High-level Cryptographic Abstractions

The interfaces exposed by commonly used cryptographic libraries are clumsy, complicated, and assume an understanding of cryptographic algorithms. The challenge is to design high-level abstractions that require minimum knowledge and effort to use while also allowing maximum control when needed. This paper proposes such high-level abstractions consisting of simple cryptographic primitives and full declarative configuration. These abstractions can be implemented on top of any cryptographic library in any language. We have implemented these abstractions in Python, and used them to write a wide variety of well-known security protocols, including Signal, Kerberos, and TLS. We show that programs using our abstractions are much smaller and easier to write than using low-level libraries, where size of security protocols implemented is reduced by about a third on average. We show our implementation incurs a small overhead, less than 5 microseconds for shared key operations and less than 341 microseconds (< 1%) for public key operations. We also show our abstractions are safe against main types of cryptographic misuse reported in the literature

Characterisation of novel biomass degradation enzymes from the genome of <i>Cellulomonas fimi</i>

Recent analyses of genome sequences belonging to cellulolytic bacteria have revealed many genes potentially coding for cellulosic biomass degradation enzymes. Annotation of these genes however, is based on few biochemically characterised examples. Here we present a simple strategy based on BioBricks for the rapid screening of candidate genes expressed in Escherichia coli. As proof of principle we identified over 70 putative biomass degrading genes from bacterium Cellulomonas fimi, expressing a subset of these in BioBrick format. Six novel genes showed activity in E. coli. Four interesting enzymes were characterised further. α-l-arabinofuranosidase AfsB, β-xylosidases BxyF and BxyH and multi-functional β-cellobiosidase/xylosidase XynF were partially purified to determine their optimum pH, temperature and kinetic parameters. One of these enzymes, BxyH, was unexpectedly found to be highly active at strong alkaline pH and at temperatures as high as 100 °C. This report demonstrates a simple method of quickly screening and characterising putative genes as BioBricks

Use of Biologic Therapy by Pregnant Women With Inflammatory Bowel Disease Does Not Affect Infant Response to Vaccines

BACKGROUND & AIMS: In women with inflammatory bowel diseases (IBDs), exposure to immunomodulator or biologic therapy has not been associated with adverse events during pregnancy or outcomes of newborns. We investigated whether exposure of patients to these agents during pregnancy affects serologic responses to vaccines in newborns. METHODS: We collected data from the Pregnancy in IBD and Neonatal Outcomes registry, which records outcomes of pregnant women with diagnosis of IBD receiving care at multiple centers in the United States, from 2007 through 2016. Serum samples collected from infants at least 7 months old were analyzed for titers of antibodies to Haemophilus influenzae B (HiB) or tetanus toxin; mothers completed a survey of vaccine practices and outcomes from July 2013 through October 2016. Umbilical cord blood samples from 33 infants were assayed for concentration of biologic agents. Vaccination response was compared between infants born to mothers exposed to biologic therapy (infliximab, adalimumab, certolizumab pegol, golimumab, natalizumab, vedolizumab, or ustekinumab-either as a single agent or in combination with an immunomodulator, at any time between conception and delivery) and infants born to unexposed mothers. RESULTS: A total of 179 women completed the vaccine survey (26 biologic unexposed, 153 exposed to a biologic agent). We found no significant difference in proportions of infants with protective antibody titers against HiB born to exposed mothers (n = 42, 71%) vs unexposed mothers (n = 8, 50%) (P = .41). We also found no difference in the proportion of infants with protective antibody titers to tetanus toxoid born to exposed mothers (80%) vs unexposed mothers (75%) (P = .66). The median concentration of infliximab in cord blood did not differ significantly between infants with vs without protective antibody titers to HiB (P = .30) or tetanus toxoid (P = .93). Mild reactions were observed in 7/40 infants who received rotavirus vaccine and whose mothers had been exposed to biologic therapies. CONCLUSIONS: Vaccination of infants against HiB and tetanus toxin, based on antibody titers measured when infants were at least 7 months old, does not appear to be affected by in utero exposure to biologic therapy

Who Benefits from KIPP?

Charter schools affiliated with the Knowledge is Power Program (KIPP) are emblematic of the No Excuses approach to public education. These schools feature a long school day, an extended school year, selective teacher hiring, strict behavior norms and a focus on traditional reading and math skills. We use applicant lotteries to evaluate the impact of KIPP Academy Lynn, a KIPP charter school that is mostly Hispanic and has a high concentration of limited English proficiency (LEP) and special-need students, groups that charter critics have argued are typically under-served. The results show overall gains of 0.35 standard deviations in math and 0.12 standard deviations in reading for each year spent at KIPP Lynn. LEP students, special education students, and those with low baseline scores benefit more from time spent at KIPP than do other students, with reading gains coming almost entirely from the LEP group.

Positive Surgical Margins in the 10 Most Common Solid Cancers.

A positive surgical margin (PSM) following cancer resection oftentimes necessitates adjuvant treatments and carries significant financial and prognostic implications. We sought to compare PSM rates for the ten most common solid cancers in the United States, and to assess trends over time. Over 10 million patients were identified in the National Cancer Data Base from 1998-2012, and 6.5 million had surgical margin data. PSM rates were compared between two time periods, 1998-2002 and 2008-2012. PSM was positively correlated with tumor category and grade. Ovarian and prostate cancers had the highest PSM prevalence in women and men, respectively. The highest PSM rates for cancers affecting both genders were seen for oral cavity tumors. PSM rates for breast cancer and lung and bronchus cancer in both men and women declined over the study period. PSM increases were seen for bladder, colon and rectum, and kidney and renal pelvis cancers. This large-scale analysis appraises the magnitude of PSM in the United States in order to focus future efforts on improving oncologic surgical care with the goal of optimizing value and improving patient outcomes

Detection of Planetary and Stellar Companions to Neighboring Stars via a Combination of Radial Velocity and Direct Imaging Techniques

13 pages, 6 figures, 4 tables, accepted for publication in the Astronomical Journal (submitted 25 Feb 2019; accepted 28 April 2019). Machine readable tables and Posteriors from the RadVel fits are available here: http://stephenkane.net/rvfits.tarThe sensitivities of radial velocity (RV) surveys for exoplanet detection are extending to increasingly longer orbital periods, where companions with periods of several years are now being regularly discovered. Companions with orbital periods that exceed the duration of the survey manifest in the data as an incomplete orbit or linear trend, a feature that can either present as the sole detectable companion to the host star, or as an additional signal overlain on the signatures of previously discovered companion(s). A diagnostic that can confirm or constrain scenarios in which the trend is caused by an unseen stellar rather than planetary companion is the use of high-contrast imaging observations. Here, we present RV data from the Anglo-Australian Planet Search (AAPS) for 20 stars that show evidence of orbiting companions. Of these, six companions have resolved orbits, with three that lie in the planetary regime. Two of these (HD 92987b and HD 221420b) are new discoveries. Follow-up observations using the Differential Speckle Survey Instrument (DSSI) on the Gemini South telescope revealed that 5 of the 20 monitored companions are likely stellar in nature. We use the sensitivity of the AAPS and DSSI data to place constraints on the mass of the companions for the remaining systems. Our analysis shows that a planetary-mass companion provides the most likely self-consistent explanation of the data for many of the remaining systems.Peer reviewedFinal Accepted Versio

A report on the piloting of a novel computer-based medical case simulation for teaching and formative assessment of diagnostic laboratory testing

Objectives: Insufficient attention has been given to how information from computer-based clinical case simulations is presented, collected, and scored. Research is needed on how best to design such simulations to acquire valid performance assessment data that can act as useful feedback for educational applications. This report describes a study of a new simulation format with design features aimed at improving both its formative assessment feedback and educational function. Methods: Case simulation software (LabCAPS) was developed to target a highly focused and well-defined measurement goal with a response format that allowed objective scoring. Data from an eight-case computer-based performance assessment administered in a pilot study to 13 second-year medical students was analyzed using classical test theory and generalizability analysis. In addition, a similar analysis was conducted on an administration in a less controlled setting, but to a much large sample (n=143), within a clinical course that utilized two random case subsets from a library of 18 cases. Results: Classical test theory case-level item analysis of the pilot assessment yielded an average case discrimination of 0.37, and all eight cases were positively discriminating (range=0.11&#x2013;0.56). Classical test theory coefficient alpha and the decision study showed the eight-case performance assessment to have an observed reliability of &#x03C3;=G=0.70. The decision study further demonstrated that a G=0.80 could be attained with approximately 3 h and 15 min of testing. The less-controlled educational application within a large medical class produced a somewhat lower reliability for eight cases (G=0.53). Students gave high ratings to the logic of the simulation interface, its educational value, and to the fidelity of the tasks. Conclusions: LabCAPS software shows the potential to provide formative assessment of medical students&#x2019; skill at diagnostic test ordering and to provide valid feedback to learners. The perceived fidelity of the performance tasks and the statistical reliability findings support the validity of using the automated scores for formative assessment and learning. LabCAPS cases appear well designed for use as a scored assignment, for stimulating discussions in small group educational settings, for self-assessment, and for independent learning. Extension of the more highly controlled pilot assessment study with a larger sample will be needed to confirm its reliability in other assessment applications

Supersymmetric Flavor Models and the B --> phi K_S Anomaly

We consider the flavor structure of supersymmetric theories that can account for the deviation of the observed time-dependent CP asymmetry in B --> phi K_S from the standard model prediction. Assuming simple flavor symmetries and effective field theory, we investigate possible correlations between sizable supersymmetric contributions to b --> s transitions and to flavor changing processes that are more tightly constrained. With relatively few assumptions, we determine the properties of minimal Yukawa and soft mass textures that are compatible with the desired supersymmetric flavor-changing effect and constraints. We then present explicit models that are designed (at least approximately) to realize these textures. In particular, we present an Abelian model based on a single U(1) factor and a non-trivial extra-dimensional topography that can explain the CP asymmetry in B --> phi K_S, while suppressing other supersymmetric flavor changing effects through a high degree of squark-quark alignment.Comment: 18 pages LaTeX, 3 eps figure