bluuebunny/crossref_metadata_2025_split huggingface dataset:
The significance of multiplex PCR/heteroduplex analysis‐based TCR‐γ gene rearrangement combined with laser‐capture microdissection in the diagnosis of early mycosis fungoides
Authors: Yang Hanjun , Xu Chen , Tang Yuan , Wan Chuan , Liu Weiping , Wang Lin 
Published: February 2012

Background: The diagnosis of early mycosis fungoides (MF) is a big challenge to dermatologists and dermatopathologists because it lacks specific clinicopathologic features.Methods: Fifty‐two paraffin‐embedded skin samples from 50 patients, including 31 with suspected MF, 10 with typical MF and 9 with benign inflammatory dermatosis (BID), were obtained from our archives. DNA was extracted both by traditional phenol‐chloroform method and by the laser‐capture microdissection (LCM)‐proteinase K approach. The TVG/TJG, V2–5/V8–12/JGT1 and BIOMED‐2‐TCR‐γ primers were used to assess TCR‐γ monoclonal rearrangement as measured by polymerase chain reaction (PCR).Results: In the suspected MF group, clonal TCR‐γ gene rearrangements were detected in 11/31 cases (35.5%) by phenol‐chloroform DNA extraction and in 25/31 cases (80.7%) by LCM‐proteinase K extraction (p < 0.05). While T‐cell clonality was detected in 8/10 cases (80%) by the phenol‐chloroform method and 10/10 cases (100%) by LCM (p > 0.05) in the typical MF group, no TCR‐γ monoclonal rearrangement was detected in the BID group.Conclusions: The strategy of multiple PCR/heteroduplex analysis for TCR‐γ gene rearrangement combined with LCM increases the detection rate of clonal TCR‐γ gene rearrangement in early MF cases and could provide strong evidence to confirm the diagnosis of early MF.Yang H, Xu C, Tang Y, Wan C, Liu W, Wang L. The significance of multiplex PCR/heteroduplex analysis‐based TCR‐γ gene rearrangement combined with laser‐capture microdissection in the diagnosis of early mycosis fungoides.
Gaps in continuity of medication management during the transition from hospital to residential care: An observational study (MedGap Study)
Authors: Elliott Rohan A , Tran Tim , Taylor Simone E , Harvey Penelope A , Belfrage Mary K , Jennings Rhonda J , Marriott Jennifer L 
Published: February 2012

Aim:  To assess continuity of medication management during transition from hospital to residential care facilities (RCFs).Method:  Telephone interviews with RCF staff were performed 24 hours after patient transfer to determine the proportion of patients with: missed or significantly delayed doses; RCF medication chart not written/updated in time for the first dose; suitably packed medications not available for the first dose; and RCF medication chart written/updated by a locum doctor. Retrospective audit was used to identify discharge summary discrepancies.Results:  Seventy‐five doses for 37/202 (18.3%) patients were missed or significantly delayed in the 24 hours after discharge. One hundred and twenty‐five (61.9%) patients did not have their medication chart written/updated and 77 (38.1%) did not have suitably packed medications available for the first dose. Locum doctors wrote RCF medication charts for 66 (32.7%) patients. One hundred and ninety‐seven of 392 (50.3%) changes to regularly scheduled medications were communicated.Conclusions:  Strategies are needed to address gaps in the continuity of medication management.
Human rights, citizenship and dementia care nursing
Authors: Kelly Fiona , Innes Anthea 
Published: February 2012

Background.  Human rights and citizenship are concepts widely used in health and social care literature. However, they are applied less frequently and less rigorously in dementia care. This paper briefly presents these concepts before exploring how they have been applied to dementia care policy and practice. We highlight areas of dementia care where human rights can be violated and citizenship can be denied. We suggest reasons why people with dementia can be denied their human and civil rights and discuss how such concepts provide a way to address cultural and practice change in dementia care.Aims and objectives.  To demonstrate how these concepts can be used to challenge and improve dementia care nursing.Conclusions.  This paper contributes to emerging discussion about dementia care nursing by challenging conventional ways of understanding dementia and the care practices that result. Taking a rights‐based approach allows nurses to examine inequity in services and address poor practice.Implications for practice.  Looking at dementia through the lenses of citizenship and human rights provides a way to broaden the scope of contemporary dementia care nursing, to enable nurses to challenge inequity and to develop and improve the direct nursing care offered to people with dementia.
Effect of plastic occlusive clips used as an alternative to mulesing on breech conformation, body weight and survival of Merino lambs
Authors: Evans IB , Lawton PW , Sergeant E , Lloyd JB 
Published: February 2012

Objective  To determine the effect of applying plastic clips to the breech and tail of lambs on the perineal and tail bare areas, breech wrinkle, dag (faecal) accumulation, urine stain, body weight and survival of lambs, compared with unclipped, unmulesed lambs and mulesed lambs.Method  The study was conducted on five commercial wool‐growing farms in southern Australia. On each study site lambs (2–12‐weeks‐old) were divided into three groups: (1) unclipped, unmulesed control (tail dock only); (2) treated with clips; and (3) treated with the mules operation. Evaluations of effects, including visual scoring, bare area measurements and body weight, were performed before treatment and on or approximately days 30, 60, 90 and 180 after treatment. On each occasion, lambs were recorded as either present or absent to allow estimates of survival.Results  The clip treatment increased the size of the perineal and tail bare areas compared with the unclipped, unmulesed control lambs (P < 0.05), although the increases were less than in mulesed lambs (P < 0.05). The clips reduced breech wrinkle, dag and urine stain to levels partway between those recorded in the unclipped, unmulesed controls and the mulesed lambs (P < 0.05). Clipped lambs weighed more than mulesed lambs after treatment (days 30–90 P < 0.001; day 180 P < 0.01) and had higher cumulative percentage survival to 90 days after treatment (P = 0.03).Conclusions  The clips successfully modified the breech region of lambs, although the changes were less than with mulesing. The clips did not reduce the body weight of lambs, compared with the unclipped, unmulesed control lambs, and improved 90‐day cumulative percentage survival compared with mulesed lambs.
The response of correlated traits following cessation of fishery‐induced selection
Authors: Salinas Santiago , Perez Kestrel O. , Duffy Tara A. , Sabatino Stephen J. , Hice Lyndie A. , Munch Stephan B. , Conover David O. 
Published: February 2012

AbstractThe application of evolutionary principles to the management of fisheries has gained considerable attention recently. Harvesting of fish may apply directional or disruptive selection to key life‐history traits, and evidence for fishery‐induced evolution is growing. The traits that are directly selected upon are often correlated (genetically or phenotypically) with a suite of interrelated physiological, behavioral, and morphological characters. A question that has received comparatively little attention is whether or not, after cessation of fishery‐induced selection, these correlated traits revert back to previous states. Here, we empirically examine this question. In experiments with the Atlantic silverside, Menidia menidia, we applied size‐selective culling for five generations and then maintained the lines a further five generations under random harvesting. We found that some traits do return to preharvesting levels (e.g., larval viability), some partially recover (e.g., egg volume, size‐at‐hatch), and others show no sign of change (e.g., food consumption rate, vertebral number). Such correlations among characters could, in theory, greatly accelerate or decelerate the recovery of fish populations. These results may explain why some fish stocks fail to recover after fishing pressure is relaxed.
Pollinator nesting guilds respond differently to urban habitat fragmentation in an oak‐savannah ecosystem
Authors: NEAME LISA A. , GRISWOLD TERRY , ELLE ELIZABETH 
Published: February 2012

Abstract.  1. Habitat fragmentation is thought to threaten biodiversity, but the response of pollinators to fragmentation is still poorly understood, and research seldom includes pollinator nesting requirements.2. We investigated pollinator community composition in a highly fragmented oak‐savannah ecosystem in south‐western British Columbia, Canada. We sampled pollinators in 19 fragments ranging from 0.3 to 31 ha and surrounded by a variety of land‐use types, including forest, low‐density suburban, and urban neighbourhoods. Pan‐trapping and netting surveys captured 4464 bees, flies, and wasps in 138 species and 48 genera.3. Contrary to expectations, overall species richness did not increase with fragment size. However, ground‐nester abundance (not diversity) and cavity‐nester diversity (not abundance) were higher in larger fragments, as expected. Floral richness and abundance did not foster pollinator diversity for either guild. Brood parasite responses were complex: host availability (ground‐nesting bees) was generally important, richness and abundance increased in fragments with high surrounding road density, and abundance also increased in fragments with other habitat fragments nearby.4. Responses of different nesting guilds to fragmentation may be related to their use of the landscape surrounding habitat fragments. Some common cavity nesters can nest in fences and gardens, but urban land use may be less hospitable for ground nesters. Brood parasites apparently respond both to host availability and landscape characteristics associated with movement among fragments.5. Consideration of nesting requirements of pollinators provided some insight into their response to habitat loss in our analysis and should be considered in future studies of fragmentation impacts on pollinator biodiversity.
Survival Analysis of Faculty Retention in Science and Engineering by Gender
Authors: Kaminski Deborah , Geisler Cheryl 
Published: February 2012

Faculty FatesAcademic careers in STEM (science, technology, engineering, and math) include challenges that may differ depending on gender.Kaminski and Geisler(p.864) analyzed the retention rates for tenure-track faculty at 14 U.S. universities in various disciplines. College catalogs, departmental Web sites, and other public sources of information were used to follow the academic careers of nearly 3000 STEM faculty. Except in mathematics faculties—where women left a couple of years earlier than men—generally, women and men were retained and promoted at the same rate.
Cross-Reactivity of Antipneumococcal Surface Protein C (PspC) Antibodies with Different Strains and Evaluation of Inhibition of Human Complement Factor H and Secretory IgA Binding via PspC
Authors: Moreno Adriana T. , Oliveira Maria Leonor S. , Ho Paulo L. , Vadesilho Cintia F. M. , Palma Giovana M. P. , Ferreira Jorge M. C. , Ferreira Daniela M. , Santos Silvia R. , Martinez Marina B. , Miyaji Eliane N. 
Published: February 2012

ABSTRACTPneumococcal surface protein C (PspC) is an important candidate for a cost-effective vaccine with broad coverage against pneumococcal diseases. Previous studies have shown thatStreptococcus pneumoniaeis able to bind to both human factor H (FH), an inhibitor of complement alternative pathway, and human secretory IgA (sIgA) via PspC. PspC was classified into 11 groups based on variations of the gene. In this work, we used three PspC fragments from different groups (PspC3, PspC5, and PspC8) to immunize mice for the production of antibodies. Immunization with PspC3 induced antibodies that recognized the majority of the clinical isolates as analyzed by Western blotting of whole-cell extracts and flow cytometry of intact bacteria, while anti-PspC5 antibodies showed cross-reactivity with the paralogue pneumococcal surface protein A (PspA), and anti-PspC8 antibodies reacted only with the PspC8-expressing strain. Most of the isolates tested showed strong binding to FH and weaker interaction with sIgA. Preincubation with anti-PspC3 and anti-PspC5 IgG led to some inhibition of binding of FH, and preincubation with anti-PspC3 partially inhibited sIgA binding in Western blotting. The analysis of intact bacteria through flow cytometry showed only a small decrease in FH binding after incubation of strain D39 with anti-PspC3 IgG, and one clinical isolate showed inhibition of sIgA binding by anti-PspC3 IgG. We conclude that although anti-PspC3 antibodies were able to recognize PspC variants from the majority of the strains tested, partial inhibition of FH and sIgA binding through anti-PspC3 antibodiesin vitrocould be observed for only a restricted number of isolates.
Identification of Clinically Relevant Corynebacterium spp., Arcanobacterium haemolyticum, and Rhodococcus equi by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Vila Jordi , Juiz Pedro , Salas Carlos , Almela Manel , de la Fuente Celia García , Zboromyrska Yuliya , Navas Jesús , Bosch Jordi , Agüero Jesús , de la Bellacasa Jorge Puig , Martínez-Martínez Luis 
Published: February 2012

ABSTRACT

The identification of 83
Corynebacterium
, 13
Arcanobacterium haemolyticum
, and 10
Rhodococcus equi
strains by conventional methods (API Coryne complemented with 16S rRNA gene sequence analysis) was compared with matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry identification. The correlation between API and MALDI-TOF results was 89%. MALDI-TOF is a rapid and accurate system for identification of the above-mentioned microorganisms.
Comparison of the GenoFlow Human Papillomavirus (HPV) Test and the Linear Array Assay for HPV Screening in an Asian Population
Authors: Wong Oscar Gee-Wan , Lo C. K. , Chow Joanne N. K. , Tsun Obe K. L. , Szeto Elaine , Liu Stephanie S. , Ngan Hextan Y. S. , Cheung Annie N. Y. 
Published: February 2012

ABSTRACT
High-risk human papillomavirus (HR-HPV) DNA detection in cervical cytology samples is useful for primary screening of cervical cancer and for triage of patients with equivocal cytological findings. The GenoFlow HPV array test (GF assay; Diagcor Bioscience Inc., Hong Kong) was recently developed to detect 33 HPV genotypes by a “flowthrough” hybridization technology. In this study, we assessed the analytical sensitivity and reproducibility of the GF assay and compared its genotyping results with those of the Linear Array (LA) assay (Roche Molecular Diagnostics, Indianapolis, IN), using 400 archived liquid-based cytology samples representing the full range of cytology findings. Genotyping findings of the GF and LA assays were concordant or compatible for 93.44% of tested samples, with a good (κ = 0.797) to very good (κ = 0.812) strength of agreement for assay-common and oncogenic HPV types, respectively. The two assays showed good (κ = 0.635) agreement in detecting infections with multiple HPV genotypes. The lowest detection limits of the GF assay for HPV16 and HPV18 were 25 copies and 20 copies, respectively. Repeat testing of 60 samples by use of two different lots of the GF assay revealed no discordant results, suggesting good reproducibility of the assay. Both assays achieved approximately 80% and 100% sensitivity for identifying cases of atypical squamous cells of undetermined significance (ASC-US) and low-grade squamous intraepithelial lesions (LSIL) with subsequent detection of LSIL+ and high-grade squamous intraepithelial lesions or higher (HSIL+) in 2 years, respectively. Among ASC-US samples, the GF assay achieved the highest specificity (23.08%) for indicating subsequent identification of HSIL compared with the LA (19.23%) and Hybrid Capture 2 (HC2) (8.97%) assays. The GF and LA assays showed significant discrepancy in detecting HPV genotypes 11, 26, 39, 52, and 66. More sensitive detection of HPV52 by GF assay offers an advantage in regions where HPV52 is more prevalent. The sensitivity of the GF assay for detecting patients with HSIL+ was noninferior to that of the LA assay.
Sequence Typing Confirms that a Predominant Listeria monocytogenes Clone Caused Human Listeriosis Cases and Outbreaks in Canada from 1988 to 2010
Authors: Knabel Stephen J. , Reimer Aleisha , Verghese Bindhu , Lok Mei , Ziegler Jennifer , Farber Jeffrey , Pagotto Franco , Graham Morag , Nadon Celine A. , Gilmour Matthew W. 
Published: February 2012

ABSTRACT

Human listeriosis outbreaks in Canada have been predominantly caused by serotype 1/2a isolates with highly similar pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MVLST) each identified a diverse population of
Listeria monocytogenes
isolates, and within that, both methods had congruent subtypes that substantiated a predominant clone (clonal complex 8; virulence type 59; proposed epidemic clone 5 [ECV]) that has been causing human illness across Canada for more than 2 decades.
Molecular Characterization of Human Enteroviruses in the Central African Republic: Uncovering Wide Diversity and Identification of a New Human Enterovirus A71 Genogroup
Authors: Bessaud Maël , Pillet Sylvie , Ibrahim Wafa , Joffret Marie-Line , Pozzetto Bruno , Delpeyroux Francis , Gouandjika-Vasilache Ionela 
Published: February 2012

ABSTRACT
Human enteroviruses (HEV) are among the most common viruses infecting humans. Their circulation has been widely studied in most parts of the world but not in sub-Saharan Africa, where poliomyelitis remains prevalent. We report here the molecular characterization of 98 nonpoliovirus (non-PV) HEV strains isolated from 93 randomly selected cell culture-positive supernatants from stool samples collected from 1997 through 2006 from children with acute flaccid paralysis living in the Central African Republic (CAR). The isolates were typed by sequencing the VP1 coding region and sequenced further in the VP2 coding region, and phylogenetic studies were carried out. Among the 98 VP1 sequences, 3, 74, 18, and 3 were found to belong to the HEV-A, -B, -C, and -D species, respectively. Overall, 42 types were detected. In most cases, the VP2 type was correlated with that of the VP1 region. Some of the isolates belonged to lineages that also contain viruses isolated in distant countries, while others belonged to lineages containing viruses isolated only in Africa. In particular, one isolate (type EV-A71) did not fall into any of the genogroups already described, indicating the existence of a previously unknown genogroup for this type. These results illustrate the considerable diversity of HEV isolates from the stools of paralyzed children in the CAR. The presence of diverse HEV-C types makes recombination between poliovirus and other HEV-C species possible and could promote the emergence of recombinant vaccine-derived polioviruses similar to those that have been implicated in repeated poliomyelitis outbreaks in several developing countries.
Detection of a Possible Bioterrorism Agent, Francisella sp., in a Clinical Specimen by Use of Next-Generation Direct DNA Sequencing
Authors: Kuroda Makoto , Sekizuka Tsuyoshi , Shinya Fumiaki , Takeuchi Fumihiko , Kanno Takayuki , Sata Tetsutaro , Asano Shigeyuki 
Published: February 2012

ABSTRACT

Deep sequencing detected a potential bioterrorism agent,
Francisella tularensis
, in a human abscess sample (Iwaki-08) of unknown etiology. Identified single-nucleotide variations suggest that the Iwaki-08 case was associated with
Francisella tularensis
subsp.
holarctica
(biovar
japonica
) but not the highly virulent type A (
Francisella tularensis
subsp.
tularensis
).
The Immune Response to a Vesicular Stomatitis Virus Vaccine Vector Is Independent of Particulate Antigen Secretion and Protein Turnover Rate
Authors: Cobleigh Melissa A. , Bradfield Clinton , Liu Yuanjie , Mehta Anand , Robek Michael D. 
Published: February 2012

ABSTRACTVesicular stomatitis virus (VSV) is a highly cytopathic virus being developed as a vaccine vector due to its ability to induce strong protective T cell and antibody responses after a single dose. However, little is known regarding the mechanisms underlying the potent immune responses elicited by VSV. We previously generated a VSV vector expressing the hepatitis B virus middle envelope surface glycoprotein (MS) that induces strong MS-specific T cell and antibody responses in mice. After synthesis in the cytoplasm, the MS protein translocates to the endoplasmic reticulum, where it forms subviral particles that are secreted from the cell. To better understand the contributions of secreted and intracellular protein to the VSV-induced immune response, we produced a vector expressing a secretion-deficient MS mutant (MSC69A) and compared the immunogenicity of this vector to that of the wild-type VSV-MS vector in mice. As expected, the MSC69Aprotein was not secreted from VSV-infected cells and displayed enhanced proteasome-mediated degradation. Surprisingly, despite these differences in intracellular protein processing, the T cell and antibody responses generated to MSC69Awere comparable to those elicited by virus expressing wild-type MS protein. Therefore, when it is expressed from VSV, the immune responses to MS are independent of particulate antigen secretion and the turnover rate of cytoplasmic protein. These results are consistent with a model in which the immune responses to VSV are strongly influenced by the replication cycle of the vector and demonstrate that characteristics of the vector have the capacity to affect vaccine efficacy more than do the properties of the antigen itself.
Level of Gene Expression Is a Major Determinant of Protein Evolution in the Viral Order Mononegavirales
Authors: Pagán Israel , Holmes Edward C. , Simon-Loriere Etienne 
Published: February 2012

ABSTRACTAlthough the rate at which proteins change is a key parameter in molecular evolution, its determinants are poorly understood in viruses. A variety of factors, including gene length, codon usage bias, protein abundance, protein function, and gene expression level, have been shown to affect the rate of protein evolution in a diverse array of organisms. However, the role of these factors in viral evolution has yet to be addressed. The polar 3′-5′ stepwise attenuation of transcription in theMononegavirales, a group of single-strand negative-sense RNA viruses, provides a unique system to explore the determinants of protein evolution in viruses. We analyzed the relative importance of a variety of factors in shaping patterns of sequence variation in full-length genomes from 13Mononegaviralesspecies. Our analysis suggests that the level of gene expression, and by extension the relative genomic position of each gene, is a key determinant of the protein evolution in these viruses. This appears to be the consequence of selection for translational robustness, but not for translational accuracy, in highly expressed genes. The small genome size and number of proteins encoded by these viruses allowed us to identify other protein-specific factors that may also play a role in virus evolution, such as host-virus interactions and functional constraints. Finally, we explored the evolutionary pressures acting on noncoding regions inMononegaviralesgenomes and observed that, despite being less constrained than coding regions, their evolutionary rates are also associated with genomic position.