gebhart/patrepeval huggingface dataset:
Morphinan Neuroprotection: New Insight into the Therapy of Neurodegeneration (2004)

Neuro-inflammation plays a pivotal role in numerous neurodegenerative disorders, such as Parkinson's disease (PD). Traditional anti-inflammatory drugs have limited therapeutic use because of their narrow spectrum and severe side effects after long-term use. Morphinans are a class of compounds containing the basic morphine structure. The following review will describe novel neuroprotective effects of several morphinans in multiple inflammatory disease models. The potential therapeutic utility and underlying mechanisms of morphinan neuroprotection are discussed.
Random Walk and Front Propagation on Watershed Adjacency Graphs for Multilabel Image Segmentation (2007)

The watershed partition of an image often results in over-segmentation. This well-known phenomenon is due to variations of intensity that do not correspond to object boundaries and produce spurious local minima in the image gradient magnitude. Filtering minima or merging watershed regions is then necessary to obtain a higher-level description of the data. In this paper, we propose new solutions to this problem by applying two interactive multilabel partitioning techniques to the adjacency graph of the watershed regions. In our first approach, the partition is derived from the probability that a "random walker" starting at an arbitrary node, first reaches a node with a pre-assigned label. In the second approach, we compute a geodesic partition of the graph using competing wavefronts starting at prescribed nodes. Both methods are based on existing segmentation techniques previously implemented on image lattices. Using a watershed adjacency graph greatly reduces their memory footprint and computational cost. We demonstrate the practicality and versatility of this approach with several experiments on 2D and 3D datasets.
The <i>trk</i> Proto-Oncogene Product: a Signal Transducing Receptor for Nerve Growth Factor (1991)

The trk proto-oncogene encodes a 140-kilodalton, membrane-spanning protein tyrosine kinase (p140prototrk) that is expressed only in neural tissues. Nerve growth factor (NGF) stimulates phosphorylation of p140prototrk in neural cell lines and in embryonic dorsal root ganglia. Affinity cross-linking and equilibrium binding experiments with 125I-labeled NGF indicate that p140prototrk binds NGF specifically in cultured cells with a dissociation constant of 10(-9) molar. The identification of p140prototrk as an NGF receptor indicates that this protein participates in the primary signal transduction mechanism of NGF.
BMP binding peptide: A BMP‐2 enhancing factor deduced from the sequence of native bovine bone morphogenetic protein/non‐collagenous protein (2004)

Forty years ago, Marshall Urist described a partially purified extract of demineralized bone matrix which induced the formation of ectopic bone. This substance, bone morphogenetic protein/non-collagenous protein (BMP/NCP), was never purified to homogeneity but other investigators used similar starting materials to clone a number of recombinant BMPs. Urist recognized that his material probably contained the BMPs which had been cloned by others but always contended that it contained another, more potent, bone inducing material which differed significantly in its physical and chemical properties from the known BMPs. We have used Urist's protocol to isolate a protein that has the chemical and physical properties of Urist's "BMP". It is an 18.5 kD fragment of the bone matrix protein, SPP-24. This fragment contains the cystatin-like domain of SPP-24. We have located a 19 amino acid region which is similar to the TGF-beta/BMP-binding region of fetuin, a member of the cystatin family of protease inhibitors. A cyclic peptide, which we call BMP binding peptide (BBP) was generated using this sequence. The peptide avidly bound rhBMP-2 with a KD of 3 x 10(-5) M. When implanted alone in mouse muscle, the peptide frequently induced dystrophic calcification. When implanted with rhBMP-2, the peptide enhanced the osteogenic activity of the recombinant molecule. We hypothesize that Urist's "BMP" was a fragment of SPP-24 which influenced bone induction by binding to bone morphogenetic proteins. BBP may be clinically useful because of its effects on other bone-inducing substances.
Modeling and Design of a Highly Compact Chaotic Cavity for Optical Gas Sensing Applications (2007)

We present a novel class of compact, robust, and potentially cost-effective chaotic cavities for trace-gas sensing applications. The cavity consists of a single, closed, reflecting surface and can support up to 15.5 meter of optical path length with a cavity volume of only 68 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The design is based on quasi-chaotic ray dynamics in a 3-dimensional (3-D) deformed sphere. Within the cavity, light traces out a quasi-stable trajectory that has been improved to achieve long optical path length and little beam overlap. The results show that the proposed chaotic cavity effectively refocuses the beam as the light bounces off the cavity wall. We modeled, fabricated, and tested a prototype cavity. The chaotic cavity can successfully achieve a 40-pass trajectory with a pulsed AlGalnP diode laser emitting at 661 nm. The experimental results agree well with calculations.
Evaluation of an ontology-content based filtering method for a personalized newspaper (2008)

A new ontological-content-based method for ranking the relevancy of items in the electronic newspapers domain is proposed. The method is being implemented in ePaper, a personalized electronic newspaper research project. The content-based part of the filtering method of ePaper utilizes a hierarchical ontology of news items. The method considers common and "close" ontology concepts appearing in the user's profile and in the item's profile, measuring the hierarchical distance between concepts in the two profiles. Based on the number of common and related concepts, and their distances from each other, the filtering algorithm computes the similarity between items and users, and rank-orders the news items according to their relevancy to each user, thus providing a personalized newspaper.
A demonstration of SQLVM (2013)

Sharing resources of a single database server among multiple tenants is common in multi-tenant Database-as-a-Service providers, such as Microsoft SQL Azure. Multi-tenancy enables cost reduction for the cloud service provider which it can pass on as savings to the tenants. However, resource sharing can adversely affect a tenant's performance due to other tenants' workloads contending for shared resources. Service providers today do not provide any assurances to a tenant in terms of isolating its performance from other co-located tenants. SQLVM, a project at Microsoft Research, is an abstraction for performance isolation which is built on a promise of reserving key database server resources, such as CPU, I/O and memory, for each tenant. The key challenge is in supporting this abstraction within a RDBMS without statically allocating resources to tenants, while ensuring low overheads and scaling to large numbers of tenants. This demonstration will show how SQLVM can effectively isolate a tenant's performance from other tenant workloads co-located at the same database server. Our demonstration will use various scripted scenarios and a data collection and visualization framework to illustrate performance isolation using SQLVM.
Metabolic reprogramming via an engineered PGC-1α improves human chimeric antigen receptor T-cell therapy against solid tumors (2023)

Our data further support a role for metabolic reprogramming in immunomodulatory treatments and highlight the utility of genes like PGC-1α as attractive candidates to include in cargo along with chimeric receptors or TCRs for cell therapy of solid tumors.
Xtalkdelay: a crosstalk-aware timing analysis tool for chip-level designs (2004)

This paper describes XTalkDelay, an industrial-strength methodology and tool for measuring the impact of crosstalk on delays of paths in a design. The main cornerstone of XTalkDelay methodology, vis-a-vis other approaches, is its high delay computation accuracy. It deliberately avoids the use of approximate models for cells and nets and interconnect reductions. XTalkDelay employs a path-based approach; uses detailed and accurately distributed RC parasitics for critical nets and their aggressors; uses BSIM3-accurate gate models; and invokes HSPICE for delay computation using only the minimum required set of input patterns. XTalkDelay has been successfully applied on two industrial designs.
Treatment with the Terminal Complement Inhibitor Eculizumab Improves Anemia in Patients with Paroxysmal Nocturnal Hemoglobinuria: Phase III Triumph Study Results. (2006)

Abstract Paroxysmal nocturnal hemoglobinuria (PNH) is a potentially life-threatening acquired hemolytic anemia in which red blood cells (RBCs) lacking complement inhibitory proteins are sensitive to complement-mediated destruction or hemolysis. Intravascular hemolysis in these patients often results in the need for clinical support with packed RBCs (PRBCs) in order to maintain tolerable hemoglobin levels. Eculizumab, a terminal complement inhibitor, has recently been shown in a placebo-controlled randomized phase III clinical trial (TRIUMPH) to reduce intravascular hemolysis and transfusion requirements in patients with PNH. Reported here is a detailed analysis of the effect of eculizumab on various parameters of anemia in these study patients. Eculizumab-treated patients, as compared to placebo, showed an 85.8% decrease in intravascular hemolysis (as measured by LDH area under the curve, p&lt;0.001). This reduction in hemolysis with eculizumab resulted in a 2.5-fold increase in PNH RBC mass from a median of 0.81x1012 cells/L at baseline to 2.05x1012 cells/L at 26 weeks (p&lt;0.001), while the PNH RBC mass in placebo-treated patients remained relatively unchanged (from a median of 1.09x1012 cells/L to 1.16x1012 cells/L). The increase in PNH RBC mass was associated with an increase in hemoglobin levels in eculizumab-treated patients relative to placebo (p&lt;0.001). The number of PRBC units transfused decreased from a median of 10.0/patient with placebo to 0.0/patient with eculizumab (p&lt;0.001), and 51.2% of eculizumab-treated patients became transfusion independent (versus 0.0% of placebo patients, p&lt;0.001). Even patients who required some transfusions while on eculizumab showed a marked reduction in transfusion requirement from a median of 10.0 units per patient with placebo to 6.0 units/patient with eculizumab (p&lt;0.001). The reduction in PRBC units transfused with eculizumab was observed regardless of transfusion requirements prior to treatment, with statistical significance reached in 3 of 3 pre-treatment transfusion strata (4 to 14 units/year; 15–25 units/year; and &gt;25 units/year, p&lt;0.001 for each stratum). Significant reductions were observed in intravascular hemolysis (LDH) in eculizumab-treated patients that achieved transfusion independence (p&lt;0.001) as well as those that did not (p&lt;0.001). Taken together, these data demonstrate that effective control of intravascular hemolysis in PNH with eculizumab results in a substantial improvement in anemia, as evidenced by an increase in endogenous RBC mass, an improvement in hemoglobin levels, and a reduction in transfusion requirements. Substantial and significant reductions in intravascular hemolysis and improvements in anemia with eculizumab are demonstrated regardless of historical transfusion requirements or whether patients achieve transfusion independence during treatment.
Activity of Friend mink cell focus-forming retrovirus during myelo-erythroid hematopoiesis. (1996)

Friend mink cell focus-forming (FMCF) viruses are recombinants between the Friend murine leukemia virus (F-MuLV) and endogenous polytropic retroviruses involved in a number of retrovirus-induced malignancies of the myelo-erythroid compartment. To analyze the contribution of the viral cis regulatory elements to the host range determinants within the hematopoietic system, we performed a series of marker gene experiments using both transient transfection and retroviral-mediated stable transduction of indicator cell lines representing distinct developmental stages. According to our data, the U3 region in the long terminal repeat (LTR) of FMCF viruses possesses an enhancer assembly that allows efficient transcription in both early and late myelo-erythroid stem and progenitor cells. Retroviral gene expression, however, is subjected to stage-dependent transcriptional controls during blood cell maturation. We obtained evidence that a repressor element overlapping with the primer binding site in the viral leader region compromises U3-mediated gene expression in a stage-dependent manner, with the strongest restriction observed in the most primitive cells analyzed, FDCP-mix. In addition, our data indicate a second hurdle for retroviral gene expression in early hematopoietic cells that is independent of the primer binding site and most likely related to inefficient utilization of U3-located enhancers. These data shed light on the mechanisms of host range restriction within the hematopoietic system and define a basis for the design of retroviral vectors aimed to overcome transcriptional inefficiency in early hematopoietic cells. Thus, we developed novel retroviral vectors combining FMCF-type U3 regions with a permissive leader from the murine embryonic stem cell virus. These vectors are highly efficient for gene transfer and expression in both early and late myelo-erythroid cells, indicating that they will be of great use for a variety of experimental and therapeutic applications.
A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains (2016)

These results suggest that retrieval of shared TCRs by NGS would be useful for the identification of potential new invariant TCRα chains. This NGS method will enable the comprehensive quantitative analysis of TCR repertoires at a clonal level.
A single dose of an adenovirus-vectored vaccine provides protection against SARS-CoV-2 challenge (2020)

Abstract The unprecedented coronavirus disease 2019 (COVID-19) epidemic has created a worldwide public health emergency, and there is an urgent need to develop an effective vaccine to control this severe infectious disease. Here, we find that a single vaccination with a replication-defective human type 5 adenovirus encoding the SARS-CoV-2 spike protein (Ad5-nCoV) protect mice completely against mouse-adapted SARS-CoV-2 infection in the upper and lower respiratory tracts. Additionally, a single vaccination with Ad5-nCoV protects ferrets from wild-type SARS-CoV-2 infection in the upper respiratory tract. This study suggests that the mucosal vaccination may provide a desirable protective efficacy and this delivery mode is worth further investigation in human clinical trials.
High-Order Harmonic Generation from Ions in a Capillary Discharge (2006)

We demonstrate a significant extension of the high-order harmonic cutoff by using a fully-ionized capillary discharge plasma as the generation medium. The preionized plasma dramatically reduces ionization-induced defocusing and energy loss of the driving laser due to ionization. This allows for significantly higher photon energies, up to 150 eV, to be generated from xenon ions, compared with the 70 eV observed previously. We also demonstrate enhancement of the harmonic flux of nearly 2 orders of magnitude at photon energies around 90 eV when the capillary discharge is used to ionize xenon, compared with harmonic generation in a hollow waveguide. The use of a plasma as a medium for high-order harmonic generation shows great promise for extending efficient harmonic generation to much shorter wavelengths using ions.
A compact broadband tunable antenna with sophisticated performance (2008)

Sensor Systems Inc. designed a novel tunable antenna covering the frequency range of 30 to 512 MHz with a maximum tuning time of 32 μs. This antenna supports SINCGARS and HAVEQUICK I/II frequency-hopping within VHF/UHF AM/FM communication. The use of our patent-pending Top Loading Fractal Element (TLFE) as a radiator provides a wide multi-band capability coupled with software- defined RF tuning architecture.
AFD-DFE using Constraint-Based RLS and Phase Noise Compensation for Uplink SC-FDMA (2016)

In this paper, we develop a constraint-based block recursive least-squares (CRLS) for an adaptive frequency-domain decision feedback equalizer (AFD-DFE) in uplink single-carrier frequency division multiple access systems. For the AFD-DFE, both the feedforward and feedback filters are implemented in the frequency domain; therefore, the CRLS complexity can be reduced substantially when compared to its time-domain counterpart by exploiting the matrix structure in the frequency domain. The performance of the CRLS algorithm is better than that of the RLS when applied to the AFD-DFE, with no increase in the computational complexity. Our designed AFD-DFE with CRLS not only enjoys a lower computational complexity when compared to the frequency-domain channel-estimate-based minimum mean square error DFE (MMSE DFE), but its performance is also better than that of the MMSE DFE with decision errors (practical case) and is close to the MMSE DFE with correct decisions (ideal case). Moreover, we iteratively compensate the transmitter and receiver phase noise using its properties in the time and frequency domains. Simulation results demonstrate the robustness of our designed AFD-DFE using CRLS.
Extending the Lifetime of Organic Flow Batteries via Redox State Management (2019)

Redox flow batteries based on quinone-bearing aqueous electrolytes have emerged as promising systems for energy storage from intermittent renewable sources. The lifetime of these batteries is limited by quinone stability. Here, we confirm that 2,6-dihydroxyanthrahydroquinone tends to form an anthrone intermediate that is vulnerable to subsequent irreversible dimerization. We demonstrate quantitatively that this decomposition pathway is responsible for the loss of battery capacity. Computational studies indicate that the driving force for anthrone formation is greater for anthraquinones with lower reduction potentials. We show that the decomposition can be substantially mitigated. We demonstrate that conditions minimizing anthrone formation and avoiding anthrone dimerization slow the capacity loss rate by over an order of magnitude. We anticipate that this mitigation strategy readily extends to other anthraquinone-based flow batteries and is thus an important step toward realizing renewable electricity storage through long-lived organic flow batteries.
Bicyclic lactam inhibitors of angiotensin converting enzyme (1984)

Syntheses of the potent angiotensin converting enzyme inhibitor 1-(carboxymethyl)-3-(mercaptomethyl)-2,3,4,5-tetrahydro-1H-1- benzazep in -2-one (4a) and the corresponding eight-membered ring analogue (4b) are described. The influence of ring size on the inhibitory potencies of these substances is discussed.
Optically heterodyned coherent Raman spectroscopy (1978)

A convenient variation of Raman-induced Kerr effect spectroscopy (RIKES) which overcomes many of the previous limitations of coherent Raman spectroscopy is introduced. Quantum limited signal-to-noise ratios may be approached by the use of optical heterodyne detection (OHD). Detector current, linearly proportional and phase sensitive to the third-order nonlinear susceptibility, and linearly proportional to the Raman scattering cross section, is produced. Heterodyne detection in coherent Raman spectroscopy enables the detection of weak Raman signals that would otherwise be obscured by noise resulting from background sources.
Liquid−Liquid Extraction Using the Composition-Induced Phase Separation Process (1996)

This paper describes a new separation process of liquid−liquid extraction. It consists of first mixing the system to be extracted with a primary solvent, which is soluble with the native solvent, and subsequently adding a modifier, which is insoluble with either the native or the primary solvent. This process is similar to the phase transition extraction, which was described in a previous paper, where the liquid mixture, together with the solute to be separated, is first heated above its critical temperature, where it forms a uniform solution, and then cooled to the region below the miscibility curve, where it separates. Both processes have the advantage that the resulting separation of the solvents is very rapid, even in the presence of emulsion-forming impurities. In addition, the extraction efficiency of the new process may be 10 times higher than that of the traditional liquid−liquid extraction. The new process is thought of having significant advantages in the extraction of products from fermentation broths, plants, and other natural sources.
View-invariant action recognition using fundamental ratios (2008)

A moving plane observed by a fixed camera induces a fundamental matrix F across multiple frames, where the ratios among the elements in the upper left 2×2 submatrix are herein referred to as the Fundamental Ratios. We show that fundamental ratios are invariant to camera parameters, and hence can be used to identify similar plane motions from varying viewpoints. For action recognition, we decompose a body posture into a set of point triplets (planes). The similarity between two actions is then determined by the motion of point triplets and hence by their associated fundamental ratios, providing thus view-invariant recognition of actions. Results evaluated over 255 semi-synthetic video data with 100 independent trials at a wide range of noise levels, and also on 56 real videos of 8 different classes of actions, confirm that our method can recognize actions under substantial amount of noise, even when they have dynamic timeline maps, and the viewpoints and camera parameters are unknown and totally different.
In vivo RNA transcript-releasing plasmid possessing a universal pseudo-terminator by means of artificial ribozymes. (1990)

RNA transcript-releasing plasmid has been constructed by means of artificial hammerhead ribozymes. In this specific construct of pGENE8459v3 the ribozyme targeted for SFL1 gene (a yeast suppressor gene for flocculation) was fused between two other ribozymes called 5'-processing and 3'-processing ribozymes. Since the "Ribozyme for SFL1" portion (cassette) can be replaced by other RNA sequences, it is now possible to produce any RNAs with defined 5'- and 3'- ends.
A Two-Dimensional Stokes Parameter Method for Determination of Cell Thickness and Twist Angle Distributions in Twisted Nematic Liquid Crystal Devices (1998)

In order to determine 2-dimensional (2D) cell thickness and twist angle distributions in twisted nematic (TN) liquid crystal (LC) devices, we propose a 2D Stokes parameter method (2DSPM). A 2DSPM system is set up using a polarizing microscope, in which some preliminary experiments are conducted to demonstrate the validity of this 2DSPM. Experimental results of 2D distributions of cell thickness and twist angle in TN LC sample cells are given for the first time. The measurement accuracy of the 2DSPM system is analyzed.