gebhart/patrepeval huggingface dataset:
Experimental Models of Immunization Against Schistosomes: Lessons for Vaccine Development (1992)

Schistosomiasis is a debilitating, and sometimes deadly, parasitic infection that afflicts hundreds of millions of people living in developing countries. One of the best hopes for control of this disease is vaccine development. Studies on experimental models of attenuated vaccines have proven that high levels of protective immunity can be achieved. In these systems, resistance has been shown to be directed against the migrating larval stages of the parasite and to have both cellular and humoral components. Several candidate vaccine immunogens have been identified on the basis of antibody reactivity. However, the level of protection induced by immunization with nonliving vaccines has at yet not approached the level observed with attenuated infection. Current challenges to vaccine development include identification of protective T cell immunogens, determination of ways to strengthen the immunogenicity of isolated parasite antigens, and development of methodologies to selectively stimulate protective, as opposed to ineffective or even detrimental, immune responses.
High-performance, low-noise digital controller for inchworm piezoelectric translators (1992)

We have designed and constructed a high-performance, low-noise digital controller for ‘‘inchworm’’ piezoelectric translators. The controller features a maximum output voltage of 700 V, an rms noise level of less than 2 mV, and is capable of driving inchworms at speeds of up to 0.23 mm/s. The controller offers substantially better performance in terms of resolution, noise, speed, and cost than commercial controllers, and is suitable for atomic resolution scanning tunneling microscopy and atomic force microscopy applications.
Theory of a solid-state cyclotron maser (1978)

A theory is developed for the cyclotron-maser interaction between an electron beam and the electromagnetic waves in a cavity formed with a semiconductor having nonparabolic energy bands. The interaction originates from the dependence of the effective mass of the electron (hence cyclotron frequency) on its velocity due to nonparabolic energy-momentum relation. This mechanism is very similar to that for the cyclotron-maser radiation in vacuum tubes where the relativistic variation of mass with velocity is utilized. The linear response of the electron beam to the cavity fields are obtained from the Vlasov equation and the Maxwell's equations, while collisions are treated with an approximate model. Analytical expressions for the beam-wave coupling coefficient, beam energy loss, and the threshold power are derived for the fundamental and higher cyclotron harmonics. The dependence of these quantities on the various parameters such as cavity length, beam position, beam energy, magnetic field, etc., are discussed.
Fast-Fourier transform analysis of signal-averaged electrocardiograms for identification of patients prone to sustained ventricular tachycardia. (1984)

Electrocardiograms obtained from patients during arrhythmia-free intervals do not identify those prone to sustained ventricular tachycardia (VT) despite the occult delayed activation that is presumably present. To determine whether frequency-domain analysis facilitates detection of this hallmark of predisposition to VT, fast-Fourier transform analysis (FFTA) procedures were developed and tested with a computer-generated mathematical model. The FFTA approach developed allows inherent limitations of high-gain amplification and a priori filtering used commonly for time-domain analysis to be avoided. After demonstrating that FFTA detected low-amplitude oscillatory waveforms in signal-averaged recordings in the frequency domain, the procedure was applied to signal-averaged X, Y, and Z lead recordings from the following three groups of patients: group I, patients with prior myocardial infarction and episodic sustained VT (n = 16); group II, patients with prior myocardial infarction without overt sustained VT (n = 35); and group III, normal control subjects (n = 10). Results of FFTA demonstrated significant (p less than .0001) differences in the decibel drop at 40 Hz and the area under the curve from the fundamental frequency to the frequency at which the spectral amplitude was decreased by 60 dB for both the terminal 40 msec of the QRS and ST segment in patients in group I compared with those in groups II and III, in whom results were similar. Results were independent of QRS duration (r = .2), left ventricular ejection fraction (r = .19), and complexity of spontaneous ventricular ectopy. Thus, patients known to manifest sustained VT also exhibited relatively greater high-frequency content in arrhythmia-free intervals in the terminal QRS and ST segment than those without VT (88%, 15%, and 0% in groups I through III, respectively). FFTA offers promise for the noninvasive detection of patients at risk for the development of sustained VT.
Phase-Array Approach to Optical Whispering Gallery Modulators (2010)

This technology leverages the well-defined orbital number of a whispering gallery modulator (WGM) to expand the range of applications for such resonators. This property rigidly connects the phase variation of the field in this mode with the azimuthal angle between the coupling locations. A WGM with orbital momentum L has exactly L instant nodes around the circumference of the WGM resonator supporting such a mode. Therefore, in two locations separated by the arc alpha, the phase difference of such a field will be equal to phi= alpha L. Coupling the field out of such locations, and into a balanced interferometer, once can observe a complete constructive or distractive interference (or have any situation in between) depending on the angle alpha. Similarly, a mode L + delta L will pick up the phase phi + alpha delta L. In all applications of a WGM resonator as a modulator, the orbital numbers for the carrier and sidebands are different, and their differences delta L are known (usually, but not necessarily, delta L = 1). Therefore, the choice of the angle alpha, and of the interferometer arms difference, allows one to control the relative phase between different modes and to perform the conversion, separation, and filtering tasks necessary.
Vitamin D–binding protein modifies the vitamin D–bone mineral density relationship (2011)

Studies examining the relationship between total circulating 25-hydroxyvitamin D [25(OH)D] levels and bone mineral density (BMD) have yielded mixed results. Vitamin D-binding protein (DBP), the major carrier protein for 25(OH)D, may alter the biologic activity of circulating vitamin D. We hypothesized that free and bioavailable 25(OH)D, calculated from total 25(OH)D, DBP, and serum albumin levels, would be more strongly associated with BMD than levels of total 25(OH)D. We measured total 25(OH)D, DBP, and serum albumin levels in 49 healthy young adults enrolled in the Metabolic Abnormalities in College-Aged Students (MACS) study. Lumbar spine BMD was measured in all subjects using dual-energy X-ray absorptiometry. Clinical, diet, and laboratory information also was gathered at this time. We determined free and bioavailable (free + albumin-bound) 25(OH)D using previously validated formulas and examined their associations with BMD. BMD was not associated with total 25(OH)D levels (r = 0.172, p = .236). In contrast, free and bioavailable 25(OH)D levels were positively correlated with BMD (r = 0.413, p = .003 for free, r = 0.441, p = .002 for bioavailable). Bioavailable 25(OH)D levels remained independently associated with BMD in multivariate regression models adjusting for age, sex, body mass index, and race (p = .03). It is concluded that free and bioavailable 25(OH)D are more strongly correlated with BMD than total 25(OH)D. These findings have important implications for vitamin D supplementation in vitamin D-deficient states. Future studies should continue to explore the relationship between free and bioavailable 25(OH)D and health outcomes.
A New Device for Hot-callusing Graft Unions1 (1981)

Abstract There are various problems associated with hot-callusing graft unions of dormant fruit and nut trees. Since the whole plant is exposed to elevated temperatures, growth is promoted not only at the graft union, but also from the scion buds and the roots. Translocation demands are placed on the graft union once growth of scion buds starts and leafing out occurs. Scion buds and leaves will desiccate if a callus bridge between rootstocks and scion is inadequately formed (1).
An Optimized GD2-Targeting Retroviral Cassette for More Potent and Safer Cellular Therapy of Neuroblastoma and Other Cancers (2016)

Neuroblastoma is the commonest extra cranial solid cancer of childhood. Despite escalation of treatment regimens, a significant minority of patients die of their disease. Disialoganglioside (GD2) is consistently expressed at high-levels in neuroblastoma tumors, which have been targeted with some success using therapeutic monoclonal antibodies. GD2 is also expressed in a range of other cancer but with the exception of some peripheral nerves is largely absent from non-transformed tissues. Chimeric Antigen Receptors (CARs) are artificial type I proteins which graft the specificity of a monoclonal antibody onto a T-cell. Clinical data with early CAR designs directed against GD2 have shown some promise in Neuroblastoma. Here, we describe a GD2-targeting CAR retroviral cassette, which has been optimized for CAR T-cell persistence, efficacy and safety.
Laser Ablation Electrospray Ionization for Atmospheric Pressure Molecular Imaging Mass Spectrometry (2010)

Laser ablation electrospray ionization (LAESI) is a novel method for the direct imaging of biological tissues by mass spectrometry. By performing ionization in the ambient environment, this technique enables in vivo studies with potential for single-cell analysis. A unique aspect of LAESI mass spectrometric imaging (MSI) is depth profiling that, in combination with lateral imaging, permits 3D molecular imaging for the first time under native conditions. With current lateral and depth resolutions of approximately 100 and approximately 40 microm, respectively, LAESI MSI helps to explore the molecular architecture of live tissues.
Novel therapeutic combination demonstrates more than additive effects in cutaneous T-cell lymphoma (2014)

Cutaneous T-cell lymphomas (CTCL) represent a group of non-Hodgkin's lymphomas comprised of skin-homing lymphocytes. Mycosis fungoides (MF), the most common form, is typically indolent, while Sezary syndrome (SS) is a less common, aggressive leukemic variant.1

Early MF is often controlled with skin-directed therapies including topical steroids, chemotherapies, retinoids, phototherapy, and electron beam therapy.2 Advanced MF and SS require systemic treatments including biologic response modifiers, extracorporeal photopheresis, or cytotoxic chemotherapy,2 and relapses are common. Often, combination therapy is used to increase response rate and duration; however, there has been only one phase I study of combinatorial treatment in CTCL.3

Romidepsin is a histone deacetylase inhibitor (HDACi), which demonstrated a 34% response rate during a phase 2 study of CTCL patients who had received prior systemic therapy.4 Histone deacetylases (HDACs) modify chromatin by catalyzing the removal of acetyl moieties from lysine, producing chromatin condensation and silencing tumor suppressor genes.5 HDAC inhibition, thus, produces open chromatin structure and alteration of transcription resulting in cell cycle arrest, apoptosis, and cellular differentiation.6 Further, HDACs deacetylate structural proteins, transcription factors, and DNA repair enzymes,7 adding to the antitumor properties of HDACi. Though romidepsin is a promising single-agent treatment, HDACi have also demonstrated additive or synergistic properties with other anticancer agents.5

Nitrogen mustard (NM, mechlorethamine hydrochloride) is a topical alkylating agent used to treat early stage CTCL with an overall response rate of up to 83%; however, this declines with disease progression.8 The alkylating effect of NM produces cellular DNA damage and results in apoptosis.9 Previous studies suggest closed chromatin structure can inhibit the formation of DNA interstrand cross-linking reactions by NM.10

We hypothesized chromatin remodeling following romidepsin treatment exposes sections of DNA that are normally protected from damage due to the effects of NM. To test our hypothesis we characterized the effects of NM and romidepsin on cell viability, apoptosis, and DNA damage. Here we present our findings demonstrating the efficacy of this combination.
Chiral tunneling of topological states: towards the efficient generation of spin current using spin-momentum locking (2014)

We show that the interplay between chiral tunneling and spin-momentum locking of helical surface states leads to spin amplification and filtering in a 3D Topological Insulator (TI). Chiral tunneling across a TI pn junction allows normally incident electrons to transmit, while the rest are reflected with their spins flipped due to spin-momentum locking. The net result is that the spin current is enhanced while the dissipative charge current is simultaneously suppressed, leading to an extremely large, gate tunable spin to charge current ratio (~20) at the reflected end. At the transmitted end, the ratio stays close to one and the electrons are completely spin polarized.
Automated detection of effective left-ventricular pacing: going beyond percentage pacing counters (2015)

A device-based algorithm for beat-by-beat monitoring of effective LV pacing is feasible.
2D-3D rigid registration to compensate for prostate motion during 3D TRUS-guided biopsy (2012)

Prostate biopsy is the clinical standard for prostate cancer diagnosis. To improve the accuracy of targeting suspicious locations, systems have been developed that can plan and record biopsy locations in a 3D TRUS image acquired at the beginning of the procedure. Some systems are designed for maximum compatibility with existing ultrasound equipment and are thus designed around the use of a conventional 2D TRUS probe, using controlled axial rotation of this probe to acquire a 3D TRUS reference image at the start of the biopsy procedure. Prostate motion during the biopsy procedure causes misalignments between the prostate in the live 2D TRUS images and the pre-acquired 3D TRUS image. We present an image-based rigid registration technique that aligns live 2D TRUS images, acquired immediately prior to biopsy needle insertion, with the pre-acquired 3D TRUS image to compensate for this motion. Our method was validated using 33 manually identified intrinsic fiducials in eight subjects and the target registration error was found to be 1.89 mm. We analysed the suitability of two image similarity metrics (normalized cross correlation and mutual information) for this task by plotting these metrics as a function of varying parameters in the six degree-of-freedom transformation space, with the ground truth plane obtained from registration as the starting point for the parameter exploration. We observed a generally convex behaviour of the similarity metrics. This encourages their use for this registration problem, and could assist in the design of a tool for the detection of misalignment, which could trigger the execution of a non-real-time registration, when needed during the procedure.
Demonstration of a wide-band image rejection microwave downconverter (2000)

A photonic image-rejection downconverter capable of down-converting radio-frequency (RF) signals over a range of 5-18 GHz into an IF band 2.1 GHz wide (3.3-5.4 GHz) is presented. RF signals received by the system are first up-converted into the passband of a 21.3-23.4-GHz filter, and then optically down-converted to 3.3-5.4 GHz. The system exhibited better than 60 dB of image rejection over its entire bandwidth and spurious signals resulting from harmonic mixing products were more than 25 dB below the downconverted signal.
Uncovering a novel function of BTLA on tumor-infiltrating CD8+ T cells (2013)

Manipulation of T-cell co-inhibitory molecules, such as CTLA-4, PD-1, and BTLA has recently moved to the forefront of cancer immunotherapy. Although these molecules serve as inhibitors of T-cell activation, they are also biomarkers for activated T cells and may in fact have positive immune
Microfluidic bubble logic (2006)

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2008.
A Manganese Superoxide Dismutase from<i>Serratia marcescens</i> (1983)

Journal Article A Manganese Superoxide Dismutase from Serratia marcescens Get access Kazutaka Maejima, Kazutaka Maejima Central Research Division, Takeda Chemical Industries, Ltd., Osaka 532, Japan Search for other works by this author on: Oxford Academic Google Scholar Kouichi Miyata, Kouichi Miyata Central Research Division, Takeda Chemical Industries, Ltd., Osaka 532, Japan Search for other works by this author on: Oxford Academic Google Scholar Katsumi Tomoda Katsumi Tomoda Central Research Division, Takeda Chemical Industries, Ltd., Osaka 532, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 47, Issue 7, 1 July 1983, Pages 1537–1543, https://doi.org/10.1080/00021369.1983.10865805 Published: 01 July 1983 Article history Received: 13 December 1982 Published: 01 July 1983
Block storage virtualization with commodity secure digital cards (2012)

Smartphones, tablets and other mobile platforms typically accommodate bulk data storage with low-cost, FAT-formatted Secure Digital cards. When one uses a mobile device to run a full-system virtual machine (VM), there can be a mismatch between 1) the VM's I/O mixture, security and reliability requirements and 2) the properties of the storage media available for VM block storage and checkpoint images. To resolve this mismatch, this paper presents a new VM disk image format called the Logging Block Store (LBS). After motivating the need for a new format, LBS is described in detail with experimental results demonstrating its efficacy. As a result of this work, recommendations are made for future optimizations throughout the stack that may simplify and improve the performance of storage virtualization systems on mobile platforms.
Continuous phase-shift lithography with a roll-type mask and application to transparent conductor fabrication (2012)

We report the development of a near-field optical nanolithography method using a roll-type phase-shift mask. Sub-wavelength resolution is achieved using near-field exposure of photoresist through a cylindrical phase mask, allowing dynamic and high throughput continuous patterning. As an application, we present the fabrication of a transparent electrode in the form of a metallic wire grid by using the roller-based optical lithography method. To fabricate a mesh-type metal pattern, a specific phase-shift mask was designed and critical experimental parameters were also studied. As a result, a transparent conductor with suitable properties was achieved with a recently built cylindrical phase-shift lithography prototype designed to pattern on 100 mm(2) of substrate area.
Label-free separation of human embryonic stem cells and their differentiating progenies by phasor fluorescence lifetime microscopy (2012)

We develop a label-free optical technique to image and discriminate undifferentiated human embryonic stem cells (hESCs) from their differentiating progenies in vitro. Using intrinsic cellular fluorophores, we perform fluorescence lifetime microscopy (FLIM) and phasor analysis to obtain hESC metabolic signatures. We identify two optical biomarkers to define the differentiation status of hESCs: Nicotinamide adenine dinucleotide (NADH) and lipid droplet-associated granules (LDAGs). These granules have a unique lifetime signature and could be formed by the interaction of reactive oxygen species and unsaturated metabolic precursor that are known to be abundant in hESC. Changes in the relative concentrations of these two intrinsic biomarkers allow for the discrimination of undifferentiated hESCs from differentiating hESCs. During early hESC differentiation we show that NADH concentrations increase, while the concentration of LDAGs decrease. These results are in agreement with a decrease in oxidative phosphorylation rate. Single-cell phasor FLIM signatures reveal an increased heterogeneity in the metabolic states of differentiating H9 and H1 hESC colonies. This technique is a promising noninvasive tool to monitor hESC metabolism during differentiation, which can have applications in high throughput analysis, drug screening, functional metabolomics and induced pluripotent stem cell generation.
Flare monitoring for petroleum refineries (2009)

In petroleum refineries, it is a common practice to flare up the exhaust gases before releasing them to the atmosphere in order to reduce the environment pollution. The area or volume of the flare indicates the quantity of gas that is getting released in the refining process and the color of the flare at any given time is decided by the constituents of the gases in the flare and the volume of the flare indicates the quantity of gas that is released. In an indirect way, these parameters of flare indicate the performance of refining process. Presently, the flare is manually observed by the operator and doing so reliably on a 24times7 basis is a difficult job. In this paper we propose an algorithm to automate this effort using video analytics and provide the alarms in case of any abnormal flaring event. The flare detection is done by estimating models for foreground and background regions and the color of the flare is analyzed by using classifiers with kernel function, such as support vector machine (SVM). The performance of these algorithms is tested on various data sets collected from refineries.
Development of Improved HDAC6 Inhibitors as Pharmacological Therapy for Axonal Charcot–Marie–Tooth Disease (2016)

Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy, with an estimated prevalence of 1 in 2500. The degeneration of motor and sensory nerve axons leads to motor and sensory symptoms that progress over time and have an important impact on the daily life of these patients. Currently, there is no curative treatment available. Recently, we identified histone deacetylase 6 (HDAC6), which deacetylates α-tubulin, as a potential therapeutic target in axonal CMT (CMT2). Pharmacological inhibition of the deacetylating function of HDAC6 reversed the motor and sensory deficits in a mouse model for mutant "small heat shock protein B1" (HSPB1)-induced CMT2 at the behavioral and electrophysiological level. In order to translate this potential therapeutic strategy into a clinical application, small drug-like molecules that are potent and selective HDAC6 inhibitors are essential. To screen for these, we developed a method that consisted of 3 distinct phases and that was based on the pathological findings in the mutant HSPB1-induced CMT2 mouse model. Three different inhibitors (ACY-738, ACY-775, and ACY-1215) were tested and demonstrated to be both potent and selective HDAC6 inhibitors. Moreover, these inhibitors increased the innervation of the neuromuscular junctions in the gastrocnemius muscle and improved the motor and sensory nerve conduction, confirming that HDAC6 inhibition is a potential therapeutic strategy in CMT2. Furthermore, ACY-1215 is an interesting lead molecule as it is currently tested in clinical trials for cancer. Taken together, these results may speed up the translation of pharmacological inhibition of HDAC6 into a therapy against CMT2.