gebhart/patrepeval huggingface dataset:
Automatic analysis of syntactic complexity in second language writing (2010)

We describe a computational system for automatic analysis of syntactic complexity in second language writing using fourteen different measures that have been explored or proposed in studies of second language development. The system takes a written language sample as input and produces fourteen indices of syntactic complexity of the sample based on these measures. The system is designed with advanced second language proficiency research in mind, and is therefore developed and evaluated using college-level second language writing data from the Written English Corpus of Chinese Learners (Wen et al. 2005). Experimental results show that the system achieves very high reliability on unseen test data from the corpus. We illustrate how the system is used in an example application to investigate whether and to what extent each of these measures significantly differentiate between different proficiency levels
Microfluidic immunomagnetic multi-target sorting – a model for controlling deflection of paramagnetic beads (2011)

We describe a microfluidic system that uses a magnetic field to sort paramagnetic beads by deflecting them in the direction normal to the flow. In the experiments we systematically study the dependence of the beads' deflection on bead size and susceptibility, magnet strength, fluid speed and viscosity, and device geometry. We also develop a design parameter that can aid in the design of microfluidic devices for immunomagnetic multi-target sorting.
Application of the enrichment approach to identify putative markers of response to 5-fluorouracil therapy in advanced colorectal carcinomas. (2000)

A wide range of tumor response is seen amongst patients with the same stage of colorectal cancer, even with the use of uniform chemotherapy. The significant economic and personal impact of chemotherapy provides the impetus for the identification of markers of response for use in guiding patient treatment. However, practical constraints prevent evaluation of all putative markers in a definitive manner. In this study, the enrichment approach was evaluated by examining the expression of a panel of putative response markers in selected patient populations with advanced colorectal cancer (i.e., those demonstrating the best and the poorest clinical response to a standardized 5-fluorouracil/folinic acid chemotherapy regimen). Patients showing a good response had a significantly increased survival when compared with poor responders (P=0.0013). Markers were then ranked for clinical importance based on differences in expression between the two groups. This allows for the relatively rapid and inexpensive investigation of multiple markers, using defined patient groups. Bcl-2 overexpression in primary colorectal tumor specimens was found to correlate with clinical response of metastatic deposits to chemotherapy (P=0.044), as did the site of the primary tumor (P=0.011). However, no clear association was observed between response status and the other examined factors (p53, PCNA, TP, MMPs 1, 2 or 9, TIMPs 1 or 2, TS, Dukes' stage at initial diagnosis, histological grade, sex or age). This approach has allowed prioritization of markers of clinical response on which larger, statistically definitive studies will be performed.
d‐Serine Regulates Proliferation and Neuronal Differentiation of Neural Stem Cells from Postnatal Mouse Forebrain (2012)

Our findings demonstrate for the first time that NSCs can synthesize D-serine and, thereby, promote themselves proliferation and neuronal differentiation, which may afford a novel therapeutic strategy for the neurological disorders that require nerve cell replenishment, such as neurodegenerative diseases and stroke.
The predictive value of pronuclear morphology of zygotes in the assessment of human embryo quality (2001)

Our results indicate that there are no significant differences in embryo quality or implantation/pregnancy rates between proposed zygote classes.
SEARCH AND PURCHASE IN INFORMATION-OVERLOADED RETAIL ELECTRONIC MARKETPLACE: DOES PRICE AND REPUTATIOIN MATTER? (2008)

This study explores buyers' search and purchase behavior in an information-overloaded retail Electronic Marketplace (EMP). Two instrumental variables, i.e. number of visitors and number of sales for an item, are used to represent buyers' search and purchase behavior. Price and reputation, two of the most frequently researched independent variables in EMP studies, are considered. The relationships between the two IVs and the two DVs are verified when transaction items are of search-type and of experience-type. This study is conducted using field data collected from Taobao (the most dominant retail EMP in China). It is found that reputation has consistent positive relationships with two DVs. Price has negative effects on two DVs. However, it might have no impacts in the case of experience-type items. Conclusively, in information overloaded EMP, reputation always matters in influencing buyers' search and purchase behavior, while price only matters in the case of search-type items.
Paragraph text segmentation into lines with Recurrent Neural Networks (2015)

The detection of text lines, as a first processing step, is critical in all text recognition systems. State-of-the-art methods to locate lines of text are based on handcrafted heuristics fine-tuned by the image processing community's experience. They succeed under certain constraints; for instance the background has to be roughly uniform. We propose to use more “agnostic” Machine Learning-based approaches to address text line location. The main motivation is to be able to process either damaged documents, or flows of documents with a high variety of layouts and other characteristics. A new method is presented in this work, inspired by the latest generation of optical models used for text recognition, namely Recurrent Neural Networks. As these models are sequential, a column of text lines in our application plays here the same role as a line of characters in more traditional text recognition settings. A key advantage of the proposed method over other data-driven approaches is that compiling a training dataset does not require labeling line boundaries: only the number of lines are required for each paragraph. Experimental results show that our approach gives similar or better results than traditional handcrafted approaches, with little engineering efforts and less hyper-parameter tuning.
Selection Criteria for c-Met-Targeted Therapies: Emerging Evidence for Biomarkers (2010)

Extensive development of targeted therapies emphasize the critical need for biomarkers and major efforts have been engaged to identify screening, prognostic, stratification and therapy-monitoring markers. One of the challenges in translating preclinical studies into effective clinical therapies remains the accurate identification of a responsive subsets of patients. Studies on trastuzumab demonstrated that patient response could be specifically correlated with the amplification of the Her2 gene. However, for the EGF receptor, it has been more difficult to find the right stratification biomarker and recent data demonstrate that genetic alterations for the EGF receptor have to be considered. Taken together, these data underline the need for a deeper understanding of both targeted receptor and human disease to determine pathways that might be investigated during early clinical trials in order to define relevant biomarkers for patient selection. This article, dealing with the c-Met tyrosine kinase receptor, provides an overview of c-Met alterations observed in cancer and proposes approaches for stratification biomarker selection.
Mechanism of synergistic cell killing by hydroxyurea and cytosine arabinoside. (1985)

Synergistic cell killing of human lymphoblastic leukemia cell line, CCRF-CEM, occurred when hydroxyurea (HU) was administered before 1-beta-D-arabinofuranosylcytosine (ara-C). At the optimal dose of HU (1mM), the ara-CTP concentration increased 4-fold and the intracellular accumulation of ara-C increased 4-fold, while the dCTP concentration decreased by more than 50%. Increased intracellular accumulation of ara-C after HU treatment was also observed in human acute myelogenous leukemic cells in circulating blood. Therefore, the synergistic cell kill of HU and ara-C may be the consequence of greater inhibition of DNA polymerase by the increased level of ara-CTP in the presence of the decreased concentration of the natural substrate of this enzyme, dCTP. This synergism was not due to an increased incorporation of ara-C into DNA since the treatment of cells with HU did not enhance the ara-C incorporation into DNA but rather suppressed it.
Cloning and Expression of the cDNA for Human γ-glutamyl Carboxylase (1991)

The cDNA for human gamma-glutamyl carboxylase, which accomplishes the post-translational modification required for the activity of all of the vitamin K-dependent proteins, was cloned. The enzyme is a 758-residue integral membrane protein and appears to have three transmembrane domains near its amino terminus. The hydrophilic COOH-terminal half of the carboxylase has 19.3 percent identity with soybean seed lipoxygenase. Expression of the cloned cDNA resulted in an increase in carboxylase activity in microsomes of transfected cells compared to mock-transfected cells.
Broadening the Spectrum of β-Lactam Antibiotics through Inhibition of Signal Peptidase Type I (2012)

The resistance of methicillin-resistant Staphylococcus aureus (MRSA) to all β-lactam classes limits treatment options for serious infections involving this organism. Our goal is to discover new agents that restore the activity of β-lactams against MRSA, an approach that has led to the discovery of two classes of natural product antibiotics, a cyclic depsipeptide (krisynomycin) and a lipoglycopeptide (actinocarbasin), which potentiate the activity of imipenem against MRSA strain COL. We report here that these imipenem synergists are inhibitors of the bacterial type I signal peptidase SpsB, a serine protease that is required for the secretion of proteins that are exported through the Sec and Tat systems. A synthetic derivative of actinocarbasin, M131, synergized with imipenem both in vitro and in vivo with potent efficacy. The in vitro activity of M131 extends to clinical isolates of MRSA but not to a methicillin-sensitive strain. Synergy is restricted to β-lactam antibiotics and is not observed with other antibiotic classes. We propose that the SpsB inhibitors synergize with β-lactams by preventing the signal peptidase-mediated secretion of proteins required for β-lactam resistance. Combinations of SpsB inhibitors and β-lactams may expand the utility of these widely prescribed antibiotics to treat MRSA infections, analogous to β-lactamase inhibitors which restored the utility of this antibiotic class for the treatment of resistant Gram-negative infections.
Redesigning of anti‐c‐Met single chain Fv antibody for the cytoplasmic folding and its structural analysis (2010)

Typically, single chain Fv antibodies are unable to fold properly under a reducing cytoplasm because of the reduction of disulfide bonds. The inability to fold limits both the production of the functional scFvs and their targeting against antigens, which are generally executed in a reducing cytoplasm. In this study, the target scFv CDR was grafted with stable human consensus framework sequences, which enabled the generation of a foldable scFv in a reducing cytoplasm of Escherichia coli. Additionally, the structural features affecting the folding efficiency of the engineered scFv were identified by analyzing the predicted structure. An anti-c-Met scFv, which was a cytoplasmic non-foldable protein, was redesigned as the model system. This study confirmed that the engineered anti-c-Met scFv was folded into its native form in the cytoplasm of E. coli BL21(DE3) without a significant loss in the specific binding activity against c-Met antigen. The structures of the wild-type anti-c-Met scFv and the engineered scFv were predicted using homology modeling. A comparative analysis based on the sequence and structure showed that the hydrophobicity of 12 solvent exposed residues decreased, and two newly formed salt bridges might have improved the folding efficiency of the engineered scFv under the reducing condition.
Yeast Glycogen Synthase Kinase 3 Is Involved in Protein Degradation in Cooperation with Bul1, Bul2, and Rsp5 (2000)

The yeast Saccharomyces cerevisiae has four genes, MCK1, MDS1 (RIM11), MRK1, and YOL128c, that encode glycogen synthase kinase 3 (GSK-3) homologs. The gsk-3 null mutant, in which these four genes are disrupted, shows temperature sensitivity, which is suppressed by the expression of mammalian GSK-3beta and by an osmotic stabilizer. Suppression of temperature sensitivity by an osmotic stabilizer is also observed in the bul1 bul2 double null mutant, and the temperature sensitivity of the bul1 bul2 double null mutant is suppressed by multiple copies of MCK1. We have screened rog mutants (revertants of gsk-3) which suppress the temperature sensitivity of the mck1 mds1 double null mutant and found that two of them, rog1 and rog2, also suppress the temperature sensitivity of the bul1 bul2 double null mutant. Bul1 and Bul2 have been reported to bind to Rsp5, a hect (for homologous to E6-associated-protein carboxyl terminus)-type ubiquitin ligase, but involvement of Bul1 and Bul2 in protein degradation has not been demonstrated. We find that Rog1, but not Rog2, is stabilized in the gsk-3 null and the bul1 bul2 double null mutants. Rog1 binds directly to Rsp5, and their interaction is dependent on GSK-3. Furthermore, Rog1 is stabilized in the npi1 mutant, in which RSP5 expression levels are reduced. These results suggest that yeast GSK-3 regulates the stability of Rog1 in cooperation with Bul1, Bul2, and Rsp5.
Gene targeting at the human CD4 locus by epitope addition. (1990)

Homologous recombination at the CD4 locus in a human T-cell line has been achieved by an approach called epitope addition. The endogenous CD4 gene provided transcription, translation, and leader sequences to a crippled introduced Thy-1 gene, resulting in the expression of murine Thy-1 epitopes on the surface of the human cells. Thy-1+ cells were selected using the Fluorescence Activated Cell Sorter (FACS). An estimated 700-fold enrichment for homologous versus nonhomologous integration events was obtained, such that 70% of cells scoring positive for Thy-1 were derived from gene targeting. Three of the Thy-1+ cell lines expressed protein only from the targeted allele; thus, these cells were functionally CD4-.
Response of Selected Weed Species to Postemergence Imazethapyr and Bentazon (1995)

Imazethapyr and bentazon were applied with petroleum oil adjuvant in a factorial arrangement to weed species in greenhouse and field research to determine if postemergence weed control by imazethapyr was antagonized when bentazon was tank-mixed. Tank-mixing 840 g/ha of bentazon with 13 or 27 g/ha of imazethapyr increased redroot pigweed and eastern black nightshade dry weight as compared to Colby's expected values in the greenhouse. However, weed control was not reduced in field studies. Subsequent greenhouse studies indicated that soil interception and resulting root uptake of imazethapyr increased redroot pigweed control. Bentazon decreased foliar absorption of 14 C-imazethapyr by 15% and translocation of 14 C from the treated leaf by more than 50% compared to l4 C-imazethapyr applied alone.
The proteins encoded by the VpreB and lambda 5 pre-B cell-specific genes can associate with each other and with mu heavy chain. (1990)

The murine pre-B cell-specific genes VpreB and lambda 5, as well as the murine gene for mu heavy chain, were introduced into Ltk- fibroblast cells which normally do not express these genes. Stable transfectants carrying these genes produced the corresponding proteins of 15.5, 21.5, and 75 kD. They secreted the three proteins as a triple complex that could be immunoprecipitated by mu heavy chain-specific antibodies, consisting of one VpreB, one lambda 5, and one mu heavy chain. The mu heavy chain and lambda 5 were disulfide-bonded with each other, while the VpreB protein was noncovalently associated. These experiments proved that the VpreB, lambda 5 and mu H chain proteins can form a heavy/light chain-like heterocomplex.
IOS-a new type of materials combination for system-on-a chip preparation (2003)

IOS (insulator-on-semiconductor) has emerged as a new type of materials combination for system-on-a chip preparation. For high frequency mobile communication systems, a thin layer of piezoelectric or ferroelectric oxide crystal such as quartz, LiTaO/sub 3/ or LiNbO/sub 3/ on Si is required for high Q-factor and low temperature coefficient SAW filters, surface resonators and oscillators. Combining these materials with Si can lead to the integration of electronic and acoustic devices on the same chip. Voltage-controlled and temperature-compensated high Q-factor crystal oscillators and resonators can thus be realized. The integration of high performance GaAs photodetectors with LiNbO/sub 3/ waveguides makes integrated optical circuits possible. By preparing a thin layer of single crystalline transition metal oxides such as magnetic garnets on Si or on III-V semiconductors, stabilized laser diodes can be realized due to the availability of on-chip thin film optical isolators and circulators. Layer transfer by wafer bonding and H-induced layer splitting provides a manufacturable technology for IOS preparation. In this study, we report feasibility study results for IOS preparation with an insulator layer of many single crystalline insulators such as c-sapphire, LaAlO/sub 2/, PLZT and LiNbO/sub 3/. We have demonstrated that surface blistering and layer splitting of these materials is possible if H implantation is performed at wafer temperatures within the specific temperature range for each material.
Rad51 expression and localization in B cells carrying out class switch recombination. (1996)

Rad51 is a highly conserved eukaryotic homolog of the prokaryotic recombination protein RecA, which has been shown to function in both recombinational repair of DNA damage and meiotic recombination in yeast. In primary murine B cells cultured with lipopolysaccharide (LPS) to stimulate heavy chain class switch recombination, Rad51 protein levels are dramatically induced. Immunofluorescent microscopy shows that anti-Rad51 antibodies stain foci that are localized within the nuclei of switching B cells. Immunohistochemical analysis of splenic sections shows that clusters of cells that stain brightly with anti-Rad51 antibodies are evident within several days after primary immunization and that Rad51 staining in vivo is confined to B cells that are switching from expression of IgM to IgG antibodies. Following switch recombination, B cells populate splenic germinal centers, where somatic hypermutation and clonal proliferation occur. Germinal center B cells are not stained by anti-Rad51 antibodies. Rad51 expression is therefore not coincident with somatic hypermutation, nor does Rad51 expression correlate simply with cell proliferation. These data suggest that Rad51, or a highly related member of the conserved RecA family, may function in class switch recombination.
Biosynthesis of a nonphysiological sialic acid in different rat organs, using N-propanoyl-D-hexosamines as precursors. (1992)

In this study it could be shown that in rat the normally occurring N-acetyl neuraminic acid can be modified in its N-acyl moiety by in vivo administration of the chemically synthesized N-propanoyl precursors, N-propanoyl-D-glucosamine or N-propanoyl-D-mannosamine. It could be shown that each of these nonphysiological amino sugar analogues was incorporated into both membrane and serum glycoproteins. After treatment of rats with radiolabeled N-[acyl-1-14C]D-mannosamine, radioactivity could be removed from serum glycoprotein fractions by incubation with neuraminidase from Clostridium perfringens or from Arthrobacter ureafaciens. Mild acid hydrolysis removed 98% of the radioactivity after in vivo labeling with N-[acetyl-1-14C]D-mannosamine and 86% after labeling with N-[propanoyl-1-14C]D-mannosamine. Chromatographic analysis yielded two compounds, i.e. N-acetyl neuraminic acid and N-propanoyl neuraminic acid, the latter being identified by gas liquid chromatography/mass spectrometry studies. Measurement of protein-bound radioactivity in different rat organs revealed a different organotropy of the natural and the nonphysiological neuraminic acid precursor. Of the glucosamine derivatives, N-acetyl-D-glucosamine showed the higher rate of uptake and incorporation in most organs (except in the submandibulary gland), and especially in kidney cortex and Morris hepatoma 7777. Natural and the unphysiological mannosamine derivatives were incorporated at similar rates, except in liver, where N-acetyl-D-mannosamine was taken up and metabolized more effectively. This finding indicates that it is possible to modify the acyl group of N-acetyl neuraminic acid in vivo by the introduction of an N-propanoyl group and possibly other homologous N-acyl groups. This procedure may provide a tool for a further characterization of the biological function of sialic acids.
Inhibition of the differentiation of human myeloid cell lines by redox changes induced through glutathione depletion (1994)

We have investigated the effect of redox changes in vivo on the differentiation of two human myeloid cell lines, HL-60 and KG-1. The glutathione-depleting agent diethyl maleate (DEM) prevented the development of differentiated features in response to phorbol esters, including adherence of the cells to plastic surfaces and repression of the myeloperoxidase and CD34 genes. Moreover, DEM abolished phorbol 12-myristate 13-acetate-induced activation of the transcription factors AP-1 and Egr-1, suggesting that inhibition of differentiation may be due, at least in part, to redox modifications of these proteins.
Thyroxine-Binding Globulin: Organization of the Gene and Variants (1996)

Thyroxine-binding globulin (TBG), the principal thyroid hormone transport protein in human serum, is synthesized by the liver and secreted into the bloodstream as a 54-kD acidic glycoprotein made up of a single polypeptide chain of 395 amino acids and four heterosaccharide units. The carbohydrate chains are important for the correct posttranslational folding, secretion and degradation of the molecule but are not required for hormone binding. TBG, encoded by a single gene copy located on Xq22, consists of five exons spanning 5.5 kbp. An upstream sequence of 218 nucleotides containing a hepatocyte nuclear factor 1 binding motif imparts to the gene a strong liver-specific transcriptional activity. Inherited TBG defects produce three phenotypes based on the level of TBG in serum of affected hemizygotes: complete TBG deficiency (TBG-CD), partial TBG deficiency (TBG-PD) and TBG excess (TBG-E). The molecular basis of the TBG defect has been identified in 12 of 16 known TBG variants. TBG-CD is caused by either premature termination of translation or an amino acid substitution resulting in failure of secretion. Point mutations resulting in single amino acid substitutions are responsible for the alteration of the properties and/or concentration of TBG-PD variants. Gene duplication and triplication has been recently identified in subjects with TBG-E.