gebhart/patrepeval huggingface dataset:
Fructosamine 3-kinase-related protein and deglycation in human erythrocytes (2004)

Fructosamine 3-kinase (FN3K), an enzyme initially identified in erythrocytes, catalyses the phosphorylation of fructosamines on their third carbon, leading to their destabilization and their removal from protein. We show that human erythrocytes also contain FN3K-related protein (FN3K-RP), an enzyme that phosphorylates psicosamines and ribulosamines, but not fructosamines, on the third carbon of their sugar moiety. Protein-bound psicosamine 3-phosphates and ribulosamine 3-phosphates are unstable, decomposing at pH 7.1 and 37 degrees C with half-lives of 8.8 h and 25 min respectively, as compared with 7 h for fructosamine 3-phosphates. NMR analysis indicated that 1-deoxy-1-morpholinopsicose (DMP, a substrate for FN3K and FN3K-RP), like 1-deoxy-1-morpholinofructose (DMF, a substrate of FN3K), penetrated erythrocytes and was converted into the corresponding 3-phospho-derivative. Incubation of erythrocytes with 50 mM allose, 200 mM glucose or 10 mM ribose for 24 h resulted in the accumulation of glycated haemoglobin, and this accumulation was approx. 1.9-2.6-fold higher if DMP, a competitive inhibitor of both FN3K and FN3K-RP, was present in the incubation medium. Incubation with 50 mM allose or 200 mM glucose also caused the accumulation of ketoamine 3-phosphates, which was inhibited by DMP. By contrast, DMF, a specific inhibitor of FN3K, only affected the glucose-dependent accumulation of glycated haemoglobin and ketoamine 3-phosphates. These data indicate that FN3K-RP can phosphorylate intracellular, protein-bound psicosamines and ribulosamines, thus leading to deglycation.
Low noise characteristics of a GaAs-AlGaAs multiple-quantum-well semiconductor laser amplifier (1990)

Low noise characteristics are experimentally demonstrated in a multiple-quantum-well laser amplifier. The measured noise figure of a GaAs-AlGaAs traveling-wave laser amplifier at a 20 dB signal gain was found to be 4.6 dB. This is the smallest value reported for semiconductor laser amplifiers. A signal gain of 20 dB was obtained at a low bias current of 23.5 mA.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modulation of the M2 Muscarinic Acetylcholine Receptor Activity with Monoclonal Anti-M2 Receptor Antibody Fragments (2004)

Antibodies directed against the second extracellular loop of G protein-coupled receptors are known to have functional activities. From a partial agonist monoclonal antibody directed against the M2 muscarinic receptor, we constructed and produced a single chain variable fragment with high affinity for its target epitope. The fragment is able to recognize its receptor on Chinese hamster ovary cells transfected with the M2 muscarinic acetylcholine receptor to block the effect of carbachol on this receptor and to exert an inverse agonist activity on the basal activity of the receptor. The antibody fragment is also able to increase the basal rhythm of cultured neonatal rat cardiomyocytes and to inhibit in a non-competitive manner the negative chronotropic effect of carbachol. This antibody fragment is able to exert its inverse agonist activity in vivo on mouse heart activity. The immunological strategy presented here could be useful to develop specific allosteric inverse agonist reagents for G protein-coupled receptors.
Geodesics of learned representations (2015)

We develop a new method for visualizing and refining the invariances of learned representations. Specifically, we test for a general form of invariance, linearization, in which the action of a transformation is confined to a low-dimensional subspace. Given two reference images (typically, differing by some transformation), we synthesize a sequence of images lying on a path between them that is of minimal length in the space of the representation (a "representational geodesic"). If the transformation relating the two reference images is linearized by the representation, this sequence should follow the gradual evolution of this transformation. We use this method to assess the invariance properties of a state-of-the-art image classification network and find that geodesics generated for image pairs differing by translation, rotation, and dilation do not evolve according to their associated transformations. Our method also suggests a remedy for these failures, and following this prescription, we show that the modified representation is able to linearize a variety of geometric image transformations.
Stable clustering through mobility prediction for large-scale multihop intelligent ad hoc networks (2004)

In this paper we present a framework for dynamically organizing mobile nodes (MNs) in large-scale mobile ad hoc networks (MANETs), with the eventual aim to support quality of service (QoS). Our dynamic, distributed clustering approach is based on intelligent mobility prediction that enables each MN to anticipate the availability of its neighbors. We present a scalable way to predict the mobility, and thus availability, of MNs, achieved with the introduction of geographically-oriented virtual clusters. We name the proposed model as the (p, t, d)-clustering model that facilitates the formation of stable clusters. Simulation results demonstrate the performance advantages of our approach.
Nicotinate Adenine Dinucleotide Phosphate (NAADP) Triggers a Specific Calcium Release System in Sea Urchin Eggs (1995)

Transient fluxes of intracellular ionized calcium (Ca2+) from intracellular stores are integral components of regulatory signaling pathways operating in numerous biological regulations, including in early stages of egg fertilization. Therefore, we explored whether NADP, which is rapidly generated by phosphorylation of NAD upon fertilization may, directly or indirectly, exert a regulatory role as a trigger of Ca2+ release from intracellular stores in sea urchin eggs. NADP had no effect, but we found that the deamidated derivative of NADP, nicotinate adenine dinucleotide phosphate (beta-NAADP), is a potent and specific stimulus (ED50 16 nM) for Ca2+ release in sea urchin egg homogenates. NAADP triggers the Ca2+ release via a mechanism which is distinct from the well-known Ca2+ release systems triggered either by inositol-1,4,5-triphosphate (IP3) or by cyclic adenosine diphospho-ribose (cADPR). The NAADP-induced release of Ca2+ is not blocked by heparin, an antagonist of IP3, or by procaine or ruthenium red, antagonists of cADPR. However, it is selectively blocked by thionicotinamide-NADP which does not inhibit the actions of IP3 or cADPR. NAADP produced by heating of NADP in alkaline (pH = 12) medium or synthetized enzymatically by nicotinic acid-NADP reaction catalyzed by NAD glycohydrolase have identical properties. The results presented herein thus describe a novel endocellular Ca(2+)-releasing system controlled by NAADP as a specific stimulus. The NAADP-controlled Ca2+ release system may be an integral component of multiple intracellular regulations occurring in fertilized sea urchin eggs, which are mediated by intracellular Ca2+ release, and may also have similar role(s) in other tissues.
Clinical spectrum of CNS aquaporin-4 autoimmunity (2012)

The spectrum of neurologic manifestations and the disease course associated with CNS AQP4 autoimmunity is broader than previously recognized.
Endogenous and exogenous interleukin-12 augment the protective immune response in mice orally challenged with Salmonella dublin (1996)

Following oral challenge with Salmonella dublin, we observed significant increases in interleukin-12 (IL-12) protein expression in the mesenteric lymph nodes. The importance of this endogenous cytokine production in the immune response against S. dublin was demonstrated by in vivo depletion of IL-12 with an anti-IL-12 monoclonal antibody prior to oral S. dublin challenge. Mice pretreated with anti-IL-12 antibody had increased salmonellosis and reduced survival times compared with mice receiving control antibody. Furthermore, administration of exogenous murine recombinant IL-12 dramatically increased survival times of mice challenged orally with S. dublin. Together, these results demonstrate that endogenous and exogenous IL-12 significantly augment the mucosal immune response against the intracellular pathogen S. dublin.
A novel RF high-Q metal-semiconductor-metal planar inter-digitated varactor based on double-channel AlGaN/GaN HEMT structure (2005)

A novel GaN-based double-channel metal-semiconductor-metal configuration planar inter-digitated varactor, fabricated with a HEMT compatible process, is presented. Our varactors achieved high Q-factor, wide tuning range, and high minimum Q-factor (Q/sub min/). The double-channel heterostructure extends the useful high Q-factor capacitance tuning range of the varactors. The operation of the varactor is explained by a physical equivalent circuit, in which the whole changing trend of extracted Q-factors over bias voltage and extracted resistance can be explained. The measurement results of the novel double-channel varactors are compared with varactors fabricated on a single channel heterostructure in order to show their superior performance.
Conversion of Glycerol to Lactic Acid under Low Corrosive Conditions with Homogeneous and Heterogeneous Catalysts (2011)

Conversion of glycerol to lactic acid was performed at 280~300°C with calcium oxide as the solid base catalyst. Different factors, including reaction time and temperature, molar ratio of CaO: glycerol and water content were studied. The best conditions were obtained at 290°C, with a reaction time of 150 min and a CaO: glycerol molar ratio of 0.3:1. The highest yield of lactic acid obtained was 40.8 mol%, with a glycerol conversion of 97.8 mol%. High water content in reactant would affect the yield of lactic acid, because CaO would react with water first forming Ca(OH)2, which has a low catalytic ability than CaO. Calcium oxide maintained its original activity in three cycles of regeneration and reuse processes, with lactic acid yield slightly affected. The utilization of CaO in conversion of crude glycerol was also investigated. For crude glycerol conversion, there is no significant influence to CaO catalytic ability when water content in crude glycerol sample was low. Also, a preliminary study on the feasibility of CaO used as catalyst for both biodiesel production and following crude glycerol conversion was conducted. Two biodiesel production methods with CaO as catalyst were tried, and lactic acid was successfully produced from crude glycerol, byproduct of biodiesel production.
Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations (2012)

Rho-associated protein kinases (ROCK1 and ROCK2) are promising targets for a number of diseases, including cardiovascular disorders, nervous system diseases, cancers, etc. Recently, we have successfully identified a ROCK1 inhibitor (1) with the triazine core. In order to gain a deeper insight into the microscopic binding of this inhibitor with ROCK1 and design derivatives with improved potency, the interactions between ROCK1 and a series of triazine/pyrimidine-based inhibitors were studied by using an integrated computational protocol that combines molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and binding energy decomposition analysis. First, three docking protocols, rigid receptor docking, induced fit docking, QM-polarized ligand docking, were used to determine the binding modes of the studied inhibitors in the active site of ROCK1. The results illustrate that rigid receptor docking achieves the best performance to rank the binding affinities of the studied inhibitors. Then, based on the predicted structures from molecular docking, MD simulations and MM/GBSA free energy calculations were employed to determine the dynamic binding process and compare the binding modes of the inhibitors with different activities. The binding free energies predicted by MM/GBSA are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. In addition, the residue-inhibitor interaction spectra were obtained by the MM/GBSA free energy decomposition analysis, and the important residues for achieving strong binding were highlighted, which affords important guidance for the rational design of novel ROCK inhibitors. Finally, a variety of derivatives of inhibitor 1 were designed and four of them showed promising potency according to the predictions. We expect that our study can provide significant insight into the development of improved inhibitors of ROCK1.
Subthreshold design considerations for insulated gate field-effect transistors (1974)

A knowledge of subthreshold behavior in an insulated gate field-effect transistor is important for circuits with low leakage specifications. This paper discusses the effect of drain voltage on the subthreshold region as the channel length becomes shorter, the effect of substrate bias on both the shift in and the slope of the subthreshold curves, and the effect of temperature on the subthreshold current characteristics. It is shown that all these effects can be incorporated into a simple one-dimensional model.
Optical beat-induced crosstalk of an acousto-optic tunable filter for WDM network application (1995)

Acousto-optic tunable filters (AOTF) using TE-TM mode conversion are attractive for wavelength routers, such as WDM add/drop multiplexers or WDM cross-connect switching fabrics, due to their multichannel selectivity. However, their multichannel selection creates optical beat-induced crosstalk, the so called "coherent crosstalk", due to the interaction of the lightwave with several acoustic waves. This paper evaluates the transmission characteristics of WDM systems employing AOTF's. First, we develop an analytical model of coherent crosstalk based on the coupled mode theory. Next, we examine coherent crosstalk induced BER degradation both theoretically and experimentally for optical WDM systems and show that the analytical studies well support the experimental results. Finally, maximum AOTF cascade number is estimated based on these results for WDM based wavelength routing networks.
Multidrug resistant Acinetobacter baumannii--the role of AdeABC (RND family) efflux pump in resistance to antibiotics. (2008)

Acinetobacter baumannii is an opportunistic pathogen which play the more and more greater role in the pathogenicity of the human. It is often attached with the hospital environment, in which is able easily to survive for many days even in adverse conditions. Acinetobacter baumannii is the species responsible for a serious nosocomial infections, especially in the intensive care units. Option of surviving in natural niches, and in the hospital environment could also be associated with the efflux pump mechanisms. Mechanisms of efflux universally appear in all cells (eukaryotic and prokaryotic) and play the physiological important role. In prokaryote, the main functions are evasion of such naturally produced molecules, removal of metabolic products and toxins. These pumps could also be involved in an early stage of infection, such as adhesion to host cells and the colonization. Importantly, they remove commonly used antibiotics from the cell in therapy of infections caused by these bacteria. Efflux pumps exemplify a unique phenomenon in drug resistance: a single mechanism causing resistance against several different classes of antibiotics. In Acinetobacter baumannii, the AdeABC efflux pump, a member of the resistance-nodulation-cell division family (RND), has been well characterized. Aminoglicosides, tetracyclines, erythromycin, chloramphenicol, trimethoprim, fluoroquinolones, some beta-lactams, and also recently tigecycline, were found to be substrates for this pump. Drugs, as substrates for the AdeABC pump, can increase the expression of the AdeABC genes, leading to multidrug resistance (MDR). From this reason, treatment failure and death caused by Acinetobacter baumannii infections or underlying diseases are common. Because the AdeABC pump is widespread in Acinetobacter baumannii, similarly to other pumps in Gram-negative and Gram-positive bacteria, exists a need of searching a new therapeutic solutions. Specific efflux inhibitors of pumps (EPIs), including AdeABC inhibitors, could be suppress the activity of pumps and restore the sensitivity of such important bacteria as Acinetobacter baumannii to commonly used antibiotic.
[Effect of inhibitors of signal transducer and activator of transcription-1/3 on expression of tumor necrosis factor-alpha induced by high mobility group box-1 protein inflammatory response in rat peritoneal macrophages]. (2006)

STAT1 and STAT3 might be involved in the regulation of TNF-alpha gene expression, but not in TNF-alpha early release (< 24 hours) induced by HMGB1 stimulation in rat peritoneal macrophages.
The dental key: a dangerous and barbarous instrument. (2005)

The dental key or turnkey, which was probably in more general use for the extraction of teeth than any other single instrument prior to the 1900s, caused more accidents and injuries than all other extraction instruments combined. However, prior to the discovery of anesthesia, it was the quickest way to remove a posterior tooth, despite its detractors and misuse.
Spatial Sigma-Delta Modulation in a Massive MIMO Cellular System (2016)

In cellular networks, frequency channels are used to separate the users. However frequency spectrum is an ever-decreasing resource as wireless units and applications increase. Thus, other means to separate the users are of interest. By using hundreds of antennas and beamforming in the system, the users can be efficiently multiplexed in the spatial domain, while using the same time-frequency resource. The large amount of antennas however requires extensive data processing and transport which is difficult and expensive to handle. Thus, an investigation of how to reduce the data bandwidth required in such a system is of interest. This master thesis project evaluates the use of the spatial dimension in a  modulator as part of the analog-to-digital conversion. It is put into the context of beamforming and evaluated. A simulator developed in MATLAB is utilized to show the properties and qualities of different modulator structures in a beamforming application. In particular, performance at low converter speeds is evaluated. The results show that by using the spatial dimension in a  modulator it is possible to reduce the bandwidth requirement, through reduction of sampling rate while still retaining the signal quality. However, this is applicable only in one direction at a time, and there are multiple implementation issues regarding the proposed design. The findings suggest that with the spatial dimension in a  modulator there are possibilities to reduce the bandwidth requirement in antenna array systems but that there are considerable challenges to overcome.
Identification of the High T<sub>c</sub> Superconductor in the System Y-Ba-Cu-O (1987)

In order to identify the superconducting phase in the Y-Ba-Cu-O system, phase search and electron microscopic study were performed. At least three unknown phases were found in a part of the system. Among these phases, perovskite-related compound (orthorhombic a =3.89, b =3.82, c =11.7 Å or possibly tetragonal a =3.83, c =11.7 Å) is the possible compound responsible for the superconductivity.
Database Applications of the FETCH-AND-ADD Instruction (1984)

The FETCH-AND-ADD instruction provides for synchronization of multiple processes in a parallel manner. This paper explores the use of FETCH-AND-ADD in the context of database systems. We show how to enqueue locks, detect lock conflicts, and release locks without resorting to critical program sections that require mutual exclusion during execution. The scheme is compatible with a variant of lock management proposed by Rosenkrantz and Stearns. A second approach to parallel lock management is based on a reservation scheme by Milenkovic. This methodology uses FETCH-AND-ADD implementation of a priority queue. An implementation of such a queue originally reported by Gottlieb and Kruskal is used for this purpose, although the storage requirements for queue management may be unacceptably large in specific cases. Both approaches described in the paper suggest that FETCH-AND-ADD is potentially effective for eliminating serial bottlenecks caused by lock conflicts in multiprocessor systems.
Lead User Analyses for the Development of New Industrial Products (1986)

Another version of this paper is available in the Sloan Working Papers collection at https://dspace.mit.edu/handle/1721.1/2145.
Fabrication and analysis of dot junction silicon solar cells (1985)

A design of solar cells with reduced junction area on the cell surface is investigated for reduction of saturation current and increase in open-circuit voltage. Equidiameter dot junctions distributed across the surface of the cell offer an efficient alternative, with variations in dot diameter and in the spacing between dots giving the required variations in the ratio of junctions area to total surface area. A simplified analysis for short-circuit current and other cell parameters, which enables cell design optimization, is presented. Efficiencies beyond 18 percent are obtainable in flat-plate terrestrial applications. Experimental solar-cell performance results, as functions of different area ratios, and bulk doping are presented. It is shown that saturation current reduction and open-circuit voltage increase is obtained by reduced junction area.
Direct electrochemical synthesis of neutral and anionic chloro- and bromo-complexes of titanium, zirconium, and hafnium (1977)

Electrochemical oxidation of titanium, zirconium, or hafnium(IV) in the presence of a solution of chlorine or bromine (X) in acetonitrile (L) leads to direct synthesis of MX 4 L 2 species in good yield. These compounds are easily transformed into other neutral adducts. On addition of tetraalkylammonium salts to the solution phase, the products are the salts (R 4 N)MCl 5 or (R 4 N) 2 MBr 6 , except that with titanium Et 4 NTiBr 4 was also formed under some conditions. The advantages of this method are discussed, and a possible reaction mechanism proposed.
Valproic Acid Prolongs Survival Time of Severe Combined Immunodeficient Mice Bearing Intracerebellar Orthotopic Medulloblastoma Xenografts (2006)

We have developed intracerebellar orthotopic models that closely recapitulated the biological features of human medulloblastomas and characterized their in vivo growth characteristics. Valproic acid treatment of these xenografts showed potent in vivo anti-medulloblastoma activity. These xenograft models should facilitate the understanding of medulloblastoma pathogenesis and future preclinical evaluation of new therapies against medulloblastoma.
Strategy without tactics (2016)

Control-flow integrity (CFI) is a general defense against code-reuse exploits that currently constitute a severe threat against diverse computing platforms. Existing CFI solutions (both in software and hardware) suffer from shortcomings such as (i) inefficiency, (ii) security weaknesses, or (iii) are not scalable. In this paper, we present a generic hardware-enhanced CFI scheme that tackles these problems and allows to enforce diverse CFI policies. Our approach fully supports multi-tasking, shared libraries, prevents various forms of code-reuse attacks, and allows CFI protected code and legacy code to co-exist. We evaluate our implementation on SPARC LEON3 and demonstrate its high efficiency.