gebhart/patrepeval huggingface dataset:
A role for interleukin-1 alpha in immunologically mediated intestinal pathology. (1993)

Interleukin-1 (IL-1) is an important mediator of inflammation and has been implicated in several forms of immunopathology. Here we have investigated whether IL-1 plays a role in the enteropathy which occurs during a graft-versus-host reaction (GVHR) in mice. Non-irradiated (CBA x BALB/c) F1 mice with GVHR had increased production of IL-1 and treatment with rabbit anti-IL-1 alpha antibodies abolished the crypt hyperplasia and significantly reduced the parallel increase in crypt length which occurs in the jejunum. Antibody treatment had no effect on the accompanying increase in intraepithelial lymphocyte (IEL) counts or on the splenomegaly. Recombinant IL-1 itself produced villus atrophy, crypt hyperplasia and increased IEL counts in normal mice and stimulated the proliferation of an intestinal epithelial cell line in vitro. We propose that IL-1 plays an effector role in immunologically mediated enteropathy, either via direct effects on epithelial cells or secondary to an action on other, stromal cells in the mucosa.
Implementing schema-theoretic models of animal behavior in robotic systems (2002)

Formal models of animal sensorimotor behavior can provide effective methods for generating robotic intelligence. We describe how schema-theoretic models of the praying mantis are implemented on a hexapod robot equipped with a real-time color vision system. The model upon which the implementation is based was developed by ethologists studying mantids. This implementation incorporates a wide range of behaviors, including obstacle avoidance, prey acquisition, predator avoidance, mating, and chantlitaxia behaviors.
Nuclear tracks in iron garnet films (1982)

Epitaxial iron garnet films of composition ${\mathrm{Y}}_{3}$${\mathrm{Fe}}_{5}$${\mathrm{O}}_{12}$, ${\mathrm{Gd}}_{3}$${\mathrm{Fe}}_{5}$${\mathrm{O}}_{12}$, and ${(\mathrm{G}\mathrm{d},\mathrm{B}\mathrm{i})}_{3}$${(\mathrm{F}\mathrm{e},\mathrm{G}\mathrm{a})}_{5}$${\mathrm{O}}_{12}$, irradiated with xenon or uranium ions of energies 1.4 and 6 MeV per nucleon exhibit nuclear tracks of lengths between 10 and 30 \ensuremath{\mu}m. These tracks were studied by saturation magnetization measurements and conversion electron M\"ossbauer spectroscopy elucidating a strong crystallographic disorder and a paramagnetic behavior in the track volume. The track diameter depends on mass and energy of the ions used for irradiation and was found to range between 15 and 20 nm for the energies investigated.
Cerebrospinal fluid trace element content in dementia (1983)

Using inductively coupled argon plasma emission spectroscopy, we measured 19 trace elements in cerebrospinal fluid of 265 patients who were undergoing diagnostic lumbar puncture. Thirty-three patients had Alzheimer-type dementia (ATD); 16 patients had other dementing illnesses; and 20 had no neurologic disease. There were seven cases of autopsy-proven Alzheimer's disease (AD) and eight autopsy controls. We found elevated CSF silicon in 24% of ATD and 71% of AD patients. We found no relationship between CSF aluminum, arsenic, lead, or manganese and ATD, AD, or other dementing illnesses.
Clinical benefit in Phase-I trials of novel molecularly targeted agents: does dose matter? (2009)

Phase-I trials traditionally involve dose-escalation to determine the maximal tolerated dose (MTD). With conventional chemotherapy, efficacy is generally deemed to be dose-dependent, but the same may not be applicable to molecularly targeted agents (MTAs). We analysed consecutive patients included in Phase-I trials at the Royal Marsden Hospital from 5 January 2005 to 6 June 2006. We considered only trials of monotherapy MTAs in which the MTD was defined. Three patient cohorts (A, B, and C) were identified according to the dose received as a percentage of the final trial MTD (0-33%, 34-65%, >66%). Potential efficacy was assessed using the non-progression rate (NPR), that is, complete/partial response or stable disease for at least 3 months by RECIST. A total of 135 patients having progressive disease before enrolment were analysed from 15 eligible trials. Median age was 57 years (20-86); male : female ratio was 1.8 : 1. Cohort A, B, and C included 28 (21%), 22 (16%), and 85 (63%) patients; NPR at 3 and 6 months was 21% and 11% (A), 50% and 27% (B), 31% and 14% (C), respectively, P=0.9. Median duration of non-progression (17 weeks; 95% CI=13-22) was not correlated with the MTD level, P=0.9. Our analysis suggests that the potential for clinical benefit is not confined to patients treated at doses close to the MTD in Phase-I trials of MTAs.
Programming languages (2008)

In this white paper, we propose a list of essential concepts of programming languages, and discuss the techniques we have used to teach these concepts.
Quotient-based control synthesis for partially observed non-deterministic plants with mu-calculus specifications (2007)

We study the control of a nondeterministic plant subject to a specification expressed in the prepositional <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> - calculus under a partial observability of events. We define a function to quotient the specification against the plant resulting in a "quotiented formula" with the property that a supervisor enforcing the desired specification exists if and only if the quotiented formula is satisfiable, and a model witnessing the satisfiability can be used as a supervisor. The quotiented formula belongs to an extended <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> -calculus, which we call <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> -calculus, where the extension is needed to express the observability constraint that cannot be expressed in the logic of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> -calculus. We present the syntax and semantics of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> - <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> -calculus and present a tableau-based satisfiability solving algorithm that also discovers a model for the quotiented formula when one exists.
Direct-Detection Based Frequency-Resolved I/Q Imbalance Calibration for Coherent Optical Transmitters (2021)

We propose a method for calibrating the frequency dependent I/Q imbalance in coherent optical transmitters. We demonstrate that with our calibration, the OSNR penalty of a 58-GBaud 256-QAM signal can be reduced by 2.5 dB.
Mixed films of TiO_2–SiO_2 deposited by double electron-beam coevaporation (1996)

We used double electron-beam coevaporation to fabricate TiO(2)-SiO(2) mixed films. The deposition process included oxygen partial pressure, substrate temperature, and deposition rate, all of which were real-time computer controlled. The optical properties of the mixed films varied from pure SiO(2) to pure TiO(2) as the composition of the films varied accordingly. X-ray diffraction showed that the mixed films all have amorphous structure with a SiO(2) content of as low as 11%. Atomic force microscopy showed that the mixed film has a smoother surface than pure TiO(2) film because of its amorphous structure. Linear and Bruggeman's effective medium approximation models fit the experimental data better than other models.
CoeViz: a web-based tool for coevolution analysis of protein residues (2016)

CoeViz represents a practical resource for a quick sequence-based protein annotation for molecular biologists, e.g., for identifying putative functional clusters of residues and structural domains. CoeViz also can serve computational biologists as a resource of coevolution matrices, e.g., for developing machine learning-based prediction models. The presented tool is integrated in the POLYVIEW-2D server (http://polyview.cchmc.org/) and available from resulting pages of POLYVIEW-2D.
Background light and atmospheric turbulence affecting the choice of space-to-ground laser communications links and communication time period program (2004)

Theoretical analysis,simulation and experimental study have been done for the relationship between the choice of space-to-ground laser communications links and communication time period program and background light and atmospheric turbulence,the general principle is given for the choice of space-to-ground laser communications links and communication time period program:1)As atmospheric turbulence is weak at night,this period is favored for space-to-ground laser communications.2)when sky is clear,space-to-ground laser communications should be avoided around the midday when sunlight is strong,the periods of morning and afternoon are favored.3)when it is overcast,it is small for background light and atmospheric turbulence to affect space-to-ground laser communications links,so if link communication light power meets the requirement of link power distribution parameters,it is practicable to conduct spact-to-ground laser communications links in the overcast sky.
Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling (2017)

Our ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell. This system has a dynamic range of ∼10,000-fold, enabling sparse labeling of proteins expressed at different abundance levels. Combined with photostable labels, this system extends the duration of automated single-molecule tracking by two orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in intact zebrafish. We found axon initial segment utilizes a "waterfall" mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor hops between clustered binding sites in spatially restricted subnuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements, enabling new experiments to quantitatively understand complex control of molecular dynamics in vivo.
Projection maskless lithography (PML2): proof-of-concept setup and first experimental results (2008)

Projection Mask-Less Lithography (PML2) is a potentially cost-effective multi electron-beam solution for the 32nm-node and beyond. PML2 is targeted on using hundreds of thousands of individually addressable electron-beams working in parallel, thereby pushing the potential throughput into the wafers per hour regime. With resolution limits <10nm, PML2 is designed to meet the requirements of several upcoming tool generations. A PML2 proof-of-concept setup was realized within the framework of the European RIMANA project. It contains all crucial components of a full-fledged PML2 tool and unambiguously demonstrates the operability of multi electron-beam projection optics with 200x reduction. In the PML2 proof-of-concept system more than 2000 switchable beams are generated by a programmable aperture plate system (APS) and projected onto wafer level with 200x demagnification. Current density (~2 A/cm<sup>2</sup>) and total current (~10 pA) of each beam are the same as in future PML2 tools, resulting in a calculated base resolution below 10nm. The PML2 proof-of-concept column has been successfully tested using resolution templates, verifying 200x reduction and the predicted 22nm hp resolution capability. Furthermore, first custom designed 32nm hp structures were printed into resist coated Si wafers using an APS test-unit. Based on the inputs obtained by the PML2 proof-of-concept system and detailed electron-optical calculations, a fully industry-compatible PML2 Alpha-tool will be realized within the European MAGIC project. Together with the infrastructure developed within MAGIC, this PML2 Alpha-tool promises to herald the introduction of mask-less lithography into the industrial environment.
System Design of an Open-Source Cloud-Based Framework for Internet of Drones Application (2019)

Unmanned Aerial Vehicles (UAV) are increasingly gaining interest in Internet of Drones (IoD) applications for automatizing the labor-intensive tasks. They are used in various areas such as infrastructure inspection. However, UAVs have limited energy resources and computational processing capabilities, which prevents them from running applications onboard and accessing the internet for gaining knowledge about their mission. In order to address these challenges imposed by limited resource on the drone, we propose a new cloud system infrastructure for building open-source IoD applications. We have designed a client-server architecture which hosts the drone as a client and the cloud as a scalable server. For validating the developed IoD application, an open-source drone simulator and flight controller are adopted to perform the tests. The overall architecture of a drone-cloud framework is presented along with a use case to show the applicability of the proposed framework.
Detection and analysis by dual‐laser flow cytometry of bacteriophage T4 DNA inside <i>Escherichia coli</i> (1991)

Bacteriophage T4 DNA was detected and analyzed inside E. coli by dual-laser flow cytometry using a dye combination of Hoechst 33258 (H33258) and chromomycin A3 (CA3) which bind to A-T- and G-C-rich regions of DNA, respectively. An exponentially-growing culture of E. coli ATCC 11303 was infected with T4 bacteriophage at a 1:1 multiplicity of infection. Samples were taken immediately and at 5 min intervals and placed on ice to interrupt viral replication. The samples were then centrifuged, ethanol-fixed, stained with H33258 and CA3, and analyzed by flow cytometry. Twenty-five minutes post-infection, a population of cells which contained T4 DNA began to appear on both a bivariate contour plot and a frequency histogram plot of the data. By 35 min, T4 DNA-containing cells could be distinguished from E. coli cells containing little or no T4 DNA. The ratio of CA3:H33258 fluorescence was then used to calculate the % G + C value for T4 DNA inside E. coli. A value of 35.6 +/- 0.2% was obtained, which agrees with % G + C values determined by traditional methods. These results demonstrate that dual-laser flow cytometry can be used to study viral DNA inside the bacterial host.
Single Cell-Based Vector Tracing in Patients with ADA-SCID Treated with Stem Cell Gene Therapy (2017)

Clinical improvement in stem cell gene therapy (SCGT) for primary immunodeficiencies depends on the engraftment levels of genetically corrected cells, and tracing the transgene in each hematopoietic lineage is therefore extremely important in evaluating the efficacy of SCGT. We established a single cell-based droplet digital PCR (sc-ddPCR) method consisting of the encapsulation of a single cell into each droplet, followed by emulsion PCR with primers and probes specific for the transgene. A fluorescent signal in a droplet indicates the presence of a single cell carrying the target gene in its genome, and this system can clearly determine the ratio of transgene-positive cells in the entire population at the genomic level. Using sc-ddPCR, we analyzed the engraftment of vector-transduced cells in two patients with severe combined immunodeficiency (SCID) who were treated with SCGT. Sufficient engraftment of the transduced cells was limited to the T cell lineage in peripheral blood (PB), and a small percentage of CD34<sup>+</sup> cells exhibited vector integration in bone marrow, indicating that the transgene-positive cells in PB might have differentiated from a small population of stem cells or lineage-restricted precursor cells. sc-ddPCR is a simplified and powerful tool for the detailed assessment of transgene-positive cell distribution in patients treated with SCGT.
Additive and interaction effects of working memory and motor sequence training on brain functional connectivity (2021)

Although shared behavioral and neural mechanisms between working memory (WM) and motor sequence learning (MSL) have been suggested, the additive and interactive effects of training have not been studied. This study aimed at investigating changes in brain functional connectivity (FC) induced by sequential (WM + MSL and MSL + WM) and combined (WM × MSL) training programs. 54 healthy subjects (27 women; mean age: 30.2 ± 8.6 years) allocated to three training groups underwent twenty-four 40-min training sessions over 6 weeks and four cognitive assessments including functional MRI. A double-baseline approach was applied to account for practice effects. Test performances were compared using linear mixed-effects models and t-tests. Resting state fMRI data were analysed using FSL. Processing speed, verbal WM and manual dexterity increased following training in all groups. MSL + WM training led to additive effects in processing speed and verbal WM. Increased FC was found after training in a network including the right angular gyrus, left superior temporal sulcus, right superior parietal gyrus, bilateral middle temporal gyri and left precentral gyrus. No difference in FC was found between double baselines. Results indicate distinct patterns of resting state FC modulation related to sequential and combined WM and MSL training suggesting a relevance of the order of training performance. These observations could provide new insight for the planning of effective training/rehabilitation.
Infectious process of the parvovirus H-1: correlation of protein content, particle density, and viral infectivity (1981)

The infectious particles of the parvovirus H-1 were characterized with respect to protein content, density in CsCl, and specific infectivity. Heavy-full and light-full particles were purified from infected simian virus 40-transformed newborn human kidney (NB) cells and from simian virus 40-transformed hamster kidney (THK) cells. Analysis of the protein content of these particles demonstrated that the ratio of viral protein VP2' to VP2 was the same in heavy-full and light-full particles derived from the same cell line, but differed significantly between the two hosts. However, the infectivity of the particles from each cell line was the same for all four viral species.. Also, in vitro conversion of VP2' to VP2 did not enhance the particle infectivity of either heavy-full or light-full virus. When the fate of input virus was studied with 125I-labeled H-1, the conversion of VP2' to VP2 occurred in a time-dependent manner up to 24 h postinfection. Simultaneous with the proteolytic cleavage, there was a shift in the density of the heavy-full virus to the light-full density. However, protein analysis of the 125I-labeled light-full virus at various times postinfection indicated that they were not enriched in VP2 when compared with heavy-full virus or the total virus population. Thus, the cleavage of VP2' to VP2 is not responsible for the shift in density from heavy-full to light-full virus, and although these events might be required for infection they appear not to be interdependent.
Features for melody spotting using hidden Markov models (2002)

The amount of digitized music stored on personal computers and available on the Internet is growing at a rapid rate. To address the access problem that this creates, we explore adapting HMM-based wordspotting techniques from speech recognition to create a system for melody-based retrieval of songs from a database of digitized music stored in a musically-unstructured format. In this paper, we present the construction of this melody spotter and evaluate its performance when trained under different feature vectors including a musical scale-based subset of the FFT and two Mel-scale based features. The results show the success of this system under the scale-based features when presented with both perfect melody queries and queries perturbed by minor errors.
A Deep Learning Method for Printing Defect Detection (2022)

In the actual printing process, the quality of printed products is often affected by many factors such as printing technology, equipment and environment. In some cases, it may cause printing defects in printed product. Product with printing defect need to be removed to ensure product quality. This paper proposes a deep learning method for printing defect detection. This method can classify printing defects into five categories. The experimental results show that the accuracy, precision and recall rate of the proposed printing defect detection method are all above 96%.
A novel photonic bandgap structure for low-pass filter of wide stopband (2000)

In this letter, a novel photonic bandgap (PBG) structure is proposed for increasing the stopband of a low-pass filter without the increasing circuit size for applications in microstrip circuits. The proposed structure is connected in two parallel periodic structures which have a different center frequency of the stopband. The wide stopband is achieved by two periodic structures of two different stopbands. We also show the performance improvement of microstrip patch antenna by etching of the proposed structure in ground plane.
Contamination resistant antireflection nano-textures in fused silica for laser optics (2013)

Anti-reflecting (AR) surface relief nano-textures have been integrated with fused silica diffraction gratings to demonstrate the potential of stable diffractive 3ω beam samplers with increased energy to target at the National Ignition Facility (NIF). TelAztec’s AR texturing process was used to etch Random-type AR (RAR) microstructures in sub-scale NIF Grating Debris Shields consisting of large pitch, shallow line gratings. This superposition yielded the desired ~3.5% increase in zero-order transmission uniformly over the full aperture without compromising the grating function. Another fused silica window fabricated with RAR nano-textures in both faces for a 3ω (351nm) transmission of 99.5%, was subjected to capillary condensation tests to evaluate the resistance of the RAR texture to the adsorption of organic compounds. It was found that for a one day exposure time to a surrogate suite of organic contaminants, the RAR textured fused silica surfaces adsorbed less than one fourth the amount of organic contaminants found on a NIF baseline hardened sol-gel AR coated optic. In two additional exposure cycles, further RAR process refinement reduced the amount of adsorbed organics to a level nearly 200 times below the current NIF baseline. Significantly, the 3ω transmission of the RAR textured window remained unchanged after all three exposure cycles, whereas the sol-gel coated windows showed losses up to 4.9% for the highest contaminant concentration. Large beam pulsed laser damage testing of RAR textured fused silica windows was conducted with the Optical Sciences Laser (OSL) at NIF. The RAR sample damage resistance was found to be equivalent to the current NIF baseline - even after multiple aggressive chemical cleaning cycles. Lastly, a series of RAR textured and sol-gel AR coated windows were subjected to commercial 3ω pulsed laser damage testing at Quantel. The results indicate an average RAR damage threshold of 26 J/cm<sup>2</sup>, a level about 80% of the two NIF fused silica samples tested, two times higher than the best performing ion beam sputtered thin-film AR coatings reported in the literature, and six times higher than catalog high power laser window coating specifications.