gebhart/patrepeval huggingface dataset:
Naming and sharing resources across administrative boundaries. (2000)

I tackle the problem of naming and sharing resources across administrative boundaries. Conventional systems manifest the hierarchy of typical administrative structure in the structure of their own mechanism. While natural for communication that follows hierarchical patterns, such systems interfere with naming and sharing that cross administrative boundaries, and therefore cause headaches for both users and administrators. I propose to organize resource naming and security, not around administrative domains, but around the sharing patterns of users. 
The dissertation is organized into four main parts. First, I discuss the challenges and tradeoffs involved in naming resources and consider a variety of existing approaches to naming. 
Second, I consider the architectural requirements for user-centric sharing. I evaluate existing systems with respect, to these requirements. 
Third, to support the sharing architecture, I develop a formal logic of sharing that captures the notion of restricted delegation. Restricted delegation ensures that users can use the same mechanisms to share resources consistently, regardless of the origin of the resource, or with whom the user wishes to share the resource next. A formal semantics gives unambiguous meaning to the logic. I apply the formalism to the Simple Public Key Infrastructure and discuss how the formalism either supports or discourages potential extensions to such a system. 
Finally, I use the formalism to drive a user-centric sharing implementation for distributed systems. I show how this implementation enables end-to-end authorization, a feature that makes heterogeneous distributed systems more secure and easier to audit. Conventionally, gateway services that bridge administrative domains, add abstraction, or translate protocols typically impede the flow of authorization information from client to server. In contrast, end-to-end authorization enables us to build gateway services that preserve authorization information, hence we reduce the size of the trusted computing base and enable more effective auditing. I demonstrate my implementation and show how it enables end-to-end authorization across various boundaries. I measure my implementation and argue that its performance tracks that of similar authorization mechanisms without end-to-end structure. 
I conclude that my user-centric philosophy of naming and sharing benefits both users and administrators.
A simple poly(3,4-ethylene dioxythiophene)/poly(styrene sulfonic acid) transistor for glucose sensing at neutral pH (2004)

We demonstrate a simple transistor based on the conducting polymer poly(3,4-ethylene dioxythiophene)/poly(styrene sulfonic acid), capable of sensing glucose in a neutral pH buffer solution by a mechanism involving sensing of hydrogen peroxide.
Comparison Analysis between Korean Central Institute for the Deaf Sentence and Korean Hearing in Noise Test Sentence (2012)

Background and ObjectivesZZHearing in Noise Test (HINT) sentences and Central Institute for the Deaf (CID) sentences are tools that are used for assessing speech cognition. The Korean versions of HINT and CID, KHINT and KCID, have been made and used for the selection of cochlear implant candidates. In this study, we analyzed the compatibility of sentences of KCID and KHINT as testing material for assessing speech performance. Materials and methodsZZA total of 36 patients selected for the study were divided into 2 groups. Group A, whose mean age was 49.9 years, was composed of 18 patients with hearing aid (range, 24 to 68 years); Group B, whose mean age was 23.5 years, was composed of 18 patients with cochlear implant (range, 10 to 63 years). Open set recognition scores of 2 sentences were compared in each group, by randomly selecting one list each of the KCID and KHINT sentences. Sentences were stimulated using recorded voice and live voice for Group A and B, respectively.
Hamiltonian Monte Carlo Without Detailed Balance (2014)

We present a method for performing Hamiltonian Monte Carlo that largely eliminates sample rejection for typical hyperparameters. In situations that would normally lead to rejection, instead a longer trajectory is computed until a new state is reached that can be accepted. This is achieved using Markov chain transitions that satisfy the fixed point equation, but do not satisfy detailed balance. The resulting algorithm significantly suppresses the random walk behavior and wasted function evaluations that are typically the consequence of update rejection. We demonstrate a greater than factor of two improvement in mixing time on three test problems. We release the source code as Python and MATLAB packages.
Regional Differences in Blood-Brain Barrier Permeability Changes and Inflammation in the Apathogenic Clearance of Virus from the Central Nervous System (2006)

The loss of blood-brain barrier (BBB) integrity in CNS inflammatory responses triggered by infection and autoimmunity has generally been associated with the development of neurological signs. In the present study, we demonstrate that the clearance of the attenuated rabies virus CVS-F3 from the CNS is an exception; increased BBB permeability and CNS inflammation occurs in the absence of neurological sequelae. We speculate that regionalization of the CNS inflammatory response contributes to its lack of pathogenicity. Despite virus replication and the expression of several chemokines and IL-6 in both regions being similar, the up-regulation of MIP-1beta, TNF-alpha, IFN-gamma, and ICAM-1 and the loss of BBB integrity was more extensive in the cerebellum than in the cerebral cortex. The accumulation of CD4- and CD19-positive cells was higher in the cerebellum than the cerebral cortex. Elevated CD19 levels were paralleled by kappa-L chain expression levels. The timing of BBB permeability changes, kappa-L chain expression in CNS tissues, and Ab production in the periphery suggest that the in situ production of virus-neutralizing Ab may be more important in virus clearance than the infiltration of circulating Ab. The data indicate that, with the possible exception of CD8 T cells, the effectors of rabies virus clearance are more commonly targeted to the cerebellum. This is likely the result of differences in the capacity of the tissues of the cerebellum and cerebral cortex to mediate the events required for BBB permeability changes and cell invasion during virus infection.
Rotationally oscillating drill (Ros‐Drill©) for mouse icsi without using mercury (2008)

Intracytoplasmic sperm injection (ICSI) is an important assisted reproductive technology (ART). Due to deployment difficulties and low efficiency of the earlier (conventional) version of ICSI, especially in the mouse, a piezo-assisted ICSI technique had evolved as a popular ART methodology in recent years. An important and remaining problem with this technique, however, is that it requires small amounts of mercury to stabilize the pipette tip when piezoelectric force pulses are applied. To eliminate this problem we developed and tested a completely different and mercury-free technology, called the "Ros-Drill" (rotationally oscillating drill). The technique uses microprocessor-controlled rotational oscillations on a spiked micropipette without mercury or piezo. Preliminary experimental results show that this new microinjection technology gives high survival rate (>70% of the injected oocytes) and fertilization rate (>80% of the survived oocytes), and blastocyst formation rates in early trials (approximately 50% of the survived oocytes). Blastocysts created by Ros-Drill ICSI were transferred into the uteruses of pseudopregnant surrogate mothers and healthy pups were born and weaned. The Ros-Drill ICSI technique is automated and therefore; it requires a very short preliminary training for the specialists, as evidenced in many successful biological trials. These advantages of Ros-Drill ICSI over conventional and piezo-assisted ICSI are clearly demonstrated and it appears to have resolved an important problem in reproductive biology.
Multiplexed Profiling of Single Extracellular Vesicles (2017)

Extracellular vesicles (EV) are a family of cell-originating, membrane-enveloped nanoparticles with diverse biological function, diagnostic potential, and therapeutic applications. While EV can be abundant in circulation, their small size (∼4 order of magnitude smaller than cells) has necessitated bulk analyses, making many more nuanced biological explorations, cell of origin questions, or heterogeneity investigations impossible. Here we describe a single EV analysis (SEA) technique which is simple, sensitive, multiplexable, and practical. We profiled glioblastoma EV and discovered surprising variations in putative pan-EV as well as tumor cell markers on EV. These analyses shed light on the heterogeneous biomarker profiles of EV. The SEA technology has the potential to address fundamental questions in vesicle biology and clinical applications.
A covalent small molecule inhibitor of glutamate-oxaloacetate transaminase 1 impairs pancreatic cancer growth (2019)

Metabolic programs are rewired in cancer cells to support survival and tumor growth. Among these, recent studies have demonstrated that glutamate-oxaloacetate transaminase 1 (GOT1) plays key roles in maintaining redox homeostasis and proliferation of pancreatic ductal adenocarcinomas (PDA). This suggests that small molecule inhibitors of GOT1 could have utility for the treatment of PDA. However, the development of GOT1 inhibitors has been challenging, and no compound has yet demonstrated selectivity for GOT1-dependent cell metabolism or selective growth inhibition of PDA cell lines. In contrast, potent inhibitors that covalently bind to the transaminase cofactor pyridoxal-5'-phosphate (PLP), within the active site of the enzyme, have been reported for kynurenine aminotransferase (KAT) and gamma-aminobutyric acid aminotransferase (GABA-AT). Given the drug discovery successes with these transaminases, we aimed to identify PLP-dependent suicide substrate-type GOT1 inhibitors. Here, we demonstrate that PF-04859989, a known KAT2 inhibitor, has PLP-dependent inhibitory activity against GOT1 and shows selective growth inhibition of PDA cell lines.
Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics (2021)

Abstract In this era of rising antibiotic resistance, in contrast to our increasing understanding of mechanisms that cause resistance, our understanding of mechanisms that influence the propensity to evolve resistance remains limited. Here, we identified genetic factors that facilitate the evolution of resistance to carbapenems, the antibiotic of “last resort,” in Klebsiella pneumoniae , the major carbapenem resistant species. In clinical isolates, we found that high-level transposon insertional mutagenesis plays an important role in contributing to high-level resistance frequencies in several major and emerging carbapenem-resistant lineages. A broader spectrum of resistance-conferring mutations for select carbapenems such as ertapenem also enables higher resistance frequencies and importantly, creates stepping-stones to achieve high-level resistance to all carbapenems. These mutational mechanisms can contribute to the evolution of resistance, in conjunction with the loss of systems that restrict horizontal resistance gene uptake, such as the CRISPR-Cas system. Given the need for greater antibiotic stewardship, these findings argue that in addition to considering the current efficacy of an antibiotic for a clinical isolate in antibiotic selection, considerations of future efficacy are also important. The genetic background of a clinical isolate and the exact antibiotic identity can and should also be considered as it is a determinant of a strain’s propensity to become resistant. Together, these findings thus provide a molecular framework for understanding acquisition of carbapenem resistance in K. pneumoniae with important implications for diagnosing and treating this important class of pathogens.
Robust Spatial Extent Inference With a Semiparametric Bootstrap Joint Inference Procedure (2019)

Spatial extent inference (SEI) is widely used across neuroimaging modalities to adjust for multiple comparisons when studying brain-phenotype associations that inform our understanding of disease. Recent studies have shown that Gaussian random field (GRF)-based tools can have inflated family-wise error rates (FWERs). This has led to substantial controversy as to which processing choices are necessary to control the FWER using GRF-based SEI. The failure of GRF-based methods is due to unrealistic assumptions about the spatial covariance function of the imaging data. A permutation procedure is the most robust SEI tool because it estimates the spatial covariance function from the imaging data. However, the permutation procedure can fail because its assumption of exchangeability is violated in many imaging modalities. Here, we propose the (semi-) parametric bootstrap joint (PBJ; sPBJ) testing procedures that are designed for SEI of multilevel imaging data. The sPBJ procedure uses a robust estimate of the spatial covariance function, which yields consistent estimates of standard errors, even if the covariance model is misspecified. We use the methods to study the association between performance and executive functioning in a working memory functional magnetic resonance imaging study. The sPBJ has similar or greater power to the PBJ and permutation procedures while maintaining the nominal type 1 error rate in reasonable sample sizes. We provide an R package to perform inference using the PBJ and sPBJ procedures.
Zoonotic origin of the human malaria parasite Plasmodium malariae from African apes (2022)

The human parasite Plasmodium malariae has relatives infecting African apes (Plasmodium rodhaini) and New World monkeys (Plasmodium brasilianum), but its origins remain unknown. Using a novel approach to characterise P. malariae-related sequences in wild and captive African apes, we found that this group comprises three distinct lineages, one of which represents a previously unknown, highly divergent species infecting chimpanzees, bonobos and gorillas across central Africa. A second ape-derived lineage is much more closely related to the third, human-infective lineage P. malariae, but exhibits little evidence of genetic exchange with it, and so likely represents a separate species. Moreover, the levels and nature of genetic polymorphisms in P. malariae indicate that it resulted from the zoonotic transmission of an African ape parasite, reminiscent of the origin of P. falciparum. In contrast, P. brasilianum falls within the radiation of human P. malariae, and thus reflects a recent anthroponosis.
Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism (2020)

Synaptic activity in neurons leads to the rapid activation of genes involved in mammalian behavior. ATP-dependent chromatin remodelers such as the BAF complex contribute to these responses and are generally thought to activate transcription. However, the mechanisms keeping such "early activation" genes silent have been a mystery. In the course of investigating Mendelian recessive autism, we identified six families with segregating loss-of-function mutations in the neuronal BAF (nBAF) subunit <i>ACTL6B</i> (originally named <i>BAF53b</i>). Accordingly, <i>ACTL6B</i> was the most significantly mutated gene in the Simons Recessive Autism Cohort. At least 14 subunits of the nBAF complex are mutated in autism, collectively making it a major contributor to autism spectrum disorder (ASD). Patient mutations destabilized ACTL6B protein in neurons and rerouted dendrites to the wrong glomerulus in the fly olfactory system. Humans and mice lacking <i>ACTL6B</i> showed corpus callosum hypoplasia, indicating a conserved role for <i>ACTL6B</i> in facilitating neural connectivity. <i>Actl6b</i> knockout mice on two genetic backgrounds exhibited ASD-related behaviors, including social and memory impairments, repetitive behaviors, and hyperactivity. Surprisingly, mutation of <i>Actl6b</i> relieved repression of early response genes including AP1 transcription factors (<i>Fos</i>, <i>Fosl2</i>, <i>Fosb</i>, and <i>Junb</i>), increased chromatin accessibility at AP1 binding sites, and transcriptional changes in late response genes associated with early response transcription factor activity. <i>ACTL6B</i> loss is thus an important cause of recessive ASD, with impaired neuron-specific chromatin repression indicated as a potential mechanism.
Field Induced Structural Transition in Mesocrystallites (1999)

We have fabricated multiply coated glass spheres with diameters of $45(\ifmmode\pm\else\textpm\fi{}2)\ensuremath{\mu}\mathrm{m}$ that exhibit appreciable magneto-, as well as electrorheological responses. Under crossed electric and magnetic fields, the microspheres were observed to form columnar crystallites with a structure that transforms from body-centered tetragonal to face-centered cubic as the ratio between the magnetic and the electric fields exceeded a minimum value. The observed transition scenario is in excellent agreement with calculations based on the model of field induced crystal formation and structural transition.
Recognition of End-of-Speed-Limit and Supplementary Signs for Improved Speed Limit Support (2008)

We present two new features for our prototype of European Speed Limit Support system: detection and recognition of end-of-speed-limit signs, as well as a framework for detection and recognition of supplementary signs located below main signs and modifying their scope (particular lane, class of vehicle, etc…). The end-of-speed-limit signs are globally recognized by a Multi-Layer Perceptron (MLP) neural network. The supplementary signs are detected by applying a rectangle-detection in a region below recognized speed-limit signs, followed by a MLP neural network recognition. A common French+German end-of-speed-limit signs recognition has been designed and successfully tested, yielding 82% detection+recognition. Results for detection and recognition of a first kind of supplementary sign (French exit-lane) are already satisfactory (78% correct detection rate), and our framework can easily be extended to handle other types of supplementary signs. To our knowledge, we are the first team presenting results on detection and recognition of supplementary signs below speed signs, which is a crucial feature for a reliable Speed Limit Support.
Experimental and theoretical study of a solar thermochemical receiver module (1984)

A few years ago, a prototype test module of a solar thermochemical receiver using an SO/sub 2//SO/sub 3/ reaction system was designed, built, and tested to establish a technical data base for future subsystem design efforts. Emphasis was placed on experimental verification of the computer simulation to establish a reliable design tool to predict the thermochemical performance of the receiver with a reasonable degree of confidence. The computational results were compared with experimental results obtained from the module tested at New Mexico State University. Reasonable agreement was found over a range of test conditions. It was concluded that the present design offers satisfactory conversion performance and operational flexibility for the construction of a complete reactor/receiver unit for use in a 10- to 15-kW dish collector system.
Performance of Scalable Video Coding for a TV broadcast network with constant video quality and heterogeneous receivers (2009)

Video broadcasters currently envision to target a variety of receiving devices of different resolutions. In such a heterogeneous TV network the transport resource consumption is likely to increase as the types and number of receiving devices increase. We estimate the required capacity for an IPTV and mobile TV network taking into account parameters as currently proposed in standardization bodies. The consumed transport capacity fluctuates over time for two reasons. First, as we target constant video quality as much as possible, the video is encoded in variable bit rate. In order to characterize the fluctuations of the bit rate associated with one channel we have encoded a representative set of video clips. Second, the user behavior causes the transport capacity demand to fluctuate because we consider a multicast-based transport system where only the requested channels are transported. We compare two modes for transporting TV channels in multiple resolutions: a mode based on the Scalable Video Coding (SVC) where all video resolutions are embedded in one stream and a simulcast (SIM) mode where all resolutions are offered in parallel. We evaluate in some realistic examples which of the two effects is dominant, i.e., the bit rate penalty of SVC or the fact that SIM transports the video streams in parallel rather than embedding them in one stream as SVC does.
Micro bead type temperature sensor with ratiometric fluorescence dyes encapsulated by Parylene (2011)

We propose a sensor for measuring temperature of micro regions with ratiometric fluorescence dye beads encapsulated by Parylene. With the proposed method, we can fabricate encapsulated micro beads with constant size and dye concentration, which is suitable and preferred for precise sensing using fluorescence intensity measurement. This micro bead type sensor can be used for micro regions, which are difficult to apply conventional methods. This type of sensor is also easy to use to measure the temperature of not only positions located on the surface of the target object but also those located deep inside its volume. We demonstrated that this sensor could measure the temperature of micro regions with the accuracy ranging from ± 0.8°C to ± 3.7°C.
AeroRIT: A New Scene for Hyperspectral Image Analysis (2020)

We investigate applying convolutional neural network (CNN) architecture to facilitate aerial hyperspectral scene understanding and present a new hyperspectral data set, AeroRIT, which is large enough for CNN training. To date, the majority of hyperspectral airborne has been confined to various subcategories of vegetation and roads, and this scene introduces two new categories: buildings and cars. To the best of our knowledge, this is the first comprehensive large-scale hyperspectral scene with nearly seven-million pixel annotations for identifying cars, roads, and buildings. We compare the performance of the three popular architectures-SegNet, U-Net, and Res-U-Net, for scene understanding and object identification via the task of dense semantic segmentation to establish a benchmark for the scene. To further strengthen the network, we add squeeze and excitation blocks for better channel interactions and use self-supervised learning for better encoder initialization. Aerial hyperspectral image analysis has been restricted to small data sets with limited train/test splits capabilities, and we believe that AeroRIT will help advance the research in the field with a more complex object distribution to perform well on. The full data set, with flight lines in radiance and reflectance domains, is available for download at https://github.com/aneesh3108/AeroRIT. This data set is the first step toward developing robust algorithms for hyperspectral airborne sensing that can robustly perform advanced tasks such as vehicle tracking and occlusion handling.