gebhart/patrepeval huggingface dataset:
O3‐04‐05: Rescue of pathology and cognitive impairment by tau immunotherapy at a moderate to severe stage of the disease in 3xTg‐alzheimer's disease mice (2015)

Neurofibrillary tangles which are made up of abnormally hyperphosphorylated tau are a hallmark brain lesion of Alzheimer disease (AD) and other tauopathies. Unlike normal tau which interacts with tubulin and promotes its assembly into microtubules, the AD P-tau sequesters normal tau, disrupts microtubules, and serves as a template for its prion-like aggregation and spread. In a previous study we showed that targeting the amino terminal region of tau could rescue not only tau pathology and cognitive impairment but also could possibly reduce Aβ pathology in 3xTg-AD mice. Female 12-13 month old 3xTg-AD mice and age- and sex-matched control WT mice received 6 weekly intravenous injections of 15 micrograms of mouse monoclonal antibody (mAb) 43D to Tau6-18, mAb 77E9 to Tau184-195, a mixture of 43D and 77E9 or, as control, mouse IgG for 6 weeks. The day after the last injection the animals were subjected to several days of behavioral tests. On day 66 the animals received the 7thinjection of the antibody or control IgG. One half of the mice were sacrificed on day 72 and the remaining animals were tested for reference memory and by novel object location test at age ∼18 months. 3xTg-AD mice exhibited reference memory impairment and short-term memory deficit and higher level of anxiety than WT control mice. Passive immunization with 43D antibody completely rescued deficits in reference memory in Morris Water Maze and short-term memory in one-trial object recognition task. Passive immunization with antibody 77E9 rescued short-term memory impairment but did not show beneficial effect in spatial learning. At 18 months the 3xTg-AD mice treated with antibody 43D but not 77E9 showed a clear trend in rescue of short-term reference memory deficit. These studies show (1) that targeting of the amino terminal region, i.e. tau6-18, is more beneficial than tau184-195 region; (2) that the beneficial effect of passive immunotherapy can last at least ∼5 months in mice; and (3) that targeting the amino terminal region of tau is potentially an especially promising strategy for the treatment of AD and possibly other tauopathies.
A multimedia 32 b RISC microprocessor with 16 Mb DRAM (2002)

This 32 b microprocessor with on-chip 2 MB DRAM is for multimedia applications that require a low-power embedded microprocessor and large memory. Using a typical 0.45 /spl mu/m DRAM process, double-metal CMOS technology, this chip integrates 17 M transistors in 19.9/spl times/7.7 mm/sup 2/. It consists of a 32 b RISC CPU, a 32 b/spl times/16 b multiply accumulator (MAC), a 2 MB DRAM, a 2 kB cache, an external bus interface unit (BIU), and control units. The CPU, DRAM, cache and BIU are connected with a single 128 b internal bus. At 66 MHz, the bus transfers a 128 b data line between the CPU and the cache in one cycle, and between CPU and DRAM in 5 cycles. The external bus is 16 b wide and operates at 16.67 MHz.
Synthesis, Self-Assembly, and Photophysical Behavior of Oligo Phenylene Ethynylenes: From Molecular to Supramolecular Properties (2008)

A pair of cationic phenylene ethynylene oligomers (OPEs) have been synthesized, and their optical properties have been studied in solution with and without added scaffold materials, including carboxymethylcellulose, carboxymethylamylose, and Laponite. The OPEs are strongly fluorescent in methanol solution, but in water, the fluorescence yield is suppressed. The addition of scaffolds to aqueous solutions of OPEs leads to a red shift in the absorption and in most cases a significant increase in the fluorescence quantum yield. The effects most likely arise because of template-induced formation of linear J-dimers or possibly because of planarization, which give rise to an effective increase in the conjugation length of OPEs.
Network Topology Inference Based on End-to-End Measurements (2006)

We consider using traceroute-like end-to-end measurement to infer the underlay topology for a group of hosts. One major issue is the measurement cost. Given N hosts in an asymmetric network without anonymous routers, traditionally full N(N-1) traceroutes are needed to determine the underlay topology. We investigate how to efficiently infer an underlay topology with low measurement cost, and propose a heuristic called Max-Delta. In the heuristic, a server selects appropriate host-pairs to measure in each iteration so as to reveal the most undiscovered information on the underlay. We further observe that the presence of anonymous routers significantly distorts and inflates the inferred topology. Previous research has shown that obtaining both exact and approximate topology in the presence of anonymous routers under certain consistency constraints is intractable. We hence propose fast algorithms on how to practically construct an approximate topology by relaxing some constraints. We investigate and compare two algorithms to merge anonymous routers. The first one uses Isomap to map routers into a multidimensional space and merges anonymous routers according to their interdistances. The second algorithm is based on neighbor router information, which trades off some accuracy with speed. We evaluate our inference algorithms on Internet-like and real Internet topologies. Our results show that almost full measurement is needed to fully discover the underlay topology. However, substantial reduction in measurements can be achieved if a little accuracy, say 5%, can be compromised. Moreover, our merging algorithms in the presence of anonymous routers can efficiently infer an underlay topology with good accuracy
PRESCIENT: platform for the rapid evaluation of antibody success using integrated microfluidics enabled technology (2020)

Identifying antibodies (Abs) that neutralize infectious agents is the first step for developing therapeutics, vaccines, and diagnostic tools for these infectious agents. However, current approaches for identifying neutralizing Abs (nAbs) typically rely on dilution-based assays that are costly, inefficient, and only survey a small subset of the entire repertoire. There are also intrinsic biases in many steps of conventional nAb identification processes. More importantly, conventional assays rely on simple Ab-antigen binding assays, which may not result in identifying the most potent nAbs, as the strongest binder may not be the most potent nAb. Droplet microfluidic systems have the capability to overcome such limitations by conducting complex multi-step assays with high reliability, resolution, and throughput in a pico-liter volume water-in-oil emulsion droplet format. Here, we describe the development of PRESCIENT (Platform for the Rapid Evaluation of antibody SucCess using Integrated microfluidics ENabled Technology), a droplet microfluidic system that can enable high-throughput single-cell resolution identification of nAb repertoires elicited in response to viral infection. We demonstrate PRESCIENT's ability to identify Abs that neutralize a model viral agent, Murine coronavirus (murine hepatitis virus), which causes high mortality rates in experimentally infected mice. In-droplet infection of host cells by the virus was first demonstrated, followed by demonstration of in-droplet neutralization by nAbs produced from a single Ab-producing hybridoma cell. Finally, fluorescence intensity analyses of two populations of hybridoma cell lines (nAb-producing and non-nAb-producing hybridoma cell lines) successfully discriminated between the two populations. The presented strategy and platform have the potential to identify and investigate neutralizing activities against a broad range of potential infectious agents for which nAbs have yet to be discovered, significantly advancing the nAb identification process as well as reinvigorating the field of Ab discovery, characterization, and development.
Isolation of the Protein Kinase TAO2 and Identification of Its Mitogen-activated Protein Kinase/Extracellular Signal-regulated Kinase Kinase Binding Domain (1999)

We previously reported the cloning of the thousand and one-amino acid protein kinase 1 (TAO1), a rat homolog of the Saccharomyces cerevisiae protein kinase sterile 20 protein. Here we report the complete sequence and properties of a related rat protein kinase TAO2. Like TAO1, recombinant TAO2 selectively activated mitogen-activated protein/extracellular signal-regulated kinase kinases (MEKs) 3, 4, and 6 of the stress-responsive mitogen-activated protein kinase pathways in vitro and copurified with MEK3 endogenous to Sf9 cells. To examine TAO2 interactions with MEKs, the MEK binding domain of TAO2 was localized to an approximately 135-residue sequence just C-terminal to the TAO2 catalytic domain. In vitro this MEK binding domain associated with MEKs 3 and 6 but not MEKs 1, 2, or 4. Using chimeric MEK proteins, we found that the MEK N terminus was sufficient for binding to TAO2. Catalytic activity of full-length TAO2 enhanced its binding to MEKs. However, neither the autophosphorylation of the MEK binding domain of TAO2 nor the activity of MEK itself was required for MEK binding. These results suggest that TAO proteins lie in stress-sensitive kinase cascades and define a mechanism by which these kinases may organize downstream targets.
A MAGE-3 Peptide Presented by HLA-DR1 to CD4+ T Cells That Were Isolated from a Melanoma Patient Vaccinated with a MAGE-3 Protein (2003)

"Cancer-germline" genes such as those of the MAGE family are expressed in many tumors and in male germline cells, but are silent in normal tissues. They encode shared tumor-specific Ags, which have been used in therapeutic vaccination trials of cancer patients. MAGE-3 is expressed in 74% of metastatic melanoma and in 50% of carcinomas of esophagus, head and neck, bladder, and lung. We report here the identification of a new MAGE-3 peptide, which is recognized by three different CD4(+) T cell clones isolated from a melanoma patient vaccinated with a MAGE-3 protein. These clones, which express different TCRs, recognize an HLA-DR1 peptide ACYEFLWGPRALVETS, which corresponds to the MAGE-3(267-282) and the MAGE-12(267-282) protein sequences. One of the T cell clones, which expresses LFA-1 at a high level, lysed tumor cells expressing DR1 and MAGE-3. Another of these DR1-restricted CD4(+) clones recognized not only the MAGE-3/12 peptide but also homologous peptides encoded by genes MAGE-1, 2, 4, 6, 10, and 11.
48 Gbit/s 16-QAM-OFDM transmission based on compact 450-nm laser for underwater wireless optical communication (2015)

We experimentally demonstrate an underwater wireless optical communications (UWOC) employing 450-nm TO-9 packaged and fiber-pigtailed laser diode (LD) directly encoded with an orthogonal frequency division multiplexed quadrature amplitude modulation (QAM-OFDM) data. A record data rate of up to 4.8 Gbit/s over 5.4-m transmission distance is achieved. By encoding the full 1.2-GHz bandwidth of the 450-nm LD with a 16-QAM-OFDM data, an error vector magnitude (EVM) of 16.5%, a signal-to-noise ratio (SNR) of 15.63 dB and a bit error rate (BER) of 2.6 × 10(-3), well pass the forward error correction (FEC) criterion, were obtained.
Prospects of β‐Secretase Inhibitors for the Treatment of Alzheimer’s Disease (2015)

β-Secretase continues to be an attractive drug discovery target for the therapeutic intervention of Alzheimer's disease (AD). This enzyme plays a critical role in the production of neurotoxic β-amyloid (Aβ) peptides in the brain. Over the years, extensive research efforts have led to the development of many promising classes of inhibitors against this protease. Many small-molecule, peptidomimetic, and nonpeptide β-secretase inhibitors have now overcome the key challenging development hurdles such as selectivity and brain penetration. A number of inhibitors have also shown further promise in reducing brain Aβ and rescuing cognitive decline in animal models. Recently, several β-secretase inhibitors have entered into preclinical and phase I studies, and at least one of these inhibitors has advanced to phase II/III human trials. The outlook on β-secretase inhibitor drugs for the treatment of AD patients is discussed herein.
Very High-Density Recording on Exchange-Coupled Trilayer Magnetically Induced Super Resolution Media without Special Initializing Magnet (1996)

We obtained a high carrier-to-noise ratio (CNR) of 47 dB and a low jitter of 8% for 0.33 µm mark length ( 0.66 µm mark pitch) on exchange-coupled trilayer magnetically induced super resolution (MSR) media. This media is composed of a readout layer, an intermediate layer, and a writing layer. The magneto-optical signal is read through an aperture at the focal point between a front mask and a rear mask. The double mask can be formed by applying a readout magnetic field smaller than 300 Oe.
Anti-Zika Activity of a Library of Synthetic Carbohydrate Receptors (2019)

Zika virus (ZIKV), a mosquito-borne flavivirus, is a global health concern because of its association with severe neurological disorders. Currently, there are no antiviral therapies that have been specifically approved to treat ZIKV, and there is an urgent need to develop effective anti-ZIKV agents. Here, we report anti-ZIKV activity of 16 synthetic carbohydrate receptors (SCRs) that inhibit ZIKV infection in Vero and HeLa cells. Using a ZIKV reporter virus particle-based infection assay, our data demonstrates these SCRs are highly potent with IC<sub>50</sub>s as low as 0.16 μM and negligible toxicity at several-fold higher concentrations. Time-of-addition studies showed that these SCRs inhibit the early stages of the virus infection, which is consistent with the proposed mode of action, where the SCRs likely inhibit binding between the virus and cell-surface glycans, thereby preventing viral entry into the cells and, as such, this study demonstrates a potential new strategy against ZIKV.
Immunization with the RgpA-Kgp Proteinase-Adhesin Complexes of<i>Porphyromonas gingivalis</i>Protects against Periodontal Bone Loss in the Rat Periodontitis Model (2002)

A major virulence factor of Porphyromonas gingivalis is the extracellular noncovalently associated complexes of Arg-X- and Lys-X-specific cysteine proteinases and adhesins designated the RgpA-Kgp complexes. In this study we investigated the ability of RgpA-Kgp as an immunogen to protect against P. gingivalis-induced periodontal bone loss in the rat. Specific-pathogen-free Sprague-Dawley rats were immunized with either formalin-killed whole P. gingivalis ATCC 33277 cells with incomplete Freund's adjuvant, RgpA-Kgp with incomplete Freund's adjuvant, or incomplete Freund's adjuvant alone. The animals were then challenged by oral inoculation with live P. gingivalis ATCC 33277 cells. Marked periodontal bone loss was observed in animals immunized with incomplete Freund's adjuvant alone; this bone loss was significantly (P < 0.05) greater than that detected in animals immunized with formalin-killed whole cells or RgpA-Kgp or in unchallenged animals. There was no significant difference in periodontal bone loss between animals immunized with formalin-killed whole cells and those immunized with RgpA-Kgp. The bone loss in these animals was also not significantly different from that in unchallenged animals. DNA probe analysis of subgingival plaque samples showed that 100% of the animals immunized with incomplete Freund's adjuvant alone and challenged with P. gingivalis ATCC 33277 were positive for the bacterium. However, P. gingivalis ATCC 33277 could not be detected in subgingival plaque samples from animals immunized with formalin-killed whole cells or with RgpA-Kgp. Immunization with formalin-killed whole cells or RgpA-Kgp induced a high-titer serum immunoglobulin G2a response. Western blot analysis of RgpA-Kgp using pooled protective antisera taken from rats immunized with RgpA-Kgp revealed immunodominant bands at 44, 39, and 27 kDa. In conclusion, immunization with RgpA-Kgp restricted colonization by P. gingivalis and periodontal bone loss in the rat.
CT Angiographic Measurement of Vascular Blood Flow Velocity by Using Projection Data (2011)

Flow velocity can be measured from row-to-row multidetector CT projectional data obtained during a single gantry revolution as a bolus of contrast material flows through a vascular phantom. With further development, this novel technique could potentially provide physiologic information to complement the anatomic CT angiographic findings of vascular disease.
<i>Z</i>-Selective Homodimerization of Terminal Olefins with a Ruthenium Metathesis Catalyst (2011)

The cross-metathesis of terminal olefins using a novel ruthenium catalyst results in excellent selectivity for the Z-olefin homodimer. The reaction was found to tolerate a large number of functional groups, solvents, and temperatures while maintaining excellent Z-selectivity, even at high reaction conversions.
Characterization of a growth factor that binds exclusively to the erbB-2 receptor and induces cellular responses. (1992)

The erbB-2 oncogene encodes a 185-kDa transmembrane protein that has been suggested to be a growth factor receptor. We have previously identified and purified a 30-kDa growth factor (gp30) that is a ligand for the p185erbB-2 protein that at high concentrations induces growth inhibition of cells with erbB-2 amplification. We now report the purification and characterization of a protein from SKBr-3 human breast cancer cells with a molecular mass of 75 kDa (p75) that is a p185erbB-2 ligand. An affinity column coupled to the extracellular domain of p185erbB-2 was used for the purification. We found that p75 induced tyrosine phosphorylation of the erbB-2 oncoprotein, as determined by in vivo and in vitro phosphorylation and phosphoamino acid analysis. p75, as well as gp30, stimulated cell proliferation and colony formation of cells overexpressing erbB-2. The specificity of this effect was confirmed by showing that the antiproliferative effects of soluble erbB-2 extracellular domain were reversed by either p75 or gp30. p75 did not show binding to the epidermal growth factor receptor and had no growth effects on cells overexpressing epidermal growth factor receptor. These data show that SKBR-3 cells, which exhibit erbB-2 amplification and overexpression, secrete a growth factor that binds and activates p185erbB-2 specifically.
Development of a test battery for evaluating speech perception in complex listening environments (2014)

In the real world, spoken communication occurs in complex environments that involve audiovisual speech cues, spatially separated sound sources, reverberant listening spaces, and other complicating factors that influence speech understanding. However, most clinical tools for assessing speech perception are based on simplified listening environments that do not reflect the complexities of real-world listening. In this study, speech materials from the QuickSIN speech-in-noise test by Killion, Niquette, Gudmundsen, Revit, and Banerjee [J. Acoust. Soc. Am. 116, 2395-2405 (2004)] were modified to simulate eight listening conditions spanning the range of auditory environments listeners encounter in everyday life. The standard QuickSIN test method was used to estimate 50% speech reception thresholds (SRT50) in each condition. A method of adjustment procedure was also used to obtain subjective estimates of the lowest signal-to-noise ratio (SNR) where the listeners were able to understand 100% of the speech (SRT100) and the highest SNR where they could detect the speech but could not understand any of the words (SRT0). The results show that the modified materials maintained most of the efficiency of the QuickSIN test procedure while capturing performance differences across listening conditions comparable to those reported in previous studies that have examined the effects of audiovisual cues, binaural cues, room reverberation, and time compression on the intelligibility of speech.
Application of phased array systems to deep brain stimulation (2009)

Deep brain stimulation (DBS) is a clinical tool adopted to treat various neurological disorders, including chronic pain, incontinence and movement disorders. One major limitation of commercial DBS systems is the inability to control the distribution of the electric field around the target region, resulting in the activation of both target and non-target neural clusters. The authors have previously proposed a method to provide controlled stimulation by the adoption of phased array technology. A model was developed to study the behavior of wavefronts, generated by phased arrays, in tissue. This study represents an improvement to this model, where the frequency-dependence of the dielectric properties of brain tissue is taken into account. Results have shown that the applicability of phased array stimulation depends on the frequency of stimulation, with frequencies in the region of GHz providing the best trade-off between field steering, focusing and tissue penetration.
Combinatorial test design in practice (2010)

Combinatorial testing is a specification based sampling technique that provides a systematic way to select combinations of program inputs or features for testing. It has been applied over the years to test input data, configurations, web forms, protocols, graphical user interfaces and for testing software product lines. This tutorial introduces the fundamentals of combinatorial testing, including both practical and theoretical foundations, to provide a comprehensive introduction that is relevant to both test practitioners and software engineering researchers. The tutorial will present an overview of Combinatorial Test Design (CTD) and describe some state of the art research advances and domains where CTD has been applied. It will present the theoretical underpinnings of CTD and explain a few algorithmic techniques used to generate CTD samples, as well as describe recent work on practical extensions to these algorithms that allow for a broader use of CTD. A session devoted to modeling test problems using CTD will follow, with attendees obtaining hands-on experience using several realistic problems.
Highly active electrolytes for rechargeable Mg batteries based on a [Mg<sub>2</sub>(μ-Cl)<sub>2</sub>]<sup>2+</sup> cation complex in dimethoxyethane (2015)

A novel [Mg2(μ-Cl)2](2+) cation complex, which is highly active for reversible Mg electrodeposition, was identified for the first time in this work. This complex was found to be present in electrolytes formulated in dimethoxyethane (DME) through dehalodimerization of non-nucleophilic MgCl2 by reacting with either Mg salts (such as Mg(TFSI)2, TFSI = bis(trifluoromethane)sulfonylimide) or Lewis acid salts (such as AlEtCl2 or AlCl3). The molecular structure of the cation complex was characterized by single crystal X-ray diffraction, Raman spectroscopy and NMR. The electrolyte synthesis process was studied and rational approaches for formulating highly active electrolytes were proposed. Through control of the anions, electrolytes with an efficiency close to 100%, a wide electrochemical window (up to 3.5 V) and a high ionic conductivity (>6 mS cm(-1)) were obtained. The understanding of electrolyte synthesis in DME developed in this work could bring significant opportunities for the rational formulation of electrolytes of the general formula [Mg2(μ-Cl)2][anion]x for practical Mg batteries.