gebhart/patrepeval huggingface dataset:
Induction of the morphology of natural language : unsupervised morpheme segmentation with application to automatic speech recognition (2006)

In order to develop computer applications that successfully process natural language data (text and speech), one needs good models of the vocabulary and grammar of as many languages as possible. According to standard linguistic theory, words consist of morphemes, which are the smallest individually meaningful elements in a language. Since an immense number of word forms can be constructed by combining a limited set of morphemes, the capability of understanding and producing new word forms depends on knowing which morphemes are involved (e.g., "water, water+s, water+y, water+less, water+less+ness, sea+water").&#13;\n&#13;\nMorpheme boundaries are not normally marked in text unless they coincide with word boundaries. The main objective of this thesis is to devise a method that discovers the likely locations of the morpheme boundaries in words of any language. The method proposed, called Morfessor, learns a simple model of concatenative morphology (word forming) in an unsupervised manner from plain text. Morfessor is formulated as a Bayesian, probabilistic model. That is, it does not rely on predefined grammatical rules of the language, but makes use of statistical properties of the input text.&#13;\n&#13;\nMorfessor situates itself between two types of existing unsupervised methods: morphology learning vs. word segmentation algorithms. In contrast to existing morphology learning algorithms, Morfessor can handle words consisting of a varying and possibly high number of morphemes. This is a requirement for coping with highly-inflecting and compounding languages, such as Finnish. In contrast to existing word segmentation methods, Morfessor learns a simple grammar that takes into account sequential dependencies, which improves the quality of the proposed segmentations.&#13;\n&#13;\nMorfessor is evaluated in two complementary ways in this work: directly by comparing to linguistic reference morpheme segmentations of Finnish and English words and indirectly as a component of a large (or virtually unlimited) vocabulary Finnish speech recognition system. In both cases, Morfessor is shown to outperform state-of-the-art solutions.&#13;\n&#13;\nThe linguistic reference segmentations were produced as part of the current work, based on existing linguistic resources. This has resulted in a morphological gold standard, called Hutmegs, containing analyses of a large number of Finnish and English word forms.
Clinical response and pharmacodynamic assessment of INVAC-1, a DNA plasmid encoding an inactive form of human telomerase reverse transcriptase (hTERT), on immune responses, immune tolerability, tumor burden and circulating tumor DNA (ctDNA) in patients with advanced solid tumors (2018)

Background: INVAC-1 is an optimized plasmid encoding an inactive form of hTERT, a tumor antigen expressed in most of human tumors with little or no expression in normal somatic cells. We report here clinical response and pharmacodynamics of INVAC-1. Methods: A two center Phase I trial evaluated INVAC-1 given monthly for 3 cycles using intra-dermal injection followed by electroporation. Immune monitoring comprised detection of autoantibodies, lymphocyte phenotyping, inflammatory cytokine levels in blood, and CD4 and CD8 anti-hTERT responses assessed by Elispot IFN-γ. Anti-tumor activity was evaluated through RECIST 1.1 adapted to immune response, and plasma ctDNA. Results: Twenty patients (pts) with refractory/progressive tumors were enrolled and treated at three escalating doses of 100 µg, 400 µg and 800 µg. 12 pts experienced stable disease according to RECIST. For 10 of them, the treatment was extended up to nine months. INVAC-1 was well tolerated with no dose-limiting toxicities. No significant biological signs of autoimmunity were observed. A majority of pts had high levels of inflammatory plasma cytokines at inclusion but no significant modification was observed after INVAC-1 administration. IFN-γ polarized anti-hTERT CD4/CD8 immune responses were detected in 55% of pts, following INVAC-1 injections. INVAC-1 triggered de novo antihTERT response or enhanced pre-existing natural anti-hTERT immunity. The majority of pts mounted anti-hTERT T cell responses following the second- or third vaccination. ctDNA was evaluated in 14 pts. The most frequent mutations were TP53, KRAS and PIK3CA. We observed a ctDNA decrease in 5 cases, a stable ctDNA level in 5 cases and an increase in 4 cases. Conclusions: Results indicate that INVAC-1 was well tolerated and immunogenic at the doses and schedule tested. Disease stabilization was obtained for the majority of pts, according to RECIST criteria or ctDNA levels. Phase II studies of INVAC-1 in solid tumors and hematologic malignancies, preferably in pts with early diseases and adequate immune functions, are starting. Clinical trial identification: NCT02301754. Legal entity responsible for the study: Invectys. Funding: Invectys. Disclosure: J. Medioni, L.O. Teixeira, L. Doucet, S. Oudard, S. Culine, O. Adotevi, M.-A. Dragon-Durey, P. Laurent-Puig: Study investigator. V. Doppler: Sponsor employee. B. Souttou: Sponsor employer. S. Wain-Hobson: Invectys co-founder. R. Defrance: Consultant for study sponsor. T. Huet: Sponsor employee. P. Langlade-Demoyen: Invectys co-founder and CEO. All other authors have declared no conflicts of interest.
Lupus autoantibodies initiate a maladaptive equilibrium sustained by HMGB1:RAGE signaling and reversed by LAIR-1:C1q signaling (2023)

Cognitive impairment is a frequent manifestation of neuropsychiatric systemic lupus erythematosus (NPSLE), present in up to 80% of patients and leading to a diminished quality of life. We have developed a model of lupus-like cognitive impairment which is initiated when anti-DNA, anti-N-methyl D-aspartate receptor (NMDAR) cross- reactive antibodies, which are present in 30% of SLE patients, penetrate the hippocampus<sup>1</sup>. This leads to immediate, self-limited excitotoxic death of CA1 pyramidal neurons followed by a significant loss of dendritic arborization in the remaining CA1 neurons and impaired spatial memory. Both microglia and C1q are required for dendritic loss<sup>1</sup>. Here we show that this pattern of hippocampal injury creates a maladaptive equilibrium that is sustained for at least one year. It requires HMGB1 secretion by neurons to bind RAGE, a receptor for HMGB1 expressed on microglia, and leads to decreased expression of microglial LAIR-1, an inhibitory receptor for C1q. The angiotensin converting enzyme (ACE) inhibitor captopril, which can restore a healthy equilibrium, microglial quiescence, and intact spatial memory, leads to upregulation of LAIR-1. This paradigm highlights HMGB1:RAGE and C1q:LAIR-1 interactions as pivotal pathways in the microglial-neuronal interplay that defines a physiologic versus a maladaptive equilibrium.
The role of carbon diffusion in densification of uranium dicarbide (1991)

Because uranium dicarbide fuel is being considered for space reactor applications, we conducted an investigation for the Department of Energy of process parameters and densification mechanisms for this fuel. Uranium dicarbide feed powder was prepared by carbothermic reduction of uranium dicarbide and graphite at 2050 K in vacuum. Uranium dicarbide pellets were prepared by cold pressing at 110 MPa and sintering at 2370 K in contact with niobium, tantalum, or tungseten substrates in an argon atmosphere. A high density front was observed to move through the pellets, starting from the pellet‐metal substrate interface. The primary factor controlling this phenomenon is the diffusion of carbon from the uranium dicarbide pellet into the metal substrate. When the carbon level reduces so that no free carbon is present, rapid densification of the uranium discarbide occurs. This technique can be used to control densification of uranium dicarbide and to control carbon level and grain size in sintered compacts. More information on the fundamental carbon transport mechanism is necessary for complete understanding of the phenomenon.
Low voltage fault ride through control in MMC-HVDC (2017)

Modular multilevel converters (MMCs) are the latest converter topology for the high voltage high power applications like the high voltage dc (HVDC) transmission. This paper presents the response of an MMC-HVDC converter during grid faults. Recent grid code requirements specify reactive current injection during low voltage fault conditions and negative sequence current injections during unbalanced faults. The impact of different current control strategies considering the positive and negative sequence current injection upon the MMC converter dynamics are analyzed and its demonstrated through time-domain simulations. It concludes that the oscillations in active power can be minimized at the cost of increased oscillation in the reactive power.
Exploiting Reconfigurability for Text Search (2006)

Since their inception, it has been clear that, in principal, FPGAs can be reconfigured at will; that is, whenever desired. In practice, however, this capability is rarely used. Typically, during application development new
Dielectric SiO2 Planarization Using MnO2 Slurry (2011)

MnO 2 slurry can polish SiO 2 film faster and planarize wide feature steps (2 ×2 mm 2 ) to a lower height than conventional silica slurry. A comparison of Gibbs free energies indicates that the MnO 2 abrasive directly reacts on the SiO 2 film. In post-Chemical mechanical polishing (CMP), the MnO 2 abrasive can be completely removed by dipping it in mixed solutions of inorganic acids and H 2 O 2 followed by scrubbing and dipping in HF solution. A comparison of Gibbs free energies clarifies that the MnO 2 abrasive on the wafer is easily dissolved in a mixed solution of an inorganic acid and H 2 O 2 .
Prolonged blockade of VEGF family members does not cause identifiable damage to retinal neurons or vessels (2008)

Several ocular diseases complicated by neovascularization are being treated by repeated intraocular injections of vascular endothelial growth factor (VEGF) antagonists. While substantial benefits have been documented, there is concern that unrecognized damage may be occurring, because blockade of VEGF may damage the fenestrated vessels of the choroicapillaris and deprive retinal neurons of input from a survival factor. One report has suggested that even temporary blockade of all isoforms of VEGF-A results in significant loss of retinal ganglion cells. In this study, we utilized double transgenic mice with doxycycline-inducible expression of soluble VEGF receptor 1 coupled to an Fc fragment (sVEGFR1Fc), a potent antagonist of several VEGF family members, including VEGF-A, to test the effects of VEGF blockade in the retina. Expression of sVEGFR1Fc completely blocked VEGF-induced retinal vascular permeability and significantly suppressed the development of choroidal neovascularization at rupture sites in Bruch's membrane, but did not cause regression of established choroidal neovascularization. Mice with constant expression of sVEGFR1Fc in the retina for 7 months had normal electroretinograms and normal retinal and choroidal ultrastructure including normal fenestrations in the choroicapillaris. They also showed no significant difference from control mice in the number of ganglion cell axons in optic nerve cross sections and the retinal level of mRNA for 3 ganglion cell-specific genes. These data indicate that constant blockade of VEGF for up to 7 months has no identifiable deleterious effects on the retina or choroid and support the use of VEGF antagonists in the treatment of retinal diseases.
Modeling Intraperitoneal Insulin Absorption in Patients with Type 1 Diabetes (2021)

Standard insulin therapy to treat type 1 diabetes (T1D) consists of exogenous insulin administration through the subcutaneous (SC) tissue. Despite recent advances in insulin formulations, the SC route still suffers from delays and large inter/intra-subject variability that limiting optimal glucose control. Intraperitoneal (IP) insulin administration, despite its higher invasiveness, was shown to represent a valid alternative to the SC one. To date, no mathematical model describing the absorption and distribution of insulin after IP administration is available. Here, we aim to fill this gap by using data from eight patients with T1D, treated by implanted IP pump, studied in a hospitalized setting, with frequent measurements of plasma insulin and glucose concentration. A battery of models describing insulin kinetics after IP administration were tested. Model comparison and selection were performed based on model ability to predict the data, precision of parameters and parsimony criteria. The selected model assumed that the insulin absorption from the IP space was described by a linear, two-compartment model, coupled with a two-compartment model of whole-body insulin kinetics with hepatic insulin extraction controlled by hepatic insulin. Future developments include model incorporation into the UVa/Padova T1D Simulator for testing open- and closed-loop therapies with IP insulin administration.
Detection of nitroaromatics in the solid, solution, and vapor phases using silicon quantum dot sensors (2016)

Silicon quantum dots (Si-QDs) represent a well-known QD fluorophore that can emit throughout the visible spectrum depending on the interface structure and surface functional group. Detection of nitroaromatic compounds by monitoring the luminescence response of the sensor material (typically fluorescent polymers) currently forms the basis of new explosives sensing technologies. Freestanding silicon QDs may represent a benign alternative with a high degree of chemical and physical versatility. Here, we investigate dodecyl and amine-terminated Si-QD luminescence response to the presence of nitrobenzene and dinitrotoluene (DNT) in various solid, solution, and vapor forms. For dinitrotoluene vapor the 3σ detection limit was 6 ppb for monomer-terminated QDs. For nitroaromatics dissolved in toluene the detection limit was on the order of 400 nM, corresponding to ∼100 pg of material distributed over ∼1 cm(2) on the sensor surface. Solid traces of nitroaromatics were also easily detectable via a simple 'touch test'. The samples showed minimal interference effects from common contaminants such as water, ethanol, and acetonitrile. The sensor can be as simple and inexpensive as a small circle of filter paper dipped into a QD solution, with a single vial of QDs able to make hundreds of these sensors. Additionally, a trial fiber-optic sensor device was tested by applying the QDs to one end of a 2 × 2 fiber coupler and exposing them to controlled DNT vapor. Finally, the quenching mechanism was explored via luminescence dynamics measurements and is different for blue (amine) and red (dodecyl) fluorescent silicon QDs.
Aggregation State Effects in Shape-Selective Hydroconversion (2007)

A unified model for the description of vapor- and liquid-phase hydroconversion has been developed. The high isomer yield, which is typical for the shape selectivity exhibited by Pt/H−ZSM-22 at vapor-phase conditions, is still observed at liquid-phase conditions. However, the molar cracking yield is enhanced by at least 10 mol % when operating at liquid-phase conditions. The latter effect is mainly due to an increased physisorption competitiveness of lighter alkanes, which also results in enhanced cracking of lighter alkanes. The effect amounts to approximately 3 orders of magnitude for a difference of 2 in carbon number. These aggregation state effects are accounted for in the model through (i) liquid phase thermodynamic nonideality, (ii) destabilization of the physisorbed state by compression of the adsorbate by the bulk fluid, and (iii) carbenium ion stabilization by sorbent solvation by the bulk fluid. F-values of the order of 103 indicate the model's adequacy in describing the observed phenomena.
A negative feedback loop involving small RNAs accelerates Vibrio cholerae’s transition out of quorum-sensing mode (2008)

Quorum sensing is a cell-to-cell communication process that allows bacteria to measure their population numbers and to synchronously alter gene expression in response to changes in cell population density. At the core of the Vibrio cholerae quorum-sensing signal transduction pathway lie four redundant small RNAs (sRNAs), named the Quorum Regulatory RNAs (Qrr1-4). Expression of qrr1-4 is cell population density-dependent due to a requirement for the quorum-sensing controlled phosphorylated response regulator LuxO-P, which is abundant only at low cell population density. When expressed, Qrr1-4 repress translation of HapR, the "master" quorum-sensing transcription factor. Here we show a negative feedback loop in which HapR activates transcription of the qrr genes, which indirectly leads to hapR repression. Efficient feedback activation of the qrr genes requires the simultaneous presence of LuxO-P (present only at low cell population density) and HapR (present only at high cell population density). For this reason, the feedback loop does not influence quorum sensing at steady-state low or high cell population density. However, LuxO-P and HapR are simultaneously present immediately following the switch from high to low cell density conditions. In this state, the HapR feedback loop dramatically accelerates V. cholerae's transition from the high to the low cell density mode.
Rock Physics Relationships between Compressional, Shear, and Density Logs in Unconventional Formations, Including Deviated Wells (2015)

Abstract This paper compares rock physics trends in the Vp-vs.-Vs crossplot and the Vp/Vs-vs.-compressional slowness crossplot. Trend uncertainties are presented with laboratory data from the Bakken, Bazhenov, Monterey, and Niobrara shales; departures from expected trends attributed to kerogen, hydrocarbon, anisotropy, and well deviation are discussed. Anisotropy models, such as ANNIE (Schoenberg et al.1996), are presented for computing Thomsen parameters and stiffness coefficients. Castagna mudrock line (Castagna et al. 1993) derived from in-situ sonic and seismic measurements provided an average linear relationship between compressional and shear-wave velocities. Brie (1995) extended previous work to include predicting gas saturation from a Vp/Vs-vs.-compressional slowness crossplot. Projecting the Castagna mudrock line onto a shear-vs.-compressional slowness crossplot proved useful for interpreting sonic data. Classical-rock physics equations were used to model compressional and shear velocities as a function of well deviation. Laboratory anisotropy models allowed for characterizing the effects of dispersion, anisotropy, and well deviation. Anisotropic-rock physics models for the Bakken, Bazhenov, Monterey, and Niobrara organic shales are presented and compared in terms of the Thomsen parameters, ε, γ, and δ, and stiffness coefficients, Cij. These models are first transposed to trend curves in Vp-vs.-Vs, Vp/Vs-vs.-compressional slowness, and shear-vs.-compressional slowness crossplots and then compared to the Castagna mudrock trend curve. The anisotropy models are then applied to characterize the effect of well deviation on these trend curves. Results are also presented for well log data from the Eagle Ford, Haynesville, and Bakken formations in the context of the discussed crossplots and then compared with the expected trend curves. The Eagle Ford data satisfies the carbonate Vp-vs.-Vs trend predicted in previous literature by Castagna et al. (1993), and the Haynesville data clearly satisfies the gas effect predicted by the Brie Vp/Vs-vs.-compressional slowness crossplot discussed. In theory, the models describing anisotropy with the Thomsen parameters or stiffness coefficients are equivalent. In practice, not all the parameters for either model can be measured from log data. Preferentially, anisotropic models should be derived by combining log data from multiple vertical, deviated, and horizontal wells for each shale reservoir.
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli (2008)

Broad-acting transcription factors (TFs) in bacteria form regulons. Here, we present a 4-step method to fully reconstruct the leucine-responsive protein (Lrp) regulon in Escherichia coli K-12 MG 1655 that regulates nitrogen metabolism. Step 1 is composed of obtaining high-resolution ChIP-chip data for Lrp, the RNA polymerase and expression profiles under multiple environmental conditions. We identified 138 unique and reproducible Lrp-binding regions and classified their binding state under different conditions. In the second step, the analysis of these data revealed 6 distinct regulatory modes for individual ORFs. In the third step, we used the functional assignment of the regulated ORFs to reconstruct 4 types of regulatory network motifs around the metabolites that are affected by the corresponding gene products. In the fourth step, we determined how leucine, as a signaling molecule, shifts the regulatory motifs for particular metabolites. The physiological structure that emerges shows the regulatory motifs for different amino acid fall into the traditional classification of amino acid families, thus elucidating the structure and physiological functions of the Lrp-regulon. The same procedure can be applied to other broad-acting TFs, opening the way to full bottom-up reconstruction of the transcriptional regulatory network in bacterial cells.
Search for Gravitational-Wave Bursts from Soft Gamma Repeaters (2008)

We present a LIGO search for short-duration gravitational waves (GWs) associated with soft gamma ray repeater (SGR) bursts. This is the first search sensitive to neutron star f modes, usually considered the most efficient GW emitting modes. We find no evidence of GWs associated with any SGR burst in a sample consisting of the 27 Dec. 2004 giant flare from SGR 1806-20 and 190 lesser events from SGR 1806-20 and SGR 1900+14. The unprecedented sensitivity of the detectors allows us to set the most stringent limits on transient GW amplitudes published to date. We find upper limit estimates on the model-dependent isotropic GW emission energies (at a nominal distance of 10 kpc) between 3x10;{45} and 9x10;{52} erg depending on waveform type, detector antenna factors and noise characteristics at the time of the burst. These upper limits are within the theoretically predicted range of some SGR models.