gebhart/patrepeval huggingface dataset:
Annealed dropout training of deep networks (2014)

Recently it has been shown that when training neural networks on a limited amount of data, randomly zeroing, or “dropping out” a fixed percentage of the outputs of a given layer for each training case can improve test set performance significantly. Dropout training discourages the detectors in the network from co-adapting, which limits the capacity of the network and prevents overfitting. In this paper we show that annealing the dropout rate from a high initial value to zero over the course of training can substantially improve the quality of the resulting model. As dropout (approximately) implements model aggregation over an exponential number of networks, this procedure effectively initializes the ensemble of models that will be learned during a given iteration of training with an enemble of models that has a lower average number of neurons per network, and higher variance in the number of neurons per network-which regularizes the structure of the final model toward models that avoid unnecessary co-adaptation between neurons. Importantly, this regularization procedure is stochastic, and so promotes the learning of “balanced” networks with neurons that have high average entropy, and low variance in their entropy, by smoothly transitioning from “exploration” with high learning rates to “fine tuning” with full support for co-adaptation between neurons where necessary. Experimental results demonstrate that annealed dropout leads to significant reductions in word error rate over standard dropout training.
Medical management of the acute radiation syndrome (2011)

The acute radiation syndrome (ARS) occurs after whole-body or significant partial-body irradiation (typically at a dose of >1 Gy). ARS can involve the hematopoietic, cutaneous, gastrointestinal and the neurovascular organ systems either individually or in combination. There is a correlation between the severity of clinical signs and symptoms of ARS and radiation dose. Radiation induced multi-organ failure (MOF) describes the progressive dysfunction of two or more organ systems over time. Radiation combined injury (RCI) is defined as radiation injury combined with blunt or penetrating trauma, burns, blast, or infection. The classic syndromes are: hematopoietic (doses >2-3 Gy), gastrointestinal (doses 5-12 Gy) and cerebrovascular syndrome (doses 10-20 Gy). There is no possibility to survive after doses >10-12 Gy. The Phases of ARS are-prodromal: 0-2 days from exposure, latent: 2-20 days, and manifest illness: 21-60 days from exposure. Granulocyte-colony stimulating factor (G-CSF) at a dose of 5 μg/kg body weight per day subcutaneously has been recommended as treatment of neutropenia, and antibiotics, antiviral and antifungal agents for prevention or treatment of infections. If taken within the first hours of contamination, stable iodine in the form of nonradioactive potassium iodide (KI) saturates iodine binding sites within the thyroid and inhibits incorporation of radioiodines into the gland. Finally, if severe aplasia persists under cytokines for more than 14 days, the possibility of a hematopoietic stem cell (HSC) transplantation should be evaluated. This review will focus on the clinical aspects of the ARS, using the European triage system (METREPOL) to evaluate the severity of radiation injury, and scoring groups of patients for the general and specific management of the syndrome.
Insulating GaN:Zn layers grown by hydride vapor phase epitaxy on SiC substrates (1999)

Fabrication of high-performance GaN microwave devices, which are the excellent candidates for new generation of high-power solid-state components, requires insulating GaN substrate materials. Due to lack of bulk GaN crystals and particularly lack of semi-insulating GaN substrates, we propose insulating GaN layers on silicon carbide as substrates for the fabrication of GaN-based microwave devices. In this work, we demonstrate insulating GaN layers on silicon carbide substrates. Insulating GaN layers doped with zinc were grown on silicon carbide substrates by hydride vapor phase epitaxy. High crystal quality of the grown material was proved by x-ray diffraction measurements showing the full width at a half maximum of ω-scan rocking curve of about 100 arcsec. Temperature dependence of specific resistivity of the GaN:Zn layers was measured in the temperature range from 200 to 500 K. The value of the specific resistivity was found to be 1012 Ω cm at 300 K and 109 Ω cm at 500 K.
A new type of electrostatic ion trap for storage of fast ion beams (1998)

A new technique for trapping of fast (keV) ion beams is presented. The trap, which is electrostatic, works on a principle similar to that of optical resonators. The main advantages of the trap are the possibility to trap fast beams without need of deceleration, the well-defined beam direction, the easy access to the trapped beam by various probes, and the simple requirement in terms of external beam injection. Results of preliminary experiments related to the radiative cooling of molecular ions are also reported.
Three-dimensional optical circuitry using two-photon-assisted polymerization (1999)

An approach using an as-formed solid bulk sample containing a blend of photocurable and thermally curable epoxies together with a highly efficient two-photon excitable fluorophore is demonstrated for in situ fabrication of three-dimensional optical circuitry with a precise control of dimension and spatial locations. Confocal volume images of a 1×2 splitter and a grating coupler are shown. End-fire coupling of a He–Ne laser beam into the 1×2 splitter has been achieved.
International Union of Pharmacology. XVIII. Nomenclature of receptors for vasoactive intestinal peptide and pituitary adenylate cyclase-activating polypeptide. (1998)

Vasoactive intestinal peptide (VIPb) and pituitary adenylate cyclase-activating polypeptide (PACAP) are members of a superfamily of structurally related peptide hormones that includes glucagon, glucagon-like peptide, secretin, and growth hormone-releasing factor (GRF). At least three receptors for
Case Studies with the Experts: Management Decisions in Atrial Fibrillation (2008)

Atrial fibrillation (AF) is the most common outpatient arrhythmia. The recent ACC/AHA/ESC guidelines outline a variety of approaches to the management of AF, but their implementation into clinical practice requires multi-faceted patient evaluations and assessments for optimizing patient care. Using a case-based approach, issues such as rate versus rhythm control, anticoagulation, cardioversion, pharmacological and catheter ablation for maintenance of sinus rhythm, and the pathophysiology of AF are discussed. These data were originally presented at a satellite symposium titled Case Studies with the Experts: Management Decisions in AF, held on May 10, 2007, during the annual Heart Rhythm Society meeting.
Differential Effects of Pneumococcal Vaccines against Serotypes 6A and 6C (2008)

PCV7 introduction has led to reductions in serotype 6A IPD but not serotype 6C IPD in the United States.
Application of SERS spectroscopy to the identification of (3,4-methylenedioxy)amphetamine in forensic samples utilizing matrix stabilized silver halides (2001)

A method based on surface-enhanced Raman scattering (SERS) spectroscopy was developed to meet the need for the reliable and rapid identification of illicit drugs such as the 'designer drug' XTC, preferably to increase the security of legal certificates. A matrix stabilized silver halide dispersion on a microtiter plate is used as the SERS-active substrate, providing an easy to use system for sample preparation and probing by means of a Raman microscope. The potential of the method is demonstrated by applying it to the identification of the psychoactive ingredients of drug containing tablets which were confiscated by the local police at techno-music events. The samples of interest were 26 different brands of XTC tablets and several pieces of evidence (powders) containing amphetamine. For reference, we show SERS and Raman spectra of pristine amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine (MDMA) and 3,4-methylenedioxyethamphetamine.
Incentive scheduling for cooperative relay in WWAN/WLAN two-hop-relay network (2005)

Non-cooperative behaviors in communication networks can significantly adversely affect the entire network. The WWAN/WLAN two-hop-relay system (Wei, H.-Y. and Gitlin, R.D., 2004) integrates two types of wireless technologies to improve wireless access throughput and coverage. Relay nodes in the two-hop-relay system can be wireless relay routers deployed by wireless service providers, or dual-mode users who voluntarily relay traffic for other users. However, it is likely that all dual-mode terminals are selfish and are not willing to relay for other users without an incentive. We propose a proper scheduling algorithm as an incentive mechanism for the hybrid wireless relay network. We use the basic concepts of game theory, especially the Nash equilibrium concept, to design our scheduling algorithms. Several scheduling algorithms, including the maximum rate C/I scheduler, the proportional fair scheduler, and the round robin scheduler, are examined to understand performance while operating under the assumption that all users are selfish. Under the C/I scheduler or the proportional fair scheduler, Nash equilibriums exist at the operating points where no user relays for other users - an undesirable situation. Under the round robin scheduler, selfish users are indifferent on relaying voluntarily or not relaying. Therefore, we are inspired to design a novel incentive scheduling algorithm to encourage relay. By applying the proposed incentive scheduler at the base station, all selfish users relay cooperatively at the Nash equilibrium.
Resource overbooking and application profiling in shared hosting platforms (2002)

In this paper, we present techniques for provisioning CPU and network resources in shared hosting platforms running potentially antagonistic third-party applications. The primary contribution of our work is to demonstrate the feasibility and benefits of overbooking resources in shared platforms, to maximize the platform yeld: the revenue generated by the available resources. We do this by first deriving an accurate estimate of application resource needs by profiling applications on dedicated nodes, and then using these profiles to guide the placement of application components onto shared nodes. By overbooking cluster resources in a controlled fashion, our platform can provide performance guarantees to applications even when overbooked, and combine these techniques with commonly used QoS resource allocation mechanisms to provide application isolation and performance guarantees at run-time. When compared to provisioning based on the worst-case, the efficiency (and consequently revenue) benefits from controlled overbooking of resources can be dramatic. Specifically, experiments on our Linux cluster implementation indicate that overbooking resources by as little as 1% can increase the utilization of the cluster by a factor of two, and a 5% overbooking yields a 300--500% improvement, while still providing useful resource guarantees to applications.
Speed Optimized Two-Qubit Gates with Laser Coherent Control Techniques for Ion Trap Quantum Computing (2003)

We propose a new concept for a two-qubit gate operating on a pair of trapped ions based on laser coherent control techniques. The gate is insensitive to the temperature of the ions, works also outside the Lamb-Dicke regime, requires no individual addressing by lasers, and can be orders of magnitude faster than the trap period, which is presently the speed limit of all two-qubit proposals.
Posttranscriptional control of bacteriophage lambda gene expression from a site distal to the gene. (1982)

The bacteriophage lambda int gene product, integrase, recombines the phage DNA with the host DNA at specific sites on each to accomplish lysogeny. The int gene is transcribed from two promoters, PL and PI, each regulated positively by lambda proteins. The expression of integrase is also controlled from a site, sib, in the b region of the phage genome. This is a unique regulatory site because it is located distal to the structural gene in relation to the promoters. The expression of int from the PL promoter is inhibited when sib is present. This effect appears to be specific for PL because sib does not cause inhibition of PI-dependent int synthesis. lambda mutants that contain alterations in the site have been isolated. Sequence analyses of the mutations reveal single base changes, spanning 37 base pairs (bp) in the b region, some 240 bp beyond the int gene. Another mutant, hef13, which has a phenotype similar to that of sib, introduces a nucleotide change within the same 37-bp region. The sib and hef mutations cluster within a region of dyad symmetry. Regulation of int synthesis by sib occurs after transcription of the int gene. There is no difference in the rate of PL-promoted int mRNA synthesis in either sib+ or sib- phage infections, yet int mRNA is less stable in the sib+ infection. Because RNase III host mutants are defective in sib regulation, processing of the PL mRNA at sib by this endoribonuclease may cause int mRNA decay and decrease int synthesis.
On the Possibility of Electromagnetic Surface Waves (1954)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Expression and folding of an interleukin‐2‐proinsulin fusion protein and its conversion into insulin by a single step enzymatic removal of the C‐peptide and the N‐terminal fused sequence (1996)

We report the expression in E. coli of a proinsulin fusion protein carrying a modified interleukin-2 N-terminal peptide linked to the N-terminus of proinsulin by a lysine residue. The key aspects investigated were: (a) the expression of the fused IL2-PI gene, (b) the folding efficiency of the insulin precursor when still carrying the N-fused peptide and (c) the selectivity of the enzymatic cleavage reaction with trypsin in order to remove simultaneously the C-peptide and the N-terminal extension. It was found that this construction expresses the chimeric proinsulin at high level (20%) as inclusion bodies; the fused protein was refolded at 100-200 micrograms/ml to yield about 80% of correctly folded proinsulin and then it was converted into insulin by prolonged reaction (5 h) with trypsin and carboxypeptidase B at a low enzyme/substrate rate (1:600). This approach is based on a single enzymatic reaction for the removal of both the N-terminal fused peptide and the C-peptide and avoids the use of toxic cyanogen bromide.
A Human-Like Senescence-Associated Secretory Phenotype Is Conserved in Mouse Cells Dependent on Physiological Oxygen (2010)

Cellular senescence irreversibly arrests cell proliferation in response to oncogenic stimuli. Human cells develop a senescence-associated secretory phenotype (SASP), which increases the secretion of cytokines and other factors that alter the behavior of neighboring cells. We show here that "senescent" mouse fibroblasts, which arrested growth after repeated passage under standard culture conditions (20% oxygen), do not express a human-like SASP, and differ from similarly cultured human cells in other respects. However, when cultured in physiological (3%) oxygen and induced to senesce by radiation, mouse cells more closely resemble human cells, including expression of a robust SASP. We describe two new aspects of the human and mouse SASPs. First, cells from both species upregulated the expression and secretion of several matrix metalloproteinases, which comprise a conserved genomic cluster. Second, for both species, the ability to promote the growth of premalignant epithelial cells was due primarily to the conserved SASP factor CXCL-1/KC/GRO-alpha. Further, mouse fibroblasts made senescent in 3%, but not 20%, oxygen promoted epithelial tumorigenesis in mouse xenographs. Our findings underscore critical mouse-human differences in oxygen sensitivity, identify conditions to use mouse cells to model human cellular senescence, and reveal novel conserved features of the SASP.
Design of a tunable GaAs/AlGaAs multiple-quantum-well resonant-cavity photodetector (1994)

We describe a tunable p-i-n photodetector using GaAs/AlGaAs multiple quantum wells (MQW) embedded in a vertical resonant cavity. The structure is similar to that employed for Fabry-Perot MQW modulators and lasers. Turnability is achieved by utilizing the quantum-confined Stark effect. The calculated response predicts a tuning range up to 20 nm. As a dual-channel wavelength-division demultiplexer, the crosstalk ratio is calculated to be >
Elevation of CXCR3-Binding Chemokines in Urine Indicates Acute Renal-Allograft Dysfunction (2004)

A noninvasive urinary test that diagnoses acute renal allograft dysfunction would benefit renal transplant patients. We aimed to develop a rapid urinary diagnostic test by detecting chemokines. Seventy-three patients with renal allograft dysfunction prompting biopsy and 26 patients with stable graft function were recruited. Urinary levels of CXCR3-binding chemokines, monokine induced by IFN-gamma (Mig/CXCL9), IFN-gamma-induced protein of 10 kDa (IP-10/CXCL10), and IFN-inducible T-cell chemoattractant (I-TAC/CXCL11), were determined by a particle-based triplex assay. IP-10, Mig and I-TAC were significantly elevated in renal graft recipients with acute rejection, acute tubular injury and BK virus nephritis. Using 100 pg/mL as the threshold level, both IP-10 and Mig had diagnostic value (sensitivity 86.4%; specificity 91.3%) in differentiating acute graft dysfunction from other clinical conditions. In terms of monitoring the response to antirejection therapy, this urinary test is more sensitive and predictive than serum creatinine. These results indicate that this rapid test is clinically useful.
Inhibition of Viral Replication by Interferon-γ-Induced Nitric Oxide Synthase (1993)

Interferons (IFNs) induce antiviral activity in many cell types. The ability of IFN-gamma to inhibit replication of ectromelia, vaccinia, and herpes simplex-1 viruses in mouse macrophages correlated with the cells' production of nitric oxide (NO). Viral replication was restored in IFN-gamma-treated macrophages exposed to inhibitors of NO synthase. Conversely, epithelial cells with no detectable NO synthesis restricted viral replication when transfected with a complementary DNA encoding inducible NO synthase or treated with organic compounds that generate NO. In mice, an inhibitor of NO synthase converted resolving ectromelia virus infection into fulminant mousepox. Thus, induction of NO synthase can be necessary and sufficient for a substantial antiviral effect of IFN-gamma.
Immunopharmacology of Thymosin α1 and Cytokine Synergy (2007)

Thymosin alpha1 (Talpha1) is a 28 amino acid biologically active protein cleaved from positions 2-29 of a precursor protein, prothymosin alpha. Since its discovery, Talpha1 has been administered to animals and humans in a wide variety of settings and its pharmacologic effects are to enhance cellular immunity. Talpha1 administration is highly effective in settings where irradiation, chemotherapy, tumor burden, or immune senescence have caused a reduction of T cell number and/or function. Recent in vitro studies, including the one reported here, suggest that Talpha1 may act via pathways commonly used by various cytokines. This raises the possibility that Talpha1 and cytokines may have synergistic activity through potentiation of cytokine activity by Talpha1. Improved control of tumor growth when tumor-bearing mice were treated with Talpha1 and high doses of IL-2 has been previously reported. We extended those studies with the Lewis lung carcinoma mouse model using IRX-2, a natural well-defined biologic containing multiple cytokines, in combination with Talpha1 (IRX-3). Although IRX-2 was effective alone (using doses that contain significantly less IL-2 than in most typical studies), adding Talpha1 led to significant improvement in survival of the tumor-bearing mice. Based on these observations, the immunopharmacology of Talpha1 predicts an important clinical role for Talpha1 in the restoration of cellular immune activity when used in combination with cytokines. Patients who experience immune suppression due to the presence of tumor, irradiation, and/or chemotherapy or aging of the host would most benefit from this treatment combination.
Compact acoustic-resolution photoacoustic imaging system with fiber-based illumination (2014)

Acoustic-resolution photoacoustic imaging enables unique high-resolution visualization of chromophores in deep tissue. However, most current systems are bulky and use complex optical components for illumination. In this study, we developed a compact acoustic-resolution photoacoustic imaging system with simple fiber-based illumination. Around the ultrasound sensor attached to an acoustic lens, four optical fibers were placed in four directions 90° apart, and the sensor plane was covered with an optically and acoustically transparent plastic spacer. The imaging head is compact (diameter, 32 mm; height, 27 mm) and lightweight (32 g) and is alignment-free, thus being suitable for in vivo applications. We assessed the uniformity and symmetry of photoacoustic excitation both by Monte Carlo simulation and experiments. A phantom study showed lateral and axial resolutions of the system to be 148 and 66 µm, respectively. With the system, high-contrast visualization of blood vessels in rat skin was demonstrated in vivo.
A Template for Stabilization of a Peptide α-Helix:  Synthesis and Evaluation of Conformational Effects by Circular Dichroism and NMR (1997)

The bicyclic diacid 1 was designed as a semi-rigid template for the hydrogen-bonding pattern of a peptide α-helix. The protected precursor 7 was synthesized in eight steps from tert-butyl 3,5-dimethoxybenzoate and linked to l-alanine and l-lactic acid to provide derivatives appropriate for coupling to a peptide. Both the amide 8-N and the ester 12-O were obtained in each of the four diastereomeric forms. The structure of R,R-8-N was determined by X-ray crystallography, which facilitated assignment of the diastereomers and confirmed the intended conformational effects of the quaternary methyl groups. The bicyclic amide and ester derivatives were appended to the peptide EALAKA-NH2, and their influence on the conformation was evaluated in aqueous solution using circular dichroism and NMR. The amide analogs have only a slight effect on the appended peptide, whereas the ester-linked template in S,S-9-O induces 32−50% helical character at 23 °C and 49−77% at 0 °C, depending on the method of determination; significant helical character persists even at 70 °C. The ability of the template 1 to induce the helical conformation is related to its structural and electronic complementarity to the N-terminus of the peptide; templating ability disappears when the carboxylate in S,S-9-O is protonated, and it is not observed in the dimethylamide S,S-9-N-a. The structural and dynamical properties of conjugate S,S-9-O were studied by NMR and compared with those of the acetylated heptapeptide 13. The dispersion and temperature dependence of amide hydrogen chemical shifts and the pattern observed for intra- and inter-residue nuclear Overhauser enhancements are all consistent with a significant population of helical conformers within the conformational ensemble of conjugate S,S-9-O, in contrast to the unstructured peptide 13. The generalized order parameter S2 was derived for each residue from the 15N T1 and T2 relaxation rate constants and 1H−15N heteronuclear NOEs determined for the 15N-labeled derivative of S,S-9-O; these parameters demonstrate a high degree of conformational rigidity along the peptide chain at 4 °C, with relative motion increasing for the C-terminal residues. These data are consistent with the chiroptical studies and demonstrate that the template is exceptionally effective in inducing helical behavior in an appended peptide.