gebhart/patrepeval huggingface dataset:
NCX1 Surface Expression (2002)

The rat Na(+)/Ca(2+) exchanger isoforms of the NCX1 gene have 14 cysteine residues. Each of these cysteines can be mutated individually to alanine or serine without loss of functional expression in transfected HEK293 cells. Yet sequential exchange starting from the amino terminal end of three or more cysteines results in reduced transport activity and surface expression. As more and more cysteines are replaced, transport activity and surface expression decrease in parallel, and the cysteineless mutant exhibits only traces of Na(+)/Ca(2+) exchange activity and surface expression. No significant differences are detected in the amount of total cell exchanger protein between the wild-type exchanger and its functional or nonfunctional cysteine mutants. Reduced surface expression of the Na(+)/Ca(2+) exchanger NCX1 is also observed when HEK293 cells expressing the transporter are treated with cyclosporin A (CsA) or with PSC833. The reductions in transport activity and surface expression are concentration dependent and parallel. No reduction is obtained in the total amount of exchanger protein by CsA or PSC833 treatment, suggesting that the effects of these drugs on NCX1 expression are posttranslational. FK506 and rapamycin treatment of HEK293 cells expressing rat NCX1 isoforms has no effect on transport activity, surface expression, or the total amount of exchanger protein in the transfected cells.
The Longitudinal Interval Follow-up Evaluation (1987)

The Longitudinal Interval Follow-up Evaluation (LIFE) is an integrated system for assessing the longitudinal course of psychiatric disorders. It consists of a semistructured interview, an Instruction booklet, a coding sheet, and a set of training materials. An interviewer uses the LIFE to collect detailed psychosocial, psychopathologic, and treatment information for a six-month follow-up interval. The weekly psychopathology measures ("psychiatric status ratings") are ordinal symptom-based scales with categories defined to match the levels of symptoms used in the Research Diagnostic Criteria. The ratings provide a separate, concurrent record of the course of each disorder initially diagnosed in patients or developing during the follow-up. Any DSM-III or Research Diagnostic Criteria disorder can be rated with the LIFE, and any length or number of follow-up intervals can be accommodated. The psychosocial and treatment information is recorded so that these data can be linked temporally to the psychiatric status ratings.
Cell culture as spheroids: an approach to multicellular resistance. (1999)

Cells cultured as spheroids present an heterogeneity similar to that of tumours in vivo. In the spheroid peripheral layers, cells are proliferating, deeper cells are non-cycling, when in the aggregate centre, cells form often a necrotic core. A multicellular resistance is related on the cell contact to other cells or to the extracellular matrix. The mechanism of this resistance remains unknown. It seems to be linked to the spheroid centre hypoxia, quiescence of a large fraction of the cell population and to the apoptose inhibition. The "classical" or "unicellular" mechanisms of resistance, as mdr1, MRP, can coexist but are not responsible of this type of resistance. This culture model is a good opportunity to study a resistance which looks close to the patient tumour resistance. A new class of therapeutic molecules appears that can reverse multicellular resistance, inhibit tumours growth and preclude metastases. The mechanism of action of this new pharmacological class is the disruption of the cell adhesion forces.
Performance debugging shared memory parallel programs using run-time dependence analysis (1997)

We describe a new approach to performance debugging that focuses on automatically identifying computation transformations to reduce synchronization and communication. By grouping writes together into equivalence classes, we are able to tractably collect information from long-running programs. Our performance debugger analyzes this information and suggests computation transformations in terms of the source code. We present the transformations suggested by the debugger on a suite of four applications. For Barnes-Hut and Shallow, implementing the debugger suggestions improved the performance by a factor of 1.32 and 34 times respectively on an 8-processor IBM SP2. For Ocean, our debugger identified excess synchronization that did not have a significant impact on performance. ILINK, a genetic linkage analysis program widely used by geneticists, is already well optimized. We use it only to demonstrate the feasibility of our approach to long-running applications.We also give details on how our approach can be implemented. We use novel techniques to convert control dependences to data dependences, and to compute the source operands of stores. We report on the impact of our instrumentation on the same application suite we use for performance debugging. The instrumentation slows down the execution by a factor of between 4 and 169 times. The log files produced during execution were all less than 2.5 Mbytes in size.
Models for the design and analysis of a large package sort facility (2002)

Abstract At the sort facility in a large overnight package delivery operation, palletized loads are moved in a container (called an inbound ULD) from a plane to a bin, unloaded from the bin, and moved by forklift one item at a time from a bin to a rack. At the rack, each palletized load is loaded into a container (called an outbound ULD) and this outbound ULD is delivered to a plane for delivery to its final delivery airport. The purpose of this study was to determine the optimal design of this sort facility that acts as a hub in a hub‐and‐spoke system. For a given topology of the sort facility (a topology being the specification of the locations of the bins and the racks), a design of this sort facility is the assignment of inbound ULDs to bins and outbound ULDs to racks and the determination of the number of forklifts needed to carry out the sort. In this paper, the Bin and Rack Assignment Model (BRAM) is developed to perform this analysis; the objective of the BRAM is to minimize the daily operating and amortized capital cost of performing the sort. Since the BRAM is computationally difficult to solve, the BAM and RAM algorithm is developed to derive heuristic solutions to the BRAM. Several examples of the BAM and RAM algorithm are presented. A modification to the BAM and RAM algorithm for solving practical‐sized problems is then presented and future directions for this analysis are discussed. © 2002 Wiley Periodicals, Inc.
160 Gbit/s error-free all-optical demultiplexing using monolithically integrated band gap shifted Mach-Zehnder interferometer (2003)

Error-free all-optical demultiplexing is demonstrated with a monolithically integrated switch for 160 Gbit/s data stream. The switch comprises 'band gap shifted' semiconductor optical amplifiers, monolithically integrated within a symmetric Mach-Zehnder interferometer.
Service differentiation in real-time main memory databases (2003)

The demand for real-time database services has been increasing. Examples include sensor data fusion, stock trading, decision support, Web information services, and data-intensive smart spaces. In these systems, it is essential to execute transactions in time using fresh (temporally consistent) data. Due to the high service demand, many transactions may miss their deadlines regardless of their importance. To address the problem, we present a service differentiation architecture for real-time databases. Transactions are classified into several service classes based on their importance. Under conditions of overload, different degrees of deadline miss ratio guarantees are provided among the service classes according to their importance. A certain data freshness guarantee is also provided for the data accessed by timely transactions which finish within their deadlines. Feedback control is applied to support the miss ratio and freshness guarantees. In a simulation study, our service differentiation approach shows a significant performance improvement compared to the baseline approaches. The specified miss ratio and freshness are supported even in the presence of unpredictable workloads and data access patterns.
Optical design and roll‐to‐roll fabrication process of microstructure film for wide viewing LCDs (2014)

Abstract We have developed a new microstructure film for wide viewing liquid crystal displays (LCDs). By attaching it to the surface of a conventional LCD, the viewing angle characteristics of LCD has drastically improved without causing a blur of the frontal image and a decrease in the contrast ratio under bright ambient light conditions. This film can be applied to various LC modes including twisted nematic and multidomain vertical alignment by changing its internal micrometer‐size 3D structure. Further, this film can be mass‐produced efficiently by self alignment roll‐to‐roll process.
Sequencing XML data and query twigs for fast pattern matching (2006)

We propose a new way of indexing XML documents and processing twig patterns in an XML database. Every XML document in the database can be transformed into a sequence of labels by prüfer's method that constructs a one-to-one correspondence between trees and sequences. During query processing, a twig pattern is also transformed into its Prüfer sequence. By performing subsequence matching on the set of sequences in the database and performing a series of refinement phases that we have developed, we can find all the occurrences of a twig pattern in the database. Our approach allows holistic processing of a twig pattern without breaking the twig into root-to-leaf paths and processing these paths individually. Furthermore, we show in the article that all correct answers are found without any false dismissals or false alarms. Experimental results demonstrate the performance benefits of our proposed techniques.
A new IC with level-crossing ADC readout architecture for PET detector signals (2012)

A technique often used in Positron Emission Tomography (PET) systems to readout pulse signals from detectors is to use a free-running ADC to digitize the pulse waveform and then use software to determine the time and energy of the pulse. The advantage of this technique over analog-based methods is the possibility of obtaining superior time resolution with software-based time discrimination algorithms and the flexibility of working with digitized values. Unfortunately, the digitized pulse waveform output from a free-running ADC is an inefficient representation of the signal. As illustrated in the paper, the rising edge, where we desire fine sampling for arrival time determination, ends up being sampled coarsely. The falling edge, which is only used for energy determination, can be coarsely sampled, but we fine sample it instead, so this solution is not cost or power optimal. The rest of this paper describes a chip which samples at user-defined voltage levels to overcome these issues.
Ode to Karl Marx (1998)

learnt to operate. So the machine it once connected to just accelerates & each new rap dance video's a perfect image of this, bodies going faster and faster, still dancing on the spot. At the moment tho' this set up works for me, being paid to sit and write & smoke, thumbing through Adorno like New Idea on a cold working day in Ballarat, where adult unemployment is 22% & all your grand schemata of intricate cause and effect work out like this: take a muscle car & wire its accelerator to the floor, take out the brakes, the gears the steering wheel & let it rip. The dumbest tattooed hoon ?mortal diamond hanging around the Mall? knows what happens next. It's fun unless you're strapped inside the car. I'm not, but the dummies they use for testing are.
7‐T <sup>1</sup>H MRS with adiabatic refocusing at short TE using radiofrequency focusing with a dual‐channel volume transmit coil (2011)

In vivo MRS of the human brain at ultrahigh field allows for the identification of a large number of metabolites at higher spatial resolutions than currently possible in clinical practice. However, the in vivo localization of single-voxel spectroscopy has been shown to be challenging at ultrahigh field because of the low bandwidth of refocusing radiofrequency (RF) pulses. Thus far, the proposed methods for localized MRS at 7 T suffer from long TE, inherent signal loss and/or a large chemical shift displacement artifact that causes a spatial displacement between resonances, and results in a decreased efficiency in editing sequences. In this work, we show that, by driving a standard volume coil with two RF amplifiers, focusing the B 1+ field in a certain location and using high-bandwidth adiabatic refocusing pulses, a semi-LASER (semi-localized by adiabatic selective refocusing) localization is feasible at short TE in the human brain with full signal acquisition and a low chemical shift displacement artifact at 7 T.
Comparison of Conventional and Catalytic in Situ Combustion Processes for Oil Recovery (2008)

Laboratory in situ combustion experiments were performed to test the concept of using in situ combustion to catalytically upgrade a medium-heavy Clair crude oil (19.8° API), using a low-pressure combustion cell. Tests were performed for both noncatalytic and catalytic procedures and for both dry and wet forward combustion runs. The results showed that the presence of catalyst promotes the combustion reactions and the resultant oil was upgraded by up to 11 points. High oil recoveries were achieved for all runs and ranged from ∼53 to 74% original oil-in-place. The highest oil recovery was achieved during wet noncatalytic tests, while the lowest was achieved during the dry catalytic tests.
[Hormonal control of the expression of alpha fetoprotein in newborn rats. Evidence for a selective action of glucocorticoids on gene transcription]. (1983)

Administration of glucocorticoid hormones to the newborn rat results in a rapid decrease in the synthesis of alpha-fetoprotein (AFP) by the liver. The molecular basis of this hormonal action was investigated by examining the steady-state levels of AFP mRNA and albumin mRNA sequences in polysomal and total RNA preparations isolated from dexamethasone-treated and control animals. Following dexamethasone treatment the number of polysomal and total mRNA sequences hybridizable to specific (32P) cDNA probes was drastically decreased for AFP while it was unchanged for albumin. These data indicate that glucocorticoids exert a selective action on AFP mRNA levels and suggest that dexamethasone operate at the transcriptional level.
Antibody Response after Vaccination with Antigen-Pulsed Dendritic Cells (2004)

Dendritic cells (DCs) are the most potent antigen-presenting cells of the immune system capable of initiating immune responses to antigens. It is also well documented that cancer patients often experience anergy against tumor antigens. In this study we selected the best protocol for inducing the production of antibodies against the HER2 oncoprotein using DCs to overcome anergy. Murine DCs were pulsed in vitro, using different protocols, with recombinant HER2 fused to a human Fc (in order to improve DC antigen uptake) and were used to vaccinate mice. The obtained results indicate that antigen-pulsed DCs can induce an antibody response and that adding CpG after antigen pulsing greatly increases anti-HER2 antibody production.
Multimode laser with an injected signal: Steady-state and linear stability analysis (1985)

We discuss the steady-state and the linearized response of a multimode laser with an injected signal. The steady-state analysis is carried out for arbitrary values of the laser gain and resonator parameters, while the linearized stability calculation is limited to parameter ranges where the mean-field assumption is a reasonable approximation. For suitably large values of the polarization and population decay rates, we review the problem of the adiabatic elimination of the atomic variables and demonstrate explicitly the existence of possible pitfalls and how to avoid them.
Absolute and arbitrary orientation of single-molecule shapes (2021)

DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. Integration of such nanoscale devices with microfabricated connectors and circuits is challenging: Large numbers of freely diffusing devices must be fixed at desired locations with desired alignment. We present a DNA origami molecule whose energy landscape on lithographic binding sites has a unique maximum. This property enabled device alignment within 3.2° on silica surfaces. Orientation was absolute (all degrees of freedom were specified) and arbitrary (the orientation of every molecule was independently specified). The use of orientation to optimize device performance was shown by aligning fluorescent emission dipoles within microfabricated optical cavities. Large-scale integration was demonstrated with an array of 3456 DNA origami with 12 distinct orientations that indicated the polarization of excitation light.
New Bioabsorbable Polylactide Ureteral Stent in the Treatment of Ureteral Lesions: An Experimental Study (1999)

The double-helical apical stent design offers some advantages over a double-J design. The risk of pressure-induced kidney damage is lowered, because there is no direct connection between the bladder and renal pelvis, and the risk of upper urinary tract infections is reduced. The biodegradation of the device necessitates the removal of the stent. These preliminary results suggest that a biodegradable SR-PLA 96 stent with more effective expansion capacity can be used for stenting after a ureteral repair.
Benign prostatic stromal cells are regulated by basic fibroblast growth factor and transforming growth factor-β1 (1996)

The current study was undertaken, using cultures of prostatic epithelial and stromal cells, to determine the functional interactions between androgens, basic fibroblast growth factor (FGF2) and transforming growth factor-beta 1 (TGF beta 1) and their importance in maintaining stromal homeostasis. Treatment of stromal cells with TGF beta 1 significantly increased intracellular FGF2 and FGF2 sequestered to the extracellular matrix. FGF2 was also detected in stromal conditioned medium (SCM), but at levels 70-fold less than found in cell lysates. TGF beta 1 (0.1 ng/ml) treatment caused an initial increase of 86% in secreted FGF2 levels, but high concentrations of TGF beta 1 (5 ng/ml) decreased FGF2 levels by 38%, relative to the untreated control. Further studies showed that epithelial conditioned medium (ECM), androgen-treated, stromal conditioned medium (ASCM), but not SCM were mitogenic for stromal cells. Both ECM and ASCM caused a threefold increase in DNA synthesis. FGF2 may be the mediator of these interactions, since the mitogenic effect of both ECM and ASCM was significantly reduced by the addition of anti-FGF2 neutralising antibody. We hypothesise that the lack of response of stromal cells to SCM is due to TGF beta 1 blocking the mitogenic effect of FGF2. Thus down-regulation of TGF beta 1 synthesis, by androgens, results in stromal proliferation by ASCM.
Eliminating popping artifacts in sheet buffer-based splatting (1998)

Splatting is a fast volume rendering algorithm which achieves its speed by projecting voxels in the form of pre-integrated interpolation kernels, or splats. Presently, two main variants of the splatting algorithm exist: (i) the original method, in which all splats are composited back-to-front, and (ii) the sheet-buffer method, in which the splats are added in cache-sheets, aligned with the volume face most parallel to the image plane, which are subsequently composited back-to-front. The former method is prone to cause bleeding artifacts from hidden objects, while the latter method reduces bleeding, but causes very visible color popping artifacts when the orientation of the compositing sheets changes suddenly as the image screen becomes more parallel to another volume face. We present a new variant of the splatting algorithm in which the compositing sheets are always parallel to the image plane, eliminating the condition for popping, while maintaining the insensitivity to color bleeding. This enables pleasing animated viewing of volumetric objects without temporal color and lighting discontinuities. The method uses a hierarchy of partial splats and employs an efficient list-based volume traversal scheme for fast splat access. It also offers more accuracy for perspective splatting as the decomposition of the individual splats facilitates a better approximation to the diverging nature of the rays that traverse the splatting kernels.
Isolation and characterization of<i>Lactobacillus delbrueckii</i>ssp.<i>bulgaricus</i>and<i>Streptococcus thermophilus</i>from plants in Bulgaria (2007)

One of the traditional ways of preparation of yogurt starter in Bulgaria is placing a branch of a particular plant species into boiled sheep's milk maintained at about 45 degrees C, which is further incubated until a dense coagulum is obtained. To investigate the possible origin of the yogurt starter bacteria, Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) and Streptococcus thermophilus (S. thermophilus), the traditional way of yogurt-starter preparation was followed. Hundreds of plant samples were collected from four regions in Bulgaria and incubated in sterile skim milk. The two target bacteria at low frequencies from the plant samples collected were successfully isolated. Phenotypic and genotypic characteristics of these bacterial isolates revealed that they were identified as L. bulgaricus and S. thermophilus. Twenty isolates of L. bulgaricus and S. thermophilus, respectively, were selected from the isolated strains and further characterized with regard to their performance in yogurt production. Organoleptic and physical properties of yogurt prepared using the isolated strains from plants were not significantly different from those prepared using commercial yogurt-starter strains. It was therefore suggested that L. bulgaricus and S. thermophilus strains widely used for commercial yogurt production could have originated from plants in Bulgaria. To our knowledge, this is the first report on the isolation and characterization of L. bulgaricus and S. thermophilus strains from plants.
A mechanism for bitter taste sensibility in peptides. (1988)

To estimate the steric distance between the bitter taste determinant sites in peptides, some cyclic dipeptides, amino acid anilides, amino acid cyclohexylamides, and benzoyl amino acids were synthesized and their tastes were evaluated. The diketopiperazine ring of cyclic dipeptides acted as a bitter taste determinant site due to its hydrophobicity. The steric distance between 2 sites was estimated as 4.1 Å from the molecule models of cyclic dipeptides composed of typical amino acids in the bitter peptides. Due to the hypothesis of two bitter taste determinant sites, which bind with the bitter taste receptor via a "binding unit" and a "stimulating unit, " a mechanism for the bitterness in peptides was postulated.