gebhart/patrepeval huggingface dataset:
Number and location of AUUUA motifs: role in regulating transiently expressed RNAs (1994)

Many RNAs coding for either cytokines or oncogenes are unstable and have a short half-life (t1/2). The AUUUA motif is a highly conserved sequence and is repeated three or more times in the 3′ untranslated region (3′UTR) of RNAs encoding many of these short-lived cytokines and oncogenes. These sequences can confer instability. In this study, we investigated the role of number and location of AUUUA motifs in stabilization of RNA. We introduced 1xATTTA, 2xATTTA, ATTTTTTTA (second adenosine of 2xATTTA was substituted with a thymidine), 3xATTTA, 5xATTTA, 7xATTTA [AT-rich sequence from granulocyte-macrophage colony- stimulating factor [GM-CSF] gene (AT-62)], and GC-62 (GC sequences were substituted for ATTTA sequences in the 7xATTTA) into the 3′UTR of rabbit beta-globin (R beta G) gene. This construct also contained the neomycin-resistance gene. These expression vectors were transfected into human lung fibroblasts (W138), which constitutively expressed low levels of GM-CSF mRNA. Stable transfectants were selected by growth in G418. Northern blot analysis of actinomycin D-treated, stably transfected cells demonstrated that the number of AUUUA sequences correlated with rapidity of turnover of the chimeric R beta G mRNA. The rank order of stability was GC-62 = 1xATTTA = 2xATTTA (no RNA decay at 4 hours) > 3xATTTA = 5xATTTA (t1/2, 4 hours) > 7xATTTA (t1/2, 2 hours). Stability of mRNA of R beta G also was reduced (t1/2, 2 to 4 hours) when AT-62 was introduced into the second exon of R beta G gene. In these same cells, the t1/2 of GM-CSF RNA was approximately 10 to 15 minutes, suggesting that the AUUUA motifs cannot alone account for the rapid degradation of this cytokine mRNA. Phorbol diesters, including 12- 0-tetradecanoyl phorbol 13-acetate (TPA), stabilize a variety of transiently expressed RNAs, including GM-CSF RNA. We found that TPA markedly increased (> 30-fold) the accumulation of GM-CSF RNA. In contrast, TPA was unable to stimulate the levels of the chimeric R beta G when either 1x, 2x, 3x, or 5xATTTA motifs were fused to 3′UTR, or when either AT-62 or GC-62 control sequences were fused to the second exon. The chimeric beta-globin construct with either AT-62 or ATTTTTTTA in the 3′UTR had only an approximately twofold to threefold increase in accumulation.
AMBIGUITY RESOLUTION IN THE SPASUR RADIO INTERFEROMETER DIRECTION FINDING SYSTEM, (1967)

A number of methods for ambiguity resolution for use in the Spasur radio interferometer direction-finding system were derived and were studied using both Monte Carlo and operational data. Implementations of the methods in both hardware and software were analyzed. The conclusion was drawn that the optimum resolution results can be obtained only by the joint optimization of the antenna configuration and the resolution process to form an optimum processing system. (Author)
Complete elimination of self-pulsations in dual-clad ytterbium-doped fiber lasers at all pumping levels (2009)

We have demonstrated suppression and elimination of self-pulsing in a watt-level, dual-clad, ytterbium-doped fiber laser. The addition of a long section of passive fiber in the laser cavity makes the gain recovery faster than the self-pulsation dynamics, allowing only stable cw lasing. This scheme provides a simple and practical method for eliminating self-pulsations in fiber lasers at all pumping levels.
Adenovirus E3-6.7K Protein Is Required in Conjunction with the E3-RID Protein Complex for the Internalization and Degradation of TRAIL Receptor 2 (2004)

Adenoviruses (Ads) encode several proteins within the early region 3 (E3) transcription unit that help protect infected cells from elimination by the immune system. Among these immunomodulatory proteins, the receptor internalization and degradation (RID) protein complex, which is composed of the RIDalpha (formerly E3-10.4K) and RIDbeta (formerly E3-14.5K) subunits, stimulates the internalization and degradation of certain members of the tumor necrosis factor (TNF) receptor superfamily, thus blocking apoptosis initiated by Fas and TNF-related apoptosis-inducing ligand (TRAIL). The experiments reported here show that TRAIL receptor 2 (TR2) is cleared from the cell surface in Ad-infected cells. Virus mutants containing deletions that span E3 were used to show that the RID and E3-6.7K proteins are both necessary for the internalization and degradation of TR2, whereas only the RID protein is required for TRAIL receptor 1 downregulation. In addition, replication-defective Ad vectors that express individual E3 proteins were used to establish that the RID and E3-6.7K proteins are sufficient to clear TR2. These data demonstrate that E3-6.7K is an important component of the antiapoptosis arsenal encoded by the E3 transcription unit of subgroup C Ads.
Geometric Robustness of Deep Networks: Analysis and Improvement (2018)

Deep convolutional neural networks have been shown to be vulnerable to arbitrary geometric transformations. However, there is no systematic method to measure the invariance properties of deep networks to such transformations. We propose ManiFool as a simple yet scalable algorithm to measure the invariance of deep networks. In particular, our algorithm measures the robustness of deep networks to geometric transformations in a worst-case regime as they can be problematic for sensitive applications. Our extensive experimental results show that ManiFool can be used to measure the invariance of fairly complex networks on high dimensional datasets and these values can be used for analyzing the reasons for it. Furthermore, we build on ManiFool to propose a new adversarial training scheme and we show its effectiveness on improving the invariance properties of deep neural networks.
Sequences and repertoire of the human T cell receptor α and β chain variable region genes in thymocytes (1987)

To compare and contrast the human T cell antigen receptor (TcR) alpha and beta chain messages found in human thymocytes to those previously isolated from human peripheral blood T lymphocytes and other nonthymic sources, 13 TcR alpha and 13 TcR beta cDNA were isolated from a human thymocyte library and the nucleotide sequences were determined. The data indicate that, as was found in the peripheral T lymphocytes, the majority of the TcR alpha and TcR beta chain thymocyte cDNA were derived from potentially functional messages. Although the thymocyte-derived TcR cDNA do not contain any unique structural features when compared to TcR cDNA from mature T lymphocytes, 4 new J alpha segments, 17 new V-gene segments (9 V alpha; 8 V beta) and 7 additional V-gene families (4 V alpha and 3 V beta) and sequences had been identified. The exon C beta O, found in many murine thymocyte TcR beta messages, was not found in over 75 human beta chain messages. Based on these new data, a revised estimate of human TcR V alpha, J alpha and V beta repertoires is calculated. The most significant change has been the increase in the estimated number of human TcR V beta-gene segments to a total of about 100 distributed among about 18 families. The V alpha families are now revised upward to 16, with a total number of V alpha segments of 50. The estimate of the J alpha segments in humans remains between 50-100.
Caracteres históricos de la Geomorfología moderna (1984)

Este artículo intenta presentar algunos rasgos de la geomorfología moderna a la luz de sus nexos históricos con la geografía y, a través de ella, con el conjunto de las ciencias sociales. Esta conexión implica una dependencia parcial del pensamiento geomorfológico en relación con la controversia metodológica entre naturalismo e historicismo, cuyo desarrollo difiere según los países. En geomorfología, como en otras ciencias, ese pluralismo ha sido un activo factor de cambio. Dentro de este intento de explicación histórica de los estudios sobre el relieve, se subraya el influjo duradero de las polémicas sobre el método ligadas a la crisis del positivismo decimonónico, que tuvo lugar en vísperas de la emergencia de la geomorfología como disciplina diferenciada. Los rasgos tardopositivistas de la síntesis davisiana son destacados especialmente para relacionarlos con determinados puntos débiles de la estructura doctrinal que se pueden apreciar en los tratados y manuales de geomorfología.
Structure-response Relationships in Noctuid Sex Pheromone Reception An Introductory Report (1975)

Electroantennogram (EAG) data reflecting response spectra of male pheromone receptors have been analyzed for 16 species of Noctuidae (Lepidoptera). The test compounds included 100 pheromone analogues, altered in chain length, in position and configuration of double bond(s), and in the functional end groups. On comparison of amounts of substance required to elicit an equivalent EAG response, a single compound was determined to be most effective on a given species: these structures, either known or proposed as the natural sex pheromones of the species, were cis-7-dodecen-1-y1 acetate, cis-7-tetradecen-1-y1 acetate, cis-9-tetradecen-1-yu acetate, trans-9-tetradecen-1-y1 acetate, cis-11-hexadecen-1-y1 acetate, cis-9, trans-12-tetradecadien-1-y1 acetate, cis-9-tetradecen-1-y1 formate, and cis-9-tetradecen-1-ol, respectively. Elongation (shortening) of the chain by 1 or 2 methylene groups, the movement of a double bond 1 carbon from the optimum, a change to the opposite geometrical isomer, or the introduction of a second double bond invariably reduced EAG responses to 1.8 to 56 times below that observed with the most stimulating compound, in all 16 species. Further alterations in chain length or in double bond position caused even greater reduction in activity, as did certain in end group (Tables I and II). A set of distinct rules could be derived from these structure-response relationships; one of these rules concerns the optimum position of the double bond(s) in relation to chain length, and another one the ratios in activity values produced by end group variations, irrespective of chain length. The same rules described here for 16 noctuid species held also for the structure-response relationships observed within various additional groups of Lepidoptera. From EAG values determined in this study, an attempt has been made to calculate physicochemical propteries of underlying acceptor structures.
Skin Mast Cells Protect Mice against Vaccinia Virus by Triggering Mast Cell Receptor S1PR2 and Releasing Antimicrobial Peptides (2011)

Mast cells (MCs) are well-known effectors of allergic reactions and are considered sentinels in the skin and mucosa. In addition, through their production of cathelicidin, MCs have the capacity to oppose invading pathogens. We therefore hypothesized that MCs could act as sentinels in the skin against viral infections using antimicrobial peptides. In this study, we demonstrate that MCs react to vaccinia virus (VV) and degranulate using a membrane-activated pathway that leads to antimicrobial peptide discharge and virus inactivation. This finding was supported using a mouse model of viral infection. MC-deficient (Kit(wsh-/-)) mice were more susceptible to skin VV infection than the wild type animals, whereas Kit(wsh-/-) mice reconstituted with MCs in the skin showed a normal response to VV. Using MCs derived from mice deficient in cathelicidin antimicrobial peptide, we showed that antimicrobial peptides are one important antiviral granule component in in vivo skin infections. In conclusion, we demonstrate that MC presence protects mice from VV skin infection, MC degranulation is required for protecting mice from VV, neutralizing Ab to the L1 fusion entry protein of VV inhibits degranulation apparently by preventing S1PR2 activation by viral membrane lipids, and antimicrobial peptide release from MC granules is necessary to inactivate VV infectivity.
Derivatives of 5-[[1-4(4-carboxybenzyl)imidazolyl]methylidene]hydantoins as orally active angiotensin II receptor antagonists (1995)

A series of 5-[[1-(4'-carboxybenzyl)imidazolyl]methylidene]hydantoins have been prepared and evaluated as in vitro and in vivo angiotensin II (Ang II) antagonists. Variation of substituents on the hydantoin ring leads to potent and selective Ang II antagonists with nanomolar IC50 values at the AT1 receptor and negligible affinity for the AT2 receptor. Preferred substituents include an n-butyl at R1 and an alkyl or heteroarylmethyl substituent at R2. The selection of the R2 substituent was guided in part by the calculation of its log P since a significant correlation was observed between CLOGP and AT1 binding affinity. The biphenyl tetrazole pharmacophore, common to a number of AT1 antagonists, could be replaced by, for example, a 4-carbomethoxyphenyl substituent resulting in potent Ang II antagonists both in vitro and in vivo. A representative compound of this series is 57, which reduced the mean arterial blood pressure of renal hypertensive rats by 40% at 30 mg/kg po and by 25% at 10 mg/kg po. In addition this compound was efficacious in the salt-deplete normotensive monkey model maximally decreasing blood pressure 27% at 10 mg/kg po. In summary, these compounds belong to a novel class of Ang II antagonists that lack the biphenyl tetrazole moiety yet display appreciable and long lasting oral activity.
Tire Cornering Simulation Using an Explicit Finite Element Analysis Code (1998)

Abstract The finite element method has been used widely in tire engineering. Most tire simulations using the finite element method are static analyses, because tires are very complex nonlinear structures. Recently, transient phenomena have been studied with explicit finite element analysis codes. In this paper, the authors demonstrate the feasibility of tire cornering simulation using an explicit finite element code, PAM‐SHOCK. First, we propose the cornering simulation using the explicit finite element analysis code. To demonstrate the efficiency of the proposed simulation, computed cornering forces for a 175SR14 tire are compared with experimental results from an MTS Flat‐Trac Tire Test System. The computed cornering forces agree well with experimental results. After that, parametric studies are conducted by using the proposed simulation.
Variational Inference for Crowdsourcing (2012)

Crowdsourcing has become a popular paradigm for labeling large datasets. How-ever, it has given rise to the computational task of aggregating the crowdsourced labels provided by a collection of unreliable annotators. We approach this prob-lem by transforming it into a standard inference problem in graphical models, and applying approximate variational methods, including belief propagation (BP) and mean field (MF). We show that our BP algorithm generalizes both major-ity voting and a recent algorithm by Karger et al. [1], while our MF method is closely related to a commonly used EM algorithm. In both cases, we find that the performance of the algorithms critically depends on the choice of a prior distribu-tion on the workers ’ reliability; by choosing the prior properly, both BP and MF (and EM) perform surprisingly well on both simulated and real-world datasets, competitive with state-of-the-art algorithms based on more complicated modeling assumptions. 1
ChemInform Abstract: SYNTHESIS AND STEREOCHEMISTRY OF 3‐(α‐HYDROXYBENZYL)‐1,4‐DIPHENYL‐2‐AZETIDINONES (1983)

Abstract Die Reaktion zwischen dem Azetidinon (Ia) und Aceton (II) ergibt nach längerer Reaktionsdauer das Derivat (III), während nach nur kurzer Reaktionszeit das Derivat (IV) entsteht, dessen Bildung auch ohne (II) erfolgt.
Ependymin, a Brain Extracellular Glycoprotein, and CNS Plasticity<sup>a</sup> (1991)

Ependymin, a glycoprotein of the brain ECF, has been implicated in the neurochemistry of memory and neuronal regeneration. Three behavioral experiments (swimming with a float, avoidance conditioning, and classical conditioning) in the goldfish and one in the mouse (T-maze learning) indicate that ependymin has a role in the synaptic changes that take place in the consolidation step of memory formation and the activity-dependent phase of sharpening of goldfish retinotectal connections during neuronal regeneration. The ECF concentration of the protein was found to decrease after the goldfish learned to associate a light stimulus (CS) with the subsequent arrival of a shock (US): paired CS-US gave changes whereas an unpaired presentation of CS-US gave no changes relative to the unstimulated controls. Ependymin is present in ECF as a mixture of three disulfide-linked dimers of two acidic (alpha and beta) polypeptide chains (37 kDa and 31 kDa). Upon removal of its N-linked glycan fragment by N-glycosidase F, the beta chain yields gamma-ependymin (26 kDa). Determinations of the amino acid sequence of gamma-ependymin indicate that it is a unique protein with no long sequence homologies to any known polypeptide. There are, however, small segments (5-7 amino acids long) with homologies to fibronectin, laminin, and tubulin. Ependymin has the capacity to polymerize into FIP (after activation by phosphorylation) in response to events that deplete ECF calcium. FIP is insoluble in 2% SDS in 6 M urea, 10 mM Ca2+Ac2, 100% acetic acid, chloroform/methanol (2/1), saturated KCNS, and even 100% trifluoroacetic acid. FIP was found to be present in goldfish brain and to be formed as a labeled product in vivo. Ependymin's FIP-forming property was used to propose a molecular hypothesis for generating synaptic changes in response to local extracellular depletions of calcium at sites of "associating inputs." The model assumes that, following NMDA receptor stimulation, the translocated PKC that is generated activates extracellular ependymin by converting it to its phosphorylated form using presynaptically released ATP. The hypothesis was tested in studies of LTP of rat hippocampal slices at CA1. After LTP, new sites that stained with antisera to ependymin, visible at 100x, were obtained in its potentiated radiatum in the CA1 region but not in the unpotentiated CA3. Electron microscopic studies showed that the horseradish peroxidase reaction product obtained was localized at synaptic clefts and postsynaptic regions. The results suggest that FIP may be formed at extracellular and postsynaptic loci where multiple associating inputs interact at CA1.
Other Contributions: Plant Parasitic Nematodes from the Lowlands and Highlands of Ecuador (1976)

Soil and root samples of 25 different crops were collected at numerous localities throughout the lowlands and highlands of Ecuador and examined for nematodes. Radopholus similis was the most abundant plant parasitic nematode of banana and caused root necrosis, toppling and reduced growth at all sites sampled. High root populations of Pratylenchus coffeae caused similar damage to abaca (Musa textilis). Meloidogyne incognita and M. hapla occurred commonly and were responsible for root galling of tomato, alfalfa, carrot, cucumber, lettuce, tree tomato, babaco and soybean. Heterodera pallida and Ditylenchus dipsaci were present in large numbers on potato and onions respectively in the highlands. Other nematodes frequently found in roots of many crops were Pratylenchus neglectus and Helicotylenchus spp.; Quinisulcius acti was commonly extracted from soils. Less frequently occurring nematodes included Pratylenchus penetrans, Criconemoides spp., Merlinius sp., Tylenchorhynchus sp., Hemicric
A DFT computational study of phosphine ligand dissociation<i>versus</i>hemilability in a Grubbs-type precatalyst containing a bidentate ligand during alkene metathesis (2008)

Using density functional theory, the metathesis reaction of 1-octene in the presence of a Grubbs-type ruthenium alkylidene complex bearing a chelating pyridinyl alcoholate ligand, [RuCl(L)(O∧ N)( = CHPh)] (L = H2IMes or PCy3, O∧ N = 1-(2′-pyridinyl)cyclohexan-1-olate)), was investigated. The complete geometry optimisation and activation energy of various activation steps in the dissociative mechanism were performed at the GGA-PW91/DNP level of theory using Accelrys Materials Studio® 4.0. Two possible precatalyst initiations were explored, i.e. the dissociation of the labile N-atom of the O∧ N-ligand as well as the dissociation of ligand L, due to the belief that ruthenium-catalysed metathesis reactions proceed through 14-electron intermediates. The formation of the catalytically active heptylidene species is kinetically favoured for both the first- and second-generation chelating complexes. The computational results are in agreement with the experimental results obtained with NMR for the second-generation system. The computational results suggest that both phosphine ligand dissociation and hemilability may play a role in the metathesis reaction with the first-generation system.
Safety and Pharmacokinetics of Intravenous Anidulafungin in Children with Neutropenia at High Risk for Invasive Fungal Infections (2006)

Anidulafungin is an echinocandin with activity against Candida species and Aspergillus species. Adult dosages under study are 50 mg/day for esophageal candidiasis and 100 mg/day for invasive candidiasis and aspergillosis. Little is known, however, about the safety and pharmacokinetics of anidulafungin in children. A multicenter, ascending-dosage study of neutropenic pediatric patients was therefore conducted. Patients were divided into two age cohorts (2 to 11 years and 12 to 17 years) and were enrolled into sequential groups to receive 0.75 or 1.5 mg/kg of body weight/day. Blood samples were obtained following the first and fifth doses. Anidulafungin was assayed in plasma, and pharmacokinetic parameters were determined. Safety was assessed using National Cancer Institute (NCI) common toxicity criteria. Pharmacokinetic parameters were determined for 12 patients at each dosage (0.75 mg/kg/day or 1.5 mg/kg/day). Concentrations and drug exposures were similar for patients between age cohorts, and weight-adjusted clearance was consistent across age. No drug-related serious adverse events were observed. One patient had fever (NCI toxicity grade of 3), and one patient had facial erythema, which resolved with slowing the infusion rate. Anidulafungin in pediatric patients was well tolerated and can be dosed based on body weight. Pediatric patients receiving 0.75 mg/kg/day or 1.5 mg/kg/day have anidulafungin concentration profiles similar to those of adult patients receiving 50 or 100 mg/day, respectively.
Osseointegration for Amputees (2020)

Osseointegrated prostheses provide a rehabilitation option for amputees offering greater mobility, better satisfaction, and higher use than traditional socket prostheses. There are several different osseointegrated implant designs, surgical techniques, and rehabilitation protocols with their own strengths and limitations. The 2 most prominent risks, infection and periprosthetic fracture, do not seem unacceptably frequent or insurmountable. Proximal amputations or situations leading to reduced mobility are exceptionally infrequent. Osseointegrated implants can be attached to advanced sensory and motor prostheses.
Mutation scanning using high-resolution melting (2009)

Mutation scanning techniques are used to detect sequence variants without the need for prior knowledge of the identity or precise location of the variant, in contrast with genotyping techniques, which determine the status of a specific variant. High-resolution melting is a recently developed method that shows great potential as a mutation scanning technique. Sensitivity and specificity for mutation detection are extremely high and the technique also has advantages of cost and throughput. Practical considerations for successful mutation scanning by high-resolution melting are also discussed in this review.