gebhart/patrepeval huggingface dataset:
Potassium Ions are More Effective than Sodium Ions in Salt Induced Peptide Formation (2013)

Prebiotic peptide formation under aqueous conditions in the presence of metal ions is one of the plausible triggers of the emergence of life. The salt-induced peptide formation reaction has been suggested as being prebiotically relevant and was examined for the formation of peptides in NaCl solutions. In previous work we have argued that the first protocell could have emerged in KCl solution. Using HPLC-MS/MS analysis, we found that K(+) is more than an order of magnitude more effective in the L-glutamic acid oligomerization with 1,1'-carbonyldiimidazole in aqueous solutions than the same concentration of Na(+), which is consistent with the diffusion theory calculations. We anticipate that prebiotic peptides could have formed with K(+) as the driving force, not Na(+), as commonly believed.
Octanoylation of the lipoyl domains of the pyruvate dehydrogenase complex in a lipoyl‐deficient strain of <i>Escherichia coli</i> (1990)

The overexpression of a subgene encoding a hybrid lipoyl domain of the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex of Escherichia coli has previously been shown to result in the formation of lipoylated and unlipoylated products. Overexpression of the same subgene in a lipoic acid biosynthesis mutant growing under lipoate-deficient conditions has now been shown to produce domains modified by octanoylation as well as unmodified domains. It was concluded from the mass of a lipoyl-binding-site peptide that the modification involves N6-octanoylation of the lysine residue (Lys244) that is normally lipoylated, and this was confirmed by the trypsin-insensitivity of the corresponding Lys244-Ala-245 bond, and the absence of modification in a mutant domain in which Lys244 is replaced by Gln. This novel protein modification raises interesting questions concerning the pathway of lipoic acid biosynthesis and the mechanism of enzyme lipoylation.
Initial hepatic removal of chylomicron remnants is unaffected but endocytosis is delayed in mice lacking the low density lipoprotein receptor. (1995)

Two endocytic receptors, the low density lipoprotein (LDL) receptor (LDLR) and the LDLR-related protein (LRP), are thought to act in concert in the hepatic uptake of partially metabolized dietary lipoproteins, the chylomicron remnants. We have evaluated the role of these two receptors in the hepatic metabolism of chylomicron remnants in normal mice and in LDLR-deficient [LDLR (-/-)] mice. The rate of chylomicron remnant removal by the liver was normal up to 30 min after intravenous injection of chylomicrons into LDLR (-/-) mice and was unaffected by receptor-associated protein (RAP), a potent inhibitor of ligand binding to LRP. In contrast, endocytosis of the remnants by the hepatocytes, measured by their accumulation in the endosomal fraction and by the rate of hydrolysis of component cholesteryl esters, was dramatically reduced in the absence of the LDLR. Coadministration of RAP prevented the continuing hepatic removal of chylomicron remnants in LDL (-/-) mice after 30 min, consistent with blockade of the slow endocytosis by a RAP-sensitive process. Taken together with previous studies, our results are consistent with a model in which the initial hepatic removal of chylomicron remnants is primarily mediated by mechanisms that do not include LDLR or LRP, possibly involving glycosaminoglycan-bound hepatic lipase and apolipoprotein E. After the remnants bind to these alternative sites on the hepatocyte surface, endocytosis is predominantly mediated by the LDLR and also by a slower and less efficient backup process that is RAP sensitive and therefore most likely involves LRP.
Metabolic engineering of <i>Escherichia coli</i> for the production of polylactic acid and its copolymers (2009)

Polylactic acid (PLA) is a promising biomass-derived polymer, but is currently synthesized by a two-step process: fermentative production of lactic acid followed by chemical polymerization. Here we report production of PLA homopolymer and its copolymer, poly(3-hydroxybutyrate-co-lactate), P(3HB-co-LA), by direct fermentation of metabolically engineered Escherichia coli. As shown in an accompanying paper, introduction of the heterologous metabolic pathways involving engineered propionate CoA-transferase and polyhydroxyalkanoate (PHA) synthase for the efficient generation of lactyl-CoA and incorporation of lactyl-CoA into the polymer, respectively, allowed synthesis of PLA and P(3HB-co-LA) in E. coli, but at relatively low efficiency. In this study, the metabolic pathways of E. coli were further engineered by knocking out the ackA, ppc, and adhE genes and by replacing the promoters of the ldhA and acs genes with the trc promoter based on in silico genome-scale metabolic flux analysis in addition to rational approach. Using this engineered strain, PLA homopolymer could be produced up to 11 wt% from glucose. Also, P(3HB-co-LA) copolymers containing 55-86 mol% lactate could be produced up to 56 wt% from glucose and 3HB. P(3HB-co-LA) copolymers containing up to 70 mol% lactate could be produced to 46 wt% from glucose alone by introducing the Cupriavidus necator beta-ketothiolase and acetoacetyl-CoA reductase genes. Thus, the strategy of combined metabolic engineering and enzyme engineering allowed efficient bio-based one-step production of PLA and its copolymers. This strategy should be generally useful for developing other engineered organisms capable of producing various unnatural polymers by direct fermentation from renewable resources.
Using Genetic Algorithms to Solve Luggage Typesetting Problem (2007)

The Bin Packing Problems play an important role in plans of production and saving cost in factories. This paper is to develop a set of Intellectual Automatic Typesetting System (IATS) for luggage factories through Bin Packing Algorithm and Genetic Algorithm. Firstly, we attain the cost of raw materials by Bill of Material (BOM) from orders. Secondly, the producing procedure of the luggage has been divided into two parts. The first part is to use the One-Dimensional Typesetting Algorithm (ODTA) to solve the problem of fabric cutting. The second part is to use the two-dimensional packing algorithm to solve the problem of leather, wood and the plastic plates cutting. Finally, we combine the IATS with mobile phone to offer an effective Quick Response/Efficient Consumer Response (QR/ECR). Hence, users can look up the minimal cost of raw materials and received the quote rapidly. It is not only more effective than traditional fabric typesetting work but also saves plenty of human resources for luggage factories.
Unique Distribution of Thrombospondin-1 in Human Ocular Surface Epithelium (2006)

In the human ocular surface epithelium, basal cells of the CE and LE, but not of the CJE, synthesize TSP-1. High levels of TSP-1 are present only just below the CE. Its unique distribution may be related to corneal avascularity and integrity.
On the placement of controllers for designing a wide area software defined networks (2017)

The newly emerged Software Defined Networks (SDN) can apply to Wide Area Network (WAN) for network control and management. To achieve this, a logically centralized but a physically distributed control architecture is normally required. This type of control architecture consists of multiple controllers. For maintaining the global consistency of the network, controller placement is a key issue in a Wide Area SDN. The controller placement problem (CPP) refers to selecting the number and proper positions of the controllers to improve the performance of the SDN control plane. Although various approaches are made to solve CPP for the small and medium-size network, still it requires an alternative solution for a large scale network like WAN. It needs enough time to select the number of controllers and their location, within a limited resource constraint. In this work, we propose two stochastic meta-heuristic techniques for finding optimal locations of the controllers that optimize the latency between the switch to a designated controller. We develop the algorithm for Particle Swarm Optimization and Firefly that solve CPP, with the fitness function as the controller to switch latency, which needs to be minimized. The extensive simulation shows that Firefly provides a better result in terms of computation time and cost that are close to optimal.
Development of layer-specific axonal arborizations in mouse primary somatosensory cortex (2005)

In the developing neocortex, pyramidal neurons use molecular cues to form axonal arbors selectively in the correct layers. Despite the utility of mice for molecular and genetic studies, little work has been done on the development of layer-specific axonal arborizations of pyramidal neurons in mice. We intracellularly labeled and reconstructed the axons of layer 2/3 and layer 5 pyramidal neurons in slices of primary somatosensory cortex from C57Bl6 mice on postnatal days 7-21. For all neurons studied, the development of the axonal arborizations in mice follows a pattern similar to that seen in other species; laminar specificity of the earliest axonal branches is similar to that of mature animals. At P7, pyramidal neurons are very simple, having only a main descending axon and few primary branches. Between P7 and P10, there is a large increase in the total number of axonal branches, and axons continue to increase in complexity and total length from P10 to P21. Unlike observations in ferrets, cats, and monkeys, two types of layer 2/3 pyramidal neurons are present in both mature and developing mice; cells in superficial layer 2/3 lack axonal arbors in layer 4, and cells close to the layer 4 border have substantial axonal arbors within layer 4. We also describe axonal and dendritic arborization patterns of three pyramidal cell types in layer 5. The axons of tall-tufted layer 5 pyramidal neurons arborize almost exclusively within deep layers while tall-simple, and short layer 5 pyramidal neurons also project axons to superficial layers.
The fault-tolerant 3B-20 processor (1981)

The 3B-20 is the first Bell System general-purpose telecommunication processor designed to meet a broad range of applications. New features such as memory management are incorporated into its design to support a modern operating system. Hardware supports are provided to efficiently execute a high-level language. The 3B-20 Processor is designed to meet ESS reliability requirements and the proven technique of self-checking duplex operation forms its basic architecture structure.
PATTERNS OF LOCAL COMMUNITY LEADERSHIP. By Linton C. Freeman. Indianapolis: Bobbs-Merrill Company, 1968. 138 pp. $2.95 (1969)

Patterns of Local Community Leadership. By Linton C. Freeman. Indianapolis: Bobbs-Merrill Company, 1968. 138 pp. $2.95 Get access Terry N. Clark Terry N. Clark University of Chicago Search for other works by this author on: Oxford Academic Google Scholar Social Forces, Volume 47, Issue 3, March 1969, Page 364, https://doi.org/10.1093/sf/47.3.364 Published: 01 March 1969
3D object watermarking by a 3D hidden object (2003)

In this paper we present a method to watermark a 3D object with another hidden 3D object using digital holography. The watermark or the hidden information is a 3D object that is embedded in the digital hologram of a 3D host object. The digital holograms are obtained optically by phase shift interferometery. The hologram of the hidden 3D object is double phase encoded before embedding it to the host 3D object hologram. Then, the watermarked hologram is double phase encoded again using different set of codes. The resultant watermarked hologram is very secure because of the multi-key nature of the watermarking process. We discuss the effect of distortion caused by hologram quantization and occlusion of some of the hologram pixels. We present tests to illustrate the effect of using a window of the hologram to reconstruct the hidden 3D object and the host 3D object. Both mathematical analysis and simulations are presented to illustrate the system performance. To the best of our knowledge, this is the first report of embedding a 3D objects within another 3D object.
Feedback into Mixture Plenums in Rotating Detonation Engines (2012)

Rotating detonation engines (RDE’s) represent a natural extension of the pulse detonation engine (PDE) concept to a continuous detonation for obtaining propulsion and power from the high efficiency detonation cycle. Although extensively studied for the last few years, RDE’s are still less understood and developed than the PDE concept. In particular, interaction between the detonation wave in the combustion chamber and the upstream mixture plenum is critical to the stability and performance of an RDE, and has not been studied in detail. In this paper, we extend our well-tested RDE models to examine the effect of pressure feedback into the mixture plenum with two and three-dimensional simulations. We examine three main injector configurations to determine their effect on stability, performance, and feedback into the mixture plenum. Results indicate that although the flow-field is considerably different, the performance of the RDE with all three modeled injection systems is close to that of assuming an ideal injection process, especially for a injector throat to injector face area ratio of 0.2. For an area ratio of 0.4, the drop in performance is more noticable, varying between 2.4% at 10 atm plenum pressure to 11.4% at 4 atm. Specific impulses for all the modeled injector cases varied from 3975 s to 5263 s. The stability at high and low pressures becomes much more of an issue when modeling specific injectors, due to an increase in flow unsteadiness from the injection. Pressure feedback into the mixture plenum appears to be relatively low for area ratios of 0.2 (less than 10% of stagnation pressure), but becomes very large for even moderate area ratios of 0.4. The cylindrical micro-injectors had the worst pressure feedback, with underpressures between 1 and 1.77 atm and overpressures between 3.09 and 3.83 atm with the large area ratio.
Error event characterization of partial response systems in magnetic recording systems with medium noise (2002)

The effective distance (d/sub eff/) of error events for partial response maximum likelihood (PRML) systems in magnetic recording channels are calculated using a realistic model for medium noise. The presence of medium noise has a strong negative impact on the minimum effective distances. The effective distances and the hierarchy of error events depend on the characteristics of the noise. In addition, due to the data dependency of medium noise, each error event corresponds to a range of d/sub eff/ depending upon which data pattern was transmitted.
Aerial Video Stream over Multi-hop Using Adaptive TDMA Slots (2017)

Unmanned Aerial Vehicles (UAVs) are rapidly becoming an important tool for applications like surveillance, target tracking and facility monitoring. In many of these contexts, one or more UAVs need to reach an area of interest (AOI) while streaming live video to a ground station (GS) where one or more operators inspect the AOI and carry out fine control of UAVs position. In remote areas, intermediate UAVs can act as relays and form a line network to extend range. Interactive control requires a live video stream where both throughput and delay are important. In this paper, we show that routing packets over CSMA/CA (native medium access protocol of WiFi, the most common wireless technology among UAVs) behaves poorly in this context due to link asymmetries. We propose a novel distributed, adaptive and self-synchronized TDMA protocol (DVSP) that both enhances delay and packet delivery while operating on commodity hardware and leveraging a standard UDP/IP protocol stack. We prove that DVSP converges to a global solution that minimizes delay using local information, only, thus in a fully distributed manner. Real world experiments with multiple UAVs show gains in delay up to 75%, and packet delivery up to 50%, without sacrificing goodput.
Myeloid cell transmigration across the CNS vasculature triggers IL-1β–driven neuroinflammation during autoimmune encephalomyelitis in mice (2016)

Growing evidence supports a role for IL-1 in multiple sclerosis and experimental autoimmune encephalomyelitis (EAE), but how it impacts neuroinflammation is poorly understood. We show that susceptibility to EAE requires activation of IL-1R1 on radiation-resistant cells via IL-1β secreted by bone marrow-derived cells. Neutrophils and monocyte-derived macrophages (MDMs) are the main source of IL-1β and produce this cytokine as a result of their transmigration across the inflamed blood-spinal cord barrier. IL-1R1 expression in the spinal cord is found in endothelial cells (ECs) of the pial venous plexus. Accordingly, leukocyte infiltration at EAE onset is restricted to IL-1R1(+) subpial and subarachnoid vessels. In response to IL-1β, primary cultures of central nervous system ECs produce GM-CSF, G-CSF, IL-6, Cxcl1, and Cxcl2. Initiation of EAE or subdural injection of IL-1β induces a similar cytokine/chemokine signature in spinal cord vessels. Furthermore, the transfer of Gr1(+) cells on the spinal cord is sufficient to induce illness in EAE-resistant IL-1β knockout (KO) mice. Notably, transfer of Gr1(+) cells isolated from C57BL/6 mice induce massive recruitment of recipient myeloid cells compared with cells from IL-1β KO donors, and this recruitment translates into more severe paralysis. These findings suggest that an IL-1β-dependent paracrine loop between infiltrated neutrophils/MDMs and ECs drives neuroinflammation.
ChemInform Abstract: Asymmetric Catalysis of the Friedel—Crafts Reaction with Fluoral by Chiral Binaphthol‐Derived Titanium Catalysts Through Asymmetric Activation. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fault Tolerance with Noisy and Slow Measurements and Preparation (2010)

It is not so well known that measurement-free quantum error correction protocols can be designed to achieve fault-tolerant quantum computing. Despite their potential advantages in terms of the relaxation of accuracy, speed, and addressing requirements, they have usually been overlooked since they are expected to yield a very bad threshold. We show that this is not the case. We design fault-tolerant circuits for the 9-qubit Bacon-Shor code and find an error threshold for unitary gates and preparation of p((p,g)thresh)=3.76×10(-5) (30% of the best known result for the same code using measurement) while admitting up to 1/3 error rates for measurements and allocating no constraints on measurement speed. We further show that demanding gate error rates sufficiently below the threshold pushes the preparation threshold up to p((p)thresh)=1/3.
The peptide binding specificity of the MHC class II I-A molecule of the Lewis rat, RT1.B<sup>1</sup> (1996)

The specificity of peptide binding to MHC molecules is defined by binding motifs composed of several relatively conserved anchor positions. The peptide binding motifs of murine MHC class II I-A molecules are functionally important but poorly characterized. Here we use peptide binding studies and isolation of naturally presented peptides to characterize the peptide binding motif of the MHC class II I-A molecule, RT1.BI, a molecule that is involved in experimental autoimmunity in the Lewis rat. We now report that, similar to other class II motifs, the RT1.BI motif consists of a nonamer sequence with four major anchor positions (P1, P4, P6 and P9). Residues at P4 and P9, rather than at P1, appeared to be particularly important for binding. Negatively charged residues were favored at P9, consistent with the presence of a serine at position 57 of the RT1.BI beta chain. This RT1.BI motif could be observed in the dominant autoantigenic T cell epitopes mapped previously in the Lewis rat. These results highlight a general similarity and some important differences in the organization of MHC class II peptide binding motifs. The reported RT1.BI motif should facilitate the prediction and design of T cell epitopes for the induction and control of experimental autoimmune diseases in Lewis rat models.
A Novel Combination Method for On-line Process Monitoring and Fault Diagnosis (2005)

on-line monitoring and fault diagnosis of chemical process is extremely important for operation safety and product quality. Principal component analysis (PCA) has been successfully as a multivariate statistical process control tool for detecting faults in processes with highly correlated variables. PCA and other statistical techniques, however, have difficulties in differentiating faults correctly in complex chemical process. Support vector machine (SVM) is a novel approach based on statistical learning theory, which has emerged for feature identification and classification. In this paper, an integrated method is applied for process monitoring and fault diagnosis, which combines PCA for fault feature extraction and multiple SVMs (MSVMs) for identification of different fault sources. This approach is verified and illustrated on the Tennessee Eastman benchmark process as a case study. Results show that the proposed PCA-MSVMs method performs good diagnosis capability and overall diagnosis correctness rate.
Bone Impactors (1986)

I have used these new instruments, designed for the reduction of nerve structure compression by the principle of impaction (driving inward of the outer surface), with success in well over 300 cases; they have proved to be useful, and often indispensible, in most cases having decompressions for lateral stenosis.
BindingDB Entry 50041981: Reversal of breast cancer resistance protein-mediated drug resistance by estrogen antagonists and agonists. (2013)

Breast cancer resistance protein (BCRP), an ATP-binding cassette transporter, confers resistance to a series of anticancer agents such as SN-38, mitoxantrone, and topotecan. In a previous study, we found that estrogens reverse drug resistance of BCRP-expressing cells. In this study, estrogen antagonists, estrogen agonists, and their derivatives were evaluated for BCRP-reversing activity. First, compounds were tested for effects on the cellular accumulation of topotecan in BCRP-transduced K562 cells (K562/BCRP). Next, these compounds were examined for their ability to reverse SN-38 and mitoxantrone resistance in K562/BCRP cells. Among commercially available estrogen antagonists and agonists tested, diethylstilbestrol showed the strongest BCRP-reversing activity. Diethylstilbestrol increased the cellular accumulation of topotecan and reversed drug resistance in K562/BCRP cells but showed marginal or no effect in parental K562 cells. The reversal activities of estrone and diethylstilbestrol were more prominent for mitoxantrone than for SN-38. Tamoxifen and toremifene were also found to enhance topotecan uptake in K562/BCRP cells. Next, various tamoxifen derivatives were screened for anti-BCRP activity. In the first cycle of screening with 14 compounds, TAG-11 showed the strongest effect. In the second cycle of screening of 25 TAG-11-related compounds, TAG-139 showed the strongest effect. Reversal of SN-38 and mitoxantrone resistance in K562/BCRP cells by TAG-139 was 5-fold stronger than that by estrone. Dose-dependent characteristics of drug resistance reversal with estrone and TAG-139 were very similar, suggesting that estrone and tamoxifen derivatives interact with the same drug-binding site of BCRP. Derivatives of antiestrogens that exhibit no other biological effects promise to be useful in overcoming BCRP-mediated drug resistance.