gebhart/patrepeval huggingface dataset:
Safety evaluation of conditionally immortalized cells for renal replacement therapy (2019)

End-stage kidney disease represents irreversible kidney failure. Dialysis and transplantation, two main treatment options currently available, present various drawbacks and complications. Innovative cell-based therapies, such as a bioartificial kidney, have not reached the clinic yet, mostly due to safety and/or functional issues. Here, we assessed the safety of conditionally immortalized proximal tubule epithelial cells (ciPTECs) for bioartificial kidney application, by using <i>in vitro</i> assays and athymic nude rats. We demonstrate that these cells do not possess key properties of oncogenically transformed cells, including anchorage-independent growth, lack of contact inhibition and apoptosis-resistance. In late-passage cells we did observe complex chromosomal abnormalities favoring near-tetraploidy, indicating chromosomal instability. However, time-lapse imaging of ciPTEC-OAT1, confined to a 3D extracellular matrix (ECM)-based environment, revealed that the cells were largely non-invasive. Furthermore, we determined the viral integration sites of SV40 Large T antigen (SV40T), human telomerase (hTERT) and OAT1 (SLC22A6), the transgenes used for immortalization and cell function enhancement. All integrations sites were found to be located in the intronic regions of endogenous genes. Among these genes, early endosome antigen 1 (EEA1) involved in endocytosis, and BCL2 Like 1 (BCL2L1) known for its role in regulating apoptosis, were identified. Nevertheless, both gene products appeared to be functionally intact. Finally, after subcutaneous injection in athymic nude rats we show that ciPTEC-OAT1 lack tumorigenic and oncogenic effects <i>in vivo</i>, confirming the <i>in vitro</i> findings. Taken together, this study lays an important foundation towards bioartificial kidney (BAK) development by confirming the safety of the cell line intended for incorporation.
Fuzzy Cluster Analysis of Positive Stress Tests: Comparison with Stress Echocardiography and Nuclear Perfusion Imaging in Patients with Triple Vessel and Left Main Coronary Disease (1999)

Fuzzy cluster analysis (FCA) was used to classify 166 outpatient positive treadmill stress tests as mildly, moderately, or severely abnormal. The method combines ST-segment change with five other stress test variables, and then computes a similarity measure to determine how closely each patient's stress test resembles a prototypical mildly, moderately, or severely abnormal stress test. All patients had coronary angiography within 1 month of their stress tests. For the 45 patients with triple vessel disease (TVD), FCA classified 34 of these stress tests as severely abnormal (sensitivity = 75%). For the 22 patients with left main disease (LM), FCA classified 19 stress tests as severely abnormal (sensitivity = 86%). For the combined group with high-grade disease (TVD + LM), the sensitivity was 79%. A literature review shows that for stress echocardiography, multiple exercise-induced wall motion abnormalities have a sensitivity in the 70-80% range for patients with high-grade disease. For nuclear stress testing, the high-risk pattern of multiple reversible defects, with or without increased lung uptake, has a sensitivity in the range of 70-80% for patients with high-grade disease. Thus classification of a positive stress test as severely abnormal by FCA has a sensitivity comparable to high-risk patterns on stress echocardiography and nuclear stress testing in patients with TVD or LM.
Sliding mode observer for triangular input form (2002)

This paper discusses the problem of designing an observer for nonlinear systems. In Drakunov and Utkin (1995) a new concept of sliding observers was introduced, where the key point is that the equivalent control concept is extensively used. Moreover, in Boukhobza, Djemai, and Barbot (1996) we use a classical sliding mode observer in order to design an observer for the largest class with the so-called output injection form. Here, our purpose is to discuss the observer design for a system in a triangular input observer form. For a system in a triangular input observer form there is no problem of singular input. The second purpose of this paper is to show how to use the anti-peaking sliding method in the case of successive equivalent vectors.
Attitude Determination and Control Hardware Development for Small Satellites (2011)

The development of a small spacecraft attitude determination and control subsystem is described. This subsystem is part of The Space Flight Laboratory's Generic Nanosatellite Bus. With a 20cm3 body, the bus has an attitude determination and control subsystem capable of full three-axis stabilization and control enabling more advanced missions previously only possible with bulkier and more power-consuming attitude control hardware. Specific contributions to the Space Flight Lab's attitude control hardware are emphasised. Particularly, the full development of a 32g three-axis nanosatellite rate sensing unit is described. This includes embedded software development, skew calibration, hardware modeling and qualification testing for the unit. Development work on a three-axis boom-mounted magnetometer is also detailed. A full hardware design is also described for a new microsatellite-sized rate sensor. Larger and more powerful than the nanosatellite rate sensors, the design ensures a low noise, low drift architecture to improve attitude determination on future microsatellite missions.
Recurrent IgA Nephropathy After Kidney Transplantation (2016)

Large numbers of patients with end-stage kidney disease caused by IgA nephropathy are transplanted every year, and each of these patients faces the risk of recurrence in their kidney graft. We review the epidemiology, diagnosis, and outcomes of recurrent IgA nephropathy. Mechanistic insights, therapeutic options, and knowledge gaps are reviewed, and we discuss future options to better understand and manage this disorder.
Molecular and cellular biology of thyrotropin-releasing hormone receptors (1996)

Thyrotropin-releasing hormone (TRH) receptor (TRH-R) complementary DNAs have been cloned from several species. The deduced amino acid sequences are compatible with TRH-R being a seven-transmembrane-spanning G protein-coupled receptor. These complementary DNAs and reagents derived from them have permitted detailed study of TRH-R biology at the molecular and cellular levels. Studies that have been performed since 1990 are reviewed in this article under the following headings: TRH-R gene, tissue distribution of TRH-R, primary structure of TRH-Rs, three-dimensional structure of the TRH-R binding pocket, TRH-R and G proteins, TRH-R activation, TRH desensitization, TRH-R endocytosis, and regulation of TRH-R number. It is evident that many new insights into the structure, function, and regulation of TRH-Rs have been gained in the last several years but that our understanding of these processes is incomplete. We look forward to even greater progress in the future.
Gefitinib monotherapy in previously treated advanced non-small cell lung cancer (NSCLC): An immunohistochemical (IHC) analysis of EGFR and its downstream molecules (2004)

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Synthesis, Characterization, and Electrical Properties of SiCN Nanowires (2008)

SiCN nanowires are prepared by pyrolysis of hexamethyldisilazane using ferrocene as a catalyst precursor with or without thiophene, at 1100 °C in a flowing Ar atmosphere. The SiCN nanowires are about 10−60 nm in diameter and on the millimeter scale in length. The addition of thiophene is found to be effective in promoting the growth of SiCN nanowires. A vapor−liquid−solid growth mechanism of the nanowires is proposed. Electrical resistivity of a single SiCN nanowire is measured at room temperature for the first time.
Expression and processing of a recombinant human macrophage colony-stimulating factor in mouse cells. (1988)

A human macrophage colony-stimulating factor encoded by a 4-kilobase cDNA was expressed with bovine papillomavirus vectors in mouse cells. Pulse-chase analyses revealed that the 62-kilodalton (kDa) translation product was glycosylated, cleaved, and efficiently secreted within 1 h of synthesis. The secreted product contained both N-linked and O-linked oligosaccharide chains. Macrophage colony-stimulating factor was present extracellularly as an 80-kDa homodimer and as a multimeric species of greater than 200 kDa that may be associated with other glycoproteins.
Homogenization of the stokes flow in a connected porous medium (1989)

In this paper we prove the convergence of the homogenization process of the Stokes equations with Dirichlet boundary condition in a periodic porous medium. We consider here the case where the solid part of the porous medium is connected, and we generalize to this case the results obtained by Tartar (1980).
Feeding inhibition of YAE to herbivorus larvae Abraxas miranda (Lepidoptera: Geometridae) and Prodenia litura (Lepidoptera: Noctuidae) (2001)

Feeding capacity and growth rate are significantly reduced since the larvae, Abraxas miranda, have taken the leaves treated with Yuan-hua (Daphne genkwa) alcohol extract (YAE). The higher the concentration, the better is the effect on the insects. The effects of inhibition on feeding and reduction of growth are much less both for YAE and beta-sitosterol at any concentrations on the larvae of Prodenia litura. The reason for these are discussed briefly.
Optical Absolute Encoder Using Spatial Filter (1987)

This paper describes a vernier-type optical encoder for angular measurement. The encoder has only two tracks, so it is much smaller and simpler than conven-tional Gray code encoders. Two spatial filter detectors are used with the to provide interpolation between encoder slit positions. Each detector consists of a LED light source on one side of the disk, and two photodiode arrays (PDA) -- one for each track of the -- on the other. The two detectors are placed at diametrically-opposed positions, and the intensities of the LED light sources are modulated in quad-rature by a sinusoidal signal. The signals from the detector arrays are combined to generate two signals, and the difference between these signals is a high-precision absolute vernier signal. The accuracy of angular measurement for a prototype encoder was as high as 1/10,000 (2.2 arc-min).
The Bean Seed Storage Protein [beta]-Phaseolin Is Synthesized, Processed, and Accumulated in the Vacuolar Type-II Protein Bodies of Transgenic Rice Endosperm (1995)

The seed storage protein [beta]-phaseolin of the common bean (Phaseolus vulgaris L.) was expressed in the endosperm of transgenic rice (Oryza sativa L.) plants. The 5.1- or 1.8-kb promoter fragment of the rice seed storage protein glutelin Gt1 gene was fused transcriptionally to either the genomic or cDNA coding sequence of the [beta]-phaseolin gene. The highest quantity of phaseolin estimated by enzyme-linked immunosorbent assay was 4.0% of the total endosperm protein in the transgenic rice seeds. The phaseolin trait was segregated as a single dominant trait with a positive gene dosage effect and was stably inherited through three successive generations. Both phaseolin genomic and cDNA coding sequences were used to synthesize four isoforms of mature phaseolin protein with apparent molecular masses of 51, 48, 47, and 45 kD. Enzyme deglycosylation experiments indicated that the 51-kD form contains high-mannose N-glycans; the 48- and 47-kD forms have further modified N-glycans; and the 45-kD form is a nonglycosylated protein. Immunolabeling studies using light and electron microscopy demonstrated that phaseolin accumulates primarily in the vacuolar type-II protein bodies located at the periphery of the endosperm near the aleurone layer. We discuss the implications of these results on nutritional improvement of rice grains.
Crystal structure of the complete integrin αVβ3 ectodomain plus an α/β transmembrane fragment (2009)

We determined the crystal structure of 1TM-alphaVbeta3, which represents the complete unconstrained ectodomain plus short C-terminal transmembrane stretches of the alphaV and beta3 subunits. 1TM-alphaVbeta3 is more compact and less active in solution when compared with DeltaTM-alphaVbeta3, which lacks the short C-terminal stretches. The structure reveals a bent conformation and defines the alpha-beta interface between IE2 (EGF-like 2) and the thigh domains. Modifying this interface by site-directed mutagenesis leads to robust integrin activation. Fluorescent lifetime imaging microscopy of inactive full-length alphaVbeta3 on live cells yields a donor-membrane acceptor distance, which is consistent with the bent conformation and does not change in the activated integrin. These data are the first direct demonstration of conformational coupling of the integrin leg and head domains, identify the IE2-thigh interface as a critical steric barrier in integrin activation, and suggest that inside-out activation in intact cells may involve conformational changes other than the postulated switch to a genu-linear state.
Transferrable single crystalline 4H-SiC nanomembranes (2016)

In this work, we demonstrate a transferrable single crystalline 4H-SiC nanomembrane (SiC NM) released from a SiC-on-insulator (SiCOI) wafer.
An Open TCP/IP Core for Reconfigurable Logic (2005)

This project is aimed at developing the full TCP/IP protocol as an open-source IP core which can be freely used, as well as to develop know-how on protocol boosting for complex protocols such as TCP/IP. The problem was quite challenging, especially if we consider that just about all commercial implementations of TCP/IP do not fully implement all of the protocol specifications.
Anonysense (2008)

Personal mobile devices are increasingly equipped with the capability to sense the physical world (through cameras, microphones, and accelerometers, for example) and the, network world (with Wi-Fi and Bluetooth interfaces). Such devices offer many new opportunities for cooperative sensing applications. For example, users' mobile phones may contribute data to community-oriented information services, from city-wide pollution monitoring to enterprise-wide detection of unauthorized Wi-Fi access points. This people-centric mobile-sensing model introduces a new security challenge in the design of mobile systems: protecting the privacy of participants while allowing their devices to reliably contribute high-quality data to these large-scale applications.
Metabolic and mitogenic activities of insulin-like growth factor-1 in interleukin-1-conditioned equine cartilage (2000)

IGF-1 at 500 ng/ml was best at overcoming detrimental effects associated with IL-1alpha in in vitro explants. These beneficial effects may be useful in horses with osteoarthritis.
Index-based code clone detection: incremental, distributed, scalable (2010)

Although numerous different clone detection approaches have been proposed to date, not a single one is both incremental and scalable to very large code bases. They thus cannot provide real-time cloning information for clone management of very large systems. We present a novel, index-based clone detection algorithm for type 1 and 2 clones that is both incremental and scalable. It enables a new generation of clone management tools that provide real-time cloning information for very large software. We report on several case studies that show both its suitability for real-time clone detection and its scalability: on 42 MLOC of Eclipse code, average time to retrieve all clones for a file was below 1 second; on 100 machines, detection of all clones in 73 MLOC was completed in 36 minutes.
Mutations in the human gene for fibrillin-1 (FBN1) in the Marfan syndrome and related disorders (1995)

The extracellular microfibril, 10-14 nm in diameter, performs a number of functions, including serving as the scaffolding for deposition of tropoelastin to form elastic fibers. A variety of proteins compose the structure of microfibrils, the most prominent of which are the two fibrillins. Fibrillin-1 is encoded by FBN1 on human chromosome 15q21 and fibrillin-2 is encoded by FBN2 on 5q23. Each fibrillin monomer contains a large number of epidermal growth factor-like motifs, most capable of binding calcium ions, and a few motifs resembling the binding protein for transforming growth factor beta. In vitro polymerization of fibrillin monomers produces 'beads on a string' structures that look on electron microscopy much like microfibrils purified from the extracellular matrices of a variety of tissues. Mutations in FBN1 produce Marfan syndrome, a pleiotropic autosomal dominant connective tissue disorder with prominent manifestations in the skeleton, eye and cardiovascular system. A number of conditions related to Marfan syndrome are also due to FBN1 mutations. Contractural arachnodactyly is due to mutations in FBN2. In this paper we review the published mutations in these genes, preliminary results of genotype-phenotype correlations, and speculations regarding molecular pathogenesis.
Sodium methoxide: a simple but highly efficient catalyst for the direct amidation of esters (2012)

A simple NaOMe catalyst provides superior accessibility to a wide variety of functionalized amides including peptides through direct amination of esters in an atom-economical and environmentally benign way.
Adrenotropic activity of mammo-somatotropic tumors in rats and mice. I. Biologic aspects. (1962)

Summary Two transplantable rat mammo-somatotropic tumor strains, MtT.F4 and MtT.W5, were studied for AtH activity. MtT.F4 caused marked enlargement of adrenals, lymphopenia, thymic atrophy, and moderate enlargement of most viscera. MtT.W5 caused thymic enlargement, no lymphopenia, and moderate enlargement of most viscera, including the adrenals. The findings suggested that both strains have growth-promoting and mammary gland-stimulating activities; MtT.F4 also has AtH activity, whereas MtT.W5 does not. Similar findings suggested that one mouse MtT (Strain 50) had AtH activity and another (Strain 48) did not. Adrenalectomy further increased body and tumor weights in the MtT.F4 hosts and had no such effect on MtT.W5 hosts. In normal rats, adrenalectomy tripled thymic weights; in MtT.F4 rats adrenalectomy not only prevented thymic involution but caused enlargement of this organ to 6 times normal, thus disclosing the somatotropic potency of its hormones. The increase in thymic weight, notably in adrenalectomized hosts, appears to be a good index of somatotropic activity and may serve as a growth hormone assay. Enhancement of tumor growth, and StH and MtH activities of strain MtT.F4 by adrenalectomy support the view that one cell produces one hormone with the three activities (MtH, StH, and AtH).
An Evaluation of Linguistically-motivated Indexing Schemes (2000)

In this article, we describe a number of indexing experiments based on indexing terms other than simple keywords. These experiments were conducted as one step in validating a linguistically-motivated indexing model. The problem is important but not new. What is new in this approach is the variety of schemes evaluated. It is important since it should not only help to overcome the well-known problems of bag-of-words representations, but also the difficulties raised by non-linguistic text simplification techniques such as stemming, stop-word deletion, and term selection. Our approach in the selection of terms is based on part-of-speech tagging and shallow parsing. The indexing schemes evaluated vary from simple keywords to nouns, verbs, adverbs, adjectives, adjacent word-pairs, and head-modifier pairs. Our findings apply to Information Retrieval and most of related areas.
Characterization of a Strain of Community-AssociatedMethicillin-Resistant <i>Staphylococcus aureus</i> WidelyDisseminated in the UnitedStates (2006)

A highly stable strain of Staphylococcus aureus with a pulsed-field gel electrophoresis type of USA300 and multilocus sequence type 8 has been isolated from patients residing in diverse geographic regions of the United States. This strain, designated USA300-0114, is a major cause of skin and soft tissue infections among persons in community settings, including day care centers and correctional facilities, and among sports teams, Native Americans, men who have sex with men, and military recruits. The organism is typically resistant to penicillin, oxacillin, and erythromycin (the latter mediated by msrA) and carries SCCmec type IVa. This strain is variably resistant to tetracycline [mediated by tet(K)]; several recent isolates have decreased susceptibility to fluoroquinolones. S. aureus USA300-0114 harbors the genes encoding the Panton-Valentine leucocidin toxin. DNA sequence analysis of the direct repeat units within the mec determinant of 30 USA300-0114 isolates revealed differences in only a single isolate. Plasmid analysis identified a common 30-kb plasmid that hybridized with blaZ and msrA probes and a 3.1-kb cryptic plasmid. A 4.3-kb plasmid encoding tet(K) and a 2.6-kb plasmid encoding ermC were observed in a few isolates. DNA microarray analysis was used to determine the genetic loci for a series of virulence factors and genes associated with antimicrobial resistance. Comparative genomics between USA300-0114 and three other S. aureus lineages (USA100, USA400, and USA500) defined a set of USA300-0114-specific genes, which may facilitate the strain's pathogenesis within diverse environments.
Viral Contamination of Blood Components and Approaches for Reduction of Infectivity (1995)

Currently, the United States blood supply offers a relatively low risk of viral infection. This is a result of careful selection of donors and extensive laboratory testing using sensitive procedures. Epidemiologic data show that there is some room for improvement in donor selection, but such improvements cannot be expected to entirely eliminate the collection of blood from infectious donors. Similarly, increased numbers of tests, along with improvements in the analytic sensitivity of these tests, may further reduce risk, but again, complete safety cannot be assured. Consequently, there is continuing interest in the development of safe and effective procedures for viral inactivation of single donor blood components. In order to establish appropriate expectations for such inactivation procedures, it is necessary to understand the titers and distributions of viral contaminants in blood components. Viruses may variously occur free in the plasma, as replicative forms in actively infected leukocytes, as integrated proviral DNA and perhaps, nonspecifically associated with cellular surfaces.
A hybrid Bayesian neural learning strategy applied to CONNECT-4 (2002)

We present a method that combines Bayesian learning, a statistical technique, with the HONEST network, a high order neural network with the property that the mapping embodied by the network can always be described by a polynomial-like equation. In a classification task, the objective is to learn to classify feature vectors into classes. When the distribution of the features is known, statistical methods can often produce better performance than backward error propagation networks. However, if the feature distribution is not known for certain, then the performance of a statistical method will depend on how well the assumed distribution matches the actual distribution. In the method we present, we first use Bayesian learning, with an assumption of a multivariate normal distribution, to learn a quadratic polynomial mapping and then use the HONEST network to improve, or fine-tune, this mapping through backward error propagation. We apply this technique to the feature combination stage of a CONNECT-4 evaluation function.