gebhart/patrepeval huggingface dataset:
Near-infrared endoscopic imaging of deep artificial approximal lesions in extracted teeth (2019)

Near-infrared (NIR) dental imaging using scanning fiber endoscope (SFE) is being developed with advantages of miniature size (1.6mm), flexible shaft, video frame rate (7Hz), and expandable field of view (60 degrees). Using 1310, 1460, and 1550 nm laser diodes, the multispectral NIR SFE provides high contrast of lesion with transparency of stained and non-calcified plaque. However, capabilities of scanned NIR imaging remain unknown. Artificial interproximal lesions are created in extracted human posterior teeth by preparing a cavitation on the mesial or distal surface and then the cavitated artificial lesions were filled with hydroxyapatite powder and sealed with cyanoacrylate resin. Lesions are prepared at different occlusal-gingival depths from marginal ridges, lesion drilling depths and lesion size. Endoscopic reflectance images were acquired and compared to micro-CT scans and 1310 nm OCT images of the lesions to evaluate performance of the nirSFE. Results show that NIR SFE can image deep lesions under sound enamel with thickness of &le;4mm. All three wavelengths can detect deep lesions through the occlusal enamel which are not visible by naked-eye. 1460 nm has the highest contrast between lesion and sound enamel while 1310nm more clearly shows the contrast between enamel and dentin. Our nirSFE system can detect artificial interproximal lesions less than 4 mm below the occlusal surface, distinguish different drilling depth both in enamel and in dentin layer. Furthermore, the nirSFE realtime imaging and video functionality renders better lesion contrast and helps distinguish specular reflection and lesion signal. In conclusion, the NIR SFE has the potential to measure volume of these lesions due to the many viewing angles achievable by the miniature and flexible probe tip.
Bounded Coordinate-Descent for Biological Sequence Classification in\n High Dimensional Predictor Space (2010)

We present a framework for discriminative sequence classification where the\nlearner works directly in the high dimensional predictor space of all\nsubsequences in the training set. This is possible by employing a new\ncoordinate-descent algorithm coupled with bounding the magnitude of the\ngradient for selecting discriminative subsequences fast. We characterize the\nloss functions for which our generic learning algorithm can be applied and\npresent concrete implementations for logistic regression (binomial\nlog-likelihood loss) and support vector machines (squared hinge loss).\nApplication of our algorithm to protein remote homology detection and remote\nfold recognition results in performance comparable to that of state-of-the-art\nmethods (e.g., kernel support vector machines). Unlike state-of-the-art\nclassifiers, the resulting classification models are simply lists of weighted\ndiscriminative subsequences and can thus be interpreted and related to the\nbiological problem.\n
Understanding the origins of metal–organic framework/polymer compatibility (2017)

The microscopic interfacial structures for a series of metal-organic framework/polymer composites consisting of the Zr-based UiO-66 coupled with different polymers are systematically explored by applying a computational methodology that integrates density functional theory calculations and force field-based molecular dynamics simulations. These predictions are correlated with experimental findings to unravel the structure-compatibility relationship of the MOF/polymer pairs. The relative contributions of the intermolecular MOF/polymer interactions and the flexibility/rigidity of the polymer with respect to the microscopic structure of the interface are rationalized, and their impact on the compatibility of the two components in the resulting composite is discussed. The most compatible pairs among those investigated involve more flexible polymers, <i>i.e.</i> polyvinylidene fluoride (PVDF) and polyethylene glycol (PEG). These polymers exhibit an enhanced contact surface, due to a better adaptation of their configuration to the MOF surface. In these cases, the irregularities at the MOF surface are filled by the polymer, and even some penetration of the terminal groups of the polymer into the pores of the MOF can be observed. As a result, the affinity between the MOF and the polymer is very high; however, the pores of the MOF may be sterically blocked due to the strong MOF/polymer interactions, as evidenced by UiO-66/PEG composites. In contrast, composites involving polymers that exhibit higher rigidity, such as the polymer of intrinsic microporosity-1 (PIM-1) or polystyrene (PS), present interfacial microvoids that contribute to a decrease in the contact surface between the two components, thus reducing the MOF/polymer affinity.
Thermodynamic Calculations and Metallorganic Chemical Vapor Deposition of Ruthenium Thin Films Using Bis(ethyl-π-cyclopentadienyl)Ru for Memory Applications (2000)

The equilibrium concentrations of the various gaseous and solid phases in metallorganic chemical vapor deposition of Ru thin films were calculated in the experimentally relevant temperature and oxygen partial pressure ranges. Although thermal decomposition of the precursor, bis(ethyl‐π‐cyclopentadienyl)Ru required a sufficient amount of oxygen, experimental results showed that up to a certain concentration of oxygen, Ru metal was deposited without any detectable impurity. Thermodynamic calculations showed that all the supplied oxygen was consumed to oxidize carbon and hydrogen, cracked from the precursor ligand, rather than Ru. Thus, metal films could be obtained. There was an optimum oxygen‐to‐precursor ratio at which the pure Ru phase could be obtained with minimum generation of not only carbon and but also detrimental hydrogen. Ru thin films with minimal carbon and contamination could be obtained by optimization of the oxygen supply at a low deposition temperature of 300°C. © 2000 The Electrochemical Society. All rights reserved.
Integrated online speaker clustering and adaptation (2011)

For many applications, it is necessary to produce speech transcriptions in a causal fashion. To produce high quality transcripts, speaker adaptation is often used. This requires online speaker clustering and incremental adaptation techniques to be developed. This paper presents an integrated approach to online speaker clustering and adaptation which allows efficient clustering of speakers using the same accumulated statistics that are normally used for adaptation. Using a consistent criterion for both clustering and adaptation should yield gains for both stages. The proposed approach is evaluated on a meetings transcription task using audio from multiple distant microphones. Consistent gains over standard clustering and adaptation were obtained.
Surface Potassium Promotion of Co4MnAlOx in Direct NO Decomposition Generates the Same Type of Active Sites as Bulk Promotion (2023)

K/Co4MnAlOx mixed oxides are active in direct NO decomposition. This work investigates the effect of the preparation method and K precursor type. Using the incipient wetness impregnation method, the modification by the required amount of K was ensured. Regardless of the K precursor type, similar NO conversions were reached for samples modified by 4 wt % K. The optimal amount of K from the KNO3 precursor was evaluated as 2–6 wt %. The physicochemical properties were carefully explored using atomic absorption spectroscopy, X-ray photoelectron spectroscopy, X-ray diffraction, Fourier transform IR spectroscopy, N2 physisorption, H2 temperature-programmed reduction, CO2 and NO temperature-programmed desorption, scanning electron microscopy, and transmission electron microscopy, correlated with catalytic properties in transient and steady state and compared with the results obtained in our previous study using bulk modified samples. The present study underlines the effect of the preparation method on the Brunauer–Emmett–Teller surface area (SBET) of prepared catalysts and thus the amount of active sites available for catalytic reaction. Moreover, the results emphasize the importance of catalyst basicity, which affects the amount of adsorbed NO2– species, the key intermediates in the direct NO catalytic reaction.
ZAP-70 is required for calcium mobilization but is dispensable for mitogen-activated protein kinase (MAPK) superfamily activation induced via CD2 in human T cells (2000)

Stimulation with specific pairs of anti-CD2 antibodies can induce T cell activation and proliferation. In this study, we investigate the significance of ZAP-70 in CD2 signaling using ZAP-70-deficient T cells derived from a CD8-deficient patient and show that ZAP-70 is necessary for cellular proliferation and cytokine production in T cells stimulated via CD2. Biochemical analyses show that CD2 stimulation induces activation of mitogen-activated protein kinase (MAPK) superfamily in ZAP-70-deficient T cells, indicating that a ZAP-70-independent pathway(s) exists for MAPK superfamily activation via CD2. In contrast, intracellular Ca2+ mobilization and activation of nuclear factor of activated T cells (NFAT) upon CD2 triggering were impaired in T cells lacking ZAP-70. Furthermore, we found that pharmacological Ca2+ elevation combined with CD2 stimulation restored NFAT activation and subsequent cytokine production in ZAP-70-deficient T cells. These results indicate that in CD2 signaling, ZAP-70 plays an essential role in Ca2+ mobilization and NFAT activation.
Diagnosis as Planning Revisited: An Abridged Report (2010)

In the spirit of past contributions to the formal characterization of diagnosis (e.g., (Reiter, 1987; de Kleer et al., 1992)) this paper presents a formal characterization of diagnosis of discrete dynamical systems, appealing to the situation calculus. It then proceeds to establish a correspondence between computing dynamical diagnoses and generating plans. It is this correspondence that we feel may be of particular interest to the DX community. Planning technology provides tailored representations and fast, efficient algorithms for automated plan generation. This paper shows how such technology can be brought to bear on the problem of generating diagnoses. Initial experiments support our claim that planning technology holds great promise for efficient generation of diagnoses.
A Minicourse on Dynamic Multithreaded Algorithms (2005)

This tutorial teaches dynamic multithreaded algorithms using a Cilk-like [11, 8, 10] model. The material was taught in the MIT undergraduate class 6.046 Introduction to Algorithms as two 80-minute lectures. The style of the lecture notes follows that of the textbook by Cormen, Leiserson, Rivest, and Stein [7], but the pseudocode from that textbook has been “Cilkified” to allow it to describe multithreaded algorithms. The first lecture teaches the basics behind multithreading, including defining the measures of work and critical-path length. It culminates in the greedy scheduling theorem due to Graham and Brent [9, 6]. The second lecture shows how parallel applications, including matrix multiplication and sorting, can be analyzed using divide-and-conquer recurrences.
Simultaneous Multi-Band, Multi-Beam, and Multi-Function TX/RX Phased Array Systems (2022)

This paper presents new TX and RX phased array systems that provide simultaneous multi-band, multi-beam, and multi-function operation over the millimeter wave region of the electromagnetic spectrum. The overall system uses separate TX and RX arrays that are based on optical up- and down-conversion as the means to implement beam forming with near-unlimited beam-bandwidth products. It does so in a non-blocking and multi-tasking manner, which enables numerous commercial and DoD applications.
Simulation and measurement of pressure dependent Q-factors in NEMS resonators (2014)

The fluidic damping and the hereof resulting Q-factor of various mechanical resonators with gaps of nanometer size between suspended part and substrate was theoretically and experimentally determined. These investigations have been carried out in the pressure regime from atmospheric pressure down to about 3 Pa. The air flow in the nanogap between the movable part of the device and the substrate was modeled by extending the mixed level model presented in [1, 2] to the slip flow and molecular dynamical regime. The pressure-dependent measurements were carried out using a Laser-Doppler vibrometer. The extracted Q factors conform very well with those expected from theory in every pressure regime. This is a noticeable result, because even at normal pressure the range of validity for a continuum-theoretical description is reached for the nanometer feature sizes considered in this work.
Cellular cholesterol homeostasis and Alzheimer's disease (2017)

Alzheimer's disease (AD) is the most common form of dementia in older adults. Currently, there is no cure for AD. The hallmark of AD is the accumulation of extracellular amyloid plaques composed of amyloid-β (Aβ) peptides (especially Aβ1-42) and neurofibrillary tangles, composed of hyperphosphorylated tau and accompanied by chronic neuroinflammation. Aβ peptides are derived from the amyloid precursor protein (APP). The oligomeric form of Aβ peptides is probably the most neurotoxic species; its accumulation eventually forms the insoluble and aggregated amyloid plaques. ApoE is the major apolipoprotein of the lipoprotein(s) present in the CNS. ApoE has three alleles, of which the <i>Apoe4</i> allele constitutes the major risk factor for late-onset AD. Here we describe the complex relationship between ApoE4, oligomeric Aβ peptides, and cholesterol homeostasis. The review consists of four parts: <i>1</i>) key elements involved in cellular cholesterol metabolism and regulation; <i>2</i>) key elements involved in intracellular cholesterol trafficking; <i>3</i>) links between ApoE4, Aβ peptides, and disturbance of cholesterol homeostasis in the CNS; <i>4</i>) potential lipid-based therapeutic targets to treat AD. At the end, we recommend several research topics that we believe would help in better understanding the connection between cholesterol and AD for further investigations.
Reliability and Determinants of Retinal Vessel Oximetry Measurements in Healthy Eyes (2014)

The Oxymap Retinal Oximeter allows reliable and repeatable retinal vessel oximetry measurements. Age is the main factor that influences retinal venular oximetry levels and should be taken into account when retinal oximetry measurements are interpreted.
Biomimetic wiring and stabilization of photosynthetic membrane proteins with block copolymer interfaces (2016)

Block copolymer membranes stabilize photosystem I in a long-lasting, high performance photocurrent generating device.
Opportunities, Constraints and Critical Supports for Achieving Sustainable Local Pharmaceutical Manufacturing in Africa: With a Focus on the Role of Finance (2021)

At the request of the Open Society Foundations Public Health Program (OSF-PHP), a Team of researchers assembled by Nova Worldwide Consulting undertook to study whether and to what extent gaps in the availability of financing are constraining the development of pharmaceutical manufacturing in Africa, especially to address COVID-19. In this context, pharmaceuticals are understood to include diagnostics, vaccines and treatments (DVT), as well as personal protective equipment (PPE). Assuming that gaps in the availability of or access to financing are acting as a constraint on local production, what steps or measures might be advocated to address those gaps?
Disruption of the CD40-CD40 ligand system prevents an oxygen-induced respiratory distress syndrome. (1998)

Oxygen therapy is a mainstay treatment for infants and adults with poor lung function. Unfortunately, oxygen itself is toxic and incites respiratory cell damage and inflammation. Therapies for oxygen-induced lung damage are nonexistent. Employing a mouse model of hyperoxic lung injury, a monoclonal anti-CD40 ligand (L) antibody (MR1), which disrupts CD40-CD40L interactions, was tested for the ability to reduce pulmonary injury. Intraperitoneal administration of MR1, either before or after oxygen exposure, was remarkably effective in reducing and in many cases preventing lung injury. The pro-inflammatory enzyme cyclooxygenase-2 (Cox-2), responsible for prostaglandin production, is massively up-regulated in the lungs after hyperoxic exposure. Immunohistochemical staining for Cox-2 revealed that MR1 greatly reduces the oxygen-induced induction of Cox-2. The remarkable effectiveness of MR1 in blunting hyperoxic lung injury in this preclinical model may be relevant to the hundreds of thousands of patients who require treatment with high oxygen and who are at risk for developing severe pulmonary inflammation and consequent fibrosis. Strategies to disrupt CD40-CD40L interactions may offer a new mode of intervention for oxygen-induced acute respiratory distress syndrome and other inflammatory lung disorders.
IBM POWER9 opens up a new era of acceleration enablement: OpenCAPI (2018)

Open Coherent Accelerator Processor Interface (OpenCAPI) is a new industry-standard device interface that enables the development of host-agnostic devices that can coherently connect to any host platform that supports the OpenCAPI standard. This in turn allows such devices to coherently cache host memory to facilitate accelerator execution, perform direct memory access and atomics to host memory, send messages and interrupts to the host, and act as a host memory home agent. OpenCAPI utilizes high-frequency differential signaling technology while providing the high bandwidth and low latency needed by advanced accelerators. OpenCAPI encapsulates the serializing cache access and address translation constructs in high-speed host silicon technology to minimize overhead and design complexity in attached silicon such as field-programmable gate arrays and application-specific integrated circuits. Finally, OpenCAPI architecturally ties together transaction layer, link layer, and physical layer attributes to optimally align to high serializer/deserializer (SerDes) ratios and enable high-bandwidth, highly parallel exploitation of attached silicon.
Image-Guided Treatment of Primary Liver Cancer in Mice Leads to Vascular Disruption and Increased Drug Penetration (2020)

Despite advances in interventional procedures and chemotherapeutic drug development, hepatocellular carcinoma (HCC) is still the fourth leading cause of cancer-related deaths worldwide with a <30% 5-year survival rate. This poor prognosis can be attributed to the fact that HCC most commonly occurs in patients with pre-existing liver conditions, rendering many treatment options too aggressive. Patient survival rates could be improved by a more targeted approach. Ultrasound-induced cavitation can provide a means for overcoming traditional barriers defining drug uptake. The goal of this work was to evaluate preclinical efficacy of image-guided, cavitation-enabled drug delivery with a clinical ultrasound scanner. To this end, ultrasound conditions (unique from those used in imaging) were designed and implemented on a Philips EPIQ and S5-1 phased array probe to produced focused ultrasound for cavitation treatment. Sonovue<sup>®</sup> microbubbles which are clinically approved as an ultrasound contrast agent were used for both imaging and cavitation treatment. A genetically engineered mouse model was bred and used as a physiologically relevant preclinical analog to human HCC. It was observed that image-guided and targeted microbubble cavitation resulted in selective disruption of the tumor blood flow and enhanced doxorubicin uptake and penetration. Histology results indicate that no gross morphological damage occurred as a result of this process. The combination of these effects may be exploited to treat HCC and other challenging malignancies and could be implemented with currently available ultrasound scanners and reagents.
P3–335: Distinct isoforms and phosphorylation states of tau expressed in human cultured cells and organs (2006)

The microtubule–associated protein tau aggregates in neurons and glial cells in brains of patients with Alzheimer's disease and other tauopathies. One of important features of tauopathies is that the isoform compositions and phosphorylation states of aggregated tau differ. The reasons are as yet unknown. To explore the possible reasons, we analyzed for the expression pattern of four–repeat tau (4Rtau) and three–repeat tau (3Rtau) in human primary cultured glial cells, neuronal and nonneuronal cell lines, and peripheral organs. The samples were analyzed using RT–PCR and Western blotting. By RT–PCR analysis, 3Rtau was weakly dominant in normal brain, heart, liver, kidney, and spleen, and, significantly, in all cell lines that were cultured over time. However, in oligodendrocytes cultured for only 2 days, the expression of 4Rtau mRNA predominated over that of 3Rtau mRNA. This pattern reversed after 7 days. In primary cultured astrocytes, a similar reversal was observed. Western blot analysis of soluble fractions, aligned with recombinant tau following dephosphorylation, showed that 4Rtau and 3Rtau proteins were present in a similar ratio to that indicated by the RT–PCR analysis for brain, heart, liver, kidney, and spleen. The amino–terminal insert of exon 2 and 3 was not observed in heart. After dephosphorylation of samples, the electrophoretic mobility of tau bands increased in brain but did not change in heart, liver, kidney, or spleen. These results suggest that tau in brain is more highly phosphorylated or more difficult to be dephosphorylated than other organs. In addition, a high molecular weight band of 120 kDa, which might correspond to big tau (i.e. containing exon 4), was detected in all organs except brain. The results of the present study suggest that tau isoform expression and the state of phosphorylation differ according to the organ and cell type. These differences may underlie the specificity of each tauopathy.
An Ultrasonic Pulse Compression System for Nondestructive Testing Using Complementary Series Phase Modulation (1990)

An ultrasonic pulse compression system is presented, which employs complementary series phase modulated signals as transmit signals to obtain theoretically zero range sidelobes and high efficiency. In correlation based signal processing, echoes are correlated with reference signals that have the same wave forms as the echoes. The effectiveness of this signal processing over the conventional one using transmit signals as reference signals is verified by experiments.
Dual-band planar electric metamaterial in the terahertz regime (2008)

We present the design, fabrication, and measurement of a dual-band planar metamaterial with two distinct electric resonances at 1.0 and 1.2 THz, as a step towards the development of frequency agile or broadband THz materials and devices. A method of defining the effective thickness of the metamaterial layer is introduced to simplify the material design and characterization. Good agreement between the simulated and measured transmission is obtained for the fabricated sample by treating the sample as multi-layer system, i. e. the effective metamaterial layer plus the rest of the substrate, as well as properly modeling the loss of the substrate. The methods introduced in this paper can be extended to planar metamaterial structures operating in infrared and optical frequency ranges.
Review Pacing in congestive heart failure (2000)

Despite the major advances in medical drug therapy, heart failure remains a syndrome associated with high mortality and morbidity. Biventricular or left ventricular (LV) short atrioventricular (AV) delay pacing is being tested in congestive heart failure patients with left bundle branch block. The aim is to resynchronise the dyscoordinate LV contraction. A number of studies are underway, but it is clear that while some patients respond remarkably, this is highly variable. Accurate identification of patients likely to benefit will be crucial. The mechanism of benefit is unclear. A greater understanding of the physiological consequences of pacing will be necessary to accurately identify these patients.