gebhart/patrepeval huggingface dataset:
Populating the equilibrium molten globule state of apomyoglobin under conditions suitable for structural characterization by NMR (1997)

Conditions have been determined under which the equilibrium molten globule state of apomyoglobin is stable and remains monomeric for periods of time sufficient for the application of three-dimensional heteronuclear NMR experiments. The quality of initial two-dimensional NMR spectra suggests that sequence-specific assignments can be made for a majority of the protein resonances under these conditions. A pH titration of the protein followed using two-dimensional 1H-15N correlation experiments indicates that the equilibrium intermediate undergoes fast exchange on the chemical shift time scale with the unfolded state and intermediate time scale exchange with the native state, and suggests a strategy to assist with backbone resonance assignments. The conditions and techniques described may be applicable to the characterization of other equilibrium folding intermediates.
Demenza vascolare sottocorticale: inquadramento clinico e diagnostico-terapeutico (2011)

L’invecchiamento della popolazione richiama l’attenzione sulle malattie croniche che accompagnano la senescenza. Tra queste, la demenza costituisce una priorità per la sua crescente prevalenza, per il grado di disabilità che comporta, per la mancanza ad oggi di cure risolutive, per il carico assistenziale che&#13;\nrichiede ai caregiver e, dati anche gli aspetti economici, alla società nel suo complesso. La demenza vascolare (VaD), seconda solo alla Malattia di Alzheimer (AD) per frequenza, è in realtà un insieme di quadri nosologici molto diversi che hanno in comune la genesi vascolare. Tra questi, la VaD sottocorticale è particolarmente frequente in età avanzata, ha un esordio subdolo, un andamento ingravescente, sintomi neuropsicologici, motori e psicoaffettivi caratteristici ed è spesso sottodiagnosticata. Ad oggi&#13;\nsi ritiene che le forme vascolari “pure” rappresentino una quota limitata dei casi di demenza e che nella maggioranza dei casi la genesi del disturbo cognitivo dell’anziano sia di tipo “misto” neurodegenerativo e vascolare. In quest’ottica, ed in considerazione della mancanza di cure efficaci, la prevenzione dei&#13;\nfattori di rischio vascolari, prima fra tutti l’ipertensione arteriosa, acquistano un ruolo fondamentale, sia in termini di prevenzione primaria, sia di rallentamento del processo patologico già in atto. In questa rassegna saranno presi in considerazione i principali aspetti epidemiologici, diagnostici e classificativi, clinici e terapeutici della VaD, in particolare della forma sottocorticale.
An Artificial Intelligence Environment for Information Retrieval Research (1988)

The CODER (COmposite Document Expert/Extended/Effective Retrieval) project is a multi-year effort to investigate how best to apply artificial intelligence methods to increase the effectiveness of information retrieval systems. Particular attention is being given to analysis and representation of heterogeneous documents, such as electronic mail digests or messages, which vary widely in style, length, topic,and structure. In order to ensure system adaptability and to allow reconfiguration for controlled experimentation, the project has been designed as a moderated expert system. This thesis covers the design problems involved in providing a unified architecture and knowledge representation scheme for such a system, and the solutions chosen for CODER. An overall object-oriented environment is constructed using a set of message-passing primitives based on a modified Prolog call paradigm. Within this environment is embedded the skeleton of a flexible expert system, where task decomposition is performed in a knowledge-oriented fashion and where subtask managers are implemented as members of a community of experts. A three-level knowledge representation formalism of elementary data types, frames, and relations is provided, and can be used to construct knowledge structures such as terms, meaning structures, and document interpretations. The use of individually tailored specialist experts coupled with standardized blackboard modules for communication and control and external knowledge bases for maintenance of factual world knowledge allows for quick prototyping, incremental development and flexibility under change. The system as a whole is structured as a set of communicating modules, defined functionally and implemented under UNIX^TM using sockets and the TCP/IP protocol for communication. Inferential modules are being coded in MU-Prolog; non-inferential modules are being prototyped in MU-Prolog and will be re-implemented as needed in C++.
Target Specific Intracellular Delivery of siRNA/PEI−HA Complex by Receptor Mediated Endocytosis (2009)

Hyaluronic acid (HA) plays important biological roles in tissue integrity, angiogenesis, wound healing, and cell motility through the interaction with receptors on cell membranes. In this work, we investigated the effect of HA modification on the receptor-mediated endocytosis labeling HA derivatives with quantum dots (QDots). HA-QDot conjugates with a degree of modification less than ca. 25 mol % appeared to be more efficiently taken up to B16F1 cells by HA receptor mediated endocytosis than QDots alone. On the basis of bioimaging study, polyethyleneimine, PEI-HA conjugate with 24.2 mol % PEI content was developed as a target specific intracellular delivery carrier of siRNA. The siRNA/PEI-HA complex exhibited higher gene silencing efficiency in B16F1 cells with HA receptors than siRNA/PEI complex. Anti-PGL3-Luc siRNA/PEI-HA complex appeared to silence PGL3-Luc gene in the range of 50%-85% depending on the serum concentration up to 50 vol %. According to in vivo biodistribution test, siRNA/PEI-HA complex accumulated mainly in the tissues with HA receptors such as liver, kidney, and tumor. Furthermore, intratumoral injection of anti-VEGF siRNA/PEI-HA complex resulted in an effective inhibition of tumor growth by the HA receptor mediated endocytosis to tumor cells in C57BL/6 mice. Considering all these results, anti-VEGF siRNA/PEI-HA complex was thought to be applied successfully as target specific antiangiogenic therapeutics for the treatment of diseases in the tissues with HA receptors, such as liver cancer and kidney cancer.
NetAffx: Affymetrix probesets and annotations (2003)

NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix. For each probeset, NetAffx lists the probe sequences, and the consensus sequence interrogated by the probes; for the larger chip sets, interactive maps display this sequence data in genomic context. Sequence annotations include Gene Ontology (GO) terms and depiction of GO graph relationships; predicted protein domains and motifs; orthologous sequences; links to relevant pathways; and links to public databases including UniGene, LocusLink, SWISS-PROT and OMIM.
Simultaneous reconstruction and motion estimation for gated cardiac ECT (2002)

The primary goal of this work has been to develop a processing method for gated cardiac emission computed tomography (ECT) that simultaneously reconstructs the pixel intensities of the gated images and estimates the motion of the cardiac wall. The simultaneous reconstruction and motion estimation is achieved using conjugate gradient optimization with an objective function that is dependent on the gated reconstructed images at two time frames and the estimated motion of the object between the two frames. The method was evaluated on simulated phantom data both with and without Poisson noise. With noise-free data, the accuracy of the motion estimate and the quality of the reconstructed images were found to be dependent on the hyperparameter selection. With noisy data, the simultaneous method produced reconstructed images with smaller squared error compared with images reconstructed without motion estimation. In a patient gated myocardial perfusion study, the estimated motion between two frames agreed with subjective assessment of wall motion.
Can Nutrients Prevent or Delay Onset of Alzheimer's Disease? (2010)

Age-related changes in nutritional status can play an important role in brain functioning. Specific nutrient deficiencies in the elderly, including omega-3 fatty acids, B-vitamins, and antioxidants among others, may exacerbate pathological processes in the brain. Consequently, the potential of nutritional intervention to prevent or delay cognitive impairment and the development of Alzheimer's disease (AD) is a topic of growing scientific interest. This review summarizes epidemiological studies linking specific nutritional deficiencies to mild cognitive impairment (MCI), as well as completed and ongoing nutritional studies in prevention of MCI and AD. Processes that underlie AD pathogenesis include: membrane/synaptic degeneration, abnormal protein processing (amyloid-beta, tau), vascular risk factors (hypertension, hypercholesterolemia), inflammation, and oxidative stress. Consideration of mechanistic evidence to date suggests that several nutritional components can effectively counteract these processes, e.g., by promoting membrane formation and synaptogenesis, enhancing memory/behavior, improving endothelial function, and cerebrovascular health. The literature reinforces the need for early intervention in AD and suggests that multi-nutritional intervention, targeting multiple aspects of the neurodegenerative process during the earliest possible phase in the development of the disease, is likely to have the greatest therapeutic potential.
A highly conserved tyrosine residue in G protein-coupled receptors is required for agonist-mediated beta 2-adrenergic receptor sequestration. (1994)

An aromatic residue, tyrosine 326 in the prototypical human beta 2-adrenergic receptor, exists in a highly conserved sequence motif in virtually all members of the G protein-coupled receptor family. The potential role of this conserved aromatic amino acid residue in the cellular processes of sequestration (a rapid internalization of the surface receptor) and down-regulation (a slower loss of total cellular receptors) associated with agonist-mediated desensitization of the beta 2-adrenergic receptor was assessed by replacing tyrosine residue 326 with an alanine residue (beta 2AR-Y326A). This mutation completely abolishes agonist-mediated receptor sequestration without affecting the ability of the receptor to activate maximally adenylyl cyclase, to undergo rapid desensitization, and to down-regulate in response to agonist. The only other major change associated with the mutated receptor is a complete loss of the ability to resensitize following rapid desensitization. These results imply that this tyrosine residue, which is part of a highly conserved sequence motif in G protein-coupled receptors, may be responsible for their agonist-mediated sequestration and that sequestration and down-regulation of the receptor are dissociable phenomena. The lack of resensitization in the sequestration-defective beta 2-adrenergic receptor mutant strongly suggests that the sequestration pathway is an important mechanism by which cells re-establish the normal responsiveness of G protein-coupled receptors following the removal of agonist.
The Yeast Phaffia rhodozyma as a Dietary Pigment Source for Salmonids and Crustaceans (1977)

The red yeast Phaffia rhodozyma contains astaxanthin as its principal carotenoid pigment. Incorporation of this yeast into the diet (15% wt/wt) of rainbow trout induced pigmentation within 43 days. However, lobsters fed the same diet did not readily accumulate the carotenoids of the yeast, though they became pigmented on a diet of live brine shrimp. The primary pigment isolated from the bodies of trout and lobsters fed the red yeast was astaxanthin. We conclude that P. rhodozyma is an excellent source of astaxanthin for cultivated salmonids. Key words: astaxanthin, carotenoid, diet, lobster, Phaffia rhodozyma, salmonids, yeast
Traumatic thoracic aortic aneurysm: treatment with endovascular stent-grafts. (1997)

Transluminal placement of endovascular stent-grafts is a technically feasible method for treatment of traumatic thoracic aortic aneurysm and may be an effective alternative to open-chest surgery.
Three-dimensional multi-layered optical card storage (1996)

Optical card storage is one of the most compact form of data storage, which stores information on plastic card of credit-card size. This method of optical storage has been intensively explored for commercial applications. However, the capacity of this storage is strictly limited. The capacity is given by the total size of memory area divided by the extent of laser-beam spot, and the minimum size of spot is as large as a half of light wavelength due to the light-wave diffraction. To overcome this limitation, we record pits into multiple layers in a volume medium in three-dimensions rather than only in the surface of the medium[1-2]. In this paper, we describe the multi-layered optical card system, which we developed.
Investigation of Organoleptic Characteristics in the Development of Soft Chews of Calcium Carbonate as Mineral Supplement (2009)

The present study was aimed at developing a soft chewable dosage form for calcium carbonate for nutraceutical application. Two different types of the formulations viz., sugar based and sugar free soft chews were prepared. The effect of various ingredients on the different organoleptic characteristics (grittiness, sweetness, hardness and mouthfeel) and the emulsion stability of the dosage form were checked and evaluated on the basis of an in-house numerical scale on healthy human volunteers. The study revealed that the type of emulsifying agent, heating temperature, particle size of the drug, ratio and quantity of sugars were found to have significant impact on the organoleptic characteristics of the dosage form. The study also indicates that the proper selection of packaging material is important in order to maintain the long term integrity of the formulation.
FRR: A proportional and worst-case fair round robin scheduler (2005)

In this paper, we propose an O(1) complexity round robin scheduler, called fair round robin (FRR), that provides good fairness and delay properties. Unlike existing O(1) complexity round robin schedulers that can only achieve long term fairness, FRR not only provides proportional fairness, but also maintains a constant normalized worst-case fair index as defined in Bennett and Zhang's work. This means that FRR guarantees both short term and long term fairness among all backlogged flows.
Function of the cytoplasmic domain of a retroviral transmembrane protein: p15E-p2E cleavage activates the membrane fusion capability of the murine leukemia virus Env protein (1994)

In the murine leukemia viruses (MuLVs), the Env complex is initially cleaved by a cellular protease into gp70SU and pre15ETM. After the virus particle is released from the cell, the C-terminal 16 residues are removed from the cytoplasmic domain of pre15E by the viral protease, yielding the mature p15ETM and p2E. We have investigated the function of this cleavage by generating a Moloney MuLV mutant, termed p2E-, in which the Env coding region terminates at the cleavage site. This mutant synthesizes only the truncated, mature form of TM rather than its extended precursor. When cells expressing this truncated Env protein are cocultivated with NIH 3T3 cells, they induce rapid cell-cell fusion. Thus, the truncated form, which is normally found in virions but not in virus-producing cells, is capable of causing membrane fusion. We conclude that the 16-residue p2E tail inhibits this activity of Env until the virus has left the cell. p2E- virions were found to be infectious, though with a lower specific infectivity than that of the wild type, showing that p2E does not play an essential role in the process of infection. Fusion was also observed with a chimeric p2E- virus in which gp70SU and nearly all of p15ETM are derived from amphotropic, rather than Moloney, MuLV. In a second mutant, an amino acid at the cleavage site was changed. The pre15E protein in this mutant is not cleaved. While the mutant Env complex is incorporated into virions, these particles have a very low specific infectivity. This result suggests that the cleavage event is essential for infectivity, in agreement with the idea that removal of p2E activates the membrane fusion capability of the Env complex.
Efficient Synthesis of Six-Membered Ring D Analogues of the Pentacyclic Alkaloid Cephalotaxine by Two Palladium-Catalyzed Reactions (2000)

D-homo-Cephalotaxine analogues 19 and 23 have been prepared by intramolecular Heck reactions of 12 and 22. The substrates 12 and 22 were obtained by alkylation and acylation, respectively, of the spirocyclic amines 17, which, in turn, were generated by intramolecular palladium-catalyzed allylic amination.
Plant Growth Substances Produced by Methylobacterium spp. and Their Effect on Tomato (Lycopersicon esculentum L.) and Red Pepper (Capsicum annuum L.) Growth (2006)

【Bacteria from the Methylobacterium genus, called pink-pigmented facultative methylotrophic bacteria (PPFMs), are common inhabitants of plants, potentially dominating the phyllosphere population, and are also encountered in the rhizosphere, seeds, and other parts of plants, being versatile in nature. The consistent success of the Methylobacterium plant association relies on methylotrophy, the ability to utilize the one-carbon compound methanol emitted by plants. However, the efficiency of Methylobacterium in plant growth promotion could be better exploited and thus has attracted increasing interest in recent years. Accordingly, the present study investigated the inoculation effects of Methylobacterium sp. strains CBMB20 and CBMB 110 on seed imbibition to tomato and red pepper on the growth and accumulation of phytohormone levels under gnotobiotic conditions. Seeds treated with the Methylobacterium strains showed a significant increase in root length when compared with either the uninoculated control or Methylobacterium extorquens $miaA^-$ knockout mutanttreated seeds. Extracts of the plant samples were used for indole-3-acetic acid (IAA), trans-zeatin riboside (t-ZR), and dihydrozeatin riboside (DHZR) assays by immunoanalysis. The treatment with Methylobacterium sp. CBMB20 or CBMB 110 produced significant increases in the accumulation of IAA and the cytokinins t-ZR and DHZR in the red pepper extracts, whereas no IAA was detected in the tomato extracts, although the cytokinin concentrations were significantly increased. Therefore, this study proved that the versatility of Methylobacterium as a plant-growth promoting bacteria could be better exploited.】
M.Ö. II. Binde Batı Anadolu’da Yakma Gömme Âdeti (2016)

Toplumların dini inanışları, sosyo-kültürel yapısı, ekonomisi ve siyasi tarihi ile ilgili önemli bilgilere arkeolojik ve filolojik verilerde rastlamak mümkündür. Anadolu‟da ve Anadolu dışındaki farklı kültürlerde toplumların dinsel inanışlarıyla ilgili önemli bilgilere her toplumun kendine özgü ölü gömme adetleri sayesinde ulaşılabilmektedir. Tarihin çeşitli dönemlerinde farklı kültür bölgelerinde yaşayan toplumların dini inanışlarını şekillendiren en önemli faktörler arasında “yaşam ve ölüm” gelmektedir. Toplumları birtakım manevi düşüncelere yönelten yaşam ve ölüm kavramları, tanrı inancı ve öbür dünya inanışları ile ilgili çeşitli düşüncelerin ortaya çıkmasına zemin hazırlamıştır. Tarihin en erken dönemlerinden itibaren ortaya çıkan yakma gömme adeti ile ilgili arkeolojik verilere, Anadolu‟da ve Anadolu dışındaki farklı kültürlerde rastlamak mümkündür. M.Ö. II. Binde Anadolu‟da yakma gömme âdetinin varlığına ilişkin bulgulara, çeşitli merkezlerde yapılan arkeolojik çalışmalar sayesinde ulaşılabilmektedir. Batı Anadolu‟da yakma gömme adeti ile ilgili önemli veriler sunan mezar ya da mezarlıklarda ele geçen buluntular, ölü gömme törenlerinin varlığına ilişkin önemli bilgiler sunması bakımından da büyük önem taşımaktadır
The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors (2012)

CD47, a "don't eat me" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.
Capture and enrichment of CD34‐positive haematopoietic stem and progenitor cells from blood circulation using P‐selectin in an implantable device (2008)

Clinical infusion of haematopoietic stem and progenitor cells (HSPCs) is vital for restoration of haematopoietic function in many cancer patients. Previously, we have demonstrated an ability to mimic physiological cell trafficking in order to capture CD34-positive (CD34+) HSPCs using monolayers of the cell adhesion protein P-selectin in flow chambers. The current study aimed to determine if HSPCs could be captured directly from circulating blood in vivo. Vascular shunt prototypes, coated internally with P-selectin, were inserted into the femoral artery of rats. Blood flow through the cell capture device resulted in a wall shear stress of 4-6 dynes/cm(2). After 1-h blood perfusion, immunofluorescence microscopy and flow cytometric analysis revealed successful capture of mononuclear cells positive for the HSPC surface marker CD34. Purity of captured CD34+ cells showed sevenfold enrichment over levels found in whole blood, with an average purity of 28%. Robust cell capture and HSPC enrichment were also demonstrated in devices that were implanted in a closed-loop arterio-venous shunt conformation for 2 h. Adherent cells were viable in culture and able to differentiate into burst-forming units. This study demonstrated an ability to mimic the physiological arrest of HSPCs from blood in an implantable device and may represent a practical alternative for adult stem cell capture and enrichment.
WILMS’ TUMOR GENE 1 (WT1) DENDRITIC CELL IMMUNOTHERAPY IN PATIENTS WITH UTERINE TUMORS: A PHASE I/II CLINICAL TRIAL (2013)

status: Published