bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic relationships of pollens from matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry data using multivariate statistics
Authors: Seifert Stephan , Weidner Steffen M. , Panne Ulrich , Kneipp Janina 
Published: May 2015

RationaleMatrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) has been suggested as a promising tool for the investigation of pollen, but the usefulness of this approach for classification and identification of pollen species has to be proven by an application to samples of varying taxonomic relations.MethodMALDI‐MS in combination with hierarchical cluster analysis (HCA) and principal component analysis (PCA) was used to delineate taxonomic relations between plants based on pollen biochemistry. To assess the robustness of the approach, pollen of 74 species of the plant orders Fagales and Coniferales were probed.ResultsDiscrimination at the levels of plant order and genus were achieved using the whole spectral range. In many cases, different species of the same genus could be distinguished. The sources of the spectral/chemical differences at the genus level can be understood using PCA. Specifically, typical mass regions for exact genus detection were identified.ConclusionsOur results indicate that the chemical information represented by MALDI‐TOFMS data is useful for reconstructing taxonomic relationships and is complementary to other chemical information on pollen from other spectroscopic data. Copyright © 2015 John Wiley & Sons, Ltd.
Letting Go of Stand‐Alone Technology
Authors: Calvert Heather 
Published: May 2015

AbstractWith the nationwide focus on increasing students understanding and use of technology, many teachers are beginning to incorporate a variety of technology into small group rotations. However, the use of technology during these rotations often does not require students to use higher level thinking or problem solving skills. By eliminating the ‘technology station' and instead providing students the chance to use technology to complete learning tasks at every work station, teachers can prepare students to be 21st century learners.
Development of a cutting force prediction model based on brittle fracture for carbon fiber reinforced polymers for rotary ultrasonic drilling
Authors: Yuan Songmei , Zhang Chong , Amin Muhammad , Fan Huitao , Liu Ming 
Published: May 2015

Abstract
Carbon fiber reinforced polymers (CFRP) T700 have got increasing demand in the aerospace industry due to their high specific strength, specific stiffness, and other unique properties. Due to their inhomogeneous, anisotropic, and thermal properties, it is challenging to achieve desired accuracy and to avoid from delamination, chip-off, cracking, and burning especially in the drilling process. The cutting force is the critical parameter which is required to minimize in order to drill a hole with better accuracy and minimize defects. In this research, the brittle fracture approach was adopted and a cutting force model was developed for CFRP-T700 based on the rotary ultrasonic drilling (RUD) process. The experimental RUD was carried out on CFRP-T700 material and found that the feed rate and spindle speed are two main parameters that affect the cutting force in RUD. The cutting force data obtained from the model and experimental setup were then analyzed and found that there is small variation even below 10 % (max value of variation is 8.5 % and the average value is 0.49 %) between simulated and measured values. So, the developed cutting force model was validated and found robust. Also, it was found that with four times increase of feed rate, there is also an increase of material removal rate (MRR) four times with the decrease in the cutting force. Moreover, this model will be much helpful to keep cutting force within limits through the optimal set of parameters as feed rate and spindle speed without extensive experimentation of such costly materials.
Retinal microvascular network attenuation in Alzheimer's disease
Authors: Williams Michael A. , McGowan Amy J. , Cardwell Chris R. , Cheung Carol Y. , Craig David , Passmore Peter , Silvestri Giuliana , Maxwell Alexander P. , McKay Gareth J. 
Published: May 2015

AbstractIntroductionCerebral small‐vessel disease has been implicated in the development of Alzheimer's disease (AD). The retinal microvasculature enables the noninvasive visualization and evaluation of the systemic microcirculation. We evaluated retinal microvascular parameters in a case‐control study of AD patients and cognitively normal controls.MethodsRetinal images were computationally analyzed and quantitative retinal parameters (caliber, fractal dimension, tortuosity, and bifurcation) measured. Regression models were used to compute odds ratios (OR) and confidence intervals (CI) for AD with adjustment for confounders.ResultsRetinal images were available in 213 AD participants and 294 cognitively normal controls. Persons with lower venular fractal dimension (OR per standard deviation [SD] increase, 0.77 [CI: 0.62–0.97]) and lower arteriolar tortuosity (OR per SD increase, 0.78 [CI: 0.63–0.97]) were more likely to have AD after appropriate adjustment.DiscussionPatients with AD have a sparser retinal microvascular network and retinal microvascular variation may represent similar pathophysiological events within the cerebral microvasculature of patients with AD.
Astrocytic β1‐integrin affects cellular composition of murine blood brain barrier in the cerebral cortex
Authors: Venkatesan Charu , Birch Derin , Peng Chian‐yu , Kessler John A. 
Published: May 2015

AbstractThe blood brain barrier (BBB) is composed of endothelial cells, astrocytes, and pericytes and maintains functional homeostasis by regulating transport of ions, fluid and cells between blood and neural tissue. The cellular and molecular pathways that contribute to the formation of the BBB in the developing brain have not been fully deciphered. β1‐integrin (β1‐itg) within endothelial cells is known to play a critical role in vasculogenesis. However, the role of astrocytic β1‐itg in BBB development is not known. Our study used a mouse glial fibrillary acidic protein (GFAP)‐cre transgenic line to selectively ablate β1‐itg within astrocytes. We found that deletion of astrocytic β1‐itg had a striking effect on the different cell types that form the BBB. Mutant mice had a decreased density of aquaporin‐4 immunoreactivity within the perivascular astrocytic end‐feet. We also found decreases in immunoreactivity for vimentin and CD‐31 within endothelial cells. These changes were not accompanied by functional changes in BBB under physiological conditions as assessed by extravasation of large and small molecular weight molecules. However, mutant mice had an increased incidence of severe cystic injury in response to neonatal hypoxia. Our findings show that astrocytic β1‐itg has an important role in defining cellular properties of the blood brain barrier in the cerebral cortex.
Permanent cardiac pacing in a patient with persistent left superior vena cava and concomitant agenesis of the right‐sided superior vena cava
Authors: Hassine M. , Hamdi S. , Chniti G. , Boussaada M. , Bouchehda N. , Mahjoub M. , Ben Hamda K. , Betbout F. , Maatouk F. , Gamra H. 
Published: May 2015

AbstractPersistent left superior vena cava (PLSVC) can be incidentally detected during pacemaker implantation from the left pectoral side. Optimal site pacing is technically difficult, and lead stability of the right ventricle (RV) can lead to such a situation. We describe a case of successful single‐chamber pacemaker implantation in a 76‐year‐old woman with a PLSVC and concomitant agenesis of the right‐sided superior vena cava, after failed attempts with the conventional procedure. The pacemaker had been working well after 12 months of follow‐up.
Comparison of the effects of bepridil and aprindine for the prevention of atrial fibrillation after cardiac and aortic surgery: A prospective randomized study
Authors: Ozawa Mahito , Komatsu Takashi , Sato Yoshihiro , Kunugita Fusanori , Tachibana Hideaki , Tashiro Atsushi , Okabayashi Hitoshi , Nakamura Motoyuki 
Published: May 2015

AbstractBackgroundApproximately one‐third of the patients undergoing cardiovascular surgery reportedly experience paroxysmal atrial fibrillation (AF) during the postoperative period. However, the usefulness of antiarrhythmic drugs for preventing postoperative AF recurrence in the Japanese population has not been extensively studied.MethodsFrom a total of 118 patients who developed postoperative paroxysmal AF between April 2009 and March 2011, 72 patients (45 men, mean age 68±8 years) requiring treatment for postoperative AF due to symptoms lasting ≥30 min were enrolled to prospectively investigate the efficacy of oral bepridil (100 mg/day, n=37) or aprindine (40 mg/day, n=35).ResultThe AF recurrence‐free survival rates at 1, 3, 7, and 14 days were 100%, 94%, 57%, and 49%, respectively, in the aprindine group, and 100%, 97%, 86%, and 76%, respectively, in the bepridil group (P=0.028, aprindine vs. bepridil).ConclusionBepridil, at a fixed dose of 100 mg/day, was considered to be more effective than a routine dose of aprindine for the prevention of postoperative AF recurrence.
Watchdogs or guard dogs: Do anti-corruption agencies need strong teeth?
Authors: Kuris Gabriel 
Published: May 2015

Abstract
Anti-corruption advocates worldwide deride “toothless” anti-corruption agencies and demand agencies “with teeth,” meaning strong law enforcement powers. However, there are drawbacks to such powers. This paper draws from the documented experiences of dozens of anti-corruption agencies worldwide to show that law enforcement powers are not determinative of agency effectiveness, nor are they always helpful. Rather, both “guard dog” agencies, which use law-enforcement powers to address crimes of corruption directly, and “watchdog” agencies, which merely uncover and report corruption issues, face unique challenges and constraints. An anti-corruption agency's powers may influence its strategic response to its operating environment, but ultimately are less critical to corruption reduction than other factors such as independence, political will, and the reliability of partner institutions.
Austrostigmidium, a new austral genus of lichenicolous fungi close to rock-inhabiting meristematic fungi in Teratosphaeriaceae
Authors: Pérez-Ortega Sergio , Garrido-Benavent Isaac , De Los Ríos Asunción 
Published: May 2015

AbstractThe new genus of lichenicolous fungi Austrostigmidium is described from Antarctica and Tierra del Fuego (Chile). It is characterized by the presence of black pseudothecia, pseudoparaphyses, fissitunicate, I−, KI− asci and 3-septate hyaline ascospores. So far, the only known species grows on Mastodia tessellata (Verrucariales, Eurotiomycetes). The new genus is compared with anatomically close genera. Based on nuLSU and nuSSU markers we inferred its phylogenetic relationships and found that it belongs to the family Teratosphaeriaceae (Capnodiales, Dothideomycetes) and is closely related to rock-inhabiting fungal species, as well as to the hyphomycetous lichenicolous fungus Xanthoriicola. Finally, the host-parasite interface has been analyzed by means of transmission electron microscopy and fluorescence microscopy in order to describe the interactions among the new fungus and the symbionts forming the host lichen.
Passions of the Intellect: A Study of Polemics
Authors: Dorschel Andreas 
Published: May 2015

AbstractPolemics are a sort of critique typically suffused with inimical emotions and passions. But how are these emotions and passions to be construed? Neither authorial expression nor actual arousal properly account for their role in polemics. Rather, the polemicist must stage an unequal battle between a polemical self and the polemical target vis-à-vis an anticipated audience, skilfully handling, through his or her words, the emotions ascribed to each of them.
Three Temperature Regimes in Superconducting Photon Detectors: Quantum, Thermal and Multiple Phase-Slips as Generators of Dark Counts
Authors: Murphy Andrew , Semenov Alexander , Korneev Alexander , Korneeva Yulia , Gol’tsman Gregory , Bezryadin Alexey 
Published: May 2015

AbstractWe perform measurements of the switching current distributions of three w ≈ 120 nm wide, 4 nm thick NbN superconducting strips which are used for single-photon detectors. These strips are much wider than the diameter of the vortex cores, so they are classified as quasi-two-dimensional (quasi-2D). We discover evidence of macroscopic quantum tunneling by observing the saturation of the standard deviation of the switching distributions at temperatures around 2 K. We analyze our results using the Kurkijärvi-Garg model and find that the escape temperature also saturates at low temperatures, confirming that at sufficiently low temperatures, macroscopic quantum tunneling is possible in quasi-2D strips and can contribute to dark counts observed in single photon detectors. At the highest temperatures the system enters a multiple phase-slip regime. In this range single phase-slips are unable to produce dark counts and the fluctuations in the switching current are reduced.
Fluorometric assay for phenotypic differentiation of drug-resistant HIV mutants
Authors: Zhu Qinchang , Yu Zhiqiang , Kabashima Tsutomu , Yin Sheng , Dragusha Shpend , El-Mahdy Ahmed F. M. , Ejupi Valon , Shibata Takayuki , Kai Masaaki 
Published: May 2015

AbstractConvenient drug-resistance testing of viral mutants is indispensable to effective treatment of viral infection. We developed a novel fluorometric assay for phenotypic differentiation of drug-resistant mutants of human immunodeficiency virus-I protease (HIV-PR) which uses enzymatic and peptide-specific fluorescence (FL) reactions and high-performance liquid chromatography (HPLC) of three HIV-PR substrates. This assay protocol enables use of non-purified enzyme sources and multiple substrates for the enzymatic reaction. In this study, susceptibility of HIV mutations to drugs was evaluated by selective formation of three FL products after the enzymatic HIV-PR reaction. This proof-of-concept study indicates that the present HPLC-FL method could be an alternative to current phenotypic assays for the evaluation of HIV drug resistance.
Eutectic Nano-Droplet Template Injection into Bulk Silicon to Construct Porous Frameworks with Concomitant Conformal Coating as Anodes for Li-Ion Batteries
Authors: Qu Fei , Li Chilin , Wang Zumin , Wen Yuren , Richter Gunther , Strunk Horst P. 
Published: May 2015

AbstractBuilding porosity in monolithic materials is highly desired to design 3D electrodes, however ex-situ introduction or in-situ generation of nano-scale sacrificial template is still a great challenge. Here Al-Si eutectic droplet templates are uniformly injected into bulk Si through Al-induced solid-solid convection to construct a highly porous Si framework. This process is concomitant with process-inherent conformal coating of ion-conductive oxide. Such an all-in-one method has generated a (continuously processed) high-capacity Si anode integrating longevity and stable electrolyte-anode diaphragm for Li-ion batteries (e.g. a reversible capacity as large as ~1800 mAh/g or ~350 μAh/cm2-μm with a CE of ~99% at 0.1 C after long-term 400 cycles).
Neurocognitive dysfunction and pharmacological intervention using guanfacine in a rhesus macaque model of self-injurious behavior
Authors: Freeman Z T , Rice K A , Soto P L , Pate K A M , Weed M R , Ator N A , DeLeon I G , Wong D F , Zhou Y , Mankowski J L , Zink M C , Adams R J , Hutchinson E K 
Published: May 2015

AbstractSelf-injurious behavior (SIB) is a common comorbidity of psychiatric disorders but there is a dearth of information about neurological mechanisms underlying the behavior, and few animal models exist. SIB in humans is characterized by any intentional self-directed behavior that leads to wounds, whereas in macaques it is not always accompanied by wounds. We describe a cohort of rhesus macaques displaying SIB as adults, in which changes within the central nervous system were associated with the SIB. In these macaques, increases in central nervous system striatal dopamine (DA) receptor binding (BPND) measured by positron emission tomography (PET) [11C]raclopride imaging correlated with severity of wounding (rs=0.662, P=0.014). Furthermore, utilizing standardized cognitive function tests, we showed that impulsivity (stop signal reaction time, SSRT) and deficits in attentional set shifting (intra-/extradimensional shift) were correlated with increased severity of SIB (rs=0.563, P=0.045 and rs=0.692, P=0.009, respectively). We also tested the efficacy of guanfacine, an α2A adrenergic agonist that acts to improve postsynaptic transmission of neuronal impulses, in reducing SIB. A subset of these animals were enrolled in a randomized experimenter-blinded study that demonstrated guanfacine decreased the severity of wounding in treated animals compared with vehicle-only-treated controls (P=0.043), with residual beneficial effects seen for several weeks after cessation of therapy. Animals with the highest severity of SIB that received guanfacine also showed the most significant improvement (rs=−0.761, P=0.009). The elevated PET BPND was likely due to low intrasynaptic DA, which in turn may have been improved by guanfacine. With underlying physiology potentially representative of the human condition and the ability to affect outcome measures of disease using pharmacotherapy, this model represents a unique opportunity to further our understanding of the biology and treatment of SIB in both animals and humans.
Classical conditioning of analgesic and hyperalgesic pain responses without conscious awareness
Authors: Jensen Karin , Kirsch Irving , Odmalm Sara , Kaptchuk Ted J. , Ingvar Martin 
Published: May 2015

Significance
It is unclear to what extent new learning can take place outside of conscious awareness. In the present study, we used psychophysical measures and classical conditioning to establish whether psychologically mediated analgesic and hyperalgesic responses could be acquired by unseen (subliminally presented) stimuli. Our study demonstrates that analgesia and hyperalgesia can be learned without conscious awareness, suggesting that higher-order cognitive processes may be affected by implicit learning mechanisms.
Substrate-binding domain conformational dynamics mediate Hsp70 allostery
Authors: Zhuravleva Anastasia , Gierasch Lila M. 
Published: May 2015

Significance
Heat shock protein 70 (Hsp70) molecular chaperones help maintain protein homeostasis. Hsp70 functions require regulated promiscuous binding and release of a wide range of protein substrates. ATP binding to the Hsp70 nucleotide-binding domain (NBD) regulates the affinity and kinetics of substrate binding to their substrate-binding domain (SBD). Our work sought deeper understanding of the role of conformational dynamics for allosteric signaling in Hsp70s: The SBD undergoes a seesaw-like conformational change from a high substrate affinity state to one with lower substrate affinity, and we show that this conformational change results in drastic changes in conformational flexibility for the SBD that are essential for efficient substrate binding and release. These insights will help efforts to use Hsp70s as therapeutic targets.
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data
Authors: Wang Bin , Cunningham John M. , (Holly) Yang Xinan 
Published: May 2015

Abstract
Summary: Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements.
Availability and implementation: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html.
Contact: xyang2@uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CoRegNet: reconstruction and integrated analysis of co-regulatory networks
Authors: Nicolle Rémy , Radvanyi François , Elati Mohamed 
Published: May 2015

Abstract
CoRegNet is an R/Bioconductor package to analyze large-scale transcriptomic data by highlighting sets of co-regulators. Based on a transcriptomic dataset, CoRegNet can be used to: reconstruct a large-scale co-regulatory network, integrate regulation evidences such as transcription factor binding sites and ChIP data, estimate sample-specific regulator activity, identify cooperative transcription factors and analyze the sample-specific combinations of active regulators through an interactive visualization tool. In this study CoRegNet was used to identify driver regulators of bladder cancer.
Availability: CoRegNet is available at http://bioconductor.org/packages/CoRegNet
Contact: remy.nicolle@issb.genopole.fr or mohamed.elati@issb.genopole.fr
Supplementary inform a tion: Supplementary data are available at Bioinformatics online.
Likelihood-based complex trait association testing for arbitrary depth sequencing data
Authors: Yan Song , Yuan Shuai , Xu Zheng , Zhang Baqun , Zhang Bo , Kang Guolian , Byrnes Andrea , Li Yun 
Published: May 2015

Abstract
Summary: In next generation sequencing (NGS)-based genetic studies, researchers typically perform genotype calling first and then apply standard genotype-based methods for association testing. However, such a two-step approach ignores genotype calling uncertainty in the association testing step and may incur power loss and/or inflated type-I error. In the recent literature, a few robust and efficient likelihood based methods including both likelihood ratio test (LRT) and score test have been proposed to carry out association testing without intermediate genotype calling. These methods take genotype calling uncertainty into account by directly incorporating genotype likelihood function (GLF) of NGS data into association analysis. However, existing LRT methods are computationally demanding or do not allow covariate adjustment; while existing score tests are not applicable to markers with low minor allele frequency (MAF). We provide an LRT allowing flexible covariate adjustment, develop a statistically more powerful score test and propose a combination strategy (UNC combo) to leverage the advantages of both tests. We have carried out extensive simulations to evaluate the performance of our proposed LRT and score test. Simulations and real data analysis demonstrate the advantages of our proposed combination strategy: it offers a satisfactory trade-off in terms of computational efficiency, applicability (accommodating both common variants and variants with low MAF) and statistical power, particularly for the analysis of quantitative trait where the power gain can be up to ∼60% when the causal variant is of low frequency (MAF &lt; 0.01).
Availability and implementation: UNC combo and the associated R files, including documentation, examples, are available at http://www.unc.edu/∼yunmli/UNCcombo/
Contact: yunli@med.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.