BACKGROUND

Collecting and managing information is a challenging task in a genome-wide profiling research project. Most databases and online computational tools require a direct human involvement. Information and computational results are presented in various multimedia formats (e.g., text, image, PDF, word files, etc.), many of which cannot be automatically processed by computers in biologically meaningful ways. In addition, the quality of computational results is far from perfect and requires nontrivial manual examination. The timely selection, integration and interpretation of heterogeneous biological information still heavily rely on the sensibility of biologists. Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information.

METHODS

We developed an information management application called GeneNotes. GeneNotes is the first application that allows users to collect and manage multimedia biological information about genes/ESTs. GeneNotes provides an integrated environment for users to surf the Internet, collect notes for genes/ESTs, and retrieve notes. GeneNotes is supported by a server that integrates gene annotations from many major databases (e.g., HGNC, MGI, etc.). GeneNotes uses the integrated gene annotations to (a) identify genes given various types of gene IDs (e.g., RefSeq ID, GenBank ID, etc.), and (b) provide quick views of genes. GeneNotes is free for academic usage. The program and the tutorials are available at: http://bayes.fas.harvard.edu/genenotes/.

CONCLUSIONS

GeneNotes provides a novel human-computer interface to assist researchers to collect and manage biological information. It also provides a platform for studying how users behave when they manipulate biological information. The results of such study can lead to innovation of more intelligent human-computer interfaces that greatly shorten the cycle of biology research.

OBJECTIVE

Assessment of endothelial dysfunction (ED) in type 2 diabetic patients with coronary artery disease (CAD) and estimation of correlation of ED with metabolic parameters: low HDL, hypertriglyceridemia, obesity, systolic blood pressure and with inflammatory-hemostatic parameters: CRP and fibrinogen.

METHODS

42 patients (age 60.0 +/- 8.5 years) with diagnosed type 2 diabetes and CAD were randomly included in a cross sectional study. B-mode ultrasound system with a linear transducer 7.5 MHz was used for evaluation of flow mediated vasodilation in brachial artery (FMV). FMV was presented as the percentage increase in brachial artery diameter, within 30 s after limb ischemia, previously provoked by cuff inflation. Percentage value up to 10% was defined as ED.

RESULTS

Bivariate linear correlation model presented significant correlation between plasma fibrinogen and FMV percentage, with r -0.47, p < 0.01. Presence of ED correlates linearly with plasma level of HDL < 1.03 mmol/L (r -0.35, p < 0.03). Multivariate analysis using Backward Wald model presented fibrinogen (OR 3.14, 95% CI 0.87-11.28) and low HDL (OR 5.16, 95% CI 0.53-60.39) as factors correlated with the presence of endothelial dysfunction.

CONCLUSIONS

These results presented plasma fibrinogen level and low HDL < 1.03 mmol/L as factors, independently correlated to the presence of endothelial dysfunction in type 2 diabetic patients with coronary artery disease (Tab. 8, Fig. 1, Ref. 25). Full Text (Free, PDF) www.bmj.sk.

Removal of the N-terminal formyl group from newly synthesized proteins by the enzyme peptide deformylase (PDF) is essential for normal growth of bacteria but not higher organisms. Recently, PDF has been explored as a target for novel antibiotics. Screening a collection of natural products for antimicrobial activity identified actinonin and two matlystatin analogs as potent PDF inhibitors. A number of synthetic analogs of these natural products were prepared and their inhibitory potency determined. Previous work has shown that PDF is an iron metalloproteinase also containing a catalytic glutamic acid residue. Ligation of the ferrous cation is an essential feature of potent inhibitors. The structures of actinonin, a matlystatin analog and a synthetic inhibitor complexed with PDF were determined by crystallography. A quantum mechanics/molecular mechanics (QM/MM) method was used to reproduce the geometry of known complexes, to predict the protonation state in the active site and to predict the geometry of additional complexes. The requirement for protonation of the active site glutamate anion is an important factor in understanding the potency of inhibitors with acidic iron-ligating groups such as hydroxamate and carboxylate. Even though potent inhibitors of PDF have been discovered, their bacteriostatic mechanism of action and the rapid development of resistance in vitro may limit their potential as antibacterial drugs.

OBJECTIVE

To provide a detailed and current characterisation of funding of a representative sample clinical trials. We also aimed to develop guidance for standardised reporting of funding information.

METHODS

We addressed the extent to which clinical trials published in 2015 in any of the 119 Core Clinical Journals included a statement on the funding source (eg, whether a not-for-profit organisation was supported by a private-for-profit organisation), type of funding, amount and role of funder. We used a stepwise approach to develop a guidance and an instrument for standardised reporting of funding information.

RESULTS

Of 200 trials, 178 (89%) included a funding statement, of which 171 (96%) reported being funded. Funding statements in the 171 funded trials indicated the source in 100%, amount in 1% and roles of funders in 50%. The most frequent sources were governmental (58%) and private-for-profit (40%). Of 54 funding statements in which the source was a not-for-profit organisation, we found evidence of undisclosed support of those from private-for-profit organisation(s) in 26 (48%). The most frequently reported roles of funders in the 171 funded trials related to study design (42%) and data analysis, interpretation or management (41%). Of 139 randomised controlled trials (RCTs) addressing pharmacological or surgical interventions, 29 (21%) reported information on the supplier of the medication or device. The proposed guidance addresses both the funding information that RCTs should report and the reporting process. Attached to the guidance is a fillable PDF document for use as an instrument for standardised reporting of funding information.

CONCLUSIONS

Although the majority of RCTs report funding, there is considerable variability in the reporting of funding source, amount and roles of funders. A standardised approach to reporting of funding information would address these limitations. Future research should explore the implications of funding by not-for-profit organisations that are supported by for-profit organisations.

Plasma of cattle infected with bovine leukemia virus (BLV) contains a factor, plasma blocking factor (PBF), that inhibits the expression of viral genome in cultured lymphocytes from BLV infected cattle. When platelet lysate was added to this culture, BLV antigen became detectable in the culture and there are some factors (PDF) in platelet lysate which have inhibitory activity against PBF. The PDF was present in platelet from BLV-free cattle as well as BLV-infected cattle at relatively high titer. The effect of platelet lysate against PBF on the expression of BLV genome seemed to be irreversible.

Probabilistic risk assessments are enjoying increasing popularity as a tool to characterize the health hazards associated with exposure to chemicals in the environment. Because probabilistic analyses provide much more information to the risk manager than standard "point" risk estimates, this approach has generally been heralded as one which could significantly improve the conduct of health risk assessments. The primary obstacles to replacing point estimates with probabilistic techniques include a general lack of familiarity with the approach and a lack of regulatory policy and guidance. This paper discusses some of the advantages and disadvantages of the point estimate vs. probabilistic approach. Three case studies are presented which contrast and compare the results of each. The first addresses the risks associated with household exposure to volatile chemicals in tapwater. The second evaluates airborne dioxin emissions which can enter the food-chain. The third illustrates how to derive health-based cleanup levels for dioxin in soil. It is shown that, based on the results of Monte Carlo analyses of probability density functions (PDFs), the point estimate approach required by most regulatory agencies will nearly always overpredict the risk for the 95th percentile person by a factor of up to 5. When the assessment requires consideration of 10 or more exposure variables, the point estimate approach will often predict risks representative of the 99.9th percentile person rather than the 50th or 95th percentile person. This paper recommends a number of data distributions for various exposure variables that we believe are now sufficiently well understood to be used with confidence in most exposure assessments. A list of exposure variables that may require additional research before adequate data distributions can be developed are also discussed.

Peptide deformylase (PDF) catalyses the hydrolytic removal of the N-terminal formyl group from nascent ribosome-synthesised polypeptides. Its activity is essential and it is present in all eubacteria. It is also present in the organelles of some eukaryotes. PDF represents a novel class of mononuclear iron protein, utilising an Fe(2+) ion to catalyse the hydrolysis of an amide bond. Due to its extreme lability, isolation and characterisation of PDF was not possible until very recently. This review will discuss the recent progress in the elucidation of the the structure and function of PDF, evaluating its suitability as a target for antibiotic design and summarising the current approaches to designing drugs that target PDF.

Recently, a compound probability density function (pdf) was proposed to model the envelope of the ultrasonic backscattered echo from tissues. This pdf will allow local and global variations in scattering cross sections and even multiple scattering in tissue. It approximates to the Nakagami, K or Rayleigh distributions under different limiting conditions, thus making it very versatile. In this work, a new parameter associated with compound pdf, speckle factor, has been introduced to characterize the scattering conditions. The usefulness of this parameter for tissue characterization has been explored through computer simulation of ultrasonic A scans and analyses of the data collected from tissue-mimicking phantoms. Results suggest the potential applications of the compound pdf and its parameters in ultrasonic tissue characterization.

Congenital muscle diseases, such as myopathies or dystrophies, occur relatively frequently, with estimated incidences of up to 4.7 per 100 000 newborns. To diagnose congenital diseases in the early stages of pregnancy, and to interpret the results of increasingly advanced in utero imaging techniques, a profound knowledge of normal human morphological development of the locomotor system and the nervous system is necessary. Muscular development, however, is an often neglected topic or is only described in a general way in embryology textbooks and papers. To provide the required detailed and updated comprehensive picture of embryologic muscular anatomy, three-dimensional (3D) reconstructions were created based on serial histological sections of a human embryo at Carnegie stage 23 (8 weeks of development, crown-rump length of 23.8 mm), using Amira reconstruction software. Reconstructed muscles, tendons, bones and nerves were exported in a 3D-PDF file to permit interactive viewing. Almost all adult skeletal muscles of the trunk and limbs could be individually identified in their relative adult position. The pectoralis major muscle was divided in three separate muscle heads. The reconstructions showed remarkable highly developed extraocular, infrahyoid and suprahyoid muscles at this age but surprisingly also absence of the facial muscles that have been described to be present at this stage of development. The overall stage of muscle development suggests heterochrony of skeletal muscle development. Several individual muscle groups were found to be developed earlier and in more detail than described in current literature.

TThe National Toxicology Program (NTP) Center for the Evaluation of Risks to Human Reproduction (CERHR) conducted an evaluation of the potential for di-n-butyl phthalate (DBP) to cause adverse effects on reproduction and development in humans. DBP is one of 7 phthalate chemicals evaluated by the NTP CERHR Phthalates Expert Panel. These phthalates were selected for evaluation because of high production volume, extent of human exposures, use in children's products, and/or published evidence of reproductive or developmental toxicity. Unlike many phthalates, DBP is not currently used as a plasticizer in polyvinyl chloride plastics. DBP is a component of latex adhesives and is used in cosmetics and other personal care products, as a plasticizer in cellulose plastics, and as a solvent for dyes. The results of this evaluation on DBP are published in a NTP-CERHR monograph which includes: 1) the NTP Brief, 2) the Expert Panel Report on the Reproductive and Developmental Toxicity of Di-n-Butyl Phthalate, and 3) public comments received on the Expert Panel Report. As stated in the NTP Brief, the NTP reached the following conclusions regarding the possible effects of exposure to DBP on human development and reproduction. First, although DBP could possibly affect human reproduction and development if exposures are sufficiently high, the NTP concludes that there is negligible concern for reproductive toxicity in exposed adults. Second, the NTP concludes that there is minimal concern for developmental effects when pregnant women are exposed to DBP levels estimated by the panel (2-10 mug/kg body weight/day). There is no direct evidence that exposure of people to DBP adversely affects reproduction or development, but studies reviewed by the expert panel show that oral exposure to high doses of DBP >>/=100 mg/kg body weight/day) may adversely affect the prenatal and early postnatal development in rodents. Finally, based on exposure estimates in women of reproductive age, the NTP concludes that there is some concern for DBP causing adverse effects to human development, particularly development of the male reproductive system. NTP-CERHR monographs are transmitted to federal and state agencies, interested parties, and the public and are available electronically in PDF format on the CERHR web site (http://cerhr.niehs.nih.gov) and in printed text or CD-ROM from the CERHR (National Institute of Environmental Health Sciences, P.O. Box 12233, MD EC-32, Research Triangle Park, NC; fax: 919-316-4511).

The resistance of the pulmonary conducting airway tree (Raw) is a consequence of the resistances of its component airways and how they are connected together. To date, theoretical calculations of Raw have been performed with the aid of mathematical models of the airway tree that are purely deterministic. That is, the mechanical properties of the component airways in these models are precisely defined functions of generation number. Such models take no account of the fact that the airways of a given generation are not all exactly the same but rather exhibit a spectrum of wall thicknesses, amounts of smooth muscle, and number of parenchymal attachments. In the present study, the properties of a 10-generation stochastic airway tree model are investigated. The lengths and radii of the airways in the tree are drawn randomly from probability distribution functions (PDFs), the means of which are deterministic functions of generation number and the standard deviations are assigned various values. Monte Carlo simulation is used to estimate the PDF of Raw itself in various conditions. We show that the relative width of the PDF of Raw may be comparable to that of the PDFs from which the individual airway radii were drawn. It is also shown that when bronchoconstriction is simulated by narrowing each airway by a random amount the resulting PDF for Raw may increase in width many times. We conclude that the variations in airway responsiveness seen in nature can only be properly understood when the distribution of airway properties within the lung are taken into account.

Mathematical phantoms are essential for the development and early stage evaluation of image reconstruction algorithms in x-ray computed tomography (CT). This note offers tools for computer simulations using a two-dimensional (2D) phantom that models the central axial slice through the FORBILD head phantom. Introduced in 1999, in response to a need for a more robust test, the FORBILD head phantom is now seen by many as the gold standard. However, the simple Shepp-Logan phantom is still heavily used by researchers working on 2D image reconstruction. Universal acceptance of the FORBILD head phantom may have been prevented by its significantly higher complexity: software that allows computer simulations with the Shepp-Logan phantom is not readily applicable to the FORBILD head phantom. The tools offered here address this problem. They are designed for use with Matlab®, as well as open-source variants, such as FreeMat and Octave, which are all widely used in both academia and industry. To get started, the interested user can simply copy and paste the codes from this PDF document into Matlab® M-files.

Legionella pneumophila is a gram-negative facultative intracellular human pathogen that can cause fatal Legionnaires' disease. Polypeptide deformylase (PDF) is a novel broad-spectrum antibacterial target, and reports of inhibitors of PDF with potent activities against L. pneumophila have been published previously. Here, we report the identification of not one but three putative pdf genes, pdfA, pdfB, and pdfC, in the complete genome sequences of three strains of L. pneumophila. Phylogenetic analysis showed that L. pneumophila PdfA is most closely related to the commonly known gamma-proteobacterial PDFs encoded by the gene def. PdfB and PdfC are more divergent and do not cluster with any specific bacterial or eukaryotic PDF. All three putative pdf genes from L. pneumophila strain Philadelphia 1 have been cloned, and their encoded products have been overexpressed in Escherichia coli and purified. Enzymatic characterization shows that the purified PDFs with Ni2+ substituted are catalytically active and able to remove the N-formyl group from several synthetic polypeptides, although they appear to have different substrate specificities. Surprisingly, while PdfA and PdfB with Zn2+ substituted are much less active than the Ni2+ forms of each enzyme, PdfC with Zn2+ substituted was as active as the Ni2+ form for the fMA substrate and exhibited substrate specificity different from that of Ni2+ PdfC. Furthermore, the catalytic activities of these enzymes are potently inhibited by a known small-molecule PDF inhibitor, BB-3497, which also inhibits the extracellular growth of L. pneumophila. These results indicate that even though L. pneumophila has three PDFs, they can be effectively inhibited by PDF inhibitors which can, therefore, have potent anti-L. pneumophila activity.

Autoclaving peritoneal dialysate fluid (PDF) degrades glucose into glucose degradation products (GDPs) that impair peritoneal mesothelial cell functions. While glycation processes leading to formation of advanced glycation end-products (AGE) were viewed commonly as being mediated by glucose present in the PDF, recent evidence indicates that certain GDPs are even more powerful inducers of AGE formation than glucose per se. In the present study, we examined the expression and modulation of AGE receptors on human peritoneal mesothelial cells (HPMC) cultured with GDPs, conventional PDF or PDF with low GDP content. HPMC cultured with GDPs differentially modulated AGE receptors (including RAGE, AGE-R1, AGE-R2 and AGE-R3) expression in a dose-dependent manner. At subtoxic concentrations, GDPs increased RAGE mRNA expression in HPMC. 2-furaldehyde (FurA), methylglyoxal (M-Glx) and 3,4-dideoxy-glucosone-3-Ene (3,4-DGE) increased the expression of AGE-R1 and RAGE, the receptors that are associated with toxic effects. These three GDPs up-regulated the AGE synthesis by cultured HPMC. In parallel, these GDPs also increased the expression of vascular endothelial growth factor (VEGF) in HPMC. PDF with lower GDP content exerted less cytotoxic effect than traditional heat-sterilized PDF. Both PDF preparations up-regulated the protein expression of RAGE and VEGF. However, the up-regulation of VEGF in HPMC following 24-h culture with conventional PDF was higher than values from HPMC cultured with PDF containing low GDP. We have demonstrated, for the first time, that in addition to RAGE, other AGE receptors including AGE-R1, AGE-R2 and AGE-R3 are expressed on HPMC. Different GDPs exert differential regulation on the expression of these receptors on HPMC. The interactions between GDPs and AGE receptors may bear biological relevance to the intraperitoneal homeostasis and membrane integrity.

OBJECTIVE

Our aim was to perform a clinical analysis of small intestinal obstructions caused by surgically treated phytobezoars.

METHODS

Twenty-four patients, with small intestinal obstructions caused by phytobezoars, underwent surgery in our department between 1998 to 2008, were reviewed retrospectively.

RESULTS

Twenty (83.3%) of 24 patients had previous gastric surgery. Preoperative computed tomography (CT) was performed in nine patients and seven (77.8%) patients, showed results consistent with a bezoar and subsequently, underwent surgery on the same day. The remaining patients had no preoperative diagnosis of a phytobezoar were typically followed-up for postoperative adhesion intestinal obstruction. Only those patients who showed no response to nonoperative treatment options underwent surgery. The phytobezoar was fragmented and milked into the cecum in 11 (45.8%) patients or extracted via longitudinal enterotomy in 12 (50%) patients; the remaining patient (4.2%) was treated via laparoscopy. Three patients had gastric phytobezoars, which were extracted via gastrotomy. There was no postoperative mortality. Two patients with previous enterotomy had either postoperative wound infection or wound infection and evisceration.

CONCLUSIONS

Phytobezoars should be considered in the differential diagnosis of acute small intestinal obstruction in patients with prior gastric surgery, poor dentition, or consume fiber-rich foods. Abdominal CT is useful for both diagnosis and for the decision to perform emergency surgery. When possible, the phytobezoar should be fragmented and milked into the cecum. Laparoscopic fragmentation may be useful in such cases (Tab. 3, Ref. 28). Full Text (Free, PDF) www.bmj.sk.

Previous studies have shown that compared with laminoplasty, anterior decompression with fusion (ADF) is superior for postoperative neurologic improvement in patients with massive cervical ossification of the posterior longitudinal ligament (OPLL) with a ≥50% canal occupying ratio. However, it is unknown which method, ADF or posterior decompression with fusion (PDF), is more effective for the treatment of massive OPLL.

This study aimed to investigate the surgical outcomes of ADF and PDF for the treatment of massive OPLL.

A multicenter retrospective case-control study was carried out.

A total of 61 OPLL patients with a ≥50% canal occupying ratio were included in this study. The mean age of the patients was 60.9 years (49 males and 12 females); 39 patients (31 males and 8 females, average age 61.1 years) underwent ADF, and 22 patients underwent PDF (18 males and 4 females, average age 60.6 years).

The data collected from both groups included age, gender, neurologic symptoms evaluated based on the Japanese Orthopedic Association score, neck pain assessed using the visual analogue scale, and radiographic parameters, including cervical lordosis and the OPLL canal occupying ratio.

Clinical and radiological outcomes were compared between the ADF and PDF groups with a minimum of 2 years follow-up.

There were no significant differences in the postoperative neurologic recovery rate between the two groups. However, in patients with kyphotic alignment (C2-C7 angle <0 degrees), the recovery rate was higher in the ADF group. Postoperative cervical pain was greater in the PDF group. The improvement in cervical alignment at C2-C7 was greater in the ADF group. The operating time was longer in the ADF group, whereas the intraoperative blood loss was greater in the PDF group. Approach-related complications were more frequently observed in the ADF group than in the PDF group.

The present study demonstrated that the postoperative recovery rate was similar in the ADF and PDF group. In patients with massive OPLL with kyphotic alignment, neurologic recovery rate in the ADF was superior to that in the PDF (in situ fusion). Additionally, postoperative neck pain was less severe in the ADF group. However, the occurrence of perioperative complications was more common in the ADF group.

OBJECTIVE

Research has shown that U.S. military veterans are at risk relative to the general adult population for excessive alcohol consumption, and veterans of the wars in Afghanistan and Iraq (Operation Enduring Freedom [OEF], Operation Iraqi Freedom [OIF], and Operation New Dawn [OND]) particularly so. The purpose of this study was to examine the efficacy of a brief personalized drinking feedback intervention tailored for veterans.

METHODS

All veterans who presented to the OEF/OIF/OND Seamless Transition Clinic at the Harry S. Truman Memorial Veterans' Hospital (Columbia, MO) were eligible to participate. Participants were 325 veterans (93% male; 82% White, 75% Army, M(age) = 32.20 years) who were randomly assigned to one of two conditions: personalized drinking feedback (PDF) or educational information (EDU). Those in the PDF condition received personalized information about their alcohol use, including social norms comparisons, risks associated with reported drinking levels, and a summary of their alcohol-related problems. Follow-up assessments were completed at 1 and 6 months after intervention (response rates = 93% and 86%, respectively).

RESULTS

Results indicated a significant (p < .05) Omnibus Group × Time effect for estimated peak blood alcohol concentration, although tests of simple main effects did not indicate between-group differences at the individual follow-up points. Among baseline abstainers, those in the PDF condition were more likely than those in the EDU condition to remain an abstainer at 6-month follow-up (p < .05).

CONCLUSIONS

These findings provide preliminary support for the efficacy of a brief, inexpensive alcohol prevention/intervention for young adult military veterans.

BACKGROUND

Non-steroidal anti-inflammatory drugs (NSAIDs) belong to most frequently used drugs worldwide. NSAIDs belong to the family of drugs that represent the biggest drug risk as to the number of adverse drug reactions (ADRs), as well as to the number of deregistered drugs.

METHODS

We analysed the whole consumption of NSAIDs from ATC class M01 in Slovakia during 1996-2007.

RESULTS

Most frequently used NSAIDs in Slovakia were ibuprofen and diclofenac. There was a marked increasing trend in piroxicam, meloxicam, ibuprofen and especially nimesulide medicines.

CONCLUSIONS

Prescription habits of doctors in Slovakia reflect the drug risk only partially, nevertheless the total consumption of dangerous medicines is decreasing and substances with safer profile remain being more used. In the prescribing process the patients' risk factors together with the differences in drug characteristics should be considered. Nevertheless some of these drugs are OTC, and their consumption is strongly influenced by pharmacists and advertisement (Tab. 2, Fig. 1, Ref. 18). Full Text (Free, PDF) www.bmj.sk.

To protect occupants from infectious diseases or possible chemical/biological agents released by a terrorist in an enclosed space, such as an airliner cabin, it is critical to identify gaseous contaminant source locations and strengths. This paper identified the source locations and strengths by solving inverse contaminant transport with the quasi-reversibility (QR) and pseudo-reversibility (PR) methods. The QR method replaces the second-order diffusion term in the contaminant transport equation with a fourth-order stabilization term. By using the airflow pattern calculated by computational fluid dynamics (CFD) and the time when the peak contaminant concentration was measured by a sensor in downstream, the QR method solves the backward probability density function (PDF) of contaminant source location. The PR method reverses the airflow calculated by CFD and solves the PDF in the same manner as the QR method. The position with the highest PDF is the location of the contaminant source. The source strength can be further determined by scaling the nominal contaminant concentration computed by CFD with the concentration measured by the sensor. By using a two-dimensional and a three-dimensional aircraft cabin as examples of enclosed spaces, the two methods can identify contaminant source locations and strengths in the cabins if the sensors are placed in the downstream location of the sources. The QR method performed slightly better than the PR method but with a longer computing time.

CONCLUSIONS

The paper presents a method that can be used to find a gaseous contaminant source location and determine its strength in enclosed spaces with the data of contaminant concentration measured by one sensor. The method can be a very useful tool to find where, what, and how the contamination has happened. The method is also useful for optimally placing sensors in enclosed spaces. The results can be applied to develop appropriate measures to protect occupants in enclosed environments from infectious diseases or chemical/biological warfare agents released by a terrorist.

OBJECTIVE

The pharmacokinetic parameters derived from dynamic contrast-enhanced (DCE) MRI have been used in more than 100 phase I trials and investigator led studies. A comparison of the absolute values of these quantities requires an estimation of their respective probability distribution function (PDF). The statistical variation of the DCE-MRI measurement is analyzed by considering the fundamental sources of error in the MR signal intensity acquired with the spoiled gradient-echo (SPGR) pulse sequence.

METHODS

The variance in the SPGR signal intensity arises from quadrature detection and excitation flip angle inconsistency. The noise power was measured in 11 phantoms of contrast agent concentration in the range [0-1] mM (in steps of 0.1 mM) and in onein vivo acquisition of a tumor-bearing mouse. The distribution of the flip angle was determined in a uniform 10 mM CuSO4 phantom using the spin echo double angle method. The PDF of a wide range of T1 values measured with the varying flip angle (VFA) technique was estimated through numerical simulations of the SPGR equation. The resultant uncertainty in contrast agent concentration was incorporated in the most common model of tracer exchange kinetics and the PDF of the derived pharmacokinetic parameters was studied numerically.

RESULTS

The VFA method is an unbiased technique for measuringT1 only in the absence of bias in excitation flip angle. The time-dependent concentration of the contrast agent measured in vivo is within the theoretically predicted uncertainty. The uncertainty in measuring K(trans) with SPGR pulse sequences is of the same order, but always higher than, the uncertainty in measuring the pre-injection longitudinal relaxation time (T10). The lowest achievable bias/uncertainty in estimating this parameter is approximately 20%-70% higher than the bias/uncertainty in the measurement of the pre-injection T1 map. The fractional volume parameters derived from the extended Tofts model were found to be extremely sensitive to the variance in signal intensity. The SNR of the pre-injection T1 map indicates the limiting precision with which K(trans) can be calculated.

CONCLUSIONS

Current small-animal imaging systems and pulse sequences robust to motion artifacts have the capacity for reproducible quantitative acquisitions with DCE-MRI. In these circumstances, it is feasible to achieve a level of precision limited only by physiologic variability.

Biomedical data may be composed of individuals generated from distinct, meaningful sources. Due to possible contextual biases in the processes that generate data, there may exist an undesirable and unexpected variability among the probability distribution functions (PDFs) of the source subsamples, which, when uncontrolled, may lead to inaccurate or unreproducible research results. Classical statistical methods may have difficulties to undercover such variabilities when dealing with multi-modal, multi-type, multi-variate data. This work proposes two metrics for the analysis of stability among multiple data sources, robust to the aforementioned conditions, and defined in the context of data quality assessment. Specifically, a global probabilistic deviation and a source probabilistic outlyingness metrics are proposed. The first provides a bounded degree of the global multi-source variability, designed as an estimator equivalent to the notion of normalized standard deviation of PDFs. The second provides a bounded degree of the dissimilarity of each source to a latent central distribution. The metrics are based on the projection of a simplex geometrical structure constructed from the Jensen-Shannon distances among the sources PDFs. The metrics have been evaluated and demonstrated their correct behaviour on a simulated benchmark and with real multi-source biomedical data using the UCI Heart Disease data set. The biomedical data quality assessment based on the proposed stability metrics may improve the efficiency and effectiveness of biomedical data exploitation and research.

Most of the existing systems and methods for laryngeal pathology detection are characterized by a classification error. One of the basic problems is the approximation and estimation of the probability density functions of the given classes. In order to increase the accuracy of laryngeal pathology detection and to eliminate the most dangerous error--classification of a patient with laryngeal disease as a normal speaker--here an approach based on modeling of the probability density functions (pdf's) of the input vectors of the normal and pathological speakers by means of two prototype distribution maps (PDM), respectively, is proposed. The pdf of the input vectors of an unknown normal or pathological speaker is also modeled by such a prototype distribution neural map--PDM(X)--and the pathology detection is done by means of a ratio of specific similarities rather than by a direct comparison of some type of distance/similarity with a threshold. The experiments show an increased classification accuracy and that the proposed method can be used for screening the laryngeal diseases. The method is applied in a consulting system for clinical practice.

A general systematic method for the detection and segmentation of bright targets is developed. We use the term "bright target" to mean a connected, cohesive object which has an average intensity distribution above that of the rest of the image. We develop an analytic model for the segmentation of targets, which uses a novel multiresolution analysis in concert with a Bayes classifier to identify the possible target areas. A method is developed which adaptively chooses thresholds to segment targets from background, by using a multiscale analysis of the image probability density function (PDF). A performance analysis based on a Gaussian distribution model is used to show that the obtained adaptive threshold is often close to the Bayes threshold. The method has proven robust even when the image distribution is unknown. Examples are presented to demonstrate the efficiency of the technique on a variety of targets.

Body temperature exhibits rhythmic fluctuations over a 24 h period (Refinetti and Menaker, 1992) and decreases during the night, which is associated with sleep initiation (Gilbert et al., 2004; Kräuchi, 2007a,b). However, the underlying mechanism of this temperature decrease is largely unknown. We have previously shown that Drosophila exhibit a daily temperature preference rhythm (TPR), in which their preferred temperatures increase during the daytime and then decrease at the transition from day to night (night-onset) (Kaneko et al., 2012). Because Drosophila are small ectotherms, their body temperature is very close to that of the ambient temperature (Stevenson, 1985), suggesting that their TPR generates their body temperature rhythm. Here, we demonstrate that the neuropeptide diuretic hormone 31 (DH31) and pigment-dispersing factor receptor (PDFR) contribute to regulate the preferred temperature decrease at night-onset. We show that PDFR and tethered-DH31 expression in dorsal neurons 2 (DN2s) restore the preferred temperature decrease at night-onset, suggesting that DH31 acts on PDFR in DN2s. Notably, we previously showed that the molecular clock in DN2s is important for TPR. Although PDF (another ligand of PDFR) is a critical factor for locomotor activity rhythms, Pdf mutants exhibit normal preferred temperature decreases at night-onset. This suggests that DH31-PDFR signaling specifically regulates a preferred temperature decrease at night-onset. Thus, we propose that night-onset TPR and locomotor activity rhythms are differentially controlled not only by clock neurons but also by neuropeptide signaling in the brain.

Body temperature rhythm (BTR) is fundamental for the maintenance of functions essential for homeostasis, such as generating metabolic energy and sleep. One major unsolved question is how body temperature decreases dramatically during the night. Previously, we demonstrated that a BTR-like mechanism, referred to as temperature preference rhythm (TPR), exists in Drosophila Here, we demonstrate that the diuretic hormone 31 (DH31) neuropeptide and pigment-dispersing factor receptor (PDFR) regulate preferred temperature decreases at night-onset via dorsal neurons 2. This is the first in vivo evidence that DH31 could function as a ligand of PDFR. Although both DH31 and PDF are ligands of PDFR, we show that DH31 regulates night-onset TPR, but PDF does not, suggesting that night-onset TPR and locomotor activity rhythms are controlled by different neuropeptides via different clock cells.