gebhart/patrepeval huggingface dataset:
Joint parsing and semantic role labeling (2005)

A striking feature of human syntactic processing is that it is context-dependent, that is, it seems to take into account semantic information from the discourse context and world knowledge. In this paper, we attempt to use this insight to bridge the gap between SRL results from gold parses and from automatically-generated parses. To do this, we jointly perform parsing and semantic role labeling, using a probabilistic SRL system to rerank the results of a probabilistic parser. Our current results are negative, because a locally-trained SRL model can return inaccurate probability estimates.
Novel macrolide‐adjustable bidirectional expression modules for coordinated expression of two different transgenes in mice (2003)

Based on their in vivo compatibility, the versatile bidirectional and macrolide-responsive expression modules represent an important advancement on the way to implementing targeted and conditional molecular interventions into a clinical reality.
Cantilever arrays for multiplexed mechanical analysis of biomolecular reactions. (2004)

Microchips containing arrays of cantilever beams have been used to mechanically detect and quantitatively analyze multiple reactions of DNA hybridization and antigen-antibody binding simultaneously. The reaction-induced deflection of a cantilever beam reflects the interplay between strain energy increase of the beam and the free energy reduction of a reaction, providing an ideal tool for investigating the connection between mechanics and chemistry of biomolecular reactions. Since free energy reduction is common for all reactions, the cantilever array forms a universal platform for label-free detection of various specific biomolecular reactions. A few such reactions and their implications in biology and biotechnology are discussed.
Identification and characterization of a lysophosphatidylcholine acyltransferase in alveolar type II cells (2006)

Pulmonary surfactant is a complex of lipids and proteins produced and secreted by alveolar type II cells that provides the low surface tension at the air-liquid interface. The phospholipid most responsible for providing the low surface tension in the lung is dipalmitoylphosphatidylcholine. Dipalmitoylphosphatidylcholine is synthesized in large part by phosphatidylcholine (PC) remodeling, and a lysophosphatidylcholine (lysoPC) acyltransferase is thought to play a critical role in its synthesis. However, this acyltransferase has not yet been identified. We have cloned full-length rat and mouse cDNAs coding for a lysoPC acyltransferase (LPCAT). LPCAT encodes a 535-aa protein of approximately 59 kDa that contains a transmembrane domain and a putative acyltransferase domain. When transfected into COS-7 cells and HEK293 cells, LPCAT significantly increased lysoPC acyltransferase activity. LPCAT preferred lysoPC as a substrate over lysoPA, lysoPI, lysoPS, lysoPE, or lysoPG and prefers palmitoyl-CoA to oleoyl-CoA as the acyl donor. This LPCAT was preferentially expressed in the lung, specifically within alveolar type II cells. Expression in the fetal lung and in rat type II cells correlated with the expression of the surfactant proteins. LPCAT expression in fetal lung explants was sensitive to dexamethasone and FGFs. KGF was a potent stimulator of LPCAT expression in cultured adult type II cells. We hypothesize that LPCAT plays a critical role in regulating surfactant phospholipid biosynthesis and suggest that understanding the regulation of LPCAT will offer important insight into surfactant phospholipid biosynthesis.
The functional valency of dodecamannosylated fullerenes with Escherichia coli FimH—towards novel bacterial antiadhesives (2010)

Fullerene hexakis-adducts bearing 12 peripheral mannose moieties have been prepared by grafting sugar derivatives onto the fullerene core and assayed as inhibitors of FimH, a bacterial adhesin, using isothermal titration calorimetry, surface plasmon resonance and hemagglutination assays.
Design and application of oncolytic HSV vectors for glioblastoma therapy (2009)

Glioblastoma multiforme is one of the most common human brain tumors. The tumor is generally highly infiltrative, making it extremely difficult to treat by surgical resection or radiotherapy. This feature contributes to recurrence and a very poor prognosis. Few anticancer drugs have been shown to alter rapid tumor growth and none are ultimately effective. Oncolytic vectors have been employed as a treatment alternative based on the ability to tailor virus replication to tumor cells. The human neurotropic herpes simplex virus (HSV) is especially attractive for development of oncolytic vectors (oHSV) because this virus is highly infectious, replicates rapidly and can be readily modified to achieve vector attenuation in normal brain tissue. Tumor specificity can be achieved by deleting viral genes that are only required for virus replication in normal cells and permit mutant virus replication selectively in tumor cells. The anti-tumor activity of oHSV can be enhanced by arming the vector with genes that either activate chemotherapeutic drugs within the tumor tissue or promote anti-tumor immunity. In this review, we describe current designs of oHSV and the experience thus far with their potential utility for glioblastoma therapy. In addition, we discuss the impediments to vector effectiveness and describe our view of future developments in vector improvement.
Electrospun polydioxanone–elastin blends: potential for bioresorbable vascular grafts (2006)

An electrospun cardiovascular graft composed of polydioxanone (PDO) and elastin has been designed and fabricated with mechanical properties to more closely match those of native arterial tissue, while remaining conducive to tissue regeneration. PDO was chosen to provide mechanical integrity to the prosthetic, while elastin provides elasticity and bioactivity (to promote regeneration in vitro/in situ). It is the elastic nature of elastin that dominates the low-strain mechanical response of the vessel to blood flow and prevents pulsatile energy from being dissipated as heat. Uniaxial tensile and suture retention tests were performed on the electrospun grafts to demonstrate the similarities of the mechanical properties between the grafts and native vessel. Dynamic compliance measurements produced values that ranged from 1.2 to 5.6%/100 mmHg for a set of three different mean arterial pressures. Results showed the 50:50 ratio to closely mimic the compliance of native femoral artery, while grafts that contained less elastin exceeded the suture retention strength of native vessel. Preliminary cell culture studies showed the elastin-containing grafts to be bioactive as cells migrated through their full thickness within 7 days, but failed to migrate into pure PDO scaffolds. Electrospinning of the PDO and elastin-blended composite into a conduit for use as a small diameter vascular graft has extreme potential and warrants further investigation as it thus far compares favorably to native vessel.
Energy balance, first ovulation and the effects of naloxone on LH secretion in early postpartum dairy cows. (1991)

Relationship among energy balance (EB), first ovulation, circulating metabolites and opioid involvement in peripheral LH concentrations were assessed in 40 multiparous Holstein cows assigned randomly to an experiment with a 2 x 2 factorial arrangement of treatments. Cows were either milked normally (2x/d) and expected to be in negative EB (LAC) or were milked for only 1 d postpartum (PP) to ensure a rapid return to positive EB (NONLAC). Blood samples were collected from NONLAC cows every 12 min for 16 h on d 7, 10, and 14 PP and from LAC cows on d 7, 14, 21 and 28 PP. Within each group, half the cows received naloxone (50 mg/h) and half received saline during h 9 to 16 of each frequent sampling series. The mean number of LH pulses/8 h for NONLAC cows was 4.3, 4.7 and 5.3 at 7, 10 and 14 d PP and for LAC cows 4.3, 5.7, 6.4 and 7.0 at 7, 14, 21 and 28 d PP, respectively. The LH pulse frequency was not different between NONLAC and LAC cows at 7 and 14 d PP, yet NONLAC cows had fewer days to first ovulation (P less than .01). Naloxone did not affect any parameters of LH secretion in either group. Following parturition, NONLAC cows averaged 4.0 d to negative EB nadir and 14.3 d to first ovulation. The LAC cows averaged 13.6 d to negative EB nadir and 27.0 d to first ovulation. Days PP to first ovulation were highly correlated (r = .85) with days PP to negative EB nadir.(ABSTRACT TRUNCATED AT 250 WORDS)
The bacterial type VI secretion machine: yet another player for protein transport across membranes (2008)

Several secretion systems have evolved that are widespread among Gram-negative bacteria. Recently, a new secretion system was recognized, which is named the type VI secretion system (T6SS). The T6SS components are encoded within clusters of genes initially identified as IAHP for IcmF-associated homologous proteins, since they were all found to contain a gene encoding an IcmF-like component. IcmF was previously reported as a component of the type IV secretion system (T4SS). However, with the exception of DotU, other T4SS components are not encoded within T6SS loci. Thus, the T6SS is probably a novel kind of complex multi-component secretion machine, which is often involved in interaction with eukaryotic hosts, be it a pathogenic or a symbiotic relationship. The expression of T6SS genes has been reported to be mostly induced in vivo. Interestingly, expression and assembly of T6SSs are tightly controlled at both the transcriptional and the post-translational level. This may allow a timely control of T6SS assembly and function. Two types of proteins, generically named Hcp and VgrG, are secreted via these systems, but it is not entirely clear whether they are truly secreted effector proteins or are actually components of the T6SS. The precise role and mode of action of the T6SS is still unknown. This review describes current knowledge about the T6SS and summarizes its hallmarks and its differences from other secretion systems.
Identification of an SCF ubiquitin-ligase complex required for auxin response in Arabidopsis thaliana (1999)

The plant hormone auxin regulates diverse aspects of plant growth and development. We report that in Arabidopsis, auxin response is dependent on a ubiquitin-ligase (E3) complex called SCFTIR1. The complex consists of proteins related to yeast Skp1p and Cdc53p called ASK and AtCUL1, respectively, as well as the F-box protein TIR1. Mutations in either ASK1 or TIR1 result in decreased auxin response. Further, overexpression of TIR1 promotes auxin response suggesting that SCFTIR1 is limiting for the response. These results provide new support for a model in which auxin action depends on the regulated proteolysis of repressor proteins.
Immunodominance among herpes simplex virus-specific CD8 T cells expressing a tissue-specific homing receptor (2003)

The study of immunodominance within microbe-specific CD8 T cell responses has been challenging. We used a previously undescribed approach to create unbiased panels of CD8 cytotoxic T lymphocyte clones specific for herpes simplex virus type 2, a pathogen with a complex genome encoding at least 85 polypeptides. Circulating herpes simplex virus type 2-specific cells were enriched and cloned after sorting for expression of the skin homing-associated receptor, cutaneous lymphocyte-associated antigen, bypassing restimulation with antigen. The specificity of the resultant cytotoxic clones was determined. Clonal frequencies were compared with each other and with the total number of cytotoxic clones. For each subject within the homing receptor-positive compartment, the CD8 cytotoxic response was dominated by T cells specific for only a few peptides. Previously undescribed antigens and epitopes in viral tegument, capsid, or scaffold proteins were immunodominant in some subjects. Clone enumeration analyses were confirmed in some subjects with dominance studies by using herpes simplex mutants, vaccinia recombinants, and/or enzyme-linked immune spots. We conclude that among circulating cells expressing a homing-associated receptor, during chronic herpes type 2 infection, the CD8 T cell response becomes quite focused despite the presence of many potential antigenic peptides.
Decameric SelA•tRNA Sec Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation (2013)

Putting Selenium in Proteins The 21st amino acid, selenocysteine (Sec), occurs in the active site of many redox enzymes. Its cognate transfer RNA (tRNA) is first loaded with Ser by seryl-tRNA synthetase and the Ser-tRNA Sec is then converted to Sec-tRNA Sec . Itoh et al. (p. 75 ) determined the crystal structures of the selenocysteine synthase, SelA, that is responsible for this conversion in bacteria, alone and in complex with tRNA. The decameric SelA complex binds to 10 tRNA Sec molecules. The structures, together with biochemistry, show how SelA discriminates tRNA Sec from tRNA Ser , give insight into the mechanism of catalysis, and show that decamerization is essential for function.
Roam: a scalable replication system for mobile computing (1999)

Nomadic users require replication to store copies of critical data on their mobile machines while disconnected or poorly connected. Existing replication services do not provide all classes of mobile users with the capabilities they require, which include: the ability for direct synchronization between any two replicas, support for large numbers of replicas, and detailed control over what files reside on their local (mobile) replica. Mobile users must adapt their behavior to match the level of service provided by today's replication systems, thereby hindering mobility and costing additional time, money, and systems management. Roam is a replication system designed to satisfy the requirements of the mobile user. Roam is based on the Ward Model, a replication architecture for mobile environments. Using the Ward Model and new distributed algorithms, Roam provides a scalable replication solution for the mobile user. We describe the motivation, design, and implementation of Roam and report its performance.
DbDMAD: a Database of DNA Methylation in Human Age-related Disease (2012)

DNA methylation plays a variety of crucial roles in cell division, proliferation, development of aging life, development of genetic diseases related to uniparental disomy, and carcinogenesis. DNA methylation can be probed by HPLC and gene chip which is very helpful to the high-through methylation test. In recent years many published articles reported that DNA methylation may be linked with human aged disease. Mining and integration of DNA methylation in human aged disease can be beneficial to novel biological discoveries. There has not been DNA methylation database repository which is exclusive for human aged disease. Therefore, we developed dbDMAD: a database of DNA methylation in human aged diseases, there are two purposes of it, one is to store DNA methylation in human aged disease datasets which were obtained from laboratory experiments, another is to find the relationship of different aged diseases. This is the first release of dbDMAD in which users can find 12 kinds of human aged diseases and relevant DNA methylation information. It can be searched by disease name and gene ID. This database also includes a visualization tool named ChainMap, by which the map of methylation pathway can be shown.
Utilization of Nuclear Matrix Proteins for Cancer Diagnosis (1996)

Circulating tumor markers have been used increasingly in recent years as clinical tools for cancer diagnosis and management. This review presents a brief discussion of currently available tumor-associated antigens. Included is an overview of different functional classes of circulating markers and their clinical applications. The limitations of some traditional tumor markers presently in widespread use are discussed in the context of the properties exhibited by an ideal tumor marker. The nuclear matrix provides structural support for the nucleus and plays a dynamic role in the spatial organization of the genome and in the control of DNA replication and transcription. The recovery of increased amounts of specific nuclear matrix proteins in several different cancers has led to the further study of some of these proteins as a new class of tumor markers. Progress on the use of a nuclear matrix protein known as NuMA as a marker for bladder cancer is presented, including results of a recently completed multisite clinical trial. Additional studies on the potential utility of nuclear matrix proteins as markers for prostate cancer are also presented. Nuclear matrix proteins could provide for the development of assays with increased efficacy for the diagnosis and treatment of cancer.
Tissue Electrical Property Mapping From Zero Echo-Time Magnetic Resonance Imaging (2014)

The capability of magnetic resonance imaging (MRI) to produce spatially resolved estimation of tissue electrical properties (EPs) in vivo has been a subject of much recent interest. In this work we introduce a method to map tissue EPs from low-flip-angle, zero-echo-time (ZTE) imaging. It is based on a new theoretical formalism that allows calculation of EPs from the product of transmit and receive radio-frequency (RF) field maps. Compared to conventional methods requiring separation of the transmit RF field (B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> ) from acquired MR images, the proposed method has such advantages as: 1) reduced theoretical error, 2) higher acquisition speed, and 3) flexibility in choice of different transmit and receive RF coils. The method is demonstrated in electrical conductivity and relative permittivity mapping in a salt water phantom, as well as in vivo measurement of brain conductivity in healthy volunteers. The phantom results show the validity and scan-time efficiency of the proposed method applied to a piece-wise homogeneous object. Quality of in vivo EP results was limited by reconstruction errors near tissue boundaries, which highlights need for image segmentation in EP mapping in a heterogeneous medium. Our results show the feasibility of rapid EP mapping from MRI without B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> mapping.
Partial restoration of T‐cell function in aged mice by in vitro blockade of the PD‐1/ PD‐L1 pathway (2010)

Programmed cell death-1 (PD-1) is a newly characterized negative regulator of immune responses. The interaction of PD-1 with its ligands (PD-L1 and PD-L2) inhibits T-cell proliferation and cytokine production in young mice. Increased PD-1 expression has been described during chronic infections, inducing chronic activation of the immune system to control it. As aging is associated with chronic immune activation, PD-1 may contribute to age-associated T-cell dysfunction. Our data showed the following results in aged mice: (i) the number of PD-1-expressing T cells and the level of expression of PD-Ls was increased on dendritic cell subsets and T cells; (ii) PD-1(+) T cells were exhausted effector memory T cells, as shown by their lower level of CD127, CD25 and CD28, as well as their limited proliferative and cytokine-producing capacity; (iii) the expression of PD-1 was up-regulated after T-cell receptor-mediated activation of CD8(+) T cells, but not of CD4(+) T cells; (iv) blockade of the PD-1/PD-L1 pathway moderately improved the cytokine production of T cells from old mice but did not restore their proliferation; and (v) blockade of the PD-1/PD-L1 pathway did not restore function of PD-1(+) T cells; its effect appeared to be exclusively mediated by increased functionality of the PD-1(-) T cells. Our data thus suggest that blockade of the PD-1/PD-L1 is not likely to be efficient at restoring exhausted T-cell responses in aged hosts, although improving the responses of PD-1(-) T cells may prove to be a helpful strategy in enhancing primary responses.
Identification of gp350 as the viral glycoprotein mediating attachment of Epstein-Barr virus (EBV) to the EBV/C3d receptor of B cells: sequence homology of gp350 and C3 complement fragment C3d (1987)

The major Epstein-Barr virus (EBV) envelope glycoprotein, gp350, was purified from the B95-8 cell line and analyzed for its ability to mediate virus attachment to the isolated EBV/C3d receptor (CR2) of human B lymphocytes. Purified gp350 and EBV, but not cytomegalovirus, exhibited dose-dependent binding to purified CR2 in dot blot immunoassays. Binding was inhibited by certain monoclonal antibodies to CR2 and to gp350. Liposomes bearing incorporated gp350 bound to CR2-positive B-cell lines but not to CR2-negative lines. Liposome binding was also inhibited by the OKB7 anti-CR2 monoclonal antibody. A computer-generated comparison of the deduced gp350 amino acid sequence with that of the human C3d complement fragment revealed two regions of significant primary sequence homology, a finding which suggests that a common region on these two unrelated proteins may be involved in CR2 binding.
Clottable Protein in Limulus: Its Localization and Kinetics of Its Coagulation by Endotoxin (1968)

Summary When blood is withdrawn from Limulus, the horseshoe crab, a cellular clot composed of amebocytes quickly forms. Amebocytes are the only type of cell in Limulus blood. During coagulation, Limulus amebocytes undergo morphological changes that are strikingly similar to those seen when mammalian platelets undergo aggregation and viscous metamorphosis. The clottable protein in Limulus blood is derived entirely from amebocytes, and gelation does not require extracellular factors. Cell free Limulus plasma is incoagulable. The cellular localization of clottable protein in Limulus blood provides a precedent for the presence of fibrinogen in mammalian platelets. The clottable protein in lysates of amebocytes has a spectral absorption pattern with a maximum at 270-275 mμ, appears to have a low sedimentation coefficient, is stable at –20° C for 1 week, and is destroyed by heating at 56° C for 30 min. The protein gels upon exposure to endotoxin; and the rate of gelation is related to the concentration of endotoxin but is independent of the concentration of protein in the range tested. The kinetics of this reaction are consistent with the concept that an enzymatic system mediates the conversion of the cellular protein into a gel by endotoxin. Increase in light scattering during the reaction detects as little as 0.004 μg of E. coli endotoxin/ml. This conversion will perhaps provide insight into one of the biological activities of endotoxins.
Software Aspects of Automated Recognition of Particles: The Example of Pollen (2006)

This chapter looked at the use of automatic techniques for the analysis of microscopic objects. It showed all stages of the analysis, from the initial hardware set-up, through the focusing procedure and object detection, to the final classification of the objects. It presented a case study of a pollen classification system that can be trained on a sample of images of pollen grains. The system was based on a flexible neural network architecture: such networks trained on individual species can be combined to produce a discriminator for the set of species. The chapter presented results based on a trial with a large number of images. Experience in the face recognition community has shown that, for small data sets, it is easy to get good results; problems arise when attempts are made to scale up techniques to realistic amounts of data. Comparing the results of different techniques is also problematic. Large public datasets are required along with protocols for testing the recognition systems.