gebhart/patrepeval huggingface dataset:
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques (2006)

Fields such as genomics and systems biology are built on the synergism between computational and experimental techniques. This type of synergism is especially important in accomplishing goals like identifying all functional transcription factor binding sites in vertebrate genomes. Precise detection of these elements is a prerequisite to deciphering the complex regulatory networks that direct tissue specific and lineage specific patterns of gene expression. This review summarizes approaches for in silico, in vitro, and in vivo identification of transcription factor binding sites. A variety of techniques useful for localized- and high-throughput analyses are discussed here, with emphasis on aspects of data generation and verification.
Measles Antibody in Vaccinated Human Immunodeficiency Virus Type 1-infected Children (1996)

These results support current recommendations to vaccinate HIV-infected children against measles. The proportion of children with detectable measles antibody among vaccinated HIV-infected children is considerably lower than in vaccinated healthy children. HIV-infected children may respond better to measles vaccine when it is administered before the first birthday. From our limited data it appears that reimmunization of previously vaccinated HIV-infected children with moderate to severe immunosuppression does not result in an antibody recall response.
Concentration of Ammonia Across Cell Membranes of Mixed Rumen Bacteria (1987)

When mixed ruminal bacteria were provided with growth rate limiting amounts of mixed carbohydrates, more than 50 mg ammonia/L were required for maximal protein synthesis. Microbial protein synthesis declined when ammonia concentration was less than 50 mg/L and unfermented carbohydrates increased. Ammonia starvation also decreased growth efficiency. Intracellular ammonia increased as a linear function of extracellular ammonia, but the intracellular concentration was always at least 160 mg/L higher than the extracellular concentration. Maximal protein synthesis was not observed until intracellular ammonia was greater than 220 mg/L. The concentration gradient of ammonia across cell membranes ranged from 15-fold to 1.8-fold and indicated that some of the ruminal bacteria may have active transport mechanisms for ammonia. These concentration gradients were, however, far less than those reported for bacteria from other habitats. The ruminal bacteria left more than 12 mg ammonia/L when carbohydrates were still available, and this observation was consistent with the assumption that active ammonium transport was not readily or maximally induced.
ChemInform Abstract: STUDIES ON TRANSITION METAL‐PEPTIDE COMPLEXES. PART 8. PARENT AND MIXED‐LIGAND COMPLEXES OF HISTIDINE‐CONTAINING DIPEPTIDES (1983)

Abstract Spektrophotometrische, pH‐metri ‐ sche und teilweise 13 C‐NMR‐spektroskopische Untersuchungen der Komplexe von Co(II), Ni(Il) und Zn(II) mit Gly‐L‐His, L‐His‐Gly und L‐Camosin zeigen die unterschiedliche Art der Koordination und die dadurch bedingte Bildung verschiedener Gemischt‐ligand‐Komplexe mit Gly, Gly‐Gly, His und 2,2′‐Bipyridyl als zweitem Liganden.
Template-based software for accurate MEMS characterization (2003)

One of the primary challenges in MEMS metrology is the large variety of shapes, lateral feature sizes, and vertical steps on MEMS devices. This paper describes a software approach by which ideal surface templates are generated for each MEMS device from the design files or prior measurements. These templates may contain multiple sub-regions, or data islands, each of which is generally characterized in a different manner. Surface measurements from a white-light interference microscope are matched with the ideal MEMS template using a variety of techniques and threshold criteria. The template-based technique is tolerant of errors both rotation and translation, allowing accurate characterization of each data island and their relative positions. This paper will explore the concepts used to generate templates, align actual data with the original template, and sources of error and robustness of each technique on several datasets. The effect of measurement and positional errors on both the overall match and on the sub-region analyses will be explored for characterization of datasets.
Osteoma in Ethmoid Sinus : a case report (2005)

We present a case of ethmoid sinus osteoma. A 66-year-old woman was referred with an asymptomatic mass of the nose. Radiographs showed a rounded homogeneous radiodense lesion in the right ethmoid sinus, suggesting an osseous lesion. Computed tomography demonstrated a multi-lobulated high density lesion (2.0×1.5 cm in size) occupying the ethmoid sinus. The lesion was attached to the nasal septum and extended to the posterior orbit. Total excision of the mass lesion was performed under general anesthesia via the oral vestibular approach with an operating microscope. Histopathological examination revealed eburneous-type osteoma. The postoperative course was uneventful.
The lymphoproliferative disease of granular lymphocytes. A heterogeneous disorder ranging from indolent to aggressive conditions (1987)

A multiparameter analysis, which included the evaluation of clinical features, cell morphology, karyotype, phenotypic and functional immunologic findings, and T-cell receptor beta-chain configuration was performed on 34 patients with lymphoproliferative disease of granular lymphocytes (LDGL). The two-fold aim of the study was to identify the most useful tools that would more accurately characterize these patients and to deal with the problem of classifying these lymphoproliferative disorders. The data presented in this article suggest that a single parameter may not be sufficient to define the nature of the proliferating cells or to predict the clinical course of the disease and prognosis for the patient. The use of a multiparameter approach, however, may reach this goal, thus providing important prognostic and therapeutic information. Our study supports the concept that lymphoproliferative disease of granular lymphocytes is a heterogeneous disorder that ranges from indolent and possibly reactive conditions to the manifestation of aggressive malignancies.
Reduction risk: criteria for choosing an appropriate design approach (1997)

The effects of the switchgear arc are strongly depending on three main factors: the fault current level; the available free space surrounding the switchgear; and the construction of the switchgear. If the fault currents are small enough, as in the case of overhead lines, the arc energy can be handled by the housing of the switch and the arc can be kept inside the housing. Also the free space in these applications is not limited because the switch is normally located about 5 to 10 m above the operator. In this case, it is enough, if hot gases are not directly downwards in direction. In this paper, the switchgear short-circuit currents are shown depending on the distance from the feeding transformer with different power line cross-section and different line voltages.
Diffusive Shock Acceleration: the Fermi Mechanism (1997)

The mechanism of diffusive Fermi acceleration at collisionless plasma shock waves is widely invoked in astrophysics to explain the appearance of non-thermal particle populations in a variety of environments, including sites of cosmic ray production, and is observed to operate at several sites in the heliosphere. This review outlines the principal results from the theory of diffusive shock acceleration, focusing first on how it produces power-law distributions in test-particle regimes, where the shock dynamics are dominated by the thermal populations that provide the seed particles for the acceleration process. Then the importance of non-linear modifications to the shock hydrodynamics by the accelerated particles is addressed, emphasizing how these subsequently influence non-thermal spectral formation.
Glyoxal als Synthon, III Eine einfache Synthese von Aminopyrrolen und Dihydropyrrolo[3,2‐<i>b</i>]pyrrolen (1989)

Abstract Die aus Glyoxaldiiminen 1 mit Alkalimetall und Dichlorsilanen leicht zugänglichen Diazasilacyclopentene 2 ergeben bei der Alkoholyse entweder 3‐aminosubstituierte Pyrrole 4 oder, mit wenig Alkohol, die N ‐substituierten Dihydropyrrolo[3,2‐ b ]pyrrole 5 . Auch bei der katalytischen Reduktion von 1 in Ethanol an wenig Palladium/Kohle mit Wasserstoff können 4 und 5 sowie ein 3,4‐Diaminopyrrol 7 , bei mehr Katalysator auch das Diaminoethan 6 als Hauptprodukt, erhalten werden. Am N , N ′‐Di‐ tert ‐butyl‐Derivat 5a wurde eine Einkristall‐Röntgenstrukturuntersuchung durchgeführt, die den erwarteten inversionssymmetrischen Bau belegt.
Treatment of recurrent brain stem gliomas and other central nervous system tumors with 5-fluorouracil, CCNU, hydroxyurea, and 6-mercaptopurine (1988)

Twenty-one patients with recurrent malignant central nervous system gliomas were treated with a combination of 5-fluorouracil, CCNU, hydroxyurea, and 6-mercaptopurine. Thirteen patients had brain stem gliomas, 3 patients had spinal cord gliomas, 3 patients had thalamic gliomas, and 2 patients had cerebellar astrocytomas. All patients had received radiation therapy, and 4 brain stem patients had also been treated with chemotherapy. Sixteen patients (76%) responded to treatment with either stabilization of disease or improvement. Nine of the 13 patients with brain stem gliomas (71%) had response or stabilization of disease. The median time to tumor progression (TTP) for the brain stem patients who responded or had stabilization of disease was 25 weeks. The median survival from recurrence for the brain stem glioma patients was 27 weeks. Patients with cerebellar, thalamic, and spinal cord tumors did very well, with an 87% response or stabilization of disease and a median TTP of 122 weeks. (Neurosurgery 22:691-693, 1988)
Solid-Phase Cobalamin Assay Using Cobalamin-Binding Protein from Dog Stomach (1975)

Ninety-five samples from 42 animals were studied for the presence of a cobalamin-binding protein fulfilling the criteria of occurring in major quantities and being homogeneous regarding size and binding constant. The binder from dog stomach thus found was made insoluble by coupling to bromoacetyl-cellulose and used for solid-phase assay of serum cobalamins. Equilibrium between free and bound radioactive cobalamin was unaffected by centrifugation of the samples, thus allowing the straightforward use of the Scatchard equation for calculation of results. The precision of the method was 0.05 to 0.10 at concentrations above 100 pmolX1(-1), the sensitivity was about 30 pmolX1(-1), the accuracy could be based on aqueous solutions of cyanocobalamin, and the reference interval was as for the Lactobacillus leichmannii method, i.e. 160-480 pmolX1(-1).
Reasoning About Parallel Architectures (1992)

Seeing architecture failures history basics the model the rule of computation the rules of program order the rules of atomicity the rules of synchronisation the rules of intra-statement order the structure of architectures out of order read operations write synchronised is write atomic ring-shaped systems a model of a shared memory multiprocessor future work.
OPC verification on cell level using fully rigorous mask topography simulation (2007)

Starting with the 45nm node, the minimum feature size on the mask has reached sub-wavelength dimension. In this regime the electromagnetic field induced in the mask is significantly impacted by the mask topography. These so called mask topography effects play an important role in the image formation process and need to be compensated for in the optical proximity correction (OPC) model. Looking ahead to the 32nm process node, mask topography effects will become even more pronounced. So, including these effects into the OPC model has become a must for advanced process nodes. Modern OPC engines start to apply electromagnetic field (EMF) compensation techniques to take these effects into account. Of course, due to the severe run time constrains for OPC models most EMF aware OPC models need to rely on approximate methods. A reliable OPC verification process needs to include a fully rigorous treatment of the mask topography effects with taking into account oblique light incidence and polarization of light. In this paper we investigate the impact of rigorous mask topography simulation on the reliability of OPC verification and determine the influence of EMF aware OPC models on OPC quality. We use lithography simulations on OPCed layout cells where we apply a fully rigorous parallelized EMF solver to the mask model. Two different OPC models are used in this study; one based on the conventional approach and another one using EMF compensation techniques. The results of the rigorous lithography simulations are used to verify both OPC models. The impact of the EMF simulation on OPC verification quality is illustrated by direct comparison with the corresponding Kirchhoff simulations for both OPC models.
Worst Case Analysis of DRAM Latency in Multi-requestor Systems (2013)

As multi-core systems are becoming more popular in real-time embedded systems, strict timing requirements for accessing shared resources must be met. In particular, a detailed latency analysis for Double Data Rate Dynamic RAM (DDR DRAM) is highly desirable. Several researchers have proposed predictable memory controllers to provide guaranteed memory access latency. However, the performance of such controllers sharply decreases as DDR devices become faster and the width of memory buses is increased. In this paper, we present a novel, composable worst case analysis for DDR DRAM that provides improved latency bounds compared to existing works by explicitly modeling the DRAM state. In particular, our approach scales better with increasing number of requestors and memory speed. Benchmark evaluations show up to 62% improvement in worst case task execution time compared to a competing predictable memory controller for a system with 8 requestors.
La Brecha entre EEUU y la “Vieja Europa” (2003)

El distanciamiento que hoy observamos entre las actitudes de los Estados Unidos (EEUU) y Francia frente a temas como el uso de la fuerza y el derecho internacional, tiene un punto algido en el debate que giro en torno a la redaccion y aprobacion de la Resolucion 1441 del Consejo de Seguridad de las Naciones Unidas (CSNU) sobre Irak. A la luz de esta brecha entre los EEUU y la Francia consideramos conveniente revisar este proceso a traves de los instrumentos analiticos ofrecidos por dos aproximaciones teoricas en Relaciones Internacionales: el neorrealismo y en el neoliberalismo. Los objetivos de este trabajo son: (1) Exponer los hechos que definieron una y otra posicion asi como el contenido final de dicha resolucion, (2) analizarlos desde la perspectiva teorica del neo-realismo y; (3) del neo-liberalismo.
From Theory to Practice (2019)

Modern video streaming uses adaptive bitrate (ABR) algorithms that run inside video players and continually adjust the quality (i.e., bitrate) of the video segments that are downloaded and rendered to the user. To maximize the quality-of-experience (QoE) of the user, ABR algorithms must stream at a high bitrate with low rebuffering and low bitrate oscillations. Further, a good ABR algorithm is responsive to user and network events and can be used in demanding scenarios such as low-latency live streaming. Recent research papers provide an abundance of ABR algorithms but fall short on many of the above real-world requirements. We develop Sabre, an open-source publicly available simulation tool that enables fast and accurate simulation of adaptive streaming environments. We empirically validated Sabre to show that it accurately simulates real-world environments. We used Sabre to design and evaluate BOLA-E and DYNAMIC, two novel ABR algorithms. We also developed a FAST SWITCHING algorithm that can replace segments that have already been downloaded with higher-bitrate (thus, higher-quality) segments. The new algorithms provide higher QoE to the user in terms of higher bitrate, fewer rebuffers, and lesser bitrate oscillations. In addition, these algorithms react faster to user events such as startup and seek, and they respond more quickly to network events such as improvements in throughput. Further, they perform very well for live streams that require low latency, a challenging scenario for ABR algorithms. Overall, our algorithms offer superior video QoE and responsiveness for real-life adaptive video streaming, in comparison to the state-of-the-art. Importantly, all three algorithms presented in this article are now part of the official DASH reference player dash.js and are being used by video providers in production environments. While our evaluation and implementation are focused on the DASH environment, our algorithms are equally applicable to other adaptive streaming formats such as Apple HLS.
Thermal-Visible Video Fusion for Moving Target Tracking and Pedestrian Classification (2007)

The paper presents a fusion-tracker and pedestrian classifier for color and thermal cameras. The tracker builds a background model as a multi-modal distribution of colors and temperatures. It is constructed as a particle filter that makes a number of informed reversible transformations to sample the model probability space in order to maximize posterior probability of the scene model. Observation likelihoods of moving objects account their 3D locations with respect to the camera and occlusions by other tracked objects as well as static obstacles. After capturing the coordinates and dimensions of moving objects we apply a pedestrian classifier based on periodic gait analysis. To separate humans from other moving objects, such as cars, we detect, in human gait, a symmetrical double helical pattern, that can then be analyzed using the Frieze Group theory. The results of tracking on color and thermal sequences demonstrate that our algorithm is robust to illumination noise and performs well in the outdoor environments.
The mRNAs of Prekallikrein, Factors XI and XII, and Kininogen, Components of the Contact Phase Cascade Are Differentially Expressed in Multiple Non-hepatic Human Tissues (2001)

Recently RT-PCR studies had demonstrated the expression of plasma prekallikrein (PPK) mRNA in extrahepatic tissues. The questions arose whether that is illegitimate or regular expression, and whether the mRNAs of blood coagulation factors XI and XII, and high molecular weight kininogen, components of the contact activation cascade of blood coagulation are also expressed in non-hepatic tissues. These questions were addressed in the present study by employing quantitative RT-PCR. The relative mRNA levels of the respective proteins determined in 16 human tissues indicate legitimate extrahepatic transcription of at least three of the genes. Transcription of all genes was highest in the liver, but only PPK mRNA was detected in all 16 tissues, especially high levels in pancreas, kidney, testis, spleen and prostate. We conclude from these results that PPK is synthesized in significant amounts in non-hepatic tissues and that this locally synthesized PPK may have special local functions.
Inflammatory response to chlorhexidine, minocycline HCl and doxycycline HCl in an in vivo mouse model (2008)

Antibacterial agents applied locally have the ability to induce an inflammatory response. They also modify the inflammatory response to P. gingivalis independent of their antimicrobial effect. CHX and doxycycline HCl appear to have the most marked anti-inflammatory effect.
Stereospecific, Enantioselective Allylation of α‐Hydrazono Esters by Using Allyltrichlorosilanes with BINAP Dioxides as Neutral‐Coordinate Organocatalysts (2004)

Excellent diastereo- and enantioselectivities were obtained in the title reaction. (E)-Crotylsilanes gave syn adducts, whereas anti adducts were obtained from (Z)-crotylsilanes (see scheme). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z461312_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Assisted History Matching of a 1.4-Million-Cell Simulation Model for Judy Creek ‘A’ Pool Waterflood/HCMF Using a Streamline-Based Workflow (2007)

Abstract We illustrate what is practical for history matching of a large and complex field like Judy Creek. Due to the size of the geomodel, the limited time available, the large amount of historical data, and the 300+ wells, manual history matching methods were ruled out. Instead, we applied a streamline-based method to update the model based on well rate mismatches and identification of streamline bundles in 3-D space that contributed to local mismatches. Knowing the bundles and the magnitude of the mismatches, we computed cell-level multipliers for any gridblock and timestep and automatically update the geomodel. This eliminated tedious manual updates as in the conventional "box multiplier" approach. However, due to the nonlinear nature of history matching, our method is not automatic but assisted, requiring engineering judgment to identify wells to focus on for matching and which timesteps to use. Approximately 60+ flow simulations and geomodel updates were required to improved the well-level match within the time-frame allowed. Results showed that while our focus was improving the history match for the waterflood period, the field-level hydrocarbon miscible flood match was also improved. Furthermore, starting with a good geologic model led to changes that were within geological realism, even though we did not include geological modeling within each model update. Lastly, conventional history matching changes such as adjustment to relative permeabilities, solvent PVT mixing parameters, and well perforations, were also required.
Lithography yield enhancement through optical rule checking (2005)

Use of simulation-based printing verification prior to mask tapeout has become standard practice for mask layers printed with low-k1 lithography processes. At 90nm and above, this methodology has proven beneficial and sufficient for guaranteeing a usable mask. However, it is anticipated that at 65nm and below, a simulation at a single point within the process window may fail to capture all important marginal areas of a mask prior to tapeout. Modern lithography simulation tools are proven capable of accurately predicting printing behavior through process window. Unfortunately, due to long run times, use of such tools is restricted to small simulation areas. Recent developments in vectorial thin-film OPC models have enabled full process window prediction on large product die. Although such models are extremely fast compared to conventional lithography simulation tools, the prospect of simulating a full chip at multiple dose and focus points is quite daunting. In an effort to reduce the expected longer run times when simulating full chips at multiple focus and dose conditions, we have developed two flows which reduce the total run time enormously. These so-called pre-targeting flows are explained, and the limitations and future prospects of the flows are described.