gebhart/patrepeval huggingface dataset:
Antibodies Elicited by Multiple Envelope Glycoprotein Immunogens in Primates Neutralize Primary Human Immunodeficiency Viruses (HIV-1) Sensitized by CD4-Mimetic Compounds (2016)

Preventing HIV-1 transmission is a high priority for global health. Eliciting antibodies that can neutralize transmitted strains of HIV-1 is difficult, creating problems for the development of an effective vaccine. We found that small-molecule CD4-mimetic compounds sensitize HIV-1 to antibodies that can be elicited in vaccinated humans and monkeys. These results suggest an approach to prevent HIV-1 sexual transmission in which a virus-sensitizing microbicide is combined with a vaccine.
Finding yourself (2004)

This work presents a robust camera pose algorithm and a working system to compute bounded-error estimates of the position and orientation of panoramic images captured within large, arbitrarily complex environments while moving the camera within a plant. A planning algorithm is used to place fiducials in an environment so as to satisfy a set of fiducial constraints, including the number of visible fiducials, the distance from the viewpoint to the fiducials, and the angle subtended by pairs of fiducials. The fiducial positions are subject to a set of constraints, which, in conjunction with an error model, enables pose estimation at any desired accuracy. Furthermore, results for several large indoor environments, consisting of multiple interconnected spaces are presented and analyzed.
Cutaneous overexpression of neurotrophin-3 (NT3) selectively restores sensory innervation in NT3 gene knockout mice (2000)

Neurotrophin-3 (NT3) is essential for development of sensory innervation to the skin. NT3 supports the postnatal survival of primary sensory neurons that mediate mechanoreception and their Merkel cell containing touch dome end organs (Airaksinen et al., 1996). In this study we determined whether NT3 overexpressed in the skin could restore innervation lost when endogenous NT3 levels were reduced. Hybrid mice that overexpress NT3 in basal keratinocytes but lack one endogenous NT3 allele (K14-NT3/NT3(+/-)) were compared to NT3 overexpresser (K14-NT3) mice, heterozygous knockout (NT3(+/-)) mice, and littermate control mice. In line with previous analyses, NT3(+/-) mice lost 63% of the Merkel cells associated with touch domes, 67% of touch dome units and the associated SAI innervation. All of these parameters were restored to overexpresser levels in K14-NT3/NT3(+/-) mice. Knockout NT3(+/-) mice also had a 31% reduction of L4/L5 dorsal root ganglion cells and a 24% reduction of myelinated axons in the saphenous cutaneous nerve. These losses were also restored in hybrid K14-NT3/NT3(+/-) mice, though only to control mouse values. These results indicate that overexpression of NT3 in skin of NT3(+/-) knockout mice rescued most cutaneous neurons lost in NT3(+/-) mice, but was unable to rescue NT3-dependent neurons that project to noncutaneous sensory targets.
Minimum Bayes Error Feature Selection for Continuous Speech Recognition (2000)

We consider the problem of designing a linear transformation \t 4 of rank , which projects the features of a classifier onto such as to achieve minimum Bayes error (or probability of misclassification). Two avenues will be explored: the first is to maximize the -average divergence between the class densities and the second is to minimize the union Bhattacharyya bound in the range of . While both approaches yield similar performance in practice, they outperform standard LDA features and show a 10% relative improvement in the word error rate over state-of-the-art cepstral features on a large vocabulary telephony speech recognition task. 1
New Non-Peptide Endothelin-A Receptor Antagonists:  Synthesis, Biological Properties, and Structure−Activity Relationships of 5-(Dimethylamino)-<i>N</i>-pyridyl-, -<i>N</i>-pyrimidinyl-, -<i>N</i>-pyridazinyl-, and -<i>N</i>-pyrazinyl-1-naphthalenesulfonamides (1997)

Use of automated synthesis led to the discovery of several 6-membered nitrogen heterocycles as replacements for the N-isoxazolyl substituent present in the 1-naphthalenesulfonamides endothelin-A (ETA) antagonist 5-(dimethylamino)-N-(3,4-dimethyl-5-isoxazolyl)-1-naphthalenesu lfo namides (BMS 182874). In each of these heterocycles, a small substituent such as halogen para to the position of attachment to the sulfonamide nitrogen atom was found to be advantageous for ETA receptor affinity. Of these heterocycles, 2-pyrazines offered the greatest scope for improving receptor affinity. Optimization of the substituents at the 3- and 5-positions in the pyrazine ring led to potent, ETA-selective compounds such as 5-(dimethylamino)-N-(5-chloro-3-methoxy-2-pyrazinyl)-1- naphthalenesulfonamides (7m, ETA pIC50 8.1). When dosed orally at 10 mg/kg to conscious, normotensive rats infused with big ET-1, compounds such as 7m showed significant inhibition of the pressor response with a duration of effect lasting for the 5-h course of the experiment.
PME-1 Modulates Protein Phosphatase 2A Activity to Promote the Malignant Phenotype of Endometrial Cancer Cells (2014)

Protein phosphatase 2A (PP2A) negatively regulates tumorigenic signaling pathways, in part, by supporting the function of tumor suppressors like p53. The PP2A methylesterase PME-1 limits the activity of PP2A by demethylating its catalytic subunit. Here, we report the finding that PME-1 overexpression correlates with increased cell proliferation and invasive phenotypes in endometrial adenocarcinoma cells, where it helps maintain activated ERK and Akt by inhibiting PP2A. We obtained evidence that PME-1 could bind and regulate protein phosphatase 4 (PP4), a tumor-promoting protein, but not the related protein phosphatase 6 (PP6). When the PP2A, PP4, or PP6 catalytic subunits were overexpressed, inhibiting PME-1 was sufficient to limit cell proliferation. In clinical specimens of endometrial adenocarcinoma, PME-1 levels were increased and we found that PME-1 overexpression was sufficient to drive tumor growth in a xenograft model of the disease. Our findings identify PME-1 as a modifier of malignant development and suggest its candidacy as a diagnostic marker and as a therapeutic target in endometrial cancer.
Pancreatic stone protein is highly increased during posttraumatic sepsis and activates neutrophil granulocytes* (2009)

We conclude that PSP/reg is up-regulated in blood after trauma, and the PSP/reg level is related to the severity of inflammation. Furthermore, PSP/reg binds to and activates neutrophils. Therefore, PSP/reg might be an acute-phase protein that could serve as a marker for posttraumatic complications.
Use of Sonochemistry in Monitoring Chlorinated Hydrocarbons in Water (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUse of Sonochemistry in Monitoring Chlorinated Hydrocarbons in WaterGrazyna E. Orzechowska, Edward J. Poziomek, Vernon F. Hodge, and William H. EngelmannCite this: Environ. Sci. Technol. 1995, 29, 5, 1373–1379Publication Date (Print):May 1, 1995Publication History Published online1 May 2002Published inissue 1 May 1995https://pubs.acs.org/doi/10.1021/es00005a033https://doi.org/10.1021/es00005a033research-articleACS PublicationsRequest reuse permissionsArticle Views128Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Immersive simulation of hearing loss and auditory prostheses (2004)

Simulation of hearing loss is useful for demonstrating the communication challenges facing hearing-impaired people. However, current simulations, most of which are only recordings, do not actually elevate thresholds; i.e., they do not simulate hearing loss, per se. The hearing loss simulator described in this talk is immersive; the user’s detection thresh- olds for ambient sounds are shifted by a prescribed degree. This threshold shift is achieved through a combination of passive attenuation (from muff-type hearing protectors) and additive masking noise (introduced by within-muff earphones). Acoustic signals picked up by microphones near each ear are processed through bandpass AGC channels and delivered via the earphones to complete the simulation of frequency-dependent hearing loss and loudness recruitment. Preliminary results validating the accuracy of specified threshold shift will be presented, along with speech-reception data comparing simulated with actual hearing losses. Subjective reactions of users engaged in one-on-one conversation suggest that strong feelings of communication disability are engendered by even moderate degrees of simulated hearing loss. The system, which is capable of simulating any degree of recruiting hearing loss along with hearing aids or cochlear implants, can provide effective interactive demonstrations of both auditory communication handicap and rehabilitation options. [Work supported by NIDCD.]
Improvements to mechanical response tissue analysis (2019)

Cortical Bone Mechanics Technology™ (CBMT) comprises certain improvements over a previous method known as Mechanical Response Tissue Analysis (MRTA). Both methods are dynamic 3-point bending tests intended for measuring the mechanical properties of cortical bone in living people. MRTA presented a theoretical potential for direct measurement of skeletal fragility, but it had acquired a reputation for error and fallen into disuse. We found sources of error in both MRTA data collection and data analysis. We describe here the fundamentals of MRTA, the major sources of error we found in MRTA, and our innovations for avoiding them. •Data collection at many sites across the mid-shaft of the ulna bone in the forearm.•Parameter estimation by fitting analytical complex compliance and stiffness transfer functions to empirical complex compliance and stiffness frequency response functions.•Optimization by selecting results from frequency response functions with the smallest deviations between fits to compliance and stiffness frequency response functions.
Unbundling Transaction Services in the Cloud (2009)

The traditional architecture for a DBMS engine has the recovery, concurrency control and access method code tightly bound together in a storage engine for records. We propose a different approach, where the storage engine is factored into two layers (each of which might have multiple heterogeneous instances). A Transactional Component (TC) works at a logical level only: it knows about transactions and their ―logical ‖ concurrency control and undo/redo recovery, but it does not know about page layout, B-trees etc. A Data Component (DC) knows about the physical storage structure. It supports a record oriented interface that provides atomic operations, but it does not know about transactions. Providing atomic record operations may itself involve DC-local concurrency control and recovery, which can be implemented using system transactions. The interaction of the mechanisms in TC and DC leads to multi-level redo (unlike the repeat history paradigm for redo in integrated engines). This refactoring of the system architecture could allow easier deployment of application-specific physical structures and may also be helpful to exploit multi-core hardware. Particularly promising is its potential to enable flexible transactions in cloud database deployments. We describe the necessary principles for unbundled recovery, and discuss implementation issues.
Histograms and Wavelets on Probabilistic Data (2008)

There is a growing realization that uncertain information is a first-class citizen in modern database management. As such, we need techniques to correctly and efficiently process uncertain data in database systems. In particular, data reduction techniques that can produce concise, accurate synopses of large probabilistic relations are crucial. Similar to their deterministic relation counterparts, such compact probabilistic data synopses can form the foundation for human understanding and interactive data exploration, probabilistic query planning and optimization, and fast approximate query processing in probabilistic database systems. In this paper, we introduce definitions and algorithms for building histogram- and wavelet-based synopses on probabilistic data. The core problem is to choose a set of histogram bucket boundaries or wavelet coefficients to optimize the accuracy of the approximate representation of a collection of probabilistic tuples under a given error metric. For a variety of different error metrics, we devise efficient algorithms that construct optimal or near optimal B-term histogram and wavelet synopses. This requires careful analysis of the structure of the probability distributions, and novel extensions of known dynamic-programming-based techniques for the deterministic domain. Our experiments show that this approach clearly outperforms simple ideas, such as building summaries for samples drawn from the data distribution, while taking equal or less time.
Investigation of an albumin‐enriched fraction of human serum and its albuminome (2007)

The removal of albumin and other high abundance proteins is a routine first step in the analysis of serum and plasma proteomes. However, as albumin can bind proteins and peptides, there is a universal concern as to how the serum proteome is changed by the removal of albumin. To address this concern, the current study was designed to identify proteins and peptides removed from the serum during albumin depletion; to determine which of these are bound to albumin (rather than copurified) and whether the bound proteins are intact proteins or peptide fragments. Sequential, independent analyses including both anti-albumin antibody (anti-HSA) affinity chromatography and SEC were used to isolate albumin-bound proteins. RP-HPLC and 1-D SDS-PAGE were then used to further separate the proteins prior to identification by MS/MS. Finally, whole protein molecular weight (MW) MS measurements coupled with protein coverage obtained by MS were combined to assess whether the bound proteins were intact or peptide fragments. Combining the results from multiple approaches, 35 proteins, of which 24 are intact, were found to be associated with albumin, and they include both known high and low abundance proteins.
Solution Assembly of a Soluble, Heteromeric, High Affinity Interleukin-2 Receptor Complex (1995)

In this study, we report the use of coiled-coil (leucine zipper) molecular recognition for the solution assembly of stable, high affinity, heteromeric interleukin-2 receptor complexes. Co-expression of interleukin-2 receptor alpha and beta extracellular domains (ectodomains), each fused to seven coiled-coil heptad repeats, resulted in the formation of heteromeric complexes that bound interleukin-2 in a cooperative fashion and with much higher affinity than similar homomeric complexes. The dissociation constants for these solution complexes are within the range of values reported for the comparable cell surface "pseudo high affinity" interleukin-2 receptor. Ligand-induced cross-linking of homomeric or heteromeric receptor subunits is the common signal transmission mechanism employed by hematopoietin receptors. Individual receptor ectodomains, however, often do not bind ligand with measurable affinity. This is the first study to demonstrate the feasibility of coiled-coil mediated preassembly of cytokine receptor complexes.
Quantitative Ultrasound and Texture Predictors of Breast Tumour Response to Chemotherapy (2018)

Previous studies have demonstrated that quantitative ultrasound (QUS)is an effective tool for monitoring breast cancer patients undergoing neo-adjuvant chemotherapy (NAC). Here, we demonstrate the clinical utility of pre-treatment and early stage treatment QUS texture features in predicting the response of breast cancer patients to NAC. Radiofrequency (RF)ultrasound data were acquired from 100 locally advanced breast cancer (LABC)patients prior to treatment, and during the first, fourth and eighth week of treatment. QUS Spectral and backscatter parameters were computed from regions of interest (ROI)in the tumour core and its margin. Subsequently, employing gray-level co-occurrence matrices (GLCM), four textural features and image quality features including core-to-margin ratio (CMR)and core-to-margin contrast ratio (CMCR)were extracted from the parametric images as potential predictive indicators. QUS results were compared with the clinical and pathological response of each patient determined at the end of their NAC. Results from the 100 patients indicate that a combined QUS and texture feature model demonstrated a favourable clinical and pathological based response prediction with area under the receiver operating characteristics curves (AUC)of 82%, 80%, 87%, and 92 % prior to treatment, during treatment at week 1, 4, and 8, respectively. Best results were obtained using a radial-basis-function support vector machine (RBF -SVM)machine learning algorithm. Only four features were selected in each binary response group classification. The findings of this study suggest that QUS features of a breast tumour are strongly linked to tumour responsiveness. The ability to identify patients that would not benefit from NAC would facilitate salvage therapy and clinical management that has minimum toxicity and maximum outcome in terms of patient survival.
New differentiation antigens associated with the growth and maturation of B lymphocytes. (1988)

Monoclonal antibodies (mAb) NDA3 and NDA4 were generated by hyperimmunizing mice with an alloreactive human T cell clone and fusing the splenocytes with the NS1 myeloma. Immunofluorescence studies indicated that these mAb react with activated, but not with resting T and B lymphocytes or with other types of cells. Immunoprecipitation studies with 125-I-labeled extracts from T and B cell lines demonstrated that the m.w. of the antigen recognized by mAb NDA3 is 36,000 and that of NDA4 is 46,000. Studies on the effect of mAb NDA3 and NDA4 on Epstein Barr Virus-transformed lymphoblastoid B cell lines (LBCL) demonstrated that these antibodies stimulate B cell proliferation and Ig synthesis. The level of expression of NDA3 and NDA4 on the membrane of LBCL is significantly augmented when cells are grown in the presence of recombinant human interferon-beta and gamma and is decreased in the presence of 12-O-tetradecanoyl-phorbol-13-acetate. These observations, in conjunction with the stimulatory effect of mAb NDA3 and NDA4 on the growth and differentiation of LBCL, suggest that these new differentiation antigens, NDA3 and NDA4, may serve as growth factor receptors.
Deleterious mechanical vibrations from dynamic loudspeaker offset by additional dynamic device (1980)

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Safe and Efficient Implementation of a Security System on ARM using Intra-level Privilege Separation (2019)

Security monitoring has long been considered as a fundamental mechanism to mitigate the damage of a security attack. Recently, intra-level security systems have been proposed that can efficiently and securely monitor system software without any involvement of more privileged entity. Unfortunately, there exists no full intra-level security system that can universally operate at any privilege level on ARM. However, as malware and attacks increase against virtually every level of privileged software including an OS, a hypervisor, and even the highest privileged software armored by TrustZone, we have been motivated to develop an intra-level security system, named Hilps . Hilps realizes true intra-level scheme in all these levels of privileged software on ARM by elaborately exploiting a new hardware feature of ARM’s latest 64-bit architecture, called TxSZ, that enables elastic adjustment of the accessible virtual address range. Furthermore, Hilps newly supports the sandbox mechanism that provides security tools with individually isolated execution environments, thereby minimizing security threats from untrusted security tools. We have implemented a prototype of Hilps on a real machine. The experimental results demonstrate that Hilps is quite promising for practical use in real deployments.
Identifying RF-DNA instances via phase differences (2009)

We developed a simple experimental testbed to collect statistical properties of the proposed RF-DNA system. It consisted of a manufactured prototype of the 5 x 10 patch antenna matrix proposed and eight benchmark RF-DNA instances manufactured using gauge-22 copper wire and DragonSkin as a plastic substrate that fixed the randomized topology of the wire once for all. The instances are illustrated. Their cost is low; each instance that we manufactured in the lab cost us less than a cent.
Analysis of a dual-twist Pancharatnam phase device with ultrahigh-efficiency large-angle optical beam steering (2015)

It has been previously shown that a Pancharatnam phase device with a dual-twist structure can deflect light up to 60° with nearly perfect efficiency. This was beyond the limits previously assumed for these types of devices, which were considered to be optically similar to Raman-Nath gratings. In this paper we first consider the range of parameters that will allow for high efficiency and show the results for a structure that demonstrates 80° deflection. We then explore the light propagation through these devices to point out interesting intensity variations in the deflected mode of light as it traverses the deflecting layer. Finally, we explain the key to understanding the efficiency of these devices, which is not the typical parameters that are important for traditional diffractive devices, but rather the control of the polarization state of light. We provide a simple design approach for optimizing the twist angle and retardation for high efficiency.
Effective Treatment of Osteomyelitis with Biodegradable Microspheres in a Rabbit Model (2004)

Biodegradable microspheres were manufactured from a high molecular weight copolymer of 50% lactic and 50% glycolic acid and the antibiotic tobramycin. It was hypothesized that the microspheres would be more effective than polymethylmethacrylate beads in the local delivery of tobramycin and that the microspheres would not inhibit bone healing. Osteomyelitis was established in 40 New Zealand White rabbits using Staphylococcus aureus. All animals had irrigation and debridement of the infected radii four weeks after inoculation and were divided into five treatment groups: debridement alone, microspheres alone, microspheres containing tobramycin plus parenteral treatment with cefazolin, polymethylmethacrylate beads containing tobramycin plus parenteral cefazolin, and parenteral cefazolin. All animals were sacrificed after 4 weeks of treatment. The group treated with microspheres plus parenteral antibiotics was the only group to have a significantly higher percentage of animals without bacteria after 4 weeks of treatment when compared with the control group. Additionally, the animals treated with microspheres had a higher degree of bone healing in the defect than the animals treated with bone cement. The most effective treatment was biodegradable microspheres combined with parenteral antibiotic in this rabbit osteomyelitis model.