CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.

SUMMARY: In recent years, the ability to generate genomic data has increased dramatically along with the demand for easily personalized and customizable genome browsers for effective visualization of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provides means for creating multiple visualization instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customizable web application for interactive visualization of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualization instances in parallel while allowing users to control and customize multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customizations made by the users allowing quick navigation between instances. Currently, the browser supports visualizing a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalized tracks, providing a whole new level of customization both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualization instance. AVAILABILITY AND IMPLEMENTATION: CRAMER is implemented in JavaScript and is publicly available on GitHub on https://github.com/FadyMohareb/cramer. The application is released under an MIT licence and can be deployed on any server running Linux or Mac OS. CONTACT: f.mohareb@cranfield.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Low osmolality and shear stress during liposuction impair cell viability in autologous fat grafting.

BACKGROUND: Liposuction and subsequent autologous fat grafting have become essential techniques for fat augmentation in plastic surgery. However, standard harvesting techniques that ensure the survival of adipocytes and stromal vascular fraction (SVF) cells and thus preserve the transplanted fat volume are lacking. In particular, the effect of different parameters of the tumescent solution has not been studied in this context. We hypothesized that the osmolality of the tumescent solution could have a significant effect on the survival of adipocytes and SVF cells. METHODS: We developed two distinct in vitro models based on freshly harvested excision fat from patients undergoing surgical treatment. First, we investigated the effect of osmolality by incubating excision fat in different tumescent solutions and analyzed the total cell survival and the differentiation potential of SVF cells. Vital whole-mount staining, isolation yield of SVF cells, clonogenicity, and osteogenic and adipogenic differentiation capacities were analyzed. Second, we addressed the additional effect of mechanical stress by simulating a liposuction on pieces of excision fat after incubation with the tumescent solutions. RESULTS: Osmolality of the tumescent solution by itself did not have a significant effect on adipocyte and SVF viability or SVF differentiation. However, when osmolality was combined with liposuction, a significant trend toward lower viability and more lipid droplets with lower osmolality was observed. Especially, SVF viability was significantly lower after liposuction with a hypotonic (150 mOsm/kg) solution. CONCLUSION: This study demonstrates the considerable effect of osmolality during liposuction and may lead to the development of "cell-protective" tumescent solutions.

The nutritional status of clinic attendees living with HIV/AIDS in St Vincent and the Grenadines / Estatus nutricional de personas con VIH/SIDA atendidas en clínicas en San Vicente y las Granadinas

OBJECTIVE: The purpose of this study was to assess nutritional status and dietary practices in persons living with HIV/AIDS (PLWHA). METHODS: A case-control design was used. Cases consisted of 36 PLWHA. Controls consisted of 37 persons within the same age range from the general population. Participants filled out a questionnaire consisting of sociodemographic, dietary and health history items. In addition, they had weight, height, upper mid-arm circumference and triceps skinfold measured using standard procedure. Biochemical and clinical data for cases were extracted from their clinic file. RESULTS: HIV-positive persons had significantly lower mean weight, BMI, upper mid-arm circumferences, arm muscle area and arm fat area than persons in the control group. They were also less likely to use multivitamins, dietary supplements, fruit and vegetables than persons in the control group. Correlation coefficients between corrected arm muscle area (CAMA) and BMI and weight ranged from 0.67 to 0.74 in cases and 0.41 to 0.68 for the control group, respectively. Screening for depleted CD4 counts using gender specific CAMA cut-offs indicative of depleted arm muscle reserves resulted in 48% sensitivity and 100% specificity in identifying PLWHA with CD4 counts < 200 cells/µL. CONCLUSION: The findings suggest that PLWHA are at increased risk for poor intakes of fruits and vegetables and depleted lean body mass. In addition, CAMA along with other clinic measures might be useful in the identification of PLWHA who might be responding adequately to treatment.

OBJETIVOS: El propósito de este estudio fue evaluar es estatus nutricional y las prácticas dietéticas de personas que viven con VIH/SIDA (PVVS). MÉTODOS: Se usó un diseño de control de casos. Los casos consistían en 36 PVVS. Los controles consistían en 37 personas en el mismo rango de edad de la población general. Los participantes llenaron un cuestionario contentivo de aspectos socio-demográficos, dietéticos, y cuestiones relacionadas con la historia de la salud. Además, se les determinó el peso, y se les tomó las medidas de la altura, la circunferencia del brazo medio superior, y el pliegue cutáneo del tríceps, usando procedimientos estándar: Los datos bioquímicos y clínicos para los casos, fueron extraídos de sus historias clínicas. RESULTADOS: Las personas VIH positivas tuvieron un promedio de peso, IMC, circunferencias del brazo medio superior, área muscular del brazo, y área adiposa del brazo, significativamente más bajo que las personas en el grupo control. También mostraron una menor tendencia a usar multivitaminas, suplementos dietéticos, frutas y vegetales, que las personas en el grupo control. Los coeficientes de correlación entre el área muscular del brazo corregida (AMBC), y el IMC y el peso tuvieron un rango de 0.67 a 0.74 en los casos y de 0.41 a 0.68 en el grupo control, respectivamente. El pesquisaje para el conteo de células CD4 agotadas usando límites de AMBC específicos del género, indicativos del agotamiento de las reservas musculares del brazo, arrojó un 48% de sensibilidad y un 100% de especificad en la identificación de PVVS con conteos de CD4 < 200 células/µL. CONCLUSIÓN: Los hallazgos sugieren que las PVVS enfrentan un riesgo mayor debido a un consumo pobre de frutas y vegetales, y a una masa corporal magra menguada. Además, la AMBC junto con las otras medidas clínicas, podría ser útil a la hora de identificar PVVS que pudieran esta respondiendo adecuadamente al tratamiento.

Optical properties and relaxation processes at femtosecond scale of bimetallic clusters.

The optical properties of Au-Ag and Ni-Ag clusters are measured by linear optical absorption spectroscopy and the time-resolved pump-probe femtosecond technique allowing a study of the influence of alloy or core-shell structure.

Acoustic vibration modes and electron-lattice coupling in self-assembled silver nanocolumns.

Using ultrafast spectroscopy, we investigated electron-lattice coupling and acoustic vibrations in self-assembled silver nanocolumns embedded in an amorphous Al2O3 matrix. The measured electron-lattice energy exchange time is smaller in the nanocolumns than in bulk silver, with a value very close to that of isolated nanospheres with comparable surface to volume ratio. Two vibration modes were detected and ascribed to the breathing and extensional mode of the nanocolumns, in agreement with numerical simulations.

The nutritional status of clinic attendees living with HIV/AIDS in St Vincent and the Grenadines.

OBJECTIVES: The purpose of this study was to assess nutritional status and dietary practices in persons living with HIV/AIDS (PLWHA). METHODS: A case-control design was used. Cases consisted of 36 PLWHA. Controls consisted of 37 persons within the same age range from the general population. Participants filled out a questionnaire consisting of sociodemographic, dietary and health history items. In addition, they had weight, height, upper mid-arm circumference and triceps skinfold measured using standard procedure. Biochemical and clinical data for cases were extracted from their clinic file. RESULTS: HIV-positive persons had significantly lower mean weight, BMI, upper mid-arm circumferences, arm muscle area and arm fat area than persons in the control group. They were also less likely to use multivitamins, dietary supplements, fruit and vegetables than persons in the control group. Correlation coefficients between corrected arm muscle area (CAMA) and BMI and weight ranged from 0.67 to 0.74 in cases and 0.41 to 0.68 for the control group, respectively. Screening for depleted CD4 counts using gender specific CAMA cut-offs indicative of depleted arm muscle reserves resulted in 48% sensitivity and 100% specificity in identifying PLWHA with CD4 counts < 200 cells/microL. CONCLUSION: The findings suggest that PLWHA are at increased risk for poor intakes of fruits and vegetables and depleted lean body mass. In addition, CAMA along with other clinic measures might be useful in the identification of PLWHA who might be responding adequately to treatment.

Expression, isolation and characterization of a mutated human plasminogen kringle 3 with a functional lysine binding site.

Each kringle of human plasminogen (HPg) except kringle 3 (K3) exhibits affinity for omega-aminocarboxylic acids. Assuming that the K3 domain contains a preformed but nonfunctional lysine binding site (LBS), Lys311 was altered by site-directed mutagenesis into Asp311 in accordance with the consensus sequence of the LBS. Cys297 involved in the interkringle disulfide bridge was mutated into Ser297 to minimize dimerization and aggregation. The mutated K3 TYQ[K3HPg/C297S/K311D]DS (r-K3mut) was expressed in Escherichia coli, isolated on an Ni2(+)-nitrilotriacetic acid-agarose column, refolded and purified on a lysine Bio-Gel column. Fluorescence titration indicates affinity of r-K3mut for omega-aminocarboxylic acids with the following association constants (Kass, mM-1): 5-aminopentanoic acid: 1.3; 6-aminohexanoic acid: 4.2; 7-aminoheptanoic acid: 0.5; trans-(aminomethyl)cyclohexanecarboxylic acid: 12.7; p-benzylaminesulfonic acid: 11.8. r-K3mut exhibits an affinity similar to native and mutated (R220G, E221D) K2. The results indicate the presence of a preformed but nonfunctional LBS in native K3 of HPg. We were able to demonstrate for the first time that an appropriate mutation in the LBS of a kringle produced a weak but distinct affinity for omega-aminocarboxylic acids.

Gastrointestinal histamine after thoracic irradiation in the mouse.

Thoracic irradiation induced duodenal lesions in mice as an indirect effect. We studied the influence of partial thoracic irradiation on endogenous histamine stores in the alimentary canal. Mice subjected to lower mediastinal irradiation had significantly higher (+19%) median gastric histamine, but lower (-44%) distal duodenal histamine than controls. They also had significantly lower proximal (-39%) and distal (-44%) duodenal histamine than mice who received upper mediastinal irradiation. Twenty-three percent of mice after lower mediastinal irradiation had duodenal lesions; these had significantly lower proximal (-30%) and distal (-44%) duodenal histamine than controls. Thus, irradiation to the lower mediastinum induced both duodenal lesions and significant changes in gastric and duodenal histamine stores. Histamine may be involved in the pathogenesis of these lesions.

Gastrointestinal histamine after gastric irradiation in the mouse.

A single dose of 9 or 15 Gy of X-rays was given to the stomach of mice. Gastric histamine formation capacity (HFC) rose in a dose-related fashion during days 4 to 11 after irradiation. This rise coincided with a dose-dependent fall in gastric mural histamine concentration. 15 Gy X-rays also resulted in a transient loss of body weight (days 4-8 after irradiation). These results suggest that irradiation of the stomach mobilizes gastric histamine and that gastric histamine stores may be radiosensitive.