bluuebunny/crossref_metadata_2025_split huggingface dataset:
IRAK2, an immune and radiation-response gene, correlates with advanced disease features but predicts high post-irradiation local control in resected oral cancer patients
Authors: Yu Chih-Chia , Lin Hon-Yi , Chan Michael W.Y. , Chiou Wen-Yen , Lee Moon-Sing , Chi Chen-Lin , Lin Ru-Inn , Hsu Feng-Chun , Chen Liang-Cheng , Chew Chia-Hui , Yang Hsuan-Ju , Hung Shih-Kai 
Published: January 2023

Abstract
Radiotherapy (RT) is an effective treatment modality for managing resected oral squamous cell carcinoma (OSCC) patients. The present study conducted gene ontology to explore the functional biological analysis of IRAK2 and performed case analysis to define its clinical role in disease progression and mediating tumor response to RT. Transcriptome sequencing data from the OML1 oral cancer cell line was analyzed to explore IR-responding genes. For identified significant IR-responsive genes, gene ontology (GO) analysis was conducted for exploring their involved bio-logical processes. From Jan. 2007 to Dec. 2014, 172 OSCC patients who received radical surgery with (n = 93) and without (n = 79) postoperative RT were identified for clinical validation. Their OSCC formalin-fixed paraffin-embedded histological samples were examined retrospectively to define IRAK2 expression. After irradiation treatments, IRAK2 upregulation was identified obviously suggesting its role as a potential radiation biomarker. Moreover, GO enrichment analysis showed IRAK2 involved ten of 14 top enriched post-irradiation biological processes, focusing on stress response and immune modulation in vitro. Clinically, high IRAK2 expression was correlated with several adverse disease features, including pT3-4 status (P = 0.01), advanced overall stage (P = 0.02), and positive bone invasion (P = 0.01). In patients who underwent RT, the IRAK2-high group was associated with fewer post-irradiation local recurrence (multivariate HR, 0.243; 95% CI, 0.071–0.838; P = 0.025) than the IRAK2-low group. However, the local control benefit did not translate into patient survival. On the other hand, for patients with no RT, IRAK2 did not predict local control. IRAK2 plays a crucial role in the radiation-induced response. In summary, patients with high IRAK2 expression demonstrated more advanced disease features but predicted higher post-irradiation local control than those with low expression. These findings support IRAK2 as a potential predictive biomarker for RT response in OSCC patients. Further prospective clinical studies are encouraged.
Genetic characterization and molecular mapping of ear height on the basis of generation mean analysis and bulked segregant analysis in maize (Zea mays)
Authors: Singh Tejinder , Singh Gagandeep , Garg Tosh , Kushwah Ashutosh , Sharma Priti , Kaur Navdeep 
Published: January 2023

Abstract
The genetic studies of ear height and its related traits were carried out by making crosses between two contrasting parents for ear height i.e, AKON40A (high ear placement) and LM23 (low ear placement) to generate F1 hybrids, which were selfed to produce F2 population and backcrossed with both parents to generate BC1.1 and BC1.2 generations. Generation mean analysis was performed on all six generations for a total of 12 morphological and phenological traits. The genetic components revealed the presence of additive gene action, additive × additive and additive × dominance gene interaction for ear height and plant height. Out of 284 SSR primer pairs, 146 primer pairs confirmed parental polymorphism, while nine primers were exhibited polymorphic in bulked segregant analysis (BSA). These nine primers were used for constructing linkage map in F2 population. Three linkage groups were formed in which LG1 spanned 26.9 cM on chromosome 3 while, LG2 and LG3 spanned 42.1 and 6.7 cM on chromosome 6 and 7, respectively. Gene governing the trait ear height was mapped on chromosome 6 between the SSR primers umc1979 and umc2317 having LOD value of ~ 3 and the phenotypic variance (R2) of 8.5. The prevalence of additive gene action for ear height suggested that recurrent selection can be utilized to improve source population for reducing ear placement by accumulating favourable alleles. Improved source population then can be utilized for inbred line development leading to maize hybrids having medium to low ear placement.
Phylogenetic relationship among species of Rubus (Rosaceae) from southern Western Ghats of India: Morphological data aligns with the combined dataset of plastic and nuclear markers
Authors: Narayanan Bhavadas , Thara Umesh B. , Ramanujan Rahul P. 
Published: January 2023

Abstract

The present study explores the taxonomic delineation of Rubus taxa within south Western Ghats of India. Most of the species are aligned in two major subgenera, Idaeobatus and Malachobatus but were lacking systematic botany. The external morphological study developed fine dichotomous key characters for the discrimination of Rubus under study, but it was inadequate for the closely allied species. Therefore, the delineation of the taxa was studied by using the alignment of molecular sequences from three barcode regions (matK, rbcL, and nrITS) and phylogenetic tree of plastid (matK + rbcL), nuclear (nrITS), and combined (plastid + nuclear) genome was constructed for taxa discrimination. Fifteen Rubus collections were comparatively analyzed for the phylogenetic analysis including the inter-specific distance of eleven taxa and the intra-specific distance of four species. It was observed that the nuclear ITS marker had much higher sequence variations compared to the other loci. Phylogenetic relationship within Rubus is well resolved in combined datasets than nuclear and plastid data separately and in this study, the analyzed samples included in both Idaeobatus and Malachobatus formed a polyphyletic clade in all datasets except plastid phylogeny. Wherein the plastid genome, subgenus Malachobatus have shown more conserved sequences than subgenus Idaeobatus. Whereas, subgenus Malachobatus had shown limited species resolution than Idaeobatus in all barcode markers because a group of species belonging to subgenus Malachobatus has shown inadequate genetic variations within species similar to its limited morphological variability. Hence we considered this group a complex species among southern Western Ghats Rubus and it is recommended further studies.
Exploring the Factors That Influence Social Harm Related to Youth Health in The Suburbs of Karaj, Iran: A Qualitative Study
Authors: Mahmoodi Zohreh , Solimannejad Tahereh , Solimannejad Mohamad , Esmaelzadeh Sara , Niazi Mohsen 
Published: January 2023

Abstract
Background
Marginalization is a global and pervasive issue and the cause of many social problems. This study seeks to explain the causes and underlying factors of social harm related to youth health in the suburbs of Karaj, Iran.
Methods
This qualitative study was conducted using content analysis in 2020 in the suburbs of Karaj, Iran. The research population consisted of 16 young people living in the region and four experts in socials harm and health. Purposeful sampling was performed with maximum variation. Semi-structured interviews were conducted individually and according to participants’ experiences and were then analyzed in MAXQDA-20 software.
Results
The data analysis led to the extraction of four categories, eight subcategories, and 52 codes. The research categories included environmental factors, family factors, cultural factors, and physical and psychological factors aggravating social harm.
Conclusion
The results of this study showed the high prevalence of the severity of social harm in the marginalized suburbs of Karaj, which was caused by social instability, peer influence, child abandonment, family breakdown, cultural deprivation, and severe traditionalism, which have led to many health problems and personal breakdown for this marginalized population. Therefore, plans should be devised to solve the problems of marginalized adolescents and to empower them so as to reduce social harms and improve their health.
Uterine Leiomyosarcoma with a Novel RAB2A-PLAG1 Gene Fusion
Authors: Sham Sunder , Hosseini Hossein , Kokabee Mostafa , Bendari Ahmed 
Published: January 2023

Abstract
Uterine leiomyosarcoma (ULMS) constitutes 1% of all uterine malignancies and is the most common subtype of uterine sarcoma. In some cases, distinguishing ULMS from endometrial stromal sarcoma (ESS) can be challenging as they may display histological and immunohistochemical overlap. In such cases, molecular studies such as RNA sequencing to detect genetic rearrangements can help arrive at the definitive diagnosis. We report a unique case on ULMS with a novel RAB21-PLAG1gene fusion, which to our knowledge, is the first case reported in the English literature.
Case Presentation:
An 80-year-old woman presented to our hospital with a one-month history of pelvic pain and abnormal uterine bleeding. Imaging was notable for a large necrotic uterine mass, a thickened endometrium, and uterine fibroids. A subsequent endometrial biopsy (EMB) revealed an unremarkable transformation zone epithelium. After 4 months, the patient presented with persistent symptoms. One solid mass within the endometrium was found on imaging. Endometrial curettage (EMC) revealed a malignant uterine mesenchymal neoplasm with histologic findings suggestive of ULMS and ESS. The patient underwent a total hysterectomy with bilateral salpingo-oophorectomy. Immunohistochemical study performed on the resection specimen was inconclusive. RNA sequencing identified a novel RAB2A-PLAG1 gene fusion, and a diagnosis of ULMS was rendered.
Conclusion:
This is the first case of a ULMS with RAB2A-PLAG1 gene fusion. Pathologists should be cognizant of the extensive morphologic and immunophenotypic overlap between various uterine mesenchymal neoplasms. In challenging cases, molecular analysis is crucial in allowing the pathologist to arrive at the final diagnosis.
The role of HIF-1α in COVID-19 pathogenesis and its correlation with IL-6 and other inflammation parameters
Authors: Khalid Hawzhin , Asadi Soheila , Palani Ayad , Faraj Rahman Karim , Muhialdin Ali Jalak , Sardar Shwan , Najafi-Ghobadi Khadijeh 
Published: January 2023

Abstract
Inflammation has a crucial role in COVID-19 pathogenesis, and previous studies have proposed an important function of IL-6 during inflammation. On the other hand, IL-6 levels and inflammation might be associated with hypoxia-inducible factor-1α (HIF-1α). Thus, due to the possible role of HIF-1α in inflammation and COVID-19 pathogenesis, we aimed to investigate the levels of HIF-1α and its correlation with inflammatory parameters (IL-6 and CRP) and D-dimer. In this case-control study, 84 patients (54 patients hospitalized in the ICU and 30 individuals as outpatient subjects) were included as the case group, and 50 healthy subjects were included as the control group. The levels of D-dimer, CRP, IL-6 (interleukin 6) and HIF-1α were assessed in all studied groups. The results of the present investigation showed that the levels of D-dimer, CRP and IL-6 were significantly increased in COVID-19 patients compared to healthy individuals. On the other hand, the level of HIF-1α significantly decreased in COVID-19 patients. In addition, there was a significant correlation between IL-6 and CRP and D-dimer, while HIF-1α was indirectly correlated with IL-6, CRP and D-dimer. Ultimately, our data indicated that the levels of CRP, D-dimer, IL-6 and HIF-1α were significantly different between ICU patients and the outpatient group with healthy individuals. Based on the study results, inflammation plays a crucial role in COVID-19 pathogenesis, and low HIF-1α is a consequence of inflammation due to COVID-19 infection and might have a protective role in COVID-19.
Experimental determination of quartz solubility in H2O-CaCl2 solutions at 600–900 °C and 0.6–1.4 GPa
Authors: Makhluf Adam R. , Newton Robert C. , Manning Craig E. 
Published: January 2023

Abstract
Fluid-mediated calcium metasomatism is often associated with strong silica mobility and the presence of chlorides in solution. To help quantify mass transfer at lower crustal and upper mantle conditions, we measured quartz solubility in H2O-CaCl2 solutions at 0.6–1.4 GPa, 600–900 °C, and salt concentrations to 50 mol%. Solubility was determined by weight loss of single-crystals using hydrothermal piston-cylinder methods. All experiments were conducted at salinity lower than salt saturation. Quartz solubility declines exponentially with added CaCl2 at all conditions investigated, with no evidence for complexing between silica and Ca. The decline in solubility is similar to that in H2O-CO2 but substantially greater than that in H2O-NaCl at the same pressure and temperature. At each temperature, quartz solubility at low salinity (XCaCl2 &lt; 0.1) depends strongly on pressure, whereas at higher XCaCl2 it is nearly pressure independent. This behavior is consistent with a transition from an aqueous solvent to a molten salt near XCaCl2 ~0.1. The solubility data were used to develop a thermodynamic model of H2O-CaCl2 fluids. Assuming ideal molten-salt behavior and utilizing previous models for polymerization of hydrous silica, we derived values for the activity of H2O (aH2O), and for the CaCl2 dissociation factor (α), which may vary from 0 (fully associated) to 2 (fully dissociated). The model accurately reproduces our data along with those of previous work and implies that, at conditions of this study, CaCl2 is largely associated (&lt;0.2) at H2O density &lt;0.85 g/cm3. Dissociation rises isothermally with increasing density, reaching ~1.4 at 600 °C, 1.4 GPa. The variation in silica molality with aH2O in H2O-CaCl2 is nearly identical to that in H2O-CO2 solutions at 800 °C and 1.0 GPa, consistent with the absence of Ca-silicate complexing. The results suggest that the ionization state of the salt solution is an important determinant of aH2O, and that H2O-CaCl2 fluids exhibit nearly ideal molecular mixing over a wider range of conditions than implied by previous modeling. The new data help interpret natural examples of large-scale Ca-metasomatism in a wide range of lower crustal and upper mantle settings.
Origin of clinopyroxene-ilmenite symplectites in mafic granulites from eastern parts of the Chotanagpur granite gneissic complex, East Indian shield
Authors: Chatterjee Somdipta , Karmakar Shreya , Mukherjee Subham , Sanyal Sanjoy , Sengupta Pulak 
Published: January 2023

Abstract
In this manuscript, we report a rare occurrence of rod-like intergrowths of clinopyroxene-ilmenite that variably replace titanite in a suite of high-pressure mafic granulites from the Chotanagpur Granite Gneissic Complex, Eastern Indian Shield. Garnet proximal to the clinopyroxene-ilmenite intergrowth is invariably replaced with symplectic clinopyroxene-plagioclase or a rind of plagioclase. Textural modeling of the reaction textures and mineral compositions suggests that the garnet-titanite became unstable and the ilmenite-clinopyroxene preferentially develop after titanite. The presence and texture of halogen rich apatites within the ilmenite-clinopyroxene symplectite are consistent with a fluid mediated process. Thermodynamic modeling in the NCFMAST (+H2O) system, demonstrates that the clinopyroxene-ilmenite symplectite was formed along a steeply decompressive retrograde P-T path (from ~13 to ~7 kbar, at ~800 °C), in the presence of partial melts. The study demonstrates that relative to Fe, Mg, and Ca, Ti was less mobile and that the mobility of Ti was restricted within the confines of titanite being replaced by the clinopyroxene-ilmenite symplectite. This study implies that besides the ligand activity, the fluid/rock ratio exerts a strong control on the length scale of Ti transport in natural rocks.
The Residual Structure of Unfolded Proteins was Elucidated from the
Standard Deviation of NMR Intensity Differences
Authors: Nishimura Chiaki , Mizuno Fuko , Aoki Saeko , Matsugami Akimasa , Hayashi Fumiaki 
Published: January 2023

Introduction:
Sensitive methods are necessary to identify the residual structure in an
unfolded protein, which may be similar to the functionally native structure. Signal intensity in NMR
experiments is useful for analyzing the line width for a dynamic structure; however, another
contribution is contained.

Methods:
Here, the signal-intensity difference along the sequence was used for probability to
calculate the standard deviation.

Results:
The relative values of the standard deviations were 0.57, 0.57, and 0.66 for alpha-synuclein
wild-type, A53T, and A30P, respectively. This revealed that the flexible region was mainly in the Cterminal
region of alpha-synuclein at higher temperatures as observed by the amide-proton exchange
studies.

Conclusion:
In particular, the flexible structure was induced by the A30P mutation.
Amyloids and Amyloid-like Protein Aggregates in Foods: Challenges and
New Perspectives
Authors: Malik Shweta , Yadav Jay Kant 
Published: January 2023

Abstract:
Protein misfolding and amyloid formations are associated with many neurodegenerative and
systemic diseases. The discovery of Alzheimer’s disease and its association with the accumulation of
Amyloid-β (Aβ) peptides in the plaques uncovered the pleiotropic nature of peptides/ proteins. As of
today, more than 50 proteins/ peptides are reported to form amyloids or amyloid-like protein aggregates
under different conditions, establishing that amyloid formation could be a generic property of many
proteins. In principle, under certain conditions, all the proteins have this property to form amyloid-like
aggregates, which can be toxic or non-toxic. The extensive research in this direction led to an understanding
of the ubiquitous nature of amyloids. Mounting evidences suggest that processed foods, particularly
protein-rich foods, could be a plethora of amyloids or amyloid-like protein aggregates. Many
are reported to be toxic, and their consumption raises health concerns. The assimilation of dietary proteins
in the human body largely depends upon their conformational states and the digestive integrity of
the gastrointestinal system. Amyloids or amyloid-like protein aggregates are usually protease resistant,
and their presence in foods is likely to reduce nutritional value. Several biochemical and biophysical
factors, commonly evident in various food processing industries, such as high temperature, the addition
of acid, etc., are likely to induce the formation of protease-resistant protein aggregates. Aging significantly
alters gastrointestinal health, predisposing aged individuals to be more susceptible to protein
aggregation-related diseases. Consumption of foods containing such protein aggregates will lead to a
poor supply of essential amino acids and might exaggerate the amyloid-related disease etiology.

:
On the other hand, the gut microbiome plays a crucial role during pathological events leading to the
development of Alzheimer’s and Parkinson’s diseases. The activity of gastrointestinal proteases, pH
change, gut microbiome, and intestinal epithelium integrity would largely determine the outcome of
consuming foods loaded with such protein aggregates. The current review outlines the recent development
in this area and a new perspective for designing safe protein-rich diets for healthy nutrition.
Rapid Quantitative Simultaneous Determination of Vitamin A and Vitamin
D in a Skin Ointment Pharmaceutical Formulation Based on Net Analyte
Signal and Partial Least Squares using the UV Spectrophotometric
Method
Authors: Hamedfam Maryam , Sohrabi Mahmoud Reza , Davallo Mehran 
Published: January 2023

Objective:
The aim of this study was to propose an easy, fast, and precise method, which can be satisfactorily applied to the simultaneous determination of the drugs in pharmaceutical dosage forms instead of the high-performance liquid chromatography (HPLC) method.

Methods:
Complicated and costly instruments, as well as spending a lot of time for analysis are the limitations of the chromatography method. Hence, UV spectrophotometric technique based on net analyte signal (NAS) and partial least squares (PLS) was proposed and validated for the simultaneous determination of vitamin A and vitamin D in binary mixtures and commercial skin ointment. The chromatographic technique was implemented to compare with the proposed approach for the simultaneous analysis of drugs.

Results:
The NAS method was able to determine vitamin A and vitamin D in the concentration range of 1–7 and 2-13 μg mL-1 at λmax=323 and λmax=261, respectively. The limit of detection (LOD) and limit of quantification (LOQ) related to the NAS method were found to be 0.092, 0.053 μg/mL and 0.214, 0.170 μg/mL for vitamin A and vitamin D, respectively. The root mean square error (RMSE) of the test series was 0.0607 and 0.0547 for vitamins A and D, respectively. Recoveries by the PLS method were found in the range of 99.98%-100.49% and 99.57%-100.88% for vitamins A and D, respectively. The results obtained from the NAS and PLS procedures were statistically compared with the reference method (HPLC) via analysis of variance (ANOVA) test, where no significant difference was observed.

Conclusion:
The spectrophotometry along with NAS and PLS methods are proper, rapid, and economic for the determination of pharmaceutical components in quality control laboratories.
In silico Study on the Binding Interactions of SSTA and 18F-SSTA Towards Somatostatin Receptor Subtype 2
Authors: Pérez David J. , Razo-Hernández Rodrigo S. , Ávila-Rodríguez Miguel A. 
Published: January 2023

Background:Somatostatin analogs (SSTAs) are versatile drugs that target a group of proteins known as somatostatin receptors. SSTAs are used for the treatment and PET-molecular imaging of Neuro Endocrine Tumors (NET), for they are labeled with the radionuclide 18F, a positron emitter radionuclide.Objective:The aim of this work was to theoretically study the binding interactions of SSTA labeled with 18F (half-life of 109.7 min) and somatostatin receptor subtype 2. As the labeling of SSTA with 18F required the use of a prosthetic group, a hydrophilicity enhancer, and a linker, the influence of these traits on the interactions of 18F-SSTA with the SSTR-2 binding site was studied.Methods:The binding modes of 18F-labeled analogues with SSTR-2 were studied by using protein homology modelling, non-equilibrium molecular dynamics, and molecular docking calculations, by means of three docking software: MVD, MOE, and VINA.Results:The results showed the main role of Asp122, Asn276, Phe272 and Phe294 from the SSTR-2 binding site, which form interactions with residues Lys, Trp, Tyr, and Thr from 18F-labeled somatostatin analogues.Conclusion:The interaction between Lys (from 18F-SSTA) and Asp122 (from SSTR-2) was identified as the most energetic and considered the one that drives the binding between 18F-SSTA and SSTR-2 (the anchor interaction). Despite the presence of prosthetic groups, linkers, and hydrophilicity enhancers, all the studied 18F-SSTA formed the anchor interaction. The trend in the results agreed with the experimental reports, identifying the main role of Asp122 in the binding of somatostatin-14 to SSTR-2.