bluuebunny/crossref_metadata_2025_split huggingface dataset:
pseudoQC: A Regression‐Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets
Authors: Wang Shisheng , Yang Hao 
Published: September 2019

AbstractVarious types of unwanted and uncontrollable signal variations in MS‐based metabolomics and proteomics datasets severely disturb the accuracies of metabolite and protein profiling. Therefore, pooled quality control (QC) samples are often employed in quality management processes, which are indispensable to the success of metabolomics and proteomics experiments, especially in high‐throughput cases and long‐term projects. However, data consistency and QC sample stability are still difficult to guarantee because of the experimental operation complexity and differences between experimenters. To make things worse, numerous proteomics projects do not take QC samples into consideration at the beginning of experimental design. Herein, a powerful and interactive web‐based software, named pseudoQC, is presented to simulate QC sample data for actual metabolomics and proteomics datasets using four different machine learning‐based regression methods. The simulated data are used for correction and normalization of the two published datasets, and the obtained results suggest that nonlinear regression methods perform better than linear ones. Additionally, the above software is available as a web‐based graphical user interface and can be utilized by scientists without a bioinformatics background. pseudoQC is open‐source software and freely available at https://www.omicsolution.org/wukong/pseudoQC/.
How demographic developments determine the management of hydrometeorological hazard risks in rural communities: The linkages between demographic and natural hazards research
Authors: Clar Christoph 
Published: September 2019

AbstractThe management of hydrometeorological hazard risks increasingly builds on the notion that the main constituents—hazard risk and vulnerability—have to be understood as dynamic processes. Natural hazards and their impacts are influenced by changes in land use and impacts of climate change, whereas the vulnerability of communities is, inter alia, determined by changes in their demographic composition. Structurally weak rural regions have to face these challenges, while their capacities to manage hydrometeorological risks are affected by major demographic developments, such as population decline and demographic aging (especially in Europe). Nonetheless, academic research regarding this issue is still in its infancy. Research on the relationship between hydrometeorological hazards and long‐term demographic change often focuses on one side of the coin: impacts of hazards on the demographic composition of communities. The impacts of demographic change onto communities' ability to prepare for, respond to and recover from natural hazards appear as disregarded link. This article gives an overview over linkages by reviewing literature at the intersection of demographic and hydrological hazard research. The review of more than 90 publications provides insights into how particular demographic factors (socioeconomic status; migration, residency, and mobility; gender and gender relations; education and knowledge; and religion and beliefs) determine the management of hydrometeorological hazard risks. Furthermore, it identifies publications which consider long‐term developments. The overview shows that we lack a thorough connection between demographic change and hydrometeorological hazard risk management, which would be crucial for in‐depth studies as well as a more dynamic understanding of respective linkages.This article is categorized under:
Science of Water > Water Extremes
Engineering Water > Planning Water
Regulations to protect groundwater resources during unconventional oil and gas extraction using fracking
Authors: Esterhuyse Surina , Vermeulen Danie , Glazewski Jan 
Published: September 2019

AbstractUnconventional oil and gas (UOG) extraction using fracking can damage groundwater resources, a crucial resource in many countries. Protecting groundwater will become more urgent as climate change and population growth increase pressure on water demand, especially in water‐scarce countries. But despite the strategic importance of groundwater, it is often poorly managed during UOG extraction. This review considers three types of regulation (command‐and‐control, market‐based and voluntary) in countries where UOG extraction is allowed, to identify the best suite of regulations to protect groundwater resources during this process. We propose a regulatory framework that includes both “hard” command‐and‐control regulations and “soft” market‐based and voluntary regulations. If regulations are to protect groundwater resources effectively, public disclosure of UOG operations must be required and the information must be stored in publicly accessible databases. This would allow for independent scientific review of data by academia and the private sector, in addition to government scrutiny of the data. These parties can then make recommendations to government, allowing timeous and appropriate adaptive management and the amendment of regulations as necessary. And, most importantly, these regulations must be properly enforced to avoid (in some cases irreversible) damage to groundwater resources.This article is characterized under:
Engineering Water > Sustainable Engineering of Water
Human Water > Water Governance
Science of Water > Water Quality
Signal transducer and activator of transcription-3 drives the high-fat diet-associated prostate cancer growth
Authors: Kwan Hiu Yee , Liu Bin , Huang Chunhua , Fatima Sarwat , Su Tao , Zhao Xiaoshan , Ho Alan H. M. , Han Quanbin , Hu Xianjing , Gong Rui-Hong , Chen Minting , Wong Hoi Leong Xavier , Bian Zhaoxiang 
Published: September 2019

AbstractProstate cancer (PCa) is the second leading cause of cancer death in men. PCa progression can be associated with obesity. Signal transducer and activator of transcription-3 (STAT3) plays a crucial role in PCa growth. However, whether STAT3 plays a role in high-fat diet (HFD)-associated PCa growth is unknown. Our data show that HFD feeding increases tumor size, STAT3 phosphorylation, and palmitic acid (PA) level in the xenograft tissues of the PCa-bearing xenograft mouse model. In vitro studies show that PA increases STAT3 expression and phosphorylation (STAT3-Y705) in PCa. Computational modeling suggests strong and stable binding between PA and unphosphorylated STAT3 at R593 and N538. The binding changes STAT3 structure and activity. Functional studies show that both STAT3 mutants (R583A and N538A) and STAT3 dominant negative significantly reduce PA-enhanced STAT3 phosphorylation, PA-increased PCa cell proliferation, migration, and invasion. In the xenograft mouse models, the HFD-increased tumor growth and STAT3 phosphorylation in tumors are reversed by STAT3 inhibition. Our study not only demonstrates the regulatory role of PA/STAT3 axis in HFD-associated PCa growth but also suggests a novel mechanism of how STAT3 is activated by PA. Our data suggest STAT3 as a therapeutic target for the treatment of HFD-associated PCa.
Transcriptome Analysis of Reticulated Platelets Reveals a Prothrombotic Profile
Authors: Bongiovanni Dario , Santamaria Gianluca , Klug Melissa , Santovito Donato , Felicetta Arianna , Hristov Michael , von Scheidt Moritz , Aslani Maria , Cibella Javier , Weber Christian , Moretti Alessandra , Laugwitz Karl-Ludwig , Peano Clelia , Bernlochner Isabell 
Published: September 2019

AbstractReticulated platelets (RPs) are larger, hyperreactive platelets that contain significantly more ribonucleic acid (RNA) compared with mature platelets (MPs). High levels of RPs in peripheral blood are predictors of an insufficient response to dual antiplatelet therapy in cardiovascular patients and of adverse cardiovascular events. However, the mechanisms underlying these correlations remain widely unknown and the biology of RPs has not been investigated yet. Here, we compared for the first time the transcriptomic profiles of RPs and MPs isolated from peripheral blood of healthy donors. Total RNA sequencing revealed 1,744 differentially expressed genes (670 downregulated, 1,074 upregulated) in RPs compared with MPs. In particular, transcripts for the collagen receptor GP6, thromboxane receptor A2 (TBXA2R), thrombin receptor PAR4 (F2RL3), and adenosine triphosphate receptors P2RX1, ORAI2, and STIM1 (both involved in calcium signaling) were significantly upregulated in RPs, whereas several RNA regulators as the ribonuclease PARN, the RISC-component TNRC6A, and the splicing factor LUC7L3 were downregulated in RPs. Gene ontology analysis revealed an enrichment of relevant biological categories in RPs including platelet activation and blood coagulation. Gene Set Enrichment Analysis showed an overrepresentation of several platelet activation pathways like thrombin, thromboxane, and glycoprotein IIb/IIIa signaling in RPs. Small-RNA sequencing reported 9 micro-RNAs significantly downregulated in RPs with targets involved in platelet reactivity. Our data show for the first time an enrichment of several prothrombotic transcripts in RPs providing a first biological explanation for their hyperreactive phenotype.
The Role of Iron and Siderophores in Infection, and the Development of Siderophore Antibiotics
Authors: Page Malcom G P 
Published: September 2019

AbstractIron is an essential nutrient for bacterial growth, replication, and metabolism. Humans store iron bound to various proteins such as hemoglobin, haptoglobin, transferrin, ferritin, and lactoferrin, limiting the availability of free iron for pathogenic bacteria. However, bacteria have developed various mechanisms to sequester or scavenge iron from the host environment. Iron can be taken up by means of active transport systems that consist of bacterial small molecule siderophores, outer membrane siderophore receptors, the TonB-ExbBD energy-transducing proteins coupling the outer and the inner membranes, and inner membrane transporters. Some bacteria also express outer membrane receptors for iron-binding proteins of the host and extract iron directly from these for uptake. Ultimately, iron is acquired and transported into the bacterial cytoplasm. The siderophores are small molecules produced and released by nearly all bacterial species and are classified according to the chemical nature of their iron-chelating group (ie, catechol, hydroxamate, α-hydroxyl-carboxylate, or mixed types). Siderophore-conjugated antibiotics that exploit such iron-transport systems are under development for the treatment of infections caused by gram-negative bacteria. Despite demonstrating high in vitro potency against pathogenic multidrug-resistant bacteria, further development of several candidates had stopped due to apparent adaptive resistance during exposure, lack of consistent in vivo efficacy, or emergence of side effects in the host. However, cefiderocol, with an optimized structure, has advanced and has been investigated in phase 1 to 3 clinical trials. This article discusses the mechanisms implicated in iron uptake and the challenges associated with the design and utilization of siderophore-mimicking antibiotics.
Secure Computing Resource Allocation Framework For Open Fog Computing
Authors: Jiang Jiafu , Tang Linyu , Gu Ke , Jia WeiJia 
Published: September 2019

AbstractFog computing has become an emerging environment that provides data storage, computing and some other services on the edge of network. It not only can acquire data from terminal devices, but also can provide computing services to users by opening computing resources. Compared with cloud computing, fog devices can collaborate to provide users with powerful computing services through resource allocation. However, as many of fog devices are not monitored, there are some security problems. For example, since fog server processes and maintains user information, device information, task parameters and so on, fog server is easy to perform illegal resource allocation for extra benefits. In this paper, we propose a secure computing resource allocation framework for open fog computing. In our scheme, the fog server is responsible for processing computing requests and resource allocations, and the cloud audit center is responsible for auditing the behaviors of the fog servers and fog nodes. Based on the proposed security framework, our proposed scheme can resist the attack of single malicious node and the collusion attack of fog server and computing devices. Furthermore, the experiments show our proposed scheme is efficient. For example, when the number of initial idle service devices is 40, the rejection rate of allocated tasks is 10% and the total number of sub-tasks is changed from 150 to 200, the total allocation time of our scheme is only changed from 15 ms to 25 ms; additionally, when the task of 5000 order matrix multiplication is tested on 10 service devices, the total computing time of our scheme is $\sim$250 s, which is better than that of single computer (where single computer needs more than 1500 s). Therefore, our proposed scheme has obvious advantages when it faces some tasks that require more computational cost, such as complex scientific computing, distributed massive data query, distributed image processing and so on.
Long-term prognostic value of morphological plaque features on coronary computed tomography angiography
Authors: Finck Tom , Stojanovic Antonija , Will Albrecht , Hendrich Eva , Martinoff Stefan , Hausleiter Jörg , Hadamitzky Martin 
Published: September 2019

Abstract

Aims
To investigate the incremental prognostic value of morphological plaque features beyond clinical risk and coronary stenosis levels. Although associated with the degree of coronary stenosis, most cardiac events occur on the basis of ruptured non-obstructive plaques and consecutive vessel thrombosis. As such, identification of vulnerable plaques is paramount for cardiovascular risk prediction and treatment decisions.

Methods and results
A total of 1615 patients with suspected but not previously diagnosed coronary artery disease (CAD) were examined by coronary computed tomography angiography and morphological plaque features were assessed. Mean follow-up was 10.5 (interquartile range 9.2–11.4) years. Cox proportional hazards analysis was used for the composite endpoint of cardiac death and non-fatal myocardial infarction. The study endpoint was reached in 51 patients (36 cardiac deaths, 15 non-fatal myocardial infarctions). In addition to quantitative parameters (presence of any calcified/non-calcified plaque or elevated plaque load), morphologic plaque features such as a spotty or gross calcification pattern and napkin-ring sign (NRS) were predictive for events. However, only spotty calcified plaques and NRS could confer additive prognostic value beyond clinical risk and coronary stenosis level. In a stepwise approach, endpoint prediction beyond clinical risk (Morise score) could be improved by inclusion of CAD severity (χ2 of 27.5, P < 0.001) and further discrimination for spotty calcified plaques (χ2 of 3.89, P = 0.049).

Conclusion
Improved cardiovascular risk prediction beyond clinical risk and coronary stenosis levels can be made by discriminating for the presence of spotty calcified plaques. Thus, an intensified prophylactic anti-atherosclerotic treatment appears to be warranted in patients with coronary plaques that show spotty calcifications.
Association of human papillomavirus infection and inflammation in cervical cancer
Authors: Hemmat Nima , Bannazadeh Baghi Hossein 
Published: September 2019

ABSTRACTHuman papillomavirus (HPV) associated cancers, and in particular cervical cancer, are considered to be directly stimulated by HPV oncogenes. Alternatively, these types of cancers could also be indirectly stimulated by HPV-induced chronic inflammations, which in turn are also caused by HPV oncogenes activity. Chronic inflammation is associated with repeated tissue injury and development of mutations in the vital tumor suppressor genes. Thus, it is important to understand that the persistent HPV infection and its associated chronic inflammation is responsible for the progression of HPV-induced cancers. HPV E5, E6 and E7 could upregulate the expression of cyclooxygenase (COX)-2 and prostaglandin (PG) E2 followed by the activation of the COX-PG pathway. This pathway is assumed to be the main cause of HPV-induced inflammation. Additionally, HPV oncogenes could have an impact on the upregulation of pro-inflammatory cytokines in HPV-positive patients. The upregulation of such cytokines accelerates the incidence of inflammation following HPV infection. Other factors such as microRNAs, which are involved in the inflammation pathways and aging, give rise to the increased level of pro-inflammatory cytokines and could also be responsible for the acceleration of HPV-induced inflammation and consequent cervical cancer. In this review, the exact roles of HPV oncogenes in the occurrence of inflammation in cervical tissue, and the effects of other factors in this event are evaluated.
Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution
Authors: Chen Qingjian , Lan Ao , Shen Xu , Wu Chung-I 
Published: September 2019

AbstractThe widely accepted view that evolution proceeds in small steps is based on two premises: 1) negative selection acts strongly against large differences and 2) positive selection favors small-step changes. The two premises are not biologically connected and should be evaluated separately. We now extend a previous approach to studying codon evolution in the entire genome. Codon substitution rate is a function of the physicochemical distance between amino acids (AAs), equated with the step size of evolution. Between nine pairs of closely related species of plants, invertebrates, and vertebrates, the evolutionary rate is strongly and negatively correlated with a set of AA distances (ΔU, scaled to [0, 1]). ΔU, a composite measure of evolutionary rates across diverse taxa, is influenced by almost all of the 48 physicochemical properties used here. The new analyses reveal a crucial trend hidden from previous studies: ΔU is strongly correlated with the evolutionary rate (R2 > 0.8) only when the genes are predominantly under negative selection. Because most genes in most taxa are strongly constrained by negative selection, ΔU has indeed appeared to be a nearly universal measure of codon evolution. In conclusion, molecular evolution at the codon level generally takes small steps due to the prevailing negative selection. Whether positive selection may, or may not, follow the small-step rule is addressed in a companion study.
Uniform Bound for the Number of Rational Points on a Pencil of Curves
Authors: Dimitrov Vesselin , Gao Ziyang , Habegger Philipp 
Published: September 2019

AbstractConsider a one-parameter family of smooth, irreducible, projective curves of genus $g\ge 2$ defined over a number field. Each fiber contains at most finitely many rational points by the Mordell conjecture, a theorem of Faltings. We show that the number of rational points is bounded only in terms of the family and the Mordell–Weil rank of the fiber’s Jacobian. Our proof uses Vojta’s approach to the Mordell Conjecture furnished with a height inequality due to the 2nd- and 3rd-named authors. In addition we obtain uniform bounds for the number of torsion points in the Jacobian that lie in each fiber of the family.
Producing a BOSS CMASS sample with DES imaging
Authors: Lee S , Huff E M , Ross A J , Choi A , Hirata C , Honscheid K , MacCrann N , Troxel M A , Davis C , Eifler T F , Cawthon R , Elvin-Poole J , Annis J , Avila S , Bertin E , Brooks D , Carnero Rosell A , Carrasco Kind M , Carretero J , da Costa L N , De Vicente J , Desai S , Flaugher B , Fosalba P , García-Bellido J , Gaztanaga E , Gerdes D W , Gruen D , Gruendl R A , Gschwend J , Gutierrez G , Hollowood D L , James D J , Jeltema T , Kuehn K , Lima M , Maia M A G , Marshall J L , Martini P , Melchior P , Menanteau F , Miller C J , Miquel R , Ogando R L C , Palmese A , Plazas A A , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Smith M , Soares-Santos M , Sobreira F , Suchyta E , Swanson M E C , Tarle G , Thomas D , Weller J , Zuntz J ,   (DES Collaboration)
Published: September 2019

ABSTRACT
We present a sample of galaxies with the Dark Energy Survey (DES) photometry that replicates the properties of the BOSS CMASS sample. The CMASS galaxy sample has been well characterized by the Sloan Digital Sky Survey (SDSS) collaboration and was used to obtain the most powerful redshift-space galaxy clustering measurements to date. A joint analysis of redshift-space distortions (such as those probed by CMASS from SDSS) and a galaxy–galaxy lensing measurement for an equivalent sample from DES can provide powerful cosmological constraints. Unfortunately, the DES and SDSS-BOSS footprints have only minimal overlap, primarily on the celestial equator near the SDSS Stripe 82 region. Using this overlap, we build a robust Bayesian model to select CMASS-like galaxies in the remainder of the DES footprint. The newly defined DES-CMASS (DMASS) sample consists of 117 293 effective galaxies covering $1244\,\deg ^2$. Through various validation tests, we show that the DMASS sample selected by this model matches well with the BOSS CMASS sample, specifically in the South Galactic cap (SGC) region that includes Stripe 82. Combining measurements of the angular correlation function and the clustering-z distribution of DMASS, we constrain the difference in mean galaxy bias and mean redshift between the BOSS CMASS and DMASS samples to be $\Delta b = 0.010^{+0.045}_{-0.052}$ and $\Delta z = \left(3.46^{+5.48}_{-5.55} \right) \times 10^{-3}$ for the SGC portion of CMASS, and $\Delta b = 0.044^{+0.044}_{-0.043}$ and $\Delta z= (3.51^{+4.93}_{-5.91}) \times 10^{-3}$ for the full CMASS sample. These values indicate that the mean bias of galaxies and mean redshift in the DMASS sample are consistent with both CMASS samples within 1σ.
Infrared-excess white dwarfs in the Gaia 100 pc sample
Authors: Rebassa-Mansergas A , Solano E , Xu(#x8BB8;#x5072;#x827A;) S , Rodrigo C , Jiménez-Esteban F M , Torres S 
Published: September 2019

Abstract
We analyse the 100 pc Gaia white dwarf volume-limited sample by means of VOSA (Virtual Observatory SED Analyser) with the aim of identifying candidates for displaying infrared excesses. Our search focuses on the study of the spectral energy distribution (SED) of 3,733 white dwarfs with reliable infrared photometry and GBP − GRP colours below 0.8 mag, a sample which seems to be nearly representative of the overall white dwarf population. Our search results in 77 selected candidates, 52 of which are new identifications. For each target we apply a two-component SED fitting implemented in VOSA to derive the effective temperatures of both the white dwarf and the object causing the excess. We calculate a fraction of infrared-excess white dwarfs due to the presence of a circumstellar disk of 1.6±0.2%, a value which increases to 2.6±0.3% if we take into account incompleteness issues. Our results are in agreement with the drop in the percentage of infrared excess detections for cool (<8,000 K) and hot (>20,000 K) white dwarfs obtained in previous analyses. The fraction of white dwarfs with brown dwarf companions we derive is ≃0.1–0.2%.