GEVALT: An integrated software tool for genotype analysis

BACKGROUND: Genotype information generated by individual and international efforts carries the promise of revolutionizing disease studies and the association of phenotypes with alleles and haplotypes. Given the enormous amounts of public genotype data, tools for analyzing, interpreting and visualizing these data sets are of critical importance to researchers. In past works we have developed algorithms for genotypes phasing and tag SNP selection, which were shown to be quick and accurate. Both algorithms were available until now only as batch executables. RESULTS: Here we present GEVALT (GEnotype Visualization and ALgorithmic Tool), a software package designed to simplify and expedite the process of genotype analysis, by providing a common interface to several tasks relating to such analysis. GEVALT combines the strong visual abilities of Haploview with our quick and powerful algorithms for genotypes phasing (GERBIL), tag SNP selection (STAMPA) and permutation testing for evaluating significance of association. All of the above are provided in a visually appealing and interactive interface. CONCLUSION: GEVALT is an integrated viewer that uses state of the art phasing and tag SNP selection algorithms. By streamlining the application of GERBIL and STAMPA together with strong visualization for assessment of the results, GEVALT makes the algorithms accessible to the broad community of researchers in genetics

Immediate versus Delayed Attachment Incorporation Impact on Prosthetic Aftercare among Mandibular Implant—Supported Overdenture Wearers

Background: Substantial effort is dedicated to finding the most favorable parameters that will ensure low aftercare demands among edentulous patients wearing mandibular implant supported overdentures (MISODs). The purpose of this retrospective cohort study was to compare prosthetic aftercare between MISOD patients with a simultaneous (group A) vs. a three-week settling in period (group B) prior to attachment incorporation. Methods: Forty-five patients enrolled in this study. Two implants per patient were placed using a two-stage implant insertion protocol. Second-stage surgery was performed after three months. All patients received ball attachments using the direct (chairside) incorporation method. Twenty-two patients received their dentures with simultaneous attachment activation and the rest—twenty-three patients—after a three-week settling in period. Patients’ files were scanned for aftercare visits. Outcome parameters included sore spot relief, attachment incorporation, and denture repair. Additionally, gingival index measurements were compared. Confounding factors included age, gender, and implant dimensions. Results: The mean follow-up for the entire cohort was 84 ± 21 months, and the range 39–120 months. The mean number of visits for group A vs. B respectively: pressure sores relieve (3.63 ± 0.84 vs. 3.71 ± 0.61, p = 0.581), liner exchange due to loss of retention (2.09 ± 1.03 vs. 2.31 ± 1.04 p = 0.487), and gingival index (1.3 ± 0.3 vs. 1.03 ± 0.2, p = 0.653) exhibited no statistically significant differences between the tested groups. No statistically significant differences between the groups were also noted for the denture repair aftercare treatments (p = 0.318) and the independent variables including age, gender, and implant length. Conclusions: Prosthetic aftercare in MISOD wearers is similar whether a simultaneous or a three-week settling in period for attachment incorporation is applied

The Earliest Lead Object in the Levant.

In the deepest section of a large complex cave in the northern Negev desert, Israel, a bi-conical lead object was found logged onto a wooden shaft. Associated material remains and radiocarbon dating of the shaft place the object within the Late Chalcolithic period, at the late 5th millennium BCE. Based on chemical and lead isotope analysis, we show that this unique object was made of almost pure metallic lead, likely smelted from lead ores originating in the Taurus range in Anatolia. Either the finished object, or the raw material, was brought to the southern Levant, adding another major component to the already-rich Late Chalcolithic metallurgical corpus known to-date. The paper also discusses possible uses of the object, suggesting that it may have been used as a spindle whorl, at least towards its deposition

The Ashalim Cave lead object.

<p>The Ashalim Cave lead object.</p

Results of lead isotope analysis.

<p>Lead isotope ratios of the Ashalim Cave lead object plotted against ores from selected regions. Details and references are provided in the text.</p

Normalized trace element concentrations (ppm) measured by WDS.

<p>Normalized trace element concentrations (ppm) measured by WDS.</p

Plan of Ashalim Cave.

<p>The plan of Ashalim Cave with the location of the lead object marked by a dot.</p