bluuebunny/crossref_metadata_2025 huggingface dataset:
The (5‐4) and (6‐4) Adducts of 1‐Methylthymine and Their Dewar Valence Isomers
Authors: Shetlar Martin D. , Chung Janet
Published: April 2011

Previous studies of the photochemical reaction of 1‐methylthymine (MeT) in frozen aqueous solution have indicated that four cyclobutane type dimers are formed. We have restudied this system and have found that, in addition to cyclobutane dimers, both a (5‐4) adduct and a (6‐4) adduct of MeT are formed in significant amounts. Upon standing in aqueous solution, the (5‐4) adduct is susceptible to reaction to form an isomeric form of the parent adduct, possibly via ring‐opening and closure reactions at C‐6 of the saturated pyrimidine ring component of the adduct. Irradiation of each of these three adducts with UVB light produces a pair of Dewar‐type adducts. The nine products were individually characterized by mass spectrometry, proton NMR spectroscopy and UV spectroscopy. A less comprehensive study showed that irradiation of thymidine in frozen aqueous solution produces a diastereomeric pair of (5‐4) adducts, along with the previously known diastereomeric pair of (6‐4) adducts.
The immunophenotypic stability of plasma cell myeloma by flow cytometry
Authors: SPEARS M. D. , OLTEANU H. , KROFT S. H. , HARRINGTON A. M.
Published: April 2011

Introduction:  Flow cytometry (FC) has become increasingly utilized in the diagnosis and monitoring of plasma cell myeloma (PCM), though few studies have evaluated the longitudinal stability of antigen expression.

Methods:  We studied 45 PCM patients by four‐color FC for shifts in CD19, CD20, CD38, CD45, CD56, and cytoplasmic light chain expression, between diagnostic/first encounter and positive follow‐up analyses. An immunophenotypic (IP) change was defined as gain, loss, or ½ log shift of antigen expression.

Results:  An IP change was observed in 14/45 (31%) patients, with single IP changes in 9/14, two changes in 2/14, and three changes in 3/14. 3/14 reverted from an aberrant to a normal plasma cell IP, while remaining light chain‐restricted. Changes in expression of CD45 occurred in 9/45 (20%), CD19 in 5/45 (11.1%), CD20 in 2/45 (4.4%), and CD56 in 5/45 (11.1%).

Conclusion:  Approximately 1/3 of PCM cases show IP changes over time, with CD45 the least stable antigen. Recognition of this relative instability is important to avoid narrow targeting of follow‐up FC analyses, especially for minimal residual disease monitoring.
Correlation of assessment of plasma cells by flow cytometry and detection of cytogenomic abnormalities by fluorescencein situhybridization in plasma cell neoplasms
Authors: LU G. , ZHANG X. X. , YOU M. J. , CHEN W.
Published: April 2011

Introduction: Increased monoclonal plasma cell count (PCC) in bone marrow (BM) is an indicator of a plasma cell neoplasm (PCN). Assessing PCC in BM by morphologic evaluation (ME) and flow cytometry (FC) is important in diagnosing PCN. Also important is fluorescencein situhybridization (FISH) to detect cytogenomic abnormalities (CAs) in PCN. Owing to FC’s short turnaround time, FC‐assessed PCC is often used as empirical reference for further FISH study. However, correlation of FC‐assessed PCs with FISH‐detected CAs has not been well studied. The purpose of this study was to validate this correlation on BM aspirates from patients with PCN.

Methods: We reviewed 224 cases of newly diagnosed PCN identified from our Lab‐database. Both FC and FISH had been performed on BM aspirates from these cases, of which 178 had been assessed by ME. The original findings from the 224 cases were also reviewed.

Results: Using a cut‐off of 3% PCs assessed by FC as an indicator for further FISH analysis, 20 (17%) FISH‐detectable PCN cases were missed; 30% of the missed cases carried high‐risk CAs and/or were highly progressive PCN.

Conclusion: In PCN cases, an FC‐assessed 3% PCC in BM aspirates should not be used as a cut‐off for further FISH testing.
Neuroprotective effect of intravitreal cell‐based glucagon‐like peptide‐1 production in the optic nerve crush model
Authors: Zhang Rong , Zhang Haijuan , Xu Liang , Ma Ke , Wallrapp Christine , Jonas Jost B.
Published: April 2011

Purpose:  To examine the effect of intraocularly produced glucagon‐like peptide‐1 (GLP‐1) on the survival rate of retinal ganglion cells in an optic nerve crush model.

Methods:  Forty‐one Sprague–Dawley rats were divided into a study group (21 animals) in which 4 beads with 3000 genetically modified cells to produce GLP‐1 were intravitreally implanted into the right eye; a saline control group (n = 12) with intravitreal saline injection; and a GLP‐1 negative bead control group (n = 8) in which 4 beads with 3000 cells without GLP‐1 production were intravitreally implanted. The right optic nerves of all animals were crushed in a standardized manner. After labeling the retinal ganglion cells by injecting 3% fluorogold into the superior colliculus, the animals were sacrificed, and the ganglion cells were counted on retinal flat mounts.

Results:  The retinal ganglion cell density of the right eyes was significantly higher in the study group (median: 2081 cells/mm2; range: 1182–2953 cells/mm2) than in the GLP‐1 bead negative control group (median: 1328 cells/mm2; range: 1007–2068 cells/mm2; p = 0.002) and than in the saline control group (median: 1777 cells/mm2; range: 1000–2405 cells/mm2; p = 0.07). Correspondingly, the survival rate (ratio of retinal ganglion cell density of right eye/left eye) was significantly higher in the study group (median: 0.72; range: 0.40–1.04) than in the GLP‐1 bead negative control group (median: 0.44; range: 0.36–0.68; p = 0.003) and than in the saline control group (median: 0.56; range: 0.36–0.89; p = 0.03).

Conclusion:  Glucagon‐like peptide‐1 produced by intravitreally implanted cell beads was associated with a higher survival rate of retinal ganglion cells after an experimental optic nerve crush in rats.
Microvascular retinopathy in subjects without diabetes: the Inter99 Eye Study
Authors: Munch Inger Christine , Kessel Line , Borch‐Johnsen Knut , Glümer Charlotte , Lund‐Andersen Henrik , Larsen Michael
Published: April 2011

Purpose:  Retinal vascular lesions such as microaneurysms and haemorrhages, while typical of diabetic retinopathy, are also seen in subjects without diabetes where they are associated with elevated cardiovascular mortality. In theory, these lesions could be a consequence of past hyperglycaemia. We examined the prevalence and risk factors for retinopathy, including lens fluorescence, a biomarker of cumulative life‐time glycaemia in adults without diabetes.

Methods:  Cross‐sectional population‐based study of 711 subjects without diabetes (WHO 1999 criteria) aged 30–60 years, including oral glucose tolerance testing, clinical and laboratory examinations, non‐invasive ocular lens fluorometry and seven‐field fundus photography.

Results:  Retinopathy was present in 8.3% (CI95 6.3–10.3%) of subjects. Higher systolic blood pressure (SBP) (p = 0.032), increasing body mass index (BMI) (p = 0.014) and wider waist circumference (p = 0.014) were significantly associated with retinopathy after adjusting for age and sex. Retinopathy was not significantly related to long‐term, short‐term or current glycaemia (lens fluorescence, HbA1c, fasting plasma glucose). In the multivariate analysis, the odds ratio (OR) for retinopathy in subjects with SBP ≥160 mmHg compared to subjects with SBP <130 mmHg was 2.68 (CI95 1.07–6.70, p = 0.036) and in subjects with BMI ≥30 compared to subjects with BMI < 25 the OR for retinopathy was 2.14 (CI95 1.01–4.57, p = 0.049) when adjusting for both variables, age, sex, the presence of impaired glucose tolerance and impaired fasting glucose.

Conclusion:  Retinopathy in subjects without diabetes was associated with hypertension and obesity. The study found no evidence that microvascular retinopathy in non‐diabetic subjects was a consequence of past hyperglycaemia.
Explaining How the Mind Works: On the Relation Between Cognitive Science and Philosophy
Authors: Trigg Jonathan , Kalish Michael
Published: April 2011

In this paper, we argue that under certain prevalent interpretations of the nature and aims of cognitive science, theories of cognition generate a forced choice between a conception of cognition which depends on the possibility of a private language, and a conception of cognition which depends on mereological confusions. We argue, further, that this should not pose a fundamental problem for cognitive scientists since a plausible interpretation of the nature and aims of cognitive science is available that does not generate this forced choice. The crucial difference between these interpretations is that on the one hand the aim of theories of cognition is to tell us what thinking (etc.) is, and on the other it is to tell us what is causally necessary if an intelligent creature is to be able to think. Our argument draws heavily on a Wittgensteinian conception of philosophy in which no philosophical theory can explain what thinking, perceiving, remembering, etc. are, either. The positive, strictly therapeutic, purpose of a philosophy of cognitive science should be to show that, since the traditional problems which constitute the philosophy of mind are chimerical, there is nothing for philosophical theorizing in cognitive science to achieve.
Philosophy for the Rest of Cognitive Science
Authors: Stepp Nigel , Chemero Anthony , Turvey Michael T.
Published: April 2011

Cognitive science has always included multiple methodologies and theoretical commitments. The philosophy of cognitive science should embrace, or at least acknowledge, this diversity. Bechtel’s (2009a) proposed philosophy of cognitive science, however, applies only to representationalist and mechanist cognitive science, ignoring the substantial minority of dynamically oriented cognitive scientists. As an example of nonrepresentational, dynamical cognitive science, we describe strong anticipation as a model for circadian systems (Stepp & Turvey, 2009). We then propose a philosophy of science appropriate to nonrepresentational, dynamical cognitive science.
Recent progress in osteogenesis imperfecta
Authors: Zhao Xiang , Yan Shi‐Gui
Published: April 2011

Osteogenesis imperfecta (OI), a rare clinical disease with abnormal type I collagen, is inherited or caused by mutation. A classification of OI into four types was proposed in 1979 and has been used up until four new types were added recently. A tough clinical challenge, OI causes abnormal blood coagulation and cardiovascular structure, airways obstruction, and delayed wound healing. The authors of the current article have reviewed recent progress in OI worldwide, including the mechanisms, classification, detection, clinical difficulties, and treatment.
Children and adolescents’ understandings of family resemblance: A study of naïve inheritance concepts
Authors: Williams Joanne M.
Published: April 2011

This paper aims to provide developmental data on two connected naïve inheritance concepts and to explore the coherence of children's naïve biology knowledge. Two tasks examined children and adolescents’ (4, 7, 10, and 14 years) conceptions of phenotypic resemblance across kin (in physical characteristics, disabilities, and personality traits). The first task required participants to predict and explain feature outcomes in both an offspring and a sibling, in a modified version of the phenotypic similarity task. In the second task, participants offered explanations for instances of parent‐offspring dissimilarity and grandparent‐offspring resemblance (phenotypic difference task). The inclusion of two tasks and a broad age range revealed significant age trends between 4 and 10 years in naïve inheritance concepts. However, there was little consistency in children's inheritance explanations within or across tasks. The findings are discussed with reference to debates concerning the development and structure of naïve biology concepts.
Optimal Design of Onshore Natural Gas Pipelines
Authors: Zhou Wenxing , Nessim Maher A.
Published: April 2011

The optimal design level for onshore natural gas pipelines was explored through a hypothetical example, whereby the pipe wall thickness was assumed to be the sole design parameter. The probability distributions of the life-cycle costs of various candidate designs for the example pipeline were obtained using Monte-Carlo simulation. The life-cycle cost included the cost of failure due to equipment impact and external corrosion, and the cost of periodic maintenance actions for external corrosion. The cost of failure included both the cost of fatality and injury as well as the cost of property damage and value of lost product. The minimum expected life-cycle cost criterion and stochastic dominance rules were employed to determine the optimal design level. The allowable societal risk level was considered as a constraint in the optimal design selection. It was found that the Canadian Standard Association design leads to the minimum expected life-cycle cost and satisfies the allowable societal risk constraint as well. A set of optimal designs for a risk-averse decision maker was identified using the stochastic dominance rules. Both the ASME and CSA designs belong to the optimal design set and meet the allowable societal risk constraint.
Plant Life Management Models: A Comparison With Analysis of Impact on Both Safety and Nonsafety Issues
Authors: Contri Paolo , Elsing Bernhard
Published: April 2011

Motivated by social and economical issues, over the last 20 years, many nuclear power plant owners started a program for the long-term operation (LTO)/plant life management (PLIM) of their older nuclear facilities. A PLIM framework requires both a detailed review of the features of the main safety programs; maintenance, surveillance, and in-service inspection (MS&I); and a complete integration of these safety programs into the general management system of the plant. Therefore, PLIM should address safety, as well as economics, knowledge management, and decision making and provide an overall framework to keep the whole plant in a safe and economically sustainable condition. Moreover, the existence of new external factors, such as extensive use of subcontractors, need for efficient management of spare parts, and request for heavy plant refurbishment programs, demands for updated techniques in the overall management of the plant. Therefore, new organizational models have to be developed to appropriately support the PLIM framework. In recent years, a network of European research organizations (SENUF) carried out many R&D tasks aimed at capturing the aspects of the maintenance programs, where research is mostly needed and at developing suitable optimized maintenance models. Using the outcome of these initiatives, this paper aims at identifying the technical attributes of the PLIM program more directly affecting the decision for a long term safe operation of a nuclear facility and the issues related to its optimal implementation. A comparison of some of the available models is presented and an analysis of the potential impact on safety and nonsafety programs is provided in order to support the development of optimized life management models.
Exact Frequency Analysis of a Rotating Cantilever Beam With Tip Mass Subjected to Torsional-Bending Vibrations
Authors: Ansari Masoud , Esmailzadeh Ebrahim , Jalili Nader
Published: April 2011

An exact frequency analysis of a rotating beam with an attached tip mass is addressed in this paper while the beam undergoes coupled torsional-bending vibrations. The governing coupled equations of motion and the corresponding boundary condition are derived in detail using the extended Hamilton principle. It has been shown that the source of coupling in the equations of motion is the rotation and that the equations are linked through the angular velocity of the base. Since the beam-tip-mass system at hand serves as the building block of many vibrating gyroscopic systems, which require high precision, a closed-form frequency equation of the system should be derived to determine its natural frequencies. The frequency analysis is the basis of the time domain analysis, and hence, the exact frequency derivation would lead to accurate time domain results, too. Control strategies of the aforementioned gyroscopic systems are mostly based on their resonant condition, and hence, acquiring knowledge about their exact natural frequencies could lead to a better control of the system. The parameter sensitivity analysis has been carried out to determine the effects of various system parameters on the natural frequencies. It has been shown that even the undamped systems undergoing base rotation will have complex eigenvalues, which demonstrate a damping-type behavior.
Estimating Changes in Speech Metrics Indicative of Fatigue Levels
Authors: Shahidi Parham , Soltan Reza A. , Southward Steve C. , Ahmadian Mehdi
Published: April 2011

In this paper, we are presenting a novel approach to estimate fatigue levels of train conductors, by analyzing the speech signal. An independent neural network joined with a Markov Model, will output the probability density, which illustrates the likelihood of the result of the first step to be accurate. Vigilance research has shown that, for most operators engaged in attention-intensive and monotonous tasks, retaining a constant level of alertness is almost impossible. Sleeping disorders, reduced hours of rest and disrupted circadian rhythms amplify this effect and lead to significantly increased fatigue levels. Increased fatigue levels manifest themselves in alterations of speech metrics, as compared to alert states of mind. To make a decision about the level of fatigue, we are proposing an alertness estimation system which uses speech metrics to generate a fatigue quotient indicative of the fatigue level. A speech pre-processor extracts metrics such as speech duration, word production rate and speech intensity from a continuous speech signal and uses a Fuzzy Logic algorithm to generate the fatigue quotient at any moment in time when speech is present. However, the nature of human interaction introduces levels of uncertainty, which make fatigue level recognition difficult. In other words, even with a perfectly trained neural network and Fuzzy Logic algorithm, we cannot make definite conclusions about the level of alertness. The reason being, that there is no guarantee that the estimated level of alertness is robust for a certain amount of time and didn’t come from drinking half a cup of coffee. Moreover, coming up with a perfect model of speech-fatigue (i.e. input-output) for humans, to train the Fuzzy algorithm is almost impossible. For this reason the study of “Risk and Uncertainty” is an integral part of this research. Motivated by the distinction between “risk” (randomness that can be fully captured by probability and statistics) and “uncertainty” (all other types of randomness), we propose a fine taxonomy: fully reducible, partially reducible, and irreducible uncertainty, that can explain some of the key differences between long term alertness and a short term change of state that makes the operator alert. An experimental study is conducted where a hyper articulated speech signal with three different levels of simulated fatigue is analyzed by the algorithm and a probability density function is assigned to the fatigue quotient to take the risk and uncertainty into account and make the overall result more reliable.
A Rail Vehicle Clearance Calculation Program
Authors: Klauder Louis T.
Published: April 2011

This paper explains and illustrates a computer program for calculating clearances between a rail vehicle and wayside objects and between a vehicle on one track and a vehicle on an adjacent track. The program includes a graphic animation illustrating the geometrical proximity of the subject vehicle to successive wayside objects and to a vehicle in successive relative locations along an adjacent track. The situations of minimum clearance for given vehicle and track geometry inputs are highlighted in a report. The main program is accompanied by an auxiliary program that uses independent logic to calculate clearances for idealized situations and that generates input files representing those situations for the main program. This provides an efficient means for verifying basic aspects of the logic of the main program.
Starve Now, Gain Later
Authors: Cheng Mickie H.
Published: April 2011

Specific, durable epigenetic changes induced in the fetus by maternal diet may spur development of type 2 diabetes in adulthood.
Patient, Heal Thyself
Authors: Hong David S.
Published: April 2011

CD40 activation boosts the antitumor response of stromal-associated macrophages in humans and mice with pancreatic cancer.
Retinoic Acid and α-Galactosylceramide Differentially Regulate B Cell ActivationIn Vitroand Augment Antibody ProductionIn Vivo
Authors: Chen Qiuyan , Mosovsky Kara L. , Ross A. Catharine
Published: April 2011

All-trans-retinoic acid (RA) promotes the maturation and differentiation of B cells, which are known as a type of professional antigen-presenting cells. We show here that CD1d, a major histocompatibility complex class I-like molecule that presents lipid antigens, is expressed in the mouse spleen B cells and is increased by RA. Thus, we hypothesized that RA and the CD1d ligand, α-galactosylceramide (αGalCer), could interact to promote the differentiation, maturation, and antibody response of antigen-activated B cells. In isolated B cells, αGalCer alone markedly stimulated, and RA further increased B cell proliferation, synergizing with the B cell antigen receptor ligation via anti-μ antibody (P< 0.05). The significantly increased cell proliferation stimulated by αGalCer was abrogated in the B cells of CD1d-null mice. RA alone and combined with αGalCer also promoted B cell differentiation by the enrichment of sIgG1-, CD138-, and PNA/Fas-positive B cells (P< 0.05), suggesting a plasmacytic cell differentiation.In vivo, wild-type mice treated with RA and/or αGalCer during primary immunization with tetanus toxoid produced a higher serum anti-tetanus IgG response and had more bone marrow anti-tetanus antibody-secreting cells as determined by enzyme-linked immunospot assay (P< 0.05) in the secondary response, a finding indicative of heightened long-term memory; however, the increased antibody secretion after αGalCer treatment was abolished in CD1d-null mice. We provide evidence here that RA, together with αGalCer, can effectively regulate B cell proliferation and differentiation, ultimately promoting a more efficient antibody response to protein antigen. The results suggest that the combination of RA and αGalCer could be a useful adjuvant combination in vaccine strategies.
Sensitivity and Specificity of Serologic Assays for Detection of Human Infection with 2009 Pandemic H1N1 Virus in U.S. Populations
Authors: Veguilla Vic , Hancock Kathy , Schiffer Jarad , Gargiullo Paul , Lu Xiuhua , Aranio Darbi , Branch Alicia , Dong Libo , Holiday Crystal , Liu Feng , Steward-Clark Evelene , Sun Hong , Tsang Byron , Wang David , Whaley Melissa , Bai Yaohui , Cronin Li , Browning Peter , Dababneh Hanan , Noland Heather , Thomas Leilani , Foster Lydia , Quinn Conrad P. , Soroka Stephen D. , Katz Jacqueline M.
Published: April 2011

Swine origin 2009 H1N1 influenza virus has spread globally to cause the first influenza pandemic of the 21st century. Serological studies can improve our understanding of the extent of human infection and risk factors associated with the transmission of this pandemic virus. The “gold standard” for serodiagnosis of human influenza virus infection is the detection of seroconversion between acute- and convalescent-stage samples. However, the timing of seroepidemiological investigations often precludes the collection of truly acute-phase sera, requiring development of serological criteria for evaluating convalescent-phase sera that optimize detection of true positives and true negatives. To guide seroepidemiological investigations into the spread of the novel 2009 pandemic H1N1 virus, we characterized serum antibody responses to 2009 H1N1 virus in 87 individuals with confirmed viral infection and 227 nonexposed U.S. individuals using microneutralization (MN) and hemagglutination inhibition (HI) assays. Sensitivity and specificity were determined for each assay alone and in combination for detection of 2009 H1N1 virus-specific antibodies in convalescent-phase sera. Although the HI assay was more specific for detecting antibody to 2009 H1N1, the MN assay was more sensitive, particularly for detecting low-titer seroconversions. A combination of titers (MN ≥ 40 and HI ≥ 20) provided the highest sensitivity (90%) and specificity (96%) for individuals aged <60 years and 92% specificity for adults aged ≥60 years for detection of serologically confirmed 2009 H1N1 infections in U.S. populations during the first pandemic waves. These studies provide an approach to optimize timely serological investigations for future pandemics or outbreaks of novel influenza viruses among humans.
Amplified Fragment Length Polymorphism Reveals Specific Epigenetic Distinctions between Mycobacterium avium Subspecies paratuberculosis Isolates of Various Isolation Types
Authors: O'Shea B. , Khare S. , Klein P. , Roussel A. , Adams L. G. , Ficht T. A. , Rice-Ficht A. C.
Published: April 2011

Amplified fragment length polymorphism (AFLP) was employed as a genetic analysis tool for the study of the genetic relatedness of
Mycobacterium avium
subsp.
paratuberculosis
isolates harvested from bovine fecal samples and from bovine or human tissues. This analysis revealed genetic differences between these two isolate types that were confirmed through cluster analysis. Dendrogram analysis separated these two isolate types based on the isolation scheme (tissue-associated versus fecal
M. avium
subsp.
paratuberculosis
isolates). Further sequence analysis of unique genetic regions from each isolation type revealed no genetic sequence differences. However, Clustal DNA alignments identified AFLP restriction enzyme sites that were undigested in the tissue-associated isolates. AFLP analysis also disclosed that the same AFLP restriction sites were digested in all of the fecal isolates. Sequence analysis further revealed a consensus sequence upstream of the undigested restriction sites for possible methyltransferase recognition in the tissue-associated
M. avium
subsp.
paratuberculosis
isolates.
Rapid Differentiation of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus by Flow Cytometry after Brief Antibiotic Exposure
Authors: Shrestha Nabin K. , Scalera Nikole M. , Wilson Deborah A. , Procop Gary W.
Published: April 2011

We noticed that methicillin-resistant
Staphylococcus aureus
(MRSA) and methicillin-susceptible
S. aureus
(MSSA) isolates yielded side-scatter (SSC) and fluorescence intensity (FI) differences on flow cytometry (FCM) following incubation in oxacillin broth. The purpose of this study was to determine whether MRSA and MSSA could be reliably differentiated by FCM.
S. aureus
isolates were incubated in oxacillin-containing Mueller-Hinton broth, stained using the FASTEST total viable organisms kit, and analyzed by FCM in the MicroPRO instrument. SSC versus FI were examined, and gates 1 and 2 were defined to encompass the majority of MSSA and MRSA signal events, respectively. A count ratio (CR) was defined as the ratio of counts in gate 2 to those in gate 1. Initially, 33 isolates were tested after 4 h of incubation for proof-of-concept. Twenty others were then tested after incubation intervals ranging from 30 min to 4 h to determine the earliest possible time for differentiation. Next, 100 separate isolates were tested to determine the best CR cutoff value. Finally, the CR was validated by using an independent cohort of 121 isolates. We noted that MRSA isolates had higher SSC and FI readings than did MSSA isolates after 2 h of incubation. The receiver-operator characteristics curve showed that a CR cutoff of 0.0445 reliably differentiated MRSA from MSSA. In the validation cohort, this cutoff had a sensitivity of 100% and a specificity of 98.7% for identifying MRSA from among
S. aureus
isolates, following 2 h of incubation. This study demonstrates that MRSA and MSSA can be accurately differentiated by FCM after 2 h of incubation in an oxacillin-containing liquid culture medium.
Complexity and Catalytic Efficiency of Hepatitis C Virus (HCV) NS3 and NS4A Protease Quasispecies Influence Responsiveness to Treatment with Pegylated Interferon plus Ribavirin in HCV/HIV-Coinfected Patients
Authors: Aparicio Ester , Franco Sandra , Parera Mariona , Andrés Cristina , Tural Cristina , Clotet Bonaventura , Martínez Miguel Angel
Published: April 2011

The role of the hepatitis C virus (HCV) NS3/4A protease in ablating the signaling pathway involved in the production of alpha/beta interferon (IFN-α/β) suggests a relationship between NS3/4A proteolytic activity and a patient's response to IFN-based therapy. To identify viral factors associated with the HCV treatment response, we analyzed the pretreatment NS3/4A protease gene quasispecies composition of 56 HCV genotype 1–HIV-1-coinfected patients treated in our clinic with pegylated IFN (pegIFN) plus ribavirin (RBV). The catalytic efficiency of the dominant (i.e., the most abundant) quasispecies was also assayed for Cardif cleavage and correlated with treatment outcome. A total of 1,745 clones were isolated and sequenced. Significantly less nucleotide quasispecies heterogeneity and lower Shannon entropy values were detected within the responder group (
P
< 0.05). A correlation was also found between the efficiency of NS3/4A protease Cardif cleavage and therapy outcome. Proteases from sustained responder patients were more efficient at processing Cardif (mean ± standard error of the mean [SEM], 0.8960 ± 0.05568;
n
= 19) than proteases from nonresponders (mean ± SEM, 0.7269 ± 0.05306;
n
= 37;
P
< 0.05). Finally, the amino acid p distance (the proportion [p] of nucleotide sites at which two sequences being compared are different) was significantly shorter in patients with an interleukin-28B (IL-28B) risk allele (
P
< 0.01), suggesting that IL-28B risk allele carriers exert a lower positive selection pressure on the NS3/4A protease. NS3/4A protease efficiency in cleaving Cardif may be associated with the pegIFN-RBV treatment response, as shown in our cohort of HIV-HCV-coinfected patients. Greater NS3/4A nucleotide heterogeneity and higher Shannon entropy values in nonresponders suggest that less HCV quasispecies complexity may favor a better response to pegIFN-RBV.
Differential Pathogenesis of Respiratory Syncytial Virus Clinical Isolates in BALB/c Mice
Authors: Stokes Kate L. , Chi Michael H. , Sakamoto Kaori , Newcomb Dawn C. , Currier Michael G. , Huckabee Matthew M. , Lee Sujin , Goleniewska Kasia , Pretto Carla , Williams John V. , Hotard Anne , Sherrill Taylor P. , Peebles R. Stokes , Moore Martin L.
Published: April 2011

Airway mucus is a hallmark of respiratory syncytial virus (RSV) lower respiratory tract illness. Laboratory RSV strains differentially induce airway mucus production in mice. Here, we tested the hypothesis that RSV strains differ in pathogenesis by screening six low-passage RSV clinical isolates for mucogenicity and virulence in BALB/cJ mice. The RSV clinical isolates induced variable disease severity, lung interleukin-13 (IL-13) levels, and gob-5 levels in BALB/cJ mice. We chose two of these clinical isolates for further study. Infection of BALB/cJ mice with RSV A2001/2-20 (2-20) resulted in greater disease severity, higher lung IL-13 levels, and higher lung gob-5 levels than infection with RSV strains A2, line 19, Long, and A2001/3-12 (3-12). Like the line 19 RSV strain, the 2-20 clinical isolate induced airway mucin expression in BALB/cJ mice. The 2-20 and 3-12 RSV clinical isolates had higher lung viral loads than laboratory RSV strains at 1 day postinfection (p.i.). This increased viral load correlated with higher viral antigen levels in the bronchiolar epithelium and greater histopathologic changes at 1 day p.i. The A2 RSV strain had the highest peak viral load at day 4 p.i. RSV 2-20 infection caused epithelial desquamation, bronchiolitis, airway hyperresponsiveness, and increased breathing effort in BALB/cJ mice. We found that RSV clinical isolates induce variable pathogenesis in mice, and we established a mouse model of clinical isolate strain-dependent RSV pathogenesis that recapitulates key features of RSV disease.
The F1 Motif of Dengue Virus Polymerase NS5 Is Involved in Promoter-Dependent RNA Synthesis
Authors: Iglesias Nestor G. , Filomatori Claudia V. , Gamarnik Andrea V.
Published: April 2011

The mechanism by which viral RNA-dependent RNA polymerases (RdRp) specifically amplify viral genomes is still unclear. In the case of flaviviruses, a model has been proposed that involves the recognition of an RNA element present at the viral 5′ untranslated region, stem-loop A (SLA), that serves as a promoter for NS5 polymerase binding and activity. Here, we investigated requirements for specific promoter-dependent RNA synthesis of the dengue virus NS5 protein. Using mutated purified NS5 recombinant proteins and infectious viral RNAs, we analyzed the requirement of specific amino acids of the RdRp domain on polymerase activity and viral replication. A battery of 19 mutants was designed and analyzed. By measuring polymerase activity using nonspecific poly(rC) templates or specific viral RNA molecules, we identified four mutants with impaired polymerase activity. Viral full-length RNAs carrying these mutations were found to be unable to replicate in cell culture. Interestingly, one recombinant NS5 protein carrying the mutations K456A and K457A located in the F1 motif lacked RNA synthesis dependent on the SLA promoter but displayed high activity using a poly(rC) template. Promoter RNA binding of this NS5 mutant was unaffected while
de novo
RNA synthesis was abolished. Furthermore, the mutant maintained RNA elongation activity, indicating a role of the F1 region in promoter-dependent initiation. In addition, four NS5 mutants were selected to have polymerase activity in the recombinant protein but delayed or impaired virus replication when introduced into an infectious clone, suggesting a role of these amino acids in other functions of NS5. This work provides new molecular insights on the specific RNA synthesis activity of the dengue virus NS5 polymerase.
CD4
+
T Cells, Including Th17 and Cycling Subsets, Are Intact in the Gut Mucosa of HIV-1-Infected Long-Term Nonprogressors
Authors: Ciccone Emily J. , Greenwald Jamieson H. , Lee Philip I. , Biancotto Angélique , Read Sarah W. , Yao Michael A. , Hodge Jessica N. , Thompson William L. , Kovacs Stephen B. , Chairez Cheryl L. , Migueles Stephen A. , Kovacs Joseph A. , Margolis Leonid B. , Sereti Irini
Published: April 2011

During acute human immunodeficiency virus (HIV) infection, there is a massive depletion of CD4
+
T cells in the gut mucosa that can be reversed to various degrees with antiretroviral therapy. Th17 cells have been implicated in mucosal immunity to extracellular bacteria, and preservation of this subset may support gut mucosal immune recovery. However, this possibility has not yet been evaluated in HIV-1-infected long-term nonprogressors (LTNPs), who maintain high CD4
+
T cell counts and suppress viral replication in the absence of antiretroviral therapy. In this study, we evaluated the immunophenotype and function of CD4
+
T cells in peripheral blood and gut mucosa of HIV-uninfected controls, LTNPs, and HIV-1-infected individuals treated with prolonged antiretroviral therapy (ART) (VL [viral load]<50). We found that LTNPs have intact CD4
+
T cell populations, including Th17 and cycling subsets, in the gut mucosa and a preserved T cell population expressing gut homing molecules in the peripheral blood. In addition, we observed no evidence of higher monocyte activation in LTNPs than in HIV-infected (HIV
−
) controls. These data suggest that, similar to nonpathogenic simian immunodeficiency virus (SIV) infection, LTNPs preserve the balance of CD4
+
T cell populations in blood and gut mucosa, which may contribute to the lack of disease progression observed in these patients.
Discrimination of Mumps Virus Small Hydrophobic Gene Deletion Effects from Gene Translation Effects on Virus Virulence
Authors: Malik Tahir , Shegogue Candie Wolbert , Werner Kellie , Ngo Laurie , Sauder Christian , Zhang Cheryl , Duprex William Paul , Rubin Steven
Published: April 2011

Deletion of the small hydrophobic (SH) protein of certain paramyxoviruses has been found to result in attenuation, suggesting that the SH protein is a virulence factor. To investigate the role of the mumps virus (MuV) SH protein in virulence, multiple stop codons were introduced into the open reading frame (ORF) of a MuV molecular clone (r88-1961
SHstop
), preserving genome structure but precluding production of the SH protein. No differences in neurovirulence were seen between the wild-type and the SH
stop
viruses. In contrast, upon deletion of the SH gene, significant neuroattenuation was observed. These data indicate that the MuV SH protein is not a neurovirulence factor and highlight the importance of distinguishing gene deletion effects from protein-specific effects.
Differential expression of microRNA-675, microRNA-139-3p and microRNA-335 in benign and malignant adrenocortical tumours
Authors: Schmitz K J , Helwig J , Bertram S , Sheu S Y , Suttorp A C , Seggewiß J , Willscher E , Walz M K , Worm K , Schmid K W
Published: April 2011

Background

For the clinical management of adrenocortical neoplasms it is crucial to correctly distinguish between benign and malignant tumours. Even histomorphologically based scoring systems do not allow precise separation in single lesions, thus novel parameters are desired which offer a more accurate differentiation. The tremendous potential of microRNAs (miRNAs) as diagnostic biomarkers in surgical pathology has recently been shown in a broad variety of tumours.

Methods

In order to elucidate the diagnostic impact of miRNA expression in adrenocortical neoplasms, a cohort of 20 adrenocortical specimens including normal adrenal tissue (n=4), adrenocortical adenomas (ACAs) (n=9), adrenocortical carcinomas (ACCs) (n=4) and metastases (n=3) was analysed using TaqMan low density arrays to identify specific miRNA profiles in order to distinguish between benign and malignant adrenocortical lesions. Results were validated in a validation cohort (n=16).

Results

Concerning the differential diagnosis of ACAs and ACCs, 159 out of 667 miRNAs were up- and 89 were down-regulated in ACAs. Using real-time PCR analysis of three of the most significantly expressed single key miRNAs allowed separation of ACAs from ACCs. ACCs exhibited significantly lower levels of miR-139-3p (up to 8.49-fold, p<0.001), miR-675 (up to 23.25-fold, p<0.001) and miR-335 (up to 5.25-fold, p<0.001). A validation cohort of 16 specimen with known Weiss score showed up-regulation of miR-335 and miR-675 in the majority of cases with probable malignant course, although overlapping values exist.

Conclusion

miRNA profiling of miR-675 and miR-335 helps in discriminating ACCs from ACAs. miRNA analysis may indicate malignant behaviour in cases with indeterminate malignant potential.
Y stenting using kissing stents for the treatment of bifurcation aneurysms
Authors: Jankowitz Brian T , Thomas Ajith , Jovin Tudor , Horowitz Michael
Published: April 2011

Background and purpose

Coiling of wide neck, bifurcation aneurysms often requires creative techniques to ensure optimal and safe embolization. The Y stenting technique utilizing kissing stents provides an alternative endovascular treatment of this complex pathology.

Materials and methods

A triple wire technique was used to place side by side stents within the parent artery and extending into the bilateral bifurcation vessels. The third wire enabled placement of a microcatheter within the aneurysm, which remained trapped by the opposing stents.

Results

9 patients obtained acceptable angiographic partial or total occlusion of their aneurysm. Follow-up was variable, ranging from none to 26 months. There were two early deaths at postprocedures day 1 and 10, with one mortality being a direct result of the intervention. One patient experienced delayed in-stent thrombosis resulting in a periprocedural morbidity and mortality of 11% and 22%, respectively. One patient required retreatment.

Conclusion

Y stenting utilizing the triple catheter technique is an alternative endovascular treatment for wide neck, bifurcation aneurysms. Caution should be used, especially in the setting of subarachnoid hemorrhage, as the complication rate and overall risk increase significantly with this technique's complexity.
Phylogenetic analysis of Austrian canine distemper virus strains from clinical samples from dogs and wild carnivores
Authors: Benetka V. , Leschnik M. , Affenzeller N. , Möstl K.
Published: April 2011

Austrian field cases of canine distemper (14 dogs, one badger [Meles meles ] and one stone marten [Martes foina ]) from 2002 to 2007 were investigated and the case histories were summarised briefly. Phylogenetic analysis of fusion (F) and haemagglutinin (H) gene sequences revealed different canine distemper virus (CDV) lineages circulating in Austria. The majority of CDV strains detected from 2002 to 2004 were well embedded in the European lineage. One Austrian canine sample detected in 2003, with a high similarity to Hungarian sequences from 2005 to 2006, could be assigned to the Arctic group (phocine distemper virus type 2‐like). The two canine sequences from 2007 formed a clearly distinct group flanked by sequences detected previously in China and the USA on an intermediate position between the European wildlife and the Asia‐1 cluster. The Austrian wildlife strains (2006 and 2007) could be assigned to the European wildlife group and were most closely related to, yet clearly different from, the 2007 canine samples. To elucidate the epidemiological role of Austrian wildlife in the transmission of the disease to dogs and vice versa, H protein residues related to receptor and host specificity (residues 530 and 549) were analysed. All samples showed the amino acids expected for their host of origin, with the exception of a canine sequence from 2007, which had an intermediate position between wildlife and canine viral strains. In the period investigated, canine strains circulating in Austria could be assigned to four different lineages reflecting both a high diversity and probably different origins of virus introduction to Austria in different years.
Comparing sediment bacterial communities in the macrophyte-dominated and algae-dominated areas of eutrophic Lake Taihu, China
Authors: Shao Keqiang , Gao Guang , Qin Boqiang , Tang Xiangming , Wang Yongping , Chi Kexu , Dai Jiangyu
Published: April 2011

Bacterial community structure and the effects of several environmental factors on bacterial community distribution were investigated in the sediment of the macrophyte-dominated and algae-dominated areas in a large, shallow, eutrophic freshwater lake (Lake Taihu, China). Surface sediment samples were collected at 6 sampling sites (3 sites from each of the 2 areas) on 15 February and 15 August 2009. Based on cluster analysis of the DGGE banding patterns, there were significant seasonal variations in the structure of the sediment bacterial community in the macrophyte- and algae-dominated areas, and site-specific variation within an area and between 2 areas. However, there were no significant between-area variations due to the large within-area variation. Analysis of DNA sequences showed that there were differences in the species composition of the sediment bacteria between the macrophyte- and algae-dominated area clone libraries. In the macrophyte-dominated area library, the bacterial community was dominated by Deltaproteobacteria, Verrucomicrobia, Acidobacteria, Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. OP10 was found in the library of this area but not in the algae-dominated area library. The algae-dominated area library was dominated by Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Acidobacteria. Cyanobacteria, Alphaproteobacteria, and Planctomycetes were found in this area library but not in the macrophyte-dominated area library. Canonical correspondence analysis demonstrated that total phosphorus and water temperature were the dominant environmental factors affecting bacterial community composition in the sediment.
ACC deaminase activity in avirulentAgrobacterium tumefaciensD3
Authors: Hao Youai , Charles Trevor C. , Glick Bernard R.
Published: April 2011

Some plant-growth-promoting bacteria encode the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, which breaks down ACC, the direct precursor of ethylene biosynthesis in all higher plants, into ammonia and α-ketobutyrate and, as a result, reduces stress ethylene levels in plants caused by a wide range of biotic and abiotic stresses. It was previously shown that ACC deaminase can inhibit crown gall development induced by Agrobacterium tumefaciens and can partially protect plants from this disease. Agrobacterium tumefaciens D3 has been previously reported to contain a putative ACC deaminase structural gene (acdS) and a regulatory gene (acdR = lrpL). In the present study, it was found that A. tumefaciens D3 is an avirulent strain. ACC deaminase activity and its regulation were also characterized. Under gnotobiotic conditions, wild-type A. tumefaciens D3 was shown to be able to promote plant root elongation, while the acdS and lrpL double mutant strain A. tumefaciens D3-1 lost that ability. When co-inoculated with the virulent strain, A. tumefaciens C58, in wounded castor bean plants, both the wild-type A. tumefaciens D3 and the mutant A. tumefaciens D3-1 were found to be able to significantly inhibit crown gall development induced by A. tumefaciens C58.
Use of protein microarray to identify gene expression changes ofYersinia pestisat different temperatures
Authors: Li Bei , Tan Yafang , Guo Jingyu , Cui Baizhong , Wang Zuyun , Wang Hu , Zhou Lei , Guo Zhaobiao , Zhu Ziwen , Du Zongmin , Yang Ruifu
Published: April 2011

Yersinia pestis is a bacterium that is transmitted between fleas, which have a body temperature of 26 °C, and mammalian hosts, which have a body temperature of 37 °C. To adapt to the temperature shift, phenotype variations, including virulence, occur. In this study, an antigen microarray including 218 proteins of Y. pestis was used to evaluate antibody responses in a pooled plague serum that was unadsorbed, adsorbed by Y. pestis cultivated at 26 °C, or adsorbed by Y. pestis cultivated at 26 and 37 °C to identify protein expression changes during the temperature shift. We identified 12 proteins as being expressed at 37 °C but not at 26 °C, or expressed at significantly higher levels at 37 °C than at 26 °C. The antibodies against 7 proteins in the serum adsorbed by Y. pestis cultivated at 26 and 37 °C remained positive, suggesting that they were not expressed on the surface of Y. pestis in LB broth in vitro or specifically expressed in vivo. This study proved that protein microarray and antibody profiling comprise a promising technique for monitoring gene expression at the protein level and for better understanding pathogenicity, to find new vaccine targets against plague.