gebhart/patrepeval huggingface dataset:
Anti-mesothelin immunotoxin induces mesothelioma eradication, anti-tumor immunity, and the development of tertiary lymphoid structures (2022)

LMB-100 is a recombinant immunotoxin composed of a Fab linked to a toxin. It kills cells expressing human mesothelin (hMSLN), which is highly expressed on the surface of mesothelioma and many other cancer cells. Clinically, we observed some patients had delayed responses to an anti-hMSLN immunotoxin treatment, suggesting the induction of anti-tumor immunity. We aimed to develop a mouse model to investigate whether immunotoxin alone can induce anti-tumor immunity and to study the mechanism of this immunity. An immunocompetent transgenic mouse was used to grow mouse mesothelioma AB1 cells expressing hMSLN in the peritoneal cavity. Mice were treated with LMB-100, and mice with complete responses (CRs) were rechallenged with tumor cells to determine whether anti-tumor immunity developed. Changes in gene expression profiles were evaluated by Nanostring, and changes in cytokines and chemokines were checked by protein arrays. The distribution of various immune cells was assessed by immunohistochemistry. Our results show that the mice with tumor reached CRs and developed anti-tumor immunity after LMB-100 treatment alone. The primary response requires CD8<sup>+</sup> T cells, CD4<sup>+</sup> T cells, and B cells. Transcriptional profiling shows that LMB-100 treatment reshapes the tumor immune microenvironment by upregulating chemotaxis signals. LMB-100 treatment upregulates genes associated with tertiary lymphoid structures (TLS) development and induces TLS formation in tumors. In sum, immunotoxin-mediated cell death induces anti-tumor immunity and the development of TLS, which provides insights into how immunotoxins cause tumor regressions.
Application-guided tool development for architecturally diverse computation (2010)

Architecturally diverse computation exploits non-traditional computing platforms (e.g., field-programmable gate arrays, graphics processors, heterogeneous chip multiprocessors) to execute user applications. We have designed the Auto-Pipe tool set with the goal of easing the task of developing applications for architecturally diverse systems. Prior to and during the course of Auto-Pipe's design, we have developed a number of real, substantial applications, and the the lessons learned during the development of these applications has had a direct bearing on the capabilities of Auto-Pipe. In this paper, we describe the relationship between our application development experience and Auto-Pipe. In short, how have applications guided the tools' evolution and development?
On using a quantum physics formalism for multidocument summarization (2012)

Multidocument summarization ( MDS ) aims for each given query to extract compressed and relevant information with respect to the different query‐related themes present in a set of documents. Many approaches operate in two steps. Themes are first identified from the set, and then a summary is formed by extracting salient sentences within the different documents of each of the identified themes. Among these approaches, latent semantic analysis ( LSA ) based approaches rely on spectral decomposition techniques to identify the themes. In this article, we propose a major extension of these techniques that relies on the quantum information access ( QIA ) framework. The latter is a framework developed for modeling information access based on the probabilistic formalism of quantum physics. The QIA framework not only points out the limitations of the current LSA ‐based approaches, but motivates a new principled criterium to tackle multidocument summarization that addresses these limitations. As a byproduct, it also provides a way to enhance the LSA ‐based approaches. Extensive experiments on the DUC 2005, 2006 and 2007 datasets show that the proposed approach consistently improves over both the LSA ‐based approaches and the systems that competed in the yearly DUC competitions. This demonstrates the potential impact of quantum‐inspired approaches to information access in general, and of the QIA framework in particular.
A Programmable Discharge Circuitry With Current Limiting Capability for a Retinal Prosthesis (2005)

Biphasic stimulation is the most commonly used electrical pattern in FES (Functional Electrical Stimulation). In such cases, a charge balanced waveform is essential to prevent any charge accumulation in the biological tissue. In a retinal prosthesis, a charge cancellation circuitry is used to discharge the stimulation sites on the retina periodically to ensure tissue safety. But discharging a node that has high voltage (due to charge accumulation) will induce large currents that might lead to unintended stimulation of the retina. This paper presents a new discharge circuitry which can act as a simple resistive discharge path for smaller voltages and a current limiter for higher voltages. In stimulation circuits which use a dual voltage scheme (positive and negative), the circuit limits the current at both polarities. The discharge profile is programmable digitally. In addition, a method to characterize inter-pixel leakage in a retinal prosthesis using this circuit is proposed.
Magnetic Ceramic Films from a Metallopolymer Resist Using Reactive Ion Etching in a Secondary Magnetic Field (2004)

Magnetic ceramic films containing metal‐rich nanoworm reticulations 200–550 nm wide have been fabricated from a highly metallized metallopolymer resist (see Figure) using oxygen or hydrogen plasma reactive ion etching in a secondary magnetic field. Applications may be found in spintronics and logic circuits.
A Dual Role for Receptor-interacting Protein Kinase 2 (RIP2) Kinase Activity in Nucleotide-binding Oligomerization Domain 2 (NOD2)-dependent Autophagy (2012)

Autophagy is triggered by the intracellular bacterial sensor NOD2 (nucleotide-binding, oligomerization domain 2) as an anti-bacterial response. Defects in autophagy have been implicated in Crohn's disease susceptibility. The molecular mechanisms of activation and regulation of this process by NOD2 are not well understood, with recent studies reporting conflicting requirements for RIP2 (receptor-interacting protein kinase 2) in autophagy induction. We examined the requirement of NOD2 signaling mediated by RIP2 for anti-bacterial autophagy induction and clearance of Salmonella typhimurium in the intestinal epithelial cell line HCT116. Our data demonstrate that NOD2 stimulates autophagy in a process dependent on RIP2 tyrosine kinase activity. Autophagy induction requires the activity of the mitogen-activated protein kinases MEKK4 and p38 but is independent of NFκB signaling. Activation of autophagy was inhibited by a PP2A phosphatase complex, which interacts with both NOD2 and RIP2. PP2A phosphatase activity inhibited NOD2-dependent autophagy but not activation of NFκB or p38. Upon stimulation of NOD2, the phosphatase activity of the PP2A complex is inhibited through tyrosine phosphorylation of the catalytic subunit in a process dependent on RIP2 activity. These findings demonstrate that RIP2 tyrosine kinase activity is not only required for NOD2-dependent autophagy but plays a dual role in this process. RIP2 both sends a positive autophagy signal through activation of p38 MAPK and relieves repression of autophagy mediated by the phosphatase PP2A.
Structural adaptation of endonuclease I from the cold-adapted and halophilic bacteriumVibrio salmonicida (2008)

The crystal structure of the periplasmic/extracellular endonuclease I from Vibrio salmonicida has been solved to 1.5 A resolution and, in comparison to the corresponding endonucleases from V. cholerae and V. vulnificus, serves as a model system for the investigation of the structural determinants involved in the temperature and NaCl adaptation of this enzyme class. The overall fold of the three enzymes is essentially similar, but the V. salmonicida endonuclease displays a significantly more positive surface potential than the other two enzymes owing to the presence of ten more Lys residues. However, if the optimum salt concentrations for the V. salmonicida and V. cholerae enzymes are taken into consideration in the electrostatic surface-potential calculation, the potentials of the two enzymes become surprisingly similar. The higher number of basic residues in the V. salmonicida protein is therefore likely to be a result, at least in part, of adaptation to the more saline habitat of V. salmonicida (seawater) than V. cholerae (brackish water). The hydrophobic core of all three enzymes is almost identical, but the V. salmonicida endonuclease has a slightly lower number of internal hydrogen bonds. This, together with repulsive forces between the basic residues on the protein surface of V. salmonicida endonuclease I and differences in the distribution of salt bridges, probably results in higher flexibility of regions of the V. salmonicida protein. This is likely to influence both the catalytic activity and the stability of the protein.
CCDC 849442: Experimental Crystal Structure Determination (2013)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
<title>Laser-induced fluorescence spectroscopy of colonic dysplasia: prospects for optical histological analysis</title> (1995)

Several groups have shown that laser-induced fluorescence spectroscopy can detect dysplastic changes in human colon tissues. We present an approach based on analysis of the underlying tissue microstructure for extracting histological information from such spectral signals. The method employs fluorescence microscopy and tissue optics to model the `bulk' fluorescence collected with an optical fiber probe in a clinical setting. For both colonic normal and adenoma, we measured the intrinsic fluorescence lineshapes, the spatial distributions of the fluorophores, and optical parameters of tissue. Numerical and analytical solutions to the radiative transfer equation were then used to compute fluorescence spectra. The results of the model were in excellent agreement with clinical spectra collected during colonoscopy, using 370 nm excitation. Four factors were found to be responsible for the spectral differences between normal tissue and adenoma: fluorescence of mucosal collagen, dysplastic cell, and submucosa, and hemoglobin attenuation. Preliminary results indicate that these parameters can be extracted from individual clinical spectra by reversing the modeling procedure.
Interchannel nonlinear transmission penalties in polarization-multiplexed 2×10Gbit?s differential phase-shift keying transmission (2005)

We discuss the performance of a multichannel 2 x 10 Gbit/s polarization-multiplexed differential phase-shift keying transmission system. Through simulations and transmission experiments we find that, despite the constant power envelope of non-return-to-zero phase-shift keying modulation formats, polarization multiplexing strongly reduces the nonlinear tolerance and transmission performance at a 2 x 10 Gbit/s line rate with multichannel transmission. This results in a 10 dB power penalty when comparing single- and nine-channel transmission. Additionally, multichannel impairments in differential phase-shift keying and on-off keying are compared for 2 x 10 Gbit/s polarization-multiplexed transmission.
Deep Multimodal Representation Learning from Temporal Data (2017)

In recent years, Deep Learning has been successfully applied to multimodal learning problems, with the aim of learning useful joint representations in data fusion applications. When the available modalities consist of time series data such as video, audio and sensor signals, it becomes imperative to consider their temporal structure during the fusion process. In this paper, we propose the Correlational Recurrent Neural Network (CorrRNN), a novel temporal fusion model for fusing multiple input modalities that are inherently temporal in nature. Key features of our proposed model include: (i) simultaneous learning of the joint representation and temporal dependencies between modalities, (ii) use of multiple loss terms in the objective function, including a maximum correlation loss term to enhance learning of cross-modal information, and (iii) the use of an attention model to dynamically adjust the contribution of different input modalities to the joint representation. We validate our model via experimentation on two different tasks: video- and sensor-based activity classification, and audio-visual speech recognition. We empirically analyze the contributions of different components of the proposed CorrRNN model, and demonstrate its robustness, effectiveness and state-of-the-art performance on multiple datasets.
High concentration testing and performance of multijunction solar cells (2003)

The use of the appropriate characterization tools along with the use of single cell assemblies that are robust, are necessary for proper evaluation of device performance and stability tests for GaInP/sub 2//GaAs/Ge triple junction (3J) concentrator solar cells. Certain discrepancies exist between the photovoltaic (PV) values from continuous outdoor illumination measurements at high concentration levels and those from the High Intensity Pulse Solar Simulator (HIPSS) measurements, which are addressed. The series resistance inferred from the current-voltage (IV) curve, however, is similar from both measurement techniques. Outdoor tests of concentrator cells yielded efficiencies near 29% (31% from HIPSS) for an average concentration of 432 suns. Both types of measurements revealed that the fill factor (FF) limited the performance of the cell at high concentrations due to the role of the series resistance. The formation of heat from the nonuniformity in the Fresnel optics also limited the device performance. Before the cell stability can be evaluated, cells are first screened for defects from the 1-sun, indoor, IV measurements. Then, the good cells are incorporated into small assemblies for further test by forward bias injection (FBI). The stability outcome of the FBI determines whether or not the cell can be used for outdoors tests. Outdoor IV measurements are then conducted. Stability test results showed that no degradation occurs in the 1-sun IV data before and after light soak of the concentrator assemblies.
Locating Microseismic Events and Determining Spatial Uncertainty Using 1C DAS Fiber Optic Strain Measurements or a Combination of 1C (DAS) and 3C (Geophones) (2022)

In typical downhole-acquired microseismic monitoring surveys, three-component (3C) sensor arrays are generally wireline conveyed, offering between five to around one hundred sensors often evenly spaced over a specific interval. Those 3C sensors are point receivers that typically measure particle velocity or acceleration. On the other hand, fiber-optic based acquisition uses the entire length of the fiber cable as a series of 1C sensors to measure the finite strain along the fiber. This allows the user to have great control over the interval for strain measurement, known as the gauge length. Conventional downhole microseismic processing requires compressional (P) and shear (S) wave arrival times along with polarization to constrain microseismic event location (hypocenter) in 3D. Since 1C sensors provide no polarization information, Distributed Acousting Sensing (DAS)–geophone hybrid systems can be considered for deployment; thus, combining the strength of each individual system (i) 3C of downhole sensors for accurate hypocenter determination and (ii) large array aperture of the sensitive fiber. A migrationbased method is a practical option to estimate hypocenters. We implement a migration-based approach for the 1C-DAS – 3C-geophone hybrid system to determine hypocenters without time-picks. Such a hybrid system minimizes event location uncertainty thanks to the long aperture of the fiber array and the polarization information provided by the geophones. In our synthetic as well as real field case studies, we observe a reduction in event location uncertainty when combining both acquisition methods vs. when relying on a traditional 3C-geophone array only. In some cases, 3C sensors are not an option and only 1C sensors can be deployed. For such configurations, we quantify the uncertainty of microseismic event location using a DAS-only system with synthetic microseismic data taking information availability and varying well configurations into account. Depth of event and distance from the well are sufficiently constrained even with a single monitoring well. While azimuth uncertainty is reduced in the dual-well configuration compared to single well, independent azimuthal information is still required to locate the microseismic event in the 3D space. This condition is also true when monitoring from a lateral well. 3D event location can be achieved using three monitoring wells without any constraints. If only downhole wells are used, one needs to consider three vertical wells or one vertical well and one lateral well to best minimize location uncertainty. Otherwise, assumptions need to be made, particularly in relation to the azimuth of events from the well.
Physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome (1997)

A physical and genetic map of the Clostridium acetobutylicum ATCC 824 chromosome was constructed. The macrorestriction map for CeuI, EagI, and SstII was created by ordering the 38 restriction sites by one- and two-dimensional pulsed-field gel electrophoresis (PFGE) and by using an original strategy based on the CeuI enzyme and indirect end labelling by hybridization on both sides of the CeuI sites with rrs (16S RNA) and 3' rrl (23S RNA) probes. The circular chromosome was estimated to be 4.15 Mb in size, and the average resolution of the physical map is 110 kb. The chromosome contains 11 rrn loci, which are localized on 44% of the chromosome in a divergent transcriptional orientation regarding the presumed location of the replication origin. In addition to these 11 rrn operons, a total of 40 identified genes were mapped by hybridization experiments with genes from C. acetobutylicum and from various other clostridia as probes. The genetic map of C. acetobutylicum was compared to that of the three other endospore-forming bacteria characterized so far: Bacillus subtilis, Clostridium beijerinckii, and Clostridium perfringens. Parodoxically, the chromosomal backbone of C. acetobutylicum showed more similarity to that of B. subtilis than to those of the clostridia.
Static CMOS latch-up considerations in HVIC design (1990)

Static latchup in CMOS devices placed on a thin epitaxial layer for high-voltage integrated circuits (HVIC) is investigated using SPICE. The layout configuration and substrate current have a major influence on CMOS latchup as compared with conventional CMOS structures. Special latchup conditions exist for NMOS devices adjacent to high-voltage devices due to an extra p-n-p-n path. The results suggest that the use of PMOS adjacent to the high-voltage is best suited, in terms of layout, to avoiding latchup conditions. It is also shown that the latchup of CMOS devices is improved by placing them in an n/sup -/ epitaxial layer on a p/sup -/ substrate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: Synthesis and Structure of E,E‐(6.2)‐(2,5)Thiophenophane‐1,5‐diene: A New Monomer for Cyclopolymerization. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Effects of climate on admission rates of schizophrenia patients to psychiatric hospitals (2004)

Data on admissions of schizophrenia- and schizoaffective disorder patients to Tel-Aviv's seven public psychiatric hospitals during 11 consecutive years were obtained along with relevant meteorological information. Mean monthly admission rates were significantly higher during the summer (for schizophrenia patients) and fall (for schizoaffective patients). Schizophrenia patients' mean monthly admission rates correlated with mean maximal monthly environmental temperature (R = 0.35, N = 132 months, P <0.001). The present study may indicate that persistent high environmental temperature may be a contributing factor for psychotic exacerbation in schizophrenia patients and their consequent admission to mental hospitals.
Targeting Inhaled Therapy beyond the Lungs (2014)

Pulmonary disease has been the primary target of inhaled therapeutics for over 50 years. During that period, increasing interest has arisen in the use of this route of administration to gain access to the systemic circulation for the treatment of a number of diseases beyond the airways. In order to effectively employ this route, the barriers to transport from the lungs following deposition of aerosols must be considered, including the nature of the disease (whether proximal, as in pulmonary hypertension, or distal, as in diabetes). Delivery to the systemic circulation begins with the efficiency of aerosol generation and subsequent deposition in the airways and proceeds to the influence of mechanisms of clearance, including absorption, metabolism, and mucociliary and cell-mediated transport, on the residence time of the drugs in the lungs. The nature of the drug (small or large molecules/low or high molecular weight), susceptibility to degradation and general physicochemical properties play a role in the chemistry of its formulation, physics of aerosol delivery and biology of disposition.
H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts (2009)

Abstract H-Invitational Database (H-InvDB; "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in 43,159 human gene clusters based on human FLcDNAs and mRNAs.H-InvDB consists of two main views, the Transcript view and the Locus view, and six auxiliary databases with web-based viewers; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view. We also provides several data mining tools such as “Navi search”: consists of 16 search contents each of which includes items for the search condition ("http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp":http://www.h-invitational.jp/hinv/c-search/hinvNaviTop.jsp), “PANDA”: Priority ANalysis for Disease Association (PANDA) system ("http://www.h-invitational.jp/panda/app":http://www.h-invitational.jp/panda/app), H-InvDB now provides web service APIs of SOAP and REST to use H-InvDB data in programs. ("http://www.h-invitational.jp/hinv/hws/doc/":http://www.h-invitational.jp/hinv/hws/doc/)
Evaluation of the signal to noise ratio in a Hadamard transform time-of-flight mass spectrometer (2001)

Evaluation of the signal to noise ratio in a Hadamard transform time-of-flight mass spectrometer