bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Bartonella quintana Extracytoplasmic Function Sigma Factor RpoE Has a Role in Bacterial Adaptation to the Arthropod Vector Environment
Authors: Abromaitis Stephanie , Koehler Jane E. 
Published: April 2013

ABSTRACT

Bartonella quintana
is a vector-borne bacterial pathogen that causes fatal disease in humans. During the infectious cycle,
B. quintana
transitions from the hemin-restricted human bloodstream to the hemin-rich body louse vector. Because extracytoplasmic function (ECF) sigma factors often regulate adaptation to environmental changes, we hypothesized that a previously unstudied
B. quintana
ECF sigma factor, RpoE, is involved in the transition from the human host to the body louse vector. The genomic context of
B. quintana
rpoE
identified it as a member of the ECF15 family of sigma factors found only in alphaproteobacteria. ECF15 sigma factors are believed to be the master regulators of the general stress response in alphaproteobacteria. In this study, we examined the
B. quintana
RpoE response to two stressors that are encountered in the body louse vector environment, a decreased temperature and an increased hemin concentration. We determined that the expression of
rpoE
is significantly upregulated at the body louse (28°C) versus the human host (37°C) temperature.
rpoE
expression also was upregulated when
B. quintana
was exposed to high hemin concentrations.
In vitro
and
in vivo
analyses demonstrated that RpoE function is regulated by a mechanism involving the anti-sigma factor NepR and the response regulator PhyR. The Δ
rpoE
Δ
nepR
mutant strain of
B. quintana
established that RpoE-mediated transcription is important in mediating the tolerance of
B. quintana
to high hemin concentrations. We present the first analysis of an ECF15 sigma factor in a vector-borne human pathogen and conclude that RpoE has a role in the adaptation of
B. quintana
to the hemin-rich arthropod vector environment.
Characterization of an
ntrX
Mutant of Neisseria gonorrhoeae Reveals a Response Regulator That Controls Expression of Respiratory Enzymes in Oxidase-Positive Proteobacteria
Authors: Atack John M. , Srikhanta Yogitha N. , Djoko Karrera Y. , Welch Jessica P. , Hasri Norain H. M. , Steichen Christopher T. , Vanden Hoven Rachel N. , Grimmond Sean M. , Othman Dk Seti Maimonah Pg , Kappler Ulrike , Apicella Michael A. , Jennings Michael P. , Edwards Jennifer L. , McEwan Alastair G. 
Published: April 2013

ABSTRACT

NtrYX is a sensor-histidine kinase/response regulator two-component system that has had limited characterization in a small number of
Alphaproteobacteria
. Phylogenetic analysis of the response regulator NtrX showed that this two-component system is extensively distributed across the bacterial domain, and it is present in a variety of
Betaproteobacteria
, including the human pathogen
Neisseria gonorrhoeae
. Microarray analysis revealed that the expression of several components of the respiratory chain was reduced in an
N. gonorrhoeae
ntrX
mutant compared to that in the isogenic wild-type (WT) strain 1291. These included the cytochrome
c
oxidase subunit (
ccoP
), nitrite reductase (
aniA
), and nitric oxide reductase (
norB
). Enzyme activity assays showed decreased cytochrome oxidase and nitrite reductase activities in the
ntrX
mutant, consistent with microarray data.
N. gonorrhoeae
ntrX
mutants had reduced capacity to survive inside primary cervical cells compared to the wild type, and although they retained the ability to form a biofilm, they exhibited reduced survival within the biofilm compared to wild-type cells, as indicated by LIVE/DEAD staining. Analyses of an
ntrX
mutant in a representative alphaproteobacterium,
Rhodobacter capsulatus
, showed that cytochrome oxidase activity was also reduced compared to that in the wild-type strain SB1003. Taken together, these data provide evidence that the NtrYX two-component system may be a key regulator in the expression of respiratory enzymes and, in particular, cytochrome
c
oxidase, across a wide range of proteobacteria, including a variety of bacterial pathogens.
Biochemical and Structural Studies of the Mycobacterium tuberculosis
O
6
-Methylguanine Methyltransferase and Mutated Variants
Authors: Miggiano Riccardo , Casazza Valentina , Garavaglia Silvia , Ciaramella Maria , Perugino Giuseppe , Rizzi Menico , Rossi Franca 
Published: April 2013

ABSTRACT

Mycobacterium tuberculosis
displays remarkable genetic stability despite continuous exposure to the hostile environment represented by the host's infected macrophages. Similarly to other organisms,
M. tuberculosis
possesses multiple systems to counteract the harmful potential of DNA alkylation. In particular, the suicidal enzyme
O
6
-methylguanine-DNA methyltransferase (OGT) is responsible for the direct repair of
O
6
-alkylguanine in double-stranded DNA and is therefore supposed to play a central role in protecting the mycobacterial genome from the risk of G·C-to-A·T transition mutations. Notably, a number of geographically widely distributed
M. tuberculosis
strains shows nonsynonymous single-nucleotide polymorphisms in their OGT-encoding gene, leading to amino acid substitutions at position 15 (T15S) or position 37 (R37L) of the N-terminal domain of the corresponding protein. However, the role of these mutations in
M. tuberculosis
pathogenesis is unknown. We describe here the
in vitro
characterization of
M. tuberculosis
OGT (
Mt
OGT) and of two point-mutated versions of the protein mimicking the naturally occurring ones, revealing that both mutated proteins are impaired in their activity as a consequence of their lower affinity for alkylated DNA than the wild-type protein. The analysis of the crystal structures of
Mt
OGT and
Mt
OGT-R37L confirms the high level of structural conservation of members of this protein family and provides clues to an understanding of the molecular bases for the reduced affinity for the natural substrate displayed by mutated
Mt
OGT. Our
in vitro
results could contribute to validate the inferred participation of mutated OGTs in
M. tuberculosis
phylogeny and biology.
Night Shift Work and Levels of 6-Sulfatoxymelatonin and Cortisol in Men
Authors: Mirick Dana K. , Bhatti Parveen , Chen Chu , Nordt Frank , Stanczyk Frank Z. , Davis Scott 
Published: April 2013

AbstractBackground: Night shift work is associated with cancer among men, but the biologic mechanism is unclear. We investigated whether male night shift workers showed changes in levels of melatonin and cortisol, potential biomarkers of cancer risk.Methods: Urine was collected from 185 night shift and 158 day shift-working male healthcare providers, aged 22 to 55 years, throughout work and sleep periods, and assayed for 6-sulfatoxymelatonin and cortisol. Morning serum was collected within 90 minutes of completing the night and assayed for cortisol.Results: Night shift workers had significantly lower 6-sulfatoxymelatonin levels during daytime sleep, nighttime work, and nighttime sleep on off-nights (57%, 62%, and 40% lower, respectively), relative to the day shift workers during nighttime sleep (P &lt; 0.0001); urinary cortisol in night shift workers was 16% higher during daytime sleep and 13% lower during nighttime sleep on off-nights (P &lt; 0.05). Morning serum cortisol post-work and post-sleep in night shift workers were 24% and 43% lower, respectively, than post-sleep levels among day shift workers (P &lt; 0.0001). Within-subject comparisons among the night shift workers revealed significantly lower melatonin levels and significantly higher urinary cortisol levels during daytime sleep and nighttime work, relative to nighttime sleep (P &lt; 0.01); morning serum cortisol levels post-work were lower than those post-sleep.Conclusions: Night shift workers have substantially lower 6-sulfatoxymelatonin during night work and daytime sleep, and levels remain low when night shift workers sleep at night. Chronic reduction in melatonin among night shift workers may be an important carcinogenic mechanism. Cortisol secretion patterns may be impacted by night shift work, which could affect cancer risk.Impact: Shift work could be an important risk factor for many types of cancer. Cancer Epidemiol Biomarkers Prev; 22(6); 1079–87. ©2013 AACR.
In Vivo Magnetization Transfer and Diffusion-Weighted Magnetic Resonance Imaging Detects Thrombus Composition in a Mouse Model of Deep Vein Thrombosis
Authors: Phinikaridou Alkystis , Andia Marcelo E. , Saha Prakash , Modarai Bijan , Smith Alberto , Botnar René M. 
Published: April 2013

Background—
Deep vein thrombosis remains a major health problem necessitating accurate diagnosis. Thrombolysis is associated with significant morbidity and is effective only for the treatment of unorganized thrombus. We tested the feasibility of in vivo magnetization transfer (MT) and diffusion-weighted magnetic resonance imaging to detect thrombus organization in a murine model of deep vein thrombosis.

Methods and Results—

Deep vein thrombosis was induced in the inferior vena cava of male BALB/C mice. Magnetic resonance imaging was performed at days 1, 7, 14, 21, and 28 after thrombus induction using MT, diffusion-weighted, inversion-recovery, and T1-mapping protocols. Delayed enhancement and T1 mapping were repeated 2 hours after injection of a fibrin contrast agent. Finally, excised thrombi were used for histology. We found that MT and diffusion-weighted imaging can detect histological changes associated with thrombus aging. MT rate (MTR) maps and percentage of MT rate (%MTR) allowed visualization and quantification of the thrombus protein content, respectively. The %MTR increased with thrombus organization and was significantly higher at days 14, 21, and 28 after thrombus induction (days 1, 7, 14, 21, 28: %MTR=2483±451, 2079±1210, 7029±2490, 10 295±4356, 32 994±25 449;
P
ANOVA
<0.05). There was a significant positive correlation between the %MTR and the histological protein content of the thrombus (
r
=0.70;
P
<0.05). The apparent diffusion coefficient was lower in erythrocyte-rich and collagen-rich thrombus (0.72±0.10 and 0.69±0.05 [×10
−3
mm
2
/s]). Thrombus at days 7 and 14 had the highest apparent diffusion coefficient values (0.95±0.09 and 1.10±0.18 [×10
−3
mm
2
/s]).

Conclusions—
MT and diffusion-weighted magnetic resonance imaging sequences are promising for the staging of thrombus composition and could be useful in guiding medical intervention.
Joyce à la Braudel: The Long-Temporality of Ulysses
Authors: George Jibu Mathew 
Published: April 2013

Abstract
Although James Joyce’s Ulysses (1922) covers only eighteen hours of a single day, the characters’ reflections and the symbolic networks of the text stretch the temporal reach of Ulysses to incredibly remote events of personal, historical, and mythical pasts. This essay focuses on a peculiar temporal dynamic in the text: by self-consciously basing itself upon the inconspicuous routine occurrences of everyday life rather than upon plot-making ‘events,’ the book hypostasizes what the Annales School of historians considers a long-temporal historical process into diurnal images. This temporal analysis of Joyce’s text draws upon Fernand Braudel, for whom history operates at multiple levels and is subject to various temporalities. Braudel’s interest lies in the imperceptibly slow-moving geographical time (longe durée), which characterizes the deep-lying “structures” of day-to-day life. Under such a micro-historical exegetical paradigm, the everyday objects and material practices of Ulysses, simultaneously synchronic and diachronic in signification, become the residual fragments of an evolving material civilization. Here Joyce’s modernist practice with regard to time provides an alibi for creating parallel narratives and histories. The long-temporality implied in the everyday furnishes Joyce with a perspectival basis on which history and its politics can be reconceived. It enables Joyce to present the claims, priorities, and challenges of the everyday lives of ordinary people, the real makers of a lasting history, as an experiential contrast to the ruptures and discontinuities of a nightmarish ‘grand history.’
Hontologie: The Chronotope of Shame in Jean Rhys’s Good Morning, Midnight
Authors: Johnson Erica L. 
Published: April 2013

Abstract
Jean Rhys’s 1939 novel, Good Morning, Midnight, is a modernist masterpiece of temporal, spatial, and linguistic fragments and collisions. This analysis begins with an application of what Bakhtin established as the mutual enmeshment in the genre of the novel of space and time, or “chronotope,” to Rhys’s novel, and goes on to identify Sasha’s primal experience of shame as the cause of temporal collapse. The mere recall of a shameful moment can ignite a blush, make the body burn—in short, erase the temporal distance between the past and the present, and Sasha exists in a state of shame so extreme that she exemplifies Bruno Chaouat’s concept of hontologie. Rhys records the violent destruction of linear time by the seismic force of the shame effect.
Emergence of Time in Quantum Gravity: Is Time Necessarily Flowing?
Authors: Martinetti Pierre 
Published: April 2013

Abstract
We discuss the emergence of time in quantum gravity and ask whether time is always “something that flows.” We first recall that this is indeed the case in both relativity and quantum mechanics, although in very different manners: time flows geometrically in relativity (i.e., as a flow of proper time in the four dimensional space-time), time flows abstractly in quantum mechanics (i.e., as a flow in the space of observables of the system). We then ask the same question in quantum gravity in the light of the thermal time hypothesis of Connes and Rovelli. The latter proposes to answer the question of time in quantum gravity (or at least one of its many aspects) by postulating that time is a state-dependent notion. This means that one is able to make a notion of time as an abstract flow—that we call the thermal time—emerge from the knowledge of both:

the algebra of observables of the physical system under investigation;
a state of thermal equilibrium of this system.

Formally, the thermal time is similar to the abstract flow of time in quantum mechanics, but we show in various examples that it may have a concrete implementation either as a geometrical flow or as a geometrical flow combined with a non-geometric action. This indicates that in quantum gravity, time may well still be “something that flows” at some abstract algebraic level, but this does not necessarily imply that time is always and only “something that flows” at the geometric level.
Emergence and the Mind-Body Problem in Roger Sperry’s Studies
Authors: Lestienne Rémy 
Published: April 2013

Abstract
Roger Sperry’s scientific career from his beginnings at Oberlin College in 1934 to his Nobel Prize in 1981 and his death in 1994 is examined from the point of view of the interaction between his scientific works and the evolution of his scientific philosophy. A progressive disengagement from the initial ambience of a reductionist and behaviorist attitude and a move toward the elaboration of an emergentist view of the mind-body problem is observed. This evolution is based on observations on the global and resistant properties of the central nervous system in animals in which the architecture of peripheral nerves has been surgically modified, on reflections on qualia (subjective global experiences such as that of pain). It follows many detailed observations of patients whose two cerebral hemispheres have been surgically disconnected for medical reasons, and in whom both the cognitive abilities of each separated cortical hemisphere and the unity of consciousness persist. Sperry’s resultant emergentist philosophy is paradigmatic of the strong form of emergence: not only is the global mind more than the sum of its parts, but in consciousness has a definite, downward causation power on subsequent and subjacent neural process. This view may be logically defendable only in a diachronic view of emergence, well in phase with a possible emergentist view of Time itself.
Emergence as a Metaphysical Fact
Authors: Barreau Hervé 
Published: April 2013

Abstract
A metaphysical fact is a fact, clearly recognizable in the course of time, for which there is no scientific explanation, that is, no legal explanation or explanation deduced in the manner recommended by modern science. I contend that life’s emergence and human thought’s emergence are metaphysical facts in this sense. These emergences are not to be explained by Darwinian principles which themselves do not seem adequate to explain genetic evolutionism. But modern cosmology has given us leave to reflect on cosmic evolution in a manner which gives sense to overall finality. There is an anthropic principle which has two forms: in the weak form, it can help science discover new legal explanations; in the strong form, it offers a teleological explanation of the laws of nature. As F. Dyson noted, we have two styles of explanation: the one is scientific; the other is metascientific (or metaphysical). We have no reason to reject teleological explanations about ontological questions.
Shoulder Muscle Fatigue During Repetitive Tasks as Measured by Electromyography and Near-Infrared Spectroscopy
Authors: Ferguson Sue A. , Allread W. Gary , Le Peter , Rose Joseph , Marras William S. 
Published: April 2013

Objective: The objective of this study was to quantify shoulder muscle fatigue during repetitive exertions similar to motions found in automobile assembly tasks. Background: Shoulder musculoskeletal disorders (MSDs) are a common and costly problem in automotive manufacturing. Method: Ten subjects participated in the study. There were three independent variables: shoulder angle, frequency, and force. There were two types of dependent measures: percentage change in near-infrared spectroscopy (NIRS) measures and change in electromyography (EMG) median frequency. The anterior deltoid and trapezius muscles were measured for both NIRS and EMG. Also, EMG was collected on the middle deltoid and biceps muscles. Results: The results showed that oxygenated hemoglobin decreased significantly due to the main effects (shoulder angle, frequency, and force). The percentage change in oxygenated hemoglobin had a significant interaction attributable to force and repetition for the anterior deltoid muscle, indicating that as repetition increased, the magnitude of the differences between the forces increased. The interaction of repetition and shoulder angle was also significant for the percentage change in oxygenated hemoglobin. The median frequency decreased significantly for the main effects; however, no interactions were statistically significant. Conclusions: There was significant shoulder muscle fatigue as a function of shoulder angle, task frequency, and force level. Furthermore, percentage change in oxygenated hemoglobin had two statistically significant interactions, enhancing our understanding of these risk factors. Application: Ergonomists should examine interactions of force and repetition as well as shoulder angle and repetition when evaluating the risk of shoulder MSDs.
Quantitative characterization of functionally modified micron–submicron fibers for tissue regeneration: a review
Authors: Jassal Manisha , Sengupta Sukalyan , Warner Steven B , Bhowmick Sankha 
Published: April 2013

Tissue regeneration relies on building carefully crafted scaffold material in the micron–submicron scale and imparting specific functionality in order to best mimic the in vivo environment in terms of chemical composition, morphology, and surface functional groups. Fibrous meshes with structural features at the micron to submicron level for ideal three-dimensional tissue regeneration scaffolds can be an inexpensive scale-up option. Bio-inert polymers lack the functional motifs for specific bioactivity; however, functionalization of the scaffolds can provide biological functions to actively induce tissue regeneration and promote cell adhesion by targeting specific cell–matrix interactions. It is therefore important to characterize the scaffolds and understand the relationship between the efficacy of the functionalization, the surface properties of the scaffolds, and their biological performance. This paper is a comprehensive review of the current understanding in functionalization and characterization of fibrous scaffolds and their biological efficacy. We begin with a compilation of various functionalization schemes including physical adsorption, co-electrospinning, wet chemical techniques, and surface graft polymerization methods and their application to fibers. After a critical literature review, the state of the art for characterization of these functionalized nano-fibers is then discussed. We emphasize the importance of covalent binding of biomolecules and the subsequent need for characterization of functional group distribution, or local density of functionalization, on the scaffold surface. Current challenges and future directions are outlined so that quantitative characterization of scaffold surfaces can aid in the development of next generation scaffolds.
Comparison between normothermic and mild hypothermic cardiopulmonary bypass in myocardial revascularization of patients with left ventricular dysfunction
Authors: Yuksel V , Canbaz S , Ege T 
Published: April 2013

Aims: The aim of this study was to investigate whether normothermic bypass is superior to mild hypothermia in patients with poor left ventricular function. This was achieved by studying defibrillation rates, postoperative requirements of cardiac pacing or other morbidity issues and mortality in patients with left ventricular dysfunction operated upon for elective coronary revascularization. Methods: Data were collected retrospectively from 252 consecutive patients with left ventricular dysfunction (ejection fraction ≤35%) undergoing coronary revascularization between January 2005 and January 2011. Patients operated upon under mild hypothermia (32ºC) were placed in Group 1 and under normothermia (≥35ºC) were placed in Group 2. Comorbidities and postoperative complications were recorded. Results: There were 128 patients in Group 1 and 124 patients in Group 2. Plasma concentrations of CK-MB and troponin T peaked at 6 hours postoperatively, with no significant difference between the groups. Despite longer aortic cross-clamp time and total bypass time in Group 2, significantly less defibrillation requirement rates after aortic declamping was observed. Hospital mortality occured in 16 patients; 8 patients in each group. Conclusions: Normothermia enables less requirement for defibrillation after aortic declamping and postoperative cardiac pacing in patients with left ventricular dysfunction, which may be interpreted as better myocardial protection under normothermic bypass. However, maintaining normothermia had no effect on postoperative stroke, postoperative atrial fibrillation, renal failure development and mortality.