gebhart/patrepeval huggingface dataset:
Pore-forming peptide of pathogenic Entamoeba histolytica. (1991)

A polypeptide that causes pore formation in target-cell membranes is implicated in the potent cytolytic activity of pathogenic Entamoeba histolytica. Pore-forming material was purified to apparent homogeneity by a multistep procedure, and its analysis by NaDodSO4/PAGE revealed one peptide of 4-5 kDa under nonreducing or under reducing conditions. Pore-forming activity was measured by depolarization of liposome membrane potential and was found to be optimally expressed at low pH. Active material preferentially inserted into negatively charged lipid vesicles. Treatment of purified amoeba peptide in solution or bound to liposomes with glutaraldehyde revealed oligomers upon NaDodSO4/PAGE, suggesting functionally relevant peptide-peptide interactions. The NH2-terminal amino acid sequence of the amoeba peptide was determined by protein sequencing and revealed a structural similarity to melittin, the membranolytic peptide of bee venom.
Oral absorption of the somatostatin analogue SMS 201–995: Theoretical and practical implications (1987)

Oral administration of SMS 201-995 (SMS), a subcutaneously injectable somatostatin analogue, was investigated in five healthy volunteers, who drank 2 mg of SMS with 75 g of glucose. Mean maximal plasma SMS concentrations after the 2 mg oral dose were comparable with those after subcutaneous injection of 50 micrograms, although the peak was delayed (90 vs 15 min). Biological activity of absorbed SMS was shown by significant and lasting suppression of plasma insulin concentrations, resulting in significant hyperglycaemia at 90 and 120 min compared with the control study. The feasibility of oral administration of SMS may extend its use in the treatment of acromegaly and gut endocrine tumours. Other peptide hormone analogues, structurally 'protected' against enzymatic degradation, may also be active orally and thus be useful therapeutically.
Leishmania RNA Virus 1-Mediated Cap-Independent Translation (1995)

Recently, a group of related Leishmania RNA viruses (Leishmania RNA virus 1 [LRV1]) has been isolated from Leishmania guyanensis and L. brasiliensis. These viruses persist in the cytoplasm and contain double-stranded RNA genomes. Miniexon sequences are absent from the 5' end of the viral RNA, and the 5' end of the viral RNA lacks a cap structure, suggesting that LRV1 has evolved a cap-independent mechanism of translation. Cap-independent translation of picornavirus genomic RNA requires a cis element, within the 5' untranslated region (UTR), referred to as an internal ribosome entry site (IRES). In order to find out if the 5' UTR of LRV1 possessed IRES activity, we modified a Leishmania expression vector, pX63NEO-GUS, so that it would produce a dicistronic transcript in which the neomycin phosphotransferase gene was separated from the downstream beta-glucuronidase (GUS) gene by the LRV1 5' UTR. High levels of GUS activity were detected in L. major stably transformed with this plasmid. Elimination of the first 120 nucleotides of the viral 5' UTR lowered GUS activity 10-fold. Furthermore, when the entire 5' UTR was eliminated, GUS activity was undetectable. These results, together with the absence of trans-spliced GUS transcripts, are consistent with the hypothesis that the 5' UTR of LRV1 functions as an IRES element. The ability to couple expression of genes via an IRES element should prove useful in genetic experiments with Leishmania spp.
NONCODE: an integrated knowledge database of non-coding RNAs (2004)

NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g. function, cellular role, cellular location, chromosomal information, etc.) in NONCODE have been confirmed manually by consulting relevant literature: more than 80% of the entries are based on experimental data. (iii) Based on the cellular process and function, which a given ncRNA is involved in, we introduced a novel classification system, labeled process function class, to integrate existing classification systems. (iv) In addition, some 1100 ncRNAs have been grouped into nine other classes according to whether they are specific to gender or tissue or associated with tumors and diseases, etc. (v) NONCODE provides a user-friendly interface, a visualization platform and a convenient search option, allowing efficient recovery of sequence, regulatory elements in the flanking sequences, secondary structure, related publications and other information. The first release of NONCODE (v1.0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn.
Expression, purification, crystallization and crystallographic characterization of the human MHC class I related protein MICA (1998)

Crystals of the human MHC-encoded molecule MICA, a homologue of MHC class I proteins, have been grown in hanging-drop vapor-diffusion trials using ammonium sulfate as a precipitating agent with recombinant protein expressed in a baculovirus-based system. Cryo-preserved crystals of MICA belong to the cubic space group F4132 with lattice constants a = b = c = 260.7 A and diffract to a resolution limit of 3.0 A when cryo-preserved. These crystals do not diffract when handled conventionally.
Improved method for recovering graded-index profile of isotropic waveguide by cubic spline function (2010)

An improved method for recovering the refractive index profile of an isotropic graded-index waveguide is presented on the basis of the cubic spline interpolation method. The surface refractive index of the waveguide can be obtained by using a polynomial function that is related with the parameters of all modes. The simulation results of several typical index distributions show that this method can be employed to recover a graded-index profile well.
Oestrogen but not testosterone increases bone density in orchiectomized rats more when fed moderately magnesium-deficient fructose than moderately magnesium-deficient cornstarch. (1994)

To investigate interactions between circulating sex hormones, dietary fructose and magnesium on bone mineral density and numbers of trabeculae, 10 weeks old orchiectomized and sham-orchiectomized rats were studied. One-third of the orchiectomized animals were injected with beta-oestradiol-3-benzoate twice per week in sesame oil; another one-third, testosterone cypionate; the remaining one-third as well as the sham-orchiectomized animals, sesame oil only. All animals were fed either fructose or cornstarch without added magnesium. After 14 weeks, a 24 h urine sample was collected for measurements of calcium, magnesium, phosphorus, and cAMP. Blood was collected for determinations of calcium, magnesium, phosphorus, 25-monohydroxy and 1,25-dihydroxycholecalciferols, oestrogen, testosterone, and parathyroid hormone. Femurs were used for measurements of bone mineral density, and tibiae, for numbers of trabeculae. Exogenous testosterone interacted with starch and magnesium deficiency to decrease serum calcium concentration significantly, which increased circulating parathyroid hormone. High circulating parathyroid hormone raised urinary cAMP and serum 1,25-dihydroxycholecalciferol. Increased parathyroid hormone, cAMP and 1,25-dihydroxycholecalciferol may be responsible for bone resorption which was noted in reductions of bone mineral density and the numbers of trabeculae in the group. In contrast, exogenous oestrogen interacted with fructose and magnesium deficiency to increase serum calcium concentration which caused a reduction of circulating parathyroid. Low parathyroid hormone, reduced 1,25-dihydroxycholecalciferol and cAMP may explain the increased bone mineral density and the numbers of trabeculae in this group.
Time Domain Identification of Moving Loads on Bridge Deck (2003)

A new time domain method is presented to identify moving loads on a bridge deck based on the measured responses. The bridge deck is modeled as an orthotropic plate and the loads are modeled as a group of four loads moving on top of the bridge deck at fixed distance apart. Dynamic behavior of the bridge deck is analyzed by the orthotropic plate theory and mode superposition technique. Like all inverse problems, this identification is an ill-conditioned problem, and a regularization technique is employed to stabilize the computations. The identified loads moving at different eccentricities are presented. Laboratory work on the force identification is also presented. The effect of incomplete measured modes in the responses is discussed, and an underestimation in the loads may result if the number of vibration mode for identification is larger than that in the responses. Computational simulations and laboratory tests show that the method is effective and practical for identification of individual wheel loads on bridge decks.
Decreased heart rate variability in survivors of sudden cardiac death not associated with coronary artery disease. (1994)

These findings suggest that there is abnormal autonomic influence on the heart in patients without coronary artery disease at risk of sudden cardiac death. Hourly analysis of heart rate variability throughout the 24 hour period may provide additional information important in the identification of high risk patients.
A Ladar-Based Pose Estimation Algorithm for Determining Relative Motion of a Spacecraft for Autonomous Rendezvous and Dock (2021)

Future autonomous space missions will require autonomous rendezvous and docking operations. The servicing spacecraft must be able to determine the relative 6 degree-of-freedom (6 DOF) motion between the vehicle and the target spacecraft. One method to determine the relative 6 DOF position and attitude is with 3D ladar imaging. Ladar sensor systems can capture close-proximity range images of the target spacecraft, producing 3D point cloud data sets. These sequentially collected point-cloud data sets were then registered with one another using a point correspondence-less variant of the Iterative Closest Points (ICP) algorithm to determine the relative 6 DOF displacements. Simulation experiments were performed and indicated that the mean-squared error (MSE), angular error, mean, and standard deviations for position and orientation estimates did not vary as a function of position and attitude and meet most minimum angular and translational error requirements for rendezvous and dock. Furthermore, the computational times required by this algorithm were comparable to previously reported variants of the point-to-point and point-to-plane-based ICP variants for single iterations when the initialization was already performed.
Immunology of atopic eczema: overcoming the Th1/Th2 paradigm (2013)

Atopic eczema (AE) is a challenge for modern medicine, because it is prevalent, severely affects quality of life of patients and their families, and causes high socioeconomic costs. The pathogenesis of AE is complex. While initial studies suggested a Th2 deviation as primary reason for the disease, numerous studies addressed a genetically predetermined impaired epidermal barrier as leading cause in a subgroup of patients. Recently, immune changes beyond the initial Th2 concept were defined in AE, with a role for specialized dendritic cells as well as newly identified T helper cell subsets such as Th17 and Th22 cells. Furthermore, trigger factors are expanded beyond classical Th2 allergens such as pollen or house dust mites to microbial products as well as self-antigens. This review pieces together our current understanding of immune as well as barrier abnormalities into the pathogenesis mosaic of AE.
Nanoscale Metal–Organic Frameworks for the Co-Delivery of Cisplatin and Pooled siRNAs to Enhance Therapeutic Efficacy in Drug-Resistant Ovarian Cancer Cells (2014)

Ovarian cancer is the leading cause of death among women with gynecological malignancies. Acquired resistance to chemotherapy is a major limitation for ovarian cancer treatment. We report here the first use of nanoscale metal-organic frameworks (NMOFs) for the co-delivery of cisplatin and pooled small interfering RNAs (siRNAs) to enhance therapeutic efficacy by silencing multiple drug resistance (MDR) genes and resensitizing resistant ovarian cancer cells to cisplatin treatment. UiO NMOFs with hexagonal-plate morphologies were loaded with a cisplatin prodrug and MDR gene-silencing siRNAs (Bcl-2, P-glycoprotein [P-gp], and survivin) via encapsulation and surface coordination, respectively. NMOFs protect siRNAs from nuclease degradation, enhance siRNA cellular uptake, and promote siRNA escape from endosomes to silence MDR genes in cisplatin-resistant ovarian cancer cells. Co-delivery of cisplatin and siRNAs with NMOFs led to an order of magnitude enhancement in chemotherapeutic efficacy in vitro, as indicated by cell viability assay, DNA laddering, and Annexin V staining. This work shows that NMOFs hold great promise in the co-delivery of multiple therapeutics for effective treatment of drug-resistant cancers.
Regulation of mouse sterol regulatory element-binding protein-1c gene (SREBP-1c) by oxysterol receptors, LXRα and LXRβ (2000)

The liver X receptors (LXRs) are members of the nuclear hormone receptor superfamily that are bound and activated by oxysterols. These receptors serve as sterol sensors to regulate the transcription of gene products that control intracellular cholesterol homeostasis through catabolism and transport. In this report, we describe a novel LXR target, the sterol regulatory element-binding protein-1c gene (SREBP-1c), which encodes a membrane-bound transcription factor of the basic helix-loop-helix-leucine zipper family. SREBP-1c expression was markedly increased in mouse tissues in an LXR-dependent manner by dietary cholesterol and synthetic agonists for both LXR and its heterodimer partner, the retinoid X receptor (RXR). Expression of the related gene products, SREBP-1a and SREBP-2, were not increased. Analysis of the mouse SREBP-1c gene promoter revealed an RXR/LXR DNA-binding site that is essential for this regulation. The transcriptional increase in SREBP-1c mRNA by RXR/LXR was accompanied by a similar increase in the level of the nuclear, active form of the SREBP-1c protein and an increase in fatty acid synthesis. Because this active form of SREBP-1c controls the transcription of genes involved in fatty acid biosynthesis, our results reveal a unique regulatory interplay between cholesterol and fatty acid metabolism.
Suppression of Hyphal Formation in Candida albicans by Mutation of a STE12 Homolog (1994)

A Candida albicans gene (CPH1) was cloned that encodes a protein homologous to Saccharomyces cerevisiae Ste12p, a transcription factor that is the target of the pheromone response mitogen-activated protein kinase cascade. CPH1 complements both the mating defect of ste12 haploids and the filamentous growth defect of ste12/ste12 diploids. Candida albicans strains without a functional CPH1 gene (cph1/cph1) show suppressed hyphal formation on solid medium. However, cph1/cph1 strains can still form hyphae in liquid culture and in response to serum. Thus, filamentous growth may be activated in C. albicans by the same signaling kinase cascade that activates Ste12p in S. cerevisiae; however, alternative pathways may exist in C. albicans.
The Advanced Glycation End Product, N∊-(Carboxymethyl)lysine, Is a Product of both Lipid Peroxidation and Glycoxidation Reactions (1996)

Nepsilon-(Carboxymethyl)lysine (CML) is an advanced glycation end product formed on protein by combined nonenzymatic glycation and oxidation (glycoxidation) reactions. We now report that CML is also formed during metal-catalyzed oxidation of polyunsaturated fatty acids in the presence of protein. During copper-catalyzed oxidation in vitro, the CML content of low density lipoprotein increased in concert with conjugated dienes but was independent of the presence of the Amadori compound, fructoselysine, on the protein. CML was also formed in a time-dependent manner in RNase incubated under aerobic conditions in phosphate buffer containing arachidonate or linoleate; only trace amounts of CML were formed from oleate. After 6 days of incubation the yield of CML in RNase from arachidonate was approximately 0.7 mmol/mol lysine compared with only 0.03 mmol/mol lysine for protein incubated under the same conditions with glucose. Glyoxal, a known precursor of CML, was also formed during incubation of RNase with arachidonate. These results suggest that lipid peroxidation, as well as glycoxidation, may be an important source of CML in tissue proteins in vivo and that CML may be a general marker of oxidative stress and long term damage to protein in aging, atherosclerosis, and diabetes.
Phase II Trial of OGX-011 in Combination with Docetaxel in Metastatic Breast Cancer (2009)

The combination of OGX-011 and docetaxel at 75 mg/m(2) is well tolerated and clinical activity was seen in these patients with metastatic breast cancer, but there was an insufficient number of responses to meet the criteria for proceeding to the second stage of accrual.
Three Abietane Diterpenes and Two Diterpenes Incorporated Sesquiterpenes from the Bark of Cryptomeria japonica (2006)

Three new abietane diterpenes, sugikurojins D (1), E (2), and F (3), and two new abietanes which incorporate cadinane, sugikurojins G (4) and H (5) were isolated from the bark of Cryptomeria japonica. These structures were elucidated primarily by extensive NMR experiments. The structure of sugikurojin D (1) was deduced to be 6alpha-acetoxy-7beta,11-dihydroxy-12-methoxy-8,11,13-abietatriene. Sugikurojin E (2) was deduced to be 6alpha-acetoxy-7beta,12-dihydroxy-8,11,13-abietatriene. Sugikurojin F (3) was 7alpha-methoxy-8,13-abietadien-11,12-dione. Sugikurojins G (4) and H (5) had a unique skeleton incorporating an alpha-cadinol or a 1alpha-hydroxy-T-cadinol in ferruginol, respectively. Also obtained in this investigation were the known diterpenes (6-14). An antibacterial activity of ten among these against Staphylococcus aureus and Escherichia coli was inactive at the (MIC: 125 microg/ml) level. Meanwhile, in the cytotoxic activity against HL-60, compounds 4, 8, and 11 showed moderate (IC50: 4, 35.4; 8, 28.0; 11, 52.4 microM) though weak (IC50: 4, 100; 8, 80.8; 11, 100 microM) activity against HCT-15.
The effects of egta and trypsin on the serum requirements for cell attachment to collagen (1979)

Cells growing on plastic or glass surfaces in vitro may be brought into suspension by proteases (e.g. trypsin) or chelating agents (e.g. EGTA). Trypsin and EGTA remove different quantities and types of molecules from cell surfaces. Previous studies have revealed that when confluent cultures of either BHK or PyBHK cells are brought into suspension by exposure to trypsin, foetal calf serum (or fibronectin) is required for cell attachment to films of denature type I collagen, but not to 3-dimensional gels of native collagen fibres. In this communication the serum requirements for the attachment of BHK and PyBHK cells to collagen substrata have been examined as a function of (a) the method used to prepare the cell suspension (EGTA or trypsin), and (b) cell density. Data are presented consistent with the view that cell surface-associated fibronectin is able to mediate cell attachment directly to films of denatured collagen.
Abstract B173: Galeterone shows anti-tumor activity in multiple pre-clinical models that express androgen receptor splice variants, supporting correlative patient data seen in ARMOR2 (2015)

Abstract Multiple experimental approaches were used to examine whether and by what mechanism galeterone affects prostate cancer growth in cells and tumors expressing androgen receptor (AR) splice variants, such as AR-V7. Galeterone is a selective, multitargeted, small molecule that disrupts androgen signaling at multiple points in the pathway. ARMOR3-SV is a Phase 3, randomized, open-label, multicenter, controlled clinical trial in metastatic castration resistant prostate cancer (mCRPC) patients whose tumors express AR splice variant-7 mRNA (AR-V7). AR-V7 is a truncated, constitutively active splice variant of the AR that lacks the ligand binding domain (LBD) and has been implicated in prostate cancer progression. The expression of AR-V7 occurs in approximately 14-26% of men with mCRPC prior to second-generation anti-androgens or chemotherapy, and AR-V7 expression has been clinically associated with resistance to enzalutamide (Xtandi) or abiraterone (Zytiga). Here we provide the pre-clinical and clinical rationale for the development of galeterone in mCRPC patients with AR-V7. Our findings show that using multiple pre-clinical approaches, galeterone reduces in vitro prostate cancer cell proliferation, androgen receptor signaling and xenograft tumor growth using cells and tumors that express AR splice variants. Reductions in AR splice variant protein were also observed in cells that also co-express wild-type AR, and prostate cancer cells that lack wild type AR, but transiently express AR splice variant protein. Clinical data further support activity of galeterone in patients with truncated androgen receptors. Galeterone's unique mechanism of AR protein downregulation occurs in both splice variant and wild-type AR, supporting that galeterone-induced AR downregulation is independent of the AR LBD. Because preclinical and clinical data support an opportunity for treatment in this setting, Tokai Pharmaceuticals designed ARMOR3-SV to test galeterone vs. enzalutamide in men with metastatic castration-resistant prostate cancer whose tumors express the AR-V7 splice variant. Citation Format: Douglas B. Jacoby, Amina Zoubeidi, Eva B. Corey, Elahe Mostaghel, Andrew K. Kwegyir-Afful, Senthilmurugan Ramalingam, Vincent Njar. Galeterone shows anti-tumor activity in multiple pre-clinical models that express androgen receptor splice variants, supporting correlative patient data seen in ARMOR2. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B173.
ChemInform Abstract: NEW POSSIBILITIES FOR THE SYNTHESIS OF POLYFUNCTIONAL CYCLOPROPANES UNDER INTERPHASE CATALYSIS CONDITIONS IN A LIQUID‐SOLID PHASE SYSTEM (1981)

Abstract Acrolein (I) bildet unter den im Formelschema angegebenen Reaktionsbedingungen mit Brommalonsäureester (II) 1,1‐Dicarbethoxy‐2‐formyl‐cyclopropan (III).
The Multicell Multiuser MIMO Uplink with Very Large Antenna Arrays and a Finite-Dimensional Channel (2013)

We consider multicell multiuser MIMO systems with a very large number of antennas at the base station (BS). We assume that the channel is estimated by using uplink training. We further consider a physical channel model where the angular domain is separated into a finite number of distinct directions. We analyze the so-called pilot contamination effect discovered in previous work, and show that this effect persists under the finite-dimensional channel model that we consider. In particular, we consider a uniform array at the BS. For this scenario, we show that when the number of BS antennas goes to infinity, the system performance under a finite-dimensional channel model with P angular bins is the same as the performance under an uncorrelated channel model with P antennas. We further derive a lower bound on the achievable rate of uplink data transmission with a linear detector at the BS. We then specialize this lower bound to the cases of maximum-ratio combining (MRC) and zero-forcing (ZF) receivers, for a finite and an infinite number of BS antennas. Numerical results corroborate our analysis and show a comparison between the performances of MRC and ZF in terms of sum-rate.