gebhart/patrepeval huggingface dataset:
Induction of murine erythroleukemia differentiation by actinomycin D (1978)

Murine erythroleukemia cells are induced to differentiate by 0.5-5 ng of actinomycin D per ml. Murine erythroleukemia cells cultured with actinomycin D prolong cell doubling time but achieve the same density after 5 days as cells without inducer. Actinomycin D causes over 95% of the cells to become benzidine-reactive. [(3)H]Actinomycin D uptake into DNA can be detected within 2 hr and reaches a maximum (approximately 0.1 pmol/10(6) cells) by 10-12 hr. It is estimated that about one out of 10(5) dG.dC pairs is bound to actinomycin D. Commitment to differentiation, assayed by transfer of cells to culture without inducer, was detected as early as 5 hr. Unlike Me(2)SO, which causes a transient prolongation in G(1) at about 15-20 hr, cells cultured with actinomycin D show a more sustained increase in the proportion of the cells in G(1). Globin mRNA accumulation was detectable by 19 hr in culture. Alteration in DNA stability in alkaline sucrose gradients was detected by 19 hr. Actinomycin D induces synthesis of Hb(maj) and Hb(min) in approximately equal amounts. A decrease in rates of synthesis of RNA, DNA, and total protein occurs in cells cultured with actinomycin D, as well as in cells cultured with Me(2)SO. No evidence for an early action of actinomycin D at the plasma membrane was obtained by measurement of changes in cell volume or (86)RbCl uptake. Taken together, the present results indicate that actinomycin D is a potent inducer of differentiation of murine erythroleukemia cells and suggest that the target of its effect may be at the level of DNA.
Personalized search engines on mining user preferences using clickthrough data (2014)

In an web based application, different users may have different search goals when they submit it to a search engine. For a broad-topic and ambiguous query it is difficult. Here we Propose a novel approach to infer user search goals by analyzing search engine query logs. A major deficiency of generic search engines is that they follow the “one size fits all” model and are not adaptable to individual users. This is typically shown in cases such as these: Different users have different backgrounds and interests. However, effective personalization cannot be achieved without accurate user profiles. We address the problem of learning the user profile within the user's ongoing behaviors by using the user search. We propose a framework that enables large-scale evaluation of personalized search. User interest is employed in the clustering process to achieve personalization effect. The goal of personalized IR (information retrieval) is to return search results that better match the user intent. First, we propose a framework to discover different user search goals for a query by clustering the proposed feedback sessions. Feedback sessions are get constructed from user click-through logs and can efficiently reflect the information needs of users. Second, we propose an approach to generate pseudo-documents to better represent the feedback sessions for clustering. Most document-based methods focus on analyzing users' clicking and browsing behaviors recorded at the users' clickthrough data. In the Web search engines, clickthrough data are important implicit feedback mechanism from users. An example of clickthrough data for the query "apple," which contains a list of ranked search results presented to the user, which contains identification on the results that was previously clicked by the user. The bolded documents that have been clicked by the user have been ranked. Several personalized systems that employ clickthrough data to capture users' interest have been proposed.
Six-Helix and Eight-Helix DNA Nanotubes Assembled from Half-Tubes (2007)

DNA nanotubes are cylinder-like structures formed from DNA double-helical molecules whose helix axes are fused at least twice by crossovers. It is potentially useful to use such tubes as sheaths around rodlike species that arise in biological systems and in nanotechnology. It seems easiest to obtain such sheathing by joining two or more components around an object rather than attempting to thread the object through a cavity in the tube. We report two examples of tubes containing a specific number of helices that are assembled from half-tube components. These tubes are a six-helix bundle and an eight-helix bundle, constructed respectively from two bent triple-crossover (BTX) molecules and from two four-helix arched motifs. Both species contain single strands in one molecule that are missing in its mate. The six-helix bundle is formed from two different BTX molecules, whereas the eight-helix species is a closed cyclic dimer of the same molecule. We demonstrate the formation of these species by gel electrophoresis, and we examine their arrangement into long one-dimensional arrays by means of atomic force microscopy.
Adenovirus-mediated gene therapy for human head and neck squamous cell cancer in a nude mouse model. (1995)

Adenovirus-mediated transfer of the herpes simplex virus thymidine kinase gene followed by ganciclovir administration was used to treat human head and neck cancer in nude mice. Tumors were generated by transcutaneous needle injection of 6 x 10(6) human squamous carcinoma cells into the floor of the mouth. After 14 days, 10(10) particles of a replication-defective recombinant adenovirus containing the herpes simplex virus thymidine kinase gene (ADV/RSV-tk) were injected directly into the tumors. The mice subsequently received ganciclovir injections for six consecutive days and were sacrificed at 21 days post tumor cell implantation. Clinical response to the treatment was assessed by computer-imaged morphometric analysis of cross sectional area of nonnecrotic tumor and mitotic activity, which were used for the calculation of a tumor index. The median tumor index value of the treatment group was 280- to 2400-fold smaller than controls which did not receive the therapeutic gene (P < 0.001-0.016), and three-quarters of the treatment group had tumor index values that were indicative of near total tumor regression. Survival studies show that 50% of the ADV/RSV-tk-treated mice are free of tumor at 160 days post adenovirus injection, while all controls died or required sacrifice within 43 days. These results demonstrate that clinically effective in vivo treatment of human squamous cell cancer can be achieved using adenovirus-mediated gene therapy.
A noncognate interaction with anti‐receptor antibody‐activated helper T cells induces small resting murine B cells to proliferate and to secrete antibody (1988)

Culture of small resting allogeneic B cells (of an irrelevant haplotype) with two clones of T helper (Th) cells that were activated by the F23.1 anti-T cell receptor antibody led to the activation of B cells to proliferate and to secrete antibody. Th cell supernatants by themselves had no effect on resting B cells (even in the presence of intact F23.1 antibody), but could induce antibody secretion by anti-Ig-preactivated B cells. Both F23.1+ clones (E9.D4 and 4.35F2) and one F23.1- clone (D2.2) could synergize with supernatants from activated E9.D4 T cells to induce B cell activation. F(ab')2 fragments of F23.1 induced E9.D4 to activate B cells as efficiently as intact F23.1 and B cell populations that had been incubated with F23.1 were not activated when cultured with E9.D4, although T cells recognized cell-presented F23.1 and were weakly activated. Reduction of the density of F23.1 adsorbed to plastic resulted in weak T cell activation, and these T cells did not induce B cell responses. Haptenated B cell populations, although recognized by E9.D4, were not activated. Separation of T and B cells by a 0.4-micron membrane prevented T-dependent B cell activation, although Th cell-derived B cell-activating lymphokines would be assayed across these membranes. These results suggest a polyclonal noncognate B cell activation that depends on physical contact between B cells and activated T cells. The requirement for a cognate interaction of Th with B cells for the production and delivery of B help can therefore be overcome by activating Th cells with high densities of T cell receptor ligands.
Studies on the mechanisms by which transforming growth factor- beta (TGF- beta ) protects against allergic encephalomyelitis. Antagonism between TGF-beta and tumor necrosis factor. (1993)

Experimental allergic encephalomyelitis (EAE) is an autoimmune disease in which peripheral lymphoid cells are activated by immunization with myelin proteins and become effector cells that traverse the central nervous system (CNS) capillaries and initiate inflammatory demyelinating lesions. The administration of transforming growth factor-beta (TGF-beta) has been shown previously to decrease the incidence and severity of EAE. In our studies we have determined: 1) the effects of TGF-beta injected at different intervals after the EAE-inducing immunization; 2) the effect of TGF-beta on the development of sensitized T cells, as assayed by the proliferative responses of T cells from lymph nodes and peripheral blood; 3) the extent of lymphoid cell infiltration in CNS of TGF-beta-treated and control mice; and 4) the role of endogenous TGF-beta and TNF in determining the severity of both acute and relapsing EAE. The onset of acute-EAE in SJL mice, induced by immunization with spinal cord homogenate in CFA and pertussigen, is on days 10 to 15. Although daily i.p. injections of 0.2 to 2 micrograms TGF-beta 1 or TGF-beta 2 on days 5 to 9 after immunization are highly protective, injections on days 1 to 5 or 9 to 13 are not. Moreover, anti-TGF-beta accelerates and aggrevates EAE when given on days 5 and 9, but not on day 12. Anti-TNF, injected on days 5 and 9, provides a comparable degree of protection as does TGF-beta. Similarly, in relapsing EAE, anti-TGF-beta increases, whereas anti-TNF decreases the incidence and severity of relapses. TGF-beta treatment on days 5 to 9 does not influence the appearance of sensitized cells in peripheral blood and lymph nodes, but does prevent the accumulation of T cells in brain and spinal cord, as assayed on days 15 to 20. It is concluded that the protective effect of TGF-beta is exerted at the level of the target organ, CNS and/or its vascular endothelium, rather than through a direct effect on lymphoid cells, and that there is a small window of 4 days in which TGF-beta exerts its protective effect.
Laser Principles (2011)

Since the construction of the first laser in the 1960s, the role that lasers play in various medical specialities, including dermatology, has steadily increased. However, within the last 2 decades, the technological advances and the use of lasers in the field of dermatology have virtually exploded. Many treatments have only become possible with the use of lasers. Especially in aesthetic medicine, lasers are an essential tool in the treatment armamentarium. Due to better research and understanding of the physics of light and skin, there is now a wide and increasing array of different lasers and devices to choose from. The proper laser selection for each indication and treatment requires a profound understanding of laser physics and the basic laser principles. Understanding these principles will allow the laser operator to obtain better results and help avoid complications. This chapter will give an in-depth overview of the physical principles relevant in cutaneous laser surgery.
DNA Triple-Helix Formation at Physiologic pH and Temperature (1991)

Oligonucleotides that form a triple helix with duplex DNA offer a novel way to site specifically regulate gene expression in vivo. Triple helices formed by homopyrimidine oligomers containing both cytosine and thymine are stabilized by acid pH and low temperature, and there is little information about triplex formation with these oligomers at both pH 7.5 and 37 degrees C. Therefore, we examined the effect of changing various conditions on triplex formation at pH 7.5. A 30-mer oligonucleotide (composed of T and 5-methyl C) at submicromolar concentrations formed a triplex with its target duplex at pH 7.5 and 37 degrees C. Association of the 30-mer oligomer with the duplex was slow, with complete association requiring about 1 h. At 37 degrees C, a 21-mer oligomer bound weakly to the target duplex but both a 25-mer and the 30-mer readily formed a triplex. This relationship of triplex formation with length was temperature dependent, as at 25 degrees C the 21-mer behaved similarly to the longer oligomers. Increasing spermine concentrations (from 0.2 to 1 mM) increased the amount of triplex formed. Spermine may be important only for the association of the oligomer to the duplex, since decreasing the spermine concentration after the triplex formed did not reduce the amount of triplex detected. At 1 mM spermine, formation of the triple-helical complex was very dependent on the concentration of KCl; increasing the KCl from 50 to 100 mM prevented triplex formation. However, the inhibitory effect of KCl could be abrogated by raising the spermine concentration to 2 mM. Our observations indicate that a triple helix can form under physiologic conditions but its formation is affected by several competing interactions.
Synthesis and biological activities of potent peptidomimetics selective for somatostatin receptor subtype 2 (1998)

A series of nonpeptide somatostatin agonists which bind selectively and with high affinity to somatostatin receptor subtype 2 (sst2) have been synthesized. One of these compounds, L-054,522, binds to human sst2 with an apparent dissociation constant of 0.01 nM and at least 3,000-fold selectivity when evaluated against the other somatostatin receptors. L-054,522 is a full agonist based on its inhibition of forskolin-stimulated adenylate cyclase activity in Chinese hamster ovary-K1 cells stably expressing sst2. L-054,522 has a potent inhibitory effect on growth hormone release from rat primary pituitary cells and glucagon release from isolated mouse pancreatic islets. Intravenous infusion of L-054,522 to rats at 50 microgram/kg per hr causes a rapid and sustained reduction in growth hormone to basal levels. The high potency and selectivity of L-054, 522 for sst2 will make it a useful tool to further characterize the physiological functions of this receptor subtype.
BLM–DNA2–RPA–MRN and EXO1–BLM–RPA–MRN constitute two DNA end resection machineries for human DNA break repair (2011)

Repair of dsDNA breaks requires processing to produce 3'-terminated ssDNA. We biochemically reconstituted DNA end resection using purified human proteins: Bloom helicase (BLM); DNA2 helicase/nuclease; Exonuclease 1 (EXO1); the complex comprising MRE11, RAD50, and NBS1 (MRN); and Replication protein A (RPA). Resection occurs via two routes. In one, BLM and DNA2 physically and specifically interact to resect DNA in a process that is ATP-dependent and requires BLM helicase and DNA2 nuclease functions. RPA is essential for both DNA unwinding by BLM and enforcing 5' → 3' resection polarity by DNA2. MRN accelerates processing by recruiting BLM to the end. In the other, EXO1 resects the DNA and is stimulated by BLM, MRN, and RPA. BLM increases the affinity of EXO1 for ends, and MRN recruits and enhances the processivity of EXO1. Our results establish two of the core machineries that initiate recombinational DNA repair in human cells.
An integrated environment for knowledge acquisition (2001)

This paper describes an integrated acquisition interface that includes several techniques previously developed to support users in various ways as they add new knowledge to an intelligent system. As a result of this integration, the individual techniques can take better advantage of the context in which they are invoked and provide stronger guidance to users. We describe the current implementation using examples from a travel planning domain, and demonstrate how users can add complex knowledge to the system.
The triptans (2009)

The migraine-specific triptans have revolutionized the treatment of migraine and are currently the drugs of choice to treat a migraine attack in progress. Over the past 15 years, triptans were released in rapid succession, with each one demonstrating some specific pharmacokinetic properties that may be translated into clinical advantages. Triptans share many similarities, but also have important differences from one another. Accordingly, herein we discuss the class of the triptans. We first define the trigeminovascular system and its importance in migraine pain, then discuss the mechanism of action of the triptans and contrast the evidence supporting the use of different triptans. We close with our view of the future and hopes for the next generation of antimigraine therapies.
Human Experimentation with Neisseria gonorrhoeae: Rationale, Methods, and Implications for the Biology of Infection and Vaccine Development (1994)

Neisseria gonorrhoeae infection is limited to the human host. Experimental urethral infection in male volunteers was used to study different aspects of the infection. Urethral installation of a variety of gonococcal variants (10(4)-10(6)) led to infection in 27 subjects, who developed pyuria and shed bacteria in urine before urethritis developed 1-6 days after gonococcal inoculation. The incubation period was affected by the inoculation procedure and size of the inoculum. Subjects were treated with intramuscular ceftriaxone (250 mg) if urethritis developed or at 6 days after inoculation. Urine cultures became negative within several hours of therapy, and symptoms resolved within 1 day of therapy. Infected patients suffered no major complications. Experimental male urethral gonococcal infection provides a unique opportunity to understand the biology and immunology of gonococcal infection and is an efficient method to test gonococcal vaccine candidates.
Using a microfluidic device for 1 l DNA microarray hybridization in 500 s (2005)

This work describes a novel and simple modification of the current microarray format. It reduces the sample/reagent volume to 1 microl and the hybridization time to 500 s. Both 20mer and 80mer oligonucleotide probes and singly labeled 20mer and 80mer targets, representative of the T-cell acute lymphocytic leukemia 1 (TAL1) gene, have been used to elucidate the performance of this hybridization approach. In this format, called shuttle hybridization, a conventional flat glass DNA microarray is integrated with a PMMA microfluidic chip to reduce the sample and reagent consumption to 1/100 of that associated with the conventional format. A serpentine microtrench is designed and fabricated on a PMMA chip using a widely available CO2 laser scriber. The trench spacing is compatible with the inter-spot distance in standard microarrays. The microtrench chip and microarray chip are easily aligned and assembled manually so that the microarray is integrated with a microfluidic channel. Discrete sample plugs are employed in the microchannel for hybridization. Flowing through the microchannel with alternating depths and widths scrambles continuous sample plug into discrete short plugs. These plugs are shuttled back and forth along the channel, sweeping over microarray probes while re-circulation mixing occurs inside the plugs. Integrating the microarrays into the microfluidic channel reduces the DNA-DNA hybridization time from 18 h to 500 s. Additionally, the enhancement of DNA hybridization reaction by the microfluidic device is investigated by determining the coefficient of variation (CV), the growth rate of the hybridization signal and the ability to discriminate single-base mismatch. Detection limit of 19 amol was obtained for shuttle hybridization. A 1 mul target was used to hybridize with an array that can hold 5000 probes.
3′-C-Trifluoromethyl Ribonucleosides (1995)

Abstract (3-C-trifluoromethyl-β-D-ribofuranosyl) nucleosides of thymine, uracil and adenine were synthesized from 5-O-benzoyl-1, 2, 3-tri-O-acetyl-3-C-trifluoromethyl-β-D-ribofuranoside, prepared by addition of CF3SiMe3 to 5-O-benzoyl-1, 2-O-isopropylidene-α-D-erythro-pentos-3-ulose. 9-(3-C-Trifluoromethyl-β-D-ribofuranosyl)adenine was active against HSV-1.
Analytical Method for Prediction of Water Permeability of Cement Paste (2008)

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Determination of alpha-toxin antibodies against Staphylococcus aureus and phagocytic ability postimmunization in rabbits (1998)

30 rabbits were inoculated i.m. 3 times, at 2-week intervals, with a S. aureus subunit bacterin preparation (10 HU of alpha-toxin, 600 æg of capsular polysaccharide, 200 æg of fibronectin binding protein). The levels of specific antibodies against alpha toxin in immunized rabbits were significantly increased over 4 weeks compared with control rabbits, which showed no response. There was no significant difference between immunized and control rabbits in bacterial clearance rate. The use of the vaccine for prevention of bovine mastitis is discussed.
Microencapsulating Properties of Whey Proteins. 2. Combination of Whey Proteins with Carbohydrates (1993)

Abstract Anhydrous milk fat was effectively microencapsulated by spray drying in wall systems consisting of combinations of whey protein with with carbohydrates lacking surface-active properties. Whey proteins were effective emulsifiers in the presence of these carbohydrates and enabled microencapsulation even at a concentration of 5% (wt/wt), respectively. All combinations of whey proteins and carbohydrates gave microencapsulation yields higher than 96%. The carbohydrates limited the extractability of the core by a solvent. Microencapsulation efficiencies were up to 93% when whey proteins were partially replaced by carbohydrates. The microencapsulating properties of wall solutions of whey proteins and commercial encapsulating agents consisting of carbohydrates were superior to those of only the carbohydrates. In all cases, spherical capsules were obtained in which the milk fat was physically well isolated from the environment. Combinations of whey proteins and carbohydrates were effective and functional microencapsulating agents.
Carrier pocket engineering applied to “strained” Si/Ge superlattices to design useful thermoelectric materials (1999)

The concept of carrier pocket engineering is applied to strained Si/Ge superlattices to obtain a large thermoelectric figure of merit ZT. In this system, the effect of the lattice strain at the Si/Ge interfaces provides another degree of freedom to control the conduction band structure of the superlattice. We explore various geometries and structures to optimize ZT for the whole three-dimensional superlattice. The resultant ZT, calculated for a symmetrized Si(20 Å)/Ge(20 Å) superlattice grown on a (111) oriented Si0.5Ge0.5 substrate, is 0.96 at 300 K and is shown to increase significantly at elevated temperatures. Such a superlattice can be grown using molecular beam epitaxy.