gebhart/patrepeval huggingface dataset:
Fully Integrated Approach Using Temperature Measurements to Describe Complex Reservoirs: Case Study from Saudi Arabia (2013)

Abstract Reservoir heterogeneity and inter-reservoir communication due to fracturing pose major challenges for our industry in terms of reservoir characterization and fluid flow modeling. Improved understanding and representation of their role in static and dynamic models is becoming a pivotal component for effective field management. Normally, multiple sources of both static and dynamic information are integrated to generate models used to simulate reservoir performance in order to identify optimal practices for efficient production and recovery. This paper presents a thorough reservoir study focused on the investigation of the use of temperature measurements to inform on fluid flow within and between reservoirs. The study addresses mainly the communication that exists in the reservoir beyond the well-bore, attributed to fracture corridors and faults. The interpretation of temperature measurements are integrated with other sources of dynamic and static information such as open-hole logs, production profiles, fluid losses, and pressure transient analysis. The study area covers a portion of an oil field that has been under peripheral water flooding for more than 30 years, producing mainly from the upper of the two reservoir units. As expected, the injected cold water imposes a significant variation in temperature profile across the reservoir which helps to describe the flood performance and understand the underlying geology. Additionally, we found that the rate of change of temperature with respect to time over the entire area shows that increasing temperatures are correlated with locations showing high structural relief. Our existing mapping shows these areas as being more densely fractured, with high fluid flow capacity. The coincidence of these factors with the temperature anomalies we observed strongly suggests that the faults and fractures in these areas may be responsible for mass and heat transfers between the two reservoirs. The outcomes of this study are used to optimize development and production plans such as balancing the off-take between high-structure and down-dip areas to prevent undesired water flood advances. They are also fully integrated with other sources of information to construct geological and flow simulation models in order to assess sweep performance and recovery estimation.
MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling (2007)

The epidermal growth factor receptor (EGFR) kinase inhibitors gefitinib and erlotinib are effective treatments for lung cancers with EGFR activating mutations, but these tumors invariably develop drug resistance. Here, we describe a gefitinib-sensitive lung cancer cell line that developed resistance to gefitinib as a result of focal amplification of the MET proto-oncogene. inhibition of MET signaling in these cells restored their sensitivity to gefitinib. MET amplification was detected in 4 of 18 (22%) lung cancer specimens that had developed resistance to gefitinib or erlotinib. We find that amplification of MET causes gefitinib resistance by driving ERBB3 (HER3)-dependent activation of PI3K, a pathway thought to be specific to EGFR/ERBB family receptors. Thus, we propose that MET amplification may promote drug resistance in other ERBB-driven cancers as well.
Hypertrophic Scar Fibroblasts Have Increased Connective Tissue Growth Factor Expression after Transforming Growth Factor-?? Stimulation (2005)

Hypertrophic scar fibroblasts have both intrinsic up-regulation of CTGF transcription and an exaggerated capacity for CTGF transcription in response to TGF-beta stimulation. These data suggest that blockage of CTGF activity may reduce pathologic scar formation.
Regulation of Enzymes Involved in Methionine Biosynthesis in Corynebacterium glutamicum (2004)

The regulatory mechanism of methionine biosynthesis in Corynebacterium glutamicum was analyzed at the protein and gene expression level. O-Acetylhomoserine sulfhydraylase (encoded by metY) was inhibited by 10 mM methionine to a residual activity of 10% level, whereas no such inhibition was found with cystathionine γ-synthase (encoded by metB) and cystathionine β-lyase (encoded by metC). The enzymatic activity of homoserine acetyltransferase (encoded by metX) was repressed to a residual activity of 25% level by 10 mM methionine which was added to the growth medium. Cystathionine γ-synthase and cystathionine β-lyase were also repressed by 10 mM methionine, but only to a residual activity of 50-70% level. O-Acetylhomoserine sulfhydrylase was very sensitive to repression by 10 mM methionine, showing residual activity of 13%. In addition, homoserine acetyltransferase was also repressed by 10 mM cysteine to 50% of its original activity. No repression of the enzymes by S-adenosyl methionine was observed. The pattern of repression by methionine indicated that the metB and aecD genes might be regulated by a common mechanism, while the metA and metY genes are differently regulated.
Born Again Neural Networks (2018)

Knowledge Distillation (KD) consists of transferring â€œknowledgeâ€ from one machine learning model (the teacher) to another (the student). Commonly, the teacher is a high-capacity model with formidable performance, while the student is more compact. By transferring knowledge, one hopes to benefit from the studentâ€™s compactness, without sacrificing too much performance. We study KD from a new perspective: rather than compressing models, we train students parameterized identically to their teachers. Surprisingly, these Born-Again Networks (BANs), outperform their teachers significantly, both on computer vision and language modeling tasks. Our experiments with BANs based on DenseNets demonstrate state-of-the-art performance on the CIFAR-10 (3.5%) and CIFAR-100 (15.5%) datasets, by validation error. Additional experiments explore two distillation objectives: (i) Confidence-Weighted by Teacher Max (CWTM) and (ii) Dark Knowledge with Permuted Predictions (DKPP). Both methods elucidate the essential components of KD, demonstrating the effect of the teacher outputs on both predicted and non-predicted classes.
Dissection of the components for PIP 2 activation and thermosensation in TRP channels (2007)

Phosphatidylinositol 4,5-bisphosphate (PIP2) plays a central role in the activation of several transient receptor potential (TRP) channels. The role of PIP2 on temperature gating of thermoTRP channels has not been explored in detail, and the process of temperature activation is largely unexplained. In this work, we have exchanged different segments of the C-terminal region between cold-sensitive (TRPM8) and heat-sensitive (TRPV1) channels, trying to understand the role of the segment in PIP2 and temperature activation. A chimera in which the proximal part of the C-terminal of TRPV1 replaces an equivalent section of TRPM8 C-terminal is activated by PIP2 and confers the phenotype of heat activation. PIP2, but not temperature sensitivity, disappears when positively charged residues contained in the exchanged region are neutralized. Shortening the exchanged segment to a length of 11 aa produces voltage-dependent and temperature-insensitive channels. Our findings suggest the existence of different activation domains for temperature, PIP2, and voltage. We provide an interpretation for channel-PIP2 interaction using a full-atom molecular model of TRPV1 and PIP2 docking analysis.
APPLICATION OF SUBSYSTEMS CHANGE RANKING METHODOLOGY IN AIRCRAFT REDESIGN PROCESS (2011)

Redesigning an aircraft is hardly a straightforward task. Due to its high susceptibility to change effects propagation, it becomes very important to select the right initiating change components to minimize redesign development risks. With realization that there are often several different ways to redesign an existing aircraft for satisfying similar requirements, designers might require assistance in selecting suitable initiating change components in their redesign plan. A methodology that systematically ranks the subsystems of the chosen baseline design according to their estimated redesign risk is proposed here. It is strongly believed that making this information available to designers during the early redesign stages will help them to make a better redesign plan. KEY WORDS: subsystems ranking, aircraft redesign, redesign plan ABSTRAK: Reka semula sesebuah pesawat udara bukanlah satu tugas yang jelas dan mudah. Memandangkan ia mudah rentan terhadap perubahan rambatan, amatlah penting untuk memilih penukaran komponen yang sesuai pada peringkat awal untuk mengurangkan masalah pembangunan reka semula. Menyedari bahawa terdapat beberapa cara untuk mereka semula pesawat udara yang sedia ada, demi memperolehi keputusan keperluan yang serupa dan memberansangkan, pereka wajar mendapatkan bantuan dari segi penukaran komponen yang sesuai pada peringkat awal pembangunan reka semula yang menepati rangka pelan reka bentuk mereka. Metodologi yang sistematik meletakkan subsistem dasar reka bentuk yang dipilih, berdasarkan anggaran risiko reka bentuk semula dicadangkan di dalam kertas kerja ini. Adalah diyakini bahawa dengan memperolehi informasi ini di peringkat permulaan reka bentuk, ia dapat menolong pereka merangka pelan reka cipta yang lebih baik.
Conformational changes in the expression domain of the Escherichia coli thiM riboswitch (2007)

The thiM riboswitch contains an aptamer domain that adaptively binds the coenzyme thiamine pyrophosphate (TPP). The binding of TPP to the aptamer domain induces structural rearrangements that are relayed to a second domain, the so-called expression domain, thereby interfering with gene expression. The recently solved crystal structures of the aptamer domains of the thiM riboswitches in complex with TPP revealed how TPP stabilizes secondary and tertiary structures in the RNA ligand complex. To understand the global modes of reorganization between the two domains upon metabolite binding the structure of the entire riboswitch in presence and absence of TPP needs to be determined. Here we report the secondary structure of the entire thiM riboswitch from Escherichia coli in its TPP-free form and its transition into the TPP-bound variant, thereby depicting domains of the riboswitch that serve as communication links between the aptamer and the expression domain. Furthermore, structural probing provides an explanation for the lack of genetic control exerted by a riboswitch variant with mutations in the expression domain that still binds TPP.
Antenatal maternal serum screening for Down's syndrome: results of a demonstration project. (1992)

Antenatal maternal serum screening for Down's syndrome is effective in practice and can be readily integrated into routine antenatal care. It is cost effective and performs better than selection for amniocentesis on the basis of maternal age alone.
Epigenetic Resensitization to Platinum in Ovarian Cancer (2012)

Preclinical studies have shown that hypomethylating agents reverse platinum resistance in ovarian cancer. In this phase II clinical trial, based upon the results of our phase I dose defining study, we tested the clinical and biologic activity of low-dose decitabine administered before carboplatin in platinum-resistant ovarian cancer patients. Among 17 patients with heavily pretreated and platinum-resistant ovarian cancer, the regimen induced a 35% objective response rate (RR) and progression-free survival (PFS) of 10.2 months, with nine patients (53%) free of progression at 6 months. Global and gene-specific DNA demethylation was achieved in peripheral blood mononuclear cells and tumors. The number of demethylated genes was greater (P < 0.05) in tumor biopsies from patients with PFS more than 6 versus less than 6 months (311 vs. 244 genes). Pathways enriched at baseline in tumors from patients with PFS more than 6 months included cytokine-cytokine receptor interactions, drug transporters, and mitogen-activated protein kinase, toll-like receptor and Jak-STAT signaling pathways, whereas those enriched in demethylated genes after decitabine treatment included pathways involved in cancer, Wnt signaling, and apoptosis (P < 0.01). Demethylation of MLH1, RASSF1A, HOXA10, and HOXA11 in tumors positively correlated with PFS (P < 0.05). Together, the results of this study suggest that low-dose decitabine altered DNA methylation of genes and cancer pathways, restoring sensitivity to carboplatin in patients with heavily pretreated ovarian cancer and resulting in a high RR and prolonged PFS.
Dyes Adsorbed at Ag‐Colloids: Substitution of Fluorescence by Similarly Efficient Surface Fluorescence and Surface Raman Scattering (1984)

Abstract With the addition of Ag‐sol to extremely diluted rhodamine 6G solutions (ca. 10 −10 M/l) the prevalent fluorescence can be replaced by surface fluorescence and surface enhanced resonance Raman scattering (SERRS) of similar intensity, however only in presence of coadsorbed anions such as chloride. For strong bands the Raman cross sections are as high as 10 −19 cm 2 sr −1 molecule −1 . Referred to the extinction of the sol which is much larger than that of the dye solution, the mean quantum yield for the surface Raman scattering is estimated to 0.0004. In addition, SERRS consisting of a set of fundamental vibrations, overtones and combination modes and a broad continuum shows throughout the spectral range a significant, but identical polarisation ( I (sp): I (ss) = 0.55), whereas the solution as well as surface fluorescence is completely depolarised.
Interpixel capacitance in nondestructive focal plane arrays (2004)

Inter-pixel capacitive coupling can exist in a non-destructive detector array if the detector nodes change voltage as they integrate charge and the design of the device allows for an electric field to exist between adjacent collection nodes. Small amounts of inter-pixel capacitance can cause large errors in the measurement of poissonian noise versus signal, and all subsequently derived measurements such as nodal capacitance and quantum efficiency. Crosstalk and MTF can also be significantly influenced by interpixel capacitance. Two 1k by 1k Raytheon SB226-based hybridized silicon PIN arrays were tested for nodal capacitance and MTF. Initial results indicated unexpected and unexplainably large nodal capacitance, poor MTF, and odd edge spread. It was hypothesized that inter-pixel capacitive coupling was responsible for these discrepancies. A stochastic method of measuring the coupling using 2D autocorrelation and Fourier Transform techniques was devised and implemented. Autocorrelation of the shot noise in the images revealed a correlation consistent with 3.2% interpixel capacitive coupling. When the effects of the measured interpixel capacitance were taken into account, the initially measured nodal capacitance of 56 fF was found to be 31% higher than the corrected nodal capacitance measurement of 43 fF. Large discrepancies between the theoretical and observed edge spread response were also greatly reduced. A simulation of the electric field in the PIN detector intrinsic region predicted an interpixel coupling very close to the observed coupling. Interpixel capacitance was also observed in a 2k by 2k Raytheon SB304-based InSb detector array, but was not strongly evident in a bare Raytheon SB226 multiplexer.
Plasmids for Therapy and Vaccination (2001)

Plasmids Structures of Plasmid DNA Genetic Vaccination with Plasmid Vectors Phase I Plasmid Gene Therapy Trials Today pAH9 - A Vector for the Treatment of Restenosis pUT649 - A Cancer Gene Therapy Vector pCMV-S2S - A Curative Immunization Approach against Hepatitis B Virus pXY53 - A Malaria Vaccine Polyvalent/Polycistronic Plasmid Vectors From Research Data to Clinical Trials with Plasmid DNA Plasmid Manufacturing - An Overview Quality Criteria for a Clinical Batch of pDNA Plasmids in Fish Vaccination.
Development of Allergic Inflammation in a Murine Model of Asthma Is Dependent on the Costimulatory Receptor Ox40 (2001)

Asthma is thought to result from an abnormal expansion of CD4 T cells reactive with airborne allergens, and pathology is controlled by several cytokines of the T helper type 2 (Th2) family. The exact molecules which are involved in generating allergen-reactive T cells are not clear. Studies with blocking reagents or knockout animals have shown that the CD28/B7 interaction partially controls development of allergic asthma in mouse models, but may not be the sole molecule involved. In this report, we have investigated the role of the tumor necrosis factor receptor family member OX40 in allergic inflammation using OX40-deficient mice. OX40 has been shown to participate in regulating clonal expansion and memory development of CD4 T cells and may synergize with CD28. Our studies demonstrate that OX40(-/)- mice, primed with the model allergen ovalbumin and challenged through the airways with aerosolized antigen, are severely impaired in their ability to generate a Th2 response characterized by high levels of interleukin (IL)-5, IL-4, and immunoglobulin E. Moreover, OX40(-/)- mice exhibit diminished lung inflammation, including an 80-90% reduction in eosinophilia and mucus production, less goblet cell hyperplasia, and significantly attenuated airway hyperreactivity. These studies highlight the potential importance of OX40 in development of allergic asthma and suggest that targeting OX40 may prove useful therapeutically.
Longitudinal evaluation of expression of virally delivered transgenes in gerbil cone photoreceptors (2008)

Delivery of foreign opsin genes to cone photoreceptors using recombinant adeno-associated virus (rAAV) is a potential tool for studying the basic mechanisms underlying cone based vision and for treating vision disorders. We used an in vivo retinal imaging system to monitor, over time, expression of virally-delivered genes targeted to cone photoreceptors in the Mongolian gerbil (Meriones unguiculatus). Gerbils have a well-developed photopic visual system, with 11-14% of their photoreceptors being cones. We used replication deficient serotype 5 rAAV to deliver a gene for green fluorescent protein (GFP). In an effort to direct expression of the gene specifically to either S or M cones, the transgene was under the control of either the human X-chromosome opsin gene regulatory elements, i.e., an enhancer termed the locus control region (LCR) and L promoter, or the human S-opsin promoter. Longitudinal fluorescence images reveal that gene expression is first detectable about 14 days post-injection, reaches a peak after about 3 months, and is observed more than a year post-injection if the initial viral concentration is sufficiently high. The regulatory elements are able to direct expression to a subpopulation of cones while excluding expression in rods and non-photoreceptor retinal cells. When the same viral constructs are used to deliver a human long-wavelength opsin gene to gerbil cones, stimulation of the introduced human photopigment with long-wavelength light produces robust cone responses.
Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium (2014)

Bifidobacteria represent one of the dominant microbial groups that are present in the gut of various animals, being particularly prevalent during the suckling stage of life of humans and other mammals. However, the overall genome structure of this group of microorganisms remains largely unexplored. Here, we sequenced the genomes of 42 representative (sub)species across the Bifidobacterium genus and used this information to explore the overall genetic picture of this bacterial group. Furthermore, the genomic data described here were used to reconstruct the evolutionary development of the Bifidobacterium genus. This reconstruction suggests that its evolution was substantially influenced by genetic adaptations to obtain access to glycans, thereby representing a common and potent evolutionary force in shaping bifidobacterial genomes.
Apoptosis of human colon carcinoma HT-29 cells induced by ceramide (2006)

Ceramide induces apoptosis of human colon carcinoma HT-29 cells by affecting the expression of Bcl-2 family gene members and impacting the mitochondrial function.
Growth of preneoplastic mammary epithelial cells in serum-free medium. (1980)

The conditions for growing preneoplastic mammary epithelial cells in primary cell cultures with serum-free factor-defined medium were established in a series of experiments. The cells, grown in Dulbecco's modified Eagle's medium with 0.6 mM Ca2+, epidermal growth factor, transferrin, insulin, and Na2SeO3, were fibroblast free, exhibited saturation densities similar to those of cells grown in serum-containing medium, and actively incorporated [3H]thymidine into DNA, as demonstrated by biochemical and autoradiography assays. The total growth fraction over a seven-day experiment was 77%. Fetuin was sufficient as a serum substitute for attachment of cells to the dish, although it was apparently not necessary for continued growth of the cells. The possible benefits of growing preneoplastic mammary epithelial cells in serum-free factor-defined medium are discussed.
Biorecognition Layer Engineering: Overcoming Screening Limitations of Nanowire-Based FET Devices (2012)

Detection of biological species is of great importance to numerous areas of medical and life sciences from the diagnosis of diseases to the discovery of new drugs. Essential to the detection mechanism is the transduction of a signal associated with the specific recognition of biomolecules of interest. Nanowire-based electrical devices have been demonstrated as a powerful sensing platform for the highly sensitive detection of a wide-range of biological and chemical species. Yet, detecting biomolecules in complex biosamples of high ionic strength (>100 mM) is severely hampered by ionic screening effects. As a consequence, most of existing nanowire sensors operate under low ionic strength conditions, requiring ex situ biosample manipulation steps, that is, desalting processes. Here, we demonstrate an effective approach for the direct detection of biomolecules in untreated serum, based on the fragmentation of antibody-capturing units. Size-reduced antibody fragments permit the biorecognition event to occur in closer proximity to the nanowire surface, falling within the charge-sensitive Debye screening length. Furthermore, we explored the effect of antibody surface coverage on the resulting detection sensitivity limit under the high ionic strength conditions tested and found that lower antibody surface densities, in contrary to high antibody surface coverage, leads to devices of greater sensitivities. Thus, the direct and sensitive detection of proteins in untreated serum and blood samples was effectively performed down to the sub-pM concentration range without the requirement of biosamples manipulation.