gebhart/patrepeval huggingface dataset:
Generation of HIV-Resistant Macrophages from IPSCs by Using Transcriptional Gene Silencing and Promoter-Targeted RNA (2018)

Highly active antiretroviral therapy (HAART) has markedly prolonged the prognosis of HIV-1 patients. However, lifelong dependency on HAART is a continuing challenge, and an effective therapeutic is much desired. Recently, introduction of short hairpin RNA (shRNA) targeting the HIV-1 promoter was found to suppress HIV-1 replication via transcriptional gene silencing (TGS). The technology is expected to be applied with hemato-lymphopoietic cell transplantation of HIV patients to suppress HIV transcription in transplanted hemato-lymphopoietic cells. Combination of the TGS technology with new cell transplantation strategy with induced pluripotent stem cell (iPSC)-derived hemato-lymphopoietic cells might contribute to new gene therapy in the HIV field. In this study, we evaluated iPSC-derived macrophage functions and feasibility of TGS technology in macrophages. Human iPSCs were transduced with shRNAs targeting the HIV-1 promoter region (shPromA) by using a lentiviral vector. The shPromA-transfected iPSCs were successfully differentiated into functional macrophages, and they exhibited strong protection against HIV-1 replication with alteration in the histone structure of the HIV-1 promoter region to induce heterochromatin formation. These results indicated that iPS-derived macrophage is a useful tool to investigate HIV infection and protection, and that the TGS technology targeting the HIV promoter is a potential candidate of new gene therapy.
Potassium Silanide (KSiH3): A Reversible Hydrogen Storage Material (2011)

KSi silicide can absorb hydrogen to directly form the ternary KSiH(3) hydride. The full structure of α-KSiD(3), which has been solved by using neutron powder diffraction (NPD), shows an unusually short Si-D lengths of 1.47 Å. Through a combination of density functional theory (DFT) calculations and experimental methods, the thermodynamic and structural properties of the KSi/α-KSiH(3) system are determined. This system is able to store 4.3 wt% of hydrogen reversibly within a good P-T window; a 0.1 MPa hydrogen equilibrium pressure can be obtained at around 414 K. The DFT calculations and the measurements of hydrogen equilibrium pressures at different temperatures give similar values for the dehydrogenation enthalpy (≈23 kJ mol(-1) H(2)) and entropy (≈54 J K(-1) mol(-1) H(2)). Owing to its relatively high hydrogen storage capacity and its good thermodynamic values, this KSi/α-KSiH(3) system is a promising candidate for reversible hydrogen storage.
Expression of a Novel Double-Mutant Dihydrofolate Reductase-Cytidine Deaminase Fusion Gene Confers Resistance to Both Methotrexate and Cytosine Arabinoside (1999)

A novel fusion gene consisting of the open reading frame of a double-mutant (Phe22-Ser31) dihydrofolate reductase (dmDHFR) cDNA fused to the open reading frame of cytidine deaminase (CD) was constructed and characterized for the purpose of conferring simultaneous resistance to methotrexate (MTX) and cytosine arabinoside (ara-C). The kinetic properties of purified recombinant dmDHFR-CD fusion protein were compared with those of purified CD and dmDHFR. The fusion protein was found to retain enzymatic properties of both dmDHFR and CD, in that the Km and Kcat values of purified dmDHFR-CD protein were found to be virtually identical to those of CD and dmDHFR alone. Retrovirus-mediated expression of dmDHFR-CD in NIH 3T3 cells conferred significant resistance (10- to 12-fold) against MTX and ara-C, compared with mock- and single gene-infected cells and the level of resistance obtained was similar to that of cells expressing both CD and dmDHFR from a retroviral bicistronic vector. Infection of mouse bone marrow cells with the dmDHFR-CD construct also showed high levels of resistance to MTX and ara-C in a CFU-GM assay. This fusion protein confers resistance to two antineoplastic agents that differ in their mechanism of action, and may be useful in the design of gene transfer strategies for protection of target cells against multiple drugs. Since high-dose ara-C and MTX are used in the treatment of lymphomas, this vector may be of value in protecting human hematopoietic progenitor cells from the toxicity of these antimetabolites.
The Center-Center Technique for the Direct Anterior Approach in Total Hip Arthroplasty: Precise Femoral Canal Preparation to Optimize Implant Fit and Fill. (2019)

The center-center technique can be used to consistently aid in proper femoral stem placement in both coronal and sagittal planes. Optimal fit and fill can be achieved safely using this technique.
<title>Bayesian tree-structured image modeling using wavelet-domain hidden Markov models</title> (1999)

ABSTRACT Wavelet-domain hidden Markov models have proven to be useful tools for statistical signal and image processing. The hiddenMarkov tree (HMT) model captures the key features of the joint density of the wavelet coefficients of real-world data. Onepotential drawback to the HMT framework is the need for cornputationallv expensive iterative training (using the Expectation-Iaximization algorithm, for example). In this paper, we propose two reduced-parameter HMT models that capture the generalstructure of a broad class of real-world images. In the image HMT (iHMT) model we use the fact that for a large class ofimages the structure of the HMT is self-similar across scale. This allows us to reduce the complexity of the iHMT to justnine easily trained parameters (independent of the size of the image and the number of wavelet scales). In the universal HMT(uHMT) we take a Bayesian approach and fix these nine parameters. The uHMT requires no training of any kind. Whilesimple, we show using a series of image estimation/denoising experiments that these two new models retain nearly all of thekey structure modeled by the full HvIT. Finally, we propose a fast shift-invariant HMT estimation algorithm that outperformsall other wavelet-based estimators in the current literature. both in mean-square error and visual metrics.
Nonintrusive monitoring for shipboard fault detection (2017)

This paper presents a case study applying nonintrusive load monitoring (NILM) for fault detection and isolation (FDI) of automated shipboard systems. A NILM system installed on an engine room subpanel of U.S. Coast Guard (USCG) Cutter SPENCER collected aggregated power consumption data for ten automated systems. A correlation-based transient identifier is used to disaggregate this data, identifying specific automated load events, including on/off events of the gray water disposal pump. A two-parameter model is calculated from these events and used for fault detection. Data collected during two operational periods of the SPENCER demonstrate the effectiveness of this model in identifying a pump sensor fault previously undetected by the crew. Early identification of such malfunctions prevents costly wear on the gray water disposal system pumps and avoids eventual catastrophic failure.
<title>Recent advances in holographic data storage in SBN</title> (1992)

In this paper we discuss recent advances in holographic data storage using ferroelectric SBN as the recording medium. A novel optical architecture involving an array of SBN fibers is discussed that allows 2 - 3 orders of magnitude faster access times than for conventional magnetic data storage devices of Gbyte size. To realize this potential we are studying fundamental materials issues related to SBN fiber growth and photorefractive processes underlying prolonged readout in SBN.
Physical characterization of nedocromil sodium hydrates (1998)

Nedocromil sodium, which is used in the treatment of reversible obstructive airway diseases, such as asthma, is found to exist in the following hydrate phases: the heptahemihydrate, the trihydrate, a monohydrate, and an amorphous phase which contains variable amounts of water (1.5-3.0 mol). An anhydrate phase is formed from the trihydrate at zero humidity at >/= 150 degrees C, but is rapidly hydrated under ambient conditions. The physical and thermodynamic properties of the four hydrate phases were characterized using differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), powder X-ray diffraction (PXRD) at ambient and elevated temperatures, hot-stage microscopy (HSM), solid phase interconversion at various relative humidities (RH), intrinsic dissolution rate (IDR), equilibrium solubility measurements, and critical RH measurements. Below 100 degrees C in open pan TGA, the heptahemihydrate and the amorphous forms lose virtually all their water, the monohydrate loses negligible amounts of water, whereas the trihydrate loses the first two moles of water. From 130 degrees C to 200 degrees C in open pan TGA the trihydrate and the monohydrate lose their last mole of water to form the anhydrate. In crimped pan DSC, the thermal events observed are analogous to those observed in open pan TGA, but the temperatures are increased by about 75 degreesC for all except the heptahemihydrate, for which the thermal events are more complex. When the heptahemihydrate is heated in a crimped pan, a melting endotherm is observed at about 75 degrees C followed by three dehydration endotherms. For the crystalline hydrate phases at 22 degrees C, the ranges of stability are as follows: the monohydrate from 0 to 6.4% RH; the trihydrate from 6.4 to 79.5% RH; the heptahemihydrate above 80% RH. A microbalance study showed that the heptahemihydrate is kinetically stable over the range 11 to 79.5% RH. The IDR in water at 25 degrees C under constant hydrodynamic conditions decreases in the rank order: monohydrate > trihydrate > heptahemihydrate, corresponding to the rank order of free energy with respect to the aqueous solution. The equilibrium aqueous solubility of the heptahemihydrate at 25.0 +/- 0.2 degrees C is 0.956 +/- 0.010 M.
Channel Parameter Estimation for Polarization Diverse Coherent Receivers (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A robust in-service estimation of fiber channel parameters from equalizer parameters of a polarization diverse coherent receiver is presented. The equations used for estimation are evolved from a theoretical fiber channel model. The theory is validated based on simulations and data from transmission experiments. </para>
A Foraging Mandala for Aquatic Microorganisms (2018)

Aquatic environments harbor a great diversity of microorganisms, which interact with the same patchy, particulate, or diffuse resources by means of a broad array of physiological and behavioral adaptations, resulting in substantially different life histories and ecological success. To date, efforts to uncover and understand this diversity have not been matched by equivalent efforts to identify unifying frameworks that can provide a degree of generality and thus serve as a stepping stone to scale up microscale dynamics to predict their ecosystem-level consequences. In particular, evaluating the ecological consequences of different resource landscapes and of different microbial adaptations has remained a major challenge in aquatic microbial ecology. Here, inspired by Ramon Margalef's mandala for phytoplankton, we propose a foraging mandala for microorganisms in aquatic environments, which accounts for both the local environment and individual adaptations. This biophysical framework distills resource acquisition into two fundamental parameters: the search time for a new resource and the growth return obtained from encounter with a resource. We illustrate the foraging mandala by considering a broad range of microbial adaptations and environmental characteristics. The broad applicability of the foraging mandala suggests that it could be a useful framework to compare disparate microbial strategies in aquatic environments and to reduce the vast complexity of microbe-environment interactions into a minimal number of fundamental parameters.
DC-AC Current Source Converter Using Coupled Inductor (2013)

This paper proposes a new current source converter using a coupled inductor, which is derived from the circuit of the matrix converter with an additional inductor. The proposed circuit has the bidirectional power conversion ability, providing step-up and step-down operation in each direction, and can switch the direction of the power flow in a few microseconds. This paper describes the principle of operation, the simulation results and the experimental results of the proposed circuit.
Impact of Polymer Excipient Molar Mass and End Groups on Hydrophobic Drug Solubility Enhancement (2017)

Solubility-enhancing amorphous solid dispersions are used in the oral delivery of hydrophobic, crystallizable drugs. Effective solid dispersion excipients enable high supersaturation drug concentrations and limit crystallization of the dissolved drug over extended times. We prepared poly(N-isopropylacrylamide)-based excipients of varying molar mass and with various end group identities, and examined their ability to improve the aqueous solubility of the Biopharmaceutical Class System Class II drug, phenytoin. Solid dispersions of these excipients and phenytoin were prepared at 10 wt % drug loading. Performance depended largely on the tendency of the polymer excipient to form micellar aggregates in aqueous buffer. We present several systems that achieved significant improvement of phenytoin solubility, with no indication of drug crystallization over 6 h. This is among the highest enhancement factors seen for phenytoin to date, and the success of these systems is ascribed to the added stability of these “self-micellizing” solid dispersions.
TutorialPlan: automated tutorial generation from CAD drawings (2013)

Authoring tutorials for complex software applications is a time consuming process. It also highly depends on the tutorial designer’s skill level and experience. This paper introduces an approach which automatically generates software tutorials using the digital artifacts produced by the users of a software program. We model this process as an optimal planning problem using software produced artifacts, software specifications and the human-computer interaction Keystroke-Level Model (KLM). We present TutorialPlan, an automated tutorial generator, which creates stepby-step text and image instructions from CAD drawings and helps users learn AutoCAD, a complex design and drafting software. In our tutorial generator, the optimal planning problem is represented and solved using DLV, a general Answer Set Programming (ASP) system. DLV offers a natural representation of both the problem and the heuristics needed to solve it efficiently. A user study shows that the tutorials generated by our system are comparable to those generated by experienced AutoCAD users. 1
New alkaline earth substituted lithium trivanadates: synthesis, characterization and lithium insertion behavior (2003)

New Mg, Ca and Ba partially substituted materials were prepared by ion exchange of Li+ in a Li1.1V3O8 precursor annealed at 350 °C. They present the same morphology as the precursor, with no well defined crystal shape. The chemical analyses lead to the general formula Li1.1−2yMyHzV3O8 (M = Mg, Ca, Ba; y ≈ 0.05–0.2; z ≈ 0.1). X-Ray diffraction analyses including Rietveld refinements have shown that the structure is basically the same as in the precursor. After the ion exchange, the materials present a larger surface area and a slightly smaller interlayer spacing. The Li insertion behaviors of the substituted materials and of the Li1.1V3O8 precursor present great similarities, confirmed by detailed studies using various galvanostatic or potentiodynamic techniques. Even if they present smaller initial capacities, the exchanged compounds exhibit both enhanced cycling capacities and decreased relative capacity losses on cycling. The diminution of relative capacity loss on cycling is believed to come from a structural stabilization by the divalent cation pillars, which better pin the layers together.
Pneumococcal Pili Are Composed of Protofilaments Exposing Adhesive Clusters of Rrg A (2008)

Pili have been identified on the cell surface of Streptococcus pneumoniae, a major cause of morbidity and mortality worldwide. In contrast to Gram-negative bacteria, little is known about the structure of native pili in Gram-positive species and their role in pathogenicity. Triple immunoelectron microscopy of the elongated structure showed that purified pili contained RrgB as the major compound, followed by clustered RrgA and individual RrgC molecules on the pilus surface. The arrangement of gold particles displayed a uniform distribution of anti-RrgB antibodies along the whole pilus, forming a backbone structure. Antibodies against RrgA were found along the filament as particulate aggregates of 2-3 units, often co-localised with single RrgC subunits. Structural analysis using cryo electron microscopy and data obtained from freeze drying/metal shadowing technique showed that pili are oligomeric appendages formed by at least two protofilaments arranged in a coiled-coil, compact superstructure of various diameters. Using extracellular matrix proteins in an enzyme-linked immunosorbent assay, ancillary RrgA was identified as the major adhesin of the pilus. Combining the structural and functional data, a model emerges where the pilus RrgB backbone serves as a carrier for surface located adhesive clusters of RrgA that facilitates the interaction with the host.
Solution Stability of Cephradine Neutralized with Arginine or Sodium Bicarbonate (1983)

The solution stability of two formulations of cephradine--one using L-arginine and the other sodium carbonate as the neutralizer--was studied. Solutions of each formulation of 1% cephradine were prepared in the following diluents: 0.9% sodium chloride injection, lactated Ringer's injection, Ringer's injection, Normosol-R injection, 5% dextrose injection, and sterile water for injection; 5 and 25% solutions were made with sterile water for injection. All solutions were maintained at 25 degrees C, and at least five samples of each were assayed at various time intervals. Assay methods were HPLC, hydroxylamine colorimetric assay, microbiological agar diffusion, and iodometric analysis. By all assay methods, degradation rates of 1% solutions were lower for the arginine-neutralized product than for the one neutralized with sodium carbonate. This may be attributable to the lower pH values of solutions of the formulation with arginine, because one mechanism of degradation is pH-dependent. At concentrations of 5%, the difference in cephradine stability between the two formulations was minimal. At the 25% concentration, the formulations containing sodium carbonate were more stable. At these higher concentrations, the effect of pH is less important because degradation occurs by a combination of mechanisms. The 1% cephradine-arginine formulation was more stable than the same strength cephradine-sodium carbonate formulation in all the i.v. diluents studied. At 5 and 25% cephradine concentrations, the differences in stability between the two formulations were not substantial.
Catalyzed additions to alkene double bonds: (I) Fumarase-catalyzed hydration of alkene double bonds (II) Alumina-catalyzed hydrochlorination of alkene double bonds (1996)

The stereospecific hydration of (5)-malate to fumarate, catalyzed by fumarase, was extensively analyzed by NMR. The NMR techniques employed were one dimensional 2H and NOE Difference, and two dimensional ^^H COSY. Various potentional substrates were tried for fumarase-promoted hydration with no sucesss. It was concluded that mesaconate is possibly the largest molecule that can fit into the active site of fumarase in the correct orientation for hydration to occur. Thionyl chloride and appropriately prepared alumina was found to promote the addition of HC1 to norbornadiene ( I ), resulting in71%(+l%) exo-5-chloronorbornene ( II ) and 29% 3-chloronortricyclene ( HI ) at room temperature, while lower temperatures favor the synthesis of the kinetic product, HI. Oxalyl chloride and alumina also produces II and HI, but the product composition slowly equilbrates mostly to the thermodynamic product, HI. Treatment of alumina with deuterium oxide was found to promote the addition of DC1 to norbornadiene, when used with thionyl chloride, to give 1 8% exo,aft'-5-chlorobicyclo[2.2.1]hept-2-ene-7-d ( VHIa ), 33% exo,exo-6-chlorobicyclo[2.2.1]hept-2-ene-5-d ( VHIb ), 21% 5-chlorotricyclo[2.2. 1 .0^2,6]heptane-3-d ( VEHc ), 20% H, and 8% HI. A higher ratio of Vmb/Vma for the catalyzed DC1 addition than for the uncatalyzed addition1 suggests that the 1 ,2-addition, when using alumina, gives a somwhat higher proportion of syn-addition.
Adaptive Representation Selection in Contextual Bandit (2018)

We consider an extension of the contextual bandit setting, motivated by
several practical applications, where an unlabeled history of contexts can
become available for pre-training before the online decision-making begins. We
propose an approach for improving the performance of contextual bandit in such
setting, via adaptive, dynamic representation learning, which combines offline
pre-training on unlabeled history of contexts with online selection and
modification of embedding functions. Our experiments on a variety of datasets
and in different nonstationary environments demonstrate clear advantages of our
approach over the standard contextual bandit.
Joint Traffic Routing and Distribution of Security Services in High Speed Networks (2008)

The continued explosion of new virus/worm and other security attacks in the Internet and the tremendous propagation speed of self-propagating attacks has led to network security being considered as a design criterion rather than an afterthought. Attack prevention, detection, and mitigation mechanisms can be broadly classified as network based or host based. Network based security mechanisms have been shown to be much more effective than host based mechanisms, primarily because of the former's ability in identifying attack traffic that is further upstream from the victim and closer to the attack source. In the context of network based mechanisms, we consider a flexible overlay network of security systems running on top of programmable (active) routers. In such an architecture, security services can be dynamically distributed across the network, which provides flexibility for load-balancing of services across nodes and addition of new services over time. Such network based mechanisms inevitably decrease network performance as all packets are analyzed for malicious content before being forwarded. In this paper, we consider traffic routing, placement of active router nodes, and distribution of security services across such nodes so as to optimize certain objectives, including (i) minimize the total number of active router deployed nodes, and (ii) minimize the maximum utilization of any router node in the network. Based on an emulation in the Deter testbed we show the benefit of the presented approach.