gebhart/patrepeval huggingface dataset:
Interferon mimetic as a therapeutic for lethal vaccinia virus infection (47.6) (2007)

Abstract We have developed small peptide mimetics of gamma interferon (IFNγ) that can bypass the poxvirus virulence factor B8R protein and can inhibit vaccinia virus replication in cell culture where intact IFNγ is ineffective. We demonstrate here that the mouse IFNγ mimetic peptide, IFNγ(95–132) with an attached lipophilic group for cell penetration, protects C57BL/6 mice against overwhelming lethal vaccinia virus infection. Intraperitoneal (IP) injection of mimetic before and at the time of intranasal (106 pfu) or IP (107 pfu) challenge with virus resulted in complete protection at 200 ug mimetic and 40 to 60 percent protection at 5 ug mimetic. Initiation of treatment of mice with IFNγ mimetic up to two days post infection resulted in complete protection against death, while initiation of treatment at six days post infection resulted in 40 percent protection. Administration of mimetic by the oral route also completely protected mice against the intranasal route of a lethal dose of vaccinia virus challenge. The mimetic also possessed adjuvant effects in boosting humoral and cellular immunity to vaccinia virus. The combination of antiviral and adjuvant effects by the IFN mimetic probably plays a role in its potent anti-vaccinia virus properties. These results suggest an effective therapeutic against ongoing, lethal poxvirus infections that taps into innate and adaptive host defenses. Supported by NIH grant AI 056152 and DoD grant W911NF-05-1-0170, both to HMJ.
IDEC-C2B8 (Rituximab) Anti-CD20 Monoclonal Antibody Therapy in Patients With Relapsed Low-Grade Non-Hodgkin's Lymphoma (1997)

IDEC-C2B8 is a chimeric monoclonal antibody (MoAb) directed against the B-cell–specific antigen CD20 expressed on non-Hodgkin's lymphomas (NHL). The MoAb mediates complement and antibody-dependent cell-mediated cytotoxicity and has direct antiproliferative effects against malignant B-cell lines in vitro. Phase I trials of single doses up to 500 mg/m2 and 4 weekly doses of 375 mg/m2 showed clinical responses with no dose-limiting toxicity. We conducted a phase II, multicenter study evaluating four weekly infusions of 375 mg/m2 IDEC-C2B8 in patients with relapsed low-grade or follicular NHL (Working Formulation groups A-D). Patients were monitored for adverse events, antibody pharmacokinetics, and clinical response. Thirty-seven patients with a median age of 58 years (range, 29 to 81 years) were treated. All patients had relapsed after chemotherapy (median of 2 prior regimens) and 54% had failed aggressive chemotherapy. Infusional side effects (grade 1-2) consisting of mild fever, chills, respiratory symptoms, and occasionally hypotension were observed mostly with the initial antibody infusion and were rare with subsequent doses. Peripheral blood B-cell depletion occurred rapidly, with recovery beginning 6 months posttreatment. There were no significant changes in mean IgG levels and infections were not increased over what would be expected in this population. Clinical remissions were observed in 17 patients (3 complete remissions and 14 partial remissions), yielding an intent to treat response rate of 46%. The onset of these tumor responses was as soon as 1 month posttreatment and reached a maximum by 4 months posttreatment. In the 17 responders, the median time to progression was 10.2 months (5 patients exceeding 20 months). Likelihood of tumor response was associated with a follicular histology, with the ability to sustain a high serum level of antibody after the first infusion, and with a longer duration of remission to prior chemotherapy. One patient developed a detectable but not quantifiable immune response to the antibody that had no clinical significance. IDEC-C2B8 in a dose of 375 mg/m2 weekly for 4 weeks has antitumor activity in patients with relapsed low-grade or follicular NHL. Results with this brief, outpatient treatment compare favorably with results with standard chemotherapy, and IDEC-C2B8 has a better safety profile. Further studies evaluating IDEC-C2B8 in other types of lymphoma either alone or combined with chemotherapy are warranted.
Stereoretentive Olefin Metathesis: An Avenue to Kinetic Selectivity (2017)

Olefin metathesis is an incredibly valuable transformation that has gained widespread use in both academic and industrial settings. Lately, stereoretentive olefin metathesis has garnered much attention as a method for the selective generation of both E- and Z-olefins. Early studies employing ill-defined catalysts showed evidence for retention of the stereochemistry of the starting olefins at low conversion. However, thermodynamic ratios E/Z were reached as the reaction proceeded to equilibrium. Recent studies in olefin metathesis have focused on the synthesis of catalysts that can overcome the inherent thermodynamic preference of an olefin, providing synthetically useful quantities of a kinetically favored olefin isomer. These reports have led to the development of stereoretentive catalysts that not only generate Z-olefins selectively, but also kinetically produce E-olefins, a previously unmet challenge in olefin metathesis. Advancements in stereoretentive olefin metathesis using tungsten, ruthenium, and molybdenum catalysts are presented.
Load Control through Incentive Regulation based on Asset Management (2020)

A novel cluster-based procedure and control principle is presented, which allows a fundamental reduction of the transmitted power down to the economic and technical minimum. The resulting, locally restricted energy use is achieved by a cluster-based approach to central assets and by a hierarchically accumulated monetary motivation of participants within the energy system. Local incentives are used to motivate grid-serving behavior, which result from the interaction of instantaneous power flow measurements and the ageing behavior, based on an asset management analysis. By accumulating the local incentives, it is also possible to influence energy flows among several clusters. This can be done with a data exchange which is reduced to a minimum.
On optimizing machine learning workloads via kernel fusion (2015)

Exploitation of parallel architectures has become critical to scalable machine learning (ML). Since a wide range of ML algorithms employ linear algebraic operators, GPUs with BLAS libraries are a natural choice for such an exploitation. Two approaches are commonly pursued: (i) developing specific GPU accelerated implementations of complete ML algorithms; and (ii) developing GPU kernels for primitive linear algebraic operators like matrix-vector multiplication, which are then used in developing ML algorithms. This paper extends the latter approach by developing fused kernels for a combination of primitive operators that are commonly found in popular ML algorithms. We identify the generic pattern of computation (alpha * X^T (v * (X * y)) + beta * z) and its various instantiations. We develop a fused kernel to optimize this computation on GPUs -- with specialized techniques to handle both sparse and dense matrices. This approach not only reduces the cost of data loads due to improved temporal locality but also enables other optimizations like coarsening and hierarchical aggregation of partial results. We also present an analytical model that considers input data characteristics and available GPU resources to estimate near-optimal settings for kernel launch parameters. The proposed approach provides speedups ranging from 2 to 67 for different instances of the generic pattern compared to launching multiple operator-level kernels using GPU accelerated libraries. We conclude by demonstrating the effectiveness of the approach in improving end-to-end performance on an entire ML algorithm.
In vitro inhibition of hemopoietic cell line growth by hepatitis B virus (1990)

The effects of hepatitis B virus (HBV) on established human cell lines of various tissue origins were evaluated by clonal or colorimetric assays in methylcellulose culture. HBV exposure inhibited the growth of six hemopoietic cell lines, while similar incubation did not affect the growth of seven nonhemopoietic carcinoma cell lines of breast, colon, liver, and stomach origin. The inhibition of hemopoietic cell line colony formation was dependent on the presence of intact viral (Dane) particles and the ratio of exposure of virions to cells and was reversible with antibodies to pre-S1, pre-S2, and S envelope protein epitopes. Purified HBV DNA, surface antigen pre-S antigens, and core antigen did not inhibit cell line growth. These results further demonstrate the tropism of HBV for cells of hemopoietic origin, confirming our previous findings on the effects of HBV on the growth of normal bone marrow progenitor cells in vitro. Established human tissue culture cell lines may be used to study the interactions of hemopoietic cells with HBV.
Collisional Pumping for the Production of Intense Spin-Polarized Neutral Beams: Target Considerations (1985)

Neutral-beam heating and/or fueling offers the possibility of establishing deuteron and triton spins oriented parallel to the magnetic field (or antiparallel to the field). It is believed that the polarizations can be maintained by guide fields until the particles are within the reactor. A beam suitable for this magnetic fusion-energy application would require five to six orders of magnitude increase in polarized beam intensity from the limits imposed by present technology, which is on the order of 10-100 ..mu..A. We have recently proposed that ampere-sized beams of nuclear-spin-polarized ions and atoms can be produced by multiple atomic collisions in an electron-spin-polarized medium. By analogy to optical pumping, we have called the process ''collisional pumping.'' Such pumping will occur when an ion beam passes through a thick electron-spinpolarized target in a low magnetic field. As an ion in the beam undergoes a succession of electron-capture and -loss collisions, polarization is transferred from the electron to the nucleus through the hyperfine interaction. After a sufficient number of charge-changing collisions, both the electron and nuclear polarization of the beam will be pumped to the electron polarization of the target. We have analyzed and theoretically demonstrated several examples of collisional pumping; the case thatmore » lends itself to earliest testing is that of a low-energy (0.1 - 10 keV/u) hydrogen or deuterium beam passing through a thick electron-spin-polarized alkalivapor target in a low magnetic field.« less
Sub-bandgap polysilicon photodetector in zero-change CMOS process for telecommunication wavelength (2015)

We report a defect state based guided-wave photoconductive detector at 1360-1630 nm telecommunication wavelength directly in standard microelectronics CMOS processes, with zero in-foundry process modification. The defect states in the polysilicon used to define a transistor gate assists light absorption. The body crystalline silicon helps form an inverse ridge waveguide to confine optical mode. The measured responsivity and dark current at 25 V forward bias are 0.34 A/W and 1.4 μA, respectively. The 3 dB bandwidth of the device is 1 GHz.
A Concise Flow Synthesis of Efavirenz (2015)

Efavirenz is an essential medicine for the treatment of HIV, which is still inaccessible to millions of people worldwide. A novel, semi-continuous process provides rac-Efavirenz with an overall yield of 45%. This streamlined proof-of-principle synthesis relies on the efficient copper-catalyzed formation of an aryl isocyanate and a subsequent intramolecular cyclization to install the carbamate core of Efavirenz in one step. The three-step method represents the shortest synthesis of this life-saving drug to date.
Functional and immunologic characterization of human immunodeficiency virus type 1 envelope glycoproteins containing deletions of the major variable regions (1993)

Deletions of the major variable regions (V1/V2, V3, and V4) of the human immunodeficiency virus type 1 (HIV-1) gp120 exterior envelope glycoprotein were created to study the role of these regions in function and antigenicity. Deletion of the V4 region disrupted processing of the envelope glycoprotein precursor. In contrast, the deletion of the V1/V2 and/or V3 regions yielded processed exterior envelope glycoproteins that retained the ability to interact with the gp41 transmembrane glycoprotein and the CD4 receptor. Shedding of the gp120 exterior glycoprotein by soluble CD4 was observed for the mutant with the V3 deletion but did not occur for the V1/V2-deleted mutant. None of the deletion mutants formed syncytia or supported virus entry. Importantly, the affinity of neutralizing antibodies directed against the CD4-binding region for the multimeric envelope glycoprotein complex was increased dramatically by the removal of both the V1/V2 and V3 structures. These results indicate that, in addition to playing essential roles in the induction of membrane fusion, the major variable regions mask conserved neutralization epitopes of the HIV-1 gp120 glycoprotein from antibodies. These results explain the temporal pattern associated with generation of HIV-1-neutralizing antibodies following infection and suggest stratagems for eliciting improved immune responses to conserved gp120 epitopes.
<i>In vitro</i> antagonistic activity of monoterpenes and their mixtures against ‘toe nail fungus’ pathogens (2003)

The antibiotic effect of the active ingredients in Meijer medicated chest rub (eucalyptus oil, camphor and menthol) as well as the inactive ingredients (thymol, oil of turpentine, oil of nutmeg and oil of cedar leaf) were studied in vitro using the fungal pathogens responsible for onychomycosis, such as the dermatophytes Tricophyton rubrum, Trichophyton mentagrophytes, Microsporum canis, Epidermophyton fl occosum and Epidermophyton stockdale. The zones of inhibition data revealed that camphor (1). menthol (2). thymol (3). and oil of Eucalyptus citriodora were the most efficacious components against the test organisms. The MIC(100) for mixtures of these four components in various carrier solvents revealed that formulations consisting of 5 mg/mL concentrations of each have a potential to be efffective in controlling onychomycosis.
Low Voltage Clock Tree Synthesis with Local Gate Clusters (2019)

In this paper, a novel local clock gate cluster-aware low voltage clock tree synthesis methodology is introduced. In low voltage/swing clocking, timing closure is a challenging problem due to tight skew and slew constraints. The clock gating makes this problem more challenging due to the high delay mismatch between the gated and the non-gated sinks. The proposed methodology preserves the power savings of the clock gating and exploits low swing clocking to further reduce the power consumption, while maintaining the same skew and slew constraints as the full swing counterpart. Experimental results performed on the large circuits of ISCAS'89 benchmarks operating at 1.5GHz in the 45nm technology node demonstrate that the proposed methodology can provide 38% power savings as compared to a full swing gated clock tree, achieving an additional 12% savings as compared to a low swing non-gated clock tree.
A monolithic resonant terahertz sensor element comprising a metamaterial absorber and micro‐bolometer (2013)

Abstract In this article a monolithic resonant terahertz sensor element with a noise equivalent power superior to that of typical commercial room temperature single pixel terahertz detectors and capable of close to real time read‐out rates is presented. The detector is constructed via the integration of a metamaterial absorber and a micro‐bolometer sensor. An absorption magnitude of 57% at 2.5 THz, a minimum NEP of and a thermal time constant of 68 ms for the sensor are measured. As a demonstration of detector capability, it is employed in a practical Nipkow terahertz imaging system. The monolithic resonant terahertz detector is readily scaled to focal plane array formats by adding standard read‐out and addressing circuitry enabling compact, low‐cost terahertz imaging.
A universal all-fiber Omnipolarizer (2013)

The all-optical control of light polarization is nowadays a fundamental issue which finds important applications in optical networks. In this field, the research has moved on the development of nonlinear methods of re-polarization of a partially coherent and initially depolarized light [1]. The main drawback of most of these devices is that they suffer from a large amount of output Relative-Intensity-Noise (RIN). However, a class of polarizers have been recently proposed which is based on the nonlinear interaction between two optical beams counter-propagating in a fiber [2]: in these devices the arbitrary state of polarization (SOP) of one of the two beams (signal) is attracted towards a specific SOP which is determined by the fixed SOP of the other beam (pump) in the fiber [2]. These polarizers turn out to be free of RIN, but they require an intense pump beam whose fixed SOP has to be also accurately stabilized.
SEDNA - Bioacoustic analysis toolbox (2011)

The possible effects of anthropogenic noise on the marine environment is becoming an important topic in the oceanic community. The exploration for fossil-fuel or alternative energy and the construction of facilities to support these endeavors often requires sizable construction efforts; which usually require permitting to study the impact of noise on the environment. Of particular interest is the variety of data products used to influence environmental impact reports and the processing time required to generate these data from large amounts of passive acoustic recordings. This paper outlines work being done by the Bioacoustics Research Program at Cornell University and the Lab of Ornithology, (BRP) for developing MATLAB tools in support of environmental compliance reporting. Due to the success of acoustic monitoring, understanding acoustic signatures is now becoming part of environmental impact assessment and required compliance for permitting. BRP has leveraged various existing tools and capabilities which result in integrated special purpose software tools within a MATLAB toolbox called SEDNA. SEDNA incorporates various tools to measure acute and chronic noise levels, detect and classify marine mammal vocalizations, and compute various metrics such as receive levels, signal excess, masking and communication space. This work will summarize the high performance computing strategy used in the SEDNA Toolbox along with the capability to integrate various layers of data within a modeling framework that incorporates ambient noise, vessel and animal data. Finally, the work will demonstrate the power of this approach through animated data visualization, showing animal, vessel and ambient noise integrated over relatively large temporal and spatial scales.
Semicarbazide-sensitive amine oxidase/vascular adhesion protein-1: a patent survey (2011)

SSAO/VAP-1 is a promising anti-inflammatory target. Another important field for therapeutic application of these inhibitors may be ophthalmology, due to their antiangiogenic effects. SSAO substrates might also be of therapeutic value in the treatment of diabetes; however, more extensive research has to be undertaken to validate this approach.
A 1-V, 5.5-GHz, CMOS LNA With Multiple Magnetic Feedback (2006)

A CMOS low-noise amplifier that utilizes multiple monolithic transformer magnetic feedback to simultaneously neutralize the gate-drain overlap capacitance of the amplifying transistor and achieve high gain at high frequencies when driving an on-chip capacitance is presented. The multiple transformer topology permits negative and positive feedback to be applied constructively, allowing for a stable design with adequate gain and large reverse isolation without noise figure (NF) degradation. Simulation results indicate voltage conversion gain of 17 dB, NF of 1.6 dB, and best-case third-order input intercept point of 13 dBm. The design is being implemented in a 0.13-mum CMOS technology
Imaging of fluorescent yield and lifetime from multiply scattered light reemitted from random media (1997)

The feasibility of employing fluorescent contrast agents to perform optical imaging in tissues and other scattering media has been examined through computational studies. Fluorescence lifetime and yield can give crucial information about local metabolite concentrations or environmental conditions within tissues. This information can be employed toward disease detection, diagnosis, and treatment if noninvasively quantitated from reemitted optical signals. However, the problem of inverse image reconstruction of fluorescence yield and lifetime is complicated because of the highly scattering nature of the tissue. Here a light propagation model employing the diffusion equation is used to account for the scattering of both the excitation and fluorescent light. Simulated measurements of frequency-domain parameters of fluorescent modulated ac amplitude and phase lag are used as inputs to an inverse image-reconstruction algorithm, which employs the diffusion model to predict frequency-domain measurements resulting from a modulated input at the phantom periphery. In the inverse image-reconstruction algorithm, a Newton-Raphson technique combined with a Marquardt algorithm is employed to converge on the fluorescent properties within the medium. The successful reconstruction of both the fluorescence yield and lifetime in the case of a heterogeneous fluorophore distribution within a scattering medium has been demonstrated without a priori information or without the necessity of obtaining absence images.
Studies on the Insulin Mediator: II. Separation of Two Antagonistic Biologically Active Materials from Fraction II (1980)

Insulin treatment significantly altered the elution profile of deproteinized muscle extracts chromatographed on Sephadex G-25 columns, particularly in fraction II, which contains the insulin mediator. Further purification of fraction II by high-voltage paper electrophoresis at pH 1.9 and 3.5 resulted in two active fractions. Fraction 1 leads to 4 stimulated the cyclic AMP-dependent protein kinase and inhibited glycogen synthase phosphoprotein phosphatase, and may be a novel substance. Fractions 1 leads to 6 and 3 leads to 6 inhibited the cyclic AMP-dependent protein kinase and stimulated glycogen synthase phosphatase. It is proposed that the insulin mediator is present in fractions 1 leads to 6 and 3 leads to 6.
A new approach to vibrational sum frequency generation spectroscopy using near infrared pulse shaping (2019)

We have developed a multipurpose vibrational sum frequency generation (vSFG) spectrometer that is uniquely capable of probing a broad range of chemical species, each requiring different experimental conditions, without optical realignment. Here, we take advantage of arbitrary near infrared (NIR) waveform generation using a 4f-pulse shaper equipped with a 2D spatial light modulator (SLM) to tailor upconversion pulses to meet sample dependent experimental requirements. This report details the experimental layout, details of the SLM calibration and implementation, and the intrinsic benefits/limitations of this new approach to vSFG spectroscopy. We have demonstrated the competency of this spectrometer by achieving an ∼3-fold increase in spectral resolution compared to conventional spectrometers by probing the model dimethyl sulfoxide/air interface. We also show the ability to suppress nonresonant background contributions from electrode interfaces using time delayed asymmetric waveforms that are generated by the NIR pulse shaper. It is expected that this advancement in instrumentation will broaden the types of samples researchers can readily study using nonlinear surface specific spectroscopies.