gebhart/patrepeval huggingface dataset:
Towards automated manufacturing of clinical scale gene-modified T cells (2014)

Meeting abstracts Adoptive immunotherapy using gene-modified T cells redirected against cancer has proven clinical efficacy and tremendous potential in several medical fields. However, such personalized medicine faces several challenges in the complexity associated with the current clinical
Hardware Information Flow Tracking (2021)

Information flow tracking (IFT) is a fundamental computer security technique used to understand how information moves through a computing system. Hardware IFT techniques specifically target security vulnerabilities related to the design, verification, testing, manufacturing, and deployment of hardware circuits. Hardware IFT can detect unintentional design flaws, malicious circuit modifications, timing side channels, access control violations, and other insecure hardware behaviors. This article surveys the area of hardware IFT. We start with a discussion on the basics of IFT, whose foundations were introduced by Denning in the 1970s. Building upon this, we develop a taxonomy for hardware IFT. We use this to classify and differentiate hardware IFT tools and techniques. Finally, we discuss the challenges yet to be resolved. The survey shows that hardware IFT provides a powerful technique for identifying hardware security vulnerabilities, as well as verifying and enforcing hardware security properties.
Determination of relative angles and anisotropic resistivity using multicomponent induction logging data (2004)

Abstract We have developed a new algorithm that retrieves information about relative dip angle, relative azimuth angle, vertical resistivity, and horizontal resistivity from multicomponent EM induction logging data. To investigate how relative dip and azimuth angles affect multicomponent induction logging data, we performed a sensitivity analysis using an anisotropic whole space model. Based upon the sensitivity analysis, we designed a two-step procedure to recover relative dip, relative azimuth, horizontal resistivity, and vertical resistivity. In the first step, the observed data are transformed into a new data set independent of the azimuth angle; a simultaneous inversion method recovers relative dip angle, vertical resistivity, and horizontal resistivity. In the second step, a 1D line search is performed to decide relative azimuth angle. Synthetic and field data tests indicate that the new inversion algorithm can extract information about relative dip and azimuth angles as well as the anisotropic resistivity structure from multicomponent induction logging data.
Segmentation assisted food classification for dietary assessment (2011)

Accurate methods and tools to assess food and nutrient intake are essential for the association between diet and health. Preliminary studies have indicated that the use of a mobile device with a built-in camera to obtain images of the food consumed may provide a less burdensome and more accurate method for dietary assessment. We are developing methods to identify food items using a single image acquired from the mobile device. Our goal is to automatically determine the regions in an image where a particular food is located (segmentation) and correctly identify the food type based on its features (classification or food labeling). Images of foods are segmented using Normalized Cuts based on intensity and color. Color and texture features are extracted from each segmented food region. Classification decisions for each segmented region are made using support vector machine methods. The segmentation of each food region is refined based on feedback from the output of classifier to provide more accurate estimation of the quantity of food consumed.
Amino-Fucoidan as a Vector for rtPA-Induced Fibrinolysis in Experimental Thrombotic Events (2018)

Acute ischaemic stroke, myocardial infarction and pulmonary embolism are the main causes of mortality and morbidity worldwide. Thrombolysis by intravenous injection of recombinant tissue plasminogen activator (rtPA) remains the most common non-interventional treatment to recanalize occluded vessels. However, this procedure is limited by significant drawbacks, including high doses and bleeding complications. Recent studies showed that fucoidan targets the intraluminal thrombus in vivo. We have developed a chimaera covalently linking fucoidan, able to target platelets within the thrombus, to dilysine, able to non-covalently bind rtPA. We hypothesize that this construct should vectorize rtPA to the thrombus, thus increasing its fibrinolytic efficacy and avoiding its deleterious effects. In vitro, rtPA mixed to dilysine fucoidan (DLF) shows a greater fibrinolytic effect than rtPA alone, both on platelet-rich thrombus and in whole blood. In vivo, occluded mesenteric vessels, carotid artery and vena cava were more efficiently recanalized by DLF complexed to rtPA than by rtPA alone. This study thus provides evidence that DLF may be a promising therapeutic tool to fight against acute thrombosis by enhancing rtPA fibrinolytic efficiency.
Magnetic-field-induced strain in Ni2MnGa shape-memory alloy (abstract) (1997)

Rare-earth/transition-metal alloys can exhibit magnetostrictive strains of order 0.17% in modest fields. Larger strains are of interest for many actuator applications. Certain alloys that undergo martensitic transformations exhibit a shape–memory effect that can yield strains up to 20% upon heating the deformed martensitic phase and they can show superelasticity upon application of a small stress. These methods of activation can be a disadvantage for many applications; magnetic activation of a shape–memory effect is desired. Several magnetic shape–memory alloys exist, among them intermetallics based on Ni2MnGa, which are the subject of this work. These materials experience a 6.6% c-axis contraction on cooling through the martensitic transition temperature, which is near 273 K; this strain is accommodated by formation of an ensemble of strained twin crystals separated by twin boundaries. Strains of several percent could be produced magnetically if the twin boundaries could be moved under application of a magnetic field. We report observations of strains of nearly 0.2% induced along [001] in unstressed crystals of Ni2MnGa with magnetic fields of 8 kOe applied at 265 K (Fig. 1). (This strain is an order of magnitude larger than the magnetostrictive strain we measure in the parent Heusler phase at 283 K.) Our data suggest that these giant strains are associated with the superelastic motion of twin boundaries in the martensitic phase, which is stable below about 274 K; the strength of the measured anisotropy energy density, MSHa/2 is comparable to the elastic energy density, eσ/2, needed for superelastic twin boundary motion.1 The strains we observe are equivalent to those achieved in terfenol-D and represent only a small fraction of the strain available if the twin variants of the martensitic phase can be oriented prior to application of a field.
Newborn Screening for Lysosomal Storage Disorders: Clinical Evaluation of a Two-Tier Strategy (2004)

Newborn screening for selected LSDs is possible with current technology. However, additional development is required to provide a broad coverage of disorders in a single, viable program.
A Microsphere-Based Vaccine Prevents and Reverses New-Onset Autoimmune Diabetes (2008)

This novel microsphere formulation represents the first diabetes-suppressive and reversing nucleic acid vaccine that confers an immunoregulatory phenotype to endogenous dendritic cells.
Petri Net Modeling and Scheduling of a Close-Down Process for Time-Constrained Single-Arm Cluster Tools (2016)

In wafer fabrication, a robotic cluster tool is required to be closed down in order for engineers to perform its on-demand and preventive maintenance and switch between different wafer lots. They often deal with a close-down process subject to wafer residency time constraints, i.e., a wafer must exit from a processing chamber before its quality degradation within a certain time limit. To obtain higher yield, it is very important to optimize a close-down process for a cluster tool. Yet the existing literature pays no or little attention to this issue. By focusing on a time-constrained single-arm cluster tool, this paper intends: 1) to build its Petri net model to analyze its schedulability and 2) to develop computationally efficient algorithms to find an optimal and feasible schedule for its closing-down process under different workloads at its steps. Industrial examples are used to illustrate the application of the proposed method.
Synthetic aperture superresolution by speckle pattern projection (2005)

We propose a method for increasing the resolution of an aperture limited optical system by illuminating the input with a speckle pattern. The high resolution of the projected speckle pattern demodulates the high frequencies of the sample and permits its passage through the system aperture. A decoding provides the superresolved image. The speckle pattern can be generated in a simple manner in contrast with other structured light superresolution methods. The method is demonstrated in microscopy test images.
A hybrid method for real-time short-term predictions of traffic flows in urban areas (2017)

Short-term traffic forecasting is driven by an increasing need of new services for user information and new systems for dynamic control. Our research focuses on reproducing anticipated traffic conditions by means of statistical methods traditionally applied in artificial intelligence problems. Although we strongly believe that the effects of specific traffic events can only be predicted through transportation model based simulations in real-time, yet the fluctuations affecting the ordinary traffic conditions of a day-type can well be forecasted without.
A capacitively loaded PIFA for compact PCS handsets (2002)

A capacitively loaded planar inverted-F antenna is studied. The finite difference time domain (FDTD) method is used to model the antenna. It is found that the capacitive load reduces the resonance length from /spl lambda//4 to /spl lambda//8. Using a capacitive feed, a match at 50 /spl Omega/ is obtained with a 5% bandwidth. Experimental verification is also provided.
ChemInform Abstract: TOTAL SYNTHESIS OF THE ANTIBIOTIC SPARSOMYCIN, A MODIFIED URACIL AMINO ACID MONOXODITHIOACETAL (1981)

Abstract Für das Antibioticum Sparsomycin (I) wird eine Synthese beschrieben und auf die entsprechenden Stereoisomeren von (I) übertragen.
Discovery and Development of Third-Generation Platinum Antitumor Agents with Oral Activity (2005)

The drug discovery process is illustrated by describing the collaborative process that was used to identify three potential platinum anti-tumor compounds (JM216 (satraplatin), AMD473 and JM335) and ultimately select two for clinical development. The selection cascade and medicinal chemistry program and selection criteria that lead to the identification of these preclinical candidate compounds is described. The additional preclinical studies and chemical development activities required to qualify these compounds as preclinical leads and ultimately as clinical candidates is described.
Protecting Military Perimeters from Approaching Human and Vehicle Using Biologically Realistic Dynamic Synapse Neural Network (2008)

The goal of this study is to detect and classify approaching human threats or vehicles, e.g. suicide bombers nearing a secured zone such as military bases. More specifically, this research is focused on (i) developing a vibration recognition system that can detect systematic vibration events; the entity might be a medium, human, animal, or a passenger vehicle, and (ii) discriminating between such a series of events vs. background and a single vibration event, e.g., falling of a tree limb. We have employed a seismic sensor to detect vibrations generated by footsteps and vehicles. A geophone is an inexpensive sensor which provides easy and instant deployment as well as long range detection capability. We have also designed a low power, low noise, and low cost hardware solution to process seismic waves locally where the sensor is located and wireless capability of the system makes it to communicate with a remote command center. Temporal features of the vibration signals were modeled by the dynamic synapse neural network (DSNN) using data recorded in the deserts of Joshua Tree, CA. The system showed 1.7% false recognition rate for the recognition of human footsteps, 6.7% for vehicle, and 0.0% for background. The models were able to reject quadrupedal animal's footsteps (in this study a trained dog). The system rejected dog's footsteps with 0.02% false recognition rate.
A Bovine Enteric Mycobacterium Infection Model to Analyze Parenteral Vaccine-Induced Mucosal Immunity and Accelerate Vaccine Discovery (2020)

Mycobacterial diseases of cattle are responsible for considerable production losses worldwide. In addition to their importance in animals, these infections offer a nuanced approach to understanding persistent mycobacterial infection in native host species. <i>Mycobacterium</i><i>avium</i> ssp. <i>paratuberculosis</i> (MAP) is an enteric pathogen that establishes a persistent, asymptomatic infection in the small intestine. Difficulty in reproducing infection in surrogate animal models and limited understanding of mucosal immune responses that control enteric infection in the natural host have been major barriers to MAP vaccine development. We previously developed a reproducible challenge model to establish a consistent MAP infection using surgically isolated intestinal segments prepared in neonatal calves. In the current study, we evaluated whether intestinal segments could be used to screen parenteral vaccines that alter mucosal immune responses to MAP infection. Using Silirum<sup>®</sup> - a commercial MAP bacterin - we demonstrate that intestinal segments provide a platform for assessing vaccine efficacy within a relatively rapid period of 28 days post-infection. Significant differences between vaccinates and non-vaccinates could be detected using quantitative metrics including bacterial burden in intestinal tissue, MAP shedding into the intestinal lumen, and vaccine-induced mucosal immune responses. Comparing vaccine-induced responses in mucosal leukocytes isolated from the site of enteric infection versus blood leukocytes revealed substantial inconsistences between these immune compartments. Moreover, parenteral vaccination with Silirum did not induce equal levels of protection throughout the small intestine. Significant control of MAP infection was observed in the continuous but not the discrete Peyer's patches. Analysis of these regional mucosal immune responses revealed novel correlates of immune protection associated with reduced infection that included an increased frequency of CD335<sup>+</sup> innate lymphoid cells, and increased expression of <i>IL21</i> and <i>IL27</i>. Thus, intestinal segments provide a novel model to accelerate vaccine screening and discovery by testing vaccines directly in the natural host and provides a unique opportunity to interrogate mucosal immune responses to mycobacterial infections.
Partial Analysis of the Genomes of Two Nontypeable <i>Haemophilus influenzae</i> Otitis Media Isolates (2004)

In 1995, The Institute for Genomic Research completed the genomic sequence of a rough derivative of Haemophilus influenzae serotype d, strain KW20. This sequence, though extremely useful in understanding the basic biology of H. influenzae, has yet to provide significant insight into our understanding of disease caused by nontypeable H. influenzae (NTHI), because serotype d strains are not generally pathogens. In contrast, NTHI strains are frequently mucosal pathogens and are the primary pathogens of chronic otitis media as well as a significant cause of acute otitis media in children. Thus, it is of great importance to further understand their biology. We used a DNA-based microarray approach to identify genes present in a clinical isolate of NTHI that were absent from strain Rd. We also sequenced the genome of a second NTHI isolate from a child with chronic otitis media to threefold coverage and then used an array of bioinformatics tools to identify genes present in this NTHI strain but absent from strain Rd. These methods were complementary in approach and results. We identified, in both strains, homologues of H. influenzae lav, an autotransported protein of unknown function; tnaA, which encodes tryptophanase; as well as a homologue of Pasteurella multocida tsaA, which encodes an alkyl peroxidase that may play a role in protection against reactive oxygen species. We also identified a number of putative restriction-modification systems, bacteriophage genes and transposon-related genes. These data provide new insight that complements and extends our ongoing analysis of NTHI virulence determinants.
Trellis precoding for channels with spectral nulls (2002)

Trellis-enhanced precoding for trellis-coded transmission over ISI channels allows coding and shaping gains to be achieved with minimal transmit power penalty for arbitrary signal constellations, provided the ISI channels are linearly invertible. If the channel exhibits spectral nulls, infinite error propagation can occur within the inverse precoder. We assume ISI channels with spectral nulls and possibly a rational transfer function. First, we investigate methods to stop error propagation in the inverse precoder. This is accomplished by exploiting knowledge about the signal region to which the transmit signal, which needs to be recovered in the inverse precoder, must be confined. Then, we consider combining the concept of feedback trellis encoding with Tomlinson-Harashima (1971, 1972) precoding, whereby error propagation is completely prevented, but only certain signal constellations are allowed. We demonstrate the effectiveness of the proposed methods for dual-duplex baseband data transmission at 100 Mbit/s over unshielded telephone-grade twisted-pair cables in office building environments.
Developments in low alloy steel powders for high strength sintered components. (1990)

The creation of high quality steel powders greatly contributes to the improvements of sintered components. A new family of low alloy steel powders has been developed to meet the requirements of heavy duty structural components mainly for the automobile industry. Composite-type alloyed steel powders containing 2%Cu or 4%Ni1.5%Cu-0.5%Mo consist of iron particles to which alloying elements are finely diffusion-bonded. The powders attain the homogeneity of sintered microstructures while maintaining the compressibility of a pure iron powder. A prealloyed steel powder containing 1.0%Ni-0.3%Cu-0.2%Mo has been designed to achieve high strength after heat-treating high density sintered compacts. The sintered materials remain soft before heat treatment and are effectively densified by repressing.
Dynamic changes in the expression of MicroRNA-31 during inflammatory bowel disease-associated neoplastic transformation (2010)

Our study reveals specific miR dysregulation as chronic inflammation progresses to dysplasia. MiR-31 expression levels increase with disease progression and accurately discriminates between distinct pathological entities that coexist in IBD patients. The novel effect of miR-31 on regulating factor inhibiting hypoxia inducible factor 1 expression provides a new insight on the pathogenesis of IBDN.
Hexanary-Feedback Contention Access With PDF-Based Multiuser Estimation for Wireless Access Networks (2004)

Most existing contention access schemes are inherently unstable resulting in exponentially deteriorating throughput under increased traffic loads. In this paper, we propose a wide-sense stable (WSS) efficient hexanary-feedback contention access (HFCA) scheme, capable of providing signaling traffic high performance while retaining maximal throughput for wireless access networks. HFCA performs incremental contention resolution, managing a small subset of users at a time via a two-phase process. In the first phase, a group of users is probabilistically admitted, with a negligible probability of the group size greater than five. In the second phase, all users in the group are efficiently resolved. The two-phase process is augmented with hexanary feedback control facilitated by a probability density function (pdf)-based multiuser estimator (PMER) implemented at the physical layer. Basically, PMER measures the exact number of transmitting users (zero to five) in a contention slot by matching the envelope-phase pdf's histograms of received signals to a preconstructed pdf's library. To formally justify the performance of HFCA, we present throughput and stability analysis in which HFCA is shown WSS and the strict-sense stability condition is derived. Finally, analytic and simulation results delineate that, HFCA is highly robust against estimation discrepancy. Significantly, HFCA achieves high performance with respect to maximum stable and saturated throughputs, access delay, and blocking probability.
Human anti- -amyloid antibodies block  -amyloid fibril formation and prevent  -amyloid-induced neurotoxicity (2003)

The accumulation of beta-amyloid (A beta) in neuritic plaques is thought to be causative for the progression of Alzheimer's disease (AD). Recently, both active immunization and passive administration of A beta antibodies dramatically attenuated amyloid plaque deposition, neuritic dystrophy, astrogliosis and behaviour deficits in transgenic animals. In addition, we and others have found that titres of naturally occurring anti-A beta antibodies in the CSF of AD patients are significantly lower than those in age-matched controls. Treatment with intravenous immunoglobulins (a preparation that contained anti-A beta antibodies) significantly lowered CSF levels of A beta in non-demented patients. In this study, anti-A beta antibodies were isolated from immunoglobulin preparations and these anti-A beta antibodies strongly block fibril formation or disrupt formation of fibrilar structures. Furthermore, these antibodies almost completely prevented neurotoxicity of A beta. In contrast, immunoglobulins depleted of anti-A beta antibodies had little effect on A beta fibril formation or protection of neuronal cells. This study supports the findings that human anti-A beta antibodies may interfere with the pathogenesis of AD by more than one mechanism, and administration of polyclonal human anti-A beta antibodies isolated from plasma is a potential therapeutic agent to prevent or slow down disease progression.
Noise and spatial resolution in SQUID microscopy (2001)

We have used a scanning SQUID microscope to image magnetic field generated by currents in integrated circuits. To obtain current paths in these circuits, we apply a magnetic inversion technique to the magnetic field data. We find that the spatial resolution obtained from this technique is related to the signal-to-noise ratio, the SQUID-sample separation and the data sampling interval. We describe in detail a mathematical model of how these parameters relate to the spatial resolution. Finally, we discuss the limitations of our apparatus, and how to achieve higher spatial resolution.