Age adjusted D-dimer in the Belfast Health and Social Care Trust: A retrospective study.

D-dimers combined with clinical pre-test probability (PTP) scores are used to determine the likelihood of a venous thromboembolic event (VTE). It is recognised that with advancing age, d-dimer values increase, leading to a cohort of patients with a d-dimer above the standard cut-off of 500µg/L. A recent systemic review, examined the accuracy of an age-adjusted D-dimer in those aged > 50 years with a low clinical risk of a VTE. This showed an increase in specificity without loss of sensitivity. Our study, aimed to examine a population of patients, who between 2011 and 2014 underwent ultrasound Doppler studies of lower limbs. By applying a corresponding age-adjusted D-dimer, we determined the sensitivity and specificity and compared this to use of conventional D-dimer.

Improving the treatment of coarse-grain electrostatics: CVCEL.

We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

Conformational analysis of nucleic acids revisited: Curves+.

We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.

Genetics of ovarian differentiation: Rspo1, a major player.

In mammals, the sex of the embryo is determined during development by its commitment either to the male or female genetic program regulating testicular or ovarian organogenesis. Major steps towards unraveling sex determination in mammals are achieved by the identification of key genes involved in human pathologies and the application of mouse genetics to analyze their function. While the expression of Sry and Sox9 is sufficient to induce the male developmental program, the molecular pathways that specify ovarian differentiation were unclear before the recent demonstration that mutations in the RSPO1 gene induce female-to-male sex reversal in XX patients. By generating the corresponding mouse model, we have shown that Rspo1 is so far the earliest known gene controlling the female genetic developmental program. Rspo1 activates the canonical beta-catenin signaling pathway required for female somatic cell differentiation and germ cell commitment into meiosis. The aim of this review is to describe the roles of R-spondins (Rspo)in developmental processes and disorders and the current knowledge obtained from murine models. A particular focus will be on Rspo1 and its crucial function in sex determination.

Generalised reduction of putative endothelial progenitors and CXCR4-positive peripheral blood cells in type 2 diabetes.

AIMS/HYPOTHESIS: In patients with type 2 diabetes, reduced levels of circulating endothelial progenitor cells have been reported and these have been correlated with disease severity. In this study, we examined a panel of markers widely used to identify progenitor and/or stem cells, and determined their association with disease severity in diabetic patients. Since expression of chemokine (C-X-C motif) receptor 4 (CXCR4) has been associated with mobilisation and recruitment of progenitor cells, CXCR4 expression was also analysed. METHODS: Peripheral blood mononuclear cells (PBMCs) from 98 patients with type 2 diabetes and 39 control individuals were analysed by flow cytometry for surface marker expression. RESULTS: Cells expressing different combinations of progenitor and/or stem cell markers were severely reduced in PBMCs of diabetic patients compared with those of control participants. Moreover, a number of these putative progenitor cell populations were negatively associated with disease severity. Reduced expression of CXCR4 and CD34/CXCR4-positive cells was also observed in diabetic patients. PBMCs expressing CXCR4 positively correlated with levels of progenitor cells in control participants but not in diabetic patients. Levels of putative progenitor and CXCR4-positive cells were further decreased in patients with diabetic complications, including cardiovascular and microvascular diseases. CONCLUSIONS/INTERPRETATION: A generalised decrease in a range of progenitor cell populations was observed in type 2 diabetic patients. This reduction was also negatively associated with disease severity.

Investigation of DAZ and RBMY1 gene expression in human testis by quantitative real-time PCR.

This study developed quantitative real-time PCR assays for the DAZ and RBMY1 genes to determine the copy number of RNA extracted from testicular biopsies from a cohort of normospermic controls (n=6) and azoospermic males (n=17) including two males with Y-chromosome microdeletions (AZFc and AZFb + c). All patients underwent testicular sperm extraction (TESE) for intracytoplasmic sperm injection (ICSI). Forty percent of the azoospermic cohort showed a significant reduction in the copies of at least one of the genes (DAZ P=0.003; RBMY1 P=0.009). The histopathology of these patients ranged from Sertoli cell only (SCO) to severe hypospermatogenesis with interstitial fibrosis. The patient with the AZFb + c deletion lacked expression of DAZ and RBMY1 and had a histopathology of SCO. The patient with the AZFc deletion had reduced expression of RBMY1 and no DAZ expression with a histopathology of spermatocyte arrest. The quantitative real-time PCR assays for DAZ and RBMY1 gave positive predictive values of 78% and 70%, respectively for the recovery of sperm from testicular biopsy.

ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes.

We present the first applications of an activated method in internal coordinate space for sampling all-atom protein conformations, the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method differs from all previous internal coordinate-based studies aimed at folding or refining protein structures in that conformational changes result from identifying and crossing well-defined saddle points connecting energy minima. Our simulations of four model proteins containing between 4 and 47 amino acids indicate that this method is efficient for exploring conformational space in both sparsely and densely packed environments, and offers new perspectives for applications ranging from computer-aided drug design to supramolecular assembly.

CAG repeat length in an infertile male population of Irish origin.

The androgen receptor (AR) gene, located on the X chromosome, is an important regulator of human spermatogenesis. In the past decade, the link between the CAG polyglutamine tract, situated on exon one of the AR gene, and reduced spermatogenesis has become a controversial one. Alterations in the length of the CAG polyglutamine tract have been associated with prostate cancer at a reduced intrinsic length and neuromuscular diseases at a CAG repeat length of > or = 40. Minimal intermediate increases have been linked with depressed spermatogenesis in infertile males. Asian and Australian groups have published an association between increased CAG repeat length and reduced spermatogenesis while many European studies have found no such association. The aim of this study was to document the association between increased CAG repeat length and reduced spermatogenesis in a group of Irish infertile males and controls known to have fathered at least one child. The study employed the ABI 377 DNA sequencer to size the CAG repeat region of exon one of the AR gene in each group. Statistical analysis revealed no actual link between the length of the CAG tract and a reduction of spermatogenesis in a cohort of infertile patients (n = 66) of Irish ethnic origin when compared to a fertile control group (n = 77) (p = 0.599).

Non-additivity in protein-DNA binding.

MOTIVATION: Localizing protein binding sites within genomic DNA is of considerable importance, but remains difficult for protein families, such as transcription factors, which have loosely defined target sequences. It is generally assumed that protein affinity for DNA involves additive contributions from successive nucleotide pairs within the target sequence. This is not necessarily true, and non-additive effects have already been experimentally demonstrated in a small number of cases. The principal origin of non-additivity involves the so-called indirect component of protein-DNA recognition which is related to the sequence dependence of DNA deformation induced during complex formation. Non-additive effects are difficult to study because they require the identification of many more binding sequences than are normally necessary for describing additive specificity (typically via the construction of weight matrices). RESULTS: In the present work we will use theoretically estimated binding energies as a basis for overcoming this problem. Our approach enables us to study the full combinatorial set of sequences for a variety of DNA-binding proteins, make a detailed analysis of non-additive effects and exploit this information to improve binding site predictions using either weight matrices or support vector machines. The results underline the fact that, even in the presence of significant deformation, non-additive effects may involve only a limited number of dinucleotide steps. This information helps to reduce the number of binding sites which need to be identified for successful predictions and to avoid problems of over-fitting. AVAILABILITY: The SVM software is available upon request from the authors.

A preliminary report on the implication of RT-PCR detection of DAZ, RBMY1, USP9Y and Protamine-2 mRNA in testicular biopsy samples from azoospermic men.

In this study, reverse transcription-polymerase chain reaction (RT-PCR) was optimized to analyse the presence of DAZ, RBMY1, USP9Y, protamine-2, SRY and actin messenger RNA (mRNA) in testicular cells of men suffering from idiopathic azoospermia. All samples (n=28), including five controls, showed normal expression of actin, SRY and USP9Y. Sperm was not recovered from eight patients after testicular biopsy. Of these, four patients showed altered mRNA levels for the fertility genes, DAZ, RBMY1 and protamine-2. One patient, who was previously shown to be azoospermia factor region (AZF)b deleted, lacked RBM mRNA and presented with reduced amplification of protamine-2 mRNA. This correlated with previous studies, which proposed that RBM expression is exclusive to AZFb and that the lack of testicular RBMY1 mRNA results in suppressed spermatogenesis. Two patients were each lacking DAZ mRNA but did show expression of RBMY1 mRNA at a reduced level, suggesting that there might be residual spermatogenesis in the absence of DAZ expression. Protamine-2 mRNA was detected in one patient and was absent in the second patient. Finally, one patient lacked DAZ, RBMY1 and protamine-2 mRNA. The 19 remaining azoospermic patients presented with normal expression patterns for each of the fertility genes studied. This study demonstrates that the expression of spermatogenesis-specific genes varies in azoospermia. The study of the expression of such genes in a larger number of patients might be useful in characterizing and identifying subpopulations of azoospermic men.

Magnesium sulfate in the treatment of refractory ventricular fibrillation in the prehospital setting.

OBJECTIVE: To determine if magnesium sulfate (MgSO(4)) improves outcome in cardiac arrest patients initially in ventricular fibrillation (VF). METHODS: Randomized, prospective, double blind, placebo-controlled, multicenter prehospital trial using 2 g of MgSO(4). Eligible patients were non-traumatic cardiac arrest patients (> or =18 years of age) presenting in VF. The protocol included those patients refractory to three electroshocks. Epinephrine and either 2 g of MgSO(4) or placebo (normal saline) were then administered. The primary outcome variable was return of spontaneous circulation (ROSC) in the field and a perfusing pulse on arrival at the ED. Secondary endpoints included admission to the hospital (ADMT) and hospital discharge (DISC). IRB approval was obtained at all participating centers. RESULTS: Total 116 patients (58 MgSO(4), 58 placebo) were enrolled during the period from 4/1992 to 10/96 with 109 available. There were no significant differences between the groups in baseline characteristics and times to cardio pulmonary resuscitation (CPR), advanced life support (ALS), and first defibrillation, except for time to study drug administration. There was no significant differences in ROSC (placebo, 18.5%, and MgSO(4), 25.5%, P=0.38), ADMT (placebo rate=16.7%, MgSO(4)=16.4%, P=1.0) or DISC (placebo rate=3.7%, MgSO(4)=3.6%, P=1.0). CONCLUSIONS: We failed to demonstrate that the administration of 2 g of MgSO(4) to prehospital cardiac arrest patients presenting in VF improves short or long term survival.

The use of capnography in the air medical environment.

We can count on two things when we receive a call as part of an air medical transport team--the patient is in critical condition, and time is of the essence. Whether the patient has experienced trauma from a motor vehicle crash, has fallen, or has suffered an insult as a consequence of poor health, our technique, skill, and judgment are tested constantly. Fortunately, we have equipment at our disposal to make our job easier. One of the more difficult aspects and responsibilities of air medical transport teams is placement of an endotracheal tube (ET). Along with the techniques used for successful endotracheal intubation (ETI), available technology can maximize patients' ventilatory status using an instrument that detects expired carbon dioxide (CO(2)) levels.

Free fluid on abdominal computed tomography without solid organ injury after blunt abdominal injury does not mandate celiotomy.

BACKGROUND: Mandatory celiotomy has been proposed for all patients with unexplained free fluid on abdominal computed tomography (CT) scanning after blunt abdominal injury. This recommendation has been based upon retrospective data and concerns over the potential morbidity from the late diagnosis of blunt intestinal injury. This study examined the rate of intestinal injury in patients with free fluid on abdominal CT after blunt abdominal trauma. METHODS: This study was a multicenter prospective series of all patients with blunt abdominal trauma admitted to four level I trauma centers over 22 months. Data were collected concurrently at the time of patient enrollment and included demographics, injury severity score, findings on CT scan, and presence or absence of blunt intestinal injury. This database was specifically queried for those patients who had free fluid without solid organ injury. RESULTS: In all, 2,299 patients were evaluated. Free fluid was present in 265. Of these, 90 patients had isolated free fluid with only 7 having a blunt intestinal injury. Conversely, 91% of patients with free fluid did not. All patients with free fluid were observed for a mean of 8 days (95% confidence interval 6.1 to 10.4, range 1 to 131). There were no missed injuries. CONCLUSIONS: Free fluid on abdominal CT scan does not mandate celiotomy. Serial observation with the possible use of other adjunctive tests is recommended.

Early trauma polymorphonuclear neutrophil responses to chemokines are associated with development of sepsis, pneumonia, and organ failure.

OBJECTIVES: The modulation of polymorphonuclear neutrophil (PMN) function by injury is unpredictable, and can predispose either to hyperimmune states (adult respiratory distress syndrome [ARDS], multiple organ failure) or to immune dysfunction, infection, and sepsis. Such outcomes have been related to excess production of the CXC chemokine interleukin (IL)-8, but PMN responses to IL-8 are mediated by both the relatively stable and IL-8 specific CXC receptor 1 (CXCR1) and the labile, promiscuous CXCR2. We hypothesized that progression to septic and multiple organ failure outcomes could be related to early differences in PMN CXC receptor status. METHODS: PMNs were isolated 12 +/- 3 hours after injury from 15 major trauma patients (Injury Severity Score of 34 +/- 2, 11 men and 4 women, age 36 +/- 4 years) who survived at least 7 days. Volunteer normal PMNs (n = 6 donors) were studied for comparison. Cells were stimulated either with the CXCR2 specific agent growth-related oncogene-alpha, or with IL-8, which stimulates CXCR1 and CXRR2. Receptor response was assessed as the mobilization of cell calcium. The development of ARDS, sepsis, and pneumonia was assessed according to standardized criteria. Day 1 receptor activity in the clinical groups was then compared by analysis of variance with Tukey's or t tests as appropriate. RESULTS: In patients that were otherwise comparable, CXCR2 responses were markedly diminished in the PMNs of patients who went on to sepsis and pneumonia, but were elevated in PMNs from the patients who went on to ARDS. CXCR1 responses were modestly lower in trauma patients than volunteers, but showed no significant variations among the various clinical outcome groups. CONCLUSION: The activity of PMN CXCR2 receptors soon after injury may be reflected in the later clinical sequelae of PMN activity. High CXCR2 activity may correlate with PMN hyperfunction and outcomes such as ARDS, whereas the loss of CXCR2 function in inflammatory environments may impair PMN functions in a manner that predisposes to pneumonia or sepsis. Early responses of PMN CXC receptors to injury may influence the clinical course of trauma patients.

Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA.

We used molecular modeling to study the optimal conformation of the complex between two p53 DNA-binding domain monomers and a 12 base-pair target DNA sequence. The complex was constructed using experimental data on the monomer binding conformation and a new approach to deform the target DNA sequence. Combined with an internal/helicoidal coordinate model of DNA, this approach enables us to bend the target sequence in a controlled way while respecting the contacts formed with each p53 monomer. The results show that the dimeric complex favors DNA bending towards the major groove at the dimer junction by a value close to experimental findings. In contrast to inferences from earlier models, the calculation of key contributions to the free energy of the complexes indicates a determinant role for DNA in the formation of the complex with the dimer of the p53 DNA-binding domains.

High-speed molecular mechanics searches for optimal DNA interaction sites.

We have recently developed a theoretical means of studying the mechanical and interaction properties of nucleic acids as a function of their base sequence. This approach, termed ADAPT, can be used to obtain the physical properties of millions of base sequences with only modest computational expense. ADAPT is based on a multi-copy algorithm using special nucleotides ("lexides") containing all four standard bases whose contribution to the energy of the molecule can be varied. We present here a deeper study of the energy minima which occur in the multi-dimensional space defined by these variable sequences. We also present an extension of the approach termed "gene threading" which enables us to scan genomic sequence data in an attempt to locate preferential binding sites. This technique is illustrated for the case of TATA-box protein binding. ADAPT enables us to demonstrate that, for this protein, DNA deformation alone explains a large part of the experimentally observed consensus binding sequence.

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.

Free energy profiles of opening of a centrally placed A:T pair within a DNA oligomer exhibits two regimes: Elastic deformation due to hydrogen bond rupture and a roughly linear region due to loss of stacking and solvation. Thymine opens equally easily into the minor and major grooves, while adenine favors the major groove direction. No significant variations from canonical backbone conformations were observed; however base opening induces considerable changes in surrounding solvent distribution, leading finally to a water channel which passes through the double helix.

Storage temperatures of medications on an air medical helicopter.

INTRODUCTION: The safety and efficacy of medications stored on air medical helicopters may be adversely affected by extreme temperatures. The purpose of this study was to determine whether temperatures inside an air medical helicopter drug box were within the U.S. Pharmacopeia recommendations for controlled room temperature. This is defined as a temperature between 15 degrees and 30 degrees C (59 degrees and 86 degrees F) with a mean kinetic temperature of less than 25 degrees C (77 degrees F). An additional goal was to determine whether time/temperature indicator labels can reliably monitor mean kinetic temperatures. METHODS: Temperatures were monitored with miniature electronic temperature recorders and color-changing time/temperature indicator labels. RESULTS: The mean kinetic temperatures for the summer and winter periods were 25.1 degrees C (77.2 degrees F) and 12.7 degrees C (54.8 degrees F), respectively. In the summer, the electronic recorders logged temperatures exceeding 25 degrees C (59 degrees F) 37% of the time and more than 30 degrees C (86 degrees F) 6% of the time. In the winter, temperatures less than 15 degrees C (59 degrees F) were recorded 83% of the time. The mean kinetic temperatures obtained from the electronic recorder and the time/temperature indicator labels differed by less than 0.7 degree C (1.3 degrees F). The results show that medications on an air medical helicopter are subject to temperatures out of the recommended range and that time/temperature indicator labels can reliably monitor mean kinetic temperatures.

A national survey of air medical infectious disease control practices.

INTRODUCTION: Caring for an infectious patient in the air medical environment presents a special challenge to all air crew members (ACMs) involved. The purpose of this study was to survey the infectious disease control practices of air medical programs (AMPs) that are members of the Association of Air Medical Services. METHODS: A structured telephone survey was designed to gather data. Using one interviewer (an undergraduate student) with no knowledge of the study's goal minimized experimental bias. AMPs from 151 geographically selected areas were called between June and August 1996. Only the programs' chief flight nurses (CFNs) were targeted as respondents. RESULTS: The response rate was 91% (138 of 151). Although no program refused to participate, 13 CFNs were unavailable to be interviewed. Mission profile was 32% scene and 68% interhospital with an annual average of 950 patient transports per program. Transport type was 61% rotor-wing aircraft, 17% fixed-wing, and 22% both. Flight physicals for ACMs were required by 57% of the AMPs. Pre-employment screenings for rubella, tuberculosis (TB), and varicella were noted. Interestingly, 17% of the AMPs reported pre-employment HIV testing. Immunization was mandated by 57% of AMPs, including hepatitis B virus, measles, rubella, and tetanus. Nine percent of the respondents refused to accept a transport with specific contagious conditions, primarily TB. A formal decontamination policy was in effect at 88% of the AMPs, and OSHA-approved filter masks were available at 70%. Pathogen exposure reporting was required by 97%. CONCLUSION: A current, comprehensive infection control program, continuing education, and 100% compliance with standard precautions will help reduce the possibility of accidental exposures. These strategies to reduce transmission also can be extended during training sessions to the prehospital and hospital personnel with whom the air medical program serves.

Optimization of nucleic acid sequences.

Base sequence influences the structure, mechanics, dynamics, and interactions of nucleic acids. However, studying all possible sequences for a given fragment leads to a number of base combinations that increases exponentially with length. We present here a novel methodology based on a multi-copy approach enabling us to determine which base sequence favors a given structural change or interaction via a single energy minimization. This methodology, termed ADAPT, has been implemented starting from the JUMNA molecular mechanics program by adding special nucleotides, "lexides," containing all four bases, whose contribution to the energy of the system is weighted by continuously variable coefficients. We illustrate the application of this approach in the case of double-stranded DNA by determining the optimal sequences satisfying structural (B-Z transition), mechanical (intrinsic curvature), and interaction (ligand-binding) properties.