bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Insulin Receptor Substrate 1 (IRS 1) Expression in the Prognosis of Head and Neck Squamous Cell Carcinoma - A Systematic Review and Meta Analysis
Authors: P Deeksheetha , Ramani Pratibha , Yuwanati Monal B , Professor Gheena. S 
Published: February 2024

Abstract

BACKGROUND
Head and neck squamous cell carcinoma (HNSCC) is the most common mucosal neoplasm to affect the head and neck region. It is the 6th most common cancer globally, most commonly seen in South Asian countries. Insulin receptor substrate 1 (IRS-1) like Insulin Receptor (IR) is an adaptor protein that integrates multiple transmembrane signals from growth factors and hormones, to regulate cell growth, survival, differentiation and metabolism. Evidence suggests that IRS 1 plays a vital role in cancer progression and nodal metastasis.
AIM
To assess the prognostic implication of the Insulin Receptor Substrate 1 expression in Head and Neck Squamous Cell Carcinoma from evidence based results.
MATERIALS AND METHODS
A systematic literature search was done to identify articles describing Insulin receptor substrate 1 (IRS 1) and head and neck squamous cell carcinoma were carried out for Pubmed, Cochrane, Google Scholar, using MeSH terms.
RESULTS
A total of 486 cases of HNSCC were included in this systematic review. Out of 3 studies, increased/high expression of IRS 1 was 67%. 64% of the cases in Stage I and stage II (TNM staging) showed higher expression of IRS 1, whereas 70% of the stage III and stage IV cases showed upregulation of IRS 1. IRS 1 was equally upregulated in cases with lymph node metastasis as well as in cases without any lymph node metastasis. 74% of the patients that showed high expression of IRS 1 showed high mortality during the follow up period of 13 months.
CONCLUSION
This review concluded that elevated levels of IRS 1 expression were associated with poor prognosis and increased lymph node metastasis
Coral Restoration in Palk Bay on the Southeast Coast of India
Authors: Sadhukhan Koushik , Shanmuagaraj T. , V Ramana Murthy M 
Published: February 2024

Abstract

Coral transplantation via asexual propagation of coral colonies has been used to restore the structure and function of degraded reefs in Palk Bay on the southeast coast of India. Successful restoration programs in India are rare. Therefore, this study aimed to implement a coral outplanting method at two different locations (Thonithurai and Munaikadu) in Palk Bay, India. Twenty metal frames and 800 cement slabs were used to make artificial substrates to install 800 small coral fragments, and the installation was performed in two sets to understand the variation in the growth and survivability of corals. The branching corals Acropora muricata, Acropora hyacinthus, Montipora digitata, and Pocillopora damicornis were used in this study. Eighteen months after coral transplantation, there was significant growth between the coral species (F = 8.0981; P = 0.0012), whereas, the growth difference between Thonithurai and Munaikadu was not significant (F = 0.0105; P = 0.91875). The average monthly growth rate of A. muricata (0.60cm/month) was the highest among all studied species, whereas A. hyacinthus, M. digitata, and P. damicornis had monthly growth rates of 0.44cm, 0.47cm, and 0.18cm, respectively. The survival rate for each species was calculated, and the survival rate for A. muricata (> 60%) and A. hyacinthus (> 50%) was the highest, whereas that for P. Damicornis was the lowest at both sites (< 35%). A large number of fish assemblages dominated by Terapon jarbua (grunter fish), Pomacentrus trilineatus (damsel fish), and Siganus javus (rabbitfish) were recorded from the sites after 9 months of transplantation. The results indicated that the coral out-planting method could be an effective tool for coral restoration in Palk Bay, and branching coral species can be considered promising contributors to artificial reef formation. Long-term restoration and multispecies out-planting can enrich the reef diversity in Palk Bay.
The Impact of Crystal Phase Transition on the Hardness and Structure of Kidney Stones
Authors: Maruyama Mihoko , Michibata Uta , Tanaka Yutaro , Yoshimura Masashi , Yoshikawa Hiroshi , Takano Kazufumi , Furukawa Yoshihiro , Momma Koichi , Tajiri Rie , Taguchi Kazumi , Hamamoto Shuzo , Okada Atsushi , Kohri Kenjiro , Yasui Takahiro , Usami Shigeyoshi , Imanishi Masayuki , Mori Yusuke 
Published: February 2024

Abstract
Calcium oxalate kidney stones, the most prevalent type of kidney stones, undergo a multi-step process of crystal nucleation, growth, aggregation, and secondary transition. The secondary transition has been rather overlooked, and thus, the effects on the disease and the underlying mechanism remain unclear. Here, we show, by periodic micro-CT images of human kidney stones in an ex vivo incubation experiment, that the growth of porous aggregates of calcium oxalate dihydrate (COD) crystals triggers the hardening of the kidney stones that causes difficulty in lithotripsy of kidney stone disease in the secondary transition. This hardening was caused by the internal nucleation and growth of precise calcium oxalate monohydrate (COM) crystals from isolated urine in which the calcium oxalate concentrations decreased by the growth of COD in closed grain boundaries of COD aggregate kidney stones. Reducing the calcium oxalate concentrations in urine is regarded as a typical approach for avoiding the recurrence. However, our results revealed that the decrease of the concentrations in closed microenvironments conversely promotes the transition of the COD aggregates into hard COM aggregates. We anticipate that the suppression of the secondary transition has the potential to manage the deterioration of kidney stone disease.
High serum 25-hydroxyvitamin D level is a risk factor for cerebral palsy：a bidirectional two-sample Mendelian randomization analysis
Authors: Liu Qiong , Liu Xiaofang , Gao Mengge , Yang Bo , Luo Miaoying , Yang Biying , Liang Goujun 
Published: February 2024

Abstract
Background: The causal relationship between the level of 25-hydroxyvitamin D(25-OH-D) in the blood and cerebral palsy (CP) remains uncertain. Prior research has indicated that the levels of 25-OH-D in the serum of children with cerebral palsy are lower compared to those in normally developing children. Nevertheless, there is a limited number of studies assessing the impact of serum 25-OH-D concentration on CP. In contrast to the prevailing notion, Mendelian randomization (MR) can be utilized to thoroughly evaluate the reciprocal causal impacts between serum 25-OH-D level and CP.
Methods: A bidirectional two-sample MR analysis was conducted by utilizing combined data from genome-wide association studies that included European populations with CP (286 individuals with CP and 216992 individuals as controls). This analysis utilized four different methods to assess the bidirectional relationship between 25-OH-D and CP. To assess the inflexibility of the findings, a sensitivity analysis was conducted. According to MR-Steiger filtering, it was found that all single nucleotide polymorphisms (SNPs) had a higher level of association with 25-OH-D compared to CP.
Results: Limited evidence suggested that there were positive causal connections between genetically predicted serum 25-OH-D level and CP, with an odds ratio of 1.88 (95% confidence interval 1.062–3.280; p= 0.036). Nevertheless, the inverse pattern did not suggest a causal relationship between CP and serum 25-OH-D level. No clear pleiotropy or heterogeneity was found in the sensitivity analysis.
Conclusion: Our analysis presents fresh evidence supporting the moderate causal influence of serum 25-OH-D level on CP. Further investigation is necessary to examine the causal impacts of CP on serum 25-OH-D levels.
eDNA based survey of non-indigenous species in Norwegian water bodies using Loop Mediated Isothermal Amplification (LAMP)
Authors: Jothinarayanan Nivedhitha , Karlsen Frank , Roseng Lars Eric 
Published: February 2024

Abstract
Monitoring of species in a habitat is important to ensure the biological diversity. Environmental DNA (eDNA) can infer the presence-absence of species and enable rapid action to avoid the threatening factor in ecosystems, in the case of non-indigenous species. LAMP assays for molecular amplification and detection are rapidly gaining popularity in the invasive species detection, but the LAMP remains an underutilized method for eDNA-based monitoring practices. The most effective combination for successful species monitoring may be the collection of eDNA or biological traces collected by nanofiltration followed by LAMP-based species detection initiatives. Here, we use LAMP analysis to detect the Northern Pike (Esox Lucius) eDNA in the Borre Lake and in the Drammen River in Norway. Northern Pike is a regionally invasive species in southeastern parts of Norway. Furthermore, the endangered species European Eel (Anguilla anguilla) and a species of least concern Atlantic Salmon (Salmon salar), have been added in our study. We developed two LAMP primers for each these species to identify the invasive, vulnerable, and least concern fish species and our study shows that eDNA is an effective tool for determining Northern Pike in freshwater bodies, using the LAMP technique.
Causal Association Between Peripheral blood immune cells and Rheumatoid Arthritis: A Bidirectional Mendelian Randomization Study
Authors: Wang Yang , Fang Peng , Wan Xin , Liu Xiaozhou , Zhao Jianning , Bao Nirong , Hao Ding , Song Dianwen 
Published: February 2024

Abstract

Immune cells play a crucial role in the onset and progression of rheumatoid Arthritis (RA). we leveraged publicly available Genome-Wide Association Studies (GWAS) data to explore the causal relationship between 731 immune cell traits and RA using the Bidirectional MR analysis. The primary method for causal analysis relies on Inverse Variance Weighting (IVW). To ensure robustness, sensitivity analyses include the Cochran Q test, MR-Egger intercept test, MR-PRESSO, and leave-one-out analysis. Additionally, gene colocalization analysis and drug target MR are employed to enhance the comprehensiveness of the study.In the forward MR analysis, after FDR correction, 731 immune cell traits had no statistically significant effect on RA. Notably, some phenotypes showed lower P values before adjustment, including 12 different immune cell traits. After gene colocalisation analysis only CD4 on HLA DR+ CD4+ T cells and CD45RA- CD28- CD8+ T cell %T cell shared the same genetic variant as RA. Inverse MR analysis showed that RA was associated with 12 immune cell traits. After gene colocalisation analysis RA was associated with CD28- CD8+ T cell %T cell, Effector Memory CD8+ T cell %T cell, CD8+ Natural Killer T Absolute Count, CD8+ Natural Killer T %lymphocyte, and CD8+ Natural Killer T %T cell share the same genetic variant. No evidence of horizontal pleiotropy or heterogeneity between genetic variants was found (P>0.05), and the "leave-one-out" test confirmed the stability and robustness of the associations. MR analyses of drug targets suggested that CCHCR1 may play an important role in the pathogenesis of RA.This study suggests that specific immune cell traits may play a key role in RA development and could serve as new biomarkers for its diagnosis. Notably, identifying CCHCR1 as a drug target unveils new paths for research and treatment, offering promising opportunities in the field.
Electromyographic Activity of the Ankle and Foot During Functional Exercises and Traditional Exercises
Authors: Baldim Isabella , Miguel Matheus , SPINOSO Deborah 
Published: February 2024

Abstract

Traditional exercises using an elastic band are often standard in clinical practice to gain muscle strength. Additionally, functional exercises are considered more representative of functional tasks or sport. However, it is unclear whether functional exercises are comparable to traditional exercises in activating the ankle joint and foot. The purpose of this study was to analyze the effects of functional exercise and traditional exercise on the muscle activity of the ankle joint and foot. Thirty women participated in this study. Using surface electromyographic, muscle activation of the Tibialis Anterior (TA), Peroneus Longus (FL), Peroneus Short (FC), Gastrocnemius Medialis (GM) and Flexor Digitorum Shortus (FCD) was measured in nine exercises (dorsiflexion with an elastic band, plantar flexion with an elastic band, inversion with an elastic band, eversion with an elastic band, towel curl, standing plantar flexion, squats with an elastic band on the foot, diagonal propulsion and propulsion with peroneal stimulation). The muscle activation was normalized by the activation in maximum voluntary isometric contraction. Functional exercises showed larger mean EMG amplitudes than the traditional exercises for all muscle groups (p > 0.05). Functional exercises provoked more activation compared with the traditional exercises. Functional exercises can be indicated to improve muscle function and functional task performance in populations that suffer dysfunction in ankle joint and foot.
Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription
Authors: Lack Nathan , Altintas Umut Berkay , Seo Ji-Heu , Giambartolomei Claudia , Ozturan Dogancan , Fortunato Brad , Nelson Geoffrey , Goldman Seth , Adelman Karen , Hach Faraz , Freedman Matthew 
Published: February 2024

Abstract

Androgen receptor (AR)-mediated transcription plays a critical role in normal prostate development and prostate cancer growth. AR drives gene expression by binding to thousands of cis-regulatory elements (CRE) that loop to hundreds of target promoters. With multiple CREs interacting with a single promoter, it remains unclear how individual AR bound CREs contribute to gene expression. To characterize the involvement of these CREs, we investigated the AR-driven epigenetic and chromosomal chromatin looping changes. We collected a kinetic multi-omic dataset comprised of steady-state mRNA, chromatin accessibility, transcription factor binding, histone modifications, chromatin looping, and nascent RNA. Using an integrated regulatory network, we found that AR binding induces sequential changes in the epigenetic features at CREs, independent of gene expression. Further, we showed that binding of AR does not result in a substantial rewiring of chromatin loops, but instead increases the contact frequency of pre-existing loops to target promoters. Our results show that gene expression strongly correlates to the changes in contact frequency. We then proposed and experimentally validated an unbalanced multi-enhancer model where the impact on gene expression of AR-bound enhancers is heterogeneous, and is proportional to their contact frequency with target gene promoters. Overall, these findings provide new insight into AR-mediated gene expression upon acute androgen simulation and develop a mechanistic framework to investigate nuclear receptor mediated perturbations.
Cardiovascular Stress Biomarkers in Response to Marathon Running in Male Athletes with Various Plasma Trimethylamine N-oxide Levels
Authors: Siekierzycka Anna , Radulska Adrianna , Woźniak Marcin , Pelikant-Małecka Iwona , Janaszak-Jasiecka Anna , Lewicka Ewa , Kalinowski Leszek , Olek Robert A. 
Published: February 2024

Abstract

Habitual physical activity is known to support cardiovascular health. However, when intensive exercise is performed for long durations, it can negatively affect the cardiovascular system. We evaluated the exercise-induced physiological responses of cardiac markers in male marathon runners with basal levels of trimethylamine-N-oxide (TMAO) plasma below (LT) and equal or above (HT) value of 4.0 µM. Blood samples from 28 marathon runners were collected two weeks before the marathon run (control before), after finishing the race (post-marathon), and two weeks after the race (control after). Serum cardiac troponin I (cTnI), endothelin-1 (ET-1), galectin-3, pentraxin-3, human growth differentiation factor 15, and neopterin were determined by the enzyme immunoassay method. Plasma trimethylamine and TMAO were measured by the ultra-high-performance liquid chromatography-mass spectrometry method. Running a marathon increased level of circulating stress biomarkers. A greater post-marathon elevation of cTnI and ET-1 was associated with higher plasma TMAO levels in the control samples prior to the marathon. A significant increase in ET-1 in post-marathon HT samples may indicate increased blood pressure and myocardial load due to increased vascular tone. Such an increase leads to greater myocardial cell membrane permeability and cTnI release. These modifications were not associated with other determined cardiovascular and inflammatory markers.
Bioprospecting of Wild Botanicals against Alternaria Leaf Blight of Radish and their Phytochemical Profiling by GC-MS
Authors: Kumar Ranjan , Ramachaandra Sudharshan Keralapura , Kaushik Snata , Austin Hans , T Rajesh 
Published: February 2024

Abstract

Cruciferous vegetables, globally important crops, face a severe threat from Alternaria blight, a pervasive and highly damaging disease, causing black spots and blight on leaves in field conditions, resulting in reduced yield and seed quality. The present study aims to evaluate the antifungal potential of different wild botanicals against the Alternaria leaf blight pathogen in in vitro and in vivo studies and to analyze the phytochemicals through Gas Chromatography Mass Spectrometry. Among fifty botanicals screened at a 10% concentration against the pathogen, the aqueous extracts of Hemidesmus indicus, Lippia alba, Chromolaena odorata, and Solanum violaceum displayed the highest mycelial inhibition. Further in vitro evaluations of these four botanicals at different concentrations (2.5%, 5.0%, 7.5%, 10.0%, and 12.5%) revealed that, at a 12.5% plant extract, H. indicus and L. alba exhibited the most effective inhibition of 82.96% and 76.60%, respectively, followed by C. odorata (71.93%) and S. violaceum (63.53%). Based on promising in vitro results, these botanicals were assessed in pot experiments at 12.5% concentration each. Among the four botanicals, the highest percentage of disease reduction was observed in H. indicus and L. alba, with 69.79% and 60.44%, respectively. Eventually, botanicals effectively reduced disease severity while increasing radish yield. GCMS analysis of phytochemicals revealed that botanicals often attributed to a combination of various bioactive compounds such as phenolics, flavonoids, saponins, and volatile compounds, known for their antimicrobial activities. This study emphasizes the potential of botanicals as a natural alternative for managing fungal diseases, offering resilient and sustainable approaches to safeguard crops from destructive fungal infections.
Association between sphingomyelin levels and gut microbiota abundance: a two-sample Mendelian randomization study
Authors: wang liping , Ding Yuyan , Yang Mengqi , Yang Zhihui , Yang Xiao , Xia Jiazeng 
Published: February 2024

Abstract
Background
Several previous observational studies have shown that abnormal sphingomyelin metabolism may be implicated in the pathogenesis of Alzheimer's disease. To determine the causal relationship between sphingolipid abundance and gut microbiota abundance at the genetic level, we conducted a Mendelian randomization (MR) investigation.
Methods
We first used the TwoSampleMR and MRPRESSO packages for conducting two-sample MR studies. Second, we utilized random effect inverse variance weighting (IVW) as the principal method of analysis and used MR‒Egger, the weighted median, the simple mode and the weighted mode as supplementary methods. Finally, we performed tests for heterogeneity and horizontal pleiotropy. These analyses were also conducted to evaluate the impact of individual SNPs on the outcomes of our analysis.
Results
The results showed that the level of sphingomyelin was correlated with the abundance of 6 gut microbiota species, among which 2 were positively correlated with the family Alcaligenaceae (p = 0.006, beta 95% CI = 0.103 [0.029, 0.178]) and the species Ruminococcus callidus (p = 0.034, beta 95% CI = 0.197 [0.015, 0.378]). There were negative correlations with the abundances of 4 gut microbiota abundencegenera, such as the genus Flavonifractor (p = 0.026, beta 95%CI = -0.218 [-0.411, -0.026]) and the genus Streptococcus (p = 0.014, beta 95% CI = -0.096 [-0.172, -0.019]). The results presented a normal distribution with no anomalous values, heterogeneity or horizontal pleiotropic effects detected.
Conclusions
This two-sample Mendelian randomization study revealed a causal relationship between sphingomyelin levels and gut microbiota abundance.
Shotgun sequencing of 512-mer copolyester allows random access to stored information
Authors: Kim Kyoung Taek , Jang Heejeong , Chu Hyunseon , Noh Hyojoo 
Published: February 2024

Abstract

Digital information encoded in polymers has been exclusively decoded by mass spectrometry. However, the size limit of analytes in mass spectrometry restricts the storage capacity per chain. In addition, sequential decoding hinders random access to the bits of interest without full-chain sequencing. Here we report the shotgun sequencing of a 512-mer sequence-defined polymer whose molecular weight (57.3 kDa) far exceeds the analytical limit of mass spectrometry. A 4-bit fragmentation code was implemented at random positions during the synthetic encoding of 512-bit information without affecting storage capacity per chain. Upon the activation of the fragmentation code, the polymer chain splits into 18 oligomeric fragments, which could be individually decoded by tandem-mass sequencing. These sequences were computationally reconstructed into a full sequence using an error-detection method. The proposed sequencing method eliminates the storage limit of a single polymer chain and allows random access to the bits of interest without full-chain sequencing.
Vpr protein regulates expression of cytokines associated with apopotsis
Authors: Xu zhen-yu , Gao jia-shi , Wu Zhenyu , Zhou Hua-ying , Chen Zi , He Yan , peng feng 
Published: February 2024

Abstract
Background: Viral protein R (Vpr) is an HIV-1 accessory protein whose function remains poorly understood. While its contribution to virus replication in dividing and non-dividing cells and to the pathogenesis of HIV-1 in many different cell types have been extensively studied. Recently, HIV-1 viral protein R (Vpr) has been demonstrated to induce host cell G2 / M phase and apoptosis in infected cells. However, its precise mechanism of apoptosis nevertheless remains enigmatic.
Methods: In this study, we established overexpression and silencing of HIV-1 Vpr gene in 293T and Jurkat cells to investigate the relationship among HIV-1 Vpr with IL-17A, IFN-γ and c-IAP2 expression.
Results: The results demonstrated that overexpression of HIV-1 Vpr gene significantly decreased IL-17A, IFN-γ concentration as well as c-IAP2 expression and induced apoptosis in Jurkat cells, but not in 293T stable cells. Meanwhile, silencing of Vprgene expression reversed the effects of Vpr on IL-17A, IFN-γ, and c-IAP2 expression, and apoptosis in Jurkat cells.
Conclusion: HIV-1 Vpr negatively regulates IL-17A, IFN-γ, and c-IAP2 expression and induce apoptosis in T lymphocytes.