gebhart/patrepeval huggingface dataset:
Gene expression signatures of response to anti-CD19 chimeric antigen receptor (CAR) T-cell therapy in patients with CLL and ALL. (2017)

137 Background: The adoptive transfer of autologous T cells genetically modified to express a CD19-specific, 4-1BB/CD3ζ-signaling CAR (CTL019) has shown remarkable activity and induces long-term remissions in a subset of patients with relapsed/refractory chronic lymphocytic leukemia (CLL) and acute lymphoblastic leukemia (ALL). In ALL, CTL019 induces a complete response (CR) in over 90% of patients while in CLL 25% of patients obtain a CR. It is not fully understood why only certain patients respond to therapy. Methods: We employed next generation sequencing of RNA (RNAseq) to identify predictive indicators of response to CTL019. We performed RNAseq on leukapheresis and manufactured product T cells prior to re-infusion from 35 CLL and 7 pediatric ALL patients with heavily pre-treated and high-risk disease. To characterize potency, we performed RNAseq on the infusion product after stimulation with the CAR. Results: We find that durable remission in CLL is associated with gene expression signatures of early memory and T-effector cells, while T cells from non-responding patients are enriched in signatures of T-regulatory cells, terminal differentiation, and exhaustion. In following the results from CLL, we find that pediatric ALL manufactured T cells are significantly enriched for an early memory, naïve T cell state and all achieved a CR. In parallel in vitro experiments, stimulation of the infusion product further demonstrated that CTL019 cells from CRs have an increased capacity for activation upon stimulation. We tested if we could extend these observations to identify a phenotype of T cells that is predictive of response prior to CTL019 manufacturing and find that the signatures predictive of response at the pre-infusion stage are also observed at the earlier leukapheresis time point. Conclusions: These findings suggest that intrinsic T cell fitness dictates response to CAR T cells. These gene expression signatures, along with additional immunological biomarkers, may be used to identify which patients are most likely to respond to adoptive transfer strategies and suggest manufacturing modifications that might potentiate the generation of maximally efficacious infusion products. Clinical trial information: NCT01029366, NCT01747486, NCT01626495.
Using hypervisor to provide data secrecy for user applications on a per-page basis (2008)

Hypervisors are increasingly utilized in modern computer systems, ranging from PCs to web servers and data centers. Aside from server applications, hypervisors are also becoming a popular target for implementing many security systems, since they provide a small and easy-to-secure trusted computing base. This paper presents a novel way of using hypervisors to protect application data privacy even when the underlying operating system is not trustable. Each page in virtual address space is rendered to user applications according to the security context the application is running in. The hypervisor encrypts and decrypts each memory page requested depending on the application's access permission to the page. The main result of this system is the complete removal of the operating system from the trust base for user applications' data privacy. To reduce the runtime overhead of the system, two optimization techniques are employed. We use page-frame replication to reduce the number ofcryptographic operations by keeping decrypted versions of a page frame. We also employ lazy synchronization to minimize overhead due to an update to one of the replicated page frame. Our system is implemented and evaluated by modifying the Xen hypervisor, showing that it increases the application execution time only by 3% for CPU and memory-intensive workloads.
CENSE: A Cognitive Navigation System for People with Special Needs (2017)

Mass Transportation provides people with access to education, employment and places in the community. However, navigating around public transportation for the visually impaired and physically challenged sections of society is a challenging task. With rapid proliferation of technology, there has been a pressing need to develop enhanced methodologies to help people with disabilities access public transportation. While there are many navigation systems, some of them leverage Global Positioning System (GPS) technology, which is useful in outdoor environments but is not effective in navigating indoor environments. Beacons are emergent sensors that are becoming popular for indoor positioning in malls and airports. They use Bluetooth Low Energy (BLE) technology, which is extensively supported by all modern day smartphones. In this paper, we propose a proof of concept (POC) for a mobile application which uses BLE beacons to provide assistance to people with special needs. This application would provide an easy to use voice interface for navigating inside stations, buses and trains. As a part of our research, we aim to use existing beacons on some regional transit centers and deploy new beacons. We plan to analyze VTA's (Valley Transportation Authority) ridership data to extract contextual data about the commuter's current environment inorder to provide commuter's with a cognitive solution and assistance during travel. The end goal of our research is to enhance the VTA travel experience for special need travelers in the San Francisco Bay Area.
Thermally Stable Blue-Light-Emitting Hybrid Organic−Inorganic Polymers Derived from Cyclotriphosphazene (2008)

The synthesis and characterization of thermally stable cyclotriphosphazene-based hybrid organic−inorganic blue-light-emitting polymers were reported. Monomers 2,4-di(4-bromoaryl)-2,4,6,6-tetra(phenoxy)-cyclotriphosphazene (3 and 4) and 2,4-di(4-bromoaryl)-2,4,6,6-tetra(ethoxy)-cyclotriphosphazene (7 and 9) were prepared beginning from hexachlorocyclotriphosphazene through a two-step reaction with the corresponding sodium 4-bromo-aryloxides. Next, 3, 4, 7, or 9 readily underwent a Suzuki cross-coupling reaction with suitable 9,9-dialkylflourene-2,7-bis(trimethyleneborate)s to afford the corresponding polymers. The structures and properties of the polymers were investigated by thermogravimetric analysis, differential scanning calorimetry, X-ray diffraction, and UV−vis and fluorescence spectroscopy. All polymers emitted blue light with high quantum yields. Subsequently, the thermal effect on the optical properties of the polymers was studied, revealing that the introduction of particular hybrid organic−inorganic three-dimensional cyclotriphosphazene in the polymer system prevented from aggregation of the polymer chain, enhanced thermal stability, and thus suppressed the undesirable green emission. On the basis of these studies, light-emitting polymer-based diode devices were fabricated.
P2‐120: INCREASED CSF MATRIX METALLOPROTEINASE‐9 (MMP‐9) AND REDUCED WHITE MATTER INTEGRITY IN HEALTHY ELDERLY (2014)

MMP-9 is s an important factor in ischemic brain insults and its genetic inactivation is protective. Elevated brain and CSF MMP-9 levels have been reported in Alzheimer's disease (AD) and implicated in the neuronal death and BBB dysfunction. Interestingly, age-related elevations in CSF MMP-9 are reported in healthy individuals with the APOE ε4 allele, the major genetic risk factor for AD. However, the relationship between MMP-9 and possible subtle brain abnormalities in this population has not been studied. Diffusion Tensor Imaging (DTI)-derived metrics have been found sensitive to subtle brain changes associated with inflammatory markers. Therefore, we employed DTI to examine the relationship between CSF MMP-9 and white matter integrity. CSF was obtained from 47 older subjects with intact cognition and an MMSE score of at least 28. MMP-9 was determined using enzyme-linked immunoassays. Magnetic Resonance Imaging (MRI) scans were performed to assess fractional anisotropy (FA), a measure of white matter integrity. Each of the DTI measures was averaged over the entire white matter compartment in images transformed into MNI space. DTI interpretations of FA included white matter hyperintensity (WHMI) ratings, mean trace diffusivity (TR), mean radial diffusivity (LR), and mean axial diffusivity (L1). Pearson's correlations were calculated to examine associations between MMP-9 and the DTI measures. MMP-9 was associated with decreased FA (r= -.35, p= .04) and with increased TR (r= +.44, p=.01), L1 (r=+ .42, p=.01), and LR (r=+ .42, p=.01 which are indicative of greater white matter pathology.. Although the number of non-e4 carriers was numerically greater than e4 carriers, only e4 carriers showed o significant correlations between MMP-9 and t DTI variables. In contrast MMP-9 was not associated with increased WHMIs. Higher CSF MMP-9 levels in healthy elderly, especially e4 carriers, are associated with subtle loss of white matter integrity in the absence of increased of macrovascular lesions such as WMHIs. Future volumetric studies should determine whether these MMP-9 associated-effects are related to loss of neurons and atrophy, or to more subtle microstructural white matter abnormalities.
A family of single-switch ZVS-CV DC-to-DC converters (2002)

A family of single-switch ZVS-CV (zero voltage switching and clamped voltage) DC/DC power converters, i.e., buck, boost, buck/boost, Cuk, Zeta, and Sepic, are presented. Each power converter is realized by employing a commutation inductor circuit which is connected in parallel with either a transistor or a freewheeling diode in a conventional PWM power converter. The steady-state characteristics of these converters are analyzed, including the voltage conversion ratio, the ZVS condition and the input and output current ripple characteristics. These analytical results are confirmed by experiments. The proposed technique is quite simple and output voltage control is easy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Dual Porosity Expanded Polytetrafluoroethylene for Soft-Tissue Augmentation (2005)

This novel dual porosity expanded polytetrafluoroethylene is associated with reduced inflammation and more extensive tissue incorporation as compared with the currently available form. These results suggest a dual porosity expanded polytetrafluoroethylene may provide a superior material for soft-tissue augmentation.
Improvement of survival in low-weight children on the Berlin Heart EXCOR ventricular assist device support† (2018)

Paediatric EXCOR ventricular assist device therapy has significantly improved for patients weighing <10 kg. Withholding a ventricular assist device is not justified on the basis of the body weight alone.
Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia (2017)

Esophageal squamous cell carcinoma (ESCC) in humans is a deadly disease associated with dietary zinc (Zn)-deficiency. In the rat esophagus, Zn-deficiency induces cell proliferation, alters mRNA and microRNA gene expression, and promotes ESCC. We investigated whether Zn-deficiency alters cell metabolism by evaluating metabolomic profiles of esophageal epithelia from Zn-deficient and replenished rats <i>vs</i> sufficient rats, using untargeted gas chromatography time-of-flight mass spectrometry (<i>n</i> = 8/group). The Zn-deficient proliferative esophagus exhibits a distinct metabolic profile with glucose down 153-fold and lactic acid up 1.7-fold (<i>P</i> < 0.0001), indicating aerobic glycolysis (the "Warburg effect"), a hallmark of cancer cells. Zn-replenishment rapidly increases glucose content, restores deregulated metabolites to control levels, and reverses the hyperplastic phenotype. Integration of metabolomics and our reported transcriptomic data for this tissue unveils a link between glucose down-regulation and overexpression of HK2, an enzyme that catalyzes the first step of glycolysis and is overexpressed in cancer cells. Searching our published microRNA profile, we find that the tumor-suppressor miR-143, a negative regulator of HK2, is down-regulated in Zn-deficient esophagus. Using <i>in situ</i> hybridization and immunohistochemical analysis, the inverse correlation between miR-143 down-regulation and HK2 overexpression is documented in hyperplastic Zn-deficient esophagus, archived ESCC-bearing Zn-deficient esophagus, and human ESCC tissues. Thus, to sustain uncontrolled cell proliferation, Zn-deficiency reprograms glucose metabolism by modulating expression of miR-143 and its target HK2. Our work provides new insight into critical roles of Zn in ESCC development and prevention.
Precise, scalable shadow mask patterning of vacuum-deposited organic light emitting devices (1999)

We demonstrate a scheme to pattern vacuum-deposited, small molecular weight organic light emitting diodes (OLEDs). Both the organic thin films and the metallic electrodes are patterned by shifting the position of a single shadow mask which accompanies the substrate throughout the deposition process. A full color, stacked OLED (SOLED) has been fabricated using this technique. The substrate movement relative to the mask was manually controlled to a root mean square accuracy of ±8 μm using a mask translating fixture. The performance of the patterned SOLED is comparable with that of devices fabricated by conventional, low tolerance methods. The limits to the display fill factor and resolution using this technique are discussed. The technique is generally applicable to all structures requiring precise patterning of vacuum-deposited thin films.
Alleviating Search Bias in Bayesian Evolutionary Optimization with Many Heterogeneous Objectives (2022)

Multi-objective optimization problems whose objectives have different evaluation costs are commonly seen in the real world. Such problems are now known as multi-objective optimization problems with heterogeneous objectives (HE-MOPs). So far, however, only a few studies have been reported to address HE-MOPs, and most of them focus on bi-objective problems with one fast objective and one slow objective. In this work, we aim to deal with HE-MOPs having more than two black-box and heterogeneous objectives. To this end, we develop a multi-objective Bayesian evolutionary optimization approach to HE-MOPs by exploiting the different data sets on the cheap and expensive objectives in HE-MOPs to alleviate the search bias caused by the heterogeneous evaluation costs for evaluating different objectives. To make the best use of two different training data sets, one with solutions evaluated on all objectives and the other with those only evaluated on the fast objectives, two separate Gaussian process models are constructed. In addition, a new acquisition function that mitigates search bias towards the fast objectives is suggested, thereby achieving a balance between convergence and diversity. We demonstrate the effectiveness of the proposed algorithm by testing it on widely used multi-/many-objective benchmark problems whose objectives are assumed to be heterogeneously expensive.
130 RENAL DENERVATION IMPROVES AUTONOMIC RESPONSES TO FALLS IN BLOOD PRESSURE (2013)

Introduction Renal denervation (RDN) decreases blood pressure (BP) in some patients with resistant hypertension. Little is known about the mechanisms through which the BP fall is achieved. It is thought that decreased afferent renal input to the brainstem results in a fall in central sympathetic outflow. We hypothesised that sympathetic baroreflex sensitivity (sBRS) would improve following RDN. Table 1 Patient ID Age (years) Sex BMI (kg/m 2 ) 1 63 M 29.8 2 48 M 38.6 3 43 F 29.4 4 72 F 26.3 5 33 F 23.4 6 65 M 27.0 7 58 M 30.0 Methods We studied seven patients with resistant hypertension (clinic systolic BP&gt;140/90 mm Hg, on ≥3 anti-hypertensive medications). Body mass index remained stable throughout. Patient demographics are in Table 1. Medications were unchanged post-RDN, except for two patients. One patient, with no BP response post-RDN, had anti-hypertensive medications increased. Another patient was symptomatic with a marked BP improvement post-RDN, and his medication was reduced. The change in medication did not alter their post-RDN BP responder status. Patients underwent RDN with the Symplicity catheter. Multiunit muscle sympathetic nerve activity (MSNA) was measured from the peroneal nerve. Sympathetic baroreflex sensitivity (sBRS) was measured at baseline, 1, and 6 months post-RDN. One patient did not undergo MSNA at 1 month. The sBRS was calculated by threshold baroreflex analysis, associating spontaneous fluctuations in diastolic BP (increases and decreases) to the occurrence of spontaneous MSNA bursts. Sensitivity is defined as the slope of the linear regression analysis. Results Response to RDN was defined as a fall in SBP ≥10 mm Hg. Four of the seven patients were responders at 1 and 6 months post-RDN. One patient was a BP non-responder at 1 month but responded by 6 months. Another patient was initially a BP responder, but a non-responder at 6 months. The sBRS improved at 1 (Δ −1.7±0.5%/mm Hg, p&lt;0.05, n=6/6) and 6 months (Δ −0.9±0.3%/mm Hg, p&lt;0.05, n=6/7) post-RDN (figure 1A). Figure 1B shows the change in the total sBRS for a single patient. Baroreflex function is dependent on whether BP is rising or falling, therefore we analysed the MSNA data for rising and falling BP separately (Figure 1A). Sympathetic BRS during falling BP was significantly improved following RDN in patients at both 1 (Δ −1.5±0.7%/mmHg, p&lt;0.05, n=4/6) and 6 months (Δ −1.8±0.4%/mm Hg, p&lt;0.05, n=6/7). In contrast, the sympathetic BRS to rising BP was unchanged at both 1 and 6 months post-RDN. Figure 1 Conclusions Four of the seven patients with resistant hypertension had a BP response to renal denervation. The sBRS to falling, but not rising, BP improved following RDN. This is important since improved baroreflex control of falling BP might help to reduce orthostatic hypotension. This is particularly relevant in patients on multiple anti-hypertensive medications. The mechanisms underpinning the improved baroreflex are unclear, but may provide a relatively early marker of procedural success in those patients that respond to RDN.
InnateDB & Cerebral: user‐friendly tools for the systems‐level analysis of innate immunity (2008)

InnateDB is a publicly available knowledgebase of genes, proteins, interactions, and pathways involved in innate immunity. It integrates known interactions and pathways from public databases and manually curated data into a centralized resource, which includes data on &gt;100,000 human and mouse interactions, cross‐references to innate immunity relevant pathways, and detailed annotation from a variety of sources. Building on this data we provide several bioinformatics tools to facilitate systems‐level investigations of the innate immune response. These include the ability to upload expression datasets, which can be integrated with network/pathway data to investigate changes in gene expression in a network of interest. This data can be investigated using our network visualization tool, Cerebral, a Cytoscape plugin which allows the generation of intuitive pathway and cell localization‐oriented views of interaction data. Cerebral allows the overlay of expression data from multiple experiments on top of interaction network data from InnateDB. We also provide orthology predictions for human, mouse &amp; bovine genes to facilitate the construction of orthologous networks in different species. InnateDB is funded by Genome Canada, the Foundation for the National Institutes of Health, &amp; the Canadian Institutes of Health Research under the Grand Challenges in Global Health Initiative.
A Study on Receiver Circuit Topology of Non-contact Charger for Electric Vehicle (2012)

This paper proposes a receiver circuit topology of a non-contact battery charger for an Electric vehicle (EV), which has a carefully designed series capacitor added to the parallel resonant circuit of the receiver. The simulation and experimental results are presented to show that the circuit can improve the power factor as well as efficiency, and as a result, enlarge the gap between the transmitter and the receiver coils.
Ray tracing with the BSP tree (2008)

One of the most fundamental concepts in computer graphics is binary space subdivision. In its purest form, this concept leads to binary space partitioning trees (BSP trees) with arbitrarily oriented space partitioning planes. In practice, however, most algorithms use kd-trees-a special case of BSP trees that restrict themselves to axis-aligned planes-since BSP trees are believed to be numerically unstable, costly to traverse, and intractable to build well. In this paper, we show that this is not true. Furthermore, after optimizing our general BSP traversal to also have a fast kd-tree style traversal path for axis-aligned splitting planes, we show it is indeed possible to build a general BSP based ray tracer that is highly competitive with state of the art BVH and kd-tree based systems. We demonstrate our ray tracer on a variety of scenes, and show that it is always competitive with-and often superior to-state of the art BVH and kd-tree based ray tracers.
Spectrum micro-trading for mobile operators (2013)

Spectrum trading is an important tool for increasing overall and local spectrum utilization, and to enable access to new and additional spectrum for mobile operators. However, the current spectrum trading regimes usually require long times to execute a trade, hence limiting the flexibility over short timescales in addition to limiting the granularity of the bandwidth and geographical units that may be traded. In this article we discuss the concept of spectrum micro-trading to enable trading of spectrum on the micro-scale in at least three dimensions: the micro-spatial, micro-temporal, and micro-frequency scales. An ecosystem for spectrum micro-trading is presented along with the most important metrics for spectrum micro-trading evaluation. Results from a simulation study for mobile operators, where spectrum is traded via auction, show that the market is viable using the proposed spectrum micro-trading model, and that spectrum utilization can be greatly improved.
Salmonella enterica Serovar Enteritidis Pathogenicity Island 1 Is Not Essential for but Facilitates Rapid Systemic Spread in Chickens (2009)

Salmonella enterica subsp. enterica serovar Enteritidis is a leading cause of human food-borne illness that is mainly associated with the consumption of contaminated poultry meat and eggs. To cause infection, S. Enteritidis is known to use two type III secretion systems, which are encoded on two salmonella pathogenicity islands, SPI-1 and SPI-2, the first of which is thought to play a major role in invasion and bacterial uptake. In order to study the role of SPI-1 in the colonization of chicken, we constructed deletion mutants affecting the complete SPI-1 region (40 kb) and the invG gene. Both DeltaSPI-1 and DeltainvG mutant strains were impaired in the secretion of SipD, a SPI-1 effector protein. In vitro analysis using polarized human intestinal epithelial cells (Caco-2) revealed that both mutant strains were less invasive than the wild-type strain. A similar observation was made when chicken cecal and small intestinal explants were coinfected with the wild-type and DeltaSPI-1 mutant strains. Oral challenge of 1-week-old chicken with the wild-type or DeltaSPI-1 strains demonstrated that there was no difference in chicken cecal colonization. However, systemic infection of the liver and spleen was delayed in birds that were challenged with the DeltaSPI-1 strain. These data demonstrate that SPI-1 facilitates systemic infection but is not essential for invasion and systemic spread of the organism in chickens.