SIG-DB: leveraging homomorphic encryption to Securely Interrogate privately held Genomic DataBases

Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic data. As the quantity and value of private genomic data grows, so does the incentive to acquire and protect such data, which creates a need to store and process these data securely. We present an algorithm for the Secure Interrogation of Genomic DataBases (SIG-DB). The SIG-DB algorithm enables databases of genomic sequences to be searched with an encrypted query sequence without revealing the query sequence to the Database Owner or any of the database sequences to the Querier. SIG-DB is the first application of its kind to take advantage of locality-sensitive hashing and homomorphic encryption to allow generalized sequence-to-sequence comparisons of genomic data.Comment: 38 pages, 3 figures, 4 tables, 1 supplemental table, 7 supplemental figure

tele-Substitution Reactions in the Synthesis of a Promising Class of 1,2,4-Triazolo[4,3-a]pyrazine-Based Antimalarials

We have discovered and studied a tele-substitution reaction in a biologically important heterocyclic ring system. Conditions that favor the tele-substitution pathway were identified: the use of increased equivalents of the nucleophile or decreased equivalents of base or the use of softer nucleophiles, less polar solvents, and larger halogens on the electrophile. Using results from X-ray crystallographic and isotope labeling experiments, a mechanism for this unusual transformation is proposed. We focused on this triazolopyrazine as it is the core structure of the in vivo active antiplasmodium compounds of Series 4 of the Open Source Malaria consortium

Kidney cell electrophoresis in space flight: Rationale, methods, results and flow cytometry applications

Cultures of human embryonic kidney cells consistently contain an electrophoretically separable subpopulation of cells that produce high levels of urokinase and have an electrophoretic mobility about 85 percent as high as that of the most mobile human embryonic kidney cells. This subpopulation is rich in large epithelioid cells that have relatively little internal structure. When resolution and throughput are adequate, free fluid electrophoresis can be used to isolate a broad band of low mobility cells which also produces high levels of plasminogen activators (PAs). In the course of performing this, it was discovered that all electrophoretic subpopulations of cultured human embryonic kidney cells produce some PAs and that separate subpopulations produce high quantities of different types of PA's. This information and the development of sensitive assays for this project have provided new insights into cell secretion mechanisms related to fibrinolysis. These advances would probably not have been made without the NASA program to explore fundamental questions of free fluid electrophoresis in space

Possibly all of that and then some: scalar implicatures are understood in two steps

Scalar implicatures often incur a processing cost in sentence comprehension tasks. We used a novel mouse-tracking technique in a sentence verification paradigm to test different accounts of this effect. We compared a two-step account, in which people access a basic meaning and then enrich the basic meaning to form the scalar implicature, against a one-step account, in which the scalar implicature is directly incorporated into the sentence representation. Participants read sentences and used a computer mouse to indicate whether each sentence was true or false. Three experiments found that when verifying sentences like “some elephants are mammals”, average mouse paths initially moved towards the true target and then changed direction mid-flight to select the false target. This supports the two-step account of implicatures. We discuss the results in relation to previous findings on scalar implicatures and theoretical accounts of pragmatic inference

Environmental conditions and vehicle disturbance influence stress behaviors in a working Harris’s Hawk (Parabuteo unicinctus)

Harris’s hawk (Parabuteo unicinctus) is used for pest control, as their presence can deter wild birds such as gulls. Working Harris’s hawk on UK waste sites is permitted in accordance with regulations and legislation. This study investigated the general environment of a waste site compound yard where a single Harris’s hawk was flown for pest control. The hawk’s behaviors were evaluated in an ethogram, alongside environmental measures, and disturbance levels. Data was analyzed using Generalised Linear Latent Variable Models (GLLVM) to elucidate the effects of disturbance and environment on hawk behaviors. Results suggested cloudy conditions encouraged grooming responses that were normal and relaxed in their nature. Rain, sun and wind conditions increased recognized stress behaviors. Frequency of disturbance by construction vehicles inside the compound increased stress behaviors, such that keepers are recommended to revise welfare conditions. Increased stress behaviors by birds worked in dynamic environments like waste recycling yards could potentially elicit damaging illness such as feather breaking behavior. Reducing stress factors for Harris’s hawk in industrial working yards combined with amending husbandry practices will improve welfare for the species

Community cleavages: gay and bisexual men's perceptions of gay and mainstream community acceptance in the post-AIDS, post-rights era

Changes in gay and bisexual men's connectedness to the gay community are related to the declining public visibility of HIV/AIDS and greater acceptance for homosexuality and bisexuality in mainstream society. Little work, however, has focused on perceived acceptance for subgroups within the gay community or broader society. Using interviews (n = 20) and a survey (n = 202) of gay and bisexual men in a mid-sized Canadian city, we find perceived hierarchies of acceptance for the various subgroups as well as an age effect wherein middle-aged men perceive the least acceptance for all groups. These differences are linked with the uneven impact of social, political, and institutional changes relevant to gay and bisexual men in Canada

Genetic structure and admixture in sheep from terminal breeds in the United States

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s FST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s FST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using ADMIXTURE, and based on cross-validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness

Further Evaluation of the Associations Between Psychopathic Traits and Symptoms of PTSD and Depression in a Nonclinical Sample

Examining psychopathic traits at the factor or facet level has revealed that various aspects of psychopathy may be differentially related, even in opposing directions, to important outcomes (e.g., intelligence, emotion regulation). Empirical work on relations between psychopathy and internalizing disorders, such as posttraumatic stress disorder (PTSD) and depression, has provided evidence for a positive association with antisocial traits. However, findings for the affective domain have been more equivocal. The current study (N = 732) sought to replicate past findings of the positive association of antisocial psychopathic traits with higher levels of PTSD and depressive symptoms, and to further explore associations between affective traits of psychopathy and these disorders using two measures of psychopathy. Results confirmed prior findings of a positive correlation between antisocial features and self-reported PTSD/Depression symptom severity, but they did not provide evidence for any association with affective traits. Future research using longitudinal designs is needed to begin establishing temporal ordering of the psychopathy–internalizing relationship

Perceptions of Precision Agriculture Technologies in the U.S. Fresh Apple Industry

Advances in precision agriculture technologies provide opportunities to improve the efficiency of agricultural production systems, especially for high-value specialty crops such as fresh apples (Malus domestica). We distributed an online survey to apple growers in Washington, New York, and Michigan to elicit stakeholder perceptions of precision agriculture technologies. Findings from this study demonstrated that growers are willing to adopt precision agriculture technologies when they receive results from applied research projects and are engaged with active extension programs. The availability of customized services and purchasing and rental options may minimize the effects of the economies of size that create barriers to adopting increasing access to technologies. Finally, respondents deemed collaborative efforts between industry and academic institutions crucial for adapting the innovation to better address the needs of growers