gebhart/patrepeval huggingface dataset:
S/MAR sequence confers long-term mitotic stability on non-integrating lentiviral vector episomes without selection (2014)

Insertional oncogene activation and aberrant splicing have proved to be major setbacks for retroviral stem cell gene therapy. Integrase-deficient human immunodeficiency virus-1-derived vectors provide a potentially safer approach, but their circular genomes are rapidly lost during cell division. Here we describe a novel lentiviral vector (LV) that incorporates human ß-interferon scaffold/matrix-associated region sequences to provide an origin of replication for long-term mitotic maintenance of the episomal LTR circles. The resulting 'anchoring' non-integrating lentiviral vector (aniLV) achieved initial transduction rates comparable with integrating vector followed by progressive establishment of long-term episomal expression in a subset of cells. Analysis of aniLV-transduced single cell-derived clones maintained without selective pressure for >100 rounds of cell division showed sustained transgene expression from episomes and provided molecular evidence for long-term episome maintenance. To evaluate aniLV performance in primary cells, we transduced lineage-depleted murine hematopoietic progenitor cells, observing GFP expression in clonogenic progenitor colonies and peripheral blood leukocyte chimerism following transplantation into conditioned hosts. In aggregate, our studies suggest that scaffold/matrix-associated region elements can serve as molecular anchors for non-integrating lentivector episomes, providing sustained gene expression through successive rounds of cell division and progenitor differentiation in vitro and in vivo.
Inactivation of T5 phage by cis-vaccenic acid, an antivirus substance from Rhodopseudomonas capsulata, and by unsaturated fatty acids and related alcohols (1991)

The antiviral extract from Rhodopseudomonas capsulata was purified and the predominant active component was defined as cis-vaccenic acid (Cl-8:1 delta 11) by gas-liquid chromatography and gas chromatography-mass spectrometry analyses. Antiviral activities of unsaturated fatty acids and related alcohols against T5 phage were also tested. Among them, linoelaidic acid, oleic acid, and petroselenyl alcohol inactivated 98%, 53%, 67% of T5 phage at the concentration of 50 micrograms/ml, respectively.
A standard multipurpose fax processor (1991)

A standard multipurpose facsimile processor aimed at adding facsimile functions to a variety of information processing systems has been developed. All the facsimile functions have been implemented on a single LSI chip, and integrated flow control was used to make this easier. The authors have also developed libraries for the basic facsimile functions, including CPUs, DMA controllers, compression functions, and serial control functions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Long-Range Structure in Ribonuclease P RNA (1991)

Phylogenetic-comparative and mutational analyses were used to elucidate the structure of the catalytically active RNA component of eubacterial ribonuclease P (RNase P). In addition to the refinement and extension of known structural elements, the analyses revealed a long-range interaction that results in a second pseudoknot in the RNA. This feature strongly constrains the three-dimensional structure of RNase P RNA near the active site. Some RNase P RNAs lack this structure but contain a unique, possibly compensating, structural domain. This suggests that different RNA structures located at different positions in the sequence may have equivalent architectural functions in RNase P RNA.
Morphine/ondansetron PCA for postoperative pain, nausea, and vomiting after skull base surgery (2006)

A-1b.
Proxy-based security protocols in networked mobile devices (2002)

We describe a resource discovery and communication system designed for security and privacy. All objects in the system, e.g., appliances, wearable gadgets, software agents, and users have associated trusted software proxies that either run on the appliance hardware or on a trusted computer. We describe how security and privacy are enforced using two separate protocols: a protocol for secure device-to-proxy communication, and a protocol for secure proxy-to-proxy communication. Using two separate protocols allows us to run a computationally-inexpensive protocol on impoverished devices, and a sophisticated protocol for resource authentication and communication on more powerful devices.We detail the device-to-proxy protocol for lightweight wireless devices and the proxy-to-proxy protocol which is based on SPKI/SDSI (Simple Public Key Infrastructure / Simple Distributed Security Infrastructure). A prototype system has been constructed, which allows for secure, yet efficient, access to networked, mobile devices. We present a quantitative evaluation of this system using various metrics.
Differential nuclear protein binding to 5-azacytosine-containing DNA as a potential mechanism for 5-aza-2'-deoxycytidine resistance. (1987)

A clonal cell line (56-42) that was stably and exclusively resistant to the toxic effects of the antileukemic agent 5-aza-2'-deoxycytidine (5-aza-CdR) was derived from C3H 10T1/2 C18 cells after multiple treatments with 5-aza-CdR. The 50% lethal dose of 5-aza-CdR for these cells was 1.3 microM, which was 15-fold greater than that for the parental cells. Cell line 56-42 was slightly cross-resistant to the ribo-analog 5-azacytidine, but was sensitive to the nucleoside analog 1-beta-D-arabinofuranosylcytosine and to colcemid. Both parental and resistant cell lines incorporated equimolar amounts of 5-aza-CdR into DNA. Resistance was therefore not due to decreased activation, increased detoxification, or reduced incorporation of the drug. The overall level of cytosine methylation in the resistant clone was 80% lower than the level in the sensitive cells. Therefore, the potential number of hemimethylated sites created by the incorporation of equivalent amounts of 5-aza-CdR into the DNA of the two cell types was much greater in the sensitive cells. Furthermore, 5-azacytosine-substituted DNA from the sensitive cells bound 100% more nuclear protein in the form of highly stable complexes. The incorporation of 5-aza-CdR opposite methylated cytosine residues in DNA of the sensitive cells thus resulted in increased nuclear protein binding at hemimethylated sites. This relative increase in tight-binding protein complexes was shown to occur in living cells and may well disrupt replication and transcription and instigate cell death. The differential binding of proteins to hypomethylated, azacytosine-containing DNA may thus mediate a novel mechanism of drug resistance.
Blend composition study of poly(3,3‴-didodecylquaterthiophene)/[6,6]-phenyl C61 butyric acid methyl ester solution processed organic solar cells (2009)

Photovoltaic devices made from blends of poly(3,3‴-didodecylquaterthiophene) (PQT-12) and [6,6]-phenyl C61 butyric acid methyl ester have been fabricated and characterized. By varying the polymer loading in the blend, an optimal power conversion efficiency (PCE) of 0.70% has been achieved for a blend consisting of 15 wt % PQT-12, which is an order of magnitude higher than the PCE for a 50 wt % blend. The apparent reason for the large difference is the fact that blends with higher PQT-12 loading are transport limited, with much larger hole-to-electron mobility ratios.
Comment on ‘‘Empirical fit to band discontinuities and barrier heights in III-V alloy systems’’ (1992)

In a recent letter Tiwari and Frank(1) “present a figure summarizing the variation of ... band discontinuity ... and gold Schottky barrier height for binary and ternary III-V semiconductors.” Figures constructed in the same way were presented earlier by McCaldin and co-workers (2-4) for binary compounds, including the III-Vs, and by Schuermeyer et al.(5) for ternary III-Vs. As for the numerical values used in the Tiwari and Frank figure, their energy values for binary III-V compounds are in excellent agreement with values presented(6) in 1976, which they seem to be unaware of. Thus yet undiscussed aspects of their letter are (1) the relevance of a previously described graphical presentation and (2) agreement with sixteen year old data.
Primary surgical treatment of anterior cruciate ligament ruptures (1990)

We reviewed 52 patients who underwent primary surgical repair of their acutely injured ACL using a multiple loop, varying depth suture technique. The average followup was 6 years and 10 months. Nine patients (17%) were considered as having failed repairs, with failure based on the presence of clinical instability (giving way) with sports participation and a positive Lachman test and/or pivot shift maneuver. In addition, of 26 patients in whom KT-1000 (MEDmetric Corp., San Diego, CA) measurements were performed, 42% were found to have abnormal laxity. Although using multiple sutures in primary repair of the anterior cruciate may work in some patients, it is an unpredictable operative procedure and resulted in a 17% failure rate in our study.
Regulation of the Natural Killer Cell Response to Interferon-α by Biogenic Amines (1992)

Monocytes, recovered from human peripheral blood by counter-current centrifugal elutriation (CCE), suppressed baseline natural killer (NK) cell cytotoxicity (NKCC) and rendered NK cells resistant to activation of cytotoxicity by human recombinant interferon-alpha (IFN-alpha) by a cell contact-dependent mechanism. Monocyte-induced suppression of resting and IFN-activated NK cells was abrogated by the biogenic amines histamine [via H2-type receptors (H2R)] and serotonin [via 5-HT1A-type receptors (5-HT1AR)]. Our data are suggestive of a monocyte/NK cell interaction that is subject to regulation by biogenic amines.
Rapid and sensitive analysis of mRNA polyadenylation states by PCR. (1995)

A rapid and sensitive technique is described that measures the length of the poly(A) tail on a specific mRNA within subnanogram quantities of total cellular RNA [the Poly(A) test (PAT)]. In a single-tube reaction, a poly(dT) primer is synthesized in situ on the poly(A) tail of mRNAs using oligo(dT) and DNA ligase. By modulating the annealing temperature and primer concentrations, a GC-rich adapter sequence is targeted to the 5' end of the poly(dT) primer. This ligated poly(dT)-anchor is then used to prime reverse transcription of the mRNA, yielding a library of PAT cDNAs. The length of a poly(A) tail is determined by PCR amplification using the oligo(dT)-anchor primer and a message-specific primer. Comparison of PCR products from different samples allows quantitative determination of changes in polyadenylation of a given mRNA. This technique overcomes many of the pitfalls associated with conventional poly(A) tail length assessments and should prove useful in studying a variety of processes relating to polyadenylation.
Degree-dependent and cascading node failures in random geometric networks (2011)

We study the problem of resilience to node failures in large-scale networks modelled by random geometric graphs. Adopting a percolation-based viewpoint, we investigates the ability of the network to maintain global communication in the presence of dependent node failures. Degree-dependent site percolation processes on random geometric graphs are examined, and the first known analytical conditions are obtained for the existence and non-existence, respectively, of a large connected component of operational network nodes after degree-dependent node failures. In electrical power networks or wireless communication and computing networks, cascading failure from power blackouts or virus epidemics may result from a small number of initial node failures triggering global failure events affecting the whole network. With the use of a simple but descriptive model, it is shown that the cascading failure problem is equivalent to a degree-dependent percolation process. The first analytical conditions are obtained for the occurrence and non-occurrence of cascading failures, respectively, in large-scale networks with geometric constraints.
High Dynamic GPS Receiver Using Maximum Likelihood Estimationand Frequency Tracking (1987)

A new high dynamic global positioning system (GPS) receiver ispresented and its performance characterized by analysis,simulation, and demonstration. The demonstration receiver is abreadboard model capable of tracking a single simulated satellitesignal in pseudorange and range rate. Pseudorange and range rateestimates are made once every 20 ms, using a maximum likelihoodestimator, and are tracked by means of a third-order fadingmemory filter in a feedback configuration. The receiver trackspseudorange with rms errors of under 1 m when subjected tosimulated 50 g, 40 g/s circular trajectories. The tracking thresholdis approximately 28 dB·Hz, which provides 12 dB margin relativethe the minimum specified signal strength, assuming 3.5 dB systemnoise figure and 0 dB antenna gain.
Inhibitors of Human Immunodeficiency Virus Type 1 (HIV-1) Attachment. 12. Structure–Activity Relationships Associated with 4-Fluoro-6-azaindole Derivatives Leading to the Identification of 1-(4-Benzoylpiperazin-1-yl)-2-(4-fluoro-7-[1,2,3]triazol-1-yl-1<i>H</i>-pyrrolo[2,3-<i>c</i>]pyridin-3-yl)ethane-1,2-dione (BMS-585248) (2013)

A series of highly potent HIV-1 attachment inhibitors with 4-fluoro-6-azaindole core heterocycles that target the viral envelope protein gp120 has been prepared. Substitution in the 7-position of the azaindole core with amides (12a,b), C-linked heterocycles (12c-l), and N-linked heterocycles (12m-u) provided compounds with subnanomolar potency in a pseudotype infectivity assay and good pharmacokinetic profiles in vivo. A predictive model was developed from the initial SAR in which the potency of the analogues correlated with the ability of the substituent in the 7-position of the azaindole to adopt a coplanar conformation by either forming internal hydrogen bonds or avoiding repulsive substitution patterns. 1-(4-Benzoylpiperazin-1-yl)-2-(4-fluoro-7-[1,2,3]triazol-1-yl-1H-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione (BMS-585248, 12m) exhibited much improved in vitro potency and pharmacokinetic properties than the previous clinical candidate BMS-488043 (1). The predicted low clearance in humans, modest protein binding, and good potency in the presence of 40% human serum for 12m led to its selection for human clinical studies.
Lilith's Midwives: Jewish Newborn Child Murder in Nineteenth-Century Vilna (2010)

This article examines a court case of newborn child murder in nineteenth-century Vilna. In 1890, the state indicted a group of Jewish women for running a lucrative baby-farming business in which they hired out unwed mothers as wet nurses and extorted their salaries in exchange for the care of their illegitimate offspring—most of whom died from neglect or abuse. I argue that this illegal network on the outskirts of town threatened the legitimate, respectable Jewish world at the center but was indispensable to it. It provided families with wet nurses, domestic servants, and even infants for childless wives to adopt. It also allowed a legitimate way for unwed mothers to abandon their unwanted offspring. Scrutiny of this lower-class women's space sheds light not only on the lives of unwed mothers but also on the complicity of Jewish society in the fate of their illegitimate children.
The Use of Optimal Cutting Temperature Compound Can Inhibit Amplification by Polymerase Chain Reaction (1997)

Optimal cutting temperature (OCT) is a widely used embedding medium for tissues for histopathologic analysis. This investigation examined the effects that OCT storage can have upon the ability to perform subsequent molecular biological analyses. Tumor material was dissected into small pieces and stored at approximately 20 degrees C both with and without OCT. DNA and RNA were then extracted from the tissue fragments and analyzed by the polymerase chain reaction (PCR), using primer sets designed to amplify a range of product sizes, and also by reverse transcriptase-PCR (RT-PCR). The storage of pathological specimens in OCT compound was found to affect significantly and irreversibly the ability to amplify DNA in the PCR, particularly as the size of the amplified fragment increased. This effect appeared to occur as a result of greater degradation of DNA extracted from tissue embedded in OCT compared to DNA extracted from tissue stored without OCT. RNA quality appeared unaffected, which may be because of the extraction protocol employed. Our results suggest that OCT-embedded frozen-tissue samples may be used for RNA isolation for subsequent RT-PCR and for the in vitro amplification of DNA targets of approximately < 300 base pairs only. We strongly advise against the routine storage of any tissue biopsy material in OCT if molecular analyses may be required.
The eternal triangle. (1970)

Nurses and Doctors-Powell Bisn= piety cannot, as a general rule, be sincere."18.. Was the dinner with Simpson and his friends at 52 Queen Street a sober occasion?Physically speaking, perhaps; intel- lectually it could hardly be.How one would like to re-create the scene!Simpson in charge, large and amiable, spreading his girth and his piesence around him;"9 and Andersen the honoured guest, tall and thin, supported on his huge feet, dressed in an odd combination of wide trousers and high, starched collar; childlike and charming withal.
A Dietary Nucleoside-Nucleotide Mixture Inhibits Endotoxin-Induced Bacterial Translocation in Mice Fed Protein-Free Diet (1995)

Nucleosides and nucleotides are important substrates utilized by the intestinal mucosa. To determine the relative effect of dietary nucleosides and nucleotides on the gut, we investigated the effects of these compounds on endotoxin-induced bacterial translocation, cecal bacterial populations and ileal histology in protein-malnourished mice. There was an inhibition of gram-negative enteric bacteria in the mesenteric lymph node and spleen of the surviving mice fed the protein-free diet supplemented with a nucleoside-nucleotide mixture compared with the nonsupplemented group. Histologically, the damage to the gut mucosal barrier was more pronounced in the nonsupplemented group than in the nucleoside-nucleotide supplemented group. However, the cecal bacterial populations in the groups were not different. The villous height, crypt depth and total wall thickness were more developed in the supplemented group compared with the nonsupplemented group, indicating that the nucleoside-nucleotide mixture blocked bacterial translocation by preventing endotoxin-induced mucosal or epithelial damage. These results suggest that the nucleoside-nucleotide mixture could be used to inhibit or reduce the incidence of bacterial translocation, decrease intestinal injury and improve survival in a lethal model of protein deficiency and endotoxemia.
Room-Temperature Self-Healing Polymers Based on Dynamic-Covalent Boronic Esters (2015)

Cross-linked polymers constructed with dynamic-covalent boronic esters were synthesized via photoinitiated radical thiol–ene click chemistry. Because the reversibility of the boronic ester cross-links was readily accessible, the resulting materials were capable of undergoing bond exchange to covalently mend after failure. The reversible bonds of the boronic esters were shown to shift their exchange equilibrium at room temperature when exposed to water. Nevertheless, the materials were observed to be stable and hydrophobic and absorbed only minor amounts of water over extended periods of time when submerged in water or exposed to humid environments. The facile reversibility of the networks allowed intrinsic self-healing under ambient conditions. Highly efficient self-healing of these bulk materials was confirmed by mechanical testing, even after subjecting a single site to multiple cut–repair cycles. Several variables were considered for their effect on materials properties and healing, including cross-link density, humidity, and healing time.
Graphitic Biocarbon from Metal-Catalyzed Hydrothermal Carbonization of Lignin (2015)

Lignin is a high-volume byproduct from the pulp and paper industry and is currently burned to generate electricity and process heat. The industry has been searching for high value-added uses of lignin to improve the process economics. In addition, battery manufacturers are seeking nonfossil sources of graphitic carbon for environmental sustainability. In this work, lignin (which is a cross-linked polymer of phenols, a component of biomass) is converted into graphitic porous carbon using a two-step conversion. Lignin is first carbonized in water at 300 °C and 1500 psi to produce biochar, which is then graphitized using a metal nitrate catalyst at 900–1100 °C in an inert gas at 15 psi. Graphitization effectiveness of three different catalysts—iron, cobalt, and manganese nitrates—is examined. The product is analyzed for morphology, thermal stability, surface properties, and electrical conductivity. Both temperature and catalyst type influenced the degree of graphitization. A good quality graphitic carbon was obtained using catalysis by Mn(NO3)2 at 900 °C and Co(NO3)2 at 1100 °C.
Reservoir Computing with Stochastic Bitstream Neurons (2005)

Reservoir Computing (RC) [6], [5], [9] is a computational framework with powerful properties and several interesting advantages compared to conventional techniques for pattern recognition. It consists essentially of two parts: a recurrently connected network of simple interacting nodes (the reservoir), and a readout function that observes the reservoir and computes the actual output of the system. The choice of the nodes that form the reservoir is very broad: spiking neurons [6], threshold logic gates [7] and sigmoidal neurons [5], [9] have been used. For this article, we will use analogue neurons to build an RC-system on a Field Programmable Gate Array (FPGA), which is a chip that can be reconfigured. A traditional neuron calculates a weighted sum of its inputs, which is then fed through a non-linearity (like a threshold or sigmoid function). This is not hardware efficient due to the extensive use of multiplications. In [2], a type of neuron is introduced that communicates using stochastic bitstreams instead of fixed-point values. This drastically simplifies the hardware implementation of arithmetic operations such as addition, the nonlinearity and multiplication. We have built an implementation of RC on FPGA, using these stochastic neurons.
Synthesis of highly active tungsten-containing MCM-41 mesoporous molecular sieve catalyst (1998)

A tungsten-containing MCM-41 mesoporous molecular sieve is synthesized by the hydrolysis of tetraethylorthosilicate and ammonium tungstate in the presence of cetylpyridinium bromide as template in acidic medium and found to be more active than the conventional WO3 catalyst in the hydroxylation of cyclohexene using H2O2 as oxidant.
Cryptanalysis of recently proposed Remote User Authentication Schemes. (2006)

Recently Manik et al. [13] proposed a novel remote user authentication scheme using bilinear pairings. Chou et al. [14] identified a weakness in Manik et al.’s scheme and made an improvement. In this paper, we show that both Manik et al.’s and Chou et al.’s schemes are insecure against forgery attack and replay attack.