gebhart/patrepeval huggingface dataset:
Vocabulary independent spoken term detection (2007)

We are interested in retrieving information from speech data like broadcast news, telephone conversations and roundtable meetings. Today, most systems use large vocabulary continuous speech recognition tools to produce word transcripts; the transcripts are indexed and query terms are retrieved from the index. However, query terms that are not part of the recognizer's vocabulary cannot be retrieved, and the recall of the search is affected. In addition to the output word transcript, advanced systems provide also phonetic transcripts, against which query terms can be matched phonetically. Such phonetic transcripts suffer from lower accuracy and cannot be an alternative to word transcripts.We present a vocabulary independent system that can handle arbitrary queries, exploiting the information provided by having both word transcripts and phonetic transcripts. A speech recognizer generates word confusion networks and phonetic lattices. The transcripts are indexed for query processing and ranking purpose.The value of the proposed method is demonstrated by the relative high performance ofour system, which received the highest overall ranking for US English speech data in the recent NIST Spoken Term Detection evaluation.
Protein Exposed Hydrophobicity Reduces the Kinetic Barrier for Adsorption of Ovalbumin to the Air−Water Interface (2003)

Using native and caprylated ovalbumin, the role of exposed hydrophobicity on the kinetics of protein adsorption to the air−water interface is studied. First, changes in the chemical properties of the protein upon caprylation were characterized followed by measurement of the changes in adsorption kinetics. No change in the molecular structure of ovalbumin was observed upon caprylation. However, aggregation of the protein was observed when more than three capryl chains were coupled per protein. A batch of caprylated ovalbumin with an average coupling of four capryl chains per protein was separated into a monomeric and an aggregated protein fraction. The exposed hydrophobicity of the monomeric and the aggregated species was measured using 8-anilino-1-naphthalenesulfonic acid fluorescence. The exposed hydrophobicity of the monomeric fraction was significantly higher than that of the nonmodified protein. The changes in adsorption kinetics were studied by measuring the increase in surface load (Γ) and in surface pressure (Π) as a function of time (t) using an ellipsometer and a Wilhelmy plate, respectively. It was found that the increase of surface load in time (even at low surface coverage) is much lower than the value that was calculated from diffusional transport. This shows that the adsorption of native ovalbumin is barrier limited. The adsorption kinetics of the caprylated protein follow the calculations from diffusional transport more closely, which shows that the energy barrier for adsorption of caprylated ovalbumin is much lower than for the native protein. The surface pressure at a certain surface load (Π−Γ) was not affected by the modification, indicating that the effect of increased hydrophobicity is limited to the adsorption process.
Light ion beam ICF program overview (1994)

The light ion fusion program at Sandia National Laboratories is reviewed. The program is based on the indirect‐drive target concept and has the long‐term objective to obtain high yield in a microfusion facility. The near‐term technical effort will focus on increasing intensity and demonstrating 100 eV temperature in an ion hohlraum. Some concepts were tested experimentally confirming the accessibility of anticipated goals. (AIP)
Abstract IA15: T-Cells targeting mutated RAS—clinical trials (2020)

Abstract Durable complete regressions of metastatic cancers can be achieved by the transfer of in vitro expanded tumor-reactive T-cells. In patients with melanoma, this can be done by giving tumor-infiltrating lymphocytes (TIL) reactive with tumor-specific mutated antigens (“neoantigens”). Unfortunately, the vast majority of immunogenic neoantigens have been shown to be totally patient specific. One exception is that T cells recognizing mutated KRAS have been found in the TIL of multiple patients. In one patient with G12D-mutated colon cancer, these cells were grown and administered to that patient (after a course of preparative immunosuppression) and mediated regression of multiple pulmonary metastases. A single lesion that had lost its presenting MHC Class I allele grew and was resected, and the patient remains disease free over 2 years later. Other patients have demonstrated additional Class I and Class II presented epitopes from mutated RAS, although they have not yet been administered clinically. In an effort to develop standardized reagents to target common RAS mutations, HLA-A11 transgenic mice were immunized with peptides containing G12D and G12V RAS mutations and HLA-A11 restricted T cells isolated. Murine T-cell receptors specific for these mutated epitopes were cloned and when retrovirally introduced into human PBL, they conferred recognition of mutated RAS but not wild-type RAS. Such cells could cause regression of established palpable pancreatic cancer xenografts in NSG mice. Two clinical trials targeting the G12D and G12V RAS variants with T-cell receptor-engineered autologous PBL in any patient who is HLA-A11 are now open to enrollment. Future efforts are under way to expand the library of receptors to encompass additional RAS mutations, other HLA alleles, and other shared mutations in common driver oncogenes. Citation Format: James Yang, Kenichi Hanada, Steven Rosenberg. T-Cells targeting mutated RAS—clinical trials [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr IA15.
Synergistic anti-HIV-1 activity of griffithsin with tenofovir, maraviroc and enfuvirtide (2011)

Background More than 60% of the total HIV-1 infections worldwide are dominated by clade B and C. To stop the epidemic, effective prevention methods (e.g. microbicidal gel) are of extreme importance. Carbohydrate binding agents (CBAs) are very good microbicide candidates. We previously showed that various CBAs act synergistic with tenofovir against HIV-1 [1]. Griffithsin (GRFT), isolated from the red alga Griffithsia sp., shows very potent and broad-spectrum anti-HIV activity and recombinant forms can easily be produced [2,3]. Materials and methods HIV-1 replication was measured in MT-4 cells and peripheral blood mononuclear cells (PBMCs) by MTS method and p24 Ag ELISA respectively. Synergism was calculated using CalcuSyn software (Biosoft, Cambridge, UK) based on the median effect principle [4]. Combination indices (CI) 1.1 are antagonistic. Results We evaluated combinations of GRFT against HIV-1 clade B and clade C isolates with various glycosylation patterns on the viral envelope in PBMCs and MT-4 cells. In all combinations tested against clade B viruses BaL (R5) and NL4.3 (X4), GRFT showed synergistic activity with tenofovir, maraviroc, AMD3100 and enfuvirtide, based on the median effect principle with combination indices (CI) varying between 0.34 and 0.64 at the calculated EC95-level. Against the clade C viruses, ZAM18, DJ259 and ETH2220 (all R5), Cl-values varied between 0.70 and 0.79. The CI correlated with increased antiviral activity of each individual compound. Conclusions The evaluated two drug combinations increase their antiviral potency and support further clinical investigation and evaluation in preexposure prophylaxis in the context of HIV-1 clade B and clade C infections. Difference in glycosylation motifs in gp120 have little, if any, effects on the antiviral activity of GRFT.
Low distortion analogue signal transmission usingvertical cavity lasers (1998)

Signal distortion in a short wavelength vertical cavity surface-emitting laser (VCSEL) is studied. The spurious free dynamic range is found to be 104.3 dB Hz2/3 at 102 MHz and 98 dB Hz2/3 at 1 GHz, which approaches the dynamic range of Fabry-Perot and DFB lasers, and is 20 dB higher than previously reported for VCSELs.
Hydrogen inhalation in rehabilitation program of the medical staff recovered from COVID-19 (2021)

Active hydrogen inhalation (H(H 2 O) m ) has powerful antioxidant and antiapoptotic effects. In recent years, it has been used in a number of experimental and clinical studies. Aim. To study the safety and effectiveness of inhalation of the “active form of hydrogen” (AFV;(H(H 2 O) m )) in the rehabilitation program of coronavirus disease 2019 (COVID-19) survivors during the recovery period. Material and methods . This randomized controlled parallel prospective study included 60 COVID-19 survivors with post-COVID-19 syndrome (ICD-10: U09.9) during the recovery period, with clinical manifestations of chronic fatigue syndrome (CFS), who received standard therapy in accordance with the management protocol of patients with CFS (ICD-10: G93.3): physiotherapy and medication therapy with drugs containing magnesium, B vitamins and L-carnitine. The patients were divided into 2 groups. The experimental group (n=30) included patients who received hydrogen inhalation for 90 minutes every day during 10 days (SUISONIA hydrogen inhalation device, Japan). The control group (n=30) consisted of patients who received standard therapy. In both groups, patients were comparable in sex and mean age: in the experimental group — 53 (22; 70) years, in the control group — 51 (25; 70) years. Biological markers of systemic inflammation, oxygen transport, lactate metabolism, intrapulmonary shunting, 6-minute walk test, and vascular endothelial function were determined in all patients on the 1 st and 10 th days of follow-up. Results. In the experimental group, a decrease in following parameters was revealed: stiffness index (SI), from 8,8±1,8 to 6,8±1,5 (p&lt;0,0001); ALT, from 24,0±12,7 to 20,22±10,61 U/L (p&lt;0,001); venous blood lactate, from 2,5±0,8 to 1,5±1,0 mmol/L (p&lt;0,001); capillary blood lactate, from 2,9±0,8 to 2,0±0,8 mmol/L (p&lt;0,0001); estimated pulmonary shunt fraction (Qs/Qt, Berggren equation, 1942) from 8,98±5,7 to 5,34±3,2 (p&lt;0,01); white blood cells, from 6,64±1,57 to 5,92±1,32 109/L. In addition, we revealed an increase in the refractive index (RI) from 46,67±13,26% to 63,32±13,44% (p&lt;0,0001), minimum blood oxygen saturation (SpO 2 ) from 92,25±2,9 to 94,25±1, 56% (p&lt;0,05), direct bilirubin from 2,99±1,41 to 3,39±1,34 pmol/L (p&lt;0,01), partial oxygen tension (PvO 2 ) from 26,9±5,0 to 34,8±5,6 mm Hg (p&lt;0,0001), venous oxygen saturation (SvO2) from 51,8±020,6 to 61,1±018,1% (p&lt;0,05), partial capillary oxygen tension (PcO 2 ) from 48,7±15,4 to 63,8±21,2 mm Hg (p&lt;0,01), capillary oxygen saturation (ScO 2 ) from 82,2±4,2 to 86,2±4,8% (p&lt;0,01), distance in 6 minute walk test from 429±45,0 to 569±60 m. Conclusion. Inhalation therapy with H(H 2 O)m in the rehabilitation program of COVID-19 survivors during the recovery period is a safe and highly effective method. Manifestations of silent hypoxemia and endothelial dysfunction decreased, while exercise tolerance increased. As for laboratory tests, a decrease in the white blood cell count, estimated pulmonary shunt fraction and lactate content parameters was revealed.
A hybrid approach for optimizing medium frequency communication networks in coal mines (2012)

This work presents a hybrid approach using transmission line (TL) equations in conjunction with commercial method of moment (MoM) codes, to aid in efficient modeling of medium frequency (MF) propagation in coal mines. All local electromagnetic phenomena can be accurately modeled by strategic placement of full wave MoM sections near transmitting and receiving antennas. Meanwhile, ideal TL models are used to calculate loading and excitation of those MoM sections. In this way, communication networks can be modeled using a hybrid approach. The TL geometry of specific interest for this work is a single wire conductor positioned much less than one wavelength away from the floor/ceiling/wall of a mine. Previous work related to this geometry is summarized for approximate solutions of TL parameters. Examples are considered to demonstrate the capacity of the hybrid approach to optimize TL networks with significantly improved speeds.
Current treatment options in patients with mastocytosis: status in 2015 and future perspectives (2015)

Mastocytosis is a term referring to a heterogeneous group of disorders characterized by abnormal mast cell (MC) accumulation in the skin and/or internal organs. In children, the disease involves mostly the skin (cutaneous mastocytosis; CM), whereas in adults, the disease is usually systemic (systemic mastocytosis; SM). Advanced SM variants with end-organ damage and reduced life expectancy have also been described, but are rare. Clinical signs and symptoms in SM result from excessive mediator release by MCs and, in aggressive forms, from organ failure related to MC infiltration. As a consequence, treatment of indolent SM aims primarily at the control of symptoms caused by MC mediator release. By contrast, in advanced SM, such as aggressive SM, MC leukemia, and MC sarcoma, intensive (chemo)therapy with or without allogeneic stem cell transplantation has to be considered. In addition, activating mutations in KIT (mostly KIT D816V in adults) are found in most patients with SM, so that targeted therapies aimed at blocking mutant KIT variants or/and downstream signaling pathways are currently being developed. Other targets, such as specific surface antigens expressed on neoplastic MCs, might be considered for the development of future therapies in advanced SM.
Femtosecond multiple pulse impulsive simulated Raman scattering in α-perylene molecular crystals (1989)

Generation of coherent optic phonons through impulsive stimulated Raman scattering (ISRS) can occur whenever a sufficiently short optical pulse passes through a Raman active medium. The first experiments demonstrating ISRS were performed with α -perylene molecular crystals 1 ; subsequently, similar observations were reported for a variety of other materials. One difficulty which can be associated with the impulsive scattering technique is an inherent lack of mode selectivity. In this paper we demonstrate multiple pulse impulsive stimulated Raman scattering, a powerful new technique for achieving mode selectivity in ISRS experiments. By using phase-only spectral filtering techniques, we efficiently generate terahertz repetition-rate bursts of femtosecond pulses, 2 which we use for repetitive impulsive excitation in our experiments. Individual phonon modes are selected by tuning the pulse repetition rate to the vibrational period. We demonstrate this concept by selectively and individually exciting the 104-cm ™1 vibrational mode and the 80-cm ™1 librational mode in α -perylene molecular crystals. This technique permits direct observation of the individual cycles of the vibrational and librational oscillations, without the mode beating which occurred in previous experiments, 1 and makes possible accurate measurements of the dephasing times.
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients (2017)

This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.
Exploration of microbial biodiversity in polar glacial ice (2013)

The polar ice caps play a key part in providing an understanding of climate variability over the last eight glacial cycles and may give information about paleoenvironmental features and changes of microbial diversity in the past. Microbiological studies on polar ice cores are rare and focused so far on silty or accreted ice. Aim of our studies is to detect, characterize, and compare the prokaryotic diversity in different Arctic and Antarctic ice cores at different depths in order to learn more about relations of past and recent communities and about alterations of ancient communities in relation to climatic changes. Critical points in ice core analytics are the strong contaminations of the outside of ice cores as well as the limited availability of sample material. Hence, preparation/decontamination protocols were tested and adapted with inoculated and artificially contaminated ice cores. Our work on real older glacial ice started with material from the uppermost 200 m of the ice shield of Dronning Maud Land, Antarctica. Some pollen grains and a low abundance of bacteria cells were detected by Sybr Green staining in combination with solid phase cytometry. From 3 other ice core samples from about 130-179 m depth, approximately 2150 years old, DNA could be extracted and amplified. DGGE-analyses of amplified DNA revealed a low bacterial diversity, but one strong DGGE band-only present in the inner part of two of the three ice cores analyzed- could be affiliated to the alpha-proteobacteria with a high similarity to Bradyrhizobium japonicum. Clone libraries and metagenomic studies supported the dominance of this bacterial type that might jointly be responsible for N2O abnormalities in glacial ice cores.
1H and 15N assignments and secondary structure of the Src SH3 domain (1993)

The 1H and 15N sequential assignments of the Src SH3 domain have been determined through a combination of 2D and 3D Nuclear Magnetic Resonance (NMR) methods. The secondary structure of the protein has been identified based on long-range NOE patterns. The SH3 domain of Src consists largely of six beta-strands that form two anti-parallel beta-sheets.
MATLAB software for recursive identification and scaling using a structured nonlinear black-box model : Revision 1 (2005)

This reports is intended as a users manual for a package of MATLAB scripts and functions, developed for recursive prediction error identification of nonlinear state space systems. The core of the package is an implementation of an output error identification and scaling algorithm. The algorithm is based on a continuous time, structured black box state space model of a nonlinear system. The software can only be run off-line, i.e. no true real time operation is possible. The algorithm is however implemented so that true on-line operation can be obtained by extraction of the main algorithmic loop. The user must then provide the real time environment. The software package contains scripts and functions that allow the user to either input live measurements or to generate test data by simulation. The scripts and functions for the setup and execution of the identification algorithm are somewhat more general than what is described in the references. There is e.g. support for automatic re-initiation of the algorithm using the parameters obtained at the end of a previous identification run. This allows for multiple runs through a set of data, something that is useful for data sets that are too short to allow convergence of the algorithm.The re-initiation step also allows the user to modify the degrees of the polynomial model structure and to specify terms that are to be excluded from the model. This makes it possible to iteratively re-fine the estimated model using multiple runs. The functionality for display of results include scripts for plotting of data, parameters, prediction errors, eigenvalues and the condition number of the Hessian. The estimated model obtained at the end of a run can be simulated and the model output plotted, alone or together with the data used for identification. Model validation is supported by two methods apart from the display functionality. First, calculation of the RPEM loss function can be performed, using parameters obtained at the end of an identification run. Secondly, the accuracy as a function of the output signal amplitude can be assessed.
The Topological Effects of Smoothing (2011)

Scientific data sets generated by numerical simulations or experimental measurements often contain a substantial amount of noise. Smoothing the data removes noise but can have potentially drastic effects on the qualitative nature of the data, thereby influencing its characterization and visualization via topological analysis, for example. We propose a method to track topological changes throughout the smoothing process. As a preprocessing step, we oversmooth the data and collect a list of topological events, specifically the creation and destruction of extremal points. During rendering, it is possible to select the number of topological events by interactively manipulating a merging parameter. The result that a specific amount of smoothing has on the topology of the data is illustrated using a topology-derived transfer function that relates region connectivity of the smoothed data to the original regions of the unsmoothed data. This approach enables visual as well as quantitative analysis of the topological effects of smoothing.
Structure−Activity Relationships for the Antileishmanial and Antitrypanosomal Activities of 1‘-Substituted 9-Anilinoacridines (1997)

Members of the class of 9-anilinoacridine topoisomerase II inhibitors bearing lipophilic electron-donating 1‘-anilino substituents are active against both the promastigote and amastigote forms of the parasite Leishmania major. A series of analogues of the known 1‘-NHhexyl lead compound were prepared and evaluated against L. major in macrophage culture to further develop structure−activity relationships (SAR). Toxicity toward mammalian cells was measured in a human leukemia cell line, and the ratio of the two IC50 values (IC50(J)/IC50(L)) was used as a measure of the in vitro therapeutic index (IVTI). A 3,6-diNMe2 substitution pattern on the acridine greatly increased toxicity to L. major without altering mammalian toxicity, increasing IVTIs over that of the lead compound. The 2-OMe, 6-Cl acridine substitution pattern used in the antimalarial drug mepacrine also resulted in potent antileishmanial activity and high IVTIs. Earlier suggestions of the utility of 2‘-OR groups in lowering mammalian cytotoxicity were not borne out in this wider study. A series of very lipophilic 1‘-NRR (symmetric dialkylamino)-substituted analogues showed relatively high antileishmanial potency, but no clear trend was apparent across the series, and none were superior to the 1‘-NH(CH2)5Me subclass. Subsets of the most active 1‘-N(R)(CH2)5Me- and 1‘-N(alkyl)2-substituted compounds against L. major were also evaluated against Leishmania donovani, Trypanosoma cruzi, and Trypanosoma brucei, but no consistent SAR could be discerned in these physiologically diverse test systems. The present study has confirmed earlier conclusions that lipophilic electron-donating groups at the 1‘-position of 9-anilinoacridines provide high activity against L. major, but the SAR patterns observed do not carry over to the other parasites studied.
Simplified Automatic Transmission Model for a Powertrain Simulator. (1999)

A powertrain simulator with a simplified automatic transmission model was developed to aid the development and verification of control schemes for automatic transmission systems. To simplify the model, characteristics of engagement, slippage and release of clutches and one-way clutches were described approximately as a single model of clutches and one-way clutches respectively. And a conventional mathematical model for geartrains which was described by 79 equations was replaced by a model which was described by 9 equations. Algebraic loops was removed in the new model, and as a result, the run-time of the simulator was reduced by about one-sixth. This simulator was used to simulate acolal simple clutch pressure control during shifting and it was confirmed that this simulator was capable to examine the effect of shift shock reduction control.