gebhart/patrepeval huggingface dataset:
A Role for Neutral Sphingomyelinase-mediated Ceramide Production in T Cell Receptor–induced Apoptosis and Mitogen-activated Protein Kinase–mediated Signal Transduction (1999)

Studying apoptosis induced by T cell receptor (TCR) cross-linking in the T cell hybridoma, 3DO, we found both neutral sphingomyelinase activation and production of ceramide upon receptor engagement. Pharmacological inhibition of ceramide production by the fungal toxin, fumonisin B1, impaired TCR-induced interleukin (IL)-2 production and programmed cell death. Addition of either exogenous ceramide or bacterial sphingomyelinase reconstituted both responses. Moreover, specific inactivation of neutral sphingomyelinase by antisense RNA inhibited IL-2 production and mitogen-activated protein kinase activation after TCR triggering. These results suggest that ceramide production by activation of neutral sphingomyelinase is an essential component of the TCR signaling machinery.
Potential Design Rules and Enzymatic Synthesis of siRNAs (2004)

Small interfering RNAs (siRNAs) have emerged as a powerful technique for sequence-specific gene silencing in a wide variety of organisms. However, the base composition of the siRNA sequence is not the only determinant of efficacy. Intrinsic factors related to mRNA structures are likely to be crucial determinants for siRNA activity. Indeed, placing the recognition site of an active siRNA into a structured mRNA region has abrogated the siRNA activity. Therefore, a successful gene-targeting project may require the design of many distinct siRNAs at a high cost. Here, potential design rules, cost-effective strategies for producing siRNAs by T7 RNA polymerase, and expression cassettes for in vivo testing are described.
Synthesis and Fluorescent Properties of Difluoroboron Dibenzoylmethane Polycaprolactone (2009)

Difluoroboron β-diketonate dyes are noted for their intense fluorescence, one- and two-photon absorption, solvatochromism, and good aqueous stability. Incorporation of these dyes into polymers leads to processable optical materials, which in some cases display additional emissive features. For example, previously we reported that difluoroboron dibenzoylmethane−polylactide (BF2dbmPLA) exhibits both fluorescence and room temperature phosphorescence (RTP). Typically RTP is ascribed to a matrix effect, where the rigid ordered medium restricts dye molecular motions, and excited-state decay via thermal pathways is hindered in favor of radiative decay. To test polymer effects on dye emissive properties, this study explores BF2dbmPCL (PCL = poly(ε-caprolactone), a semicrystalline polymer) of different molecular weights ranging from ∼3 to 18 kDa. PCL materials exhibit the expected intense fluorescence and molecular weight dependent emission but, surprisingly, no RTP. Phosphorescence is evident at lower temperatures (0 to −78 °C), however, and both intensities and lifetimes increase as the temperature is dropped. Polymer thermal properties were also examined. Aside from in the lowest molecular weight sample, the dye end group showed little effect on melting and glass transition temperatures. These dye-modified materials lend useful optical imaging capability to PCL, a polymer commonly used in drug delivery and tissue engineering applications.
Fabrication of gold nanowires on insulating substrates by field-induced mass transport (2001)

A method for the fabrication of nanometer size gold wires on insulating surfaces is presented. An oscillating gold-coated atomic force microscope tip is brought into close proximity of a silicon dioxide surface. The application of a negative sample voltage produces the transport of gold atoms from the tip to the surface. The voltage is applied when there is a tip–surface separation of ∼3 nm. The finite tip–surface separation enhances the tip lifetime. It also allows the application of sequences of multiple voltage pulses. Those sequences allow the fabrication of continuous nanowires. The atomic force microscope gold deposition is performed at room temperature and in ambient conditions which makes the method fully compatible with standard lithographic techniques. Electron transport measurements of the wires show a clear metallic behavior. Electrical resistivities of ∼3×10−7 Ω m and current densities of up to 5×1011 A m−2 are reported.
High genetic diversity at the regional scale and possible speciation in Sebacina epigaea and S. incrustans (2013)

Our results suggest that recombination and negative selection have played significant roles in generating genetic diversity within these morphological species at small geographical scales. Concordance between gene genealogies identified lineages/cryptic species that have evolved independently for a relatively long period of time. These putative species were not associated with geographic provenance, geographic barrier, host preference or distinct phenotypic innovations.
The signigicance of communication within the family for the development of behavior disturbances in primary school children (1994)

Cilj ovog rada je utvrđivanje prediktivnih vrijednosti komunikacije u obitelji na ponasanje djece starije osnovnoskolske dobi. Rezultati se temelje na samopercepciji i samoiskazu ucenika sedmih i osmih razreda osnovnih skola grada Zagreba (N – 484) o njihovom ponasanju (PON) i kvaliteti komunikacije u obitelji (KUO). Pomocu regresijske analize temeljene na sedam latentnih dimenzija prostora ponasanja i manifestnih varijabli (150) prostora komunikacije u obitelji, utvrđena je visoka povezanost promatranih prostora, odnosno svaki faktor ponasanja moguce je objasniti specificnim modalitetima komunikacije u obitelji. Rezultati upucuju na vrijednost ucenja komunikacije i drugih socijalnih vjestina kao prevencije specificnih oblika ponasanja djece, odnosno podizanja kvalitete obiteljskog života.
Density Functional Calculations of Proton Chemical Shifts in Model Peptides (1997)

Density-functional chemical shielding calculations are reported for the alanine dipeptide with a variety of backbone torsion angles and for methane and N-methylacetamide complexes with rare gases, monatomic ions, water, and other amides. These fragment systems model electrostatic, nonbonded, and hydrogen bonding interactions in proteins and have been investigated at a variety of geometries. The results are compared to empirical formulas that relate intermolecular shielding effects to peptide group magnetic anisotropies, electrostatic polarization of the C−H and N−H bonds, magnetic contributions from C−C and C−H bonds, and close contact effects. Close contacts are found to deshield protons involved in close nonbonded contacts that typically occur in hydrogen bonds. “Lone pair” charges improve the model for electrostatic effects and are important for understanding the angular dependence of shifts for protons involved in hydrogen bonds. C−C and C−H bond anisotropy contributions help to explain the torsional dependence of amide proton shifts in alanine dipeptide. Good agreement is found between the empirical formulas and the quantum chemistry results, allowing a reassessment of empirical formulas that are used in the analysis of chemical shift dispersion in proteins.
Anatomy, histology and immunohistochemistry of normal human skin. (2003)

The skin is the largest organ of the body, accounting for about 15% of the total body weight in adult humans. It exerts multiple vital protective functions against environmental aggressions, rendered possible thanks to an elaborate structure, associating various tissues of ectodermal and mesodermal origin, arranged in three layers, including (from top to bottom) the epidermis (and its appendages), the dermis and the hypodermis. This article reviews the main data concerning the anatomy, histology and immunohistochemistry of normal human skin.
An overview of hepatocellular carcinoma study by omics-based methods (2009)

Hepatocellular carcinoma (HCC) is one of the most deadly malignancies worldwide. Scientists have been studying the molecular mechanism of HCC for years, but the understanding of it remains incomplete and scattered across the literature at different molecular levels. Chromosomal aberrations, epigenetic abnormality and changes of gene expression have been reported in HCC. High-throughput omics technologies have been widely applied, aiming at the discovery of candidate biomarkers for cancer staging, prediction of recurrence and prognosis, and treatment selection. Large amounts of data on genetic and epigenetic abnormalities, gene expression profiles, microRNA expression profiles and proteomics have been accumulating, and bioinformatics is playing a more and more important role. In this paper, we review the current omics-based studies on HCC at the levels of genomics, transcriptomics and proteomics. Integrating observations from multiple aspects is an essential step toward the systematic understanding of the disease.
Chromosome 1 abnormalities in myeloid malignancies: a literature survey and karyotype–phenotype associations (2009)

Chromosome 1 is the largest human chromosome and contains over 1600 known genes and 1000 novel coding sequences or transcripts. It is, therefore, not surprising that recurrent chromosome 1 abnormalities are regularly encountered in both neoplastic and non-neoplastic medical conditions. The current review is focused on myeloid malignancies where we summarize the relevant published literature and discuss specific karyotype-phenotype associations. We show that chromosome 1 abnormalities are most frequent in BCR-ABL-negative classic myeloproliferative neoplasms (MPN): polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). Specific abnormalities include duplications (e.g. 1q12-->1q32 in PV, 1q21-32-->1q32-44 in post-PV MF or PMF), deletions (e.g. 1p13-36-->pter in PV or PMF, 1q21 in PMF) and unbalanced translocations involving chromosome 6, such as der(6)t(1;6)(q21-25;p21.3-23), and other partner chromosomes involving 1q10/1p11 and 1q21-25 breakpoints. Although occasionally seen in chronic phase MPN, unbalanced 1;7 translocations, e.g. der(1;7)(q10;p10), are usually seen in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and post-MPN AML/MDS. These observations suggest that certain chromosome 1 regions, especially 1q21-1q32 and 1p11-13, might harbor oncogenes or tumor suppressor genes that are pathogenetically relevant to both chronic and advanced phases of MPN.
A polymorphism in the GALNT2 gene and ovarian cancer risk in four population based case-control studies. (2010)

Recent epidemiologic evidence supports a role for MUC1 in ovarian carcinogenesis; therefore, we hypothesized that common genetic variation in the genes responsible for glycosylation of MUC1 may influence ovarian cancer risk. In a genome-wide association study of ovarian cancer, we observed an association between a non-synonymous SNP (rs2271077) in the UDP-N-acetyl-alpha-d-galactosamine: polypeptide N-acetylgalactosainyltransferase 2 (GALNT2) gene and ovarian cancer risk (p=0.005). We sought to validate the association in four population based ovarian cancer case-control studies collaborating through the Ovarian Cancer Association Consortium. Although rs2271077 was associated with a significantly increased risk (Odds Ratio (OR) = 1.37, 95% Confidence Interval (CI) = 1.06-1.77) in one study with 961 cases and 922 controls, we observed no association in the remaining three studies including 1452 cases and 1954 controls (OR=0.83, 95% CI= 0.66-1.04). Therefore, there appears to be no strong evidence of association between GALNT2 SNP rs2271077 and ovarian cancer risk.
Mucin and proteoglycan functions in embryo implantation (1998)

Embryo implantation is a complex series of events that involves changes in pattern of expression of embryonic as well as uterine cell surface components. In the case of the embryo, these changes are driven by the developmental program. In the case of the uterus, these changes are triggered by both maternal hormonal influences as well as embryo-derived factors. Aspects of the implantation process vary among species; however, interaction between the external surface of the embryonic trophectoderm and the apical surface of the lumenal uterine epithelium is a common event. Progress is being made in defining the molecular players in these cell surface interactions. Large-molecular-weight mucin glycoproteins such as MUC1 are present at the apical surface of the uterine epithelium under most conditions. Under most circumstances, these mucins appear to protect the mucosal surface from infection and the action of degradative enzymes. These mucins are antiadhesive and also appear to represent a barrier to embryo attachment. Consistent with this model, reduction of mucin expression is observed in uterine lumenal epithelia in many species. Nonetheless, mucin expression persists in the human uterus during the proposed receptive phase. It is possible that mucin loss is localized to implantation sites in humans. Alternatively, mucins may function differently within the context of human implantation than in other species. Studies primarily performed in mice indicate that heparan sulfate proteoglycans, in particular, perlecan, appears on the exterior trophectodermal surface coincident with the acquisition of attachment competence. Various in vitro studies indicate that heparan sulfate proteoglycans support embryo attachment activity that may represent an early event in embryo-uterine interaction. Uterine epithelia cells express several complementary heparan sulfate-binding proteins that may participate in these attachment processes. Use of molecular genetic approaches in mouse models, as well as careful studies of the expression and function of these molecules in the context of implantation in various species are beginning to shed light on the key molecular events of implantation.
New three-dimensional integration technology using self-assembly technique (2006)

To achieve ultimate super chip integration, we have developed a three-dimensional integration technology called super-smart-stack technology using a self-assembly technique. The chip alignment accuracy of within 1mum is obtained by the self-assembly technique. We demonstrated for the first time that 3D SRAM test chip with ten memory layers was successfully fabricated using the super-smart-stack (SSS) technology
Two-dimensional separations: concept and promise (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTwo-dimensional separations: concept and promiseJ. Calvin GiddingsCite this: Anal. Chem. 1984, 56, 12, 1258A–1270APublication Date (Print):October 1, 1984Publication History Published online22 September 2008Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/ac00276a003https://doi.org/10.1021/ac00276a003research-articleACS PublicationsRequest reuse permissionsArticle Views1865Altmetric-Citations460LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Dissection of immunoglobulin E and T lymphocyte reactivity of isoforms of the major birch pollen allergen Bet v 1: potential use of hypoallergenic isoforms for immunotherapy. (1996)

We dissected the T cell activation potency and the immunoglobulin (Ig) E-binding properties (allergenicity) of nine isoforms of Bet v 1 (Bet v 1a-Bet v 1l), the major birch pollen allergen. Immunoblot experiments showed that Bet v 1 isoforms differ in their ability to bind IgE from birch pollen-allergic patients. All patients tested displayed similar IgE-binding patterns toward each particular isoform. Based on these experiments, we grouped Bet v 1 isoforms in three classes: molecules with high IgE-binding activity (isoforms a, e, and j), intermediate IgE-binding (isoforms b, c, and f), and low/no IgE-binding activity (isoforms d, g, and 1). Bet v 1a, a recombinant isoform selected from a cDNA expression library using IgE immunoscreening exhibited the highest IgE-binding activity. Isoforms a, b, d, e, and 1 were chosen as representatives from the three classes for experimentation. The potency of each isoallergen to activate T lymphocytes from birch pollen-allergic patients was assayed using peripheral blood mononuclear cells, allergen-specific T cell lines, and peptide-mapped allergen-specific T cell clones. Among the patients, some displayed a broad range of T cell-recognition patterns for Bet v 1 isoforms whereas others seemed to be restricted to particular isoforms. In spite of this variability, the highest scores for T cell proliferative responses were observed with isoform d (low IgE binder), followed by b, 1, e, and a. In vivo (skin prick) tests showed that the potency of isoforms d and 1 to induce typical urticarial type 1 reactions in Bet v 1-allergic individuals was significantly lower than for isoforms a, b, and e. Taken together, our results indicate that hypoallergenic Bet v 1 isoforms are potent activators of allergen-specific T lymphocytes, and Bet v 1 isoforms with high in vitro IgE-binding activity and in vivo allergenicity can display low T cell antigenicity. Based on these findings, we propose a novel approach for immunotherapy of type I allergies: a treatment with high doses of hypoallergenic isoforms or recombinant variants of atopic allergens. We proceed on the assumption that this measure would modulate the quality of the T helper cell response to allergens in vivo. The therapy form would additionally implicate a reduced risk of anaphylactic side effects.
Intravitreal Bevacizumab (Avastin) Treatment of Neovascular Glaucoma in Ocular Ischemic Syndrome (2009)

We report a case of ocular ischemic syndrome accompanied by neovascular glaucoma that was successfully treated with Bevacizumab. A 70-year-old male patient diagnosed with neovascular glaucoma of the left eye 3-4 years prior complained of continuous left eye pain and declining visual acuity despite receiving the latest treatment methods. At the time of admission the patient had no light perception in the left eye and his intraocular pressure was 30 mmHg. Anterior segment and fundus examinations revealed neovascularization of the iris and stenosis of the retinal vessel. Hypofluorescence of the choroid and retinal vessels was observed on fluorescence fundus angiography. Left internal carotid artery stenosis was observed on a brain MRI. Despite being treated with eye solution and oral medication, intraocular pressure was not controlled. After 7 days, we performed an intravitreal Bevacizumab 1.25 mg/0.05mL injection. One day after the intravitreal Bevacizumab injection, the neovascularization had nearly regressed and intraocular pressure was 30 mmHg. Intravitreal Bevacizumab injection produced regression of neovascularization and proved effective for treatment of neovascular glaucoma in this case of ocular ischemic syndrome.
Protein-tyrosine Phosphatase 1B Potentiates IRE1 Signaling during Endoplasmic Reticulum Stress (2004)

Protein-tyrosine phosphatase 1B (PTP-1B) is the prototypic tyrosine phosphatase whose function in insulin signaling and metabolism is well established. Although the role of PTP-1B in dephosphorylating various cell surface receptor tyrosine kinases is clear, the mechanisms by which it modulates receptor function from the endoplasmic reticulum (ER) remains an enigma. Here, we provide evidence that PTP-1B has an essential function in regulating the unfolded protein response in the ER compartment. The absence of PTP-1B caused impaired ER stress-induced IRE1 signaling. More specifically, JNK activation, XBP-1 splicing, and EDEM (ER degradation-enhancing alpha-mannosidase-like protein) gene induction, as well as ER stress-induced apoptosis, were attenuated in PTP-1B knock-out mouse embryonic fibroblasts in response to two ER stressors, tunicamycin and azetidine-2 carboxylic acid. We demonstrate that PTP-1B is not just a passive resident of the ER but on the contrary has an essential role in potentiating IRE1-mediated ER stress signaling pathways.
The Plasmid RK2 Replication Initiator Protein (TrfA) Binds to the Sliding Clamp β Subunit of DNA Polymerase III: Implication for the Toxicity of a Peptide Derived from the Amino-Terminal Portion of 33-Kilodalton TrfA (2006)

The broad-host-range plasmid RK2 is capable of replication and stable maintenance within a wide range of gram-negative bacterial hosts. It encodes the essential replication initiation protein TrfA, which binds to the host initiation protein, DnaA, at the plasmid origin of replication (oriV). There are two versions of the TrfA protein, 44 and 33 kDa, resulting from alternate in-frame translational starts. We have shown that the smaller protein, TrfA-33, and its 64-residue amino-terminal peptide (designated T1) physically interact with the Escherichia coli beta sliding clamp (beta(2)). This interaction appears to be mediated through a QLSLF peptide motif located near the amino-terminal end of TrfA-33 and T1, which is identical to the previously described eubacterial clamp-binding consensus motif. T1 forms a stable complex with beta(2) and was found to inhibit plasmid RK2 replication in vitro. This specific interaction between T1 and beta(2) and the ability of T1 to block DNA replication have implications for the previously reported cell lethality caused by overproduction of T1. The toxicity of T1 was suppressed when wild-type T1 was replaced with mutant T1, carrying an LF deletion in the beta-binding motif. Previously, T1 toxicity has been shown to be suppressed by Hda, an intermediate regulatory protein which helps prevent over-initiation in E. coli through its interaction with the initiator protein, DnaA, and beta(2). Our results support a model in which T1 toxicity is caused by T1 binding to beta(2), especially when T1 is overexpressed, preventing beta(2) from interacting with host replication proteins such as Hda during the early events of chromosome replication.
On the feasibility of remote palpation using acoustic radiation force (2001)

A method of acoustic remote palpation, capable of imaging local variations in the mechanical properties of tissue, is under investigation. In this method, focused ultrasound is used to apply localized (on the order of 2 mm3) radiation force within tissue. and the resulting tissue displacements are mapped using ultrasonic correlation based methods. The tissue displacements are inversely proportional to the stiffness of the tissue, and thus a stiffer region of tissue exhibits smaller displacements than a more compliant region. In this paper, the feasibility of remote palpation is demonstrated experimentally using breast tissue phantoms with spherical lesion inclusions, and in vitro liver samples. A single diagnostic transducer and modified ultrasonic imaging system are used to perform remote palpation. The displacement images are directly correlated to local variations in tissue stiffness with higher contrast than the corresponding B-mode images. Relationships between acoustic beam parameters, lesion characteristics and radiation force induced tissue displacement patterns are investigated and discussed. The results show promise for the clinical implementation of remote palpation.
Rationale and design of a large registry on renal denervation: the Global SYMPLICITY registry (2013)

The rationale, design and first baseline data from the Global SYMPLICITY registry are presented.