gebhart/patrepeval huggingface dataset:
Ultrathin Spider Silk Films: Insights into Spider Silk Assembly on Surfaces (2019)

β-Sheets in natural spider dragline silk proteins are typically formed by polyalanine (An) as well as alanine-glycine (AG) and GGA sequences flanking these An regions. The hydrophobic β-sheet-rich regions are embedded in a hydrophilic amorphous matrix, and this phenomenon can be reflected as microphase separation, similar to that of block copolymers. Microphase separation occurs not only in fibers but also in cast spider silk films. Micellar-like structures form within the bulk of the film, while substrate surface as well as the film/air interface trigger explicit secondary structure formation in these layers. So far, only limited information is available concerning the mechanism of film assembly and microphase separation of spider silk proteins on surfaces. In this work, self-assembly and folding of eADF4(C16) was analyzed on steady silicon surfaces, dependent on the spider silk layer number and thickness. Based on the results, a model for structural features of spider silk films is proposed, combining block copolymer microphase separation theory with folding properties of recombinant eADF4(C16).
PTZ camera network calibration from moving people in sports broadcasts (2012)

In sports broadcasts, networks consisting of pan-tilt-zoom (PTZ) cameras usually exhibit very wide baselines, making standard matching techniques for camera calibration very hard to apply. If, additionally, there is a lack of texture, finding corresponding image regions becomes almost impossible. However, such networks are often set up to observe dynamic scenes on a ground plane. Corresponding image trajectories produced by moving objects need to fulfill specific geometric constraints, which can be leveraged for camera calibration. We present a method which combines image trajectory matching with the self-calibration of rotating and zooming cameras, effectively reducing the remaining degrees of freedom in the matching stage to a 2D similarity transformation. Additionally, lines on the ground plane are used to improve the calibration. In the end, all extrinsic and intrinsic camera parameters are refined in a final bundle adjustment. The proposed algorithm was evaluated both qualitatively and quantitatively on four different soccer sequences.
Multi-channel sentence classification for spoken dialogue language modeling (2003)

In traditional language modeling word prediction is based on the local context (e.g. n-gram). In spoken dialog, language statistics are affected by the multidimensional structure of the human-machine interaction. In this paper we investigate the statistical dependencies of users’ responses with respect to the system’s and user’s channel. The system channel components are the prompts’ text, dialogue history, dialogue state. The user channel components are the Automatic Speech Recognition (ASR) transcriptions, the semantic classifier output and the sentence length. We describe an algorithm for language model rescoring using users’ response classification. The user’s response is first mapped into a multidimensional state and the state specific language model is applied for ASR rescoring. We present perplexity and ASR results on the How May I Help You ? sm 100K spoken dialogs.
A Phase 2 Study Evaluating the Safety, Tolerability, and Immunogenicity of Two 3-Dose Regimens of a Clostridium difficile Vaccine in Healthy US Adults Aged 65 to 85 Years (2019)

NCT02561195.
Design of a lightweight, multipurpose underwater vehicle (1993)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Ocean Engineering, 1993.
Adversarial Examples that Fool both Human and Computer Vision (2018)

Machine learning models are vulnerable to adversarial examples: small changes to images can cause computer vision models to make mistakes such as identifying a school bus as an ostrich. However, it is still an open question whether humans are prone to similar mistakes. Here, we create the first adversarial examples designed to fool humans, by leveraging recent techniques that transfer adversarial examples from computer vision models with known parameters and architecture to other models with unknown parameters and architecture, and by modifying models to more closely match the initial processing of the human visual system. We find that adversarial examples that strongly transfer across computer vision models influence the classifications made by time-limited human observers.
Osteomodulin impacts positively the bone remodeling process in osteoarthritis (2021)

peer reviewed
Drug-Induced Extrapyramidal Reactions (1961)

A common form of Parkinsonism today is that induced by certain ataractic drugs, particularly phenothiazines containing a piperazine moiety. Mild to severe extrapyramidal symptoms can appear and disappear within hours or days of commencing or withdrawing the drugs. With rare exceptions the syndrome is completely reversible. This study was based on the postulate that the syndrome is due to interference with the normal functioning of central catecholamines, particularly dopamine, and of central histamine. Extrapyramidal reactions caused by reserpine or 1 of 3 phenothiazines were treated with from 4 to 32 gm. per day of dihydroxyphenylalanine (dopa, the precursor of the catecholamines), with 0.4 to 0.6 gm. per day of diphenhydramine (an antihistamine), or with each in turn. Dopa was mildly beneficial in 4 out of 22 patients, whereas diphenhydramine was completely effective in each of 11
Bacterial-Derived Outer Membrane Vesicles are Potent Adjuvants that Drive Humoral and Cellular Immune Responses (2021)

Discovery and development of novel adjuvants that can improve existing or next generation vaccine platforms have received considerable interest in recent years. In particular, adjuvants that can elicit both humoral and cellular immune responses would be particularly advantageous because the majority of licensed vaccines are formulated with aluminum hydroxide (alum) which predominantly promotes antibodies. We previously demonstrated that bacterial-derived outer membrane vesicles (OMV) possess inherent adjuvanticity and drive antigen-specific antibody and cellular immune responses to OMV components. Here, we investigated the ability of OMVs to stimulate innate and adaptive immunity and to function as a stand-alone adjuvant. We show that OMVs are more potent than heat-inactivated and live-attenuated bacteria in driving dendritic cell activation in vitro and in vivo. Mice immunized with OMVs admixed with heterologous peptides generated peptide-specific CD4 and CD8 T cells responses. Notably, OMV adjuvant induced much greater antibody and B cell responses to co-delivered ovalbumin compared to the responses elicited by the adjuvants alum and CpG DNA. Additionally, pre-existing antibodies raised against the OMVs did not impair OMV adjuvanticity upon repeat immunization. These results indicate that vaccines adjuvanted with OMVs elicit robust cellular and humoral immune responses, supporting further development of OMV adjuvant for use in next-generation vaccines.
MAP Kinase Pathway Alterations in BRAF -Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition (2013)

Treatment of BRAF-mutant melanoma with combined dabrafenib and trametinib, which target RAF and the downstream MAP-ERK kinase (MEK)1 and MEK2 kinases, respectively, improves progression-free survival and response rates compared with dabrafenib monotherapy. Mechanisms of clinical resistance to combined RAF/MEK inhibition are unknown. We performed whole-exome sequencing (WES) and whole-transcriptome sequencing (RNA-seq) on pretreatment and drug-resistant tumors from five patients with acquired resistance to dabrafenib/trametinib. In three of these patients, we identified additional mitogen-activated protein kinase (MAPK) pathway alterations in the resistant tumor that were not detected in the pretreatment tumor, including a novel activating mutation in MEK2 (MEK2(Q60P)). MEK2(Q60P) conferred resistance to combined RAF/MEK inhibition in vitro, but remained sensitive to inhibition of the downstream kinase extracellular signal-regulated kinase (ERK). The continued MAPK signaling-based resistance identified in these patients suggests that alternative dosing of current agents, more potent RAF/MEK inhibitors, and/or inhibition of the downstream kinase ERK may be needed for durable control of BRAF-mutant melanoma.
Cooperative effects of genes controlling the G2/M checkpoint (2000)

It is believed that multiple effectors independently control the checkpoints permitting transitions between cell cycle phases. However, this has not been rigorously demonstrated in mammalian cells. The p53-induced genes p21 and 14-3-3sigma are each required for the G(2) arrest and allow a specific test of this fundamental tenet. We generated human cells deficient in both p21 and 14-3-3sigma and determined whether the double knockout was more sensitive to DNA damage than either single knockout. p21(-/-) 14-3-3sigma(-/-) cells were significantly more sensitive to DNA damage or to the exogenous expression of p53 than cells lacking only p21 or only 14-3-3sigma. Thus, p21 and 14-3-3sigma play distinct but complementary roles in the G(2)/M checkpoint, and help explain why genes at the nodal points of growth arrest pathways, like p53, are the targets of mutation in cancer cells.
BACE: Lead Target for Orchestrated Therapy of Alzheimer's Disease. Edited by Varghese John. (2010)

Wiley, Hoboken 2010. 266 pp., hardcover $ 99.95.—ISBN 978-0-470-29342-3
2012 British Transplant Society 15TH ANNUAL CONGRESS (2012)

Messenger RNA Levels in Peripheral Blood and Urine Can Potentially Stratify Risk of Rejection Following Renal Transplantation<br/>
Reverberation Noise Suppression in the Aperture Domain Using 3D Fully Convolutional Neural Networks (2018)

Reverberation clutter is image noise resulting from multiple reflections between tissue layers and leads to image degradation. We propose a 3D fully convolutional neural network (FCNN) to selectively remove reverberation noise from ultrasound channel data. A training set was generated using Field II Pro to simulate full synthetic aperture channel data. Reverberation noise was approximated by adding bandpass filtered noise to the noise-free simulated channel data. This channel data, with and without noise, was used to train a 3D FCNN with a custom architecture to remove the reverberation and thermal noise. The network was evaluated on a simulated validation set and on an ATS 549 phantom using a L12-3v transducer connected to a Verasonics Vantage 256 system with reverberation noise. The resulting network shows significant reverberation noise reduction. Across the validation set, the normalized RMS loss between the noisy and noise free images decreased from 77% to 39% after being decluttered using 3D FCNN.
The complex evolutionary paths of local infrared bright galaxies: a high-angular resolution mid-infrared view (2016)

We investigate the evolutionary connection between local infrared (IR)-bright galaxies (logLIR ≥11.4 Lʘ) and quasars. We use high-angular resolution (∼0.3–0.4 arcsec∼few hundred parsecs) 8–13µm ground-based spectroscopy to disentangle the active galactic nuclei (AGN) id-IR properties from those of star formation. The comparison between the nuclear 11.3µm polycyclic aromatic hydrocarbon feature emission and that measured with Spitzer/Spitzer Infrared Spectrograph indicates that the star formation is extended over a few kpc in the IRbright galaxies. The AGN contribution to the total IR luminosity of IR-bright galaxies is lower than in quasars. Although the dust distribution is predicted to change as IR-bright galaxies evolve to IR-bright quasars and then to optical quasars, we show that the AGN mid-IR emission of all the quasars in our sample is not significantly different. In contrast, the nuclear emission of IR-bright galaxies with low AGN contributions appears more heavily embedded in dust although there is no clear trend with the interaction stage or projected nuclear separation. This suggests that the changes in the distribution of the nuclear obscuring material may be taking place rapidly and at different interaction stages washing out the evidence of an evolutionary path. When compared to normal AGN, the nuclear star formation activity of quasars appears to be dimming, whereas it is enhanced in some IR-bright nuclei, suggesting that the latter are in an earlier star formation-dominated phase.
Altered Methylation of Ribosomal RNA in an Erythromycin-Resistant Strain of Staphylococcus aureus (1971)

In certain strains of Staphylococcus aureus, a concentration of erythromycin between 10(-8) and 10(-7) M can induce resistance to concentrations of this drug as high as 10(-4) M. In one such strain studied, S. aureus (1206), N(6)-dimethyladenine is not normally present in 23S rRNA; however, a compound presumptively identified (on the basis of paper chromatography in three different solvents) as N(6)-dimethyladenine appears in the 23S rRNA of growing cells that have been incubated in a medium containing 10(-7) M erythromycin. It has been shown previously that the induction of the erythromycin-resistant phenotype that occurs under these conditions requires 10(-8)-10(-7) M erythromycin for maximal expression within 1 hr and that induction results in modified 50S ribosomal subunits, which are then unable to bind erythromycin or lincomycin. Methylated adenine is also found in the 16S rRNA from the strain of S. aureus studied; however, in contrast to the situation with 23S rRNA, the amount in 16S rRNA is not affected by erythromycin. These findings provide the first example of a correlation between the methylation of rRNA and altered ribosomal function.
FlexCam (2012)

FlexCam is a novel compound camera platform that explores interactions with color photographic prints using thinfilm flexible color displays. FlexCam augments a thinfilm color Flexible Organic Light Emitting Diode (FOLED) photographic viewfinder display with an array of lenses at the back. Our prototype allows for the photograph to act as a camera, exploiting flexibility of the viewfinder as a means to dynamically re-configure images captured by the photograph. FlexCam's flexible camera array has altered optical characteristics when flexed, allowing users to dynamically expand and contract the camera's field of view (FOV). Integrated bend sensors measure the amount of flexion in the display. The degree of flexion is used as input to software, which dynamically stitches images from the camera array and adjusts viewfinder size to reflect the virtual camera's FOV. Our prototype envisions the use of photographs as cameras in one aggregate flexible, thin-film device.
Encoding with Bursting, Subthreshold Oscillations, and Noise in Mammalian Cold Receptors (1996)

Mammalian cold thermoreceptors encode steady-state temperatures into characteristic temporal patterns of action potentials. We propose a mechanism for the encoding process. It is based on Plant's ionic model of slow wave bursting, to which stochastic forcing is added. The model reproduces firing patterns from cat lingual cold receptors as the parameters most likely to underlie the thermosensitivity of these receptors varied over a 25 degrees C range. The sequence of firing patterns goes from regular bursting, to simple periodic, to stochastically phase-locked firing or "skipping." The skipping at higher temperatures is shown to necessitate an interaction between noise and a subthreshold endogenous oscillation in the receptor. The basic period of all patterns is robust to noise. Further, noise extends the range of encodable stimuli. An increase in firing irregularity with temperature also results from the loss of stability accompanying the approach by the slow dynamics of a reverse Hopf bifurcation. The results are not dependent on the precise details of the Plant model, but are generic features of models where an autonomous slow wave arises through a Hopf bifurcation. The model also addresses the variability of the firing patterns across fibers. An alternate model of slow-wave bursting (Chay and Fan 1993) in which skipping can occur without noise is also analyzed here in the context of cold thermoreception. Our study quantifies the possible origins and relative contribution of deterministic and stochastic dynamics to the coding scheme. Implications of our findings for sensory coding are discussed.
Detection of antibodies against avian antigens in bronchoalveolar lavage from patients with pigeon breeder's disease: Usefulness of enzyme‐linked immunosorbent assay and enzyme immunotransfer blotting (1990)

The study reported here evaluated the usefulness of the enzyme-linked immunosorbent assay (ELISA) in the detection of antibodies against pigeon antigens in the serum and bronchoalveolar lavage (BAL) of patients with clinical, radiological, and functional evidence of interstitial lung disease (ILD) with and without pigeon breeder's disease (PBD). The results were compared with those obtained by the simultaneous use of counterimmunoelectrophoresis (CIE) in the same patients. In PBD, ELISA detected antibodies against pigeon's sera in both serum and BAL in 100% of patients, while CIE failed to detect the antibodies in the serum of one patient and in most of the samples of BAL. In addition, we used enzyme immunotransfer blotting to determine the number of epitopes in pigeon serum recognized by antibodies present in serum and BAL. There was a heterogeneous response in both fluids, but the reaction pattern demonstrated that patient's sera recognize to-25 different pigeon epitopes. We conclude that ELISA is a highly sensitive and specific method for the detection of antibodies against pigeon antigens in the serum and BAL of patients with PBD and that the host response involves a great number of avian antigens.
Broadband terahertz radiation from metal targets irradiated by a short pulse laser (2020)

The generation of low-frequency radiation from sub-picosecond laser pulses incident on metal targets is investigated. The laser field drives time-varying currents in a thin sub-surface layer of the metal, which emits broadband radiation that peaks at terahertz frequencies. We present a one-dimensional electrostatic model for copper appropriate for the interaction of laser pulses at normal incidence combined with a radiation model for an infinitely thin disk. The latter uses as input a single parameter, the temporal dependence of the integrated current density on axis, which is derived from the electrostatic model. The salient characteristics of the emitted radiation, such as power, energy, and spectra, are calculated for laser pulses with various intensities and pulse durations. The radiated energy per unit solid angle peaks at a small angle off the target normal and tapers off at larger angles. Analytical scaling of radiated energy with incident laser energy, in the low frequency limit, is obtained in the form εrad∼εlaser3/2. For accurate results, it is imperative to use the full expression for the heat capacity of electrons, in both the degenerate and ideal gas limits. Failure to do so may result in inaccuracies for the computed radiated energy, as large as one order of magnitude. A comparison of calculated and measured radiation energy in the 8–12 GHz frequency range indicates a similar trend with laser energy and comparable magnitude (∼1 fJ).
Prejunctional modulatory action of neuropeptide Y on peripheral terminals of capsaicin‐sensitive sensory nerves (1989)

1. We have determined the effect of neuropeptide Y (NPY) on motor responses produced by activation of capsaicin-sensitive primary afferents in the guinea-pig isolated left atria (reserpine-pretreatment, atropine in the bath) and bronchi (atropine and indomethacin in the bath) using capsaicin itself and electrical field stimulation as stimuli. 2. In both preparations, NPY inhibited or suppressed the response produced by electrical field stimulation while leaving the response to a submaximal concentration of capsaicin unaffected. 3. NPY had no effect on motor responses produced by a submaximal concentration of calcitonin gene-related peptide (atria) or neurokinin A (bronchi), the putative endogenous mediators of the responses produced by activation of the 'efferent' function of sensory fibres in these preparations. 4. We conclude that NPY exerts a prejunctional inhibitory action on transmitter release from peripheral endings of capsaicin-sensitive nerves. Failure of NPY to modulate responses activated by capsaicin provides further evidence for the existence of two independent modes of activation of the 'efferent' function of capsaicin-sensitive sensory nerves.
Mass densification and defect restoration in chemical vapor deposition silicon dioxide film using Ar plasma excited by microwave (2014)

Silicon dioxide (SiO2) films formed by chemical vapor deposition (CVD) have been treated with Ar plasma excited by microwave. The changes of the mass densities, carrier trap densities, and thicknesses of the CVD-SiO2 films with the Ar plasma treatments were investigated. The mass density depth profiles were estimated with X-Ray Reflectivity (XRR) analysis using synchrotron radiation. The densities of carrier trap centers due to defects of Si-O bond network were estimated with X-ray Photoelectron Spectroscopy (XPS) time-dependent measurement. The changes of the thicknesses due to the oxidation of Si substrates were estimated with the XRR and XPS. The mass densities of the CVD-SiO2 films are increased by the Ar plasma treatments. The carrier trap densities of the films are decreased by the treatments. The thicknesses of the films are not changed by the treatments. It has been clarified that the mass densification and defect restoration in the CVD-SiO2 films are caused by the Ar plasma treatments without the oxidation of the Si substrates.
Design and synthesis of a peptide derived from positions 195-244 of human cdc25C phosphatase (1999)

We have designed, synthesized and purified a 51 amino acid peptide derived from an essential domain of human cdc25C phosphatase. In vivo, differential phosphorylation of this domain regulates either the induction of mitotic processes, or the checkpoint arrest of eukaryotic cells in response to DNA damage. Peptide synthesis was achieved using the stepwise Fmoc strategy and resulted in an important yield of highly pure peptide. The final peptide was identified by amino acid analysis, electrospray mass spectrometry and nuclear magnetic resonance, which revealed that one of the two methionines within the peptide was oxidized into its sulphoxide derivative We investigated whether this 51 amino acid peptide folded into secondary structures in solution by circular dichroism and observed the formation of alpha helices in TFE. Finally, we verified that this peptide could bind to its biologically relevant 14-3-3 partner in vitro by fluorescence spectroscopy.
Vadose Zone Transport Field Study: 3D Casing Tomography And High Resolution Resistivity (2002)

Using a cluster of 18-meter-long steel casings as electrodes we have dynamically&lt;br&gt;imaged, in three-dimensions, controlled injection events for both Columbia River water&lt;br&gt;and sodium thiosulfate solutions.&lt;br&gt;These results were part of the Vadose Zone Transport Field Study (VZTFS)&lt;br&gt;performed at the Hanford Nuclear Reservation located in Richland, Washington under the&lt;br&gt;direction of Pacific Northwest National Laboratory during the past two years. Several&lt;br&gt;geophysical methods were evaluated during the VZTFS. Our responsibility included high&lt;br&gt;resolution resistivity (HRR) and steel casing resistivity tomography (SCRT).&lt;br&gt;Thirty-two, six-inch, steel casings arranged in a radial pattern allowed electrical&lt;br&gt;resistivity measurements to be made using five different casing arrays including a single,&lt;br&gt;“buried” electrode in the non-conducting injection well. Additional non-invasive&lt;br&gt;electrical measurements were made using a 100-electrode surface array. All results are&lt;br&gt;compared to neutron density data obtained in the same 32 casings.