gebhart/patrepeval huggingface dataset:
Characterization of the human CD4 gene promoter: transcription from the CD4 gene core promoter is tissue-specific and is activated by Ets proteins. (1993)

We analyzed the 5' transcription control sequences of the human CD4 gene. We located the transcription initiation site and showed that the CD4 core promoter (positions -40 to +16) lacks a classical "TATA" or initiator positioning consensus sequence but directs precise and efficient transcription when coupled to the ubiquitously active simian virus 40 enhancer. The transcriptional activity of the CD4 gene promoter correlated with CD4 expression in various cell types. Interestingly, the CD4 core promoter also displayed a tissue-specific transcriptional activity. Within this fragment, three nucleic acid sequences are completely conserved in the murine CD4 gene. One of these sequences contains a perfect ETS consensus sequence. Another ETS consensus sequence is located 1060 nt upstream. Electrophoretic-mobility-shift assays showed that the core promoter ETS motif binds an Ets-related protein specifically expressed at high levels in CD4+ cells. Moreover, in CD4- cells, overexpression of Ets-1 or Ets-2 efficiently and specifically activated transcription from the CD4 promoter and core promoter. These data indicate that Ets transcription factors play a central role in controlling CD4 gene expression, by binding to both a classical remote site and an unusual proximal activator sequence.
Multicolor detection of rare tumor cells in blood using a novel flow cytometry‐based system (2013)

The presence and number of circulating tumor cells (CTCs) in the blood of patients with solid tumors are predictive of their clinical outcomes. To date, the CellSearch system is the only US Food and Drug Administration-approved CTC enumeration system for advanced breast, prostate, and colon cancers. However, sensitivity issues due to epithelial cellular adhesion molecule (EpCAM)-based enrichment and limited capability for subsequent molecular analysis must be addressed before CTCs can be used as predictive markers in the clinical setting. We have developed a multicolor CTC detection system using cross-contamination-free flow cytometry, which permits the enumeration and characterization of CTCs for multiple molecular analyses. Tumor cell lines with different expression levels of EpCAM were spiked into peripheral blood obtained from healthy donors. Spike-in samples were negatively enriched using anti-CD45-coated magnetic beads to remove white blood cells, and this was followed by fixation and labeling with CD45-Alexa Fluor 700, EpCAM-phycoerythrin, cytokeratin (CK)-fluorescein isothiocyanate antibodies, and/or 7-aminoactinomycin D for nuclei staining. Excellent detection (slope = 0.760-0.888) and a linear performance (R(2) = 0.994-0.998) were noted between the observed and expected numbers of tumor cells, independent of EpCAM expression. The detection rate was markedly higher than that obtained using the CellSearch system, suggesting the superior sensitivity of our system in detecting EpCAM- tumor cells. Additionally, the incorporation of an epithelial-mesenchymal transition (EMT) marker allowed us to detect EpCAM-/CK- cells and EMT-induced tumor cells. Taken together, our multicolor CTC detection system may be highly efficient in detecting previously unrecognized populations of CTCs.
Accuracy evaluation of surface-based registration methods in a computer navigation system for hip surgery performed through a posterolateral approach (2001)

Slice thickness and reconstruction pitch affected the accuracy of registration. As the sampling area was expanded from the periarticular area to the distant peripheral area, accuracy increased slightly. Accuracy did not increase when the whole area was used, but in fact decreased, especially in the femur. The positive effect of increasing the number of sampling points was saturated at 30 points when the surface of the periarticular area was sampled. The following trade-off between accuracy and invasiveness, in terms of various parameters of preoperative and intraoperative data, is proposed as clinically optimal: perform the CT scan with 3-mm slice thickness and 1-mm reconstruction pitch, and sample the periarticular area with 30 sampling points. With these parameters, the accuracy of registration was 1.2 mm and 0.9 degrees of bias with 0.7 mm and 0.3 degrees of RMS in the pelvis, and 1.4 mm and 0.6 degrees of bias with 1.3 mm and 0.3 degrees of RMS in the femur.
Local Voltage-Stability Index Using Tellegen's Theorem (2006)

In the paper, the Tellegen's theorem and adjoint networks are used to derive a new, local voltage-stability index. The new approach makes it possible to determine the Thevenin's parameters in a different way than adaptive curve-fitting techniques, from two consecutive phasor measurements. The new index was rigorously tested on different test systems. The results were obtained on a static two-bus test system and on the dynamic Belgian-French 32-bus test system that includes full dynamic models of all power-system components crucial to the voltage instability analysis. The results show advantages of the proposed index: it is simple, computationally very fast, and easy to implement in the wide-area monitoring and control center or locally in a numerical relay
Pricing in computer networks: motivation, formulation, and example (1993)

The role of pricing policies in multiple service class networks is studied. An abstract formulation of service disciplines and pricing policies that allows the interplay between service disciplines and pricing policies in determining overall network performance to be described more clearly is presented. Effective multiclass service disciplines allow networks to focus resources on performance-sensitive applications, while effective pricing policies allows the benefits of multiple service classes to be spread around to all users. Furthermore, the incentives formed by service disciplines and pricing policies must be carefully tuned so that user self-interest leads to optimal overall network performance. These concepts are illustrated through simulation of several simple example networks. It is found that it is possible to set the prices so that users of every application type are more satisfied with the combined cost and performance of a network with service-class-sensitive prices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The LX39 latent fingerprint matcher (1978)

A procedure is described for automatically determining if a latent scene-of-crime fingerprint matches an inked, rolled file fingerprint. The procedure uses the x and y coordinates and the individual directions of the minutiae (ridge endings and bifurcations). The identity of the latent print with a print on file is indicated by a high score resulting from computations based on differences in angle and coordinate values of minutiae that are found in going from one of the fingerprints to the other.
Interactive Software Development Using Workflow (2009)

Workflow in interactive media and software development can be used to improve the development process as well as adding new features to the system as opposed to using classical software development approaches. Three types of workflow are distinguished to be sequential, state-machine, and rule-based workflow. This paper shows how these approaches can be used to improve the software quality and the development process. To demonstrate the capability of workflow-based approach to interactive software development, two different types of interactive applications are chosen and developed using different workflow methods: a computer game (Sudoku) and an internal Web-based application (employee ticket reservation system(ETRS)). For each one of these applications the improvement of development time, modification time, and adding a subsystem are measured and compared to the same factor using classical approaches.
C-reactive protein velocity to distinguish febrile bacterial infections from non-bacterial febrile illnesses in the emergency department (2009)

CRPv improved differentiation between febrile bacterial infections and non-bacterial febrile illnesses compared with CRP alone, and could identify individuals who need prompt therapeutic intervention.
Pluronic Surfactants (2000)

Poly (ethyleneoxide) /poly (propyleneoxide) triblock copolymers, with the commercial name of Pluronics are receiving increasingly more attention for their low toxicity and stimulus compared to other nonionic surfactants. Aqueous solution of these copolymers have unique properties. The capacity of micelle and gel formation is determined considerably by temperature. Various physical properties and applications of these copolymers are discussed.
Severe congenital neutropenia resulting from G6PC3 deficiency with increased neutrophil CXCR4 expression and myelokathexis (2010)

Mutations in more than 15 genes are now known to cause severe congenital neutropenia (SCN); however, the pathologic mechanisms of most genetic defects are not fully defined. Deficiency of G6PC3, a glucose-6-phosphatase, causes a rare multisystem syndrome with SCN first described in 2009. We identified a family with 2 children with homozygous G6PC3 G260R mutations, a loss of enzymatic function, and typical syndrome features with the exception that their bone marrow biopsy pathology revealed abundant neutrophils consistent with myelokathexis. This pathologic finding is a hallmark of another type of SCN, WHIM syndrome, which is caused by gain-of-function mutations in CXCR4, a chemokine receptor and known neutrophil bone marrow retention factor. We found markedly increased CXCR4 expression on neutrophils from both our G6PC3-deficient patients and G6pc3(-/-) mice. In both patients, granulocyte colony-stimulating factor treatment normalized CXCR4 expression and neutrophil counts. In G6pc3(-/-) mice, the specific CXCR4 antagonist AMD3100 rapidly reversed neutropenia. Thus, myelokathexis associated with abnormally high neutrophil CXCR4 expression may contribute to neutropenia in G6PC3 deficiency and responds well to granulocyte colony-stimulating factor.
A general scheme for constructing inversion algorithms for conebeam CT (2003)

Given a rather general weight function n 0 , we derive a new cone beam transform inversion formula. The derivation is explicitly based on Grangeat′s formula (1990) and the classical 3D Radon transform inversion. The new formula is theoretically exact and is represented by a 2D integral. We show that if the source trajectory C is complete in the sense of Tuy (1983) (and satisfies two other very mild assumptions), then substituting the simplest weight n 0 ≡ 1 gives a convolution‐based FBP algorithm. However, this easy choice is not always optimal from the point of view of practical applications. The weight n 0 ≡ 1 works well for closed trajectories, but the resulting algorithm does not solve the long object problem if C is not closed. In the latter case one has to use the flexibility in choosing n 0 and find the weight that gives an inversion formula with the desired properties. We show how this can be done for spiral CT. It turns out that the two inversion algorithms for spiral CT proposed earlier by the author are particular cases of the new formula. For general trajectories the choice of weight should be done on a case‐by‐case basis.
Gene expression profiles in febrile children with defined viral and bacterial infection (2013)

Viral infections are common causes of fever without an apparent source in young children. Despite absence of bacterial infection, many febrile children are treated with antibiotics. Virus and bacteria interact with different pattern recognition receptors in circulating blood leukocytes, triggering specific host transcriptional programs mediating immune response. Therefore, unique transcriptional signatures may be defined that discriminate viral from bacterial causes of fever without an apparent source. Gene expression microarray analyses were conducted on blood samples from 30 febrile children positive for adenovirus, human herpesvirus 6, or enterovirus infection or with acute bacterial infection and 22 afebrile controls. Blood leukocyte transcriptional profiles clearly distinguished virus-positive febrile children from both virus-negative afebrile controls and afebrile children with the same viruses present in the febrile children. Virus-specific gene expression profiles could be defined. The IFN signaling pathway was uniquely activated in febrile children with viral infection, whereas the integrin signaling pathway was uniquely activated in children with bacterial infection. Transcriptional profiles classified febrile children with viral or bacterial infection with better accuracy than white blood cell count in the blood. Similarly accurate classification was shown with data from an independent study using different microarray platforms. Our results support the paradigm of using host response to define the etiology of childhood infections. This approach could be an important supplement to highly sensitive tests that detect the presence of a possible pathogen but do not address its pathogenic role in the patient being evaluated.
Highly Luminescent BODIPY-Based Organoboron Polymer Exhibiting Supramolecular Self-Assemble Structure (2008)

A novel class of rod-coil type-organoboron polymers with p-phenylene-ethynylene as the rod segment and long alkyl chain (decyl group) as coil segment has been prepared from a Sonogashira-Hagihara coupling reaction of a BODIPY-based monomer having bis-iodophenyl and decyl groups with diyne monomers, 1,4-diethynylbenzene (a), 1,4-diethynyl-2,5-bis(trifluoromethyl)benzene (b), and 2,7-diethynyl-9,9-dihexyl-9H-fluorene (c). The characterization by means of scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed the strong tendency of the obtained polymers, 2a, 2b, and 2c, to self-assemble into particles in solution and as-casted films on a micron-nm scale. Especially, 2a showed the presence of nm-sized particles and micron-sized fiber-like structures formed by aggregation of each particle. Further, in CHCl3, the gelation of 2a by three-dimensional aggregation of each fiber was observed at room temperature after 24 h. Their luminescent properties showed high energy transfer efficiency from pi-conjugated polymer linkers to BODIPY moieties (PhiF > 71%).
Applications of Rare‐Earth Magnets to the Small Motor Industry (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
The early genes E6 and E7 of cancer associated human papilloma viruses as targets of tumor suppression? (1991)

We have transplanted HPV 18 positive nontumorigenic hybrid cells and tumorigenic hybrid segregants as well as nontumorigenic and tumorigenic human keratinocytes immortalized by HPV 16-DNA transfection (HPK cells and HPK-ras cells) into nude mice and grown them under in vivo conditions for different periods of time. By analyzing gene expression at the mRNA level of the early viral genes E6/E7 and a number of cytoskeletal cellular genes we wanted to test the hypothesis that the nontumorigenic phenotype of these cells in vivo may be determined by the specific downregulation of expression of the oncogenic E6/E7 genes by the product(s) of tumor suppressor gene(s). The results obtained showed that: 1) The nontumorigenic hybrid cells (in contrast to tumorigenic segregants) stopped to proliferate about 3 days after transplantation. At this time E6/E7 gene expression was already drastically reduced, whereas at day 2 expression was still high. This suppression specifically affected the HPV 18 E6/E7 genes and preceded cell death by at least 10 days. 2) The same specific suppression of HPV E6/E7 gene expression occurred during in vivo growth of the nontumorigenic HPK cells. These cells gave rise to transiently growing cysts, but had retained the in vivo differentiation potential of normal keratinocytes (orderly expression of cytokeratins 1 and 10, involucrin and filaggrin). HPV 16 E6/E7 gene expression was very low and clearly restricted to a small subset of basal cells, thus showing an inverse relationship to terminal differentiation. In contrast, in the tumors induced by HPK-ras cells E6/E7 gene expression extended from the basal cells into suprabasal cells and terminal differentiation was retarded. These results support the hypothesis that during in vivo growth tumor suppressor gene(s) negatively regulated HPV E6/E7 gene expression resulting in the stop of proliferation of the nontumorigenic cells.
Induced Expression of the Conditionally Cytotoxic Herpes Simplex Virus <i>thymidine kinase</i> Gene by Means of a Parvoviral Regulatory Circuit (1994)

As a step toward the achievement of targeted expression of toxic genes, we have established a model system using the selective trans-activation of the late promoter P38 of Minute Virus of Mice (MVMp) by the parvoviral nonstructural protein NS-1. The conditionally toxic herpes simplex virus type 1 thymidine kinase (tk) gene (HSV1-tk) was cloned under the control of the P38 promoter and transfected into NIH-3T3 TK- cells. Treatment of the stably transfected cells with acyclovir (ACV) followed by infection with MVMp reduced cell survival by 3.5- to 5-fold compared to the toxic effects of ACV or MVMp alone. These results indicate that it should be possible to combine the genuine cytopathic action of parvoviruses with a specific activation of toxic genes driven by parvoviral promoters, to achieve the targeted destruction of parvovirus-expressing (in particular tumor) cells.
The applicability of CPP-GMR heads for magnetic recording (2002)

In this paper, we mainly discuss the extendability of current perpendicular to plane giant magnetoresistive (CPP-GMR) heads beyond 100 Gbpsi by using micromagnetic simulation and simulation techniques. An area map of CPP-GMR's resistance-area product (RA) and magnetoresistive ratio for several areal densities is made, which suggests that downsizing of a CPP-GMR head does not cause a decrease in output voltage differently from a current in plane GMR (CIP-GMR) head. At this point, a CPP-GMR has the advantage of extendability to a higher areal density over CIP-GMR, and is the major candidate for the next generation. A CIP-GMR seems to have a scalability limit around 100-200 Gbpsi. On the other hand, the area map also suggests that the RA of the CPP-GMR is a more important keyfactor for higher areal density than for CIP-GMR. The CPP-GMR, therefore, requires not only higher MR, but also less RA as areal density gets higher. Tunneling MR (TMR) has exactly the same problem, so CPP-GMR also has many advantages over TMR, with too high an RA. Additionally, we present CPP-GMR films with the potential for around 500 Gbpsi and discuss a suitable read-head structure for CPP-GMR. Micromagnetic simulation results indicate that the read track width will be controlled by a magnetic field due to the sense current of CPP. We will discuss overall studies on scalability of CPP-GMR.
Heat shock proteins and cell proliferation in human breast cancer biopsy samples. (1997)

Human breast cancers may overexpress certain heat shock protein (hsp) family members, proteins which are involved with cell proliferation and differentiation as well as with disease prognosis and drug resistance. Here, we have studied the relationship between the expression of two hsps (hsp27 and hsp70) and the proliferative activity of tumor cells in 40 biopsies from breast cancer patients. Twenty of these tumors were selected for a detailed colocalization study. Immunocytochemistry was done using specific antibodies against hsp27 and hsp70. Cell proliferation was studied analyzing the expression of proliferating cell nuclear antigen (PCNA) (late G1, S, and G2 phases of the cell cycle) and the number of silver-staining nucleolar organizer regions (AgNORs) (G1 phase). The colocalization study revealed a statistically significant inverse correlation between hsp27 expression and cell proliferation in 16/19 (84%) of the cases evaluated by PCNA immunostaining, and in 11/16 (69%) of the cases evaluated by AgNORs. In contrast, a statistically significant positive correlation between hsp70 expression and elevated cell proliferation was seen in almost 85% of the cases evaluated by PCNA staining, and in almost 50% of the cases evaluated by AgNORs. Moreover, in 22% (9/40) of the breast cancer samples examined, hsp70 was clearly associated with the mitotic spindle. A Western blot analysis revealed that hsp70 was coprecipitated with taxol-polymerized tubulin. The association of hsp70 with the mitotic spindle was not clearly noted in lung carcinoma samples (N = 20) or in normal cells displaying elevated mitotic activity. These studies thus demonstrate that in a significant percentage of clinical breast cancers hsp27 overexpression is inversely correlated with cell proliferation, while hsp70 is clearly associated with the mitotic spindle and cell proliferation. These results add evidence to the concept that in human breast cancers hsp27 may be involved in cell growth arrest and increased differentiation while, in contrast, hsp70 may be involved in cell proliferation; further studies will be necessary to elucidate these possible cause-and-effect relationships.
Autoimmunity in a Phase I Trial of a Fully Human Anti-Cytotoxic T-Lymphocyte Antigen-4 Monoclonal Antibody With Multiple Melanoma Peptides and Montanide ISA 51 for Patients With Resected Stages III and IV Melanoma (2004)

Dose-related autoimmune adverse events, predominantly skin and GI toxicities, were reversible. Patients mounted an antigen-specific immune response to a peptide vaccine when combined with a human anti-CTLA-4 antibody.
Postpartum Low-Back Pain (1992)

To determine the prevalence of back pain and its development over the first postpartum period, 817 women who had been followed through pregnancy were studied a minimum of 12 months after delivery. More than 67% of the women experienced back pain directly after delivery, whereas 37% said they had back pain at the follow-up examination. Most of the women who had recovered became pain-free within 6 months. Factors that correlated to persistent postpartum back pain were the presence of back pain before pregnancy, the presence of back pain during pregnancy, physically heavy work, and multipregnancy. Of these four factors, physically heavy work was found to have the strongest association with persistent back pain at 12 months.
Android taint flow analysis for app sets (2014)

One approach to defending against malicious Android applications has been to analyze them to detect potential information leaks. This paper describes a new static taint analysis for Android that combines and augments the FlowDroid and Epicc analyses to precisely track both inter-component and intra-component data flow in a set of Android applications. The analysis takes place in two phases: given a set of applications, we first determine the data flows enabled individually by each application, and the conditions under which these are possible; we then build on these results to enumerate the potentially dangerous data flows enabled by the set of applications as a whole. This paper describes our analysis method, implementation, and experimental results.