gebhart/patrepeval huggingface dataset:
PLTP deficiency improves the anti-inflammatory properties of HDL and reduces the ability of LDL to induce monocyte chemotactic activity (2004)

We reported that phospholipid transfer protein (PLTP) deficiency decreased atherosclerosis in mouse models. Because the decreased atherosclerosis was accompanied by a significant decrease in plasma HDL levels, we examined the properties of PLTP knockout (PLTP0) HDL and tested its ability to prevent LDL-induced monocyte chemotactic activity in human artery wall cell cocultures. We isolated HDL and LDL from LDL receptor knockout/PLTP knockout (LDLr0/PLTP0) mice and from apolipoprotein B transgenic (apoBTg)/PLTP0 mice as well as their controls. PLTP0 HDL was relatively rich in protein and depleted in phosphatidylcholine. Turnover studies revealed a 3.5- to 4.0-fold increase in the turnover of protein and cholesteryl ester in HDL from PLTP0 mice compared with control mice. The ability of HDL from LDLr0/PLTP0 and apoBTg/PLTP0 mice to prevent the induction of monocyte chemotactic activity in human artery wall cell cocultures exposed to human LDL was dramatically better than that in controls. Moreover, LDL from PLTP0 mice was markedly resistant to oxidation and induced significantly less monocyte chemotactic activity compared with that in controls. In vitro, PLTP0 HDL removed significantly more oxidized phospholipids from LDL than did control HDL. We conclude that PLTP deficiency improves the anti-inflammatory properties of HDL in mice and reduces the ability of LDL to induce monocyte chemotactic activity.
Amino Acid and Peptide Bioconjugates of Copper(II) and Zinc(II) Complexes with a ModifiedN,N-Bis(2-picolyl)amine Ligand (2005)

Four chelating nitrogen ligands 2-5 derived from N,N-bis(2-picolyl)amine (bpa, 1) were synthesized, namely, (PyCH(2))(2)N-CH(2)-p-C(6)H(4)-CO(2)R (R = Me, 2, and R = H, 3) and (PyCH(2))(2)N-(CH(2))(n)-CO(2)H (n = 2, 4, and n = 5, 5). Amino acid conjugates 6 and 7 were formed by condensation of 3 with H-Phe-OMe and H-betaAla-OMe, respectively. Cu(II) and Zn(II) complexes of 1-7 were prepared and fully characterized. The X-ray structures of 1(Zn), 2(Zn), 4(Cu), and 7(Cu) were determined. The Zn complexes 1(Zn) and 2(Zn) as well as 7(Cu) show a distorted trigonal bipyramidal coordination environment in the solid state. An octahedral complex is observed for 4(Cu) which forms chains along the crystallographic b axis by intermolecular coordination of the carboxylic acid to the metal ion of a neighboring complex. Ligand 3 was used to prepare the peptide bioconjugate 8 (3-Ahx-Pro-Lys-Lys-Lys-Arg-Lys-Phe-NH(2)) with a nuclear localization signal (nls) heptapeptide by solid phase synthesis. Cu(II) and Zn(II) complexes of 8 were synthesized in situ and studied by FAB-MS, ESI-MS, UV/vis, and EPR (for 8(Cu)), and FAB-MS, ESI-MS, and NMR (for 8(Zn)). All spectroscopic results clearly support metal coordination to the bpa ligand in the bioconjugates 8(M), even in the presence of other potential ligands from amino acid side chains of the peptide. We suggest metal-peptide conjugates like 8(M) as artificial metallochaperones because they have the potential to deliver metal ions to specific compartments in the cell as determined by the peptide moieties.
Interaction of the Factor XIII Activation Peptide with α-Thrombin (2000)

The serine protease thrombin proteolytically activates blood coagulation factor XIII by cleavage at residue Arg(37); factor XIII in turn cross-links fibrin molecules and gives mechanical stability to the blood clot. The 2.0-A resolution x-ray crystal structure of human alpha-thrombin bound to the factor XIII-(28-37) decapeptide has been determined. This structure reveals the detailed atomic level interactions between the factor XIII activation peptide and thrombin and provides the first high resolution view of this functionally important part of the factor XIII molecule. A comparison of this structure with the crystal structure of fibrinopeptide A complexed with thrombin highlights several important determinants of thrombin substrate interaction. First, the P1 and P2 residues must be compatible with the geometry and chemistry of the S1 and S2 specificity sites in thrombin. Second, a glycine in the P5 position is necessary for the conserved substrate conformation seen in both factor XIII-(28-37) and fibrinopeptide A. Finally, the hydrophobic residues, which occupy the aryl binding site of thrombin determine the substrate conformation further away from the catalytic residues. In the case of factor XIII-(28-37), the aryl binding site is shared by hydrophobic residues P4 (Val(34)) and P9 (Val(29)). A bulkier residue in either of these sites may alter the substrate peptide conformation.
GPS Signal Availability in Land Mobile Applications (1989)

This paper summarizes the results of a series of direct measurements conducted to characterize the GPS signal environment in land vehicular operations for a variety of highway, city, and railroad situations. The basic instrumentation for these observations consisted of a NAVCORE I (TM) GPS receiver configured to output key measurements to a microcomputer as a data recording device. The results of these tests are presented in tables of the percentages of distance traveled in which one or more and two or more satellite outages were encountered, and in histograms of the outage probabilities as functions of the distance durations of the outages. The equipment was installed both in a van-type vehicle for highway and city street tests, and in a “Hy-Rail” vehicle for operation on railroad tracks.
Doubling direct-detection data rate by polarization multiplexing of 16-QAM without active polarization control (2013)

We introduce and simulate a technique enabling to utilize the polarization dimension in direct-detection optical transmission, supporting polarization multiplexing (POL-MUX) over direct-detection (DD) methods previously demonstrated for a single polarization such as direct-detection OFDM. POL-MUX is currently precluded in self-coherent DD with remotely transmitted pilot, as signal x pilot components may randomly fade out. We propose POL-MUX transmission of advanced modulation formats, such as 16-QAM and higher, by means of a novel low-complexity photonic integrated optical front-end and adaptive 3x2 MIMO DSP. The principle of operation is as follows: an additional X x Y cross-polarizations signal is generated, providing three projections onto an over-complete frame of three dependent vectors. This enables to resiliently reconstruct the received state of polarization even when the remotely transmitted pilot fades along one of the received polarization axes.
Growth restriction of influenza A virus by M2 protein antibody is genetically linked to the M1 protein. (1989)

The M2 protein of influenza A virus is a 97-amino acid integral membrane protein expressed at the surface of infected cells. Recent studies have shown that a monoclonal antibody (14C2) recognizes the N terminus of M2 and restricts the replication of certain influenza A viruses. To investigate the mechanism of M2 antibody growth restriction, 14C2 antibody-resistant variants of strain A/Udorn/72 have been isolated. Most of the variant viruses are not conventional antigenic variants as their M2 protein is still recognized by the 14C2 antibody. A genetic analysis of reassortant influenza viruses prepared from the 14C2 antibody-resistant variants and an antibody-sensitive parent virus indicates that M2 antibody growth restriction is linked to RNA segment 7, which encodes both the membrane protein (M1) and the M2 integral membrane protein. Nucleotide sequence analysis of RNA segment 7 from the variant viruses predicts single amino acid substitutions in the cytoplasmic domain of M2 at positions 71 and 78 or at the N terminus of the M1 protein at residues 31 and 41. To further examine the genetic basis for sensitivity and resistance to the 14C2 antibody, the nucleotide sequences of RNA segment 7 of several natural isolates of influenza virus have been obtained. Differences in the M1 and M2 amino acid sequences for some of the naturally resistant strains correlate with those found for the M2 antibody variant viruses. The possible interaction of M1 and M2 in virion assembly is discussed.
Matched rabbit monoclonal antibodies against αv-series integrins reveal a novel αvβ3-LIBS epitope, and permit routine staining of archival paraffin samples of human tumors (2012)

The relationship between integrin expression and function in pathologies is often contentious as comparisons between human pathological expression and expression in cell lines is difficult. In addition, the expression of even integrins αvβ6 and αvβ8 in tumor cell lines is not comprehensively documented. Here, we describe rabbit monoclonal antibodies (RabMabs) against the extracellular domains of αv integrins that react with both native integrins and formalin fixed, paraffin embedded (FFPE) human tissues. These RabMabs, against αvβ3 (EM22703), αvβ5 (EM09902), αvβ6 (EM05201), αvβ8 (EM13309), and pan-αv (EM01309), recognize individual integrin chains in Western blots and in flow cytometry. EM22703 detected a ligand-induced binding site (LIBS), reporting an epitope enhanced by the binding of an RGD-peptide to αvβ3. αvβ8 was rarely expressed in human tumor specimens, and weakly expressed in non-small-cell lung carcinoma (NSCLC). However, ovarian carcinoma cell lines expressed αvβ8, as did some melanoma cells, whereas U87MG glioma lacked αvβ8 expression. We observed an unexpected strong expression of αvβ6 in tumor samples of invasive ductal breast adenoma, colorectal carcinoma (CRC), and NSCLC. αvβ3 was strongly expressed in some invasive NSCLC cohorts. Interestingly, PC3 prostate cell and human prostate tumors did not express αvβ3. The RabMabs stained plasma membranes in FFPE-immunohistochemistry (IHC) samples of tumor cell lines from lung, ovary, colon, prostate, squamous cell carcinoma of head and neck (SCCHN), breast, and pancreas carcinomas. The RabMabs are unique tools for probing αv integrin biology, and suggest that especially αvβ6 and αvβ8 biologies still have much to reveal.
Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis (2019)

Microglia, the main immune cells of the central nervous system, are increasingly implicated in Alzheimer's disease (AD). Manifold transcriptomic studies in the brain have not only highlighted microglia's role in AD pathogenesis, but also mapped crucial pathological processes and identified new therapeutic targets. An important component of many of these transcriptomic studies is the investigation of gene expression networks in AD brain, which has provided important new insights into how coordinated gene regulatory programs in microglia (and other cell types) underlie AD pathogenesis. Given the rapid technological advancements in transcriptional profiling, spanning from microarrays to single-cell RNA sequencing (scRNA-seq), tools used for mapping gene expression networks have evolved to keep pace with the unique features of each transcriptomic platform. In this article, we review the trajectory of transcriptomic network analyses in AD from brain to microglia, highlighting the corresponding methodological developments. Lastly, we discuss examples of how transcriptional network analysis provides new insights into AD mechanisms and pathogenesis.
A Fuzzy Relative of the ISODATA Process and Its Use in Detecting Compact Well-Separated Clusters (1973)

Abstract Two fuzzy versions of the k-means optimal, least squared error partitioning problem are formulated for finite subsets X of a general inner product space. In both cases, the extremizing solutions are shown to be fixed points of a certain operator T on the class of fuzzy, k-partitions of X, and simple iteration of T provides an algorithm which has the descent property relative to the least squared error criterion function. In the first case, the range of T consists largely of ordinary (i.e. non-fuzzy) partitions of X and the associated iteration scheme is essentially the well known ISODATA process of Ball and Hall. However, in the second case, the range of T consists mainly of fuzzy partitions and the associated algorithm is new; when X consists of k compact well separated (CWS) clusters, Xi , this algorithm generates a limiting partition with membership functions which closely approximate the characteristic functions of the clusters Xi . However, when X is not the union of k CWS clusters, the limiting partition is truly fuzzy in the sense that the values of its component membership functions differ substantially from 0 or 1 over certain regions of X. Thus, unlike ISODATA, the “fuzzy” algorithm signals the presence or absence of CWS clusters in X. Furthermore, the fuzzy algorithm seems significantly less prone to the “cluster-splitting” tendency of ISODATA and may also be less easily diverted to uninteresting locally optimal partitions. Finally, for data sets X consisting of dense CWS clusters embedded in a diffuse background of strays, the structure of X is accurately reflected in the limiting partition generated by the fuzzy algorithm. Mathematical arguments and numerical results are offered in support of the foregoing assertions.
Antitumor effects of interleukin-7 and adoptive immunotherapy on human colon carcinoma xenografts. (1993)

The antitumor properties of recombinant human IL-7 (rhIL-7) on a human tumor was evaluated by engrafting a human colon carcinoma into immunodeficient mice and then treating the mice with rhIL-7 and adoptively transferred human peripheral blood T cells. It was found that rhIL-7 alone had no effect on the survival of the tumor-bearing recipients. However, the combination of rhIL-7 and human T cells significantly promoted the survival of the recipients compared with mice receiving either treatment by itself. When the surviving mice were analyzed 6 mo later for the degree of human cell engraftment, the recipients receiving both rhIL-7 and human T cells had greater numbers of human CD8+ T cells in the spleens. However, the human T cells recovered from the surviving mice showed low lytic activity against the tumor in vitro. Supernatants from human T cells cultured with the tumor and rhIL-7 in vitro were found to inhibit tumor growth and were demonstrated to contain high levels of IFN-gamma. Antibodies to IFN-gamma neutralized the growth inhibition of the tumor both in vitro and in vivo demonstrating that the in vivo mechanism underlying the antitumor effects of this regimen was partly dependent on the production of IFN-gamma by the T cells and not their cytolytic capability. Interestingly, systemic administration of rhIFN-gamma to tumor-bearing mice yielded little antitumor effect suggesting that adoptive immunotherapy with rhIL-7 was superior possibly because of the continuous local release of the cytokines. Therefore, rhIL-7 may be of clinical use as an antineoplastic agent and the human/mouse model is a potentially important preclinical model for in vivo evaluation of the efficacy of this and other immunotherapies.
Data collection of Japanese dialects and its influence into speech recognition (2002)

Reports the successful completion of a Japanese POLYPHONE project-the Voice Across Japan (VAJ) data collection project. The database has the following characteristics: (1) a large speaker database (8,866 speakers) through a telephone line, (2) gathering of the participants' personal information such as gender, age, place where they grew up, and so on, and (3) data segmented by phone or word boundaries. This paper describes several aspects of Japanese dialects and also reports the results of experiments. How much does dialect influence speech recognition? In our results, dialect influences the speech recognition rate by 2-4%. The results are useful information for building practical speech recognition systems as well as for data collection.
Novel 3-hydroxy-2(1H)-pyridinones. Synthesis, iron(III)-chelating properties and biological activity (1990)

The synthesis of a range of novel bidentate and hexadentate ligands containing the chelating moiety 3-hydroxy-2(1H)-pyridinone is described. The pKa values of the ligands and the stability constants of their iron(III) complexes have been determined. The stability constant of the iron(III) complex of one of the hexadentate ligands is comparable to that of desferrioxamine B. The distribution coefficients of the ligands and their iron(III) complexes were also determined. One of the novel hexadentate compounds has been shown to markedly enhance iron(III) excretion from both hepatocytes and iron-overloaded mice.
Elevated Serum Cytokines Correlated with Altered Behavior, Serum Cortisol Rhythm, and Dampened 24-Hour Rest-Activity Patterns in Patients with Metastatic Colorectal Cancer (2005)

Significant correlations were found between serum levels of TGF-alpha and IL-6, circadian patterns in wrist activity and serum cortisol and tumor-related symptoms in patients with metastatic colorectal cancer. These data support the hypothesis that some cancer patient's symptoms of fatigue, poor QOL, and treatment outcome are related to tumor or host generated cytokines and could reflect cytokine effects on the circadian timing system. This interplay between cytokine signaling pathways, the hypothalamic-pituitary-adrenal axis, the autonomic nervous system, and efferent pathways of the suprachiasmatic nucleus that control circadian physiology, opens the way to new rational interventions for symptom management in cancer patients.
Steroidal regulation of connective tissue growth factor (CCN2; CTGF) synthesis in the mouse uterus (2001)

Maternal factors are principal cues for CCN2 (CTGF) and TGF-beta1 production in the uterus because (1) their expression during pseudopregnancy is comparable to that seen in pregnancy and (2) they are regulated by ovarian steroids. TGF-beta dependent and independent mechanisms of ccn2 (ctgf) gene transcription exist in the uterus that are variably regulated by steroid hormones. Collectively, the data support a role for CCN2 (CTGF) in mediating the effects of steroid hormones and TGF-beta on endometrial function.
Example-based composite sketching of human portraits (2004)

Creating a portrait in the style of a particular artistic tradition or a particular artist is a difficult problem. Elusive to codify algorithmically, the nebulous qualities which combine to form artwork are often well captured using example-based approaches. These methods place the artist in the process, often during system training, in the hope that their talents may be tapped. Example based methods do not make this problem easy, however. Examples are precious, so training sets are small, reducing the number of techniques which may be employed. We propose a system which combines two separate but similar subsystems, one for the face and another for the hair, each of which employs a global and a local model. Facial exaggeration to achieve the desired stylistic look is handled during the global face phase. Each subsystem uses a divide-and-conquer approach, but while the face subsystem decomposes into separable subproblems for the eyes, mouth, nose, etc., the hair needs to be subdivided in a relatively arbitrary way, making the hair subproblem decomposition an important step which must be handled carefully with a structured model and a detailed model.
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays (1999)

Oligonucleotide arrays can provide a broad picture of the state of the cell, by monitoring the expression level of thousands of genes at the same time. It is of interest to develop techniques for extracting useful information from the resulting data sets. Here we report the application of a two-way clustering method for analyzing a data set consisting of the expression patterns of different cell types. Gene expression in 40 tumor and 22 normal colon tissue samples was analyzed with an Affymetrix oligonucleotide array complementary to more than 6,500 human genes. An efficient two-way clustering algorithm was applied to both the genes and the tissues, revealing broad coherent patterns that suggest a high degree of organization underlying gene expression in these tissues. Coregulated families of genes clustered together, as demonstrated for the ribosomal proteins. Clustering also separated cancerous from noncancerous tissue and cell lines from in vivo tissues on the basis of subtle distributed patterns of genes even when expression of individual genes varied only slightly between the tissues. Two-way clustering thus may be of use both in classifying genes into functional groups and in classifying tissues based on gene expression.
ICOS Co-Stimulation: Friend or Foe? (2016)

Over the last 15 years, the inducible T cell co-stimulator (ICOS) has been implicated in various immune outcomes, including the induction and regulation of Th1, Th2, and Th17 immunity. In addition to its role in directing effector T cell differentiation, ICOS has also been consistently linked with the induction of thymus-dependent (TD) antibody (Ab) responses and the germinal center (GC) reaction. ICOS co-stimulation, therefore, appears to play a complex role in dictating the course of adaptive immunity. In this article, we summarize the initial characterization of ICOS and its relationship with the related co-stimulatory molecule CD28. We then address the contribution of ICOS in directing an effector T cell response, and ultimately disease outcome, against various bacterial, viral, and parasitic infections. Next, we assess ICOS in the context of TD Ab responses, connecting ICOS signaling to follicular helper T cell differentiation and its role in the GC reaction. Finally, we address the link between ICOS and human autoimmune disorders and evaluate potential therapies aiming to mitigate disease progression by modulating ICOS signaling.
The ArabidopsisERECTAgene is expressed in the shoot apical meristem and organ primordia (1998)

In Arabidopsis thaliana (L.) Heynh, the mutation in ERECTA is known to confer a compact inflorescence by a reduction in the lengths of internodes and pedicels. We analyzed the expression pattern of this gene during plant development. In situ hybridization and histochemical analysis using transgenic plants carrying chimeric gene fusions, with the ERECTA promoter fused to the beta-glucuronidase (GUS) gene, showed that ERECTA was predominantly expressed in the shoot apical meristems and organ primordia. ERECTA expression in the shoot apical meristem was weak early in plant development but increased with the transition from the vegetative to the reproductive growth phase. ERECTA was also strongly expressed in organ primordia and immature organs but weakly in mature organs. Thus, ERECTA was expressed in a cell-specific and developmentally regulated manner. In order to identify the regulatory mechanism responsible for the expression pattern of ERECTA, the cis-acting regions in the ERECTA promoter were defined by study of the expression of the chimeric genes that consist of the 5'- or internal deleted promoter and a GUS reporter gene in transgenic plants. The results showed that the essential cis-regulatory elements governing the spatially and temporally specific expression of ERECTA are located between positions -462 and -228 bp and between positions -228 and -153 bp with respect to the transcriptional initiation site.