gebhart/patrepeval huggingface dataset:
Shape Deformation in Two-Dimensional Electrical Impedance Tomography (2012)

Electrical impedance tomography (EIT) uses measurements from surface electrodes to reconstruct an image of the conductivity of the contained medium. However, changes in measurements result from both changes in internal conductivity and changes in the shape of the medium relative to the electrode positions. Failure to account for shape changes results in a conductivity image with significant artifacts. Previous work to address shape changes in EIT has shown that in some cases boundary shape and electrode location can be uniquely determined for isotropic conductivities; however, for geometrically conformal changes, this is not possible. This prior work has shown that the shape change problem can be partially addressed. In this paper, we explore the limits of compensation for boundary movement in EIT using three approaches. First, a theoretical model was developed to separate a deformation vector field into conformal and nonconformal components, from which the reconstruction limits may be determined. Next, finite element models were used to simulate EIT measurements from a domain whose boundary has been deformed. Finally, an experimental phantom was constructed from which boundary deformation measurements were acquired. Results, both in simulation and with experimental data, suggest that some electrode movement and boundary distortions can be reconstructed based on conductivity changes alone while reducing image artifacts in the process.
Human CAR T cells with cell-intrinsic PD-1 checkpoint blockade resist tumor-mediated inhibition (2016)

Following immune attack, solid tumors upregulate coinhibitory ligands that bind to inhibitory receptors on T cells. This adaptive resistance compromises the efficacy of chimeric antigen receptor (CAR) T cell therapies, which redirect T cells to solid tumors. Here, we investigated whether programmed death-1–mediated (PD-1–mediated) T cell exhaustion affects mesothelin-targeted CAR T cells and explored cell-intrinsic strategies to overcome inhibition of CAR T cells. Using an orthotopic mouse model of pleural mesothelioma, we determined that relatively high doses of both CD28- and 4-1BB–based second-generation CAR T cells achieved tumor eradication. CAR-mediated CD28 and 4-1BB costimulation resulted in similar levels of T cell persistence in animals treated with low T cell doses; however, PD-1 upregulation within the tumor microenvironment inhibited T cell function. At lower doses, 4-1BB CAR T cells retained their cytotoxic and cytokine secretion functions longer than CD28 CAR T cells. The prolonged function of 4-1BB CAR T cells correlated with improved survival. PD-1/PD-1 ligand [PD-L1] pathway interference, through PD-1 antibody checkpoint blockade, cell-intrinsic PD-1 shRNA blockade, or a PD-1 dominant negative receptor, restored the effector function of CD28 CAR T cells. These findings provide mechanistic insights into human CAR T cell exhaustion in solid tumors and suggest that PD-1/PD-L1 blockade may be an effective strategy for improving the potency of CAR T cell therapies.
The Escherichia coli mazEF Suicide Module Mediates Thymineless Death (2003)

In 1954, Cohen and Barner discovered that a thymine auxotrophic (thyA) mutant of Escherichia coli undergoes cell death in response to thymine starvation. This phenomenon, called thymineless death (TLD), has also been found in many other organisms, including prokaryotes and eukaryotes. Though TLD has been studied intensively, its molecular mechanism has not yet been explained. Previously we reported on the E. coli mazEF system, a regulatable chromosomal suicide module that can be triggered by various stress conditions. MazF is a stable toxin, and MazE is an unstable antitoxin. Here, we show that cell death that is mediated by the mazEF module can also be activated by thymine starvation. We found that TLD depends on E. coli mazEF and that under thymine starvation, the activity of the mazEF promoter P(2) is significantly reduced. Our results, which describe thymine starvation as a trigger for a built-in death program, have implications for programmed cell death in both prokaryotes and eukaryotes.
Focal aberrations indicate EYA2 and hsa‐miR‐375 as oncogene and tumor suppressor in cervical carcinogenesis (2012)

Cervical cancer results from persistent infection with high-risk human papillomavirus (hrHPV). Common genetic aberrations in cervical (pre)cancers encompass large genomic regions with numerous genes, hampering identification of driver genes. This study aimed to identify genes functionally involved in HPV-mediated transformation by analysis of focal aberrations (<3 Mb) in high-grade cervical intraepithelial neoplasia (hgCIN). Focal chromosomal aberrations were determined in high-resolution array comparative genomic hybridization data of 60 hgCIN. Genes located within focal aberrations were validated using 2 external gene expression datasets or qRT-PCR. Functional roles of candidate genes EYA2 (20q13) and hsa-miR-375 (2q35) were studied by siRNA-mediated knock-down and overexpression, respectively, in hrHPV-containing cell lines. We identified 74 focal aberrations encoding 305 genes. Concurrent altered expression in hgCIN and/or cervical carcinomas compared with normal cervical samples was shown for ATP13A3, HES1, OPA1, HRASLS, EYA2, ZMYND8, APOBEC2, and NCR2. Gene silencing of EYA2 significantly reduced viability, migratory capacity, and anchorage-independent growth of HPV16-transformed keratinocytes. For hsa-miR-375, a direct correlation between a (focal) loss and significantly reduced expression was found. Downregulation of hsa-miR-375 expression was confirmed in an independent series of cervical tissues. Ectopic expression of hsa-miR-375 in 2 cervical carcinoma cell lines reduced cellular viability. Our data provide a proof of concept that chromosomal aberrations are actively contributing to HPV-induced carcinogenesis and identify EYA2 and hsa-miR-375 as oncogene and tumor suppressor gene, respectively.
A DHT-Based Process Migration Policy for Mobile Clusters (2010)

A mobile cluster experiences disruption in execution of long-running applications because of its highly dynamic nature. Process migration is a solution for handling such dynamism to have seamless computing with minimal disruption. The challenge in process migration is that it should take considerably less time. This work is a novel effort at such a goal that employs a heap-based super P2P structure for the cluster. The P2P cluster transfers process state in terms of object migration between the peers through the base station. Also, while migrating processes, care is taken to maintain load balancing. As the mobile cluster has heterogeneous nodes with varying processing capabilities, we devise a mechanism for computing the capabilities of these nodes. Considering the capability and current load of the nodes the destination for process migration is chosen.
Evaluation and extension of maximum entropy models with inequality constraints (2003)

A maximum entropy (ME) model is usually estimated so that it conforms to equality constraints on feature expectations. However, the equality constraint is inappropriate for sparse and therefore unreliable features. This study explores an ME model with box-type inequality constraints, where the equality can be violated to reflect this unreliability. We evaluate the inequality ME model using text categorization datasets. We also propose an extension of the inequality ME model, which results in a natural integration with the Gaussian MAP estimation. Experimental results demonstrate the advantage of the inequality models and the proposed extension.
The p24 leucocyte membrane antigen: Modulation associated with lymphocyte activation and differentiation (1989)

Monoclonal antibodies of the CD9 cluster recognize a 24 kD protein (p24) found on platelets and endothelium, and expressed by lymphocytes at restricted stages of maturation and activation. In this study, we explore the possibility that p24 is involved in the response of lymphocytes to signals delivered by lymphokines. p24 is expressed only very weakly by resting B lymphocytes. We found no increase in expression when cells were activated with anti-immunoglobulin together with interleukin-4, or induced to proliferate by low-molecular weight B cell growth factor (LMW-BCGF). Culture of activated B cells with B cell differentiation factor was associated with an increased mean expression of p24. In cells from a patient with chronic lymphocytic leukaemia (CLL), culture with LMW-BCGF up-regulated p24 expression. Resting T cells (p24-negative) were induced to express p24 strongly when activated with antibody against CD3. CD9 antibody did not modulate B or T cell responses to activation stimuli. The results suggest that the p24 molecule is not involved in the primary interaction of cells with lymphokine, but rather may be involved in a secondary reaction, such as ion flux, which follows as a consequence of the action of lymphokines on cells.
In-fiber common-path optical coherence tomography using a conical-tip fiber (2009)

Common-path optical coherence tomography (CPOCT) is known to reduce group velocity dispersion and polarization mismatch between the reference and the sample arm as both arms share the same physical path. Existing implementations of CPOCT typically require one to incorporate an additional cover glass within the beam path of the sample arm to provide a reference signal. In this paper, we aim to further reduce this step by directly making use of the back-reflected signal, arising from a conical lens-tip fiber, as a reference signal. The conical lens, which is directly manufactured onto the optical fiber tip via a simple selective-chemical etching process, fulfils two functions acting as both the imaging lens and the self-aligning reference plane. We use a Fourier-domain OCT system to demonstrate the feasibility of this technique upon biological tissue. An in-fiber CPOCT technique may prove potentially useful in endoscopic OCT imaging.
Isolation and characterization of the three polypeptide components of 4-chlorobenzoate dehalogenase from Pseudomonas sp. strain CBS-3 (1992)

The three genes encoding the 4-chlorobenzene dehalogenase polypeptides were excised from a Pseudomonas sp. CBS-3 DNA fragment and separately cloned and expressed in Escherichia coli. The three enzymes were purified from the respective subclones by using an ammonium sulfate precipitation step followed by one or two column chromatographic steps. The 4-chlorobenzoate:coenzyme A ligase was found to be a homodimer (57-kDa subunit size), to require Mg2+ (Co2+ and Mn2+ are also activators) for activity, and to turn over MgATP (Km = 100 microM), coenzyme A (Km = 80 microM), and 4-chlorobenzoate (Km = 9 microM) at a rate of 30 s-1 at pH 7.5 and 25 degrees C. Benzoate, 4-bromobenzoate, 4-iodobenzoate, and 4-methylbenzoate were shown to be alternate substrates while 4-hydroxybenzoate, 4-aminobenzoate, 2-aminobenzoate, 2,3-dihydroxybenzoate, 4-coumarate, palmate, laurate, caproate, butyrate, and phenylacetate were not substrate active. The 4-chlorobenzoate-coenzyme A dehalogenase was found to be a homotetramer (30 kDa subunit size) to have a Km = 15 microM and kcat = 0.3 s-1 at pH 7.5 and 25 degrees C and to be catalytically inactive toward hydration of crotonyl-CoA, alpha-methylcrotonyl-CoA, and beta-methylcrotonyl-CoA. The 4-hydroxybenzoate-coenzyme A thioesterase was shown to be a homotetramer (16 kDa subunit size), to have a Km = 5 microM and kcat = 7 s-1 at pH 7.5 and 25 degrees C, and to also catalyze the hydrolyses of benzoyl-coenzyme A and 4-chlorobenzoate-coenzyme A. Acetyl-coenzyme A, hexanoyl-coenzyme A, and palmitoyl-coenzyme A were not hydrolyzed by the thioesterase.
Angiogenesis and Progression in Human Melanoma (2010)

In tumor growth, angiogenesis, the process of new-formation of blood vessels from pre-existing ones, is uncontrolled and unlimited in time. The vascular phase is characterized by the new-formation of vascular channels that enhances tumor cell proliferation, local invasion and hematogenous metastasis. Human malignant melanoma is a highly metastatic tumor with poor prognosis, and high resistance to treatment. Parallel with progression, melanoma acquires a rich vascular network, whereas an increasing number of tumor cells express the laminin receptor, which enables their adhesion to the vascular wall, favouring tumor cell extravasation and metastases. Melanoma neovascularization has been correlated with poor prognosis, overall survival, ulceration and increased rate of relapse. Secretion of various angiogenic cytokines, i.e. VEGF-A, FGF-2, PGF-1 and -2, IL-8, and TGF-1 by melanoma cells promote the angiogenic switch and has been correlated to transition from the radial to the vertical growth phase, and to the metastatic phase. Moreover, melanoma cells overexpress alphavbeta3, alphavbeta5, alpha2beta1 and alpha5beta1 integrins and release, together with stromal cells, higher amount of metalloproteases that increasing their invasive potential and angiogenesis. Basing on these observations, different molecular targets of antiangiogenic molecules has be recognized and various antiangiogenic agents are currently in preclinical and clinical trials for melanoma.
Remote palpation technology (1995)

One of a surgeon's most important tools is a highly developed sense of touch. Surgeons rely on sensations from the finger tips to guide manipulation and to perceive a wide variety of anatomical structures and pathologies. Unfortunately, new surgical techniques separate the surgeon's hands from the surgical site. These techniques include minimally invasive procedures such as laparoscopy and thoracoscopy, and new techniques involving robotic manipulators. In these situations the surgeon's perception is limited to visual feedback from a video camera, or gross motion and force feedback through the handles of long instruments. The authors are working to develop new technology to rectify this sensory deficit by relaying tactile information from the surgical site to the surgeon. They have developed a variety of tactile sensors that can be mounted in a probe or surgical instrument. The tactile information provided by these sensors may then be conveyed through the tactile display devices the authors have developed to recreate the tactile stimulus directly on the surgeon's finger tip. By using these remote palpation devices, the surgeon may regain some of the perceptual and manipulative skills present in conventional open-incision surgery. Among the tactile feedback parameters the authors are investigating are force reflection, vibration, and small-scale shape.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Autolink-a tool for automatic test generation from SDL specifications (2002)

Due to an increasing interest in SDL (Specification and Description Language), MSC (Message Sequence Charts) and TTCN (Tree and Tabular Combined Notation) based tools for validation and test generation, Telelogic AB and the Institute for Telematics at the University of Lu/spl uml/beck are cooperating in a research and development project which adds new test generation facilities to Telelogic's Tau tool set. The result of that cooperation is Autolink, a software tool which supports the automatic generation of TTCN test suites based on SDL and MSC specifications. The project follows a pragmatic approach and is driven by practical experience. Autolink has been used by the European Telecommunications Standards Institute (ETSI) to develop a test suite for Core INAP CS-2 (Intelligent Network Application Protocol, Capability Set 2).
Determination of small angular displacement by moiré fringes of matched radial–parallel gratings (1997)

We investigate the properties of the moiré fringes of matched radial-parallel (MRP) gratings that are useful for the fine visual indication of angular displacements. Moiré patterns formed by overlapping two different MRP gratings of angular pitches, P(theta) and P(theta)? (<P(theta)), can provide a simple fringe-counting method for determining both the angle and the direction of the relative angular displacement of the gratings within the accuracy of (P(theta)?/M(theta)), where M(theta) is the angular magnification for radial vernier fringes.
Developmental expression of troponin I isoforms in fetal human heart (1991)

We have used antibodies specific for troponin I proteins to examine human cardiac development and have detected a transiently expressed developmental isoform. This isoform is distinct from adult cardiac troponin I (TnIc) but is indistinguishable, on the basis of electrophoretic mobility and antibody reactivity, from the isoform found in slow skeletal muscle (TnIs). Furthermore, we show that mRNA for TnIs is present in fetal, but not adult, heart. Analysis of a developmental series of fetal samples indicates that there is a transition in expression from TnIs to TnIc which occurs between 20 weeks fetal and 9 months postnatal development.
[Combined sciatic/3-in-1 block. III. Prilocaine 1% versus mepivacaine 1%]. (1988)

In a randomized, double-blind study, the efficacy of prilocaine 1% (group 1, 30 patients) was compared to mepivacaine 1% (group 2, 30 patients). All patients had a combined sciatic/femoral block for surgery of the lower extremities; a tourniquet was applied in each case. In each patient the block was done using 50 ml of a 1% solution of local anesthetic: 20 ml for the sciatic and 30 ml for the 3-in-1 block. The time to onset of sensory block was approx. 4 min in both groups; the onset of motor blockade averaged 6 min and after 10-12 and 15 min sensory and motor blockades, respectively, were complete. On the average, patients were pain-free for 254 min with prilocaine and 267 min with mepivacaine. Four of 30 patients (= 13%) in group 1 an 6 of 30 patients (= 20%) in group 2 had an unsatisfactory blockade and had to be supplemented by analgesics or general anesthesia. The finding of a significant correlation between the voltage necessary for stimulation and the efficacy of the blockade underlines the importance of correct stimulation when identifying the nerves.
A wearable diffuse reflectance sensor for continuous monitoring of cutaneous blood content (2009)

An optical diffuse reflectance sensor for characterization of cutaneous blood content and optimized for continuous monitoring has been developed as part of a non-invasive multisensor system for glucose monitoring. A Monte Carlo simulation of the light propagation in the multilayered skin model has been performed in order to estimate the optimal geometrical separation of the light source and detector for skin and underlying tissue. We have observed that the pathlength within the upper vascular plexus of the skin which defines the sensor sensitivity initially grows with increasing source-detector distance (SDD) before reaching a maximum at 3.5 mm and starts to decay with further increase. At the same time, for distances above 2.4 mm, the sensor becomes sensitive to muscle blood content, which decreases the specificity to skin perfusion monitoring. Thus, the SDDs in the range from 1.5 mm to 2.4 mm satisfy the requirements of sensor sensitivity and specificity. The hardware implementation of the system has been realized and tested in laboratory experiments with a venous occlusion procedure and in an outpatient clinical study in 16 patients with type 1 diabetes mellitus. For both testing procedures, the optical sensor demonstrated high sensitivity to perfusion change provoking events. The general build-up of cutaneous blood under the sensor has been observed which can be associated with pressure-induced vasodilation as a response to the sensor application.
Dietary Migraine: Recent Progress in the Red (And White) Wine Story (1995)

The concept of dietary migraine as a clinical entity remains controversial. We review here such objective evidence that has been put forward for its existence. Red wine, in particular, is commonly alleged to initiate attacks in susceptible individuals. We discuss how some of its recently described pharmacological properties might trigger off the sequence of events leading to migrainous headache.
Affinity Chromatography of B-Glucosidase and Endo-B-Glucanase from Aspergillus Niger on Concanavalin A-Sepharose: Implications for Cellulase Component Purification and Immobilization (1986)

Affinity chromatography of a commercial preparation of beta-glucosidase from Aspergillus niger using concanavalin A-Sepharose (CAS) was employed as a means of purifying this glycoprotein. However, mannose (up to 1.08 M) was ineffective as an eluent of this enzyme from CAS, as were several other sugars and their derivatives, including 0.5 M glucose. Also, washing the CAS: beta-glucosidase complex with buffer at pH 3.5 in the absence of MnCl2 and CaCl2 (required to preserve the binding activity of concanavalin A below pH 5.0) did not result in elution of this enzyme. On the contrary, endoglucanase activity present in a crude cellulase complex (A. niger) which bound to CAS could be eluted by mannose (0.5-0.7 M) and was fractionated into at least two components. The CAS: beta-glucosidase complex hydrolyzed cellobiose to glucose and possessed an activity of 2,158 units/g dry CAS. It could be used, therefore, for continuous cellobiose hydrolysis without leakage of enzyme from the support.
Neuroprotective Effects of α2 -Adrenergic Receptor Agonists (2007)

Alpha2-adrenergic receptor agonists exert potent analgesic and sedative/hypnotic effects. In addition, they have been shown to be neuroprotective in various experimental models, but the molecular pathways leading to these actions are still poorly defined. This review summarizes the available literature and discusses potential mechanisms of alpha2-adrenergic receptor agonist mediated neuroprotection.
Detection of activated ras oncogenes in human thyroid carcinomas. (1988)

Focus formation following DNA transfection of mouse 3T3-Vill cells was used to search for the presence of activated oncogenes in human thyroid tumors. Oncogenes belonging to the ras family were detected in four out of six thyroid carcinomas (Ki-ras in one anaplastic tumor and one follicular moderately differentiated tumor and Ha-ras and N-ras in two papillary tumors). Normal thyroid tissue samples obtained from two patients, one with an anaplastic tumor and one with a benign adenoma, and samples from 4 benign adenomas and from one toxic goiter of a patient with Graves' disease gave negative results. In one case, restriction enzyme analysis demonstrated the presence of a mutation in codon 12 of the activated Ha-ras oncogene. Our data show that all three ras proto-oncogenes can become activated in malignant thyroid tumors.
HLA–DRB1 genotype associations in 793 white patients from a rheumatoid arthritis inception cohort: Frequency, severity, and treatment bias (2002)

This large inception cohort study confirms previously identified major associations and provides additional insights. Only one dominant association was found: *0401, which differs from other SE alleles in a single Lys-for-Arg substitution. The association of the rare DRB1*10 allele has not previously been postulated. Sex associations were confirmed. Associations with seronegative RA were not seen. Not all genotypes containing an SE copy showed increased susceptibility to RA. The association of SE genotypes found in this study related to disease susceptibility rather than severity.