gebhart/patrepeval huggingface dataset:
Isolation of Cross-Clade HIV-Neutralizing Human Antibodies from Memory B Cell Repertoires Using Short Term Culture and High-Throughput Primary Neutralization Screens (38.17) (2010)

Abstract Background. We have recently isolated 2 broadly neutralizing monoclonal antibodies (bNAbs), PG9 and PG16, from an HIV-infected subject in an African Protocol G cohort that are more potent than the bNAbs discovered in the past decade. The discovery highlights our human antibody (Ab) discovery approach based on short-term memory B cell culture, high-throughput primary microneutralization screening, and recombinant monoclonal antibody (mAb) reconstitution (Walker LM, et al, 2009, Science, 326:285-9). The epitope specificities of PG9 and PG16 reveal a novel target for designing vaccine immunogens that may elicit broad anti-HIV protection. To identify additional epitopes for vaccine design, we extended the bNAb discovery to more HIV-infected subjects. Method. We selected several HIV-infected subjects with broad neutralization activity in serum. Memory B cells from these elite neutralizers were activated and the IgG-containing culture media were screened for neutralizing activity against multiple pseudotyped viruses. mAbs were rescued from selected B cell culture wells by RT-PCR and subcloning. Results. From an HIV-infected elite neutralizer, we have identified in the primary screen multiple human Abs that cross-neutralize MGRM-C-26 of clade C, and 93BR020 and JR-CSF of clade B. Antibodies that neutralize either MGRM-C-26 alone or 94UG103 of clade A alone were also detected. Recombinant mAbs are currently being rescued for further characterization. (Supported by IAVI and USAID)
ESTIMATION OF DETECTION LIMITS OF THE PHAGE-INVASION BASED IDENTIFICATION OF BACTERIA (2005)

Recently a new method, SEnsing of Phage-Triggered Ion Cascade (SEPTIC) was proposed for the rapid detection and identification of bacteria via the electrical field caused by the stochastic emission of ions during phage infection. In this Letter, we present linear network theoretical considerations about the detection limits of the method. The considerations are based on our published data of the E. coli detection experiments and on the assumption of a linear response between the number of bacteria and the measured power density spectrum of the fluctuation-signal. Some practical limits of the detectability of the present agents with possible noise measurement arrangements are discussed in this paper. The calculations indicate that the detection and identification of a single bacterium can be achieved with natural (wild) phages with reasonable efforts within a time window of 10 minutes.
Glucose-6-phosphate dehydrogenase: a novel therapeutic target in cardiovascular diseases. (2008)

Vascular dysfunction associated with diabetes, heart failure and pulmonary hypertension is the major cause of morbidity and mortality worldwide. Although the causes of vascular dysfunction remain unclear, altered glucose metabolism appears to be a common factor in these diseases. For example, in diabetes, increased glucose-6-phosphate dehydrogenase (G6PD) activity and elevated NADPH levels are associated with endothelial and vascular dysfunction. Also, there is a 10-fold increase in myocardial G6PD expression and a 2-fold increase in G6PD activity in pacing-induced heart failure compared with normal hearts. In addition, the inhibition of G6PD ameliorates chronic hypoxic pulmonary hypertension. Lastly, G6PD plays a role in mediating angiotensin II-induced hypertrophy of smooth muscle and in the development of atherosclerosis. While it is understood that G6PD-derived NADPH, which is a cofactor for NADPH oxidase, enhances superoxide anion generation and elevates oxidative stress in diabetes, heart failure, and angiotensin II-induced hypertrophy of smooth muscle, there are no specific drugs available to study the role of G6PD and G6PD-derived NADPH in organ function and the development of human diseases. This warrants the development of new drugs or genetic approaches to target G6PD for investigational and clinical use. This review discusses the specificity and side effects of existing investigational G6PD inhibitors.
Biocompatible silk step-index optical waveguides (2015)

Biocompatible optical waveguides were constructed entirely of silk fibroin. A silk film (n=1.54) was encapsulated within a silk hydrogel (n=1.34) to form a robust and biocompatible waveguide. Such waveguides were made using only biologically and environmentally friendly materials without the use of harsh solvents. Light was coupled into the silk waveguides by direct incorporation of a glass optical fiber. These waveguides are extremely flexible, and strong enough to survive handling and manipulation. Cutback measurements showed propagation losses of approximately 2 dB/cm. The silk waveguides were found to be capable of guiding light through biological tissue.
Kinetics of Aqueous-Phase Hydrogenation of Lactic Acid to Propylene Glycol (2002)

The kinetics of aqueous-phase hydrogenation of lactic acid to propylene glycol over a 5 wt % Ru/carbon catalyst have been characterized in a stirred batch reactor. A thorough analysis of mass-transfer resistances based on measurements of hydrogen solubility and gas−liquid mass-transfer coefficients, application of correlations in the literature, and intraparticle diffusion calculations show that mass-transfer resistances are negligible at the temperatures (403−423 K) and hydrogen pressures (6.8−13.6 MPa) studied. A Langmuir−Hinshelwood (L−H) model is proposed and used to fit lactic acid conversion kinetics. The kinetic model provides insight into the catalytic reaction mechanism and forms the basis for design and further investigation of the aqueous-phase hydrogenation.
Sinusoidal phase modulating absolute distance measurement interferometer combining frequency-sweeping and multi-wavelength interferometry (2018)

A sinusoidal phase modulating absolute distance measurement (ADM) interferometer combining frequency-sweeping interferometry (FSI) and multi-wavelength interferometry (MWI) is proposed in this paper. The swept frequency in FSI and the wavelengths for MWI are calibrated by an optical frequency comb, so the distance measurement can be directly traced back to the SI definition of a meter. With a simple optical structure, an ADM interferometer consisting of a measurement interferometer and a monitor interferometer is constructed without polarization optics. A near-infrared external cavity diode laser (ECDL) calibrated by an optical frequency comb is used as a work source of the measurement interferometer for frequency sweeping and hopping. The monitor interferometer using a He-Ne laser runs parallel to the measurement interferometer to monitor the fluctuation of the measured distance during the measurement. Experiments for absolute distance measurements in a range of 8.25 m were carried out to verify the feasibility of the proposed ADM interferometer. The experimental results show that the maximum measurement error is less than 1 μm compared with an incremental-type laser interferometer.
Scarcity of <i>ars</i> sequences isolated in a morphogenesis mutant of the yeast <i>Yarrowia lipolytica</i> (1991)

Previous attempts is isolate autonomously replicating sequences (ars) from the dimorphic yeast Yarrowia lipolytica have been unsuccessful. We isolated a Fil- mutant unable to produce hyphae and growing only in a yeast form to facilitate ars isolation. This mutant was transformed with a Y. lipolytica DNA bank and several unstable clones were obtained. Extrachromosomal plasmids were evidenced in yeast, recovered in Escherichia coli and characterized by restriction mapping. They were able to retransform Fil- and Fil+ yeast strains at high frequency and transformants displayed a slightly unstable phenotype. The detailed analysis of the plasmids showed that only two different ars sequences had been isolated, each of them corresponding to a unique sequence in the Y. lipolytica genome. We concluded that functional ars sequences that can be cloned on plasmids are rare in this yeast.
A Fast Low-Energy Acquisition Technology For GPS Receivers (1999)

We have developed a high-speed, low-power, parallel-correlation
technique that dramatically reduces GPS
signal-acquisition time and energy. For example, a brute-force
search over 2046 code-offset positions for 24
satellite codes in 13 frequency bins consumes only
0.065 Joules and takes only 0.68 seconds. This is very
important for battery-powered applications and for rapid
direct acquisition of the military P(Y) GPS signals in a
jamming environment. The dramatic time reduction is
achieved by storing a short acquisition-signal segment in
a digital memory and then rapidly searching this stored
segment for all desired GPS signals. Ultra-low energy
consumption is achieved by reducing the receiver “on”
time, and by using a novel and extremely efficient
parallel-correlator architecture. In the following sections,
we describe the new correlator technique, the architecture
of the fabricated prototype IC, and conclude with
preliminary IC-testing results.
Silk fibroin and polyethylene glycol‐based biocompatible tissue adhesives (2011)

Tissue sealants have emerged in recent years as strong candidates for hemostasis. A variety of formulations are currently commercially available and though they satisfy many of the markets' needs there are still key aspects of each that need improvement. Here we present a new class of blends, based on silk fibroin and chemically active polyethylene glycols (PEGs) with strong adhesive properties. These materials are cytocompatible, crosslink within seconds via chemical reaction between thiols and maleimides present on the constituent PEGs and have the potential to further stabilize through β-sheet formation by silk. Based on the silk concentration in the final formulation, the adhesive properties of these materials are comparable or better than the current leading PEG-based sealant. In addition, the silk-PEG based materials show decreased swelling and longer degradation times. Such properties would make them suitable for applications for which the current sealants are contraindicated.
The identification and characterization of human Sister-of-Mammalian Grainyhead (SOM) expands the grainyhead-like family of developmental transcription factors (2003)

The Drosophila gene grainyhead is the founding member of a large family of genes encoding developmental transcription factors that are highly conserved from fly to human. The family consists of two main branches, with grainyhead as the ancestral gene for one branch and the recently cloned Drosophila CP2 as the ancestral gene for the other. We now extend this family with the identification of another novel mammalian member, Sister-of-Mammalian Grainyhead (SOM), which is phylogenetically aligned with grainyhead. SOM is closely related to the other mammalian homologues of grainyhead, including Mammalian Grainyhead (MGR) and Brother-of-MGR, sharing a high degree of sequence identity with these factors in the functional DNA-binding, protein dimerization and activation domains. Protein interaction studies demonstrate that SOM can heterodimerize with MGR and Brother-of-MGR, but not with the more distant members of the family. Like grainyhead, the SOM gene too produces several distinct isoforms with differing functional properties through alternative splicing. The tissue distributions of these isoforms differ and all display highly restricted expression patterns. These findings indicate that SOM, like its family members, may play important roles in mammalian development.
Synthesis of a heulandite-type zeolite by hydrothermal conversion of zeolite P1 (1996)

A synthetic analogue of the zeolite heulandite is synthesized by hydrothermal treatment of zeolite P1 with solutions containing CaCl_2 and NaOH.
D32 Improvement of In-process Measurement of Surface Roughness Using Thermoelectric Effect in Grinding (2008)

The purpose of this study is the development of in-process measurement technique of surface roughness in grinding using the thermoelectric effect. In the proposed measurement, the electromotive force generates depending on the surface roughness of workpiece when the sensor with separate thermocouple wires rubs on the workpiece surface. In this report, the sensor was improved by adjustment of measurement point and attaching the elastic support pad. As a result, the in-process measurement of surface roughness can be carried out quantitatively with high stability.
Cell adhesion on poly(propylene fumarate‐<i>co</i>‐ethylene glycol) hydrogels (2002)

We synthesized poly(propylene fumarate-co-ethylene glycol) block copolymers [P(PF-co-EG)] that were crosslinked to form hydrogels and investigated the effect of copolymer composition on cell adhesion to the hydrogels. These copolymers were water soluble when the molar ratio of ethylene glycol repeating unit to propylene fumarate repeating unit was higher than 4.4. The water content of swollen hydrogels increased from 29 to 63% and the water contact angle decreased from 38 to 21 degrees as the molar ratio increased from 0.6 to 4.4. No significant change in either property was observed for ratios higher than 4.4. In a cell adhesion assay under serum-free conditions, the number of adherent platelets and smooth muscle cells decreased from 21 to 2% and from 78 to 20% of the initial seeding density, respectively, as the molar ratio increased from 0.6 to 7.8. Adherent smooth muscle cells did not spread on the hydrogels of the compositions tested. Adherent platelets did not show any filopodia. These results suggest that the hydrophilicity of P(PF-co-EG) hydrogels is one of the factors affecting cell adhesion, and that copolymer modification may be required for enhancing cell adhesion for an application involving the copolymers as in situ crosslinkable cell carriers.
Switched capacitor system for automatic series battery equalization (2002)

A clocked switched-capacitor circuit can exchange charge between adjacent batteries in a series string. This exchange drives all batteries to identical voltages, without regard to component values, battery technology, or state of charge. This equalization process can proceed while the batteries are in use or under charge, or separately. Transformer-based and transformerless implementations are given, and results of experimental tests are provided. The process is much faster and less stressful than the conventional approach, and is simpler than some active approaches.
A Popularity-Based Approach for Effective Cloud Offload in Fog Deployments (2018)

Recent research has put forward the concept of Fog computing, a deported intelligence for IoT networks. Fog clusters are meant to complement current cloud deployments, providing compute and storage resources directly in the access network - which is particularly useful for low-latency applications. However, Fog deployments are expected to be less elastic than cloud platforms, since elasticity in Cloud platforms comes from the scale of the data-centers. Thus, a Fog node dimensioned for the average traffic load of a given application will be unable to handle sudden bursts of traffic. In this paper, we explore such a use-case, where a Fog-based latency-sensitive application must offload some of its processing to the Cloud. We build an analytical queueing model for deriving the statistical response time of a Fog deployment under different request Load Balancing (LB) strategies, contrasting a naive, an ideal (LFU-LB, assuming a priori knowledge of the request popularity) and a practical (LRU-LB, based on online learning of the popularity with an LRU filter) scheme. Using our model, and confirming the results through simulation, we show that the LRU-LB achieves close-to-ideal performance, with high savings on Cloud offload cost with respect to a request-oblivious strategy in the explored scenarios.
Dynamic Tree Bitmap for IP Lookup and Update (2007)

We propose a data structure-dynamic tree bitmap-for the representation of dynamic IP router tables that must support very high lookup and update rates. In fact, the dynamic tree bitmap is able to support updates at the same rate as lookups and is very competitive with other structures-tree bitmap and BaRT-proposed earlier for dynamic tables. Although the dynamic tree bitmap requires more memory than is required by the tree bitmap and BaRT structures, the required memory remains reasonable. The real value of our structure is its ability to support a very high update rate.
Generation, characterization and preclinical studies of a human anti-L1CAM monoclonal antibody that cross-reacts with rodent L1CAM (2016)

L1 cell adhesion molecule (L1CAM) is aberrantly expressed in malignant tumors and plays important roles in tumor progression. Thus, L1CAM could serve as a therapeutic target and anti-L1CAM antibodies may have potential as anticancer agents. However, L1CAM is expressed in neural cells and the druggability of anti-L1AM antibody must be validated at the earliest stages of preclinical study. Here, we generated a human monoclonal antibody that is cross-reactive with mouse L1CAM and evaluated its pharmacokinetic properties and anti-tumor efficacy in rodent models. First, we selected an antibody (Ab4) that binds human and mouse L1CAM from the human naïve Fab library using phage display, then increased its affinity 45-fold through mutation of 3 residues in the complementarity-determining regions (CDRs) to generate Ab4M. Next, the affinity of Ab4M was increased 1.8-fold by yeast display of single-chain variable fragment containing randomly mutated light chain CDR3 to generate Ab417. The affinities (KD) of Ab417 for human and mouse L1CAM were 0.24 nM and 79.16 pM, respectively. Ab417 specifically bound the Ig5 domain of L1CAM and did not exhibit off-target activity, but bound to the peripheral nerves embedded in normal human tissues as expected in immunohistochemical analysis. In a pharmacokinetics study, the mean half-life of Ab417 was 114.49 h when a single dose (10 mg/kg) was intravenously injected into SD rats. Ab417 significantly inhibited tumor growth in a human cholangiocarcinoma xenograft nude mouse model and did not induce any adverse effect in in vivo studies. Thus, Ab417 may have potential as an anticancer agent.
Progressive inter-scale and intra-scale non-blind image deconvolution (2008)

Ringing is the most disturbing artifact in the image deconvolution. In this paper, we present a progressive inter-scale and intra-scale non-blind image deconvolution approach that significantly reduces ringing. Our approach is built on a novel edge-preserving deconvolution algorithm called bilateral Richardson-Lucy (BRL) which uses a large spatial support to handle large blur. We progressively recover the image from a coarse scale to a fine scale (inter-scale), and progressively restore image details within every scale (intra-scale). To perform the inter-scale deconvolution, we propose a joint bilateral Richardson-Lucy (JBRL) algorithm so that the recovered image in one scale can guide the deconvolution in the next scale. In each scale, we propose an iterative residual deconvolution to progressively recover image details. The experimental results show that our progressive deconvolution can produce images with very little ringing for large blur kernels.
Response to atrial arrhythmias in an atrioventricular synchronous ventricular leadless pacemaker: A case report in a paroxysmal atrial fibrillation patient (2018)

The recent introduction of leadless pacing technologies in real-world practice has been successful, demonstrating a high procedural success rate (99.6%) with a low rate of major complications (1.51%) through 30 days postimplant, and reaffirming the positive results observed in the investigational trial.1,2 Existing leadless pacing systems, however, are designed as single-chamber pacemakers, limiting their potential use to 14%–32% of all pacemaker implantations.3,4 Among patients with complete atrioventricular (AV) block and preserved sinus node function, maintenance of AV synchrony has been shown to improve stroke volume and quality of life and to decrease the risk of development of pacemaker syndrome.
Synergistic Inhibition of Human α-1,3-Fucosyltransferase V (1996)

Human α-1,3-fucosyltransferase V (FucT V), which catalyzes the transfer of l-fucose moiety from guanosine diphosphate β-l-fucose (GDP-Fuc) to an acceptor sugar to form sialyl Lewis x (sLex), was shown to proceed through an ordered, sequential mechanism by product inhibition studies. The designed azatrisaccharide propyl 2-acetamido-2-deoxy-4-O-(β-d-galactopyranosyl)-3-O-(2-(N-(β-l-homofuconojirimycinyl))ethyl)-α-d-glucopyranoside (2), prepared by covalently linking the N-group of β-l-homofuconojirimycin (1) to the 3-OH of LacNAc through an ethylene unit, in the presence of GDP was found to be an effective inhibitor of FucT V. In the presence of 30 μM GDP, the concentration of 2 necessary to cause 50% inhibition was reduced 77-fold to 31 μM. Presumably, the azatrisaccharide and GDP form a complex which mimics the transition state of the enzymatic reaction. Given the low affinity of FucT V for its substrate LacNAc (Km = 35 mM), the designed azatrisaccharide in the presence of GDP represents the most potent synergistic inhibitor complex reported so far.
Coherent rake reception using noisy channel estimates (2005)

With traditional Rake reception, channel estimates are used to combine despread values. In this paper, a maximum-likelihood approach is used to reformulate the Rake combining weights, accounting for the channel estimation error. Specifically, Ling's formulation is extended to include fading, noise, and channel estimation error correlation between fingers. The resulting combining weights are similar to the generalized Rake receiver, except that the known channel response is replaced by a minimum mean-square error (MMSE) estimate, and the noise covariance matrix is augmented by a term related to channel estimation. The performance of this and other combining approaches are compared, showing how performance depends on the available energy for channel estimation and the Rake finger placement strategy.
Elucidation of a protein signature discriminating six common types of adenocarcinoma (2006)

Pathologists are commonly facing the problem of attempting to identify the site of origin of a metastatic cancer when no primary tumor has been identified, yet few markers have been identified to date. Multitumor classifiers based on microarray based RNA expression have recently been described. Here we describe the first approximation of a tumor classifier based entirely on protein expression quantified by two-dimensional gel electrophoresis (2DE). The 2DE was used to analyze the proteomic expression pattern of 77 similarly appearing (using histomorphology) adenocarcinomas encompassing 6 types or sites of origin: ovary, colon, kidney, breast, lung and stomach. Discriminating sets of proteins were identified and used to train an artificial neural network (ANN). A leave-one-out cross validation (LOOCV) method was used to test the ability of the constructed network to predict the single held out sample from each iteration with a maximum predictive accuracy of 87% and an average predictive accuracy of 82% over the range of proteins chosen for its construction. These findings demonstrate the use of proteomics to construct a highly accurate ANN-based classifier for the detection of an individual tumor type, as well as distinguishing between 6 common tumor types in an unknown primary diagnosis setting.