bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Sequencing (RNA-seq) Analysis of the Effects of Metal Nanoparticle Exposure on the Transcriptome of Chlamydomonas reinhardtii
Authors: Simon Dana F. , Domingos Rute F. , Hauser Charles , Hutchins Colin M. , Zerges William , Wilkinson Kevin J. 
Published: June 2013

ABSTRACT

The widespread use of nanoparticles (NPs) raises concern over their potential toxicological effects in humans and ecosystems. Here we used transcriptome sequencing (RNA-seq) to evaluate the effects of exposure to four different metal-based NPs, nano-Ag (nAg), nano-TiO
2
(nTiO
2
), nano-ZnO (nZnO), and CdTe/CdS quantum dots (QDs), in the eukaryotic green alga
Chlamydomonas reinhardtii
. The transcriptome was characterized before and after exposure to each NP type. Specific toxicological effects were inferred from the functions of genes whose transcripts either increased or decreased. Data analysis resulted in important differences and also similarities among the NPs. Elevated levels of transcripts of several marker genes for stress were observed, suggesting that only nZnO caused nonspecific global stress to the cells under environmentally relevant conditions. Genes with photosynthesis-related functions were decreased drastically during exposure to nTiO
2
and slightly during exposures to the other NP types. This pattern suggests either toxicological effects in the chloroplast or effects that mimic a transition from low to high light. nAg exposure dramatically elevated the levels of transcripts encoding known or predicted components of the cell wall and the flagella, suggesting that it damages structures exposed to the external milieu. Exposures to nTiO
2
, nZnO, and QDs elevated the levels of transcripts encoding subunits of the proteasome, suggesting proteasome inhibition, a phenomenon believed to underlie the development and progression of several major diseases, including Alzheimer's disease, and used in chemotherapy against multiple myeloma.
Biodegradation of Endocrine Disruptors in Solid-Liquid Two-Phase Partitioning Systems by Enrichment Cultures
Authors: Villemur Richard , dos Santos Silvia Cristina Cunha , Ouellette Julianne , Juteau Pierre , Lépine François , Déziel Eric 
Published: June 2013

ABSTRACT

Naturally occurring and synthetic estrogens and other molecules from industrial sources strongly contribute to the endocrine disruption of urban wastewater. Because of the presence of these molecules in low but effective concentrations in wastewaters, these endocrine disruptors (EDs) are only partially removed after most wastewater treatments, reflecting the presence of these molecules in rivers in urban areas. The development of a two-phase partitioning bioreactor (TPPB) might be an effective strategy for the removal of EDs from wastewater plant effluents. Here, we describe the establishment of three ED-degrading microbial enrichment cultures adapted to a solid-liquid two-phase partitioning system using Hytrel as the immiscible water phase and loaded with estrone, estradiol, estriol, ethynylestradiol, nonylphenol, and bisphenol A. All molecules except ethynylestradiol were degraded in the enrichment cultures. The bacterial composition of the three enrichment cultures was determined using 16S rRNA gene sequencing and showed sequences affiliated with bacteria associated with the degradation of these compounds, such as
Sphingomonadales
. One
Rhodococcus
isolate capable of degrading estrone, estradiol, and estriol was isolated from one enrichment culture. These results highlight the great potential for the development of TPPB for the degradation of highly diluted EDs in water effluents.
Development of a New Method for Detection and Identification of Oenococcus oeni Bacteriophages Based on Endolysin Gene Sequence and Randomly Amplified Polymorphic DNA
Authors: Doria Francesca , Napoli Chiara , Costantini Antonella , Berta Graziella , Saiz Juan-Carlos , Garcia-Moruno Emilia 
Published: June 2013

ABSTRACTMalolactic fermentation (MLF) is a biochemical transformation conducted by lactic acid bacteria (LAB) that occurs in wine at the end of alcoholic fermentation.Oenococcus oeniis the main species responsible for MLF in most wines. As in other fermented foods, where bacteriophages represent a potential risk for the fermentative process,O. oenibacteriophages have been reported to be a possible cause of unsuccessful MLF in wine. Thus, preparation of commercial starters that take into account the different sensitivities ofO. oenistrains to different phages would be advisable. However, currently, no methods have been described to identify phages infectingO. oeni. In this study, two factors are addressed: detection and typing of bacteriophages. First, a simple PCR method was devised targeting a conserved region of the endolysin (lys) gene to detect temperateO. oenibacteriophages. For this purpose, 37O. oenistrains isolated from Italian wines during different phases of the vinification process were analyzed by PCR for the presence of thelysgene, and 25 strains gave a band of the expected size (1,160 bp). This is the first method to be developed that allows identification of lysogenicO. oenistrains without the need for time-consuming phage bacterial-lysis induction methods. Moreover, a phylogenetic analysis was conducted to type bacteriophages. After the treatment of bacteria with UV light, lysis was obtained for 15 strains, and the 15 phage DNAs isolated were subjected to two randomly amplified polymorphic DNA (RAPD)-PCRs. By combining the RAPD profiles andlyssequences, 12 differentO. oeniphages were clearly distinguished.
The Plasma Membrane Proton Pump PMA-1 Is Incorporated into Distal Parts of the Hyphae Independently of the Spitzenkörper in Neurospora crassa
Authors: Fajardo-Somera Rosa A. , Bowman Barry , Riquelme Meritxell 
Published: June 2013

ABSTRACTMost models for fungal growth have proposed a directional traffic of secretory vesicles to the hyphal apex, where they temporarily aggregate at the Spitzenkörper before they fuse with the plasma membrane (PM). The PM H+-translocating ATPase (PMA-1) is delivered via the classical secretory pathway (endoplasmic reticulum [ER] to Golgi) to the cell surface, where it pumps H+out of the cell, generating a large electrochemical gradient that supplies energy to H+-coupled nutrient uptake systems. To characterize the traffic and delivery of PMA-1 during hyphal elongation, we have analyzed by laser scanning confocal microscopy (LSCM) strains ofNeurospora crassaexpressing green fluorescent protein (GFP)-tagged versions of the protein. In conidia, PMA-1-GFP was evenly distributed at the PM. During germination and germ tube elongation, PMA-1-GFP was found all around the conidial PM and extended to the germ tube PM, but fluorescence was less intense or almost absent at the tip. Together, the data indicate that the electrochemical gradient driving apical nutrient uptake is generated from early developmental stages. In mature hyphae, PMA-1-GFP localized at the PM at distal regions (>120 μm) and in completely developed septa, but not at the tip, indicative of a distinct secretory route independent of the Spitzenkörper occurring behind the apex.
Activation of CpxRA in Haemophilus ducreyi Primarily Inhibits the Expression of Its Targets, Including Major Virulence Determinants
Authors: Gangaiah Dharanesh , Zhang Xinjun , Fortney Kate R. , Baker Beth , Liu Yunlong , Munson Robert S. , Spinola Stanley M. 
Published: June 2013

ABSTRACTHaemophilus ducreyicauses chancroid, a genital ulcer disease that facilitates the transmission of human immunodeficiency virus type 1. In humans,H. ducreyiis surrounded by phagocytes and must adapt to a hostile environment to survive. To sense and respond to environmental cues, bacteria frequently use two-component signal transduction (2CST) systems. The only obvious 2CST system inH. ducreyiis CpxRA; CpxR is a response regulator, and CpxA is a sensor kinase. Previous studies by Hansen and coworkers showed that CpxR directly represses the expression ofdsrA, thelspB-lspA2operon, and theflpoperon, which are required for virulence in humans. They further showed that CpxA functions predominantly as a phosphatasein vitroto maintain the expression of virulence determinants. Since acpxAmutant is avirulent while acpxRmutant is fully virulent in humans, CpxA also likely functions predominantly as a phosphatasein vivo. To better understand the role ofH. ducreyiCpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. Activation of CpxR by deletion ofcpxArepressed nearly 70% of its targets, including seven established virulence determinants. Inactivation of CpxR by deletion ofcpxRdifferentially regulated few genes and increased the expression of one virulence determinant. We identified a CpxR binding motif that was enriched in downregulated but not upregulated targets. These data reinforce the hypothesis that CpxA phosphatase activity plays a critical role in controllingH. ducreyivirulencein vivo. Characterization of the downregulated genes may offer new insights into pathogenesis.
Role of the Ribosomal P-Site Elements of m
2
G966, m
5
C967, and the S9 C-Terminal Tail in Maintenance of the Reading Frame during Translational Elongation in Escherichia coli
Authors: Arora Smriti , Bhamidimarri Satya Prathyusha , Weber Michael H. W. , Varshney Umesh 
Published: June 2013

ABSTRACT

The ribosomal P-site hosts the peptidyl-tRNAs during translation elongation. Which P-site elements support these tRNA species to maintain codon-anticodon interactions has remained unclear. We investigated the effects of P-site features of methylations of G966, C967, and the conserved C-terminal tail sequence of Ser, Lys, and Arg (SKR) of the S9 ribosomal protein in maintenance of the translational reading frame of an mRNA. We generated
Escherichia coli
strains deleted for the SKR sequence in S9 ribosomal protein, RsmB (which methylates C967), and RsmD (which methylates G966) and used them to translate LacZ from its +1 and −1 out-of-frame constructs. We show that the S9 SKR tail prevents both the +1 and −1 frameshifts and plays a general role in holding the P-site tRNA/peptidyl-tRNA in place. In contrast, the G966 and C967 methylations did not make a direct contribution to the maintenance of the translational frame of an mRNA. However, deletion of
rsmB
in the S9Δ3 background caused significantly increased −1 frameshifting at 37°C. Interestingly, the effects of the deficiency of C967 methylation were annulled when the
E. coli
strain was grown at 30°C, supporting its context-dependent role.
Discovery of Catalases in Members of the Chlamydiales Order
Authors: Rusconi Brigida , Greub Gilbert 
Published: June 2013

ABSTRACTCatalase is an important virulence factor for survival in macrophages and other phagocytic cells. InChlamydiaceae, no catalase had been described so far. With the sequencing and annotation of the full genomes ofChlamydia-related bacteria, the presence of different catalase-encoding genes has been documented. However, their distribution in theChlamydialesorder and the functionality of these catalases remain unknown. Phylogeny of chlamydial catalases was inferred using MrBayes, maximum likelihood, and maximum parsimony algorithms, allowing the description of three clade 3 and two clade 2 catalases. Only monofunctional catalases were found (no catalase-peroxidase or Mn-catalase). All presented a conserved catalytic domain and tertiary structure. Enzymatic activity of cloned chlamydial catalases was assessed by measuring hydrogen peroxide degradation. The catalases are enzymatically active with different efficiencies. The catalase ofParachlamydia acanthamoebaeis the least efficient of all (its catalytic activity was 2 logs lower than that ofPseudomonas aeruginosa). Based on the phylogenetic analysis, we hypothesize that an ancestral class 2 catalase probably was present in the common ancestor of all currentChlamydialesbut was retained only inCriblamydia sequanensisandNeochlamydia hartmannellae. The catalases of class 3, present inEstrella lausannensisandParachlamydia acanthamoebae, probably were acquired by lateral gene transfer fromRhizobiales, whereas forWaddlia chondrophilathey likely originated fromLegionellalesorActinomycetales. The acquisition of catalases on several occasions in theChlamydialessuggests the importance of this enzyme for the bacteria in their host environment.
Clinical scaphoid score (CSS) to identify scaphoid fracture with MRI in patients with normal x-ray after a wrist trauma
Authors: Bergh Torbjørn Hiis , Lindau Tommy , Soldal Lars Atle , Bernardshaw Soosaipillai V , Behzadi Mehdi , Steen Knut , Brudvik Christina 
Published: June 2013

IntroductionThe aim of this study was to compare a combination of three commonly used tests to identify scaphoid fractures with MRI in patients with normal x-ray after a wrist trauma.Patients and methodsThis prospective MRI study included patients between 18 years and 49 years, who attended the Emergency Department, Bergen, Norway after sustaining an acute wrist trauma within the previous week. Initial x-rays of the wrist were normal. MRI was done within a median of 1 day after the trauma. The study period lasted 1 year. The patients were examined with three commonly used clinical scaphoid tests; tenderness in the anatomical snuffbox with the wrist in ulnar deviation (3 points), tenderness over the scaphoid tubercle (2 points) and pain upon longitudinal compression of the thumb (1 point). The clinical scaphoid score (CSS) is a sum of these points, which was compared with MRI verified fracture of the scaphoid.ResultsWe included 154 patients with wrist sprain and normal x-rays; 13 had occult scaphoid fracture. A CSS of 4 or more was the only statistically significant ‘cut-off’ value to identify occult scaphoid fractures (p<0.05). Diagnostic sensitivity increased with more experienced Emergency Department doctors.ConclusionsIf a patient with wrist pain after injury and normal x-ray has a CSS≥4 (pain in the anatomical snuffbox in addition to pain at scaphoid tubercle or longitudinal compression or both) we recommend MRI. A CSS <4 has a negative predictive value of 96%, which makes scaphoid fracture unlikely.
ALK Rearrangements Are Mutually Exclusive with Mutations in EGFR or KRAS: An Analysis of 1,683 Patients with Non–Small Cell Lung Cancer
Authors: Gainor Justin F. , Varghese Anna M. , Ou Sai-Hong Ignatius , Kabraji Sheheryar , Awad Mark M. , Katayama Ryohei , Pawlak Amanda , Mino-Kenudson Mari , Yeap Beow Y. , Riely Gregory J. , Iafrate A. John , Arcila Maria E. , Ladanyi Marc , Engelman Jeffrey A. , Dias-Santagata Dora , Shaw Alice T. 
Published: June 2013

Abstract
Purpose: Anaplastic lymphoma kinase (ALK) gene rearrangements define a distinct molecular subset of non–small cell lung cancer (NSCLC). Recently, several case reports and small series have reported that ALK rearrangements can overlap with other oncogenic drivers in NSCLC in crizotinib-naïve and crizotinib-resistant cancers.
Experimental Design: We reviewed clinical genotyping data from 1,683 patients with NSCLC and investigated the prevalence of concomitant EGFR or KRAS mutations among patients with ALK-positive NSCLC. We also examined biopsy specimens from 34 patients with ALK-positive NSCLC after the development of resistance to crizotinib.
Results: Screening identified 301 (17.8%) EGFR mutations, 465 (27.6%) KRAS mutations, and 75 (4.4%) ALK rearrangements. EGFR mutations and ALK rearrangements were mutually exclusive. Four patients with KRAS mutations were found to have abnormal ALK FISH patterns, most commonly involving isolated 5′ green probes. Sufficient tissue was available for confirmatory ALK immunohistochemistry in 3 cases, all of which were negative for ALK expression. Among patients with ALK-positive NSCLC who acquired resistance to crizotinib, repeat biopsy specimens were ALK FISH positive in 29 of 29 (100%) cases. Secondary mutations in the ALK kinase domain and ALK gene amplification were observed in 7 of 34 (20.6%) and 3 of 29 (10.3%) cases, respectively. No EGFR or KRAS mutations were identified among any of the 25 crizotinib-resistant, ALK-positive patients with sufficient tissue for testing.
Conclusions: Functional ALK rearrangements were mutually exclusive with EGFR and KRAS mutations in a large Western patient population. This lack of overlap was also observed in ALK-positive cancers with acquired resistance to crizotinib. Clin Cancer Res; 19(15); 4273–81. ©2013 AACR.
Different Patterns of Bundle-Branch Blocks and the Risk of Incident Heart Failure in the Women’s Health Initiative (WHI) Study
Authors: Zhang Zhu-ming , Rautaharju Pentti M. , Soliman Elsayed Z. , Manson JoAnn E. , Martin Lisa W. , Perez Marco , Vitolins Mara , Prineas Ronald J. 
Published: June 2013

Background—
We evaluated the risk of incident heart failure (HF) associated with bundle-branch blocks (BBBs) in postmenopausal women.

Methods and Results—
Cox’s regression was used to evaluate hazard ratios with 95% confidence intervals for HF among 65 975 participants of the Women’s Health Initiative (WHI) study during an average follow-up of 14 years. BBBs observed in 1676 women at baseline were categorized into left, right, and indetermined-type BBBs (LBBB, RBBB, and intraventricular conduction defect, respectively). Compared with women with no BBB, LBBB, and intraventricular conduction defect were strong predictors of incident HF in multivariable-adjusted risk models (hazard ratio, 3.79; confidence interval, 2.95–4.87 for LBBB and hazard ratio, 3.53; confidence interval, 2.14–5.81 for intraventricular conduction defect). RBBB was not a significant predictor of incident HF in multivariable-adjusted risk model, but the combination of RBBB and left anterior fascicular block was a strong predictor (hazard ratio, 2.96; confidence interval, 1.77–4.93). QRS duration was an independent predictor of incident HF only in LBBB, with more pronounced risk at QRS ≥140 ms than at <140 ms. QRS nondipolar voltage (RNDPV) was an independent predictor in both RBBB and LBBB and, in addition, in LBBB, QRS/STT angle and ST J-point depression in aVL were independent predictors.

Conclusions—
LBBB, intraventricular conduction defect, and RBBB combined with left anterior fascicular block are strong predictors of incident HF in multivariable-adjusted risk models, but RBBB is not a significant predictor. QRS duration ≥140 ms may warrant consideration in LBBB as an indication for further diagnostic evaluation for possible therapeutic and preventive action.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00000611.
Acute Failure of Catheter Ablation for Ventricular Tachycardia Due to Structural Heart Disease: Causes and Significance
Authors: Tokuda Michifumi , Kojodjojo Pipin , Tung Stanley , Tedrow Usha B. , Nof Eyal , Inada Keiichi , Koplan Bruce A. , Michaud Gregory F. , John Roy M. , Epstein Laurence M. , Stevenson William G. 
Published: June 2013

Background

Acute end points of catheter ablation for ventricular tachycardia (
VT
) remain incompletely defined. The aim of this study is to identify causes for failure in patients with structural heart disease and to assess the relation of this acute outcome to longer‐term management and outcomes.

Methods and Results

From 2002 to 2010, 518 consecutive patients (84% male, 62±14 years) with structural heart disease underwent a first ablation procedure for sustained
VT
at our institution. Acute ablation failure was defined as persistent inducibility of a clinical
VT
. Acute ablation failure was seen in 52 (10%) patients. Causes for failure were: intramural free wall
VT
in 13 (25%), deep septal
VT
in 9 (17%), decision not to ablate due to proximity to the bundle of His, left phrenic nerve, or a coronary artery in 3 (6%), and endocardial ablation failure with inability or decision not to attempt to access the epicardium in 27 (52%) patients. In multivariable analysis, ablation failure was an independent predictor of mortality (hazard ratio 2.010, 95%
CI
1.147 to 3.239,
P
=0.004) and
VT
recurrence (hazard ratio 2.385, 95%
CI
1.642 to 3.466,
P
<0.001).

Conclusions

With endocardial or epicardial ablation, or both, acute ablation failure was seen in 10% of patients, largely due to anatomic factors. Persistence of a clinical
VT
is associated with recurrence and comparatively higher mortality.
Supposition Theory and Porretan Theology: Summa Zwettlensis and Dialogus Ratii et Everardi
Authors: Valente Luisa 
Published: June 2013

Abstract
The article investigates how the problem of (linguistic) reference is treated in the theology of two pupils of Gilbert of Poitiers by means of suppo* terms (supponere; suppositus,-a,-um; suppositio). Supposition is for Gilbert an action performed by a speaker, not a property of terms, and he considers language as a system for communication between human beings: key notions are the ‘sense in the author’s mind’ and the ‘interpreter’s understanding’. In contrast, the two Porretans tend to objectify language as a formal system of terms. Suppositio becomes in the Summa Zwettlensis the name itself as subject term in a proposition, and is divided into many kinds; formal rules are described which govern the influence of the predicate on the subject term’s denotation. In Everard of Ypres’ Dialogus Ratii et Everardi, supponere is a function (officium) of the name, and ‘human is a species of individuals’ is, as in some logical treatises and differently from Gilbert, a case of rhetorical transfer.
Suppositum between Logic and MetaphysicsSimon of Faversham and his Contemporaries(1270-1290)
Authors: Murè Dafne 
Published: June 2013

Abstract
This article is the result of research on the occurrences of the terms suppositio, supponere and their linguistic derivations in the literature on fallacies (comments on the Sophistical Refutations) of the second half of the thirteenth century. The authors analysed are Albert the Great, Giles of Rome, Simon of Faversham, the so-called Incerti Auctores (Anonymous C and SF), the Anonymous of Prague (P) and John Duns Scotus. The central elements that emerge are the role played by the notion of suppositum and by the linguistic context (adiuncta, determinatio) to determine the denotation of an expression, and the importance of the metaphysical problem of the unity and identity of suppositum in both the theory of predication and the theory of inference. Both subjects, obviously, are closely connected.
Scotus on Supposition
Authors: Marmo Costantino 
Published: June 2013

Abstract
In his commentaries on Porphyry and Aristotle’s Organon (Categories, Peri hermeneias, Sophistici elenchi, and Topics) and in his other works, John Duns Scotus shows his knowledge of both the modistic theory of language and the theory of supposition. My contribution sheds some light on the relationship between Scotus’ philosophy of language and the theory of supposition, collecting and commenting on all the passages in which he makes use of it or discusses some theoretical points. I take into special account the almost unknown commentary on the Topics, which is preserved in a Vatican manuscript.
Supposition and Predication in Medieval Trinitarian Logic
Authors: Knuuttila Simo 
Published: June 2013

Abstract
Many fourteenth-century logicians took affirmative propositions to maintain that the subject term and the predicate term stand or supposit for the same. This is called the identity theory of predication by historians and praedicatio identica (or one form of praedicatio identica) by Paul of Venice and others. The identity theory of predication was an important part of early fourteenth-century Trinitarian discussions as well, but what was called praedicatio identica by Duns Scotus and his followers in this context was something different. After some remarks on Scotus’s view and its background, I shall analyse Adam Wodeham’s explanation of Scotus’s praedicatio identica and how he understood the assumptions pertaining to supposition in the Scotist approach. I also describe Wodeham’s own solution to Trinitarian sophisms, which did not deviate from the identity theory of predication.