An introduction to scripting in Ruby for biologists

<p>Abstract</p> <p>The Ruby programming language has a lot to offer to any scientist with electronic data to process. Not only is the initial learning curve very shallow, but its reflection and meta-programming capabilities allow for the rapid creation of relatively complex applications while still keeping the code short and readable. This paper provides a gentle introduction to this scripting language for researchers without formal informatics training such as many wet-lab scientists. We hope this will provide such researchers an idea of how powerful a tool Ruby can be for their data management tasks and encourage them to learn more about it.</p

Congenital syphilis, still a reality in 21st century: a case report

Congenital syphilis is a preventable disease and its presence reflects a failure of prenatal care delivery systems, as well as syphilis control programmes. The procedure to prevent congenital syphilis through antenatal screening and treatment is well established. But implementation of effective programmes has proved very difficult especially in resource constrained countries

Prescribing practices of primary-care veterinary practitioners in dogs diagnosed with bacterial pyoderma

Concern has been raised regarding the potential contributions of veterinary antimicrobial use to increasing levels of resistance in bacteria critically important to human health. Canine pyoderma is a frequent, often recurrent diagnosis in pet dogs, usually attributable to secondary bacterial infection of the skin. Lesions can range in severity based on the location, total area and depth of tissue affected and antimicrobial therapy is recommended for resolution. This study aimed to describe patient signalment, disease characteristics and treatment prescribed in a large number of UK, primary-care canine pyoderma cases and to estimate pyoderma prevalence in the UK vet-visiting canine population

Chronic multichannel neural recordings from soft regenerative microchannel electrodes during gait

Reliably interfacing a nerve with an electrode array is one of the approaches to restore motor and sensory functions after an injury to the peripheral nerve. Accomplishing this with current technologies is challenging as the electrode-neuron interface often degrades over time, and surrounding myoelectric signals contaminate the neuro-signals in awake, moving animals. The purpose of this study was to evaluate the potential of microchannel electrode implants to monitor over time and in freely moving animals, neural activity from regenerating nerves. We designed and fabricated implants with silicone rubber and elastic thin-film metallization. Each implant carries an eight-by-twelve matrix of parallel microchannels (of 120\u2009 7\u2009110\u2009\u3bcm2 cross-section and 4\u2009mm length) and gold thin-film electrodes embedded in the floor of ten of the microchannels. After sterilization, the soft, multi-lumen electrode implant is sutured between the stumps of the sciatic nerve. Over a period of three months and in four rats, the microchannel electrodes recorded spike activity from the regenerating sciatic nerve. Histology indicates mini-nerves formed of axons and supporting cells regenerate robustly in the implants. Analysis of the recorded spikes and gait kinematics over the ten-week period suggests firing patterns collected with the microchannel electrode implant can be associated with different phases of gait

Does training with amplitude modulated tones affect tone-vocoded speech perception?

Temporal-envelope cues are essential for successful speech perception. We asked here whether training on stimuli containing temporal-envelope cues without speech content can improve the perception of spectrally-degraded (vocoded) speech in which the temporal-envelope (but not the temporal fine structure) is mainly preserved. Two groups of listeners were trained on different amplitude-modulation (AM) based tasks, either AM detection or AM-rate discrimination (21 blocks of 60 trials during two days, 1260 trials; frequency range: 4Hz, 8Hz, and 16Hz), while an additional control group did not undertake any training. Consonant identification in vocoded vowel-consonant-vowel stimuli was tested before and after training on the AM tasks (or at an equivalent time interval for the control group). Following training, only the trained groups showed a significant improvement in the perception of vocoded speech, but the improvement did not significantly differ from that observed for controls. Thus, we do not find convincing evidence that this amount of training with temporal-envelope cues without speech content provide significant benefit for vocoded speech intelligibility. Alternative training regimens using vocoded speech along the linguistic hierarchy should be explored

Cancer Incidence among Former Love Canal Residents

Ba c k g r o u n d: The Love Canal was a rectangular 16-acre, 10-ft-deep chemical waste landfill situated in a residential neighborhood in Niagara Falls, New York. This seriously contaminated site came to public attention in 1978. Only one prior study examined cancer incidence in former residents of the Love Canal neighborhood (LC). Objective: In this study we aimed to describe cancer incidence in former LC residents from 1979 to 1996 and to investigate whether it differs from that of New York State (NYS) and Niagara County (NC). Me t h o d s: From 1978 to 1982, we interviewed 6,181 former residents, and 5,052 were eligible to be included in this study. In 1996, we identified 304 cancer diagnoses in this cohort using the NYS Cancer Registry. We compared LC cancer incidence with that of NYS and NC using standardized incidence ratios (SIRs), and we compared risks within the LC group by potential exposure to the landfill using survival analysis. Res u l t s: SIRs were elevated for cancers of the bladder [SIR NYS = 1.44; 95 % confidence interval (CI), 0.91–2.16] and kidney (SIR NYS = 1.48; 95 % CI, 0.76–2.58). Although CIs included 1.00, other studies have linked these cancers to chemicals similar to those found at Love Canal. We also found higher rates of bladder cancer among residents exposed as children, based on two cases. Co n c l u s i o n s: In explaining these excess risks, the role of exposure to the landfill is unclear given such limitations as a relatively small and incomplete study cohort, imprecise exposure measurements, and the exclusion of cancers diagnosed before 1979. Given the relatively young age of the cohort, further surveillance is warranted. Key w o r d s: cancer, community health, exposure assessment, hazardous waste sites, Love Canal. Environ Health Perspect 117:1265–1271 (2009). doi:10.1289/ehp.0800153 available vi

Renal function during rofecoxib therapy in patients with metastatic cancer: retrospective analysis of a prospective phase II trial

German Clinical Trials Register DRKS: DRKS0000011

Circumstellar disks and planets. Science cases for next-generation optical/infrared long-baseline interferometers

We present a review of the interplay between the evolution of circumstellar disks and the formation of planets, both from the perspective of theoretical models and dedicated observations. Based on this, we identify and discuss fundamental questions concerning the formation and evolution of circumstellar disks and planets which can be addressed in the near future with optical and infrared long-baseline interferometers. Furthermore, the importance of complementary observations with long-baseline (sub)millimeter interferometers and high-sensitivity infrared observatories is outlined.Comment: 83 pages; Accepted for publication in "Astronomy and Astrophysics Review"; The final publication is available at http://www.springerlink.co