bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of an acute, outpatient physiotherapy exercise program following pediatric heart or lung transplantation
Authors: Deliva R. D. , Hassall A. , Manlhiot C. , Solomon M. , McCrindle B. W. , Dipchand A. I. 
Published: October 2012

AbstractThis prospective interventional study investigated the impact of a three‐month, ambulatory HA or HB, semi‐individualized, PT‐prescribed exercise program following pediatric HTx or LTx. SMW distance, strength, and flexibility were assessed at start and completion of the program and one yr after enrollment. Subjects received either an HB or HA exercise program three times per week. The cohort demonstrated clinically and statistically significant improvements in SMW distances at three months (425.7 ± 109.4–500.6 ± 93.6 m, p < 0.001) and at one yr (528.5 ± 66.6 m, p = 0.001), although there was no difference between the two groups at any time. Similar improvements were also observed in strength and flexibility measures. Correlates with higher SMW distance at three months and one yr included older age, male gender, and underlying diagnosis other than CHD. Male gender and diagnosis other than CHD were associated with a slower improvement in the SMW distance. This is the first report of institutionally based, outpatient exercise rehabilitation in the recovery following pediatric thoracic transplantation. We found similar improvements to HB interventions up to one yr after surgery. Further study of the role of exercise rehabilitation and long‐term fitness outcomes is needed.
Detection of Legionella bozemanae, a New Cause of Septic Arthritis, by PCR Followed by Specific Culture
Authors: Just Søren Andreas , Knudsen John Bonde , Uldum Søren Anker , Holt Hanne Marie 
Published: October 2012

ABSTRACT

Legionella bozemanae
is a rare isolate in clinical specimens. We describe a case of joint infection due to
L. bozemanae
in an immunocompromised patient with dermatomyositis. Without the use of PCR screening or culture on specialized medium, the organism would not have been detected.
Diversity of Bipolaris Species in Clinical Samples in the United States and Their Antifungal Susceptibility Profiles
Authors: da Cunha K. C. , Sutton D. A. , Fothergill A. W. , Cano J. , Gené J. , Madrid H. , De Hoog S. , Crous P. W. , Guarro J. 
Published: October 2012

ABSTRACTA set of 104 isolates from human clinical samples from the United States, morphologically compatible withBipolaris, were morphologically and molecularly identified through the sequence analysis of the internal transcribed space (ITS) region of the nuclear ribosomal DNA (rDNA). The predominant species wasBipolaris spicifera(67.3%), followed byB. hawaiiensis(18.2%),B. cynodontis(8.6%),B. micropus(2.9%),B. australiensis(2%), andB. setariae(1%).Bipolaris cynodontis,B. micropus, andB. setariaerepresent new records from clinical samples. The most common anatomical sites where isolates were recovered were the nasal region (30.7%), skin (19.2%), lungs (14.4%), and eyes (12.5%). The antifungal susceptibilities of 5 species ofBipolaristo 9 drugs are provided. With the exception of fluconazole and flucytosine, the antifungals tested showed good activity.
Evaluation of Clostridium difficile Fecal Load and Limit of Detection during a Prospective Comparison of Two Molecular Tests, the illumigene C. difficile and Xpert C. difficile/Epi Tests
Authors: Gyorke Clare E. , Wang Susan , Leslie Jhansi L. , Cohen Stuart H. , Solnick Jay V. , Polage Christopher R. 
Published: October 2012

ABSTRACT

In a large prospective comparison, the illumigene test detected
Clostridium difficile
in 98% of toxin-positive and 58% of toxin-negative samples confirmed positive by other methods. The Xpert was uniformly sensitive. Most samples with discrepant results had
C. difficile
concentrations below the illumigene limit of detection. The significance of low-level
C. difficile
detection needs investigation.
Association of Relapse of Clostridium difficile Disease with BI/NAP1/027
Authors: Marsh Jane W. , Arora Rangolee , Schlackman Jessica L. , Shutt Kathleen A. , Curry Scott R. , Harrison Lee H. 
Published: October 2012

ABSTRACT

Recurrent
Clostridium difficile
infection (CDI) occurs in up to 35% of patients. Recurrences can be due to either relapse with the same strain or reinfection with another strain. In this study, multilocus variable-number tandem-repeat analysis (MLVA) was performed on
C. difficile
isolates from patients with recurrent CDI to distinguish relapse from reinfection. In addition, univariate and multivariate analyses were performed to identify risk factors associated with relapse. Among patients with a single recurrence, relapse due to the original infecting strain was more prevalent than reinfection and the interval between episodes was shorter than among patients who had reinfections. Among patients with >1 recurrence, equal distributions of relapse and reinfection or a combination of the two episode types were observed. Initial infection with the BI/NAP1/027 epidemic clone was found to be a significant risk factor for relapse. This finding may have important implications for patient therapy. Classification of recurrent CDI episodes by MLVA can be utilized to make informed patient care decisions and to accurately define new CDI cases for infection control and reimbursement purposes.
Point-Counterpoint: Is the Era of Viral Culture Over in the Clinical Microbiology Laboratory?
Authors: Hodinka Richard L. , Kaiser Laurent , Hodinka Richard L. , Kaiser Laurent 
Published: October 2012

ABSTRACT
Conventional tube culture systems have long been the mainstay in clinical virology for the growth and identification of viruses from clinical specimens. Innovations such as centrifugation-enhanced shell vial and multiwell plate cultures and the use of genetically engineered and mixed cell lines, coupled with faster detection of viral replication, have allowed for reasonable turnaround times for even some of the most slowly growing clinically important human viruses. However, molecular methods, in particular, the PCR, have usurped the role of viral culture in many laboratories, limiting the use of this traditional method of virus detection or replacing it altogether. Advances and improvements in molecular technology over time have also resulted in newer generations of more rapid and accurate molecular assays for the detection, quantification, and genetic characterization of viruses. For this point-counterpoint, we have asked two individuals, Richard L. Hodinka of the Children's Hospital of Philadelphia, a clinical virologist whose laboratory has completely eliminated viral culture in favor of molecular methods, and Laurent Kaiser, head of the Virology Laboratory at the University of Geneva Hospital, who continues to be a strong advocate of viral culture, to discuss the relevance of viral culture in the molecular age.
Differences between Two Clinical Staphylococcus capitis Subspecies as Revealed by Biofilm, Antibiotic Resistance, and Pulsed-Field Gel Electrophoresis Profiling
Authors: Cui Bintao , Smooker Peter M. , Rouch Duncan A. , Daley Andrew J. , Deighton Margaret A. 
Published: October 2012

ABSTRACT

Coagulase-negative staphylococci have been identified as major causes of late-onset neonatal bacteremia in neonatal intensive care units. Sixty isolates of
Staphylococcus capitis
obtained from blood cultures of neonates between 2000 and 2005 were examined in this study. Biochemical analysis confirmed that 52 of these isolates belonged to the subsp.
urealyticus
, and the remaining 8 belonged to the subsp.
capitis.
Isolates of the predominant subsp.
urealyticus
clones were characterized by their resistance to penicillin, erythromycin, and oxacillin and their biofilm formation ability, whereas subsp.
capitis
isolates were generally antibiotic susceptible and biofilm negative. Pulsed-field gel electrophoresis (PFGE) after SacII digestion separated the 60 isolates into five major clusters. Sequence analysis showed that, in
S. capitis
, the
ica
operon plus the negative regulator
icaR
was 4,160 bp in length. PCRs demonstrated the presence of the
ica
operon in all isolates. Further analysis of five isolates (two biofilm-positive subsp.
urealyticus
, one biofilm-negative subsp.
urealyticus
, and two biofilm-negative subsp.
capitis
) revealed that the
ica
operons were identical in all of the biofilm-positive subsp.
urealyticus
strains; however, the biofilm-negative isolates showed variations. The distinctive phenotypic and genotypic characteristics revealed by this study may affect the epidemiology of the two subspecies of
S. capitis
in the clinical setting. These results may provide a better understanding of the contribution of these two species to bloodstream infections in neonates.
Structure and Function of AvtR, a Novel Transcriptional Regulator from a Hyperthermophilic Archaeal Lipothrixvirus
Authors: Peixeiro N. , Keller J. , Collinet B. , Leulliot N. , Campanacci V. , Cortez D. , Cambillau C. , Nitta K. R. , Vincentelli R. , Forterre P. , Prangishvili D. , Sezonov G. , van Tilbeurgh H. 
Published: October 2012

ABSTRACT

The structural and functional analysis of the protein AvtR encoded by
Acidianus
filamentous virus 6 (AFV6), which infects the archaeal genus
Acidianus
, revealed its unusual structure and involvement in transcriptional regulation of several viral genes. The crystal structure of AvtR (100 amino acids) at 2.6-Å resolution shows that it is constituted of a repeated ribbon-helix-helix (RHH) motif, which is found in a large family of bacterial transcriptional regulators. The known RHH proteins form dimers that interact with DNA using their ribbon to create a central β-sheet. The repeated RHH motifs of AvtR superpose well on such dimers, but its central sheet contains an extra strand, suggesting either conformational changes or a different mode of DNA binding. Systematic evolution of ligands by exponential enrichment (SELEX) experiments combined with systematic mutational and computational analysis of the predicted site revealed 8 potential AvtR targets in the AFV6 genome. Two of these targets were studied in detail, and the complex role of AvtR in the transcriptional regulation of viral genes was established. Repressing transcription from its own gene,
gp29
, AvtR can also act as an activator of another gene,
gp30
. Its binding sites are distant from both genes' TATA boxes, and the mechanism of AvtR-dependent regulation appears to include protein oligomerization starting from the protein's initial binding sites. Many RHH transcriptional regulators of archaeal viruses could share this regulatory mechanism.
Long-Distance RNA-RNA Interactions in the Coronavirus Genome Form High-Order Structures Promoting Discontinuous RNA Synthesis during Transcription
Authors: Mateos-Gomez Pedro A. , Morales Lucia , Zuñiga Sonia , Enjuanes Luis , Sola Isabel 
Published: October 2012

ABSTRACT
Coronavirus (CoV) transcription requires a high-frequency recombination process that links newly synthesized minus-strand subgenomic RNA copies to the leader region, which is present only once, at the 5′ end of the genome. This discontinuous RNA synthesis step is based on the complementarity between the transcription-regulating sequences (TRSs) at the leader region and those preceding each gene in the nascent minus-strand RNA. Furthermore, the template switch requires the physical proximity of RNA genome domains located between 20,000 and 30,000 nucleotides apart. In this report, it is shown that the efficacy of this recombination step is promoted by novel additional long-distance RNA-RNA interactions between RNA motifs located close to the TRSs controlling the expression of each gene and their complementary sequences mapping close to the 5′ end of the genome. These interactions would bring together the motifs involved in the recombination process. This finding indicates that the formation of high-order RNA structures in the CoV genome is necessary to control the expression of at least the viral N gene. The requirement of these long-distance interactions for transcription was shown by the engineering of CoV replicons in which the complementarity between the newly identified sequences was disrupted. Furthermore, disruption of complementarity in mutant viruses led to mutations that restored complementarity, wild-type transcription levels, and viral titers by passage in cell cultures. The relevance of these high-order structures for virus transcription is reinforced by the phylogenetic conservation of the involved RNA motifs in CoVs.
The N-Terminal Region of IFITM3 Modulates Its Antiviral Activity by Regulating IFITM3 Cellular Localization
Authors: Jia Rui , Pan Qinghua , Ding Shilei , Rong Liwei , Liu Shan-Lu , Geng Yunqi , Qiao Wentao , Liang Chen 
Published: October 2012

ABSTRACTInterferon-inducible transmembrane (IFITM) protein family members IFITM1, -2, and -3 restrict the infection of multiple enveloped viruses. Significant enrichment of a minor IFITM3 allele was recently reported for patients who were hospitalized for seasonal and 2009 H1N1 pandemic flu. This IFITM3 allele lacks the region corresponding to the first amino-terminal 21 amino acids and is unable to inhibit influenza A virus. In this study, we found that deleting this 21-amino-acid region relocates IFITM3 from the endosomal compartments to the cell periphery. This finding likely underlies the lost inhibition of influenza A virus that completes its entry exclusively within endosomes at low pH. Yet, wild-type IFITM3 and the mutant with the 21-amino-acid deletion inhibit HIV-1 replication equally well. Given the pH-independent nature of HIV-1 entry, our results suggest that IFITM3 can inhibit viruses that enter cells via different routes and that its N-terminal region is specifically required for controlling pH-dependent viruses.
RNA Interference as a Cellular Defense Mechanism against the DNA Virus Baculovirus
Authors: Jayachandran Balachandran , Hussain Mazhar , Asgari Sassan 
Published: October 2012

ABSTRACT

In insects, the RNA interference (RNAi) pathway plays a major role in antiviral responses, as shown against many RNA viruses. The response includes the cleavage of double-stranded RNA genome or intermediates, produced during replication, into viral short interfering RNAs (v-siRNAs). Using deep sequencing, we found that a large number of small reads of ∼20 nucleotides from
Helicoverpa armigera
larvae infected with
Helicoverpa armigera
single nucleopolyhedrovirus (HaSNPV) were mapped to certain open reading frames in the viral genome (hot spots) that are mostly structural and auxiliary late genes. After excluding the possibility of these small RNAs being microRNAs, it was determined that Dicer-2, the main enzyme implicated in the RNAi response in insects, is involved in the generation of v-siRNAs. In
Dicer-2
- but not
Dicer-1
-silenced cells, higher transcript levels of the hot spot genes were detected, and as a consequence the virus replicated more efficiently. The results suggest that the viral transcripts are degraded by the RNAi response of the host. This may, however, be to the advantage of the virus by preventing overreplication of the virus, which may otherwise lead to the premature death of the host cells.
Endovascular approach and technique for treatment of transverse-sigmoid dural arteriovenous fistula with cortical reflux: the importance of venous sinus sacrifice
Authors: Carlson Andrew Phillip , Alaraj Ali , Amin-Hanjani Sepideh , Charbel Fady T , Aletich Victor 
Published: October 2012

BackgroundTreatment of dural arteriovenous fistula involving the transverse-sigmoid region with cortical reflux is complex and treatment options may require sacrifice of the fistulous segment of the sinus.ObjectiveTo review our results in this subset of patients and describe current endovascular decision-making and approaches.MethodsWe reviewed cases of endovascular sinus sacrifice for dural fistulas at our institution from 2007 to 2012. Demographic, decision-making, technical and outcome data were collected.ResultsSeven patients were identified who underwent endovascular sinus sacrifice for treatment of dural fistula during this 4-year period. Determination of the fistulous sinus segment was based on the pattern of cortical drainage. Endovascular access to the sinus was achieved by transarterial, transvenous or via open surgery in one case. Complete cure of the target fistula was obtained in all cases. One patient had transient post-procedure headache. There were no hemorrhages, new neurological deficits or signs of increased intracranial pressure. Six of the seven patients had angiographic follow-up at least 6 months after treatment with no recurrence.ConclusionsFistulas of the transverse-sigmoid sinuses with cortical reflux may require sacrifice of the parent sinus for cure. Defining the fistulous segment and occluding this segment deliberately, completely and precisely is essential for cure. Several modalities and approaches can be used to achieve this. For properly selected patients, cure of the lesions can be achieved with this method with low risk of morbidity.
Translation caching
Authors: Barr Thomas W. , Cox Alan L. , Rixner Scott 
Published: October 2012

This paper explores the design space of MMU caches that accelerate virtual-to-physical address translation in processor architectures, such as x86-64, that use a radix tree page table. In particular, these caches accelerate the page table walk that occurs after a miss in the Translation Lookaside Buffer. This paper shows that the most effective MMU caches are translation caches, which store partial translations and allow the page walk hardware to skip one or more levels of the page table.
In recent years, both AMD and Intel processors have implemented MMU caches. However, their implementations are quite different and represent distinct points in the design space. This paper introduces three new MMU cache structures that round out the design space and directly compares the effectiveness of all five organizations. This comparison shows that two of the newly introduced structures, both of which are translation cache variants, are better than existing structures in many situations.
Finally, this paper contributes to the age-old discourse concerning the relative effectiveness of different page table organizations. Generally speaking, earlier studies concluded that organizations based on hashing, such as the inverted page table, outperformed organizations based upon radix trees for supporting large virtual address spaces. However, these studies did not take into account the possibility of caching page table entries from the higher levels of the radix tree. This paper shows that any of the five MMU cache structures will reduce radix tree page table DRAM accesses far below an inverted page table.
Shared caches in multicores
Authors: Irwin Mary Jane 
Published: October 2012

As we transition from clock-frequency performance scaling to performance scaling with multicores, the pressure on the memory hierarchy is increasing dramatically. Many different on-chip cache topologies have been proposed/implemented; effective management of these shared caches is crucial to multicore performance.
This talk will begin with a description of a cache miss classification scheme for multicores (compulsory, inter-core misses, intra-core misses) that gives insight into the interactions between memory transactions of the different cores on a chip sharing a cache. Ways to improve the on-chip cache performance with architectural enhancements, compiler enhancements, and runtime system enhancements will then be discussed. If the application thread mapping and the on-chip topology is static (i.e., does not change during runtime), then compiler enhancements that support cache topology aware code optimization can be used to significantly improve an application's performance. Results from such an augmented compiler, where the topology is exposed to the compiler and where the compiler also does thread-to-core mapping assignments, will be presented. If the application thread mapping or the on-chip topology is dynamic, then other alternatives exist. For example, a thread scheduler, or allocator, can make decisions about moving threads to different cores during runtime in the hopes of improving overall cache performance. Initial experiments with the REEact system being developed by researchers at Penn State-UPittsburgh-UVirginia that "reacts" to hardware conditions (such as cache miss rates, hot-spots, etc.) by reallocating threads at runtime will be outlined. Finally, if the on-chip cache topology itself is dynamic (i.e., is designed to be reconfigurable at runtime), large performance benefits might be obtained. However, both hardware and software design challenges to realizing such a dynamic system abound. Some of these challenges will be briefly discussed.
Security refresh
Authors: Seong Nak Hee , Woo Dong Hyuk , Lee Hsien-Hsin S. 
Published: October 2012

Phase change memory (PCM) is an emerging memory technology for future computing systems. Compared to other non-volatile memory alternatives, PCM is more matured to production, and has a faster read latency and potentially higher storage density. The main roadblock precluding PCM from being used, in particular, in the main memory hierarchy, is its limited write endurance. To address this issue, recent studies proposed to either reduce PCM's write frequency or use wear-leveling to evenly distribute writes. Although these techniques can extend the lifetime of PCM, most of them will not prevent deliberately designed malicious codes from wearing it out quickly. Furthermore, all the prior techniques did not consider the circumstances of a compromised OS and its security implication to the overall PCM design. A compromised OS will allow adversaries to manipulate processes and exploit side channels to accelerate wear-out.
In this paper, we argue that a PCM design not only has to consider normal wear-out under normal application behavior, most importantly, it must take the worst-case scenario into account with the presence of malicious exploits and a compromised OS to address the durability and security issues simultaneously. In this paper, we propose a novel, low-cost hardware mechanism called Security Refresh to avoid information leak by constantly migrating their physical locations inside the PCM, obfuscating the actual data placement from users and system software. It uses a dynamic randomized address mapping scheme that swaps data using random keys upon each refresh due. The hardware overhead is tiny without using any table. The best lifetime we can achieve under the worst-case malicious attack is more than six years. Also, our scheme incurs around 1% performance degradation for normal program operations.