bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular and genetic diversity in the metastatic process of melanoma
Authors: Harbst Katja , Lauss Martin , Cirenajwis Helena , Winter Christof , Howlin Jillian , Törngren Therese , Kvist Anders , Nodin Björn , Olsson Eleonor , Häkkinen Jari , Jirström Karin , Staaf Johan , Lundgren Lotta , Olsson Håkan , Ingvar Christian , Gruvberger‐Saal Sofia K , Saal Lao H , Jönsson Göran
Published: January 2014

Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene‐expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene‐expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
Reactive compatibilization of poly(l‐lactide)/poly(butylene succinate) blends through polyester maleation: from materials to properties
Authors: Persenaire Olivier , Quintana Robert , Lemmouchi Yahia , Sampson John , Martin Stuart , Bonnaud Leïla , Dubois Philippe
Published: January 2014

The melt blending of poly(l‐lactide) (PLLA) with biodegradable poly(butylene succinate) (PBS) is considered with a view to fine‐tuning its mechanical properties and its degradability. For this purpose, both maleic‐anhydride‐grafted PLLA (PLLA‐g‐MA) and maleic‐anhydride‐grafted PBS (PBS‐g‐MA) were prepared and used as reactive compatibilizers. The influence of PBS melt viscosity on the morphology and mechanical properties of PLLA/PBS blends was studied. Interestingly, the blending of low viscosity PBS with PLLA allows PLLA to be toughened while the use of high viscosity PBS led to PLLA/PBS blends exhibiting co‐continuous morphology. The nanostructure of the co‐continuous blends may be tuned through the joint action of organo‐modified clays and reactive compatibilizers. The effect of PBS on PLLA degradability was also investigated. The accelerated weathering testing of blends reveals that such combination of biodegradable polymers allows their degradability rate to be tailored. It is found that the addition of 20 wt% PBS to PLLA allows the molar mass loss fraction to be doubled after 425 h of testing. © 2014 Society of Chemical Industry
Lower Extremity Muscle Activation During Functional Exercises in Patients With and Without Chronic Ankle Instability
Authors: Feger Mark A. , Donovan Luke , Hart Joseph M. , Hertel Jay
Published: January 2014

Objective

To determine whether individuals with chronic ankle instability (CAI) exhibit altered neuromuscular control as demonstrated by surface electromyography (EMG) amplitudes compared with healthy controls during single‐limb eyes‐closed balance, Star Excursion Balance Test, forward lunge, and lateral hop exercises.

Design

A cross‐sectional laboratory study.

Setting

A research laboratory.

Participants

Fifteen young adults with CAI and 15 healthy controls.

Interventions

The subjects performed functional exercises while surface EMG signals were recorded from the tibialis anterior, peroneus longus, lateral gastrocnemius, rectus femoris, biceps femoris, and gluteus medius.

Main Outcome Measurements

Surface EMG amplitudes (root mean square area) for each muscle, muscles of the shank (distal 3 muscles), muscles of the thigh (proximal 3 muscles), and total muscle activity (all 6 muscles) of the lower extremity were analyzed and compared between the groups.

Results

Individuals with CAI demonstrated significantly less EMG activity in the muscles of the lower extremity during all 4 functional exercises. Effect sizes for significant differences between groups ranged from −0.75 to −1.08, none of which had 95% confidence intervals that crossed zero, which indicates moderate to large decreases in muscle activity in patients with CAI compared with healthy controls.

Conclusions

Patients with CAI demonstrated decreased muscle activity of ankle, knee, and hip musculature during common functional rehabilitative tasks. Clinicians may benefit from implementing functional exercises for patients with CAI that target both distal and proximal muscles of the lower extremity.
Deconversion and Disaffiliation in Contemporary US Roman Catholicism
Authors: Beaudoin Tom
Published: January 2014

Disaffiliation—when members of religious communities leave—has recently become a popular topic for theological and social scientific investigation. Today, fewer Roman Catholics than in recent memory describe themselves as strong members of their church. Many have left to seek other spiritual paths, and many of those who remain do not believe and practice as the Church teaches that they should. These essays propose that the theoretical framework of “deconversion” provides a broader and more effective way to understand forms of religious change that are occurring in contemporary America. In the classroom, teaching theology can take on a specific productive shape when the surrounding culture challenges theologians to take deconversion seriously as an element of, and larger context for, spiritual identity today. Theology remains vital when patient curiosity about the current adventure of religious identity is foregrounded pedagogically. Concluding thoughts sketch some important characteristics of an evangelical church, more concerned with its mission and witness in the world than with maintaining its internal life.
Dust grain surface potential in a non-Maxwellian dusty plasma with negative ions
Authors: ABID A. A. , ALI S. , MUHAMMAD R.
Published: January 2014

Dust charging processes involving the collection of electrons and positive/negative ions in a non-equilibrium dusty plasma are revisited by employing the power-law kappa (κ)-distribution function. In this context, the current balance equation is solved to obtain dust grain surface potential in the presence of negative ions. Numerically, it is found that plasma parameters, such as the κ spectral index, the negative ion-to-electron temperature ratio (γ), the negative–positive ion number density ratio (α), and the negative ion streaming speed (U0) significantly modify the dust grain potential profiles. In particular, for large kappa values, the dust grain surface potential reduces to the Maxwellian case, and at lower kappa values the magnitude of the negative dust surface potential increases. An increase in γ and U0 leads to the enhancement of the magnitude of the dust grain surface potential, while α leads to an opposite effect. The relevance of present results to low-temperature laboratory plasmas is discussed.
Novel inhibitors of the Plasmodium falciparum electron transport chain
Authors: STOCKS P. A. , BARTON V. , ANTOINE T. , BIAGINI G. A. , WARD S. A. , O'NEILL P. M.
Published: January 2014

Due to an increased need for new antimalarial chemotherapies that show potency against Plasmodium falciparum, researchers are targeting new processes within the parasite in an effort to circumvent or delay the onset of drug resistance. One such promising area for antimalarial drug development has been the parasite mitochondrial electron transport chain (ETC). Efforts have been focused on targeting key processes along the parasite ETC specifically the dihydroorotate dehydrogenase (DHOD) enzyme, the cytochrome bc1 enzyme and the NADH type II oxidoreductase (PfNDH2) pathway. This review summarizes the most recent efforts in antimalarial drug development reported in the literature and describes the evolution of these compounds.
Acute Effects of Alcohol on Brain Perfusion Monitored with Arterial Spin Labeling Magnetic Resonance Imaging in Young Adults
Authors: Marxen Michael , Gan Gabriela , Schwarz Daniel , Mennigen Eva , Pilhatsch Maximilian , Zimmermann Ulrich S , Guenther Matthias , Smolka Michael N
Published: January 2014

While a number of studies have established that moderate doses of alcohol increase brain perfusion, the time course of such an increase as a function of breath alcohol concentration (BrAC) has not yet been investigated, and studies differ about regional effects. Using arterial spin labeling (ASL) magnetic resonance imaging, we investigated (1) the time course of the perfusion increase during a 15-minute linear increase of BrAC up to 0.6 g/kg followed by a steady exposure of 100 minutes, (2) the regional distribution, (3) a potential gender effect, and (4) the temporal stability of perfusion effects. In 48 young adults who participated in the Dresden longitudinal study on alcohol effects in young adults, we observed (1) a 7% increase of global perfusion as compared with placebo and that perfusion and BrAC are tightly coupled in time, (2) that the increase reaches significance in most regions of the brain, (3) that the effect is stronger in women than in men, and (4) that an acute tolerance effect is not observable on the time scale of 2 hours. Larger studies are needed to investigate the origin and the consequences of the effect, as well as the correlates of inter-subject variations.
Activation and Regulation of Cellular Inflammasomes: Gaps in Our Knowledge for Central Nervous System Injury
Authors: de Rivero Vaccari Juan Pablo , Dietrich W Dalton , Keane Robert W
Published: January 2014

The inflammasome is an intracellular multiprotein complex involved in the activation of caspase-1 and the processing of the proinflammatory cytokines interleukin-1 β (IL-1 β) and IL-18. The inflammasome in the central nervous system (CNS) is involved in the generation of an innate immune inflammatory response through IL-1 cytokine release and in cell death through the process of pyroptosis. In this review, we consider the different types of inflammasomes (NLRP1, NLRP2, NLRP3, and AIM2) that have been described in CNS cells, namely neurons, astrocytes, and microglia. Importantly, we focus on the role of the inflammasome after brain and spinal cord injury and cover the potential activators of the inflammasome after CNS injury such as adenosine triphosphate and DNA, and the therapeutic potential of targeting the inflammasome to improve outcomes after CNS trauma.
A Multiscale Model of Interleukin‐6–Mediated Immune Regulation in Crohn's Disease and Its Application in Drug Discovery and Development
Authors: Dwivedi G , Fitz L , Hegen M , Martin SW , Harrold J , Heatherington A , Li C
Published: January 2014

In this study, we have developed a multiscale systems model of interleukin (IL)‐6–mediated immune regulation in Crohn's disease, by integrating intracellular signaling with organ‐level dynamics of pharmacological markers underlying the disease. This model was linked to a general pharmacokinetic model for therapeutic monoclonal antibodies and used to comparatively study various biotherapeutic strategies targeting IL‐6–mediated signaling in Crohn's disease. Our work illustrates techniques to develop mechanistic models of disease biology to study drug–system interaction. Despite a sparse training data set, predictions of the model were qualitatively validated by clinical biomarker data from a pilot trial with tocilizumab. Model‐based analysis suggests that strategies targeting IL‐6, IL‐6Rα, or the IL‐6/sIL‐6Rα complex are less effective at suppressing pharmacological markers of Crohn's than dual targeting the IL‐6/sIL‐6Rα complex in addition to IL‐6 or IL‐6Rα. The potential value of multiscale system pharmacology modeling in drug discovery and development is also discussed.

CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e89; doi:10.1038/psp.2013.64; advance online publication 8 January 2014
In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system
Authors: Lee On On , Wang Yong , Tian Renmao , Zhang Weipeng , Shek Chun Shum , Bougouffa Salim , Al-Suwailem Abdulaziz , Batang Zenon B. , Xu Wei , Wang Guang Chao , Zhang Xixiang , Lafi Feras F. , Bajic Vladmir B. , Qian Pei-Yuan
Published: January 2014

Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.
Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate
Authors: Tateishi-Karimata Hisae , Nakano Miki , Sugimoto Naoki
Published: January 2014

The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.
Development and validation of a stability-indication LC-UV method for determination of daptomycin injectable form and kinetic study in alkaline medium
Authors: Christ Ana Paula , Machado Mariana Souto , Rosa Priscila , Codevilla Cristiane Franco , Bueno Rolim Clarice Madalena , Horn Adams Andréa Inês
Published: January 2014

Development and validation of LC-UV method to quantify daptomycin in injectable form, in accordance with the ICH requirements.
FACS-based immunoassay of troponin-I using E. coli cells with autodisplayed Z-domains
Authors: Park Min , Bong Ji-Hong , Chang Young Wook , Yoo Gu , Jose Joachim , Kang Min-Jung , Pyun Jae-Chul
Published: January 2014

Fluorescence-activated cell sorter (FACS)-based immunoassays usingE. colicells with autodisplayed Z-domains were performed.
The response comparison of a hydrogen-bond acidic polymer to sarin, soman and dimethyl methyl phosphonate based on a surface acoustic wave sensor
Authors: Wang Yang , Du Xiaosong , Long Yin , Tang Xianzhong , Tai Huiling , Jiang Yadong
Published: January 2014

Responses of a DKAP coated SAW sensor to sarin, soman and dimethyl methyl phosphonate at 1 mg m−3and 10 mg m−3.
Screening and quantification of 304 pesticides and related organic pollutants in surface water using dispersive liquid–liquid microextraction coupled with gas chromatography-mass spectrometry
Authors: Chen Bo , Jin Baohui , Jiang Ruifen , Xie Liqi , Lin Yankui , Feng Wen , Ouyang Gangfeng
Published: January 2014

DLLME coupled with GC-MS was used to quantify and semi-quantify 304 pesticides and related organic pollutants in surface water.
Coordination and conformational isomers in mononuclear iron complexes with pertinence to the [FeFe] hydrogenase active site
Authors: Orthaber Andreas , Karnahl Michael , Tschierlei Stefanie , Streich Daniel , Stein Matthias , Ott Sascha
Published: January 2014

6 Fe complexes of the type [Fe(X-bdt)(PR2NPh2)(CO)] were prepared and the possibility to tune their electronic properties by ligand modification was demonstrated. IR spectroscopic and computational studies suggest that the compounds exist as a mixture of isomers in solution.
An unprecedented high nuclearity catecholato-based Ti(iv)-architecture bearing labile pyridine ligands
Authors: Chaumont Clément , Mobian Pierre , Henry Marc
Published: January 2014

The original behaviour in solution associated with the visible light absorption properties of the S4-symmetry [Ti10O12(cat)8(py)8] complex makes this compound a good candidate for generating titanium-based coordination polymers.
Solar energy: setting the economic bar from the top-down
Authors: McFarland E. W.
Published: January 2014

Sunlight is thermal radiation from sustained nuclear reactions within our sun. Our challenge is to harness this solar energy at a cost less than 10% of our GDP.
Preparation of Dufulin imprinted polymer on surface of silica gel and its application as solid-phase extraction sorbent
Authors: Miao Shan Shan , Wang Hua Zi , Lu Yi Chen , Geng Hao Ran , Yang Hong
Published: January 2014

A new molecularly imprinted polymer based on silica-gel surface was developed using Dufulin (Duf) as template.
A putative role of the Sup35p C-terminal domain in the cytoskeleton organization during yeast mitosis
Authors: Na Insung , Reddy Krishna D. , Breydo Leonid , Xue Bin , Uversky Vladimir N.
Published: January 2014

Based on structural analysis of several effectors and partners, Sup35pC is proposed to serve as actin modulator during mitosis.
Heterocycle-fused lupane triterpenoids inhibit Leishmania donovani amastigotes
Authors: Haavikko Raisa , Nasereddin Abedelmajeed , Sacerdoti-Sierra Nina , Kopelyanskiy Dmitry , Alakurtti Sami , Tikka Mari , Jaffe Charles L. , Yli-Kauhaluoma Jari
Published: January 2014

The synthesis of heterocyclic betulin derivatives and their activity against Leishmania donovani are reported.
Spin-induced band modifications of graphene through intercalation of magnetic iron atoms
Authors: Sung S. J. , Yang J. W. , Lee P. R. , Kim J. G. , Ryu M. T. , Park H. M. , Lee G. , Hwang C. C. , Kim Kwang. S. , Kim J. S. , Chung J. W.
Published: January 2014

Fe adatoms are intercalated through epitaxial graphene to form a bilayer graphene, which shows spin-polarized Dirac bands arising from spin-injected C atoms.
High throughput electron transfer from carbon dots to chloroplast: a rationale of enhanced photosynthesis
Authors: Chandra Sourov , Pradhan Saheli , Mitra Shouvik , Patra Prasun , Bhattacharya Ankita , Pramanik Panchanan , Goswami Arunava
Published: January 2014

Microwave assisted synthesis of carbon dots and their direct involvement in whole chain electron transfer processes, yielding augmentation in photosynthesis.
Efficient synthesis of functionalized dihydroquinolines, quinolines and dihydrobenzo[b]azepine via an iron(iii) chloride-catalyzed intramolecular alkyne–carbonyl metathesis of alkyne tethered 2-amino benzaldehyde/acetophenone derivatives
Authors: Jalal Swapnadeep , Bera Krishnendu , Sarkar Soumen , Paul Kartick , Jana Umasish
Published: January 2014

Iron-catalyzed synthesis of dihydroquinolines, quinolines and dihydrobenzo[b]azepine.
Reversible deactivation radical polymerization in the presence of zero-valent metals: from components to precise polymerization
Authors: Wang Wenxiang , Zhao Junfei , Zhou Nianchen , Zhu Jian , Zhang Wei , Pan Xiangqiang , Zhang Zhengbiao , Zhu Xiulin
Published: January 2014

We highlight recent work from the advent of zero-valent metal-mediated RDRP looking at advances in its components and the synthesis of well-defined polymers.
Multifunctional photo-crosslinked polymeric ionic hydrogel films
Authors: He Hongkun , Adzima Brian , Zhong Mingjiang , Averick Saadyah , Koepsel Richard , Murata Hironobu , Russell Alan , Luebke David , Takahara Atsushi , Nulwala Hunaid , Matyjaszewski Krzysztof
Published: January 2014

The crosslinked ionic hydrogel films prepared by photopolymerization have multiple applications as magnetic, catalytic, antibiotic, and fluorescent materials.
Reactivity enhancement of N-CNTs in green catalysis of C2H2 hydrochlorination by a Cu catalyst
Authors: Zhou Kai , Si Jiangkun , Jia Jinchao , Huang Jiaqi , Zhou Jun , Luo Guohua , Wei Fei
Published: January 2014

We reported the prominent effect of nitrogen-doped carbon nanotubes (N-CNTs) on reactivity enhancement in catalyzing acetylene hydrochlorination, which improved the TOF of Cu to ca. 1.2 min−1, proving that N-CNTs is a potential green substrate, and that the Cu-based catalyst is an alternative to the toxic conventional HgCl2 catalyst.
Actuation based on thermo/photosalient effect: a biogenic smart hybrid driven by light and heat
Authors: Chandra Sahoo Subash , Nath Naba K. , Zhang Lidong , Semreen Mohamad H. , Al-Tel Taleb H. , Naumov Panče
Published: January 2014

Crystals of a thermosalient (jumping) solid were employed as a mechanically active “backbone” to actuate “tissue” from natural protein matrix by both light and heat in a way similar to actuation in muscles.
Single porous SnO2 microtubes templated from Papilio maacki bristles: new structure towards superior gas sensing
Authors: Zhang Wang , Tian Junlong , Wang Yu'an , Fang Xiaotian , Huang Yiqiao , Chen Weixin , Liu Qinglei , Zhang Di
Published: January 2014

Templated from the bristles on Papilio maacki wings, single porous SnO2 microtubes (SPSMs) have been synthesized by soaking and sintering.
Selective laser sintering of TiO2 nanoparticle film on plastic conductive substrate for highly efficient flexible dye-sensitized solar cell application
Authors: Ming Liqun , Yang Huan , Zhang Wenjun , Zeng Xianwei , Xiong Dehua , Xu Zhen , Wang Huan , Chen Wei , Xu Xiaobao , Wang Mingkui , Duan Jun , Cheng Yi-Bing , Zhang Jie , Bao Qiaoliang , Wei Zhanhua , Yang Shihe
Published: January 2014

Fast and selective laser sintering is efficient for the treatment of TiO2 nanoparticle film for flexible DSC applications.
Nitrogen-doped carbon and iron carbide nanocomposites as cost-effective counter electrodes of dye-sensitized solar cells
Authors: Xu Hongxia , Zhang Chuanjian , Wang Zaiwei , Pang Shuping , Zhou Xinhong , Zhang Zhongyi , Cui Guanglei
Published: January 2014

The hierarchical nanocomposites (Fe3C@N–C) of iron carbide encaged in nitrogen-doped carbon counter electrode were fabricated for low-cost, highly efficient dye-sensitized solar cells.
New tandem type ion source based on electron cyclotron resonance for universal source of synthesized ion beams
Authors: Kato Yushi , Kurisu Yosuke , Nozaki Dai , Yano Keisuke , Kimura Daiju , Kumakura Sho , Imai Youta , Nishiokada Takuya , Sato Fuminobu , Iida Toshiyuki
Published: January 2014

A new tandem type source has been constructed on the basis of electron cyclotron resonance (ECR) plasma for producing synthesized ion beams. We investigate feasibility and hope to realize the device which has wide range operation window in a single device to produce many kinds of ion beams based on ECR ion source (ECRIS). It is considered that ECR plasmas are necessary to be available to individual operations with different plasma parameters. Both of analysis of ion beams and investigation of plasma parameters are conducted on produced plasmas. We describe construction of the new tandem type ion source based on ECRIS with wide operation window for aiming at producing synthesized ion beams as this new source can be a universal source.
Prediction of 1P Rydberg energy levels of beryllium based on calculations with explicitly correlated Gaussians
Authors: Bubin Sergiy , Adamowicz Ludwik
Published: January 2014

Benchmark variational calculations are performed for the seven lowest 1s22s np (1P), n = 2…8, states of the beryllium atom. The calculations explicitly include the effect of finite mass of 9Be nucleus and account perturbatively for the mass-velocity, Darwin, and spin-spin relativistic corrections. The wave functions of the states are expanded in terms of all-electron explicitly correlated Gaussian functions. Basis sets of up to 12 500 optimized Gaussians are used. The maximum discrepancy between the calculated nonrelativistic and experimental energies of 1s22s np (1P) →1s22s2 (1S) transition is about 12 cm−1. The inclusion of the relativistic corrections reduces the discrepancy to bellow 0.8 cm−1.
Expansions at small Reynolds numbers for the locomotion of a spherical squirmer
Authors: Khair Aditya S. , Chisholm Nicholas G.
Published: January 2014

The locomotion of a spherical squirmer — a model organism that achieves self-propulsion via steady tangential movement of its surface — is quantified at small Reynolds number R. Matched asymptotic expansions are employed to calculate the swimming velocity of the squirmer through O(R2). Approximations to the velocity and vorticity fields around the squirmer that are uniformly valid to O(R) are also constructed.
Imaging the condensation and evaporation of molecularly thin ethanol films with surface forces apparatus
Authors: Zhao Gutian , Tan Qiyan , Xiang Li , Zhang Di , Ni Zhonghua , Yi Hong , Chen Yunfei
Published: January 2014

A new method for imaging condensation and evaporation of molecularly thin ethanol films is reported. It is found that the first adsorbed layer of ethanol film on mica surface behaves as solid like structure that cannot flow freely. With the increase of exposure time, more ethanol molecules condense over the mica surface in the saturated ethanol vapor condition. The first layer of adsorbed ethanol film is about 3.8 Å thick measured from the surface forces apparatus, which is believed to be the average diameter of ethanol molecules while they are confined in between two atomically smooth mica surfaces.
Study of nonlinear electron-acoustic solitary and shock waves in a dissipative, nonplanar space plasma with superthermal hot electrons
Authors: Han Jiu-Ning , Duan Wen-Shan , Li Jun-Xiu , He Yong-Lin , Luo Jun-Hua , Nan Ya-Gong , Han Zhen-Hai , Dong Guang-Xing
Published: January 2014

With the consideration of the superthermal electron distribution, we present a theoretical investigation about the nonlinear propagation of electron-acoustic solitary and shock waves in a dissipative, nonplanar non-Maxwellian plasma comprised of cold electrons, superthermal hot electrons, and stationary ions. The reductive perturbation technique is used to obtain a modified Korteweg-de Vries Burgers equation for nonlinear waves in this plasma. We discuss the effects of various plasma parameters on the time evolution of nonplanar solitary waves, the profile of shock waves, and the nonlinear structure induced by the collision between planar solitary waves. It is found that these parameters have significant effects on the properties of nonlinear waves and collision-induced nonlinear structure.
Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer
Authors: Veselkov Kirill A. , Mirnezami Reza , Strittmatter Nicole , Goldin Robert D. , Kinross James , Speller Abigail V. M. , Abramov Tigran , Jones Emrys A. , Darzi Ara , Holmes Elaine , Nicholson Jeremy K. , Takats Zoltan
Published: January 2014

Significance

Mass spectrometry imaging (MSI) technology represents a highly promising approach in cancer research. Here, we outline current roadblocks in translational MSI and introduce a comprehensive workflow designed to address current methodological limitations. An integrated bioinformatics platform is presented that allows intuitive histology-directed interrogation of MSI datasets. We show that this strategy permits the analysis of multivariate molecular signatures with direct correlation to morphological regions of interest, which can offer new insights into how different tumor microenvironmental populations interact with one another and generate novel region-of-interest specific biomarkers and therapeutic targets.
Redox-dependent stability, protonation, and reactivity of cysteine-bound heme proteins
Authors: Zhong Fangfang , Lisi George P. , Collins Daniel P. , Dawson John H. , Pletneva Ekaterina V.
Published: January 2014

Significance

Metal thiolates are common components of electron transfer proteins, enzymes, and redox sensors. Reduction of ferric thiolate hemes often involves protonation of the Cys ligand and ligand loss or substitution. These reactions contribute to enzyme inactivation and form the basis of sensing functions, but their mechanistic details are not well understood, particularly in proteins. A neutral thiol is a viable ligand to the heme; however, analysis of this interaction has been challenging. Herein, we describe a series of model proteins that offer detailed spectroscopic and thermodynamic characterization of ferric thiolate and ferrous thiol species as well as their interconversions. Results have shed light on the forces that control a particular heme ligation and redox reactivity of these key bioinorganic centers.
A Contractarian Solution to the Experimenter’s Regress
Authors: Teira David
Published: January 2014

Debiasing procedures are experimental methods aimed at correcting errors arising from the cognitive biases of the experimenter. We discuss two of these methods, the predesignation rule and randomization, showing to what extent they are open to the experimenter’s regress: there is no metarule to prove that, after implementing the procedure, the experimental data are actually free from biases. We claim that, from a contractarian perspective, these procedures are nonetheless defensible since they provide a warrant of the impartiality of the experiment: we only need proof that the result has not been intentionally manipulated for prima facie acceptance.
Is Race a Cause?
Authors: Marcellesi Alexandre
Published: January 2014

Advocates of the counterfactual approach to causal inference argue that race is not a cause, and this despite the fact that it is commonly treated as such by scientists in many disciplines. I object that their argument is unsound since two of its premises are false. I also sketch an argument to the effect that racial discrimination cannot be explained unless one assumes race to be a cause.
The Explanatory Relevance of Nash Equilibrium: One-Dimensional Chaos in Boundedly Rational Learning
Authors: Wagner Elliott
Published: January 2014

Game theory is often used to explain behavior. Such explanations often proceed by demonstrating that the behavior in question is a Nash equilibrium. Agents are in Nash equilibrium if each agent’s strategy maximizes her payoff given her opponents’ strategies. Nash equilibriums are fundamentally static, but it is usually assumed that equilibriums will be the outcome of a dynamic process of learning or evolution. This article demonstrates that, even in the most simple setting, this need not be true. In two-strategy games with just a single equilibrium, a family of imitative learning dynamics does not lead to equilibrium.
On the Debate Concerning the Proper Characterization of Quantum Dynamical Evolution
Authors: Cuffaro Michael E. , Myrvold Wayne C.
Published: January 2014

There has been a long-standing and sometimes passionate debate between physicists over whether a dynamical framework for quantum systems should incorporate not completely positive (NCP) maps in addition to completely positive (CP) maps. Despite the reasonableness of the arguments for complete positivity, we argue that NCP maps should be allowed, with a qualification: these should be understood, not as reflecting ‘not completely positive’ evolution, but as linear extensions, to a system’s entire state space, of CP maps that are only partially defined. Beyond the domain of definition of a partial-CP map, we argue, much may be permitted.
A Generalized Manifold Topology for Branching Space-Times
Authors: Müller Thomas
Published: January 2014

The logical theory of branching space-times, which provides a relativistic framework for studying objective indeterminism, remains mostly disconnected from discussions of space-time theories in philosophy of physics. Earman has criticized the branching approach and suggested “pruning some branches from branching space-time.” This article identifies the different—order-theoretic versus topological—perspective of both discussions as a reason for certain misunderstandings and tries to remove them. Most important, we give a novel, topological criterion of modal consistency that usefully generalizes an earlier criterion, and we introduce a differential-geometrical version of branching space-times as a non-Hausdorff (generalized) manifold.
Human Nature in a Post-essentialist World
Authors: Ramsey Grant
Published: January 2014

In this essay I examine a well-known articulation of human nature skepticism, a paper by Hull. I then review a recent reply to Hull by Machery, which argues for an account of human nature that he claims is both useful and scientifically robust. I challenge Machery’s account and introduce an alternative account—the “life-history trait cluster” conception of human nature—that I hold is scientifically sound and makes sense of (at least some of) our intuitions about—and desiderata for—human nature.
Synthetic Modeling and Mechanistic Account: Material Recombination and Beyond
Authors: Knuuttila Tarja , Loettgers Andrea
Published: January 2014

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic modeling as a kind of material recomposition strategy also points beyond the mechanistic paradigm.
Evaluation of an Antimicrobial Stewardship Approach to Minimize Overuse of Antibiotics in Patients with Asymptomatic Bacteriuria
Authors: Kelley Denise , Aaronson Patrick , Poon Elaine , McCarter Yvette S. , Bato Ben , Jankowski Christopher A.
Published: January 2014

An antimicrobial stewardship educational initiative provided to physicians and pharmacists was evaluated at an academic medical center to minimize inappropriate treatment of asymptomatic bacteriuria (ASB). A significant decrease in empirical antimicrobial use for ASB was observed after education. Multifaceted educational initiatives can reduce inappropriate antimicrobial treatment of ASB.
Karcher means and Karcher equations of positive definite operators
Authors: Lawson Jimmie , Lim Yongdo
Published: January 2014

The Karcher or least-squares mean has recently become an important tool for the averaging and studying of positive definite matrices. In this paper we show that this mean extends, in its general weighted form, to the infinite-dimensional setting of positive operators on a Hilbert space and retains most of its attractive properties. The primary extension is via its characterization as the unique solution of the corresponding Karcher equation. We also introduce power means

P
t

P_t

in the infinite-dimensional setting and show that the Karcher mean is the strong limit of the monotonically decreasing family of power means as

t
→

0
+

t\to 0^+

. We show that each of these characterizations provide important insights about the Karcher mean.
Recovering Individual Preferences for Non‐Market Goods: A Collective Travel‐Cost Model
Authors: Menon Martina , Perali Federico , Veronesi Marcella
Published: January 2014

Traditional recreation demand models do not make a distinction between a household and an individual as the reference decision‐making unit, thus assuming that a family maximizes a single utility function, even if the family consists of different individuals. Such models ignore the possibility of family members' divergent preferences for non‐market goods. This study proposes a novel approach—the collective travel‐cost model (CTCM)—to eliciting individual preferences for a non‐market good, such as a recreation site, by using revealed preference data. This approach accounts for the intra‐household resource allocation and the role of each household member's preferences. We show that the collective travel‐cost model can be applied to estimating a recreation demand model that yields individual welfare estimates appropriate for policy analysis of non‐market goods, such as the willingness to pay to access a recreation site. We find that how resources are distributed within the household reflects significant differences in welfare measures.
A design protocol for tailoring ice-templated scaffold structure
Authors: Pawelec K. M. , Husmann A. , Best S. M. , Cameron R. E.
Published: January 2014

In this paper, we show, for the first time, the key link between scaffold architecture and latent heat evolution during the production of porous biomedical collagen structures using freeze-drying. Collagen scaffolds are used widely in the biomedical industry for the repair and reconstruction of skeletal tissues and organs. Freeze-drying of collagen slurries is a standard industrial process, and, until now, the literature has sought to characterize the influence of set processing parameters including the freezing protocol and weight percentage of collagen. However, we are able to demonstrate, by monitoring the local thermal events within the slurry during solidification, that nucleation, growth and annealing processes can be controlled, and therefore we are able to control the resulting scaffold architecture. Based on our correlation of thermal profile measurements with scaffold architecture, we hypothesize that there is a link between the fundamental freezing of ice and the structure of scaffolds, which suggests that this concept is applicable not only for collagen but also for ceramics and pharmaceuticals. We present a design protocol of strategies for tailoring the ice-templated scaffold structure.
Rates of genomic divergence in humans, chimpanzees and their lice
Authors: Johnson Kevin P. , Allen Julie M. , Olds Brett P. , Mugisha Lawrence , Reed David L. , Paige Ken N. , Pittendrigh Barry R.
Published: January 2014

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.
Parental effects improve escape performance of juvenile reef fish in a high-CO2world
Authors: Allan Bridie J. M. , Miller Gabrielle M. , McCormick Mark I. , Domenici Paolo , Munday Philip L.
Published: January 2014

Rising CO2levels in the oceans are predicted to have serious consequences for many marine taxa. Recent studies suggest that non-genetic parental effects may reduce the impact of high CO2on the growth, survival and routine metabolic rate of marine fishes, but whether the parental environment mitigates behavioural and sensory impairment associated with high CO2remains unknown. Here, we tested the acute effects of elevated CO2on the escape responses of juvenile fish and whether such effects were altered by exposure of parents to increased CO2(transgenerational acclimation). Elevated CO2negatively affected the reactivity and locomotor performance of juvenile fish, but parental exposure to high CO2reduced the effects in some traits, indicating the potential for acclimation of behavioural impairment across generations. However, acclimation was not complete in some traits, and absent in others, suggesting that transgenerational acclimation does not completely compensate the effects of high CO2on escape responses.
Competition induces allelopathy but suppresses growth and anti-herbivore defence in a chemically rich seaweed
Authors: Rasher Douglas B. , Hay Mark E.
Published: January 2014

Many seaweeds and terrestrial plants induce chemical defences in response to herbivory, but whether they induce chemical defences against competitors (allelopathy) remains poorly understood. We evaluated whether two tropical seaweeds induce allelopathy in response to competition with a reef-building coral. We also assessed the effects of competition on seaweed growth and seaweed chemical defence against herbivores. Following 8 days of competition with the coralPorites cylindrica, the chemically rich seaweedGalaxaura filamentosainduced increased allelochemicals and became nearly twice as damaging to the coral. However, it also experienced significantly reduced growth and increased palatability to herbivores (because of reduced chemical defences). Under the same conditions, the seaweedSargassum polycystumdid not induce allelopathy and did not experience a change in growth or palatability. This is the first demonstration of induced allelopathy in a seaweed, or of competitors reducing seaweed chemical defences against herbivores. Our results suggest that the chemical ecology of coral–seaweed–herbivore interactions can be complex and nuanced, highlighting the need to incorporate greater ecological complexity into the study of chemical defence.
Integrating multiple lines of evidence into historical biogeography hypothesis testing: aBison bisoncase study
Authors: Metcalf Jessica L. , Prost Stefan , Nogués-Bravo David , DeChaine Eric G. , Anderson Christian , Batra Persaram , Araújo Miguel B. , Cooper Alan , Guralnick Robert P.
Published: January 2014

One of the grand goals of historical biogeography is to understand how and why species' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species's demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level.
How body mass and lifestyle affect juvenile biomass production in placental mammals
Authors: Sibly Richard M. , Grady John M. , Venditti Chris , Brown James H.
Published: January 2014

In mammals, the mass-specific rate of biomass production during gestation and lactation, here called maternal productivity, has been shown to vary with body size and lifestyle. Metabolic theory predicts that post-weaning growth of offspring, here termed juvenile productivity, should be higher than maternal productivity, and juveniles of smaller species should be more productive than those of larger species. Furthermore because juveniles generally have similar lifestyles to their mothers, across species juvenile and maternal productivities should be correlated. We evaluated these predictions with data from 270 species of placental mammals in 14 taxonomic/lifestyle groups. All three predictions were supported. Lagomorphs, perissodactyls and artiodactyls were very productive both as juveniles and as mothers as expected from the abundance and reliability of their foods. Primates and bats were unproductive as juveniles and as mothers, as expected as an indirect consequence of their low predation risk and consequent low mortality. Our results point the way to a mechanistic explanation for the suite of correlated life-history traits that has been called the slow–fast continuum.
Habitat collapse due to overgrazing threatens turtle conservation in marine protected areas
Authors: Christianen Marjolijn J. A. , Herman Peter M. J. , Bouma Tjeerd J. , Lamers Leon P. M. , van Katwijk Marieke M. , van der Heide Tjisse , Mumby Peter J. , Silliman Brian R. , Engelhard Sarah L. , van de Kerk Madelon , Kiswara Wawan , van de Koppel Johan
Published: January 2014

Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more ‘natural’ conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging for and consuming rhizomes and roots, turtles create abundant bare gaps, thereby enhancing erosion and reducing seagrass regrowth. A fully parametrized model reveals that the ecosystem is approaching a tipping point, where consumption overwhelms regrowth, which could potentially lead to complete collapse of the seagrass habitat. Seagrass recovery will not ensue unless turtle density is reduced to nearly zero, eliminating the MPA's value as a turtle reserve. Our results reveal an unrecognized, yet imminent threat to MPAs, as sea turtle densities are increasing at major nesting sites and the decline of seagrass habitat forces turtles to concentrate on the remaining meadows inside reserves. This emphasizes the need for policy and management approaches that consider the interactions of protected species with their habitat.