Sweet Summer Breeze

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Short-Term Relapse Quantitation as a Fully Surrogate Endpoint for Long-Term Sustained Progression of Disability in RRMS Patients Treated with Natalizumab

Time to sustained worsening in the expanded disability status scale as the standard for evaluating the accumulation of disability has been used as a measure of clinical efficacy in many relapsing-remitting multiple sclerosis (RRMS) clinical trials. However, this measurement usually requires a large sample and long-term study to demonstrate the treatment effect. Annualized relapse rate or time to first relapse is also widely used as alternative measurements of clinical efficacy. A formal statistical validation of short-term relapse activity as a surrogate endpoint for long-term sustained progression of disability could potentially permit smaller, shorter, and less expensive clinical trials in RRMS. Four statistical validation/evaluation approaches consistently showed that relapse activity through one year of treatment serves as statistically valid surrogate endpoint for time to sustained progression of disability. The analysis demonstrates that long-term sustained progression of disability can be predicted by short-term relapse measures with 4 consistent validations of statistical approaches, including a formal statistical hypothesis test. This was demonstrated in a large phase III trial of natalizumab and showed that the beneficial clinical effect of natalizumab on sustained progression of disability at 2 years in patients with RRMS can be predicted by the total number of relapses at 1 year

Parameterized Complexity of the k-anonymity Problem

The problem of publishing personal data without giving up privacy is becoming increasingly important. An interesting formalization that has been recently proposed is the $k$-anonymity. This approach requires that the rows of a table are partitioned in clusters of size at least $k$ and that all the rows in a cluster become the same tuple, after the suppression of some entries. The natural optimization problem, where the goal is to minimize the number of suppressed entries, is known to be APX-hard even when the records values are over a binary alphabet and $k=3$, and when the records have length at most 8 and $k=4$ . In this paper we study how the complexity of the problem is influenced by different parameters. In this paper we follow this direction of research, first showing that the problem is W[1]-hard when parameterized by the size of the solution (and the value $k$). Then we exhibit a fixed parameter algorithm, when the problem is parameterized by the size of the alphabet and the number of columns. Finally, we investigate the computational (and approximation) complexity of the $k$-anonymity problem, when restricting the instance to records having length bounded by 3 and $k=3$. We show that such a restriction is APX-hard.Comment: 22 pages, 2 figure

Trust and reputation policy-based mechanisms for self-protection in autonomic communications

Currently, there is an increasing tendency to migrate the management of communications and information systems onto the Web. This is making many traditional service support models obsolete. In addition, current security mechanisms are not sufficiently robust to protect each management system and/or subsystem from web-based intrusions, malware, and hacking attacks. This paper presents research challenges in autonomic management to provide self-protection mechanisms and tools by using trust and reputation concepts based on policy-based management to decentralize management decisions. This work also uses user-based reputation mechanisms to help enforce trust management in pervasive and communications services. The scope of this research is founded in social models, where the application of trust and reputation applied in communication systems helps detect potential users as well as hackers attempting to corrupt management operations and services. These so-called “cheating services” act as “attacks”, altering the performance and the security in communication systems by consumption of computing or network resources unnecessarily

Multitrophic enemy escape of invasive Phragmites australis and its introduced herbivores in North America

© 2015, Springer International Publishing Switzerland. One explanation for why invasive species are successful is that they escape natural enemies from their native range or experience lower attack from natural enemies in the introduced range relative to native species (i.e., the enemy-release hypothesis). However, little is known about how invasive plants interact with co-introduced herbivores or natural enemies of the introduced herbivores. We focus on Phragmites australis, a wetland grass native to Europe (EU) and North America (NA). Within the past 100–150 years, invasive European genotypes of P. australis and several species of specialist Lipara gall flies have spread within NA. On both continents we surveyed P. australis patches for Lipara infestation (proportion of stems infested) and Lipara mortality from natural enemies. Our objectives were to assess evidence for enemy-release in the invaded (NA) versus native (EU) range and whether Lipara infestation or mortality differed between invasive and native P. australis genotypes in NA. Enemy-release varied regionally; Lipara were absent throughout most of NA, supporting enemy-release of Phragmites. However, where Lipara were present, the proportion of invasive P. australis stems infested with Lipara was higher in the introduced (11 %) than native range (\u3c1 \u3e%). This difference may be explained by the absence of Lipara parasitoids in our NA survey, strongly supporting enemy-release of Lipara. In NA, native P. australis genotypes exhibited higher Lipara infestation (32 %) than invasive genotypes (11 %), largely driven by L. rufitarsis. We attribute genotypic differences in infestation to a combination of Lipara exhibiting 34 % greater performance (gall diameter) and suffering four times less vertebrate predation on native than invasive genotypes. Our study suggests that complex interactions can result from the co-introduction of plants and their herbivores, and that a multitrophic perspective is required for investigating how biotic interactions influence invasion success

Opportunities and Challenges: Hepatitis C Testing and Treatment Access Experiences Among People in Methadone and Buprenorphine Treatment During COVID-19, Arizona, 2021

Introduction: The purpose of this study was to characterize hepatitis C virus screening and treatment access experiences among people in treatment for opioid use disorder in Arizona during COVID-19. Methods: Arizonans receiving treatment for opioid use disorder from methadone clinics and buprenorphine providers during COVID-19 were interviewed about hepatitis C virus testing, curative treatment, and knowledge about screening recommendations. Interviews were conducted with 121 people from August 4, 2021 to October 10, 2021. Qualitative data were coded using the categories of hepatitis C virus testing, knowledge of screening recommendations, diagnosis, and experiences seeking curative treatment. Data were also quantitated for bivariate testing with outcome variables of last hepatitis C virus test, diagnosis, and curative treatment process. Findings were arrayed along an adapted hepatitis C virus cascade framework to inform program and policy improvements. Results: Just over half of the sample reported ever having tested for hepatitis C virus (51.2%, n=62) and of this group, 58.1% were tested in the past 12 months. Among those who were ever tested, 54.8% reported a hepatitis C virus diagnosis and 16.1% reported either being in treatment or having been declared cured of the hepatitis C virus. Among those who were diagnosed with hepatitis C, 14.7% indicated that they unsuccessfully tried to access curative treatment and would not attempt to again. Reasons cited for not accessing or receiving curative treatment included beliefs about treatment safety, barriers created by access requirements, natural resolution of the infection, and issues with healthcare coverage and authorization. Conclusions: Structural barriers continue to prevent curative hepatitis C virus treatment access. Given that methadone and buprenorphine treatment providers serve patients who are largely undiagnosed or treated for hepatitis C virus, opportunities exist for them to screen their patients regularly and provide support for and/or navigation to hepatitis C virus curative treatment

Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer.

Functional redundancy shared by paralog genes may afford protection against genetic perturbations, but it can also result in genetic vulnerabilities due to mutual interdependency1-5. Here, we surveyed genome-scale short hairpin RNA and CRISPR screening data on hundreds of cancer cell lines and identified MAGOH and MAGOHB, core members of the splicing-dependent exon junction complex, as top-ranked paralog dependencies6-8. MAGOHB is the top gene dependency in cells with hemizygous MAGOH deletion, a pervasive genetic event that frequently occurs due to chromosome 1p loss. Inhibition of MAGOHB in a MAGOH-deleted context compromises viability by globally perturbing alternative splicing and RNA surveillance. Dependency on IPO13, an importin-β receptor that mediates nuclear import of the MAGOH/B-Y14 heterodimer9, is highly correlated with dependency on both MAGOH and MAGOHB. Both MAGOHB and IPO13 represent dependencies in murine xenografts with hemizygous MAGOH deletion. Our results identify MAGOH and MAGOHB as reciprocal paralog dependencies across cancer types and suggest a rationale for targeting the MAGOHB-IPO13 axis in cancers with chromosome 1p deletion

Modeling genomic diversity and tumor dependency in malignant melanoma

The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and "druggable" effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative "driver" events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors

A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS)

<p>Abstract</p> <p>Background</p> <p>Cardiomyopathy syndrome (CMS) is a severe disease affecting large farmed Atlantic salmon. Mortality often appears without prior clinical signs, typically shortly prior to slaughter. We recently reported the finding and the complete genomic sequence of a novel piscine reovirus (PRV), which is associated with another cardiac disease in Atlantic salmon; heart and skeletal muscle inflammation (HSMI). In the present work we have studied whether PRV or other infectious agents may be involved in the etiology of CMS.</p> <p>Results</p> <p>Using high throughput sequencing on heart samples from natural outbreaks of CMS and from fish experimentally challenged with material from fish diagnosed with CMS a high number of sequence reads identical to the PRV genome were identified. In addition, a sequence contig from a novel totivirus could also be constructed. Using RT-qPCR, levels of PRV in tissue samples were quantified and the totivirus was detected in all samples tested from CMS fish but not in controls. <it>In situ </it>hybridization supported this pattern indicating a possible association between CMS and the novel piscine totivirus.</p> <p>Conclusions</p> <p>Although causality for CMS in Atlantic salmon could not be proven for either of the two viruses, our results are compatible with a hypothesis where, in the experimental challenge studied, PRV behaves as an opportunist whereas the totivirus might be more directly linked with the development of CMS.</p

Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis

A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an analysis of somatic copy-number aberrations in 486 gastrointestinal adenocarcinomas including 296 esophageal and gastric cancers. Focal amplifications were substantially more prevalent in gastric/esophageal adenocarcinomas than colorectal tumors. We identified 64 regions of significant recurrent amplification and deletion, some shared and others unique to the adenocarcinoma types examined. Amplified genes were noted in 37% of gastric/esophageal tumors, including in therapeutically targetable kinases such as ERBB2, FGFR1, FGFR2, EGFR, and MET, suggesting the potential use of genomic amplifications as biomarkers to guide therapy of gastric and esophageal cancers where targeted therapeutics have been less developed compared with colorectal cancers. Amplified loci implicated genes with known involvement in carcinogenesis but also pointed to regions harboring potentially novel cancer genes, including a recurrent deletion found in 15% of esophageal tumors where the Runt transcription factor subunit RUNX1 was implicated, including by functional experiments in tissue culture. Together, our results defined genomic features that were common and distinct to various gut-derived adenocarcinomas, potentially informing novel opportunities for targeted therapeutic interventions