gebhart/patrepeval huggingface dataset:
Hardware/software organization of a high-performance ATM host interface (1993)

A successful hardware/software architecture that resolves performance bottlenecks at the workstation-to-network host interface and offers high end-to-end performance is described. The solution reported carefully splits protocol processing functions into hardware and software implementations. The interface hardware is highly parallel and performs all per-cell functions with dedicated logic to maximize performance. Software provides support for the transfer of data between the interface and application memory, as well as the state management necessary for virtual circuit setup and maintenance. In addition, all higher-level protocol processing is implemented with host software. The prototype connects a RISC System/6000 to a SONET-based asynchronous transfer model (ATM) network carrying data at the OC-3c rate of 155 Mb/s. An experimental evaluation of the interface hardware and software has been performed. Several conclusions are drawn about this host interface architecture and the workstations to which it is connected.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The radial bulk annular resonator: towards a 50Ω RF MEMS filter (2004)

This paper presents a new electrostatic RF MEMS resonator design: the radial bulk annular resonator (RBAR). The RBAR utilizes the bulk radial resonant modes of an annulus. The theory behind the RBAR, and its predecessor the bulk longitudinal resonator (BLR), will be developed and discussed. It is found that the RBAR is capable of achieving an arbitrarily low motional resistance for any desired resonant frequency at the cost of increased average annular radius. This feature makes the RBAR attractive for minimizing insertion loss in bandpass filters.
First X-ray phase contrast images obtained with conventional X-ray source under exposure conditions compatible with real-world applications (2010)

X-ray phase contrast imaging (XPCi) is a novel technique that allows detecting small variations in structure and composition of objects that would be undetectable when employing conventional X-ray absorption imaging. We have recently proposed a modification of the technique, called coded-aperture XPCi, which allows recording phase contrast images using conventional laboratory X-ray sources. Unlike other methods based on conventional sources, the coded-aperture approach does not require any collimation or aperturing of the emitted beam to increase the source coherence, which would result in suppressing the source output thus leading to excessively long exposure times. This opens up the possibilities of using XPCi in various applications from medical imaging to security applications. Here we will present the results obtained with the laboratory coded-aperture XPCi setup that show drastic improvement in sensitivity compared to conventional absorption imaging.
Critical Role of Position 10 Residue in the Polymyxin Antimicrobial Activity (2023)

Polymyxins (polymyxin B and colistin) are lipopeptide antibiotics used as a last-line treatment for life-threatening multidrug-resistant (MDR) Gram-negative bacterial infections. Unfortunately, their clinical use has been affected by dose-limiting toxicity and increasing resistance. Structure-activity (SAR) and structure-toxicity (STR) relationships are paramount for the development of safer polymyxins, albeit very little is known about the role of the conserved position 10 threonine (Thr) residue in the polymyxin core scaffold. Here, we synthesized 30 novel analogues of polymyxin B<sub>1</sub> modified explicitly at position 10 and examined the antimicrobial activity against Gram-negative bacteria and <i>in vivo</i> toxicity and performed molecular dynamics simulations with bacterial outer membranes. For the first time, this study revealed the stereochemical requirements and role of the β-hydroxy side chain in promoting the correctly folded conformation of the polymyxin that drives outer membrane penetration and antibacterial activity. These findings provide essential information for developing safer and more efficacious new-generation polymyxin antibiotics.
Bayesian sparse‐based reconstruction in bioluminescence tomography improves localization accuracy and reduces computational time (2017)

Bioluminescence tomography (BLT) provides fundamental insight into biological processes in vivo. To fully realize its potential, it is important to develop image reconstruction algorithms that accurately visualize and quantify the bioluminescence signals taking advantage of limited boundary measurements. In this study, a new 2-step reconstruction method for BLT is developed by taking advantage of the sparse a priori information of the light emission using multispectral measurements. The first step infers a wavelength-dependent prior by using all multi-wavelength measurements. The second step reconstructs the source distribution based on this developed prior. Simulation, phantom and in vivo results were performed to assess and compare the accuracy and the computational efficiency of this algorithm with conventional sparsity-promoting BLT reconstruction algorithms, and results indicate that the position errors are reduced from a few millimeters down to submillimeter, and reconstruction time is reduced by 3 orders of magnitude in most cases, to just under a few seconds. The recovery of single objects and multiple (2 and 3) small objects is simulated, and the recovery of images of a mouse phantom and an experimental animal with an existing luminescent source in the abdomen is demonstrated. Matlab code is available at https://github.com/jinchaofeng/code/tree/master.
Soluble Copolymers of Yellow Jacket, Yellow Hornet and White Faced Hornet with Human Albumin for Venom Immunotherapy (1989)

Soluble polymers have been prepared by polymerizing human serum albumin (HSA) with either yellow jacket venom (YJV), yellow hornet venom (YHV) or white faced hornet venom (WFHV). The venom-albumin polymer preparations were fractionated on Sephacryl S-300 to have a molecular weight range higher than catalase (2.4 x 10(5) daltons). Rabbits were immunized with either yellow jacket venom-albumin polymer (YJVAP), yellow hornet venom-albumin polymer (YHVAP) or white faced hornet venom-albumin polymer (WFHVAP). Rabbits immunized with venom-albumin polymer (VAP) produced IgG antibody to VAP and venom, as measured by enzyme-linked immunosorbent assay (ELISA). Experiments to demonstrate antigenic completeness and absence of new antigenic determinants in the polymer were performed using WFHVAP. IgG against WFHVAP was completely inhibited by a mixture of WFHV and HSA demonstrating the absence of new antigenic determinants in WFHVAP. IgG against WFHV in sera from patients receiving maintenance doses of WFHV immunotherapy was completely inhibited by WFHVAP, demonstrating antigenic completeness. We have previously described similar results with bee venom-albumin polymer and wasp venom-albumin polymer. We now conclude that VAP preparations of all five clinically relevant hymenoptera venoms have potential value in the treatment of hymenoptera anaphylaxis.
Effect of Dietary Forage Concentration and Buffer Addition on Duodenal Flow of Trans-C18:1 Fatty Acids and Milk Fat Production in Dairy Cows (1997)

Milk fat depression in cows fed high grain diets has been shown to be related to increased trans-C18:1 fatty acids in milk. Trans-C18:1 fatty acids are produced as a result of incomplete biohydrogenation of dietary polyunsaturated fatty acids in the rumen. The objective of this study was to determine the effects of varying amounts of dietary concentrate and buffer addition on duodenal flow, apparent absorption, and incorporation of trans-C18:1 fatty acids into milk fat. Four ruminally and duodenally cannulated multiparous Holstein cows in midlactation were fed diets consisting of 60% (high) or 25% (low) forage with or without buffer (1.5% NaHCO3 and 0.5% MgO). Treatments were arranged in a 2 x 2 factorial within a 4 x 4 Latin square design. The diet containing low forage and no buffer increased the flow of trans-C18:1 fatty acids to the duodenum compared with the effects of other diets (120 vs. 57 to 66 g/d). Ruminal pH was lower for cows fed the low forage diets. The addition of buffer increased ruminal pH by 0.19 and 0.02 units for cows fed the low forage and high forage diets, respectively. Cows fed the diet containing low forage and no buffer produced milk with a lower fat percentage. The addition of buffer to the low forage diet partially corrected milk fat depression. Milk trans-C18:1 fatty acids were higher for cows fed the low forage diet without buffer than for cows fed the other diets (5.8% vs. 3.0%). Altered ruminal function resulting from low ruminal pH for cows fed the low forage diet and no buffer may play a role in the increased production of trans-C18:1 fatty acids in the rumen.
Potential tumor- or organ-imaging agents. 27. Polyiodinated 1,3-disubstituted and 1,2,3-trisubstituted triacylglycerols (1986)

A series of glyceryl 1,3-bis- and 1,2,3-tris[omega-(3-amino-2,4,6-triiodophenyl)alkanoates] were synthesized, radioiodinated with iodine-125, and evaluated for their ability to selectively localize in the liver for potential use as hepatographic imaging agents. Of the nine target compounds synthesized and evaluated in rats, glyceryl 1,2,3-tris[3-(3-amino-2,4,6-triiodophenyl)propionate] (5b) displayed rapid and sustained liver specificity. This agent was found to accumulate in the liver in concentrations of 60, 75, and 86% of the administered dose at 5 min, 30 min, and 24 h, respectively. Moreover, the 24-h liver-to-blood ratio of 235 justifies further studies in higher animal species.
SPIN-TUNNELING IN FERROMAGNETIC JUNCTIONS (1999)

▪ Abstract Based on the spin conservation in electron tunneling across an insulator (I) and the spin polarization of conduction electrons in ferromagnets (FM) established by Meservey and Tedrow, Jullière put forward a quantitative model (1975) showing that tunneling in FM-I-FM junctions should lead to a large junction magnetoresistance (JMR). This conjecture was realized with repeatable results only in 1995, and since then JMR values >30% have been achieved at room temperature. This phenomenon has tremendous potential for applications as nonvolatile magnetic memory elements, read heads, and picotesla field sensors. We review the experimental results and the current theoretical understanding of FM-I-FM tunneling and its dependence on bias, temperature, and barrier characteristics. The influence of inelastic tunneling processes and material properties on the JMR is extensively discussed. Early theories are reviewed and their relationship to the linear response theory is presented. Future directions, both from the point of fundamental physics as well as applications, are also covered.
Efficient Graph-Based Semi-Supervised Learning of Structured Tagging Models (2010)

We describe a new scalable algorithm for semi-supervised training of conditional random fields (CRF) and its application to partof-speech (POS) tagging. The algorithm uses a similarity graph to encourage similar n-grams to have similar POS tags. We demonstrate the efficacy of our approach on a domain adaptation task, where we assume that we have access to large amounts of unlabeled data from the target domain, but no additional labeled data. The similarity graph is used during training to smooth the state posteriors on the target domain. Standard inference can be used at test time. Our approach is able to scale to very large problems and yields significantly improved target domain accuracy. 1
Mechanism for Modulation Response Improvement in Mutually Injection-Locked Semiconductor Lasers (2011)

The modulation response (MR) improvement in mutually injection-locked semiconductor lasers is analyzed. We show that the system becomes increasingly sensitive to the modulation when its operation point approaches the lock band boundary, suggesting that the MR enhancement results from a modulation-induced transition between locked and unlocked operations of the laser system.
DARN: Dynamic Baselines for Real-time Network Monitoring (2018)

Network monitoring is necessary so as to ensure high reliability and availability in telecom networks. One of the main challenges posed by state-of-the-art monitoring tools is the creation of network baselines. Such baselines include thresholds that can be used to determine whether monitored values (with a given context, e.g. time) represent normal network operation or not. The size and complexity of current (and future) networks makes it infeasible to manually determine and set baselines for each network operator and metric, let alone adapting the thresholds to changes in network conditions. This leads to the use of default baselines and/or setting baselines only once and never changing them throughout the lifetime of network elements. This does not only cause inefficient operation, but could have implications for network reliability and availability. In this paper, we present the design, implementation, and evaluation of DARN: a collection of analytics and machine learning-based algorithms aimed at ensuring that network baselines are automatically adapted to different metric evolution. DARN has been comprehensively evaluated on a deployment with real traffic to confirm accuracy of generated baselines, a 22% improvement in accuracy due to baseline adaptation, and a 72% reduction in false alarms.
Sub-μm, planarized, Nb-AlO<i>x</i>-Nb Josephson process for 125 mm wafers developed in partnership with Si technology (1991)

We have demonstrated a new planarized all-refractory technology for low Tc superconductivity (PARTS). With the exception of the Nb-AlOx-Nb trilayer preparation, the processing is done almost exclusively within an advanced Si technology fabrication facility. This approach has allowed us to leverage highly off of existing state-of-the-art lithography, metal etching, materials deposition, and planarization capabilities. Using chemical-mechanical polish as the planarization technique we have fabricated Josephson junctions ranging in size from 0.5–100 μm2. Junction quality is excellent with the figure of merit Vm typically exceeding 70 mV. PARTS has yielded fully functional integrated Josephson devices including magnetometers, gradiometers, and soliton oscillators.
Properties of Pristine Graphene Composites Arising from the Mechanism of Graphene-Stabilized Emulsion Formation (2016)

Inexpensive, strong, and electrically conductive pristine graphene composites are synthesized from graphene-stabilized emulsions. These materials do not utilize oxidized graphite (GO) or reduced oxidized graphite (rGO), instead taking advantage of the recently demonstrated surfactant qualities of pristine graphene sheets. Using monomer as the oil phase, water-in-oil emulsions stabilized by graphene are polymerized to form porous composites with a continuous network of hollow graphene lined spheres. The effects of graphite flake size, emulsion settling, graphite concentration, and solvent ratio on composite properties such as electrical conductivity, strength, and density are investigated. We relate changes in the composite morphology to the observed property changes, and discuss the cause and effect of larger sphere sizes in the composite materials. Controlling and understanding properties such as conductivity and strength is a critical requirement for envisioned applications such as batteries, capacitors, and structural materials.
Biotin Analogues with Antibacterial Activity Are Potent Inhibitors of Biotin Protein Ligase (2012)

There is a desperate need to develop new antibiotic agents to combat the rise of drug-resistant bacteria, such as clinically important Staphylococcus aureus. The essential multifunctional enzyme, biotin protein ligase (BPL), is one potential drug target for new antibiotics. We report the synthesis and characterization of a series of biotin analogues with activity against BPLs from S. aureus, Escherichia coli, and Homo sapiens. Two potent inhibitors with K i < 100 nM were identified with antibacterial activity against a panel of clinical isolates of S. aureus (MIC 2-16 μg/mL). Compounds with high ligand efficiency and >20-fold selectivity between the isozymes were identified and characterized. The antibacterial mode of action was shown to be via inhibition of BPL. The bimolecular interactions between the BPL and the inhibitors were defined by surface plasmon resonance studies and X-ray crystallography. These findings pave the way for second-generation inhibitors and antibiotics with greater potency and selectivity.
Key handling with control vectors (1991)

A method is presented for controlling cryptographic key usage based on control vectors. Each cryptographic key has an associated control vector that defines the permitted uses of the key within the cryptographic system. At key generation, the control vector is cryptographically coupled to the key via a special encryption process. Each encrypted key and control vector is stored and distributed within the cryptographic system as a single token. Decryption of a key requires respecification of the control vector. As part of the decryption process, the cryptographic hardware also verifies that the requested use of the key is authorized by the control vector. This paper focuses mainly on the use of control vectors in cryptosystems based on the Data Encryption Algorithm.
Design and Fabrication of a Disposable Dental Handpiece for Clinical Use of a New Laser-Based Therapy-Monitoring System (2015)

Dental caries, the breakdown of tooth enamel by bacteria infection that causes cavities in the enamel, is the most common chronic disease in individuals 6–19 years of age in the U.S. Optical detection of caries has been shown to be sensitive to the presence of bacteria and the resulting demineralization of enamel. The scanning fiber endoscope (SFE) is a miniature camera system that can detect early stages of caries by performing high-quality imaging and laser fluorescence spectroscopy with 405 nm excitation. Because optical imaging of caries does not involve radiation risk, repeated imaging of the teeth is acceptable during treatment of the bacterial infection to monitor healing. A disposable handpiece was designed and fabricated to position the flexible fiber optic SFE probe for quantitative measurements. Plastic 3D-printed handpiece prototypes were tested with the SFE and a fluorescence calibration standard to verify mechanical fit and absence of signal contamination. Design feedback was provided by pediatric dentists and staff engineers to guide iterations. The final design configuration was based on the need to image interproximal regions (contact surfaces between adjacent teeth), ergonomics, and probe safety. The final handpiece design: (1) is safe for both the patient and the probe, (2) allows easy SFE insertion and removal, (3) does not interfere with spectral measurements, (4) standardizes the SFE's positioning during imaging by maintaining a consistent distance from the target surface, and (5) is significantly less expensive to produce and use than purchasing sanitary endoscope sheaths. The device will be used to help determine if new medicinal therapies can arrest caries and repair early interproximal demineralization under the clinical monitoring program. Ultimately, we anticipate that this handpiece will help us move closer toward widespread implementation of a dental diagnostic laser system that is safer and more sensitive than conventional methods for early caries detection.
Electrical Domain Compensation of Optical Dispersion (2005)

Recent advances in the electrical equalization of optical systems are presented in the context of standard methods. We report 10 Gb/s transmission over 60,000 ps/nm of optical dispersion from 3840 km of NDSF.
Localization of the Sperm Protein SP22 and Inhibition of Fertility In Vivo and In Vitro (2002)

We previously established that levels of the sperm membrane protein, SP22, are highly correlated with the fertility of sperm from the cauda epididymidis of rats exposed to both epididymal and testicular toxicants, and that a testis-specific SP22 transcript is expressed in postmeiotic germ cells. In this study, polyclonal and monoclonal antibodies were generated to study the expression of SP22 in the testis and epididymis, and to determine whether SP22 plays a coincidental or causal role in fertility. Polyclonal antiserum was raised in sheep against full-length recombinant rat SP22 (rSP22). Hybridoma clones were generated from mice immunized with rSP22 and boosted with native SP22; positive clones were used for ascites production. Immunoblots indicated that affinity-purified anti-rSP22 immunoglobulin (Ig) and ascites Ig recognized denatured and native SP22, respectively. Linear epitope mapping of the 189-amino acid SP22 sequence revealed 3 distinct peptide sequences recognized by anti-rSP22 Ig, and 1 sequence recognized by ascites Ig. Cytoplasm of round spermatids and heads of elongating/elongated spermatids immunostained with both anti-rSP22 and ascites antibodies. Isolated rete testis sperm revealed discrete staining over the cytoplasmic droplet, whereas staining was apparent over the equatorial segment of the head by the time sperm reached the caput epididymidis. Clear cells were, interestingly, immunostained along the length of the epididymis. Ascites Ig and anti-SP22 Ig each recognized the equatorial segment of sperm heads from rat, hamster, bull, rabbit, and human. Ascites Ig and affinity-purified anti-rSP22 Ig each significantly inhibited the fertility of cauda epididymal sperm from the rat in vivo, as well as the fertilization rates of cauda epididymal sperm in vitro. Moreover, affinity-purified anti-rSP22 significantly inhibited in vitro fertilization of both zona-intact and zona-free hamster oocytes, suggesting that SP22 may play a role in both the zona penetration and membrane fusion steps of fertilization.
Immunochemical localization and amino acid sequences of crossreactive epitopes within the group A streptococcal M6 protein. (1986)

mAbs 10A11, 10B6, and 10F5, raised against the native group A streptococcal M6 protein, were examined for their crossreactivity with non-laboratory passaged clinical isolates, representing 58 M serotypes, by bacterial dot blot immunoassay. mAb 10A11 crossreacted with 9, mAb 10B6 with 30, and mAb 10F5 with 30 different non-M6 serotypes. To identify the epitopes for these antibodies, the native M6 protein was cleaved with pepsin or staphylococcal V8 protease. Resultant peptides were purified by HPLC, examined for binding to crossreactive mAbs in ELISA, and reactive peptides were subjected to amino acid sequence analysis. Peptides were aligned with the amino acid sequence of the entire M6 protein predicted by the DNA sequence of the M6 gene. Competitive inhibition studies using peptides synthesized on the basis of peptide and DNA sequences, in concert with selective blocking of amino acid residues, allowed for the further identification and placement of these crossreactive epitopes within the M6 molecule. The 10A11 epitope was located within the six amino acid residues at position 134-139, which repeat at positions 159-164 and 184-189 within the variable amino terminal half of the native molecule. The conserved 10B6 and 10F5 epitopes were positioned within a 15-amino-acid span at position 275-289, with the possibility that either epitope could have been repeated at residues 239-247. Chemical modification of amino acids within this sequence aided in the differentiation of these two epitopes. Such studies should aid in the recognition of a sequence(s) common to a greater number of M serotypes, which may be useful for future vaccine development or group A streptococcal identification.
Diffraction Compensation of Masks for High Channel-Count Phase-Only Sampled Fiber Bragg Gratings (2003)

Full C-band phase-only sampled gratings are fabricated using the standard proximity side-writing technique. The mask is designed by a simple and novel method that compensates for very significant diffraction effects from the mask to the fiber core.