bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE
Authors: Crook Oliver , Davies Colin , Gatto Laurent , Kirk Paul , Lilley Kathryn 
Published: January 2021

Abstract
The steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different sub-cellular niches upon perturbation of the subcellular environment. Differential localisation provides a step towards mechanistic insight of subcellular protein dynamics. Aberrant localisation has been implicated in a number of pathologies, thus differential localisation may help characterise disease states and facilitate rational drug discovery by suggesting novel targets. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we propose a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation, as well quantifying the uncertainty in these estimates. Furthermore, BANDLE allows information to be shared across spatial proteomics datasets to improve statistical power. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to datasets studying EGF stimulation and AP-4 dependent localisation recovers well studied translocations, using only two-thirds of the provided data. Moreover, we implicate TMEM199 with AP-4 dependent localisation. In an application to cytomegalovirus infection, we obtain novel insights into the rewiring of the host proteome. Integration of high-throughput transcriptomic and proteomic data, along with degradation assays, acetylation experiments and a cytomegalovirus interactome allows us to provide the functional context of these data.
Super-elasticity at 4K of Covalently Crosslinked Polyimide Aerogels with Ultrahigh Negative Poisson’s Ratio
Authors: Cheng Yang , Zhang Xiang , Qin Yixiu , Dong Pei , Yao Wei , Matz John , Ajayan Pulickel , Shen Jianfeng , Ye Mingxin 
Published: January 2021

Abstract
The deep cryogenic temperatures encountered in aerospace present significant challenges for the performance of elastic materials in spacecrafts and related apparatus. Reported elastic carbon or ceramic aerogels overcome the low-temperature brittleness in conventional elastic polymers. However, complicated fabrication process and high costs greatly limited their applications. In this work, super-elasticity at deep cryogenic temperature of covalently crosslinked polyimide (PI) aerogels is achieved based on scalable and low-cost directional dimethyl sulfoxide crystals assisted freeze-gelling and freeze-drying strategy. The covalently crosslinked chemical structure, cellular architecture, negative Poisson’s ratio (-0.2), extremely low volume shrinkage (3.1%) and ultralow density (6.1 mg/cm3) endow the PI aerogels with an elastic compressive strain up to 99% even in liquid helium (4K), almost zero loss of resilience after dramatic thermal shocks (∆T = 569 K), and fatigue resistance over 5000 times compressive cycles. This work provides a new pathway for constructing polymer-based materials with super-elasticity at deep cryogenic temperature, demonstrating much promise for extensive applications in ongoing and near-future aerospace exploration.
Influence of Old Age on Risk of Lymph Node Metastasis and Survival in Patients With T1 Colorectal Cancer: A Population-Based Analysis
Authors: Ye Hua , Zheng Bin , Zheng Qi , Chen Ping 
Published: January 2021

Abstract
Background We aimed at determining the influence of old age on lymph node metastasis (LNM) and prognosis in T1 colorectal cancer (CRC). Methods We collected data from eligible patients in Surveillance, Epidemiology, and End Results database between 2004 and 2015. Independent predictors of LNM were identified by the logistic regression analysis. Cox regression analysis, propensity score-matched analysis and competing risks analysis were used to analyze the associations between old age and lymph node (LN) status, and to validate the prognostic value of old age on cancer-specific survival (CSS).Results In total, 10092 patients were identified. Among them, 6423 patients (63.6%) had greater than or equal to 12 examined lymph nodes (LNs) (LNE ³12), and 5777 patients (57.7%) were of 65 years or older. The observed rate of LNM was 14.9 % (960 out of 6423). Logistic regression models demonstrated that tumor size ³3cm (odds ratio, OR = 1.316, P = 0.038), poorly differentiated (OR = 3.716, P <0.001), older age (OR = 0.633 for age 65–79 years, OR= 0.477 for age over 80 years, both P < 0.001), and negative CEA level (OR = 0.71, P =0.007) were independent prognostic factors. Cox regression analysis demonstrated CSS was not significantly different between elderly patients undergoing radical resection with LNE³12 and those with LNE <12 (HR= 0.865, P = 0.153), which were firmly validated after propensity score-matched analysis by a competing risks model.Conclusions We found that tumor size<3cm, well/moderately differentiated, negative CEA level and adenocarcinoma in elderly patients with T1 colorectal cancer who were suitable for Local excision.
Conjugate Buoyant Convective Transport of Different Nanofluids in An Enclosed Annular Geometry
Authors: Sankar M. , Reddy N. Keerthi , Do Younghae 
Published: January 2021

Abstract
A vertical annular configuration with differently heated cylindrical surfaces and horizontal adiabatic boundaries is extensively studied due to many industrial applications. In this paper, we investigate the effects of conjugate buoyant heat transport within water based nanofluid with different nanoparticles such as alumina, titanium oxide or copper, which is contained in the gap of the enclosed annulus. The enclosed annulus is constituted by a thick inner cylinder with a constant high temperature, an exterior boundary with a constant low temperature and thermally insulated upper and lower surfaces. By investigating heat transport for broad spectrum of Rayleigh number, solid wall thickness, thermal conductivity ratio and nanoparticle volume fraction, we found that the influence of wall thickness on thermal dissipation rate along wall and interface greatly depend on conductivity ratio and vice-versa. In particular, we uncover that the choice of nanoparticle in a nanofluid and its concentration are key factors in enhancing the thermal transport along the interface. Specially, copper based nanofluids produces higher heat transport among other nanoparticles, and increasing nanoparticle concentration leads to enhanced thermal dissipation along interface. Our results are applicable to choose nanofluids along with other critical parameters for the desired heat transport.
Survival after Surgery among Patients with Cholangiocarcinoma in Northeast Thailand According to Anatomical and Morphological Classification
Authors: Thawarungruang Chaiwat , Khuntikeo Narong , Chamadol Nittaya , Laopaiboon Vallop , Thuanman Jaruwan , Thinkhamrop Kavin , Kelly Matthew , Thinkhamrop Bandit 
Published: January 2021

Abstract
Background: Cholangiocarcinoma (CCA) has been categorized based on tumor location as intrahepatic (ICCA), perihilar (PCCA) or distal (DCCA), and based on the morphology of the tumor of the bile duct as mass forming (MF), periductal infiltrating (PI) or intraductal (ID). To date, there is limited evidence available regarding the survival of CCA among these different anatomical and morphological classifications. This study aimed to evaluate the survival rate and median survival time after curative surgery among CCA patients according to their anatomical and morphological classifications, and to determine the association between these classifications and survival. Methods: This study included CCA patients who underwent curative surgery with a pathological diagnosis from the Cholangiocarcinoma Screening and Care Program (CASCAP), Northeast Thailand. Survival rates of CCA and median survival time since the date of CCA surgery and 95% confidence intervals (CI) were calculated. Multiple cox regression was performed to evaluate factors associated with survival which were quantified by hazard ratios (HR) and their 95% CIs. Results: Of the 746 CCA patients, 514 had died at the completion of the study which constituted 15,643.6 person-months of data recordings. The mortality rate was 3.3 per 100 patients per month (95% CI: 3.0-3.6), with median survival time of 17.8 months (95% CI: 15.4-20.2), and 5-year survival rate of 24.6% (95% CI: 20.7­28.6). The longest median survival time was 21.8 months (95% CI: 16.3-27.3) while the highest 5-year survival rate of 34.8% (95% CI: 23.8-46.0) occurred in the DCCA group. A combination of anatomical and morphological classifications, PCCA+ID, was associated with the longest median survival time of 40.5 months (95% CI: 17.9-63.0) and the highest 5-year survival rate of 42.6% (95% CI: 25.4-58.9). The ICCA+MF combination was associated with survival (adjusted HR: 1.45; 95% CI: 1.01-2.09; P = 0.013) compared to ICCA+ID patients. Conclusions: Among patients receiving surgical treatment, those with PCCA+ID had the highest 5-year survival rate, which was higher than in groups classified by only anatomical characteristics. Additionally, the patients with ICCA+MF showed the highest survival association. Therefore, further investigations into CCA imaging should focus on patients with a combination of anatomical and morphological classifications.
β-Conglycinin Regulates Intestinal Immunity through the CIITA-mediated MHC II-PI3K/Akt/mTOR Pathway in Hybrid Grouper: The Ameliorative Effects of Sodium Butyrate (NaB)
Authors: Yin Bin , Liu Hongyu , Tan Beiping , Dong Xiaohui , Chi Shuyan , Yang Qihui , Zhang Shuang 
Published: January 2021

Abstract
We investigated the effects of low and high doses of 7S and the ameliorative effects of NaB (based on high-dose 7S) on the growth performance, serum immunity, distal histopathology, and CIITA-mediated MHC II-PI3K/Akt/mTOR pathway in hybrid groupers. The results revealed that the specific growth rate of groupers significantly increased, decreased, and increased in the low-level 7S (bL), high-level 7S (bH) high-level 7S plus NaB (bH-NaB) groups, respectively. The feed coefficient ratio was significantly increased in the bH and bH-NaB groups, whereas serum levels of IFN-γ, IL-1β, and TNF-α were upregulated in the bH group. The intestinal diameter/plica height ratio was significantly increased in the bH group. Furthermore, there were increases in nitric oxide, nitric oxide synthase (NOS), and peroxynitrite anion (ONOO−) in the bH group, and decreases in NOS and ONOO− in the bH-NaB group. The mRNA levels in distal intestine of TSC1, mTOR C2, CIITA, and CREB1 were significantly upregulated in all three treatment groups, whereas those of IKKα, Rheb, mTOR C1, mLST8, EIF4B, NFY, GILT, and AEP were upregulated and downregulated in the bH and bH-NaB groups, respectively. These indicate 7S has a regulatory effect on serum immunity and affect distal intestinal development by modulating hindgut injury-related parameters. Within the distal intestinal tract, 7S can induce intestinal inflammation by activating the CIITA-mediated MHC II-PI3K/Akt/mTOR pathway, which eventually manifests as a reduction in growth performance. Supplementing feed with NaB represents an effective approach for enhancing serum immunity, and also protects the intestines from damage caused by high-dose 7S.
Seminal Plasma piRNA Array Analysis Identifies Possible Biomarker piRNAs for the Diagnosis of Asthenozoospermia
Authors: he ling , wu Xing , wu rong , guo ping , sun Wan , he wen , chen he 
Published: January 2021

Abstract
Asthenozoospermia (AZS) is characterized by reduced sperm motility, and its pathogenesis remains poorly understood. Piwi-interacting RNAs (piRNAs) have been recognized to play important roles in spermatogenesis. However, little is known about the correlation of piRNAs with AZS. In this study, small RNA sequencing was performed on samples from AZS patients and fertile controls. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate the small RNA-seq results. Bioinformatics analyses were performed to predict the functions of differentially expressed piRNAs. Logistic regression models were constructed, and receiver operating characteristic curve (ROC) analysis was used to evaluate their diagnostic performance. A total of 114 upregulated and 169 downregulated piRNAs were detected in AZS patients. GO and KEGG analyses showed that the differentially expressed piRNAs were mainly associated with transcription, signal transduction, cell differentiation, metal ion binding and focal adhesion. These results were verified by qRT-PCR of 8 selected piRNAs. Among the differentially expressed piRNAs tested, piR-hsa-32694, piR-hsa-26591, piR-hsa-18725, piR-hsa-18586 and piR-hsa-2912 produced qRT-PCR results consistent with the sequencing results in AZS compared with controls in the first cohort, whereas the other three genes did not show significant differences in expression. piR-hsa-32694, piR-hsa-26591, piR-hsa-18725, and piR-hsa-18586 were significantly upregulated in AZS. The diagnostic power of the four piRNAs was further analysed using ROC analysis; piR-hsa-26591 exhibited an area under the ROC curve (AUC) of 0.913 (95% CI: 0.795-0.994). Logistic regression modelling and subsequent ROC analysis indicated that the combination of the 4 piRNAs reached good diagnostic efficacy (AUC: 0.935).
TGFB-Induced Factor Homeobox 1 (TGIF) Expression in Breast Cancer
Authors: Stürken Christine , Möbus Volker , Milde-Langosch Karin , Schmatloch Sabine , Fasching Peter , Rüschoff Josef , Stickeler Elmar , Henke Rolf-Peter , Denkert Carsten , Hanker Lars , Schem Christian , Vladimirova Valentina , Karn Thomas , Nekljudova Valentina , Köhne Claus-Henning , Marmé Frederik , Schumacher Udo , Loibl Sibylle , Müller Volkmar 
Published: January 2021

Abstract
Background: Breast cancer (BC) is the most frequent female cancer its which preferentially metastasizes to bone. Mechanisms of bone tropism are poorly understood, however, the transcription factor TGFB-induced factor homeobox 1 (TGIF) is involved in bone metabolism and thus of potential interest.Methods: TGIF expression was analyzed by immunohistochemistry in 1197 formalin-fixed, paraffin-embedded tissue from BC patients treated in the GAIN study with two adjuvant dose-dense schedules of chemotherapy with or without bisphosphonate ibandronate. TGIF expression was categorized into negative/low and moderate/strong staining.Results: In 1197 samples, we found associations of higher TGIF protein expression with smaller tumor size (p = 0.015), well differentiated phenotype (p < 0.001) and estrogen receptor (ER)-positive BC (p < 0.001). Patients with higher TGIF expression levels showed a significantly better disease-free (log-rank p 0.019) and overall survival (log-rank p = 0.018), but no association with time to bone metastasis as first site of relapse. Stratified univariate analysis in molecular subgroups emphasized that elevated TGIF expression was prognostic for both DFS and OS in ER-positive BC patients (DFS: log-rank p = 0.009; OS: log-rank p = 0.008) and in the HER2-negative subgroup (DFS: log-rank p = 0.004; OS: log-rank p = 0.002).Conclusions: Our findings suggest that a loss of TGIF expression is associated with BC progression, especially in luminal carcinomas.Trial registration: This clinical trial has been registered with ClinicalTrials.gov; registration number: NCT00196872.
Determination of Dy Substitution Site in Nd2-xDyxFe14B by HAADF-STEM and Illustration of Magnetic Anisotropy of “g” and “f” Sites, Before and After Substitution
Authors: Kang Young , Haider Syed , Kang Min-Chul , Hong Jisang , Yang Cheol-Woong , Kim Dongsoo 
Published: January 2021

Abstract
Nd2Fe14B and Nd2 − xDyxFe14B (x = 0.25,0.50) particles were prepared by the modified co-precipitation followed by reduction-diffusion process. Bright field scanning transmission electron microscope (BF-STEM) image revealed the formation of Nd-Fe-B trigonal prisms in [-101] viewing zone axis, confirming the formation of Nd2Fe14B/Nd2 − xDyxFe14B. Accurate site for the Dy substitution in Nd2Fe14B crystal structure was determined as “f” site by using high-angle annular dark field scanning transmission electron microscope (HAADF-STEM). It was found that all the “g” sites are occupied by the Nd, where’s and Dy occupied only the “f” site. Anti-ferromagnetic coupling at “f” site decreased the magnetic moment values for Nd1.75Dy0.25Fe14B (23.48 µB) and Nd1.5Dy0.5Fe14B (21.03 µB) as compared to Nd2Fe14B (25.50 µB). Reduction of magnetic moment increased the squareness ratio, coercivity and energy product. Analysis of magnetic anisotropy at constant magnetic field confirmed that “f” site substitution did not change the patterns of the anisotropy. Furthermore, magnetic moment of Nd2Fe14B, Nd2 − xDyxFe14B, Nd (“f” site), Nd (“g” site) and Dy (“f” site) was recorded for all angles between 0-180o.
Parameter Study of the High Temperature MOCVD Numerical Model for AlN Growth Using Orthogonal Test Design
Authors: an jiadai , dai xianying , feng lansheng , zheng jieming 
Published: January 2021

Abstract
We investigated the process parameters of the high temperature MOCVD (HT-MOCVD) numerical model for the AlN growth based on CFD simulation using orthogonal test design. It is believed that high temperature growth condition is favorable for improving efficiency and crystallization quality for AlN film, while the flow field in the HT-MOCVD reactor is closely related to the process parameters, which will affect the uniformity of the film. An independently developed conceptual HT-MOCVD reactor was established for the AlN growth to carry out the CFD simulation. To evaluate the role of the parameters systematically and efficiently on the growth uniformity, the process parameters based on CFD simulation were analyzed using orthogonal test design. The advantages of the range, matrix and variance methods were considered and the results were analyzed comprehensively and the optimal process parameters were obtained as follows, susceptor rotational speed 400 rpm, operating pressure 40 Torr, gas flow rate 50 slm, substrate temperature 1550 K.
Association Between Smoking Status and Outcomes in ST-Segment Elevation and Non-ST-Segment Elevation Myocardial Infarction Patients Undergoing Percutaneous Coronary Intervention
Authors: Sia Ching-Hui , Ko Junsuk , Zheng Huili , Ho Andrew , Foo David , Foo Ling-Li , Lim Patrick , Liew Boon , Chai Ping , Yeo Tiong-Cheng , Tan Huay-Cheem , Chua Terrance , Chan Mark , Tan Jack , Bulluck Heerajnarain , Hausenloy Derek 
Published: January 2021

Abstract
Smoking is one of the leading risk factors for cardiovascular diseases, including ischemic heart disease and hypertension. However, in acute myocardial infarction (AMI) patients, smoking has been associated with better clinical outcomes, a phenomenon termed the “smoker’s paradox.” Given the known detrimental effects of smoking on the cardiovascular system, it has been proposed that the beneficial effects of smoking on outcomes is due to age differences between smokers and non-smokers and is therefore a smoker’s pseudoparadox. The aim of this study was to evaluate the association between smoking status and clinical outcomes in ST-segment elevation (STEMI) and non-STEMI (NSTEMI) patients treated by percutaneous coronary intervention (PCI), using a national multi-ethnic Asian registry. In unadjusted analyses, current smokers had better clinical outcomes following STEMI and NSTEMI. However, after adjusting for age, the protective effect of smoking was lost, confirming a smoker’s pseudoparadox. Interestingly, although current smokers had increased risk for recurrent MI within 1 year after PCI in both STEMI and NSTEMI patients, there was no increase in mortality. In summary, we confirm the existence of a smoker’s pseudoparadox in a multi-ethnic Asian cohort of STEMI and NSTEMI patients and report increased risk of recurrent MI, but not mortality, in smokers.
The Value of Alveolar Lavage Fluid mNGS in The Peripheral Pulmonary Among Children
Authors: Qiu Kun-yin , Liao Xiong-yu , Fang Jian-pei , Zhou Dun-hua 
Published: January 2021

Abstract
Objectives The aim of this study was to evaluate the value of alveolar lavage fluid mNGS in the diagnosis of peripheral pulmonary infectious lesions among children. Methods Twenty-eight consecutive pediatric patients suspected of pulmonary infections were retrospectively. Result The detection rate of traditional pathogen method was 17.9%, while the detection rate of mNGS was 71.4% (P < 0.01,). The smoothing curve also showed that, there is a negative linear correlation between WBC and microbial reads (P < 0.05,). Further we found when CRP is less than 60mg/dl, CRP increases with the increase of microbial sequencing reads. With the ROC curves, we demonstrated the different detection methods of alveolar lavage fluid in the diagnosis of peripheral pulmonary infectious lesions.The results showed that mNGS was more sensitive (100%) and specific (90.9%) compared to traditional method (83.3%, 18.2%). The PPV and NPV of mNGS were 100% and 75%. The AUC of mNGS was 95.45%, while the AUC of traditional methods was 50.76%, which was with a significant difference (P < 0.001). The PPV and NPV of traditional pathogen detection were 80% and 21.7%. Conclusions Metagenomic NGS analysis can provided fast and precise pathogen detection and identification among children, and WBC and CRP could be used biomarkers of anti-infective efficacy.
Pharmacognostic Study and Development of Quality Control Parameters for Different Parts of Lavatera Cashmeriana
Authors: Majid Neelofar , Raja Weekar Y. , Nissar Saduf , Nawchoo Irshad A. , Bhat Zulfikar Ali , Rashid Kausar 
Published: January 2021

Abstract
Lavatera cashmeriana Camb. is an endemic and important medicinal plant species of Kashmir Himalaya. It is widely used locally and is sold as crude drug in Kashmir markets due to its various medicinal properties. However, despite its traditional usage there is limited information pertaining to pharmacognostic characterization of L. cashmeriana. So, the present study was carried out to investigate the pharmacognostical and physicochemical profile of different parts of L. cashmeriana. The measures taken for pharmacognostical characterization were organoleptic study, macroscopy, anatomy, powder microscopy, foreign matter analysis, ash values, loss on drying, swelling index, foaming index, ph values, fluorescence analysis and extractive yield. Organoleptic and macroscopic studies revealed that L. cashmeriana is a perennial herb with very thick branched tap root system; orbicular, palmate, slightly cordate at base, upper surface of leaves with dense simple, fascicled or stellate hairs, lower surface densely stellate hairy, lobes ovate or obtuse, stipule linear lanceolate; axillary, solitary or in terminal sub-racemes inflorescence; fruit discoid mericarps and seeds glabrous, dark brown. Anatomical studies and powder microscopy revealed some important diagnostic features in the plant species. The pharmacognostic profile studies generated helpful data to set up standards for the plant. The present study for the first time endows with an inclusive pharmacognostic profiling of L. cashmeriana, thereby, acting as a platform for accurate identification, authentication and development of quality control parameters of the species. Data obtained may be used as a standard for future studies.