gebhart/patrepeval huggingface dataset:
AntMap: Constructing Genetic Linkage Maps Using an Ant Colony Optimization Algorithm (2006)

High-throughput assay of molecular markers enables to utilize large amounts of markers in linkage mapping. To incorporate numerous markers into a linkage map, the development of a highly efficient method for linkage mapping is indispensable. When the number of loci is large, locus ordering is a major difficulty in linkage mapping, since the number of possible orders becomes very large. To address this problem, we developed a new algorithm for locus ordering and used it in a newly developed computer program called AntMap. The algorithm is based on ant colony optimization, which is a set of metaheuristic algorithms inspired by the cooperative behavior of real ants in finding the shortest path from their nest to a food source. Using this algorithm, AntMap seeks the linear order of loci that minimizes the sum of adjacent recombination fractions or that maximizes the log likelihood of locus order. Analyses based on simulated data sets indicated that our algorithm displayed a high efficiency level. The high performance of the algorithm enabled to save time and labor, and also to validate an estimated order by bootstrap tests. Our algorithm and AntMap should enable to construct high-throughput systems for linkage mapping. AntMap is available under a GNU general public license at http://cse.naro.affrc.go.jp/iwatah/antmap/index.html. Source codes and executables of AntMap can be obtained there.
Conversion of rod-shaped gold nanoparticles to spherical forms and their effect on biodistribution in tumor-bearing mice (2012)

Gold nanorods that have an absorption band in the near-infrared region and a photothermal effect have been used as nanodevices for near-infrared imaging and thermal therapy. Choice of the optimal shape of gold nanorods which relates optical properties and in vivo biodistribution is important for their applications. In the present study, to investigate the relationship between the shape of gold nanorods and their biodistribution after intravenous injection, we first prepared two types of gold nanorods that had distinct aspect ratios but had the same volume, zeta potential, and PEG density on the gold surface. Biodistributions of the two types of gold nanorods after intravenous injection into tumor-bearing mice were then compared. Although a slight difference in accumulation in the spleen was observed, no significant difference was observed in the liver, lung, kidney, and tumors. These results suggest that biodistribution of the gold nanorods in the aspect ratio range of 1.7 to 5.0, diameter of 10 to 50 nm, and volume of approximately 4 × 103 nm3 was dependent mainly on surface characteristics, PEG density, and zeta potential.
The Construction of Semantic Memory: Grammar-Based Representations Learned from Relational Episodic Information (2011)

After acquisition, memories underlie a process of consolidation, making them more resistant to interference and brain injury. Memory consolidation involves systems-level interactions, most importantly between the hippocampus and associated structures, which takes part in the initial encoding of memory, and the neocortex, which supports long-term storage. This dichotomy parallels the contrast between episodic memory (tied to the hippocampal formation), collecting an autobiographical stream of experiences, and semantic memory, a repertoire of facts and statistical regularities about the world, involving the neocortex at large. Experimental evidence points to a gradual transformation of memories, following encoding, from an episodic to a semantic character. This may require an exchange of information between different memory modules during inactive periods. We propose a theory for such interactions and for the formation of semantic memory, in which episodic memory is encoded as relational data. Semantic memory is modeled as a modified stochastic grammar, which learns to parse episodic configurations expressed as an association matrix. The grammar produces tree-like representations of episodes, describing the relationships between its main constituents at multiple levels of categorization, based on its current knowledge of world regularities. These regularities are learned by the grammar from episodic memory information, through an expectation-maximization procedure, analogous to the inside-outside algorithm for stochastic context-free grammars. We propose that a Monte-Carlo sampling version of this algorithm can be mapped on the dynamics of "sleep replay" of previously acquired information in the hippocampus and neocortex. We propose that the model can reproduce several properties of semantic memory such as decontextualization, top-down processing, and creation of schemata.
The derivation and maturation of vascular smooth muscle cells from human pluripotent stem cells (2011)

Vascular diseases include conditions that cause artery, vein, or lymph vessel damage and disorders that affect blood circulation, such as cardiovascular disease, and peripheral vascular disease. A promising treatment for vascular diseases is cell therapy using human pluripotent stem cells (hPSCs) for vascular regeneration. The differentiation of hPSCs depends on biochemical cues (e.g. growth factors) as well as biomechanical cues (e.g. strain/stress). We first used the growth factors TGF-β and PDGF-BB to derive vascular smooth muscle cells (v-SMCs) from hPSCs i.e. human embryonic stem cells and induced pluripotent stem cells. The application of uniaxial cyclic strain and serum starvation was utilized to induce maturation of the v-SMC derivatives. v-SMCs derivatives were analyzed using immunofluorescence staining for v-SMC markers including SMA, calponin, SM22 and SM-MHC. The production and secretion of Collagen 1 and Fibronectin was also investigated. Western blot and RT-PCR quantified the proteins and mRNA levels of the various markers. . Our results indicate that short term culture and exposure to TGF-β and PDGF-BB promote a more contractile phenotype while long term exposure produces a more synthetic phenotype. Additionally, the application of strain has varying effects on the expression of different v-SMC markers. This research was partially funded by the March of Dimes.
Ultra-wideband tellurite-based Raman fibre amplifier (2001)

The first wideband tellurite-based Raman fibre amplifier is described. The amplifier provided a 160 nm bandwidth with a gain of over 10 dB and a noise figure below 10 dB from 1490 to 1650 nm with a tellurite-based fibre only 250 m in length pumped by 4 wavelength channel LDs.
Refining Fitts' law models for bivariate pointing (2003)

We investigate bivariate pointing in light of the recent progress in the modeling of univariate pointing. Unlike previous studies, we focus on the effect of target shape (width and height ratio) on pointing performance, particularly when such a ratio is between 1 and 2. Results showed unequal impact of amplitude and directional constraints, with the former dominating the latter. Investigating models based on the notion of weighted Lp norm, we found that our empirical findings were best captured by an Euclidean model with one free weight. This model significantly outperforms the best model to date.
Handling Missing Annotations in Supervised Learning Data (2020)

Data annotation is an essential stage in supervised learning. However, the annotation process is exhaustive and time consuming, specially for large datasets. Activities of Daily Living (ADL) recognition is an example of systems that exploit very large raw sensor data readings. In such systems, sensor readings are collected from activity-monitoring sensors in a 24/7 manner. The size of the generated dataset is so huge that it is almost impossible for a human annotator to give a certain label to every single instance in the dataset. This results in annotation gaps in the input data to the adopting supervised learning system. The performance of the recognition system is negatively affected by these gaps. In this work, we propose and investigate three different paradigms to handle these gaps. In the first paradigm, the gaps are taken out by dropping all unlabeled readings. A single "Unknown" or "Do-Nothing" label is given to the unlabeled readings within the operation of the second paradigm. The last paradigm handles these gaps by giving every one of them a unique label identifying the encapsulating deterministic labels. Also, we propose a semantic preprocessing method of annotation gaps by constructing a hybrid combination of some of these paradigms for further performance improvement. The performance of the proposed three paradigms and their hybrid combination is evaluated using an ADL benchmark dataset containing more than $2.5\times 10^6$ sensor readings that had been collected over more than nine months. The evaluation results emphasize the performance contrast under the operation of each paradigm and support a specific gap handling approach for better performance.
Faculty Opinions recommendation of Somatic NF1 inactivation is a frequent event in sporadic pheochromocytoma. (2012)

Germline mutations in the RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, MAX, TMEM127, NF1 or VHL genes are identified in about 30% of patients with pheochromocytoma or paraganglioma and somatic mutations in RET, VHL or MAX genes are reported in 17% of sporadic tumors. In the present study, using mutation screening of the NF1 gene, mapping of chromosome aberrations by single nucleotide polymorphism (SNP) array, microarray-based expression profiling and immunohistochemistry (IHC), we addressed the implication of NF1 somatic alterations in pheochromocytomas and paragangliomas. We studied 53 sporadic tumors, selected because of their classification with RET/NF1/TMEM127-related tumors by genome wide expression studies, as well as a second set of 11 independent tumors selected on their low individual levels of NF1 expression evaluated by microarray. Direct sequencing of the NF1 gene in tumor DNA identified the presence of an inactivating NF1 somatic mutation in 41% (25/61) of analyzed sporadic tumors, associated with loss of the wild-type allele in 84% (21/25) of cases. Gene expression signature of NF1-related tumors highlighted the downregulation of NF1 and the major overexpression of SOX9. Among the second set of 11 tumors, two sporadic tumors carried somatic mutations in NF1 as well as in another susceptibility gene. These new findings suggest that NF1 loss of function is a frequent event in the tumorigenesis of sporadic pheochromocytoma and strengthen the new concept of molecular-based targeted therapy for pheochromocytoma or paraganglioma. PMID: 22962301
Ciphertext-Policy Attribute-Based Encryption (2007)

In several distributed systems a user should only be able to access data if a user posses a certain set of credentials or attributes. Currently, the only method for enforcing such policies is to employ a trusted server to store the data and mediate access control. However, if any server storing the data is compromised, then the confidentiality of the data will be compromised. In this paper we present a system for realizing complex access control on encrypted data that we call ciphertext-policy attribute-based encryption. By using our techniques encrypted data can be kept confidential even if the storage server is untrusted; moreover, our methods are secure against collusion attacks. Previous attribute-based encryption systems used attributes to describe the encrypted data and built policies into user's keys; while in our system attributes are used to describe a user's credentials, and a party encrypting data determines a policy for who can decrypt. Thus, our methods are conceptually closer to traditional access control methods such as role-based access control (RBAC). In addition, we provide an implementation of our system and give performance measurements.
Cutaneous Horn (1945)

No extract is available for articles shorter than 400 words.
Evaluation of PSMA-Targeted PAMAM Dendrimer Nanoparticles in a Murine Model of Prostate Cancer (2019)

The prostate-specific membrane antigen (PSMA) is a validated target for detection and management of prostate cancer (PC). It has also been utilized for targeted drug delivery through antibody–drug conjugates and polymeric micelles. Polyamidoamine (PAMAM) dendrimers are emerging as a versatile platform in a number of biomedical applications due to their unique physicochemical properties, including small size, large number of reactive terminal groups, bulky interior void volume, and biocompatibility. Here, we report the synthesis of generation 4 PSMA-targeted PAMAM dendrimers [G4(MP-KEU)] and evaluation of their targeting properties in vitro and in vivo using an experimental model of PC. A facile, one-pot synthesis gave nearly neutral nanoparticles with a narrow size distribution of 5 nm in diameter and a molecular weight of 27.3 kDa. They exhibited in vitro target specificity with a dissociation constant (Kd) of 0.32 ± 0.23 μm and preferential accumulation in PSMA+ PC3 PIP tumors versus isogenic PSMA– PC3 flu tumors. Positron emission tomography-computed tomography imaging and ex vivo biodistribution studies of dendrimers radiolabeled with 64Cu, [64Cu]G4(MP-KEU), demonstrated high accumulation in PSMA+ PC3 PIP tumors at 24 h post-injection (45.83 ± 20.09% injected dose per gram of tissue, %ID/g), demonstrating a PSMA+ PC3 PIP/PSMA– PC3 flu ratio of 7.65 ± 3.35. Specific accumulation of G4(MP-KEU) and [64Cu]G4(MP-KEU) in PSMA+ PC3 PIP tumors was inhibited by the known small-molecule PSMA inhibitor, ZJ-43. On the contrary, G4(Ctrl), control dendrimers without PSMA-targeting moieties, showed comparable low accumulation of ∼1%ID/g in tumors irrespective of PSMA expression, further confirming PSMA+ tumor-specific uptake of G4(MP-KEU). These results suggest that G4(MP-KEU) may represent a suitable scaffold by which to target PSMA-expressing tissues with imaging and therapeutic agents.
Unperturbed dimensions of poly(ethylene oxide) (1969)

Abstract The intrinsic viscosities of fractions of poly(ethylene oxide) in the molecular weight range 1.5 × 10 3 to 10 6 have been measured at 25°C in benzene, carbon tetrachloride, and acetone; at 35°C in 0.45 M aqueous potassium sulfate; and at 50°C in methyl isobutyl ketone and diethylene glycol diethyl ether. The latter three are practically theta solvents. The value of ( r 0 2 / M ) 1/2 for poly(ethylene oxide) is calculated to be 0.84 Å from the molecular weights of the high molecular weight fractions, and their intrinsic viscosities in the theta solvents and acetone. Erroneous values result if the usual methods of determination are applied to the data obtained for the low molecular weight (&lt;10 4 ) fractions or to the intrinsic viscosities in the very good solvents, benzene and carbon tetrachloride.
Robust multicast protocols for wireless multihop networks (2014)

The problem of multicasting in wireless multihop networks was studied in this dissertation. Nodes in the multicast routing structures were classified into different classes based on their roles in the multicast routing structures. Optimal multicast routing strategies for different classes were analyzed using the most accurate interference model. Based on the analyses, two algorithms to create interference-aware multicast routing tree and three algorithms to create interference-aware multicast routing mesh were proposed. The proposed multicast routing structures were evaluated using wireless network simulations. To improve the credibility of the wireless network simulations, a frame-level bursty link model was proposed and implemented in ns-3 network simulator. The results showed that, by taking interference into account when building multicast routing structures, the proposed multicast routing structures provided improved performance over other multicast routing structures that do not consider wireless interference when building multicast routing structures.
An optical implementation of a packet-based (Ethernet) MAC in a WDM passive optical network overlay (2002)

We propose and demonstrate an optical implementation of an Ethernet (CSMA/CD) MAC on a WDM PON using spectrally slicing and novel AWG wiring connections. Fairness and throughput are demonstrated and compared to theory and simulations.
누리장나무 꽃의 Flavonoid 성분 (2015)

Seven flavonoids were isolated from the flower of Clerodendrum trichotomum. Their structures were identified as apigenin (1), genistein (2), chrysoeriol (3), genistein 7-O-glucoside (4), kaempferol 3-O-glucoside (5), isorhamnetin 3-O-glucoside (6) and apigenin 7-O-glucoside (7) on the basis of spect...
Math-Modeling and Analysis of the Error of Flange-Measure Tool (2012)

Flange measure apparatus is a kind of measure tool that is used for sub-sea pipe installing.Flange measure apparatus can measure the space relation of platform riser and sub-sea pipe(the space relation of two straight lines which are in different surface).There is bug with the flange measure apparatus used in construction at present,and the measure precision is affected.For this problem of flange measure apparatus,a method solved the problem is presented,a math-models is get up(the space relation of two straight lines which are in different surface),and the error in theory is analyzed.These will be useful for improving and error-repairing of the flange measure apparatus.
Shape‐ and Size‐Controlled Synthesis of Uniform Anatase TiO2 Nanocuboids Enclosed by Active {100} and {001} Facets (2011)

Abstract Uniform anatase TiO 2 nanocuboids enclosed by active {100} and {001} facets over a wide size range (60–830 nm in length) with controllable aspect ratios were solvothermally synthesized through hydrolysis of titanium tetraisopropoxide (TTIP) using acetic acid (HAc) as the solvent and the ionic liquid 1‐butyl‐3‐methylimidazolium tetrafluoroborate ([bmim][BF 4 ]) as the capping agent. The size and aspect ratio of the anatase TiO 2 nanocuboids can be readily adjusted by changing the composition parameters including the contents of [bmim][BF 4 ], water, and HAc in the quaternary solution system. It was revealed that [bmim][BF 4 ] played an important role in stabilizing both the {100} and {001} facets of the anatase TiO 2 nanocuboids. On the one hand, [bmim][BF 4 ] acted as a fluoride source to release F − ions for stabilizing the {001} facets; on the other hand, the [bmim] + ions acted as effective capping ions to preferentially stabilize the {100} facets. The obtained near‐monodisperse anatase TiO 2 nanocuboids exhibited an interesting self‐assembly behavior during deposition. These single‐crystalline anatase nanocuboids showed extremely high crystalline phase stability, retaining the pure phase of anatase as well as the morphology even after being calcined at 900 °C. Moreover, the anatase nanocuboids exhibited considerably enhanced photocatalytic activity owing the wholly exposed active {100} and {001} facets.
Processing Windows for Forming Silk Fibroin Biomaterials into a 3D Porous Matrix (2005)

In the present study we clarify phase diagrams related to silk fibroin processing into three-dimensional porous structures useful for biomaterials and for scaffolds in tissue engineering. All-aqueous and organic solvent (hexafluoroisopropanol) modes of processing are compared relative to solution concentration of silk protein polymer and size of porogen (NaCl particles). The results clarify the range of conditions under which these biomaterial matrices can be formed, with a broader range of pore sizes and smoother surface morphology generated from the organic solvent process. These structures are directly applicable to fundamental studies of protein-based biomaterial assembly as well as cell interactions and tissue formation with these systems.
Acetate inhibits NFAT activation in T cells via importin β1 interference (2007)

Acetate is a principal short chain fatty acid produced by bacterial fermentation in the colon and a major end product of alcohol metabolism. In the present study, we assessed the effects of acetate on T cell activation and found that acetate inhibited NFAT activation but not NF-kappaB activation. Moreover, acetate impaired the nuclear translocation of NFAT but not that of NF-kappaB. Unlike cyclosporin A (CsA), acetate did not affect the dephosphorylation of NFAT and calcineurin activity. Acetate impaired the binding of NFAT to importin beta1, which is involved in NFAT nuclear translocation. NFAT is a critical transcription factor in cytokine and early response gene expression in activated T cells. Agents targeting NFAT such as CsA are used to suppress harmful immune responses in inflammatory diseases. Therefore, we also evaluated the efficacy of acetate in murine models of inflammatory diseases, and found that acetate administration (as well as administration of dexamethasone) attenuated trinitrobenzenesulfonic acid-induced colitis and dinitrofluorobenzene-induced dermatitis. These findings indicate for the first time that acetate inhibits NFAT activation by interfering with the interaction between NFAT and importin beta1 in T cells and that acetate can potentially act as an anti-inflammatory agent.
Fluorescence lifetime imaging microscopy: fundamentals and advances in instrumentation, analysis, and applications (2020)

FLIM is advantageous for probing molecular environments of fluorophores to inform on fluorophore behavior that cannot be elucidated with intensity measurements alone. Development of FLIM technologies, analysis, and applications will further advance biological research and clinical assessments.
Translocational pausing of apolipoprotein B can be regulated by membrane lipid composition (1998)

One potential mechanism by which apolipoprotein (apo) B secretion is regulated is via transient pausing during translocation across the endoplasmic reticulum membrane. We have previously shown that translocation and secretion of full-length and truncated variants of apoB 100 are impaired in hepatocytes in which microsomal membranes are enriched in the phospholipid phosphatidylmonomethylethanolamine (PMME). We have now investigated whether or not the decreased translocation of apoB is the result of altered membrane lipid composition having an impact on translocational pausing. Our experiments showed that less in vitro translated apoB-15 (the N-terminal 15% of human apoB-100) was translocated into the lumen of PMME-enriched microsomes than of control microsomes. Proteinase K treatment of the translocation products yielded discrete N-terminal fragments of apoB indicating that both types of microsomal membranes contained translocationally paused nascent chains. Similarly, apoB generated from a truncated mRNA lacking a stop codon was also found to be translocationally paused. However, restarting of translocation after translocational pausing was impaired in PMME-enriched, but not in control, microsomes. These data suggest that secretion of apoB-containing lipoproteins can be regulated by membrane lipid composition at the level of translocational pausing.
Targeting matrix metalloproteases to improve cutaneous wound healing (2006)

Wound repair is a physiological event in which tissue injury initiates a repair process leading to restoration of structure and function of the tissue. Cutaneous wound repair can be divided into a series of overlapping phases including formation of fibrin clot, inflammatory response, granulation tissue formation incorporating re-epithelialisation and angiogenesis and finally, matrix formation and remodelling. Matrix metalloproteases (MMPs) are a family of neutral proteases that play a vital role throughout the entire wound healing process. They regulate inflammation, degrade the extracellular matrix (ECM) to facilitate the migration of cells and remodel the new ECM. However, excessive MMP activity contributes to the development of chronic wounds. Selective control of MMP activity may prove to be a valuable therapeutic approach to promote healing of chronic ulcers. Recent evidence indicates that the anticoagulant, activated protein C may be useful in the treatment of non-healing wounds by preventing excessive protease activity through inhibition of inflammation and selectively increasing MMP-2 activity to enhance angiogenesis and re-epithelialisation.