gebhart/patrepeval huggingface dataset:
Well Placement and Geological Evaluation of a North Sea Horizontal Water Injector Using LWD Technology (2017)

Abstract During the late life of the Siri field in the Danish North Sea, an infill water injection well was drilled to provide enhanced reservoir sweep and to help improve tail-end field production. Dynamic reservoir modeling indicated that a down-dip horizontal water injector on the southwestern flank of the field using injection inflow control devices (ICDs) could provide the necessary uplift for producers near the crest of the field. The Siri field is characterized as a high permeability, remobilized glauconitic sand package comprising multiple stacked and amalgamated sand bodies deposited from high density gravity flows in the Paleocene-Eocene Siri fairway. Seismic, well logging, and production data indicate that fluid flow is influenced by vertical and horizontal baffling. The internal flow channeling and baffle effects are likely caused by a combination of siliciclastic diagenesis, subseismic faulting, and multiple calcite-cemented paleo oil/water contacts. These baffles are capable of maintaining significant pressure differentials. They consequently have a major effect on field scale horizontal permeability and reservoir sweep efficiency. During the last decade of drilling horizontal development wells in the Siri area, Dong Energy has obtained extensive in-house experience and knowledge in the use of deep reading resistivity technology for reservoir mapping, as well as in positioning long horizontal development wells in challenging settings, such as ultra-thin reservoirs sands and thin oil columns. This paper discusses the well placement and geological evaluation of the Siri reservoir with regard to the acquired logging while drilling (LWD) data, which includes resistivity inversion, neutron porosity/bulk density imaging, and formation pressure measurements. The well trajectory was adjusted in real time to reduce footage exposure to tight facies, as well as to identify fluid boundaries related to the flow channeling present within the reservoir. Borehole resistivity inversion provides evidence that the mineralized permeability barriers are not always high-angle features. This paper also discusses insights into the Siri reservoir geology in light of the horizontal well data acquisition program and potential implications for future ICD behavior.
Analysis of cocaine receptor site ligand binding by three-dimensional Voronoi site modeling approach (1993)

The Voronoi approach has been used to obtain a three-dimensional model for the binding of the cocaine analogues at the cocaine receptor site. The method has been used to determine the geometric details and the physicochemical properties of the binding regions in the receptor site. With only eight compounds in the training set, the Voronoi site model, consisting of four regions, not only fully explains the binding affinity of the input compounds but is also successful in correctly predicting another eight compounds of the test set. The phenyl substituent at the 3-position of the tropane ring of cocaine was found to be the most significant functionality relevant for activity, while moderate contribution results from the hydrophobic interactions of the tropane ring with the binding regions. Some of the problems associated with the approach are discussed, and we report a new procedure for evaluating the validity of the model obtained from our approach.
Overexpression and knock-down studies highlight that a disintegrin and metalloproteinase 28 controls proliferation and migration in human prostate cancer (2016)

Prostate cancer is one of the most prevalent cancers in men. It is critical to identify and characterize oncogenes that drive the pathogenesis of human prostate cancer. The current study builds upon previous research showing that a disintegrin and metallproteinase (ADAM)28 is involved in the pathogenesis of numerous cancers. Our novel study used overexpression, pharmacological, and molecular approaches to investigate the biological function of ADAM28 in human prostate cancer cells, with a focus on cell proliferation and migration. The results of this study provide important insights into the role of metalloproteinases in human prostate cancer.The expression of ADAM28 protein levels was assessed within human prostate tumors and normal adjacent tissue by immunohistochemistry. Immunocytochemistry and western blotting were used to assess ADAM28 protein expression in human prostate cancer cell lines. Functional assays were conducted to assess proliferation and migration in human prostate cancer cells in which ADAM28 protein expression or activity had been altered by overexpression, pharmacological inhibition, or by siRNA gene knockdown.The membrane bound ADAM28 was increased in human tumor biopsies and prostate cancer cell lines. Pharmacological inhibition of ADAM28 activity and/or knockdown of ADAM28 significantly reduced proliferation and migration of human prostate cancer cells, while overexpression of ADAM28 significantly increased proliferation and migration.ADAM28 is overexpressed in primary human prostate tumor biopsies, and it promotes human prostate cancer cell proliferation and migration. This study supports the notion that inhibition of ADAM28 may be a potential novel therapeutic strategy for human prostate cancer.
694. Improved Therapeutic Efficacy Following AAV2/8-Mediated Expression of α-Galactosidase A in Fabry Mice (2004)

Fabry disease is an inherited disorder that is caused by a deficiency of the lysosomal enzyme α-galactosidase A. This results in the progressive accumulation of the glycosphingolipid, globotriaocylceramide (GL-3) in the lysosomes of endothelial, perithelial and smooth muscle cells. Substrate deposition also occurs in structures of the central, peripheral and autonomic nervous system. Previously, we showed that intravenous administration of 5 × 1011 particles of a recombinant AAV2 vector encoding human α-galactosidase A under the transcriptional control of a liver-restricted enhancer/promoter (DC190) into Fabry mice resulted in expression of therapeutic levels of the enzyme that was sustained for 12 months. Treatment resulted in a reduction of GL-3 in the liver, spleen and heart to basal levels and in the kidney by approximately 40% at 8 weeks. To improve the therapy to the kidney, different AAV serotypes (1, 5, and 8) with reportedly higher hepatic transduction activity were evaluated. A very modest improvement in expression of α-galactosidase A was seen with the AAV pseudotypes 2/1 and 2/5 when compared to 2/2. However, the corresponding AAV2/8 vector generated approximately 100 fold greater levels of the enzyme than the AAV2/2 vector. Moreover, the kinetics of expression from the AAV2/8 vector was more rapid, with α-galactosidase A in the serum detected as early as 1 week post-treatment. Intravenous administration of 5 × 1010 particles of the AAV2/8 virus into Fabry mice resulted in higher levels of expression of the enzyme and more rapid clearance of GL-3 from the affected tissues than with a 10 fold higher dose of the corresponding AAV2/2 vector. Clearance of GL-3 from the AAV2/8-treated tissues including kidney was essentially complete by 4 instead of 8 weeks. Hence a significant improvement in potency was realized with the AAV2/8 pseudotyped vector. In addition to correcting the aberrant GL-3 levels, an improvement in the thermal sensitivity of the treated Fabry mice was also realized. Fabry mice demonstrate a delayed response to placement on a hot plate that is equilibrated to 55°C (as demonstrated by a flick of its hindlimbs) when compared to unaffected normal mice (129/Sv). The response time of untreated Fabry mice became progressively longer over a period of 8 months. In contrast, Fabry mice treated at 5 weeks of age with the AAV2/8 vector demonstrated short response times that were similar to those for age-matched normal 129/Sv mice throughout the study. The hindlimb footpads of the mice, as well as dorsal root ganglia of the spinal cord have been examined histologically to show if the pathology corresponded to the improvement in thermal sensitivity. Finally, we demonstrated that the immune tolerance to α-galactosidase A observed previously using an AAV2/2 vector harboring a liver-restricted promoter also applied to the AAV2/8 vector. Together, these data support the continued development of AAV2/8-mediated gene therapy for Fabry disease.
A Simulated Annealing Algorithm for RFID Reader Networks (2007)

In consideration of the reader collision problem in radio frequency identification (RFID) networks, we present an algorithm that deploys RFID reader networks so that they are flexible and efficient. We formulate the deployment issue as 0/1 integer programming problem, and propose a simulated annealing-based heuristic algorithm to solve it.
Electrophoresis of metal-dielectric Janus particles with dipolar director symmetry in nematic liquid crystals (2022)

We study the electrophoresis of metal-dielectric Janus particles with dipolar director symmetry in two nematic liquid crystals (LCs) having the same sign of conductivity anisotropy (Δ<i>σ</i>) but opposite signs of dielectric anisotropy (Δ<i>ε</i>). The applied ac electric field is parallel and perpendicular to the director for positive and negative dielectric anisotropy LCs, respectively. We show that the Janus dipolar particles propel faster than the non-Janus dipolar particles in both LCs. The propelling speed of the Janus dipolar particles is also significantly higher compared to the quadrupolar Janus particles studied previously. We map the electroosmotic flow fields surrounding a Janus dipolar particle using microparticle image velocimetry (μ-PIV) and show that the flow on a metal hemisphere is stronger than that on a dielectric hemisphere. Altogether, Janus dipolar particles demonstrate efficient electrophoresis compared to both Janus and non-Janus quadrupolar particles. These findings may be useful for applications in active matter, microrobotic and microfluidic devices.
Extracting collective probabilistic forecasts from web games (2001)

Game sites on the World Wide Web draw people from around the world with specialized interests, skills, and knowledge. Data from the games often reflects the players' expertise and will to win. We extract probabilistic forecasts from data obtained from three online games: the Hollywood Stock Exchange (HSX), the Foresight Exchange (FX), and the Formula One Pick Six (F1P6) competition. We find that all three yield accurate forecasts of uncertain future events. In particular, prices of so-called "movie stocks" on HSX are good indicators of actual box office returns. Prices of HSX securities in Oscar, Emmy, and Grammy awards correlate well with observed frequencies of winning. FX prices are reliable indicators of future developments in science and technology. Collective predictions from players in the F1 competition serve as good forecasts of true race outcomes. In some cases, forecasts induced from game data are more reliable than expert opinions. We argue that web games naturally attract well-informed and well-motivated players, and thus offer a valuable and oft-overlooked source of high-quality data with significant predictive value.
Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes (2016)

We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.
Learning Dynamic Robot-to-Human Object Handover from Human Feedback (2016)

Object handover is a basic, but essential capability for robots interacting with humans in many applications, e.g., caring for the elderly and assisting workers in manufacturing workshops. It appears deceptively simple, as humans perform object handover almost flawlessly. The success of humans, however, belies the complexity of object handover as collaborative physical interaction between two agents with limited communication. This paper presents a learning algorithm for dynamic object handover, for example, when a robot hands over water bottles to marathon runners passing by the water station. We formulate the problem as contextual policy search, in which the robot learns object handover by interacting with the human. A key challenge here is to learn the latent reward of the handover task under noisy human feedback. Preliminary experiments show that the robot learns to hand over a water bottle naturally and that it adapts to the dynamics of human motion. One challenge for the future is to combine the model-free learning algorithm with a model-based planning approach and enable the robot to adapt over human preferences and object characteristics, such as shape, weight, and surface texture.
Erratum: Isotope and temperature shifts of direct and indirect band gaps in diamond-type semiconductors (1992)

We calculate the isotope and temperature shifts of the indirect and direct band gaps in natural silicon (M\ifmmode\bar\else\textasciimacron\fi{}=28.09 u), in natural diamond $^{12}\mathrm{C}$ and its isotope $^{13}\mathrm{C}$, in natural germanium (M\ifmmode\bar\else\textasciimacron\fi{}=72.59 u), and the isotope $^{70}\mathrm{Ge}$, and in the isotope mixture $^{75.7}\mathrm{Ge}$, due to the deformation-potential-type electron-phonon interaction (within the pseudopotential-bond-charge-model framework). We compare these results to existing experimental information and to data obtained by us with spectroscopic ellipsometry. We find that there are small, but noticeable shifts of the band gaps between different isotopes (about 13 meV for diamond, 1 meV for germanium). The isotopic influence on the broadenings of the ${\mathit{E}}_{1}$ transition in Ge is also observed.
Protein engineering of α2,3/2,6-sialyltransferase to improve the yield and productivity of in vitro sialyllactose synthesis (2013)

In the large-quantity production of α2,3- and α2,6-sialyllactose (Neu5Ac(α2,3)Galβ1,4Glc (3'-SL) and Neu5Ac(α2,6)Galβ1,4Glc (6'-SL)) using sialyltransferases (STs), there are major hurdles to overcome for further improvement in yield and productivity of the enzyme reactions. Specifically, Pasteurella multocida α2,3-sialyltransferase (α2,3PST) forms a by-product to a certain extent, owing to its multifunctional activity at pH below 7.0, and Photobacterium damselae α2,6-sialyltransferase (α2,6PdST) shows relatively low ST activity. In this study, α2,3PST and α2,6PdST were successfully engineered using a hybrid approach that combines rational design with site-saturation mutagenesis. Narrowly focused on the substrate-binding pocket of the STs, putative functional residues were selected by multiple sequence alignment and alanine scanning, and subsequently subjected to site-saturation mutagenesis. In the case of α2,3PST, R313N single mutation improved its activity slightly (by a factor of 1.5), and further improvement was obtained by making the double mutants (R313N/T265S and R313H/T265S) resulting in an overall 2-fold improvement in its specific α2,3 ST activity, which is mainly caused by the increase in kcat. It was revealed that the R313 mutations to N, D, Y, H or T greatly reduced the α2,6 ST side-reaction activity of α2,3PST at below pH 7.0. In the case of α2,6PdST, single-mutation L433S/T and double-mutation I411T/L433T exhibited 3- and 5-fold enhancement of the α2,6 ST-specific activity compared with the wild-type, respectively, via increase in kcat values. Our results show a very good model system for enhancing ST activity and demonstrate that the generated mutants could be used efficiently for the mass production of 3'-SL and 6'-SL with enhanced productivity and yield.
TAPER: Time-Aware Patient EHR Representation (2020)

Effective representation learning of electronic health records is a challenging task and is becoming more important as the availability of such data is becoming pervasive. The data contained in these records are irregular and contain multiple modalities such as notes, and medical codes. They are preempted by medical conditions the patient may have, and are typically recorded by medical staff. Accompanying codes are notes containing valuable information about patients beyond the structured information contained in electronic health records. We use transformer networks and the recently proposed BERT language model to embed these data streams into a unified vector representation. The presented approach effectively encodes a patient's visit data into a single a distributed representation, which can be used for downstream tasks. Our model demonstrates superior performance and generalization on mortality, readmission and length of stay tasks using the publicly available MIMIC-III ICU dataset.
Roles of aggrecan domains in biosynthesis, modification by glycosaminoglycans and product secretion (2001)

Aggrecan is a member of the chondroitin sulphate (CS) proteoglycan family, which also includes versican/PG-M, neurocan and brevican. Members of this family exhibit structural similarity: a G1 domain at the N-terminus and a G3 domain at the C-terminus, with a central sequence for modification by CS chains. A unique feature of aggrecan is the insertion of three additional domains, an inter-globular domain (IGD), a G2 domain and a keratan sulphate (KS) domain (sequence modified by KS chains), between the G1 domain and the CS domain (sequence modified by CS chains). The G1 and G3 domains have been implicated in product secretion, but G2, although structurally similar to the tandem repeats of G1, performs an unknown function. To define the functions of each aggrecan domain in product processing, we cloned and expressed these domains in various combinations in COS-7 cells. The results indicated that the G3 domain enhanced product secretion, alone or in combination with the KS or CS domain, and promoted glycosaminoglycan (GAG) chain attachment. Constructs containing the G1 domain were not secreted. Addition of a CS domain sequence to G1 reduced this inhibition, but GAG chain attachment was still decreased. The potential GAG chain attachment site in the IGD was occupied by GAGs, and IGD product was secreted efficiently. The KS domain was modified by GAG chains and secreted. Finally, the G2 domain was expressed but not secreted, and inhibited secretion of the IGD when expressed as an IGD–G2 combination.
Spinal 5-HT2 and 5-HT3 receptors mediate low, but not high, frequency TENS-induced antihyperalgesia in rats (2003)

Transcutaneous electrical nerve stimulation (TENS) is a form of non-pharmacological treatment for pain. Involvement of descending inhibitory systems is implicated in TENS-induced analgesia. In the present study, the roles of spinal 5-HT and alpha(2)-adrenoceptors in TENS analgesia were investigated in rats. Hyperalgesia was induced by inflaming the knee joint with 3% kaolin-carrageenan mixture and assessed by measuring paw withdrawal latency (PWL) to heat before and 4 h after injection. The (1). alpha(2)-adrenergic antagonist yohimbine (30 microg), (2). 5-HT antagonist methysergide (5-HT(1). and 5-HT(2). 30 microg), one of the 5-HT receptor subtype antagonists, (3). NAN-190 (5-HT(1A), 15 microg), (4). ketanserin (5-HT(2A), 30 microg), (5). MDL-72222 (5-HT(3), 12 microg), or (6). vehicle was administered intrathecally prior to TENS treatment. Low (4 Hz) or high (100 Hz) frequency TENS at sensory intensity was then applied to the inflamed knee for 20 min and PWL was determined. Selectivity of the antagonists used was confirmed using respective agonists administered intrathecally. Yohimbine had no effect on the antihyperalgesia produced by low or high frequency TENS. Methysergide and MDL-72222 prevented the antihyperalgesia produced by low, but not high, frequency TENS. Ketanserin attenuated the antihyperalgesic effects of low frequency TENS whereas NAN-190 had no effect. The results from the present study show that spinal 5-HT receptors mediate low, but not high, frequency TENS-induced antihyperalgesia through activation of 5-HT(2A) and 5-HT(3) receptors in rats. Furthermore, spinal noradrenergic receptors are not involved in either low or high frequency TENS antihyperalgesia.
High Hydrostatic Pressure Effects on the Texture of Meat and Meat Products (2009)

High hydrostatic pressure (HHP) treatment can influence meat protein conformation and induce protein denaturation, aggregation, or gelation. The means whereby HHP treatment exerts effects on meat protein structure change are due to the rupture of noncovalent interactions within protein molecules, and to the subsequent re-formation of intra- and inter-molecular bonds within or among protein molecules. Depending upon the meat protein system, the pressure, the temperature, and the duration of the pressure treatment, meat can be either tenderized or toughened. Muscle texture variation induced by heat treatment is due to breakage of hydrogen bonds, whereas changes from high pressure treatment are due to the rupture of hydrophobic and electrostatic interactions. Pressure treatment has little effect on the toughness of connective tissue. Juiciness, springiness, and chewiness are increased upon HHP treatment. Prerigor HHP treatment tenderizes meat, whereas tenderizing effects of postrigor HHP treatment are only measureable if pressure and heat treatment are combined. The limitations and future applications of high pressure technology are also discussed.
A Chain Structure of Switched Capacitor for Improved Cell Balancing Speed of Lithium-Ion Batteries (2013)

Among various active cell balancing circuits, a switched capacitor circuit is promising because it can be implemented with low cost and small size. However, when the switched capacitor is applied in the lithium-ion battery, cell balancing speed is generally slow when the number of batteries is high. Therefore, this paper proposes the chain structure of the switched capacitor to increase balancing speed, particularly among outer cells. In this paper, the cell balancing principle of the conventional switched capacitor is explained, and the reason why slow cell balancing of the switched capacitor is shown in the lithium-ion battery is analyzed. To improve cell balancing speed, two circuits with chain structure are proposed. The balancing performance of the proposed circuits is confirmed by computer simulation, and a comparison between conventional and proposed circuits is presented. The theoretical analysis on the cell balancing speed of conventional structures and the proposed chain structure is also shown in this paper. Experimental tests were carried out to verify the validity of the proposed structures, and the experimental results show an improved balancing performance of the proposed circuit.