bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing Breast Cancer Neoadjuvant Therapy Prediction with Proximity Analysis of CD8 + T Cells and Immune Landscape Integration
Authors: Liang Hongling , Huang Jianqing , Li Hongsheng , He Weixing , Ao Xiang , Xie Zhi , Chen Yu , Lv Zhiyi , zhang Leyao , Zhong Yanghua , Tan Xiaojun , Han Guodong , Zhou Jie , Qiu Ni , Jiang Ming , Xia Haoming , Zhan Yongtao , Jiao Lei , Ma Jie , Radisky Derek , Huang Jia , Zhang Xuchao 
Published: May 2024

Abstract

Background: In breast cancer, the spatial relationship between immune and tumor cells is increasingly recognized as critical in determining the efficacy of neoadjuvant therapy (NAT). This study investigated how the distribution of immune cells, particularly CD8+ T cells, relative to tumor cells affects treatment outcomes.
Methods: Biopsies from 104 breast cancer patients were examined, both pre- and post-NAT, using multiplex immunohistochemistry (mIHC). This study focused on the density and distribution of CD8+ T cells, CD68+ macrophages, FoxP3+ regulatory T cells, and other immune markers.
Results: The spatial proximity of CD8+ T cells within 20 µm of cancer cells (N20-CD8+T) was strongly correlated with improved clinical outcomes across diverse tumor subtypes and NAT regimens. A significant post-NAT decrease in CD4+, CD68+, and FoxP3+ cells highlights notable shifts in the tumor immune landscape. A noteworthy finding was the positive correlation between CXCL9 expression and N20-CD8+T cells, suggesting a mechanism for immune cell recruitment and interaction within the tumor microenvironment. These results highlight the complex interplay among NAT, immune cell modifications, and patient outcomes.
Conclusions: This study revealed that the proximity of N20-CD8+ T cells to tumor cells is consistently associated with favorable NAT outcomes, transcending tumor subtypes, and treatment differences. This highlights the potential of immune cell dynamics, especially CD8+ T cells, as predictive biomarkers for therapeutic responses in breast cancer, underscoring their vital role in tumor immunity.
Significance of neutrophil-to-lymphocyte ratio in predicting the efficacy of anamorelin treatment for cancer cachexia
Authors: Nakazawa Yusuke , Watanabe Kanako , Gannichida Ako , Uwagawa Tadashi , Kawakubo Takashi 
Published: May 2024

Abstract

Purpose: Cancer cachexia is a multifactorial syndrome characterized by persistent loss of skeletal muscle mass, adversely affecting chemotherapy tolerability and life expectancy. Despite the expected therapeutic effect of anamorelin’s appetite-promotion,its efficacy has not been investigated in clinical practice. Given the involvement of cancer-inducing cytokines in cancer cachexia, we investigated whether the inflammatory biomarker neutrophil-to-lymphocyte ratio (NLR) could predict treatment outcomes.
Methods: This study included patients receiving anamorelin for cancer cachexia associated with pancreatic, nonsmall-cell lung, gastric, and colorectal cancers between April 2021 and December 2023. Patients were classified based on their NLR (<5 or ≥5) at 4 weeks postanamorelin administration. The NLR changes before and 4 weeks after of anamorelin therapy and 1-year overall survival (OS) rates were compared between the two groups.
Results: Out of 66 patients who received anamorelin, those with NLR <5 (n = 50) at 4 weeks postanamorelin administration showed a significant decrease in mean NLR from 3.71 ± 3.12 to 2.44 ± 1.23. Conversely, patients with an NLR ≥5 at 4 weeks (n = 16) had a significant increase from 5.70 ± 2.78 to 9.52 ± 4.85. The 1-year OS was significantly increased in patients with NLR of <5. Receiver–operating characteristic (ROC) analysis suggested that an NLR <4.4 before treatment potentially change to NLR <5 after anamorelin treatment, indicating NLR’s potential as a prognostic marker.
Conclusion: NLR was suggested to be an effective indicator for predicting the therapeutic effect of anamorelin.
Genetic ancestry and male founder effects explain differences in height and lactose tolerance in 60 Caucasian populations
Authors: Grasgruber Pavel 
Published: May 2024

Abstract

This study aimed to examine geographical associations of genetic factors (24 Y haplogroups, 10 autosomal ancestry components) with mean male height and the occurrence of lactose tolerance-associated alleles in a sample of 60 genetically interconnected Caucasian populations of Europe, the Near East, and North Africa. The results show that Y haplogroups or their combinations often match almost perfectly the geographical occurrence of a particular autosomal ancestry (correlation coefficients reaching up to r = 0.99), demonstrating that male founder effects played a crucial role in shaping population history. Male height adjusted for major environmental factors is positively related mainly to ancestry components BHG (Baltic hunter-gatherers), Villabruna, and Yamnaya, and the combined frequency of five Y haplogroups (I1, I2a-P37.2, N, Q, R1b-U106). The frequency of the European lactose tolerance-associated allele 13910*T correlates primarily with Yamnaya ancestry and with the combination of six Y haplogroups (I1, I2a-M223, Q, R1a, R1b-S116, R1b-U106), whereas the Near Eastern allele 13915*G is predicted by Natufian ancestry and three Y haplogroups typical of Arab populations (E1b-M123, J1, T). Of further note is the fact that country-level relationships between body height and ancestry components show both concordance and stark differences with genetic studies using individual-level relationships, which can potentially have important implications. In summary, many of the findings achieved are extremely impressive and their causality can often be inferred from already documented findings. Others offer hypotheses that could be tested with more sophisticated research.
Oscillating Spatiotemporal Patterns of COVID-19 in the United States
Authors: Jalal Hawre , Lee Kyueun , Burke Donald 
Published: May 2024

Abstract

COVID-19 case rates in the USA wax and wane in wave-like patterns over time, but the spatial patterns of these temporal epidemic waves have not been well characterized. By analyzing state- and county-level COVID-19 case rate data for spatiotemporal decomposition modes and oscillatory patterns, we demonstrate that the transmission dynamics of COVID-19 feature recurrent spatiotemporal patterns. In addition to the well-recognized national level annual mid-winter surges, we demonstrate a prominent but previously unrecognized six-month north-south oscillation in the eastern USA (Eastern US COVID Oscillator – EUCO) that gives rise to regional sub-epidemics and travelling epidemic waves. We also demonstrate a second less prominent pattern that oscillates east-west in the northern USA (Northern US COVID Oscillator – NUCO). The drivers of these newly recognized oscillatory epidemic patterns remain to be elucidated. Since the first documented case of SARS-CoV-2 in the USA in January of 2020, the virus has caused nearly 100 million reported infections and more than 1 million deaths.1 COVID-19 incidences have waxed and waned several times a year, with month-to-month variations in intensity in different regions of the country.1 The spatiotemporal granularity of available COVID-19 data in the USA provides an unprecedented opportunity to investigate detailed epidemiological dynamics of an infectious disease. In this study, we examine this spatiotemporal data in the USA to reveal patterns that can aid in the understanding COVID-19 waves and their oscillatory behavior in the United States.
Description of BCG and Tuberculosis Disease in a Cohort of 79 Patients with Chronic Granulomatous Disease
Authors: León-Lara Ximena , Pérez-Blanco Uriel , Yamazaki-Nakashimada Marco A , Bustamante-Ogando Juan Carlos , Aguilar-Gómez Nancy , Cristerna-Tarrasa Hernán , Staines-Boone Aidé Tamara , Saucedo-Ramírez Omar J , Fregoso-Zuñiga Eunice , Macías-Robles Ana Paola , Canseco-Raymundo María R , Venancio-Hernández Marco , Moctezuma-Trejo Cristina , Gámez-González Berenise , Zarate-Hernández Carmen , Ramírez-Rivera Roselia , Scheffler-Mendoza Selma , Jiménez-Polvo Nancy , Hernández-Nieto Leticia , Carmona-Vargas Jocelyn , García-Cruz María L , Zavaleta-Martínez Óscar , Román-Montes Carla M , Cervantes-Parra Victoria , González-Reynoso Anelena , Guzmán-Cotaya Rogelio , Espinosa-Rosales Francisco , Saltigeral-Simental Patricia , Espinosa-Padilla Sara , Galicia Lizbeth Blancas 
Published: May 2024

Abstract

Purpose.
Chronic granulomatous disease (CGD) is an inherited immunodeficiency caused by pathogenic variants of genes encoding the enzyme complex NADPH oxidase. In countries where tuberculosis (TB) is endemic and the Bacillus Calmette–Guérin (BCG) vaccine is routinely administered, mycobacteria are major disease-causing pathogens in CGD. However, information on the clinical evolution and treatment of mycobacterial diseases in patients with CGD is limited. The present study describes the adverse reactions to BCG and TB in Mexican patients with CGD.
Methods.
Patients with CGD who were evaluated at the Immunodeficiency Laboratory of the National Institute of Pediatrics between 2013 and 2024 were included. Medical records were reviewed to determine the clinical course and treatment of adverse reactions to BCG and TB disease.
Results.
A total of 79 patients with CGD were included in this study. Adverse reactions to BCG were reported in 55 (72%) of 76 patients who received the vaccine. Tuberculosis was diagnosed in 19 (24%) patients. Relapse was documented in three (10%) of 31 patients with BGC-osis and six (32%) of 19 patients with TB, despite antituberculosis treatment. There was no difference in the frequency of BCG and TB disease between patients with pathogenic variants of the X-linked CYBB gene versus recessive variants.
Conclusions.
This report highlights the importance of considering TB in endemic areas and BCG in children with CGD to enable appropriate diagnostic and therapeutic approaches to improve prognosis and reduce the risk of relapse.
Prognostic value of natural killer cells in colorectal carcinomas
Authors: Helal Imen , Aissi Wafa , Abdallah Khouloud Ben , Cherif Mouna , Khanchel Fatma , Laamari Hajer , Sabbah Mariem , Brahim Ehsen Ben , Jouini Raja , Debbiche Aschraf Chadly 
Published: May 2024

Abstract

Backgrounds:
Although natural killer cells are considered valuable prognostic factors in several solid tumors, their role in colorectal carcinomas remains obscure. Thus, we aimed to determine the prognostic value of NK cells in colorectal carcinomas.
Methods:
We reviewed patients who were diagnosed with stage I to IV colorectal carcinomas and who underwent curative resection of the tumor. We first determined and marked the areas with the most important lymphocyte infiltration in the center and the invasive margin of the tumor. Subsequently, we identified natural killer cells by performing an immune histochemical study with a anti-CD56 antibody via the tissue microarray technique. Afterwards, we manually counted the marked cells. Multivariate analysis was performed to determine the independent prognostic factors for death.
Results:
Our study included 104 patients. The mean age was 61.6 ± 1.4 years. The median numbers of natural killer cells in the tumor center and in the invasive margin were 1/punch and 0/punch respectively. The median total number of natural killer cells/tumor was 2. The total number of natural killer cells was ≥ 2 in 49 (47.1%) tumors. No significant difference was found in the survival curves between the group of tumors with Natural Killer cells ≥ 2 and that with Natural Killer cells < 2 (p = 0.117). According to multivariate analysis, a low immunoscore and the histological subtype of mucinous adenocarcinomas were found to be independent prognostic factors associated with poor overall survival.
Conclusion:
There are few natural killer cells in tumor tissue. They have no prognostic impact on the overall survival of patients with colorectal carcinomas.
Trial registration:
The Habib Thameur Hospital Ethics Committee HTHEC-2023-23 (retrospectively registered)
Switching Behavior and Changes in Smoking Behavior by Menthol Cigarette Preference and Menthol Heated Tobacco Product Use Among Adults Who Smoke Cigarettes: An Actual Use Study
Authors: Karelitz Joshua , He Yisha , Becker Elizabeth , Vansickel Andrea 
Published: May 2024

Abstract

Background: Heated tobacco products (HTPs) deliver nicotine with significantly lower toxicant exposure relative to combustible cigarettes. HTPs may serve as viable tobacco harm reduction options for adults who smoke (AS) but are not able or willing to stop consuming nicotine-containing products. There is limited information on switching away from or reducing combusted cigarette consumption among AS provided with HTPs, and none assessing differences due to menthol cigarette preference or menthol HTP use.
Methods: In a six-week actual use study of HTP, AS ages 21-64 (n=615) who were not planning to quit smoking combusted cigarettes were offered free choice of HTPs (one non-menthol and two menthol varieties) to use ad libitum. Preference for smoking menthol or non-menthol cigarettes was assessed upon study entry (374 menthol; 241 non-menthol). The number of HTP sticks and combusted cigarettes consumed were measured daily. Complete switching was defined as reporting consuming zero combusted cigarettes while continuing to use the HTP research product in Week 6.
Results: Overall, 247 participants completely switched to HTP, corresponding to 21.1% of all those enrolled at baseline (n=1173) or 40.2% of the analytic sample (n=615). Among the analytic sample, we observed greater switching among AS who preferred menthol versus non-menthol cigarettes (46.8% vs 29.9%). Probability of switching increased with greater proportional use of menthol versus non-menthol HTPs. Non-menthol cigarette-preferring AS had greater increases in switching when using proportionally more menthol than non-menthol HTPs; switching remained consistently high among menthol-preferring AS. Among participants who did not switch and continued smoking at Week 6, preference for menthol cigarettes and use of proportionally greater menthol versus non-menthol HTPs were each associated with greater reductions in cigarette consumption.
Conclusions: HTP use facilitated switching away from or reducing consumption of combusted cigarettes among AS, especially when using menthol HTPs. Most AS used menthol HTPs, regardless of their incoming preference for smoking menthol or non-menthol cigarettes. Availability of HTPs in menthol and non-menthol varieties offers an increased tobacco harm reduction opportunity over non-menthol only by providing AS with smoke-free alternatives that they find appealing, reduce toxicant exposure, and can effectively support their transition away from combusted cigarettes.
Prioritizing disease-related rare variants by integrating gene expression data
Authors: Guo Hanmin , Urban Alexander Eckehart , Wong Wing Hung 
Published: May 2024

Abstract

Rare variants, comprising a vast majority of human genetic variations, are likely to have more deleterious impact on human diseases compared to common variants. Here we present carrier statistic, a statistical framework to prioritize disease-related rare variants by integrating gene expression data. By quantifying the impact of rare variants on gene expression, carrier statistic can prioritize those rare variants that have large functional consequence in the diseased patients. Through simulation studies and analyzing real multi-omics dataset, we demonstrated that carrier statistic is applicable in studies with limited sample size (a few hundreds) and achieves substantially higher sensitivity than existing rare variants association methods. Application to Alzheimer's disease reveals 16 rare variants within 15 genes with extreme carrier statistics. We also found strong excess of rare variants among the top prioritized genes in diseased patients compared to that in healthy individuals. The carrier statistic method can be applied to various rare variant types and is adaptable to other omics data modalities, offering a powerful tool for investigating the molecular mechanisms underlying complex diseases.
Ethnobotany of traditional plant cosmetics utilized by women; A study in Northern Ghana
Authors: Ameade Evans Paul Kwame , Aparku Josephine , Adom Emmanuel 
Published: May 2024

Abstract

Background
Plants with cosmetic properties have been often abandoned in research as they mostly focus on plants with medicinal value or properties and their use as food. The study therefore assessed the use of plants for cosmetic purposes among female residents in Tamale metropolis the in the Northern Region of Ghana.
Method
A cross-sectional study was thus conducted among women in the Tamale metropolis to specifically identify plants used as cosmetics and determine the level of usage among women. A convenience sampling method was used in selecting the 383 participants from 20 randomly selected communities in Tamale. A semi-structured questionnaire-guided interview was used to collect the data which was then analyzed using Microsoft Excel version 2310 and IBM Statistical Package for Social Sciences (SPSS) software version 25.0. The results of the data analysis were presented in tables and graphs. Also, multivariate analysis was used to determine the association between some variables. Statistical significance is assumed at p < 0.05 at a confidence level of 95%.
Results
A total of 19 plants belonging to 18 families were listed by women in Tamale to be used for cosmetic purposes. Out of the 383 respondents, 228 use plants for cosmetic purposes. The most preferred application areas were skin, hair and private parts whereas the main cosmetic uses were skin smoothening (33.4%), skin protection (8.1%), hair growth (13.3%), treatment of acne (11.7%), body odour (9.9%) and vaginal hygiene (5.7%). Employment status (p-value = 0.325), level of education (p – value = 0.709), the origin of growth (p-value = 0.455) and type of accommodation (p – value = 0.925) which measured the economic status of the women had no association with their usage of plants for cosmetic purposes. Marital status however had a significant association with plant cosmetic usage (p – value = 0.020).
Conclusion:
Shea butter (Vitellaria paradoxa) was the most used plant by females for smoothening the skin and enhancing hair growth. This study provided an understanding of the abandoned areas of plants concerning their cosmetic values. Continuous research is encouraged to record and preserve this indigenous knowledge.
Neural correlates of resilience under different operational definitions: A resting-state fMRI study
Authors: Tai Alan P. L. , Leung Mei-Kei , Yuen Kevin C. P. , Geng Xiujuan , Lau Way K. W. 
Published: May 2024

Abstract

Different operationalizations of psychological resilience, the ability to rebound from adversity, have been adopted in the literature, each representing a specific dimension of resilience. This study aims to explore the underlying neural correlates of different operational definitions of resilience in the same participant using resting-state fMRI. Fifty-eight healthy university students in Hong Kong who underwent resting-state fMRI brain scanning were included. Their self-perceived overall, state and trait, and outcome-based resilience levelswere measured by different resilience scales. Multiple regression analyses were performed between the different measures of resilience and the whole-brain regional homogeneity (ReHo), and between resilience measures and long-range functional connectivity from both a whole-brain and a seed-based approach using fourteen preselected brain regions. The State Resilience Scale was found to be negatively associated with the ReHo of the hippocampus and parahippocampal gyrus. The outcome-based measure of resilience was negatively associated with the ReHo of the angular gyrus and insula. The Trait Resilience Scale was found to be negatively associated with the functional connectivity between the amygdala and inferior frontal gyrus from both a whole-brain and a seed-based approach. No overlapping regions or pathways were found, indicating that different operationalizations of resilience represent distinct areas of resilience.
Optimizing Anterior Urethral Stricture Assessment: Leveraging AI-Assisted Three-Dimensional Sonourethrography in Clinical Practice
Authors: Feng Chao , Lu Qi-Jie , Xue Jing-Dong , Shu Hui-Quan , Sa Ying-Long , Xu Yue-Min , Chen Lei 
Published: May 2024

Abstract

Purpose
This investigation sought to validate the clinical precision and practical applicability of AI-enhanced three-dimensional sonographic imaging for the identification of anterior urethral stricture.
Methods
The study enrolled 63 male patients with diagnosed anterior urethral strictures alongside 10 healthy volunteers to serve as controls. The imaging protocol utilized a high-frequency 3D ultrasound system combined with a linear stepper motor, which enabled precise and rapid image acquisition. For image analysis, an advanced AI-based segmentation process using a modified U-net algorithm was implemented to perform real-time, high-resolution segmentation and three-dimensional reconstruction of the urethra. A comparative analysis was performed against the surgically measured stricture lengths. Spearman’s correlation analysis was executed to assess the findings.
Results
The AI model completed the entire processing sequence, encompassing recognition, segmentation, and reconstruction, within approximately 5 minutes. The mean intraoperative length of urethral stricture was determined to be 14.452 ± 8.385 mm. Notably, the mean lengths of the urethral strictures reconstructed by manual and AI models were 13.092 ± 7.463 mm and 13.419 ± 7.216 mm, respectively. Interestingly, no statistically significant disparity in urethral stricture length between manually reconstructed and AI-reconstructed images was observed. Spearman’s correlation analysis underscored a more robust association of AI-reconstructed images with intraoperative urethral stricture length than manually reconstructed 3D images (0.869811 vs. 0.8201756). Furthermore, AI-reconstructed images provided detailed views of the corpus spongiosum fibrosis from multiple perspectives.
Conclusions
The research heralds the inception of an innovative, efficient AI-driven sonographic approach for three-dimensional visualization of urethral strictures, substantiating its viability and superiority in clinical application
Meta-SCI app: a comprehensive transcriptional reference for understanding the severity and progression of spinal cord injury
Authors: Grillo-Risco Rubén , Hidalgo Marta R. , Rojas Beatriz Martínez , Moreno-Manzano Victoria , García-García Francisco 
Published: May 2024

Abstract

Background
Spinal cord injury (SCI) is a devastating condition that leads to motor, sensory, and autonomic dysfunction. Current therapeutic options remain limited, emphasizing the need for a comprehensive understanding of the underlying SCI-associated molecular mechanisms.
Results
This study characterized distinct SCI phases and severities at the gene and functional levels, focusing on biomarker gene identification. Our approach involved a systematic review, individual transcriptomic analysis, gene meta-analysis, and functional characterization. We compiled a total of fourteen studies with 273 samples, leading to the identification of severity-specific biomarker genes for injury prognosis (e.g., Srpx2, Hoxb8, Acap1, Snai1, Aadat) and phase-specific genes for the precise classification of the injury profile (e.g., Il6, Fosl1, Cfp, C1qc, Cp). We investigated the potential transferability of severity-associated biomarkers and identified a twelve-gene signature that predicted injury prognosis from human blood samples. We also report the development of MetaSCI-app - an interactive web application designed for researchers - that allows the exploration and visualization of all generated results (https://metasci-cbl.shinyapps.io/metaSCI).
Conclusions
Overall, we present a transcriptomic reference and provide a comprehensive framework for assessing SCI considering severity and time perspectives, all integrated into a user-friendly tool.