bluuebunny/crossref_metadata_2025_split huggingface dataset:
A glycolysis-related signature to improve the current treatment and prognostic evaluation for breast cancer
Authors: Feng Sijie , Ning Linwei , Zhang Huizhen , Wang Zhenhui , Lu Yunkun 
Published: August 2024

Background
As a heterogeneous malignancy, breast cancer (BRCA) shows high incidence and mortality. Discovering novel molecular markers and developing reliable prognostic models may improve the survival of BCRA.

Methods
The RNA-seq data of BRCA patients were collected from the training set The Cancer Genome Atlas (TCGA)-BRCA and validation set GSE20685 in the Gene Expression Omnibus (GEO) databases. The “GSVA” R package was used to calculate the glycolysis score for each patient, based on which all the patients were divided into different glycolysis groups. The “limma” package was employed to perform differentially expression genes (DEGs) analysis. Key signature genes were selected by performing un/multivariate and least absolute shrinkage and selection operator (LASSO) C regression and used to develop a RiskScore model. The ESTIMATE and MCP-Counter algorithms were used for quantifying immune infiltration level. The functions of the genes were validated using Western blot, colony formation, transwell and wound-healing assay.

Results
The glycolysis score and prognostic analysis showed that high glycolysis score was related to tumorigenesis pathway and a poor prognosis in BRCA as overactive glycolysis inhibited the normal functions of immune cells. Subsequently, we screened five key prognostic genes using the LASSO Cox regression analysis and used them to establish a RiskScore with a high classification efficiency. Based on the results of the RiskScore, it was found that patients in the high-risk group had significantly unfavorable immune infiltration and prognostic outcomes. A nomogram integrating the RiskScore could well predict the prognosis for BRCA patients. Knockdown of PSCA suppressed cell proliferation, invasion and migration of BRCA cells.

Conclusion
This study developed a glycolysis-related signature with five genes to distinguish between high-risk and low-risk BRCA patients. A nomogram developed on the basis of the RiskScore was reliable to predict BRCA survival. Our model provided clinical guidance for the treatment of BRCA patients.
Yield Trait Association Studies through Principal Component Analysis in Bi-Parental Population Derived from indica/tropical japonica Inter Sub-Specific Cross in Rice (Oryza sativa L.)
Authors: Haranal Abhishek Ashok , KB Eswari , Badri Jyothi , P Raghuveer Rao 
Published: August 2024

In the present investigation, a mapping population consisting of 189 lines derived from an inter sub-specific cross between an indica cultivar, ‘Samba Mahsuri’ and a tropical japonica accession, ‘Cuba 65’ was investigated to assess the trait contribution to variability employing principal component analysis (PCA). The study aimed at determination of inter-relationships among various yield attributing traits vis-à-vis individuals of the mapping population. Out of eleven principal components (PC), first four PCs exhibited Eigen value more than one accounting to a total of 68.73% cumulative variance among the characters. The first PC accounted for the highest variability (PC1 31.6%) to the total variability, followed by 14.51% (PC2), 12.69% (PC3) and 9.91% (PC4). The highest positive Eigen value observed for the tiller number (0.33) and panicle number (0.32) in PC1 indicated their pronounced effect in the overall variation in the population. The analysis revealed the traits that contribute maximum for the variation. PCA also revealed negligible effect of days to fifty percent flowering, grain size and spikelet fertility to the variability in the mapping population. Although all the studied traits except grain size showed significant positive association with grain yield; negative correlation was observed between some of the component traits. Panicle weight, thousand grain weight and grain number showed negative association with tiller number and panicle number. The latter two traits contributed to the maximum variability in the population. The trait associations identified in the present investigation will help in determining the selection criteria to be adopted in the development of high yielding cultivars involving indica/tropical japonica populations.
Effect of land‐atmosphere coupling strength on impacts from Amazonian deforestation
Authors: Lorenz Ruth , Pitman Andy J. 
Published: August 2014

AbstractWe use a global climate model to explore how increasing the spatial scale of deforestation affects rainfall and temperature over Amazonia. We gradually increase the scale of deforestation separately over a “weakly” and a “strongly” land‐atmosphere coupled region. The rate at which deforestation triggers a response in air temperature increases faster when deforestation is imposed on a strongly coupled region, especially during the dry season. A small deforestation signal in a strongly coupled region can have a larger impact on temperature than a large deforestation signal in a weakly coupled region. Capturing the impact of deforestation, therefore, requires the perturbation to be colocated with the appropriate land‐atmosphere coupling strength. It is unclear from our results whether the impact of deforestation on rainfall depends on coupling strength. Reducing these uncertainties will require larger ensembles of model simulations to be interpreted in the context of coupling strength.
Low calcium carbonate saturation state in an Arctic inland sea having large and varying fluvial inputs: The Hudson Bay system
Authors: Azetsu‐Scott Kumiko , Starr Michel , Mei Zhi‐Ping , Granskog Mats 
Published: August 2014

AbstractThe Hudson Bay system (HBS) is a shallow inland sea in the Arctic, composed of Hudson Strait, Foxe Basin/Channel, James Bay, and Hudson Bay. Dissolved inorganic carbon (DIC) and total alkalinity (TA) measurements were used to investigate the state of ocean acidification, specifically calcium carbonate saturation states (Ω) and pH. The freshwater sources were identified from the relationship between oxygen isotope composition (δ18O) and salinity to understand the role of freshwater in ocean acidification. The saturation state of seawater with respect to calcium carbonate (Ω) in surface water (<10 m) of the HBS was strongly influenced by river runoff. Aragonite under‐saturation (Ωarg < 1) was observed in the surface water of the south‐eastern Hudson Bay, where the river runoff fraction was high (>10%). The watershed characteristics, however, influenced the alkalinity of river runoff in different parts of Hudson Bay, which contributed to Ω variation in the coastal region. In southwestern Hudson Bay where the watershed is dominated by limestone, Ω was higher compared to eastern Hudson Bay, where the watershed consists of an igneous rock formation. In deeper waters, low Ω is caused by remineralization of organic matter. The highest DIC concentrations (>2300 µmol/kg) were observed in the depths of central Hudson Bay with a pHtotal of 7.49 and Ωarg of 0.37. Over 67% and 22% of the bottom water of Hudson Bay was undersaturated with respect to aragonite and calcite respectively, despite Hudson Bay being very shallow (less than 250 m deep). The aragonite saturation horizon in the central Hudson Bay was around 50 m.
The role of aerosol absorption in driving clear‐sky solar dimming over East Asia
Authors: Persad Geeta G. , Ming Yi , Ramaswamy V. 
Published: August 2014

AbstractSurface‐based observations indicate a significant decreasing trend in clear‐sky downward surface solar radiation (SSR) over East Asia since the 1960s. This “dimming” is thought to be driven by the region's long‐term increase in aerosol emissions, but little work has been done to quantify the underlying physical mechanisms or the contribution from aerosol absorption within the atmospheric column. Given the distinct climate impacts that absorption‐driven dimming may produce, this constitutes an important, but thus far rather neglected, line of inquiry. We examine experiments conducted in the Geophysical Fluid Dynamics Laboratory's atmospheric general circulation models, AM2.1 and AM3, in order to analyze the model‐simulated East Asian clear‐sky SSR trends. We also use the models' stand‐alone radiation module to examine the contribution from various aerosol characteristics in the two models (such as burden, mixing state, hygroscopicity, and seasonal distribution) to the trends. Both models produce trends in clear‐sky SSR that are comparable to that observed but via disparate mechanisms. Despite their different aerosol characteristics, the models produce nearly identical increases in aerosol absorption since the 1960s, constituting as much as half of the modeled clear‐sky dimming. This is due to a compensation between the differences in aerosol column burden and mixing state assumed in the two models, i.e., plausible clear‐sky SSR simulations can be achieved via drastically different aerosol parameterizations. Our novel results indicate that trends in aerosol absorption drive a large portion of East Asian clear‐sky solar dimming in the models presented here and for the time periods analyzed and that mechanistic analysis of the factors involved in aerosol absorption is an important diagnostic in evaluating modeled clear‐sky solar dimming trends.
WWBs, ENSO predictability, the spring barrier and extreme events
Authors: Lopez Hosmay , Kirtman Ben P. 
Published: August 2014

AbstractThis study examines how semi‐stochastic Westerly Wind Bursts (WWBs) affect El Niño Southern Oscillation (ENSO) predictability. An ensemble ENSO prediction experiment is presented in which the Community Climate System Model version 3 (CCSM3) and CCSM3 with a state‐dependent WWB parameterization are used as both “truth” and as predictor systems. Inclusion of WWBs has little effect on ENSO predictability if the “truth” lacks WWBs. If the “truth” includes WWBs, the limit of ENSO predictability is larger for a forecast system that captures the correct statistics of WWBs. Predictability drops considerably if a forecast system that lacks WWB events is used to predict a “truth” that includes WWBs. At longer lead times, predictability is more dependent on the dynamical properties of the truth; that is, the importance of capturing the WWB statistics becomes less important and the statistics (e.g., signal‐to‐noise ratio) of the truth determine the limit of predictability. At short leads, ENSO predictability depends on the prediction system and the “truth.” ENSO prediction skill is model and phase dependent. Predictability of extreme warm events remains a challenge as the number of ensemble members required to capture these events is on the order of 100 members. Finally, we examine real ENSO predictions with and without the WWB parameterization. It is found that including WWBs in the prediction system significantly increases ENSO prediction skill compared with a prediction system that lacks WWBs. Also, it is found that the so‐called forecast spring prediction barrier is, at least partially, caused by the lack of WWB representation in the forecast system.
West African monsoon demise: Climatology, interannual variations, and relationship to seasonal rainfall
Authors: Zhang Gang , Cook Kerry H. 
Published: August 2014

AbstractThe climatology and interannual variations of the West African monsoon demise are investigated using the Tropical Rainfall Measuring Mission and the Global Precipitation Climatology Project precipitation data sets along with the ERA‐Interim reanalysis. During monsoon demise, the rainfall maximum progresses southward from the Sahel to the Gulf of Guinea. The West African monsoon demise is smooth, with no evidence of a meridional jump of the rainfall maximum as occurs during monsoon onset. The climatological monsoon demise date, defined by using a 2 mm d−1 rainfall threshold for the Sahel, is 20 October. The demise date varies up to 25 days during the period 1979–2012, between 5 and 30 October. An early (late) demise is associated with an anomalously strong (weak) North Atlantic subtropical high, which extends over the Mediterranean and the Sahara throughout the demise period. The monsoon season total rainfall is found to be significantly correlated with the demise date. In a composite of early (late) demise cases, northerly (southerly) moisture flux anomalies, which enhance (reduce) moisture divergence, are associated with an anomalously strong (weak) North Atlantic subtropical high. In addition, the early (late) demise of the West African monsoon is accompanied by cold (warm) sea surface temperature anomalies in the subtropical North Atlantic.
Aquarius: Status and recent results
Authors: Le Vine D. M. , Dinnat E. P. , Lagerloef G. S. E. , de Matthaeis P. , Abraham S. , Utku C. , Kao H. 
Published: August 2014

AbstractAquarius is a combination active/passive instrument at L band designed to map sea surface salinity globally from space. The radiometer (passive) is the primary instrument for retrieving salinity, and the scatterometer (active) provides information to correct for a major source of error, sea surface roughness (waves). In addition, the radiometer includes a number of special features designed to meet the goal for this challenging measurement, including measurement of the third Stokes parameter to help with the correction for Faraday rotation and rapid sampling to help with the mitigation of radio frequency interference. Aquarius was launched on 10 June 2011 aboard the Aquarius/SAC‐D observatory and has been working well. The salinity retrieval continues to improve, and the special features suggest the potential for new applications of remote sensing from space at L band.
Oxygen Reduction Reaction in a Droplet on Graphite: Direct Evidence that the Edge Is More Active than the Basal Plane
Authors: Shen Anli , Zou Yuqin , Wang Qiang , Dryfe Robert A. W. , Huang Xiaobing , Dou Shuo , Dai Liming , Wang Shuangyin 
Published: August 2014

AbstractCarbon‐based metal‐free electrocatalysts for the oxygen reduction reaction (ORR) in alkaline medium have been extensively investigated with the aim of replacing the commercially available, but precious platinum‐based catalysts. For the proper design of carbon‐based metal‐free electrocatalysts for the ORR, it would be interesting to identify the active sites of the electrocatalyst. The ORR was now studied with an air‐saturated electrolyte solution droplet (diameter ca. 15 μm), which was deposited at a specified position either on the edge or on the basal plane of highly oriented pyrolytic graphite. Electrochemical measurements suggest that the edge carbon atoms are more active than the basal‐plane ones for the ORR. This provides a direct way to identify the active sites of carbon materials for the ORR. Ball‐milled graphite and carbon nanotubes with more exposed edges were also prepared and showed significantly enhanced ORR activity. DFT calculations elucidated the mechanism by which the charged edge carbon atoms result in the higher ORR activity.
Rhodium(III)‐Catalyzed CC and CO Coupling of Quinoline N‐Oxides with Alkynes: Combination of CH Activation with O‐Atom Transfer
Authors: Zhang Xueyun , Qi Zisong , Li Xingwei 
Published: August 2014

Abstract[Cp*RhIII]‐catalyzed CH activation of arenes assisted by an oxidizing NO or NN directing group has allowed the construction of a number of hetercycles. In contrast, a polar NO bond is well‐known to undergo O‐atom transfer (OAT) to alkynes. Despite the liability of NO bonds in both CH activation and OAT, these two important areas evolved separately. In this report, [Cp*RhIII] catalysts integrate both areas in an efficient redox‐neutral coupling of quinoline N‐oxides with alkynes to afford α‐(8‐quinolyl)acetophenones. In this process the NO bond acts as both a directing group for CH activation and as an O‐atom donor.
Regulation of Structure and Function of Sarcomeric Actin Filaments in Striated Muscle of the Nematode Caenorhabditis elegans
Authors: Ono Shoichiro 
Published: August 2014

ABSTRACTThe nematode Caenorhabditis elegans has been used as a valuable system to study structure and function of striated muscle. The body wall muscle of C. elegans is obliquely striated muscle with highly organized sarcomeric assembly of actin, myosin, and other accessory proteins. Genetic and molecular biological studies in C. elegans have identified a number of genes encoding structural and regulatory components for the muscle contractile apparatuses, and many of them have counterparts in mammalian cardiac and skeletal muscles or striated muscles in other invertebrates. Applicability of genetics, cell biology, and biochemistry has made C. elegans an excellent system to study mechanisms of muscle contractility and assembly and maintenance of myofibrils. This review focuses on the regulatory mechanisms of structure and function of actin filaments in the C. elegans body wall muscle. Sarcomeric actin filaments in C. elegans muscle are associated with the troponin–tropomyosin system that regulates the actin–myosin interaction. Proteins that bind to the side and ends of actin filaments support ordered assembly of thin filaments. Furthermore, regulators of actin dynamics play important roles in initial assembly, growth, and maintenance of sarcomeres. The knowledge acquired in C. elegans can serve as bases to understand the basic mechanisms of muscle structure and function. Anat Rec, 297:1548–1559, 2014. © 2014 Wiley Periodicals, Inc.
Probing Muscle Ankyrin‐Repeat Protein (MARP) Structure and Function
Authors: Lun Alexander Shiang , Chen Ju , Lange Stephan 
Published: August 2014

ABSTRACTMuscle ankyrin‐repeat proteins (MARPs) have been shown to serve diverse functions within cardiac and skeletal muscle cells. Apart from their interactions with sarcomeric proteins like titin or myopalladin that locate them along myofilaments, MARPs are able to shuttle to the nucleus where they act as modulators for a variety of transcription factors. The deregulation of MARPs in many cardiac and skeletal myopathies contributes to their use as biomarkers for these diseases. Many of their functions are attributed to their domain composition. MARPs consist of an N‐terminal coiled‐coil domain responsible for their dimerization. The C‐terminus contains a series of ankyrin repeats, whose best‐characterized function is to bind to the N2A region of the giant sarcomeric protein titin. Here we investigate the nature of their dimerization and their interaction with titin more closely. We demonstrate that the coiled‐coil domain in all MARPs enables their homo‐ and hetero‐dimerization in antiparallel fashion. Protein complementation experiments indicate further antiparallel binding of the ankyrin repeats to titin's N2A region. Binding of MARP to titin also affects its PKA mediated phosphorylation. We demonstrate further that MARPs themselves are phosphorylated by PKA and PKC, potentially altering their structure or function. These studies elucidate structural relationships within the stretch‐responsive MARP/titin complex in cross‐striated muscle cells, and may relate to disease relevant posttranslational modifications of MARPs and titin that alter muscle compliance. Anat Rec, 297:1615–1629, 2014. © 2014 Wiley Periodicals, Inc.
Understanding Cardiac Sarcomere Assembly With Zebrafish Genetics
Authors: Yang Jingchun , Shih Yu‐huan , Xu Xiaolei 
Published: August 2014

ABSTRACTMutations in sarcomere genes have been found in many inheritable human diseases, including hypertrophic cardiomyopathy. Elucidating the molecular mechanisms of sarcomere assembly shall facilitate understanding of the pathogenesis of sarcomere‐based cardiac disease. Recently, biochemical and genomic studies have identified many new genes encoding proteins that localize to the sarcomere. However, their precise functions in sarcomere assembly and sarcomere‐based cardiac disease are unknown. Here, we review zebrafish as an emerging vertebrate model for these studies. We summarize the techniques offered by this animal model to manipulate genes of interest, annotate gene expression, and describe the resulting phenotypes. We survey the sarcomere genes that have been investigated in zebrafish and discuss the potential of applying this in vivo model for larger‐scale genetic studies. Anat Rec, 297:1681–1693, 2014. © 2014 Wiley Periodicals, Inc.
Tenascin‐C in Development and Disease of Blood Vessels
Authors: Imanaka‐Yoshida Kyoko , Yoshida Toshimichi , Miyagawa‐Tomita Sachiko 
Published: August 2014

ABSTRACTTenascin‐C (TNC) is an extracellular glycoprotein categorized as a matricellular protein. It is highly expressed during embryonic development, wound healing, inflammation, and cancer invasion, and has a wide range of effects on cell response in tissue morphogenesis and remodeling including the cardiovascular system. In the heart, TNC is sparsely detected in normal adults but transiently expressed at restricted sites during embryonic development and in response to injury, playing an important role in myocardial remodeling. Although TNC in the vascular system appears more complex than in the heart, the expression of TNC in normal adult blood vessels is generally low. During embryonic development, vascular smooth muscle cells highly express TNC on maturation of the vascular wall, which is controlled in a way that depends on the embryonic site of cell origin. Strong expression of TNC is also linked with several pathological conditions such as cerebral vasospasm, intimal hyperplasia, pulmonary artery hypertension, and aortic aneurysm/ dissection. TNC synthesized by smooth muscle cells in response to developmental and environmental cues regulates cell responses such as proliferation, migration, differentiation, and survival in an autocrine/paracrine fashion and in a context‐dependent manner. Thus, TNC can be a key molecule in controlling cellular activity in adaptation during normal vascular development as well as tissue remodeling in pathological conditions. Anat Rec, 297:1747–1757, 2014. © 2014 Wiley Periodicals, Inc.
Mechanochromic Luminescence of Fluorenyl‐Substituted Ethylenes
Authors: Lv Yun , Liu Yang , Guo Dan , Ye Xin , Liu Guangfeng , Tao Xutang 
Published: August 2014

AbstractIt has been reported several times that some organic luminogens with aggregation‐induced emission (AIE) characteristics exhibit the abnormal phenomenon of crystallization‐induced blueshift fluorescence, which makes them suitable for utilization as luminescence color‐switching materials. Because of the attractive application potential and the numerous underlying structure–property relationships in such materials, we investigated a series of fluorenyl‐containing tetrasubstituted ethylenes for their novel optical properties and structural features. The dyes show morphology‐dependent luminescence. Their emission color can be switched between green and blue by means of mechanical grinding and solvent fuming. The transformation between crystalline and amorphous accounts for the luminescence changing. Through single‐crystal and X‐ray diffraction (XRD) analysis, the twisted molecular geometries and loose packing motifs in the crystalline samples are believed to be the intrinsic origin of the external‐stimuli‐induced structural transformation.