bluuebunny/crossref_metadata_2025_split huggingface dataset:
SIRPB1 regulates inflammatory factor expression in the glioma microenvironment via SYK: functional and bioinformatics insights
Authors: Geng Ren , Zhao Yao , Xu Wanzhen , Ma Xiaoshan , Jiang Yining , Han Xuefei , Zhao Liyan , Li Yunqian 
Published: April 2024

Abstract
Background
SIRPB1 expression is upregulated in various tumor types, including gliomas, and is known to contribute to tumor progression; nevertheless, its function in the immune milieu of gliomas is still mainly unknown.

Methods
This study, we analyzed 1152 normal samples from the GTEx database and 670 glioma samples from the TCGA database to investigate the relationship between the expression of SIRPB1 and clinicopathological features. Moreover, SIRPB1 gene knockout THP-1 cell lines were constructed using CRISPR/Cas9 and were induced into a co-culture of macrophages and glioma cells in vitro to learn more about the role of SIRPB1 in the glioma immune milieu. Lastly, we established a prognostic model to predict the effect of SIRPB1 on prognosis.

Results
Significantly higher levels of SIRPB1 expression were found in gliomas, which had an adverse effect on the immune milieu and correlated poorly with patient survival. SIRPB1 activation with certain antibodies results in SYK phosphorylation and the subsequent activation of calcium, MAPK, and NF-κB signaling pathways. This phenomenon is primarily observed in myeloid-derived cells as opposed to glioma cells. In vitro co-culture demonstrated that macrophages with SIRPB1 knockout showed decreased IL1RA, CCL2, and IL-8, which were recovered upon ectopic expression of SIRPB1 but reduced again following treatment with SYK inhibitor GS9973. Critically, a lower overall survival rate was linked to increased SIRPB1 expression. Making use of SIRPB1 expression along with additional clinicopathological variables, we established a nomogram that showed a high degree of prediction accuracy.

Conclusions
Our study demonstrates that glioma cells can be activated by macrophages via SIRPB1, subsequently reprogramming the TME, suggesting that SIRPB1 could serve as a promising therapeutic target for gliomas.
A portable system to measure knee extensor spasticity after spinal cord injury
Authors: De Santis Dalia , Perez Monica A. 
Published: April 2024

Abstract
Background
The pendulum test is a quantitative method used to assess knee extensor spasticity in humans with spinal cord injury (SCI). Yet, the clinical implementation of this method remains limited. The goal of our study was to develop an objective and portable system to assess knee extensor spasticity during the pendulum test using inertial measurement units (IMU).

Methods
Spasticity was quantified by measuring the first swing angle (FSA) using a 3-dimensional optical tracking system (with external markers over the iliotibial band, lateral knee epicondyle, and lateral malleolus) and two wireless IMUs (positioned over the iliotibial band and mid-part of the lower leg) as well as a clinical exam (Modified Ashworth Scale, MAS).

Results
Measurements were taken on separate days to assess test–retest reliability and device agreement in humans with and without SCI. We found no differences between FSA values obtained with the optical tracking system and the IMU-based system in control subjects and individuals with SCI. FSA values from the IMU-based system showed excellent agreement with the optical tracking system in individuals with SCI (ICC > 0.98) and good agreement in controls (ICC > 0.82), excellent test–retest reliability across days in SCI (ICC = 0.93) and good in controls (ICC = 0.87). Notably, FSA values measured by both systems showed a strong association with MAS scores ($$\uprho$$
ρ
~ −0.8) being decreased in individuals with SCI with higher MAS scores, reflecting the presence of spasticity.

Conclusions
These findings suggest that our new portable IMU-based system provides a robust and flexible alternative to a camera-based optical tracking system to quantify knee extensor spasticity following SCI.
A phenotypic screening approach to target p60AmotL2-expressing invasive cancer cells
Authors: Fonseca Pedro , Cui Weiyingqi , Struyf Nona , Tong Le , Chaurasiya Ayushi , Casagrande Felipe , Zhao Honglei , Fernando Dinura , Chen Xinsong , Tobin Nicholas P. , Seashore-Ludlow Brinton , Lundqvist Andreas , Hartman Johan , Göndör Anita , Östling Päivi , Holmgren Lars 
Published: April 2024

Abstract
Background
Tumor cells have the ability to invade and form small clusters that protrude into adjacent tissues, a phenomenon that is frequently observed at the periphery of a tumor as it expands into healthy tissues. The presence of these clusters is linked to poor prognosis and has proven challenging to treat using conventional therapies. We previously reported that p60AmotL2 expression is localized to invasive colon and breast cancer cells. In vitro, p60AmotL2 promotes epithelial cell invasion by negatively impacting E-cadherin/AmotL2-related mechanotransduction.

Methods
Using epithelial cells transfected with inducible p60AmotL2, we employed a phenotypic drug screening approach to find compounds that specifically target invasive cells. The phenotypic screen was performed by treating cells for 72 h with a library of compounds with known antitumor activities in a dose-dependent manner. After assessing cell viability using CellTiter-Glo, drug sensitivity scores for each compound were calculated. Candidate hit compounds with a higher drug sensitivity score for p60AmotL2-expressing cells were then validated on lung and colon cell models, both in 2D and in 3D, and on colon cancer patient-derived organoids. Nascent RNA sequencing was performed after BET inhibition to analyse BET-dependent pathways in p60AmotL2-expressing cells.

Results
We identified 60 compounds that selectively targeted p60AmotL2-expressing cells. Intriguingly, these compounds were classified into two major categories: Epidermal Growth Factor Receptor (EGFR) inhibitors and Bromodomain and Extra-Terminal motif (BET) inhibitors. The latter consistently demonstrated antitumor activity in human cancer cell models, as well as in organoids derived from colon cancer patients. BET inhibition led to a shift towards the upregulation of pro-apoptotic pathways specifically in p60AmotL2-expressing cells.

Conclusions
BET inhibitors specifically target p60AmotL2-expressing invasive cancer cells, likely by exploiting differences in chromatin accessibility, leading to cell death. Additionally, our findings support the use of this phenotypic strategy to discover novel compounds that can exploit vulnerabilities and specifically target invasive cancer cells.
Clinical-functional correlation with brain volumetry in severe perinatal asphyxia: a case report
Authors: Velasquez-Minoli Juan Pablo , Cardona-Ramirez Natalia , Garcia-Arias Hernan Felipe , Restrepo-Restrepo Feliza , Porras-Hurtado Gloria Liliana 
Published: April 2024

Abstract
Background
Hypoxic-ischemic encephalopathy (HIE) appears in neurological conditions where some brain areas are likely to be injured, such as deep grey matter, basal ganglia area, and white matter subcortical periventricular áreas. Moreover, modeling these brain areas in a newborn is challenging due to significant variability in the intensities associated with HIE conditions. This paper aims to evaluate functional measurements and 3D machine learning models of a given HIE case by correlating the affected brain areas with the pathophysiology and clinical neurodevelopmental.

Case presentation
A comprehensive analysis of a term infant with perinatal asphyxia using longitudinal 3D brain information from Machine Learning Models is presented. The clinical analysis revealed the perinatal asphyxia diagnosis with APGAR <5 at 5 and 10 minutes, umbilical arterial pH of 7.0 BE of -21.2 mmol / L), neonatal seizures, and invasive ventilation mechanics. Therapeutic interventions: physical, occupational, and language neurodevelopmental therapies. Epilepsy treatment: vagus nerve stimulation, levetiracetam, and phenobarbital. Furthermore, the 3D analysis showed how the volume decreases due to age, exhibiting an increasing asymmetry between hemispheres. The results of the basal ganglia area showed that thalamus asymmetry, caudate, and putamen increase over time while globus pallidus decreases. Clinical outcomes: spastic cerebral palsy, microcephaly, treatment-refractory epilepsy.

Conclusions
Slight changes in the basal ganglia and cerebellum require 3D volumetry for detection, as standard MRI examinations cannot fully reveal their complex shape variations. Quantifying these subtle neurodevelopmental changes helps in understanding their clinical implications. Besides, neurophysiological evaluations can boost neuroplasticity in children with neurological sequelae by stimulating new neuronal connections.
Outcome prediction of cardiac arrest with automatically computed gray-white matter ratio on computed tomography images
Authors: Tsai Hsinhan , Chi Chien-Yu , Wang Liang-Wei , Su Yu-Jen , Chen Ya-Fang , Tsai Min-Shan , Wang Chih-Hung , Hsu Cheyu , Huang Chien-Hua , Wang Weichung 
Published: April 2024

Abstract

Background

This study aimed to develop an automated method to measure the gray-white matter ratio (GWR) from brain computed tomography (CT) scans of patients with out-of-hospital cardiac arrest (OHCA) and assess its significance in predicting early-stage neurological outcomes.

Methods

Patients with OHCA who underwent brain CT imaging within 12 h of return of spontaneous circulation were enrolled in this retrospective study. The primary outcome endpoint measure was a favorable neurological outcome, defined as cerebral performance category 1 or 2 at hospital discharge. We proposed an automated method comprising image registration, K-means segmentation, segmentation refinement, and GWR calculation to measure the GWR for each CT scan. The K-means segmentation and segmentation refinement was employed to refine the segmentations within regions of interest (ROIs), consequently enhancing GWR calculation accuracy through more precise segmentations.

Results

Overall, 443 patients were divided into derivation N=265, 60% and validation N=178, 40% sets, based on age and sex. The ROI Hounsfield unit values derived from the automated method showed a strong correlation with those obtained from the manual method. Regarding outcome prediction, the automated method significantly outperformed the manual method in GWR calculation (AUC 0.79 vs. 0.70) across the entire dataset. The automated method also demonstrated superior performance across sensitivity, specificity, and positive and negative predictive values using the cutoff value determined from the derivation set. Moreover, GWR was an independent predictor of outcomes in logistic regression analysis. Incorporating the GWR with other clinical and resuscitation variables significantly enhanced the performance of prediction models compared to those without the GWR.

Conclusions

Automated measurement of the GWR from non-contrast brain CT images offers valuable insights for predicting neurological outcomes during the early post-cardiac arrest period.
Effect of volume infusion on left atrial strain in acute circulatory failure
Authors: Cicetti Marta , Bagate François , Lapenta Cristina , Gendreau Ségolène , Masi Paul , Mekontso Dessap Armand 
Published: April 2024

Abstract
Background
Left atrial strain (LAS) is a measure of atrial wall deformation during cardiac cycle and reflects atrial contribution to cardiovascular performance. Pathophysiological significance of LAS in critically ill patients with hemodynamic instability has never been explored. This study aimed at describing LAS and its variation during volume expansion and to assess the relationship between LAS components and fluid responsiveness.

Methods
This prospective observational study was performed in a French ICU and included patients with acute circulatory failure, for whom the treating physician decided to proceed to volume expansion (rapid infusion of 500 mL of crystalloid solution). Trans-thoracic echocardiography was performed before and after the fluid infusion. LAS analysis was performed offline. Fluid responsiveness was defined as an increase in velocity-time integral (VTI) of left ventricular outflow tract ≥ 10%.

Results
Thirty-eight patients were included in the final analysis. Seventeen (45%) patients were fluid responders. LAS analysis had a good feasibility and reproducibility. Overall, LAS was markedly reduced in all its components, with values of 19 [15 – 32], -9 [-19 – -7] and − 9 [-13 – -5] % for LAS reservoir (LASr), conduit (LAScd) and contraction (LASct), respectively. LASr, LAScd and LASct significantly increased during volume expansion in the entire population. Baseline value of LAS did not predict fluid responsiveness and the changes in LAS and VTI during volume expansion were not significantly correlated.

Conclusions
LAS is severely altered during acute circulatory failure. LAS components significantly increase during fluid administration, but cannot be used to predict or assess fluid responsiveness.
Psychometric evaluation of the near activity visual questionnaire presbyopia (NAVQ-P) and additional patient-reported outcome items
Authors: Sims Joel , Sloesen Brigitte , Bentley Sarah , Naujoks Christel , Arbuckle Rob , Chiva-Razavi Sima , Pascoe Ben , Stochl Jan , Findley Amy , O’Brien Paul , Wolffsohn James S. 
Published: April 2024

Abstract
Background
The Near Visual Acuity Questionnaire Presbyopia (NAVQ-P) is a patient-reported outcome (PRO) measure that was developed in a phakic presbyopia population to assess near vision function impacts. The study refined and explored the psychometric properties and score interpretability of the NAVQ-P and additional PRO items assessing near vision correction independence (NVCI), near vision satisfaction (NVS), and near vision correction preference (NVCP).

Methods
This was a psychometric validation study conducted using PRO data collected as part of a Phase IIb clinical trial (CUN8R44 A2202) consisting of 235 randomized adults with presbyopia from the US, Japan, Australia, and Canada. Data collected at baseline, week 2, and months 1, 2, and 3 during the 3-month trial treatment period were included in the analyses to assess item (question) properties, NAVQ-P dimensionality and scoring, reliability, validity, and score interpretation.

Results
Item responses were distributed across the full response scale for most NAVQ-P and additional PRO items. Confirmatory factor analysis supported the pre-defined unidimensional structure and calculation of a NAVQ-P total score as a measure of near vision function. Item deletion informed by item response distributions, dimensionality analyses, item response theory, and previous qualitative findings, including clinical input, supported retention of 14 NAVQ-P items. The 14-item NAVQ-P total score had excellent internal consistency (α = 0.979) and high test-retest reliability (Intraclass Correlation Coefficients > = 0.898). There was good evidence of construct-related validity for all PROs supported by strong correlations with concurrent measures. Excellent results for known-groups validity and ability to detect change analyses were also demonstrated. Anchor-based and distribution-based methods supported interpretation of scores through generation of group-level and within-individual estimates of meaningful change thresholds. A meaningful within-patient change in the range of 8-15-point improvement on the NAVQ-P total score (score range 0–42) was recommended, including a more specific responder definition of 10-point improvement.

Conclusions
The NAVQ-P, NVCI, and NVS are valid and reliable instruments which have the ability to detect change over time. Findings strongly support the use of these measures as outcome assessments in clinical/research studies and in clinical practice in the presbyopia population.
Gigantopithecus blacki extinction and human threats to Tapanuli orangutans: lessons from past and present challenges
Authors: Silva Heslley Machado 
Published: April 2024

Abstract
Background
This letter explores the historical challenges faced by Gigantopithecus blacki, a colossal ape, during the Pleistocene period in southern China, emphasizing its extinction approximately 300,000 years ago due to climate change. Main body: Drawing parallels, the research sheds light on the imminent threat to Tapanuli orangutans in Southeast Asia, underscoring the role of human intervention. The paradox emerges as Homo sapiens, despite claiming wisdom, becomes a significant threat through climate change and deforestation, exacerbated by the dissemination of scientific misinformation. Conclusion: The text urges humanity to reorient its development, emphasizing the need for responsible environmental stewardship to ensure a sustainable and balanced future for both Earth and its primate inhabitants.
Combining ability of Egyptian cotton (Gossypium barbadense L.) reveals genetic potential for improved yield and fiber quality
Authors: Abdelghany Ahmed M. , El-Banna Aly A. A. , Lamlom Sobhi F. , El-Sorady Gawhara A. , Salama Ehab A. A. , Ren Honglei , Shaibu Abdulwahab S. , Yehia Waleed M. B. 
Published: April 2024

Abstract
Background
As the most widely cultivated fiber crop, cotton production depends on hybridization to unlock the yield potential of current varieties. A deep understanding of genetic dissection is crucial for the cultivation of enhanced hybrid plants with desired traits, such as high yield and fine fiber quality. In this study, the general combining ability (GCA) and specific combining ability (SCA) of yield and fiber quality of nine cotton parents (six lines and three testers) and eighteen F1 crosses produced using a line × tester mating design were analyzed.

Results
The results revealed significant effects of genotypes, parents, crosses, and interactions between parents and crosses for most of the studied traits. Moreover, the effects of both additive and non-additive gene actions played a notably significant role in the inheritance of most of the yield and fiber quality attributes. The F1 hybrids of (Giza 90 × Aust) × Giza 86, Uzbekistan 1 × Giza 97, and Giza 96 × Giza 97 demonstrated superior performance due to their favorable integration of high yield attributes and premium fiber quality characteristics. Path analysis revealed that lint yield has the highest positive direct effect on seed cotton yield, while lint percentage showed the highest negative direct effect on seed cotton yield. Principal component analysis identified specific parents and hybrids associated with higher cotton yield, fiber quality, and other agronomic traits.

Conclusion
This study provides insights into identifying potential single- and three-way cross hybrids with superior cotton yield and fiber quality characteristics, laying a foundation for future research on improving fiber quality in cotton.
Turkish population-based screening for first identified changes of BRCA1 and BRCA2 genes in breast and/or ovarian cancer patients
Authors: Semerci Sevimli Tuğba , Sevimli Murat , Manguoğlu Ayşe Esra , Lüleci Güven 
Published: April 2024

Abstract
Introduction
It is known that BRCA1 and BRCA2 genes’ mutation carriers are predisposed to breast and ovarian cancers and other organ cancers such as prostate, colon and cervix. In the previous study performed at X University, all coding exons of both genes were screened by denaturing gradient gel electrophoresis (DGGE). In addition to various nonsense, missense mutations, polymorphisms and intronic region changes, seven novel missense mutations, including H513L, H816P and S1517Y in BRCA1 and S326R, G258P, E2903K and N2742S in BRCA2, had been identified.

Methods
To determine whether these unclassified variants are pathogenic, DNA samples of 150 healthy individuals without a known cancer history in the family were screened in this study for these seven novel missense mutations. These DNA samples were recruited from archives of previous polymorphism studies. PCR performed DNA amplifications, and denaturing high-performance liquid chromatography (DHPLC) techniques did mutation screenings.

Results
Peak patterns suggestive of a change in DNA fragments were considered for sequencing analyses. Analyses revealed that none of the 150 DNA samples had any change in the seven screened fragments. As a result, it is assumed that these seven mutations might be novel pathogenic mutations described in the Turkish population.

Conclusion
In conclusion, these carriers must be informed about the mutation and given appropriate genetic counseling by their physicians. In addition, genetic testing must be offered to high-risk individuals (men/women) in the family so that it would be possible for other family members to have genetic counseling and contribute to disease prevention. On the other hand, these findings would contribute to current literature with novel results and shed light on future research.
Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants
Authors: Feng Shuyan , Li Nan , Chen Huilong , Liu Zhuo , Li Chunjin , Zhou Rong , Zhang Yingchao , Cao Rui , Ma Xiao , Song Xiaoming 
Published: April 2024

AbstractThe auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.