bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6
Authors: Saski Christopher A , Feltus Frank A , Staton Margaret E , Blackmon Barbara P , Ficklin Stephen P , Kuhn David N , Schnell Raymond J , Shapiro Howard , Motamayor Juan Carlos 
Published: August 2011

AbstractBackgroundThe fermented dried seeds ofTheobroma cacao(cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robustT. cacaocultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected.ResultsHere, we describe the construction of a BAC-based integrated genetic-physical map of theT. cacaocultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size ofT. cacaois 374.6 Mbp. A comparative analysis withA. thaliana, V. vinifera, andP. trichocarpasuggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the twoT. cacaocultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed.ConclusionsThe results presented in this study are a stand-alone resource for functional exploitation and enhancement ofTheobroma cacaobut are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of theT. cacaogenome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.
A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog
Authors: Nicholas Thomas J , Baker Carl , Eichler Evan E , Akey Joshua M 
Published: August 2011

AbstractBackgroundStructural variation contributes to the rich genetic and phenotypic diversity of the modern domestic dog,Canis lupus familiaris, although compared to other organisms, catalogs of canine copy number variants (CNVs) are poorly defined. To this end, we developed a customized high-density tiling array across the canine genome and used it to discover CNVs in nine genetically diverse dogs and a gray wolf.ResultsIn total, we identified 403 CNVs that overlap 401 genes, which are enriched for defense/immunity, oxidoreductase, protease, receptor, signaling molecule and transporter genes. Furthermore, we performed detailed comparisons between CNVs located within versus outside of segmental duplications (SDs) and find that CNVs in SDs are enriched for gene content and complexity. Finally, we compiled all known dog CNV regions and genotyped them with a custom aCGH chip in 61 dogs from 12 diverse breeds. These data allowed us to perform the first population genetics analysis of canine structural variation and identify CNVs that potentially contribute to breed specific traits.ConclusionsOur comprehensive analysis of canine CNVs will be an important resource in genetically dissecting canine phenotypic and behavioral variation.
An evaluation of ciprofloxacin pharmacokinetics in critically ill patients undergoing continuous veno-venous haemodiafiltration
Authors: Spooner Almath M , Deegan Catherine , D'Arcy Deirdre M , Gowing Caitriona M , Donnelly Maria B , Corrigan Owen I 
Published: August 2011

AbstractBackgroundThe study aimed to investigate the pharmacokinetics of intravenous ciprofloxacin and the adequacy of 400 mg every 12 hours in critically ill Intensive Care Unit (ICU) patients on continuous veno-venous haemodiafiltration (CVVHDF) with particular reference to the effect of achieved flow rates on drug clearance.MethodsThis was an open prospective study conducted in the intensive care unit and research unit of a university teaching hospital. The study population was seven critically ill patients with sepsis requiring CVVHDF.Blood and ultrafiltrate samples were collected and assayed for ciprofloxacin by High Performance Liquid Chromatography (HPLC) to calculate the model independent pharmacokinetic parameters; total body clearance (TBC), half-life (t1/2) and volume of distribution (Vd). CVVHDF was performed at prescribed dialysate rates of 1 or 2 L/hr and ultrafiltration rate of 2 L/hr. The blood flow rate was 200 ml/min, achieved using a Gambro blood pump and Hospal AN69HF haemofilter.ResultsSeventeen profiles were obtained. CVVHDF resulted in a median ciprofloxacin t1/2of 13.8 (range 5.15-39.4) hr, median TBC of 9.90 (range 3.10-13.2) L/hr, a median Vdssof 125 (range 79.5-554) L, a CVVHDF clearance of 2.47+/-0.29 L/hr and a clearance of creatinine (Clcr) of 2.66+/-0.25 L/hr. Thus CVVHDF, at an average flow rate of ~3.5 L/hr, was responsible for removing 26% of ciprofloxacin cleared. At the dose rate of 400 mg every 12 hr, the median estimated Cpmax/MIC and AUC0-24/MIC ratios were 10.3 and 161 respectively (for a MIC of 0.5 mg/L) and exceed the proposed criteria of >10 for Cpmax/MIC and > 100 for AUC0-24/MIC. There was a suggestion towards increased ciprofloxacin clearance by CVVHDF with increasing effluent flow rate.ConclusionsGiven the growing microbial resistance to ciprofloxacin our results suggest that a dose rate of 400 mg every 12 hr, may be necessary to achieve the desired pharmacokinetic - pharmacodynamic (PK-PD) goals in patients on CVVHDF, however an extended interval may be required if there is concomitant hepatic impairment. A correlation between ciprofloxacin clearance due to CVVHDF and creatinine clearance by the filter was observed (r2= 0.76), providing a useful clinical surrogate marker for ciprofloxacin clearance within the range studied.Trial RegistrationCurrent Controlled TrialsISRCTN52722850
Incorporation of n-3 PUFA and γ-linolenic acid in blood lipids and red blood cell lipids together with their influence on disease activity in patients with chronic inflammatory arthritis - a randomized controlled human intervention trial
Authors: Dawczynski Christine , Hackermeier Ursula , Viehweger Martin , Stange Rainer , Springer Monika , Jahreis Gerhard 
Published: August 2011

Abstract

Background and aim
Marine n-3 fatty acids and γ-linolenic acid both have anti-inflammatory effects and may be useful to help treat inflammatory diseases. The effects of these alone or combined were examined in patients with arthritis in a randomized controlled trial.

Design
Patients with rheumatoid arthritis or psoriatic arthritis were randomized into four groups in a double-blind, placebo-controlled parallel designed study. Patients received the respective capsules (1: 3.0 g n-3 LC-PUFA/d; 2: 3.2 g γ-linolenic acid/d; 3: 1.6 g n-3 LC-PUFA + 1.8 g γ-linolenic acid/d; 4: 3.0 g olive oil) for a twelve week period. Clinical status was evaluated and blood samples were taken at the beginning and at the end of the period. Differences before and after intervention were tested with paired t-test or with Wilcoxon test for non-normal data distribution.

Results
60 patients (54 rheumatoid arthritis, 6 psoriatic arthritis) were randomised, 47 finished per protocol. In group 1, the ratio of arachidonic acid (AA)/eicosapentaenoic acid (EPA) decreased from 6.5 ± 3.7 to 2.7 ± 2.1 in plasma lipids and from 25.1 ± 10.1 to 7.2 ± 4.7 in erythrocyte membranes (p ≤ 0.001). There was no significant influence on AA/EPA ratio due to interventions in group 2-4. In group 2, the intake of γ-linolenic acid resulted in a strong rise of γ-linolenic acid and dihomo-γ-linolenic acid concentrations in plasma lipids, cholesteryl esters, and erythrocyte membranes. The combination of n-3 LC-PUFA and γ-linolenic acid (group 3) led to an increase of γ-linolenic acid and dihomo-γ-linolenic acid concentrations in plasma lipids, cholesteryl esters, and erythrocyte mem-branes. This increase was only half of that in group 2.

Conclusions
Incorporation of eicosanoid precursor FAs was influenced by an intake of n-3 LC-PUFA and γ-linolenic acid suggesting a possible benefit for therapy of chronic inflammatory diseases.

Trial Registration
ClinicalTrials NCT01179971
Accumulation and aberrant composition of cholesteryl esters in Scrapie-infected N2a cells and C57BL/6 mouse brains
Authors: Vascellari Sarah , Banni Sebastiano , Vacca Claudia , Vetrugno Vito , Cardone Franco , Di Bari Michele A , La Colla Paolo , Pani Alessandra 
Published: August 2011

Abstract

Objective
Cholesterol changes have been described in prion-cell models and in experimental rodent scrapie; yet, the pattern of this association is still controversial.

Methods
To shed light on the matter, we analysed and compared cholesterol variations in ScN2a cells and in brains of Scrapie-infected C57Bl/6 mice, using two different methods: a fluorimetric-enzymatic cholesterol assay, and high performance liquid chromatography-mass spectroscopy (HPLC-MS).

Results
Compared to uninfected controls, similar cholesterol metabolism anomalies were observed in infected cells and brains by both methods; however, only HPLC-MS revealed statistically significant cholesterol variations, particularly in the cholesteryl esters (CE) fraction. HPLC-MS analyses also revealed different fatty acid composition of the CE fraction in cells and brains. In N2a cells, their profile reflected that of serum, while in normal brains cholesteryl-linoleate only was found at detectable levels. Following prion infection, most CE species were increased in the CE pool of ScN2a cells, whereas a conspicuous amount of cholesteryl-arachidonate only was found to contribute to the cerebral increase of CE. Of interest, oral pravastatin administration to Scrapie-infected mice, was associated with a significant reduction of cerebral free cholesterol (FC) along with a concomitant further increase of the CE pool, which included increased amounts of both cholesteryl-linoleate and cholesteryl-arachidonate.

Conclusion
Although mechanistic studies are needed to establish the pathophysiological relevance of changes in cerebral CE concentrations, to the best of our knowledge this is the first report to provide evidence of increased cholesterol esterification in brains of prion-infected mice, untreated and treated with pravastatin.
The laval questionnaire: a new instrument to measure quality of life in morbid obesity
Authors: Therrien Fanny , Marceau Picard , Turgeon Nathalie , Biron Simon , Richard Denis , Lacasse Yves 
Published: August 2011

Abstract

Background
Our recent review of the literature uncovered eleven obesity-specific quality of life questionnaires, all with incomplete demonstration of their measurement properties. Our objective was to validate a new self-administered questionnaire specific to morbid obesity to be used in clinical trials. The study was carried out at the bariatric surgery clinic of Laval Hospital, Quebec City, Canada.

Methods
This study followed our description of health-related quality of life in morbid obesity from which we constructed the Laval Questionnaire. Its construct validity and responsiveness were tested by comparing the baseline and changes at 1-year follow-up in 6 domain scores (symptoms, activity/mobility, personal hygiene/clothing, emotions, social interactions, sexual life) with those of questionnaires measuring related constructs (SF-36, Impact of Weight on Quality of Life-Lite, Rosenberg Self-Esteem Scale and Beck Depression Inventory-II).

Results
112 patients (67 who got bariatric surgery, 45 who remained on the waiting list during the study period) participated in this study. The analysis of the discriminative function of the questionnaire showed moderate-to-high correlations between the scores in each domain of our instrument and the corresponding questionnaires. The analysis of its evaluative function showed (1) significant differences in score changes between patients with bariatric surgery and those without, and (2) moderate-to-high correlations between the changes in scores in the new instrument and the changes in the corresponding questionnaires. Most of these correlations met the a priori predictions we had made regarding their direction and magnitude.

Conclusion
The Laval Questionnaire is a valid measure of health-related quality of life in patients with morbid obesity and is responsive to treatment-induced changes.
Yolk sac tumor in a patient with transverse testicular ectopia
Authors: Zhu Yi-Ping , Zhang Shi-Lin , Ye Ding-Wei , Shi Guo-hai , Xiao Wen-jun 
Published: August 2011

Abstract
Transverse testicular ectopia (TTE) is a rare anomaly in which both testes descend through a single inguinal canal. We report a case of yolk sac tumor in the ectopic testis of a patient with TTE. A 24-year-old man presented to our hospital with a left inguinal-mass, right cryptorchidism and elevated alpha-fetoprotein (AFP). A left herniotomy 3 years earlier demonstrated both testes in the left scrotum, one above another positionally. Four months ago, a left scrotal mass appeared and radical orchiectomy of both testes revealed testicular yolk sac tumor of the ectopic testis. An enlarging left inguinal-mass appeared 2 months ago and he was referred to our hospital. Laboratory data showed an elevation of AFP (245.5 ng/ml) and a 46 XY karyotype. He underwent bilateral retroperitoneal lymph node dissection and simultaneous left inguinal mass dissection. Histopathologic examination revealed a diagnosis of recurrent yolk sac tumor in the left inguinal mass. The retroperitoneal lymph node was not enlarged and, on histopathology, was not involved. The patient has now been followed up for 8 months without evidence of biochemical or radiological recurrence.
Performance of the Tariff Method: validation of a simple additive algorithm for analysis of verbal autopsies
Authors: James Spencer L , Flaxman Abraham D , Murray Christopher JL 
Published: August 2011

Abstract

Background
Verbal autopsies provide valuable information for studying mortality patterns in populations that lack reliable vital registration data. Methods for transforming verbal autopsy results into meaningful information for health workers and policymakers, however, are often costly or complicated to use. We present a simple additive algorithm, the Tariff Method (termed Tariff), which can be used for assigning individual cause of death and for determining cause-specific mortality fractions (CSMFs) from verbal autopsy data.

Methods
Tariff calculates a score, or "tariff," for each cause, for each sign/symptom, across a pool of validated verbal autopsy data. The tariffs are summed for a given response pattern in a verbal autopsy, and this sum (score) provides the basis for predicting the cause of death in a dataset. We implemented this algorithm and evaluated the method's predictive ability, both in terms of chance-corrected concordance at the individual cause assignment level and in terms of CSMF accuracy at the population level. The analysis was conducted separately for adult, child, and neonatal verbal autopsies across 500 pairs of train-test validation verbal autopsy data.

Results
Tariff is capable of outperforming physician-certified verbal autopsy in most cases. In terms of chance-corrected concordance, the method achieves 44.5% in adults, 39% in children, and 23.9% in neonates. CSMF accuracy was 0.745 in adults, 0.709 in children, and 0.679 in neonates.

Conclusions
Verbal autopsies can be an efficient means of obtaining cause of death data, and Tariff provides an intuitive, reliable method for generating individual cause assignment and CSMFs. The method is transparent and flexible and can be readily implemented by users without training in statistics or computer science.
Phonologically-based biomarkers for major depressive disorder
Authors: Trevino Andrea Carolina , Quatieri Thomas Francis , Malyska Nicolas 
Published: August 2011

Abstract
Of increasing importance in the civilian and military population is the recognition of major depressive disorder at its earliest stages and intervention before the onset of severe symptoms. Toward the goal of more effective monitoring of depression severity, we introduce vocal biomarkers that are derived automatically from phonologically-based measures of speech rate. To assess our measures, we use a 35-speaker free-response speech database of subjects treated for depression over a 6-week duration. We find that dissecting average measures of speech rate into phone-specific characteristics and, in particular, combined phone-duration measures uncovers stronger relationships between speech rate and depression severity than global measures previously reported for a speech-rate biomarker. Results of this study are supported by correlation of our measures with depression severity and classification of depression state with these vocal measures. Our approach provides a general framework for analyzing individual symptom categories through phonological units, and supports the premise that speaking rate can be an indicator of psychomotor retardation severity.
Enhanced Inhibitory Synaptic Transmission in the Spinal Dorsal Horn Mediates Antinociceptive Effects of TC-2559
Authors: Cheng Long-Zhen , Han Lei , Fan Jing , Huang Lan-Ting , Peng Li-Chao , Wang Yun 
Published: August 2011

Background: TC-2559 is a selective α4β2 subtype of nicotinic acetylcholine receptor (nAChR) partial agonist and α4β2 nAChR activation has been related to antinociception. The aim of this study is to investigate the analgesic effect of TC-2559 and its underlying spinal mechanisms. Results: 1) In vivo bioavailability study: TC-2559 (3 mg/kg) had high absorption rate in rats with maximal total brair concentration reached over 4.6 μM within first 15 min after administration and eliminated rapidly with brain half life of about 20 min after injection. 2) In vivo behavioral experiments: TC-2559 exerts dose dependent antinociceptive effects in both formalin test in mice and chronic constriction injury (CCI) model in rats by activation of α4β2 nAChRs; 3) Whole-cell patch-clamp studies in the superficial dorsal horn neurons of the spinal cord slices: perfusion of TC-2559 (2 μM) significantly increased the frequency, but not amplitude of spontaneous inhibitory postsynaptic currents (sIPSCs). The enhancement of sIPSCs was blocked by pre-application of DHpE (2 μM), a selective α4β2 nicotinic receptor antagonist. Neither the frequency nor the amplitude of spontaneous excitatory postsynaptic currents (sEPSCs) of spinal dorsal horn neurons were affected by TC-2559. Conclusions: Enhancement of inhibitory synaptic transmission in the spinal dorsal horn via activation of α4β2 nAChRs may be one of the mechanisms of the antinociceptive effects of TC-2559 on pathological pain models. It provides further evidence to support the notion that selective α4β2 subtype nAChR agonist may be developed as new analgesic drug for the treatment of neuropathic pain.
Accumulation of Kv7.2 Channels in Putative Ectopic Transduction Zones of Mice Nerve-End Neuromas
Authors: Roza Carolina , Castillejo Sol , Lopez-García Jose A 
Published: August 2011

Background: Modulation of M-type currents has been proposed as a new strategy for the treatment of neuropathic pain due to their role in regulating neuronal excitability. Using electrophysiological techniques we showed previously that the opening of Kv7 channels with retigabine, blocked ectopic discharges from axotomized fibers but did not alter transduction at intact skin afferents. We hypothesized that after nerve damage, accumulation of Kv7 channels in afferent fibers may increase M-type currents which then acquired a more important role at regulating fiber excitability. Findings: In this study, we used an immunohistochemical approach to examine patterns of expression of Kv7.2 channels in afferent fibers after axotomy and compared them to patterns of expression of voltage gated Na+ channels (Nav) which are key electrogenic elements in peripheral axons known to accumulate in experimental and human neuromas. Axotomy induced an enlargement and narrowing of the nodes of Ranvier at the proximal end of the neuroma together with a dramatic demyelination and loss of structure at its distal end in which naked accumulations of Nav were present. In addition, axotomy also induced accumulations of Kv7.2 that co-localized with those of Nav channels. Conclusions: Whilst Nav channels are mandatory for initiation of action potentials, (i.e. responsible for the generation/propagation of ectopic discharges) an increased accumulation of Kv7.2 channels after axotomy may represent a homeostatic compensation to over excitability in axotomized fibers, opening a window for a peripheral action of M-current modulators under conditions of neuropathy.
Cellular Prion Protein Protects from Inflammatory and Neuropathic Pain
Authors: Gadotti Vinicius M , Zamponi Gerald W 
Published: August 2011

Cellular prion protein (PrPC) inhibits N-Methyl- D-Aspartate (NMDA) receptors. Since NMDA receptors play an important role in the transmission of pain signals in the dorsal horn of spinal cord, we thus wanted to determine if PrPC null mice show a reduced threshold for various pain behaviours. We compared nociceptive thresholds between wild type and PrPC null mice in models of inflammatory and neuropathic pain, in the presence and the absence of a NMDA receptor antagonist. 2-3 months old male PrPC null mice exhibited an MK-801 sensitive decrease in the paw withdrawal threshold in response both mechanical and thermal stimuli. PrPC null mice also exhibited significantly longer licking/biting time during both the first and second phases of formalin-induced inflammation of the paw, which was again prevented by treatment of the mice with MK-801, and responded more strongly to glutamate injection into the paw. Compared to wild type animals, PrPC null mice also exhibited a significantly greater nociceptive response (licking/biting) after intrathecal injection of NMDA. Sciatic nerve ligation resulted in MK-801 sensitive neuropathic pain in wild-type mice, but did not further augment the basal increase in pain behaviour observed in the null mice, suggesting that mice lacking PrPC may already be in a state of tonic central sensitization. Altogether, our data indicate that PrPC exerts a critical role in modulating nociceptive transmission at the spinal cord level, and fit with the concept of NMDA receptor hyperfunction in the absence of PrPC.