However, our findings reveal that the response to incoherent motion is larger than the response to coherent motion for a wide variety of stimulus parameters and adaptation regimes, suggesting that the observed reduced response to coherent stimuli is most likely due to the activation of smaller neuronal populations, in alignment with the second hypothesis. Hence, adaptation and differential neuronal recruitment work together to give rise to the observed hemodynamic responses. This computational work sheds light on experimental results and enriches our understanding of the mechanisms involved in neural adaptation, particularly in the context of heterogeneous neuronal populations.
Structures of transcription-translation coupling complexes at each stage of the translation cycle
Authors: Zhang Jing , Lu Guoliang , Zhou Wei , Yang Mingxia , Li Li , Shao Huihui , Zhou Xiaogen , Chen Changbin , Ebright Richard H. , Gao Yue , Lin Jinzhong , Wang Chengyuan 
Published: March 2024

AbstractBacterial transcription and translation are frequently linked through a transcribing RNA polymerase following the leading ribosome, a process termed transcription-translation coupling (TTC). Three distinct TTC structures, the “collided expressome” (TTC-A), the “coupled expressome” (TTC-B) and the “long-range coupled expressome” (TTC-LC) have been reported, but the biological significance of all complexes is still subject to uncertainty. Furthermore, all of the ribosomes in the structures are determined in a static state. The underlying translation dynamics within these TTCs remain elusive. Here, we reconstitute the complete active transcription-translation system, using antibiotics and a series of different lengths of mRNAs to trap intermediate coupling states, and determine Cryo-EM structures showing the snapshots for the dynamic reaction trajectory. The results show five states of TTC-B representing the whole stages of the translation elongation cycle. TTC-B is compatible with ribosome conformational changes during translation elongation and coordinates transcription elongation with translation elongation. The results show two distinct TTC-A in translational pre-translocation and translocation intermediate states in which the RNAP becomes unstable as the translation progresses. The results further show that TTC-A is the crucial state where the ribosomes could exert mechanical force on RNAP, leading to the potential transition between TTC-A and TTC-B within mRNA spacer ranging from 7 to 9 codons and suggesting a ribosome-dependent transcription termination within mRNA spacer shorter than 7 codons. The results further show TTC-LC is also compatible with ribosome conformational changes during translation elongation cycle but with less stability compared with TTC-B and shows the potential transition with TTC-B within mRNA spacer of 13 codons. Our results provide a comprehensive blueprint detailing the dynamic interplay of transcription-translation coupling.
Escherichia coli grown in cost-effective conical tubes produces more plasmid DNA
Authors: Marquez Mayra , Chen Qian , Cachaco Silvia , Sui Hongyan , Imamichi Tomozumi 
Published: March 2024

AbstractBefore the COVID-19 pandemic, we grew plasmid-transformedEscherichia coliin Falcon round-bottom-polypropylene tubes (F-Round-PP) and isolated plasmid using a Miniprep kit. When obtaining sufficient quantities of F-Round-PP became problematic during the pandemic and the inflation, we grew them using any available tubes. Notably, we observed that plasmid yield from cells grown in a cost-effective Oxford conical-polypropylene tubes (O-Conical-PP) was higher than that from F-Round-PP. We assessed the impact using O-Conical-PP and other conical brand tubes. As a result, the plasmid yield from O-Conical-PP (the list price is nearly 1/3 of F-Round-PP) was 1.5-fold higher than other PP tubes (p<0.001). We propose that researchers may need to re-assess the effectiveness of their laboratory supplies to optimize the budget during this inflationary period.
Biophysical metabolic modeling of complex bacterial colony morphology
Authors: Dukovski Ilija , Golden Lauren , Zhang Jing , Osborne Melisa , Segrè Daniel , Korolev Kirill S. 
Published: March 2024

SummaryMicrobial colony growth is shaped by the physics of biomass propagation and nutrient diffusion, and by the metabolic reactions that organisms activate as a function of the surrounding environment. While microbial colonies have been explored using minimal models of growth and motility, full integration of biomass propagation and metabolism is still lacking. Here, building upon our framework for Computation of Microbial Ecosystems in Time and Space (COMETS), we combine dynamic flux balance modeling of metabolism with collective biomass propagation and demographic fluctuations to provide nuanced simulations ofE. colicolonies. Simulations produced realistic colony morphology, consistent with our experiments. They characterize the transition between smooth and furcated colonies and the decay of genetic diversity. Furthermore, we demonstrate that under certain conditions, biomass can accumulate along “metabolic rings” that are reminiscent of coffee-stain rings, but have a completely different origin. Our approach is a key step towards predictive microbial ecosystems modeling.
Enhanced Data Pre-processing for the Identification of Alzheimer’s Disease-Associated SNPs
Authors: Alves Juliana F , Costa Eduardo , Xavier Alencar , Brito Luiz , Cerri Ricardo 
Published: March 2024

AbstractAlzheimer’s Disease (AD) is a complex neurodegenerative disorder that has gained significant attention in scientific research, particularly since the Human Genome Project. Based on twin studies that utilize the resemblance of Alzheimer’s disease risk between pairs of twins, it has been found that the overall heritability of the disease is estimated at 0.58. When shared environmental factors are taken into account, the maximum heritability reaches 0.79. This suggests that approximately 58-79% of the susceptibility to late-onset Alzheimer’s disease can be attributed to genetic factors [4]. In 2022, it is estimated that AD will affect over 50 million people worldwide, and its economic burden exceeds a trillion US dollars per year. One promising approach is Genome-Wide Association Studies (GWAS), which allow the identification of genetic variants associated with AD susceptibility. Of particular interest are Single Nucleotide Polymorphisms (SNPs), which represent variations in a single nucleotide base in the DNA sequence. In this study, we investigated the association between SNPs and AD susceptibility by applying various quality control (QC) parameters during data pre-processing and rank the SNP associations through mixed linear models-based GWAS implemented in BLUPF90. Our findings indicate that the identified SNPs are located in regions already associated with Alzheimer’s Disease, including non-coding regions. We also investigated the impact of incorporating demographic data into our models. However, the results indicated that the inclusion of such data did not yield any benefits for the model. This study highlights the importance of GWAS in identifying potential genetic risk factors for AD and underscores the need for further research to gain a better understanding of the complex genetic mechanisms underlying this debilitating disease.
Creating an Early Diagnostic Method for Glaucoma Using Convolutional Neural Networks
Authors: Alqarni Areej A. , Al Harbi Sanad H. , Subhan Irshad A. 
Published: March 2024

AbstractAccording to the World Health Organization, glaucoma is a leading cause of blindness, accounting for over 12% of global blindness as it affects one in every 100 people. In fact, 79.6 million people worldwide live with blindness caused by glaucoma. This is because the current method for diagnosing glaucoma is by examining retinal fundus images. However, it is considerably difficult to distinguish the lesions’ features solely through manual observations by ophthalmologists, especially in the early phases. This study introduces a novel glaucoma detection method using attention-enhanced convolutional neural networks, achieving 98.9% accuracy and a swift 30-second detection time, vastly surpassing traditional diagnostic methods. The attention mechanism is utilized to learn pixel-wise features for accurate prediction. Several attention strategies have been developed to guide the networks in learning the important features and factors that affect localization accuracy. The algorithms were trained for glaucoma detection using Python 2.7, TensorFlow, Py Torch, and Keras Machine Learning-Based Applications. The methods were evaluated on Drishti-GS and RIM-ONE datasets with 361 training and 225 test sets, consisting of 344 healthy and 242 glaucomatous images. The proposed algorithms can achieve impressive results that show an increase in overall diagnostic efficiency, as the algorithm displays a 30-second detection time with 98.9% accuracy compared to the 72.3% accuracy of traditional testing methods. Finally, this algorithm has been implemented as a webpage, allowing patients to test for glaucoma. This webpage offers various services such as: connecting the patient to the nearest care setup; offering scientific articles regarding glaucoma; and a video game that supports eye-treatment yogic exercises to strengthen vision and focus. This early diagnostic method has the near future potential to decrease the percentage of irreversible vision loss due to glaucoma by 42.79% (the percentage was calculated using the mean absolute error function), which could prevent glaucoma from remaining the leading cause of blindness worldwide. Our glaucoma diagnostic webpage can be found at:Glaucoma Detector(glaucomadiagnosis.com)
Association between fruit and vegetable consumption and chronic diseases among food pantry users
Authors: Chen Jiacheng , Hosler Akiko S. , O’Grady Thomas J. , Romeiko Xiaobo X. 
Published: March 2024

AbstractIntroductionFruit and vegetable (FV) consumption can be a protective factor for chronic diseases, but few studies have investigated FV’s impact on health in the context of food/nutrition assistance system.MethodsWe used three health survey data collected in Upstate New York communities to construct a predictive model of food pantry use. The model was applied to a Northeastern US regional subset of SMART Behavioral Risk Factor Surveillance System (BRFSS) data to identify potential food pantry users. The associations between FV intake and diabetes, hypertension, and BMI were examined through multivariable logistic regression and linear regression analyses with food pantry use as a potential effect modifier.ResultsThe analysis dataset had 5,257 respondents, and 634 individuals were estimated as food pantry users. Consumption of vegetables was associated with decreased odds of hypertension and a lower BMI regardless of food pantry use. Consumption of fruits was associated with decreased odds of diabetes regardless of food pantry use. The association between fruit consumption and BMI was modified by food pantry use. Among food pantry users, consumption of fruits was associated with a greater BMI, while among food pantry non-users, it was associated with a lower BMI.ConclusionThe overall protective effects of increased FV consumption on chronic diseases suggest that increasing FV availability in food pantries may not only alleviate hunger but also improve health. Further research is needed to investigate the role of fruit including 100% fruit juice consumption and BMI among food pantry users.
Direct Ink Writing of Graphene Oxide Reinforced 13-93B1 Bioactive Glass Scaffolds for Bone Tissue Engineering Applications
Authors: Dixit Kartikeya , Vishwakarma Ashok , Kumar Hitendra , Kim Keekyoung , Sinha Niraj 
Published: March 2024

AbstractGraphene-reinforced bioactive glass scaffolds have gained significant attention in the field of bone tissue engineering due to their unique combination of mechanical strength, bioactivity, and electrical conductivity. Additive manufacturing techniques, such as 3D printing, provide a versatile platform for fabricating these scaffolds with precise control over their architecture and composition. Consequently, in this work, we have fabricated graphene oxide (GO)-reinforced 13-93B1 bioactive glass scaffold using the direct ink writing technique. A Pluronic F-127- based ink was prepared for scaffold fabrication, and its rheological properties were assessed for shear thinning behaviour, structural support, and recovery. Further, the fabricated scaffolds were characterized using micro-computed tomography, scanning electron microscopy, and energy dispersive x-ray spectroscopy. Additionally, computational fluid dynamics simulations with Dulbecco’s modified eagle medium and blood were performed to evaluate the perfusion kinetics of the scaffolds. The inclusion of GO enhanced the compressive strength of the fabricated scaffolds by ∼225%. The morphological characterization based on micro-computed tomography showed that additively manufactured scaffolds have appropriate porosity, pore size, pore throat size, and interconnectivity. The live-dead assay results showed no cytotoxicity towards C2C12 mouse myoblast cells. Also, cell adhesion and cell viability results show better cell growth on the nanocomposite scaffolds. Overall, the fabricated scaffold is found suitable for bone tissue engineering applications.