gebhart/patrepeval huggingface dataset:
Comparing Rule-Based and Statistical Approaches to Speech Understanding in a Limited Domain Speech Translation System (2004)

The paper directly compares two versions of a medical speech translation system, one with a grammar based language model (GLM) recognizer and the other with a statistical language model (SLM) recognizer. We construct the GLM using a corpus-based method, so that both the GLM and the SLM can be derived from the same corpus; evaluation is carried out with respect to performance on the speech translation task. Despite using a very small training set for both the GLM and the SLM, the SLM delivers much better word error rates on unseen test material. Nonetheless, evaluating both systems on translation performance rather than word error rates, the GLM-based version of the system outperforms the SLM on the actual translation task. 1.
Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments (2009)

Widespread use of microarrays has generated large amounts of data, the interrogation of the public microarray repositories, identifying similarities between microarray experiments is now one of the major challenges. Approaches using defined group of genes, such as pathways and cellular networks (pathway analysis), have been proposed to improve the interpretation of microarray experiments. We propose a novel method to compare microarray experiments at the pathway level, this method consists of two steps: first, generate pathway signatures, a set of descriptors recapitulating the biologically meaningful pathways related to some clinical/biological variable of interest, second, use these signatures to interrogate microarray databases. We demonstrate that our approach provides more reliable results than with gene-based approaches. While gene-based approaches tend to suffer from bias generated by the analytical procedures employed, our pathway based method successfully groups together similar samples, independently of the experimental design. The results presented are potentially of great interest to improve the ability to query and compare experiments in public repositories of microarray data. As a matter of fact, this method can be used to retrieve data from public microarray databases and perform comparisons at the pathway level.
The TRPV4 channel is a novel regulator of intracellular Ca2+ in human esophageal epithelial cells (2011)

The esophageal epithelium has sensory properties that enable it to sustain normal barrier function. Transient receptor potential vanilloid 4 (TRPV4) is a Ca(2+)-permeable channel that is activated by extracellular hypotonicity, polyunsaturated fatty acids, phorbol esters, and elevated temperature. We found that TRPV4 is expressed in both human esophageal tissue and in HET-1A cells, a human esophageal epithelial cell line. Specific activation of TRPV4 by the phorbol ester 4α-phorbol 12,13-didecanoate (4α-PDD) increased intracellular Ca(2+) in a subset of HET-1A cells. Elevated temperature strongly potentiated this effect at low concentrations of 4α-PDD, and all of the responses were inhibited by the TRPV antagonist ruthenium red. TRPV4 activation differentially affected cell proliferation and cell viability; HET-1A cell proliferation was increased by 1 μM 4α-PDD, whereas higher concentrations (10 μM and 30 μM) significantly decreased cell viability. Transient TRPV4 activation triggered ATP release in a concentration-dependent manner via gap-junction hemichannels, including pannexin 1 and connexin 43. Furthermore, TRPV4 activation for 24 h did not increase the production of interleukin 8 (IL-8) but reduced IL-1β-induced IL-8 production. Small-interference RNA targeted to TRPV4 significantly attenuated all of the 4α-PDD-induced responses in HET-1A cells. Collectively, these findings suggest that TRPV4 is a novel regulator of Ca(2+)-dependent signaling pathways linked to cell proliferation, cell survival, ATP release, and IL-8 production in human esophageal epithelial cells.
Immunodynamics of explanted human tumors for immuno‐oncology (2020)

Decision making in immuno-oncology is pivotal to adapt therapy to the tumor microenvironment (TME) of the patient among the numerous options of monoclonal antibodies or small molecules. Predicting the best combinatorial regimen remains an unmet medical need. Here, we report a multiplex functional and dynamic immuno-assay based on the capacity of the TME to respond to ex vivo stimulation with twelve immunomodulators including immune checkpoint inhibitors (ICI) in 43 human primary tumors. This "in sitro" (in situ/in vitro) assay has the potential to predict unresponsiveness to anti-PD-1 mAbs, and to detect the most appropriate and personalized combinatorial regimen. Prospective clinical trials are awaited to validate this in sitro assay.
A flexible module library for custom DSP applications in a multiprocessor environment (1990)

The module library for the Cathedral-II synthesis environment is discussed. The underlying architectural style of the environment is defined as a hierarchical composition of flexible and parameterizable data paths, microcoded control units, interprocessor communication protocols, and input/output interfaces. A data path is called an execution unit (EXU), which consists of three parts: an input block, an output block, and a core. Only the core varies for the different EXUs. The topology and functionality of an EXU can be influenced by a set of parameters. The module library consists of two parts, a leaf-cell library and a procedure library, to place and interconnect the leaf cells to create functional building blocks that compose one EXU. The EXUs are guaranteed to work at 10 MHz. The described modules have been implemented and tested. The main features of this system are a very powerful parameterization, the technology independence of the CAD tools, and the generation speed of the modules. The current library is specially dedicated towards application-specific IC (ASIC) customized processors, although it can be used for more hardwired architectures, oriented towards higher throughput.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of a Ryanodine Receptor-Ca 2+ Channel that is Regulated by TGF-β (1992)

Ryanodine receptors (RyRs) are intracellular channels that release calcium ions from the sarcoplasmic reticulum (SR) in response to either plasma membrane depolarization (in skeletal muscle) or increases in the concentration of intracellular free Ca2+ (in the heart). A gene (beta 4) encoding a ryanodine receptor (similar to, but distinct from, the muscle RyRs) was identified. The beta 4 gene was expressed in all tissues investigated, with the exception of heart. Treatment of mink lung epithelial cells (Mv1Lu) with transforming growth factor beta (TGF-beta) induced expression of the beta 4 gene together with the release of Ca2+ in response to ryanodine (but not in response to caffeine, the other drug active on muscle RyRs). This ryanodine receptor may be important in the regulation of intracellular Ca2+ homeostasis.
Supplementary Table Legends from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma (2023)

&lt;p&gt;PDF file 73K, This file contains legends for the five supplementary tables&lt;/p&gt;
Membrane Culture of Bone Marrow Stromal Cells Yields Better Tissue Than Pellet Culture for Engineering Cartilage-Bone Substitute Biphasic Constructs in a Two-Step Process (2011)

Our long-term goal is to treat osteochondral lesions with bioengineered biphasic constructs. We have previously demonstrated that biphasic constructs, created in vitro with primary chondrocytes harvested from healthy joints and a porous calcium polyphosphate (CPP) substrate bone substitute, could successfully repair a focal defect in sheep joints. However, primary chondrocytes are limited in supply and cannot be used in engineering constructs large enough for clinical use. Thus, we developed a robust protocol to predifferentiate sheep bone marrow-derived stromal cells to chondrocytes on collagen-coated polytetrafluoroethane membrane inserts, and harvest the chondrocytes that develop and subsequently culturing these predifferentiated cells scaffold-free on the intended articulation surface of the CPP. Chondrocytes predifferentiated on membrane culture accumulated similar matrix as those in conventional pellet culture, but expressed less Col1a1 RNA. Membrane culture predifferentiated cells gave rise to a functionally superior hyaline cartilage tissue compared to pellet culture predifferentiated cells. Studies demonstrated that 2 weeks of membrane predifferentiation culture followed by 8 weeks of biphasic construct culture was the optimal culture period at which the compressive mechanical strength and the accumulation of extracellular matrix were maximized while avoiding tissue mineralization. This protocol will be used to generate implants for preclinical study to determine their ability to repair osteochondral lesions.
Spatiotemporal controlled delivery of nanoparticles to injured vasculature (2010)

There are a number of challenges associated with designing nanoparticles for medical applications. We define two challenges here: ( i ) conventional targeting against up-regulated cell surface antigens is limited by heterogeneity in expression, and ( ii ) previous studies suggest that the optimal size of nanoparticles designed for systemic delivery is approximately 50–150 nm, yet this size range confers a high surface area-to-volume ratio, which results in fast diffusive drug release. Here, we achieve spatial control by biopanning a phage library to discover materials that target abundant vascular antigens exposed in disease. Next, we achieve temporal control by designing 60-nm hybrid nanoparticles with a lipid shell interface surrounding a polymer core, which is loaded with slow-eluting conjugates of paclitaxel for controlled ester hydrolysis and drug release over approximately 12 days. The nanoparticles inhibited human aortic smooth muscle cell proliferation in vitro and showed greater in vivo vascular retention during percutaneous angioplasty over nontargeted controls. This nanoparticle technology may potentially be used toward the treatment of injured vasculature, a clinical problem of primary importance.
Primary Angioplasty of a Super Dominant Left Anterior Descending Coronary Artery (2016)

The posterior descending artery usually arises from either the right coronary artery or the left circumflex artery. Here we report an unusual case of super-dominant left anterior descending coronary artery continuing as the posterior descending artery beyond the crux which was totally occluded in a patient who presented with acute anterior wall myocardial infarction. Successful primary angioplasty and stenting of the super-dominant left anterior descending coronary artery was performed.JCMS Nepal. 2016;12(2):81-82
Supp. Figure 5 from LIM Kinase Inhibitor Pyr1 Reduces the Growth and Metastatic Load of Breast Cancers (2023)

&lt;p&gt;RPPA results of tubulin acetylation, tubulin detyrosination and cofilin phosphorylation levels in tumors of mice treated with vehicle, Pyr1 and PTX&lt;/p&gt;
Using an Integrated Silicon Emitter to Generate Two Coaxial Orbital-Angular-Momentum Beams with Tunable Mode Orders and Broad Bandwidth (2019)

We design and simulate a broadband integrated silicon emitter to generate two coaxial orbital-angular-momentum beams with tunable mode orders (l = {-1,0} or {0,+ 1}). Crosstalk <-15 dB is achieved over 1500–1600 nm. © 2019 The Author(s)
Support Recovery of Sparse Signals in the Presence of Multiple Measurement Vectors (2011)

This paper studies the problem of support recovery of sparse signals based on multiple measurement vectors (MMV). The MMV support recovery problem is connected to the problem of decoding messages in a Single-Input Multiple-Output (SIMO) multiple access channel (MAC), thereby enabling an information theoretic framework for analyzing performance limits in recovering the support of sparse signals. Sharp sufficient and necessary conditions for successful support recovery are derived in terms of the number of measurements per measurement vector, the number of nonzero rows, the measurement noise level, and especially the number of measurement vectors. Through the interpretations of the results, in particular the connection to the multiple output communication system, the benefit of having MMV for sparse signal recovery is illustrated providing a theoretical foundation to the performance improvement enabled by MMV as observed in many existing simulation results. In particular, it is shown that the structure (rank) of the matrix formed by the nonzero entries plays an important role on the performance limits of support recovery.
Multiple source localization using Estimation Consistency in the Time-Frequency domain (2017)

The extraction of multiple Direction-of-Arrival (DoA) information from estimated spatial spectra can be challenging when such spectra are noisy or the sources are adjacent. Smoothing or clustering techniques are typically used to remove the effect of noise or irregular peaks in the spatial spectra. As we will explain and show in this paper, the smoothing-based techniques require prior knowledge of minimum angular separation of the sources and the clustering-based techniques fail on noisy spatial spectrum. A broad class of localization techniques give direction estimates in each Time Frequency (TF) bin. Using this information as input, a novel technique for obtaining robust localization of multiple simultaneous sources is proposed using Estimation Consistency (EC) in the TF domain. The method is evaluated in the context of spherical microphone arrays. This technique does not require prior knowledge of the sources and by removing the noise in the estimated spatial spectrum makes clustering a reliable and robust technique for multiple DoA extraction from estimated spatial spectra. The results indicate that the proposed technique has the strongest robustness to separation with up to 10° median error for 5° to 180° separation for 2 and 3 sources, compared to the baseline and the state-of-the-art techniques.
Neuronal expression of enhanced green fluorescent protein directed by 5′ flanking sequences of the rat aldolase C gene in transgenic mice (2003)

The rat aldolase C gene encodes a glycolytic enzyme strongly expressed in adult brain. We previously reported that a combination of distal and proximal 5' flanking sequences, the A + C + 0.8 kilobase (kb) pairs fragments, ensured high brain-specific expression in vivo (Skala et al. 1998). We show here that the expression pattern conferred by these sequences, when placed in front of the chloramphenicol acetyltransferase (CAT) or the enhanced green fluorescent protein (EGFP) reporter genes in transgenic mice, is similar to the distribution of the endogenous mRNA and protein. Double immunostaining for neuronal or glial cell-specific markers and for the EGFP protein indicates that the A + C + 0.8 kb genomic sequences from the rat aldolase C gene direct a predominant expression in neuronal cells of adult brain.
Comparative Genomics (2018)

Maize (Zea mays ssp. mays L.) is an important source of food and nutritional security for millions of people in the developing world, especially in sub Saharan Africa (SSA) and Latin America. The crop provides over 20% of total calories in human diets in 21 countries, and over 30% in 12 countries that are home to a total of more than 310 million people (Shiferaw et al. 2011). For 900 million farmers and consumers in low-and middle-income countries, maize is a preferred crop or food. The importance of improving maize production and productivity in the developing world could be gauged from the fact that one-third of all malnourished children are found in systems where maize is among the top three crops (Hyman et al. 2008).
Supplementary Table 1 from A Multi-Institution Phase I Trial of Ruxolitinib in Patients with Chronic Myelomonocytic Leukemia (CMML) (2023)

&lt;p&gt;Table summarizing cohort escalation rules for this clinical trial.&lt;/p&gt;
An antibody with Fab-constant domains exchanged for a pair of CH3 domains (2018)

We have designed a complete antibody-like construct where the CH1 and Cκ domains are exchanged for a pair of the CH3 domains and efficient pairing of the heavy and light variable domain is achieved using "Knobs-into-Holes" strategy. This construct, composed of only naturally occurring immunoglobulin sequences without artificial linkers, expressed at a high level in mammalian cells, however exhibited low solubility. Rational mutagenesis aimed at the amino acid residues located at the interface of the variable domains and the exchanged CH3 domains was applied to improve the biophysical properties of the molecule. The domain-exchanged construct, including variable domains of the HER2/neu specific antibody trastuzumab, was able to bind to the surface of the strongly HER2/neu positive cell line SK-BR3 4-fold weaker than trastuzumab, but could nevertheless incite a more potent response in an antibody-dependent cell cytotoxicity (ADCC) reporter assay with FcγRIIIa-overexpressing T-cells. This could be explained with a stronger binding to the FcγRIIIa. Importantly, the novel construct could mediate a specific ADCC effect with natural killer cells similar to the parental antibody.
Adjusting bit-stream video watermarking systems to cope with HTTP adaptive streaming transmission (2014)

HTTP adaptive streaming has become the dominant solution for broadband streaming delivery. Essentially, the server delivers small chunks of content in response to queries from a player, that can alternate between different qualities of content depending on its rendering capabilities and the network condition. In this paper, we highlight that the frequent switches of this popular delivery mechanism are deemed to interfere with the payload modulation of bit-stream video watermarking systems. We then propose a generic strategy to cope with such transmission and showcase its efficiency in practice with a watermarking system that operates directly in the H.264/AVC CABAC bit-stream. Eventually, we evaluate the robustness of the proposed solution against standard attacks.
Age-Related Differences in the Biaxial Biomechanical Behavior of Human Abdominal Aorta (2002)

The biomechanical response of abdominal aortic tissue to uniaxial loading conditions has been reported previously [1]. This testing identified the uniaxial mechanical response of aortic tissue to specimens oriented in the longitudinal and circumferential directions, but did not provide significant evidence for the isotropy or anisotropy of this tissue. The information taken from uniaxial tensile testing is insufficient for the characterization of the multi-axial mechanical response of aortic tissue. In particular, the uniaxial response of a biological tissue in a given direction does not incorporate the effects of loading in an orthogonal direction. For these reasons, there exists a need for an enhanced description of the mechanical response of aortic tissue to loading in multiple planar directions. For the current investigation, biaxial tensile testing was performed on normal abdominal aortic tissue in order to gain insight into the anisotropy and age related differences of the biomechanical response of this tissue.
Selective inhibition of .gamma.-aminobutyric acid aminotransferase by (3R,4R), (3S,4S)- and (3R,4S), (3S,4R)-4-amino-5-fluoro-3-phenylpentanoic acids (1990)

(3R,4R),(3S,4S)- and (3R,4S),(3S,4R)-4-amino-5-fluoro-3-phenylpentanoic acid (1a and 1b) were synthesized and studied as selective inactivators of gamma-aminobutyric acid (GABA) aminotransferase. Neither compound caused time-dependent inactivation of the enzyme. Neither compound underwent enzyme-catalyzed transamination nor was fluoride ion eliminated from either compound by the enzyme. No 3-phenyllevulinic acid, the product of elimination of HF followed by enamine hydrolysis, was detected. However, both 1a and 1b were competitive reversible inhibitors of GABA aminotransferase; the Ki for 1a was smaller than the Km for GABA. These results suggest that 1a and 1b bind to the active site of GABA aminotransferase, but gamma-proton removal does not occur. Whereas (S)-4-amino-5-fluoropentanoic acid (AFPA) is a potent inhibitor of L-glutamic acid decarboxylase (GAD), neither 1a nor 1b at concentrations 40 times the Ki of AFPA caused any detectable competitive inhibition of GAD. Therefore, the incorporation of a phenyl substituent at the 3-position of AFPA confirms selective inhibition of GABA aminotransferase over GAD.
Hybrid Lipid Polymer Nanoparticles for Combined Chemo- and Photodynamic Therapy (2019)

Retinoblastoma is a malignant tumor of the retina in infants. Conventional therapies are associated to severe side effects and some of them induce secondary tumors. Photodynamic therapy (PDT) thus appears as a promising alternative as it is nonmutagenic and generates minimal side effects. The effectiveness of PDT requires the accumulation of a photosensitizer (PS) in the tumor. However, most porphyrins are hydrophobic and aggregate in aqueous medium. Their incorporation into a nanocarrier may improve their delivery to the cell cytoplasm. In this work, we designed biodegradable liponanoparticles (LNPs) consisting of a poly(d,l)-lactide (PDLLA) nanoparticle coated with a phospholipid (1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine/1,2-dioleoyl-3-trimethylammonium-propane) bilayer. An anticancer drug, beta-lapachone (β-Lap) and a PS, <i>m</i>-THPC, were co-encapsulated for combined chemo- and PDT because it has been suggested that they may have a synergistic effect based on the activation of β-Lap by PDT-induced over-expression of the enzyme NQO1. Using dynamic light scattering measurements, cryogenic transmission electron microscopy, and fluorescence confocal microscopy, we selected the appropriate conditions for the encapsulation of the compounds. LNPs were internalized in retinoblastoma cells within few hours. No obvious synergistic effect related to the activation of β-Lap by PDT was observed. Conversely, the LNPs were cytotoxic at lower doses of the two encapsulated compounds as compared to the single therapies. Analysis of the combinatorial treatment showed that PDT and chemotherapy had an additive effect on the viability of retinoblastoma cells.
Multi-physics simulation and reliability analysis for RF-MEMS devices (2008)

RF-MEMS is a disruptive technology, commonly regarded as key for future telecommunication systems as it potentially alleviates several of the natural trade-offs presented by current telecommunication systems. This new technology however does not percolate in the industry by lack of realized reliability. This can be attributed to a lack of understanding of the very specific failure mechanisms of RF-MEMS devices and detailed underlying physical behaviours. In this paper, we introduce the basic design of electrostatically actuated capacitive RF-MEMS devices produced in thin-film technologies. We stress the specific reliability issues associated with these devices and the environment they have to function in. We highlight the issues related to the dielectric charging, the packaging, the thermal stability and finally the RF-specific power- handling issues.