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In this paper, we describe the design and implementation of anautomated 802.11 wireless network diagnostic system called Shaman. Since theend-to-end performance of user traffic is some combination of factors acrossall network layers, Shaman incorporates comprehensive, cross-layer models of802.11 network behavior and performance. These mod- els include broadbandinterference at the physical layer, per- packet link layer media access delaysand losses, network layer device mobility and association management, andtrans- port layer congestion and flow control. No one anomaly, fail- ure orinteraction is singularly responsible for all network problems, and that aholistic analysis is necessary to cover the range of problems experienced inreal networks. When users experience unsatisfactory performance at a particulartime, they can query Shaman for a diagnosis. Shaman will then profile auser’s traffic at that time, deter- mine the network events that shape theperformance profile, infer the causal sources of those events, and report there- sults to the user. We demonstrate the use of Shaman on an enterprisewireless network deployed in a university campus building, and illustrate theunderlying analysis Shaman per- forms on real network trouble reports submittedby users of the enterprise network.Pre-2018 CSE ID: CS2010-0959

Modern enterprise networks are of sufficient complexity that evensimple faults can be difficult to diagnose --- let alone transientoutages or service degradations. Nowhere is this problem more apparent than inthe 802.11-based wireless access networks now ubiquitous in the enterprise. Inaddition to the myriad complexities of the wired network, wireless networksface the additional challenges of shared spectrum, user mobility andauthentication management. Not surprisingly, few organizations have theexpertise, data or tools to decompose the underlying problems and interactionsresponsible for transient outages or performance degradations. In this paper,we present a set of analysis techniques and models to precisely determine allsources of data transfer delay due to media access and mobility in 802.11networks --- from the physical layer to the transport layer --- as well as theinteractions among them. While some sources of delay can be directly measured,many of the delay components, such as AP queuing, backoffs, contention, etc.,must be inferred. To infer these delays from measurements, we develop adetailed model of MAC protocol behavior, both as it is described in the 802.11specification as well as how it is implemented in vendor hardware. Combinedwith comprehensive traces of wireless activity taken from an enterprisenetwork, we produce a complete delay breakdown for packet transmissions andpinpoint problems that constrain connectivity or limit performance.Pre-2018 CSE ID: CS2007-0885

Purpose: Approximate dose calculation methods were used in the nominal dose distribution and the perturbed dose distributions due to uncertainties in a commercial treatment planning system (CTPS) for robust optimization in intensity‐modulated proton therapy (IMPT). We aimed to investigate whether the approximations influence plan quality, robustness, and interplay effect of the resulting IMPT plans for the treatment of locally advanced lung cancer patients. Materials and methods: Ten consecutively treated locally advanced nonsmall cell lung cancer (NSCLC) patients were selected. Two IMPT plans were created for each patient using our in‐house developed TPS, named "Solo," and also the CTPS, EclipseTM (Varian Medical Systems, Palo Alto, CA, USA), respectively. The plans were designed to deliver prescription doses to internal target volumes (ITV) drawn by a physician on averaged four‐dimensional computed tomography (4D‐CT). Solo plans were imported back to CTPS, and recalculated in CTPS for fair comparison. Both plans were further verified for each patient by recalculating doses in the inhalation and exhalation phases to ensure that all plans met clinical requirements. Plan robustness was quantified on all phases using dose‐volume‐histograms (DVH) indices in the worst‐case scenario. The interplay effect was evaluated for every plan using an in‐house developed software, which randomized starting phases of each field per fraction and accumulated dose in the exhalation phase based on the patient's breathing motion pattern and the proton spot delivery in a time‐dependent fashion. DVH indices were compared using Wilcoxon rank‐sum test. Results: Compared to the plans generated using CTPS on the averaged CT, Solo plans had significantly better target dose coverage and homogeneity (normalized by the prescription dose) in the worst‐case scenario [ITV D95%: 98.04% vs 96.28%, Solo vs CTPS, P = 0.020; ITV D5%–D95%: 7.20% vs 9.03%, P = 0.049] while all DVH indices were comparable in the nominal scenario. On the inhalation phase, Solo plans had better target dose coverage and cord Dmax in the nominal scenario [ITV D95%: 99.36% vs 98.45%, Solo vs CTPS, P = 0.014; cord Dmax: 20.07 vs 23.71 Gy(RBE), P = 0.027] with better target coverage and cord Dmax in the worst‐case scenario [ITV D95%: 97.89% vs 96.47%, Solo vs CTPS, P = 0.037; cord Dmax: 24.57 vs 28.14 Gy(RBE), P = 0.037]. On the exhalation phase, similar phenomena were observed in the nominal scenario [ITV D95%: 99.63% vs 98.87%, Solo vs CTPS, P = 0.037; cord Dmax: 19.67 vs 23.66 Gy(RBE), P = 0.039] and in the worst‐case scenario [ITV D95%: 98.20% vs 96.74%, Solo vs CTPS, P = 0.027; cord Dmax: 23.47 vs 27.93 Gy(RBE), P = 0.027]. In terms of interplay effect, plans generated by Solo had significantly better target dose coverage and homogeneity, less hot spots, and lower esophageal Dmean, and cord Dmax [ITV D95%: 101.81% vs 98.68%, Solo vs CTPS, P = 0.002; ITV D5%–D95%: 2.94% vs 7.51%, P = 0.002; cord Dmax: 18.87 vs 22.29 Gy(RBE), P = 0.014]. Conclusions: Solo‐generated IMPT plans provide improved cord sparing, better target robustness in all considered phases, and reduced interplay effect compared with CTPS. Consequently, the approximation methods currently used in commercial TPS programs may have space for improvement in generating optimal IMPT plans for patient cases with locally advanced lung cancer. [ABSTRACT FROM AUTHOR]

This Note analyzes Nepal's attempts to establish accountability and the rule of law in the aftermath of its ten-year civil war. It compares Nepal's treatment of persons implicated in gross human rights violations with the international human rights legal framework surrounding a state's international obligations, particularly in its use of transitional justice mechanisms. It argues that Nepal's failure to bring either administrative sanctions or criminal prosecutions against officials accused of human rights abuses--and its reliance instead on truth commissions--undermines the rule of law and violates the country's international human rights obligations. [ABSTRACT FROM AUTHOR]

Cough is an important symptom in children with acute and chronic respiratory disease. Daily cough is common in Cystic Fibrosis (CF) and increased cough is a symptom of pulmonary exacerbation. To date, cough assessment is primarily subjective in clinical practice and research. Attempts to develop objective, automatic cough counting tools have faced reliability issues in noisy environments and practical barriers limiting long-term use. This single-center pilot study evaluated usability, acceptability and performance of a mechanoacoustic sensor (MAS), previously used for cough classification in adults, in 36 children with CF over brief and multi-day periods in four cohorts. Children whose health was at baseline and who had symptoms of pulmonary exacerbation were included. We trained, validated, and deployed custom deep learning algorithms for accurate cough detection and classification from other vocalization or artifacts with an overall area under the receiver-operator characteristic curve (AUROC) of 0.96 and average precision (AP) of 0.93. Child and parent feedback led to a redesign of the MAS towards a smaller, more discreet device acceptable for daily use in children. Additional improvements optimized power efficiency and data management. The MAS's ability to objectively measure cough and other physiologic signals across clinic, hospital, and home settings is demonstrated, particularly aided by an AUROC of 0.97 and AP of 0.96 for motion artifact rejection. Examples of cough frequency and physiologic parameter correlations with participant-reported outcomes and clinical measurements for individual patients are presented. The MAS is a promising tool in objective longitudinal evaluation of cough in children with CF.

Drug resistance is a consequence of how most modern medicines work. Drugs exert pressure on cells that causes death or the evolution of resistance. Indeed, highly specific drugs are rendered ineffective by a single DNA mutation. In this study, we apply the drug methotrexate, which is widely used in cancer and rheumatoid arthritis, and perform evolution experiments on Baker's yeast to ask the different ways in which cells become drug resistant. Because of the conserved nature of biological pathways between yeast and man, our results can inform how the same mechanism may operate to render human cells resistant to treatment. Exposure of cells to small molecules and drug therapies imposes a strong selective pressure. As a result, cells rapidly acquire mutations in order to survive. These include resistant variants of the drug target as well as those that modulate drug transport and detoxification. To systematically explore how cells acquire drug resistance in an unbiased manner, rapid cost-effective approaches are required. Methotrexate, as one of the first rationally designed anticancer drugs, has served as a prototypic example of such acquired resistance. Known methotrexate resistance mechanisms include mutations that increase expression of the dihydrofolate reductase (DHFR) target as well as those that maintain function yet reduce the drug's binding affinity. Recent evidence suggests that target-independent, epistatic mutations can also result in resistance to methotrexate. Currently, however, the relative contribution of such unlinked resistance mutations is not well understood. To address this issue, we took advantage of Saccharomyces cerevisiae as a model eukaryotic system that combined with whole-genome sequencing and a rapid screening methodology, allowed the identification of causative mutations that modulate resistance to methotrexate. We found a recurrent missense mutation in SEC21 (orthologous to human COPG1), which we confirmed in 10 de novo methotrexate-resistant strains. This sec21 allele (S96L) behaves as a recessive, gain-of-function allele, conferring methotrexate resistance that is abrogated by the presence of a wild-type copy of SEC21 These observations indicate that the Sec21p/COPI transport complex has previously uncharacterized roles in modulating methotrexate stress., (Copyright © 2017 Wong et al.)

Systematic analyses of essential gene function using mutant collections in Saccharomyces cerevisiae have been conducted using collections of heterozygous diploids, promoter shut-off alleles, through alleles with destabilized mRNA, destabilized protein, or bearing mutations that lead to a temperature-sensitive (ts) phenotype. We previously described a method for construction of barcoded ts alleles in a systematic fashion. Here we report the completion of this collection of alleles covering 600 essential yeast genes. This resource covers a larger gene repertoire than previous collections and provides a complementary set of strains suitable for single gene and genomic analyses. We use deep sequencing to characterize the amino acid changes leading to the ts phenotype in half of the alleles. We also use high-throughput approaches to describe the relative ts behavior of the alleles. Finally, we demonstrate the experimental usefulness of the collection in a high-content, functional genomic screen for ts alleles that increase spontaneous P-body formation. By increasing the number of alleles and improving the annotation, this ts collection will serve as a community resource for probing new aspects of biology for essential yeast genes., (Copyright © 2015 Kofoed et al.)