bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delayed seroconversion to STLV-1 infection is associated with mutations in the pol and rex genes
Authors: Dube Syamalima , Saksena Nitin , Spicer Timothy , Healey Jayne , Benz Patricia , Dube Dipak K , Poiesz Bernard J 
Published: September 2013

Abstract

Background
Simian T-cell lymphoma/leukemia virus-1 (STLV-1) infection of non-human primates can serve as a model for human T-cell lymphoma/leukemia virus infection.

Methods
Two tantalus and 2 patas monkeys were transfused with intraspecies whole blood infected with STLV-1. Infection was determined by ELISA, western blot and DNA PCR analyses. The entire genome of the STLV-1 Tan 90 strain and some of the STVL-1 Pat74 strain were amplified using over-lapping primer-pairs and subsequently sequenced.

Results
Followup studies conducted over 2 years indicated that all 4 monkeys remained healthy despite being infected with STLV-1, as determined by PCR, cloning and sequencing analyses. ELISA and Western blot analyses indicated that both patas monkeys seroconverted within 2 months of transfusion, while one tantalus monkey required one year to seroconvert and the other never fully seroconverted. The tantalus monkey which never fully seroconverted, failed to react to HTLV-1 p24 Gag antigen. Sequence analyses indicated that, while unique, the deduced p24 Gag amino acid sequence of the STLV-1 Tan 90 strain used for infection was still highly homologous to the HTLV-1 p24 Gag amino acids present in the ELISA and WB assays. However, a mutation in the pol sequence of STLV-1 Tan 90 encoded a putative stop codon, while a common deletion in the pol/rex regulatory gene causes significant changes in the Pol, and p27 Rex proteins. These same mutations were also observed in the viral DNA of both recipient infected tantalus monkeys and were not present in the STLV-1 Pat 74 strain.

Conclusion
Our data suggest that seroconversion to STLV-1 infection may be prolonged due to the above mutations, and that compensatory molecular events must have occurred to allow for virus transmission.
Prevalence of avian paramyxovirus type 1 in Mallards during autumn migration in the western Baltic Sea region
Authors: Tolf Conny , Wille Michelle , Haidar Ann-Katrin , Avril Alexis , Zohari Siamak , Waldenström Jonas 
Published: September 2013

Abstract

Background
Newcastle disease virus (NDV) is the causative agent of the Newcastle disease, a severe disease in birds associated with substantial economic losses to the poultry industry worldwide. Sweden is situated along the Western European waterfowl flyway and applies a non-vaccination policy combined with directives of immediate euthanisation of NDV infected flocks. During the last decades there have been several outbreaks with NDV in poultry in Sweden. However, less is known about the virus prevalence in the wild bird population including waterfowl, a well-established reservoir of avian paramyxovirus type 1 (APMV-1), the paramyxovirus serotype that include pathogenic NDV.

Methods
The survey constituted of 2332 samples from Mallards (Anas platyrhynchos), trapped in the southern part of Sweden during autumn migration in 2010. These samples were screened for APMV-1 by real-time reverse transcription PCR, and viral strains from positive samples were isolated and characterized by sequence analysis of the fusion gene and by phylogenetic analysis.

Conclusions
Twenty of these samples were positive for APMV-1, hence a virus prevalence of 0.9% (95% Confidence Interval [95% CI]=0.54%, 1.35%). The highest APMV-1 prevalence was detected in juvenile Mallards sampled in November (n=887, prevalence 1.24% ([95% CI])=0.67%, 2.24%). Sequence analysis and evaluation of phylogenetic relatedness indicated that isolated APMV-1 strains were lentogenic, and phylogenetically most closely related to genotype Ib strains within the clade of class II viruses. The sampling system employed enabled us to follow APMV-1 infections and the shedding of one particular viral strain in one individual bird over several days. Furthermore, combining previous screening results with the APMV-1 detections in this study showed that more than 50% of Mallards that tested positive for APMV-1 RNA were co-infected with influenza A virus.
Comparison of viremia of type II porcine reproductive and respiratory syndrome virus in naturally infected pigs by zip nucleic acid probe-based real-time PCR
Authors: Lin Chao-Nan , Lin Wei-Hao , Hung Li-Ning , Wang Sheng-Yuan , Chiou Ming-Tang 
Published: September 2013

Abstract

Background
Porcine reproductive and respiratory syndrome virus (PRRSV) is a RNA virus with high genetic variation. This virus causes significant economic losses in most pig-producing countries. The clinical presentation of PRRSV ranges from asymptomatic to devastating. In this study, we developed a sensitive and specific zip nucleic acid probe-based real-time PCR assay to evaluate the viremia of natural PRRSV-infected pigs in Taiwan. Serum samples were collected from 577 pigs aged 5–12 weeks. These include 444 clinically healthy pigs and 133 symptomatic pigs were confirmed to have porcine respiratory disease complex (PRDC).

Results
Viremia was quantified in 79 of the 444 (17.8%) clinically healthy pigs and in 112 of the 133 (84.2%) PRDC cases. Viremias were significantly more common in pigs with PRDC compared with the clinically healthy pigs (P <0.0001). These results suggest that a high viral load is a major feature of PRRSV-affected pigs.

Conclusions
ZNA probe-based real-time PCR can be a useful tool to diagnose symptomatic and asymptomatic PRRSV-infected pigs. The presence of this marker in a sample of animals with high PRRSV loads (>104.2 PRRSV genomes/μl of serum) seems to indicate that it correlates with the presence of PRDC in pigs.
Resolution of five-component mixture using mean centering ratio and inverse least squares chemometrics
Authors: Issa Mahmoud Mohamed , Nejem R’afat Mahmoud , Shanab Alaa Mohamed Abu , Shaat Nahed Talab 
Published: September 2013

Abstract

Background
A comparative study of the use of mean centering of ratio spectra and inverse least squares for the resolution of paracetamol, methylparaben, propylparaben, chlorpheniramine maleate and pseudoephedrine hydrochloride has been achieved showing that the two chemometric methods provide a good example of the high resolving power of these techniques. Method (I) is the mean centering of ratio spectra which depends on using the mean centered ratio spectra in four successive steps that eliminates the derivative steps and therefore the signal to noise ratio is improved. The absorption spectra of prepared solutions were measured in the range of 220–280 nm. Method (II) is based on the inverse least squares that depend on updating developed multivariate calibration model. The absorption spectra of the prepared mixtures in the range 230–270 nm were recorded.

Results
The linear concentration ranges were 0–25.6, 0–15.0, 0–15.0, 0–45.0 and 0–100.0 μg mL-1 for paracetamol, methylparaben, propylparaben, chlorpheniramine maleate and pseudoephedrine hydrochloride, respectively. The mean recoveries for simultaneous determination were between 99.9-101.3% for the two methods. The two developed methods have been successfully used for prediction of five-component mixture in Decamol Flu syrup with good selectivity, high sensitivity and extremely low detection limit.

Conclusion
No published method has been reported for simultaneous determination of the five components of this mixture so that the results of the mean centering of ratio spectra method were compared with those of the proposed inverse least squares method. Statistical comparison was performed using t-test and F-ratio at P = 0.05. There was no significant difference between the results.
Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data
Authors: Chu Hsueh-Ting , Lin Han , Tsao Theresa Tsun-Hui , Chang Chun-Fan , Hsiao William WL , Yeh Tze-Jung , Chang Ching-Mao , Liu Yen-Wenn , Wang Tse-Yi , Yang Ko-Chun , Chen Tsung-Jui , Chen Jen-Chih , Chen Kuang-Chi , Kao Cheng-Yan 
Published: September 2013

Abstract

Background
Neutrophil antigens are involved in a variety of clinical conditions including transfusion-related acute lung injury (TRALI) and other transfusion-related diseases. Recently, there are five characterized groups of human neutrophil antigen (HNA) systems, the HNA1 to 5. Characterization of all neutrophil antigens from whole genome sequencing (WGS) data may be accomplished for revealing complete genotyping formats of neutrophil antigens collectively at genome level with molecular variations which may respectively be revealed with available genotyping techniques for neutrophil antigens conventionally.

Results
We developed a computing method for the genotyping of human neutrophil antigens. Six samples from two families, available from the 1000 Genomes projects, were used for a HNA typing test. There are 500 ~ 3000 reads per sample filtered from the adopted human WGS datasets in order for identifying single nucleotide polymorphisms (SNPs) of neutrophil antigens. The visualization of read alignment shows that the yield reads from WGS dataset are enough to cover all of the SNP loci for the antigen system: HNA1, HNA3, HNA4 and HNA5. Consequently, our implemented Bioinformatics tool successfully revealed HNA types on all of the six samples including sequence-based typing (SBT) as well as PCR sequence-specific oligonucleotide probes (SSOP), PCR sequence-specific primers (SSP) and PCR restriction fragment length polymorphism (RFLP) along with parentage possibility.

Conclusions
The next-generation sequencing technology strives to deliver affordable and non-biased sequencing results, hence the complete genotyping formats of HNA may be reported collectively from mining the output data of WGS. The study shows the feasibility of HNA genotyping through new WGS technologies. Our proposed algorithmic methodology is implemented in a HNATyping software package with user’s guide available to the public at http://sourceforge.net/projects/hnatyping/.
Pronuclear morphology evaluation for fresh in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) cycles: a systematic review
Authors: Nicoli Alessia , Palomba Stefano , Capodanno Francesco , Fini Maria , Falbo Angela , La Sala Giovanni Battista 
Published: September 2013

Abstract
The current systematic review was aimed to assess the effectiveness of the zygote morphology evaluation in fresh in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) cycles. All available studies reporting on zygote morphology and clinical and/or biological outcomes were analyzed. Forty studies were included in the final analysis. Fourteen different zygote scoring systems were employed. Zygote morphology correlated significantly with embryo quality and cleavage, blastocyst stage, embryonic chromosome status, in a high proportion of the studies which assessed the specific outcome [15/25 (60%), 15/20 (75%), 7/8 (87.5%), 6/6 (100%), respectively]. On the other hand, only a reduced proportion of papers showed a statistically significant relationship between implantation, pregnancy and delivery/live-birth rates and zygote morphology score [12/23 (52.2%), 12/25 (48%), 1/4 (25%), respectively]. In conclusion, our findings demonstrate the lack of conclusive data on the clinical efficacy of the zygote morphology evaluation in fresh IVF/ICSI cycles, even if biological results showing a good relationship with embryo viability suggest a role in cycles in which the transfer/freezing is performed at day 1.
Renal replacement therapy with net fluid removal lowers intra-abdominal pressure and volumetric indices in critically ill patients
Authors: De laet Inneke , Deeren Dries , Schoonheydt Karen , Van Regenmortel Niels , Dits Hilde , Malbrain Manu LNG 
Published: September 2013

Abstract

Background
Little is known about the effects of renal replacement therapy (RRT) with fluid removal on intra-abdominal pressure (IAP). The global end-diastolic volume index (GEDVI) and extravascular lung water index (EVLWI) can easily be measured bedside by transpulmonary thermodilution (TPTD). The aim of this study is to evaluate the changes in IAP, GEDVI and EVLWI in critically ill patients receiving slow extended daily dialysis (SLEDD) or continuous venovenous haemofiltration (CVVH) with the intention of net fluid removal.

Methods
We performed a retrospective cohort study in ICU patients who were treated with SLEDD or CVVH and in whom IAP was also measured, and RRT sessions were excluded when the dose of vasoactive medication needed to be changed between the pre- and post-dialysis TPTD measurements and when net fluid loss did not exceed 500 ml. The TPTD measurements were performed within 2 h before and after SLEDD; in case of CVVH, before and after an interval of 12 h.

Results
We studied 25 consecutive dialysis sessions in nine patients with acute renal failure and cardiogenic or non-cardiogenic pulmonary oedema. The GEDVI and EVLWI values before dialysis were 877 ml/m² and 14 ml/kg, respectively. Average net ultrafiltration per session was 3.6 l, with a net fluid loss 1.9 l. The GEDVI decreased significantly during dialysis, but not more than 47.8 ml/m² (p = 0.008), as also did the EVLWI with 1 ml/kg (p = 0.03). The IAP decreased significantly from 12 to 10.5 mmHg (p < 0.0001).

Conclusions
Net fluid removal by SLEDD or CVVH in the range observed in this study decreased IAP, GEDVI and EVLWI in critically ill patients although EVLWI reduction was modest.
Cardioprotective effects of adenosine within the border and remote areas of myocardial infarction
Authors: Bousquenaud Mélanie , Maskali Fatiha , Poussier Sylvain , Zangrando Jennifer , Marie Pierre-Yves , Boutley Henri , Fay Renaud , Karcher Gilles , Wagner Daniel R , Devaux Yvan 
Published: September 2013

Abstract

Background
Adenosine may have beneficial effects on left ventricular function after myocardial infarction (MI), but the magnitude of this effect on remote and MI areas is controversial. We assessed the long-term effects of adenosine after MI using electrocardiogram-triggered 18 F-fluorodeoxyglucose positron emission tomography.

Methods
Wistar rats were subjected to coronary ligation and randomized into three groups treated daily for 2 months by NaCl (control; n = 7), 2-chloroadenosine (CADO; n = 8) or CADO with 8-sulfophenyltheophilline, an antagonist of adenosine receptors (8-SPT; n = 8).

Results
After 2 months, control rats exhibited left ventricular remodelling, with increased end-diastolic volume and decreased ejection fraction. Left ventricular remodelling was not significantly inhibited by CADO. Segmental contractility, as assessed by the change in myocardial thickening after 2 months, was improved in CADO rats compared to control rats (+1.6% ± 0.8% vs. −2.3% ± 0.8%, p < 0.001). This improvement was significant in border (+5.6% ± 0.8% vs. +1.5% ± 0.8%, p < 0.001) and remote (−4.0% ± 1.0% vs. −10.4% ± 1.3%, p < 0.001) segments, but absent in MI segments. Histological analyses revealed that CADO reduced fibrosis, cardiomyocyte hypertrophy and apoptosis. Protective effects of CADO were blunted by 8-SPT.

Conclusion
Long-term administration of adenosine protects the left ventricle from contractile dysfunction following MI.
Effect of low-level laser therapy on the expression of inflammatory mediators and on neutrophils and macrophages in acute joint inflammation
Authors: Alves Ana Carolina Araruna , Vieira Rodolfo de Paula , Leal-Junior Ernesto Cesar Pinto , dos Santos Solange Almeida , Ligeiro Ana Paula , Albertini Regiane , Junior Jose Antonio Silva , de Carvalho Paulo de Tarso Camillo 
Published: September 2013

Abstract
Introduction
Inflammation of the synovial membrane plays an important role in the pathophysiology of osteoarthritis (OA). The synovial tissue of patients with initial OA is characterized by infiltration of mononuclear cells and production of proinflammatory cytokines and other mediators of joint injury. The objective was to evaluate the effect of low-level laser therapy (LLLT) operating at 50 mW and 100 mW on joint inflammation in rats induced by papain, through histopathological analysis, differential counts of inflammatory cells (macrophages and neutrophils), as well as gene expression of interleukin 1-beta and 6 (IL-1β and IL-6), and protein expression of tumor necrosis factor alpha (TNFα).

Methods
Male Wistar rats (n = 60) were randomly divided into four groups of 15 animals, namely: a negative control group; an inflammation injury positive control group; a 50 mW LLLT group, subjected to injury and treated with 50 mW LLLT; and a 100 mW LLLT group, subjected to injury and treated with 100 mW LLLT. The animals were subject to joint inflammation (papain solution, 4%) and then treated with LLLT (808 nm, 4 J, 142.4 J/cm2, spot size 0.028 for both groups). On the day of euthanasia, articular lavage was collected and immediately centrifuged; the supernatant was saved for analysis of expression of TNFα protein by enzyme-linked immunosorbent assay and expression of IL-1β and IL-6 mRNA by real-time polymerase chain reaction. A histologic examination of joint tissue was also performed. For the statistical analysis, analysis of variance with Tukey's post-hoc test was used for comparisons between each group. All data are expressed as mean values and standard deviation, with P < 0.05.

Results
Laser treatment with 50 mW was more efficient than 100 mW in reducing cellular inflammation, and decreased the expression of IL-1β and IL-6. However, the 100 mW treatment led to a higher reduction of TNFα compared with the 50 mW treatment.

Conclusions
LLLT with 50 mW was more efficient in modulating inflammatory mediators (IL-1β, IL-6) and inflammatory cells (macrophages and neutrophils), which correlated with the histology that showed a reduction in the inflammatory process.
Predicting persistent inflammatory arthritis amongst early arthritis clinic patients in the UK: is musculoskeletal ultrasound required?
Authors: Pratt Arthur G , Lorenzi Alice R , Wilson Gill , Platt Philip N , Isaacs John D 
Published: September 2013

Abstract
Introduction
Analyses of large clinical datasets from early arthritis cohorts permit the development of algorithms that may be used for outcome prediction in individual patients. The value added by routine use of musculoskeletal ultrasound (MSUS) in an early arthritis setting, as a component of such predictive algorithms, remains to be determined.

Methods
The authors undertook a retrospective analysis of a large, true-to-life, observational inception cohort of early arthritis patients in Newcastle upon Tyne, UK, which included patients with inflammatory arthralgia but no clinically swollen joints. A pragmatic, 10-minute MSUS assessment protocol was developed, and applied to each of these patients at baseline. Logistic regression was used to develop two "risk metrics" that predicted the development of a persistent inflammatory arthritis (PIA), with or without the inclusion of MSUS parameters.

Results
A total of 379 enrolled patients were assigned definitive diagnoses after ≥12 months follow-up (median 28 months), of whom 162 (42%) developed a persistent inflammatory arthritis. A risk metric derived from 12 baseline clinical and serological parameters alone had an excellent discriminatory utility with respect to an outcome of PIA (area under receiver operator characteristic (ROC) curve 0.91; 95% CI 0.88 to 0.94). The discriminatory utility of a similar metric, which incorporated MSUS parameters, was not significantly superior (area under ROC curve 0.91; 95% CI 0.89 to 0.94). Neither did this approach identify an added value of MSUS over the use of routine clinical parameters in an algorithm for discriminating PIA patients whose outcome diagnosis was rheumatoid arthritis (RA).

Conclusions
MSUS use as a routine component of assessment in an early arthritis clinic did not add substantial discriminatory value to a risk metric for predicting PIA.
Induced expression and functional effects of aquaporin-1 in human leukocytes in sepsis
Authors: Vassiliou Alice G , Maniatis Nikolaos A , Orfanos Stylianos E , Mastora Zafeiria , Jahaj Edison , Paparountas Triantafillos , Armaganidis Apostolos , Roussos Charis , Aidinis Vassilis , Kotanidou Anastasia 
Published: September 2013

Abstract
Introduction
Gene expression profiling was performed via DNA microarrays in leukocytes from critically ill trauma patients nonseptic upon admission to the ICU, who subsequently developed either sepsis (n = 2) or severe sepsis and acute respiratory distress syndrome (n = 3). By comparing our results with published expression profiling studies in animal models of sepsis and lung injury, we found aquaporin-1 to be differentially expressed across all studies. Our aim was to determine how the water channel aquaporin-1 is involved in regulating the immune response in critically ill patients during infection acquired in the ICU.

Methods
Following the results of the initial genetic screening study, we prospectively followed aquaporin-1 leukocyte expression patterns in patients with ICU-acquired sepsis who subsequently developed septic shock (n = 16) versus critically ill patients who were discharged without developing sepsis (n = 13). We additionally determined aquaporin-1 expression upon lipopolysaccharide (LPS) exposure and explored functional effects of aquaporin-1 induction in polymorphonuclear granulocytes (PMNs).

Results
Leukocyte aquaporin-1 expression was induced at the onset of sepsis (median 1.71-fold increase; interquartile range: 0.99 to 2.42, P = 0.012 from baseline) and was further increased upon septic shock (median 3.00-fold increase; interquartile range: 1.20 to 5.40, P = 0.023 from sepsis, Wilcoxon signed-rank test); no difference was observed between baseline and discharge in patients who did not develop sepsis. Stimulation of PMNs by LPS led to increased expression of aquaporin-1 in vitro, which could be abrogated by the NF-κB inhibitor EF-24. PMN hypotonic challenge resulted in a transient increase of the relative cell volume, which returned to baseline after 600 seconds, while incubation in the presence of LPS resulted in persistently increased cell volume. The latter could be abolished by blocking aquaporin-1 with mercury and restored by incubation in β-mercaptoethanol, which abrogated the action of mercury inhibition.

Conclusions
Aquaporin-1 is induced in leukocytes of patients with ICU-acquired sepsis and exhibits higher expression in septic shock. This phenomenon may be due to LPS-triggered NF-κB activation that can also lead to alterations in plasma membrane permeability.