Hot Clones, Maintaining a Link Between Software Clones Across Repositories

Code duplication is common in current programming-practice: programmers search for snippets of code, incorporate them into their projects and then modify them to their needs. In today's practice, no automated scheme is in place to inform both parties of any distant changes of the code. As code snippets continues to evolve both on the side of the user and on the side of the author, both may wish to benefit from remote bug fixes or refinements --- authors may be interested in the actual usage of their code snippets, and researchers could gather information on clone usage. We propose maintaining a link between software clones across repositories and outline how the links can be created and maintained.

A novel technique, dynamic intraligamentary stabilization creates optimal conditions for primary ACL healing: A preliminary biomechanical study

BACKGROUND Anterior cruciate ligament (ACL) rupture is a common lesion. Current treatment emphasizes arthroscopic ACL reconstruction via a graft, although this approach is associated with potential drawbacks. A new method of dynamic intraligamentary stabilization (DIS) was subjected to biomechanical analysis to determine whether it provides the necessary knee stability for optimal ACL healing. METHODS Six human knees from cadavers were harvested. The patellar tendon, joint capsule and all muscular attachments to the tibia and femur were removed, leaving the collateral and the cruciate ligaments intact. The knees were stabilized and the ACL kinematics analyzed. Anterior-posterior (AP) stability measurements evaluated the knees in the following conditions: (i) intact ACL, (ii) ACL rupture, (iii) ACL rupture with primary stabilization, (iv) primary stabilization after 50 motion cycles, (v) ACL rupture with DIS, and (vi) DIS after 50 motion cycles. RESULTS After primary suture stabilization, average AP laxity was 3.2mm, which increased to an average of 11.26mm after 50 movement cycles. With primary ACL stabilization using DIS, however, average laxity values were consistently lower than those of the intact ligament, increasing from an initial AP laxity of 3.00mm to just 3.2mm after 50 movement cycles. CONCLUSIONS Dynamic intraligamentary stabilization established and maintained close contact between the two ends of the ruptured ACL, thus ensuring optimal conditions for potential healing after primary reconstruction. The present ex vivo findings show that the DIS technique is able to restore AP stability of the knee.

Objective consensus from decision trees

BackgroundConsensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources.MethodsBased on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus.ResultsBased on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters.ConclusionRecommendations represented as decision trees can serve as a basis for objective consensus among multiple parties.

GOCE: precise orbit determination for the entire mission

The Gravity field and steady-state Ocean Circulation Explorer (GOCE) was the first Earth explorer core mission of the European Space Agency. It was launched on March 17, 2009 into a Sun-synchronous dusk-dawn orbit and re-entered into the Earth’s atmosphere on November 11, 2013. The satellite altitude was between 255 and 225 km for the measurement phases. The European GOCE Gravity consortium is responsible for the Level 1b to Level 2 data processing in the frame of the GOCE High-level processing facility (HPF). The Precise Science Orbit (PSO) is one Level 2 product, which was produced under the responsibility of the Astronomical Institute of the University of Bern within the HPF. This PSO product has been continuously delivered during the entire mission. Regular checks guaranteed a high consistency and quality of the orbits. A correlation between solar activity, GPS data availability and quality of the orbits was found. The accuracy of the kinematic orbit primarily suffers from this. Improvements in modeling the range corrections at the retro-reflector array for the SLR measurements were made and implemented in the independent SLR validation for the GOCE PSO products. The satellite laser ranging (SLR) validation finally states an orbit accuracy of 2.42 cm for the kinematic and 1.84 cm for the reduced-dynamic orbits over the entire mission. The common-mode accelerations from the GOCE gradiometer were not used for the official PSO product, but in addition to the operational HPF work a study was performed to investigate to which extent common-mode accelerations improve the reduced-dynamic orbit determination results. The accelerometer data may be used to derive realistic constraints for the empirical accelerations estimated for the reduced-dynamic orbit determination, which already improves the orbit quality. On top of that the accelerometer data may further improve the orbit quality if realistic constraints and state-of-the-art background models such as gravity field and ocean tide models are used for the reduced-dynamic orbit determination.

What percentage of people in the general population satisfies the current clinical at-risk criteria of psychosis?

The clinical validity of at-risk criteria of psychosis had been questioned based on epidemiological studies that have reported much higher prevalence and annual incidence rates of psychotic-like experiences (PLEs as assessed by either self rating questionnaires or layperson interviews) in the general population than of the clinical phenotype of psychotic disorders (van Os et al., 2009). Thus, it is unclear whether “current at-risk criteria reflect behaviors so common among adolescents and young adults that a valid distinction between ill and non-ill persons is difficult” (Carpenter, 2009). We therefore assessed the 3-month prevalence of at-risk criteria by means of telephone interviews in a randomly drawn general population sample from the at-risk age segment (age 16–35 years) in the Canton Bern, Switzerland. Eighty-five of 102 subjects had valid phone numbers, 21 of these subjects refused (although 6 of them signaled willingness to participate at a later time), 4 could not be contacted. Sixty subjects (71% of the enrollment fraction) participated. Two participants met exclusion criteria (one for being psychotic, one for lack of language skills). Twenty-two at-risk symptoms were assessed for their prevalence and severity within the 3 months prior to the interview by trained clinical raters using (i) the Structured Interview for Prodromal Syndromes (SIPS; Miller et al., 2002) for the evaluation of 5 attenuated psychotic and 3 brief limited intermittent psychotic symptoms (APS, BLIPS) as well as state-trait criteria of the ultra-high-risk (UHR) criteria and (ii) the Schizophrenia Proneness Instrument, Adult version (SPI-A; Schultze-Lutter et al., 2007) for the evaluation of the 14 basic symptoms included in COPER and COGDIS (Schultze-Lutter et al., 2008). Further, psychiatric axis I diagnoses were assessed by means of the Mini-International Neuropsychiatric Interview, M.I.N.I. (Sheehan et al., 1998), and psychosocial functioning by the Scale of Occupational and Functional Assessment (SOFAS; APA, 1994). All interviewees felt ‘rather’ or ‘very’ comfortable with the interview. Of the 58 included subjects, only 1 (2%) fulfilled APS criteria by reporting the attenuated, non-delusional idea of his mind being literally read by others at a frequency of 2–3 times a week that had newly occurred 6 weeks ago. BLIPS, COPER, COGDIS or state-trait UHR criteria were not reported. Yet, twelve subjects (21%) described sub-threshold at-risk symptoms: 7 (12%) reported APS relevant symptoms but did not meet time/frequency criteria of APS, and 9 (16%) reported COPER and/or COGDIS relevant basic symptoms but at an insufficient frequency or as a trait lacking increase in severity; 4 of these 12 subjects reported both sub-threshold APS and sub-threshold basic symptoms. Table 1 displays type and frequency of the sub-threshold at-risk symptoms.

Current state of evidence on 'off-label' therapeutic options for systemic lupus erythematosus, including biological immunosuppressive agents, in Germany, Austria and Switzerland--a consensus report

Systemic lupus erythematosus (SLE) can be a severe and potentially life-threatening disease that often represents a therapeutic challenge because of its heterogeneous organ manifestations. Only glucocorticoids, chloroquine and hydroxychloroquine, azathioprine, cyclophosphamide and very recently belimumab have been approved for SLE therapy in Germany, Austria and Switzerland. Dependence on glucocorticoids and resistance to the approved therapeutic agents, as well as substantial toxicity, are frequent. Therefore, treatment considerations will include 'off-label' use of medication approved for other indications. In this consensus approach, an effort has been undertaken to delineate the limits of the current evidence on therapeutic options for SLE organ disease, and to agree on common practice. This has been based on the best available evidence obtained by a rigorous literature review and the authors' own experience with available drugs derived under very similar health care conditions. Preparation of this consensus document included an initial meeting to agree upon the core agenda, a systematic literature review with subsequent formulation of a consensus and determination of the evidence level followed by collecting the level of agreement from the panel members. In addition to overarching principles, the panel have focused on the treatment of major SLE organ manifestations (lupus nephritis, arthritis, lung disease, neuropsychiatric and haematological manifestations, antiphospholipid syndrome and serositis). This consensus report is intended to support clinicians involved in the care of patients with difficult courses of SLE not responding to standard therapies by providing up-to-date information on the best available evidence.

[Lymphadenectomy for bladder cancer: current status and controversies]

Pelvic lymph node dissection is an integral part of the radical cystectomy procedure for patients with muscle-invasive bladder cancer. The optimal extent of the lymphadenectomy (LND) and mainly the proximal template boundary remain controversial issues. In view of the existing mapping studies and retrospective analyses, extended LND up to the mid-upper third of the common iliac vessels appears to provide further prognostic and therapeutic benefit and therefore should be defined as standard LND. This applies for all procedures irrespective of the choice of surgical approach (open surgery, minimally invasive approach). In this context total lymph node count is not a quality criterion because nodal yield is overly influenced by the individual patient's anatomy, surgical technique, template applied and pathological work-up. Consecutively, considerable inter-institutional differences result, which render any comparison impossible. Lymph node density is thought to be a superior prognostic factor, but it is similarly influenced by the above-mentioned factors. Concerning molecular techniques to improve the sensitivity of postoperative nodal staging further research is necessary. The two ongoing prospective randomized trials will potentially help to further define the optimal LND template.

[Erectile dysfunction in depression and under treatment with antidepressants -- current treatment options]

Erectile dysfunction (ED) is a common problem in the general population, but also a symptom of both treated and untreated depression. As a side effect of antidepressant medication, erectile dysfunction appears to be one of the principal reasons for discontinuing antidepressant treatment. Avoiding or switching antidepressants is problematic, as this may lead to an increase in depressive symptoms. Our review shows that oral phosphodiesterase inhibitors are an option in treating both ED resulting from depression and from antidepressant medication.

The impact of statin treatment on presentation mode and early outcomes in acute coronary syndromes

OBJECTIVES: The role of statin use in the treatment of acute coronary syndromes (ACS) is not clear. The aim of our study was to evaluate the role of statins in ACS. METHODS: Using data from the Acute Myocardial Infarction in Switzerland (AMIS Plus) Project, we compared the effects of chronic statin use, statin therapy after admission and no statin therapy on presentation mode and outcomes in ACS. RESULTS: Available data from the period 2001-2006 including 11,603 patients were analyzed. Major cardiac event rates and in-hospital mortality were more common in statin-naive patients compared to patients who received statins. CONCLUSIONS: Our results support the importance of statin treatment in ACS. Chronic statin therapy seems to alter the initial presentation of ACS but it is questionable whether it provides an additional effect on early outcomes compared to the establishment of statin therapy after admission in statin-naive patients.

[A-mode ultrasonic pointer for navigated pelvic surgery]

Surgical navigation has proven to be a minimally invasive procedure that enables precise surgical interventions with reduced exposure to irradiation for patient and personnel. Fluoroscopy-based modules have prevailed on the market. For certain operations of the pelvis computed tomography is necessary with its high imaging quality and considerably larger scan volume. To enable navigation in these cases, matching of the CT data set and the patient's real pelvic bone is essential. The common pair point-matching algorithm is complemented by the surface-matching algorithm to achieve an even higher overall precision of the system. For conventional surface matching with a solid pointer, the bone has to be exposed from soft tissue quite extensively, using a solid pointer. This conflicts with the claim of computer-assisted surgery to be minimally invasive. We integrated an A-mode ultrasonic pointer with the intention to perform extended surface matching on the pelvic bone noninvasively. Related to the conventional method, comparable and to some extent even improved precision conditions could be established.

Erosion Damage Mapping: Assessing Current Soil Erosion Damage in Switzerland

Within the scope of a comprehensive assessment of the degree of soil erosion in Switzerland, common methods have been used in the past including test plot measurements, artificial rainfall simulation, and erosion modelling. In addition, mapping guidelines for all visible erosion features have been developed since the 1970s and are being successfully applied in many research and soil conservation projects. Erosion damage has been continuously mapped over a period of 9 years in a test region in the central Bernese plateau. In 2005, two additional study areas were added. The present paper assesses the data gathered and provides a comparison of the three study areas within a period of one year (from October 2005 to October 2006), focusing on the on-site impacts of soil erosion. During this period, about 11 erosive rainfall events occurred. Average soil loss rates mapped at each study site amounted to 0.7 t ha-1, 1.2 t ha-1 and 2.3 t ha-1, respectively. About one fourth of the total arable land showed visible erosion damage. Maximum soil losses of about 70 t ha-1 occurred on individual farm plots. Average soil erosion patterns are widely used to underline the severity of an erosion problem (e.g. impacts on water bodies). But since severe rainfall events, wheel tracks, headlands, and other “singularities” often cause high erosion rates, analysis of extreme erosion patterns such as maximum values led to a more differentiated understanding and appropriate conclusions for planning and design of soil protection measures. The study contains an assessment of soil erosion in Switzerland, emphasizing questions about extent, frequency and severity. At the same time, the effects of different types of land management are investigated in the field, aiming at the development of meaningful impact indicators of (un-)sustainable agriculture/soil erosion risk as well as the validation of erosion models. The results illustrate that conservation agriculture including no-till, strip tillage and in-mulch seeding plays an essential role in reducing soil loss as compared to conventional tillage.

Determination of the minimum alveolar concentration of isoflurane in Shetland ponies using constant current or constant voltage electrical stimulation

OBJECTIVE: To determine the minimum alveolar concentration (MAC) of isoflurane in Shetland ponies using a sequence of three different supramaximal noxious stimulations at each tested concentration of isoflurane rather than a single stimulation. STUDY DESIGN: Prospective, experimental trial. ANIMALS: Seven 4-year-old, gelding Shetland ponies. METHODS: The MAC of isoflurane was determined for each pony. Three different modes of electrical stimulation were applied consecutively (2 minute intervals): two using constant voltage (90 V) on the gingiva via needle- (CVneedle) or surface-electrodes (CVsurface) and one using constant current (CC; 40 mA) via surface electrodes applied to the skin over the digital nerve. The ability to clearly interpret the responses as positive, the latency of the evoked responses and the inter-electrode resistance were recorded for each stimulus. RESULTS: Individual isoflurane MAC (%) values ranged from 0.60 to 1.17 with a mean (+/-SD) of 0.97 (+/-0.17). The responses were more clearly interpreted with CC, but did not reach statistical significance. The CVsurface mode produced responses with a longer delay. The CVneedle mode was accompanied by variable inter-electrode resistances resulting in uncontrolled stimulus intensity. At 0.9 MAC, the third stimulation induced more positive responses than the first stimulation, independent of the mode of stimulation used. CONCLUSIONS: The MAC of isoflurane in the Shetland ponies was lower than expected with considerable variability among individuals. Constant current surface electrode stimulations were the most repeatable. A summation over the sequence of three supramaximal stimulations was observed around 0.9 MAC. CLINICAL RELEVANCE: The possibility that Shetland ponies require less isoflurane than horses needs further investigation. Constant current surface-electrode stimulations were the most repeatable. Repetitive supramaximal stimuli may have evoked movements at isoflurane concentrations that provide immobility when single supramaximal stimulation was applied.

Current practice in neuropsychological outcome reporting after aneurysmal subarachnoid haemorrhage

BACKGROUND Neuropsychological deficits (NPD) are common in patients with aneurysmal subarachnoid haemorrhage (aSAH). NPD are one of the major limiting factors for patients with an otherwise acceptable prognosis for sustained quality of life. There are only a few studies reporting outcome after aSAH, which used a standardized neuropsychological test battery as a primary or secondary outcome measure. Aim of this study was to determine the current practice of reporting NPD following aSAH in clinical studies. METHODS A MEDLINE analysis was performed using the search term "subarachnoid haemorrhage outcome". The latest 1,000 articles were screened. We recorded study design, number of patients, and the presence of neuropsychological outcome report. Additionally, the time of testing after aSAH, the neuropsychological tests administered, as well as the percentage of patients with NPD were analyzed. RESULTS A total of 324 publications between 2009 and 2012 were selected for further review. Of those, 21 studies (6.5%) reported neuropsychological outcome, in 2,001 of 346,666 patients (0.6%). The assessment of NPD differed broadly using both subjective and objective cognitive evaluation, and a large variety of tests were used. CONCLUSION Neuropsychological outcome is underreported, and there is great variety in assessment in currently published clinical articles on aSAH. Prospective randomized trials treating aSAH may benefit from implementing more comprehensive and standardized neuropsychological outcome measures. This approach might identify otherwise unnoticed treatment effects in future interventional studies of aSAH patients.