bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors analysis and survival prediction model establishment of patients with lung adenocarcinoma based on different pyroptosis-related gene subtypes
Authors: Wen Ziang , Pei Bei , Dai Longfei , Lu Peng , Li Xiangyu , Zhang Chengxin , Ge Shenglin 
Published: December 2023

Abstract
Background
Lung adenocarcinoma (LUAD) is a common cancer with a poor prognosis. Pyroptosis is an important process in the development and progression of LUAD. We analyzed the risk factors affecting the prognosis of patients and constructed a nomogram to predict the overall survival of patients based on different pyroptosis-related genes (PRGs) subtypes.

Methods
The genomic data of LUAD were downloaded from the TCGA and GEO databases, and all data were filtered and divided into TCGA and GEO cohorts. The process of data analysis and visualization was performed via R software. The data were classified based on different PRGs subtypes using the K-means clustering method. Then, the differentially expressed genes were identified between two different subtypes, and risk factors analysis, survival analysis, functional enrichment analysis, and immune cells infiltration landscape analysis were conducted. The COX regression analysis was used to construct the prediction model.

Results
Based on the PRGs of LUAD, the patients were divided into two subtypes. We found the survival probability of patients in subtype 1 is higher than that in subtype 2. The results of the logistics analysis showed that gene risk score was closely associated with the prognosis of LUAD patients. The results of GO analysis and KEGG analysis revealed important biological processes and signaling pathways involved in the differentially expressed proteins between the two subtypes. Then we constructed a prediction model of patients’ prognosis based on 13 genes, including IL-1A, P2RX1, GSTM2, ESYT3, ZNF682, KCNF1, STK32A, HHIPL2, GDF10, NDC80, GSTA1, BCL2L10, and CCR2. This model was strongly related to the overall survival (OS) and also reflects the immune status in patients with LUAD.

Conclusion
In our study, we examined LUAD heterogeneity with reference to pyroptosis and found different prognoses between the two subtypes. And a novel prediction model was constructed to predict the OS of LUAD patients based on different PRGs signatures. The model has shown excellent predictive efficiency through validation.
The Human Genome Organisation (HUGO) and a vision for Ecogenomics: the Ecological Genome Project
Authors: Capps Benjamin , Chadwick Ruth , Lederman Zohar , Lysaght Tamra , Mills Catherine , Mulvihill John J. , Oetting William S. , Winship Ingrid ,   HUGO Committee on Ethics, Law and Society,   HUGO Executive Board
Published: December 2023

Abstract
Background
The following outlines ethical reasons for widening the Human Genome Organisation’s (HUGO) mandate to include ecological genomics.

Main
The environment influences an organism’s genome through ambient factors in the biosphere (e.g. climate and UV radiation), as well as the agents it comes into contact with, i.e. the epigenetic and mutagenic effects of inanimate chemicals and pollution, and pathogenic organisms. Emerging scientific consensus is that social determinants of health, environmental conditions and genetic factors work together to influence the risk of many complex illnesses. That paradigm can also explain the environmental and ecological determinants of health as factors that underlie the (un)healthy ecosystems on which communities rely. We suggest that The Ecological Genome Project is an aspirational opportunity to explore connections between the human genome and nature. We propose consolidating a view of Ecogenomics to provide a blueprint to respond to the environmental challenges that societies face. This can only be achieved by interdisciplinary engagement between genomics and the broad field of ecology and related practice of conservation. In this respect, the One Health approach is a model for environmental orientated work. The idea of Ecogenomics—a term that has been used to relate to a scientific field of ecological genomics—becomes the conceptual study of genomes within the social and natural environment.

Conclusion
The HUGO Committee on Ethics, Law and Society (CELS) recommends that an interdisciplinary One Health approach should be adopted in genomic sciences to promote ethical environmentalism. This perspective has been reviewed and endorsed by the HUGO CELS and the HUGO Executive Board.
Pharmacotherapy for attention deficit/hyperactivity disorder in youth with avoidant restrictive food intake disorder: a case series of patients prescribed stimulant medication in a partial hospitalization program for eating disorders
Authors: Finn Daphna M. , Menzel Jessie E. , Gray Emily , Schwartz Terry 
Published: December 2023

Abstract
Background
Appetite suppression and weight loss are established potential side effects of most medications for attention deficit/hyperactivity disorder (ADHD). These side effects may be especially problematic when using stimulants to treat ADHD in the context of a restrictive eating disorder, such as avoidant restrictive food intake disorder (ARFID), although these diagnoses are often comorbid in children. This paper presents a combined approach to treating ADHD comorbid with ARFID using stimulant medication and behavior management within a partial hospitalization program (PHP) and intensive outpatient program (IOP)for eating disorders. The aim of this paper is to determine if the continued or new use of stimulant medication allows for adequate weight restoration by reviewing a series of cases receiving the combined treatment.

Case presentations
Consecutive patients with a historical or new diagnosis of ADHD when presenting for treatment for ARFID were included in this case series. This series included 10 patients (8 male, 2 female) who received pharmacotherapy using stimulants and behavior management interventions involving structured mealtimes and contingency management. All treatment occurred within the context of a PHP/IOP for childhood eating disorders. All youth were able to effectively continue on stimulant medication, show clinical benefit in core ADHD symptoms, and able to gradually restore weight. In all cases, stimulant medications were not discontinued, but in some cases, doses were optimized (increased or decreased), switched to a different stimulant, or augmented with non-ADHD medication, such as mirtazapine, to support the management of ADHD while concurrently assisting in weight gain as necessary for the treatment of ARFID. Only one patient was newly started on a stimulant medication; as this was near the end of her treatment stay, limited conclusions can be drawn from this case.

Conclusions
These findings support the use of pharmacotherapy, including continuing stimulant medication, when combined with behavior management strategies as a potentially effective treatment approach for ADHD in youth with ARFID in the PHP/IOP setting. Future studies using more rigorous methodology, longer follow-up times, and within other treatment settings are needed.
Challenges and opportunities of AI in inclusive education: a case study of data-enhanced active reading in Japan
Authors: Toyokawa Yuko , Horikoshi Izumi , Majumdar Rwitajit , Ogata Hiroaki 
Published: December 2023

AbstractIn inclusive education, students with different needs learn in the same context. With the advancement of artificial intelligence (AI) technologies, it is expected that they will contribute further to an inclusive learning environment that meets the individual needs of diverse learners. However, in Japan, we did not find any studies exploring current needs in an actual special needs context. In this study, we used the learning and evidence analysis framework (LEAF) as a learning analytics-enhanced learning environment and employed Active Reading as an example learning task to investigate the challenges and possibilities of applying AI to inclusive education in the future. Two students who attended a resource room formed the context. We investigated learning logs in the LEAF system while each student executed a given learning task. We detected specific learning behaviors from the logs and explored the challenges and future potential of learning with AI technology, considering human involvement in orchestrating inclusive educational practices.
Seismic wave attenuation (1/Qp) in the crust underneath the Eastern and eastern Southern Alps (Europe): imaging effects of faults, fractures, and fluids
Authors: Jozi Najafabadi Azam , Haberland Christian , Handy Mark R. , Le Breton Eline , Weber Michael 
Published: December 2023

AbstractWe present a novel three-dimensional model of compressional wave attenuation (1/QP) for the Eastern and eastern Southern Alps in Europe that includes the eastern part of the Adriatic indenter, termed here the Dolomites Sub-Indenter. Our approach employed waveform data from the SWATH-D network, a dense temporary network operational between 2017 and 2019, as well as selected stations of the larger AlpArray Seismic Network. A spectral inversion method using frequency-independent quality factor QP, was applied to derive 3578 path-averaged attenuation values (t*) from 126 local earthquakes. These were then inverted using the damped least square inversion (local earthquake tomography) for the attenuation structure. The resulting QP model, which builds on and complements a previously calculated 3-D velocity model (VP and VP/VS), exhibits good resolution down to ~ 20 km depth. Several anomalies can be correlated with the distribution of other physical parameters (VP and VP/VS) and regional tectonic features. Notably, the Friuli-Venetian region exhibits the highest attenuation (lowest QP) anomaly, coinciding with low VP values and increased VP/VS. This anomaly is likely associated with a high density of faults and fractures, as well as the presence of fluid-filled sediments along the active thrust front in the eastern segment of the Southern Alps. Another intriguing observation is the low attenuation (high QP) anomaly along the northwestern edge of the Dolomites Sub-Indenter (NWDI), located south of the Periadriatic fault and east of the Giudicarie fault, where seismicity is notably absent. This anomaly coincides with Permian magmatic rocks at the surface and may be a measure of their strength at depth.
Graphical Abstract
Redefining precision and efficiency in orthognathic surgery through virtual surgical planning and 3D printing: a narrative review
Authors: Lee Yong-Chan , Kim Seong-Gon 
Published: December 2023

AbstractOrthognathic surgery, essential for addressing jaw and facial skeletal irregularities, has historically relied on traditional surgical planning (TSP) involving a series of time-consuming steps including two-dimensional radiographs. The advent of virtual surgical planning (VSP) and 3D printing technologies has revolutionized this field, bringing unprecedented precision and customization to surgical processes. VSP facilitates 3D visualization of the surgical site, allowing for real-time adjustments and improving preoperative stress for patients by reducing planning time. 3D printing dovetails with VSP, offering the creation of anatomical models and surgical guides, enhancing the predictability of surgical outcomes despite higher initial setup and material costs. The integration of VSP and 3D printing promises innovative and effective solutions in orthognathic surgery, surpassing the limitations of traditional methods. Patient-reported outcomes show a positive post-surgery impact on the quality of life, underlining the significant role of these technologies in enhancing self-esteem and reducing anxiety. Economic analyses depict a promising long-term fiscal advantage with these modern technologies, notwithstanding the higher initial costs. The review emphasizes the need for large-scale randomized controlled trials to address existing research gaps and calls for a deeper exploration into the long-term impacts and ethical considerations of these technologies. In conclusion, while standing on the cusp of a technological renaissance in orthognathic surgery, it is incumbent upon the medical fraternity to foster a collaborative approach, balancing innovation with scrutiny to enhance patient care. The narrative review encourages the leveraging of VSP and 3D printing technologies for more efficient and patient-centric orthognathic surgery, urging the community to navigate uncharted territories in pursuit of precision and efficiency in the surgical landscape.
The study of serum muscarinic acetylcholine receptor subtype 3 (m3AChR)-Specific autoantibodies level in rheumatoid arthritis patients with secondary sjogren syndrome
Authors: Fakher Hagar Elsayed , El Gazzar Nagat Mohammed , Mabrouk Maaly Mohamed , Nada Doaa Waseem 
Published: December 2023

Abstract
Background
Dry eyes and mouth are symptoms of Sjogren syndrome, which can occur on its own and be referred to as primary Sjogren syndrome or in conjunction with other rheumatic diseases like rheumatoid arthritis and be referred to as secondary Sjogren syndrome. Anti-muscarinic type 3 receptors have been linked to neurological issues as well as secretory dysfunction in Sjogren patients. Consequently, the purpose of this study is to determine the serum level of muscarinic acetylcholine receptor subtype 3 (m3AChR)-specific autoantibodies in rheumatoid arthritis (RA) patients and evaluate its relationship to disease activity, functional disability, and to study its role in the development of secondary Sjogren syndrome manifestations in those patients.

Methods
In this cross-sectional study, 30 RA patients with secondary Sjogren syndrome signs and 30 RA patients without secondary Sjogren syndrome manifestations were included, along with 30 healthy volunteers who were aged, and sex matched as controls. All participants underwent thorough clinical examination, evaluation of disease activity using the DAS28 score, assessment of functional status using the modified health assessment questionnaire (MHAQ), and evaluation of the serum level of (m3AChR) by (ELISA).

Results
When compared to RA patients without secondary Sjogren syndrome and healthy controls (20.09 ± 4.24, 18.36 ± 3.59 ng/ml respectively), the serum level of m3AChR antibodies among 30 RA patients with secondary Sjogren syndrome considerably increased (mean 25.98 ± 4.81 ng/ml).Analysis of the m3AChR’s (ROC)-curve revealed that the three groups under study differed significantly (P < 0.001), with the AUC (0.806), cutoff (> 22.63ng/ml), sensitivity (73.33%), and specificity (86.67%) all exceeding the threshold. Additionally, there was a significant positive connection between the serum level of m3AChR and the following variables (P < 0.05): DAS scores, MHAQ score, number of tender & swollen joints, and acute phase reactants.

Conclusion
Autoantibodies against m3AChR may be one of the serum components involved in the pathophysiology of secondary Sjogren syndrome in RA patients, and because of their high sensitivity and specificity, they can be utilized as a diagnostic marker in these individuals.
The effect of an adapted digital mental health intervention for sickle cell disease on engagement: a pilot randomized controlled trial
Authors: Nardo Emily V. , Parchuri Ektha , O’Brien Julia A. , Crosby Lori , Porter Jerlym , Palermo Tonya , Nikolajski Cara , Treadwell Marsha , Hillery Cheryl A. , Szigethy Eva , Jonassaint Charles R. 
Published: December 2023

Abstract
Introduction
Despite promising outcomes, lack of engagement and poor adherence are barriers to treating mental health using digital CBT, particularly in minority groups. After conducting guided focus groups, a current mental health app was adapted to be more inclusive for minorities living with SCD.

Methods
Patients between the ages of 16–35 with SCD who reported experiencing anxiety or depression symptoms were eligible for this study. Once enrolled, participants were randomly assigned to receive one of two versions of a mental health app: 1) the current version designed for the general population or 2) the adapted version. Baseline measures for depression, anxiety, pain, and self-efficacy were completed at the start of the study and again at post-intervention (minimum 4 weeks).

Results
Compared to baseline, mean scores for pain decreased an average of 3.29 (p = 0.03) on a 10-point scale, self-efficacy improved 3.86 points (p = 0.007) and depression symptoms decreased 5.75 points (p = 0.016) for the group that received the adapted app. On average, control participants engaged with the app 5.64 times while the participants in the experimental group engaged 8.50 times (p = 0.40). Regardless of group assignment, a positive relationship (r = 0.47) was shown between app engagement and a change in depression symptoms (p = 0.042).

Discussion
Target enrollment for this study sought to enroll 40 participants. However, after difficulties locating qualified participants, enrollment criteria were adjusted to expand the population pool. Regardless of these efforts, the sample size for this study was still smaller than anticipated (n = 21). Additionally, irrespective of group approximately 40% of participants did not engage with the app. However, despite a small sample size and poor engagement, this study 1) demonstrated the feasibility of implementing socially relevant changes into a mental health app and 2) indicated that participants in the intervention group displayed better outcomes and showed trends for greater app interaction.

Conclusion
These promising results should encourage future researchers to continue exploring ideal adaptations for implementing digital CBT in minority populations. Future studies should also consider implementing post-intervention surveys to help identify common factors relating to a lack of engagement.

Trial registration
This trial (NCT04587661) was registered on August 12th, 2020.
Awakening adult neural stem cells: NOX signalling as a positive regulator of the quiescence-to-proliferation transition in the Xenopus retina
Authors: Donval Alicia , Hernandez Puente Cinthia Violeta , Lainé Anaïs , Roman Diana , Vessely Romain , Leclercq Julien , Perron Muriel , Locker Morgane 
Published: December 2023

ABSTRACT
A growing wealth of data suggest that reactive oxygen species (ROS) signalling might be crucial in conferring embryonic or adult stem cells their specific properties. However, how stem cells control ROS production and scavenging, and how ROS in turn contribute to stemness, remain poorly understood. Using the Xenopus retina as a model system, we first investigated the redox status of retinal stem cells (RSCs). We discovered that they exhibit higher ROS levels compared with progenitors and retinal neurons, and express a set of specific redox genes. We next addressed the question of ROS functional involvement in these cells. Using pharmacological or genetic tools, we demonstrate that inhibition of NADPH oxidase-dependent ROS production increases the proportion of quiescent RSCs. Surprisingly, this is accompanied by an apparent acceleration of the mean division speed within the remaining proliferating pool. Our data further unveil that such impact on RSC cell cycling is achieved by modulation of the Wnt/Hedgehog signalling balance. Altogether, we highlight that RSCs exhibit distinctive redox characteristics and exploit NADPH oxidase signalling to limit quiescence and fine-tune their proliferation rate.
Sensory nerve regulates progenitor cells via FGF-SHH axis in tooth root morphogenesis
Authors: Pei Fei , Ma Li , Guo Tingwei , Zhang Mingyi , Jing Junjun , Wen Quan , Feng Jifan , Lei Jie , He Jinzhi , Janečková Eva , Ho Thach-Vu , Chen Jian-Fu , Chai Yang 
Published: December 2023

ABSTRACT
Nerves play important roles in organ development and tissue homeostasis. Stem/progenitor cells differentiate into different cell lineages responsible for building the craniofacial organs. The mechanism by which nerves regulate stem/progenitor cell behavior in organ morphogenesis has not yet been comprehensively explored. Here, we use tooth root development in mouse as a model to investigate how sensory nerves regulate organogenesis. We show that sensory nerve fibers are enriched in the dental papilla at the initiation of tooth root development. Through single cell RNA-sequencing analysis of the trigeminal ganglion and developing molar, we reveal several signaling pathways that connect the sensory nerve with the developing molar, of which FGF signaling appears to be one of the important regulators. Fgfr2 is expressed in the progenitor cells during tooth root development. Loss of FGF signaling leads to shortened roots with compromised proliferation and differentiation of progenitor cells. Furthermore, Hh signaling is impaired in Gli1-CreER;Fgfr2fl/fl mice. Modulation of Hh signaling rescues the tooth root defects in these mice. Collectively, our findings elucidate the nerve-progenitor crosstalk and reveal the molecular mechanism of the FGF-SHH signaling cascade during tooth root morphogenesis.
Longitudinal Changes in Quadriceps Morphology over the First Three Months Following Anterior Cruciate Ligament Reconstruction
Authors: Johnston Christopher D. , Dewig Derek R. , Pietrosimone Brian , Padua Darin , Ryan Eric D. , Hart Joe , Spang Jeffrey , Blackburn Troy 
Published: December 2023

ABSTRACTPurposeNeuromuscular deficits and atrophy following anterior cruciate ligament reconstruction (ACLR) may be accompanied by changes in muscle composition and poor quadriceps muscle quality (QMQ). Quadriceps atrophy occurs following ACLR, but improves within the first three post-operative months, yet this hypertrophy could be attributable to increases in non-contractile tissue (i.e. poor QMQ). The purposes of this study were to evaluate changes in QMQ following ACLR and determine if changes in QMQ and cross-sectional area (CSA) occur in parallel or independently.MethodsA longitudinal prospective cohort design was implemented to evaluate QMQ and CSA in 20 individuals with ACLR and 12 healthy controls. Participants completed three testing sessions (baseline/pre-surgery, 1 month, and 3 months) during which ultrasound images were obtained from the vastus lateralis (VL) and rectus femoris (RF). QMQ was calculated as the echo intensity (EI) of each image, with high EI representing poorer QMQ. Anatomical CSA was also obtained from each image.ResultsRF and VL EI were greater at 1 and 3 months in the ACLR limb compared to baseline and the contralateral limb, and did not change between 1 and 3 months. VL and RF CSA in the ACLR limb were smaller at 1 and 3 months compared to the contralateral limb and controls (VL only), but increased from 1 to 3 months. Changes in QMQ and CSA were not correlated.ConclusionsQMQ declines within the first month following ACLR and does not improve by 3 months even though hypertrophy occurs, suggesting that these morphological characteristics change independently following ACLR. Poorer QMQ represents greater concentration of noncontractile tissues within the muscle and potentially contributes to chronic quadriceps dysfunction observed following ACLR.