bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RNA-Binding Domain of Bacteriophage P22 N Protein Is Highly Mutable, and a Single Mutation Relaxes Specificity toward λ
Authors: Cocozaki Alexis I. , Ghattas Ingrid R. , Smith Colin A. 
Published: September 2008

ABSTRACT

Antitermination in bacteriophage P22, a lambdoid phage, uses the arginine-rich domain of the N protein to recognize boxB RNAs in the nut site of two regulated transcripts. Using an antitermination reporter system, we screened libraries in which each nonconserved residue in the RNA-binding domain of P22 N was randomized. Mutants were assayed for the ability to complement N-deficient virus and for antitermination with P22 boxB
left
and boxB
right
reporters. Single amino acid substitutions complementing P22 N
−
virus were found at 12 of the 13 positions examined. We found evidence for defined structural roles for seven nonconserved residues, which was generally compatible with the nuclear magnetic resonance model. Interestingly, a histidine can be replaced by any other aromatic residue, although no planar partner is obvious. Few single substitutions showed bias between boxB
left
and boxB
right
, suggesting that the two RNAs impose similar constraints on genetic drift. A separate library comprising only hybrids of the RNA-binding domains of P22, λ, and φ21 N proteins produced mutants that displayed bias. P22 N
−
plaque size plotted against boxB
left
and boxB
right
reporter activities suggests that lytic viral fitness depends on balanced antitermination. A few N proteins were able to complement both λ N- and P22 N-deficient viruses, but no proteins were found to complement both P22 N- and φ21 N-deficient viruses. A single tryptophan substitution allowed P22 N to complement both P22 and λ N
−
. The existence of relaxed-specificity mutants suggests that conformational plasticity provides evolutionary transitions between distinct modes of RNA-protein recognition.
Identification of a Repressor of a Truncated Denitrification Pathway in
Moraxella catarrhalis
Authors: Wang Wei , Richardson Anthony R. , Martens-Habbena Willm , Stahl David A. , Fang Ferric C. , Hansen Eric J. 
Published: September 2008

ABSTRACT

Growth of
Moraxella catarrhalis
in a biofilm resulted in marked upregulation of two open reading frames (ORFs),
aniA
and
norB
, predicted to encode a nitrite reductase and a nitric oxide reductase, respectively (W. Wang, L. Reitzer, D. A. Rasko, M. M. Pearson, R. J. Blick, C. Laurence, and E. J. Hansen, Infect. Immun. 75:4959-4971, 2007). An ORF designated
nsrR
, which was located between
aniA
and
norB
, was shown to encode a predicted transcriptional regulator. Inactivation of
nsrR
resulted in increased expression of
aniA
and
norB
in three different
M. catarrhalis
strains, as measured by both DNA microarray analysis and quantitative reverse transcriptase PCR. Provision of a wild-type
nsrR
gene in
trans
in an
nsrR
mutant resulted in decreased expression of the AniA protein. DNA microarray analysis revealed that two other ORFs (MC ORF 683 and MC ORF 1550) were also consistently upregulated in an
nsrR
mutant. Consumption of both nitrite and nitric oxide occurred more rapidly with cells of an
nsrR
mutant than with wild-type cells. However, growth of
nsrR
mutants was completely inhibited by a low level of sodium nitrite. This inhibition of growth by nitrite was significantly reversed by introduction of an
aniA
mutation into the
nsrR
mutant and was completely reversed by the presence of a wild-type
nsrR
gene in
trans
. NsrR regulation of the expression of
aniA
was sensitive to nitrite, whereas NsrR regulation of
norB
was sensitive to nitric oxide.
Nitric Oxide and Oxygen Regulate Truncated Hemoglobin Gene Expression inFrankiaStrain CcI3
Authors: Niemann James , Tisa Louis S. 
Published: September 2008

ABSTRACTTheFrankiagenome contains two truncated hemoglobin genes (hboNandhboO) whose functions remain to be determined. Nitric oxide (NO) generated by the addition of 400 μM SNAP (S-nitroso-N-acetylpenicillamine) caused a 10-fold increase inhboNgene expression but had no effect onhboOexpression. The addition of the NO scavenger, carboxy-PT10, reduced the effect of SNAP.hboOgene expression increased under low-oxygen conditions, whilehboNexpression was unaffected. These results suggest that HboN may function in protection from nitrosative stress and that HboO may act as an oxygen transport molecule for increased respiration in hypoxic environments.
Comparative Genomics of Regulation of Fatty Acid and Branched-Chain Amino Acid Utilization in Proteobacteria
Authors: Kazakov Alexey E. , Rodionov Dmitry A. , Alm Eric , Arkin Adam Paul , Dubchak Inna , Gelfand Mikhail S. 
Published: September 2008

ABSTRACT

Bacteria can use branched-chain amino acids (ILV, i.e., isoleucine, leucine, valine) and fatty acids (FAs) as sole carbon and energy sources converting ILV into acetyl-coenzyme A (CoA), propanoyl-CoA, and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR, and GntR families binding to 11 distinct DNA motifs. The ILV degradation genes in gamma- and betaproteobacteria are regulated mainly by a novel regulator from the MerR family (e.g., LiuR in
Pseudomonas aeruginosa
) (40 species); in addition, the TetR-type regulator LiuQ was identified in some betaproteobacteria (eight species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in
Shewanella
species. The FA degradation genes are controlled by four regulators including FadR in gammaproteobacteria (34 species), PsrA in gamma- and betaproteobacteria (45 species), FadP in betaproteobacteria (14 species), and LiuR orthologs in alphaproteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from functional and evolutionary points of view.
Dipeptidyl Aminopeptidase IV fromStenotrophomonas maltophiliaExhibits Activity against a Substrate Containing a 4-Hydroxyproline Residue
Authors: Nakajima Yoshitaka , Ito Kiyoshi , Toshima Tsubasa , Egawa Takashi , Zheng Heng , Oyama Hiroshi , Wu Yu-Fan , Takahashi Eiji , Kyono Kiyoshi , Yoshimoto Tadashi 
Published: September 2008

ABSTRACTThe crystal structure of dipeptidyl aminopeptidase IV fromStenotrophomonas maltophiliawas determined at 2.8-Å resolution by the multiple isomorphous replacement method, using platinum and selenomethionine derivatives. The crystals belong to space groupP43212, with unit cell parametersa=b= 105.9 Å andc= 161.9 Å. Dipeptidyl aminopeptidase IV is a homodimer, and the subunit structure is composed of two domains, namely, N-terminal β-propeller and C-terminal catalytic domains. At the active site, a hydrophobic pocket to accommodate a proline residue of the substrate is conserved as well as those of mammalian enzymes.Stenotrophomonasdipeptidyl aminopeptidase IV exhibited activity toward a substrate containing a 4-hydroxyproline residue at the second position from the N terminus. In theStenotrophomonasenzyme, one of the residues composing the hydrophobic pocket at the active site is changed to Asn611 from the corresponding residue of Tyr631 in the porcine enzyme, which showed very low activity against the substrate containing 4-hydroxyproline. The N611Y mutant enzyme was generated by site-directed mutagenesis. The activity of this mutant enzyme toward a substrate containing 4-hydroxyproline decreased to 30.6% of that of the wild-type enzyme. Accordingly, it was considered that Asn611 would be one of the major factors involved in the recognition of substrates containing 4-hydroxyproline.
The impact of urinary stress incontinence in young and middle-age women practising recreational sports activity: an epidemiological study
Authors: Salvatore S , Serati M , Laterza R , Uccella S , Torella M , Bolis P-F 
Published: September 2008

Objectives:To evaluate the prevalence of urinary stress incontinence (USI) in menstruating women practising recreational sports activity, to detect specific sports with a stronger association with urinary incontinence (UI) and to evaluate risk factors possibly related to this condition.Design:Epidemiological study.Setting:Non-competitive sports organisations in the province of Varese, Italy.Participants:679 women of fertile age, practising recreational sports activity.Intervention:Anonymous questionnaire on UI.Main outcome measurements:The questionnaire included questions about patients’ general characteristics, occurrence of UI in relation to sport or daily general activities, time of onset of this condition, frequency of leakage episodes, correlation of incontinence with types of movements or sports, subjective impression of being limited on such occasions and/or necessity to modify the type of sport.Results:UI was reported by 101 women (14.9%). Of these, 32 (31.7%) complained of UI only during sports activity, 48 (47.5%) only during daily life and 21 (20.8%) in both circumstances. Body mass index and parity were significantly associated with the risk of UI. Looking at the different sports activities, a higher rate of incontinence was found in women participating in basketball (16.6%), athletics (15%), and tennis or squash (11%). 10.4% of women abandoned their favourite sport, because of USI, and a further 20% limited the way they practised their favourite sport to reduce leakage episodes.Conclusions:Female UI affects a significant proportion of young women practising non-competitive sports activity; it can cause abandonment of the sport or limitation of its practice.
A clinical prediction rule for identifying patients with patellofemoral pain who are likely to benefit from foot orthoses: a preliminary determination
Authors: Vicenzino Bill , Collins Natalie , Cleland Joshua , McPoil Thomas 
Published: September 2008

ObjectiveTo develop a clinical prediction rule to identify patients with patellofemoral pain (PFP) who are more likely to benefit from foot orthoses.DesignPosthoc analysis of one treatment arm of a randomised clinical trial.SettingSingle-centre trial in a community setting in Brisbane, Australia.Participants42 participants (mean age 27.9 years) with a clinical diagnosis of PFP (median duration 36 months).InterventionsFoot orthoses fitted by a physiotherapist.Main Outcome MeasuresFive-point global improvement scale at 12-week follow-up, dichotomised with marked improvement equalling success.ResultsPotential predictor variables identified by univariate analyses were age, height, pain severity, anterior knee pain scale score, functional index questionnaire score, foot morphometry (arch height ratio, mid-foot width difference from non-weight bearing to weight bearing) and overall orthoses comfort. Parsimonious fitting of these variables to a model that explained success with orthoses identified the following: age (>25 years), height (<165 cm), worst pain visual analogue scale (<53.25 mm) and a difference in mid-foot width from non-weight bearing to weight bearing (>10.96 mm). The pretest success rate of 40% increased to 86% if the patient exhibited three of these variables (positive likelihood ratio 8.8; 95% CI 1.2 to 66.9).ConclusionPost-hoc analysis identified age, height, pain severity and mid-foot morphometry as possible predictors of successful treatment of PFP with foot orthoses, thereby providing practitioners with information for prescribing foot orthoses in PFP and stimulating further research.
Functional Specialization and Convergence in the Occipito-temporal Cortex Supporting Haptic and Visual Identification of Human Faces and Body Parts: An fMRI Study
Authors: Kitada Ryo , Johnsrude Ingrid S. , Kochiyama Takanori , Lederman Susan J. 
Published: September 2008

Abstract
Humans can recognize common objects by touch extremely well whenever vision is unavailable. Despite its importance to a thorough understanding of human object recognition, the neuroscientific study of this topic has been relatively neglected. To date, the few published studies have addressed the haptic recognition of nonbiological objects. We now focus on haptic recognition of the human body, a particularly salient object category for touch. Neuroimaging studies demonstrate that regions of the occipito-temporal cortex are specialized for visual perception of faces (fusiform face area, FFA) and other body parts (extrastriate body area, EBA). Are the same category-sensitive regions activated when these components of the body are recognized haptically? Here, we use fMRI to compare brain organization for haptic and visual recognition of human body parts. Sixteen subjects identified exemplars of faces, hands, feet, and nonbiological control objects using vision and haptics separately. We identified two discrete regions within the fusiform gyrus (FFA and the haptic face region) that were each sensitive to both haptically and visually presented faces; however, these two regions differed significantly in their response patterns. Similarly, two regions within the lateral occipito-temporal area (EBA and the haptic body region) were each sensitive to body parts in both modalities, although the response patterns differed. Thus, although the fusiform gyrus and the lateral occipito-temporal cortex appear to exhibit modality-independent, category-sensitive activity, our results also indicate a degree of functional specialization related to sensory modality within these structures.
Optimizing Functional Accuracy of TMS in Cognitive Studies: A Comparison of Methods
Authors: Sack Alexander T. , Cohen Kadosh Roi , Schuhmann Teresa , Moerel Michelle , Walsh Vincent , Goebel Rainer 
Published: September 2008

Abstract
Transcranial magnetic stimulation (TMS) is a tool for inducing transient disruptions of neural activity noninvasively in conscious human volunteers. In recent years, the investigative domain of TMS has expanded and now encompasses causal structure–function relationships across the whole gamut of cognitive functions and associated cortical brain regions. Consequently, the importance of how to determine the target stimulation site has increased and a number of alternative methods have emerged. Comparison across studies is precluded because different studies necessarily use different tasks, sites, TMS conditions, and have different goals. Here, therefore, we systematically compare four commonly used TMS coil positioning approaches by using them to induce behavioral change in a single cognitive study. Specifically, we investigated the behavioral impact of right parietal TMS during a number comparison task, while basing TMS localization either on (i) individual fMRI-guided TMS neuronavigation, (ii) individual MRI-guided TMS neuronavigation, (iii) group functional Talairach coordinates, or (iv) 10–20 EEG position P4. We quantified the exact behavioral effects induced by TMS using each approach, calculated the standardized experimental effect sizes, and conducted a statistical power analysis in order to calculate the optimal sample size required to reveal statistical significance. Our findings revealed a systematic difference between the four approaches, with the individual fMRI-guided TMS neuronavigation yielding the strongest and the P4 stimulation approach yielding the smallest behavioral effect size. Accordingly, power analyses revealed that although in the fMRI-guided neuronavigation approach five participants were sufficient to reveal a significant behavioral effect, the number of necessary participants increased to n = 9 when employing MRI-guided neuronavigation, to n = 13 in case of TMS based on group Talairach coordinates, and to n = 47 when applying TMS over P4. We discuss these graded effect size differences in light of the revealed interindividual variances in the actual target stimulation site within and between approaches.
Neural Evidence of Statistical Learning: Efficient Detection of Visual Regularities Without Awareness
Authors: Turk-Browne Nicholas B. , Scholl Brian J. , Chun Marvin M. , Johnson Marcia K. 
Published: September 2008

AbstractOur environment contains regularities distributed in space and time that can be detected by way of statistical learning. This unsupervised learning occurs without intent or awareness, but little is known about how it relates to other types of learning, how it affects perceptual processing, and how quickly it can occur. Here we use fMRI during statistical learning to explore these questions. Participants viewed statistically structured versus unstructured sequences of shapes while performing a task unrelated to the structure. Robust neural responses to statistical structure were observed, and these responses were notable in four ways: First, responses to structure were observed in the striatum and medial temporal lobe, suggesting that statistical learning may be related to other forms of associative learning and relational memory. Second, statistical regularities yielded greater activation in category-specific visual regions (object-selective lateral occipital cortex and word-selective ventral occipito-temporal cortex), demonstrating that these regions are sensitive to information distributed in time. Third, evidence of learning emerged early during familiarization, showing that statistical learning can operate very quickly and with little exposure. Finally, neural signatures of learning were dissociable from subsequent explicit familiarity, suggesting that learning can occur in the absence of awareness. Overall, our findings help elucidate the underlying nature of statistical learning.
ERP Evidence for Flexible Adjustment of Retrieval Orientation and Its Influence on Familiarity
Authors: Ecker Ullrich K. H. , Zimmer Hubert D. 
Published: September 2008

Abstract
The assumption was tested that familiarity memory as indexed by a mid-frontal ERP old–new effect is modulated by retrieval orientation. A randomly cued category-based versus exemplar-specific recognition memory test, requiring flexible adjustment of retrieval orientation, was conducted. Results show that the mid-frontal ERP old–new effect is sensitive to the manipulation of study-test congruency—that is, whether the same object is repeated identically or a different category exemplar is presented at test. Importantly, the effect pattern depends on subjects' retrieval orientation. With a specific orientation, only same items elicited an early old–new effect (same &gt; different = new), whereas in the general condition, the old–new effect was graded (same &gt; different &gt; new). This supports the view that both perceptual and conceptual processes can contribute to familiarity memory and demonstrates that the rather automatic process of familiarity is not only data driven but influenced by top–down retrieval orientation, which subjects are able to adjust on a flexible basis.
Aspects of Technicity in Heidegger's Early Philosophy: Rereading Aristotle's Techné and Hexis
Authors: Wolff Ernst 
Published: September 2008

AbstractThe article aims to advance our understanding of what the early Heidegger had in mind when he spoke about technics. Taking GA 18, Grundbegriffe der aristotelischen Philosophie, as a guiding text, Heidegger's “destructive” reading of the two notions most directly associated with Aristotle's presentation of technics—τεχνη and εξις—will be examined, especially with reference to the portrayal of technics in the Nicomachean Ethics. It will be argued that Aristotle already exaggerated the distinction between virtue and skill and that, instead of insisting on their similarities (as will be argued to be desirable), Heidegger drove the two notions even further apart. This enabled him to form a warped picture of technical life, which he exploited as a counter image to develop an unrealistically non-technical notion of πρα;ξις, which Heidegger implicitly advocates.
And the Rest Is Sigetik: Silencing Logic and Dialectic in Heidegger's Beiträge zur Philosophie
Authors: Gonzalez Francisco 
Published: September 2008

AbstractFaced with the impossibility of saying Being directly given that all language is language of beings, Heidegger proposes an overcoming of logic in favor of what he calls Sigetik: a way of addressing Being in and through silence, i.e., without asserting anything of Being. After considering what such a Sigetik actually involves and how it is possible, this paper asks why Heidegger rejects the alternative of that indirect saying of Being that he identifies with dialectic. It is then argued both that Heidegger's arguments against dialectic are not compelling and that the Beiträge itself, in mostly failing to achieve and sustain the Sigetik it prescribes, cannot fully escape some form of dialectic. Sigetik may prove a lure more threatening to philosophical questioning than the dialectic it seeks, unsuccessfully, to overcome.
Waiting and Lateness: The Context, Implications, and Basic Argumentation of Derrida's “Awaiting (at) the Arrival” (S'attendre à l'arrivée) in Aporias
Authors: Lawlor Leonard 
Published: September 2008

AbstractIn Derrida's last book (posthumously published in 2006), L'animal que donc je suis, there is a kind of refrain: “il ne suffit pas de …” (it is not sufficient or enough to . . . ). Derrida utters this refrain in relation to all the discourses on animality and animal suffering found in the Western philosophical tradition. None of these discourses are sufficient. This last book revolves then around the idea of an insufficient (not enough) response. The idea of an insufficient response is not restricted to the problem of animal suffering; it extends to what we must call, following Derrida, “the problem of the worst.” The worst is the end, in the sense of total violence or total suicide: apocalypse. In this essay, I have tried to construct the beginnings of a more sufficient response that urges us to move toward the least amount of violence towards all living beings, while recognizing nevertheless that even this response is not sufficient. The more sufficient response is based on Derrida's transformation of the concept of waiting into being late found in Aporias. This transformation is at the heart of Derrida's thought of the messianic. We are so late in relation to the problem of the apocalypse that we can no longer wait for someone else to come and save us. We are so late that we—there's no one else coming—must take action now.
Derrida's Cat (Who Am I?)
Authors: Bruns Gerald 
Published: September 2008

AbstractWhat is it to be seen (naked) by one's cat? In “L'animal que donc je suis” (2006), the first of several lectures that he presented at a conference on the “autobiographical animal,” Jacques Derrida tells of his discomfort when, emerging from his shower one day, he found himself being looked at by his cat. Th experience leads him, by way of reflections on the question of the animal, to what is arguably the question of his philosophy: Who am I? It is not so much that Derrida wants to answer this question as to be free of it. His task here is to determine the sense of it— where it leads, for example, when it comes to the nature of the diff erence between himself and his cat. Unlike animal rights activists (and unlike philosophers Martha Nussbaum and Cora Diamond, who have recently addressed this issue), Derrida does not want to erase this difference but wants to multiply it in order (among other things) to affirm the absolute alterity or singularity of his cat, which cannot be subsumed by any category (such as the animal). His cat is an Other in a way that no human being (supposing there to be such a thing, which Derrida is not prepared to grant) could ever be. And here is where “the question who?” leads as well, namely, to a path of escape from absorption into any identity-machine. As Derrida puts it in A Taste for the Secret: Who am I when I am not one of you? In a hospitable world one would be free not to answer.