bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil microbial communities, soil nutrition, and seedling growth of a Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) plantation in response to three weed control methods
Authors: Wang Song , Sun Honggang , Santos Edson , Soares Alvaro 
Published: February 2022

Abstract
Background and aims Competitive vegetation in forest stands influence seedling growth by changing soil nutrient availability. However, studies on the effects of different weed control methods on seedling growth of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) are rare. Methods We applied three weed control methods, comprising artificial sickle weeding (ASW), woody disc weeding (WDW), and nonwoven cloth weeding (nWCW), to explore their effect on growth of Chinese fir seedlings in a plantation in Jiangxi Province, China. Results The weed control methods affected the shoot height and root-collar diameter of the seedlings. The contents of sugar, glucose, triglycerides, total cholesterol, and free fatty acids in newly developed leaves were increased after ASW and nWCW treatment, and were consistent with the expression of genes associated with glucokinase, sucrose phosphate synthase, and sucrose synthase. Weeding method influenced soil properties, including pH, moisture, total nitrogen (N), ammonium-N, nitrate-N, total phosphorus, available phosphorus, and dissolved organic carbon contents. Moisture content was the main factor that influenced the soil bacterial community and leaf nutrition. High-throughput sequencing of the bacterial 16S rRNA gene revealed that the weeding methods affected bacterial community structure. Specifically, compared with ASW and nWCW, WDW contributed to lower soil bacterial diversity, simpler bacterial interaction, and increase in pathogenic bacteria potential. Conclusions The weeding methods differ in influence on soil bacterial community structure, soil properties, and plant growth, which are potentially useful as indices of biomass productivity to improve the growth of Chinese fir seedlings.
A Pan-cancer Analysis of Thioredoxin-interacting Protein as an Immunological and Prognostic Biomarker
Authors: Guo Xuxue , Huang Mei , Zhang Haonan , Chen Qianhui , Hu Ying , Meng Yan , Wu Changjie , Tu Chenge , Liu Yongfeng , Li Aimin , Li Qingyuan , Zhou Peirong , Liu Side 
Published: February 2022

Abstract
Background: The critical role of thioredoxin-interacting protein (TXNIP) in cellular sulfhydryl redox homeostasis and inflammasome activation is already widely known, however, no pan-cancer analysis is currently available. Methods: We thus first explored the potential roles of TXNIP across thirty-three tumors mainly based on The Cancer Genome Atlas and Gene Expression Omnibus datasets. Results: TXNIP is lowly expressed in most cancers, and distinct associations exist between TXNIP expression and the prognosis of tumor patients. TXNIP expression was associated with tumor mutational burden, microsatellite instability, mismatch repair genes, tumor infiltrating immune cell abundance as well as cancer-associated fibroblasts. Moreover, ubiquitin mediated proteolysis, protein post-translational modification and other related pathways were involved in the functional mechanisms of TXNIP. Conclusions: Our first pan-cancer study comprehensively revealed the carcinostatic role of TXNIP across different tumors. And this molecule may be considered as a potential immunological and prognostic biomarker.
Spectroscopic sensing of eight metal ions in aqueous solutions using silver nanoparticles
Authors: Tamilselvan Selvaraj , Soniya Rathnavelu Murali , Vasantharaja Raguraman , Kannan Malaichamy , Supriya Subrahmanian , Govindaraju Kasivelu 
Published: February 2022

Abstract
Anthropogenic releases from different outlets of industry, municipal sewage and the road traffic can give rise to higher concentrations of the heavy metals in the food commodities which imposes a threat to human health and environment. A simple silver nanoparticle (Ag NPs) used for the sensing of heavy metal ions, Cd2+, Cu2+, Fe2+, Hg2+, Mn2+, Ni2+, Pb2+ and Zn2+ in aqueous solution is described by qualitative and quantitatively using spectroscopic tool. FE-SEM and TEM images confirmed that the particles are spherical in shape with an average diameter of 23.4 nm. In presence of heavy metal ions with Ag NPs, a new peak at around 925, 898, 643, 665, 688, and 838 nm of Cd2+, Cu2+, Fe2+, Hg2+, Mn2+ and Zn2+ appeared in addition to the peak found at 410 nm of Ag NPs. Further, the addition of Ni2+ and Pb2+ metal ion solution with Ag NPs increased the SPR band from 410 nm to 436 and 462 nm respectively. Citrate functionalized Ag NPs are aggregated in solution in the presence of divalent metal ions by an ions-template chelating process and easily measurable change in the UV-vis absorption spectrum of the particles. Further, studies also confirmed the interaction of Ag NPs with metal ions using FT-IR spectroscopy. The proposed method was found to be useful for simple UV-vis spectroscopic sensing of metal ions in aqueous solutions and real contaminated samples.
Developing and Evaluating a High Resistant Starch Menu and Glycemic Response in Adults with Prediabetes: A Non-Randomized Pilot Study
Authors: Maiya Madhura , Cartagenova Alba D , Fitko Kendall Altizer , Roa Shannon , Law Christina , Patterson Mindy A 
Published: February 2022

Abstract
Background
The nondigestible fiber, resistant starch (RS), is found in beans, peas, and legumes, bread, cereals and grains, plantains, and potatoes. Here, we determined the feasibility of developing, preparing, and distributing a 7-day menu with a weekly average of ~30 g RS/d, as well as the likability of the foods.
Methods
First, a menu was formulated using a database, then prepared, stored, and delivered to mimic a future clinical trial. The RS content in each food item was quantified “as consumed” using an assay. Second, adults with prediabetes (n = 15) evaluated the likeability of the food items using a 9-point Likert scale. Likeability was acceptable if the overall score was ≥7 and >75% of the food items were consumed. Anthropometrics (n = 11), and fasting and postprandial (15, 30, 60, and 120 min) blood were collected to determine changes in weight, BMI, glucose, and insulin before and after the intervention.
Results
The feasibility of preparing, storing, and distributing the menu was verified and a weekly average of ~30 g RS/d at consumption was sustained. The menu provided ~2,000 kcal and 44.1 ± 9.5 g fiber per day. The feasibility of distributing the food items was acceptable where 100% compliance was achieved with the food preparation and participant pick-up schedules. Overall, 78.6% of the food items were consumed with an overall likeability score of 7.1 ± 1.9, meeting likeability targets. Frozen meals were the highest (94.1 ± 5.8%; 8.1 ± 1.4) and soups the lowest (61.4 ± 6.6%; 6 ± 2.4) amount consumed and mean likeability, respectively. Body weight and BMI changed -1.6 kg; 95% CI -2.6 to -0.7 and -0.5 kg/m2; 95% CI -2.8 to 8, respectively. The total area under the curve(0−120 min) for glucose and insulin changed by -655 and -1178 units, respectively, following high RS menu intake.
Conclusions
It is feasible to formulate, prepare, and distribute a high RS menu that is consumed and liked by adults with prediabetes. Due to small sample size, decreases in body weight, BMI, and glycemic indices should be interpreted with caution and tested using a randomized, cross-over intervention trial.
Trial registration:
Not applicable.
Concordance of the Risk of Neonatal Respiratory Morbidity Assessed by Quantitative Ultrasound Lung Texture Analysis in Fetuses of Twin Pregnancies
Authors: Moreno-Espinosa Ana L. , Hawkins-Villarreal Ameth , Burgos-Artizzu Xavier P. , Coronado-Gutierrez David , Castelazo Santiago , Lip-Sosa Diana L. , Fuenzalida Javiera , Gallo Dahiana M. , Peña-Ramirez Tatiana , Zuazagoitia Paula , Muñoz Miriam , Parra-Cordero Mauro , Gratacòs Eduard , Palacio Montse 
Published: February 2022

Abstract
Objective: To evaluate the concordance of the risk of neonatal respiratory morbidity (NRM) assessed by quantitative ultrasound lung texture analysis (QuantusFLM®) in fetuses of twin pregnancies.Methods: Prospective study conducted in twin pregnancies. Fetal ultrasound lung images were obtained at 26.0–38.6 weeks of gestation. Categorical (high or low) and continuous results of the risk of NRM were compared between twins.Results Fetal ultrasound lung images from 131 pairs of twins were included. The images were classified into three gestational age ranges: Group 1: 26.0 to 29.6 weeks (29.8%); Group 2: 30.0 to 33.6 weeks (37.4%) and Group 3: 34.0 to 38.6 weeks (32.8%). Concordance was good in Groups 1 and 3 and moderate in Group 2. In Groups 2 and 3 at least one fetus presented high-risk results in 26.5 % and 11.6% of twin pairs, respectively. Only gestational age <32 weeks, gestational diabetes mellitus and in vitro fertilization were associated with a high risk of NRM in Group 2.Conclusions There was good concordance of the risk of NRM between twins <30.0 weeks and >34.0 weeks. From 30.0 to 33.6 weeks 26.5% of the twin pairs had discordant results, with moderate concordance of the risk of NRM.
Sternomental Displacement and Neck Circumference. A New Look for the Neck as a Difficult Airway Predictor in Obese Surgical Patients. A Cohort Study
Authors: Gorgy Antony , Ahmed Abeer , Atef Mohamed , Mekawy Nevan El , Nagy Heba , Sami Wael 
Published: February 2022

Abstract
Background
Sternomental displacement (SMDD) is a surrogate indicator for cervical spine (C-spine) mobility. SMDD revealed good potentials to predict difficult airway, but its validity in obese patients is not evident. This study assessed the performance of SMDD with neck circumference (NC) in predicting difficult airway in obese surgical patients.
Methods
The study involved 135 adult patients with BMI ≥ 35 kg/m2, scheduled for elective surgeries under general anesthesia with endotracheal tubes (ETT) inserted using Macintosh laryngoscopes. The airway was assessed using SMDD, NC, and Modified Malampati test (MMT). Difficult laryngoscopy view (DLV) was defined as Cormack–Lehane (C-L) grade ≥ 3. The accuracy of the SMDD in predicting DLV was set as the primary endpoint, while the accuracy of the SMDD compared to that of NC, MMT, and NC/SMDD ratio in predicting difficult airway was set as the secondary endpoint.
Results
The DLV cases were 28 of 135 (20.7%), with a mean body mass index (BMI) of 41.1 ± 3.3 kg/m2. SMDD < 5cm and NC > 43 cm could predict DLV with an area under the receiver operating characteristic curve (AUROC) of 0.97 and 0.83 respectively. SMDD and NC revealed a good negative correlation (r = - 0.6; 95% CI= 0.7 to 0.4; p= 0.0001). The NC/SMDD ratio had the best predition for DLV (AUROC of 0.98 at a cut-off value > 7.8).
Conclusion
In obese surgical patients, the SMDD and NC/SMDD ratio are excellent predictors for DLV when the cut-off values are < 5cm and > 7.8, respectively.
Trial registration
: ClinicalTrials.gov identifier: ID: NCT04524546 Registered in August 2020.
Nuclear Morphometry and Chromatin Texture Changes in Hepatocellular Carcinoma Samples May Predict Liver Transplant Patients’ Outcomes
Authors: Santos Jordan Boeira dos , Starosta Rodrigo Tzovenos , Pilar Emily Ferreira Salles , Kunz Jefferson Daniel , Tomedi Joelson , Cerski Carlos Thadeu Schmidt , Ruppenthal Rúbia Denise 
Published: February 2022

Abstract
Background: Nuclear changes are typical in the carcinogenesis of hepatocellular carcinoma (HCC). Morphometry and chromatin texture analysis are quantitative methods for their quantification. In this study, we analyzed nuclear morphometry and chromatin texture parameters in samples of hepatocellular carcinoma from liver transplant patients and their associations with clinicopathologic variables. Methods: Samples of HCC and adjacent tissue from 34 individuals were collected in tissue microarray blocks. Stained slides were microphotographed using an optical microscope and nuclear parameters analyzed in ImageJ (FracLac plug-in). ROC curve analysis was used to find accurate cut-offs for differentiation of neoplastic and non-neoplastic cells. The inter-rater agreement was also evaluated. Results: Nuclear morphometric and textural differences were observed between the samples of HCC and adjacent tissue of liver transplant patients. Lower mean gray value (p=0.034) and Feret diameter (p=0.024) were associated with higher Model for End-Stage Liver Disease (MELD) scores. Nuclei with larger area (p=0.014) and Feret diameter (p=0.035) were associated with lower survival. Lower aspect ratio was associated with HCC recurrence after the transplant (p=0.048). The cut-off of 1.13μm (p=<0.001) for aspect ratio and cut-off of 21.15μm (p=0.038) for perimeter were established for the differentiation of neoplastic and non-neoplastic cells. The morphometric analysis was reproducible to area, circularity, Feret diameter, mean gray value and aspect ratio between observers (p=<0,001). Conclusions: Nuclear morphometric differences between the HCC and the adjacent tissue samples were associated with prognostic variables (MELD scores, recurrence and survival) and may predict liver transplant patients’ outcomes.
Ultrasound-Based Radiomics Analysis for Preoperative Prediction of Central and Lateral Cervical Lymph Node Metastasis in Papillary Thyroid Carcinoma: A Multi-Institutional Study
Authors: Tong Yuyang , Zhang Jingwen , Wei Yi , Yu Jinhua , Zhan Weiwei , Xia Hansheng , Zhou Shichong , Wang Yuanyuan , Chang Cai 
Published: February 2022

Abstract
Background

An accurate preoperative assessment of cervical lymph node metastasis (LNM) is important for choosing optimal therapeutic strategy for papillary thyroid carcinoma (PTC) patients. This study aimed to develop and validate two ultrasound (US) nomograms for the individual prediction of central and lateral compartment LNM in patients with PTC.
Methods

A total of 720 PTC patients from 3 institutions were enrolled in this study. They were categorized into a primary cohort, an internal validation, and two external validation cohorts. Radiomics features were extracted from conventional US images. LASSO regression was used to select optimized features to construct the radiomics signature. Two nomograms integrating independent clinical variables and radiomics signature were established with multivariate logistic regression. The performance of the nomograms was assessed with regard to discrimination, calibration, and clinical usefulness.
Results

The radiomics scores were significantly higher in patients with central/lateral LNM. A radiomics nomogram indicated good discrimination for central compartment LNM, with an area under the curve (AUC) of 0.875 in the training set, the corresponding value in the validation sets were 0.856, 0.870 and 0.870, respectively. Another nomogram for predicting lateral LNM also demonstrated good performance with a training AUC of 0.938, an internal validation AUC of 0.905, and two external validation AUC of 0.881 and 0.903, respectively. The clinical utility of the nomograms was confirmed by the decision curve analysis.
Conclusion

The nomograms proposed here have favorable performance for preoperatively predicting cervical LNM, and hold promise for optimizing the personalized treatment, which may improve the survival outcome in PTC patients.
Individualized Prognostic Score for Lung Adenocarcinoma Based on Immune Status
Authors: Chen Peng , Abdurazik Mihray , Huo Gengwei , Du Ye , Zuo Ran , Zhu Fuyi , Cui Jinfang , Yuan Dongqi 
Published: February 2022

Abstract
Background: Lung adenocarcinoma (LUAD) is the prevalent non-small cell lung cancer (NSCLC) histological subtype, with rising morbidity and mortality. This study was conducted with the motive to develop a prognostic model by examining the relation between immune-related gene (IRGs) profiles.Methods: We combined immune-related gene (IRG) expression profiles and progression-free intervals (PFIs) in 594 LUAD patients by using TCGA dataset. The COX regression analysis and computational difference technique were used to predict survival-associated and differentially expressed IRGs in LUAD patients. Computational biology was also used to investigate the characteristics and molecular mechanisms of these LUAD-specific IRGs. Using multivariable COX analysis, a novel prognostic index based on immune-related genes was established.Results: There was a strong correlation between the clinical outcome of LUAD patients and 58 differentially expressed immune-related genes. These genes were found to be actively involved in a KEGG pathway involving cytokines and cytokine receptors, as demonstrated by functional enrichment analysis. A prognostic signature comprised of IRGs (CRABP1, S100A16, FGF2, RBP2, FURIN, SLC11A1, ANGPTL4, VIPR1, BDNF, IL11, INHA, SEMA4B, TNFRSF11A) performed relatively well in prognostic prediction and was associated with tumour stage, tumour burden, age, number of lesions, and metastasis. Surprisingly, the IRG-based prognostic index effectively predicted immune cell infiltration.Conclusions: Our findings collectively identified multiple clinically relevant IRGs, identified regulators of the immunological repertoire, as well as established the critical role of a tailored, surveillance, IRG-based immune signature in the diagnosis, and prognosis of LUAD.
Severe Combined Immunodeficiency (SCID) Screening in Arizona: Lessons Learned from the First 2 Years
Authors: Booth Natalie A , Freeman Catherine M , Wright Benjamin L , Rukasin Christine , Badia Priscila , Daines Michael , Bauer Cindy S , Miller Holly 
Published: February 2022

Abstract
Purpose:The incidence of severe combined immunodeficiency (SCID) in the United States was reported as 1 in 58,000 live births. In Arizona, it was anticipated that newborn screening would identify two to four cases of SCID per year. This estimate did not consider ethnic nuances in Arizona, with higher percentages of American Indian and Hispanic populations compared to national percentages. The true incidence of SCID and non SCID T-cell lymphopenia have not previously been reported in Arizona. Methods:A retrospective chart review was performed of abnormal SCID Newborn Screening (NBS) tests from January 1, 2018 to December 31, 2019, using data from the Arizona Department of Health Service and the Phoenix Children’s Hospital’s electronic medical record [IRB# 20-025]. Results: Seven infants were diagnosed with SCID, yielding an incidence of 1 in 22,819 live births. Four of these infants had Artemis type SCID. Eighteen infants were identified with an abnormal initial NBS which ultimately did not lead to a diagnosis of SCID. Four of these infants were diagnosed with congenital syndromes associated with T-cell lymphopenia. Infants of Hispanic ethnicity were over-represented in this cohort. Conclusion: NBS in Arizona confirmed an incidence more than 2.5 times that reported nationally. This increased incidence is likely reflective of Arizona’s unique population profile, with a higher percentage of American Indian population. The findings in our non-SCID cohort are in alignment with previously published data, except for a higher than anticipated number of infants of Hispanic/Latino ethnicity, likely related to Arizona’s higher percentage of Hispanic/Latino population.
Therapeutic Effects of Tocotrienol-Rich Fraction on Rhinitis Symptoms in Platelet-Activating Factor Induced Allergic Rhinitis
Authors: Teo Cheryl Wei Ling , Png Stephanie Jia Ying , Ung Yee Wei , Yap Wei Ney 
Published: February 2022

Abstract
Background: Platelet-activating factor (PAF) has been suggested to be a potent inflammatory mediator in Allergic rhinitis (AR) pathogenesis. Vitamin E is known as a potential therapeutic agent for airway allergic inflammation. This study aimed to investigate the beneficial effects of palm-derived Tocotrienol-rich fraction (TRF) on PAF-induced AR in a rat model. Methods: Sprague Dawley rats were randomly assigned into 3 groups: Control, PAF-induced AR and PAF-induced AR with TRF treatment. To induce AR, 50 μl of 16 μg/ml PAF was nasally instilled into each nostril. From day 1 to 7 after AR induction, 10 μl of 16 μg/μl TRF was delivered intranasally to the TRF treatment group. Complete upper skulls were collected for histopathological evaluation on day 8.Results: The average severity scores of AR were significantly higher in the PAF-induced AR rats compared to both control and PAF-induced AR with TRF treatment. The histologic examination of the nasal structures showed moderate degree of inflammation and polymorphonuclear cells infiltration in the lamina propria, mucosa damage and vascular congestion in the PAF-induced AR rats. TRF was able to ameliorate the AR symptoms by restoring the nasal structures back to normal. H&E staining demonstrated a statistically significant benefit upon TRF treatment, where minimal degree of inflammation, and a reduction in the infiltration of polymorphonuclear cells, mucosa damage and vascular congestion were observed. Conclusion: TRF exhibited symptomatic relief action in AR potentially due to its antioxidant, anti-inflammatory and anti-allergic properties.
Identification of Prostate Cancer Subtypes Based on Immune Signature Scores in Bulk and Single Cell Transcriptomes
Authors: Chen Canping , Wang Xiaosheng 
Published: February 2022

Abstract
Prostate cancer (PC) is heterogeneous in the tumor immune microenvironment (TIME). Subtyping of PC based on the TIME could provide new insights into intratumor heterogeneity and its correlates of clinical features. Based on the enrichment scores of 28 immune cell types in the TIME, we performed unsupervised clustering to identify immune-specific subtypes of PC. The clustering analysis was performed in ten different bulk tumor transcriptomic datasets and in a single cell RNA-Seq (scRNA-seq) dataset, respectively. We identified two PC subtypes: PC immunity high (PC-ImH) and PC immunity low (PC-ImL), consistently in these datasets. Compared to PC-ImL, PC-ImH displayed stronger immune signatures, worse clinical outcomes, higher epithelial-mesenchymal transition (EMT) signature, tumor stemness, intratumor heterogeneity (ITH) and genomic instability, and lower incidence of TMPRSS2-ERG fusion. Tumor mutation burden (TMB) showed no significant difference between PC-ImH and PC-ImL, while copy number alteration (CNA) was more significant in PC-ImL than in PC-ImH. PC-ImH could be further divided into two subgroups, which had significantly different immune infiltration levels and clinical features. In conclusion, “hot” PCs have stronger anti-tumor immune response while worse clinical outcomes versus “cold” PCs. CNA instead of TMB plays a crucial role in the regulation of TIME in PC. TMPRSS2-ERG fusion correlates with decreased anti-tumor immune response while better disease-free survival in PC. The identification of immune-specific subtypes has potential clinical implications for PC immunotherapy.