gebhart/patrepeval huggingface dataset:
Independent Validation of Candidate Breast Cancer Serum Biomarkers Identified by Mass Spectrometry (2005)

Evaluation of biomarkers in independent sample sets can help determine the broader utility of candidate markers, and protein identification permits understanding of their molecular basis. C3a(desArg) appears to lack specificity among patients with benign diseases, limiting its utility as a stand-alone tumor marker, but it may still be useful in a multimarker panel for early detection of breast cancer.
Bis Tertiary Amide Inhibitors of the HIV-1 Protease Generated via Protein Structure-Based Iterative Design (1996)

A series of potent nonpeptide inhibitors of the HIV protease have been identified. Using the structure of compound 3 bound to the HIV protease, bis tertiary amide inhibitor 9 was designed and prepared. Compound 9 was found to be about 17 times more potent than 3, and the structure of the protein-ligand complex of 9 revealed the inhibitor binds in an inverted binding mode relative to 3. Examination of the protein-ligand complex of 9 suggested several modifications in the P1 and P1' pockets. Through these modifications it was possible to improve the activity of the inhibitors another 100-fold, highlighting the utility of crystallographic feedback in inhibitor design. These compounds were found to have good antiviral activity in cell culture, were selective for the HIV protease, and were orally available in three animal models.
A practical ply-based appearance model of woven fabrics (2020)

Simulating the appearance of woven fabrics is challenging due to the complex interplay of lighting between the constituent yarns and fibers. Conventional surface-based models lack the fidelity and details for producing realistic close-up renderings. Micro-appearance models, on the other hand, can produce highly detailed renderings by depicting fabrics fiber-by-fiber, but become expensive when handling large pieces of clothing. Further, neither surface-based nor micro-appearance model has not been shown in practice to match measurements of complex anisotropic reflection and transmission simultaneously. In this paper, we introduce a practical appearance model for woven fabrics. We model the structure of a fabric at the ply level and simulate the local appearance of fibers making up each ply. Our model accounts for both reflection and transmission of light and is capable of matching physical measurements better than prior methods including fiber based techniques. Compared to existing micro-appearance models, our model is light-weight and scales to large pieces of clothing.
On the security of iterated message authentication codes (1999)

The security of iterated message authentication code (MAC) algorithms is considered, and in particular, those constructed from unkeyed hash functions. A new MAC forgery attack applicable to all deterministic iterated MAC algorithms is presented, which requires on the order of 2/sup n/2/ known text-MAC pairs for algorithms with n bits of internal memory, as compared to the best previous general attack which required exhaustive key search. A related key-recovery attack is also given which applies to a large class of MAC algorithms including a strengthened version of CBC-MAC found in ANSI X9.19 and ISO/IEC 9797, and envelope MAC techniques such as "keyed MD5". The security of several related existing MACs based directly on unkeyed hash functions, including the secret prefix and secret suffix methods, is also examined.
A Supramolecular Approach for Preparation of Size‐Controlled Nanoparticles (2009)

A supramolecular approach has been developed for the preparation of supramolecular nanoparticles (SNPs) with variable sizes (30-450 nm) from three different molecular building blocks using a cyclodextrin/adamantane recognition system. Positron emission tomography (PET) was employed to study the biodistribution and lymph node drainage of the SNPs in mice. The sizes of the SNPs affect their in vivo characteristics (see picture).
Abstract 2527: Potent, highly selective peptidomimetic prodrugs targeting the SH2 domain of Stat3 decrease vasculogenic mimicry, invasion, and anchorage independent growth of cancer cells (2010)

Abstract Signal transducer and activator of transcription 3 (Stat3) transmits signals from IL-6 family cytokines, EGF and VEGF. Stat3 is constitutively activated in lung, head and neck, breast, and prostate cancers, AML and other malignancies, providing a target for cancer drug design. To uncouple Stat3 from its roles in proliferation, survival, angiogenesis, and invasion, we are targeting its SH2 domain with phosphopeptide mimetics derived from the recognition sequence, pTyr-Leu-Pro-Gln. Molecular modeling indicated that a methyl group attached to the β-position of a pTyr mimic would enhance affinity due to hydrophobic contact. This modification increased affinity 2-3 fold in a series of peptidomimetics based on pCinn-Xxx-Yyy-Gln-NHBn (pCinn = 4-phosphorylcinnamic acid), resulting in IC50 values of 35 − 112 nM in a biochemical fluorescence polarization assay. Conversion of these to bis-pivaloyloxymethyl (POM) protected difluoromethylphosphonate prodrugs resulted in complete inhibition of the phosphorylation of Tyr705 of Stat3 at concentrations of 0.5 − 1 μM in breast, ovarian, and melanoma cells. Prodrugs were selective for Stat3 over other SH2 domain-containing proteins such as Stat1, Stat5, Src, and PI3K p85. Quantitative RT-PCR showed that prodrugs inhibited Stat3-targeted gene expression. Prodrugs were not cytotoxic to cells grown in 2D cultures on plastic dishes. However, potent inhibition of Stat3-driven processes such as vasculogenic mimicry, invasion, and anchorage independent growth in soft agar was observed. Conclusions: 1. peptidomimetic prodrugs are highly potent and selective inhibitors of Stat3; 2. cultured tumor cells do not depend on phosphorylation of Tyr705 of Stat3 for survival; 3. highly selective inhibitors of Stat3 phosphorylation are likely to be effective antitumor agents due to inhibition of invasion and angiogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2527.
Relaxing the stability limit of adaptive control systems in the presence of unmodelled dynamics (2017)

It is known that a closed-loop dynamical system subject to an adaptive controller remains stable either if there does not exist significant unmodelled dynamics or the effect of system uncertainties is negligible. This implies that these controllers cannot tolerate large system uncertainties even when the unmodelled dynamics satisfy a set of conditions. In this paper, we present an adaptive control architecture such that the proposed adaptive controller is augmented with an adaptive robustifying term. Unlike standard adaptive controllers, the proposed architecture allows the closed-loop dynamical system to remain stable in the presence of large system uncertainties when the unmodelled system dynamics satisfy a set of conditions. A numerical example is provided to demonstrate the efficacy of the proposed approach.
ChemInform Abstract: REDUCTIVE ENZYMIC SYNTHESIS OF L‐CARNITINE WITH REGENERATION OF THE NADH USED (1980)

Abstract Die enzymatische Synthese von L‐Carnitin (II) erfolgt durch Reduktion der Carbonylfunktion von 3‐Dehydrocarnitin (I) mit NADH unter Verwendung von Carnitindehydrogenase (CARH) als Katalysator und einem NADH‐regenerierenden System (NARS).
Demonstration of Kaposi's Sarcoma-Associated Herpes Virus Cyclin D Homolog in Cutaneous Kaposi's Sarcoma by Colorimetric In Situ Hybridization Using a Catalyzed Signal Amplification System (1998)

Kaposi's sarcoma-associated herpes virus (KSHV)/human herpes virus 8 (HHV8) DNA sequences have been demonstrated in Kaposi's sarcoma (KS), as well as in some acquired immunodeficiency syndrome (AIDS)-related non-Hodgkin's lymphomas (NHL) and in multicentric Castleman's disease. Although KSHV DNA generally is abundant in KSHV-associated lymphomas, few copies of the virus are present in KS, a property that confounds detection by in situ methods. Previous in situ studies, which identified KSHV in lesions of KS, relied on the use of polymerase chain reaction (PCR) to amplify target DNA sequences before in situ hybridization (ISH) for localization or used ISH with radioactively-labeled probes to obtain adequate levels of detection sensitivity. In this study, a novel nonisotopic nucleic acid ISH method using catalyzed signal amplification and colorimetric detection without PCR-dependent target amplification was used to identify KSHV-specific sequences. The level of sensitivity was increased further by using a probe that detects viral cyclin D homolog transcripts, which are expressed at significant levels during latent viral infection. Thirty cutaneous lesions of KS (25 AIDS-related and five classical European type) were evaluated. AIDS-related NHL and cell lines derived from patients with AIDS-related NHL, all of which were known to harbor KSHV by Southern blot analysis, were used as positive controls. NHL and benign cutaneous vascular lesions not associated with AIDS were used as negative controls. For each of the 30 KS lesions studied, hybridization signals were detected in most of the spindle cells surrounding the atypical slit-like vascular channels and also were detected in some endothelial cells in well-formed blood vessels in the perilesional dermis. Plaque and nodular lesions generally contained more labeled cells than did early patch lesions. All AIDS-related NHL and cell lines contained KSHV-specific sequences; however, the non-AIDS-related NHLs and benign vascular lesions were negative. These results confirm the presence of KSHV sequences in cutaneous KS and provide in situ evidence of infection by this virus in early patch-stage lesions. This study also defines the in situ expression of the KSHV cyclin D homolog viral oncogene in cutaneous KS. The use of this sensitive nonisotopic ISH method should allow detection of other KSHV-specific gene products, further defining the pathobiology of this virus.
TensorFlow Quantum: A Software Framework for Quantum Machine Learning (2020)

We introduce TensorFlow Quantum (TFQ), an open source library for the rapid prototyping of hybrid quantum-classical models for classical or quantum data. This framework offers high-level abstractions for the design and training of both discriminative and generative quantum models under TensorFlow and supports high-performance quantum circuit simulators. We provide an overview of the software architecture and building blocks through several examples and review the theory of hybrid quantum-classical neural networks. We illustrate TFQ functionalities via several basic applications including supervised learning for quantum classification, quantum control, simulating noisy quantum circuits, and quantum approximate optimization. Moreover, we demonstrate how one can apply TFQ to tackle advanced quantum learning tasks including meta-learning, layerwise learning, Hamiltonian learning, sampling thermal states, variational quantum eigensolvers, classification of quantum phase transitions, generative adversarial networks, and reinforcement learning. We hope this framework provides the necessary tools for the quantum computing and machine learning research communities to explore models of both natural and artificial quantum systems, and ultimately discover new quantum algorithms which could potentially yield a quantum advantage.
Benefits of oxytocin administration in obstructive sleep apnea (2017)

Activation of oxytocin receptors has shown benefits in animal models of obstructive sleep apnea (OSA). We tested if nocturnal oxytocin administration could have beneficial effects in OSA patients. Eight patients diagnosed with OSA were administered intranasal oxytocin (40 IU). Changes in cardiorespiratory events during sleep, including apnea and hypopnea durations and frequency, risk of event-associated arousals, and heart rate variability, were assessed. Oxytocin significantly increased indexes of parasympathetic activity, including heart rate variability, total sleep time, and the postpolysommogram sleep assessment score, an index of self-reported sleep satisfaction. Although the apnea-hypopnea index was not significantly changed with oxytocin administration, when apnea and hypopnea events were compared independently, the frequency of hypopneas, but not apneas, was significantly (<i>P</i> ≤ 0.005) decreased with oxytocin treatment. Both apneas and hypopneas were significantly shortened in duration with oxytocin treatment. Oxytocin treatment significantly decreased the percent of apnea and hypopnea events that were accompanied with an arousal. Oxytocin administration has the potential to restore cardiorespiratory homeostasis and reduce some clinically important (objective and patient-reported) adverse events that occur with OSA. Additional studies are needed to further understand the mechanisms by which oxytocin promotes these changes in cardiorespiratory and autonomic function in OSA patients.
InGaN/GaN nanowires epitaxy on large-area MoS<sub>2</sub> for high-performance light-emitters (2017)

High-quality nitride nanowires on large-area layered transition metal dichalcogenides are first reported, which yielded light-emitting diodes (LEDs) with superior performance.
The TLX-miR-219 cascade regulates neural stem cell proliferation in neurodevelopment and schizophrenia iPSC model (2016)

Dysregulated expression of miR-219, a brain-specific microRNA, has been observed in neurodevelopmental disorders, such as schizophrenia (SCZ). However, its role in normal mammalian neural stem cells (NSCs) and in SCZ pathogenesis remains unknown. We show here that the nuclear receptor TLX, an essential regulator of NSC proliferation and self-renewal, inhibits miR-219 processing. miR-219 suppresses mouse NSC proliferation downstream of TLX. Moreover, we demonstrate upregulation of miR-219 and downregulation of TLX expression in NSCs derived from SCZ patient iPSCs and DISC1-mutant isogenic iPSCs. SCZ NSCs exhibit reduced cell proliferation. Overexpression of TLX or inhibition of miR-219 action rescues the proliferative defect in SCZ NSCs. Therefore, this study uncovers an important role for TLX and miR-219 in both normal neurodevelopment and in SCZ patient iPSC-derived NSCs. Moreover, this study reveals an unexpected role for TLX in regulating microRNA processing, independent of its well-characterized role in transcriptional regulation.
Development of a video‐rate rangefinder system using light intensity modulation with scanning laser light (2006)

Abstract We have developed an active rangefinder system that can obtain depth images at video field rates by improving Carrihill's intensity ratio depth sensor. Although the depth sensor can be made at low cost, its depth precision is affected by background light, video noise, and the motion of objects. To reduce such influences, first we used a laser line pattern scanned by a rotating mirror as a light source and a camera with an optical narrow‐bandpass filter—an interference filter—to overcome the background light. Second, we corrected the projected light power at the camera's peripheral field to decrease depth error there. Third, we performed inter‐field median filtering of measured depths to decrease the influence of object motion. As a result, we achieved standard deviations of depths 1.4% and 2.1% in a range of 2.2 to 3 and 3.2 to 4 m, respectively. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(3): 20–31, 2006; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/scj.20423
Rapid Mycobacterial Liquid Culture-Screening Method for<i>Mycobacterium avium</i>Complex Based on Secreted Antigen-Capture Enzyme-Linked Immunosorbent Assay (2009)

ABSTRACT Sensors in automated liquid culture systems for mycobacteria, such as MGIT, BacT/Alert 3D, and Trek ESP II, flag growth of any type of bacteria; a positive signal does not mean that the target mycobacteria are present. All signal-positive cultures thus require additional and often laborious testing. An immunoassay was developed to screen liquid mycobacterial cultures for evidence of Mycobacterium avium complex (MAC). The method, called the MAC-enzyme-linked immunosorbent assay (ELISA), relies on detection of MAC-specific secreted antigens in liquid culture. Secreted MAC antigens were captured by the MAC-ELISA with polyclonal anti- Mycobacterium avium subsp. paratuberculosis chicken immunoglobulin Y (IgY), detected using rabbit anti-MAC IgG, and then revealed using horseradish peroxidase-conjugated goat anti-rabbit IgG. When the MAC-ELISA was evaluated using pure cultures of known mycobacterial ( n = 75) and nonmycobacterial ( n = 17) organisms, no false-positive or false-negative MAC-ELISA results were found. By receiver operator characteristic (ROC) analysis of 1,275 previously identified clinical isolates, at the assay optimal cutoff the diagnostic sensitivity and specificity of the MAC-ELISA were 92.6% (95% confidence interval [95% CI], 90.3 to 94.5) and 99.9% (95% CI, 99.2 to 100), respectively, with an area under the ROC curve of 0.992. Prospective evaluation of the MAC-ELISA with an additional 652 clinical samples inoculated into MGIT ParaTB medium and signaling positive per the manufacturer's instructions found that the MAC-ELISA was effective in determining those cultures that actually contained MAC species and warranting the resources required to identify the organism by PCR. Of these 652 MGIT-positive cultures, the MAC-ELISA correctly identified 96.8% (of 219 MAC-ELISA-positive cultures) as truly containing MAC mycobacteria, based on PCR or high-performance liquid chromatography (HPLC) as reference tests. Only 6 of 433 MGIT signal-positive cultures (1.4%) were MAC-ELISA false negative, and only 7 of 219 MGIT signal-negative cultures (3.2%) were false positive. The MAC-ELISA is a low-cost, rapid, sensitive, and specific test for MAC in liquid cultures. It could be used in conjunction with or independent of automated culture reading instrumentation. For maximal accuracy and subspecies-specific identification, use of a confirmatory multiplex MAC PCR is recommended.
Truly bistable twisted nematic liquid crystal display (2004)

Truly bistable twisted nematic liquid crystal display has been demonstrated. This display can be switched between the-22.5/spl deg/ and 157.5/spl deg/ twist states by breaking of the anchoring on one of the substrates. Bistability is achieved through the application of a new photo-alignable polymer SDA-1. Both theoretical and experimental results show that this mode has excellent contrast ratio and wide viewing angles.
<title>Mark topography for alignment and registration in projection electron lithography</title> (1996)

We have studied two mark geometries for possible use in a projection e-beam lithography system using SCALPEL (scattering with angular limitation in projection electron lithography). These are V-grooves and vertically etched geometries, pedestals or trenches. We report results of measurements of backscattered electron (BSE) contrast form topographic marks of varying size and as a function of energy up to 100 kV. The marks were fabricated on silicon wafers. The measurements were taken both in a scanning electron microscope and in an experimental SCALPEL machine operating in focused probe mode. The V-grooves ranged from 1.0 to 30 micrometers wide. The vertical etched features ranged from 2 to 30 micrometers wide and 0.6 and 50 micrometers depth. The results depended not only on the feature width and depth, but also on whether the features were isolated or in line and space patterns. Using a BSE ratio of 1.05 as a criterion for acceptable contrast from an alignment mark, V-grooves and vertical etched features had acceptable contrast with exception of the smallest and shallowest features for both geometries.
Increase in levels of serum keratan sulfate following cartilage proteoglycan degradation in the rabbit knee joint (1988)

Following injection of chymopapain into a single knee joint in rabbits, serum keratan sulfate levels rose sharply and remained elevated for at least 48 hours before returning to preinjection levels. These changes were accompanied by depletion of proteoglycans from articular cartilage in the injected joint. We conclude that serum keratan sulfate levels rise predictably following acute loss of proteoglycan from a single joint.
Multi-channel real time active noise control system for infant incubators (2009)

Excessive noise levels inside infants incubators in neonatal intensive care units (NICU) contribute to number of harmful effects on the infant's health. This paper develops and implements practical active noise control (ANC) systems for the infant incubators. The filtered-X least mean square (FXLMS) algorithm is used to cancel the noise inside the incubator. The multi-channel and pseudo multi-channel ANC systems are proposed to enhance the noise cancellation performance in terms of cancellation gain and quiet zone. An experimental setup based on real Giraffe incubator from GE Healthcare is used for real-time experiments. The results show that the ANC system can dramatically reduce the noise and cost effective.
The Effect of Thermal Shunt on the Current Instability of Multiple-Emitter-Finger Heterojunction Bipolar Transistors (1993)

The occurrence of thermally-induced instability in multi-emitter finger heterojunction bipolar transistors (HBTs) is described. An equivalent circuit is used to model the effect of thermal on this instability. It is shown that the shunt is superior to the ballast resistor for improving power characteristics, without sacrificing microwave performance. An HBT implementing the shunt technique has demonstrated a microwave power density of more than 10 mW/pm2 of emitter area. I. INTRODUCTION Due to the demand for high power microwave circuits, GaAs-based heterojunction bipolar transistors (HBTs) have been under intensive development. Power performance of AIGaAs/GaAs HBTs built by conventional upright processing techniques has been demonstrated with an output RF power density of 4 mW/pm2 of emitter area at X band frequencies[l]. As the power performance approaches the ultimate limit determined by the electronic properties of device materials, heat dissipation becomes, a great concern. Junction temperature rise causes the dc current-voltage (I-V) characteristics to be adversely altered from the ideal isothermal performance and degrades the microwave performance. The destruction of Si power devices by runaway is well established[2,3]. It is also known that Si power transistors with multiple emitter fingers show thermallyinduced instability[4,5]. These phenomena are fundamental to all bipolar transistors. AIGaAsIGaAs HBTs, with low substrate conductivity and high operating power, are expected to be more vulnerable to these effects than Si devices. A theoretical study[6] taking into account the nonuniform junction temperature distribution showed that multi-emitter finger HBTs exhibit an I-V current in the linear active region. The device can be operated in and out of the crush region many times without permanent damage, since electro-thermal stability is usually preserved. In other words, the formation of localized hot spots does not necessarily destroy an HBT, but it may pose a long term reliability concern. This thermally-induced instability (TICI), which is one form of runaway, imposes a limitation on the power output of HBTs.
Silicon Micromachined Modulated Metasurface Antennas in the Terahertz Range (2016)

This paper explores the capabilities of a class of metasurface (MTS), which consists of metalized cylinders on a ground plane, for the realization of modulated MTS antennas at terahertz (THz) frequencies. The proposed structure is particularly appropriate for being micromachined out of a silicon wafer by means of deep reactive ion etching (DRIE). The constraints that DRIE imposes in the design of the MTS unit cell are discussed, along with the advantages of silicon micromachined modulated MTSs with respect to other fabrication approaches in the THz range.