gebhart/patrepeval huggingface dataset:
An aggregation sensing reporter identifies leflunomide and teriflunomide as polyglutamine aggregate inhibitors (2011)

Intracellular protein aggregation is a common pathologic feature in neurodegenerative diseases such as Huntington' disease, amyotrophic lateral sclerosis and Parkinson' disease. Although progress towards understanding protein aggregation in vitro has been made, little of this knowledge has translated to patient therapy. Moreover, mechanisms controlling aggregate formation and catabolism in cellulo remain poorly understood. One limitation is the lack of tools to quantitatively monitor protein aggregation and disaggregation. Here, we developed a protein-aggregation reporter that uses huntingtin exon 1 containing 72 glutamines fused to the N-terminal end of firefly luciferase (httQ72-Luc). httQ72-Luc fails to aggregate unless seeded by a non-luciferase-containing polyglutamine (polyQ) protein such as Q80-cfp. Upon co-aggregation, httQ72-luc becomes insoluble and loses its enzymatic activity. Using httQ72-Luc with Q80(CFP/YFP) as seeds, we screened the Johns Hopkins Clinical Compound Library and identified leflunomide, a dihydroorotate dehydrogenase inhibitor with immunosuppressive and anti-psoriatic activities, as a novel drug that prevents polyQ aggregation. Leflunomide and its active metabolite teriflunomide inhibited protein aggregation independently of their known role in pyrimidine biosynthesis, since neither uridine treatment nor other pyrimidine biosynthesis inhibitors affected polyQ aggregation. Inducible cell line and cycloheximide-chase experiments indicate that these drugs prevent incorporation of expanded polyQ into an aggregate. This study demonstrates the usefulness of luciferase-based protein aggregate reporters for high-throughput screening applications. As current trials are under-way for teriflunomide in the treatment of multiple sclerosis, we propose that this drug be considered a possible therapeutic agent for polyQ diseases.
Measures of wound healing rate (2002)

Several wound healing rate measures have been introduced to date, with the main goal to enable quantification of effects of various therapeutic modalities on healing of skin wounds. Different definitions of wound healing rate render comparison of clinical results impossible. The goal of the authors' study was to discuss measures of wound healing rate based on wound size. Measures founded on two wound size measurements and measures based on several wound area measurements over time. Wound healing data obtained in a clinical trial revealed exponential behaviour of the healing process with delay of wound healing process initialisation. Due to the nonlinear nature of the healing process, it was concluded that wound healing rate cannot be correctly determined from just two wound size measurements. Optimally the wound healing rate measure should be deduced from the wound healing model with three parameters. Fitting with the delayed exponential model requires at least four wound size measurements over time. In further analysis the authors compared the wound healing measure based solely on wound area measurements with the measure additionally containing wound shape information. It was found that wound perimeter data does not facilitate wound healing rate expression. Thus it was concluded that wound area measurements should be transformed to percent of initial wound area and fitted to delayed exponential model. The slope of the curve fitted to the transformed wound area measurements over time after initial delay well describes wound healing rate.
Predictions of Hole Mobilities in Oligoacene Organic Semiconductors from Quantum Mechanical Calculations (2004)

We estimate the hole mobility for oligoacene crystals using quantum mechanics (QM) to calculate the reorganization energy and electron-transfer coupling matrix elements and molecular dynamics (MD) to do the thermal averaging. Using an incoherent transport model we calculate a hole mobility of 6.5 cm2/(V s) for pentacene crystals at 300 K. This can be compared to recent experimental results of 5 cm2/(V s). However, we find that an alternative packing into the crystal could lead to a hole mobility of 15.2 cm2/(V s). This suggests that current materials might still be improved by a factor of ∼3. Such calculations might be useful for finding solid-state structures that would increase the hole mobility for use in high-performance molecular devices.
Innovative airborne inventory and inspection technology for electric power line condition assessments and defect reporting (2002)

A cost-effective and innovative airborne inventory and inspection patrol system for distributed assets such as transmission lines, pipelines, and roadways has been developed and evaluated. Results show that aerial high-resolution digital visual and spectral images tagged by Global Positioning Satellite (GPS) coordinates can be successfully used to cost-effectively identify the majority of conditions/defects on electric power lines. Experiments show that the condition and defect detection rate of the airborne inventory and inspection system is significantly higher than rates derived from traditional patrols and comparable to values achieved from driving patrols. Geographic information systems (GIS) based mapping tools can be used to quickly and efficiently interpret digital images collected from aerial platforms. Digital images provide an archival record of the condition of the distributed assets to estimate the long-term performance of the assets and to define cost-effective maintenance and replacement schedules.
A photolithographic process for grossly non-planar substrates (2008)

We describe a technique whereby photolithography has been extended to the patterning of near micron-scale features onto grossly non-planar substrates. Examples will be given of track widths down to ten microns patterned over surfaces with vertical dimensions in excess of one centimetre - far outside the normal bounds of photolithography. The technique enables many novel microsystem packaging schemes and provides an alternative to the direct-write methods that are traditionally employed for patterning non-planar surfaces. The technique is based on the computation of the phase/amplitude distribution on the mask that, when illuminated with light of sufficient spatial coherence, will recreate the desired non-planar light distribution. This has some similarities to existing RET and inverse lithography techniques, but is extended to grossly non-planar surfaces. Exposure of an electrophoretic photoresist-coated substrate to the light field created by the mask enables the non-planar pattern to be transferred to the substrate. The holographic mask contains localized Fresnel patterns. We discuss the analytical methods used for their computation, the approximations necessary to enable mask manufacture and the effects of these approximations on image quality. We also discuss more general numerical methods of mask computation.
In vivo restoration of T cell functions by human IL-1 <i>beta</i> or its 163-171 nonapeptide in immunodepressed mice. (1988)

The immunorestorative capacities of human (hu) IL-1 beta or its synthetic fragment 163-171 (VQGEESNDK) were assessed in vivo in mice immunodepressed by aging, sublethal irradiation, or both. Subcutaneous administration of hu rIL-1 beta into immunodepressed animals immediately after carrier (horse red blood cells, HRBC) priming could restore to normal levels Th cell activity. This was measured as the ability of spleen cells from HRBC-primed mice to induce a hapten-specific antibody response in spleen cells from nonimmune mice in vitro stimulated with the hapten-carrier conjugate TNP-HRBC. In parallel, the ability of spleen cells from hu rIL-1 beta-treated immunodepressed animals to produce T cell growth factor activity upon in vitro mitogen stimulation was also increased significantly as compared to that of untreated mice and approached that of immunocompetent controls. The immunorestorative activity of hu rIL-1 beta on Th cell activity and T cell growth factor production could be mimicked by the synthetic nonapeptide 163-171 which, at the doses used, produced in most instances even greater effects than the whole protein. Although the optimal immunorestorative doses of the 163-171 peptide were several orders of magnitude higher than those of hu rIL-1 beta, the complete lack of IL-1-like inflammatory and toxic effects suggests that the synthetic hu IL-1 beta fragment may be successfully used as immunomodulating agent in the therapy of T cell immunodeficiencies.
Complete nucleotide sequence of the gene encoding bacteriophage E endosialidase: implications for K1E endosialidase structure and function (1995)

Bacteriophage E specifically recognizes and infects strains of Escherichia coli which display the alpha-2,8-linked polysialic acid K1 capsule. Bacteriophage E endosialidase, which is thought to be responsible for initial absorption of the phage to the host bacterium, was purified, and the N-terminal amino acid sequences of the polypeptide monomer and cyanogen bromide fragments were determined. Synthetic oligonucleotide probes were designed from the N-terminal amino acid sequences and used to identify restriction fragments of bacteriophage E DNA encoding the endosialidase. The primary nucleotide sequence of the bacteriophage E endosialidase gene contains an open reading frame encoding a 90 kDa polypeptide which is processed to give a mature 74 kDa protein. The native enzyme is probably a trimer of identical 74 kDa subunits. In the bacteriophage E genome the K1E endosialidase open reading frame is preceded by a putative upstream promoter region with homology to a bacteriophage SP6 promoter. A central region of 500 amino acids of the deduced protein sequence of the K1E endosialidase was found to have 84% identity to K1F endosialidase. Both endosialidases contain two copies of a sialidase sequence motif common to many bacterial and viral sialidases. These sequences flank the region of greatest identity between the two endosialidase forms, which suggests that this central domain is involved in binding and hydrolysis of the polysialic acid substrate.
Increase in the cerebrospinal fluid content of neurosteroids in patients with unipolar major depression who are receiving fluoxetine or fluvoxamine (1998)

We recently reported that fluoxetine or paroxetine, two selective serotonin reuptake inhibitors (SSRIs), when administered to rats, increase the brain content of the neurosteroid 3alpha-hydroxy-5alpha-pregnane-20-one (3alpha5alpha-ALLO) without altering the brain content of other neurosteroids. ALLO (3alpha5alpha and 3alpha5beta isomers) binds with high affinity to various gamma-aminobutyric acid (GABA) receptor A subtypes and facilitates the action of GABA at these receptors. We hypothesized that the increase of ALLO brain content induced by treatment with SSRIs could contribute to alleviating the anxiety and dysphoria associated with the symptomatology of major unipolar depression. We measured ALLO content in four cisternal-lumbar fractions of cerebrospinal fluid (CSF) before and 8-10 weeks after treatment with fluoxetine or fluvoxamine in 15 patients with unipolar major depression. The concentration of ALLO ( approximately 40 fmol/ml in each CSF fraction of three control subjects) was about 60% lower in patients with major unipolar depression. However, in the same patients, fluoxetine or fluvoxamine treatment normalized the CSF ALLO content. Moreover, a statistically significant correlation (r = 0.58; P < 0.023; n = 15) existed between symptomatology improvement (Hamilton Rating Scale for Depression scores) and the increase in CSF ALLO after fluoxetine or fluvoxamine treatment. The CSF content of PREG and PROG remained unaltered after treatment and failed to correlate with the SSRI-induced increase of CSF ALLO. The normalization of CSF ALLO content in depressed patients appears to be sufficient to mediate the anxiolytic and antidysphoric actions of fluoxetine or fluvoxamine via its positive allosteric modulation of GABA type A receptors.
High-performance Ge-on-Si photodetector with optimized DBR location (2017)

We investigated the Ge-on-Si photodetector's performance enhancement by optimizing the detector length, therefore, the location of the distributed Bragg reflector (DBR). Since the unabsorbed signal light in the photodetector oscillates between the germanium and silicon layers, but the DBR is on the silicon layer, the optimized location of the DBR will result in shorter devices, with increased bandwidth, reduced dark current, and consistent responsivity. The 5 μm long photodetector with an optimized DBR location shows responsivity of 0.72 A/W, at least 31.7 GHz 3 dB bandwidth; the dark current is only 7 nA at 1550 nm.
Opening the Red Cross International Tracing Service Archive, 26 J. Marshall J. Computer & Info. L. 161 (2008) (2008)

The Red Cross International Tracing Service Archive in Bad Arolsen contains nearly 17.5 million names and nearly 50 million World War II and post-war era documents. The Bonn Accords designated the International Tracing Service (“ITS”) as the sole caretaker of these documents. A recent revision to the Bonn Accords has resulted in a reopening of archives at Bad Arolsen. ITS has started to digitize materials, and the data has been distributed to designated research institutions. The revision also resulted in access to the archives for research purposes. This expanded availability of the information has raised a number of important questions about access to these documents. The significance of making the archives at Bad Arolsen available within organizations cannot be understated. The new records will effectively double the U.S. Holocaust Memorial Museum’s current holdings and it will be easier for interested survivors and families to explore the fates of specific categories of prisoners. The materials will provide the fullest account of Nazi persecutions on record to both scholars and students of the Holocaust. Nonetheless, many survivors and families continue to argue for direct remote access to the records without the approval of museum gatekeepers. While access to the records will continue to be hotly debated, the archives will remain a valuable window into the life and experiences of prisoners, which may help to further explain the complex social structure that developed in Nazi prisons during World War II.
ADAPTIVE ALGORITHMS FOR ACOUSTIC ECHO CANCELLATION IN SPEECH PROCESSING (2011)

Adaptive filtering constitutes one of the core technologies in digital signal processing and finds numerous application areas in science as well as in industry. Adaptive filtering techniques are used in a wide range of applications, including echo cancellation, adaptive equalization, adaptive noise cancellation, and adaptive beamforming. Acoustic echo cancellation is a common occurrence in today’s telecommunication systems. The signal interference caused by acoustic echo is distracting to users and causes a reduction in the quality of the communication. This paper focuses on the use of LMS and NLMS algorithms to reduce this unwanted echo, thus increasing communication quality.
Hydrophilic (Hydrogen-Bonding) Polystyrene Surface by Substrate-Induced Surface Segregation of Benzene Groups (2000)

The measurement of contact angle on polystyrene (PS) films solvent cast on acid-cleaned glass substrates was used in conjunction with the Lifshitz−van der Waals/acid−base approach in order to investigate the surface functional-group compositions as well as the physical nature and the strength of intermolecular interactions between the film surfaces and various testing liquids. The static contact angle for water observed on the air-side surface of the films (80°) was consistent with the literature. However, the glass-side surface of the films was found to be hydrophilic with a water contact angle of 62°. This hydrophilic character was shown to arise from (i) the substrate-induced surface segregation of benzene groups in the film casting process with consequent formation of benzene-rich PS surface and (ii) the relatively strong hydrogen-bond-accepting (electron-donating) character of the aromatic rings of polymer. The strength of hydrogen bond between the water molecule and the aromatic moiety was estimated to be ≥10.6 kJ/mol.
<i>C</i><scp><i>IC</i></scp> inactivating mutations identify aggressive subset of 1p19q codeleted gliomas (2015)

CIC mutations result in protein inactivation with upregulation of CIC target genes, activation of proliferative pathways, inhibition of differentiation, and poorer outcome in patients with a 1p19q codeleted glioma.
Walker carcinosarcoma 256 in study of anticancer agents. I. Method for simultaneous assessment of therapeutic value and toxicity. (1966)

Summary Described is the screening system with the Walker tumor in rats currently used at the Chester Beatty Research Institute. The biologic criterion of activity is defined in terms of the chemotherapeutic index measured in a combined therapeutic-toxicity assay.
Cultured Epidermal Keratinocytes on a Microspherical Transport System Are Feasible to Reconstitute the Epidermis in Full-Thickness Wounds (1999)

Research efforts to modify cultured autologous skin transplants for large full-thickness burn wounds and in chronic ulcers have shifted from multilayered differentiated grafts ("sheet" grafts) toward smaller units of basal undifferentiated single cell suspensions in a transport medium and subconfluently covered static carriers. It has been shown that wounds transplanted with single cell suspensions reconstitute the epidermis. However, this technique requires the detachment of the keratinocytes from the culture flasks by enzymatic digestion-digestion that might alter the anchoring proteins of the cells. A new approach might be to circumvent the enzymatic digestion to harvest the keratinocytes. This study reports a technique to culture epidermal cells on spherical microcarriers as a suspension culture and transport vehicle. The spherical microcarrier consists of a 100-microm-diameter collagen-coated dextran carrier (Cytodex 3 Pharmacia) and has been used previously for enzyme production commercially. With this new approach, we seeded the human keratinocytes in a spinner-like system onto microspheres and transplanted these micrografts onto full-thickness wounds on the back of nude mice. After 14 days, we showed a reconstituted epithelium that was multilayered and keratinized compared to control wounds. We believe that this is the first step of a new approach to increase the cell yield for seeding without altering the anchoring proteins by enzymatic steps, leading to a superior transplantation method for keratinocytes.
Video Coding Focusing on Block Partitioning and Occlusion (2009)

Among the existing block partitioning schemes, the pattern-based video coding (PVC) has already established its superiority at low bit-rate. Its innovative segmentation process with regular-shaped pattern templates is very fast as it avoids handling the exact shape of the moving objects. It also judiciously encodes the pattern-uncovered background segments capturing high level of interblock temporal redundancy without any motion compensation, which is favoured by the rate-distortion optimizer at low bit-rates. The existing PVC technique, however, uses a number of content-sensitive thresholds and thus setting them to any predefined values risks ignoring some of the macroblocks that would otherwise be encoded with patterns. Furthermore, occluded background can potentially degrade the performance of this technique. In this paper, a robust PVC scheme is proposed by removing all the content-sensitive thresholds, introducing a new similarity metric, considering multiple top-ranked patterns by the rate-distortion optimizer, and refining the Lagrangian multiplier of the H.264 standard for efficient embedding. A novel pattern-based residual encoding approach is also integrated to address the occlusion issue. Once embedded into the H.264 Baseline profile, the proposed PVC scheme improves the image quality perceptually significantly by at least 0.5 dB in low bit-rate video coding applications. A similar trend is observed for moderate to high bit-rate applications when the proposed scheme replaces the bi-directional predictive mode in the H.264 High profile.
The performance of protocols based on locks with ordered sharing (1994)

There is growing evidence that for a wide variety of database workloads and system configurations, locking-based concurrency control outperforms other types of concurrency control strategies. However, in the presence of increased data contention, locking protocols such as two-phase locking perform poorly. In this paper, we analyze a family of locking-based protocols that employ a new relationship between locks called ordered sharing. Using a centralized database simulation model, we demonstrate that these protocols exhibit comparable performance to that of traditional locking-based protocols when data contention is low, and they exhibit superior performance when data contention is high. Furthermore, we show that the performance of these protocols improves as resources become more plentiful. This is particularly significant because the performance of two-phase locking degrades as a result of data contention, not resource contention. Thus, introducing additional resources improves the performance of the proposed protocols, though it does not benefit two-phase locking significantly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
OPERATIONAL LEVEL-OF-SERVICE INDEX MODEL FOR RAIL RAPID TRANSIT (1997)

In planning a new transit system or considering alternatives to improve services of an existing transit system, it is essential to consider both the system capacity and the levels of service. However, the concept of transit level of service, unlike that of highways, is not well established. Although the level of service is directly related to capacity, their relationship is poorly understood. A level-of-service index model is described that attempts to establish levels of service for rail rapid transit on the basis of vehicle load factors and headways. The model clearly demonstrates the relationship between level of service and system capacity. It may be used as the basis for developing practical tools for assisting transit agencies to plan a new system or for rail rapid transit operators to better manage train operation, including, for instance, selection of optimal operating schemes and assurance of service quality. The proposed model also makes it possible to compare the levels of service offered by different rail rapid transit systems on a common basis, and it may be used to develop a standard service guideline, which may be adopted by local transit agencies with modifications to reflect local conditions.
Credibility assessments: operational issues and technology impact for law enforcement applications (2003)

Law Enforcement personnel are faced with new challenges to rapidly assess the credibility of statements made by individuals in airports, border crossings, and a variety of environments not conducive to interviews. New technologies may offer assistance to law enforcement personnel in the interview and interrogation process. Additionally, homeland defense against terrorism challenges scientists to develop new methods of assessing truthfulness and credibility in humans. Current findings of four advanced research projects looking at emerging technologies in the credibility assessment are presented for discussion. This paper will discuss research efforts on four emerging technologies now underway at DoDPI and other institutions. These include: (1) Thermal Image Analysis (TIA); (2) Laser Doppler Vibrometry (LDV); (3) Eye Movement based Memory Assessment (EMMA); and (4) functional Magnetic Resonance Imaging (fMRI). A description each technique, the current state of these research efforts, and an overview of the potential for each of these emerging technologies will be provided.