gebhart/patrepeval huggingface dataset:
A lock-free B+tree (2012)

Lock-free data structures provide a progress guarantee and are known for facilitating scalability, avoiding deadlocks and livelocks, and providing guaranteed system responsiveness. In this paper we present a design for a lock-free balanced tree, specifically, a B+tree. The B+tree data structure has an important practical applications, and is used in various storage-system products. As far as we know this is the first design of a lock-free, dynamic, and balanced tree, that employs standard compare-and-swap operations.
Fibroblast growth factor receptor 2 (FGFR2)-mediated reciprocal regulation loop between FGF8 and FGF10 is essential for limb induction (1998)

FGFR2 is a membrane-spanning tyrosine kinase that serves as a high affinity receptor for several members of the fibroblast growth factor (FGF) family. To explore functions of FGF/FGFR2 signals in development, we have mutated FGFR2 by deleting the entire immunoglobin-like domain III of the receptor. We showed that murine FGFR2 is essential for chorioallantoic fusion and placenta trophoblast cell proliferation. Fgfr2(DeltaIgIII/DeltaIgIII) embryos displayed two distinct defects that resulted in failures in formation of a functional placenta. About one third of the mutants failed to form the chorioallantoic fusion junction and the remaining mutants did not have the labyrinthine portion of the placenta. Consequently, all mutants died at 10-11 days of gestation. Interestingly, Fgfr2(DeltaIgIII/DeltaIgIII) embryos do not form limb buds. Consistent with this defect, the expression of Fgf8, an apical ectodermal factor, is absent in the mutant presumptive limb ectoderm, and the expression of Fgf10, a mesenchymally expressed limb bud initiator, is down regulated in the underlying mesoderm. These findings provide direct genetic evidence that FGF/FGFR2 signals are absolutely required for vertebrate limb induction and that an FGFR2 signal is essential for the reciprocal regulation loop between FGF8 and FGF10 during limb induction.
Separation and Purification of Angiotensin I Converting Enzyme Inhibitory Peptide in Peptic Hydrolyzate of Oyster. (1994)

オイスターのプロテアーゼ分解エキスを製造する過程で最も官能的に優れたエキスを与える酵素剤を選択し,そのエキス(PA-1)中に含まれるACE阻害活性ペプチドの単離と配列決定を行い,以下の結果を得た.(1) 分解に用いるプロテアーゼとして11種類の市販食品用プロテアーゼを検索し,官能的に最も評価の高かった酵素としてデナチームAPを選抜した.(2) PA-1はIC50値0.55mg-protein/mlを有していた.PA-1をODS充填カラムに通し, 25%エタノールで溶出することにより,高いACE阻害活性(IC50=0.085mg-protein/ml)を有するペプチド画分(A-3)を得た.画分A-3にはSP-Sephadexによるイオン交換クロマトグラフィーの結果, 3つの主要な活性画分が含まれていた.(3) SP-Sephadexから0.1Mギ酸アンモニウムで最初に溶出したA画分を,トヨパールHW-40カラムおよび逆相HPLCで分離した結果,多くのACE阻害活性を有するペプチドが含まれていた.(4) 逆相HPLCで高い活性を有していた画分(AT-B) につきアサヒパックGS-320と逆相HPLCによるリクロマトを行いACE阻害ペプチドを単離した.そのペプチドの構造はLeu-Pheであり, IC50値は126μMであった.
Cancer chemotherapy pocket guide (1998)

Guidelines for prescribing cytotoxic drugs use of haemotopoietic growth factors adult chemotherapy regimens paediatric cancers antiemetic therapy in the cancer patient pain management of the cancer patient management of tumour lysis and hypercalcemia management of malignant effusions bone marrow transplant supportive care management of dissemination intravascular coagulation in patients with acute leukemia.
Animal cell mutants defective in glycosaminoglycan biosynthesis. (1985)

We have obtained Chinese hamster ovary cell mutants defective in the biosynthesis of glycosaminoglycans by screening replicate colonies immobilized on polyester cloth. Depending upon the strain, the mutants accumulated less 35S-labeled glycosaminoglycans per microgram of cell protein by a factor of 6-60 compared to the wild type. Some of the mutants incorporated [6-3H]glucosamine into glycosaminoglycans to the same extent as the wild type, suggesting that sulfate addition was specifically altered. In contrast, five strains failed to generate 3H-labeled glycosaminoglycans normally. In four of these, the initiation of glycosaminoglycan assembly was specifically altered, since the addition of p-nitrophenyl-beta-xyloside restored sulfation to normal. Enzymatic assay of the xylosyltransferase in extracts prepared from these mutants revealed that one of the strains, S745, contained less enzyme activity by a factor of 15 than the wild type. This mutant provides genetic evidence that the xylosyltransferase assayed in vitro is responsible for the initiation of chondroitin sulfate and heparan sulfate biosynthesis in vivo.
Expression of the Tomato Pto Gene in Tobacco Enhances Resistance to Pseudomonas syringae pv tabaci Expressing avrPto (1995)

Roger L. Thilmony, Zutang Chen, Ray A. Bressan, Gregory B. Martin, Expression of the Tomato Pto Gene in Tobacco Enhances Resistance to Pseudomonas syringae pv tabaci Expressing avrPto, The Plant Cell, Vol. 7, No. 10 (Oct., 1995), pp. 1529-1536
Risk factors and outcome of transfusion-related acute lung injury in the critically ill: A nested case–control study* (2010)

Transfusion-related acute lung injury is common in critically ill patients. Transfusion-related acute lung injury may contribute to an adverse outcome associated with transfusion. This study identifies transfusion-related acute lung injury risk factors, which may aid in assessing the risks and benefits of transfusion in critically ill patients.
Enterococcus faecalis Infection and Reactive Oxygen Species Down-Regulates the miR-17-92 Cluster in Gastric Adenocarcinoma Cell Culture (2014)

Chronic inflammation due to bacterial overgrowth of the stomach predisposes to the development of gastric cancer and is also associated with high levels of reactive oxygen species (ROS). In recent years increasing attention has been drawn to microRNAs (miRNAs) due to their role in the pathogenesis of many human diseases including gastric cancer. Here we studied the impact of infection by the gram-positive bacteria Enterococcus faecalis (E. faecalis) on global miRNA expression as well as the effect of ROS on selected miRNAs. Human gastric adenocarcinoma cell line MKN74 was infected with living E. faecalis for 24 h or for 5 days or with E. faecalis lysate for 5 days. The miRNA expression was examined by microarray analysis using Affymetrix GeneChip miRNA Arrays. To test the effect of ROS, MKN74 cells were treated with 100 mM tert-Butyl hydroperoxide (TBHP). Following 5 days of E. faecalis infection we found 91 differentially expressed miRNAs in response to living bacteria and 2 miRNAs responded to E. faecalis lysate. We verified the down-regulation of the miR-17-92 and miR-106-363 clusters and of other miRNAs involved in the oxidative stress-response by qRT-PCR. We conclude that only infection by living E. faecalis bacteria caused a significant global response in miRNA expression in the MKN74 cell culture. E. faecalis infection as well as ROS stimulation down-regulated the expression of the miR-17-92 cluster. We believe that these changes could reflect a general response of gastric epithelial cells to bacterial infections.
Relationship between structure and antiproliferative activity of polymethoxyflavones towards HL60 cells. (2012)

As part of our continuing investigation of polymethoxyflavone (PMF) derivatives as potential anticancer substances, a series of PMF derivatives was synthesized. The synthesized compounds were evaluated for cytotoxicity against the promyelocytic leukemic HL60 cell line, and structure-activity relationship correlations were investigated along with previously isolated PMFs from the peel of king orange (Citrus nobilis). 7,3'-Dimethoxyflavone demonstrated the most potent activity among the synthetic PMFs. Consideration of correlation between the methoxylation pattern and antiproliferative activity revealed the importance of the 3'-methoxyl group and the higher degree of methoxylation on the A-ring moiety of PMFs.
Role of the tyrosine kinase pyk2 in the integrin-dependent activation of human neutrophils by TNF (1999)

Secretion of inflammatory products from neutrophils can be induced by a combination of signals from ligated integrins and receptors for soluble, physiological agonists such as TNF. Here we identify pyk2 in primary human neutrophils; localize it to focal adhesions and podosomes; and demonstrate its tyrosine phosphorylation, activation, and association with paxillin during stimulation of adherent cells by TNF. Tyrphostin A9 emerged as the most potent and selective of 51 tyrosine kinase inhibitors tested against the TNF-induced respiratory burst. Tyrphostin A9 inhibited TNF-induced tyrosine phosphorylation of pyk2 without blocking the cells' bactericidal activity. Wortmannin, an inhibitor of phosphatidylinositol-3-kinase, potently blocked the TNF-induced respiratory burst and selectively inhibited tyrosine phosphorylation of pyk2. Thus, pyk2 appears to play an essential role in the ability of neutrophils to integrate signals from beta(2) integrins and TNF receptors.
ChemInform Abstract: Design and Synthesis of Metal—Organic Frameworks Using Metal—Organic Polyhedra as Supermolecular Building Blocks (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Inhibitors of Androgen Receptor Activation Function-2 (AF2) Site Identified through Virtual Screening (2011)

The androgen receptor (AR) is one of the most studied drug targets for the treatment of prostate cancer. However, all current anti-androgens directly interact with the AR at the androgen binding site, which is prone to resistant mutations, calling for new strategies of the AR inhibition. The current study represents the first attempt to use virtual screening to identify inhibitors of activation function-2 (AF2) of the human AR. By combining large-scale docking with experimental approaches, we were able to identify several small molecules that interact with the AF2 and effectively prevent the transcriptional activation of the AR. The crystallographic structure of one of these inhibitors in complex with the AR provides critical insight into the corresponding protein-ligand interactions and suitable for future hit optimization. Taken together, our results provide a promising ground for development of novel anti-androgens that can help to address the problem of drug resistance in prostate cancer.
Build‐up of Polypeptide Multilayer Coatings with Anti‐Inflammatory Properties Based on the Embedding of Piroxicam–Cyclodextrin Complexes (2004)

Abstract We describe the build‐up of biomaterial coatings based on polypeptide multilayers possessing anti‐inflammatory properties. Poly( L ‐lysine) (PLL) and poly( L ‐glutamic acid) (PGA) are used as polypeptides, and piroxicam (Px) is used as the anti‐inflammatory agent. In order to embed high enough amounts of Px, the drug is incorporated in the films in the form of complexes with a charged 6 A ‐carboxymethylthio‐β‐cyclodextrin (cCD). It is shown that this cyclodextrin can solubilize higher amounts of Px than the cyclodextrins used commercially. The anti‐inflammatory properties are evaluated by determining the inhibition of TNFα production by human monocytic THP‐1 cells stimulated with lipopolysaccharide (LPS) bacterial endotoxin. Using Fourier‐transform (FT) Raman spectroscopy, we show that Px is mainly in the neutral form in cCD–Px complexes in solution, and that it remains biologically active under this form, whereas up to now only the zwitterionic form was reported to possess anti‐inflammatory properties. When incorporated in PLL/PGA multilayers, Px in the cCD–Px complexes changes from the neutral to the zwitterionic form. It is shown that these films present anti‐inflammatory properties, which can be delayed, and whose duration can be tuned by changing the film architecture.
Differential effects of IL-21 and IL-15 on perforin expression, lysosomal degranulation, and proliferation in CD8 T cells of patients with human immunodeficiency virus-1 (HIV) (2006)

An urgent need exists to devise strategies to augment antiviral immune responses in patients with HIV who are virologically well controlled and immunologically stable on highly active antiretroviral therapy (HAART). The objective of this study was to compare the immunomodulatory effects of the cytokines interleukin (IL)-21 with IL-15 on CD8 T cells in patients with HIV RNA of less than 50 copies/mL and CD4 counts greater than 200 cells/mm.(3) Patient CD8 T cells displayed skewed maturation and decreased perforin expression compared with healthy controls. Culture of freshly isolated patient peripheral-blood mononuclear cells (PBMCs) for 5 hours to 5 days with IL-21 resulted in up-regulation of perforin in CD8 T cells, including memory and effector subsets and virus-specific T cells. IL-21 did not induce T-cell activation or proliferation, nor did it augment T-cell receptor (TCR)-induced degranulation. Treatment of patient PBMCs with IL-15 resulted in induction of perforin in association with lymphocyte proliferation and augmentation of TCR-induced degranulation. Patient CD8 T cells were more responsive to cytokine effects than the cells of healthy volunteers. We conclude that CD8 T cells of patients with HIV can be modulated by IL-21 to increase perforin expression without undergoing overt cellular activation. IL-21 could potentially be useful for its perforin-enhancing properties in anti-HIV immunotherapy.
Oral delivery of DNA vaccines using attenuatedSalmonella typhimuriumas carrier (2000)

The efficacious delivery of eukaryotic expression plasmids to inductive cells of the immune system constitutes a key prerequisite for the generation of effective DNA vaccines. Here, we have explored the use of bacteria as vehicles to orally deliver expression plasmids. Attenuated Salmonella typhimurium aroA harbouring eukaryotic expression plasmids that encoded virulence factors of Listeria monocytogenes were administered orally to BALB/c mice. Strong cytotoxic and helper T cell responses as well as antibody production were elicited even after a single administration. Mice immunised four times with Salmonella that carried a eukaryotic expression plasmid encoding the secretory listerial protein listeriolysin were protected against a subsequent lethal challenge with this pathogen. A single dose was already partially protective. The efficiency of this vaccination procedure was due to transfer of the expression plasmid from the bacterial carrier to the mammalian host. Evidence for such an event could be obtained in vivo and in vitro. Expression of the desired antigen in various lymphoid tissues was already detectable 1 day after administration of the DNA vaccine and persisted for at least 1 month in spleen and mesenteric lymph nodes. Induction of cytotoxic and helper T cell responses was observed in all mouse strains tested including outbred strains whereas antibodies were mainly detected in BALB/c. Furthermore, we could show that immunogenicity could be improved by increasing the invasiveness of the bacterial carrier.
Parietal cells express high levels of Na-K-2Cl cotransporter on migrating into the gastric gland neck (1999)

Na-K-2Cl cotransport and Cl/HCO3 exchange are prominent mechanisms for Cl- uptake in Cl--secreting epithelial cells. We used immunofluorescence microscopy to delineate the distributions of Na-K-2Cl cotransporter-1 (NKCC1) and anion exchanger-2 (AE2) proteins in rat gastric mucosa (zymogenic zone). Parietal cells (PCs) above the neck of the gastric gland contained abundant AE2 but little or no NKCC1, whereas those in the neck and base contained high NKCC1 but diminished AE2. Lower levels of NKCC1 were detected in surface mucous cells and in cells comprising the blind ends of all glands. Pulse labeling of proliferating cells with bromodeoxyuridine indicated that new PCs originate in the isthmus with scant NKCC1; the subset of PCs that migrate downward expresses NKCC1 abruptly on entering the neck, within 7 days of cell division. Our results suggest that downwardly migrating PCs replace one mechanism for Cl- entry (Cl/HCO3 exchange) with another (Na-K-2Cl cotransport).
Bone Resorption by Osteoclasts (2000)

Osteoporosis, a disease endemic in Western society, typically reflects an imbalance in skeletal turnover so that bone resorption exceeds bone formation. Bone resorption is the unique function of the osteoclast, and anti-osteoporosis therapy to date has targeted this cell. The osteoclast is a specialized macrophage polykaryon whose differentiation is principally regulated by macrophage colony-stimulating factor, RANK ligand, and osteoprotegerin. Reflecting integrin-mediated signals, the osteoclast develops a specialized cytoskeleton that permits it to establish an isolated microenvironment between itself and bone, wherein matrix degradation occurs by a process involving proton transport. Osteopetrotic mutants have provided a wealth of information about the genes that regulate the differentiation of osteoclasts and their capacity to resorb bone.
Five-Point Motion Estimation Made Easy (2006)

Estimating relative camera motion from two calibrated views is a classical problem in computer vision. The minimal case for such problem is the so-called five-point problem, for which the state-of-the-art solution is Nist´er’s algorithm [1][2]. However, due to the heuristic nature of the procedures it applies, to implement it needs much effort for non-expert user. This paper provides a simpler algorithm based on the hidden variable resultant technique. Instead of eliminating the unknown variables one by one (i.e, sequentially) using the Gauss-Elimination as in [1], our algorithm eliminates many unknowns at once. Moreover, in the equation solving stage, instead of back-substituting and solve all the unknowns sequentially, we compute the minimal singular vector of the coefficient matrix, by which all the unknown parameters can be estimated simultaneously. Experiments on both simulation and real images have validated the new algorithm.
BCL2 gene activation and protein expression in follicular lymphoma: a report on 64 cases. (1993)

Rearrangements of the BCL2 gene and expression of bcl-2 protein were analyzed in a series of 64 cases of follicular lymphomas in order to establish a relationship between the rearrangements and the protein overexpression. Of the 64 cases, 41 showed BCL2 rearrangement involving one of the three breakpoint clusters: 30 in mbr, eight in mcr, and three in vcr. A double rearrangement mbr+vcr was detected in two cases. Twenty cases with bcl-2 protein expression in tumor cells exhibited no apparent rearrangement, suggesting the possible existence of other mechanisms activating the gene. Interestingly, expression of the LMP1 protein, the Epstein-Barr virus (EBV) encoded gene, whose capacity to induce BCL2 has been recently demonstrated, was only found in 2/41 cases in which BCL2 was rearranged. These data suggest that EBV infection is not an important mechanism in the activation of BCL2 in follicular lymphoma.
Nanotube‐Based Ultrafast Electrochromic Display (2005)

An ultrafast electrochromic display is fabricated based upon well defined nanotube arrays of poly(3,4-ethylenedioxythiophene), PEDOT (see Figure). The thin nature of the nanotube walls (10 – 20 nm) offers a short ion-diffusion distance, which results in an ultrafast switching rate (color-switching time < 10 ms). The arrayed long nanotube structure furnishes strong coloration.
Inhibition of 7,12-dimethylbenz(a)anthracene-induced skin papillomas and carcinomas by dehydroepiandrosterone and 3-beta-methylandrost-5-en-17-one in mice. (1985)

Topical application of the adrenal steroid, dehydroepiandrosterone, or the synthetic steroid, 3-beta-methylandrost-5-en-17-one, which unlike dehydroepiandrosterone is not demonstrably uterotrophic, inhibits 7,12-dimethylbenz(a)anthracene-induced skin papillomas and carcinomas in the CD-1 mouse.
Rollout strategies for sequential fault diagnosis (2003)

Test sequencing is a binary identification problem wherein one needs to develop a minimal expected cost testing procedure to determine which one of a finite number of possible failure sources, if any, is present. The problem can be solved optimally using dynamic programming or AND/OR graph search methods (AO/sup */, CF, and HS). However, for large systems, the associated computation with dynamic programming or AND/OR graph search methods is substantial, due to the rapidly increasing number of OR nodes (denoting ambiguity states) and AND nodes (denoting tests) in the search graph. In order to overcome the computational explosion, the one-step or multistep lookahead heuristic algorithms have been developed to solve the test sequencing problem. In this paper, we propose to apply rollout strategies, which can be combined with the one-step or multistep lookahead heuristic algorithms, in a computationally more efficient manner than the optimal strategies, to obtain solutions superior to those using the one-step or multistep lookahead heuristic algorithms. The rollout strategies are illustrated and tested using a range of real-world systems. We show computational results, which suggest that the information-heuristic based rollout policies are significantly better than other rollout policies based on Huffman coding and entropy.
Structure of the Lowest Temperature Phase of the Solid Benzene–Hexafluorobenzene Adduct (1992)

Similarities with a number of liquid-crystal systems are revealed by the structural characterization of the low-temperature phases II—IV of the solid adduct from benzene and hexafluorobenzene (right). As the temperature is raised, increased rotation leads to a reduction in the interactions between neighboring columns of alternating C6H6 and C6F6 molecules. These results could only be obtained by using a combination of powder diffraction techniques with neutrons and synchrotron radiation.
Detection of mitochondrial DNA mutations in primary breast cancer and fine-needle aspirates. (2001)

To determine the frequency and distribution of mitochondrial DNA mutations in breast cancer, 18 primary breast tumors were analyzed by direct sequencing. Twelve somatic mutations not present in matched lymphocytes and normal breast tissues were detected in 11 of the tumors screened (61%). Of these mutations, five (42%) were deletions or insertions in a homopolymeric C-stretch between nucleotides 303-315 (D310) within the D-loop. The remaining seven mutations (58%) were single-base substitutions in the coding (ND1, ND4, ND5, and cytochrome b genes) or noncoding regions (D-loop) of the mitochondrial genome. In three cases (25%), the mutations detected in coding regions led to amino acid substitutions in the protein sequence. We then screened an additional 46 primary breast tumors with a rapid PCR-based assay to identify poly-C alterations in D310, and we found seven more cancers with alterations. Using D310 mutations as clonal marker, we detected identical changes in five of five matched fine-needle aspirates and in four of four metastases-positive lymph nodes. The high frequency of D310 alterations in primary breast cancer combined with the high sensitivity of the PCR-based assays provides a new molecular tool for cancer detection.