bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-Depth Quantification of Cell Division and Elongation Dynamics at the Tip of Growing Arabidopsis Roots Using 4D Microscopy, AI-Assisted Image Processing and Data Sonification
Authors: Goh Tatsuaki , Song Yu , Yonekura Takaaki , Obushi Noriyasu , Den Zeping , Imizu Katsutoshi , Tomizawa Yoko , Kondo Yohei , Miyashima Shunsuke , Iwamoto Yutaro , Inami Masahiko , Chen Yen-Wei , Nakajima Keiji 
Published: October 2023

Abstract
One of the fundamental questions in plant developmental biology is how cell proliferation and cell expansion coordinately determine organ growth and morphology. An amenable system to address this question is the Arabidopsis root tip, where cell proliferation and elongation occur in spatially separated domains, and cell morphologies can easily be observed using a confocal microscope. While past studies revealed numerous elements of root growth regulation including gene regulatory networks, hormone transport and signaling, cell mechanics and environmental perception, how cells divide and elongate under possible constraints from cell lineages and neighboring cell files has not been analyzed quantitatively. This is mainly due to the technical difficulties in capturing cell division and elongation dynamics at the tip of growing roots, as well as an extremely labor-intensive task of tracing the lineages of frequently dividing cells. Here, we developed a motion-tracking confocal microscope and an Artificial Intelligence (AI)-assisted image-processing pipeline that enables semi-automated quantification of cell division and elongation dynamics at the tip of vertically growing Arabidopsis roots. We also implemented a data sonification tool that facilitates human recognition of cell division synchrony. Using these tools, we revealed previously unnoted lineage-constrained dynamics of cell division and elongation, and their contribution to the root zonation boundaries.
Ablation of OCT4 function in cattle embryos by double electroporation of CRISPR-Cas for DNA and RNA targeting (CRISPR-DART)
Authors: Nix Jada L , Schettini Gustavo P , Speckhart Savannah L , Ealy Alan D , Biase Fernando H 
Published: October 2023

Abstract
CRISPR-Cas ribonucleoproteins are important tools for gene editing in pre-implantation embryos. However, the inefficient production of biallelic deletions in cattle zygotes has hindered mechanistic studies of gene function. In addition, the presence of maternal RNAs that support embryo development until embryonic genome activation may cause confounding phenotypes. Here, we aimed to improve the efficiency of biallelic deletions and deplete specific maternal RNAs in cattle zygotes using CRISPR-Cas editing technology. Two electroporation sessions with Cas9D10A ribonucleoproteins targeting exon 1 and the promoter of OCT4 produced biallelic deletions in 91% of the embryos tested. In most cases, the deletions were longer than 1000 nucleotides long. Electroporation of Cas13a ribonucleoproteins prevents the production of the corresponding proteins. We electroporated Cas9D10A ribonucleoproteins targeting exon 1, including the promoter region, of OCT4 in two sessions with inclusion of Cas13a ribonucleoproteins targeting OCT4 mRNAs in the second session to ablate OCT4 function in cattle embryos. A lack of OCT4 resulted in embryos arresting development prior to blastocyst formation at a greater proportion (13%) than controls (31.6%, P&lt;0.001). The few embryos that developed past the morula stage did not form a normal inner cell mass. Transcriptome analysis of single blastocysts, confirmed to lack exon 1 and promoter region of OCT4, revealed a significant (FDR&lt;0.1) reduction in transcript abundance of many genes functionally connected to stemness, including markers of pluripotency (CADHD1, DPPA4, GNL3, RRM2). The results confirm that OCT4 is key regulator of genes that modulate pluripotency and is required to form a functional blastocyst in cattle.
An organ-effective modulation for non-contrast chest computed tomography imaging: effect on image quality and thyroid exposure reduction
Authors: Li Qianling , Zhao Zicheng , Yang Chen , Zhu Fandong , Sun Chenweng , Zhao Zhenhua 
Published: October 2023

Abstract
We investigate the efficacy of organ-effective modulation (OEM) technique for thyroid dose reduction among various body habitus and its impact on image quality in chest non-contrast computed tomography (CT). We prospectively enrolled 64 patients who underwent non-contrast chest CT from January to May 2022. The skin-absorbed radiation dose over the thyroid (Dthyroid) was obtained using a thermoluminescence dosemeter. Signal-to-noise ratio and image noise was also quantitatively assessed. In subjective analyses, two radiologists independently evaluated images based on a 5-point scale. The OEM group showed a markedly decrease in Dthyroid when compared with the non-OEM group (p &lt; 0.05). No significant difference was observed regarding the image noise (p &lt; 0.05), except for the ventral air space. The subjective scores of two radiologists showed no significant differences between the non-OEM and OEM groups. OEM can effectively reduce the radiation exposure of thyroid without compromising on image quality in non-contrast chest CT.
Gene Transfer-Based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory
Authors: Katriel Guy , Mahanaymi Udi , Brezner Shelly , Kezel Noor , Koutschan Christoph , Zeilberger Doron , Steel Mike , Snir Sagi 
Published: October 2023

Abstract
The genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analyzing the point mutations of standard markers is often too crude and slow for fine-scale phylogenetics. Nevertheless, genome dynamics (GD) events provide alternative, often richer information. The synteny index (SI) between a pair of genomes combines gene order and gene content information, allowing the comparison of genomes of unequal gene content, together with order considerations of their common genes. Recently, genome dynamics has been modeled as a continuous-time Markov process, and gene distance in the genome as a birth–death–immigration process. Nevertheless, due to complexities arising in this setting, no precise and provably consistent estimators could be derived, resulting in heuristic solutions. Here, we extend this modeling approach by using techniques from birth–death theory to derive explicit expressions of the system’s probabilistic dynamics in the form of rational functions of the model parameters. This, in turn, allows us to infer analytically accurate distances between organisms based on their SI. Subsequently, we establish additivity of this estimated evolutionary distance (a desirable property yielding phylogenetic consistency). Applying the new measure in simulation studies shows that it provides accurate results in realistic settings and even under model extensions such as gene gain/loss or over a tree structure. In the real-data realm, we applied the new formulation to unique data structure that we constructed—the ordered orthology DB—based on a new version of the EggNOG database, to construct a tree with more than 4.5K taxa. To the best of our knowledge, this is the largest gene-order-based tree constructed and it overcomes shortcomings found in previous approaches. Constructing a GD-based tree allows to confirm and contrast findings based on other phylogenetic approaches, as we show.
Molecular mechanisms underlying mitochondrial damage, endoplasmic reticulum stress, and oxidative stress induced by environmental pollutants
Authors: Li Kang , Geng Yanpei , Lin Bencheng , Xi Zhuge 
Published: October 2023

Abstract
Mitochondria and endoplasmic reticulum (ER) are essential organelles playing pivotal roles in the regulation of cellular metabolism, energy production, and protein synthesis. In addition, these organelles are important targets susceptible to external stimuli, such as environmental pollutants. Exposure to environmental pollutants can cause the mitochondrial damage, endoplasmic reticulum stress (ERS), and oxidative stress, leading to cellular dysfunction and death. Therefore, understanding the toxic effects and molecular mechanisms of environmental pollution underlying these processes is crucial for developing effective strategies to mitigate the adverse effects of environmental pollutants on human health. In the present study, we summarized and reviewed the toxic effects and molecular mechanisms of mitochondrial damage, ERS, and oxidative stress caused by exposure to environmental pollutants as well as interactions inducing the cell apoptosis and the roles in exposure to environmental pollutants.
Revision of the darkling beetle genusEurynotus(Blaptinae: Platynotini) and new records of ovovivipary in Tenebrionidae
Authors: Lumen Ryan , Kamiński Marcin J 
Published: October 2023

AbstractThe taxonomic concepts and monophyly of the southern African genus Eurynotus and its subgeneric components (Biolus and Neosolenopistoma) are tested using cladistic analyses. Seventy morphological characters were scored and analysed using maximum parsimony and Bayesian inference for 26 Eurynotina species, including all Eurynotus. Comprehensive revision of Biolus and Eurynotus resulted in Neosolenopistoma becoming a junior synonym of the genus Biolus stat. nov. (elevated to generic rank), restoration of one species (B. asperipennis stat. res.), recognition of seven new combinations, and descriptions of two new species (Biolus brunoi sp. nov. and Eurynotus privisolum sp. nov.). Lectotypes are designated for previously described species from syntype material, and a key to species of Biolus and Eurynotus is provided. Three species were confirmed as ovoviviparous (two Biolus and one Eurynotus) bringing the number of recorded ovoviviparous Tenebrionidae to 14. Shortened ovipositors are discounted as requisite for ovovivipary based on elongate paraprocts in Biolus and Eurynotus. Principal component analyses were used to examine three lineages of ovoviviparous tenebrionids; however, no single set of climatic variables was correlated with ovovivipary. Southern African, Malagasy, and Guadeloupe lineages of ovoviviparous Tenebrionidae probably have additional and/or separate evolutionary origins and selection pressures to consider when examining this reproductive strategy.
The Self-Perceived E-Learning Environment Scale: Development and Psychometric Properties in a Nursing Students Samples
Authors: Dal Santo Letizia , Peña-Jimenez Marco , Canzan Federica , Saiani Luisa , Battistelli Adalgisa 
Published: October 2023

Abstract

AIM
E-learning is increasingly used in education, creating a learning environment that needs to be studied thoroughly for developing new learning opportunities.

BACKGROUND
Drawing from the community of inquiry framework, the present work provides the theoretical foundation and measurement validation of the Self-Perceived E-Learning Environment Scale (SEES). The SEES measures core aspects of the e-learning context: autonomous strategic planning, social interaction, and teacher feedback.

METHOD
Through two studies carried out in sample of nursing students, an exploratory (n = 302) and confirmatory (n = 245) factor analysis revealed a three-factor structure.

RESULT
The results provide empirical evidence of appropriate psychometric properties (i.e., reliability, validity).

CONCLUSION
The SEES can be used in a higher education context, particularly in nursing education programs. Theoretical, methodological, and practical implications for exploring the e-learning environment in nursing educational settings are discussed.
Feasibility and safety of percutaneous nephrolithotomy in the management of renal stones with emphysematous pyelonephritis following control of infection
Authors: Singh Anshuman , K.R. Surag , Choudhary Anupam , Reddy Suraj Jayadeva , Gali Kasi Viswanath , Shah Abhijit 
Published: October 2023

Abstract

Background
Management of renal calculi in the presence of emphysematous pyelonephritis (EPN) is challenging. The optimal management strategy for patients with EPN and renal calculi remains unclear. This study aimed to evaluate the safety and efficacy of percutaneous nephrolithotomy (PCNL) in the management of these patients and to provide insights into the postoperative outcomes and complications of PCNL according to the modified Clavien-Dindo classification.

Materials and methods
This retrospective study included patients with EPN and renal stones who underwent PCNL, after initial conservative management, between January 2012 and December 2021. Patient demographics, presenting symptoms, features of septicemia, preoperative drainage, postoperative complications, and outcomes were recorded. Postoperative complications were categorized according to the modified Clavien-Dindo classification.

Results
A total of 48 patients with EPN and renal calculi were included in this study. Percutaneous nephrolithotomy was performed 4–6 weeks later after obtaining a negative urine culture or under appropriate antibiotic coverage if the culture was unsterile. Of the total, 39 (81.25%) patients had postoperative complications, but only 9 (18.75%) patients had grade III or higher complications. Of these, 3 (6.25%) patients had grade IIIa complications, 3 (6.25%) had grade IIIb complications, 2 (4.1%) had grade IVa complications, and 1 (2.08%) had grade IVb complications and was admitted to the intensive care. No mortality was observed during the postoperative period.

Conclusions
Initial conservative management of EPN followed by PCNL after initial infection control is an effective strategy for managing these patients. Patients with higher EPN grades have a higher risk of major postoperative complications after PCNL for renal stones. Specifically, patients with an EPN class 3 or 4 had a higher risk of complications than those with an EPN class 2 or lower. Patients with EPN class 1 have a relatively uncomplicated postoperative course after PCNL.
Dynamic Prevalence of and Factors Associated With Fatigue Following Traumatic Brain Injury: A Systematic Review and Meta-analysis of Observational Studies
Authors: Liu I-Hsing , Lin Chia-Jou , Romadlon Debby Syahru , Lee Shu-Chun , Huang Hui-Chung , Chen Pin-Yuan , Chiu Hsiao-Yean 
Published: October 2023

Objective:
To implement a systematic review and meta-analysis to comprehensively synthesize the prevalence of and factors associated with fatigue following traumatic brain injury (TBI).

Methods:
We systematically searched the PubMed, EMBASE, Cochrane Library, Cumulated Index to Nursing and Allied Health Literature, PsycINFO, and ProQuest Dissertations and Theses A&I databases in all fields from their inception to March 31, 2021. We included observational studies investigating fatigue at specific time points following TBI or factors associated with post-TBI fatigue. All data were analyzed using a random-effects model.

Results:
This meta-analysis included 29 studies that involved 12 662 patients with TBI and estimated the prevalence of post-TBI fatigue (mean age = 41.09 years); the meta-analysis also included 23 studies that involved 6681 patients (mean age = 39.95 years) and investigated factors associated with post-TBI fatigue. In patients with mild-to-severe TBI, the fatigue prevalence rates at 2 weeks or less, 1 to 3 months, 6 months, 1 year, and 2 years or more after TBI were 52.2%, 34.6%, 36.0%, 36.1%, and 48.8%, respectively. Depression (r = 0.48), anxiety (r = 0.49), sleep disturbance (r = 0.57), and pain (r = 0.46) were significantly associated with post-TBI fatigue. No publication bias was identified among the studies, except for those assessing fatigue prevalence at 6 months after TBI.

Conclusion:
The pooled prevalence rates of post-TBI fatigue exhibited a U-shaped pattern, with the lowest prevalence rates occurring at 1 to 3 months after TBI. Depression, anxiety, sleep disturbance, and pain were associated with post-TBI fatigue. Younger patients and male patients were more likely to experience post-TBI fatigue. Our findings can assist healthcare providers with identifying appropriate and effective interventions targeting post-TBI fatigue at specific periods.
The Relationship of Health Literacy to Health Outcomes Among Individuals With Traumatic Brain Injury: A Traumatic Brain Injury Model Systems Study
Authors: Pappadis Monique R. , Sander Angelle M. , Juengst Shannon B. , Leon-Novelo Luis , Ngan Esther , Bell Kathleen R. , Corrigan John D. , Driver Simon , Dreer Laura E. , Lequerica Anthony H. 
Published: October 2023

Objective:
To examine the associations between health literacy and health outcomes among individuals with traumatic brain injury (TBI) at least a year post-injury.

Setting:
Community following discharge from inpatient rehabilitation.

Participants:
A total of 205 individuals with complicated mild to severe TBI who completed a TBI Model Systems National Database follow-up interview and a web-based health literacy measure.

Design:
A multicenter, cross-sectional, observational study.

Main Measures:
The Health Literacy Assessment Using Talking Touchscreen Technology (Health LiTT), number of comorbid conditions (Medical and Mental Health Comorbidities Interview [MMHCI]), perceived physical and mental health (PROMIS Global Physical and Mental Health subscales), Patient Health Questionnaire-9 (PHQ-9), and Generalized Anxiety Disorder-7 (GAD-7).

Results:
After controlling for sociodemographic, injury, cognition, and time post-injury, adequate health literacy was associated with higher odds of greater perceived physical health compared with participants with marginal/inadequate health literacy (odds ratio = 4.10; CI = 1.52-11.70]. Participants with inadequate/marginal health literacy had 3.50 times greater odds of depression (PHQ-9 ≥ 10) compared with those with adequate health literacy. Participants 45 years and older reported a greater number of MMHCI physical health conditions, but fewer MMHCI mental health conditions and GAD-7 anxiety symptoms compared with those who were younger. Non-Hispanic White participants and those with mild/moderate TBI were more likely to report a greater number of MMHCI mental health conditions compared with non-Hispanic Black participants or those with severe TBI. Greater time post-injury was associated with greater number of chronic physical and mental health conditions, and less odds of good-to-excellent perceived global mental health.

Conclusions:
Inadequate health literacy is associated with worse perceived physical health and greater depressive symptoms among adults with TBI. Greater efforts are needed to explore the mechanisms by which health literacy influences chronic disease management and mental health after TBI to improve postinjury health status and outcomes, particularly among those with limited health literacy skills.
Electrostimulation of the white matter of the posterior insula and medial operculum: perception of vibrations, heat, and pain
Authors: Mandonnet Valéry , Obaid Sami , Descoteaux Maxime , St-Onge Etienne , Devaux Bertrand , Levé Charlotte , Froelich Sébastien , Rheault François , Mandonnet Emmanuel 
Published: October 2023

Abstract
This study aimed to characterize the sensory responses observed when electrically stimulating the white matter surrounding the posterior insula and medial operculum (PIMO). We reviewed patients operated on under awake conditions for a glioma located in the temporoparietal junction. Patients' perceptions were retrieved from operative reports. Stimulation points were registered in the Montreal Neurological Institute template. A total of 12 stimulation points in 8 patients were analyzed. Painful sensations in the contralateral leg were reported (5 sites in 5 patients) when stimulating the white matter close to the parcel OP2/3 of the Glasser atlas. Pain had diverse qualities: burning, tingling, crushing, or electric shock. More laterally, in the white matter of OP1, pain and heat sensations in the upper part of the body were described (5 sites in 2 patients). Intermingled with these sites, vibration sensations were also reported (3 sites in 2 patients). Based on the tractograms of 44 subjects from the Human Connectome Project data set, we built a template of the pathways linking the thalamus to OP2/3 and OP1. Pain sites were located in the thalamo-OP2/3 and thalamo-OP1 tracts. Heat sites were located in the thalamo-OP1 tract. In the 227 awake surgeries performed for a tumor located outside of the PIMO region, no patients ever reported pain or heat sensations when stimulating the white matter. Thus, we propose that the thalamo-PIMO connections constitute the main cortical inputs for nociception and thermoception and emphasize that preserving these fibers is of utmost importance to prevent the postoperative onset of a debilitating insulo-opercular pain syndrome.
Targeted transcriptional upregulation of SENP1 by CRISPR activation enhances deSUMOylation pathways to elicit antinociception in the spinal nerve ligation model of neuropathic pain
Authors: Gomez Kimberly , Allen Heather N. , Duran Paz , Loya-Lopez Santiago , Calderon-Rivera Aida , Moutal Aubin , Tang Cheng , Nelson Tyler S. , Perez-Miller Samantha , Khanna Rajesh 
Published: October 2023

Abstract
The voltage-gated sodium channel NaV1.7 is an essential component of human pain signaling. Changes in NaV1.7 trafficking are considered critical in the development of neuropathic pain. SUMOylation of collapsin response mediator protein 2 (CRMP2) regulates the membrane trafficking and function of NaV1.7. Enhanced CRMP2 SUMOylation in neuropathic pain correlates with increased NaV1.7 activity. Pharmacological and genetic interventions that interfere with CRMP2 SUMOylation in rodents with neuropathic pain have been shown to reverse mechanical allodynia. Sentrin or SUMO-specific proteases (SENPs) are vital for balancing SUMOylation and deSUMOylation of substrates. Overexpression of SENP1 and/or SENP2 in CRMP2-expressing cells results in increased deSUMOylation and decreased membrane expression and currents of NaV1.7. Although SENP1 is present in the spinal cord and dorsal root ganglia, its role in regulating NaV1.7 function and pain is not known. We hypothesized that favoring SENP1 expression can enhance CRMP2 deSUMOylation to modulate NaV1.7 channels. In this study, we used a clustered regularly interspaced short palindromic repeats activation (CRISPRa) SENP1 lentivirus to overexpress SENP1 in dorsal root ganglia neurons. We found that SENP1 lentivirus reduced CRMP2 SUMOylation, NaV1.7–CRMP2 interaction, and NaV1.7 membrane expression. SENP1 overexpression decreased NaV1.7 currents through clathrin-mediated endocytosis, directly linked to CRMP2 deSUMOylation. Moreover, enhancing SENP1 expression did not affect the activity of TRPV1 channels or voltage-gated calcium and potassium channels. Intrathecal injection of CRISPRa SENP1 lentivirus reversed mechanical allodynia in male and female rats with spinal nerve injury. These results provide evidence that the pain-regulating effects of SENP1 overexpression involve, in part, the modulation of NaV1.7 channels through the indirect mechanism of CRMP2 deSUMOylation.