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

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

Caregiving can be costly : a qualitative study of barriers and facilitators to conducting kangaroo mother care in a US tertiary hospital neonatal intensive care unit

Preterm birth is a leading cause of morbidity and mortality in children under five and often requires a newborn to have an extended stay in a neonatal intensive care unit (NICU). Maternal engagement, such as visiting the NICU to provide kangaroo mother care (KMC), can improve outcomes for preterm infants but requires significant investment of time and resources. This study sought to understand barriers and facilitators to provision of KMC in the NICU.; We conducted semi-structured in-depth interviews with mothers of preterm infants (N = 20) at a large academic medical center in Massachusetts. A series of open-ended interview questions were designed to elicit all aspects of mothers' experiences and to understand how these experiences influence provision of KMC. All interviews were recorded and transcribed verbatim. We conducted an inductive thematic analysis to identify themes in the data with a focus on the barriers and facilitators of KMC provision in the NICU.; Findings show that engaging in KMC is heavily influenced by the mental, emotional, and physical effects of preterm birth on the birth mother, such as stress around preterm birth and difficulty recovering from birth. These challenges are compounded by structural barriers such as costly accommodations, unreliable transportation, lack of child care, and inadequate maternity leave policies that limit the frequency and duration of KMC and parental ability to provide care.; A complex array of mental, emotional, physical, and structural factors determine a mother's ability to visit the NICU and provide kangaroo mother care. Providing social supports, such as improved maternity leave policies and reliable hospital access through child care, accommodation, and transportation services, may address the structural barriers that inhibit KMC, reduce burdensome costs, and improve the health of mothers and their preterm infants

Neural correlates of enhanced visual short-term memory for angry faces: An fMRI study

Copyright: © 2008 Jackson et al.Background: Fluid and effective social communication requires that both face identity and emotional expression information are encoded and maintained in visual short-term memory (VSTM) to enable a coherent, ongoing picture of the world and its players. This appears to be of particular evolutionary importance when confronted with potentially threatening displays of emotion - previous research has shown better VSTM for angry versus happy or neutral face identities.Methodology/Principal Findings: Using functional magnetic resonance imaging, here we investigated the neural correlates of this angry face benefit in VSTM. Participants were shown between one and four to-be-remembered angry, happy, or neutral faces, and after a short retention delay they stated whether a single probe face had been present or not in the previous display. All faces in any one display expressed the same emotion, and the task required memory for face identity. We find enhanced VSTM for angry face identities and describe the right hemisphere brain network underpinning this effect, which involves the globus pallidus, superior temporal sulcus, and frontal lobe. Increased activity in the globus pallidus was significantly correlated with the angry benefit in VSTM. Areas modulated by emotion were distinct from those modulated by memory load.Conclusions/Significance: Our results provide evidence for a key role of the basal ganglia as an interface between emotion and cognition, supported by a frontal, temporal, and occipital network.The authors were supported by a Wellcome Trust grant (grant number 077185/Z/05/Z) and by BBSRC (UK) grant BBS/B/16178

Distribution and determinants of pneumonia diagnosis using Integrated Management of Childhood Illness guidelines: a nationally representative study in Malawi

Background: Pneumonia remains the leading cause of child mortality in sub-Saharan Africa. The Integrated Management of Childhood Illness (IMCI) strategy was developed to standardise care in low-income and middle-income countries for major childhood illnesses and can effectively improve healthcare worker performance. Suboptimal clinical evaluation can result in missed diagnoses and excess morbidity and mortality. We estimate the sensitivity of pneumonia diagnosis and investigate its determinants among children in Malawi. Methods: Data were obtained from the 2013–2014 Service Provision Assessment survey, a census of health facilities in Malawi that included direct observation of care and re-examination of children by trained observers. We calculated sensitivity of pneumonia diagnosis and used multilevel log-binomial regression to assess factors associated with diagnostic sensitivity. Results: 3136 clinical visits for children 2–59 months old were observed at 742 health facilities. Healthcare workers completed an average of 30% (SD 13%) of IMCI guidelines in each encounter. 573 children met the IMCI criteria for pneumonia; 118 (21%) were correctly diagnosed. Advanced practice clinicians were more likely than other providers to diagnose pneumonia correctly (adjusted relative risk 2.00, 95% CI 1.21 to 3.29). Clinical quality was strongly associated with correct diagnosis: sensitivity was 23% in providers at the 75th percentile for guideline adherence compared with 14% for those at the 25th percentile. Contextual factors, facility structural readiness, and training or supervision were not associated with sensitivity. Conclusions: Care quality for Malawian children is poor, with low guideline adherence and missed diagnosis for four of five children with pneumonia. Better sensitivity is associated with provider type and higher adherence to IMCI. Existing interventions such as training and supportive supervision are associated with higher guideline adherence, but are insufficient to meaningfully improve sensitivity. Innovative and scalable quality improvement interventions are needed to strengthen health systems and reduce avoidable child mortality

Rifaximin Treatment in Hepatic Encephalopathy

Background Hepatic encephalopathy is a chronically debilitating complication of hepatic cirrhosis. The efficacy of rifaximin, a minimally absorbed antibiotic, is well documented in the treatment of acute hepatic encephalopathy, but its efficacy for prevention of the disease has not been established. Methods In this randomized, double-blind, placebo-controlled trial, we randomly assigned 299 patients who were in remission from recurrent hepatic encephalopathy resulting from chronic liver disease to receive either rifaximin, at a dose of 550 mg twice daily (140 patients), or placebo (159 patients) for 6 months. The primary efficacy end point was the time to the first breakthrough episode of hepatic encephalopathy. The key secondary end point was the time to the first hospitalization involving hepatic encephalopathy. Results Rifaximin significantly reduced the risk of an episode of hepatic encephalopathy, as compared with placebo, over a 6-month period (hazard ratio with rifaximin, 0.42; 95% confidence interval [CI], 0.28 to 0.64; P Conclusions Over a 6-month period, treatment with rifaximin maintained remission from hepatic encephalopathy more effectively than did placebo. Rifaximin treatment also significantly reduced the risk of hospitalization involving hepatic encephalopathy. (ClinicalTrials.gov number, NCT00298038.

The immortalized UROtsa cell line as a potential cell culture model of human urothelium.

The UROtsa cell line was isolated from a primary culture of normal human urothelium through immortalization with a construct containing the SV40 large T antigen. It proliferates in serum-containing growth medium as a cell monolayer with little evidence of uroepithelial differentiation. The working hypothesis in the present study was that this cell line could be induced to differentiate and express known features of in situ urothelium if the original serum-containing growth medium was changed to a serum-free formulation. We demonstrated that the UROtsa cells could be successfully placed into a serum-free growth medium consisting of a 1:1 mixture of Dulbeco\u27s modified Eagle\u27s medium and Ham\u27s F-12 supplemented with selenium (5 ng/mL), insulin (5 microg/mL), transferrin (5 microg/mL), hydrocortisone (36 ng/mL), triiodothyronine (4 pg/mL), and epidermal growth factor (10 ng/mL). Under serum-free growth conditions, confluent UROtsa cells were shown by light microscopy to produce raised, three-dimensional structures. Routine ultrastructural examination disclosed these three-dimensional areas to consist of a stratified layer of cells that strongly resembled in situ urothelium. The cells displayed numerous desmosomal connections, complex interactions of the lateral membranes, and abundant intermediate filaments within the cytoplasm. Freeze fracture analysis demonstrated that the cells possessed tight-junction sealing strands and gap junctions. The overall morphology was most consistent with that found in the intermediate layers of in situ urothelium. The basal expression patterns of the metallothionein (MT) and heat shock proteins 27, 60, and 70 were determined in these cells, and expression was in agreement with that known to occur for in situ urothelium. The cells were also successfully tested for their ability to be stably transfected using expression vectors containing the MT-3 or MT-2A genes. The findings suggest that the UROtsa cells grown with a serum-free medium could be a valuable adjunct for studying environmental insult to the human urothelium in general and for the stress response in particular

Adjuvant chemotherapy in upper tract urothelial carcinoma (the POUT trial): a phase 3, open-label, randomised controlled trial

Background: Urothelial carcinomas of the upper urinary tract (UTUCs) are rare, with poorer stage-for-stage prognosis than urothelial carcinomas of the urinary bladder. No international consensus exists on the benefit of adjuvant chemotherapy for patients with UTUCs after nephroureterectomy with curative intent. The POUT (Peri-Operative chemotherapy versus sUrveillance in upper Tract urothelial cancer) trial aimed to assess the efficacy of systemic platinum-based chemotherapy in patients with UTUCs. Methods: We did a phase 3, open-label, randomised controlled trial at 71 hospitals in the UK. We recruited patients with UTUC after nephroureterectomy staged as either pT2–T4 pN0–N3 M0 or pTany N1–3 M0. We randomly allocated participants centrally (1:1) to either surveillance or four 21-day cycles of chemotherapy, using a minimisation algorithm with a random element. Chemotherapy was either cisplatin (70 mg/m²) or carboplatin (area under the curve [AUC]4·5/AUC5, for glomerular filtration rate <50 mL/min only) administered intravenously on day 1 and gemcitabine (1000 mg/m²) administered intravenously on days 1 and 8; chemotherapy was initiated within 90 days of surgery. Follow-up included standard cystoscopic, radiological, and clinical assessments. The primary endpoint was disease-free survival analysed by intention to treat with a Peto-Haybittle stopping rule for (in)efficacy. The trial is registered with ClinicalTrials.gov, NCT01993979. A preplanned interim analysis met the efficacy criterion for early closure after recruitment of 261 participants. Findings: Between June 19, 2012, and Nov 8, 2017, we enrolled 261 participants from 57 of 71 open study sites. 132 patients were assigned chemotherapy and 129 surveillance. One participant allocated chemotherapy withdrew consent for data use after randomisation and was excluded from analyses. Adjuvant chemotherapy significantly improved disease-free survival (hazard ratio 0·45, 95% CI 0·30–0·68; p=0·0001) at a median follow-up of 30·3 months (IQR 18·0–47·5). 3-year event-free estimates were 71% (95% CI 61–78) and 46% (36–56) for chemotherapy and surveillance, respectively. 55 (44%) of 126 participants who started chemotherapy had acute grade 3 or worse treatment-emergent adverse events, which accorded with frequently reported events for the chemotherapy regimen. Five (4%) of 129 patients managed by surveillance had acute grade 3 or worse emergent adverse events. No treatment-related deaths were reported. Interpretation: Gemcitabine–platinum combination chemotherapy initiated within 90 days after nephroureterectomy significantly improved disease-free survival in patients with locally advanced UTUC. Adjuvant platinum-based chemotherapy should be considered a new standard of care after nephroureterectomy for this patient population. Funding: Cancer Research UK

Advanced mobile networking, sensing, and controls.

This report describes an integrated approach for designing communication, sensing, and control systems for mobile distributed systems. Graph theoretic methods are used to analyze the input/output reachability and structural controllability and observability of a decentralized system. Embedded in each network node, this analysis will automatically reconfigure an ad hoc communication network for the sensing and control task at hand. The graph analysis can also be used to create the optimal communication flow control based upon the spatial distribution of the network nodes. Edge coloring algorithms tell us that the minimum number of time slots in a planar network is equal to either the maximum number of adjacent nodes (or degree) of the undirected graph plus some small number. Therefore, the more spread out that the nodes are, the fewer number of time slots are needed for communication, and the smaller the latency between nodes. In a coupled system, this results in a more responsive sensor network and control system. Network protocols are developed to propagate this information, and distributed algorithms are developed to automatically adjust the number of time slots available for communication. These protocols and algorithms must be extremely efficient and only updated as network nodes move. In addition, queuing theory is used to analyze the delay characteristics of Carrier Sense Multiple Access (CSMA) networks. This report documents the analysis, simulation, and implementation of these algorithms performed under this Laboratory Directed Research and Development (LDRD) effort