bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deprivation and exposure to public activities during the COVID-19 pandemic in England and Wales
Authors: Beale Sarah , Braithwaite Isobel , Navaratnam Annalan MD , Hardelid Pia , Rodger Alison , Aryee Anna , Byrne Thomas E , Fong Erica Wing Lam , Fragaszy Ellen , Geismar Cyril , Kovar Jana , Nguyen Vincent , Patel Parth , Shrotri Madhumita , Aldridge Robert , Hayward Andrew 
Published: October 2021

BackgroundDifferential exposure to public activities may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes but has not been directly investigated. We set out to investigate whether participants in Virus Watch—a large community cohort study based in England and Wales—reported differential exposure to public activities and non-household contacts during the autumn–winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.MethodsParticipants (n=20 120–25 228 across surveys) reported their daily activities during 3 weekly periods in late November 2020, late December 2020 and mid-February 2021. Deprivation was quantified based on participants’ residential postcode using English or Welsh Index of Multiple Deprivation quintiles. We used Poisson mixed-effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.ResultsRelative to participants in the least deprived areas, participants in the most deprived areas exhibited elevated risk of exposure to vehicle sharing (adjusted risk ratio (aRR) range across time points: 1.73–8.52), public transport (aRR: 3.13–5.73), work or education outside of the household (aRR: 1.09–1.21), essential shops (aRR: 1.09–1.13) and non-household contacts (aRR: 1.15–1.19) across multiple survey periods.ConclusionDifferential exposure to essential public activities—such as attending workplaces and visiting essential shops—is likely to contribute to inequalities in infection risk and outcomes. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.
Revisiting the cosmic distance duality relation with machine learning reconstruction methods: the combination of HII galaxies and ultra-compact radio quasars
Authors: Liu Tonghua , Cao Shuo , Zhang Sixuan , Gong Xiaolong , Guo Wuzheng , Zheng Chenfa 
Published: October 2021

AbstractIn this paper, we carry out an assessment of cosmic distance duality relation (CDDR) based on the latest observations of HII galaxies acting as standard candles and ultra-compact structure in radio quasars acting as standard rulers. Particularly, two machine learning reconstruction methods [Gaussian Process (GP) and Artificial Neural Network (ANN)] are applied to reconstruct the Hubble diagrams from observational data. We show that both approaches are capable of reconstructing the current constraints on possible deviations from the CDDR in the redshift range $$z\sim 2.3$$

z
∼
2.3

. Considering four different parametric methods of CDDR, which quantify deviations from the CDDR and the standard cosmological model, we compare the results of the two different machine learning approaches. It is observed that the validity of CDDR is in well agreement with the current observational data within $$1\sigma $$

1
σ

based on the reconstructed distances through GP in the overlapping redshift domain. Moreover, we find that ultra-compact radio quasars could provide $$10^{-3}$$

10

-
3

-level constraints on the violation parameter at high redshifts, when combined with the observations of HII galaxies. In the framework of ANN, one could derive robust constraints on the violation parameter at a precision of $$10^{-2}$$

10

-
2

, with the validity of such distance duality relation within $$2\sigma $$

2
σ

confidence level.
Value of Thyroid Imaging Reporting and Data System in Initial Bethesda Category III Thyroid Nodules
Authors: Yan Caoxin , Luo Zhiyan , Lin Zimei , Xu Shouxing , Luo Yunkai , Chen Jian 
Published: October 2021

Background. To evaluate the role of Thyroid Imaging Reporting and Data System (TI-RADS) in predicting malignancy for cytological Bethesda system III nodules. Method. The study included 188 thyroid nodules with first Bethesda system III cytology on surgery or repeat FNA. Patients' clinicopathologic parameters and ultrasonographic (US) nodule characteristics were evaluated according to benignity and malignancy. Using the TI-RADS classification system, thyroid nodules were categorized. Results. The size of malignant nodules was significantly lower than that of benign nodules (

P

< 0.001). Thyroid nodules associated with concomitant thyroid carcinoma had a significantly increased risk of malignancy (

P

< 0.001). Univariate analysis indicated that there were significant differences in the images of benign and malignant nodules in terms of solid composition, hypoechogenicity or marked hypoechogenicity, a taller-than-wide or irregular shape, ill-defined margins, and microcalcifications presence (

P

< 0.05). TI-RADS categories 4c (OR = 8.3, 95% CI 3.8–18.1;

P

= 0.043) and 5 (OR = 9.4; 95% CI 1.2–74.2;

P

= 0.026) were predictive for malignancy. Conclusions. The TI-RADS US evaluation may assist the physician in deciding whether to proceed with follow-up, repeating FNA, or surgical intervention.
Long‐Term Health Utilization and Outcomes in Chronic Suppurative Otitis Media
Authors: Thai Anthony , Aaron Ksenia A. , Kaufman Adam C. , Santa Maria Peter L. 
Published: October 2021

ObjectiveTo report health utilization patterns and outcomes of medical and surgical management in patients with chronic suppurative otitis media (CSOM).Study DesignRetrospective cohort.SettingAcademic otology clinic.MethodsThis study included 175 patients with CSOM with a first clinic visit at our institution between March 2011 and November 2016. All patients displayed a diagnosis of CSOM by International Classification of Diseases code, had at least 1 episode of active CSOM (defined as perforation with otorrhea), and had a documented history of chronic ear infections. The mean age was 49.5 ± 1.5 years, 53% were female, and mean follow‐up time was 3.5 ± 0.3 years.ResultsPatients had an average of 9.5 ± 0.5 otology visits, 4.7 ± 0.4 prescriptions, and 1.7 ± 0.1 surgeries, with estimated per patient cost ranging from $3927 to $20,776. Under medical management, 69% of patients displayed recurrence of disease, with a median time to recurrence of 4 months. For tympanoplasty and tympanomastoidectomy, median time to recurrence was similar at 5 and 7 years, respectively (P =. 73). At the most recent visit, the prevalence of all patients with CSOM displaying moderate or worse sensorineural hearing loss (SNHL) was 41%.ConclusionsCSOM represents a major public health issue with high health care utilization and associated costs. Surgery is superior to medical therapy for achieving short‐ to medium‐term inactive disease. Patients with CSOM display a high SNHL burden.
Electrocardiogram abnormalities in residents in cold homes: a cross-sectional analysis of the nationwide Smart Wellness Housing survey in Japan
Authors: Umishio Wataru , Ikaga Toshiharu , Kario Kazuomi , Fujino Yoshihisa , Suzuki Masaru , Ando Shintaro , Hoshi Tanji , Yoshimura Takesumi , Yoshino Hiroshi , Murakami Shuzo ,   on behalf of the SWH Survey Group
Published: October 2021

Abstract
Background
Excess winter mortality caused by cardiovascular disease is particularly profound in cold houses. Consistent with this, accumulating evidence indicates that low indoor temperatures at home increase blood pressure. However, it remains unclear whether low indoor temperatures affect other cardiovascular biomarkers. In its latest list of priority medical devices for management of cardiovascular diseases, the World Health Organization (WHO) included electrocardiography systems as capital medical devices. We therefore examined the association between indoor temperature and electrocardiogram findings.

Methods
We collected electrocardiogram data from 1480 participants during health checkups. We also measured the indoor temperature in the living room and bedroom for 2 weeks in winter, and divided participants into those living in warm houses (average exposure temperature ≥ 18 °C), slightly cold houses (12–18 °C), and cold houses (< 12 °C) in accordance with guidelines issued by the WHO and United Kingdom. The association between indoor temperature (warm vs. slightly cold vs. cold houses) and electrocardiogram findings was analyzed using multivariate logistic regression models, with adjustment for confounders such as demographics (e.g., age, sex, body mass index, household income), lifestyle (e.g., eating habit, exercise, smoking, alcohol drinking), and region.

Results
The average temperature at home was 14.7 °C, and 238, 924, and 318 participants lived in warm, slightly cold, and cold houses, respectively. Electrocardiogram abnormalities were observed in 17.6%, 25.4%, and 30.2% of participants living in warm, slightly cold, and cold houses, respectively (p = 0.003, chi-squared test). Compared to participants living in warm houses, the odds ratio of having electrocardiogram abnormalities was 1.79 (95% confidence interval: 1.14–2.81, p = 0.011) for those living in slightly cold houses and 2.18 (95% confidence interval: 1.27–3.75, p = 0.005) for those living in cold houses.

Conclusions
In addition to blood pressure, living in cold houses may have adverse effects on electrocardiogram. Conversely, keeping the indoor thermal environment within an appropriate range through a combination of living in highly thermal insulated houses and appropriate use of heating devices may contribute to good cardiovascular health.

Trial registration
The trial was retrospectively registered on 27 Dec 2017 to the University hospital Medical Information Network Clinical Trials Registry (UMIN-CTR, https://www.umin.ac.jp/ctr/, registration identifier number UMIN000030601).
CirPred, the first structure modeling and linker design system for circularly permuted proteins
Authors: Chen Teng-Ruei , Lin Yen-Cheng , Huang Yu-Wei , Chen Chih-Chieh , Lo Wei-Cheng 
Published: October 2021

Abstract
Background
This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors.

Results
Here we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy.

Conclusions
The CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at http://10.life.nctu.edu.tw/CirPred/ and http://lo.life.nctu.edu.tw/CirPred/.
Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis
Authors: Pu Yiyi , Li Chao , Yuan Haining , Wang Xiaoju 
Published: October 2021

Abstract
Background
Detecting prostate cancer at a non-aggressive stage is the main goal of prostate cancer screening. DNA methylation has been widely used as biomarkers for cancer diagnosis and prognosis, however, with low clinical translation rate. By taking advantage of multi-cancer data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), we aimed to identify prostate cancer specific biomarkers which can separate between non-aggressive and aggressive prostate cancer based on DNA methylation patterns.

Results
We performed a comparison analysis of DNA methylation status between normal prostate tissues and prostate adenocarcinoma (PRAD) samples at different Gleason stages. The candidate biomarkers were selected by excluding the biomarkers existing in multiple cancers (pan-cancer) and requiring significant difference between PRAD and other urinary samples. By least absolute shrinkage and selection operator (LASSO) selection, 8 biomarkers (cg04633600, cg05219445, cg05796128, cg10834205, cg16736826, cg23523811, cg23881697, cg24755931) were identified and in-silico validated by model constructions. First, all 8 biomarkers could separate PRAD at different stages (Gleason 6 vs. Gleason 3 + 4: AUC = 0.63; Gleason 6 vs. Gleason 4 + 3 and 8–10: AUC = 0.87). Second, 5 biomarkers (cg04633600, cg05796128, cg23523811, cg23881697, cg24755931) effectively detected PRAD from normal prostate tissues (AUC ranged from 0.88 to 0.92). Last, 6 biomarkers (cg04633600, cg05219445, cg05796128, cg23523811, cg23881697, cg24755931) completely distinguished PRAD with other urinary samples (AUC = 1).

Conclusions
Our study identified and in-silico validated a panel of prostate cancer specific DNA methylation biomarkers with diagnosis value.
Immunogenicity of a new enhanced tetanus-reduced dose diphtheria-acellular pertussis (Tdap) vaccine against Bordetella pertussis in a murine model
Authors: Kang Kyu Ri , Huh Dong Ho , Kim Ji Ahn , Kang Jin Han 
Published: October 2021

Abstract
Background
The necessity of the tetanus-reduced dose diphtheria-acellular pertussis (Tdap) vaccine in adolescence and adults has been emphasized since the resurgence of small-scale pertussis in Korea and worldwide due to the waning effect of the vaccine and variant pathogenic stains in the late 1990s. GreenCross Pharma (GC Pharma), a Korean company, developed the Tdap vaccine GC3111 in 2010. Recently, they enhanced the vaccine, GC3111, produced previously in 2010 to reinforce the antibody response against filamentous hemagglutinin (FHA). In this study, immunogenicity and efficacy of the enhanced Tdap vaccine compared and evaluated with two Tdap vaccines, GC3111 vaccine produced in 2010 previously and commercially available Tdap vaccine in a murine model.

Methods
Two tests groups and positive control group of Balb/c mice were primed with two doses of the diphtheria-tetanus-acellular pertussis (DTaP) vaccine followed by a single booster Tdap vaccine at 9 week using the commercially available Tdap vaccine or 2 Tdap vaccines from GC Pharma (GC3111, enhanced GC3111). Humoral response was assessed 1 week before and 2 and 4 weeks after Tdap booster vaccination. The enhanced GC3111 generated similar humoral response compare to the commercial vaccine for filamentous hemagglutinin (FHA). The interferon gamma (IFN-γ) (Th1), interleukin 5 (IL-5) (Th2) and interleukin 17 (IL-17) (Th17) cytokines were assessed 4 weeks after booster vaccination by stimulation with three simulators: heat inactivated Bordetella pertussis (hBp), vaccine antigens, and hBp mixed with antigens (hBp + antigen). A bacterial challenge test was performed 4 weeks after booster vaccination.

Results
Regarding cell-mediated immunity, cytokine secretion differed among the three simulators. However, no difference was found between two test groups and positive control group. All the vaccinated groups indicated a Th1 or Th1/Th2 response. On Day 5 post-bacterial challenge, B. pertussis colonies were absent in the lungs in two test groups and positive control group.

Conclusions
Our results confirmed the immunogenicity of GC Pharma’s Tdap vaccine; enhanced GC3111 was equivalent to the presently used commercial vaccine in terms of humoral response as well as cell-mediated cytokine expression.
Developing an efficient DNA barcoding system to differentiate between Lilium species
Authors: Liu Yixin , Zhang Mingfang , Chen Xuqing , Chen Xi , Hu Yue , Gao Junlian , Pan Wenqiang , Xin Yin , Wu Jian , Du Yunpeng , Zhang Xiuhai 
Published: October 2021

Abstract
Background
Lilium is an important ornamental bulb, possesses medicinal properties, and is also edible. Species within the Lilium genus share very similar morphology and macroscopic characteristics, thus they cannot be easily and clearly distinguished from one another. To date, no efficient species-specific markers have been developed for classifying wild lily species, which poses an issue with further characterizing its medicinal properties.

Results
To develop a simple and reliable identification system for Lilium, 45 representative species from 6 sections were used to develop a DNA barcoding system, which was based on DNA sequence polymorphisms. In this study, we assessed five commonly used DNA barcode candidates (ITS, rbcL, ycf1b, matK and psbA-trnH) and five novel barcode candidates obtained from highly variable chloroplast genomic regions (trnL-trnF, trnS-trnG, trnF-ndhJ, trnP-psaJ-rpI33 and psbB-psbH). We showed that a set of three novel DNA barcodes (ITS + trnP-psaJ-rpI33 + psbB-psbH) could be efficiently used as a genetic marker to distinguish between lily species, as assessed by methods including DNAsp, BI and ML tree, and Pair Wise Group (PWG).

Conclusions
A rapid and reliable DNA barcoding method was developed for all 45 wild Lilium species by using ITS, trnP-psaJ-rpI33, and psbB-psbH as DNA barcoding markers. The method can be used in the classification of wild Lilium species, especially endangered species, and also provides an effective method for selective lily breeding.
Effects of repeated drought stress on the physiological characteristics and lipid metabolism of Bombax ceiba L. during subsequent drought and heat stresses
Authors: Zheng Yanling , Xia Zhining , Wu Jianrong , Ma Huancheng 
Published: October 2021

Abstract
Background
Trees of Bombax ceiba L. could produce a large number of viable seeds in the dry-hot valleys. However, the seedling regeneration of the species is difficult in these areas as mild drought often occur repeatedly which might be followed by heat stress. However, how the repeated drought affects the subsequent drought and heat tolerance of B. ceiba is not clear. In this study, chlorophyll fluorescence, soluble sugar content and lipid metabolism were measured for the drought-treated seedlings and heat-treated seedlings with or without drought hardening.

Results
Neither the first nor third dehydration treatments affected the photosynthetic activity and soluble sugar content of B. ceiba seedlings. However, they differentially affected the fluidity of the local membranes and the levels of diacylglycerol and phosphatidic acid. Heat shock severely decreased the photosynthetic efficiency but drought priming reduced the effects of heat shock. Moreover, heat shock with or without drought priming had differential effects on the metabolism of soluble sugars and some lipids. In addition, the unsaturation level of membrane glycerolipids increased following heat shock for non-drought-hardened seedlings which, however, maintained for drought-hardened seedlings.

Conclusions
The results suggest that two cycles of dehydration/recovery can affect the metabolism of some lipids during the third drought stress and may enhance the heat tolerance of B. ceiba by adjusting lipid composition and membrane fluidity.
Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency
Authors: Chen Zhijian , Song Jianling , Li Xinyong , Arango Jacobo , Cardoso Juan Andres , Rao Idupulapati , Schultze-Kraft Rainer , Peters Michael , Mo Xiaohui , Liu Guodao 
Published: October 2021

Abstract
Background
Phosphorus (P) is an essential macronutrient for plant growth that participates in a series of biological processes. Thus, P deficiency limits crop growth and yield. Although Stylosanthes guianensis (stylo) is an important tropical legume that displays adaptation to low phosphate (Pi) availability, its adaptive mechanisms remain largely unknown.

Results
In this study, differences in low-P stress tolerance were investigated using two stylo cultivars (‘RY2’ and ‘RY5’) that were grown in hydroponics. Results showed that cultivar RY2 was better adapted to Pi starvation than RY5, as reflected by lower values of relative decrease rates of growth parameters than RY5 at low-P stress, especially for the reduction of shoot and root dry weight. Furthermore, RY2 exhibited higher P acquisition efficiency than RY5 under the same P treatment, although P utilization efficiency was similar between the two cultivars. In addition, better root growth performance and higher leaf and root APase activities were observed with RY2 compared to RY5. Subsequent RNA-seq analysis revealed 8,348 genes that were differentially expressed under P deficient and sufficient conditions in RY2 roots, with many Pi starvation regulated genes associated with P metabolic process, protein modification process, transport and other metabolic processes. A group of differentially expressed genes (DEGs) involved in Pi uptake and Pi homeostasis were identified, such as genes encoding Pi transporter (PT), purple acid phosphatase (PAP), and multidrug and toxin extrusion (MATE). Furthermore, a variety of genes related to transcription factors and regulators involved in Pi signaling, including genes belonging to the PHOSPHATE STARVATION RESPONSE 1-like (PHR1), WRKY and the SYG1/PHO81/XPR1 (SPX) domain, were also regulated by P deficiency in stylo roots.

Conclusions
This study reveals the possible mechanisms underlying the adaptation of stylo to P deficiency. The low-P tolerance in stylo is probably manifested through regulation of root growth, Pi acquisition and cellular Pi homeostasis as well as Pi signaling pathway. The identified genes involved in low-P tolerance can be potentially used to design the breeding strategy for developing P-efficient stylo cultivars to grow on acid soils in the tropics.