gebhart/patrepeval huggingface dataset:
Creation of an NCI comparative brain tumor consortium: informing the translation of new knowledge from canine to human brain tumor patients (2020)

On September 14–15, 2015, a meeting of clinicians and investigators in the fields of veterinary and human neuro-oncology, clinical trials, neuropathology, and drug development was convened at the National Institutes of Health campus in Bethesda, Maryland. This meeting served as the inaugural event launching a new consortium focused on improving the knowledge, development of, and access to naturally occurring canine brain cancer, specifically glioma, as a model for human disease. Within the meeting, a SWOT (strengths, weaknesses, opportunities, and threats) assessment was undertaken to critically evaluate the role that naturally occurring canine brain tumors could have in advancing this aspect of comparative oncology aimed at improving outcomes for dogs and human beings. A summary of this meeting and subsequent discussion are provided to inform the scientific and clinical community of the potential for this initiative. Canine and human comparisons represent an unprecedented opportunity to complement conventional brain tumor research paradigms, addressing a devastating disease for which innovative diagnostic and treatment strategies are clearly needed.
An Unsupervised Approach to Sentence Classification. (2010)

Many real-life databases include columns containing textual data, which need to be processed to produce novel and actionable insights. We consider the novel problem of identifying specific sentences in the given text, since they tend to be actionable and novel. We demonstrate that specific sentences in the textual responses collected in an employee satisfaction survey and a product review are useful in understanding concrete issues, grievances and actionable suggestions for improvements. We propose an unsupervised approach for identifying specific sentences: We define and compute several features for each sentence and compute a specificity score for each sentence. Top k sentences in terms of this score are identified as specific. Some features are semantic in the sense that they use a supporting ontology (that of WordNet). We use the theory of speech acts to build an unsupervised (knowledgebased) classifier to further classify the identified specific sentences into suggestion and complaint classes. Our contributions here include treating suggestion and complaint as speech acts as well as the use of sentiment analysis in identifying speech acts. We demonstrate the utility of the proposed work in two real-life domains: employee surveys and product reviews.
Poster (2015)

Each year, consumers carry an increasing number of gadgets on their person: mobile phones, tablets, smartwatches, etc. As a result, users must remember to recharge each device, every day. Wireless charging promises to free users from this burden, allowing devices to remain permanently unplugged. Today's wireless charging, however, is either limited to a single device, or is highly cumbersome, requiring the user to remove all of her wearable and handheld gadgets and place them on a charging pad. This paper introduces MultiSpot, a new wireless charging technology that can charge multiple devices, even as the user is wearing them or carrying them in her pocket. A MultiSpot charger acts as an access point for wireless power. When a user enters the vicinity of the MultiSpot charger, all of her gadgets start to charge automatically. We have prototyped MultiSpot and evaluated it using off-the-shelf mobile phones, smartwatches, and tablets. Our results show that MultiSpot can charge 6 devices at distances of up to 50cm.
The Thermal Outgassing Rate of Materials Used in Vacuum Systems (2021)

There are many rarely used materials in vacuum systems that are poorly investigated in terms of vacuum properties. For example, phosphors, scintillating materials, ferrites, various adhesives, etc. In addition, new organic materials are being developed with mechanical properties similar to those of conventional steel. The use of such materials is very promising in vacuum technology. This article presents the thermal degassing performance of several rarely used materials and promising materials for vacuum applications.
Quantifying the Impact of FEXT on Eye Margin for Coupled Lines in Inhomogeneous Media (2015)

Increase in printed circuit board costs is leading to denser routing of high-speed signal traces and to the use of low-cost dielectric materials for high-volume manufacturing. This, in turn, is increasing crosstalk among the traces. The crosstalk between the coupled traces in adjacent layers and the same layers is becoming an important factor to take into account as the signal speed increases. The dielectric media in the vertical stackup may not be homogeneous, and this increases the far-end crosstalk (FEXT) and insertion loss (THRU); thereby, reducing the signal to noise ratio of the high-speed link. This paper investigates the FEXT crosstalk impact on eye opening at a specified bit error rate at different signal speeds for differential coupled traces in inhomogeneous media and compares the results against homogeneous media models. A set of design guidelines regarding the material, coupled length, and stackup parameter selection is formulated for designers based on the signaling speeds.
Design and experimental demonstration of a hardware-efficient integrated optical neural network (2022)

The optical neural network (ONN) is a promising neuromorphic framework for implementing deep learning tasks thanks to the key features of light, such as high parallelism, low latency, and low power consumption. As the size of deep neural networks (DNNs) continues to grow, so do the training and control difficulties of the corresponding photonic hardware accelerators. Therefore, it is essential to reduce the complexity of ONNs while maintaining accuracy. Here we propose an ONN architecture based on structured neural networks to reduce the optical component utilization as well as the chip footprint. The model complexity of our proposed ONN can be further optimized by incorporating current DNN pruning strategies. Meanwhile, a hardware-aware on-chip training flow is also proposed to improve the learnability, trainability, and robustness of our architecture. Finally, we experimentally demonstrate the reliability of this architecture with a programmable photonic neural chip and benchmarked its performance on multiple datasets.
Towards low loss non-volatile phase change materials in mid index\n waveguides (2021)

Photonic integrated circuits currently use platform intrinsic thermo-optic and electro-optic effects to implement dynamic functions such as switching, modulation and other processing. Currently, there is a drive to implement field programmable photonic circuits, a need which is only magnified by new neuromorphic and quantum computing applications. The most promising non-volatile photonic components employ phase change materials such as GST and GSST, which had their origin in electronic memory. However, in the optical domain, these compounds introduce significant losses potentially preventing a large number of applications. Here, we evaluate the use of two newly introduced low loss phase change materials, Sb2S3 and Sb2Se3, on a silicon nitride photonic platform. We focus the study on Mach-Zehnder interferometers that operate at the O and C bands to demonstrate the performance of the system. Our measurements show an insertion loss below 0.04 dB/um for Sb2S3 and lower than 0.09 dB/um for Sb2Se3 cladded devices for both amorphous and crystalline phases. The effective refractive index contrast for Sb2S3 on SiNx was measured to be 0.05 at 1310 nm and 0.02 at 1550 nm, whereas for Sb2Se3, it was 0.03 at 1310 nm and 0.05 at 1550 nm highlighting the performance of the integrated device.
Biofunctional Polyelectrolyte Multilayers and Microcapsules: Control of Non‐Specific and Bio‐Specific Protein Adsorption (2005)

Abstract Layers of the polyelectrolytes poly(allylamine hydrochloride) (PAH, polycationic) and poly(styrene sulfonate) (PSS, polyanionic) are consecutively adsorbed on flat silicon oxide surfaces, forming stable, ultrathin multilayer films. Subsequently, a final monolayer of the polycationic copolymer poly( L ‐lysine)‐ graft ‐poly(ethylene glycol) (PLL‐ g ‐PEG) is adsorbed onto the PSS‐terminated multilayer in order to impart protein resistance to the surface. The growth of each of the polyelectrolyte layers and the protein resistance of the resulting [PAH/PPS] n (PLL‐ g ‐PEG) multilayer ( n = 1–4) are followed quantitatively ex situ using X‐ray photoelectron spectroscopy and in situ using real‐time optical‐waveguide lightmode spectroscopy. In a second approach, the same type of [PAH/PSS] n (PLL‐ g ‐PEG) multilayer coatings are successfully formed on the surface of colloidal particles in order to produce surface‐functionalized, hollow microcapsules after dissolution of the core materials (melamine formaldehyde (MF) and poly(lactic acid) (PLA; colloid diameters: 1.2–20 μm). Microelectrophoresis and confocal laser scanning microscopy are used to study multilayer formation on the colloids and protein resistance of the final capsule. The quality of the PLL‐ g ‐PEG layer on the microcapsules depends on both the type of core material and the dissolution protocols used. The greatest protein resistance is achieved using PLA cores and coating the polyelectrolyte microcapsules with PLL‐ g ‐PEG after dissolution of the cores. Protein adsorption from full serum on [PAH/PPS] n (PLL‐ g ‐PEG) multilayers (on both flat substrates and microcapsules) decreases by three orders of magnitude in comparison to the standard [PAH/PPS] n layer. Finally, biofunctional capsules of the type [PAH/PPS] n (PLL‐ g ‐PEG/PEG‐biotin) (top copolymer layer with a fraction of the PEG chains end‐functionalized with biotin) are produced which allow for specific recognition and immobilization of controlled amounts of streptavidin at the surface of the capsules. Biofunctional multilayer films and capsules are believed to have a potential for future applications as novel platforms for biotechnological applications such as biosensors and carriers for targeted drug delivery.
Spectral Features Of Higher-Order Side-Channel Countermeasures (2018)

This brief deals with the problem of mathematically formalizing hardware circuits' vulnerability to side-channel attacks. We investigate whether spectral analysis is a useful analytical tool for this purpose by building a mathematically sound theory of the vulnerability phenomenon. This research was originally motivated by the need for deeper, more formal knowledge around vulnerable nonlinear circuits. However, while building this new theoretical framework, we discovered that it can consistently integrate known results about linear ones as well. Eventually, we found it adequate to formally model side-channel leakage in several significant scenarios. In particular, we have been able to find the vulnerability perimeter of a known cryptographic primitive (i.e., Keccak \cite{Bertoni:2010ug}) and thus tackle the analysis of vulnerability when signal glitches are present. We believe the conceptual framework we propose will be useful for researchers and practitioners in the field of applied cryptography and side-channel attacks.
Sorption of Gases and Vapors in an Amorphous Glassy Perfluorodioxole Copolymer (1999)

Gas and vapor sorption properties of a random copolymer of 87 mol % 2,2-bis(trifluoromethyl)-4,5-difluoro-1,3-dioxole and 13% tetrafluoroethylene (AF2400) are reported. Using both pressure decay and inverse gas chromatography (IGC) methods, a wide range of solutes was studied: He, N2, O2, CO2, C1−C13 n-alkanes, CF4, C2F6, C6F6, and C6F5CF3. These solutes have critical temperatures ranging from 5 to 677 K. AF2400 has very large solubility coefficients, S, relative to other glassy and rubbery polymers. Only poly(1-trimethylsilyl-1-propyne), the most permeable polymer known, exhibits higher solubility coefficients. The large solubility coefficients in AF2400 are mainly due to high Henry's law solubility coefficients. Fluorocarbon solutes exhibit higher solubility than their hydrocarbon analogues. A novel linear correlation between the logarithm of S and Tc2, where Tc is the solute critical temperature, was observed. On the basis of IGC results, the microcavity size in this perfluoropolymer is larger than in conventional hydrocarbon-based glassy polymers.
Abstract 4799: Promoter methylation of leukemia inhibitory factor receptor gene in colorectal carcinoma (2011)

Abstract Aberrant methylation of gene promoters and corresponding loss of gene expression plays a critical role in the initiation and progression of colorectal cancer. An IL-6-type cytokine receptor, leukemia inhibitory factor receptor (LIFR), is a component of cell-surface receptor complexes for multifunctional cytokines such as LIF. Herein, we report that LIFR is methylated in human colon cancer. LIFR promoter was methylated in primary tumor tissues with high frequency (65%, 52/80). Quantitative methylation-specific PCR (TaqMan-MSP) demonstrated differential promoter methylation of LIFR in primary colorectal cancer tissues as compared to normal colon tissues (5%, 4/80). LIFR methylation was not detectable in 13 normal colon mucosa samples obtained from patients without cancer. The mRNA expression of LIFR was significantly down-regulated in colon cancer tissues as compared to corresponding normal tissues. A strong expression of LIFR protein was observed in all non-malignant normal and adjacent normal colon mucosa tissues whereas down-regulated LIFR protein expression was observed in primary tumors. These results implicate that cancer-specific methylation and a specific decrease of LIFR expression are a common inactivation event in colon cancer development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4799. doi:10.1158/1538-7445.AM2011-4799
Synchronization and noncoherent communication (2008)

In Chapter 3, we established a framework for demodulation over AWGN channels under the assumption that the receiver knows and can reproduce the noiseless received signal for each possible transmitted signal. These provide “templates” against which we can compare the noisy received signal (using correlation), and thereby make inferences about the likelihood of each possible transmitted signal. Before the receiver can arrive at these templates, however, it must estimate unknown parameters such as the amplitude, frequency and phase shifts induced by the channel. We discuss synchronization techniques for obtaining such estimates in this chapter. Alternatively, the receiver might fold in implicit estimation of these parameters, or average over the possible values taken by these parameters, in the design of the demodulator. Noncoherent demodulation, discussed in detail in this chapter, is an example of such an approach to dealing with unknown channel phase. Noncoherent communication is employed when carrier synchronization is not available (e.g., because of considerations of implementation cost or complexity, or because the channel induces a difficult-to-track time-varying phase, as for wireless mobile channels). Noncoherent processing is also an important component of many synchronization algorithms (e.g., for timing synchronization, which often takes place prior to carrier synchronization).
Floating-Point Exponentiation Units for Reconfigurable Computing (2013)

The high performance and capacity of current FPGAs makes them suitable as acceleration co-processors. This article studies the implementation, for such accelerators, of the floating-point power function x y as defined by the C99 and IEEE 754-2008 standards, generalized here to arbitrary exponent and mantissa sizes. Last-bit accuracy at the smallest possible cost is obtained thanks to a careful study of the various subcomponents: a floating-point logarithm, a modified floating-point exponential, and a truncated floating-point multiplier. A parameterized architecture generator in the open-source FloPoCo project is presented in details and evaluated.
Multimode Fiber Optic Pressure Sensor With Extended Range (1988)

Absolute and differential fiber optic pressure sensors are described in this paper that have .1% resolution and are produced by integrated circuit techniques with yields of thousands per 3&quot; wafer. Sensor performance can be tailored to application with full scale responses ranging from 5&quot; of water (9 mmHg) to greater than 1000 psi (700KPa).
Long-range detection and length estimation of light filaments using extra-attenuation of terawatt femtosecond laser pulses propagating in air (2005)

High-energy femtosecond laser pulses propagating in the atmosphere undergo self-focusing resulting in the appearance of the phenomenon of filamentation. We observed an extra-attenuation of such (terawatt) femtosecond laser pulses propagating in the atmosphere when compared with long pulses (200 ps) with the same energy. This is because, in contrast to the linear propagation of the long pulse, the input femtosecond laser pulse is attenuated owing to either absorption through multiphoton ionization/tunnel ionization or to scattering on the laser-induced plasma; self-phase-modulation and self-steepening further convert partially the energy initially contained in the fundamental bandwidth into the broad side bands of the laser, becoming eventually a white-light laser pulse (supercontinuum). The experimental data allow us to extract an effective extra-attenuation coefficient for an exponential decay of the input pulse energy with the propagation distance. Such a coefficient allows us to estimate an upper bound of the filament length under the experimental conditions used. More generally, our observation leads to a new technique to remotely detect light filaments in the atmosphere.
Supplemental Figure S1 from <i>KRAS</i> Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine (2023)

&lt;p&gt;Cell viability is shown for sensitive (IC50 &lt; 150 nM, red) and resistant (IC50 &gt; 150 nM, blue) cell lines after nine days of treatment with decitabine. KRAS mutation status is marked with an asterisk (*). Data are representative of two independent experiments each measured in 14 replicates (mean, error bars removed for clarity).&lt;/p&gt;
Hormesis and health: a little of what you fancy may be good for you. (2000)

The term hormesis refers to beneficial effects from low doses of potentially harmful substances. Although there are many laboratory examples of this phenomenon, it remains controversial and has never become widely accepted by the health community. This review goes beyond the laboratory and describes many clinical and common sense, real-world examples of hormesis that often go unrecognized. Many vitamins and minerals are essential for life at low doses but toxic at higher ones. Similarly, exercise, caloric restriction, and alcohol consumption are examples of processes that are harmful in the extreme but beneficial in moderation. This review also highlights possible reasons why acceptance of the hormetic paradigm has lagged. These include high-dose toxicologic testing that precludes the demonstration of low-level effects and the threat posed by hormesis to the currently accepted precautionary principle, which assumes that any dose of a chemical is potentially harmful.
Windows Detection Using K-means in CIE-Lab Color Space (2010)

In this paper, we present a method for window detection, robust enough to process complex façades of historical buildings. This method is able to provide results even for facades under severe perspective distortion. Our algorithm is able to detect many different window types and does not require a learning step. We achieve these features thanks to an extended gradient projection method and introduction of a façade color descriptor based on a k-means clustering in a CIE-Lab color space into the process. This method is an important step towards creating large 3D city models in an automated workflow from large online image databases, or industrial systems. As such, it was designed to provide a high level of robustness for processing a large variety of façade types.
Base-free oxidation of glucose to gluconic acid using supported gold catalysts (2015)

1% Au/TiO<sub>2</sub> catalysts prepared by a variety of methods were studied for the base-free oxidation of glucose.
uORF‐introducing variants in the 5′UTR of the NIPBL gene as a cause of Cornelia de Lange syndrome (2022)

Cornelia de Lange syndrome (CdLS) is a clinically-recognizable rare developmental disorder. About 70% of patients carry a missense or loss-of-function pathogenic variant in the NIPBL gene. We hypothesized that some variants in the 5'-untranslated region (UTR) of NIPBL may create an upstream open reading frame (uORF), putatively leading to a loss of function. We searched for NIPBL 5'-UTR variants potentially introducing uORF by (i) reannotating NGS data of 102 unsolved CdLS patients and (ii) literature and variant databases search. We set up a green fluorescent protein (GFP) reporter assay and studied NIPBL expression in a lymphoblastoid cell line (LCL). We identified two variants introducing a novel ATG codon sequence in the 5'-UTR of NIPBL, both predicted to introduce uORF: a novel c.-457_-456delinsAT de novo mutation in a 15-year-old male with classic CdLS, and a c.-94C>T variant in a published family. Our reporter assay showed a significant decrease of GFP levels in both mutant contexts, with similar levels of messenger RNA (mRNA) as compared to wt constructs. Assessment of LCL of one patient showed consistent results with decreased NIPBL protein and unchanged mRNA levels. 5'-UTR uORF-introducing NIPBL variants may represent a rare source of pathogenic variants in unsolved CdLS patients.
Crystallization and preliminary X‐ray diffraction analysis of gingipain R2 from Porphyromonas gingivalis in complex with H‐D‐Phe‐Phe‐Arg‐chloromethylketone (1998)

Gingipain R2 is a 50 kDa proteinase from the oral pathogenic bacterium Porphyromonas gingivalis. This proteinase, which displays no significant sequence homology to any protein previously analyzed by X-ray crystallography, has been crystallized using the vapor diffusion method. Two different crystal forms were obtained from a solution containing polyethylene glycol (MW 8,000) (space group P2(1)2(1)2(1)) or magnesium sulfate (space group R3) as precipitating agent. Complete diffraction data sets have been collected up to 2.0 and 2.9 A resolution, respectively. Cell dimensions are a = 51.9 A, b = 79.9 A, and c = 99.6 A (P2(1)2(1)2(1)), and a = b = 176.6 A, and c = 143.4 A (R3). Considerations of the possible values of Vm accounts for the presence of one monomer per asymmetric unit in the case of the orthorhombic crystal form, whereas the rhombohedral crystal form, together with the analysis of the self-rotation function, could accommodate a tetramer in the asymmetric unit.
Resonant pumped erbium-doped waveguide lasers using distributed Bragg reflector cavities (2016)

This Letter reports on an optical pumping scheme, termed resonant pumping, for an erbium-doped distributed feedback (DFB) waveguide laser. The scheme uses two mirrors on either side of the DFB laser, forming a pump cavity that recirculates the unabsorbed pump light. Symmetric distributed Bragg reflectors are used as the mirrors and are designed by matching the external and internal quality factors of the cavity. Experimental demonstration shows lasing at an optical communication wavelength of around 1560 nm and an improvement of 1.8 times in the lasing efficiency, when the DFB laser is pumped on-resonance.