gebhart/patrepeval huggingface dataset:
Book Review: Plasmalogens: Workhorse Lipids of Membranes in Normal and Injured Neurons and Glia (2001)

Plasmalogens are unique glycerophospholipids because they have an enol ether double bond at the sn-1 position of the glycerol backbone. They are found in all mammalian tissues, with ethanolamine plasmalogens 10-fold higher than choline plasmalogens except in muscles. The enol ether double bond at the sn-1 position makes plasmalogens more susceptible to oxidative stress than the corresponding ester-bonded glycerophospholipids. Plasmalogens are not only structural membrane components and a reservoir for second messengers but may also be involved in membrane fusion, ion transport, and cholesterol efflux. Plasmalogens may also act as antioxidants, thus protecting cells from oxidative stress. Receptor-mediated degradation of plasmalogens by plasmalogen-selective phospholipase A2 results in the generation of arachidonic acid, eicosanoids, and platelet activating factor. Low levels of these metabolites have trophic effects, but at high concentration they are cytotoxic and may be involved in allergic response, inflammation, and trauma. Levels of plasmalogens are decreased in several neurological disorders including Alzheimer's disease, ischemia, and spinal cord trauma. This may be due to the stimulation of plasmalogen-selective phospholipase A2. A deficiency of plasmalogens in peroxisomal disorders and Niemann-Pick type C disease indicates that this deficiency may be due to the decreased activity of plasmalogen synthesizing enzymes that occur in peroxisomes.
Oxidative Dehydrogenation of Ethane: Common Principles and Mechanistic Aspects (2013)

Abstract The increasing demand for light olefins and the changing nature of basic feedstock has stimulated substantial research activity into the development of new process routes. Steam cracking remains the most industrially relevant pathway, but other routes for light‐olefin production have emerged. Fluid catalytic cracking only produces ethene in minor concentrations. Challenged by marked catalyst deactivation, in contrast, catalytic dehydrogenation ethane up opens a more selective route to ethene. The oxidative dehydrogenation (ODH) of ethane, which couples the endothermic dehydration of ethane with the strongly exothermic oxidation of hydrogen, would potentially be the most attractive alternative route because it avoids the need for excessive internal heat input, but also consumes valuable hydrogen. In this Review, the current state of the ODH of ethane is compared with other routes for light‐olefin production, with a focus on the catalyst and reactor system variants. New catalyst systems and reactor designs have been developed to improve the industrial competitiveness of the ODH reaction of ethane. The current state of our fundamental understanding of the ODH of light alkanes, in particular in terms of catalyst and reactor development, is critically reviewed. The proposed mechanisms and the nature of the active site for the ODH reaction are described and discussed in detail for selected promising catalysts. The reported catalytic performance and the possible limitations of these ODH catalysts will be examined and the performance of the emerging approaches is compared to the currently practiced methods.
Potentiation of Virulence by Group B Streptococcal Polysaccharides (1984)

The ability of group B streptococcal (GBS) capsular polysaccharides to potentiate virulence was examined. Incubation of soluble type Ia or III polysaccharide in hypogammaglobulinemic human serum inhibited classical complement-dependent opsonophagocytic killing of type Ia strain 515. When functional complement components were measured, C1 activity increased in sera with added polysaccharide whereas C4 activity decreased 80%-90%. Incubation of purified C1 with type Ia polysaccharide inhibited lysis of EAC4 cells in a C1 transfer assay. In a mouse lethality model, tail-vein injection of 50 micrograms of type Ia or III polysaccharide decreased the 50% lethal dose (LD50) from 3.2 X 10(6) to 2.2 X 10(5). Total hemolytic complement levels in mice immediately after polysaccharide injection were increased over levels in control mice, but this difference was not seen 30 min later. The LD50 in mice depleted of C3 (with cobra venom factor) was 6 X 10(5) and simultaneous injection of polysaccharide did not further lower the LD50.
Expression of PD-1, PD-L1, and PD-L2 in the Liver in Autoimmune Liver Diseases (2007)

Modulation of PD-1/PD-L1 and PD-L2 systems may play a role in the development of autoimmune liver diseases.
Phase unwrapping with a regularized phase-tracking system (1998)

We develop a regularized phase-tracking (RPT) technique tounwrap phase maps. The phase maps that can be unwrapped with thisnew method may be bounded by arbitrarily shaped boundaries. Moreover, the RPT unwrapper has a higher noise robustness than previously reported phase-unwrapping schemes.
Syntheses, structures, and complexation of <i>cis</i>‐ and <i>trans</i>‐cycloheptane‐1,2‐diyl‐fused crown thioethers ([12]ansS<sub>4</sub>) (2011)

Abstract cis ‐ and trans ‐Cycloheptane‐1,2‐diyl‐fused crown thioethers ([12]ansS 4 ), 2,3‐ cis ‐ and 2,3‐ trans ‐cycloheptano‐1,4,7,10‐tetrathiacyclododecanes ( cis ‐ 2 and (±)‐ trans ‐ 2 ), were synthesized from newly prepared cis ‐ and trans ‐cycloheptane‐1,2‐ditiols, respectively. X‐ray diffraction analyses on cis ‐ 2 and (–)‐ trans ‐ 2 , which was obtained by optical resolution of (±)‐ trans ‐ 2 with a chiral column, showed that in cis ‐ 2 the S‐C‐C‐S part fused with the cis ‐cycloheptane‐1,2‐diyl adopted a gauche orientation and that in (–)‐ trans ‐ 2 all S‐C‐C‐S parts took anti‐conformations. A competitive complexation experiment of cis ‐ 2 and (±)‐ trans ‐ 2 with AgOTf revealed that cis ‐ 2 was more favorable than (±)‐ trans ‐ 2 for the complexation. The structure of [Ag( cis ‐ 2 )]NO 3 was analyzed by X‐ray crystallography. © 2011 Wiley Periodicals, Inc. Heteroatom Chem 22:388–396, 2011; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20695
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles (2006)

dibernardo@tigem.it SUPLEMENTARY INFORMATION: Supplementary data are available at http://dibernado.tigem.it
<i>In vitro</i> and <i>in vivo</i> antitumor properties of the cyclin dependent kinase inhibitor CYC202 (R‐roscovitine) (2002)

Abstract CDK2 inhibitors have been proposed as effective anti‐cancer therapeutics. We show here that CYC202 ( R ‐roscovitine) is a potent inhibitor of recombinant CDK2/cyclin E kinase activity (IC 50 = 0.10 μM) with an average cytotoxic IC 50 of 15.2 μM in a panel of 19 human tumour cell lines, and we also demonstrate selectivity for rapidly proliferating cells over non‐proliferating cells. A study of the cell cycle effects of CYC202 in Lovo colorectal carcinoma cells showed that the major effect was not the predicted arrest in one part of the cycle, but rather an induction of cell death from all compartments of the cell cycle. The maximum tolerated dose given intravenously to mice was in excess of 20 mg/kg. Doses up to 2,000 mg/kg were tolerated when administered orally in mice. Following repeated intraperitoneal administration (3 times daily for 5 days) of 100 mg/kg to nude mice bearing the Lovo human colorectal tumour, CYC202 induced a significant antitumour effect with a 45% reduction in tumour growth compared to controls. A second experiment using the human uterine xenograft MESSA‐DX5 treated with orally administered CYC202 (500 mg/kg 3 times daily for 4 days) also exhibited a significant reduction in the rate of growth of the tumour (62%). These data, showing enzyme and cellular potency together with antitumour activity, confirm the potential of CDK2 inhibitors such as CYC202 as anticancer drugs. © 2002 Wiley‐Liss, Inc.
History of the Discovery of the Antipsychotic Dopamine D2 Receptor: A Basis for the Dopamine Hypothesis of Schizophrenia (2013)

The 1975 publication of Seeman et al. (Proc Nat Acad Sci, USA), reporting the discovery of the antipsychotic receptor in the brain, is a classic example of translational medicine research. In searching for a pathophysiological mechanism of psychosis, the team sought to identify sites that bound the antipsychotic drug haloperidol. Their criterion was that haloperidol bound to the site at one to two nanomoles per liter, corresponding to haloperidol concentrations found in spinal fluid or plasma water in treated patients. They requested de novo synthesis of tritiated haloperidol, and it readily detected specific haloperidol binding sites in brain striatum. With dopamine binding the haloperidol-labeled sites with higher potency than other neurotransmitters, the sites were named antipsychotic/dopamine receptors (now designated dopamine D2 receptors). Most significantly, they found that all antipsychotics bound these sites at concentrations and with a rank order of potencies that were directly related to the mean daily antipsychotic dose taken by patients with schizophrenia. Their findings enabled screening for new antipsychotics, initiated D2 receptor measurements in brain of living patients, and determination of minimum occupancy (65%) of D2 receptors for antipsychotic benefit. The collective work is generally viewed as providing a fundamental basis for the dopamine hypothesis of schizophrenia.
Versatile Transcoding Proxy for Internet Content Adaptation (2008)

Recent technology advances in multimedia communication have ushered in a new era of personal communication. Users can ubiquitously access the Internet via various mobile devices. For the mobile devices featured with lower bandwidth network connectivity, transcoding can be used to reduce the object size by lowering the quality of a multimedia object. In view of the monolithic transcoders which only provide transcoding services and have limited performances due to the unknown data types and protocols in the prior research, we propose the architecture of versatile transcoding proxy (VTP). Based on the concept of the agent system, the VTP architecture can accept and execute the transcoding preference script provided by the client or the server to transform the corresponding data or protocol according to the user's specification. In order to enhance the effectiveness of the VTP architecture, we adopt the concept of dynamic cache categories and propose the scheme maximum profit replacement with dynamic cache categories (DCC-MPR). Based on the weighted transcoding graph, scheme DCC-MPR performs cache replacement according to the content in the caching candidate set, which is generated by the concept of dynamic programming. The experimental results show that the proposed architecture VTP and the corresponding scheme DCC-MPR have better performances in many aspects compared to the conventional transcoding proxy systems.
Frequent beta-catenin mutation and cytoplasmic/nuclear accumulation in pancreatic solid-pseudopapillary neoplasm. (2001)

Significance of Wnt signaling with beta-catenin mutations on solid-pseudopapillary neoplasm (SPN) of the pancreas was studied by immunohistochemistry and molecular analysis. On immunohistochemistry, all 18 SPNs tested showed diffuse cytoplasmic/nuclear positivity for beta-catenin. Upon direct DNA sequencing of exon 3 of the beta-catenin gene, 15 (83%) of the 18 SPNs showed 1-bp missense mutation in codons 32 (5 cases), 33 (3 cases), 34 (3 cases), 37 (3 cases), and 41 (1 case). Immunoreactivity for cyclin D1, one of the intranuclear targets of beta-catenin complexes, was found in tumor cells of more than half the tumor cells of all of the 18 SPNs. The present study strongly suggested a significant role of Wnt signaling, mostly associated with beta-catenin mutations in the tumorigenesis of SPN.
Synthesis and recognition studies with a ditopic, photoswitchable deep cavitand (2013)

We describe the synthesis and photochemical behavior of open-ended container modules connected by a 4,4'-azobiphenyl spacer. Both trans and cis azo configurations of the host can be accessed and their binding of guest molecules was characterized by NMR methods.
Expression of MUC1 and MUC2 mucin antigens in intrahepatic bile duct tumors: Its relationship with a new morphological classification of cholangiocarcinoma (1999)

Our previous immunohistochemical study on intrahepatic bile duct tumors showed that invasive cholangiocarcinoma (ICC) with a poor outcome expressed MUC1 mucin but was negative for MUC2 mucin, whereas bile duct cystadenocarcinoma (BDCC) with a favorable outcome was MUC1 negative and MUC2 positive. In the present study, ICC was further subdivided into 2 subtypes: intraductal growth type and/or periductal infiltrating type (ICC-IP) and mass forming type (ICC-M). The survival of patients with BDCC or ICC-IP is significantly better than that of patients with ICC-M. We examined these subtypes (ICC-IP and ICC-M) and BDCC for their expression of MUC1 mucins of different glycoforms. ICC-M showed significantly higher MUC1 expression rates (90%, 95%, and 85% positive rates as measured with the DF3, MY.1E12, and MUC1-Glycoprotein antibodies, respectively) than BDCC and ICC-IP (14% and 33%, 58% and 58%, and 0% and 50% positive respectively, as measured by the same antibodies). In contrast, BDCC (86% positive) and ICC-IP (67% positive) showed significantly higher MUC2 expression rates than ICC-M (25% positive) as measured with the anti-MRP antibody. Thus, the immunohistochemical staining pattern of ICC-IP resembled the pattern of BDCC more than they resembled ICC-M. In general, MUC1 expression is associated with poor patient outcome, irrespective of the glycosylation status. In particular, high expression of more sialylated forms of MUC1 mucins was correlated with poor survival. In contrast, expression of non-sialylated MUC2 mucin is a favorable prognostic indicator. These results suggest that ICC-IP is a different entity from ICC-M. This reclassification may have value in determining prognosis and treatment method.
<i>In Vitro</i> Reconstruction of Nonribosomal Peptide Biosynthesis Directly from DNA Using Cell-Free Protein Synthesis (2016)

Genome sequencing has revealed that a far greater number of natural product biosynthetic pathways exist than there are known natural products. To access these molecules directly and deterministically, a new generation of heterologous expression methods is needed. Cell-free protein synthesis has not previously been used to study nonribosomal peptide biosynthesis, and provides a tunable platform with advantages over conventional methods for protein expression. Here, we demonstrate the use of cell-free protein synthesis to biosynthesize a cyclic dipeptide with correct absolute stereochemistry. From a single-pot reaction, we measured the expression of two nonribosomal peptide synthetases larger than 100 kDa, and detected high-level production of a diketopiperazine. Using quantitative LC-MS and synthetically prepared standard, we observed production of this metabolite at levels higher than previously reported from cell-based recombinant expression, approximately 12 mg/L. Overall, this work represents a first step to apply cell-free protein synthesis to discover and characterize new natural products.
Antimicrobial activities of pomegranate rind extracts: enhancement by addition of metal salts and vitamin C (2008)

This is the first report demonstrating the enhanced efficacy of PRE/metal salt combinations in the presence of the stabilising agent vitamin C, to which all isolates were sensitive with the exception of B. subtilis. This study has validated the exploration of PRE along with additives such as metal salts and vitamin C as novel antimicrobial combinations.
A Polymer with “Locked” Degradability: Superior Backbone Stability and Accessible Degradability Enabled by Mechanophore Installation (2020)

Though numerous applications require degradable polymers, there are surprisingly few polymer systems that combine superior stability and controllable degradability. Particularly, the degradability of a conventional degradable polymer is typically enabled by cleavable groups on the backbone, which can be attacked by stimuli in ambient conditions, causing undesirable material deterioration. Here we report a general strategy to overcome this issue: "locking" the degradability during handling and use of the polymers and "unlocking" it when degradation is needed. This strategy is demonstrated with a cyclobutane-fused lactone (CBL) polymer. The cyclobutane keeps polymer backbone intact under conditions that hydrolyze the lactone and allows the ester group to be recovered when undesirable hydrolysis occurs. When backbone degradation is needed, the degradability can be unlocked by mechanochemical activation that converts the polyCBL into a linear polyester. The rare combination of two intrinsically conflicting properties, i.e., backbone stability and accessible degradability, can make this polymer a potential option for new sustainable materials.
Taper time for mining sector (2013)

Global investors have been fretting about the impact of a possible US Federal Reserve tapering. But a new report from PIMCO warns that Australian investors should be factoring in the fallout from another form of tapering: the tapering of mining investment in Australia.
Aberrant Glycosylation of E-cadherin Enhances Cell-Cell Binding to Suppress Metastasis (1996)

Introduction of the beta1-4 N-acetylglucosaminyltransferase (GnT-III) gene was reported to suppress metastasis in highly metastatic B16-hm murine melanoma cells (Yoshimura, M., Nishikawa, A. , Ihara, Y., Taniguchi, S., and Taniguchi, N.(1995) Proc. Natl. Acad. Sci. U. S. A. 92, 8754-8758). In this study, the effect of GnT-III gene transfer on E-cadherin was studied, since E-cadherin acts as a suppressor of metastasis. E-cadherin expression at cell-cell contacts of B16-hm cells expressing high GnT-III activity was greater than controls without affecting transcription. Lectin blotting showed that E-cadherin from GnT-III transfectants was glycosylated by ectopically expressed GnT-III. The glycosylated E-cadherin exhibited the delayed turnover and the decreased release from cell surface, as compared with the native E-cadherin, resulting in the elevated expression at the cell-cell border of GnT-III transfectants. Furthermore, cell-cell aggregation was enhanced in GnT-III transfectants, indicating that the glycosylated E-cadherin is biologically functional. These results suggest that the glycosylated E-cadherin contributes to the suppression of metastasis by the introduction of GnT-III gene into melanoma cells.
Multivariate Optical Computation for Predictive Spectroscopy (1998)

A novel optical approach to predicting chemical and physical properties based on principal component analysis (PCA) is proposed and evaluated using a data set from earlier work. In our approach, a regression vector produced by PCA is designed into the structure of a set of paired optical filters. Light passing through the paired filters produces an analog detector signal that is directly proportional to the chemical/physical property for which the regression vector was designed. This simple optical computational method for predictive spectroscopy is evaluated in several ways, using the example data for numeric simulation. First, we evaluate the sensitivity of the method to various types of spectroscopic errors commonly encountered and find the method to have the same susceptibilities toward error as standard methods. Second, we use propagation of errors to determine the effects of detector noise on the predictive power of the method, finding the optical computation approach to have a large multiplex advantage over conventional methods. Third, we use two different design approaches to the construction of the paired filter set for the example measurement to evaluate manufacturability, finding that adequate methods exist to design appropriate optical devices. Fourth, we numerically simulate the predictive errors introduced by design errors in the paired filters, finding that predictive errors are not increased over conventional methods. Fifth, we consider how the performance of the method is affected by light intensities that are not linearly related to chemical composition (as in transmission spectroscopy) and find that the method is only marginally affected. In summary, we conclude that many types of predictive measurements based on use of regression (or other) vectors and linear mathematics can be performed more rapidly, more effectly, and at considerably lower cost by the proposed optical computation method than by traditional dispersive or interferometric instrumentation. Although our simulations have used Raman experimental data, the method is equally applicable to Near-IR, UV-vis, IR, fluorescence, and other spectroscopies.
Review article: Obesity as a risk factor for development and poor prognosis of breast cancer (2006)

The evidence that obesity adversely affects women's health is overwhelming and indisputable. The risk of postmenopausal breast cancer increases with obesity; measured as weight gain, body mass index, waist-hip ratio or percent body fat. It is also established that obesity is associated with poor prognosis of breast cancer. This review examines in detail the possible mechanisms by which obesity causes poor prognosis of breast cancer such as estrogenic activity, advanced or more aggressive disease at diagnosis and high likelihood of both local and systemic treatment failure. After careful consideration of the available evidence, the author concludes that obesity contributes towards development and poor prognosis of breast cancer; therefore, weight management should be an integral part of any strategy to prevent and improve the outcome of breast cancer.
Lonidamine in malignant brain tumors. (1991)

Among new therapeutic modalities for both primary and secondary brain tumors, selective manipulation of metabolic pathways seems attractive. In human malignant gliomas and cell lines from a glioblastoma multiform, lonidamine has been shown to interfere with aerobic glycolysis with a decrease of lactate production by the inhibition of a mitochondrially-bound hexokinase; this selective reduction of the energetic capabilities of glioma cells would be a limiting factor for processes requiring energy, such as cell growth and recovery from potentially lethal damage after radiotherapy or chemotherapy. The activity of lonidamine in malignant gliomas after surgery in association with conventional radiotherapy is being investigated, while previous studies have suggested a limited, but clear therapeutic activity of the drug in recurrent malignant gliomas. In brain metastases lonidamine has not been effective as a radiation enhancer, but has been shown to potentiate systemic chemotherapy. Most common side effects were myalgias, testicular pain and ototoxicity with no serious organ toxicity or myelosuppression.