bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Puzzle about Consent in Research and in Practice
Authors: CHWANG ERIC 
Published: February 2010

abstractIn this paper, I will examine a puzzling discrepancy between the way clinicians are allowed to treat their patients and the way researchers are allowed to treat their subjects: in certain cases, researchers are legally required to disclose quite a bit more information when obtaining consent from prospective subjects than clinicians are when obtaining consent from prospective patients. I will argue that the proper resolution of this puzzling discrepancy must appeal to a pragmatic criterion of disclosure for informed consent: that what needs to be disclosed in order for consent to be valid depends on what the patient/subject needs to know in order to make a decision. I will then use this pragmatic criterion of disclosure to argue that when obtaining consent researchers should be permitted to omit the same information clinicians are, given certain qualifications. I will also examine how this puzzle forces us to confront some perhaps surprising truths about valid consent. My broader aim in this paper is to examine, not so much the puzzle itself, but rather what this particular puzzle can teach us about more theoretical issues surrounding informed consent.
The spatial arrangement of the human large intestinal wall blood circulation
Authors: Kachlik David , Baca Vaclav , Stingl Josef 
Published: February 2010

AbstractThe aim of the study was to describe and depict the spatial arrangement of the colon microcirculatory bed as a whole. Various parts of the large intestine and terminal ileum were harvested from either cadaver or section material or gained peroperatively. Samples were then injected with India ink or methylmetacrylate Mercox resin for microdissection and corrosion casting for scanning electron microscopy. The results showed that extramural vasa recta ramified to form the subserous plexus, some of them passing underneath the colon taeniae. Branches of both short and long vasa recta merged in the colon wall, pierced the muscular layer and spread out as the submucous plexus, which extended throughout the whole intestine without any interruption. The muscular layer received blood via both the centrifugal branches of the submucous plexus and the minor branches sent off by the subserous plexus. The mucosa was supplied by the mucous plexus, which sent capillaries into the walls of intestinal glands. The hexagonal arrangement of the intestinal glands reflected their vascular bed. All three presumptive critical points are only gross anatomical points of no physiological relevance in healthy individuals. Neither microscopic weak points nor regional differences were proven within the wall of the whole large intestine. The corrosion casts showed a huge density of capillaries under the mucosa of the large intestine. A regular hexagonal pattern of the vascular bed on the inner surface was revealed. No microvascular critical point proofs were confirmed and a correlation model to various pathological states was created.
Recombination and the maintenance of plant organelle genome stability
Authors: Maréchal Alexandre , Brisson Normand 
Published: February 2010

SummaryLike their nuclear counterpart, the plastid and mitochondrial genomes of plants have to be faithfully replicated and repaired to ensure the normal functioning of the plant. Inability to maintain organelle genome stability results in plastid and/or mitochondrial defects, which can lead to potentially detrimental phenotypes. Fortunately, plant organelles have developed multiple strategies to maintain the integrity of their genetic material. Of particular importance among these processes is the extensive use of DNA recombination. In fact, recombination has been implicated in both the replication and the repair of organelle genomes. Revealingly, deregulation of recombination in organelles results in genomic instability, often accompanied by adverse consequences for plant fitness. The recent identification of four families of proteins that prevent aberrant recombination of organelle DNA sheds much needed mechanistic light on this important process. What comes out of these investigations is a partial portrait of the recombination surveillance machinery in which plants have co‐opted some proteins of prokaryotic origin but have also evolved whole new factors to keep their organelle genomes intact. These new features presumably optimized the protection of plastid and mitochondrial genomes against the particular genotoxic stresses they face.

Contents

Summary
299

I.
Introduction
299

II.
Roles of recombination in organelle genome stability
301

III.
Recombination surveillance machinery in plant organelles
304

IV.
Conclusion and perspectives
312

Acknowledgements
313

References
313
The Effect of a Cultural Intervention on Adherence to Latent Tuberculosis Infection Therapy in Latino Immigrants
Authors: Ailinger Rita L. , Martyn Diona , Lasus Howard , Lima Garcia Natalie 
Published: February 2010

ABSTRACT
Objective: The purpose of this study was to examine the effect of a cultural intervention (CI) on increasing adherence to latent tuberculosis infection (LTBI) therapy among Latino immigrants.Design and Sample: This clinical study used a preexperimental design. A nonprobability sample of 86 Latino immigrant clients who were starting LTBI therapy were enrolled in the intervention. The comparison group was an historical sample of 131 clients' records randomly selected from the previous year.Intervention: The CI, designed by the principal investigator, was delivered by 2 Spanish‐speaking interventionist nurses at each of 9 clinic visits. The intervention was based on Latino cultural values and included 5 components.Measures: The patients' adherence was measured by a self‐report of the number of pills taken.Results: The findings of this study were that clients in the CI group took a significantly greater number of doses of INH than those in the historical sample.Conclusions: Using a CI to increase adherence to LTBI therapy shows promise for public health nursing practice.
Willingness of University Nursing Students to Volunteer During a Pandemic
Authors: Yonge Olive , Rosychuk Rhonda J. , Bailey Tracey M. , Lake Rob , Marrie Thomas J. 
Published: February 2010

ABSTRACT
Objective: The global threat of an influenza pandemic continues to grow and thus universities have begun emergency preparedness planning. This study examined stakeholder's knowledge, risk‐perception, and willingness to volunteer.Design and Sample: The design of this study is a cross‐sectional survey. Questionnaires were sent to 1,512 nursing students and were returned by 484, yielding a response rate of 32% for this subgroup. Nursing students may be a much‐needed human resource in the event of an influenza pandemic.Measures: The measurement tool was a Web‐based questionnaire regarding pandemic influenza designed by a subgroup of researchers on the Public Health Response Committee.Results: Most nursing students (67.9%) said they were likely to volunteer in the event of a pandemic if they were able to do so. An even higher number (77.4%) said they would volunteer if provided protective garments. Overall, 70.7% of students supported the proposition that nursing students have a professional obligation to volunteer during a pandemic. Nursing students indicated that they have had a wealth of volunteer experience in the past and they would apply this service ethic to a pandemic situation.Conclusions: Emergency preparedness competencies should be integrated into existing nursing curricula and other health science programs. University administrations need to engage in planning to create protocol for recruitment, practice, and protection of volunteers.
Is Apolipoprotien E codon 112 Polymorphisms Associated with Recurrent Pregnancy Loss?
Authors: Ozornek Hakan , Ergin Elif , Jeyendran Rajasingam S. , Ozay Alev T. , Pillai Delanie , Coulam Carolyn 
Published: February 2010

Citation Ozornek H, Ergin E, Jeyendran RS, Ozay AT, Pillai D, Coulam C. Is Apolipoprotien E codon 112 polymorphisms associated with recurrent pregnancy loss? Am J Reprod Immunol 2010; 64: 87–92Problem  To compare the prevalence of 112T>C point mutations among women experiencing RPL with fertile control women.Method of Study  Buccal swabs were obtained from 232 individuals: 136 with a history of ≥2 abortions, 37 with at least 2 live births and 59 with a history of deep vein thrombosis (DVT). DNA was extracted and PCR amplification of Apo E codons was performed.Results  The allelic frequency of a cytosine at position 112 was 11.4% (31/272) among patients experiencing RPL, compared with a frequency of 5.4% (4/74) among the fertile controls (P = 0.19) and 19.5% (23/118) among individuals with a history of DVT. However, significantly more E3/E4 and E4/E4 genotypes were seen among individuals experiencing RPL and DVT than fertile controls (P < 0.05).Conclusion  Apo E4 codon 112C point mutation is, by itself, not associated with an elevated risk of recurrent pregnancy loss, but rather codon 112C in association with codon 158C is a risk factor for RPL.
Limits of Predictability in Human Mobility
Authors: Song Chaoming , Qu Zehui , Blumm Nicholas , Barabási Albert-László 
Published: February 2010

Predictable Travel RoutinesWhile people rarely perceive their actions to be random, current models of human activity are fundamentally stochastic. Processes that rely on human mobility patterns, like the prediction of new epidemics, traffic engineering, or city planning, could benefit from highly accurate predictive models. To investigate the predictability of human dynamics,Songet al.(p.1018) used the recorded trajectories of millions of mobile phone users, collected by mobile phone companies and anonymized for research purposes. They hypothesized that given the wide range of travel patterns that different users follow, there would be significant differences between their predictability as well: Users who travel less should be easier to predict than those who are constantly on the road. Surprisingly, there was 93% predictability across the whole user base, and individuals' predictability did not in general fall significantly below 80%.
Pharmacokinetics and Disposition of Rilpivirine (TMC278) Nanosuspension as a Long-Acting Injectable Antiretroviral Formulation
Authors: van ′t Klooster Gerben , Hoeben Eva , Borghys Herman , Looszova Adriana , Bouche Marie-Paule , van Velsen Frans , Baert Lieven 
Published: February 2010

ABSTRACTThe next-generation human immunodeficiency virus type 1 (HIV-1) nonnucleoside reverse transcriptase inhibitor rilpivirine (TMC278) was administered in rats and dogs as single intramuscular (IM) or subcutaneous (SC) injections, formulated as a 200-nm nanosuspension. The plasma pharmacokinetics, injection site concentrations, disposition to lymphoid tissues, and tolerability were evaluated in support of its potential use as a once-monthly antiretroviral agent in humans. Rilpivirine plasma concentration-time profiles showed sustained and dose-proportional release over 2 months in rats and over 6 months in dogs. The absolute bioavailability approached 100%, indicating a complete release from the depot, in spite of rilpivirine concentrations still being high at the injection site(s) 3 months after administration in dogs. For both species, IM administration was associated with higher initial peak plasma concentrations and a more rapid washout than SC administration, which resulted in a stable plasma-concentration profile over at least 6 weeks in dogs. The rilpivirine concentrations in the lymph nodes draining the IM injection site exceeded the plasma concentrations by over 100-fold 1 month after administration, while the concentrations in the lymphoid tissues decreased to 3- to 6-fold the plasma concentrations beyond 3 months. These observations suggest uptake of nanoparticles by macrophages, which generates secondary depots in these lymph nodes. Both SC and IM injections were generally well tolerated and safe, with observations of a transient inflammatory response at the injection site. The findings support clinical investigations of rilpivirine nanosuspension as a long-acting formulation to improve adherence during antiretroviral therapy and for preexposure prophylaxis.
Three Surface Exoglycosidases fromStreptococcus pneumoniae, NanA, BgaA, and StrH, Promote Resistance to Opsonophagocytic Killing by Human Neutrophils
Authors: Dalia Ankur B. , Standish Alistair J. , Weiser Jeffrey N. 
Published: February 2010

ABSTRACTStreptococcus pneumoniae(the pneumococcus) is a major human pathogen and a leading cause of inflammatory infections such as pneumonia and otitis media. An important mechanism for host defense againstS. pneumoniaeis opsonophagocytic killing by neutrophils. To persist in the human host, the pneumococcus has developed strategies to evade opsonization and subsequent neutrophil-mediated killing. Utilizing a genomic approach, we identified NanA, the major pneumococcal neuraminidase, as a factor important for resistance to opsonophagocytic killing in ex vivo killing assays using human neutrophils. The effect of NanA was shown using both type 4 (TIGR4) and type 6A clinical isolates. NanA promotes this resistance by acting in conjunction with two other surface-associated exoglycosidases, BgaA, a β-galactosidase, and StrH, anN-acetylglucosaminidase. Experiments using human serum showed that these exoglycosidases reduced deposition of complement component C3 on the pneumococcal surface, providing a mechanism for this resistance. Additionally, we have shown that antibodies in human serum do not contribute to this phenotype. These results demonstrate that deglycosylation of a human serum glycoconjugate(s) by the combined effects of NanA, BgaA, and StrH, is important for resistance to complement deposition and subsequent phagocytic killing ofS. pneumoniae.
Comparison of Two Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Methods with Conventional Phenotypic Identification for Routine Identification of Bacteria to the Species Level
Authors: Cherkaoui Abdessalam , Hibbs Jonathan , Emonet Stéphane , Tangomo Manuela , Girard Myriam , Francois Patrice , Schrenzel Jacques 
Published: February 2010

ABSTRACT
Bacterial identification relies primarily on culture-based methodologies requiring 24 h for isolation and an additional 24 to 48 h for species identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is an emerging technology newly applied to the problem of bacterial species identification. We evaluated two MALDI-TOF MS systems with 720 consecutively isolated bacterial colonies under routine clinical laboratory conditions. Isolates were analyzed in parallel on both devices, using the manufacturers' default recommendations. We compared MS with conventional biochemical test system identifications. Discordant results were resolved with “gold standard” 16S rRNA gene sequencing. The first MS system (Bruker) gave high-confidence identifications for 680 isolates, of which 674 (99.1%) were correct; the second MS system (Shimadzu) gave high-confidence identifications for 639 isolates, of which 635 (99.4%) were correct. Had MS been used for initial testing and biochemical identification used only in the absence of high-confidence MS identifications, the laboratory would have saved approximately US$5 per isolate in marginal costs and reduced average turnaround time by more than an 8-h shift, with no loss in accuracy. Our data suggest that implementation of MS as a first test strategy for one-step species identification would improve timeliness and reduce isolate identification costs in clinical bacteriology laboratories now.
Validation of Factor 6d Antiserum for Serotyping
Streptococcus pneumoniae
Serotype 6C
Authors: Jacobs Michael R. , Dagan Ron , Bajaksouzian Saralee , Windau Anne R. , Porat Nurith 
Published: February 2010

ABSTRACT

Factor 6d antiserum reacts with the new
Streptococcus pneumoniae
serotype 6C. Serogroup 6 isolates, consisting of 49 6A, 42 6B and 98 6C strains from the United States and Israel, serotyped in parallel by PCR and capsular swelling methods, were all identified correctly. The new factor 6d antiserum accurately identifies serotype 6C.
Rapid Detection of Rifampicin- and Isoniazid-ResistantMycobacterium tuberculosisby High-Resolution Melting Analysis
Authors: Ong Danny C. T. , Yam Wing-Cheong , Siu Gilman K. H. , Lee Ann S. G. 
Published: February 2010

ABSTRACTWe have developed a high-resolution melting (HRM) assay to scan for mutations in therpoB,inhA,ahpC, andkatGgenes and/or promoter regions for the detection of rifampin and isoniazid resistance inMycobacterium tuberculosis. For assay development, 23 drug-resistant isolates ofM. tuberculosishaving 29 different mutations, together with 40 drug-susceptible isolates, were utilized. All 29 mutations were accurately detected by our assay. We further validated the assay with a series of 59 samples tested in a blind manner. All sequence alterations that were within the regions targeted by the HRM assay were correctly identified. Compared against results of DNA sequencing, the sensitivity and specificity of our HRM assay were 100%. For the blinded samples, the specificities and sensitivities were 89.3% and 100%, respectively, for detecting rifampin resistance and 98.1% and 83.3%, respectively, for detecting isoniazid resistance, as isolates with mutations in regions not encompassed by our assay were not detected. A C-to-T sequence alteration at position −15 of theahpCregulatory region, which was previously reported to be associated with isoniazid resistance, may possibly be a polymorphism, as it was detected in an isoniazid-susceptibleM. tuberculosisisolate. HRM is a rapid, accurate, simple, closed-tube, and low-cost method. It is thus an ideal assay to be used in countries with a high prevalence of drug-resistantM. tuberculosisand where cost-effectiveness is essential. As a mutation-scanning assay for detecting drug-resistantM. tuberculosis, it can potentially lead to better treatment outcomes resulting from earlier treatment with the appropriate antibiotics.
Molecular Identification and Analysis of Nonserotypeable Human Enteroviruses
Authors: Zhou Fei , Kong Fanrong , McPhie Kenneth , Ratnamohan Mala , Gilbert Gwendolyn L. , Dwyer Dominic E. 
Published: February 2010

ABSTRACT
Conventional approaches to characterizing human enteroviruses (HEVs) are based on viral isolation and neutralization. Molecular typing methods depend largely on reverse transcription-PCR (RT-PCR) and nucleotide sequencing of the entire or partial VP1 gene. A modified RT-PCR-based reverse line blot (RLB) hybridization assay was developed as a rapid and efficient way to characterize common and nonserotypeable (by neutralization) HEVs. Twenty HEV serotypes accounted for 87.1% of all HEVs isolated at a reference laboratory from 1979 to 2007; these common serotypes were identified using one sense and three antisense primers and a set of 80 serotype-specific probes in VP1 (F. Zhou et al., J. Clin. Microbiol. 47:2737-2743, 2009). In this study, one HEV-specific primer pair, two probes in the 5′ untranslated region (UTR), and a new set of 80 serotype-specific probes in VP1 were designed. First, we successfully applied the modified RT-PCR-RLB (using two HEV-specific probes and two sets of serotype-specific probes) to synchronously detect the 5′ UTR and VP1 regions of 131/132 isolates previously studied (F. Zhou et al., J. Clin. Microbiol. 47:2737-2743, 2009). Then, this method was used to identify 73/92 nonserotypeable HEV isolates; 19 nonserotypeable isolates were hybridized only with HEV-specific probes. The VP1 region of 92 nonserotypeable HEV isolates was sequenced; 73 sequences corresponded with one or both RLB results and 19 (not belonging to the 20 most common genotypes) were identified only by sequencing. Two sets of serotype-specific probes can capture the majority of strains belonging to the 20 most common serotypes/genotypes simultaneously or complementarily. Synchronous detection of the 5′ UTR and VP1 region by RT-PCR-RLB will facilitate the identification of HEVs, especially nonserotypeable isolates.
Role of the GTPase Rab1b in
Ebolavirus
Particle Formation
Authors: Yamayoshi Seiya , Neumann Gabriele , Kawaoka Yoshihiro 
Published: February 2010

ABSTRACT

The
Ebolavirus
matrix protein VP40 is essential for virion assembly and egress. Recently, we reported that the coat protein complex II (COPII) transport system plays an important role in the transport of VP40 to the plasma membrane. Here, we show that dominant-negative mutants of the GTPase Rab1b interfere with VP40-mediated particle formation. Rab1b activates GBF1 (Golgi-specific BFA [brefeldin A] resistance factor 1), a critical factor in the assembly of COPI vesicles. Activated GBF1 stimulates ARF1 (ADP ribosylation factor 1), which recruits coat protein to cellular membranes for the assembly of COPI vesicles. Here, we demonstrate that GBF1 and ARF1 are involved in
Ebolavirus
virion formation, suggesting that both the COPII and COPI transport systems play a role in
Ebolavirus
VP40-mediated particle formation. These findings provide new insights into the cellular pathways employed for
Ebolavirus
virion formation.
T-Cell Correlates of Vaccine Efficacy after a Heterologous Simian Immunodeficiency Virus Challenge
Authors: Martins Mauricio A. , Wilson Nancy A. , Reed Jason S. , Ahn Chanook D. , Klimentidis Yann C. , Allison David B. , Watkins David I. 
Published: February 2010

ABSTRACT

Determining the “correlates of protection” is one of the challenges in human immunodeficiency virus vaccine design. To date, T-cell-based AIDS vaccines have been evaluated with validated techniques that measure the number of CD8
+
T cells in the blood that secrete cytokines, mainly gamma interferon (IFN-γ), in response to synthetic peptides. Despite providing accurate and reproducible measurements of immunogenicity, these methods do not directly assess antiviral function and thus may not identify protective CD8
+
T-cell responses. To better understand the correlates of vaccine efficacy, we analyzed the immune responses elicited by a successful T-cell-based vaccine against a heterologous simian immunodeficiency virus challenge. We searched for correlates of protection using a viral suppression assay (VSA) and an IFN-γ enzyme-linked immunospot assay. While the VSA measured
in vitro
suppression, it did not predict the outcome of the vaccine trial. However, we found several aspects of the vaccine-induced T-cell response that were associated with improved outcome after challenge. Of note, broad vaccine-induced prechallenge T-cell responses directed against Gag and Vif correlated with lower viral loads and higher CD4
+
lymphocyte counts. These results may be relevant for the development of T-cell-based AIDS vaccines since they indicate that broad epitope-specific repertoires elicited by vaccination might serve as a correlate of vaccine efficacy. Furthermore, the present study demonstrates that certain viral proteins may be more effective than others as vaccine immunogens.