gebhart/patrepeval huggingface dataset:
Isolation and characterization of an autonomously replicating sequence from Ustilago maydis. (1988)

DNA fragments that function as autonomously replicating sequences (ARSs) have been isolated from Ustilago maydis. When inserted into an integrative transforming vector, the fragments increased the frequency of U. maydis transformation several-thousandfold. ARS-containing plasmids were transmitted in U. maydis as extrachromosomal elements through replication. They were maintained at a level of about 25 copies per cell but were mitotically unstable. One ARS characterized in detail, which we called UARS1, was localized to a 1.7-kilobase fragment. UARS1 contained a cluster of active sequences. This element could be reduced further into three separate subfragments, each of which retained ARS activity. The smallest one was 383 base pairs (bp) long. Although not active itself in yeast, this small fragment contained seven 8-bp direct repeats, two contiguous 30-bp direct repeats, and five 11-bp units in both orientations with sequences similar but not identical to the consensus sequence found to be crucial for ARS activity in Saccharomyces cerevisiae.
Electrical properties of Au/ and YBa2Cu3O7−<i>x</i>/SrTi1−<i>y</i>Nb<i>y</i>O3 diodes (1991)

Electrical properties of Au/ and YBa2Cu3O7−x/SrTi1−yNbyO3 heterojunctions were studied by measuring their capacitance-voltage, current-voltage, and conductance-voltage characteristics. The heterostructures were made by depositing Au or YBa2Cu3O7−x films on SrTi1−yNbyO3 substrates. The results of the capacitance-voltage measurement indicated that there was an interfacial layer having a dielectric constant lower than that of bulk SrTiO3 at the Au/SrTiO3 and YBa2Cu3O7−x/SrTiO3 interfaces. The current-voltage characteristics of the Au/SrTi1−yNbyO3 diodes with substrate Nb concentrations of 0.05 and 0.005 wt. % matched characteristics normally associated Schottky junctions and had a large ideality factor, n, consistent with the low-dielectric-constant interfacial layers. When the carrier concentration of the n-SrTiO3 substrate was 2×1019 cm−3, the Au and YBa2Cu3O7−x junctions showed interfacial-layer tunneling characteristics. The YBa2Cu3O7−x junctions exhibited two peaks in their conductance-voltage relations whose peak structures relies on the superconducting state density in YBa2Cu3O7−x films.
Characterization and exploitation of narrow-width loads (2010)

This paper exploits small-value locality to accelerate the execution of memory instructions. We find that narrow-width loads (NWLDs) --- loads with small-value operands of 8 bits or less --- comprise 26% of all executed loads across 40 applications of the SPEC benchmark suites. We establish that the frequency of NWLDs are almost independent of compiler and input data. We introduce narrow-width caches (NWC) to cache small-value memory words. NWCs provide a significant speedup for several memory-intensive applications with a negligible chip-area overhead. NWCs also reduce the overall energy dissipation and memory traffic.
Shape‐Persistent Macrocycles: Structures and Synthetic Approaches from Arylene and Ethynylene Building Blocks (2006)

Shape-persistent arylene ethynylene macrocycles have attracted much attention in supramolecular chemistry and materials science because of their unique structures and novel properties. In this Review we describe recent examples of macrocycle synthesis by cross-coupling (Sonogashira: aryl acetylene macrocycle or Glaser: aryl diacetylene macrocycle) and dynamic covalent chemistry. The primary disadvantage of the coupling methods is the kinetically determined product distribution, since a significant portion of oligomers grow beyond the length of the cyclic targets ("overshooting"). Better results have been obtained recently by a dynamic covalent approach involving reversible metathesis reactions that afford macrocycles in one step. Mechanistic studies demonstrate that macrocycle formation is thermodynamically controlled by this route. Remaining synthetic challenges include the efficient preparation of site-specifically functionalized structures and larger, more complex two- and three-dimensional molecules.
Automated Visual Tracking for Behavioral Analysis of Biological Model Organisms (2008)

Capturing the detailed motion and behavior of biological organisms plays an important role in a wide variety of research disciplines. Many studies in biomechanics, neuroethology, and developmental biology rely on analysis of video sequences to understand the underlying behavior. However, the efficient and rapid quantification of these complex behavioral traits imposes a major bottleneck on the elucidation of many interesting scientific questions. The goal of this thesis is to develop a suite of model-based visual tracking algorithms that will apply across a variety of model organisms used in biology. These automated tracking algorithms operate in a high-throughput, high-resolution manner needed for a productive synthesis with modern genetic approaches. To this end, I demonstrate automated estimation of the detailed body posture of nematodes, zebrafish, and fruit flies from calibrated video. The current algorithm utilizes a generative geometric model to capture the organism's shape and appearance. To accurately predict the organism's motion between video frames, I incorporate a motion model that matches tracked motion patterns to patterns in a training set. This technique is invariant with respect to the organism's velocity and can easily incorporate training data from completely different motion patterns. The prediction of the motion model is refined using measurements from the image. In addition to high-contrast feature points, I introduce a region, segmentation model based on level sets that are formally integrated into the observation framework of an Iterated Kalman Filter (IKF). The prior knowledge provided by the geometric and motion models improves tracking accuracy in the presence of partial occlusions and misleading visual cues. The method is used to track the position and shape of multiple nematodes during mating behavior, zebrafish of different ages during escape response, and fruit flies during take off maneuvers. These applications demonstrate the modular design of this model-based visual tracking system, where the user can specify which components are appropriate to a given experiment. In contrast to other approaches, which are customized to a particular organism or experimental setup, my approach provides a foundation that requires little re-engineering whenever the experimental parameters are changed.
<title>Smart composite material system with sensor, actuator, and processor functions: a model of holding and releasing a ball</title> (2002)

A smart composite material system which has three smart functions of sensor, actuator and processor has been developed intend to apply to structure of house for controlling ambient temperature and humidity, hands of robot for holding and feeling an object, and so on. A carbon fiber reinforced plastics (CFRP) is used as matrix in the smart composite. The size of the matrix is 120mm x 24mm x 0.45mm. The CFRP plate is combined two Ni-Ti shape memory alloy (SMA) wires with an elastic rubber to construct a composite material. The composite material has a characteristic of reversible response with respect to temperature. A photo-sensor and temperature sensor are embedded in the composite material. The composite material has a processor function to combine with a simple CPU (processor) unit. For demonstrating the capability of the composite material system, a model is built up for controlling certain behaviors such as gripping and releasing a spherical object. The amplitude of gripping force is (3.0 plus/minus 0.3) N in the measurement, which is consistent with our calculation of 2.7 N. Out of a variety of functions to be executed by the CPU, it is shown to exert calculation and decision making in regard to object selection, object holding, and ON-OFF control of action by external commands.
Transcription factors in human leukaemias. (1992)

At the present time, two general mechanisms account for deregulation and subsequent oncogenic conversion of transcriptional proteins in human leukaemias. One involves quantitative alterations in expression, suggesting that activity of the involved factors is primarily controlled by their accessibility within the cell. Neoplastic transformation may result from excessive expression or, conversely, complete loss of functional products (eg tumour suppressor proteins not described here). The second mechanism involves mutation by protein fusion (or truncation) and illustrates the modular composition of transcriptional proteins. The loss or inappropriate combination of specific modules creates chimaeric proteins with presumably altered transcriptional properties that may contribute to the neoplastic phenotype. Both mechanisms underscore the importance of cognate interactions, particularly heterodimerization between various transcriptional proteins with other members of the transcription complex. Future efforts will continue to focus on the interactions of oncogenic transcription factors with other cellular proteins and their biologically relevant target genes.
A coding and retransmission protocol for mobile radio data transmission (2003)

Mobile radio systems suffer from severe channel impairments. As services are moving toward a full extension of those available over fixed networks, new coding strategies are being developed to support data traffic beside the more usual voice communication. This paper presents a modified type II hybrid FEC/ARQ protocol in which each packet to be transmitted is decomposed into sub-packets each of which can be independently tested for correctness and retransmitted if necessary. The complete coding and transmission scheme is designed to be compatible with the frame format used in GSM networks. The performances of the proposed algorithm are evaluated by computer simulation using the system specifications contained in the ETSI-GSM recommendations. Throughput comparison with a traditional selective repeat (SR) protocol is presented to support the robustness and effectiveness of the presented scheme.
The role of mesalamine in the treatment of ulcerative colitis. (2007)

Ulcerative colitis (UC) is a chronic inflammatory condition of unclear etiology affecting the large bowel, most commonly the rectum and extending proximally in a continuous fashion. The overall principle in the pathophysiolgy of ulcerative colitis is the dysregulation of the normal immune system against an antigenic trigger leading to a prolonged mucosal inflammatory response. The diagnosing of UC is made by combining the clinical picture, tissue biopsy with the endoscopic appearance of mucosal ulceration, friable, edematous, erythematous granular appearing mucus. The approach to therapy of UC has been dependent on severity of symptoms with frontline therapy being salicylate based sulfasalazine. Newer formulations of salicylates based drugs with fewer side-effects have been developed. These are free of the sulphur component and are composed of 5-ASA, without the sulfapyridine carrier molecule. Mesalamine is one of these 5-ASA based agents that are currently available and indicated for treatment of UC. In mild/moderate active disease mesalamine has response rates between 40%-70% and remission rates of 15%-20%. Considering that the efficacy of 5-ASA is dose dependent, 4.8 g/day and 2.4 g/day have been shown to be the optimal dosages for mild-moderate distal active disease and for maintenance therapy, respectively. Patients with moderately active ulcerative colitis treated with 4.8 g/d of mesalamine are significantly more likely to achieve overall improvement at week 6 compared to patients treated with 2.4 g/d. In the setting of left-sided distal colitis (proctitis), topical (rectal) formulations have been found to be superior to oral aminosalicylates at inducing remission. Mesalamine has been shown to be safe in short term use with a dose-response efficacy without dose-related toxicity.
Characteristics of InAs/AlGaAs self-organized quantum dot modulation doped field effect transistors (1998)

We have investigated the dc characteristics of InGaAs/AlGaAs modulation doped field effect transistors in which a layer of self-organized InAs quantum dots is inserted adjacent to the pseudomorphic quantum well channel. Distinct steps and a negative differential resistance are observed in the current–voltage characteristics at room temperature and lower temperatures. These are attributed to conduction through the bound states in the quantum dots.
Rapid purification of ferritin from lysates of red blood cells using proteinase-K (1989)

A simple, rapid, and novel procedure for purifying ferritin from the postnuclear supernatant of red blood cell lysates is described. This report establishes the resistance of commercially available holo- and apo-ferritins to proteinase-K digestion, and documents how the use of this enzyme, in conjunction with the well-documented resistance of ferritins to heat denaturation (75-80 degrees C for 10 min), makes it possible to obtain high yields (greater than 90%) of pure, undegraded ferritin from the postnuclear supernatant of hypotonically or Triton X-100 lysed red blood cells. The resultant purified ferritin contains the same amount of iron as ferritin not treated with proteinase-K and, as judged by one- and two-dimensional gel electrophoresis and electron microscopy, consists of intact ferritin with a subunit isoform composition identical in molecular mass and isoelectric points to that obtained from ferritin prepared in the absence of this enzyme.
Identification of a brain-specific APC homologue, APCL, and its interaction with beta-catenin. (1998)

We isolated a novel gene, APCL, that showed significant homology to the adenomatous polyposis coli (APC) tumor suppressor gene. This novel gene, located on chromosome 19p13.3, encodes a protein of 2303 amino acids that is expressed specifically in the brain. The predicted protein of APCL contains five copies of a 20-amino-acid motif (FXVEXTPXCFSRXSSLSSLS). Like APC, this domain of APCL was able to bind to beta-catenin and deplete the intracellular beta-catenin pool. A reporter-gene assay revealed that APCL could also regulate interaction of beta-catenin with T cell-specific transcription factor, although less actively than APC. These results suggest that the APCL protein may be involved in the Wnt/Wingless signal pathway, and the identification of a novel relative of APC may provide new insights into the function of APC.
A Cross-linked Large Channel Organic Coordination Solid (2001)

A new approach to fully covalent crystalline networks is revealed. It is a template technique in which a metal salt is co-crystallized with a mesoscopic organic molecule. The Figure shows a phenylacetylenenitrile silver triflate molecule, which is reacted with silyl ditriflates to form high molecular weight polymers. Details of the technique and physical properties are discussed.
The Improving of IKE with PSK for Using in Mobile Computing Environments (2009)

The rapid increase in using mobile communication networks for transmitting confidential data and conducting commercial transactions such as mobile e-commerce is creating large demands in designing secure mobile business systems. However, the mobile devices and mobile communication network have some weakness. It can cause some problems using traditional VPN technologies in mobile computing environments immediately. Currently, mobile users' authentication in IKE is being done using certificates or PSK with aggressive mode commonly. They have serious security related issues (for PSK with aggressive mode) and need high deployment and maintain cost (for certificates). In this paper, we propose a new approach that is based on PSK where the IKE negotiation phase is modified for using in mobile computing environments. The modified IKE consists of four messages, and the responder doesn't need to store any state while receiving message 1. It uses strong cookies and pre-calculated DHpp stack, etc technologies to counter IP flooding attacks and man-in-the-middle DoS attacks, because it does not require the responder to perform heavy computations before the initiator has authenticated itself. Otherwise, for one mobile user, it has a group of PSKs to be random selected, and the initiator and responder exchange identity info and agree on PSK with Hash (PSK-ID|IDi) or Hash (PSK-ID|IDr) info. Therefore, it provides the initiator and responder's identity protection and prevention of passive dictionary based attacks on pre-shared keys.
Expiratory flow limitation during mechanical ventilation detected by the forced oscillation method (1996)

We have previously observed large phasic variations of respiratory mechanical impedance in chronic obstructive pulmonary disease (COPD) patients mechanically-ventilated for acute respiratory failure, and postulated that they were due to expiratory flow limitation (EFL). The aim of this study was to test that assumption experimentally and to assess the value of impedance for automatic and noninvasive detection of EFL during mechanical ventilation. The study was performed: 1) in a mechanical analogue, including a flow-limiting element; and 2) in eight anaesthetized and paralysed rabbits, before and during histamine infusion. In both instances, EFL was obtained by lowering the expiratory pressure, using a computer-controlled ventilator; the absence of flow increase when expiratory pressure was further lowered was taken as evidence of EFL. Impedance was measured by applying 15 Hz oscillations at the airway opening. Its real (Re) and imaginary (Im) parts were measured separately during the inspiratory and the expiratory phases, and their differences were related to the mean inspiratory modulus. With the analogue, EFL was accompanied by large decreases both of Re and Im during the expiratory phase. In the rabbits, phasic variations of Re were variable in sign and were not significantly different with and without EFL. In contrast, EFL systematically and specifically decreased Im during the expiratory phase. A threshold of -50% provided a sensitivity of 96% and a specificity of 100% for detecting EFL. The observed phasic variations may be explained by airway wall shunt properties. The study suggests that a large decrease of the imaginary part of impedance during the expiratory phase is a sensitive and specific index of expiratory flow limitation during artificial ventilation.
Recepteur d'Origine Nantais Tyrosine Kinase Is a Direct Target of Hypoxia-inducible Factor-1α-mediated Invasion of Breast Carcinoma Cells (2009)

Hypoxia-inducible factor-1alpha (HIF-1alpha) overexpression was shown to be associated with invasion and metastasis of tumors and tumor cell lines. The identification of molecular targets that contribute to HIF-1alpha-mediated invasion is under intensive investigation. We have analyzed the role of recepteur d'origine nantais (RON), a tyrosine kinase receptor for macrophage-stimulating protein (MSP) that plays a role in breast cancer cell invasion as one of the molecular targets of HIF-1alpha. Analysis of a panel of breast cancer cell lines indicated a correlation between HIF-1alpha and RON expression. Treatment of HIF-1alpha- and RON-positive breast cancer cells with HIF-1alpha inhibitor, echinomycin, led to the inhibition of HIF-1alpha activity and RON expression. We have identified HIF-1alpha binding site on the RON promoter. Chromatin immunoprecipitation analysis and site-directed mutagenesis of the RON promoter confirmed the binding of HIF-1alpha to RON promoter. HIF-1alpha inhibitor-, echinomycin-, or short hairpin RNA-mediated selective knockdown of HIF-1alpha or HIF-1alpha target RON tyrosine kinase abrogated RON gene expression, and the RON ligand macrophage-stimulating protein mediated invasion of breast cancer cells. Consequently, the data presented herein demonstrated RON as a novel molecular target of HIF-1alpha and suggest a potential therapeutic role for HIF-1alpha or RON tyrosine kinase inhibitors in the blockade of RON tyrosine kinase-mediated invasion of carcinoma cells.
Software Directed Issue Queue Power Reduction (2005)

The issue logic of a superscalar processor dissipates a large amount of static and dynamic power. Furthermore, its power density makes it a hot-spot requiring expensive cooling systems and additional packaging. In this paper we present a novel software assisted approach to power reduction where the processor dynamically resizes the issue queue based on compiler analysis. The compiler passes information to the processor about the number of entries needed which limits the number of instructions dispatched and resident in the queue. This saves power without adversely affecting performance. Compared with recently proposed hardware techniques, our approach is faster, simpler and saves more power. Using a simplistic scheme we achieve 47% dynamic and 31% static power savings in the issue queue with only a 2.2% performance loss. We then show that the performance loss can be reduced to less than 1.3% with 45% dynamic and 30% static power savings, outperforming all current approaches.
5:3 Ultra Low Power Bright Reflective Displays using <i>BiNem</i> ® Technology Fabricated by Standard Manufacturing Equipment (2002)

Abstract We have developed reflective bistable nematic BiNem® LCDs with 160×160 and VGA resolutions. On state reflectance reaches 30% and contrast ratio exceeds 9 at normal incidence, with excellent viewing angle. Infinite bistability coupled to low driving voltage enable ultra low power consumption. Manufacturing process uses standard passive LCD fabrication equipment.
High-precision mask repair using nanomachining (2002)

Nanomachining has recently been introduced as a new option for the repair of photomasks. The RAVE nm1300 system is a high precision system for subtractive removal of opaque mask defects. The first such system was installed at the Infineon Mask House in Munich, Germany. This paper presents the results of the acceptance testing. Programmed pattern defects on binary chrome on glass masks, alternating phase shifting masks and both 248nm and 193nm halftone phase shifting masks were used for these tests. Some examples of carbon patch trimming, sequential defect removing as well as repairing of 'non-removable' particles and irregularly shaped quartz bump defects demonstrate the unique capabilities of the tool.
Effectiveness of mouthpiece nebulization and nasal swab stick packing for topical anesthesia in awake fiberoptic nasotracheal intubation. (2007)

In the present study technique of topical anesthesia using 2% lidocaine 5 mL mouthpiece nebulization and 10% cocaine 1 mL soaked nasal swab stick packing is useful and safe for awake fiberoptic nasotracheal intubation in patients with suspected difficult intubation. 76.7% of the patient did not require more local anesthesia and 80% were satisfied with this technique.
Tracking of deformable human hand in real time as continuous input for gesture-based interaction (2007)

Gesture input is a natural and effective interactive model. The tracking of deformable hand gesture is a very important task in gesture-based interaction. A novel real-time tracking approach is proposed to capture hand motion with single camera. It combines the characters of model-based and appearance-based method. The presented approach achieves auto-initialization by posture recognition and matching with image features. It solves the problem of interference among fingers successfully by the integration of K-Means clustering and Particle Filters. Moreover, tracking detection realizes resumption from tracking failure and automatic update of hand model. Experiments show that, the proposed method can achieve continuous real-time tracking of deformable hand gesture, and meets the requirements for gesture-based Human-Computer Interaction.