gebhart/patrepeval huggingface dataset:
Comparative Study of Different Procedures for the Collection and Banking of Umbilical Cord Blood (1995)

Different procedures for umbilical cord blood (CB) collection, separation, and cryopreservation were compared to evaluate the feasibility of large-scale CB banking for unrelated transplant. CB collection using an open system was associated with a 12.5% rate of bacterial contamination, whereas this rate fell to 3.3% using a closed collection system. When the umbilical cord was clamped within 30 s after delivery, on 378 occasions it was possible to collect 77 +/- 23 ml of CB without risk to mother or infant. Considering that engraftment can be obtained in recipients of 20 x 10(3) CFU-GM/kg, 86% and 28% of CB samples with a volume larger than 50 ml were found to contain a sufficient number of CFU-GM to engraft patients of 20 and 70 kg, respectively. Both Ficoll and gelatin purification procedures were associated with a recovery of 86-92% of CFU-GM, BFU-E, CFU-GEMM, and HPP-CFC, but the gelatin method appears to be more suitable for large-scale CB banking in vials. After cryopreservation, the recovery of clonogenic progenitors was similar for both CB samples stored as whole blood or as mononuclear cells separated using Ficoll or gelatin. In conclusion, large-scale CB banking seems feasible, and CB cell separation could allow storage of a large number of CB samples in a limited liquid nitrogen space.
Identification, molecular cloning, and characterization of the chromosome 12 breakpoint cluster region of uterine leiomyomas (1994)

Recent molecular cytogenetic analysis of uterine leiomyoma cell lines with chromosome 12 aberrations has indicated that their chromosome 12 breakpoints map between linkage locus D12S8 and the CHOP gene. Here, we report fluorescence in situ hybridization (FISH) and molecular cloning studies of the chromosome 12 breakpoints in a panel of seven such uterine leiomyoma cell lines; five with the frequently observed t(12;14)(q15;q24), one with t(12;15)(q15;q24), and one with ins(12;11)(q14;q21qter). Directional chromosome walking studies starting from D12S8 and the CHOP gene resulted in the isolation of a relatively large number of overlapping YAC clones, including Y5355 (465 kbp), Y7673 (360 kbp), and Y9899 (275 kbp). In total, the inserts of these three YAC clones span an 800 kbp long and presumably contiguous stretch of human genomic DNA. All chromosome 12 breakpoints of the uterine leiomyoma cell lines studied were found by FISH analysis to be mapping within a 445 kbp subfragment of this region and, furthermore, to be dispersed over a DNA region which is at least 150 kbp in size. The chromosome 12 breakpoint of t(12;14)(q15;q24) in uterine leiomyoma cell line LM-30.1/SV40 was tentatively mapped within the 60 kbp region between YAC clones Y9899 and Y5355. From this 60 kbp region and close to sequence-tagged site RM99, we isolated probe pRM118-A, which showed in Southern blot analysis that it detected a rearrangement in LM-30.1/SV40 DNA, and generated restriction maps of the normal and rearranged genomic DNA regions detected with this probe. Finally, we molecularly cloned part of one of those rearranged DNA fragments using a vectorette-PCR-based technique and demonstrated that it consisted of 12q13-q15 sequences fused to DNA sequences derived from 14q23-24 and most likely represented the translocation junction on der(14) in LM-30.1/SV40 cells. Our studies strongly suggest that we have identified and isolated the uterine leiomyoma cluster region of chromosome 12 breakpoints, which we designate ULCR12, and molecularly cloned and characterized the der(14) translocation junction in cells derived from a uterine leiomyoma carrying the frequently observed t(12;14)(q15;q24).
Web question answering (2002)

This paper describes a question answering system that is designed to capitalize on the tremendous amount of data that is now available online. Most question answering systems use a wide variety of linguistic resources. We focus instead on the redundancy available in large corpora as an important resource. We use this redundancy to simplify the query rewrites that we need to use, and to support answer mining from returned snippets. Our system performs quite well given the simplicity of the techniques being utilized. Experimental results show that question answering accuracy can be greatly improved by analyzing more and more matching passages. Simple passage ranking and n-gram extraction techniques work well in our system making it efficient to use with many backend retrieval engines.
Laser-Induced Explosion of Gold Nanoparticles: Potential Role for Nanophotothermolysis of Cancer (2006)

Explosion of nanoparticles may be accompanied by optical plasma, generation of shock waves with supersonic expansion and particle fragmentation with fragments of high kinetic energy, all of which can contribute to the killing of cancer cells.
Staphylococcal enterotoxin A gene is associated with a variable genetic element. (1984)

The genetic determinant of Staphylococcus aureus enterotoxin A (SEA) has been cloned in pBR322 in Escherichia coli and found to be expressed and secreted into the periplasmic space in that organism. The SEA gene (entA) is within a 2.5-kilobase-pair HindIII fragment that is part of a discrete genetic element 8-12 kilobase pairs in length. This entA element has a standard chromosomal location [between the purine (pur) and isoleucine-valine (ilv) markers] in most S. aureus strains. In some strains it is unlinked to pur-ilv. However, its internal structure is conserved at different locations. Some naturally occurring SEA-nonproducer (EntA-) strains lack the entire entA element, and one instance of its spontaneous loss is reported. Other naturally occurring strains have EntA- structural variants of the element at the same pur-ilv location at which the intact element is most commonly found. Some of these strains are EntA-, others are EntA+; the latter have a second, unlinked copy of the element containing their functional entA gene. These results suggest that entA is associated with a structurally unstable, possibly mobile, discrete genetic element.
Oxidation of low-density lipoprotein with hypochlorite causes transformation of the lipoprotein into a high-uptake form for macrophages (1993)

Oxidation of low-density lipoprotein (LDL) lipid is thought to represent the initial step in a series of oxidative modification reactions that ultimately transform this lipoprotein into an atherogenic high-uptake form that can cause lipid accumulation in cells. We have studied the effects of hypochlorite, a powerful oxidant released by activated monocytes and neutrophils, on isolated LDL. Exposure of LDL to reagent hypochlorite (NaOCl) at 4 degrees C resulted in immediate and preferential oxidation of amino acid residues of apoprotein B-100, the single protein associated with LDL. Neither lipoprotein lipid nor LDL-associated antioxidants, except ubiquinol-10, represented major targets for this oxidant. Even when high concentrations of NaOCl were used, only low levels of lipid hydroperoxides could be detected with the highly sensitive h.p.l.c. post-column chemiluminescence detection method. Lysine residues of apoprotein B-100 quantitatively represented the major target, scavenging some 68% of the NaOCl added, with tryptophan and cysteine together accounting for an additional 10% of the oxidant. Concomitant with the loss of LDL's amino groups, chloramines were formed and the anionic surface charge of the lipoprotein particle increased, indicated by a 3-4-fold increase in electrophoretic mobility above that of native LDL on agarose gels. While both these changes could be initially reversed by physiological reductants such as ascorbic acid and methionine, incubation of the NaOCl-modified LDL at 37 degrees C resulted in increasing resistance of the modified lysine residues against reductive reversal. Exposure of mouse peritoneal macrophages to NaOCl-oxidized LDL resulted in increased intracellular concentrations of cholesterol and cholesteryl esters. These findings suggest that lipid-soluble antioxidants associated with LDL do not efficiently protect the lipoprotein against oxidative damage mediated by hypochlorite, and that extensive lipid oxidation is not a necessary requirement for oxidative LDL modification that leads to a high-uptake form of the lipoprotein.
Tumour necrosis factor-alpha inhibitors and the reactivation of latent tuberculosis infection. (2003)

Infliximab (Remicade) is a chimeric (part human, part mouse) antibody that targets tumour necrosis factor-α (TNF-α), a potent proinflammatory cytokine implicated in different inflammatory diseases, such as Crohn's disease and rheumatoid arthritis.[1][1],[2][2] (Cytokines are molecules secreted
Phosphorylation of insulin receptor substrate 1 by glycogen synthase kinase 3 impairs insulin action (1997)

The phosphorylation of insulin receptor substrate 1 (IRS-1) on tyrosine residues by the insulin receptor (IR) tyrosine kinase is involved in most of the biological responses of insulin. IRS-1 mediates insulin signaling by recruiting SH2 proteins through its multiple tyrosine phosphorylation sites. The phosphorylation of IRS-1 on serine/threonine residues also occurs in cells; however, the particular protein kinase(s) promoting this type of phosphorylation are unknown. Here we report that glycogen synthase kinase 3 (GSK-3) is capable of phosphorylating IRS-1 and that this modification converts IRS-1 into an inhibitor of IR tyrosine kinase activity in vitro. Expression of wild-type GSK-3 or an "unregulated" mutant of the kinase (S9A) in CHO cells overexpressing IRS-1 and IR, resulted in increased serine phosphorylation levels of IRS-1, suggesting that IRS-1 is a cellular target of GSK-3. Furthermore, insulin-induced tyrosine phosphorylation of IRS-1 and IR was markedly suppressed in cells expressing wild-type or the S9A mutant, indicating that expression of GSK-3 impairs IR tyrosine kinase activity. Taken together, our studies suggest a new role for GSK-3 in attenuating insulin signaling via its phosphorylation of IRS-1 and may provide new insight into mechanisms important in insulin resistance.
Balancing between immunity and tolerance: an interplay between dendritic cells, regulatory T cells, and effector T cells (2007)

Dendritic cells (DC), professional antigen-presenting cells of the immune system, exert important functions both in induction of T cell immunity, as well as tolerance. It is well established that the main function of immature DC (iDC) in their in vivo steady-state condition is to maintain peripheral tolerance to self-antigens and that these iDC mature upon encounter of so-called danger signals and subsequently promote T cell immunity. Previously, it was believed that T cell unresponsiveness induced after stimulation with iDC is caused by the absence of inflammatory signals in steady-state in vivo conditions and by the low expression levels of costimulatory molecules on iDC. However, a growing body of evidence now indicates that iDC can also actively maintain peripheral T cell tolerance by the induction and/or stimulation of regulatory T cell populations. Moreover, several reports indicate that traditional DC maturation can no longer be used to distinguish tolerogenic and immunogenic properties of DC. This review will focus on the complementary role of dendritic cells in inducing both tolerance and immunity, and we will discuss the clinical implications for dendritic cell-based therapies.
Antibodies to Butyrate-Inducible Antigens of Kaposi's Sarcoma–Associated Herpesvirus in Patients with HIV-1 Infection (1996)

The presence of antibodies to a KSHV antigenic peptide correlates with the presence of Kaposi's sarcoma in a high-risk population and provides further evidence of an etiologic role for KSHV.
Regulation of Aryl Hydrocarbon Receptor Function by Selective Estrogen Receptor Modulators (2009)

Selective estrogen receptor modulators (SERMs), such as tamoxifen (TAM), have been used extensively for the treatment and prevention of breast cancer and other pathologies associated with aberrant estrogen receptor (ER) signaling. These compounds exhibit cell-selective agonist/antagonist activities as a consequence of their ability to induce different conformational changes in ER, thereby enabling it to recruit functionally distinct transcriptional coregulators. However, the observation that SERMs can also regulate aspects of calcium signaling and apoptosis in an ER-independent manner in some systems suggests that some of the activity of drugs within this class may also arise as a consequence of their ability to interact with targets other than ER. In this study, we demonstrate that 4-hydroxy-TAM (4OHT), an active metabolite of TAM, directly binds to and modulates the transcriptional activity of the aryl hydrocarbon receptor (AHR). Of specific interest was the observation, that in the absence of ER, 4OHT can induce the expression of AHR target genes involved in estradiol metabolism, cellular proliferation, and metastasis in cellular models of breast cancer. The potential role for AHR in SERM pharmacology was further underscored by the ability of 4OHT to suppress osteoclast differentiation in vitro in part through AHR. Cumulatively, these findings provide evidence that it is necessary to reevaluate the relative roles of ER and AHR in manifesting the pharmacological actions and therapeutic efficacy of TAM and other SERMs.
Phenylmorphans and analogs: opioid receptor subtype selectivity and effect of conformation on activity (1992)

The morphine-like (+)-phenylmorphan, the atypical (-)-enantiomer, and some analogues have been tested in receptor binding assays selective for opioid mu 1, mu 2, delta, kappa 1, and kappa 3 receptors. The affinities of all of the compounds except one, including the atypical (-)-phenylmorphan, were greatest for mu 1 and mu 2 receptors. The only exception was the (+)-9 alpha-methyl analogue which had slightly greater affinity for the kappa 1 receptor. The selective receptor binding assays provide evidence that opioids in which the phenyl ring is constrained to be equatorial on the piperidine ring can have considerable affinity for mu receptors. In addition, dose-response curves were determined for (+)- and (-)-phenylmorphan using the mouse tail-flick assay with the (+)-enantiomer found to be about 7 times more potent. Pretreatment with the selective opioid antagonists beta-FNA (mu 1 and mu 2), naloxonazine (mu 1), nor-BNI (kappa 1), and naltrindole (delta) suggests that the antinociceptive activity of both enantiomers is mediated through mu receptors. The pretreatment with naloxonazine, which attenuated the antinociceptive effect, shows that both (+)- and (-)-phenylmorphan are mu 1 agonists while intrathecal administration shows that both are mu 2 agonists. Conformational energy calculations on the compounds were also performed using the MM2-87 program. Consistent with previous conformational results for the phenylmorphans (J. Med. Chem. 1984, 27, 1234-1237), the most potent antinociceptive compounds preferred a particular orientation of the phenyl ring.
Acetalins: opioid receptor antagonists determined through the use of synthetic peptide combinatorial libraries. (1993)

A synthetic peptide combinatorial library made up of 52,128,400 hexapeptides, each having an acetyl group at the N terminus and an amide group on the C terminus, was screened to find compounds able to displace tritiated [D-Ala2,MePhe4,Gly-ol5]enkephalin from mu opioid receptor binding sites in crude rat brain homogenates. Individual peptides with mu receptor affinity were found using an iterative process for successively determining the most active peptide mixtures. Upon completion of this iterative process, the three peptides with the highest affinity were Ac-RFMWMT-NH2, Ac-RFMWMR-NH2, and Ac-RFMWMK-NH2. These peptides showed high affinity for mu and kappa 3 opioid receptors, somewhat lower affinity for delta receptors, weak affinity for kappa 1 receptors, and no affinity for kappa 2 receptors. They were found to be potent mu receptor antagonists in the guinea pig ileum assay and relatively weak antagonists in the mouse vas deferens assay. These peptides represent a class of opioid receptor ligands that we have termed acetalins (acetyl plus enkephalin).
Finite-state Markov model for Rayleigh fading channels (1999)

We form a finite-state Markov channel model to represent Rayleigh fading channels. We develop and analyze a methodology to partition the received signal-to-noise ratio (SNR) into a finite number of states according to the time duration of each state. Each state corresponds to a different channel quality indicated by the bit-error rate (BER). The number of states and SNR partitions are determined by the fading speed of the channel. Computer simulations are performed to verify the accuracy of the model.
UNC569, a Novel Small-Molecule Mer Inhibitor with Efficacy against Acute Lymphoblastic Leukemia In Vitro and In Vivo (2013)

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. Although survival rates have improved, patients with certain biologic subtypes still have suboptimal outcomes. Current chemotherapeutic regimens are associated with short- and long-term toxicities and novel, less toxic therapeutic strategies are needed. Mer receptor tyrosine kinase is ectopically expressed in ALL patient samples and cell lines. Inhibition of Mer expression reduces prosurvival signaling, increases chemosensitivity, and delays development of leukemia in vivo, suggesting that Mer tyrosine kinase inhibitors are excellent candidates for targeted therapies. Brain and spinal tumors are the second most common malignancies in childhood. Multiple chemotherapy approaches and radiotherapies have been attempted, yet overall survival remains dismal. Mer is also abnormally expressed in atypical teratoid/rhabdoid tumors (AT/RT), providing a rationale for targeting Mer as a therapeutic strategy. We have previously described UNC569, the first small-molecule Mer inhibitor. This article describes the biochemical and biologic effects of UNC569 in ALL and AT/RT. UNC569 inhibited Mer activation and downstream signaling through ERK1/2 and AKT, determined by Western blot analysis. Treatment with UNC569 reduced proliferation/survival in liquid culture, decreased colony formation in methylcellulose/soft agar, and increased sensitivity to cytotoxic chemotherapies. MYC transgenic zebrafish with T-ALL were treated with UNC569 (4 μmol/L for two weeks). Fluorescence was quantified as indicator of the distribution of lymphoblasts, which express Mer and enhanced GFP. UNC569 induced more than 50% reduction in tumor burden compared with vehicle- and mock-treated fish. These data support further development of Mer inhibitors as effective therapies in ALL and AT/RT.
Perl Cookbook (1998)

From the Publisher:
The Perl Cookbook is a comprehensive collection of problems, solutions, and practical examples for anyone programming in Perl. Topics range from beginner questions to techniques that even the most experienced Perl programmers can learn from. More than just a collection of tips and tricks, the Perl Cookbook is the long-awaited companion volume to Programming Perl, filled with previously unpublished Perl arcana.
Short-Time Infusion of Fish Oil-Based Lipid Emulsions, Approved for Parenteral Nutrition, Reduces Monocyte Proinflammatory Cytokine Generation and Adhesive Interaction with Endothelium in Humans (2003)

Potential impact of omega-3 fatty acids, as contained in fish oil, on immunological function has been suggested because observations of reduced inflammatory diseases in Greenland Inuit were published. A fish oil-based lipid emulsion has recently been approved for parenteral nutrition in many countries. We investigated the influence of a short infusion course of fish oil-based (omega-3) vs conventional (omega-6) lipid emulsion on monocyte function. In a randomized design, twelve healthy volunteers received omega-3 or omega-6 lipid infusion for 48 h, with cross-over repetition of the infusion course after 3 mo. Fatty acid profiles, monocyte cytokine release and adhesive monocyte-endothelium interaction were investigated. Resultant omega-6 lipid emulsion increased plasma-free fatty acids including arachidonic acid, whereas the omega-3/omega-6 fatty acid ratio in monocyte membranes remained largely unchanged. It also caused a tendency toward enhanced monocyte proinflammatory cytokine release and adhesive monocyte-endothelium interaction. In contrast, omega-3 lipid emulsion significantly increased the omega-3/omega-6 fatty acid ratio in the plasma-free fatty acid fraction and in monocyte membrane lipid pool, markedly suppressing monocyte generation of TNF-alpha, IL-1, IL-6, and IL-8 in response to endotoxin. In addition, it also significantly inhibited both monocyte-endothelium adhesion and transendothelial monocyte migration, although monocyte surface expression of relevant adhesive molecules (CD11b, CD18, CD49 days, CCR2) was unchanged. Although isocaloric, omega-3 and omega-6 lipid emulsions exert differential impact on immunological processes in humans. In addition to its nutritional value, fish oil-based omega-3 lipid emulsion significantly suppresses monocyte proinflammatory cytokine generation and features of monocyte recruitment.
An efficient route to asymmetrically diconjugated tris(heteroleptic) complexes of Ru(ii) (2016)

A highly efficient and versatile route to the preparation of tris(heteroleptic) Ru(<sc>ii</sc>) polypyridyl complexes is described which permits access to two or more independently conjugatable termini in the final structure.
A Day and Night Vision MOS Imager With Robust Photonic-Crystal-Based RGB-and-IR (2008)

This paper demonstrates a day and night vision MOS imager with red, green, blue (RGB) and extra near-infrared filters placed over individual pixels. The on-chip RGB and IR filters are fabricated from an inorganic photonic crystal color filter (PCCF) technology, thereby realizing a robust and reliable camera module for indoor and outdoor use without mounting a mechanical IR-cut filter. These PCCFs allow the IR band as well as the RGB bands to pass through to the RGB photodiodes from which RGB signals, each involving some amount of IR component, are derived. During the daytime, however, chromatically almost pure RGB colors are reproduced by subtracting a weighed IR signal of an extra IR pixel from the raw RGB signals of the surrounding IR pixels. As a result, the IR components in the resultant RGB signals are minimized from 25%, 21%, and 50% to 9%, 4%, and 21%, respectively. During the night, on the other hand, an IR image having a resolution match with a conventional IR imager can be captured by using the IR components of the raw RGB signals with the IR signal.
Diag-Join: An Opportunistic Join Algorithm for 1:N Relationships (1998)

Abstract Time of creation is one of the predominant (often implicit) clustering strategies found not only in Data Warehouse systems: line items are created together with their corresponding order, objects are created together with their subparts and so on. The newly created data is then appended to the existing data. We present a new join algorithm, called DiagJoin, which exploits time-of-creation clustering. If we are able to take advantage of timeof-creation clustering, then the performance evaluation reveals the superiority of Diag-Join over standard join algorithms like block-wise nested-loop join, GRACE hash join, and index nested-loop join. We also present an analytical cost model for Diag-Join. 1 Introduction During the evaluation of queries in Data Warehouses, relations containing millions or even billions of tuples need to be joined. Joins involving fact tables are very costly operations. Evidently, fast join algorithms are very important in this environment.