gebhart/patrepeval huggingface dataset:
TBL2, a novel transducin family member in the WBS deletion: characterization of the complete sequence, genomic structure, transcriptional variants and the mouse ortholog (1999)

Williams-Beuren syndrome (WBS) is a developmental disorder with multi-system manifestations caused by haploinsufficiency for contiguous genes deleted in chromosome region 7q11.23. The size of the deletion is similar in most patients due to a genomic duplication that predisposes to unequal meiotic crossover events. While hemizygosity at the elastin locus is responsible for the cardiovascular features, the contribution of other genes to the WBS phenotype remains to be demonstrated. We have identified a novel gene, TBL2, in the common WBS deletion. TBL2 is expressed as a 2. 4-kb transcript predominantly in testis, skeletal muscle, heart and some endocrine tissues, with a larger approximately 5-kb transcript detected ubiquitously at lower levels. TBL2 encodes a protein with four putative WD40-repeats. An alternatively spliced transcript in TBL2 introduces a novel second exon with an in frame stop codon. This mRNA encodes a 75 amino acid protein with 43 amino acids identical to TBL2 at the N-terminus and no known functional domain. The mouse homolog, Tbl2, shows 84% sequence identity at the nucleotide level and 92% similarity at the amino acid level. Comparison of the mouse and human sequences identifies a conserved region that extends upstream of the previously published sequence with an initiation codon common to both species that adds 21 amino acids at the N-terminus. The Tbl2 gene has been mapped to mouse chromosome 5 in a region of conserved synteny with human 7q11.23. Since haploinsufficiency has been shown for other WD-repeat containing proteins, hemizygosity of TBL2 may contribute to some of the aspects of the complex WBS phenotype.
Gene delivery from polymer scaffolds for tissue engineering (2004)

The combination of gene therapy with tissue engineering offers the potential to direct progenitor cell proliferation and differentiation into functional tissue replacements. Many approaches to engineering tissue replacements feature a polymer scaffold to create and maintain a space, support cell adhesion, and organize tissue formation. Polymer scaffolds, either natural, synthetic, or a combination of the two, have also been adapted to serve as delivery vehicles for viral and nonviral vectors, which can induce the expression of tissue inductive factors. Gene delivery is a versatile approach, capable of targeting any cellular process through localized expression of tissue inductive factors. The design and application of tissue engineering scaffolds for localized gene transfer are reviewed. Scaffolds are designed either to release the vector into the local tissue environment or maintain the vector at the polymer surface, which is regulated by the effective affinity of the vector for the polymer. Polymeric delivery can enhance gene transfer locally, promote and extend transgene expression, avoid vector distribution to distant tissues, and reduce the immune response to the vector. Scaffolds capable of controlled DNA delivery can provide a fundamental tool for directing progenitor cell function, which has applications with the engineering of numerous types of tissue. The utility of this approach will increase with the development of design parameters that correlate release and transgene expression, and with continued research into the biology of tissue formation.
Gold(iii) compounds containing a chelating, dicarbanionic ligand derived from 4,4′-di-tert-butylbiphenyl (2014)

An oligomeric gold(III) compound containing dicarbanionic chelating 4,4'-di-tert-butylbiphenyl was prepared via transmetallation using the corresponding organotin(IV) compound. The reactivity of the chloro-bridged oligomer with various species including neutral N-, P-, and C-donor ligands as well as monoanionic S- and Se-ligands was investigated. Some of the products were characterised by X-ray crystallography. The photophysical properties of two derivatives were studied.
T-cell determinants and antibody binding sites on the major mycobacterial secretory protein MPB59 of Mycobacterium bovis (1994)

Among the first proteins encountered by the host immune system upon infection or vaccination with mycobacteria are those secreted by the bacillus during growth. The antigen 85 complex of Mycobacterium bovis bacillus Calmette-Gúerin (BCG) is composed of three closely related members. The mature 85B protein of M. bovis (MPB59) has a high degree of amino acid identity with the M. bovis 85A protein (76%) and the Mycobacterium tuberculosis 85B (99%) and 85A (76%) proteins. We have examined the regions of MPB59 which stimulate human T- and B-cell responses by use of a set of 28 synthetic peptides, 20 amino acids (aa) in length and overlapping by 10 aa. Initial proliferative assays with recombinant MPB59 demonstrated that peripheral blood mononuclear cells from 95% of BCG vaccinees and 52% of tuberculosis patients responded to the whole mature protein. Peripheral blood mononuclear cells from MPB59 responders, but not nonresponders, were stimulated by peptides in a dose-dependent fashion. Five peptides were reactive in more than half of the MPB59 responders. The T-cell-reactive regions were essentially identical in the M. bovis and M. tuberculosis 85B proteins. Subjects with a variety of HLA-DR phenotypes responded to a number of these peptides. The dominant T-cell-reactive regions were distinct from the peptides recognized by sera from tuberculosis patients (aa 71 to 100) and the murine monoclonal antibody HYT27 (aa 61 to 90). The region reactive with antibodies overlapped part of the MPB59 sequence recently shown to participate in the binding of MPB59 to fibronectin.
Mid infrared pulse shaping by optical parametric amplification and its application to optical free induction decay measurement (2003)

We produce microjoule energy shaped mid infrared (MIR) pulses in an optical parametric amplification (OPA) process by imposing the phase and amplitude profile of an arbitrarily shaped pump pulse onto the idler pulse. Using phase locked pulses created using this technique, we measure for the first time, complex optical free induction decay (OFID) of the vibrational coherence of a C-H stretching mode.
Modeling Power Systems as Complex Adaptive Systems (2004)

Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We review and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.
BR96-Doxorubicin Conjugate (BMS-182248) Versus Doxorubicin: A Comparative Toxicity Assessment in Rats (1994)

The toxicity of BMS-182248, an immunoglobulin (cBR96)-cytotoxic drug (doxorubicin) conjugate, was investigated in Sprague-Dawley rats at single intravenous doses of 508, 1,200, and 2,550 mg/m2 (conjugated doxorubicin doses of 14.7, 34.8, and 74 mg/m2, respectively) and compared to that obtained from administration of free doxorubicin at single doses of 33.6 and 72 mg/m2 (approximately equivalent to that contained in the 1,200- and 2,550-mg/m2 doses of BMS-182248, respectively). Necropsies were conducted on day 8, upon death/moribund sacrifice, or after an approximate 3-mo observation period following completion of treatment. Death/moribundity of all rats that received 72 mg/m2 and of 9 of 20 rats given 33.6 mg/m2 free doxorubicin were attributed primarily to delayed cardiotoxicity and glomerulonephropathy. With BMS-182248, death from glomerulonephropathy and cardiotoxicity occurred in only 4 of 20 rats given 2,550 mg/m2 (74 mg/m2 doxorubicin equivalent). No deaths or cardiotoxicity occurred in rats given 508 or 1,200 mg/m2 BMS-182248. Additional effects noted with either drug included testicular atrophy, axonal degeneration of sciatic nerve and nerve tracts of brain and spinal cord, teeth (incisor) abnormalities, thymic atrophy, bone marrow hypocellularity, splenic lymphoid and red-pulp depletion, and increased extramedullary hematopoiesis in the spleen and liver. Also noted were altered chief cells in the stomach, vacuolation of adrenal gland and corpora lutea in the ovary, uterine and seminal vesicle atrophy, ulceration and myocyte regeneration/degeneration in the tongue, increased osteoclasts and osteoblasts in bone, and lymphoid hyperplasia of mandibular lymph node. In general, these effects were more severe in doxorubicin-treated rats. All changes observed with BMS-182248 were considered primarily due to the effects of doxorubicin and were substantially less severe (most notably cardiotoxicity) compared to those produced by an equivalent amount of doxorubicin.
Effect of Inositol Hexakisphosphate Kinase 2 on Transforming Growth Factor β-activated Kinase 1 and NF-κB Activation (2007)

We previously showed that inositol hexakisphosphate kinase 2 (IHPK2) functions as a growth-suppressive and apoptosis-enhancing kinase during cell stress. Overexpression of IHPK2 sensitized ovarian carcinoma cell lines to the growth-suppressive and apoptotic effects of interferon beta (IFN-beta), IFN-alpha2, and gamma-irradiation. Expression of a kinase-dead mutant abrogated 50% of the apoptosis induced by IFN-beta. Because the kinase-dead mutant retained significant response to cell stressors, we hypothesized that a portion of the death-promoting function of IHPK2 was independent of its kinase activity. We now demonstrate that IHPK2 binds to tumor necrosis factor (TNF) receptor-associated factor (TRAF) 2 and interferes with phosphorylation of transforming growth factor beta-activated kinase 1 (TAK1), thereby inhibiting NF-kappaB signaling. IHPK2 contains two sites required for TRAF2 binding, Ser-347 and Ser-359. Compared with wild type IHPK2-transfected cells, cells expressing S347A and S359A mutations displayed 3.5-fold greater TAK1 activation following TNF-alpha. This mutant demonstrated a 6-10-fold increase in NF-kappaB DNA binding following TNF-alpha compared with wild type IHPK2-expressing cells in which NF-kappaB DNA binding was inhibited. Cells transfected with wild type IHPK2 or IHPK2 mutants that lacked S347A and S359A mutations displayed enhanced terminal deoxynucleotidyltransferase-mediated dUTP nick end-labeling staining following TNF-alpha. We believe that IHPK2-TRAF2 binding leads to attenuation of TAK1- and NF-kappaB-mediated signaling and is partially responsible for the apoptotic activity of IHPK2.
Holographic optical coherence imaging of tumor spheroids (2003)

We present depth-resolved coherence-domain images of living tissue using a dynamic holographic semiconductor film. An AlGaAs photorefractive quantum-well device is used in an adaptive interferometer that records coherent backscattered (image-bearing) light from inside rat osteogenic sarcoma tumor spheroids up to 1 mm in diameter in vitro. The data consist of sequential holographic image frames at successive depths through the tumor represented as a visual video “fly-through.” The images from the tumor spheroids reveal heterogeneous structures presumably caused by necrosis and microcalcifications characteristic of human tumors in their early avascular growth.
Distinguishing Single- and Double-Stranded Nucleic Acid Molecules Using Solid-State Nanopores (2009)

Solid-state nanopores offer a promising method for rapidly probing the structural properties of biopolymers such as DNA and RNA. We have for the first time translocated RNA molecules through solid-state nanopores, comparing the signatures of translocating double-stranded RNA molecules and of single-stranded homopolymers poly(A), poly(U), poly(C). On the basis of their differential blockade currents, we can rapidly discriminate between both single- and double-stranded nucleic-acid molecules, as well as separate purine-based homopolymers from pyrimidine-based homopolymers. Molecule identification is facilitated through the application of high voltages ( approximately 600 mV), which contribute to the entropic stretching of these highly flexible molecules. This striking sensitivity to relatively small differences in the underlying polymer structure greatly improves the prospects for using nanopore-based devices for DNA or RNA mapping.
Modeling Compressive Strength Of Recycled Aggregate Concrete Using Neural Networks And Regression Analysis (2013)

Recycled aggregates are used in concrete and is called as Recycled Aggregate Concrete (RAC). This paper aims at predicting the 28 day compressive strength of RAC using two techniques namely Artificial Neural Network (ANN) and Non-linear regression (NLR). Five ANN and NLR models were developed with input parameters as per cubic proportions of cement, sand, natural coarse aggregate , recycled coarse aggregate, water , admixtures used in the mix designs and non-dimensional parameters sand aggregate ratio , water to total materials ratio and the replacement ratio of recycled coarse aggregates to natural aggregates(by volume) in concrete. The effects of each parameter on networks in both techniques were studied. Comparing the techniques shows that ANN performs better than NLR equations. With limited amount of input parameters also, ANN1 predicted the strength of RAC better as compared to NLR1. The performance of ANN models and NLR models improved with the use of non-dimensional parameters.
Six-Degree-of-Freedom Sensor Fish Design and Instrumentation (2007)

Fish passing through dams may be injured or killed despite advances in turbinedesign, project operations and other fish bypass systems. The six-degree-of-freedom (6DOF)Sensor Fish device is an autonomous sensor package that characterizes the physical conditionsand physical stresses to which fish are exposed when they pass through complex hydraulicenvironments. It has been used to identify the locations and operations where conditions aresevere enough to injure or kill fish. During the design process, a set of governing equationsof motion for the Sensor Fish was derived and simulated to understand the design implica-tions of instrument selection and placement within the body of the device. The Sensor Fishpackage includes three rotation sensors, three acceleration sensors, a pressure sensor, and atemperature sensor with a sampling frequency of 2,000 Hz. Its housing is constructed of clearpolycarbonate plastic. It is 24.5 mm in diameter and 90 mm in length and weighs about 43 g,similar to the size and density of a yearling salmon smolt. The accuracy of the pressure sensorwas determined to be within 0.2 psi. In laboratory acceptance tests, the relative errors of boththe linear acceleration and angular velocity measurements were determined to be less than5%. An exposure is defined as a significant event when the acceleration reaches predefinedthresholds. Based on the different characteristic of acceleration and rotation velocities, theexposure event is categorized as either a collision between the Sensor Fish and a solid struc-ture or shear caused by turbulence. Since its development in 2005, the 6DOF Sensor Fish hasbeen deployed successfully at many major dams in the United States.
The minK potassium channel exists in functional and nonfunctional forms when expressed in the plasma membrane of Xenopus oocytes (1994)

The minK protein induces a slowly activating voltage-dependent potassium current when expressed in Xenopus oocytes. In order to measure the levels of minK protein in the plasma membrane, we have modified the minK gene by inserting a 9 amino acid epitope into the N-terminal domain of the protein sequence. When intact live oocytes are injected with the modified minK RNA and subsequently incubated with an antibody to this epitope, specific binding is detected, indicating that the N-terminal domain is extracellular. We found that when oocytes are injected with amounts of minK mRNA up to 50 ng, the levels of protein at the surface are proportional to the amount of injected mRNA. In contrast, the amplitude of the minK current recorded in the oocytes saturates at 1 ng of injected mRNA. Although the amplitude of the currents is not altered by increasing mRNA levels above 1 ng, the kinetics of activation of the current differ in oocytes with high or low levels of minK RNA. In particular, activation is slower with higher levels of minK protein in the plasma membrane. Finally, we find that increasing intracellular cAMP levels, which increases the amplitude of minK currents, does not alter surface expression of the minK protein but produces a small increase in the rate of activation of the current. Our results support a model in which minK protein forms functional potassium channels by association with a factor endogenous to the oocyte.
O6 alkylguanine-DNA alkyltransferase activity in human myeloid cells. (1985)

The association between alkylating agent exposure and acute nonlymphocytic leukemia in humans indicates that myeloid cells may be particularly susceptible to mutagenic damage. Alkylating agent mutagenesis is frequently mediated through formation and persistence of a particular DNA base adduct, O6alkylguanine, which preferentially mispairs with thymine rather than cytosine, leading to point mutations. O6alkylguanine is repaired by O6alkylguanine-DNA alkyltransferase (alkyltransferase), a protein that removes the adduct, leaving an intact guanine base in DNA. We measured alkyltransferase activity in myeloid precursors and compared it with levels in other cells and tissues. In peripheral blood granulocytes, monocytes, T lymphocytes, and B lymphocytes, there was an eightfold range of activity between individuals but only a twofold range in the mean activity between cell types. Normal donors maintained stable levels of alkyltransferase activity over time. In bone marrow T lymphocytes and myeloid precursors, there was an eightfold range of alkyltransferase activity between donors. Alkyltransferase activity in the two cell types was closely correlated in individual donors, r = 0.69, P less than 0.005, but was significantly higher in the T lymphocytes than the myeloid precursors, P less than 0.05. Liver contained the highest levels of alkyltransferase of all tissues tested. By comparison, small intestine contained 34%, colon 14%, T lymphocytes 11%, brain 11%, and myeloid precursors 6.6% of the activity found in liver. Thus, human myeloid precursors have low levels of O6alkylguanine-DNA alkyltransferase compared with other tissues. Low levels of this DNA repair protein may increase the susceptibility of myeloid precursors to malignant transformation after exposure to certain alkylating agents.
Vasculature of the normal and arthritic synovial joint. (2001)

The vasculature of the normal and arthritic knee is described. The joint contains a number of different tissues, many of which are heterogeneous and each with varying degrees of vascularization. In the normal joint the vasculature is highly organised, some tissues are highly vascular with well defined vascular organisation, whilst other tissues are avascular. During arthritis vascular turnover is increased. This vascular plasticity leads to redistribution of the vascular bed and may compromise its functional ability. The normal joint is able to regulate its blood flow, but this ability may be compromised by the inflammation and increased synovial fluid volume that are associated with joint disease. Growth of the subchondral vasculature into the articular cartilage may also occur, leading to ossification of the articular cartilage.
Feature bagging for outlier detection (2005)

Outlier detection has recently become an important problem in many industrial and financial applications. In this paper, a novel feature bagging approach for detecting outliers in very large, high dimensional and noisy databases is proposed. It combines results from multiple outlier detection algorithms that are applied using different set of features. Every outlier detection algorithm uses a small subset of features that are randomly selected from the original feature set. As a result, each outlier detector identifies different outliers, and thus assigns to all data records outlier scores that correspond to their probability of being outliers. The outlier scores computed by the individual outlier detection algorithms are then combined in order to find the better quality outliers. Experiments performed on several synthetic and real life data sets show that the proposed methods for combining outputs from multiple outlier detection algorithms provide non-trivial improvements over the base algorithm.
A system for saccular intracranial aneurysm analysis and virtual stent planning (2012)

Recent studies have found correlation between the risk of rupture of saccular aneurysms and their morphological characteristics, such as volume, surface area, neck length, among others. For reliably exploiting these parameters in endovascular treatment planning, it is crucial that they are accurately quantified. In this paper, we present a novel framework to assist physicians in accurately assessing saccular aneurysms and efficiently planning for endovascular intervention. The approach consists of automatically segmenting the pathological vessel, followed by the construction of its surface representation. The aneurysm is then separated from the vessel surface through a graph-cut based algorithm that is driven by local geometry as well as strong prior information. The corresponding healthy vessel is subsequently reconstructed and measurements representing the patient-specific geometric parameters of pathological vessel are computed. To better support clinical decisions on stenting and device type selection, the placement of virtual stent is eventually carried out in conformity with the shape of the diseased vessel using the patient-specific measurements. We have implemented the proposed methodology as a fully functional system, and extensively tested it with phantom and real datasets.
Network characteristics of video streaming traffic (2011)

Video streaming represents a large fraction of Internet traffic. Surprisingly, little is known about the network characteristics of this traffic. In this paper, we study the network characteristics of the two most popular video streaming services, Netflix and YouTube. We show that the streaming strategies vary with the type of the application (Web browser or native mobile application), and the type of container (Silverlight, Flash, or HTML5) used for video streaming. In particular, we identify three different streaming strategies that produce traffic patterns from non-ack clocked ON-OFF cycles to bulk TCP transfer. We then present an analytical model to study the potential impact of these streaming strategies on the aggregate traffic and make recommendations accordingly.