bluuebunny/crossref_metadata_2025_split huggingface dataset:
Filifactor alocis collagenase can modulate apoptosis of normal oral keratinocytes
Authors: Chioma O. , Aruni A.W. , Milford T.‐A. , Fletcher H.M. 
Published: May 2016

SummaryTo successfully colonize host cells, pathogenic bacteria must circumvent the host's structural barrier such as the collagen‐rich extracellular matrix (ECM), as a preliminary step to invasion and colonization of the periodontal tissue. Filifactor alocis possesses a putative Peptidase U32 family protein (HMPREF0389_00504) with collagenase activity that may play a significant role in colonization of host tissue during periodontitis by breaking down collagen into peptides and disruption of the host cell. Domain architecture of the HMPREF0389_00504 protein predicted the presence of a characteristic PrtC‐like collagenase domain, and a peptidase domain. Our study demonstrated that the recombinant F. alocis peptidase U32 protein (designated PrtFAC) can interact with, and degrade, type I collagen, heat‐denatured collagen and gelatin in a calcium‐dependent manner. PrtFAC decreased viability and induced apoptosis of normal oral keratinocytes (NOKs) in a time and dose‐dependent manner. Transcriptome analysis of NOK cells treated with PrtFAC showed an upregulation of the genes encoding human pro‐apoptotic proteins: Apoptotic peptidase activating factor 1 (Apaf1) cytochrome C, as well as caspase 3 and caspase 9, suggesting the involvement of the mitochondrial apoptotic pathway. There was a significant increase in caspase 3/7 activity in NOK cells treated with PrtFAC. Taken together, these findings suggest that F. alocis PrtFAC protein may play a role in the virulence and pathogenesis of F. alocis.
Physics and Causation
Authors: Blanchard Thomas 
Published: May 2016

AbstractMore than a century ago, Russell launched a forceful attack on causation, arguing not only that modern physics has no need for causal notions but also that our belief in causation is a relic of a pre‐scientific view of the world. He thereby initiated a debate about the relations between physics and causation that remains very much alive today. While virtually everybody nowadays rejects Russell's causal eliminativism, many philosophers (although by no means all) have been convinced by Russell that the fundamental physical structure of our world doesn't contain causal relations. This raises the question of how to reconcile the central role of causal concepts in the special sciences and in common sense with the putative absence of causation in fundamental physics.
Quantifying learning‐dependent changes in the brain: Single‐trial multivoxel pattern analysis requires slow event‐related fMRI
Authors: Visser Renée M. , de Haan Michelle I. C. , Beemsterboer Tinka , Haver Pia , Kindt Merel , Scholte H. Steven 
Published: May 2016

AbstractSingle‐trial analysis is particularly useful for assessing cognitive processes that are intrinsically dynamic, such as learning. Studying these processes with fMRI is problematic, as the low signal‐to‐noise ratio of fMRI requires the averaging over multiple trials, obscuring trial‐by‐trial changes in neural activation. The superior sensitivity of multivoxel pattern analysis over univariate analyses has opened up new possibilities for single‐trial analysis, but this may require different fMRI designs. Here, we measured fMRI and pupil dilation responses during discriminant aversive conditioning, to assess associative learning in a trial‐by‐trial manner. The impact of design choices was examined by varying trial spacing and trial order in a series of five experiments (total n = 66), while keeping stimulus duration constant (4.5 s). Our outcome measure was the change in similarity between neural response patterns related to two consecutive presentations of the same stimulus (within‐stimulus) and between patterns related to pairs of different stimuli (between‐stimulus) that shared a specific outcome (electric stimulation vs. no consequence). This trial‐by‐trial similarity analysis revealed clear single‐trial learning curves in conditions with intermediate (8.1–12.6 s) and long (16.5–18.4 s) intervals, with effects being strongest in designs with long intervals and counterbalanced stimulus presentation. No learning curves were observed in designs with shorter intervals (1.6–6.1 s), indicating that rapid event‐related designs—at present, the most common designs in fMRI research—are not suited for single‐trial pattern analysis. These findings emphasize the importance of deciding on the type of analysis prior to data collection.
The human motor neuron pools receive a dominant slow‐varying common synaptic input
Authors: Negro Francesco , Yavuz Utku Şükrü , Farina Dario 
Published: May 2016

Key points
Motor neurons in a pool receive both common and independent synaptic inputs, although the proportion and role of their common synaptic input is debated.
Classic correlation techniques between motor unit spike trains do not measure the absolute proportion of common input and have limitations as a result of the non‐linearity of motor neurons.
We propose a method that for the first time allows an accurate quantification of the absolute proportion of low frequency common synaptic input (<5 Hz) to motor neurons in humans.
We applied the proposed method to three human muscles and determined experimentally that they receive a similar large amount (>60%) of common input, irrespective of their different functional and control properties.
These results increase our knowledge about the role of common and independent input to motor neurons in force control.
AbstractMotor neurons receive both common and independent synaptic inputs. This observation is classically based on the presence of a significant correlation between pairs of motor unit spike trains. The functional significance of different relative proportions of common input across muscles, individuals and conditions is still debated. One of the limitations in our understanding of correlated input to motor neurons is that it has not been possible so far to quantify the absolute proportion of common input with respect to the total synaptic input received by the motor neurons. Indeed, correlation measures of pairs of output spike trains only allow for relative comparisons. In the present study, we report for the first time an approach for measuring the proportion of common input in the low frequency bandwidth (<5 Hz) to a motor neuron pool in humans. This estimate is based on a phenomenological model and the theoretical fitting of the experimental values of coherence between the permutations of groups of motor unit spike trains. We demonstrate the validity of this theoretical estimate with several simulations. Moreover, we applied this method to three human muscles: the abductor digiti minimi, tibialis anterior and vastus medialis. Despite these muscles having different functional roles and control properties, as confirmed by the results of the present study, we estimate that their motor pools receive a similar and large (>60%) proportion of common low frequency oscillations with respect to their total synaptic input. These results suggest that the central nervous system provides a large amount of common input to motor neuron pools, in a similar way to that for muscles with different functional and control properties.
Microtubule doublets are double-track railways for intraflagellar transport trains
Authors: Stepanek Ludek , Pigino Gaia 
Published: May 2016

Stay on the right track
Cilia contain a well-ordered array of microtubule doublets along their length. A longstanding question in cilium structure and function is why the microtubule arrangement in cilia is so complex. Stepanek and Pigino developed a time-resolved correlative fluorescence and three-dimensional electron microscopy method to show that the doublets provide directionality to intraflagellar transport. One microtubule in the pair moves cargoes up to the ciliary tip. Meanwhile, the other microtubule moves cargoes back to the cell body. These results explain why the axoneme is built out of microtubule doublets and suggest a mechanistic picture of how the logistics of bidirectional intraflagellar transport are regulated.

Science
, this issue p.
721
Draft Genome Sequence of
Cylindrospermopsis raciborskii
(Cyanobacteria) Strain ITEP-A1 Isolated from a Brazilian Semiarid Freshwater Body: Evidence of Saxitoxin and Cylindrospermopsin Synthetase Genes
Authors: Lorenzi Adriana Sturion , Silva Genivaldo Gueiros Z. , Lopes Fabyano Alvares Cardoso , Chia Mathias Ahii , Edwards Robert A. , Bittencourt-Oliveira Maria Carmo 
Published: May 2016

ABSTRACT

Cylindrospermopsis raciborskii
ITEP-A1 is a saxitoxin-producing cyanobacterium. We report the draft genome sequence of ITEP-A1, which comprised 195 contigs that were assembled with SPAdes and annotated with Rapid Annotation using Subsystem Technology. The identified genome sequence had 3,605,836 bp, 40.1% G+C, and predicted 3,553 coding sequences (including the synthetase genes).
Draft Genome Sequence of Klebsiella pneumoniae UCD-JA29 Isolated from a Patient with Sepsis
Authors: Alexiev Alexandra , Coil David A. , Jospin Guillaume , Eisen Jonathan A. , Adams Jason Y. 
Published: May 2016

ABSTRACT

Here, we present the 6,155,188-bp draft genome sequence of
Klebsiella pneumoniae
UCD-JA29, isolated from blood cultures from a patient with sepsis at the University of California, Davis Medical Center in Sacramento, California, USA.
Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica
Authors: Parmeciano Di Noto Gisela , Vázquez Susana C. , MacCormack Walter P. , Iriarte Andrés , Quiroga Cecilia 
Published: May 2016

ABSTRACT

We present the draft genome of
Shewanella frigidimarina
Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution.
Genome Sequence of
Ustilaginoidea virens
IPU010, a Rice Pathogenic Fungus Causing False Smut
Authors: Kumagai Toshitaka , Ishii Tomoko , Terai Goro , Umemura Myco , Machida Masayuki , Asai Kiyoshi 
Published: May 2016

ABSTRACT

Ustilaginoidea virens
is a rice pathogenic fungus that causes false smut disease, a disease that seriously damages the yield and quality of the grain. Analysis of the
U. virens
IPU010 33.6-Mb genome sequence will aid in the understanding of the pathogenicity of the strain, particularly in regard to effector proteins and secondary metabolic genes.
Draft Genome Sequence of Zhouia amylolytica AD3, Isolated from Tidal Flat Sediment
Authors: Jia Baolei , Jin Hyun Mi , Lee Hyo Jung , Jeon Che Ok 
Published: May 2016

ABSTRACT

Zhouia amylolytica
AD3 was isolated from tidal flat sediment at Taean, South Korea. We report here the draft genome sequence of
Z. amylolytica
AD3, which is the first report of a genome sequence of the genus
Zhouia
. The genomic information will provide a better understanding of the physiology, adaptation, and evolution of
Zhouia
species.
Complete Genome Sequence of an NADC30-Like Porcine Reproductive and Respiratory Syndrome Virus Characterized by Recombination with Other Strains
Authors: Li Yingying , Ji Guobiao , Wang Juan , Tan Feifei , Zhuang Jinshan , Li Xiangdong , Tian Kegong 
Published: May 2016

ABSTRACT
We report here the complete genome sequence of an NADC30-like porcine reproductive and respiratory syndrome virus (PRRSV), HNyc15, which was characterized by recombination with VR-2332 and CH-1a PRRSV strains in open reading frames (ORFs) 2 to 4.
Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology
Authors: He Jingxuan , Sundararajan Anitha , Devitt Nicholas P. , Schilkey Faye D. , Ramaraj Thiruvarangan , Melançon Charles E. 
Published: May 2016

ABSTRACT

Here, we report the complete genome sequence of
Streptomyces venezuelae
ATCC 15439, a producer of the methymycin/pikromycin family of macrolide antibiotics and a model host for natural product studies, obtained exclusively using PacBio sequencing technology. The 9.03-Mbp genome harbors 8,775 genes and 11 polyketide and nonribosomal peptide natural product gene clusters.
MORPHOLOGY EFFECT OF Ni–Ag/CARBON NANOMATERIALS ON THEIR ELECTROCATALYTIC ACTIVITY FOR GLUCOSE OXIDATION
Authors: OUYANG RUIZHUO , LI WEIWEI , YANG YANG , ZHANG WANGYAO , FENG KAI , ZONG TIANYU , AN YARUI , ZHOU SHUANG , MIAO YUQING 
Published: May 2016

We presented here three carbon-nanomaterials-based modified glassy carbon electrodes (GCE) with Ni–Ag nanohybrid nanoparticles (NPs) deposited upon, including single-wall carbon nanotubes (SWCNTs), multi-wall carbon nanotubes (MWCNTs) and the mesoporous carbons (MPCs), and compared their morphology effects on both Ni–Ag deposition quality and electrocatalytic performances toward Glu oxidation. After being deposited with Ni–Ag NPs, a homogenous surface with very small Ni–Ag NPs was obtained for Ni–Ag/SWCNTs/GCE, while heterogeneous, coarse surfaces with obvious embedment with large Ni–Ag particles were observed for both Ni–Ag/MWCNTs/GCE and Ni–Ag/MPC/GCE. All three modified electrodes were well characterized in terms of surface morphology, electron transfer rate, hydrophilicity, interference resistance, stability, electrocatalytic behaviors as well as practicability in real samples, based on which Ni–Ag/SWCNTs/GCE was always proved to be more advantageous over other two composite electrodes. Such advantage of Ni–Ag/SWCNTs/GCE was attributed to its desirable surface morphology good for Ni–Ag deposition and exposure of as many active sites as possible to Glu oxidation, leading to the extraordinary electrocatalytic performance.
Some remarks on Mathieu subspaces over associative algebras
Authors: de Bondt Michiel 
Published: May 2016

In [9] (which is [W. Zhao, Mathieu subspaces of associative algebras, J. Algebra 350(1) (2012) 245–272]), the author takes a closer look at algebraic elements of radicals of Mathieu subspaces (of associative algebras) over a field, and suggests to look at integral elements with rings other than fields. But it seems more useful to look at so-called co-integral elements. We generalize his theory about algebraic radicals over fields to co-integral radicals over commutative rings with unity. Furthermore, we show that over Artin rings, the concepts of integrality and co-integrality coincide. In addition, we define so-called uniform Mathieu subspaces, inspired by the fact that Mathieu subspaces with co-integral radicals are always of this type. Besides broadening the theory of [9] by means of the new concepts co-integrality and uniformity, we generalize many of the results of [9] in other ways as well. Furthermore, we obtain several new results. In the last section, we disprove a conjecture by the author of [9] (in a version of [9] prior to finding the counterexample), by showing that so-called strongly simple algebras do not need to be fields over theirselves.
A 25 myr chronostratigraphy of ignimbrites in south Peru: implications for the volcanic history of the Central Andes
Authors: Thouret Jean-Claude , Jicha Brian R. , Paquette Jean-Louis , Cubukcu Evren H. 
Published: May 2016

With an area exceeding 25 000 km
2
and volumes
c.
5000 km
3
, south Peru hosts the Andes’ second largest Neogene ignimbrite field. We document the extent, stratigraphy and chronology of 12 ignimbrite sheets in the Río Ocoña–Cotahuasi–Marán and Colca deep canyons. Based on 74
40
Ar/
39
Ar and U/Pb age determinations, ignimbrite-forming episodes span 25 myr. Prior to 9 Ma, eight large-volume ignimbrites were produced every 2.4 myr. After 9 Ma, average lulls between small- to moderate-volume ignimbrites decreased to 0.85 myr. The refined volcanic stratigraphy reveals three main features. (1) Larger volume ignimbrites were emplaced by punctuated flare-ups between 25 and 9 Ma during uplift of the Western Cordillera. (2) Numerous smaller ignimbrites were emplaced after 9 Ma as the ignimbrite production rate decreased threefold. This decrease may be due to the declining crustal melting rate, decreasing plate convergence rate after 9 Ma, or more magma stagnation in the shallow crust, which promoted the growth of composite cones. (3) Growth of two volcanic arcs has added twice as much volume (
c.
53 km
3
Ma
−1
) to the Río Ocoña–Cotahuasi–Marán volcanic field than the ignimbrites after 2.27 Ma. Estimated linear arc magma output has, however, decreased twofold (0.15 – 0.08 km
3
km
−1
Ma
−1
) from the Early Quaternary to the Pleistocene–Holocene.

Supplementary materials:
Supplementary text, tables 1–3 and figures 1–4 are available at
http://doi.org/10.6084/m9.figshare.c.3147100
.
Challenging the Cancer Molecular Stratification Dogma: Intratumoral Heterogeneity Undermines Consensus Molecular Subtypes and Potential Diagnostic Value in Colorectal Cancer
Authors: Dunne Philip D. , McArt Darragh G. , Bradley Conor A. , O'Reilly Paul G. , Barrett Helen L. , Cummins Robert , O'Grady Tony , Arthur Ken , Loughrey Maurice B. , Allen Wendy L. , McDade Simon S. , Waugh David J. , Hamilton Peter W. , Longley Daniel B. , Kay Elaine W. , Johnston Patrick G. , Lawler Mark , Salto-Tellez Manuel , Van Schaeybroeck Sandra 
Published: May 2016

Abstract
Purpose: A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer with potential diagnostic utility, culminating in publication of a colorectal cancer Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.
Experimental Design: We performed multiregion tissue RNA extraction/transcriptomic analysis using colorectal-specific arrays on invasive front, central tumor, and lymph node regions selected from tissue samples from 25 colorectal cancer patients.
Results: We identified a consensus 30-gene list, which represents the intratumoral heterogeneity within a cohort of primary colorectal cancer tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential HR = 2.914 (confidence interval 0.9286–9.162) in stage II/III colorectal cancer patients, but in addition, we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread epithelial–mesenchymal transition. Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analyzed.
Conclusions: Gene expression profiles derived from the nonmalignant stromal region can influence assignment of colorectal cancer transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision making in colorectal cancer. Clin Cancer Res; 22(16); 4095–104. ©2016 AACR.
See related commentary by Morris and Kopetz, p. 3989
Crise da água na Região Metropolitana de São Paulo: a injustiça ambiental e a privatização de um bem comum
Authors: Fracalanza Ana Paula , Freire Thais Magalhães 
Published: May 2016

O objetivo deste artigo é discutir a água enquanto bem comum, direito de todos, e a injustiça ambiental envolvida na crise hídrica da água na Região Metropolitana de São Paulo - RMSP. Conclui-se pela existência de injustiça ambiental no caso da crise hídrica na Região Metropolitana de São Paulo, já que é a população de mais baixa renda e mais vulnerável dos pontos de vista econômico e ambiental que apresenta maiores dificuldades de acesso à água enquanto bem comum em quantidade e qualidade para sua sobrevivência. Por outro lado, a população de mais alta renda tem maiores possibilidades de obtenção da água, de maneira privada. Isto contribui para acentuar o crescimento da apropriação privada da água enquanto mercadoria, acentuando a privatização de um bem comum.
Low-Density Lipoprotein Receptor–Dependent and Low-Density Lipoprotein Receptor–Independent Mechanisms of Cyclosporin A–Induced Dyslipidemia
Authors: Kockx Maaike , Glaros Elias , Leung Betty , Ng Theodore W. , Berbée Jimmy F.P. , Deswaerte Virginie , Nawara Diana , Quinn Carmel , Rye Kerry-Anne , Jessup Wendy , Rensen Patrick C.N. , Meikle Peter J. , Kritharides Leonard 
Published: May 2016

Objective—

Cyclosporin A (CsA) is an immunosuppressant commonly used to prevent organ rejection but is associated with hyperlipidemia and an increased risk of cardiovascular disease. Although studies suggest that CsA-induced hyperlipidemia is mediated by inhibition of low-density lipoprotein receptor (LDLr)–mediated lipoprotein clearance, the data supporting this are inconclusive. We therefore sought to investigate the role of the LDLr in CsA-induced hyperlipidemia by using
Ldlr
-knockout mice (
Ldlr
−/−
).

Approach and Results—

Ldlr
−/−
and wild-type (wt) C57Bl/6 mice were treated with 20 mg/kg per d CsA for 4 weeks. On a chow diet, CsA caused marked dyslipidemia in
Ldlr
−/−
but not in wt mice. Hyperlipidemia was characterized by a prominent increase in plasma very low–density lipoprotein and intermediate-density lipoprotein/LDL with unchanged plasma high-density lipoprotein levels, thus mimicking the dyslipidemic profile observed in humans. Analysis of specific lipid species by liquid chromatography–tandem mass spectrometry suggested a predominant effect of CsA on increased very low–density lipoprotein–IDL/LDL lipoprotein number rather than composition. Mechanistic studies indicated that CsA did not alter hepatic lipoprotein production but did inhibit plasma clearance and hepatic uptake of [
14
C]cholesteryl oleate and glycerol tri[
3
H]oleate-double-labeled very low–density lipoprotein–like particles. Further studies showed that CsA inhibited plasma lipoprotein lipase activity and increased levels of apolipoprotein C-III and proprotein convertase subtilisin/kexin type 9.

Conclusions—
We demonstrate that CsA does not cause hyperlipidemia via direct effects on the LDLr. Rather, LDLr deficiency plays an important permissive role for CsA-induced hyperlipidemia, which is associated with abnormal lipoprotein clearance, decreased lipoprotein lipase activity, and increased levels of apolipoprotein C-III and proprotein convertase subtilisin/kexin type 9. Enhancing LDLr and lipoprotein lipase activity and decreasing apolipoprotein C-III and proprotein convertase subtilisin/kexin type 9 levels may therefore provide attractive treatment targets for patients with hyperlipidemia receiving CsA.