gebhart/patrepeval huggingface dataset:
Modular Approach to Silicon‐Bridged Biaryls: Palladium‐Catalyzed Intramolecular Coupling of 2‐(Arylsilyl)aryl Triflates (2008)

Bridge of Si: Intramolecular direct arylation of 2-(arylsilyl)aryl triflates is catalyzed smoothly by Pd(OAc)2/PCy3 in the presence of Et2NH in dimethylacetamide (DMA), giving rise to the corresponding silicon-bridged biaryls in good to excellent yields. The new approach has led to the synthesis of a silicon-bridged 2-phenylindole (see scheme) that exhibits blue photoluminescence in the solid state with extremely high quantum yields.
Low loss, heat-resistant optical waveguides using new fluorinated polyimides (1993)

Two types of polymer ridge optical waveguide are prepared using new fluorinated polyimides with excellent transparency and refractive index controllability. One has a polyimide core with a refractive index n of 1.573 and an SiO2 undercladding layer. The other has a polyimid e core (n = 1.521) and a polyimide undercladding layer (n = 1.520). These waveguides exhibit a low loss of 0.3dB/cm at 1.3μm. In addition, they have high thermal stability because of high temperature curing (above 350°C).
Quantitative Trait Loci for Root Architecture Traits Correlated with Phosphorus Acquisition in Common Bean (2006)

Low soil P availability is a primary constraint to common bean ( Phaseolus vulgaris L.) production in Latin America and Africa. Substantial genotypic variation in bean adaptation to low phosphorus (LP) availability has been linked with root traits that enhance the efficiency of soil foraging. The objectives of this study were to identify quantitative trait loci (QTLs) for P accumulation and associated root architectural traits, to facilitate genetic improvement and to reveal physiological relationships. Eighty‐six F 5.7 recombinant inbred lines (RILs) were developed from a cross between G19833, an Andean landrace with high total P accumulation, and DOR 364, a Mesoamerican cultivar with low total P accumulation in LP conditions. A genetic map constructed with restriction fragment length polymorphisms (RFLPs), microsatellites, and PCR‐based markers covering 1703 centimorgans (cM) total genetic distance and all eleven linkage groups (LGs) was used for QTL analysis. Seventy‐one RILs were evaluated in the field at high phosphorus (HP) and LP for P accumulation, total root length (RL), specific RL, and plant dry weight (DW), while all 86 RILs were evaluated in a hydroponic system in the greenhouse for tap, basal, total, and specific RL and plant DW. Phosphorus accumulation in the field correlated with root parameters measured in the greenhouse. A total of 26 individual QTLs were identified for P accumulation and associated root characters using composite interval mapping (CIM) analysis. Phosphorus accumulation QTLs often coincided with those for basal root development, thus, basal roots appear to be important in P acquisition. Independent QTLs were identified for basal and taproot development, and for specific RL. Distinct QTLs for greater specific RL had positive, null and negative effects on P accumulation. Our results confirm the importance of root structure for LP adaptation and highlight the need for a more detailed understanding of root architectural traits for phenotypic as well as marker‐aided selection of more P‐efficient crops.
The G glycoprotein of human respiratory syncytial viruses of subgroups A and B: extensive sequence divergence between antigenically related proteins. (1987)

Two major antigenic subgroups (designated A and B) have been described for human respiratory syncytial virus (RSV). Previously, on the basis of reactivity patterns with monoclonal antibodies, the greatest intersubgroup variation was shown to occur in the G protein, the putative attachment glycoprotein. To delineate the molecular basis for this variation, we have determined the nucleotide and deduced amino acid sequences of the G mRNAs and proteins representing a subgroup A (Long strain) and a subgroup B (18537 strain) virus. These sequences were compared to the available G mRNA sequence for another subgroup A (A2 strain) virus. The Long G protein shared 94% amino acid identity with the A2 G protein. In contrast, the 18537 G protein shared only 53% amino acid identity with the A2 sequence; interestingly, most of the sequence divergence occurred in the proposed extracellular domain of the G protein. This extensive divergence for the G protein was significantly greater than that observed for other RSV proteins. Despite this considerable divarication, the proposed extracellular domains of the G proteins contained a single region of highly conserved sequence and secondary structure that may represent a conserved structural or function domain, perhaps involved in attachment to cellular receptors. Furthermore, this conserved region may comprise part of an epitope that is shared between the two subgroup G proteins and may significantly contribute to the fact that, despite extensive overall amino acid sequence divergence, the RSV G proteins maintain significant antigenic relatedness.
The base-pairing specificity of cellulose-pdT9 (1975)

The stability of the interaction of oligoadenylates, containing single nucleotide substitutions, with cellulose-pdT9 has been studied by thermal elution. In the case of oligodeoxyriboadenylates, the replacement of an internal dA by dC, dG or dT caused destabilization. In the case of oligoriboadenylates, replacement of an internal A residue by C or U resulted in a significantly lesser destabilization. The results indicate that caution should be exercised in extrapolation of data on the specificity of deoxyribonpolynucleotide-deoxyribopolynucleotide hybridization to structure of the type deoxyribopolynucleotide-ribopolynucleotide.
Selective Delivery of Estradiol to Bone by Aspartic Acid Oligopeptide and Its Effects on Ovariectomized Mice (2001)

We have developed a novel osteotropic prodrug of estradiol (E(2)) conjugated with L-Asp-hexapeptide (E(2).3D(6)), which has very low affinity for estrogen receptors, and in this study, we examined its pharmacokinetic behavior and pharmacological potential. After a single iv injection of E(2) x 3D(6) to mice, the half-time for elimination from plasma was about 100 min; however, E(2) was selectively delivered to the bone and eliminated very slowly, declining to the endogenous level at about 7 days. After a single iv injection of E(2), the half-time in plasma was about 70 min, whereas E(2) was highly distributed to the uterus, and the bone concentration of E(2) was only slightly increased at 6 h. When E(2) (0.37 micromol/kg, sc, every third day) or E(2) x 3D(6) (0.11 to 1.1 micromol/kg, sc, every seventh day) was administered to OVX mice for 4 weeks, E(2) increased the bone mineral density (BMD) together with weights of liver and uterus, whereas E(2) x 3D(6) increased only the BMD, in a dose-dependent manner. E(2) x 3D(6) enhanced the expression of messenger RNAs of bone matrix proteins (osteopontin, bone sialoprotein, type I collagen alpha) of OVX mice at 4 h after administration, but E(2) did very slightly. These results indicate that the E(2) prodrug was delivered to the bone, where it gradually released E(2), thereby ameliorating bone loss. This acidic oligopeptide appears to be a good candidate for selective drug delivery to bone.
Extracellular matrix of human amnion manufactured into tubes as conduits for peripheral nerve regeneration (2002)

The human amnion consists of the epithelial cell layer and underlying connective tissue. After removing the epithelial cells, the resulting acellular connective tissue matrix was manufactured into thin dry sheets called amnion matrix sheets. The sheets were further processed into tubes, amnion matrix tubes (AMTs), of varying diameters, with the walls of varying numbers of amnion matrix sheets with or without a gelatin coating. The AMTs were implanted into rat sciatic nerves. Regenerating nerves extended in bundles through tubes of 1-2 mm in diameter and further elongated into host distal nerves 1-3 weeks after implantation. Morphometrical analysis of the regenerated nerve cable at the middle of each amnion matrix tube 3 weeks after implantation was performed. The average numbers of myelinated axons were almost the same (ca. 80-112/10(4) microm(2)) in AMTs of 1-2 mm in diameter, as in the normal sciatic nerve (ca. 95/10(4) microm(2)). No myelinated fibers were found in AMTs composed of multiple thin tubes of 0.2 mm in diameter. The myelinated axons were thinner in implanted tubes than those in the normal sciatic nerve. The rate of occurrences of myelinated axons less than 4 microm in diameter was significantly higher in the AMTs, whereas axons in the normal sciatic nerve were diverse in distribution, with the highest population at 8-12 microm in diameter. Reinnervation to the gastrocnemius muscle was demonstrated electrophysiologically 9 months after implantation. It was concluded that the extracellular matrix sheet from the human amnion is an effective conduit material for peripheral nerve regeneration.
Screening and evaluation of anticancer agents. (1988)

The screening and evaluation procedures for the development of anticancer agents indicated that the entire process is a rather difficult task. This is particularly true in choosing screening models and criteria for activity. If the criteria were set too low, then some clinically false-positive results may be faced; and if the criteria were set too high, some agents could be missed which might be effective against certain types of human cancer. Presently, active compounds are selected by prescreening and screening against transplanted mouse tumors and human tumor xenografts as well as by the in vitro systems. Xenografts of human tumor in athymic nude animals represent metabolic characteristics of human malignant disease which appear to be of value in the preclinical screening. Human tumor cloning assays have gained increased attention as a promising in vitro test system for the screening as well as for the prediction of patient responses. Application of chemosensitivity tests in the prediction of the responses of individuals to chemotherapy, especially in the identification of drug resistant tumors are, in general, quite reliable. Human tumor xenografts, human tumor cloning assays and chemosensitivity tests may be regarded as the major impetus in screening during the past decade. After promising agents are selected from the screening procedures, before the filing of an investigational new drug application, the preclinical toxicology and pharmacology should be completed. Information on the nature of toxicity, dose-response effects, and dose schedule are necessary for predicting the effects of the drug in man. The new drugs then go through three phases of clinical trials to assure safety, effectiveness, and reliability of the drugs. During the past fifteen years eight-three antineoplastic drugs were evaluated clinically under the NCI sponsorship and twenty-four are active in at least one disease. Among these active drugs, eleven possess novel clinical structure, the remaining thirteen are analogues of known active compounds already in clinical trials. After an investigational anticancer drug is approved by the U.S. Food and Drug Administration it becomes a commercial product on the market and the benefits can be shared by the general public. The time required for evaluation and development from the first discovery of activity to final FDA approval for fifty-two therapeutic drugs are tabled. The average interval is 8.8 years, but in the 1950s the average was only 2.8 years, in the 1960s, 6.5 years; in the 1970s, 13.9 years; and in the 1980s, 16.0 years. This reflects the increasing stricter requirements for an antineoplastic drug to be officially recognize
The chloromethylketone protease inhibitor AAPFCMK also targets ATP‐dependent helicases and SAP‐domain proteins (2006)

We have been studying a nuclear protease, which appears to be involved in cellular transformation, as well as in infections with high-risk human papillomaviruses (HPVs). This protease has a chymotrypsin-like substrate specificity and the chloromethylketone inhibitor AAPF(CMK) is a potent (and relatively selective) inhibitor of it. Recently, we have observed that AAPF(CMK) has potent effects in some model systems which appear not to be mediated by decreases in the nuclear protease. Here we show that AAPF(CMK) selectively reacts with ATP-dependent helicases as well as a limited spectrum of proteins in other DNA repair/chromatin remodeling nuclear complexes, including for example Cohesin complex components and proteins containing SAP-domains. In vitro, AAPF(CMK) selectively reacts with SV40 large T antigen, and inhibits its helicase activity.
Dna density in mitotic and meiotic metaphase chromosomes of plants and animals (1983)

Studies of chromosome disposition at metaphase using serial thin-sectioning and three-dimensional reconstruction techniques have produced accurate estimates of the total volume of chromosomes per cell in 15 plant and two animal species. Comparing this character with the 4C DNA amount showed no indiction of systemic differences in DNA density between either organisms with widely different (greater than 200-fold) C values or different groups or organisms. For example, there was no significant difference between the density of DNA in somatic metaphase chromosomes of man (0.141 pg/micrometers3) and its mean in 14 angiosperm plant species (0.182 pg/micrometers3), or between four dicotyledons (0.180 pg/miocrometers3) and 10 monocotyledons (0.182 pg/micrometers3). However, evidence was found showing that DNA density can vary significantly within a species. Thus, although the total chromosome volume per cell was closely correlated (r greater than 0.97) with 4C DNA amount in somatic and meiotic cells, the density of DNA in metaphase chromosomes was significantly lower in meiocytes (0.131 pg/micrometers3) than in somatic metaphase cells (0.19 pg/micrometers3).
Identification, Phylogeny, and Evolution of Retroviral Elements Based on Their Envelope Genes (2001)

Phylogenetic analyses of retroviral elements, including endogenous retroviruses, have relied essentially on the retroviral pol gene expressing the highly conserved reverse transcriptase. This enzyme is essential for the life cycle of all retroid elements, but other genes are also endowed with conserved essential functions. Among them, the transmembrane (TM) subunit of the envelope gene is involved in virus entry through membrane fusion. It has also been reported to contain a domain, named the immunosuppressive domain, that has immunosuppressive properties most probably essential for virus spread within the host. This domain is conserved among a large series of retroviral elements, and we have therefore attempted to generate phylogenetic links between retroviral elements identified from databases following tentative alignments of the immunosuppressive domain and adjacent sequences. This allowed us to unravel a conserved organization among TM domains, also found in the Ebola and Marburg filoviruses, and to identify a large number of human endogenous retroviruses (HERVs) from sequence databases. The latter elements are part of previously identified families of HERVs, and some of them define new families. A general phylogenetic analysis based on the TM proteins of retroelements, and including those with no clearly identified immunosuppressive domain, could then be derived and compared with pol-based phylogenetic trees, providing a comprehensive survey of retroelements and definitive evidence for recombination events in the generation of both the endogenous and the present-day infectious retroviruses.
The 1997 HTK broadcast news transcription system (1998)

This paper presents the recent development of the HTK broadcast news transcription system. Previously we have used data type specific modelling based on adapted Wall Street Journal trained HMMs. However, we are now using data for which no manual preclassification or segmentation is available and therefore automatic techniques are required and compatible acoustic modelling strategies must be adopted. A number of recognition experiments are presented that compare data-type specific and non-specific models; differing amounts of training data; the use of gender-dependent modelling and the effects of automatic data-type classification. Based on these experiments, the HTK system for the 1997 broadcast news evaluation was designed. A detailed description of this system is given which includes a class-based language modelling component. The complete system yields an overall word error rate of 22.0% on the 1996 unpartitioned broadcast news development test data and just 15.8% on the 1997 evalua...
572. Intermediates for the synthesis of optically active methyl-substituted long-chain acids. Part II (1957)

The first page of this article is displayed as the abstract.
Meta-analysis of anti-VEGF class adverse events from three double-blind (Db) placebo (Pbo)-controlled phase III trials with IV aflibercept (Afl). (2012)

561 Background: Three Db Pbo controlled studies were conducted with IV Afl in metastatic cancer patients [colorectal (CRC) Afl+FOLFIRI (WCGC 2011 abstract O-0024), lung (LC) Afl+docetaxel (WCLC 2011, abstract 511) and pancreatic (PC) Afl+gemcitabine (WCGC 2009 abstract O-0006)]. Each study used the same weekly Afl dose intensity (4 mg/kg q2w for CRC and PC; 6mg/kg q3w for LC). A safety meta-analysis of anti-VEGF class adverse events (AE) was performed on data from these studies. Methods: A fixed-effect logistic regression model was used, including study, treatment and study-by-treatment interaction factors as covariates to test the consistency of treatment effect across studies for each of the considered AE. When no evidence of heterogeneity of treatment effects was found across studies, relative risks (RR) and 95% confidence intervals (CI) were estimated. Summary incidences (% of patients [pts]) and RR are presented for NCI grade 3-4 events. Results: Safety data from total of 2,662 pts (Afl: 1,333; Pbo: 1,329) were included for analysis (Table). Among pts treated with Afl, 0.4 and 0.5% experienced grade 4 hypertension and nephrotic syndrome, respectively. Conclusions: The addition of Afl to concurrent chemotherapies did not increase the risk of VTE. The risk of grade 3-4 anti-VEGF class AEs was increased when adding Afl to concurrent chemotherapies. This increased risk was statistically significant ( ** ) only for hypertension, proteinuria and hemorrhage. Further analyses, when more data are available, should improve the precision of these results. Studies were sponsored by Sanofi NCT00561470 , NCT00532155 , and NCT00574275 . [Table: see text]
Uptake of endocytic markers into mitotic yeast cells (1991)

[3H]alpha-Factor and Lucifer yellow were used to measure receptor mediated and fluid-phase endocytosis in the yeast Saccharomyces cerevisiae, arrested in mitosis by depolymerization of the microtubules or due to a mutation preventing nuclear division (cdc16). Both processes continued at roughly the same level as during interphase. This shows that in yeast endocytosis is not interrupted during mitosis like in mammalian cells.
Surface Plasmon Polaritons and Their Role in the Enhanced Transmission of Light through Periodic Arrays of Subwavelength Holes in a Metal Film (2004)

We present results of the transmitted, reflected, and absorbed power associated with the enhanced transmittance of light through a silver film pierced by a periodic array of subwavelength holes. Comparing experimentally acquired dispersion curves under different polarization conditions shows that the transmission features of the array are consistent with p-polarized resonant modes of the structure. By exploring the regime in which no propagating diffracted orders are allowed, we further show that the transmittance maxima are associated with both reflectance minima and absorption maxima. These new results provide strong experimental evidence for transmission based on diffraction, assisted by the enhanced fields associated with surface plasmon polaritons.
Cellular Toxicity of Polyglutamine Expansion Proteins (2004)

The expression of polyglutamine-expanded mutant proteins in Huntington's disease and other neurodegenerative disorders is associated with the formation of intraneural inclusions. These aggregates could potentially cause cellular toxicity by sequestering essential proteins possessing normal polyQ repeats, including the transcription factors TBP and CBP. We show, in vitro and in cells, that monomers or small soluble oligomers of huntingtin exon1 accumulate in the nucleus and inhibit the function of TBP in a polyQ-dependent manner. FRET experiments indicate that these toxic forms are generated through a conformational rearrangement in huntingtin. Interaction of toxic huntingtin with the benign polyQ repeat of TBP structurally destabilizes the transcription factor, independent of the formation of insoluble coaggregates. Hsp70/Hsp40 chaperones interfere with the conformational change in mutant huntingtin and inhibit the deactivation of TBP. These results outline a molecular mechanism of cellular toxicity in polyQ disease and can explain the beneficial effects of molecular chaperones.
Physical mapping of complex genomes by cosmid multiplex analysis. (1989)

A rapid and powerful approach for linking individual clones of a cosmid library and the assembly of a large physical map is presented, which depends on the simultaneous analysis of many cosmid clones for overlapping regions. This method uses cosmid vectors that contain endogenous bacteriophage T3 and T7 promoters to allow for the identification of overlapping clones through the synthesis of end-specific RNA probes. A genomic library is constructed and organized as an ordered matrix such that each clone is assigned an identifying coordinate. DNA from mixtures of cosmid clones is pooled such that each pool contains only one common member with any other pool, RNA probes are prepared from mixtures of cosmid clones, and groups of clones overlapping with the constituents of the mixtures are determined by hybridization. Pooled probes are most simply prepared by grouping clones according to the rows and columns of the library matrix. The pairwise comparison of data generated by the hybridization of mixed probes can be decoded by using simple algorithms that predict the order and linkage of all clones in the collection and organize them into predicted contigs. To demonstrate the feasibility of multiplexed analysis of cosmids, a genomic library was prepared from a mouse-human somatic cell hybrid that contains a portion of the long arm of human chromosome 11. Preparation, arrangement on a matrix, and analysis of pooled cosmid clones from this collection resulted in the detection of 1099 linked pairs of cosmids, which could be assembled into 315 contigs. Thus, with a minimal amount of effort, a substantial portion of this genomic region has been linked in multiple overlapping contigs. This method may have practical applications in the large-scale mapping and sequencing of mammalian genomes.