bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and optimization of quantitative PCR for the diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid
Authors: Khot Prasanna D , Ko Daisy L , Hackman Robert C , Fredricks David N 
Published: May 2008

Abstract

Background
The diagnosis of invasive pulmonary aspergillosis (IPA) remains challenging. Culture and histopathological examination of bronchoalveolar lavage (BAL) fluid are useful but have suboptimal sensitivity and in the case of culture may require several days for fungal growth to be evident. Detection of Aspergillus DNA in BAL fluid by quantitative PCR (qPCR) offers the potential for earlier diagnosis and higher sensitivity. It is important to adopt quality control measures in PCR assays to address false positives and negatives which can hinder accurate evaluation of diagnostic performance.

Methods
BAL fluid from 94 episodes of pneumonia in 81 patients was analyzed. Thirteen episodes were categorized as proven or probable IPA using Mycoses Study Group criteria. The pellet and the supernatant fractions of the BAL were separately assayed. A successful extraction was confirmed with a human 18S rRNA gene qPCR. Inhibition in each qPCR was measured using an exogenous DNA based internal amplification control (IAC). The presence of DNA from pathogens in the Aspergillus genus was detected using qPCR targeting fungal 18S rRNA gene.

Results
Human 18S rRNA gene qPCR confirmed successful DNA extraction of all samples. IAC detected some degree of initial inhibition in 11 samples. When culture was used to diagnose IPA, the sensitivity and specificity were 84.5% and 100% respectively. Receiver-operating characteristic analysis of qPCR showed that a cutoff of 13 fg of Aspergillus genomic DNA generated a sensitivity, specificity, positive and negative predictive value of 77%, 88%, 50%, 96% respectively. BAL pellet and supernatant analyzed together resulted in sensitivity and specificity similar to BAL pellet alone. Some patients did not meet standard criteria for IPA, but had consistently high levels of Aspergillus DNA in BAL fluid by qPCR.

Conclusion
The Aspergillus qPCR assay detected Aspergillus DNA in 76.9% of subjects with proven or probable IPA when the concentrated BAL fluid pellet fraction was used for diagnosis. There was no benefit from analyzing the BAL supernatant fraction. Use of both extraction and amplification controls provided optimal quality control for interpreting qPCR results and therefore may increase our understanding of the true potential of qPCR for the diagnosis of IPA.
Acute pancreatitis and subdural haematoma in a patient with severe falciparum malaria: Case report and review of literature
Authors: Seshadri Pratibha , Dev Anand Vimal , Viggeswarpu Surekha , Sathyendra Sowmya , Peter John Victor 
Published: May 2008

Abstract

Plasmodium falciparum infection is known to be associated with a spectrum of systemic complications ranging from mild and self-limiting to life-threatening. This case report illustrates a patient who had a protracted course in hospital due to several rare complications of falciparum malaria. A 21-year old man presented with a five-day history of high-grade fever, jaundice and abdominal pain and a two-day history of altered conscious state. A diagnosis of severe falciparum malaria was made based on the clinical presentation and a positive blood smear with parasitaemia of 45%. Despite adequate anti-malarial therapy with artesunate, the patient had persistent and worsening abdominal pain. Investigations suggested a diagnosis of acute pancreatitis, a rare association with falciparum malaria. However, in spite of supportive therapy for acute pancreatitis and a 10-day course of intravenous artesunate and oral doxycycline at recommended doses, he continued to be febrile with peripheral blood smear showing persistence of ring forms. Antimalarial therapy was, therefore, changed to quinine on the suspicion of possible artesunate resistance. On the 17th day of stay in hospital, the patient developed generalized tonic-clonic seizures. Computerized tomography of the brain showed bilateral fronto-parietal subdural haematomas that were surgically drained. His fever persisted beyond 30-days despite broad-spectrum antibiotics, quinine therapy and negative malarial smears. A possibility of drug fever was considered and all drugs were ceased. He subsequently became afebrile and was discharged on the 38th hospital admission day. Recognition of complications and appropriate management at each stage facilitated successful outcome. This report has been presented to highlight the occurrence of several rare complications of falciparum malaria in the same patient.
The elusive link between high sensitivity C-reactive protein and carotid subclinical atherosclerosis in coronary artery bypass grafting candidates: A cross-sectional study
Authors: Shakouri Parvin , Nezami Nariman , Tarzamni Mohammad Kazem , Rashid Reza Javad 
Published: May 2008

Abstract

Background
Previous studies demonstrated a modest association between C-Reactive Protein (CRP), stenosis of carotid artery, and carotid Intima-Media Thickness (IMT) in general population. During present study, we aimed to evaluate the relationship between High Sensitivity C-Reactive Protein (hsCRP) and Common Carotid Intima-Media Thickness (CCIMT) in patients who candidate for Coronary Artery Bypass Grafting (CABG).

Methods
The study subjects were enrolled from patients with coronary arteries disease referred from Shahid Madani Hospital (Tabriz, Iran), who have been candidate for elective CABG from January 2005 to August 2007. The common carotid arteries were evaluated with high-resolution B-mode ultrasonography using a 7.5- MHz linear-array transducer to determine the IMT and grade of stenosis. Serum hsCRP level was measured using commercially available enzyme linked immunosorbent assay kit.

Results
Finally, information of 176 CABG candidates was analysed. The mean age of participants was 62.71 ± 9.45 years with 1.63 male to female ratio. The mean of CCIMT was 0.69 ± 0.54 mm. Although there was no significant correlation between serum hsCRP level and CCIMT in patients without carotid stenosis (p=0.113, r=0.186), participants with common carotid artery stenosis had higher levels of serum hsCRP than participants without stenosis (2.42+/-1.30 vs. 1.20+/-0.97 mg/dl; p=0.009).

Conclusion
Study results showed that there was no correlation between serum hsCRP level and CCIMT in patients without carotid stenosis, but patients with common carotid artery stenosis had higher levels of serum hsCRP than patients without stenosis.
Nef does not contribute to replication differences between R5 pre-AIDS and AIDS HIV-1 clones from patient ACH142
Authors: Olivieri Kevin C , Scoggins Robert M , Broderick Brooks , Powell Maria LC , Alexander Melissa A , Hammarskjöld Marie-Louise , Rekosh David , Camerini David 
Published: May 2008

Abstract
AIDS-associated, CCR5-tropic (R5) HIV-1 clones, isolated from a patient that never developed CXCR4-tropic HIV-1, replicate to a greater extent and cause greater cytopathic effects than R5 HIV-1 clones isolated before the onset of AIDS. Previously, we showed that HIV-1 Env substantially contributed to the enhanced replication of an AIDS clone. In order to determine if Nef makes a similar contribution, we cloned and phenotypically analyzed nef genes from a series of patient ACH142 derived R5 HIV-1 clones. The AIDS-associated Nef contains a series of residues found in Nef proteins from progressors [1]. In contrast to other reports [1–3], this AIDS-associated Nef downmodulated MHC-I to a greater extent and CD4 less than pre-AIDS Nef proteins. Additionally, all Nef proteins enhanced infectivity similarly in a single round of replication. Combined with our previous study, these data show that evolution of the HIV-1 env gene, but not the nef gene, within patient ACH142 significantly contributed to the enhanced replication and cytopathic effects of the AIDS-associated R5 HIV-1 clone.
An optimized high-performance liquid chromatography (HPLC) method for benzoylmesaconine determination in Radix Aconiti Lateralis Preparata (Fuzi, aconite roots) and its products
Authors: Xie Ying , Zhou Hua , Wong Yuen Fan , Liu Zhongqiu , Xu Hongxi , Jiang Zhihong , Liu Liang 
Published: May 2008

Abstract

Background
Benzoylmesaconine (BMA) is the main Aconitum alkaloid in Radix Aconiti Lateralis Preparata (Fuzi, aconite roots) with potent pharmacological activities, such as analgesia and anti-inflammation. The present study developed a simple and reliable method using BMA as a marker compound for the quality control of processed aconite roots and their products.

Methods
After extraction, a high-performance liquid chromatography (HPLC) determination of BMA was conducted on a RP-C18 column by gradient elution with acetonitrile and aqueous phase, containing 0.1% phosphoric acid adjusted with triethylamine to pH 3.0.

Results
A distinct peak profile was obtained and separation of BMA was achieved. Method validation showed that the relative standard deviations (RSDs) of the precision of BMA in all intra-day and inter-day assays were less than 1.36%, and that the average recovery rate was 96.95%. Quantitative analysis of BMA showed that the content of BMA varied significantly in processed aconite roots and their products.

Conclusion
This HPLC method using BMA as a marker compound is applicable to the quality control of processed aconite roots and their products.
Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
Authors: Tomazou Eleni M , Rakyan Vardhman K , Lefebvre Gregory , Andrews Robert , Ellis Peter , Jackson David K , Langford Cordelia , Francis Matthew D , Bäckdahl Liselotte , Miretti Marcos , Coggill Penny , Ottaviani Diego , Sheer Denise , Murrell Adele , Beck Stephan 
Published: May 2008

Abstract

Background
The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome.

Methods
To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls.

Results
Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation.

Conclusion
A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.
Conditioning response to granulocyte colony-stimulating factor via the dipeptidyl peptidase IV-adenosine deaminase complex
Authors: Focosi Daniele , Kast Richard Eric , Galimberti Sara , Petrini Mario 
Published: May 2008

AbstractG-CSF is routinely used to mobilize hematopoietic stem cells (HSCs) from bone marrow (BM) into peripheral blood before aphaeresis, but HSC harvesting can be suboptimal. On the other hand, transplanted HSCs sometimes fail to engraft a recipient BM microenvironment when G-CSF is used after transplantation, as pushing-CSF will push HSCs away from marrow. So, G-CSF action needs to be potentiated by other drugs. Marrow stromal cells establish a local CXCL12 concentration gradient that is the primary homing signal for HSCs. Pharmacological interventions that modify this gradient, therefore, have potential to help HSC mobilization (by decreasing CXCL12) and engraftment (by increasing CXCL12). CXCL12 inactivation is primarily mediated by dipeptidyl peptidase-IV. We review here the currently available drugs affecting this enzyme that could be used in the clinic to achieve phase-specific help for G-CSF.
Separate endocytic pathways regulate IL-5 receptor internalization and signaling
Authors: Lei Jonathan T , Martinez-Moczygemba Margarita 
Published: May 2008

AbstractEosinophils are critically dependent on IL-5 for their activation, differentiation, survival, and augmentation of cytotoxic activity. We previously showed that the cytoplasmic domain of the hematopoietic receptor, βc, which is shared by IL-5, IL-3, and GM-CSF, is directly ubiquitinated and degraded by the proteasomes in a JAK2-dependent manner. However, studies describing the spatial distribution, endocytic regulation, and trafficking of βc-sharing receptors in human eosinophils are currently lacking. Using deconvolution microscopy and biochemical methods, we clearly demonstrate that IL-5Rs reside in and are internalized by clathrin- and lipid raft-dependent endocytic pathways. Microscopy analyses in TF1 cells and human eosinophils revealed significant colocalization of βc, IL-5Rα, and Cy3-labeled IL-5 with transferrin- (clathrin) and cholera toxin-B- (lipid raft) positive vesicles. Moreover, whereas internalized IL-5Rs were detected in both clathrin- and lipid raft-positive vesicles, biochemical data revealed that tyrosine phosphorylated, ubiquitinated, and proteasome-degraded IL-5Rs partitioned to the soluble, nonraft fractions (clathrin-containing). Lastly, we show that optimal IL-5-induced signaling requires entry of activated IL-5Rs into the intracellular compartment, as coimmunoprecipitation of key signaling molecules with the IL-5R was completely blocked when either endocytic pathway was inhibited. These data provide the first evidence that IL-5Rs segregate and traffic into two distinct plasma membrane compartments, and they further establish that IL-5R endocytosis regulates signaling both positively and negatively.
Delays in discharging elderly psychiatric in-patients
Authors: Hanif Irfan , Rathod Bhupendra 
Published: May 2008

Aims and MethodThe issue of elderly psychiatric patients remaining in hospitals after being declared medically fit is of concern to doctors, hospital managers and politicians alike. This article sets out the findings from a study involving elderly psychiatric patients at a district general hospital, undertaken to establish the actual lengths, reasons for and financial implications of delays in discharge. The study involved 50 in-patients, all of whom had been discharged over the 3-month study period.ResultsMore than half of the patients in the sample were subject to some delay in discharge and for patients waiting for Elderly Mentally Infirm (EMI) placements this averaged 50 days. Collectively, nearly 25% of the time spent in hospital was due to delay. The cost to the hospital was estimated at more than £700 000 in 1 year.Clinical ImplicationsPatients are being put at extra risk in terms of their health by being delayed in hospital. Issues of institutionalisation, nosocomial infections and falls are of primary concern.
Comparative survey of comorbidities in people with learning disability with and without epilepsy
Authors: Pawar Deepak G. , Akuffo Emmanuel O. 
Published: May 2008

Aims and MethodTo ascertain the prevalence of epilepsy and understand the differences in the comorbidities of non-epileptic and epileptic patients with learning disabilities. A simple comparative survey was undertaken between the two main groups of patients: non-epileptic and epileptic.ResultsThe prevalence of epilepsy in the study group was 30%. A total of 70% of patients with any type of challenging behaviour were in the non-epileptic group compared with 59% in the epileptic group. Depression was the most common diagnosis in both groups, being slightly more in the non-epileptic group.Clinical ImplicationsOur study suggests that there is no association between epilepsy and the prevalence of challenging behaviour of psychiatric conditions within the learning disabilities population.
Evaluation of thyroid-mediated otolith growth of larval and juvenile tilapia
Authors: Shiao Jen-Chieh , Wu Su-Mei , Hwang Yi-Ping , Wu Done-Ping , Hwang Pung-Pung 
Published: May 2008

SUMMARYThyroid-mediated otolith growth in tilapia was evaluated by the ontogenic triiodothyronine (T3) profile revealed by radioimmunoassay during the first month after hatching. Thyroid hormone receptor genes(TRα and TRβ) were cloned and only the expression of TRα mRNA, quantified by real-time PCR, was similar to the T3 profile. Variations in otolith growth showed median correlation with the T3 profile and TRα mRNA expression pattern. Hypothyroidism and hyperthyroidism were induced in tilapia juveniles and larvae by administration of different concentrations of thiourea (TU) and T3, respectively, for 13 days. T3 and TU had little effect on otolith growth during the larval stage. However, T3increased otolith growth and TU retarded, or stopped, otolith growth during the juvenile stage. Furthermore, TU treatment caused permanent changes in otolith shape in the ventral area. Otolith growth recovered slowly from hypothyroidism, requiring 2 days to form an increment during the first week. These results suggest that otolith growth, at least during the juvenile stage,is regulated by the thyroid hormones and the process may be mediated by TRα.
Two-voice complexity from a single side of the syrinx in northern mockingbirdMimus polyglottosvocalizations
Authors: Zollinger Sue Anne , Riede Tobias , Suthers Roderick A. 
Published: May 2008

SUMMARYThe diverse vocal signals of songbirds are produced by highly coordinated motor patterns of syringeal and respiratory muscles. These muscles control separate sound generators on the right and left side of the duplex vocal organ, the syrinx. Whereas most song is under active neural control, there has been a growing interest in a different class of nonlinear vocalizations consisting of frequency jumps, subharmonics, biphonation and deterministic chaos that are also present in the vocal repertoires of many vertebrates,including many birds. These nonlinear phenomena may not require active neural control, depending instead on the intrinsic nonlinear dynamics of the oscillators housed within each side of the syrinx. This study investigates the occurrence of these phenomena in the vocalizations of intact northern mockingbirds Mimus polyglottos. By monitoring respiratory pressure and airflow on each side of the syrinx, we provide the first analysis of the contribution made by each side of the syrinx to the production of nonlinear phenomena and are able to reliably discriminate two-voice vocalizations from potentially similar appearing, unilaterally produced, nonlinear events. We present the first evidence of syringeal lateralization of nonlinear dynamics during bilaterally produced chaotic calls. The occurrence of unilateral nonlinear events was not consistently correlated with fluctuations in air sac pressure or the rate of syringeal airflow. Our data support previous hypotheses for mechanical and acoustic coupling between the two sides of the syrinx. These results help lay a foundation upon which to understand the communicative functions of nonlinear phenomena.
The effects of fasting and cold exposure on metabolic rate and mitochondrial proton leak in liver and skeletal muscle of an amphibian, the cane toad Bufo marinus
Authors: Trzcionka M. , Withers K. W. , Klingenspor M. , Jastroch M. 
Published: May 2008

SUMMARY
Futile cycling of protons across the mitochondrial inner membrane contributes significantly to standard metabolic rate in a variety of ectothermic and endothermic animals, but adaptations of the mitochondrial bioenergetics to different environmental conditions have rarely been studied in ectotherms. Changes in ambient temperature and nutritional status have a great effect on the physiological demands of ectothermic amphibians and may require the adjustment of mitochondrial efficiency. In order to investigate the effect of temperature and nutritional status on the mitochondrial level,we exposed male cane toads to either 10°C or 30°C and fasted half of the animals in each group. Cold exposure resulted in a fourfold reduction of the resting metabolic rate whereas nutritional status had only minor effects. The mitochondrial adjustments to each condition were observed by comparing the proton leak kinetics of isolated liver and skeletal muscle mitochondria at 25°C. In response to cold exposure, liver mitochondria showed a decrease in proton conductance while skeletal muscle mitochondria were unchanged. Additional food deprivation had minor effects in skeletal muscle, but in liver we uncovered surprising differences in energy saving mechanisms between the acclimation temperatures: in warm-acclimated toads, fasting resulted in a decrease of the proton conductance whereas in cold-acclimated toads, the activity of the respiratory chain was reduced. To investigate the molecular mechanism underlying mitochondrial proton leakage, we determined the adenine-nucleotide transporter (ANT) content, which explained tissue-specific differences in the basal proton leak, but neither the ANT nor uncoupling protein (UCP) gene expression correlated with alterations of the proton leak in response to physiological stimuli.
Population origin, development and temperature of development affect the amounts of HSP70, HSP90 and the putative hypoxia-inducible factor in the tadpoles of the common frogRana temporaria
Authors: Nikinmaa Mikko , Leveelahti Lotta , Dahl Emma , Rissanen Eeva , Rytkönen Kalle T. , Laurila Anssi 
Published: May 2008

SUMMARYWe raised Rana temporaria tadpoles from three different populations from southern, mid and northern Sweden (the total north-to-south distance between populations is approximately 1500 km) at two temperatures,and measured the differences in HSP70, HSP90 and putative HIF-1α levels(Rana temporaria HIF-1α was sequenced in the present study)with immunoblotting. The levels of the studied proteins increased with developmental stage. Also, the levels increased with latitude at the lower but not at the higher developmental temperature. This shows that there is a clear difference between the populations at the molecular level but that this difference can be modified by the environmental conditions experienced during development. The proteins analyzed may be involved in the regulation of developmental processes. If this is the case, the tadpoles from the northernmost population have the most advanced complement of regulatory proteins at developmental stages approaching metamorphosis.