gebhart/patrepeval huggingface dataset:
An efficiently updatable index scheme for structured documents (2002)

We propose an efficiently updatable index scheme for XML documents. This index scheme consists of four types of indices. Content index manages occurrence positions of words, element names, attribute names and attribute values. Local structure index manages logical structure of each document. Global structure index summarizes logical structure of document instances for a DTD. The last one is called structure meta index, and keeps, for each element, the number of local structure indices and global structure indices which include the element. Using our four types of indices, therefore, a wide range of queries over structured documents can be processed efficiently. We compare our indices with existing indices in terms of index size, update cost and retrieval cost.
De NovoDesign of Sequences for Nucleic Acid Structural Engineering (1990)

An interactive procedure has been developed to assign sequences for the design of nucleic acid secondary structure. The primary goal of the procedure is to facilitate macromolecular architecture studies through the design of branched nucleic acid mono- and oligo-junction constructs in a convenient fashion. The essential feature of the sequence-symmetry minimization algorithm employed is the treatment of short sequences as vocabulary elements whose repetition decreases control over the resulting secondary structure. Both manual and semi-automatic application of this approach are available. The design of linear nucleic acid molecules or molecules containing single-stranded loops or connectors is also possible through application of the procedure.
Prostate-specific antigen in serum occurs predominantly in complex with alpha 1-antichymotrypsin (1991)

Immunologic measurements of the serum concentration of prostate-specific antigen (PSA), an abundant prostatic-secreted serine proteinase, are frequently used to monitor patients with prostate cancer, though it has not been ascertained whether this immunoreactivity represents a PSA zymogen, the active proteinase, or PSA complexed to extracellular proteinase inhibitors. To characterize the PSA immunoreactivity in serum, we used monoclonal antibodies produced against PSA and a polyclonal rabbit IgG against alpha 1-antichymotrypsin in the design of three noncompetitive PSA assays: assay T, which detected PSA both when present as the active proteinase and when complexed to alpha 1-antichymotrypsin; assay F, which recognized the active proteinase but most poorly detected PSA complexed to alpha 1-antichymotrypsin; and assay C, which was specific for PSA complexed to alpha 1-antichymotrypsin. We used the three assays to measure PSA immunoreactivity in 64 patients' sera and in the effluent after gel chromatography of sera from four patients. This identified an 80- to 90-kDa complex between PSA and alpha 1-antichymotrypsin as the predominant fraction of the PSA immunoreactivity in blood plasma; an immunoreactive 25- to 40-kDa compound was the minor fraction.
Common Channel Interoffice Signaling: 4A Toll Crossbar Application (1978)

The No. 4 toll crossbar switching system is presently the backbone of the Direct Distance Dialing (DDD) network. Conversion of No. 4 offices equipped with the Electronic Translator System (ETS) is vital to the rapid introduction of CCIS to the DDD network. CCIS capability represents a major increase in the role of the ETS software in the call switching process. Significant changes and additions to the switching equipment are required to support this expanded software control.
Characterization of collagen synthesized by normal and chemically transformed rat liver epithelial cell lines (1980)

A rat liver epithelial cell line (K16) and a 2-[N-(acetoxyacetyl)amino]fluorine-transformed K16 cell line (W8) [Weinstein, I.B., Yamaguchi, R., Gerbert, R., & Kaighn, M.E. (1975) In Vitro 11, 130-141] synthesize and secrete similar quantities of collagenous proteins. The transformed cells produce more total protein so that the percent collagen produced is decreased compared to that of the parent cell line. The type of collagen produced by the transformants differed from that of the parent cell line. After limited pepsin digestion, the pepsin-resistant collagen molecules synthesized by K16 cells precipitated at 2.6 M NaCl and contained both alpha 1 (I) and alpha 2 chains in a 2.5:1 ratio. The collagen synthesized by the W8 cells precipitated at higher salt concentrations, and no pepsin-resistant alpha 2 chains could be demonstrated by CM-cellulose chromatography or gel electrophoresis. The cyanogen bromide peptides of the W8 alpha 1 chains did not cochromatograph with type I rat skin collagen cyanogen bromide peptides on CM-cellulose chromatography, whereas the alpha 1 chains of the K16 cells did cochromatograph. The conversion of procollagen to collagen was also decreased in the transformant cells. Therefore, the chemical transformation of K16 produced transformants with increased protein synthesis and altered collagen metabolism.
New insights into the pathophysiology and in vivo function of IgG Fc receptors through gene deletion studies. (2003)

Fc-receptors for IgG (FcyRs) are critically involved at multiple stages of an immune response, ranging from antigen presentation and regulation of antibody production to the end-stage effector mechanisms of inflammation. IgG autoantibodies that are detectable in the majority of autoimmune diseases are ligands for FcgammaRs. The three classes, FcgammaRI, FcgammaRII, and FcgammaRIII, vary in their antibody affinity, cellular expression and in vivo function. We review the current knowledge on the regulation and diverse functions of the distinct FcgammaRs and describe the evidence of their important immunoregulatory roles in autoimmunity based on recent work in animal models.
Impact of single-residue mutations on the structure and function of ovispirin/novispirin antimicrobial peptides (2002)

We studied three model antibacterial peptides that resembled the N-terminal 18 amino acids of SMAP-29, an alpha-helical, antimicrobial peptide of sheep. Although the parent compound, ovispirin-1 (KNLRR IIRKI IHIIK KYG), was potently antimicrobial, it was also highly cytotoxic to human epithelial cells and hemolytic for human erythrocytes. Single residue substitutions to ovispirin-1 yielded two substantially less cytotoxic peptides (novispirins), with intact antimicrobial properties. One of these, novispirin G-10, differed from ovispirin-1 only by containing glycine at position 10, instead of isoleucine. The other, novispirin T-7, contained threonine instead of isoleucine at position 7. We determined the three-dimensional solution structures of all three peptides by circular dichroism spectroscopy and two-dimensional nuclear magnetic resonance spectroscopy. Although all retained an amphipathic helical structure in 2,2,2-trifluoroethanol, they manifested subtle fine-structural changes that evidently impacted their activities greatly. These findings show that simple structural modifications can 'fine-tune' an antimicrobial peptide to minimize unwanted cytotoxicity while retaining its desired activity.
Augmented cell-graphs for automated cancer diagnosis (2005)

This work reports a novel computational method based on augmented cell-graphs (ACG), which are constructed from low-magnification tissue images for the mathematical diagnosis of brain cancer (malignant glioma). An ACG is a simple, undirected, weighted and complete graph in which a node represents a cell cluster and an edge between a pair of nodes defines a binary relationship between them. Both the nodes and the edges of an ACG are assigned weights to capture more information about the topology of the tissue. In this work, the experiments are conducted on a dataset that is comprised of 646 human brain biopsy samples from 60 different patients. It is shown that the ACG approach yields sensitivity of 97.53% and specificities of 93.33 and 98.15% (for the inflamed and healthy, respectively) at the tissue level in glioma diagnosis.
Survival advantage from imatinib compared with the combination interferon-α plus cytarabine in chronic-phase chronic myelogenous leukemia: historical comparison between two phase 3 trials (2006)

In the multinational IRIS study comparing imatinib with interferon plus cytarabine (IFN/Ara-C) in patients with newly diagnosed chronic-phase chronic myelogenous leukemia (CP CML), imatinib demonstrated significantly higher rates of complete cytogenetic responses (CCyRs) and improved progression-free survival (PFS). However, because of a high early crossover rate to imatinib, survival benefit was not assessable. Here, we report the result of a study comparing long-term outcome of patients included in 2 prospective randomized trials: 551 patients assigned to imatinib in the IRIS trial from 2000 to 2001 and 325 patients who received the combination IFN/Ara-C in the CML91 trial between 1991 and 1996 before imatinib was available. With a follow-up of 42 months for both groups of patients, estimated CCyR, survival free of transformation, and overall survival were significantly higher with imatinib compared with IFN/Ara-C (P < .001, P = .004, and P < .001, respectively). Improved overall survival was also confirmed within different Sokal prognostic risk groups. Of interest, among all patients who achieved major cytogenetic response or CCyR at 12 months, the survival rate was similar irrespective of their treatment. In conclusion, within the limitation of this historical comparison, there is a survival advantage from first-line therapy with imatinib over IFN/Ara-C.
Further evidence for a susceptibility locus on chromosome 10p14-p11 in 72 families with schizophrenia by nonparametric linkage analysis (1998)

Recent reports on potential linkage by Faraone and the NIMH Genetics Initiative-Millennium Schizophrenia Consortium [1997: Am J Med Genet 74:557], and by Straub et al. [1997: Am J Med Genet 74:558], prompted us to study chromosome 10 in a sample of 72 families containing 2 or more affected sibs with schizophrenia for additional evidence of linkage. We obtained highest allele sharing for the two markers D10S582 (61.5% allele sharing, χ2 = 7.6, P = 0.0058) and D10S1423 (59% allele sharing, χ2 = 4.76, P = 0.029). D10S1423 is one of the markers with the highest lod scores in the study of Faraone and the NIMH Genetics Initiative-Millennium Schizophrenia Consortium [1997: Am J Med Genet 74:557]. GENEHUNTER analysis revealed a nonparametric lod score (NPL) of 3.2 (P = 0.0007) for the marker D10S1714, which lies in the same region. Multipoint affected sib-pair lod score analysis (identity by descent) calculated by ASPEX revealed a lod score of 1.72 for all possible sib-pair combinations (107) and of 2.13, when only independent sib-pairs (87) were counted. Our study provides further evidence for a potential susceptibility locus for schizophrenia on chromosome 10p. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 81:302–307, 1998. © 1998 Wiley-Liss, Inc.
Nonapical and Cytoplasmic Expression of Interleukin-8, CXCR1, and CXCR2 Correlates with Cell Proliferation and Microvessel Density in Prostate Cancer (2005)

We propose that the concurrent increase in IL-8 and IL-8 receptor expression in human prostate cancer induces autocrine signaling that may be functionally significant in initiating and promoting the progression of prostate cancer by underpinning cell proliferation and angiogenesis.
Behavior and Use of Nonaqueous Media without Supporting Electrolyte in Capillary Electrophoresis and Capillary Electrochromatography (1997)

Five nonaqueous solvents (acetonitrile, methanol, N,N-dimethylformamide, dimethyl sulfoxide, formamide) and deionized water were investigated for their ability to support electroosmotic flow (EOF) without electrolytic additives. In general, flow was found to be equal to or greater than flow with typical CE buffer systems. The magnitude of EOF was determined for each solvent by open tubular capillary electrophoresis (CE) and related to viscosity (eta), dielectric constant (epsilon), and the ratio of dielectric constant to viscosity (eta/epsilon). Zeta potentials (zeta) were derived indirectly from flow data and tabulated. Comparisons of flow behavior and zeta were made between pure solvents and conventional CE buffers, and questions of equilibrium and reproducibility were addressed. Similar experiments were performed using hydroorganic mobile phases (ACN/water, MeOH/water) across the complete compositional range (100% water-100% organic), with flow characteristics and zeta reported for each mobile phase system. Packed capillary columns (5-microns ODS) were evaluated for flow and retention stability under capillary electrochromatographic (CEC) conditions. A separation of 11 polycyclic aromatic hydrocarbons was performed in under 13 min by CEC with an ACN/water mobile phase. Reduced plate heights (h) were calculated between 2.5 and 3.0 for solutes with capacity factors (k') up to 4.5 for the most retained solute.
Efficient recolonisation of progenitor‐depleted areas of the CNS by adult oligodendrocyte progenitor cells (2002)

A widely quoted hypothesis for the failure of remyelination in multiple sclerosis (MS) is the exhaustion of the oligodendrocyte progenitor cell (OPC) pool that is strongly implicated as the source of remyelinating oligodendrocytes in demyelinating lesions. Despite this, little is known about the responses of adult OPCs to adjacent areas of the CNS from which their numbers are depleted. We have developed an experimental model to study the pattern and rate of repopulation of OPC-depleted zones, by endogenous OPCs in the adult rat spinal cord. By X-irradiating short lengths of the spinal cord with 40 Gy of X-irradiation, we were able to produce a highly localised depletion of OPCs that allowed us to study the responses of cells located in adjacent normal areas, to this local depletion. Using both NG2 immunohistochemistry and PDGFalphaR in situ hybridisation to identify OPCs, we demonstrate that endogenous OPCs repopulated the depleted areas slowly, but completely. This repopulation occurred at the rate of approximately 0.5 mm/week in the first month. Most cells at the leading edge of repopulation had complex, branching morphologies. The repopulation process was capable of restoring the density of progenitors in repopulated areas to that of normal tissue and was not associated with a secondary progenitor loss in tissue from which progenitor cells were generated. These findings indicate that depletion of the OPC population around lesions is not likely to be the primary explanation for remyelination failure in MS.
Protein Translocation Across Membranes (1988)

Many newly synthesized proteins must be translocated across a membrane to reach their final destinations. Translocation requires a signal on the protein itself, a loose conformation of the protein, energy, and receptor-like components in the cytosol and on the target membrane.
Genome-wide Spatial Expression Profiling in FFPE Tissues (2020)

Abstract Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here we present a procedure to perform genome-wide spatial analysis of mRNA in FFPE tissue sections. The procedure takes advantage of well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3’ end of mRNA molecules in tissue sections. First, we conducted expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method’s capability to delineate anatomical regions from a molecular perspective. Second, we explored the spatial composition of transcriptomic signatures in ovarian carcinosarcoma samples using data driven analysis methods, exemplifying the method’s potential to elucidate molecular mechanisms in heterogeneous clinical samples.
Miniaturizing free‐flow electrophoresis – a critical review (2008)

Free-flow electrophoresis (FFE) separation methods have been developed and investigated for around 50 years and have been applied not only to many types of analytes for various biomedical applications, but also for the separation of inorganic and organic substances. Its continuous sample preparation and mild separation conditions make it also interesting for online monitoring and detection applications. Since 1994 several microfluidic, miniaturized FFE devices were developed and experimentally characterized. In contrast to their large-scale counterparts microfluidic FFE (mu-FFE) devices offer new possibilities due to the very rapid separations within several seconds or below and the requirement for sample volumes in the microliter range. Eventually, these mu-FFE systems might find application in so-called lab-on-a-chip devices for real-time monitoring and separation applications. This review gives detailed information on the results so far published on mu-FFE chips, comprising its four main modes, namely free-flow zone electrophoresis (FFZE), free-flow IEF (FFIEF), free-flow ITP (FFITP), and free-flow field-step electrophoresis (FFFSE). The principles of the different FFE modes and the basic underlying theory are given and discussed with special emphasis on miniaturization. Different designs as well as fabrication methods and applied materials are discussed and evaluated. Furthermore, the separation results shown indicate that similar separation quality with respect to conventional FFE systems, as defined by the resolution and peak capacity, can be achieved with mu-FFE separations when applying much lower electrical voltages. Furthermore, innovations still occur and several approaches for hyphenated, more integrated systems have been proposed so far, some of which are discussed here. This review is intended as an introduction and early compendium for research and development within this field.
<title>Fast computation of the covariance of MAP reconstructions of PET images</title> (1999)

We develop an approximate theoretical formula for fast computation of the covariance of PET images reconstructed using maximum a posteriori (MAP) estimation. The results assume a Poisson likelihood for the data and a quadratic prior on the image. The covariance for each voxel is computed using 2D FFTs and is a function of a single data dependent parameter. This parameter is computed using a modified backprojection. For a small region of interest (ROI), the correlation can be assumed to be locally stationary so that computation of the variance of an ROI can be performed very rapidly. Previous approximate formulae for the variance of MAP estimators have performed poorly in areas of low activity since they do not account for the non- negativity constraints that are routinely used in MAP algorithms. Here a `truncated Gaussian' model is used to compensate for the effect of the non-negativity constraints. Accuracy of the theoretical expressions is evaluated using both Monte Carlo simulations and a multiple-frame <SUP>15</SUP>O- water brain study. The Monte Carlo studies show that the truncated Gaussian model is effective in compensating for the effect of the non-negativity constraint. These results also show good agreement between Monte Carlo covariances and the theoretical approximations. The <SUP>15</SUP>O-water brain study further confirms the accuracy of the theoretical approximations.
A myosignal-based powered exoskeleton system (2001)

This paper studies the integration of a human arm with a powered exoskeleton (orthotic device) and its experimental implementation in an elbow joint, naturally controlled by the human. The human-machine interface was set at the neuromuscular level, by using the neuromuscular signal (EMG) as the primary command signal for the exoskeleton system. The EMG signal along with the joint kinematics were fed into a myoprocessor which in turn predicted the muscle moments on the elbow joint. The moment-based control system integrated myoprocessor moment prediction with feedback moments measured at the human arm/exoskeleton and external load/exoskeleton interfaces. The exoskeleton structure under study was a two-link, two-joint mechanism, corresponding to the arm limbs and joints, which was mechanically linked by the human operator. Four indices of performance were used to define the quality of the human/machine integration and to evaluate the operational envelope of the system. Experimental results indicate the feasibility of an EMG-based power exoskeleton system as an integrated human-machine system using high-level neurological signals.
Sphingosine 1-Phosphate and Isoform-specific Activation of Phosphoinositide 3-Kinase β (2001)

Sphingosine 1-phosphate (S1P) is a platelet-derived sphingolipid that elicits diverse biological responses, including angiogenesis, via the activation of G protein-coupled EDG receptors. S1P activates the endothelial isoform of nitric-oxide synthase (eNOS), associated with eNOS phosphorylation at Ser-1179, a site phosphorylated by protein kinase Akt. We explored the proximal signaling pathways that mediate Akt activation and eNOS regulation by S1P/EDG receptors. Akt is regulated by the lipid kinase phosphoinositide 3-kinase (PI3-K). We found that bovine aortic endothelial cells (BAEC) express both alpha and beta isoforms of PI3-K, while lacking the gamma isoform. S1P treatment led to the rapid and isoform-specific activation of PI3-Kbeta in BAEC. PI3-Kbeta can be regulated by G protein betagamma subunits (Gbetagamma). The overexpression of a peptide inhibitor of Gbetagamma attenuated S1P-induced eNOS enzyme activation, as well as S1P-induced phosphorylation of eNOS and Akt. In contrast, bradykinin, a classical eNOS agonist, neither activated any PI3-K isoform nor induced eNOS phosphorylation at Ser-1179, despite activating eNOS in BAEC. Vascular endothelial growth factor activated both PI3-Kalpha and PI3-Kbeta via tyrosine kinase pathways and promoted eNOS phosphorylation that was unaffected by Gbetagamma inhibition. These findings indicate that PI3-Kbeta (regulated by Gbetagamma) may represent a novel molecular locus for eNOS activation by EDG receptors in vascular endothelial cells. These studies also indicate that different eNOS agonists activate distinct signaling pathways that diverge proximally following receptor activation but converge distally to activate eNOS.
Prophylaxis of venous thrombosis following total hip and total knee replacement using antithrombin III and heparin. (1991)

We have performed prospective clinical studies to investigate the potential value of postoperative AT III replacement in combination with low-dose heparin in preventing venous thromboembolic disease following THR or TKR
eLearning based on the semantic web (2001)

eLearning is efficient, task relevant and just-in-time learning grown from the learningrequirements of the new, dynamically changing, distributed business world. The term &amp;quot;Semantic Web&amp;quot; encompasses efforts to build a new WWW architecture that enhances content with formal semantics, which enables better possibilities for navigating through the cyberspace and accessing its contents. As such, the Semantic Web represents a promising technology for realizing eLearning requirements.