gebhart/patrepeval huggingface dataset:
Interchromosomal Crossover in Human Cells Is Associated with Long Gene Conversion Tracts (2007)

Crossovers have rarely been observed in specific association with interchromosomal gene conversion in mammalian cells. In this investigation two isogenic human B-lymphoblastoid cell lines, TI-112 and TSCER2, were used to select for I-SceI-induced gene conversions that restored function at the selectable thymidine kinase locus. Additionally, a haplotype linkage analysis methodology enabled the rigorous detection of all crossover-associated convertants, whether or not they exhibited loss of heterozygosity. This methodology also permitted characterization of conversion tract length and structure. In TI-112, gene conversion tracts were required to be complex in tract structure and at least 7.0 kb in order to be selectable. The results demonstrated that 85% (39/46) of TI-112 convertants extended more than 11.2 kb and 48% also exhibited a crossover, suggesting a mechanistic link between long tracts and crossover. In contrast, continuous tracts as short as 98 bp are selectable in TSCER2, although selectable gene conversion tracts could include a wide range of lengths. Indeed, only 16% (14/95) of TSCER2 convertants were crossover associated, further suggesting a link between long tracts and crossover. Overall, these results demonstrate that gene conversion tracts can be long in human cells and that crossovers are observable when long tracts are recoverable.
Five recent books on Swift (1997)

Eighteenth-Century Life - Volume 21, Number 3, November 1997
Transpapillary Drug Delivery to the Breast (2014)

The study was aimed at investigating localized topical drug delivery to the breast via mammary papilla (nipple). 5-fluorouracil (5-FU) and estradiol (EST) were used as model hydrophilic and hydrophobic compounds respectively. Porcine and human nipple were used for in-vitro penetration studies. The removal of keratin plug enhanced the drug transport through the nipple. The drug penetration was significantly higher through the nipple compared to breast skin. The drug's lipophilicity had a significant influence on drug penetration through nipple. The ducts in the nipple served as a major transport pathway to the underlying breast tissue. Results showed that porcine nipple could be a potential model for human nipple. The topical application of 5-FU on the rat nipple resulted in high drug concentration in the breast and minimal drug levels in plasma and other organs. Overall, the findings from this study demonstrate the feasibility of localized drug delivery to the breast through nipple.
Purification and Properties of β-Glucosidase from <i>Aspergillus terreus</i> (1982)

A beta-glucosidase (EC 3.2.1.21) from the fungus Aspergillus terreus was purified to homogeneity as indicated by disc acrylamide gel electrophoresis. Optimal activity was observed at pH 4.8 and 50 degrees C. The beta-glucosidase had K(m) values of 0.78 and 0.40 mM for p-nitrophenyl-beta-d-glucopyranoside and cellobiose, respectively. Glucose was a competitive inhibitor, with a K(i) of 3.5 mM when p-nitrophenyl-beta-d-glucopyranoside was used as the substrate. The specific activity of the enzyme was found to be 210 IU and 215 U per mg of protein on p-nitrophenyl-beta-d-glucopyranoside and cellobiose substrates, respectively. Cations, proteases, and enzyme inhibitors had little or no effect on the enzyme activity. The beta-glucosidase was found to be a glycoprotein containing 65% carbohydrate by weight. It had a Stokes radius of 5.9 nm and an approximate molecular weight of 275,000. The affinity and specific activity that the isolated beta-glucosidase exhibited for cellobiose compared favorably with the values obtained for beta-glucosidases from other organisms being studied for use in industrial cellulose saccharification.
Collaborative Action of Brca1 and CtIP in Elimination of Covalent Modifications from Double-Strand Breaks to Facilitate Subsequent Break Repair (2010)

Topoisomerase inhibitors such as camptothecin and etoposide are used as anti-cancer drugs and induce double-strand breaks (DSBs) in genomic DNA in cycling cells. These DSBs are often covalently bound with polypeptides at the 3' and 5' ends. Such modifications must be eliminated before DSB repair can take place, but it remains elusive which nucleases are involved in this process. Previous studies show that CtIP plays a critical role in the generation of 3' single-strand overhang at "clean" DSBs, thus initiating homologous recombination (HR)-dependent DSB repair. To analyze the function of CtIP in detail, we conditionally disrupted the CtIP gene in the chicken DT40 cell line. We found that CtIP is essential for cellular proliferation as well as for the formation of 3' single-strand overhang, similar to what is observed in DT40 cells deficient in the Mre11/Rad50/Nbs1 complex. We also generated DT40 cell line harboring CtIP with an alanine substitution at residue Ser332, which is required for interaction with BRCA1. Although the resulting CtIP(S332A/-/-) cells exhibited accumulation of RPA and Rad51 upon DNA damage, and were proficient in HR, they showed a marked hypersensitivity to camptothecin and etoposide in comparison with CtIP(+/-/-) cells. Finally, CtIP(S332A/-/-)BRCA1(-/-) and CtIP(+/-/-)BRCA1(-/-) showed similar sensitivities to these reagents. Taken together, our data indicate that, in addition to its function in HR, CtIP plays a role in cellular tolerance to topoisomerase inhibitors. We propose that the BRCA1-CtIP complex plays a role in the nuclease-mediated elimination of oligonucleotides covalently bound to polypeptides from DSBs, thereby facilitating subsequent DSB repair.
<i>Acinetobacter baumannii</i> Increases Tolerance to Antibiotics in Response to Monovalent Cations (2009)

Acinetobacter baumannii is well adapted to the hospital environment, where infections caused by this organism are associated with significant morbidity and mortality. Genetic determinants of antimicrobial resistance have been described extensively, yet the mechanisms by which A. baumannii regulates antibiotic resistance have not been defined. We sought to identify signals encountered within the hospital setting or human host that alter the resistance phenotype of A. baumannii. In this regard, we have identified NaCl as being an important signal that induces significant tolerance to aminoglycosides, carbapenems, quinolones, and colistin upon the culturing of A. baumannii cells in physiological NaCl concentrations. Proteomic analyses of A. baumannii culture supernatants revealed the release of outer membrane proteins in high NaCl, including two porins (CarO and a 33- to 36-kDa protein) whose loss or inactivation is associated with antibiotic resistance. To determine if NaCl affected expression at the transcriptional level, the transcriptional response to NaCl was determined by microarray analyses. These analyses highlighted 18 genes encoding putative efflux transporters that are significantly upregulated in response to NaCl. Consistent with this, the effect of NaCl on the tolerance to levofloxacin and amikacin was significantly reduced upon the treatment of A. baumannii with an efflux pump inhibitor. The effect of physiological concentrations of NaCl on colistin resistance was conserved in a panel of multidrug-resistant isolates of A. baumannii, underscoring the clinical significance of these observations. Taken together, these data demonstrate that A. baumannii sets in motion a global regulatory cascade in response to physiological NaCl concentrations, resulting in broad-spectrum tolerance to antibiotics.
Hunter standoff killer team (HSKT) ground and flight test results (2007)

Since the inception of powered flight, manned aerial vehicles have been a force multiplier on the battlefield. With the emergence of new technology, the structure of the military battlefield is changing. One such technology, the Unmanned Aerial Vehicle (UAV) has emerged as a valuable asset for today's war fighter. UAVs have traditionally been operated by ground control stations, yet minimum research has been targeted towards UAV connectivity. Airborne Manned Unmanned System Technology Baseline (AMUST-Baseline) was a concept that demonstrated the battlefield synergy gained by Manned and Unmanned Vehicle teaming. AMUST-Baseline allowed an Apache Longbow's (AH-64D) co-pilot gunner (CPG) to have Level IV control of a Hunter fixed wing UAV. Level IV control of a UAV includes payload control, flight control and direct data receipt. With the success of AMUST-Baseline, AATD, Lockheed Martin, Northrop Grumman, and the Boeing Company worked towards enhanced Manned and Unmanned connectivity through a technology investment agreement. This effort named Airborne Manned Unmanned System Technology Demonstration (AMUST-D) focused on the connectivity between two manned platforms, Apache Longbow (AH-64D) and Command and Control (C2) Blackhawk, and Hunter UAV. It allows robust communication from the UAV to each platform through the Tactical Common Data Link (TCDL). AMUST-D used decision aiding technology developed under the Rotorcraft Pilots Associate (RPA) Advanced Technology Demonstration (ATD) as to assist in control of the Hunter UAV, as well as assist the pilot in regularly performed duties. Through the use of decision aiding and UAV control, the pilot and commander were better informed of potential threats and targets, thus increasing his situational awareness. The potential benefits of improved situational awareness are increased pilot survivability, increased lethality, and increased operational effectiveness. Two products were developed under the AMUST-D program, the Warfighter's Associate (WA) which was integrated onto the Apache Longbow, and the Mobile Commanders Associate (MCA) which was integrated onto the Army Airborne Command and Control System (A2C2S) UH-60 Blackhawk. In this paper we will discuss what WA and MCA provided to the warfighter, and the results of the HSKT ground and flight testing.
Study of field driven electroluminescence in colloidal quantum dot solids (2012)

Semiconductor nanocrystals, or quantum dots (QDs), promise to drive advances in electronic light generation. It was recently shown that long range transport of charge, which is typically required for electric excitation and which is inherently limited in nanosized materials, can be avoided by developing devices that operate through local, field-assisted generation of charge. We investigate such devices that consist of a thin film of CdSe/ZnS core-shell QD placed between two dielectric layers and that exhibit electroluminescence under pulsed, high field excitation. Using electrical and spectroscopic measurements, we are able to elucidate the dynamics of charge within the QD layer and determine that charge trapping and field-induced luminescence quenching are the main limitations of device performance.
Sox10 directs neural stem cells toward the oligodendrocyte lineage by decreasing Suppressor of Fused expression (2010)

Oligodendrocyte precursor cells (OPCs) are lineage-restricted progenitors generally limited in vivo to producing oligodendrocytes. Mechanisms controlling genesis of OPCs are of interest because of their importance in myelin development and their potential for regenerative therapies in multiple sclerosis and dysmyelinating syndromes. We show here that the SoxE transcription factors (comprising Sox8, 9, and 10) induce multipotent neural precursor cells (NPCs) from the early postnatal subventricular zone (SVZ) to become OPCs in an autonomous manner. We performed a chromatin immunoprecipitation-based bioinformatic screen and identified Suppressor of Fused (Sufu) as a direct target of repression by Sox10. In vitro, overexpression of Sufu blocked OPC production, whereas RNAi-mediated inhibition augmented OPC production. Furthermore, mice heterozygous for Sufu have increased numbers of OPCs in the telencephalon during development. We conclude that Sox10 acts to restrict the potential of NPCs toward the oligodendrocyte lineage in part by regulating the expression of Sufu.
An exact mapping between the Variational Renormalization Group and Deep\n Learning (2014)

Deep learning is a broad set of techniques that uses multiple layers of\nrepresentation to automatically learn relevant features directly from\nstructured data. Recently, such techniques have yielded record-breaking results\non a diverse set of difficult machine learning tasks in computer vision, speech\nrecognition, and natural language processing. Despite the enormous success of\ndeep learning, relatively little is understood theoretically about why these\ntechniques are so successful at feature learning and compression. Here, we show\nthat deep learning is intimately related to one of the most important and\nsuccessful techniques in theoretical physics, the renormalization group (RG).\nRG is an iterative coarse-graining scheme that allows for the extraction of\nrelevant features (i.e. operators) as a physical system is examined at\ndifferent length scales. We construct an exact mapping from the variational\nrenormalization group, first introduced by Kadanoff, and deep learning\narchitectures based on Restricted Boltzmann Machines (RBMs). We illustrate\nthese ideas using the nearest-neighbor Ising Model in one and two-dimensions.\nOur results suggests that deep learning algorithms may be employing a\ngeneralized RG-like scheme to learn relevant features from data.\n
Oxygen controlled product formation in CCl{sub 4} dechlorination using zero-valent iron (1995)

Carbon tetrachloride (CCl{sub 4}) was abiotically dechlorinated using zero-valent iron powder (Fe{sup o}) to yield chloroform (CHCl{sub 3}) and methylene chloride (CH{sub 2}Cl{sub 2}), which did not undergo further dechlorination. Dechlorination was rapid and approximated first-order kinetics in the range of concentrations tested (CCl{sub 4}: 1.5 to 5.5 {mu}M; Fe{sup o}: 1 to 10 g per 265 mL distilled deionized water). Initial dechlorination rate coefficients for anoxic batch reactors (0.290 {plus_minus} 0.009 hr{sup -1} for 1 g Fe{sup o}; 1.723 {plus_minus} 0.078 hr{sup -1} for 10 g Fe{sup o}) increased with iron surface area (initially 2.4 {plus_minus} 0.2 m{sup 2}/g). Dechlorination also occurred under oxic conditions, although rates were significantly slower (e.g., 0.085 {plus_minus} 0.041 hr{sup -1} for 1 g Fe{sup o} and 7.4 mg/L initial dissolved oxygen). Rate coefficients increased with time, probably due to an increase in reactive surface area from pitting and dissolution of the iron surface. A rapid pH increase was synchronous to dissolved oxygen consumption, and the pH remained constant after oxygen depletion. This was attributed to the proton and oxygen consuming aerobic corrosion of the Fe{sup o} surface. Recalcitrant CH{sub 2}Cl{sub 2} was decreased in the presence of dissolved oxygen, which reacted with dechlorinatedmore » intermediates to yield less environmentally onerous products such as formic acid and carbon monoxide.« less
RESPONSE OF THE NON-MYELINATED NERVE TERMINAL IN PACINIAN CORPUSCLES TO MECHANICAL AND ANTIDROMIC STIMULATION AND THE EFFECT OF PROCAINE, CHOLINE AND COOLING (1963)

1. Potential changes in response to antidromic and mechanical stimuli were recorded across an oil-saline interface placed close to or at the non-myelinated terminal of the Pacinian corpuscle, of which the lamellae had been removed up to the central core.2. An antidromic stimulus produced a diphasic potential indicating that an antidromic impulse can invade the terminal, while a mechanical stimulus generated a diphasic response of an all-or-nothing nature superimposed on a graded response, or on the receptor potential. This all-or-nothing response to mechanical stimuli can be abolished and the antidromic impulse becomes monophasic when procaine, choline or cooling is applied to the terminal.3. When a mechanical stimulus was delivered within a few msec after an antidromic impulse, the all-or-nothing response to mechanical stimuli was abolished, and only the receptor potential was observed during the refractory period of the terminal. The amplitude of the receptor potential became smaller as the interval between the mechanical and antidromic stimuli was shortened. The depression of the receptor potential could not be observed, when the terminal was made inexitable by procaine, choline and cooling so that antidromic impulses could not invade the terminal.4: The relative amplitude of the maximum receptor potential, the all-ornothing impulse at the terminal and the mechanically and antidromatically elicited impulses at the first node of Ranvier was measured; their average ratio being 0.49: 0.36: 0.85: 1.5. The receptor potential has a rise time of about 1 msec and the time constant of decay of its exponential falling phase is 0.9 msec, which is smaller than that obtained in intact Pacinian corpuscles.
John Gatenby Bolton, 5 June 1922 - 6 July 1993 (1995)

Abstract Since World War II astronomy has lived through its golden age undergoing a complete transformation. Before the war, astronomy meant optical astronomy and observations were confined to the use of the narrow range of visible spectrum capable of penetrating the earth’s atmosphere - about 1 octave in all. Since that time new advances have made it possible to observe at radio, infrared, ultra-violet, X-ray and gamma-ray wavelengths covering a spectrum of some 56 octaves. An exciting consequence of the new era has been the discovery of new classes of galaxies with extraordinarily high energy and luminosity, pushing back the limits of the observable universe beyond all expectations. What started this great revolution? It may be fairly said that it all began in 1948 in Sydney, Australia, when a three-man team led by a 26-year old Yorkshireman named John Bolton discovered that three distant objects, known from optical observations, were, extremely powerful emitters of radio waves. One, which Bolton called ‘Taurus A’, was located in our own galaxy; the Crab Nebula. The other two (‘Virgo A’ and ‘Centaurus A’) were external galaxies. This discovery marked the beginning of the new era in which the universe could be explored by means of its high- energy galaxies. The pursuit of this subject became the main theme of Bolton’s scientific life.
Four hundred-million-year-old vesicular arbuscular mycorrhizae. (1994)

The discovery of arbuscules in Aglaophyton major, an Early Devonian land plant, provides unequivocal evidence that mycorrhizae were established >400 million years ago. Nonseptate hyphac and arbuscules occur in a specialized meristematic region of the cortex that continually provided new cells for fungal infection. Arbuscules are morphologically identical to those of living arbuscular mycorrhizae in consisting of a basal trunk and repeatedly branched bush-like tuft within the plant cell. Although interpretations of the evolution of mycorrhizal mutualisms continue to be speculative, the existence of arbuscules in the Early Devonian indicates that nutrient transfer mutualism may have been in existence when plants invaded the land.
Carbon Dioxide Mitigation: Carbon Nano‐Onions Made Directly from CO<sub>2</sub> by Molten Electrolysis for Greenhouse Gas Mitigation (Adv. Sustainable Syst. 10/2019) (2019)

In article number 1900056, Stuart Licht and co-workers, the first high yield electrosynthesis of carbon nano-onions (CNOs) by low cost molten carbonate electrolysis is shown. The only reactant, CO2, becomes a useful, valuable resource rather than a greenhouse pollutant as a response to mitigate anthropogenic CO2. The synthesis is achieved by excluding nucleating agents from the molten carbonate growth medium resulting in a profusion of uniform CNOs.
Identification of the True Product of the Urate Oxidase Reaction (1997)

The O2-dependent oxidation of urate catalyzed by urate oxidase has been examined in order to identify the immediate product of the enzymatic reaction. Specifically labeled [13C]urates were utilized as substrates, and the time courses were monitored by 13C NMR. On the basis of chemical shift values and 18O labeling, the product of the reaction was identified as 5-hydroxyisourate. This identification was substantiated by calculation of the 13C NMR spectrum of 5-hydroxyisourate using ab initio density functional theory methods. The predominant tautomers of urate and allantoin in aqueous solution were identified from 13C NMR titration data; the ionization behavior of urate and 5-hydroxyisourate were also examined by computational methods. The nonenzymatic pathway for production of allantoin from 5-hydroxyisourate was delineated; the reaction proceeds by the hydrolysis of the N1−C6 bond, followed by an unusual 1,2-carboxylate shift and decarboxylation to form allantoin.
Criteria Documents Revisited (1982)

Professor of Occupational Medicine, from the School of Public Health, the University of Texas Health Science Center at Houston, P.O. Box 20186, Houston, TX 77025
Nucleic acid amphiphiles: synthesis and self-assembled nanostructures (2011)

This review provides an overview of a relatively new class of bio-conjugates, DNA amphiphiles, which consist of oligonucleotides covalently bonded to synthetic hydrophobic units. The reader will find the basic principles for the structural design and preparation methods of the materials. Moreover, the self-assembly into superstructures of higher order will be highlighted. Finally, some potential applications will be described.
Transparent Solar Concentrator for Flat Panel Display (2012)

A new concept of the transparent solar concentrator for flat panel display is experimentally demonstrated without adversely affecting the visual effects. The solar concentrator is based on a solar light-guide plate with micro prisms, not only increasing the absorption area of solar energy but also enhancing the conversion efficiency. The incident light is guided by the designed solar light-guide plate according to the total internal reflection (TIR), and converted into electrical power by photovoltaic solar cells. The designed transparent solar concentrator was made and measured with high transparency, namely 94.8%. The developed solar energy system for display can store energy and supply the bias voltage to light on two light-emitting diodes (LEDs) successfully.
Adaptive Interrogation for Fast Optical Sensing Based on Cascaded Micro-Ring Resonators (2010)

An adaptive interrogation technique that employs integrated semiconductor micro-ring resonators (MRR) for fast-response sensing applications is proposed and numerically studied. The basic sensing scheme consists of two MRRs in an add/drop signal configuration; the first MRR plays the role of the measuring sensor, while the second one acts as a reference optical filter that converts any frequency shift induced in the spectral characteristics of the measuring sensor into optical power variations. The proposed photonic sensor has the potential to adjust its transfer function dynamically, due to the varying response of the MMRs to different operating conditions, exhibiting either an ultra-low resolution operation capable of detecting extremely small refractive index changes, or an operation with a wide dynamic range. Finally, we propose a more sophisticated approach for simultaneous interrogation that incorporates multiple MRR sensors, based on thermal heaters that modulate the response of each MRR sensor with different modulation frequencies. In contrast to the conventional interrogation techniques, the proposed configurations enable ultra-high sampling rates crucial for studying fast biochemical reactions, such as enzyme kinetics.