On evaluating parallel computer systems

A workshop was held in an attempt to program real problems on the MIT Static Data Flow Machine. Most of the architecture of the machine was specified but some parts were incomplete. The main purpose for the workshop was to explore principles for the evaluation of computer systems employing new architectures. Principles explored were: (1) evaluation must be an integral, ongoing part of a project to develop a computer of radically new architecture; (2) the evaluation should seek to measure the usability of the system as well as its performance; (3) users from the application domains must be an integral part of the evaluation process; and (4) evaluation results should be fed back into the design process. It is concluded that the general organizational principles are achievable in practice from this workshop

Survival following the placement of gastrostomy tube in patients with multiple sclerosis

Background Around a third of people with multiple sclerosis (MS) experience dysphagia. There is a need for disease-specific information on survival following placement of gastrostomy tube in people with MS. Objective We aimed to study survival following gastrostomy in patients with MS. Methods We reviewed medical records, home enteral feeding database and death certificates of people with MS who had gastrostomy from 2005 to 2017. Cox regression analysis was performed to identify independent predictors associated with mortality after gastrostomy. Results Median survival of 53 patients with MS after gastrostomy was 21.73 months. Median duration of hospital stay after gastrostomy was 14 days (IQR 5.25, 51.5). Survival at 30 days, 3 months, 1, 2, 5 and 10 years were 100% (53/53), 98.1% (52/53), 81.1% (43/53), 54.7% (29/53), 22.4% (11/49) and 6.8% (3/44), respectively. Of 53 patients, 24 died due to respiratory tract infection. Patients who had gastrostomy tube before 50 years of age survived longer (median 28.48 months) compared with those who had the gastrostomy after age 50 years (median 17.51 months) (p = 0.040). Conclusion Around 54% of patients with MS survived two or more years following gastrostomy. Younger patients had better survival. The most frequent cause of death was respiratory infection

White paper: A plan for cooperation between NASA and DARPA to establish a center for advanced architectures

Large, complex computer systems require many years of development. It is recognized that large scale systems are unlikely to be delivered in useful condition unless users are intimately involved throughout the design process. A mechanism is described that will involve users in the design of advanced computing systems and will accelerate the insertion of new systems into scientific research. This mechanism is embodied in a facility called the Center for Advanced Architectures (CAA). CAA would be a division of RIACS (Research Institute for Advanced Computer Science) and would receive its technical direction from a Scientific Advisory Board established by RIACS. The CAA described here is a possible implementation of a center envisaged in a proposed cooperation between NASA and DARPA

Prochlo: Strong Privacy for Analytics in the Crowd

The large-scale monitoring of computer users' software activities has become commonplace, e.g., for application telemetry, error reporting, or demographic profiling. This paper describes a principled systems architecture---Encode, Shuffle, Analyze (ESA)---for performing such monitoring with high utility while also protecting user privacy. The ESA design, and its Prochlo implementation, are informed by our practical experiences with an existing, large deployment of privacy-preserving software monitoring. (cont.; see the paper

Bioluminescence imaging of human embryonic stem cells transplanted in vivo in murine and chick models

Research into the behavior, efficacy, and biosafety of stem cells with a view to clinical transplantation requires the development of noninvasive methods for in vivo imaging of cells transplanted into animal models. This is particularly relevant for human embryonic stem cells (hESCs), because transplantation of undifferentiated hESCs leads to tumor formation. The present study aimed to monitor hESCs in real time when injected in vivo. hESCs were stably transfected to express luciferase, and luciferase expression was clearly detected in the undifferentiated and differentiated state. When transfected hESCs were injected into chick embryos, bioluminescence could be detected both ex and in ovo. In the SCID mouse model, undifferentiated hESCs were detectable after injection either into the muscle layer of the peritoneum or the kidney capsule. Tumors became detectable between days 10-30, with approximately a 3 log increase in the luminescence signal by day 75. The growth phase occurred earlier in the kidney capsule and then reached a plateau, whilst tumors in the peritoneal wall grew steadily throughout the period analysed. These results show the widespread utility of bioluminescent for in vivo imaging of hESCs in a variety of model systems for preclinical research into regenerative medicine and cancer biology. © Copyright 2009, Mary Ann Liebert, Inc

Itraconazole associated quadriparesis and edema: a case report

<p>Abstract</p> <p>Introduction</p> <p>Itraconazole is an anti-fungal agent widely used to treat various forms of mycosis. It is particularly useful in allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitization. Side effects are uncommon and usually mild. Mild neuropathy is noted to occur very rarely. We present an unusual and, to the best of our knowledge, as yet unreported case of severe neuropathy and peripheral edema due to itraconazole in the absence of a concomitant risk factor.</p> <p>Case presentation</p> <p>A 72-year-old Caucasian man was started on itraconazole following diagnosis of severe asthma with fungal sensitization. One month later he presented with severe bilateral ankle edema with an elevated serum itraconazole level. The itraconazole dose was reduced but his ankle edema persisted and he developed weakness of all four limbs. Itraconazole was completely stopped leading to improvement in his leg edema but he became bed bound due to weakness. He gradually improved with supportive care and neurorehabilitation. On review at six months, our patient was able to mobilize with the aid of two elbow crutches and power had returned to 5/5 in distal extremities and 4+/5 in proximal extremities. The diagnosis was established based on the classical presentation of drug-induced neuropathy and negative investigatory findings for any alternative diagnoses.</p> <p>Conclusion</p> <p>We report the case of a patient presenting with an unusual complication of severe neuropathy and peripheral edema due to itraconazole. Clinicians should be alert to this association when encountered with neuropathy and/or edema in an itraconazole therapy recipient.</p

\u3ci\u3eCorrigendum to\u3c/i\u3e “Incorporation of crop phenology in Simple Biosphere Model (SiBcrop) to improve land-atmosphere carbon exchanges from croplands” published in Biogeosciences, 6, 969–986, 2009

In the above mentioned manuscript a mistake in Fig. 11 occured. The corrected version of the figure is as follows

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

Integration of Static and Dynamic Analysis Techniques for Checking Noninterference

In this article, we present an overview of recent combinations of deductive program verification and automatic test generation on the one hand and static analysis on the other hand, with the goal of checking noninterference. Noninterference is the non-functional property that certain confidential information cannot leak to certain public output, i.e., the confidentiality of that information is always preserved. We define the noninterference properties that are checked along with the individual approaches that we use in different combinations. In one use case, our framework for checking noninterference employs deductive verification to automatically generate tests for noninterference violations with an improved test coverage. In another use case, the framework provides two combinations of deductive verification with static analysis based on system dependence graphs to prove noninterference, thereby reducing the effort for deductive verification