bluuebunny/crossref_metadata_2025_split huggingface dataset:
No evidence for a pathogen associated with pulmonary MALT lymphoma: a metagenomics investigation
Authors: Borie Raphael , Cao Valerie , Nunes Hilario , Kambouchner Marianne , Cazes Aurelie , Antoine Martine , Crestani Bruno , Leroy Karen , Copie-Bergman Christiane , Kwasiborski Aurelia , Hennequin Christophe , Vandenbogaert Mathias , Hourdel Veronique , Cadranel Jacques 
Published: February 2021

Abstract
Mucosa-associated lymphoid tissue (MALT) lymphoma is generally associated with chronic antigen stimulation: auto-antigens or of microbial origin. Only one study suggested association between Achromobacter xylosoxidans and pulmonary MALT lymphoma. We aimed to investigate the presence of virus or any infectious agents in pulmonary MALT lymphoma by using metagenomic next-generation sequencing (mNGS).All lung samples were centrally reviewed. The t(11;18) (q21;q21) was evaluated by FISH analysis. The snap frozen large lung biopsies were analyzed by mNGS. After lung biopsies homogenization total nucleic acids (RNA and DNA) were extracted, amplified and classified according to their taxonomic assignment, after exclusion of host DNA.We included 13 samples from pulmonary MALT lymphoma (mean age: 60.3 years, 7 women, 3 with auto-immune background) and 10 controls. The diagnosis of MALT lymphoma was confirmed for the 13 samples, 3 showed API2-MALT1 translocation (23%). No evidence of the presence of a specific pathogen was clearly identified in the group of patients with pulmonary MALT lymphoma. We identified A. xylosoxidans sequence in 4/13 patients and in 4/10 controls.This study did not find evidence for a DNA or RNA virus, a fungi, a parasite or a bacteria associated with pulmonary MALT lymphoma either in the stroma or in tumor cells.
III-Nitride nanophotonics for beyond-octave soliton generation and self-referencing
Authors: Liu Xianwen , Gong Zheng , Bruch Alexander , Surya Joshua , Lu Juanjuan , Tang Hong 
Published: February 2021

Abstract
Frequency microcombs, successors to mode-locked laser and fiber combs, enable miniature rulersof light for applications including precision metrology, molecular fingerprinting and exoplanet discoveries. To enable frequency ruling functions, microcombs must be stabilized by locking their carrier-envelop offset frequency. So far, the microcomb stabilization remains compounded by the elaborate optics external to the chip, thus evading its scaling benefit. To address this challenge, here we demonstrate a nanophotonic chip solution based on aluminum nitride thin films, which simultaneously offer optical Kerr nonlinearity for generating octave soliton combs and Pockels nonlinearity for enabling heterodyne detection of the offset frequency. The agile dispersion control of crystalline III-Nitride photonics permits high-fidelity generation of solitons with features including 1.5-octave spectral span, dual dispersive waves and sub-terahertz repetition rates down to 220 gigahertz. These attractive characteristics, aided by on-chip phase-matched aluminum nitride waveguides, allow the full determination of the offset frequency. Our proof-of-principle demonstration represents an important milestone towards fully-integrated self-locked microcombs for portable optical atomic clocks and frequency synthesizers
Reliability of the Freehand Region-of-Interest Method in Quantitative Cerebral Diffusion Tensor Imaging
Authors: Hakulinen Ullamari , Brander Antti , Ilvesmäki Tero , Helminen Mika , Öhman Juha , Luoto Teemu , Eskola Hannu 
Published: February 2021

Abstract
Background: Diffusion tensor imaging (DTI) is a magnetic resonance imaging (MRI) technique used for evaluating changes in the white matter in brain parenchyma. The reliability of quantitative DTI analysis is influenced by several factors, such as the imaging protocol, pre-processing and post-processing methods, and selected diffusion parameters. Of the post-processing methods, the region-of-interest (ROI) method is most widely used because it is found in commercial programs. The focus of our research was to study the reliability of the freehand ROI method using various intra- and inter-observer analyses.Methods: This study included 40 neurologically healthy participants who underwent diffusion MRI of the brain with a 3T scanner. The measurements were performed at nine different anatomical locations using a freehand ROI method. The data extracted from the ROIs included the regional mean values, intra- and inter-observer variability and reliability. The used DTI parameters were fractional anisotropy (FA), the apparent diffusion coefficient (ADC), and axial (AD) and radial (RD) diffusivity.Results: The average ICC of the intra-observer was found to be 0.9 (excellent). The single ICC results were excellent (> 0.8) or adequate (> 0.69) in eight out of the nine regions in terms of FA and ADC. The most reliable results were found in the frontobasal regions. In terms of the regional mean values, significant differences between age groups were found in the frontobasal regions. Specifically, the FA and AD values were significantly higher and the RD values lower in the youngest age group (18-30 years) compared to the other age groups.Conclusions: The quantitative freehand ROI method can be considered highly reliable for the average ICC and mostly adequate for the single ICC. The freehand method is suitable for research work with a well-experienced observer. Measurements should be performed at least twice in the same region to ensure that the results are sufficiently reliable. In our study, reliability was undermined by artifacts in some regions such as the cerebral peduncle, corona radiata and centrum semiovale. From a clinical point of view, the results are most reliable in adults under the age of 30, when age-related changes in brain white matter have not yet occurred.
Knowledge on intrapartum care practices among skilled birth attendants in Cambodia – a cross-sectional study.
Authors: Matsui Mitsuaki , Saito Yuko , Po Rithy , Taing Bunsreng , Nhek Chamnan , Tung Rathavy , Masaki Yoko , Iwamoto Azusa 
Published: February 2021

Abstract
Background Delivery is a critical moment for pregnant women and babies, and careful monitoring is essential throughout the delivery process. The partograph is a useful tool for monitoring and assessing labour progress as well as maternal and foetal conditions; however, it is often used inaccurately or inappropriately. A gap between practices and evidence-based guidelines has been reported in Cambodia, perhaps due to a lack of evidence-based knowledge in maternity care. This study aims to address: i) to what extent skilled birth attendants in the first-line health services in Cambodia have knowledge on the management of normal delivery, and ii) what factors are associated with their level of knowledge. Methods Midwives and nurses were recruited working in maternity in first-line public health facilities in Phnom Penh municipality, Kampong Cham and Svay Rieng provinces. Two self-administered questionnaires were applied. The first consisted of three sections with questions on monitoring aspects of the partograph: progress of labour, foetal, and maternal conditions. The second consisted of questions on diagnostic criteria, normal ranges, and standard intervals of monitoring during labour. A multiple linear regression analysis was performed to identify relationships between characteristics of the participants and the questionnaire scores. Results Of 542 eligible midwives and nurses, 523 (96%) participated. The overall mean score was 58%. Only 3% got scores of more than 90%. Multivariate analysis revealed that ‘Kampong Cham province’, ‘younger age’, and ‘higher qualification’ were significantly associated with higher scores. Previous training experience was not associated with the score. Substantial proportions of misclassification of monitoring items during labour were found; for example, 61% answered uterine contraction as a foetal condition, and 44% answered foetal head descent and 26% answered foetal heart rate as a maternal condition. ﻿Conclusion This study found that knowledge was low on delivery management among skilled birth attendants. Previous training experience did not influence the knowledge level. A lack of understanding of physiology and anatomy was implied. Further experimental approaches should be attempted to improve the knowledge and quality of maternity services in Cambodia.
Potent Inhibition of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by photosensitizers
Authors: Yu Shujuan , Sun Gaohui , Sui Yaqun , Li Hanlin , Zhang Ning , Bi Yuhai , Gao George , Jiang Longguang , Xu Peng , Yuan Cai , Yang Yang , Huang Mingdong 
Published: February 2021

Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has exploded since December 2019, and causes more than 2 million death with more than 95 million people infected as of Jan. 21th, 2021 globally1,2. Angiotensin-converting enzyme 2 (ACE2), expressed in the lungs, arteries, heart, kidney, intestines, and nasal epithelium3, has been shown to be the primary entry point targeted by the surface spike protein of SARS-CoV-2. Currently, no proven antiviral treatment for SARS-CoV-2 infection is available. In this study, we screened a number of photosensitizers for photodynamic viral inactivation, and found compounds pentalysine β-carbonylphthalocyanine zinc (ZnPc5K) and chlorin e6 (ce6) potently inhibited the viral infection and replication in vitro with half-maximal effective concentrations (EC50) values at nanomolar level. Such viral inactivation strategy is implementable, and has unique advantages, including resistance to virus mutations, affordability compared to the monoclonal antibodies, and lack of long-term toxicity.
The Consumption of Sugar-Sweetened Beverages in Jamaica and Its Association With Household Expenditure Allocation
Authors: Paraje Guillermo , Gomes Fabio S 
Published: February 2021

Abstract
Background. Overweight and obesity are important drivers for the increasing healthcare and other social costs. Apart from present social costs, consumption of SSB may have an effect on future outcomes, from family future wellbeing to national economic growth. If expenditures on SSB decrease expenditures on other goods and services, such as education and healthcare, this “crowding-out” may have a lasting effect. The objective of this article is to estimate the statistical association between the decision of spending in SSB and budget allocation in JamaicaMethods. Using the Jamaican Household Expenditure Survey 2004-2005 a generalized ordered probit model was estimated to examine the association between socioeconomic variables and the decision to purchase SSB. Seemingly Unrelated Regression Equations (SURE) of all the expenditure groups (except the SSB group) were used to estimate the association between the decision of buying SSB and budget allocation on other goods and services.Results. Purchases of SSB are negatively affected by the size of the household and the area of residence (rural households purchase more SSB than urban ones), while having a larger proportion of children (15 or younger) and having a larger total budget is associated to more expenditures on SSB. Households with positive expenditure on SSB allocate significantly less budget to “Health” and “Education”, when compared to those who did not buy SSB. Conclusions. SSB purchases may crowd-out expenditures in essential goods and services, which implies that decreasing the amount spent on SSB may have important present and future consequences on poorer households’ welfare.
Sleep Duration, Vegetable Consumption and All-Cause Mortality Among Older Adults in China: A 6-Year Prospective Study
Authors: Bai Chen , Guo Muqi , Yao Yao , Ji John S. , Gu Danan , Zeng Yi 
Published: February 2021

Abstract
BackgroundSleep duration and vegetable consumption are associated with mortality at old age (termed as sleep-mortality linkage and vegetable-mortality linkage, respectively). Yet, little is known about the interplay of sleep duration and vegetable consumption on mortality. MethodsA dataset of nationwide longitudinal survey with 13,441 participants aged 65 years or older recruited in 2008 and followed up till 2014 was used. Sleep duration was classified into five groups (≤5, 6, 7-8, 9, and ≥10 hours/day). Vegetable consumption was classified as either high frequency (eating vegetables almost daily) or low frequency. We used parametric Weibull hazard regression models to estimate associations of sleep duration and frequency of vegetable consumption with mortality, adjusting for demographics, socioeconomic factors, family/social support, health practice, and health conditions. ResultsOver the six-year study period, when only demographics were present, participants sleeping ≤5, 6, 9, and ≥10 hours/day had hazard ratios (HR) of mortality 1.18 (p<0.001), 1.14(p<0.01), 1.06 (p>0.1), and 1.30 (p<0.001), respectively, compared to those sleeping 7-8 hours/day. The HRs were attenuated to 1.08 (p<0.05), 1.08 (p<0.05), 1.09 (p<0.1), 1.18(p<0.001), respectively, when all other covariates were additionally adjusted for. High frequency of eating vegetables was associated with 22% lower risk of mortality (HR=0.78, p<0.001) compared to low frequency in the demographic model, and with 9% lower risk (HR=0.91, p<0.05) in the full model. Subpopulation and interaction analyses show that the sleeping-mortality linkage was stronger in female, urban, oldest-old (aged ≥80), and illiterate participants compared to their respective male, rural, young-old, and literate counterparts. High frequency of vegetable intakes could offset the higher mortality risk in participants with short-sleeping duration, but low frequency of eating vegetables could exacerbate mortality risk for participants with either short or long sleep duration; and except for few cases, these findings held in subpopulations. Conclusions Too short and too long sleep durations were associated with higher mortality risk, and infrequent vegetable consumption could exacerbate the risk, although frequent vegetable intake could offset the risk for short sleep duration. The relationship between these two lifestyles and mortality was complex and varied among subpopulations.
Identification of the Most Suitable Reference Gene for Gene Expression Studies With Development and Abiotic Stress Response in Bromus Sterilis
Authors: Sen Madhab Kumar , Hamouzova Katerina , Kosnarova Pavlina , Roy Amit , Soukup Josef 
Published: February 2021

Abstract
Bromus sterilis is an annual weedy grass, causing high yield losses in winter cereals. Frequent use of herbicides had led to the evolution of herbicide-resistance in this species. Mechanisms underlying herbicide resistance in B. sterilis must be uncovered because this problem is becoming a global threat. qRT-PCR and the next-generation sequencing technologies can contribute to elucidation of the resistance mechanisms. Although qRT-PCR can calculate precise fold changes, its preciseness depends on the expression of reference genes. Regardless of stable expression in any given condition, no gene can act as a universal reference gene. Hence, it is necessary to identify the suitable reference gene for each species. To our knowledge, there are no reports on the suitable reference gene in any brome species so far. Thus, in this paper, the stability of eight genes were evaluated using qRT-PCR experiments followed by expression stability ranking via five most commonly used softwares for reference gene selection. Our findings suggest using a combination of 18S rRNA and ACCase to normalise the qRT-PCR data in B. sterilis. Besides, reference genes are also recommended for different experimental conditions. The present study outcomes will facilitate future molecular work in B. sterilis and other related grass species.
Multifunctional Rural Transition Along China’s Yangtze River Transect: Spatial differentiation and Economic Relevance
Authors: Jiang Tianhe , Shi Guoqing , Zhang Yingnan 
Published: February 2021

Abstract
To understand rural sustainability, it is necessary to scrutinize the relationship between rural transition and economic growth. The article uses rural multifunctionality as an analytical lens through which to view the processes of the development of rural occupancy. There is a pressing need to ascertain how to quantify rural multifunctionality and reveal its spatial differentiation, as well as garner and investigate how multifunctional rural transition (MRT) responds to economic growth. This paper employed the concept of Transect to compensate for data deficiencies in a long temporal series and established the indicator system from three different aspects- “living function, production function, and ecological function”, to measure MRT along China’s Yangtze River Transect. Our analysis showed that living function and production function display an increasing trend from underdeveloped western regions to eastern economically prosperous regions, and represent a high degree surrounding urban agglomerations, while economic growth only leads to a statistically insignificant decreasing trend in ecological function. The MRT resulting from multiple factors is much diverse, complex, sophisticated, therefore, it should be understood within a framework incorporating both endogenous and exogenous factors. According to the results, it is thus important to formulate differentiated managerial countermeasures corresponding to the economic development level rather than the uniform regulations.
Transforming Growth Factor -β Level&nbsp;Might&nbsp;Be An Independent Factor Related to Occurrence of Chronic Hepatitis B
Authors: Li Ming-hui , Lu Yao , Sun Fang-fang , Chen Qi-qi , Zhang Lu , Lu Hui-hui , Zeng Zhan , Yi Wei , Xie Yao 
Published: February 2021

Abstract
To investigate association between immune cell-related cytokines and development of chronic hepatitis B (CHB). Patients with chronic hepatitis B virus (HBV) infection in immune tolerance (IT, n=30) and hepatitis B envelope antigen (HBeAg) positive CHB (n=250) were enrolled in the study. HBV virus, serological indicators, and plasma cytokine levels were detected at the time of enrollment. The results showed that there were significant differences in median age of patients (27 vs. 31y), alanine aminotransferase level (ALT, 29.85 vs 234.70 U/L), alanine aminotransferase level (AST, 23.40 vs. 114.90 U/L), HBsAg level (4.79 vs. 3.88 log10 IU/ml), HBeAg (1606.36 vs. 862.47 S/CO) and HBV DNA load (8.17 vs 6.71 log10 IU/ml) between IT and CHB groups (all P<0.01). The median values of Fms-like tyrosine kinase 3 ligand (FLT3-L), interferon-γ (IFN-γ), interleukin- 17A (IL-17A) and transforming growth factor- beta (TGF-β1) in IT group were significantly higher than those in CHB group (FLT3-L: 41.62 vs. 27.47 pg/ml; IFN-γ: 42.48 vs. 33.18 pg/ml; IL-17A: 15.66 vs. 8.90 pg/ml; TGF-β1: 4921.50 vs. 2234 pg/ml. All P<0.01). The median values of IFN-a2, TGF-β3 and IL-10 levels in IT group were significantly lower than those in CHB group (IFN-α2: 15.24 vs. 35.78 pg/ml, P=0.000; TGF-β3: 131.69 vs. 162.61 pg/ml, P=0.025; IL-10: 5.02 vs. 7.9 pg/ml, P=0.012). The multivariate logistic regression analysis indicated that TGF-β 1 (OR=0.999, 95% CI 0.999-1.000, P<0.001) and TGF-β2 levels (OR=1.008, 95%CI 1.004-1.012, P <0.001) were significantly associated with the incidence of CHB. The results suggest that TGF-β level might be an independent factor related to the occurrence of CHB.
WITHDRAWN: Low-Intensity Pulsed Ultrasound-Generated Singlet Oxygen Induces Telomere Damage Leading to Glioma Stem Cell Awakening From Quiescence
Authors: Song Sirong , Ma Dongbin , Xu Lixia , Wang Qiong , Liu Lanxiang , Tong Xiaoguang , Yan Hua 
Published: February 2021

Abstract
Background: Cancer stem cells, quiescent and drug-resistant, have become a therapeutic target. Low-intensity pulsed ultrasound (LIPUS), a new noninvasive physical device, promotes pluripotent stem cell differentiation and is mainly applied in tissue engineering but rarely in oncotherapy. We explored the effect and mechanism of LIPUS on glioma stem cell (GSC) expulsion from quiescence.Methods: Immunofluorescence staining and flow cytometry were used to detect changes of stem hallmarkers. RT-PCR results showed the gene expression levels of stem-related transcription factors. Brud and RNA-seq were performed for cell cycle analysis. Western blotting showed different expressions of key point proteins. Telomeres damage was found by FISH and IF-FISH. Fluorescence detection was used for mitochondrial membrane potential assay and singlet oxygen detection. Tumor xenograft and immunohistochemical staining were performed to confirm the role of low intensity pulsed ultrasound.Results: We found that LIPUS led to attenuated expression of GSC hallmarks, promoted GSC escape from G0 quiescence, and significantly weakened the stemness-related Wnt and Hh pathways. Next, Interestingly, LIPUS transferred sonomechanical energy into recombinant cytochrome C and B5 proteins in vitro, which converted oxygen molecules into singlet oxygen, triggering a telomere crisis. The results in vivo and in vitro confirmed that LIPUS enhanced GSC sensitivity to temozolomide.Conclusion: These results demonstrated that LIPUS “wakes up” GSCs to improve chemotherapy by transferring energy to cyt families and leading to telomere crisis.
Symptomatic Metastases have Poorer Prognosis in Breast Cancer Patients Under Intensive Surveillance
Authors: Jung Sung Mi , Ryu Jai Min , Chae Byung Joo , Yu Jonghan , Lee Jeong Eon , Kim Seok Won , Nam Seok Jin , Lee Se Kyung 
Published: February 2021

Abstract
Purpose The purpose of this study was to investigate risk factors for post-metastasis overall survival (PMOS), and to analyze the effect of early detection of distant metastases before symptoms occur on survival in breast cancer patients under intensive surveillance.Methods A total of 7,840 patients underwent surgery for breast cancer from January 2010 to December 2014 at Samsung Medical Center; of these, we retrospectively studied 316 metastatic breast cancer patients. The patients were divided into two groups based on method of metastases detection, routine surveillance without symptoms (asymptomatic group) or follow-up for new-onset symptoms (symptomatic group).Results Multivariate analysis of PMOS showed that the patients with multiple metastases had a 1.872 fold risk of PMOS (p = 0.011) compared to the patients with bone metastasis only. The hazard ratio for the symptomatic group was higher than that for the asymptomatic group (p < 0.001). When patients were stratified by tumor subtype, patients who were HR-positive and asymptomatic on diagnosis of distant metastasis had a better prognosis than those who were HR-positive and symptomatic on diagnosis. However, patients who were HER2-positive showed no significant survival difference between two groups.Conclusion Breast cancer patients who were diagnosed with distant metastasis after symptoms occurred had a poorer prognosis than patients who were diagnosed before symptoms had developed. It is important to follow up patients regularly for symptoms related to distant metastases. Our findings validate the need for intensive surveillance, suggesting reconsideration of the guidelines for metastases screening in breast cancer patients.