bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing Gene Expression Predictions Using Deep Learning and Functional Annotations
Authors: Ramprasad Pratik , Ren Jingchen , Pan Wei 
Published: September 2024

ABSTRACTTranscriptome‐wide association studies (TWAS) aim to uncover genotype–phenotype relationships through a two‐stage procedure: predicting gene expression from genotypes using an expression quantitative trait locus (eQTL) data set, then testing the predicted expression for trait associations. Accurate gene expression prediction in stage 1 is crucial, as it directly impacts the power to identify associations in stage 2. Currently, the first stage of such studies is primarily conducted using linear models like elastic net regression, which fail to capture the nonlinear relationships inherent in biological systems. Deep learning methods have the potential to model such nonlinear effects, but have yet to demonstrably outperform linear methods at this task. To address this gap, we propose a new deep learning architecture to predict gene expression from genotypic variation across individuals. Our method utilizes a learnable input scaling layer in conjunction with a convolutional encoder to capture nonlinear effects and higher‐order interactions without compromising on interpretability. We further augment this approach to allow for parameter sharing across multiple networks, enabling us to utilize prior information for individual variants in the form of functional annotations. Evaluations on real‐world genomic data show that our method consistently outperforms elastic net regression across a large set of heritable genes. Furthermore, our model statistically significantly improved predictive performance by leveraging functional annotations, whereas elastic net regression failed to show equivalent gains when using the same information, suggesting that our method can capture nonlinear functional information beyond the capability of linear models.
Studies to assess natural resource recovery and evaluate monitoring methods for restored bottomland hardwood forests
Authors: Hooper Michael J. , Struckhoff Matthew A. , Isanhart John P. , Albers Janice L. , Grabner Keith W. , Green Nicholas S. , Kunz Bethany K. , Victoria McDonald M. , West Benjamin M. 
Published: September 2024

Abstract
The Natural Resource Damage Assessment and Restoration process assesses natural resource injury due to oil or chemical spills and calculates the damages to compensate the public for those injuries. Ecological restoration provides a means for recovering resources injured or lost due to contamination from oil or chemical spills by restoring the injured site after remediation, or acquiring or reconstructing equivalent resources off site to replace those lost due to the spill. In the case of restored forests, once restoration is implemented, monitoring of forest ecology helps keep recovery on track, with the maturation of forest vegetation, recovered soil conditions, and development of microbial, fungal, and faunal communities, necessary for ecologically functioning forests. This series of papers focuses on applying methods for monitoring restoration progress in forest vegetation and soils, and amphibian, avian, and mammalian communities, assessing strengths and weaknesses of different methods, and evaluating levels of effort needed to obtain accurate indications of forest ecological condition. Integr Environ Assess Manag 2024;20:1912–1916. © 2024 The Author(s). Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
Key Points
Ecological restorations recover resources injured or lost due to contamination from oil or chemical spills, by restoring the injured site after remediation, or by acquiring or reconstructing equivalent resources off site to replace those lost due to the spill. In the case of forests, once restoration is implemented, monitoring is important to track the progress of indicators of ecological function, such as maturation of forest vegetation, recovered soil conditions, and development of faunal communities. Articles in this special series describe the recovery of vegetation and soils, and amphibian, avian, and mammalian communities in forest restorations of multiple ages, while simultaneously comparing the strengths, weaknesses, and relative efficiency of different monitoring methods.
Study on the effects of beta cyclodextrin‐zinc oxide nanoparticles as heterogeneous catalysts in microbial oil fermentation
Authors: Ravi Kumar Janice , Anandan Dayanandan , Kaliyaperumal Viswanathan 
Published: September 2024

AbstractIn order to study the catalytic activity of beta cyclodextrin‐encapsulated zinc oxide (ZnO) nanoparticles in microbial oil synthesis, rice‐washed waste water (RWW) was used as the fermentation medium and streptomyces fradiae as the microbe. The introduction of zinc oxide nanoparticles during fermentation had an impact on output and growth. The biomass percentage was 1.5 times greater and the fatty acid profile was better than in the control samples. The analysis of the induction period (IP) revealed that samples containing zinc oxide nanoparticles had maximum oxidation stability for up to 120 days of storage, along with a considerable reduction in autoxidation. The cetane number and calorific value, however, increased with the addition of ZnO nanoparticles. A new study discovered that the use of ZnO nanoparticles encapsulated in β‐CD led to much increased production (63.5 g/L) of microbial oil than the control sample (42.5 g/L). Therefore, it is anticipated that these nanoparticles would find utility in energy‐related applications.
Dissecting SOX9 dynamics reveals its differential regulation in osteoarthritis
Authors: Govindaraj Kannan , Kannan Sakshi , Coutinho de Almeida Rodrigo , Jansen Klomp Lucas , Karperien Marcel , Meulenbelt Ingrid , Post Janine N. 
Published: September 2024

AbstractThe transcription factor SOX9 is integral to tissue homeostasis and is implicated in skeletal malformation, campomelic dysplasia, and osteoarthritis (OA). Despite extensive research, the complete regulatory landscape of SOX9 transcriptional activity, interconnected with signaling pathways (TGFβ, WNT, BMP, IHH, NFκB, and HIF), remains challenging to decipher. This study focuses on elucidating SOX9 signaling in OA pathology using Fluorescence Recovery After Photobleaching (FRAP) to assess SOX9 activity directly in live human primary chondrocytes (hPCs). Single cell FRAP data revealed two distinct subpopulations with differential SOX9 dynamics, showing varied distribution between healthy and OA hPCs. Moreover, inherently elevated SOX9‐DNA binding was observed in healthy hPCs compared to preserved and OA counterparts. Anabolic factors (BMP7 and GREM1) and catabolic inhibitors (DKK1 and FRZb) were found to modulate SOX9 transcriptional activity in OA‐hPCs. These findings provide valuable insights into the intricate regulation of SOX9 signaling in OA, suggesting potential therapeutic avenues for modulating SOX9 activity in diseased states.
Simulator practice of temporary anchorage device (TAD) insertion on inter‐radicular sites improves learning and confidence in dental residency
Authors: Duan Duoni , Gan Mark Joo Seng , Lim Li Zhen , Foong Kelvin Weng Chiong 
Published: September 2024

AbstractPurposeThis exploratory study elicited the procedural considerations and inter‐radicular site placement techniques of experts and investigated how the use of a simulator, with and without feedback, influenced novice learners’ procedural considerations, placement techniques, and confidence.MethodsThree orthodontic/oral maxillofacial surgery expert clinicians participated in a temporary anchorage device (TAD) insertion assessment accompanied by a think‐aloud protocol. Expert transcripts were coded according to a coding scheme to analyze clinicians’ (N = 18) procedural considerations and placement techniques. Residents were randomly allocated to control and intervention groups. Two placement sessions were conducted at two inter‐radicular sites with audio recordings. The intervention group received real‐time feedback on root contact from the simulator's sensor and postoperative radiographs for self‐assessed feedback. Residents’ confidence levels were compared before and after placements, and subjective feedback about the simulator was obtained.ResultsThis study utilized the think‐aloud protocol to capture experts’ procedural considerations and placement techniques during TAD insertion and revealed a disparity between residents’ and experts’ thought processes. Only four out of 15 expert themes were mentioned by more than 50% of the residents. The use of the TAD insertion simulator in combination with feedback broadened residents’ procedural considerations after one round of placement. Residents’ confidence increased significantly in both groups (p < 0.05), but there was no significant difference between them (p > 0.482).ConclusionWhen used in conjunction with feedback, simulator practice of TAD insertion broadened residents’ procedural considerations after one round of placement. It improved residents’ confidence level and was well received as a learning tool.
Pediatric Dentistry Program Directors as stakeholders in the process of Board certification
Authors: Caffrey Erica M. , Dhar Vineet 
Published: September 2024

AbstractPurpose/objectivesBoard certification is an important credential for pediatric dentists to achieve for purposes of career advancement, hospital privileges, and reputation. The purpose of this pilot study was to assess the engagement of residency Program Directors (PDs) with the Board certification process in terms of criteria for clinical readiness, curriculum development, and value. An additional objective was to identify challenges and ways in which PDs may need support as they prepare residents for Board certification.MethodsEighty‐seven PDs were invited to participate in this study, out of which 32 agreed to participate (36% response rate). The study included a digital non‐validated survey and verbal interviews. Digital and verbal survey results were analyzed using descriptive statistics.ResultsPDs had recurrent themes in their descriptions of clinical readiness, including information gathering, application of knowledge, and professional awareness. Half of the participants used the American Board of Pediatric Dentistry (ABPD) exam domains as a guideline in their curriculum development. Of the verbal interview participants (N = 32), 30(94%) felt that Board certification was very important to their residents and program. Many barriers to successful completion of the Board exam were discussed, and a diverse array of suggestions were made for mechanisms to better support PDs as they prepare residents for Board certification.ConclusionsBoard certification is valued by PDs and influences their criteria for clinical readiness. Increased engagement with the ABPD will facilitate better support for PDs and will enhance the consistency of training standards in residency programs.
Functional Verification of Transcription Factor comp54181_c0 in Monascus purpureus
Authors: Zhang Chan , Wang Haijiao , Ablimit Arzugul , Zhao Yufei , Sun Qing , Dong HuiJun , Zhang Bobo , Liu Chengjian , Wang Chengtao 
Published: September 2024

ABSTRACTMonacolin K is a valuable secondary metabolite produced after a period of fermentation by Monascus purpureus; however, our current understanding of the regulatory mechanisms of its synthesis remains incomplete. This study conducted functional analysis on the key transcription factor, comp54181_c0, that is involved in the synthesis of monacolin K in Monascus. Mutant strains with either knockout or overexpression of comp54181_c0 were constructed using CRISPR/Cas9. A comparison between the knockout and overexpression strains revealed changes in fungal morphology and growth, with a significant increase in the production of Monascus pigments and monacolin K when comp54181_c0 was absent. Real‐time fluorescence quantitative PCR analysis revealed that comp54181_c0 significantly influenced the transcription of key genes related to monacolin K biosynthesis in Monascus. In conclusion, our study elucidates the crucial role of comp54181_c0 in Monascus, enriches our understanding of fungal secondary metabolite development and regulation, and provides a foundation for the development and regulation of Monascus and monacolin K production.
Knowledge assessment tool for pediatric parenteral nutrition: A validation study
Authors: Fleet Sarah E. , Sideridis Georgios , Wolbrink Traci 
Published: September 2024

AbstractBackgroundParenteral nutrition (PN) is a high‐risk medication, and its prescription and administration requires extensive training. Difficulties inherent with bedside teaching have made teaching these concepts challenging. Currently, no knowledge assessment tools with validity evidence exist to test the effectiveness of new PN teaching interventions. We sought to develop and provide validity evidence for a pediatric PN knowledge test to measure the effectiveness of future teaching interventions.MethodsWe created a multiple‐choice question knowledge assessment tool that underwent content validation by PN experts and was emailed to potential participants. We evaluated the knowledge assessment tool for factorial validity, internal consistency reliability, and discriminant validity.ResultsWe enrolled 103 medical students (40%), residents and fellow trainees (55%), and attending physicians (5%) into the study between October 2021 and October 2022. Five of the 30 questions performed poorly based on their nonsignificant contribution to the primary aim of assessing pediatric PN knowledge. Following the exclusion of those questions, the knowledge assessment tool demonstrated an acceptable model fit, and the root mean squared error of approximation was <5%. The omega coefficient was 0.829, indicating acceptable levels of reliability, and using an analysis of variance test (ANOVA) demonstrated significant differences between groups, showing good discrimination between levels of experience (F[2, 80] = 39.002; P < 0.001).ConclusionWe have developed and provided validity evidence for a multiple‐choice question knowledge test that may be used by educators and programs to evaluate knowledge of pediatric PN in physicians and trainees.
Chemometrics analysis of the flow and thermal properties of cardaba banana starch
Authors: Olawoye Babatunde , Olaoye Isaac Olatunde 
Published: September 2024

AbstractBACKGROUNDStarch from a non‐conventional source such as cardaba banana is relatively underexplored compared to conventional sources such as potato, maize or tapioca. Its high amylose content, however, suggests its suitability for specific industrial uses. Understanding the flowability, rheology and thermal properties of cardaba banana starch could lead to its novel application in food product formulation and pharmaceutical industry. Therefore, the present study aimed to examine the effect of modification on the bulk material characterization (powder flowability), granule size and shape (measured by light microscope), rheology and thermal properties of cardaba banana starch.RESULTSThe flowability of cross‐linked starch was affected significantly by the granule size (105 892.7 μm), shape (circularity 0.78) and compressibility (0.20), making it a more free‐flowing powder than other starch powders. The rheological behavior of the starch paste revealed that the Herschel–Bulkley model best predicts the rheological behavior with the highest coefficient of determinant (R2 > 0.9).CONCLUSIONCross‐linked Cardaba banana starch with an excellent characteristic will find good application in food products that require free‐flowing behavior. © 2024 Society of Chemical Industry.
Inkjet‐printed quantum dot light‐emitting diodes: Development and challenges for display applications
Authors: Han Changyeol , Lee Sooho , Ko Yunhyuk , Cho Jungho , Jung Yun Ku , Kang Dong Jin , Kwak Donghoon , Kim Sehun , Ha Jaekook , Yoon Yeo‐geon , Lee Changhee 
Published: September 2024

AbstractQuantum dot (QD) technology is rapidly advancing and draws much attention for display applications where accurate and vibrant color reproduction is highly required. Currently, significant research is being conducted in developing quantum dot light‐emitting diode (QD‐LED) as next‐generation displays. QD‐LEDs offer several advantages, including high color purity, wide color gamut, and lower manufacturing costs. Recent advancements in QD synthesis and device engineering have significantly improved the performance of QD‐LEDs, but several challenges must be addressed for the successful commercialization. In this article, we provide an overview of QD‐LED developments and key issues that are required to be solved for realizing practical inkjet‐printed QD‐LED displays.
Classifiers of anterior cruciate ligament status in female and male adolescents using return‐to‐activity criteria
Authors: Girard Céline I. , Romanchuk Nicholas J. , Del Bel Michael J. , Carsen Sasha , Chan Adrian D. C. , Benoit Daniel L. 
Published: September 2024

AbstractPurposeA lack of standardization exists for functional tasks in return‐to‐activity (RTA) guidelines for adolescents with anterior cruciate ligament injury (ACLi). Identifying the variables that discern ACLi status among adolescents is a first step in the creation of such guidelines following surgical reconstruction. This study investigated the use of classification models to discern ACLi status of adolescents with and without injury using spatiotemporal variables from functional tasks typically used in RTA guidelines for adults.MethodsSixty‐four adolescents with ACLi and 70 uninjured adolescents completed single‐limb hops, lunges, squats, countermovement jumps and drop‐vertical jumps. Jumping distances, heights, and depths were collected. Decision trees (DTs) were used to classify ACLi status and were evaluated using the F‐measure (F1), kappa statistic (ĸ) and area under the precision–recall curve (PRC). Independent t tests and effect sizes were calculated for each important classifier of the DT models.ResultsA five‐variable model classified ACLi status with an accuracy of 67.5% (F1 = 0.6842; ĸ = 0.350; PRC = 0.491) with sex as a classifier. Significant differences were found in three of the four spatiotemporal variables (p ≤ 0.002). Separate models then classified ACLi status in males and females with an accuracy of 53.3% (F1 = 0.5882; ĸ = 0.0541; PRC = 0.476) and 76.9% (F1 = 0.7692; ĸ = 0.541; PRC = 0.528), respectively, with significant differences for all variables (p ≤ 0.013).ConclusionsAmong the DT models, females were better able to classify ACLi status compared to males, highlighting the importance of sex‐specific rehabilitation guidelines for adolescents.Level of EvidenceLevel III.
Newborn Hearing Screening Success… Patient Care Failure
Authors: Jennings Akailah , Isaacson Glenn 
Published: September 2024

ObjectiveTo assess the efficacy of a newborn hearing screening program in an urban hospital 24 years after a longitudinal study identified failings in its program and recommended solutions.MethodsA hospital‐specific, Pennsylvania database was queried to determine rates of in‐hospital testing, referral, and diagnosis for Temple University Hospital (TUH), and to compare these with reporting sites statewide. At TUH, interviews with newborn hearing screeners and audiologists were conducted to identify barriers to care.ResultsIn the year 2022, 2,006/2,069 newborns (97%) were successfully screened prior to hospital discharge at TUH. (63 babies were never tested). There were 73 who did not pass automated auditory brainstem response testing (ABR) in at least one ear. All of these 73 infants returned for repeat automated ABR testing and 50/73 passed in both ears. 23/2006 (1%) were referred to diagnostic testing. 13/23 were successfully scheduled. 11/23 passed in both ears. 2/13 were found to have hearing losses. 10 infants (43%) were lost to follow‐up and were never diagnosed. Examining lost‐to‐follow‐up rates statewide, we identified a relationship between successful follow‐up and local median family income.ConclusionLegislation on the state level and improvements in audiometric technology have led to highly successful in‐hospital screening with relatively low false‐positive rates. Despite this, inadequate outpatient follow‐up testing and inequities in the American health care system continue to delay audiometric diagnosis and habilitation of congenital hearing loss. Lack of transportation, childcare for siblings, and newborn insurance status impede access to diagnostic testing.Level of Evidence3 evidence—retrospective review comparing cases and controls Laryngoscope, 135:942–947, 2025
Soil Nutrients Inversion in Open‐Pit Coal Mine Reclamation Area of Loess Plateau, China: A Study Based on ZhuHai‐1 Hyperspectral Remote Sensing
Authors: Wang Hongyu , Wang Juan , Ma Rongrong , Zhou Wei 
Published: September 2024

ABSTRACTSoil nutrients are crucial to assess land reclamation quality, and the use of various types of remote sensing data for soil nutrient inversion has been a key focus for soil monitoring. However, fewer studies have been conducted using satellite‐based hyperspectral remote sensing. To explore the potential of satellite‐based hyperspectral remote sensing in soil nutrient monitoring, this study selected soil organic matter, total nitrogen, available phosphorus, and available potassium content data from 83 sample sites using ZhuHai‐1 hyperspectral data. After spectral transformation and feature extraction, various inversion models were constructed, including partial least squares regression, support vector machine, recurrent neural network, and random forest. After verification by accuracy, the best spectral‐model combination was used for inversion. The results showed that the R‐squared range of the inversion models was 0.67748–0.78115. High content areas of soil organic matter and available potassium exhibited concentrated and contiguous features, while high content areas of total nitrogen and available phosphorus were more fragmented and fine‐grained. Alfalfa grassland plays a vital role in improving reconstructed soil in the early reclamation stage, and agricultural activities have differential impacts on soil nutrient accumulation. This study provides a theoretical basis for verifying the application capability of ZhuHai‐1 hyperspectral satellite data in soil monitoring.