gebhart/patrepeval huggingface dataset:
Modeling Magneto-Active Elastomer Composites Using the Finite Element Method (2014)

Magneto-active elastomers (MAE) are a new branch of smart materials that consist of hard-magnetic particles such as barium ferrite in an elastomer matrix. Under the application of a uniform magnetic field, the MAE material undergoes large deformation as the material bends due to magnetic torques acting on the distribution of hard-magnetic particles. This behavior demonstrates the potential of MAEs to act as remote actuators. MAEs vary from magnetorheological elastomers (MRE) which use soft-magnetic iron particles in place of the hard-magnetic particles and they are driven by magnetic interactions between particles. In this work, MAEs were fabricated using 30% v/v 325 mesh M-type barium ferrite (BaM) particles in Dow Corning HS II silicone elastomers. Prior to curing, the samples were placed in a uniform (∼2 Tesla) magnetic field to align the magnetic particles and produce a magnetization oriented in the direction of the applied magnetic field. The specimens were bonded to a passive poldymethylsiloxane (PDMS) substrate to form a two-segment accordion structure where the MAEs with magnetization, M, were placed in opposing orientations a prescribed distance apart. The application of a uniform magnetic field perpendicular to the magnetization of the undeformed MAEs would result in a bend (on the PDMS) that is dependent upon the orientation of the magnetic particles and the direction of the applied field. This behavior of the composite structure highlights the ability of the MAE material to perform work. Experimental testing of the MAEs used a two-segment accordion structure with fixed boundary-conditions on both ends of the PDMS substrate and a uniform magnetic field was applied to the structure. The resulting deformation roughly represented either a mountain or valley fold (dependent upon the orientation of the applied field). The resulting axial force was observed and compared to computational simulations which utilized numerical techniques to develop approximate solutions. This procedure was repeated with a prescribed displacement on one of the two fixed boundary conditions to induce bending prior to the application of a uniform magnetic field. Results show a decrease in magnetic work potential with increases in the aforementioned prescribed displacement; results also show an increase in magnetic work potential with increases in the applied magnetic field.
Structure of retroviral RNAs produced by cell lines derived from spontaneous lymphomas of AKR mice (1982)

The retrovirus expression of eight independent lymphoid cell lines derived from spontaneous thymomas of AKR mice was investigated. The RNase T1 fingerprints of viral 70S RNA produced by these cell lines were compared with genome structures of the non-leukemogenic Akv virus and with two types of cloned leukemogenic viruses derived from one of the thymoma cell lines. Viral RNAs from three cell lines, SL3, 4, and 7, were indistinguishable from one another. The fingerprint patterns indicated that these cell lines produce equal amounts of two prototype, leukomogenic SL viruses that were previously isolated from the SL3 cell line. Viral RNA produced by the SL1 and SL2 cell lines contained similar components, but at a different ratio. Two other cell lines (SL5 and SL11) produced viral RNAs that resemble those of AKR mink cell focus-forming viruses. One additional line, SL9, produced viral RNA of a novel structure. The complex pattern of viral RNA expression observed for these lymphoid cell lines can be interpreted in terms of recombination among three types of endogenous viral sequences: the Akv virus, a xenotropic virus, and an SL (for spontaneous leukemia) virus.
Human epidermal cells from ultraviolet light-exposed skin preferentially activate autoreactive CD4+2H4+ suppressor-inducer lymphocytes and CD8+ suppressor/cytotoxic lymphocytes. (1988)

In vivo exposure of human epidermis to UV abrogates the function of T6+DR+ Langerhans cells and induces the appearance of Ag-presenting T6-DR+ OKM5+ cells in the epidermis. Since UV exposure of murine skin results in Ts lymphocyte activation, we investigated the capacity of human epidermal cells (EC) harvested 3 days after in vivo UV exposure to activate regulatory and effector autologous T lymphocyte subsets. T lymphocytes were separated into CD8+ suppressor/cytotoxic lymphocytes and CD4+ helper/inducer lymphocytes by C lysis and panning. The CD4+ subset was further divided by using the 2H4 mAB to obtain CD4+2H4+ lymphocytes (inducers of TS lymphocytes) and CD4+2H4- lymphocytes (inducers of B cell Ig production and inducers of cytotoxic T cells). Unirradiated suction blister-derived EC from control skin (C-EC) and from skin exposed in vivo to UV (UV-EC) were cultured with purified autologous T lymphocyte subsets in the absence of added Ag. The resultant T lymphocyte proliferation was detected by [3H]thymidine uptake. UV-EC were highly effective in the stimulation of CD4+ lymphocytes, whereas C-EC were poor stimulators. The stimulator effect of UV-EC was abrogated after depletion of DR+ UV-EC. When CD4+ lymphocytes were fractionated, UV-EC consistently demonstrated enhanced ability to stimulate suppressor-inducer CD4+2H4+ lymphocytes relative to C-EC. Although less responsive than CD4+2H4+ lymphocytes, CD4+2H4- lymphocytes also demonstrated greater proliferation to UV-EC than to C-EC. Neither UV-EC nor C-EC were able to activate CD8+ lymphocytes devoid of CD4+ lymphocytes. However, after addition of rIL-2 at concentrations that allow binding only to the high affinity IL-2R on T lymphocytes, UV-EC induced vigorous proliferation of CD8+ lymphocytes, whereas C-EC induced only background levels of proliferation. C lysis of leukocytes resident within UV-EC resulted in 66 to 70% reduction of CD8+ lymphocyte proliferation. In conclusion, UV-EC may activate CD8+ lymphocytes by at least two pathways: (1) UV-EC activation of CD4+2H4+ lymphocytes may induce differentiation/proliferation of CD8+ suppressor cells and (2) UV-EC activation of CD4+ cells may induce IL-2 production, that, in combination with UV-induced epidermal leukocytes, stimulates CD8+ cells.
A Sub-Ev Resolution Soft-X-Ray Spectrometer for a Transmision Electron Microscope to Obtain the Density of States of the Valence Band (2001)

Abstract We developed a high energy-resolution electron energy-loss spectroscopy (EELS) microscope to investigate electronic structures from specified small specimen areas [1]. EELS gives us information of the dielectric properties and the partial density of states (DOS) of the conduction band. Together with the DOS of the conduction band (unoccupied states), the DOS of the valence band (occupied states) is imperative to understand the whole electronic structure. Unfortunately, the DOS of the valence band cannot be reached directly by EELS. A partial DOS of the valence band can be obtained by fluorescent X-ray emission spectroscopy (XES). A conventional EELS instrument attached to a TEM usually takes spectra with an energy resolution of about 1 eV, by which the DOS of conduction bands has been studied using ELNES until now. Thus, an energy resolution of about 1 eV is at least necessary for the study of the DOS of the valence band.
Femtosecond-Assisted Anterior Lamellar Corneal Staining-Tattooing in a Blind Eye With Leukocoria (2009)

: The technique of FALT is simple and efficient for treating cosmetically blind eyes with leukocoria and may overcome the limitations of previously reported techniques. The long-term safety of the commercially available corneal tattoo dyes should be studied further.
Multi-step control over self-assembled hydrogels of peptide-derived building blocks and a polymeric cross-linker (2015)

We present a detailed study of self-assembled hydrogels of bundled and cross-linked networks consisting of positively charged amyloid-like nanofibers and a triblock copolymer with negatively charged end blocks as a cross-linker. In a first step small oligopeptides self-assemble into macrocycles which are held together by reversible disulfide bonds. Interactions between the peptides cause the macrocycles to assemble into nanofibers, which form a reversible hydrogel. The physical properties of the hydrogel are tuned using various methods such as control over the fibre length, addition of a cross-linking copolymer, and addition of salt. We establish a relationship between the bulk mechanical properties, the properties of the individual fibers and the hydrogel morphology using characterization techniques operating at different length scales such as rheology, atomic force microscopy (AFM) and cryo transmission electron microscopy (Cryo-TEM). This allows for a precise control of the elastic behaviour of these networks.
The Flavonoid 7,4′‐Dihydroxyflavone Inhibits MUC5AC Gene Expression, Production, and Secretion via Regulation of NF‐κB, STAT6, and HDAC2 (2015)

Mucus overproduction is a significant component of the pathophysiology of obstructive lung diseases. Currently, there are only a few medications available that inhibit mucus production. Previous studies showed that glycyrrhizin, a triterpenoid in Glycyrrhiza uralensis inhibits mucin 5AC (MUC5AC) mRNA and protein expression. Other potential mucus production inhibitory compounds contained within in G. uralensis have not been fully investigated. The aim of the present study was to determine if the G. uralensis flavonoid 7,4'-dihydroxyflavone (7,4'-DHF) inhibits MUC5AC gene expression, mucus production, and secretion, and if so, to elucidate the mechanism of this inhibition. 7,4'-Dihydroxyflavone significantly decreased phorbol 12-myristate 13-acetate-stimulated NCI-H292 human airway epithelial cell MUC5AC gene expression and mucus production, at a 28-fold lower concentration than glycyrrhizin (The half maximal inhibitory concentration IC50 value of 1.4 μM vs 38 μM, respectively); 7,4'-DHF also inhibited MUC5AC mucus secretion. Inhibition was associated with the suppression of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), signal transducer and activator of transcription 6 (STAT6) activation, and enhanced histone deacetylase 2 (HDAC2) expression. In a murine model of asthma, 7,4'-DHF-treated mice exhibited a marked reduction in MUC5AC secretion in the bronchoalveolar lavage fluid compared with control mice. These findings, together with previous findings linking NF-κB, STAT6, and HDAC2 modulation to the control of MUC5AC expression, demonstrate that 7,4'-DHF is a newly identified component of G. uralensis that regulates MUC5AC expression and secretion via regulation of NF-κB, STAT6, and HDAC2.
A High Resolution, Light-Weight, Synthetic Aperture Radar for UAV Application (1999)

(U) Sandia National Laboratories in collaboration with General Atomics (GA) has designed and built a high resolution, light-weight, Ku-band Synthetic Aperture Radar (SAR) known as "Lynx". Although Lynx can be operated on a wide variety of manned and unmanned platforms, its design is optimized for use on medium altitude Unmanned Aerial Vehicles (UAVS). In particular, it can be operated on the Predator, I-GNAT, and Prowler II platforms manufactured by GA. (U) The radar production weight is less than 120 lb and operates within a 3 GHz band from 15.2 GHz to 18.2 GHz with a peak output power of 320 W. Operating range is resolution and mode dependent but can exceed 45 km in adverse weather (4 mm/hr rain). Lynx has operator selectable resolution and is capable of 0.1 m resolution in spotlight mode and 0.3 m resolution in stripmap mode, over substantial depression angles (5 to 60 deg) and squint angles (broadside &plusmn;45 deg). Real-time Motion Compensation is implemented to allow high-quality image formation even during vehicle turns and other maneuvers.
Molecular Stacking Effect on Small-Molecular Organic Light-Emitting Diodes Prepared with Solution Process (2020)

The light-emitting layer (EML) is generally prepared by mixing the host and dopant to realize an organic light-emitting diode (OLED). However, phase separation is often observed during the fabrication process to prepare OLEDs, depending on the structure of the host materials. In particular, phase separation because of π-π stacking is frequently observed during thermal annealing for the solution process. The annealing process is required for solvent removal and complete relaxation of the molecule. Hence, the materials with a high glass transition temperature (<i>T</i><sub>g</sub>) are ideal because phase separation occurs because of π-π stacking during the annealing process, if <i>T</i><sub>g</sub> is too low. To understand this phenomenon, we compared two host materials with similar molecular weights but different three-dimensional connectivity, which causes different rotational freedom. Then, we investigated the effect on the device properties, depending on the annealing conditions. In both materials, when the annealing temperature rises above 120 °C, the dopant completely escaped from the EML. However, the material that does not disturb the molecular stacking order by annealing because of its limited free rotation through the internal bond shows much better device characteristics even after annealing at a higher temperature than <i>T</i><sub>g</sub>. The results show that interdiffusion at the interface and unstable internal density distribution with annealing temperature are responsible for the device degradation behavior.
Compositional Dynamic Test Generation (Extended Abstract) (2007)

Dynamic test generation is a form of dynamic program analysis that attempts to compute test inputs to drive a program along a specific program path. Directed Automated Random Testing, or DART for short, blends dynamic test generation with model checking techniques with the goal of systematically executing all feasible program paths of a program while detecting various types of errors using run-time checking tools (like Purify, for instance). Unfortunately, systematically executing all feasible program paths does not scale to large, realistic programs. This paper addresses this major limitation and proposes to perform dynamic test generation compositionally, by adapting known techniques for interprocedural static analysis. Specifically, we introduce a new algorithm, dubbed SMART for Systematic Modular Automated Random Testing, that extends DART by testing functions
HUMAN FAMSD-BASE: High Quality Protein Structure Model Database for the Human Genome Using the FAMSD Homology Modeling Method (2010)

Almost all proteins express their biological functions through the structural conformation of their specific amino acid sequences. Therefore, acquiring the three-dimensional structures of proteins is very important to elucidate the role of a particular protein. We had built protein structure model databases, which is called RIKEN FAMSBASE (http://famshelp.gsc.riken.jp/famsbase/). The RIKEN FAMSBASE is a genome-wide protein structure model database that contains a large number of protein models from many organisms. The HUMAN FAMSBASE that is one part of the RIKEN FAMSBASE contains many protein models for human genes, which are significant in the pharmaceutical and medicinal fields. We have now implemented an update of the human protein modeling database consisting of 242918 constructed models against the number of 20743 human protein sequences with an improved modeling method called Full Automatic protein Modeling System Developed (FAMSD). The results of our benchmark test of the FAMSD method indicated that it has an excellent capability to pack amino acid side-chains with correct torsion angles in addition to the main-chain, while avoiding the formation of atom-atom collisions that are not found in experimental structures. This new protein structure model database for human genes, which is named HUMAN FAMSD-BASE, is open to the public as a component part of the RIKEN FAMSBASE at http://mammalia.gsc.riken.jp/human_famsd/. A significant improvement of the HUMAN FAMSD-BASE in comparison with the preceding HUMAN FAMSBASE was verified in the benchmark test of this paper. The HUMAN FAMSD-BASE will have an important impact on the progress of biological science.
Medication continuation and compliance: a comparison of patients treated with clozapine and haloperidol. (2000)

Continuation with medication is greater with clozapine than haloperidol and is partly explained by greater symptom improvement and reduced side effects. No differences were found in regimen compliance.
scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling (2018)

Cellular barcoding of 3' mRNAs enabled massively parallel profiling of single-cell gene expression and has been implemented in droplet and microwell based platforms. The latter further adds the value for compatibility with low input samples, optical imaging, scalability, and portability. However, cell lysis in microwells remains challenging despite the recently developed sophisticated solutions. Here, we present scFTD-seq, a microchip platform for performing single-cell freeze-thaw lysis directly toward 3' mRNA sequencing. It offers format flexibility with a simplified, widely adoptable workflow that reduces the number of preparation steps and hands-on time, with the quality of data and cost per sample matching that of the state-of-the-art scRNA-seq platforms. Freeze-thaw, known as an unfavorable lysis method resulting in possible RNA fragmentation, turns out to be fully compatible with 3' scRNA-seq. We applied it to the profiling of circulating follicular helper T cells implicated in systemic lupus erythematosus pathogenesis. Our results delineate the heterogeneity in the transcriptional programs and effector functions of these rare pathogenic T cells. As scFTD-seq decouples on-chip cell isolation and library preparation, we envision it to allow sampling at the distributed sites including point-of-care settings and downstream processing at centralized facilities, which should enable wide-spread adoption beyond academic laboratories.
Acquisition and extinction of conditioned suppression of a graft-vs-host response in the rat. (1984)

Injection of rats with cyclophosphamide (CY) after their consumption of a novel saccharin-flavored drinking solution results in a conditioned aversion to saccharin and a conditioned suppression of immune responses. In this study, female Lewis X Brown Norwegian F1 rats were conditioned by pairing saccharin with 50 mg/kg CY. Seven weeks later (day 0), a graft-vs-host response (GvHR) was induced in these animals by injecting splenic leukocytes from Lewis donors into a rear footpad. At this time, some conditioned animals were reexposed to saccharin, the conditioned stimulus. During the 7-wk interval between conditioning and immunization, subgroups of conditioned rats were given 0, 4, 9, or 18 extinction trials (saccharin followed by saline injections). Animals receiving 4, 9, or 18 extinction trials showed a greater preference for saccharin on day 0 than did animals receiving no extinction trials, but these groups did not differ among themselves; all conditioned groups showed a lower preference for saccharin than placebo-treated animals. There was a clear effect of number of extinction trials on the GvHR. Animals receiving 9 or 18 extinction trials did not differ from controls, whereas animals receiving 0 or 4 trials had a milder GvHR than did conditioned rats that were not reexposed to saccharin at the time of immunization. These results confirm a previous report of conditioned suppression of a GvHR, demonstrate that conditioned immunopharmacologic responses are subject to experimental extinction, and indicate that conditioned immunosuppression can be dissociated from conditioned taste aversion.
An integrated test generation tool for enhanced coverage of simulink/stateflow models (2012)

Simulink/Stateflow (SL/SF) is the primary modeling notation for the development of control systems in automotive and aerospace industries. In model based testing, test cases derived from a design model are used to show model-code conformance. Safety standards such as ISO 26262 recommend model based testing to show the conformance of a software with the corresponding model. From our experiments with various test generation techniques, we have observed that their coverage capabilities are complementary in nature. With this observation in mind, we have developed a new tool called SmartTestGen which integrates different test generation techniques. In this paper, we discuss SmartTestGen and the different test generation techniques utilized -- random testing, constraint solving, model checking and heuristics. We experimented with 20 production-quality SL/SF models and compared the performance of our tool with that of two prominent commercial tools.
New and Preliminary Evidence on Altered Oral and Gut Microbiota in Individuals with Autism Spectrum Disorder (ASD): Implications for ASD Diagnosis and Subtyping Based on Microbial Biomarkers (2019)

Autism Spectrum Disorder (ASD) is a complex neurological and developmental disorder characterized by behavioral and social impairments as well as multiple co-occurring conditions, such as gastrointestinal abnormalities, dental/periodontal diseases, and allergies. The etiology of ASD likely involves interaction between genetic and environmental factors. Recent studies suggest that oral and gut microbiome play important roles in the pathogenesis of inflammation, immune dysfunction, and disruption of the gut-brain axis, which may contribute to ASD pathophysiology. The majority of previous studies used unrelated neurotypical individuals as controls, and they focused on the gut microbiome, with little attention paid to the oral flora. In this pilot study, we used a first degree-relative matched design combined with high fidelity 16S rRNA (ribosomal RNA) gene amplicon sequencing in order to characterize the oral and gut microbiotas of patients with ASD compared to neurotypical individuals, and explored the utility of microbiome markers for ASD diagnosis and subtyping of clinical comorbid conditions. Additionally, we aimed to develop microbiome biomarkers to monitor responses to a subsequent clinical trial using probiotics supplementation. We identified distinct features of gut and salivary microbiota that differed between ASD patients and neurotypical controls. We next explored the utility of some differentially enriched markers for ASD diagnosis and examined the association between the oral and gut microbiomes using network analysis. Due to the tremendous clinical heterogeneity of the ASD population, we explored the relationship between microbiome and clinical indices as an attempt to extract microbiome signatures assocociated with clinical subtypes, including allergies, abdominal pain, and abnormal dietary habits. The diagnosis of ASD currently relies on psychological testing with potentially high subjectivity. Given the emerging role that the oral and gut microbiome plays in systemic diseases, our study will provide preliminary evidence for developing microbial markers that can be used to diagnose or guide treatment of ASD and comorbid conditions. These preliminary results also serve as a starting point to test whether altering the oral and gut microbiome could improve co-morbid conditions in patients with ASD and further modify the core symptoms of ASD.
Performance Analysis and Improvement of OpenMP on Software Distributed Shared Memory Systems (2003)

Abstract. In this paper, the performance of the portable OpenMP compiler on SDSM JIAJIA is analyzed using SPEC OMPM2001 benchmark. The overheads of parallel execution have been investigated from the aspects of thread management and task schedule, memory access and synchronization. To improve the performance, the page placement and data privatization techniques have been implemented for the optimization of the compiler. 1