gebhart/patrepeval huggingface dataset:
Elastic computing (2010)

Over the past decade, system architectures have started on a clear trend towards increased parallelism and heterogeneity, often resulting in speedups of 10x to 100x. Despite numerous compiler and high-level synthesis studies, usage of such systems has largely been limited to device experts, due to significantly increased application design complexity. To reduce application design complexity, we introduce elastic computing - a framework that separates functionality from implementation details by enabling designers to use specialized functions, called elastic functions, which enable an optimization framework to explore thousands of possible implementations, even ones using different algorithms. Elastic functions allow designers to execute the same application code efficiently on potentially any architecture and for different runtime parameters such as input size, battery life, etc. In this paper, we present an initial elastic computing framework that transparently optimizes application code onto diverse systems, achieving significant speedups ranging from 1.3x to 46x on a hyper-threaded Xeon system with an FPGA accelerator, a 16-CPU Opteron system, and a quad-core Xeon system.
Systematic chemical screening identifies disulfiram as a repurposed drug that enhances sensitivity to cisplatin in bladder cancer: a summary of preclinical studies (2019)

The present study highlighted the advantage of drug repurposing to enhance the efficacy of anticancer chemotherapy. Repurposing of DSF to a chemotherapy sensitiser may provide additional efficacy with less expense by using an available drug with a well-characterised safety profile.
Chemogenetic inhibition of the medial prefrontal cortex reverses the effects of REM sleep loss on sucrose consumption (2016)

Rapid eye movement (REM) sleep loss is associated with increased consumption of weight-promoting foods. The prefrontal cortex (PFC) is thought to mediate reward anticipation. However, the precise role of the PFC in mediating reward responses to highly palatable foods (HPF) after REM sleep deprivation is unclear. We selectively reduced REM sleep in mice over a 25-48 hr period and chemogenetically inhibited the medial PFC (mPFC) by using an altered glutamate-gated and ivermectin-gated chloride channel that facilitated neuronal inhibition through hyperpolarizing infected neurons. HPF consumption was measured while the mPFC was inactivated and REM sleep loss was induced. We found that REM sleep loss increased HPF consumption compared to control animals. However, mPFC inactivation reversed the effect of REM sleep loss on sucrose consumption without affecting fat consumption. Our findings provide, for the first time, a causal link between REM sleep, mPFC function and HPF consumption.
Low-Band-Gap Small Molecule for Efficient Organic Solar Cells with a Low Energy Loss below 0.6 eV and a High Open-Circuit Voltage of over 0.9 V (2017)

Small molecule organic solar cells (SMOSCs) have received considerable attention in recent years. However, one of the key factors limiting the performance of SMOSCs is their large energy loss (Eloss), which is typically between 0.6 and 1.0 eV, and therefore significantly higher than those of perovskite solar cells and inorganic solar cells (Eloss < 0.5 eV). Herein, we successfully report a new acceptor–donor–acceptor (A–D–A) type dimeric squaraine electron donor (D-IDTT-SQ) with a low optical band gap of 1.49 eV and deep HOMO energy level of −5.20 eV. Consequently, a high open-circuit voltage (Voc) of 0.93 V with an impressive power conversion efficiency (PCE) of 7.05% is achieved for solution-processed bulk heterojunction SMOSCs, showing an Eloss of only 0.56 eV. This is the first report wherein SMOSCs result in such a low Eloss, while simultaneously exhibiting a considerably high Voc over 0.9 V and an excellent PCE above 7.0%.
Fabrication of Oligonucleotide Chips by Using Parallel Cantilever‐Based Electrochemical Deposition in Picoliter Volumes (2007)

The use of a parallel cantilever-based deposition system as an electrospotting tool in picoliter volumes is demonstrated. Applied in conjunction with polypyrrole electrochemistry, this generic approach for fabricating biochips is optimized for oligonucleotide chips featuring micrometer spots of different sequences with high reproducibility and specificity (see figure).
Predicting hypertension onset using logistic regression models with labs and/or easily accessible variables: the role of blood pressure measurements (2021)

Hypertension is a critical condition that represents a leading risk factor for mortality. The identification of subjects at risk of developing hypertension is important to improve life expectancy and reduce the burden of healthcare systems. Available models to predict hypertension onset in some years in the future mainly include blood pressure (BP) measurements as well as blood test and lifestyle variables. However, systolic and diastolic BP are inevitably strong predictors of the disease and their presence in such models may hide a possible key role of other covariates. The aim of this work is to develop predictive models of hypertension onset both with and without the use of BP measurements to investigate if and how BP variables influence the feature selection process. By involving a large dataset on individuals socio-economic status, demographics, wellbeing, lifestyle, medical history and blood exams, logistic regression models (w/ and w/o BP) have been trained using a stepwise selection procedure to select only highly predictive variables. The model with systolic and diastolic BP selected as important variables HDL cholesterol, hemoglobin, marital status, depression scale and alcohol drinking, achieving an area under the receiver-operating characteristic curve (AU-ROC) of 0.80. The model without BP variables exploits heart rate, waist, age and marital status, and achieves AU-ROC=0.74. As expected, the model employing BP measurements performs better than the one that does not consider them. However, also without BP, it was possible to develop a model with satisfactory performance involving only easily accessible information that do not require laboratory tests.
Design and implementation of an enterprise grid (2004)

This paper presents the design and implementation of intraGrid, an experimental grid based on the Globus Toolkit™ and deployed on the IBM intranet. The architecture and the main components of intraGrid are described. Then, the major technical challenges and their solutions are reviewed, including software packaging and distribution, the interface for administrative tasks, and the design and implementation of the three major services: information services, management services, and job submission services. The paper also describes the extensions and modifications to intraGrid that were required to create the ISD grid, a grid that is used for joint projects with customers and thus requires access by external users. The paper reviews the use of intraGrid by various teams of IBM researchers to date and outlines the plans for future applications. The work in progress to migrate the intraGrid to an OGSA-based (Open Grid Services Architecture-based) grid is also described.
Transport studies ofLa2−xSrxCuO4near the insulator-metal-superconductor transition (1989)

We have measured the temperature-dependent resistivities of a series of samples of ${\mathrm{La}}_{2\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Sr}}_{\mathrm{x}}$${\mathrm{CuO}}_{4}$ with 0.02\ensuremath{\le}x\ensuremath{\le}0.1 over the temperature range 0.05 K\ensuremath{\le}T\ensuremath{\le}300 K. We find the onset of superconductivity as x is increased to be correlated with a substantial drop in the magnitude of the normal-state resistivity. We observe no change, however, in the qualitative shape of the resistivity as the superconducting threshold is crossed. We also find that the low-temperature (T\ensuremath{\le}8.0 K) resistivities of the least concentrated samples can be described by variable range hopping, with a crossover between Coulomb gap and single-particle behavior occurring as x is increased.
Targeting the Oligomerization Domain of ETO Interferes with RUNX1/ETO Oncogenic Activity in t(8;21)-Positive Leukemic Cells (2007)

About 12% of all de novo acute myeloid leukemias are characterized by the translocation t(8;21), which generates the oncogenic fusion protein RUNX1/ETO. RUNX1/ETO has a modular structure and contains several docking sites for heterologous proteins, including transcriptional co-repressors like N-CoR, SMART, and mSIN3A. RUNX1/ETO is found in high molecular weight complexes, which are crucial for the block in myeloid differentiation observed in RUNX1/ETO-transformed cells. Essential for high molecular weight complex formation is the nervy homology region 2 (NHR2) within ETO, which serves as interacting surface for oligomerization as well as association with members of the ETO protein family. Here, we show that the expression of a fusion peptide consisting of 128 amino acids (NC128), including the entire NHR2 domain of ETO, disrupts the stability of the RUNX1/ETO high molecular weight complexes, restores transcription of RUNX1/ETO target genes, and reverts the differentiation block induced by RUNX1/ETO in myeloid cells. In the presence of NC128, RUNX1/ETO-transformed cells lose their progenitor cell characteristics, are arrested in cell cycle progression, and undergo cell death. Our results indicate that selective interference with the oligomerization domain of ETO could provide a promising strategy to inhibit the oncogenic properties of the leukemia-associated fusion protein RUNX1/ETO.
Subwavelength Multilayer Binary Grating Design for Implementing Photonic Crystals (1997)

Subwavelength multilayer binary gratings (SMBG) can be seen as a 2-D periodic structures (see Fig.1a) with two periodic directions along the grating vector and the multilayer cascading direction. Such structures combine strong form- birefringence 1 , 2 of the subwavelength grating with high reflectivity due the multilayer structure allowing us to design polarization sensitive microdevices, such as polarization selective mirror and polarizing beam splitter. Recently 3 we introduce a new polarizing beam splitter (PBS) microdevice design built of SMBGs. Not only this novel design increases the angular and spectral range of the PBS microdevice in comparison to conventional PBS designs, but most importantly, our microdevice can operate with normally incident light, acting as a high-efficiency polarization-selective mirror. Microdevice with such features are critical for microlaser designs. Since the SMBG is a 2-D periodic structure, it can also be used to design a 2-D photonic crystal. In this manuscript, we summarize the design, modeling, and characterization of the SMBG structure designed to implement polarization sensitive microdevice, and also introduce and discuss a 2-D photonic crystal design based on SMBG.
Selective Binding to mRNA Duplex Regions by Chemically Modified Peptide Nucleic Acids Stimulates Ribosomal Frameshifting (2017)

Minus-one programmed ribosomal frameshifting (-1 PRF) allows the precise maintenance of the ratio between viral proteins and is involved in the regulation of the half-lives of cellular mRNAs. Minus-one ribosomal frameshifting is activated by several stimulatory elements such as a heptameric slippery sequence (X XXY YYZ) and an mRNA secondary structure (hairpin or pseudoknot) that is positioned 2-8 nucleotides downstream from the slippery site. Upon -1 RF, the ribosomal reading frame is shifted from the normal zero frame to the -1 frame with the heptameric slippery sequence decoded as XXX YYY Z instead of X XXY YYZ. Our research group has developed chemically modified peptide nucleic acid (PNA) L and Q monomers to recognize G-C and C-G Watson-Crick base pairs, respectively, through major-groove parallel PNA·RNA-RNA triplex formation. L- and Q-incorporated PNAs show selective binding to double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). The sequence specificity and structural selectivity of L- and Q-modified PNAs may allow the precise targeting of desired viral and cellular RNA structures, and thus may serve as valuable biological tools for mechanistic studies and potential therapeutics for fighting diseases. Here, for the first time, we demonstrate by cell-free in vitro translation assays using rabbit reticulocyte lysate that the dsRNA-specific chemically modified PNAs targeting model mRNA hairpins stimulate -1 RF (from 2% to 32%). An unmodified control PNA, however, shows nonspecific inhibition of translation. Our results suggest that the modified dsRNA-binding PNAs may be advantageous for targeting structured RNAs.
Diffusion spreadability as a probe of the microstructure of complex media across length scales (2021)

Understanding time-dependent diffusion processes in multiphase media is of great importance in physics, chemistry, materials science, petroleum engineering, and biology. Consider the time-dependent problem of mass transfer of a solute between two phases and assume that the solute is initially distributed in one phase (phase 2) and absent from the other (phase 1). We desire the fraction of total solute present in phase 1 as a function of time, $\mathcal{S}(t)$, which we call the spreadability, since it is a measure of the spreadability of diffusion information as a function of time. We derive exact direct-space formulas for $\mathcal{S}(t)$ in any Euclidean space dimension $d$ in terms of the autocovariance function as well as corresponding Fourier representations of $\mathcal{S}(t)$ in terms of the spectral density, which are especially useful when scattering information is available experimentally or theoretically. These are singular results because they are rare examples of mass transport problems where exact solutions are possible. We derive closed-form general formulas for the short- and long-time behaviors of the spreadability in terms of crucial small- and large-scale microstructural information, respectively. The long-time behavior of $\mathcal{S}(t)$ enables one to distinguish the entire spectrum of microstructures that span from hyperuniform to nonhyperuniform media. For hyperuniform media, disordered or not, we show that the ``excess'' spreadability, $\mathcal{S}(\ensuremath{\infty})\ensuremath{-}\mathcal{S}(t)$, decays to its long-time behavior exponentially faster than that of any nonhyperuniform two-phase medium, the ``slowest'' being antihyperuniform media. The stealthy hyperuniform class is characterized by an excess spreadability with the fastest decay rate among all translationally invariant microstructures. We obtain exact results for $\mathcal{S}(t)$ for a variety of specific ordered and disordered model microstructures across dimensions that span from hyperuniform to antihyperuniform media. Moreover, we establish a remarkable connection between the spreadability and an outstanding problem in discrete geometry, namely, microstructures with ``fast'' spreadabilities are also those that can be derived from efficient ``coverings'' of space. We also identify heretofore unnoticed, to our best knowledge, remarkable links between the spreadability $\mathcal{S}(t)$ and NMR pulsed field gradient spin-echo amplitude as well as diffusion MRI measurements. This investigation reveals that the time-dependent spreadability is a powerful, dynamic-based figure of merit to probe and classify the spectrum of possible microstructures of two-phase media across length scales.
Proceedings of the 4th international workshop on Adversarial information retrieval on the web (2008)

Before the advent of the World Wide information retrieval algorithms were developed for relatively small and coherent document collections such as newspaper articles or book catalogs in a library. In comparison to these collections, the is massive, much less cohe-rent, changes more rapidly, and is spread over geographically distributed computers. Scal-ing information retrieval algorithms to the World Wide is a challenging task. Success to date is depicted by the ubiquitous use of engines to access Internet content.

From the point of view of a engine, the is a mix of two types of content: the Web and the open Web. The closed web comprises a few high-quality controlled collections which a engine can fully trust. The open Web, on the other hand, in-cludes the vast majority of pages, which lack an authority asserting their quality. The openness of the has been the key to its rapid growth and success. However, this open-ness is also a major source of new challenges for information retrieval methods.

Adversarial Information Retrieval addresses tasks such as gathering, indexing, filtering, re-trieving and ranking information from collections wherein a subset has been manipulated maliciously. On the the predominant form of such manipulation is search engine spamming or spamdexing, i.e.: malicious attempts to influence the outcome of ranking al-gorithms, aimed at getting an undeserved high ranking for some items in the collection. There is an economic incentive to rank higher in engines, considering that a good ranking on them is strongly correlated with more traffic, which often translates to more revenue.
Wavelet methods for shape perception in electro-sensing (2016)

This paper aims at presenting a new approach to the electro-sensing problem using wavelets. It provides an efficient algorithm for recognizing the shape of a target from micro-electrical impedance measurements. Stability and resolution capabilities of the proposed algorithm are quantified in numerical simulations.
Knowledge Enhanced Attention for Robust Natural Language Inference (2019)

Neural network models have been very successful at achieving high accuracy on natural language inference (NLI) tasks. However, as demonstrated in recent literature, when tested on some simple adversarial examples, most of the models suffer a significant drop in performance. This raises the concern about the robustness of NLI models. In this paper, we propose to make NLI models robust by incorporating external knowledge to the attention mechanism using a simple transformation. We apply the new attention to two popular types of NLI models: one is Transformer encoder, and the other is a decomposable model, and show that our method can significantly improve their robustness. Moreover, when combined with BERT pretraining, our method achieves the human-level performance on the adversarial SNLI data set.
New Methods for Simulation Speed-up and Test Qualification with Analog Fault Simulation (2015)

With SOCs being increasingly designed for communication and embedded processing applications, the content of analog, mixed-signal (AMS) and RF components in them has increased. Large SOCs are often dominated by these components, which in turn also contribute to the overall incurred test time, attainable test quality and time required for silicon debug and characterisation. Existing test methods based on the use of specification based tests and use of design verification test-benches are increasingly difficult to adopt in such SOCs (as compared to standalone IP chips) since a large number of such modules and their interactions must be tested in the budgeted test time. The paper describes the practical use of fault simulation for AMS circuits to address the above issues. The main contributions of this paper are two-fold. (i) Enhancements are proposed to a commercially available analog fault simulation flow to handle specific SOC requirements of accuracy and speed, using smart management of models and/or fault lists across different fault conditions and fault sites. (ii) Efficient test generation methods targeting the analog -- digital interface are built by identifying uncovered regions/operating modes of the circuit. These are novel extensions to the commercial analog EDA tools supporting regular fault simulation. Experiments are performed on industrial designs and benefits are highlighted. It is expected that such techniques will be increasingly required to be integrated into the design flows for mixed-signal SOCs.
Through Silicon Via (TSV) Technology Creates Electro-Optical Interfaces (2012)

Silicon is a most versatile material, it is readily etched into a multitude of shapes and it has very highly desirable electrical properties .Through Silicon Via (TSV) technology is emerging as an essential method for allowing circuits on one side of an IC to be accessible from the other. This ability is not only essential for devices requiring covers, such as image sensors and MEMs but for stacking ICs as well. Much has been reported about the interconnecting and stacking of devices, such as, memory-on-memory and memory-on-logic devices. TSV fabrication is a micro-machining process for silicon. The micro-machining properties of silicon can also be utilized to etch and form features other than vias, such as the ability to etch precise channels which can be used to align and secure the fiber cables in an interposer. The interposer is one of the main elements in short length multimode (MMF) electro-optical transceivers capable of data rates exceeding 10 Gb/sec.
Control of In droplets for self-catalyzed growth of InP nanowires by VLS-MBE on silicon substrates (2014)

May, 11-15, 2014
Breast Cancer: Evaluation of Response to Neoadjuvant Chemotherapy with 3.0-T MR Imaging (2011)

The diagnostic accuracy of breast MR imaging is better in more aggressive than in less aggressive cancers. When MR imaging is used for surgical planning, caution should be taken with HER2-negative hormone receptor-positive cancers.
EC610 Revised 1944 Helpful Practices in Producing Milk and Cream (1944)

Extension circular 610 is a 1944 revision of the original circular. It contains helpful practices in producing milk and cream.