gebhart/patrepeval huggingface dataset:
Simple, distance-based measurement for paper analytical devices (2013)

Paper-based analytical devices (PADs) represent a growing class of elegant, yet inexpensive chemical sensor technologies designed for point-of-use applications. Most PADs, however, still utilize some form of instrumentation such as a camera for quantitative detection. We describe here a simple technique to render PAD measurements more quantitative and straightforward using the distance of colour development as a detection motif. The so-called distance-based detection enables PAD chemistries that are more portable and less resource intensive compared to classical approaches that rely on the use of peripheral equipment for quantitative measurement. We demonstrate the utility and broad applicability of this technique with measurements of glucose, nickel, and glutathione using three different detection chemistries: enzymatic reactions, metal complexation, and nanoparticle aggregation, respectively. The results show excellent quantitative agreement with certified standards in complex sample matrices. This work provides the first demonstration of distance-based PAD detection with broad application as a class of new, inexpensive sensor technologies designed for point-of-use applications.
Designing a Three‐dimensional Expanded Polytetrafluoroethylene–Poly(lactic‐co‐glycolic acid) Scaffold for Tissue Engineering (2009)

The purpose of this study was to design a three-dimensional expanded polytetrafluoroethylene (ePTFE)-poly(lactic-co-glycolic acid) (PLGA) scaffold for tissue engineering. To test the feasibility of this composite scaffold, a series of two-dimensional culture experiments were performed to investigate the behavior of anterior cruciate ligament (ACL) cells on the ePTFE and PLGA membranes. It was found PLGA provided a cell-favorable substrate for cell adhesion, migration, and growth, indicating PLGA is an ACL cell-conductive material. Conversely, poor adhesion and proliferation of ACL cells were observed on the ePTFE, even on the collagen-coated ePTFE. Therefore, the scaffold was not fabricated by coating PLGA on the ePTFE surface because it is difficult to coat anything on the extremely hydrophobic ePTFE surface. Instead, the ePTFE embedded in the PLGA matrix was prepared by immersing ePTFE scrim yarns into the PLGA solution, and then precipitating PLGA to form a three-dimensional construction with porous morphology. The role of ePTFE is regarded as a reinforcing constituent to improve the mechanical strength of porous PLGA matrix to provide early repair strength for tissue healing. However, porous PLGA matrix acts as a supportive environment for allowing cell adhesion, migration, and growth to guide the repair and regeneration of ligament tissue. To test this assumption, a preliminary animal experiment of rabbit ACL wound healing with this three-dimensional ePTFE-PLGA scaffold was performed. These results are very encouraging because such a new scaffold made of ePTFE scrim yarns embedded in PLGA may serve as ACL prostheses in the ligament tissue engineering.
Stoichiometry of Gata4, Mef2c, and Tbx5 Influences the Efficiency and Quality of Induced Cardiac Myocyte Reprogramming (2014)

Our results demonstrate that stoichiometry of G, M, T protein expression influences the efficiency and quality of iCM reprogramming. The established optimal G, M, T expression condition will provide a valuable platform for future iCM studies.
Detection of Hypermethylated Genes in Women with and Without Cervical Neoplasia (2005)

Aberrant promoter methylation analysis on exfoliated cell samples is a potential diagnostic tool for cervical cancer screening that potentially may be used alone or in conjunction with cytology and/or human papillomavirus testing.
Immune regulation by non-lymphoid cells in transplantation (2009)

Regulatory cells play a crucial role in the induction and maintenance of tolerance by controlling T cell as well as B and natural killer (NK) cell-mediated immunity. In transplantation, CD4+CD25+forkhead box P3+ T regulatory cells are instrumental in the maintenance of immunological tolerance, as are several other T cell subsets such as NK T cells, double negative CD3+ T cells, gammadelta T cells, interleukin-10-producing regulatory type 1 cells, transforming growth factor-beta-producing T helper type 3 cells and CD8+CD28(-) cells. However, not only T cells have immunosuppressive properties, as it is becoming increasingly clear that both T and non-T regulatory cells co-operate and form a network of cellular interactions controlling immune responses. Non-T regulatory cells include tolerogenic dendritic cells, plasmacytoid dendritic cells, mesenchymal stem cells, different types of stem cells, various types of alternatively activated macrophages and myeloid-derived suppressor cells. Here, we review the mechanism of action of these non-lymphoid regulatory cells as they relate to the induction or maintenance of tolerance in organ transplantation.
Premalignant Lesions as Targets for Cancer Vaccines (2003)

The job of the immune system is to respond to signals released by tissues that are being destroyed by foreign invaders, such as viruses and bacteria, and to destroy the invaders. These signals have been termed “danger” signals ([1][1]). Destruction of tissues by uncontrolled cell growth
Characterization of protein tyrosine kinases from human breast cancer: involvement of the c-src oncogene product. (1992)

Tyrosine phosphorylation is an important regulatory mechanism in response to the action of growth factors and oncogenes. Since many oncogenes code for tyrosine kinases, increased or altered oncogene expression may be reflected in increased tyrosine kinase activity. In a recent study (Hennipman et al., Cancer Res., 49: 516-521, 1989), we found that the tyrosine kinase activity of the cytosolic and membrane fractions of malignant human breast tissue was significantly higher compared to the benign or the normal breast tissue. Moreover, the increase in the cytosolic fractions was found to be of prognostic value. In the present study we determined the protein tyrosine kinase (PTK) activity of another 72 breast cancer specimens, and it could be shown again that the PTK activity in all 72 of these tumors was elevated compared to normal controls. We characterized these cytosolic PTKs by anion exchange chromatography using fast protein liquid chromatography, and it could be shown that at least two different forms of PTK exist. Using antibodies against a number of known oncogene products, we could determine that at least 70% of the PTK activity in the cytosol originated from the presence of the c-src oncogene product. Both of the PTK activity peaks seen in the fast protein liquid chromatography patterns could be precipitated with the anti-Src antibody. Furthermore, using the MCF-7 breast cancer cell line, it could be shown that the antibody against c-src also precipitated a part of the cytosolic PTK activity. In normal human peripheral lymphocytes, no precipitation of the cytosolic and membrane PTK activity could be achieved using the anti-Src antibody. Inasmuch as the cytosolic PTK activity parallels the malignancy in breast tumors (Hennipman et al., Cancer Res., 49: 516-521, 1989), and the majority of this activity is precipitated by anti-Src antibodies, the c-src protooncogene may play a key role in the manifestation of breast cancer.
Modular Arrangement of Cartilage- and Neural Tissue-specificcis-Elements in the Mouse α2(XI) Collagen Promoter (1998)

Type XI collagen, a heterotrimer specific to cartilage matrix, plays an important role in cartilage morphogenesis. We analyzed various alpha2(XI) collagen promoter-lacZ reporter gene constructs in transgenic mice to understand tissue-specific transcriptional regulation. The -530 promoter sequence was sufficient to direct reporter gene expression specifically to cartilage. Further deletion to -500 abolished reporter gene expression in cartilage but activated the expression specific to neural tissues such as brain and neural tube. An additional 47-base pair deletion resulted in random tissue expression patterns. A 24-base pair sequence from -530 to -507 of the alpha2(XI) promoter was able to switch the activity of the heterologous neurofilament light gene promoter from neural tissues to cartilage. These results suggest that the alpha2(XI) collagen gene is regulated by at least three modular elements: a basal promoter sequence distal to -453, a neural tissue-specific element (-454 to -500), and a cartilage-specific element (-501 to -530), which inhibits expression in neural tissues and induces expression in cartilage.
Monoclonal Antibody K1 Reacts With Epithelial Mesothelioma but not With Lung Adenocarcinoma (1992)

Immunoperoxidase histochemical staining of cryostat sections from human tumor tissues revealed that a murine monoclonal antibody (MAb), K1, can distinguish epithelial mesotheliomas from lung adenocarcinomas. All of 15 epithelial-type mesotheliomas and all four mixed type mesothelioma samples, but none of 23 lung adenocarcinomas with different degrees of histologic differentiation demonstrated reactivity with antibody K1. Of the cell populations in each mesothelioma tested, 80% to 100% showed strong and homogeneous staining with MAb K1. Immunofluorescence analysis of live cultured cells from an epithelioid mesothelioma (H-meso) and several lung carcinoma cell lines as well as a pleural effusion of a patient with mesothelioma also showed selective reactivity of K1 with the mesothelioma cells. These data indicate that K1 can be useful as a mesothelial cell marker for the differential pathological diagnosis of the epithelial form of mesothelioma; K1 may also be useful in the study of the pathogenesis, immunodiagnosis, and immunotherapy of epithelial-type and mixed-type human malignant mesothelioma.
Requiem: a novel zinc finger gene essential for apoptosis in myeloid cells. (1994)

To identify genes mediating programmed cell death triggered by interleukin 3 (IL-3)-deprivation of myeloid cells, the IL-3-dependent murine myeloid cell line FDCP-1 was used to screen a mammalian cell expression library for cDNAs that would promote survival following withdrawal of IL-3. A unique 892-base pair cDNA was cloned that prevented the programmed cell death response following IL-3 deprivation by causing antisense suppression of an endogenous 2.4-kilobase (kb) mRNA. A 2.3-kb cDNA containing the identical 892-base pair over-lapping sequence was cloned that encoded a deduced 371-amino acid protein containing a single Kruppel-type zinc finger and a cluster of 4 cysteine/histidine-rich repeats resembling atypical zinc fingers. The 2.4-kb mRNA was found to be ubiquitously expressed in murine tissues and its abundance in FDCP-1 cells was not altered in response to IL-3 deprivation. Since expression of this 2.4-kb mRNA was a prerequisite for the apoptosis response following IL-3 deprivation, the gene encoding it was named requiem. Requiem is likely to encode a transcription factor required for the apoptosis response following survival factor withdrawal from myeloid cells.
The MicroRNA: Overview of the RNA Gene That Modulates Gene Functions (2006)

MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes. When a transposon is inserted in the intron, it becomes an intronic miRNA, taking advantage of the protein synthesis machinery, i.e., mRNA transcription and splicing, as a means for processing and maturation. Recently, miRNAs have been found to play an important, but not life-threatening, role in embryonic development. They might play a pivotal role in diverse biological systems in various organisms, facilitating a quick response and accurate plotting of body physiology and structures. Based on these unique properties, manufactured intronic miRNAs have been developed for in vitro evaluation of gene function, in vivo gene therapy, and generation of transgenic animal models. The biogenesis and identification of miRNAs, potential applications, and future directions for research are presented in this chapter, hopefully providing a guideline for further miRNA and gene function studies.
Near-Infrared Fluorescent Imaging of Matrix Metalloproteinase Activity After Myocardial Infarction (2005)

This study demonstrates that the activity of MMPs in the myocardium may be imaged by use of specific activity-dependent molecular probes.
Targeting macrophages in the tumour environment to enhance the efficacy of αOX40 therapy (2012)

The treatment of high-grade tumours must consider a tumour environment dominated by cells that support cancer growth. In addition to directing angiogenesis and invasion, alternatively activated macrophages in the tumour provide protection from adaptive immunity and permit tumour growth. Agonist antibodies to the tumour necrosis factor receptor family member OX40 are an effective therapy for cancer in a range of murine models; however, as with many immune therapies, αOX40 therapy is less effective as the tumour grows and develops an immune suppressive environment. We demonstrate that αOX40 directly activates T cells and that this T-cell activation alters macrophage differentiation in the tumour environment. We demonstrate that macrophages in the tumour limit the efficacy of αOX40 therapy, and that combining αOX40 therapy with inhibitors of arginase significantly enhances survival of tumour-bearing mice. These data demonstrate that macrophages in the tumour environment limit the effectiveness of OX40-based immunotherapy, and combination therapies that target both the cell-mediated immune response and the suppressive tumour environment will be required for translation of effective immunotherapies to patients with established tumours.
Therapeutic Role of TGF-β–Neutralizing Antibody in Mouse Cyclosporin A Nephropathy (2003)

TGF-beta is believed to play a central role in the development of Cyclosporin A (CsA)-induced nephropathy. This study investigated the effects of 1D11, a murine pan-specific TGF-beta-neutralizing monoclonal antibody, in an ICR mouse model of chronic CsA nephropathy. Mice were administered a low-salt diet (0.01% sodium) for 1 wk followed by CsA treatment (30 mg/kg, subcutaneously, daily) for 4 wk. 1D11 was administered (2.5 mg/kg, intraperitoneally, 3 times/wk) beginning immediately after the termination of CsA dosing and continued through 8 wk. CsA caused extensive renal histopathologic alterations, including tubular damage, interstitial infiltrates and fibrosis, deposition of collagen III, and apoptosis of tubular epithelial cells. 1D11 ameliorated the CsA-induced histopathologic alterations, with significant reduction in collagen III expression and deposition. Additionally, elevated levels of mRNA encoding TGF-beta1 and TGF-beta2 were significantly reduced. 1D11 also protected tubular epithelial cells from apoptosis by 48% (P < 0.05). In contrast, 13C4 (a control antibody) had no significant effect on any of the endpoints described above. Importantly, the effects of 1D11 on the CsA-induced morphologic alterations were followed by a reduction in serum creatinine level when compared with CsA mice treated with 13C4 (13C4, 0.45 +/- 0.09; 1D11, 0.30 +/- 0.08; P < 0.05) after 8 wk of treatment. Endothelial nitric oxide synthase (eNOS), inducible NOS (iNOS), nitrotyrosine, and tissue hypoxia were examined by immunostaining using specific antibodies. eNOS was significantly reduced in the endothelium of arterioles in the kidneys of mice treated with CsA, whereas iNOS was induced in the cortical tubules. Tissue hypoxia was found in both the arterioles and tubules, whereas nitrotyrosine was localized in the tubules. Administration of 1D11 improved tissue hypoxia and reduced nitrotyrosine formation. Moreover, the reciprocal changes in iNOS and eNOS expression were normalized by 1D11. This study demonstrates that 1D11 administration ameliorated morphologic alterations and preserved renal function in the context of existing chronic CsA nephropathy.
Long-term Use of Inhaled Corticosteroids and the Risk of Pneumonia in Chronic Obstructive Pulmonary Disease (2009)

Among patients with COPD, inhaled corticosteroid use for at least 24 weeks is associated with a significantly increased risk of serious pneumonia, without a significantly increased risk of death.
Culture of Human Pancreatic Islet Cells (2003)

The pancreatic islet is a microorgan composed of four types of hormone-producing cells. In the human pancreas, the islets comprise about l-2%; of the pancreatic mass, and the islet number is approx 1-2 × 10(6). The majority of cells, which are mainly located in the center of the islet, are the insulin-producing ß;β-cells In the periphery, α-cells and δ-cells synthesizing glucagon and somatostatin, respectively, are found. Finally, a small number of cells containing pancreatic polypeptide (PP) are scattered within the islets (1). In addition, in the intact pancreatic islet nerve cell fibers, vascular tissue as well as a few residing immune cells can also be observed. Owing to the requirements to study the in vitro function of the ß;cells for various aspects of diabetes research, methods have been developed to isolate and culture free pancreatic islets.
Expression of HIV in lymph node cells of LAS patients. Immunohistology, in situ hybridization, and identification of target cells. (1988)

Monoclonal antibodies (MAb) anti-HIV core and envelope proteins and in situ hybridization, using cDNA HIV probe, were employed to determine which lymph node cells in LAS patients express viral antigens and viral nucleic acids. The results have been correlated with the histologic phases of LAS and with the germinal center lysis detected using DRC-1 MAb directed against follicular dendritic reticulum cells (FDRC). Viral antigens occasionally were detected on high endothelial cells of paracortical venules and frequently on germinal center FDR accessory cells; this last finding correlates well with the extent of FDRC lysis and of CD4+ and CD8+ lymphocyte infiltration in germinal centers. HIV replication, detected by in situ hybridization, was observed in mononucleated cells present in T and B areas and, in one case, in flat endothelium.
Diversas caracterizaciones de distribuciones hipergeométricas negativas (2001)

Probamos que las distribuciones discretas con soporte en los enteros no negativos cuya razon de Mill sea una funcion lineal son distribuciones hipergeometricas negativas de tipo I y II o bien distribuciones geometricas en el caso en que la funcion lineal sea constante. Como aplicacion presentamos caracterizaciones de distribuciones mediante regresion lineal de records debiles, fuertes y de estadisticos ordenados
Hyperexpression of CD40 Ligand (CD154) in Inflammatory Bowel Disease and Its Contribution to Pathogenic Cytokine Production (1999)

CD40 ligand (CD40L or CD154), a type II membrane protein with homology to TNF, is transiently expressed on activated T cells and known to be important for B cell Ig production and for activation and differentiation of monocytes and dendritic cells. Both Crohn's disease and ulcerative colitis are characterized by local production of cytokines such as TNF and by an influx of activated lymphocytes into inflamed mucosa. Herein, we investigated whether CD40L signaling participates in immune responses in these diseases. Our results demonstrated that CD40L was expressed on freshly isolated lamina propria T cells from these patients and was functional to induce IL-12 and TNF production by normal monocytes, especially after IFN-gamma priming. The inclusion of a blocking mAb to CD40L or CD40 in such cocultures significantly decreased monocyte IL-12 and TNF production. Moreover, lamina propria and peripheral blood T cells from these patients, after in vitro activation with anti-CD3, showed increased and prolonged expression of CD40L as compared with controls. Immunohistochemical analyses indicated that the number of CD40+ and CD40L+ cells was significantly increased in inflamed mucosa, being B cells/macrophages and CD4+ T cells, respectively. These findings suggest that CD40L up-regulation is involved in pathogenic cytokine production in inflammatory bowel disease and that blockade of CD40-CD40L interactions may have therapeutic effects for these patients.
Cynical Selection of Language Model Training Data (2017)

The Moore-Lewis method of "intelligent selection of language model training data" is very effective, cheap, efficient... and also has structural problems. (1) The method defines relevance by playing language models trained on the in-domain and the out-of-domain (or data pool) corpora against each other. This powerful idea-- which we set out to preserve-- treats the two corpora as the opposing ends of a single spectrum. This lack of nuance does not allow for the two corpora to be very similar. In the extreme case where the come from the same distribution, all of the sentences have a Moore-Lewis score of zero, so there is no resulting ranking. (2) The selected sentences are not guaranteed to be able to model the in-domain data, nor to even cover the in-domain data. They are simply well-liked by the in-domain model; this is necessary, but not sufficient. (3) There is no way to tell what is the optimal number of sentences to select, short of picking various thresholds and building the systems. We present a greedy, lazy, approximate, and generally efficient information-theoretic method of accomplishing the same goal using only vocabulary counts. The method has the following properties: (1) Is responsive to the extent to which two corpora differ. (2) Quickly reaches near-optimal vocabulary coverage. (3) Takes into account what has already been selected. (4) Does not involve defining any kind of domain, nor any kind of classifier. (6) Knows approximately when to stop. This method can be used as an inherently-meaningful measure of similarity, as it measures the bits of information to be gained by adding one text to another.
An Activation Switch in the Rhodopsin Family of G Protein-coupled Receptors (2005)

We aimed at understanding molecular events involved in the activation of a member of the G protein-coupled receptor family, the thyrotropin receptor. We have focused on the transmembrane region and in particular on a network of polar interactions between highly conserved residues. Using molecular dynamics simulations and site-directed mutagenesis techniques we have identified residue Asn-7.49, of the NPxxY motif of TM 7, as a molecular switch in the mechanism of thyrotropin receptor (TSHr) activation. Asn-7.49 appears to adopt two different conformations in the inactive and active states. These two states are characterized by specific interactions between this Asn and polar residues in the transmembrane domain. The inactive gauche+ conformation is maintained by interactions with residues Thr-6.43 and Asp-6.44. Mutation of these residues into Ala increases the constitutive activity of the receptor by factors of approximately 14 and approximately 10 relative to wild type TSHr, respectively. Upon receptor activation Asn-7.49 adopts the trans conformation to interact with Asp-2.50 and a putatively charged residue that remains to be identified. In addition, the conserved Leu-2.46 of the (N/S)LxxxD motif also plays a significant role in restraining the receptor in the inactive state because the L2.46A mutation increases constitutive activity by a factor of approximately 13 relative to wild type TSHr. As residues Leu-2.46, Asp-2.50, and Asn-7.49 are strongly conserved, this molecular mechanism of TSHr activation can be extended to other members of the rhodopsin-like family of G protein-coupled receptors.