bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic factor analysis for patient outcome of PD-L1 expression in thoracic oesophageal squamous cell carcinoma
Authors: Wu Bo , Gao Jianhua , Ma Muyuan , Wu Yuanyuan , Ye Xiaofeng 
Published: May 2021

Abstract

OBJECTIVES
The purpose of this study was to determine the expression of PD-L1 in oesophageal squamous cell carcinoma (OSCC) and the prognostic factors.

METHODS
PD-L1 expression was investigated by immunohistochemical staining of resected specimens from 50 OSCC patients who were randomly selected from 104 patients with complete follow-up data. The relationships among PD-L1 expression, clinicopathological factors and prognosis were assessed by statistical analysis.

RESULTS
The expression of PD-L1 was positive in 27 (54%, positive cells’ proportion &gt; 25%) and negative in 23 (46%, positive cells proportion ≤25%) of 50 cases, and PD-L1 expression was negative in all pericarcinomatous tissues (P &gt; 0.05). The 5-year survival rate of patients with PD-L1-positive expression was 22.2% (6 of 27), which was less than that of patients with PD-L1-negative expression (47.8%; 11 of 23) (P &lt; 0.05). The results showed significant differences in the depth of tumour invasion, lymph node status, postoperative pathological stage and PD-L1 expression (P &lt; 0.05). Multivariable analysis showed that PD-L1 expression was an independent prognostic factor for survival.

CONCLUSIONS
The depth of tumour invasion, lymph node status, postoperative pathological stage and PD-L1 expression are important factors affecting the prognosis of patients with thoracic OSCC; in particular, high PD-L1 expression was a significant independent poor prognostic factor in thoracic OSCC patients.
Performance analysis in a stochastic supply chain with reverse flows: a DEA-based approach
Authors: Amirteimoori Alireza , Khoshandam Leila , Kordrostami Sohrab , Jahani Sayyad Noveiri Monireh , Matin Reza Kazemi 
Published: May 2021

Abstract
Traditional efficiency studies on network data envelopment analysis (DEA) consider decision-making units as black boxes that use a set of crisp inputs to produce a set of crisp outputs and that ignore intermediate measures and reverse flows. In real applications, however, we are faced with network systems with reverse flows in an uncertain environment. In this paper, therefore, a chance-constrained multistage DEA model is introduced to analyze the relative performances of supply chains and components in the presence of reverse flows and random factors. A real case in the sugar illustrates the proposed method. The results demonstrate the validity and applicability of the model.
Human Immunotypes Impose Selection on Viral Genotypes Through Viral Epitope Specificity
Authors: Gabrielaite Migle , Bennedbæk Marc , Zucco Adrian G , Ekenberg Christina , Murray Daniel D , Kan Virginia L , Touloumi Giota , Vandekerckhove Linos , Turner Dan , Neaton James , Lane H Clifford , Safo Sandra , Arenas-Pinto Alejandro , Polizzotto Mark N , Günthard Huldrych F , Lundgren Jens D , Marvig Rasmus L 
Published: May 2021

AbstractBackgroundUnderstanding the genetic interplay between human hosts and infectious pathogens is crucial for how we interpret virulence factors. Here, we tested for associations between HIV and host genetics, and interactive genetic effects on viral load (VL) in HIV-positive antiretroviral treatment-naive clinical trial participants.MethodsHIV genomes were sequenced and the encoded amino acid (AA) variants were associated with VL, human single nucleotide polymorphisms (SNPs), and imputed HLA alleles using generalized linear models with Bonferroni correction.ResultsHuman (388 501 SNPs) and HIV (3010 variants) genetic data were available for 2122 persons. Four HIV variants were associated with VL (P &lt; 1.66 × 10–5). Twelve HIV variants were associated with a range of 1–512 human SNPs (P &lt; 4.28 × 10–11). We found 46 associations between HLA alleles and HIV variants (P &lt; 1.29 × 10–7). HIV variants and immunotypes when analyzed separately were associated with lower VL, whereas the opposite was true when analyzed in concert. Epitope binding predictions supported our observations.ConclusionsOur results show the importance of immunotype specificity on viral antigenic determinants, and the identified genetic interplay emphasizes that viral and human genetics should be studied in the context of each other.Clinical Trials Registration: NCT00867048.
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review
Authors: Guo Yi , Zhang Yahan , Lyu Tianchen , Prosperi Mattia , Wang Fei , Xu Hua , Bian Jiang 
Published: May 2021

AbstractObjectiveTo summarize how artificial intelligence (AI) is being applied in COVID-19 research and determine whether these AI applications integrated heterogenous data from different sources for modeling.Materials and MethodsWe searched 2 major COVID-19 literature databases, the National Institutes of Health’s LitCovid and the World Health Organization’s COVID-19 database on March 9, 2021. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline, 2 reviewers independently reviewed all the articles in 2 rounds of screening.ResultsIn the 794 studies included in the final qualitative analysis, we identified 7 key COVID-19 research areas in which AI was applied, including disease forecasting, medical imaging-based diagnosis and prognosis, early detection and prognosis (non-imaging), drug repurposing and early drug discovery, social media data analysis, genomic, transcriptomic, and proteomic data analysis, and other COVID-19 research topics. We also found that there was a lack of heterogenous data integration in these AI applications.DiscussionRisk factors relevant to COVID-19 outcomes exist in heterogeneous data sources, including electronic health records, surveillance systems, sociodemographic datasets, and many more. However, most AI applications in COVID-19 research adopted a single-sourced approach that could omit important risk factors and thus lead to biased algorithms. Integrating heterogeneous data for modeling will help realize the full potential of AI algorithms, improve precision, and reduce bias.ConclusionThere is a lack of data integration in the AI applications in COVID-19 research and a need for a multilevel AI framework that supports the analysis of heterogeneous data from different sources.
Rapamycin administration during an acute heat stress challenge in growing pigs
Authors: Mayorga Edith J , Horst Erin A , Goetz Brady M , Rodríguez-Jiménez Sonia , Abeyta Megan A , Al-Qaisi Mohmmad , Lei Samantha , Rhoads Robert P , Selsby Joshua T , Baumgard Lance H 
Published: May 2021

Abstract
Study objectives were to determine the effects of rapamycin (Rapa) on biomarkers of metabolism and inflammation during acute heat stress (HS) in growing pigs. Crossbred barrows (n = 32; 63.5 ± 7.2 kg body weight [BW]) were blocked by initial BW and randomly assigned to 1 of 4 environmental-therapeutic treatments: 1) thermoneutral (TN) control (n = 8; TNCon), 2) TN and Rapa (n = 8; TNRapa), 3) HS control (n = 8; HSCon), or 4) HS and Rapa (n = 8; HSRapa). Following 6 d of acclimation to individual pens, pigs were enrolled in two experimental periods (P). During P1 (10 d), pigs were fed ad libitum and housed in TN conditions (21.3 ± 0.2°C). During P2 (24 h), HSCon and HSRapa pigs were exposed to constant HS (35.5 ± 0.4°C), while TNCon and TNRapa pigs remained in TN conditions. Rapamycin (0.15 mg/kg BW) was orally administered twice daily (0700 and 1800 hours) during both P1 and P2. HS increased rectal temperature and respiration rate compared to TN treatments (1.3°C and 87 breaths/min, respectively; P &lt; 0.01). Feed intake (FI) markedly decreased in HS relative to TN treatments (64%; P &lt; 0.01). Additionally, pigs exposed to HS lost BW (4 kg; P &lt; 0.01), while TN pigs gained BW (0.7 kg; P &lt; 0.01). Despite marked changes in phenotypic parameters caused by HS, circulating glucose and blood urea nitrogen did not differ among treatments (P &gt; 0.10). However, the insulin:FI increased in HS relative to TN treatments (P = 0.04). Plasma nonesterified fatty acids (NEFA) increased in HS relative to TN treatments; although this difference was driven by increased NEFA in HSCon compared to TN and HSRapa pigs (P &lt; 0.01). Overall, circulating white blood cells, lymphocytes, and monocytes decreased in HS compared to TN pigs (19%, 23%, and 33%, respectively; P ≤ 0.05). However, circulating neutrophils were similar across treatments (P &gt; 0.31). The neutrophil-to-lymphocyte ratio (NLR) was increased in HS relative to TN pigs (P = 0.02); however, a tendency for reduced NLR was observed in HSRapa compared to HSCon pigs (21%; P = 0.06). Plasma C-reactive protein tended to differ across treatments (P = 0.06) and was increased in HSRapa relative to HSCon pigs (46%; P = 0.03). Circulating haptoglobin was similar between groups. In summary, pigs exposed to HS had altered phenotypic, metabolic, and leukocyte responses; however, Rapa administration had limited impact on outcomes measured herein.
Retinoic acid stimulates transcription of the rat SHARP-2 gene via multiple pathways
Authors: Hayashi Momoko , Misaki Toshinori , Yoshida Sena , Tokutake Hiroshi , Aruga Tomoki , Yoda Kazuya , Kenmochi Eri , Saito Kaho , Togashi Momo , Nakano Mai , Maejima Misato , Amemiya Riho , Sakuma Airi , Nakazawa Yuuri , Takagi Katsuhiro , Tsukada Akiko , Yamada Kazuya 
Published: May 2021

Abstract
Members of the enhancer of split- and hairy-related protein (SHARP) family, SHARP-1 and SHARP-2, are basic helix−loop−helix transcriptional repressors and belong to the clock genes. In this study, an effect of retinoic acid (RA) on the SHARP family gene expression in the differentiated cells was examined. RA rapidly and temporarily induced the SHARP-2 mRNA expression in hepatic H4IIE cells. Then, whether the SHARP-2 mRNA expression is altered by dexamethasone (Dex), insulin, and the combination of RA and Dex or RA and insulin was examined. Dex had different effects on the expression of SHARP-2 mRNA in the presence or absence of RA. Then, the molecular mechanisms were investigated using inhibitors of various signaling molecules. The RA-induction of SHARP-2 mRNA level was mainly inhibited by LY294002, staurosporine, and actinomycin D, respectively. Finally, whether RA acts on the transcriptional regulatory region of the SHARP-2 gene was analysed using luciferase reporter gene assay. At least two RA-responsive regions were mapped at the nucleotide sequences between −3,700 and −1,600 of the SHARP-2 gene. In addition, this effect was dependent on the RA receptor and retinoid X receptor. Thus, we conclude that RA stimulated transcription of the SHARP-2 gene via multiple pathways.
Cissus quadrangularis extract attenuates diabetic nephropathy by altering SIRT1/DNMT1 axis
Authors: Syed Anees Ahmed , Reza Mohammad Irshad , Garg Richa , Goand Umesh K , Gayen Jiaur R 
Published: May 2021

Abstract

Objectives
Hyperglycemia-induced SIRT1, DNMT1, SODs, as well as oxidative stress, play a pivotal role in the progression of diabetic nephropathy. Cissus quadrangularis, holds antioxidant and hypoglycemic activity; however, a direct link between its activity and prevention of diabetic nephropathy has not been ascertained yet. Accordingly, we aimed to delineate the protective effect of ethanolic extract of Cissus quadrangularis (EECQ) against high-fat diet/streptozotocin (HFD/STZ) induced diabetic nephropathy rats.

Methods
The control group was fed with a normal chow diet. Rats kept on an HFD for 12 weeks with a single low dose of STZ manifested the features of diabetic nephropathy. The treatment was done by the oral administration of EECQ (200 mg/kg) for six weeks (six rats in each group).

Key findings
Treatment with EECQ demonstrated substantial attenuation of elevated insulin resistance, lipid profile and creatinine level. Additionally, EECQ restored albuminuria, glomerular filtration rate and creatinine clearance in diabetic nephropathy rats. Furthermore, HFD consumption in rats culminated in reduced SIRT1 and enhanced DNMT1 expression, nonetheless, rescued by EECQ. Moreover, EECQ augmented the SOD 1 and 3 levels, thereby safeguarded from oxidative damage and renal inflammation. Besides, treatment protected from renal fibrosis by downregulating TGFβ, Smad2/3 and col1/3 expression in diseased rats.

Conclusions
Thus, based on the above findings, we conclude that EECQ shows a protective effect against diabetic nephropathy.
SmKFB5 protein regulates phenolic acid biosynthesis by controlling the degradation of phenylalanine ammonia-lyase inSalvia miltiorrhiza
Authors: Yu Haizheng , Li Dongyue , Yang Dongfeng , Xue Zheyong , Li Jie , Xing Bingcong , Yan Kaijing , Han Ruilian , Liang Zongsuo 
Published: May 2021

AbstractPhenolic acids are the major secondary metabolites and significant bioactive constituents of the medicinal plant Salvia miltiorrhiza. Many enzyme-encoding genes and transcription factors involved in the biosynthesis of phenolic acids have been identified, but the underlying post-translational regulatory mechanisms are poorly understood. Here, we demonstrate that the S. miltiorrhiza Kelch repeat F-box protein SmKFB5 physically interacts with three phenylalanine ammonia-lyase (PAL) isozymes and mediates their proteolytic turnover via the ubiquitin-26S proteasome pathway. Disturbing the expression of SmKFB5 reciprocally affected the abundance of SmPAL protein and the accumulation of phenolic acids, suggesting that SmKFB5 is a post-translational regulator responsible for the turnover of PAL and negatively controlling phenolic acids. Furthermore, we discovered that treatment of the hairy root of S. miltiorrhiza with methyl jasmonate suppressed the expression of SmKFB5 while inducing the transcription of SmPAL1 and SmPAL3. These data suggested that methyl jasmonate consolidated both transcriptional and post-translational regulation mechanisms to enhance phenolic acid biosynthesis. Taken together, our results provide insights into the molecular mechanisms by which SmKFB5 mediates the regulation of phenolic acid biosynthesis by jasmonic acid, and suggest valuable targets for plant breeders in tailoring new cultivars.
In da club: the cytoplasmic kinase MAZZA joins CLAVATA signaling and dances with CLV1-like receptors
Authors: Müller-Xing Ralf , Xing Qian 
Published: May 2021

This article comments on:
Blümke P, Schlegel J, Gonzalez-Ferrer C, Becher S, Pinto K, Monaghan J, Simon R. 2021. Receptor-like cytoplasmickinase MAZZA mediates developmental processes with CLAVATA1 family receptors in Arabidopsis. Journal of Experimental Botany 72, 4853–4870.
Association of Plasma Fibrinogen Levels on Postoperative Day 1 with 2-Year Survival of Orthotopic Liver Transplantation for HBV-Related HCC
Authors: Liu Xia , Guo Renyong , Tian Jie 
Published: May 2021

Abstract

Objective
To clarify the prognostic values of hemostatic parameters to predict the survival of patients undergoing orthotopic liver transplantation (OLT) for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC).

Methods
The data of 182 consecutive adult patients who underwent OLT for HBV-related HCC were subjected to univariate and multivariate analyses.

Results
Ascites and fibrinogen levels on postoperative day (POD) 1 were independent predictors of postoperative 2-year mortality (both P &lt;.05). Kaplan-Meier survival analysis showed that the higher the fibrinogen level on POD 1, the better the 1- and 2-year survival of patients with ascites (P &lt;.05), whereas the fibrinogen level on POD 1 was associated with 1-year (P &lt;.05) but not 2-year survival of patients without ascites.

Conclusion
Fibrinogen on POD 1 is a predictor of 2-year post-OLT survival of patients with HBV-related HCC with ascites.
Mode identification and seismic study of δ Scuti, the prototype of a class of pulsating stars
Authors: Daszyńska-Daszkiewicz J , Pamyatnykh A A , Walczak P , Handler G , Pigulski A , Szewczuk W 
Published: May 2021

ABSTRACT
We present a seismic study of δ Scuti based on a mode identification from multicoulor photometry. The dominant frequency can be associated only with a radial mode and the second frequency is, most probably, a dipole mode. The other six frequencies have more ambiguous identifications. The photometric mode identification provided also some constraints on the atmospheric metallicity [m/H] ≈ +0.5 and microturbulent velocity ξt ≈ 4 km s−1. For models reproducing the dominant frequency, we show that only the fundamental mode is possible and the first overtone is excluded. However, the location of δ Scuti near the terminal age main sequence requires the consideration of three stages of stellar evolution. For the star to be on the main sequence, it is necessary to include overshooting from the convective core with a parameter of at least αov = 0.25 at the metallicity greater than Z = 0.019. It turned out that the value of the relative amplitude of the bolometric flux variations (the non-adiabatic parameter f) is mainly determined by the position of the star in the HR diagram, i.e. by its effective temperature and luminosity, whereas the effect of the evolutionary stage is minor. On the other hand, the convective efficiency in the subphotospheric layers has a dominant effect on the value of the parameter f. Comparing the theoretical and empirical values of f for the radial dominant mode, we obtain constraints on the mixing length parameter αMLT which is less than about 1.0, independently of the adopted opacity data and chemical mixture. This value of αMLT is substantially smaller than for a calibrated solar model indicating rather low to moderately efficient convection in the envelope of δ Scuti.
Deep Extragalactic VIsible Legacy Survey (DEVILS): SED fitting in the D10-COSMOS field and the evolution of the stellar mass function and SFR–M⋆ relation
Authors: Thorne Jessica E , Robotham Aaron S G , Davies Luke J M , Bellstedt Sabine , Driver Simon P , Bravo Matías , Bremer Malcolm N , Holwerda Benne W , Hopkins Andrew M , Lagos Claudia del P , Phillipps Steven , Siudek Malgorzata , Taylor Edward N , Wright Angus H 
Published: May 2021

ABSTRACT
We present catalogues of stellar masses, star formation rates (SFRs), and ancillary stellar population parameters for galaxies spanning 0 &lt; z &lt; 9 from the Deep Extragalactic VIsible Legacy Survey (DEVILS). DEVILS is a deep spectroscopic redshift survey with very high completeness, covering several premier deep fields including COSMOS (D10). Our stellar mass and SFR estimates are self-consistently derived using the spectral energy distribution (SED) modelling code ProSpect, using well-motivated parametrizations for dust attenuation, star formation histories, and metallicity evolution. We show how these improvements, and especially our physically motivated assumptions about metallicity evolution, have an appreciable systematic effect on the inferred stellar masses, at the level of ∼0.2 dex. To illustrate the scientific value of these data, we map the evolving galaxy stellar mass function (SMF) and the SFR–M⋆ relation for 0 &lt; z &lt; 4.25. In agreement with past studies, we find that most of the evolution in the SMF is driven by the characteristic density parameter, with little evolution in the characteristic mass and low-mass slopes. Where the SFR–M⋆ relation is indistinguishable from a power law at z &gt; 2.6, we see evidence of a bend in the relation at low redshifts (z &lt; 0.45). This suggests evolution in both the normalization and shape of the SFR–M⋆ relation since cosmic noon. It is significant that we only clearly see this bend when combining our new DEVILS measurements with consistently derived values for lower redshift galaxies from the Galaxy And Mass Assembly (GAMA) survey: this shows the power of having consistent treatment for galaxies at all redshifts.
A lander radio science experiment for the estimation of the gravity field and rotation of comet 133P/Elst-Pizarro
Authors: Gao Wutong , Yan Jianguo , Wang Bo , Xi Guo , Ye Mao , Jin Weitong , Barriot Jean-Pierre 
Published: May 2021

ABSTRACT
The main belt comet 133P/Elst-Pizarro is one of the targets of the proposed Chinese small body exploration mission. The rotation and gravity of this comet will be modelled at the end of the mission phase. To prepare this mission, we performed a radio science simulation based on the current knowledge of the characteristics of 133P/Elst-Pizarro. Simulated two-way Earth–orbiter and orbiter–lander range rate tracking data with a lander positioned at the comet equator were used to determine the gravity field coefficients and the rotational parameters. Our simulation results show that the introduction of the orbiter–lander range rate data can significantly decrease the uncertainty in the initial state vector of the orbiter as well as the uncertainty in the rotation and gravity parameters.
A highly accreting low-mass black hole hidden in the dust: Suzaku and NuSTAR observations of the NLS1 Mrk 1239
Authors: Jiang Jiachen , Baloković Mislav , Brightman Murray , Liu Honghui , Harrison Fiona A , Lansbury George B 
Published: May 2021

ABSTRACT
We present torus modelling for the X-ray spectra of a nearby narrow-line Seyfert 1 galaxy Mrk 1239 (z = 0.0199), based on archival Suzaku, NuSTAR, and Swift observations. Our model suggests very soft intrinsic power-law continuum emission of Γ ≈ 2.57 in 2019 and Γ ≈ 2.98 in 2007. By applying a correction factor to the unabsorbed X-ray luminosity, we find that Mrk 1239 is accreting near or around the Eddington limit. Our best-fitting spectral model also suggests a torus with a column density of log (NH,ave/ cm−2) = 25.0 ± 0.2 and a high covering factor of 0.90 in Mrk 1239, indicating that this source is most likely to be viewed almost face-on with i ≈ 26°. Our line of sight might cross the edge of the torus with NH,los = 2–5 × 1023 cm−2. The high Eddington ratio and the high line-of-sight column density makes Mrk 1239 one of the active galactic nuclei that are close to the limit where wind may form near the edge of the torus due to high radiation pressure.
Broad-band spectral and timing properties of MAXI J1348–630 using AstroSat and NICER observations
Authors: Jithesh V , Misra Ranjeev , Maqbool Bari , Mall Gitika 
Published: May 2021

ABSTRACT
We present broad-band X-ray spectral-timing analysis of the new Galactic X-ray transient MAXI J1348–630 using five simultaneous AstroSat and NICER observations. Spectral analysis using AstroSat data identify the source to be in the soft state for the first three observations and in a faint and bright hard state for the next two. Quasi-periodic oscillations at ∼0.9 and ∼6.9 Hz, belonging to the type-C and type-A class are detected. In the soft state, the power density spectra are substantially lower (by a factor &gt;5) for the NICER (0.5–12 keV) band compared to the AstroSat/LAXPC (3–80 keV) one, confirming that the disc is significantly less variable than the Comptonization component. For the first time, energy-dependent fractional rms and time lag in the 0.5–80 keV energy band was measured at different Fourier frequencies, using the bright hard state observation. Hard time lag is detected for the bright hard state, while the faint one shows evidence for soft lag. A single-zone propagation model fits the LAXPC results in the energy band 3–80 keV with parameters similar to those obtained for Cygnus X–1 and MAXI J1820+070. Extending the model to lower energies, reveals qualitative similarities but having quantitative differences with the NICER results. These discrepancies could be because the NICER and AstroSat data are not strictly simultaneous and because the simple propagation model does not take into account disc emission. The results highlight the need for more joint coordinated observations of such systems by NICER and AstroSat.