gebhart/patrepeval huggingface dataset:
Defects in galactose metabolism and glycoconjugate biosynthesis in UDP‐glucose pyrophosphorylase‐deficient fibroblasts are reversed by supplementing the cell growth medium with galactose (2012)

UDP‐glucose (UDP‐Glc) is required for galactose metabolism and glycoconjugate biosynthesis and is synthesised from glucose‐1‐ phosphate by UDP‐Glc pyrophosphorylase (UGPP). UGPP‐deficient fibroblasts displaying reduced UDP‐Glc, impaired mitochondrial function and increased glucose regulated protein expression have been described. We have now characterised glycoconjugate biosynthesis and galactose metabolism in these cells and show that they display: 1) reduced [6‐ 3 H]galactose incorporation into UDP‐[6‐ 3 H]‐galactose; 2) an inability to glucosylate the dolichol‐linked oligosaccharide required for protein N ‐glycosylation; 3) hypo‐ N ‐glycosylated PrP C ; 4) truncated O‐glycans, and 5) reduced glucosylceramide and NeuAcα2,3Galβ1,4Glcβ‐ceramide levels. Transfection of the cells with wild type UGPP restores all the above defects except mitochondrial function. Surprisingly, it was discovered that the effects of transfecting the mutant cells with wild type UGPP were reproduced by prolonged cultivation of the cells with galactose. Accordingly, we describe a novel reversable model with which to study defects in galactose metabolism and glycoconjugate biosynthesis.
Probing the surface forces of monolayer films with an atomic-force microscope (1990)

Using an atomic force microscope (AFM), we have studied the attractive and adhesive forces between a cantilever tip and sample surfaces as a function of sample surface energy. The measured forces systematically increased with surface energy. The AFM is very sensitive; changes in the surface forces (i.e., attraction and adhesion) of monolayer covered samples could be clearly discerned when only the surface group of the monolayer film was changed from -${\mathrm{CH}}_{3}$ to -${\mathrm{CF}}_{3}$.
The incredible shrinking world of DNA microarrays (2008)

The efficacy of microarrays in examining gene expression, gene and genome structure, protein-DNA interactions, whole-genome similarities and differences, microRNA expression, methylation (and more) is no longer in question. It is a fast-developing, cutting edge technology that has grown up along with massive sequence databases and is likely to become part of everyday patient care. Many advances have recently expanded the power and utility of microarrays; among them is our development of a new array tiling technique that dramatically increases the scope of coverage of an oligonucleotide tiling array without substantially increasing its cost.
The Beauty of the Commons: Optimal Load Sharing by Base Station Hopping in Wireless Sensor Networks (2014)

In wireless sensor networks (WSNs), the base station (BS) is a critical sensor node whose failure causes severe data losses. Deploying multiple fixed BSs improves the robustness, yet requires all BSs to be installed with large batteries and large energy-harvesting devices due to the high energy consumption of BSs. In this paper, we propose a scheme to coordinate the multiple deployed BSs such that the energy supplies required by individual BSs can be substantially reduced. In this scheme, only one BS is selected to be active at a time and the other BSs act as regular sensor nodes. We first present the basic architecture of our system, including how we keep the network running with only one active BS and how we manage the handover of the role of the active BS. Then, we propose an algorithm for adaptively selecting the active BS under the spatial and temporal variations of energy resources. This algorithm is simple to implement but is also asymptotically optimal under mild conditions. Finally, by running simulations and real experiments on an outdoor testbed, we verify that the proposed scheme is energy-efficient, has low communication overhead and reacts rapidly to network changes.
Requirement for Bbp1p in the Proper Mitotic Functions of Cdc5p inSaccharomyces cerevisiae (2004)

The polo-box domain of the budding yeast polo kinase Cdc5p plays an essential role for targeting the catalytic activity of Cdc5p to spindle pole bodies (SPBs) and cytokinetic neck-filaments. Here, we report the isolation of Bbp1p as a polo-box interacting protein by a yeast two-hybrid screen. Bbp1p localizes to the periphery of the central plaque of the SPB and plays an important role in SPB duplication. Similarly, Cdc5p localized to the cytoplasmic periphery of the SPB. In vitro binding studies showed that Cdc5p interacted with the N-terminal domain of Bbp1p (Bbp1pDeltaC), but apparently not with Mps2p, a component shown to form a stable complex with Bbp1p. In addition, Bbp1p, but likely not Mps2p, was required for proper localization of Cdc5p to the SPB. The C-terminal coiled-coil domain of Bbp1p (Bbp1p(243-385)), which is crucial for both the homodimerization and the SPB localization, could target the localization-defective Cdc5pDeltaC to the SPB and induce the release of Cdc14p from the nucleolus. Consistent with this observation, expression of CDC5DeltaC-BBP1(243-385) under CDC5 promoter control partially complemented the cdc5Delta defect. These data suggest that Bbp1pDeltaC interacts with the polo-box domain of Cdc5p, and this interaction is critical for the subcellular localization and mitotic functions of Cdc5p.
A New Stick-Slip Prevention System (2009)

Abstract Stick-slip is a dysfunction of rotary drilling, characterized by large cyclic variations of the drive torque and the rotational bit speed. It is recognized as a major source of problems, such as excessive bit wear, premature tool failures and poor drilling rate. This paper presents a new system for curing and preventing stick-slip motion. Like other competitive systems it fights the stick-slip oscillations by smart control of the drive. But in contrast to other active systems it does not use any kind of torque feed-back, not even the motor current. Fundamentally, the system is a PI-type speed controller that is tuned to effectively dampen torsional vibrations at the observed stick-slip frequency. In addition to automatic tuning of the speed controller the system includes a suite of support functions, such as automatic determination of the stick-slip frequency, estimation of the instantaneous bit rotation speed and calculation of the stick-slip severity, defined as the normalized downhole speed amplitude. All software is implemented in a standard programmable logic controller (PLC). The paper also includes results from a field test and from Hardware-In-the-Loop (HIL) simulation tests. In the latter tests utilizing the HIL, the software runs on a PLC communicating with an advanced real-time computer model for the drive and the drill string. HIL testing has proved to be cost efficient because the PLC software can easily be tested over a wide range of different downhole conditions that rarely occur in the field.
Changes in the electrocardiogram during treatment with tricyclic antidepressant drugs in endogenous depression. (1979)

In a previous study the authors proposed a law of visco-elasticity with three parameters to describe the influence on blood of a forced test according Couette's schedule. The changes produced by different plasma substitutes are studied under equilibrium conditions and under altered conditions. Marked changes were noted in the various parameters. It would appear that these changes are related to the cohesion of erythrocyte rouleaux.
Function Cultivation in Transparent Oxides Utilizing Natural and Artificial Nanostructures (2006)

In this chapter, we review the recent progress in optoelectronic applications of transparent wide band gap oxides. We concentrate especially on creating new functions in transparent oxides by forming or utilizing nanostructures embedded in the materials. First, our material design concept is introduced in relation to the electronic structures of the oxides. Then optoelectronic properties, electronic structures, and device applications are reviewed for (1) layered oxychalcogenides LnCuOCh (Ln = lanthanide, Ch = chalcogen), and (2) nanoporous crystal 12CaO.7Al2O3 (C12A7). Finally, fabrication of periodic nanostructures in transparent materials by interfering femtosecond (fs) laser pulses is reviewed. Sharp blue-to-UV light emission was observed in LnCuOCh originating from room-temperature stable exciton and the stability of exciton is discussed in relation to their two-dimensional electronic structures. C12A7 has free oxygen ions clathrated in its subnanometer-sized cages, and new functions may be added to C12A7 by replacing the free oxygen ions with active anions. Quantum calculations indicate that cages trapping electrons in C12A7 can be regarded as quantum dots. Micro/nano-processing techniques using fs pulses is an emerging approach to adding new functions to transparent materials. A distributed feedback laser structure was fabricated solely using the laser pulses and its oscillation at room temperature was demonstrated.
Regulation of Glucocorticoid Receptor Function through Assembly of a Receptor‐Heat Shock Protein Complexa (1993)

Incubation of immunopurified, hormone-free mouse glucocorticoid receptors with rabbit reticulocyte lysate results in ATP-dependent and monovalent cation-dependent assembly of the GR into a heterocomplex with hsp90, hsp70, and hsp56. Heterocomplex assembly is accompanied by conversion of the receptor from a form that does not bind steroid to a high affinity steroid-binding conformation. Reticulocyte lysate also promotes ATP-dependent dissociation of unliganded receptors from a prebound receptor-DNA complex. Receptor released from DNA has been reconstituted into the heat shock protein heterocomplex and converted to the non-DNA-binding state. The reticulocyte lysate also reconstitutes pp60v-src into a heterocomplex containing hsp90 and p50, both of which are components of the native heterocomplex form of the tyrosine kinase in cytoplasm. Although the c-Raf-1 serine/threonine kinase has never been found in native association with hsp90, it can be assembled into a heat shock protein heterocomplex by the ATP-dependent system in reticulocyte lysate.
Synthesis and Properties of a-Thiagra. A Substituted 5-(2-Thienyl)pyrazolo[4,3-d]pyrimidin-7-one Bioisostere of Viagra® (2000)

For structure-activity manipulations, the compound α-thiagra (3), a thiophene bioisostere of viagra ® , has been prepared and its X-Ray structure determined.The crystallographic data show that the thiophene and pyrazolo[4,3-d]-pyrimidone hetero-ring systems are nearly coplanar by virtue of an adequate intramolecular hydrogen-bond between the pyrimidone NH and the oxygen lone pair of the 3'-ethoxy group.
Sliced Wasserstein Kernels for Probability Distributions (2016)

Optimal transport distances, otherwise known as Wasserstein distances, have recently drawn ample attention in computer vision and machine learning as powerful discrepancy measures for probability distributions. The recent developments on alternative formulations of the optimal transport have allowed for faster solutions to the problem and have revamped their practical applications in machine learning. In this paper, we exploit the widely used kernel methods and provide a family of provably positive definite kernels based on the Sliced Wasserstein distance and demonstrate the benefits of these kernels in a variety of learning tasks. Our work provides a new perspective on the application of optimal transport flavored distances through kernel methods in machine learning tasks.
Evaluating the impact of high Pluronic® F68 concentrations on antibody producing CHO cell lines (2014)

Pluronic® F68 (P-F68) is an important component of chemically-defined cell culture medium because it protects cells from hydrodynamic and bubble-induced shear in the bioreactor. While P-F68 is typically used in cell culture medium at a concentration of 1 g/L (0.1%), higher concentrations can offer additional shear protection and have also been shown to be beneficial during cryopreservation. Recent industry experience with variability in P-F68-associated shear-protection has opened up the possibility of elevated P-F68 concentrations in cell culture media, a topic that has not been previously explored in the context of industrial cell culture processes. Recognizing this gap, we first evaluated the effect of 1-5 g/L P-F68 concentrations in shake flask cultures over ten 3-day passages for cell lines A and B. Increase in terminal cell density and cell size was seen over time at higher P-F68 concentrations but protein productivity was not impacted. Results from this preliminary screening study suggested no adverse impact of high P-F68 concentrations. Subsequently fed-batch bioreactor experiments were conducted at 1 and 5 g/L P-F68 concentrations with both cell lines where cell growth, viability, metabolism, and product quality were examined under process conditions reflective of a commercial process. Results from these bioreactor experiments confirmed findings from the preliminary screen and also indicated no impact of elevated P-F68 concentration on product quality. If additional shear protection is desired, either due to raw material variability, cell line sensitivity, or a high-shear cell culture process, our results suggest this can be accomplished by elevating the P-F68 concentration in the cell culture medium without impacting cell culture performance and product quality.
A Bacterial Strain with a Unique Quadruplet Codon Specifying Non‐native Amino Acids (2014)

The addition of noncanonical amino acids to the genetic code requires unique codons not assigned to the 20 canonical amino acids. Among the 64 triplet codons, only the three nonsense "stop" codons have been used to encode non-native amino acids. Use of quadruplet "frame-shift" suppressor codons provides an abundant alternative but suffers from low suppression efficiency as a result of competing recognition of their first three bases by endogenous host tRNAs or release factors. Deletion of release factor 1 in a genomically recoded strain of E. coli (E. coli C321), in which all endogenous amber stop codons (UAG) are replaced with UAA, abolished UAG mediated translation termination. Here we show that a Methanocaldococcus jannaschii-derived frame-shift suppressor tRNA/aminoacyl-tRNA synthetase pair enhanced UAGN suppression efficiency in this recoded bacterial strain. These results demonstrate that efficient quadruplet codons for encoding non-native amino acids can be generated by eliminating competing triplet codon recognition at the ribosome.
Hemagglutinin-specific neutralization of subacute sclerosing panencephalitis viruses (2018)

Subacute sclerosing panencephalitis (SSPE) is a progressive, lethal complication of measles caused by particular mutants of measles virus (MeV) that persist in the brain despite high levels of neutralizing antibodies. We addressed the hypothesis that antigenic drift is involved in the pathogenetic mechanism of SSPE by analyzing antigenic alterations in the MeV envelope hemagglutinin protein (MeV-H) found in patients with SSPE in relation to major circulating MeV genotypes. To this aim, we obtained cDNA for the MeV-H gene from tissue taken at brain autopsy from 3 deceased persons with SSPE who had short (3-4 months, SMa79), average (3.5 years, SMa84), and long (18 years, SMa94) disease courses. Recombinant MeVs with a substituted MeV-H gene were generated by a reverse genetic system. Virus neutralization assays with a panel of anti-MeV-H murine monoclonal antibodies (mAbs) or vaccine-immunized mouse anti-MeV-H polyclonal sera were performed to determine the antigenic relatedness. Functional and receptor-binding analysis of the SSPE MeV-H showed activity in a SLAM/nectin-4-dependent manner. Similar to our panel of wild-type viruses, our SSPE viruses showed an altered antigenic profile. Genotypes A, G3, and F (SSPE case SMa79) were the exception, with an intact antigenic structure. Genotypes D7 and F (SSPE SMa79) showed enhanced neutralization by mAbs targeting antigenic site IIa. Genotypes H1 and the recently reported D4.2 were the most antigenically altered genotypes. Epitope mapping of neutralizing mAbs BH015 and BH130 reveal a new antigenic site on MeV-H, which we designated Φ for its intermediate position between previously defined antigenic sites Ia and Ib. We conclude that SSPE-causing viruses show similar antigenic properties to currently circulating MeV genotypes. The absence of a direct correlation between antigenic changes and predisposition of a certain genotype to cause SSPE does not lend support to the proposed antigenic drift as a pathogenetic mechanism in SSPE.
Necklace‐like Nitrogen‐Doped Tubular Carbon 3D Frameworks for Electrochemical Energy Storage (2020)

Abstract The design and synthesis of a necklace‐like nitrogen‐doped tubular carbon (NTC) are presented by growing microporous polyhedral ZIF‐8 particles and a uniform layer of ZIF‐8 on sacrificial ZnO tetrapods (ZTPs). Oxygen vacancies together with defect regions on the surface of the ZTPs result in the formation of ZIF‐8 polyhedra in conjunction with a very thin shell. This necklace‐like NTC structure has a high N content, very large surface area, ultrahigh microporosity, and quite high electrical conductivity. NTC‐based symmetrical supercapacitor and zinc‐ion capacitor (ZIC) devices are fabricated and their electrochemical performance is measured. The NTC supercapacitor shows an ultrahigh rate capability (up to 2000 mV s −1 ) and promising cycle life, retaining 91.5% of its initial performance after 50 000 galvanostatic charge–discharge cycles. An aqueous ZIC, constructed using the NTC, has a specific capacitance of 341.2 F g −1 at a current density of 0.1 A g −1 and an energy density of 189.6 Wh kg −1 with a 2.0‐V voltage window, respectively. The outstanding performance is attributed to the NTC high N‐doping content, a continuous “polyhedral 3D hollow” architecture and the highly porous microtubular arms exhibiting very high surface area.
Original Articles WAROSCOPIC RADICAL NEPHRECTOMY FOR RENAL TUMOR: THE WASHINGTON UNIVERSITY EXPERIENCE (1996)

Purpose: We report our experience with laparoscopic radical nephrectomy in 17 consecutive patients with renal tumors. Materials and Methods: The clinical data on 17 consecutive patients undergoing laparoscopic radical nephrectomy were reviewed. Of the patients 12 with stage pT1 or pT2 renal cell carcinoma 7 cm. in diameter or smaller undergoing laparoscopic radical nephrectomy were compared to 12 undergoing open radical nephrectomy for stage pT1 or pT2 renal cell carcinoma 6 cm. in diameter or smaller. Results: Among the 17 patients undergoing laparoscopic radical nephrectomy average operative time was 6.9 hours (range 4.5 to 9) and average estimated blood loss was 105 cc (range 50 to 600). Average weight of the surgical specimen was 402 gm. (range 190 to 1,100). In 12 of 16 patients in whom laparoscopic radical nephrectomy was completed the specimen was removed intact. The patients required an average of 24 mg. morphine sulfate equivalent (range 2 to 220) for postoperative pain. Average hospital stay was 4.5 days (range 3 to 11) and average interval to resume normal activities was 3.5 weeks (range 2 to 4). The 12 patients in the open and laparoscopic radical nephrectomy groups were similar with respect to age, American Society of Anesthesiologists score and interval of surgery. Laparoscopic radical nephrectomy required significantly more operative time than open radical nephrectomy (6.9 versus 2.2 hours, respectively). However, the laparoscopic radical nephrectomy group compared to the open radical nephrectomy group had significantly less postoperative pain (24 versus 40 mg, morphine sulfate equivalent required for postoperative analgesia), shorter interval to resuming oral intake (1 versus 3 days), more rapid discharge from the hospital (4.5 versus 8.4 days) and more rapid return to normal activities (3.5 versus 5.1 weeks). The laparoscopic nephredomy group also fully recovered more rapidly than the open surgical group (5.8 versus 39 weeks). To date, during a 4-year period there was no retroperitoneal recurrence or seeding of a port site. Conclusions: Laparoscopic radical nephrectomy is a lengthy and demanding procedure. However, it affords patients with renal cell carcinoma a markedly improved postoperative course while accomplishing the necessary surgical goals.
Computing on Authenticated Data. (2011)

In tandem with recent progress on computing on encrypted data via fully homomorphic encryption, we present a framework for computing on authenticated data via the notion of slightly homomorphic signatures, or P-homomorphic signatures. With such signatures, it is possible for a third party to derive a signature on the object m ′ from a signature of m as long as P (m, m ′ ) = 1 for some predicate P which captures the “authenticatable relationship ” between m ′ and m. Moreover, a derived signature on m ′ reveals no extra information about the parent m. Our definition is carefully formulated to provide one unified framework for a variety of distinct concepts in this area, including arithmetic, homomorphic, quotable, redactable, transitive signatures and more. It includes being unable to distinguish a derived signature from a fresh one even when given the original signature. The inability to link derived signatures to their original sources prevents some practical privacy and linking attacks, which is a challenge not satisfied by most prior works. Under this strong definition, we then provide generic constructions for all univariate and closed predicates, and specific efficient constructions for a broad class of natural predicates such as quoting, subsets, weighted sums, averages, and Fourier transforms. To our knowledge, these are the first efficient constructions for these predicates (excluding subsets) that provably satisfy this strong security notion. Supported by NSF, DARPA, and AFOSR. Applying to all authors, the views and conclusions contained in this
Hydrajetting Applications in Horizontal Completions to Improve Hydraulic Fracturing Stimulations and Improve ROI (2009)

Abstract This paper reviews applications of hydrajet perforating during the past 6+ years specifically as they apply to horizontal and highly deviated completions for both oil and gas reservoirs. Many benefits to hydraulic fracturing through hydrajetted perfs instead of shape charge perforations will often exist. Also, a key feature to more economic applications has been coupling this process with a method that includes multi-stage fracturing operations. This feature can shorten the completion time needed to achieve multistage frac treatments. During this decade, horizontal wells that need fracture stimulation are being drilled deeper and, especially, with longer lateral sections requiring larger numbers of fracturing stages. This has increasingly challenged the limits of conventional jetting systems and methods, while requiring higher pressure limits for the wellhead, treatment tubing, and pumping equipment. Three primary methods for using hydrajet perforating have been part of the surge of horizontal well applications. Listed in the order of their emergence of significant application during the present decade, they are: hydrajet fracturing (HJF), hydrajet perforating, annulus path fracturing (HPAP), and standalone use of hydrajetted perforating (SHJP) followed by conventional wellbore stimulation and isolation applications.
Diamond volume crystal growth in HF-CVD and monitoring gas phase with laser absorption spectroscopy (2007)

In hot-filament CVD we synthesized single diamond crystals up to 100 μm in diameter [1]. In order to enhance growth rate and impede growth defects, it is intended to employ a new gas feeding system. This allows CH4 to be separately applied from H2 to the reactor locally at the substrate position. The effect of this concept on the gas phase was analyzed by Infrared Tuneable Diode Laser Absorption Spectroscopy (IR-TDLAS). The changes in species concentrations of CH4, CH3 and C2H2 with the substrate distance from filaments as well as first growth results are shown.