bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anisotropic slope limiting for discontinuous Galerkin methods
Authors: Aizinger Vadym , Kosík Adam , Kuzmin Dmitri , Reuter Balthasar 
Published: January 2017

SummaryIn this paper, we present an anisotropic version of a vertex‐based slope limiter for discontinuous Galerkin methods. The limiting procedure is carried out locally on each mesh element utilizing the bounds defined at each vertex by the largest and smallest mean value from all elements containing the vertex. The application of this slope limiter guarantees the preservation of monotonicity. Unnecessary limiting of smooth directional derivatives is prevented by constraining the x and y components of the gradient separately. As an inexpensive alternative to optimization‐based methods based on solving small linear programming problems, we propose a simple operator splitting technique for calculating the correction factors for the x and y derivatives. We also provide the necessary generalizations for using the anisotropic limiting strategy in an arbitrary rotated frame of reference and in the vicinity of exterior boundaries with no Dirichlet information. The limiting procedure can be extended to elements of arbitrary polygonal shape and three dimensions in a straightforward fashion. The performance of the new anisotropic slope limiter is illustrated by two‐dimensional numerical examples that employ piecewise linear discontinuous Galerkin approximations. Copyright © 2017 John Wiley & Sons, Ltd.
Mapping complementary features of cross‐species structural connectivity to construct realistic “Virtual Brains”
Authors: Bezgin Gleb , Solodkin Ana , Bakker Rembrandt , Ritter Petra , McIntosh Anthony R. 
Published: January 2017

AbstractModern systems neuroscience increasingly leans on large‐scale multi‐lab neuroinformatics initiatives to provide necessary capacity for biologically realistic modeling of primate whole‐brain activity. Here, we present a framework to assemble primate brain's biologically plausible anatomical backbone for such modeling initiatives. In this framework, structural connectivity is determined by adding complementary information from invasive macaque axonal tract tracing and non‐invasive human diffusion tensor imaging. Both modalities are combined by means of available interspecies registration tools and a newly developed Bayesian probabilistic modeling approach to extract common connectivity evidence. We demonstrate how this novel framework is embedded in the whole‐brain simulation platform called The Virtual Brain (TVB). Hum Brain Mapp 38:2080–2093, 2017. © 2017 Wiley Periodicals, Inc.
Closing the PDF gap: ReadCube’s experiments in reader‐focused design
Authors: Hodgson Alex , Schlager Lucas 
Published: January 2017

Key points

Twenty years ago, a fraction of articles were paired with supplements; now, one in five research stories go beyond PDF.
Why has the evolution of research content's delivery vehicles lagged behind the evolution of the research story?
Hyperlinked in‐line references are the most used feature of the Enhanced PDF – exposing faster, easier ways to follow the path of research.
Discovery need not start and end with the search engine – it can start within the PDF itself.
Discovery is not a solitary process; therefore, content platforms must support collaboration to drive readership.
Hyperbranched Polymers Formed through Irreversible Step Polymerization of AB2‐Type Monomer in a Continuous Flow Stirred‐Tank Reactor (CSTR)
Authors: Tobita Hidetaka 
Published: January 2017

Hyperbranched polymers formed through step polymerization of AB2‐type monomer with equal reactivity for both B groups in a continuous flow stirred‐tank reactor (CSTR) are investigated theoretically. The weight fraction distribution at high molecular weight tail follows a power law, W(P) ∝ P
−1/ξ for ξ ≤ 0.5 with , where is the mean residence time. The degree of branching (DB) at the large degree of polymerization (P) limit is DB
P→∞ = 0.6 irrespective of the ξ‐value, which is larger than the case for the corresponding batch polymerization that gives DB
P→∞ = 0.5. The relationship between the radius of gyration 〈s
2〉0 and P shows that the hyperbranched polymers formed in a CSTR are very compact, and the 〈s
2〉0‐values for large polymers are even smaller than the smallest possible case for a batch reactor with DB
P→∞ = 1. For large polymers, the power law 〈s
2〉0∝P
1/3 holds, which is 〈s
2〉0∝P
1/2 for batch polymerization.
image
Combined miRNA profiling and proteomics demonstrates that different miRNAs target a common set of proteins to promote colorectal cancer metastasis
Authors: Torres Sofía , Garcia‐Palmero Irene , Bartolomé Rubén A , Fernandez‐Aceñero María Jesús , Molina Elena , Calviño Eva , Segura Miguel F , Casal J Ignacio 
Published: January 2017

AbstractThe process of liver colonization in colorectal cancer remains poorly characterized. Here, we addressed the role of microRNA (miRNA) dysregulation in metastasis. We first compared miRNA expression profiles between colorectal cancer cell lines with different metastatic properties and then identified target proteins of the dysregulated miRNAs to establish their functions and prognostic value. We found that 38 miRNAs were differentially expressed between highly metastatic (KM12SM/SW620) and poorly metastatic (KM12C/SW480) cancer cell lines. After initial validation, we determined that three miRNAs (miR‐424‐3p, −503, and −1292) were overexpressed in metastatic colorectal cancer cell lines and human samples. Stable transduction of non‐metastatic cells with each of the three miRNAs promoted metastatic properties in culture and increased liver colonization in vivo. Moreover, miR‐424‐3p and miR‐1292 were associated with poor prognosis in human patients. A quantitative proteomic analysis of colorectal cancer cells transfected with miR‐424‐3p, miR‐503, or miR‐1292 identified alterations in 149, 129, or 121 proteins, respectively, with an extensive overlap of the target proteins of the three miRNAs. Importantly, down‐regulation of two of these shared target proteins, CKB and UBA2, increased cell adhesion and proliferation in colorectal cancer cells. The capacity of distinct miRNAs to regulate the same mRNAs boosts the capacity of miRNAs to regulate cancer metastasis and underscores the necessity of targeting multiple miRNAs for effective cancer therapy. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Application of metal − organic frameworks
Authors: Pettinari Claudio , Marchetti Fabio , Mosca Nello , Tosi Giovanni , Drozdov Andrei 
Published: January 2017

AbstractThe burgeoning field of metal − organic frameworks or porous coordination polymers has received increasing interest in recent years. In the last decade these microporous materials have found several applications including storage and separation of gases, sensors, catalysis and functional materials. In order to better design new metal − organic frameworks and porous coordination polymers with specific functionalities a fundamental issue is to achieve a basic understanding of the relationship between molecular parameters and structures, preferred adsorption sites and properties by using using modern theoretical methods. The focus of this mini‐review is a description of the potential and emerging applications of metal − organic frameworks. © 2017 Society of Chemical Industry
An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences
Authors: Knutson Stacy T. , Westwood Brian M. , Leuthaeuser Janelle B. , Turner Brandon E. , Nguyendac Don , Shea Gabrielle , Kumar Kiran , Hayden Julia D. , Harper Angela F. , Brown Shoshana D. , Morris John H. , Ferrin Thomas E. , Babbitt Patricia C. , Fetrow Jacquelyn S. 
Published: January 2017

AbstractProtein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.
Using PyMOL as a platform for computational drug design
Authors: Yuan Shuguang , Chan H.C. Stephen , Hu Zhenquan 
Published: January 2017

PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing, and making movies. This Python‐based software, alongside many Python plugin tools, has been developed to enhance its utilities and facilitate the drug design in PyMOL. To gain an insightful view of useful drug design tools and their functions in PyMOL, we present an extensive discussion on various molecular modeling modules in PyMOL, covering those for visualization and analysis enhancement, protein–ligand modeling, molecular simulations, and drug screening. This review provides an excellent introduction to present 3D structures visualization and computational drug design in PyMOL. WIREs Comput Mol Sci 2017, 7:e1298. doi: 10.1002/wcms.1298This article is categorized under:

Structure and Mechanism > Molecular Structures
Computer and Information Science > Visualization
Molecular and Statistical Mechanics > Molecular Mechanics
Partial Splenectomy is Superior to Total Splenectomy for Selected Patients with Hemangiomas or Cysts
Authors: Wang Lei , Xu Jianwei , Li Feng , Zhan Hanxiang , Liu Han , Chen Wei , Hu Sanyuan 
Published: January 2017

AbstractBackgroundThe superiority of partial splenectomy (PS) as a treatment for benign tumors has not well been confirmed. This study aimed to identify the short‐ and long‐term outcomes of PS, to compare laparoscopic and laparotomic PS, and to demonstrate whether the effects of PS are superior to that of total splenectomy (TS).MethodsPatients with either a hemangioma or cyst who underwent PS or TS from 2009 to 2015 at Qilu Hospital of Shandong University were included. Clinical parameters were collected and analyzed.ResultsA total of 17 patients underwent PS were collected, including 2 men and 15 women with a mean age of 43.9 ± 11.3 years old. Patients who underwent laparoscopic PS (9 cases) had a longer operative time and shorter postoperative hospital stay than those who underwent laparotomy (8 cases). Compared with TS (22 cases), PS significantly decreased the incidence of thrombocytosis, shortened time until drainage removal, and shortened postoperative hospital stay. After an average follow‐up of 34.8 months, patients who underwent TS showed a higher incidence of thrombocytosis and splenic vein thrombosis compared with patients underwent PS.ConclusionsPS is technically feasible and provides favorable short‐ and long‐term outcomes for selected patients with either a hemangioma or cyst compared with TS. Laparoscopic PS shows lower morbidity and equal therapeutic efficacy compared with laparotomic PS and can be widely performed.
The Impact of Fatty Acid Composition on Transportation Fuel Yields via the Non‐Catalytic Cracking of Triacylglyceride Oils
Authors: Seames Wayne , Linnen Michael , Sander Blake , Wills Robert 
Published: January 2017

AbstractA wide spectrum of triacylglyceride (TG) oils were decomposed in batch lab and continuous pilot‐scale reactors to generate an extensive database, which was then used to construct a model to predict the detailed composition of products generated during non‐catalytic cracking. The model was then coupled with additional simulated process steps to determine the yields of transportation products and other chemical co‐products meeting specifications of their petroleum analogs as validated with laboratory testing. A statistical study was then performed to use the model to analyze the impact that changes in TG oil composition have upon target product yields. In this study, the model was used to simulate a viable suite of products for every TG oil analyzed. The model predicts minor differences in the ratio of products from various different fatty acid compositions. For example, it was found that stearic (C18:0), oleic (C18:1), and erucic (C22:1) acids show a positive effect on fuel yields. By contrast, palmitic (C16:0), linoleic (C18:2), and linolenic (C18:3) acids have negative impacts on fuel yields. From these results, a hypothetical “ideal” TG oil was constructed. This oil turns out to have a composition that is very close to the composition of high oleic sunflower oil.
Inpatient Urine Cultures Are Frequently Performed Without Urinalysis or Microscopy: Findings From a Large Academic Medical Center
Authors: Carlson Abigail L. , Munigala Satish , Russo Anthony J. , McMullen Kathleen M. , Wood Helen , Jackups Ronald , Warren David K. 
Published: January 2017

OBJECTIVETo describe the frequency of urine cultures performed in inpatients without additional testing for pyuriaDESIGNRetrospective cohort studySETTINGA 1,250-bed academic tertiary referral centerPATIENTSHospitalized adultsMETHODSThis study included urine cultures drawn on 4 medical and 2 surgical wards from 2009 to 2013 and in the medical and surgical intensive care units (ICUs) from 2012 to 2013. Patient and laboratory data were abstracted from the hospital’s medical informatics database. We identified catheter-associated urinary tract infections (CAUTIs) in the ICUs by routine infection prevention surveillance. Cultures without urinalysis or urine microscopy were defined as “isolated.” The primary outcome was the proportion of isolated urine cultures obtained. We used multivariable logistic regression to assess predictors of isolated cultures.RESULTSDuring the study period, 14,743 urine cultures were obtained (63.5 cultures per 1,000 patient days) during 11,820 patient admissions. Of these, 2,973 cultures (20.2%) were isolated cultures. Of the 61 CAUTIs identified, 31 (50.8%) were identified by an isolated culture. Predictors for having an isolated culture included male gender (adjusted odds ratio [aOR], 1.22; 95%; confidence interval [CI], 1.11–1.35], urinary catheterization (aOR, 2.15; 95% CI, 1.89–2.46), ICU admission (medical ICU aOR, 1.72; 95% CI, 1.47–2.00; surgical ICU aOR, 1.82; 95% CI, 1.51–2.19), and obtaining the urine culture ≥1 calendar day after admission (1–7 days aOR, 1.91; 95% CI. 1.71–2.12; >7 days after admission aOR, 2.81; 95% CI, 2.37–3.34).CONCLUSIONSIsolated urine cultures are common in hospitalized patients, particularly in patients with urinary catheters and those in ICUs. Interventions targeting inpatient culturing practices may improve the diagnosis of urinary tract infections.Infect Control Hosp Epidemiol2017;38:455–460
A Randomized Trial to Determine the Impact of an Educational Patient Hand-Hygiene Intervention on Contamination of Hospitalized Patient’s Hands with Healthcare-Associated Pathogens
Authors: Sunkesula Venkata C. K. , Kundrapu Sirisha , Knighton Shanina , Cadnum Jennifer L. , Donskey Curtis J. 
Published: January 2017

We conducted a non-blinded randomized trial to determine the impact of a patient hand-hygiene intervention on contamination of hospitalized patients’ hands with healthcare-associated pathogens. Among patients with negative hand cultures on admission, recovery of pathogens from hands was significantly reduced in those receiving the intervention versus those receiving standard care.Infect Control Hosp Epidemiol 2017;38:595–597
Low-Flow Pressure Gradient Pumping for Active Absorption of CO2 on a Molecular Sieve
Authors: Cheng Peng , Wu Shugang , Fu Yunchong , Xiong Xiaohu , Niu Zhenchuan , Fan Yukun 
Published: January 2017

AbstractThe authors have developed an active absorption system combining a molecular sieve with a pressure gradient as a way to overcome the shortcomings of the phosphoric acid solution displacement method. Taking advantage of the pressure gradient produced between the inside and outside of a bottle, as water moves through it, CO2 in the atmosphere can actively be absorbed onto a molecular sieve in its pathway. A comparative study showed that the technique was in agreement with the phosphoric acid displacement method, within error. We applied the new method to collect not only atmospheric CO2 samples, but also CO2 samples from soil respiration to verify its utility. Simple yet practical, our method is well suited to extended collection times in a variety of environments, and capable of providing relatively large amounts of carbon for high-precision accelerator mass spectrometry (AMS) 14C analyses of atmospheric samples.
Preparation Methods of μg Carbon Samples for14C MeasuremenTS
Authors: Steier Peter , Liebl Jakob , Kutschera Walter , Wild Eva Maria , Golser Robin 
Published: January 2017

AbstractSystematic investigations and experience from several application projects on small carbon samples over a number of years have resulted in measuring the radiocarbon content of 10 μg C samples with an overall precision of typically 1%. A substantial reduction of the carbon contamination during graphitization was achieved, resulting in 31±30 ng modern and <100 ng14C-free carbon. Thus, graphitization is no longer the limiting factor because earlier sample preparation steps usually introduce much larger contamination. The method has been extended to a variety of materials and applied to various projects. Realistic conditions for procedure development can only be achieved in the context of applications on true samples; methods developed are the lyophilization of samples in solution, combustion, ultraviolet oxidation, or carbonate hydrolysis with phosphoric acid, which allows to prepare samples for a wide range of applications. Insights gained from systematic investigations and from real applications are presented.
Co-morbid obsessive–compulsive disorder and depression: a Bayesian network approach
Authors: McNally R. J. , Mair P. , Mugno B. L. , Riemann B. C. 
Published: January 2017

BackgroundObsessive–compulsive disorder (OCD) is often co-morbid with depression. Using the methods of network analysis, we computed two networks that disclose the potentially causal relationships among symptoms of these two disorders in 408 adult patients with primary OCD and co-morbid depression symptoms.MethodWe examined the relationship between the symptoms constituting these syndromes by computing a (regularized) partial correlation network via the graphical LASSO procedure, and a directed acyclic graph (DAG) via a Bayesian hill-climbing algorithm.ResultsThe results suggest that the degree of interference and distress associated with obsessions, and the degree of interference associated with compulsions, are the chief drivers of co-morbidity. Moreover, activation of the depression cluster appears to occur solely through distress associated with obsessions activating sadness – a key symptom that ‘bridges’ the two syndromic clusters in the DAG.ConclusionsBayesian analysis can expand the repertoire of network analytic approaches to psychopathology. We discuss clinical implications and limitations of our findings.
Neural indicators of interpersonal anger as cause and consequence of combat training stress symptoms
Authors: Gilam G. , Lin T. , Fruchter E. , Hendler T. 
Published: January 2017

BackgroundAngry outbursts are an important feature of various stress-related disorders, and commonly lead to aggression towards other people. Findings regarding interpersonal anger have linked the ventromedial prefrontal cortex (vmPFC) to anger regulation and the locus coeruleus (LC) to aggression. Both regions were previously associated with traumatic and chronic stress symptoms, yet it is unclear if their functionality represents a consequence of, or possibly also a cause for, stress symptoms. Here we investigated the relationship between the neural trajectory of these indicators of anger and the development and manifestation of stress symptoms.MethodA total of 46 males (29 soldiers, 17 civilians) participated in a prospective functional magnetic resonance imaging experiment in which they played a modified interpersonal anger-provoking Ultimatum Game (UG) at two-points. Soldiers were tested at the beginning and end of combat training, while civilians were tested at the beginning and end of civil service. We assumed that combat training would induce chronic stress and result in increased stress symptoms.ResultsSoldiers showed an increase in stress symptoms following combat training while civilians showed no such change following civil service. All participants were angered by the modified UG irrespective of time point. Higher post-combat training stress symptoms were associated with lower pre-combat training vmPFC activation and with higher activation increase in the LC between pre- and post-combat training.ConclusionsResults suggest that during anger-provoking social interactions, flawed vmPFC functionality may serve as a causal risk factor for the development of stress symptoms, and heightened reactivity of the LC possibly reflects a consequence of stress-inducing combat training. These findings provide potential neural targets for therapeutic intervention and inoculation for stress-related psychopathological manifestations of anger.
World Factory: Theatre, Labor, and China's “New Left”
Authors: Steen Shannon 
Published: January 2017

In today's China, how are we supposed to understand the notion of “work,” after the chaos of the socialist period, and after the conversion to capitalism, and now after globalization? Marx said that labor makes people, this was one of his fundamental principles. So how are we supposed to understand labor today? What does it mean for us?—Grass Stage,World FactoryThe insistence on “socialism with Chinese characteristics” often sounds quite vacuous, and yet it is a constant reminder of the Chinese resistance to dissolution into capitalism and the continued reaffirmation of one kind of socialist past in the search for another kind of socialist future.—Arif Dirlik, “Back to the Future”