gebhart/patrepeval huggingface dataset:
Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development. (1994)

When starved for nitrogen, MATa/MAT alpha cells of the budding yeast Saccharomyces cerevisiae undergo a dimorphic transition to pseudohyphal growth. A visual genetic screen, called PHD (pseudohyphal determinant), for S. cerevisiae pseudohyphal growth mutants was developed. The PHD screen was used to identify seven S. cerevisiae genes that when overexpressed in MATa/MAT alpha cells growing on nitrogen starvation medium cause precocious and unusually vigorous pseudohyphal growth. PHD1, a gene whose overexpression induced invasive pseudohyphal growth on a nutritionally rich medium, was characterized. PHD1 maps to chromosome XI and is predicted to encode a 366-amino-acid protein. PHD1 has a SWI4- and MBP1-like DNA binding motif that is 73% identical over 100 amino acids to a region of Aspergillus nidulans StuA. StuA regulates two pseudohyphal growth-like cell divisions during conidiophore morphogenesis. Epitope-tagged PHD1 was localized to the nucleus by indirect immunofluorescence. These facts suggest that PHD1 may function as a transcriptional regulatory protein. Overexpression of PHD1 in wild-type haploid strains does not induce pseudohyphal growth. Interestingly, PHD1 overexpression enhances pseudohyphal growth in a haploid strain that has the diploid polar budding pattern because of a mutation in the BUD4 gene. In addition, wild-type diploid strains lacking PHD1 undergo pseudohyphal growth when starved for nitrogen. The possible functions of PHD1 in pseudohyphal growth and the uses of the PHD screen to identify morphogenetic regulatory genes from heterologous organisms are discussed.
3'-Modified oligonucleotides by reverse DNA synthesis (2003)

Reverse DNA oligonucleotide synthesis (i.e. from 5'-->3') is a strategy that has yet to be exploited fully. While utilized previously for the construction of alternating 3'-3'- and 5'-5'-linked antisense oligonucleotides, the use of nucleoside 5'-phosphoramidites has not generally been used for the elaboration of (modified) oligonucleotides. Presently, the potential of reverse oligonucleotide synthesis for the facile synthesis of 3'-modified DNAs is illustrated using a phosphoramidite derived from tyrosine. The derived oligonucleotide was shown to have chromatographic and electrophoretic properties identical with the modified oligonucleotide resulting from the proteinase K digestion of the vaccinia topoisomerase I-DNA covalent complex. The results confirm the nature of the structure previously assigned to this product, and establish the facility with which proteinase K is able to complete the digestion of the polypeptide backbone of the DNA oligonucleotide-linked topoisomerase I.
A Distinct Endothelial Cell Recognition System That Controls Lymphocyte Traffic into Inflamed Synovium (1986)

Lymphocytes are essential mediators of normal tissue inflammatory reactions and of pathologic tissue damage in, for example, rheumatoid arthritis and other autoimmune diseases. In a study of the mechanisms controlling lymphocyte entry into sites of inflammation from the blood, the function and specificity of lymphocyte-endothelial interactions were examined in inflamed joint tissue (synovium) from patients with rheumatoid arthritis. Synovial high endothelial venules (HEV) supported the binding of normal peripheral blood lymphocytes in vitro. The characteristics of this binding, which were similar to those of lymphocyte-HEV interactions controlling lymphocyte migration into organized lymphoid tissues, included a requirement for calcium ions, a dependence on metabolic activity, and a preferential adherence of circulating lymphocytes as opposed to immature thymocytes. However, the binding of lymphocytes to synovial HEV was not inhibited by a monoclonal antibody to lymphocyte receptors for lymph node HEV, and synovial HEV failed to bind either lymph node HEV-specific or mucosal HEV-specific B lymphoblastoid cells. The results suggest that a lymphocyte-endothelial cell recognition system that is distinct from such systems in organized lymphoid tissues directs the extravasation of normal lymphocytes as well as pathologically important effector cells into inflamed synovium.
A Priority Scheme for IEEE 802. 11 DCF Access Method (1999)

this paper, we propose a method to modify the CSMA/CA protocol such that station priorities can be supported. The method is simple, e#cient and easy to implement in comparison to point coordination function (PCF), another access method in IEEE 802.11 based on access points (base stations). Simulations are conducted to analyze the proposed scheme. The results show that DCF is able to carry the prioritized tra#c with the proposed scheme.
Allergy and Allergic Diseases (2001)

Allergic rhinitis, asthma, and atopic eczema are among the commonest causes of chronic ill health. These diseases are increasing in prevalence, and they add considerably to the burden of health care costs. In Sweden, for example, the number of children with allergic rhinitis, asthma, or eczema roughly doubled over a 12-year period,1 and in the United States the annual cost of treating asthma is about $6 billion.2 The term “allergy” was introduced in 1906 by von Pirquet, who recognized that in both protective immunity and hypersensitivity reactions, antigens had induced changes in reactivity.3 With the passage of time the word . . .
Incorporation of adhesion peptides into nonadhesive hydrogels useful for tissue resurfacing (1998)

Photopolymerized crosslinked networks of poly(ethylene glycol; PEG) diacrylate (MW 8000) were derivitized throughout their bulk with Arg-Gly-Asp (RGD)-containing peptide sequences. Incorporation was achieved by functionalizing the amine terminus of the peptide with an acrylate moiety, thereby enabling the adhesion peptide to copolymerize rapidly with the PEG diacrylate upon photoinitiation. PEG diacrylate hydrogels derivitized with RGD peptide at surface concentrations ranging from 0.001 to 1 pmol/cm2 were studied in vitro for their ability to promote spreading of human foreskin fibroblasts over 24 h. Hydrogels not derivitized with peptides were poor substrates for adhesion, permitting spreading of only 5% of the seeded cells. When immobilized with no spacer arm, both RGD and RDG (inactive control) supported spreading of approximately 50% and approximately 15% of cells at 1 and 0.1 pmol/cm2 surface concentrations respectively; lower concentrations did not promote spreading. When a MW 3400 PEG spacer arm was incorporated between the hydrogel and the peptide linkage, incorporation of 1 pmol/cm2 RGD promoted 70% spreading whereas RDG at the same concentration did not promote spreading. In addition, when cells were seeded in serum-free medium, only RGD peptides incorporated with a spacer arm were able to promote spreading. Thus peptide incorporated into PEG 8000 diacrylate hydrogels without a spacer arm nonspecifically mediated cell spreading whereas incorporation via a MW 3400 PEG spacer arm was required to permit cell spreading to be specifically mediated.
Overgrowth of Fat Autotransplanted for Correction of Localized Steroid-Induced Atrophy (2000)

A case is presented in which regional subcutaneous atrophy in the lateral thigh after steroid injection was treated with autologous fat grafting. More than 1 year after treatment, an increase in the volume of the transplanted site necessitated a secondary procedure to debulk the area. We believe that this is a case in which the transplanted adipocytes (or preadipocytes) survived and subsequently (for an unclear reason) increased significantly in volume. This case report supports the cell survival theory of fat autotransplantation. Animal studies using radioisotope-labeled lipocytes might provide further understanding of the mechanisms of fat graft "survival."
Palladium-Catalyzed Allylic Fluorination of Cinnamyl Phosphorothioate Esters (2012)

A highly regioselective, Pd-catalyzed allylic fluorination of phosphorothioate esters is reported. This chemistry addresses several limitations of previously reported methods in which elimination and lack of reactivity were problematic. Preliminary mechanistic investigations reveal that these reactions are stereospecific and provide fluorinated products with net retention of stereochemical configuration. In analogy to other Pd-catalyzed allylic substitution reactions, this process likely proceeds through a palladium π-allyl intermediate.
Familial Combined Hyperlipidemia in Mexicans (2005)

This study, the first to extensively investigate the genetic component of the common FCHL disorder in Mexicans, provides independent evidence for the role of USF1 in FCHL in an outbred population and links the 16q24.1 region to an FCHL-component trait in Mexicans.
A Constitutively Active Gα Subunit Provides Insights into the Mechanism of G Protein Activation (2012)

The activation of Gα subunits of heterotrimeric G proteins by G protein-coupled receptors (GPCRs) is a critical event underlying a variety of biological responses. Understanding how G proteins are activated will require structural and biochemical analyses of GPCRs complexed to their G protein partners, together with structure-function studies of Gα mutants that shed light on the different steps in the activation pathway. Previously, we reported that the substitution of a glycine for a proline at position 56 within the linker region connecting the helical and GTP-binding domains of a Gα chimera, designated αT*, yields a more readily exchangeable state for guanine nucleotides. Here we show that GDP-GTP exchange on αT*(G56P), in the presence of the light-activated GPCR, rhodopsin (R*), is less sensitive to the β1γ1 subunit complex than to wild-type αT*. We determined the X-ray crystal structure for the αT*(G56P) mutant and found that the G56P substitution leads to concerted changes that are transmitted to the conformationally sensitive switch regions, the α4-β6 loop, and the β6 strand. The α4-β6 loop has been proposed to be a GPCR contact site that signals to the TCAT motif and weakens the binding of the guanine ring of GDP, whereas the switch regions are the contact sites for the β1γ1 complex. Collectively, these biochemical and structural data lead us to suggest that αT*(G56P) may be adopting a conformation that is normally induced within Gα subunits by the combined actions of a GPCR and a Gβγ subunit complex during the G protein activation event.
The case for GPGPU spatial multitasking (2012)

The set-top and portable device market continues to grow, as does the demand for more performance under increasing cost, power, and thermal constraints. The integration of Graphics Processing Units (GPUs) into these devices and the emergence of general-purpose computations on graphics hardware enable a new set of highly parallel applications. In this paper, we propose and make the case for a GPU multitasking technique called spatial multitasking. Traditional GPU multitasking techniques, such as cooperative and preemptive multitasking, partition GPU time among applications, while spatial multitasking allows GPU resources to be partitioned among multiple applications simultaneously. We demonstrate the potential benefits of spatial multitasking with an analysis and characterization of General-Purpose GPU (GPGPU) applications. We find that many GPGPU applications fail to utilize available GPU resources fully, which suggests the potential for significant performance benefits using spatial multitasking instead of, or in combination with, preemptive or cooperative multitasking. We then implement spatial multitasking and compare it to cooperative multitasking using simulation. We evaluate several heuristics for partitioning GPU stream multiprocessors (SMs) among applications and find spatial multitasking shows an average speedup of up to 1.19 over cooperative multitasking when two applications are sharing the GPU. Speedups are even higher when more than two applications are sharing the GPU.
Can Cytokines be Removed by Hemofiltration or Hemoadsorption? (2000)

To study the removability of pro-inflammatory cytokines by hemofiltration (HF), we performed experimental HF with various high-flux membranes (HFM) using a closed circuit system filled with monocyte-free human plasma, which contained TNFα, IL-1β, and IL-6. Plasma and filtrate samples were taken before and 1, 2, 3, and 4 hours after the initiation of HF, and each cytokine was determined by enzyme-linked immunosorbent assay. IL-1β was well removed through filtration during experimental HF using HFM (PAN>CTA>PMMA>PS). TNFα and IL-6 were only minimally filtered out by HF using HFM. TNFα was removed to some extent by using PS, and IL-6 was partially removed by using PMMA during experimental HF through other mechanisms, such as adsorption, than the filtration. IL-1β and IL-6 were effectively removed by HA using charcoal adsorbent column, especially during the first 2 hours, while TNFα was only partly removed.
Two Genome-wide Association Studies of Aggressive Prostate Cancer Implicate Putative Prostate Tumor Suppressor Gene DAB2IP (2007)

A genetic variant in DAB2IP may be associated with the risk of aggressive prostate cancer and should be evaluated further.
[The pathogenic role of macrophage migration inhibitory factor in acute respiratory distress syndrome]. (2002)

OBJECTIVE To investigate the expression and pathogenic role of macrophage migration inhibitory factor( MIF) in human acute respiratory distress syndrome(ARDS) METHODS The serum level of MIF in ARDS patients and normal persons were measured by ELISA method. Peripheral blood mononuclear cell (PBMC) MIF expression was determined by flow- cytometry. The expression of MIF mRNA and protein in the lung tissues were detected by using double immuno histochemistry labeling and in situ hybridization. RESULTS The serum level of MIF increased significantly in ARDS patients as compared with normal persons (P < 0.01). The percentage of PBMC MIF expression was higher in ARDS patients than in normal controls (P < 0.01). In situ hybridization and immunohistochemistry showed undetectable or weak MIF mRNA and protein expression in normal lungs. In contrast, there was marked upregulation of MIF mRNA and protein expression in the ARDS lungs. In ARDS macro phages infiltrated the alveolar space and interstitium, most of which also expressed MIF. Infiltrating macrophages were almost restricted to the areas of severe tissue damage. The MIF expression level showed a strong correlation with the number of infiltrating macrophages. CONCLUSIONS The serum level of MIF and PBMC MIF expression increased in ARDS patients with enhanced pulmonary MIF expression and macrophage infiltration, which suggests that MIF plays a pivotal role in the pathogenesis of ARDS.
Actin filament organization is required for proper cAMP-dependent activation of CFTR (1999)

Previous studies have indicated a role of the actin cytoskeleton in the regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel. However, the exact molecular nature of this regulation is still largely unknown. In this report human epithelial CFTR was expressed in human melanoma cells genetically devoid of the filamin homologue actin-cross-linking protein ABP-280 [ABP(-)]. cAMP stimulation of ABP(-) cells or cells genetically rescued with ABP-280 cDNA [ABP(+)] was without effect on whole cell Cl(-) currents. In ABP(-) cells expressing CFTR, cAMP was also without effect on Cl(-) conductance. In contrast, cAMP induced a 10-fold increase in the diphenylamine-2-carboxylate (DPC)-sensitive whole cell Cl(-) currents of ABP(+)/CFTR(+) cells. Further, in cells expressing both CFTR and a truncated form of ABP-280 unable to cross-link actin filaments, cAMP was also without effect on CFTR activation. Dialysis of ABP-280 or filamin through the patch pipette, however, resulted in a DPC-inhibitable increase in the whole cell currents of ABP(-)/CFTR(+) cells. At the single-channel level, protein kinase A plus ATP activated single Cl(-) channels only in excised patches from ABP(+)/CFTR(+) cells. Furthermore, filamin alone also induced Cl(-) channel activity in excised patches of ABP(-)/CFTR(+) cells. The present data indicate that an organized actin cytoskeleton is required for cAMP-dependent activation of CFTR.
Analysis of eIF4E and 4EBP1 mRNAs in head and neck cancer (2011)

Elevated 4E:4EBP1 significantly correlated with increased disease recurrence. Because 4EBP1 modulates eIF4E activity, our results highlight the importance of incorporating a joint analysis of eIF4E and 4EBP1 mRNAs in HNSCC patient care decisions.
Regular models of phonological rule systems (1994)

This paper presents a set of mathematical and computational tools for manipulating and reasoning about regular languages and regular relations and argues that they provide a solid basis for computational phonology. It shows in detail how this framework applies to ordered sets of context-sensitive rewriting rules and also to grammars in Koskenniemi's two-level formalism. This analysis provides a common representation of phonological constraints that supports efficient generation and recognition by a single simple interpreter.
Abstract 3691: Collagen 1 fiber content may predict for recurrence in non-small cell lung cancer (2018)

Abstract Non-small cell lung carcinoma (NSCLC) comprises 85% of all lung cancers. Approximately 30-50% of NSCLC recur despite curative resection. There is a major unmet need to identify NSCLC that are likely to recur so that these patients may be treated with more aggressive therapies. Collagen 1 (Col1) fibers are a major structural component of the extracellular matrix (ECM) of tumors. While increased Col1 fibers have been associated with increased metastasis in breast cancer, the role of Col1 in NSCLC and its relationship to recurrence has not been previously examined. We performed a blinded second harmonic generation (SHG) microscopy study on tumor tissue obtained from 5 patients with nonrecurrent NSCLC and 5 patients with recurrent NSCLC. Col1 fibers were detected with SHG microscopy that detects an intrinsic signal derived from the noncentrosymmetric molecular structure of Col1 fibers. SHG microscopy of tumor regions was performed on the H&amp;E sections to quantify Col1 fiber volume and inter fiber distance in the tumors. At least 10 fields of view were analyzed from 1-2 sections obtained from each tumor. We additionally performed Haralick feature analyses to further analyze Col1 fiber patterns. Adjacent sections were immunostained for CD44 and α-SMA to identify cancer associated fibroblasts (CAFs) and understand their role in these tumors. We observed a significant increase of Col1 fiber volume and a significant decrease of inter fiber distance in recurrent NSCLC. Four Haralick features (orientation, contrast, energy and homogeneity) were also significantly higher in the recurrent tumors compared to the non recurrent tumors. We are currently analyzing the CAFs in the tumor sections to understand their role in the significant differences observed in Col1 fibers between recurrent and nonrecurrent tumors. If these preliminary data are confirmed in an expanded sample set, Col1 fiber analysis may provide a companion diagnostic test that can be performed rapidly on H&amp;E tumor sections, using a confocal microscope, to evaluate the likelihood of tumor recurrence. These studies provide new insights into the role of the tumor microenvironment in NSCLC recurrence, and identify new targets for future therapeutic strategies. This work was supported in part by NIH R35CA209960. Citation Format: Samata Kakkad, Peng Huang, Malcolm Brock, Balaji Krishnamachary, Zaver M. Bhujwalla. Collagen 1 fiber content may predict for recurrence in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3691.
RcaE is a complementary chromatic adaptation photoreceptor required for green and red light responsiveness (2004)

The recent discovery of large numbers of phytochrome photoreceptor genes in both photosynthetic and non-photosynthetic prokaryotes has led to efforts to understand their physiological roles in environmental acclimation. One receptor in this class, RcaE, is involved in controlling complementary chromatic adaptation, a process that regulates the transcription of operons encoding light-harvesting proteins in cyanobacteria. Although all previously identified phytochrome responses are maximally sensitive to red and far red light, complementary chromatic adaptation is unique in that it is responsive to green and red light. Here, we present biochemical and genetic evidence demonstrating that RcaE is a photoreceptor and that it requires the cysteine at position 198 to ligate an open chain tetrapyrrole covalently in a manner analogous to chromophore attachment in plant phytochromes. Furthermore, although the wild-type rcaE gene can rescue red and green light photoresponses of an rcaE null mutant, a gene in which the codon for cysteine 198 is converted to an alanine codon rescues the red light but not the green light response. Thus, RcaE is a photoreceptor that is required for both green and red light responsiveness during complementary chromatic adaptation and is the first identified phytochrome class sensor that is involved in sensing and responding to green and red light rather than red and far red light.
2ndPEGS Annual Symposium on Antibodies for Cancer Therapy (2012)

The 2nd Annual Antibodies for Cancer Therapy symposium, organized again by Cambridge Healthtech Institute as part of the Protein Engineering Summit, was held in Boston, USA from April 30th to May 1st, 2012. Since the approval of the first cancer antibody therapeutic, rituximab, fifteen years ago, eleven have been approved for cancer therapy, although one, gemtuzumab ozogamicin, was withdrawn from the market. The first day of the symposium started with a historical review of early work for lymphomas and leukemias and the evolution from murine to human antibodies. The symposium discussed the current status and future perspectives of therapeutic antibodies in the biology of immunoglobulin, emerging research on biosimilars and biobetters, and engineering bispecific antibodies and antibody-drug conjugates. The tumor penetration session was focused on the understanding of antibody therapy using ex vivo tumor spheroids and the development of novel agents targeting epithelial junctions in solid tumors. The second day of the symposium discussed the development of new generation recombinant immunotoxins with low immunogenicity, construction of chimeric antigen receptors, and the proof-of-concept of 'photoimmunotherapy'. The preclinical and clinical session presented antibodies targeting Notch signaling and chemokine receptors. Finally, the symposium discussed emerging technologies and platforms for therapeutic antibody discovery.