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

Micro-Raman Study of Stress Distribution Generated in Silicon During Proximity Rapid Thermal Diffusion

proximity rapid thermal diffusion (RTD). A compressive stress was found on the whole silicon wafer after 15 s RTD. After 165 s RTD, the distribution of the stress across the wafer was found to be different: compressive at the edge and tensile at the middle. Thermal stress was relieved in the RTD wafers via slip dislocations. These slip dislocations were observed in the product wafers using optical microscopy. Slip lines propagated from the wafer edge to the wafer centre in eight preferred positions of maximum induced stress. The thermally induced stress and the slip dislocation density increased with time spent at the RTD peak temperature

Clinicopathologic features of endometrial cancer with mismatch repair deficiency

The inclusion of DNA mismatch repair (MMR) evaluation as a standard of care for endometrial cancer management will result in a growing population of patients with MMR deficiency and negative germline Lynch syndrome testing (MMR-deficient). In this systematic review and study, the clinicopathologic features of endometrial cancer in patients with MMR-intact, MLH1 methylation positive, MMR-deficient or Lynch syndrome are evaluated. A systematic search of online databases between 1990 and 2018 identified studies of endometrial cancer patients with tumour testing (MMR protein immunohistochemistry or microsatellite instability) and germline assessment for Lynch syndrome. Extracted data included tumour testing, germline genetic testing, age, body mass index (BMI), family history, tumour stage, grade and histologic type. Associations between MMR-intact, MLH1 methylation positive, MMR-deficient and Lynch syndrome groups were analysed using descriptive statistics. The comprehensive search produced 4,400 publications, 29 met inclusion criteria. A total of 7,057 endometrial cancer cases were identified, 1,612 with abnormal immunohistochemistry, 977 with microsatellite instability. Nine-hundred patients underwent germline genetic testing, identifying 212 patients with Lynch syndrome. Patients in the Lynch syndrome and MMR-deficient groups were significantly younger than patients in the MMR-intact and MLH1 methylation positive groups. Patients with MMR-intact tumours had the highest BMI, followed by MMR-deficient, then Lynch syndrome. MMR-intact tumours were more likely to be grade I at diagnosis than other groups. Patients with Lynch syndrome and MMR-deficient tumours were less likely to have stage I disease as compared to patients with MMR-intact tumours. Endometrial cancer patients with MMR-deficient tumours have similar features to those with germline Lynch syndrome mutations, including age, grade, histology and stage. Even in the absence of a germline mutation, tumour evaluation for MMR status may have important clinical implications

Interfacial characteristics and microstructural evolution of ceramics exposed to high temperature sand laden combustion environments

Sand laden combustion environments are a current challenge plaguing ceramic thermal barrier coatings (TBCs) and environmental barrier coatings (EBCs) on metallic and emerging ceramic matrix composite (CMC) turbomachinery components. Exposure of thermal and environmental barrier coatings on ceramic matrix composites to environmental particulate laden deteriorates the ceramic structure via chemical reactions and infiltration into pore structures. The challenge of environmental particulates, collectively referred to as calcium-magnesium-aluminosilicate (CMAS), is expected to be exacerbated in future components that utilize ceramic matric composites (CMCs), since the higher operating temperatures will accelerate particulate melting, infiltration, and diffusion kinetics. This study first presents efforts at ARL to develop sandphobic coatings resistant to CMAS infiltration and deposition. The results of a recent full scale sand ingestion engine test used to evaluate several ARL layered and blended coating compositions are presented. The study also includes the evaluation of interactions of CMAS plasma sprayed environmental barrier coatings and HfO2-Si bond coats on SiC/SiC CMCs in rig simulated engine test conditions. The focus is on the microstructural evolution of the coatings and the interfacial characteristics between the TBCs and EBCs and CMAS. Interfaces between coating constituents are also of interest in order to tailor coatings with superior thermal, structural, and chemical characteristics. Controlled studies on YSZ-based ceramic compacts are also performed in order to gain a more fundamental understanding of the effect of porosity on infiltration kinetics, as well as the nature of interfaces and interfacial products wrought by CMAS infiltration into YSZ ceramic grain boundaries. These model studies on YSZ are conducted by immersing the ceramic compacts into AFRL-02 sand and exposing the system to temperatures of up to 1300 °C. X-ray diffraction, scanning electron microscopy, transmission electron microscopy, electron back scattered diffraction, and focused ion beam (milling and imaging) are utilized for microstructural and interfacial characterization of the CMAS reacted thermal and environmental barrier coating systems

Ballistic InSb Nanowires and Networks via Metal-Sown Selective Area Growth

Selective area growth is a promising technique to realize semiconductor-superconductor hybrid nanowire networks, potentially hosting topologically protected Majorana-based qubits. In some cases, however, such as the molecular beam epitaxy of InSb on InP or GaAs substrates, nucleation and selective growth conditions do not necessarily overlap. To overcome this challenge, we propose a metal-sown selective area growth (MS SAG) technique, which allows decoupling selective deposition and nucleation growth conditions by temporarily isolating these stages. It consists of three steps: (i) selective deposition of In droplets only inside the mask openings at relatively high temperatures favoring selectivity, (ii) nucleation of InSb under Sb flux from In droplets, which act as a reservoir of group III adatoms, done at relatively low temperatures, favoring nucleation of InSb, and (iii) homoepitaxy of InSb on top of the formed nucleation layer under a simultaneous supply of In and Sb fluxes at conditions favoring selectivity and high crystal quality. We demonstrate that complex InSb nanowire networks of high crystal and electrical quality can be achieved this way. We extract mobility values of 10※000-25※000 cm V s consistently from field-effect and Hall mobility measurements across single nanowire segments as well as wires with junctions. Moreover, we demonstrate ballistic transport in a 440 nm long channel in a single nanowire under a magnetic field below 1 T. We also extract a phase-coherent length of ∼8 μm at 50 mK in mesoscopic rings

HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention

Despite a high current standard of care in antiretroviral therapy for HIV, multidrug-resistant strains continue to emerge, underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic. We report a new class of small molecule antiretroviral compounds that directly target HIV-1 capsid (CA) via a novel mechanism of action. The compounds exhibit potent antiviral activity against HIV-1 laboratory strains, clinical isolates, and HIV-2, and inhibit both early and late events in the viral replication cycle. We present mechanistic studies indicating that these early and late activities result from the compound affecting viral uncoating and assembly, respectively. We show that amino acid substitutions in the N-terminal domain of HIV-1 CA are sufficient to confer resistance to this class of compounds, identifying CA as the target in infected cells. A high-resolution co-crystal structure of the compound bound to HIV-1 CA reveals a novel binding pocket in the N-terminal domain of the protein. Our data demonstrate that broad-spectrum antiviral activity can be achieved by targeting this new binding site and reveal HIV CA as a tractable drug target for HIV therapy

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Accelerating cryoprotectant diffusion kinetics improves cryopreservation of pancreatic islets

Funder: W. D. Armstrong Fund (School of Technology, University of Cambridge)Abstract: Cryopreservation offers the potential to increase the availability of pancreatic islets for treatment of diabetic patients. However, current protocols, which use dimethyl sulfoxide (DMSO), lead to poor cryosurvival of islets. We demonstrate that equilibration of mouse islets with small molecules in aqueous solutions can be accelerated from > 24 to 6 h by increasing incubation temperature to 37 °C. We utilize this finding to demonstrate that current viability staining protocols are inaccurate and to develop a novel cryopreservation method combining DMSO with trehalose pre-incubation to achieve improved cryosurvival. This protocol resulted in improved ATP/ADP ratios and peptide secretion from β-cells, preserved cAMP response, and a gene expression profile consistent with improved cryoprotection. Our findings have potential to increase the availability of islets for transplantation and to inform the design of cryopreservation protocols for other multicellular aggregates, including organoids and bioengineered tissues

Formulation Pre-screening of Inhalation Powders Using Computational Atom–Atom Systematic Search Method

The synthonic modeling approach provides a molecule-centered understanding of the surface properties of crystals. It has been applied extensively to understand crystallization processes. This study aimed to investigate the functional relevance of synthonic modeling to the formulation of inhalation powders by assessing cohesivity of three active pharmaceutical ingredients (APIs, fluticasone propionate (FP), budesonide (Bud), and salbutamol base (SB)) and the commonly used excipient, α-lactose monohydrate (LMH). It is found that FP (−11.5 kcal/mol) has a higher cohesive strength than Bud (−9.9 kcal/mol) or SB (−7.8 kcal/mol). The prediction correlated directly to cohesive strength measurements using laser diffraction, where the airflow pressure required for complete dispersion (CPP) was 3.5, 2.0, and 1.0 bar for FP, Bud, and SB, respectively. The highest cohesive strength was predicted for LMH (−15.9 kcal/mol), which did not correlate with the CPP value of 2.0 bar (i.e., ranking lower than FP). High FP–LMH adhesive forces (−11.7 kcal/mol) were predicted. However, aerosolization studies revealed that the FP–LMH blends consisted of agglomerated FP particles with a large median diameter (∼4–5 μm) that were not disrupted by LMH. Modeling of the crystal and surface chemistry of LMH identified high electrostatic and H-bond components of its cohesive energy due to the presence of water and hydroxyl groups in lactose, unlike the APIs. A direct comparison of the predicted and measured cohesive balance of LMH with APIs will require a more in-depth understanding of highly hydrogen-bonded systems with respect to the synthonic engineering modeling tool, as well as the influence of agglomerate structure on surface–surface contact geometry. Overall, this research has demonstrated the possible application and relevance of synthonic engineering tools for rapid pre-screening in drug formulation and design