gebhart/patrepeval huggingface dataset:
The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries (1997)

Current approaches to the design of combinatorial libraries assume that structural diversity in the reactant pools corresponds to structural diversity in the combinatorial libraries that result from reacting these pools together. In experiments with three different published libraries, dissimilarity-based compound selection (DBCS) is applied at two levels. First, the DBCS algorithm is applied at the reactant level, a library is built, and its diversity is measured. Second, the DBCS algorithm is applied to the full set of products generated by enumeration of all the reactants and the diversity of the subset is measured. Results show that reactant-based selection, which attempts to maximize diversity in the pools, results in noticeably less diverse libraries than if the selection is performed at the product level. Experiments are reported to estimate the upperbound to diversity achievable using DBCS, and it appears that DBCS is very effective at finding maximally diverse subsets. However, applying DBCS selection at the product level is synthetically inefficient since it does not result in a combinatorial library. We thus describe a genetic algorithm for selecting combinatorial libraries from the fully enumerated products and demonstrate that these libraries are significantly more diverse than those generated using reactant-based selection.
Molecular replacement by evolutionary search (2001)

Stochastic search algorithms can be used to perform rapid six-dimensional molecular-replacement searches. A molecular-replacement procedure has been developed that uses an evolutionary algorithm to simultaneously optimize the orientation and position of a search model in a unit cell. Here, the performance of this algorithm and its dependence on search model quality and choice of target function are examined. Although the evolutionary search procedure is capable of finding solutions with search models that represent only a small fraction of the total scattering matter of the target molecule, the efficiency of the search procedure is highly dependent on the quality of the search model. Polyalanine models frequently provide better search efficiency than all-atom models, even in cases where the side-chain positions are known with high accuracy. Although the success of the search procedure is not highly dependent on the statistic used as the target function, the correlation coefficient between observed and calculated structure-factor amplitudes generally results in better search efficiency than does the R factor. An alternative stochastic search procedure, simulated annealing, provides similar overall performance to evolutionary search. Methods of extending the evolutionary search algorithm to include internal optimization, selection and construction of the search model are now beginning to be investigated.
A Electric Way to Measure the Wear of Gear Device in Auto T ransmission System (2001)

This paper introduces a way to measure the wear mosa ic content of lubrication oil in auto transmission system gear device by a new type of magnetic resistance sensor,the wear degree of gear device in transmissio n system can be monitored in this way.
Infiltrating leukocyte populations and T-lymphocyte subsets in head and neck squamous cell carcinomas from patients receiving perilymphatic injections of recombinant interleukin 2. A pathologic and immunophenotypic study. (1990)

Nine patients with squamous cell carcinoma of the oral cavity and oropharynx underwent preoperative perilymphatic administration of recombinant interleukin 2 (rIL-2). A more marked eosinophil and lymphocyte infiltration and more extensive edema than in 13 untreated cases were observed in surgical specimens. Necrosis was present in five of nine cases, but involved no more than 10% of the neoplastic tissue; in three of nine cases, characteristic necrotic changes with intense eosinophil infiltration possibly induced by lymphokines involved the peritumoral soft tissues. Of the tumor-infiltrating lymphocytes, T-lymphocytes (mostly CD4+ cells) prevailed over B-lymphocytes. CD4+ and CD8+ cells were mainly located close to the neoplastic sheets. Moderate amounts of CD38+ and CD11c+ cells (macrophages) and few CD16+ and CD56+ lymphocytes were found in all cases. CD25+ and LAK1+ cells were significantly more numerous in treated than in untreated cases. This suggests that local administration of rIL-2 induces an increase in activated T-lymphocyte subsets infiltrating the neoplastic tissue, thus eliciting a tumor-specific T-lymphocyte reactivity.
Molecular characterization of a rat negative regulator with a basic helix-loop-helix structure predominantly expressed in the developing nervous system. (1992)

We report here the cDNA cloning and characterization of a rat basic helix-loop-helix (HLH) factor, designated HES-5. This factor has a distant sequence homology to Drosophila hairy and Enhancer-of-split proteins, both of which are required for normal neurogenesis. DNase I footprinting analyses show that HES-5 binds to the sequence CACNAG (called N box), a recognition sequence of Enhancer-of-split proteins. Although HES-5 does not bind to the sequence CANNTG (called E box) recognized by other HLH factors, it attenuates the binding of E47, an HLH activator, to E box by forming a hetero-oligomer. In cotransfection analyses using NIH 3T3 cells, HES-5 significantly represses transcription originating from the promoter containing the N box sequences. Furthermore, HES-5 also partially inhibits the E47-induced expression from the promoter containing E boxes. Northern blot, RNase protection, and in situ hybridization analyses demonstrate that the HES-5 mRNA is specifically expressed in the nervous system. Prominent expression is observed in the ventricular zones of the embryonal brain vesicles and the outer nuclear layer of the neural retina. These results suggest that the negative regulator HES-5 may play an important role in neural development.
Lipid advanced glycosylation: pathway for lipid oxidation in vivo. (1993)

To address potential mechanisms for oxidative modification of lipids in vivo, we investigated the possibility that phospholipids react directly with glucose to form advanced glycosylation end products (AGEs) that then initiate lipid oxidation. Phospholipid-linked AGEs formed readily in vitro, mimicking the absorbance, fluorescence, and immunochemical properties of AGEs that result from advanced glycosylation of proteins. Oxidation of unsaturated fatty acid residues, as assessed by reactive aldehyde formation, occurred at a rate that paralleled the rate of lipid advanced glycosylation. Aminoguanidine, an agent that prevents protein advanced glycosylation, inhibited both lipid advanced glycosylation and oxidative modification. Incubation of low density lipoprotein (LDL) with glucose produced AGE moieties that were attached to both the lipid and the apoprotein components. Oxidized LDL formed concomitantly with AGE-modified LDL. Of significance, AGE ELISA analysis of LDL specimens isolated from diabetic individuals revealed increased levels of both apoprotein- and lipid-linked AGEs when compared to specimens obtained from normal, nondiabetic controls. Circulating levels of oxidized LDL were elevated in diabetic patients and correlated significantly with lipid AGE levels. These data support the concept that AGE oxidation plays an important and perhaps primary role in initiating lipid oxidation in vivo.
Glutathionylation of beta-actin via a cysteinyl sulfenic acid intermediary (2007)

We conclude that glutathionylation of beta-actin may occur via spontaneous oxidation of a cysteinyl residue to a sulfenic acid that readily reacts with GSH to form a mixed disulfide. We also show that the reactivity and oxidation to a reactive protein thiol intermediary differ between different actin isoforms.
Differential Outcome of IL-2/Anti–IL-2 Complex Therapy on Effector and Memory CD8+ T Cells following Vaccination with an Adenoviral Vector Encoding EBV Epitopes (2011)

IL-2/anti-IL-2 complex-based therapy has been proposed as a potential adjunct therapeutic tool to enhance in vivo efficacy of T cell-based immunotherapeutic strategies for chronic viral infections and human cancers. In this study, we demonstrate that IL-2 complex therapy can have discerning effects on CD8(+) T cells depending on their stage of differentiation. To delineate the underlying mechanism for these opposing effects on CD8(+) T cells, we examined the effects of IL-2 therapy during early priming, effector, and memory phases of T cell responses generated following immunization with an adenoviral vector encoding multiple EBV CD8(+) epitopes. IL-2 complex treatment during the early priming phase, which coincided with low levels of IL-2Rβ (CD122) and higher levels of IL-2Rα (CD25) on CD8(+) T cells, did not induce the expansion of effector T cells. In contrast, IL-2 complex treatment following the establishment of memory enhanced the expansion of Ag-specific T cells. Additionally, central memory T cells preferentially expanded following treatment at the expense of effector memory T cell populations. These studies demonstrate how differentiation status of the responding CD8(+) T cells impacts on their responsiveness to IL-2 complexes and highlight that timing of treatment should be considered before implementing this therapy in a clinical setting.
Synthesis of (1R,4R)- and (1S,4S)-2,5-Diazabicyclo[2.2.1]heptanes and TheirN-Substituted Derivatives (1990)

Derivatives of the (1R,4R)- and (1S,4S)-2,5-diazabicyclo- [2.2.1]heptane ring system are prepared in enantiomerically pure form from trans-4-hydroxy-L-proline (2). The target compounds are precursors of antibacterial quinolone carboxyclic acids.
Activation of tat-defective human immunodeficiency virus by ultraviolet light. (1990)

Ultraviolet light (UV) is known to cause activation of gene expression from the human immunodeficiency virus type 1 (HIV-1) promoter. To address the question of whether tat-defective HIV-1 provirus could be rescued by UV irradiation we examined its effect on HeLa cells containing integrated proviruses with tat mutations. Exposure of these cells to an optimal dose of UV resulted in the production of infectious viruses. The degree of UV activation and reversion to infectious virus appeared to depend on the nature of the original tat mutation. Two of the mutants required cocultivation with tat-expressing cells to fully generate replication competent viruses, while a third mutant required only cocultivation with H9 cells. Sequencing of cDNA from cells infected with this last mutant demonstrated that the parental mutant sequence was retained and that genotypic revertants to the wild-type as well as new mutant sequences were generated. These results suggest that tat-defective HIV-1 provirus can be activated by UV and can subsequently revert to wild-type virus. This study raises the possibility that UV exposure of immune cells in the skin plays a role in the activation of defective HIV-1 in vivo.
Anti-inflammatory activity and neutrophil reductions mediated by the JAK1/JAK3 inhibitor, CP-690,550, in rat adjuvant-induced arthritis (2010)

Results from this investigation suggest that CP-690,550 is a potent inhibitor of JAK1 and JAK3 with potentially reduced cellular potency for JAK2. In rat AIA, as in the case of human RA, PBNC were decreased at efficacious exposures of CP-690,550. Inflammatory end points were similarly reduced, as judged by attenuation of paw edema and cytokines IL-6 and IL-17. Plasma concentration at these exposures was consistent with inhibition of JAK1 and JAK3 but not JAK2. Decreases in PBNC following CP-690,550 treatment may thus be related to attenuation of inflammation and are likely not due to suppression of granulopoiesis through JAK2 inhibition.
Identification of Committed Mononuclear Precursors for Osteoclast-Like Cells Formed in Long Term Human Marrow Cultures* (1990)

Nonadherent marrow mononuclear cells enriched for hematopoietic progenitor cells were cultured in semisolid medium with recombinant human granulocyte-macrophage colony-stimulating factor for 9 days to form colony forming unit-granulocyte macrophage (CFU-GM) colonies. 1,25-Dihydroxyvitamin D was then gently layered over the cultures. After 2 weeks, approximately 30% of the colonies that formed were composed of cells with a unique polygonal morphology. One hundred percent of the polygonal cells in these colonies crossreacted with the monoclonal antibody 23c6, which preferentially recognizes osteoclasts. Homogenous populations of these polygonal cells formed multinucleated cells (MNC) in suspension culture, 100% of which cross-reacted with the 23c6 monoclonal antibody, and greater than 90% of the MNC contracted in response to calcitonin. Approximately 20% of these MNC formed resorption lacunae on calcified matrices. These results suggest that 1) early osteoclast precursors are derived from CFU-GM, the committed granulocyte-macrophage progenitor; 2) committed mononuclear osteoclast precursors have a distinct polygonal morphology and cross-react with monoclonal antibodies that recognize mature osteoclasts; and 3) these mononuclear precursors are capable of forming multinucleated cells which fulfill the functional criteria for osteoclasts.
Comparison of defined culture systems for feeder cell free propagation of human embryonic stem cells (2010)

There are many reports of defined culture systems for the propagation of human embryonic stem cells in the absence of feeder cell support, but no previous study has undertaken a multi-laboratory comparison of these diverse methodologies. In this study, five separate laboratories, each with experience in human embryonic stem cell culture, used a panel of ten embryonic stem cell lines (including WA09 as an index cell line common to all laboratories) to assess eight cell culture methods, with propagation in the presence of Knockout Serum Replacer, FGF-2, and mouse embryonic fibroblast feeder cell layers serving as a positive control. The cultures were assessed for up to ten passages for attachment, death, and differentiated morphology by phase contrast microscopy, for growth by serial cell counts, and for maintenance of stem cell surface marker expression by flow cytometry. Of the eight culture systems, only the control and those based on two commercial media, mTeSR1 and STEMPRO, supported maintenance of most cell lines for ten passages. Cultures grown in the remaining media failed before this point due to lack of attachment, cell death, or overt cell differentiation. Possible explanations for relative success of the commercial formulations in this study, and the lack of success with other formulations from academic groups compared to previously published results, include: the complex combination of growth factors present in the commercial preparations; improved development, manufacture, and quality control in the commercial products; differences in epigenetic adaptation to culture in vitro between different ES cell lines grown in different laboratories.
Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies (2014)

The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.
Twin pregnancy: the role of ultrasound in management (2001)

Determination of chorionicity is one of the most important issues in the management of twin pregnancy. Modern ultrasound equipment has made it possible to accurately assess placentation already in the first trimester with the lambda sign. With regard to prenatal diagnosis, it is important to know the chorionicity in order to calculate the risk of chromosomally abnormal fetuses. Accurate chorionicity offers the obstetricians the opportunity to observe the monochorionic twins more intensively than is required for twins with dichorionic placentation. This review gives an update of the state of the art for clinicians caring for twin pregnancies.
Physiology of Heat Regulation and the Science of Clothing (1950)

This significant volume is a progress report of the research work on the most efficient and practical methods of protecting man against the extremes of external temperatures such as encountered in the polar regions, in equatorial deserts and at high altitudes in the air. This work, by competent biologists, medical doctors and engineers during the late war, was inaugurated by our Armed Forces. Fifteen authors contribute to the 12 chapters of the report. Each chapter is provided with an extensive bibliography. This valuable report shows how far the extremes of environmental temperatures can be mitigated by scientifically protective covering of man. The studies are being continued by both military and civilian groups.
Basal-Like Breast Cancer Defined by Five Biomarkers Has Superior Prognostic Value than Triple-Negative Phenotype (2008)

The expanded surrogate immunopanel of estrogen receptor, progesterone receptor, human HER-2, EGFR, and cytokeratin 5/6 provides a more specific definition of basal-like breast cancer that better predicts breast cancer survival.
BRCA2 and homologous recombination (2001)

Two recent papers provide new evidence relevant to the role of the breast cancer susceptibility gene BRCA2 in DNA repair. Moynahan et al provide genetic data indicating a requirement for BRCA2 in homology-dependent (recombinational) repair of DNA double-strand breaks. The second paper, by Davies et al, begins to address the mechanism through which BRCA2 makes its contribution to recombinational repair. BRCA2 appears to function in recombination via interactions with the major eukaryotic recombinase RAD51 [1,2,3]. We briefly review the context in which the two studies were carried out, we comment on the results presented, and we discuss models designed to account for the role of BRCA2 in RAD51-mediated repair.
Hepatic Accumulation of Glutamic Acid Branched Neogalactosyllipid Modified Liposomes. (1997)

We synthesized branched type galactosyllipid derivatives for liposome modification for the targeting of asialoglycoprotein receptors on the surface of liver cells. Galactose was coupled to the alpha- and gamma-carboxyl groups of glutamic acid via a triethyleneglycol spacer, then this glutamic moiety was bound to the lipid anchor. Ricinus communis agglutinin (RCA120) induced the agglutination of liposomes modified with mono-, bi- and tri-antennary neogalactosyllipid. With the bi- or tri-antennary derivatives, agglutination was observed at fewer galactosyl residues on the liposomes. We examined the effect of the branching structure in vivo. The difference in accumulation of liposomes between non-branched type neogalactosyllipid and branched type neogalactosyllipid was not large. Liver accumulation of liposomes depended on the galactosyl residues. The number of galactosyl residues was more effective for accumulation in the liver than for branching. We studied the effect of asialofetuin preinjection on the hepatic accumulation of neogalactosyllipid modified liposomes. Hepatic accumulation of liposomes was inhibited by preinjection of asialofetuin. The effect of preinjection was almost equal among the ligands. These results show that the saccharide density on the liposome surface seemed to be a more important factor than the branching structure of the ligand for liver targeting.
Short-term aromatase inhibition: effects on glucose metabolism and serum leptin levels in young and elderly men (2008)

Short-term aromatase inhibition appears to affect glucose metabolism in young men, and lipid metabolism, including leptin secretion, in young and elderly men. Furthermore, the short period of exposure suggests that these changes might be mediated by direct effects of sex steroids rather than by changes in body composition.
A new approach in intelligent trailer parking (2010)

In this article a new approach for parking the trailer was suggested, using fuzzy ration in a dynamic environment. This method, contrasting with previous methods, in which only the trailer's backward movement was allowed, the capability of forward movement to find the optimal path beside backward movement exists. Sometimes the angel of the trailer's position may be in a way that the possibility of backward movement does not exist. In this article, three separate fuzzy controllers were used for directing the trailer; one is used for forward movement realization in order to stop crashing with the used walls, which organize the forward movement, the second controller is for finding the target, and the third for staying away from the obstacles. In the first case, obstacles are assumed to be fixed, while the second condition includes moving obstacles through which the trailer should be directed toward the parking dock. The method is designed in a way to be used in conditions with infinite number of obstacles at arbitrary places. In any case, to find the parking dock, the trailer movement must be adapted to that of obstacles. While there is no obstacle around, the target finder controller is in use; and in the cases where the trailer gets close to obstacles the obstacle avoider controller is activated. The proposed method is employed for parking a trailer model through fixed and moving obstacles.