gebhart/patrepeval huggingface dataset:
Site-Specific DNA–Doxorubicin Conjugates Display Enhanced Cytotoxicity to Breast Cancer Cells (2014)

Doxorubicin (Dox) is widely used for breast cancer treatment but causes serious side effects including cardiotoxicity that may adversely impact patient lifespan even if treatment is successful. Herein, we describe selective conjugation of Dox to a single site in a DNA hairpin resulting in a highly stable complex that enables Dox to be used more effectively. Selective conjugation of Dox to G15 in the hairpin loop was verified using site-specific labeling with [2-(15)N]-2'-deoxyguanosine in conjunction with [(1)H-(15)N] 2D NMR, while 1:1 stoichiometry for the conjugate was validated by ESI-QTOF mass spectrometry and UV spectroscopy. Molecular modeling indicated covalently bound Dox also intercalated into the stem of the hairpin and stability studies demonstrated the resulting Dox-conjugated hairpin (DCH) complex had a half-life >30 h, considerably longer than alternative covalent and noncovalent complexes. Secondary conjugation of DCH with folic acid (FA) resulted in increased internalization into breast cancer cells. The dual conjugate, DCH-FA, can be used for safer and more effective chemotherapy with Dox and this conjugation strategy can be expanded to include additional anticancer drugs.
Development of the Structural Basis for Antimicrobial and Hemolytic Activities of Peptides Based on Gramicidin S and Design of Novel Analogs Using NMR Spectroscopy (2000)

The structures of 14-residue head-to-tail cyclic gramicidin S peptides have been investigated to develop the structural rationale for their antimicrobial and hemolytic profiles. The basis for these studies is GS14 (cyclo(VKLKVdYPLKVKLdYP)), designed as an extension of the naturally occurring antimicrobial peptide. The structure of GS14 has been determined using NMR methods and was found to exist in a highly amphipathic antiparallel beta-sheet conformation. Systematic enantiomeric substitutions within the framework of the GS14 peptide were found to decrease the amphipathicity of this molecule. These results indicated that there was a direct correlation between the high amphipathic character and potent hemolytic activity in the diastereomers, whereas an inverse correlation existed between amphipathicity and antimicrobial function. To define the structural consequences of changing the amphipathic nature of GS14 analogs to maximize antimicrobial activity and to minimize hemolysis, NMR structures were determined in water and the membrane-mimetic solvent trifluoroethanol. The structures show that these attributes are the result of induction of the beta-sheet character in a membrane environment and the positioning of charged side chains on the hydrophobic face of the cyclic framework, thus decreasing the amphipathicity and directed hydrophobicity of these molecules. Implications for the design of more effective antimicrobials are discussed.
Cancer metastasis: negative regulation by an invasion-suppressor complex. (1995)

Invasion is the hallmark of tumor malignancy. We situate invasion within microecosystems comprising neoplastic cells as well as host cells. Modulation of invasion within such systems is ascribed to balances between promoter and suppressor pathways. The E-cadherin/alpha-, beta-, gamma-catenin complex has an invasion-suppressor function as evidenced by transfections either with sense cDNA encoding these molecules or with antisense cDNA inhibiting their expression. Loss of heterozygosity at the E-Cadherin (uvo) locus has been reported, but mutations in the E-cadherin gene seem to be rare. Downregulation of E-cadherin occurred at the level of transcription or of mRNA stability. Ex vivo cultures from invasive tumors or metastases produced cells that were homogeneously E-cadherin-positive and noninvasive in vitro. These observations have led to the idea that factors in the host downmodulate the E-cadherin complex and promote invasion most probably in a transient way.
Genetics and molecular immunology (1986)

Outline of Contents: Molecular approaches to immunology Immunoglobulin genetics Genetics of the major histocompatibility complex Resources.
Pilot study of combination therapy with ribavirin and interferon alfa for the retreatment of chronic hepatitis B e antibody-positive patients (2000)

Twenty-four patients with chronic hepatitis B virus (HBV), antibody to hepatitis B e antigen (anti-HBe), HBV DNA positivity, and alanine transaminase (ALT) elevation who failed previous interferon alfa (IFN-alpha) therapy were included in a pilot study of combination therapy with ribavirin and IFN-alpha. The patients received daily oral ribavirin (1,000-1,200 mg according to body weight) plus 5 million units (MU) IFN-alpha2b three times a week for 12 months and were followed-up for 12 months. The median viremia level decreased significantly at the end of treatment (1.2 x 10(3) copies/mL) and follow-up (4.0 x 10(2) copies/mL) compared with the baseline (3.0 x 10(6) copies/mL; P <.05). After 12 months, 8 of 24 (33%) patients had cleared HBV DNA and 12 (50%) had normal ALT levels. At the end of the study virological and biochemical response was 50% and 21%, respectively. Thus, virological and biochemical response sustained in 5 of 24 (21%) patients retreated with ribavirin and IFN-alpha; none of them lost hepatitis B surface antigen (HBsAg). Liver histology improved in 2 of 4 sustained responders but in none of the 12 nonresponders with paired biopsies (P =.05). The response was independent of dose and duration of previous treatment, viral load, or the distribution of HBV precore wild-type/mutant variants. However, sustained responders had significantly higher necroinflammation (P =.036) and fibrosis (P =.007) scores. IFN-alpha-related side effects were mild and reversible on discontinuation. In 4 (17%) patients who suffered nausea and diarrhea the ribavirin dosage was reduced by 50% after 1 month of therapy and finally discontinued in all of them. No patient had liver disease decompensation. In summary, combination therapy with ribavirin and IFN-alpha may be efficacious to treat viremic anti-HBe-positive patients with chronic hepatitis B who have failed previous IFN therapy.
The elaborate structure of spider silk (2008)

Biomaterials, having evolved over millions of years, often exceed man-made materials in their properties. Spider silk is one outstanding fibrous biomaterial which consists almost entirely of large proteins. Silk fibers have tensile strengths comparable to steel and some silks are nearly as elastic as rubber on a weight to weight basis. In combining these two properties, silks reveal a toughness that is two to three times that of synthetic fibers like Nylon or Kevlar. Spider silk is also antimicrobial, hypoallergenic and completely biodegradable. This article focuses on the structure-function relationship of the characterized highly repetitive spider silk spidroins and their conformational conversion from solution into fibers. Such knowedge is of crucial importance to understanding the intrinsic properties of spider silk and to get insight into the sophisticated assembly processes of silk proteins. This review further outlines recent progress in recombinant production of spider silk proteins and their assembly into distinct polymer materials as a basis for novel products.
The value of position-specific priors in motif discovery using MEME (2010)

We conclude that using position-specific priors can substantially increase the power of EM-based motif discovery algorithms such as MEME algorithm.
Procognitive Compounds Promote Neurite Outgrowth (2015)

The results of this study indicate that some procognitive compounds may possess a disease-modifying potential.
In vivo spectroscopic quantification of theN-acetyl moiety, creatine, and choline from large volumes of brain gray and white matter: Effects of normal aging (1999)

Volumetric proton magnetic resonance spectroscopic imaging (MRSI) was used to generate brain metabolite maps in 15 young and 19 elderly adult volunteers. All subjects also had structural MR scans, and a model, which took into account the underlying structural composition of the brain contributing to each metabolite voxel, was developed and used to estimate the concentration of the N-acetyl-moiety (NAc), creatine (Cr), and choline (Cho) in gray matter and white matter. NAc concentration (signal intensity per unit volume of brain) was higher in gray than white matter and did not differ between young and old subjects despite significant gray matter volume deficits in the older subjects. To the extent that NAc is an index of neuronal integrity, the available gray matter appears to be intact in these older healthy adults. Cr concentrations were much higher in gray than white matter and significantly higher in the old than young subjects. Cho concentration in gray matter was also significantly higher in old than young subjects. Independent determination of metabolite values rather than use of ratios is essential for characterizing age-related changes in brain MRS metabolites.
Stem Cell Factor: A Hemopoietic Cytokine with Important Targets in Asthma (2003)

We review evidence that Stem Cell Factor (SCF) plays an important role in the pathophysiology of asthma. SCF is produced by a wide variety of cells present in asthmatic lung, including mast cells and eosinophils. Its receptor, c-kit, is broadly expressed on mature mast cells and eosinophils. SCF promotes recruitment of mast cell progenitors into tissues, as well as their local maturation and activation. It also promotes eosinophil survival, maturation and functional activation. SCF enhances IgE-dependent release of mediators from mast cells, including histamine, leukotrienes, cytokines (TNF-alpha, IL-5, GM-CSF) and chemokines (RANTES/CCL5, MCP-1/CCL2, TARC/CCL17 e MDC/CCL22); it is required for IL-4 production in mast cells. SCF, acting in concert with IgE, also upregulates the expression and function of CC chemokine receptors in mast cells. Structural and resident airway cells express increased levels of SCF in the bronchus of asthmatic patients. In a murine model of asthma, allergen exposure increased production of SCF by epithelial cells and alveolar macrophages, which was transient and paralleled by histamine release. SCF induced long-lived airway hyperreactivity, which was prevented by local neutralization of SCF, as well as by inhibitors of the production or activity of cysteinyl-leukotrienes. Together, these observations suggest that SCF has an important role in asthma.
Full-duplex Wireless: Design, Implementation and Characterization (2012)

One of the fundamental assumptions made in the design of wireless networks is that the wireless devices have to be half-duplex, i.e., they cannot simultaneously transmit and receive in the same frequency band. The key deterrent in implementing a full-duplex wireless device, which can simultaneously transmit and receive in the same frequency band, is the large power differential between the self-interference from a device's own transmissions and the signal of interest coming from a distant source. In this thesis, we revisit this basic assumption and propose a full-duplex radio design. The design suppresses the self-interference signal by employing a combination of passive suppression, and active analog and digital cancellation mechanisms. The active cancellations are designed for wideband, multiple subcarrier (OFDM), and multiple antenna (MIMO) wireless communications systems. We then implement our design as a 20 MHz MIMO OFDM system with a 2.4 GHz center frequency, suitable for Wi-Fi systems. We perform extensive over-the-air tests to characterize our implementation. Our main contributions are the following: (a) the average amount of active cancellation increases as the received self-interference power increases and as a result, the rate of a full-duplex link increases as the transmit power of communicating devices increases, (b) applying digital cancellation after analog cancellation can sometimes increase the self-interference and the effectiveness of digital cancellation in a full-duplex system will depend on the performance of the cancellation stages that precede it, (c) our full-duplex device design achieves an average of 85 dB of self-interference cancellation over a 20 MHz bandwidth at 2.4 GHz, which is the best cancellation performance reported to date, (d) our full-duplex device design achieves 30-84% higher ergodic rates than its half-duplex counterpart for received powers in the range of [-75, -60] dBm. As a result, our design is the first one to achieve Wi-Fi ranges; in comparison, no implementation to date has achieved Wi-Fi ranges. Consequently, we have conclusively demonstrated that Wi-Fi full-duplex is practically feasible and hence shown that one of the commonly made assumptions in wireless networks is not fundamental.
Biochemical Method for Inserting New Genetic Information into DNA of Simian Virus 40: Circular SV40 DNA Molecules Containing Lambda Phage Genes and the Galactose Operon of Escherichia coli (1972)

We have developed methods for covalently joining duplex DNA molecules to one another and have used these techniques to construct circular dimers of SV40 DNA and to insert a DNA segment containing lambda phage genes and the galactose operon of E. coli into SV40 DNA. The method involves: (a) converting circular SV40 DNA to a linear form, (b) adding single-stranded homodeoxypolymeric extensions of defined composition and length to the 3' ends of one of the DNA strands with the enzyme terminal deoxynucleotidyl transferase (c) adding complementary homodeoxypolymeric extensions to the other DNA strand, (d) annealing the two DNA molecules to form a circular duplex structure, and (e) filling the gaps and sealing nicks in this structure with E. coli DNA polymerase and DNA ligase to form a covalently closed-circular DNA molecule.
Adenosine Triphosphate Concentration and β-d-Glucuronidase Activity as Indicators of Sea Bass Semen Quality (2004)

The most common parameters used to evaluate sperm quality are motility rate and duration and fertilization ability. In this study, chemical and biochemical parameters of sea bass (Dicentrarchus labrax) sperm were investigated to find an alternative method for evaluating sperm fertilization ability before and after cryopreservation. The biochemical and chemical analyses were performed with fresh and frozen-thawed sperm and seminal plasma. To cryopreserve sperm, 250-microl straws were used. Fertilization ability was evaluated by inseminating eggs (obtained from hormonally stimulated females) with fresh and cryopreserved sperm. The results revealed a linear relationship (P < 0.05) between semen fertilization capacity and some seminal plasma (beta-D-glucuronidase activity, potassium concentration) and sperm (ATP concentration, aspartate aminotransferase activity) parameters. Variations in semen fertilization rate could be best described by two multiple regression models: one including the sperm parameters and another including the seminal plasma parameters. For practical application, the use of simple regression models is of value. Fertilization rate in both fresh and cryopreserved sperm was reliably predicted by determining the ATP concentration or the beta-D-glucuronidase activity or both.
Radioimmunoassay for plasma C-type natriuretic peptide determination: a methodological evaluation (2005)

C-Type natriuretic peptide (CNP) is a member of the family of natriuretic peptides with vasodilatory properties, and is produced and secreted by endothelial cells. It seems to play a central role in the paracrine vasomotor control of tone and to be important in several clinical conditions characterized by endothelial dysfunction. We evaluated the analytical performance of a commercially available radioimmunoassay for CNP after a preliminary extraction with Sep-Pak C18. Its analytical reliability was checked by determination of CNP plasma levels in healthy subjects (n = 23) and in patients with different diseases, likely characterized by endothelial dysfunction, such as chronic heart failure (n = 133) and cirrhosis (n = 84). The extraction yield was 78+/-3%. Accuracy of the radiommunological determination was evaluated by dilution (45-370 microL of extracted plasma) and recovery tests (>80%). Between- and within-assay variabilities were < or = 10% and analytical sensitivity was 0.41+/-0.015 pg/tube. Plasma CNP in patients with chronic heart failure and with cirrhosis was significantly raised compared to controls (p<0.0001 and p = 0.001, respectively). The sensitivity, accuracy and variability levels of the method proposed for CNP assay was suitable for reliable detection of changes in CNP plasma levels in the clinical setting.
Lattice Vacancies and Interstitials in Silicon (1977)

A review is given of what is known about the simple intrinsic lattice point defects in silicon. This information has come primarily from high energy electron irradiation studies at cryogenic temperatures (4.2 K, 20.4 K) and observation in situ by electron paramagnetic resonance (EPR). Isolated vacancies have been observed as well as divacancies and higher aggregates of vacanies. Also a large number of vacancy-impurity pairs have been identified. Isolated interstitial silicon atoms have eluded detection but a variety of interstitial-impurity pairs, and possibly di-interstitials, have been studied. Current interests center around the effect of electron-hole recombination at the defects on their mobility, stability, and reaction kinetics. Evidence will be cited that the energy released upon recombination at a vacancy can cause it to diffuse at hermally through the lattice. The failure to detect isolated interstitial silicon has also been attributed to its lack of stability in the presence of ionizing radiation.
The Use of NMDA-Receptor Antagonists in the Treatment of Chronic Pain (2000)

Chronic pain can be maintained by a state of sensitization within the central nervous system that is mediated in part by the excitatory amino acids glutamate and aspartate binding to the N-methyl-D-aspartate (NMDA) receptor. A number of antagonists to the NMDA receptor are antinociceptive in animal models but are associated with significant dose-limiting side effects. Commercially available NMDA-receptor antagonists include ketamine, dextromethorphan, memantine, and amantadine. The opioids methadone, dextropropoxyphene, and ketobemidone are also antagonists at the NMDA receptor. The NMDA-receptor antagonists have a significant impact on the development of tolerance to opioid analgesics. Consequently, NMDA-receptor antagonists may represent a new class of analgesics and may have potential as coanalgesics when used in combination with opioids.
Structure of Raw Starch-Digesting Bacillus cereus β-Amylase Complexed with Maltose, (1999)

The crystals of beta-amylase from Bacillus cereus belong to space group P21 with the following cell dimensions: a = 57.70 A, b = 92.87 A, c = 65.93 A, and beta =101.95 degrees. The structures of free and maltose-bound beta-amylases were determined by X-ray crystallography at 2.1 and 2.5 A with R-factors of 0.170 and 0.164, respectively. The final model of the maltose-bound form comprises 516 amino acid residues, four maltose molecules, 275 water molecules, one Ca2+, one acetate, and one sulfate ion. The enzyme consists of a core (beta/alpha)8-barrel domain (residues 5-434) and a C-terminal starch-binding domain (residues 435-613). Besides the active site in the core where two maltose molecules are bound in tandem, two novel maltose-binding sites were found in the core L4 region and in the C-terminal domain. The structure of the core domain is similar to that of soybean beta-amylase except for the L4 maltose-binding site, whereas the C-terminal domain has the same secondary structure as domain E of cyclodextrin glucosyltransferase. These two maltose-binding sites are 32-36 A apart from the active site. These results indicate that the ability of B. cereus beta-amylase to digest raw starch can be attributed to the additional two maltose-binding sites.
Cell Growth Modulation of Human Cells Irradiated in Vitro with Low-Level Laser Therapy (2004)

Our results are a confirmation of previous observations carried out on human cells, where only the proliferation of slowly growing cell populations appeared to be stimulated by laser light.
Impairment of rod cGMP-gated channel alpha-subunit expression leads to photoreceptor and bipolar cell degeneration. (2000)

Impairment of rod cGMP-gated channel alpha subunit expression leads to photoreceptor and bipolar cell degeneration. These transgenic mice are the first model of retinal degeneration caused by an alteration in the expression of the rod cGMP-gated channel. This model system can be used to test therapies designed to slow or stalled retinal degenerations.
Ultrastructural Comparison of Oncovirinae (Type C), Spumavirinae, and Lentivirinae: Three Subfamilies of Retroviridae Found in Farm Animals (1984)

The successive steps of maturation of seven retroviruses from five species of farm animals and one retrovirus from a mouse were compared in cell cultures. The viruses included three type C oncoviruses, one spumavirus, and three lentiviruses. Although members of the 3 subfamilies shared some gross morphologic features such as budding on plasma membranes, core, and surface projections, differences were noted in the ultrastructural detail of these features. Type C oncoviruses did not show any structural differentiation in identifiable form in the cytoplasm as opposed to characteristic features observed in the spumavirus and lentivirus subfamilies, respectively. Budding viruses were distinct among the 3 subfamilies. The type C bovine leukemia virus budding on vacuole membranes differed from the two other type C viruses by lacking an electron-lucent intermediate layer as did the lentiviruses. Differentiation between type C oncoviruses and lentiviruses could be confusing because of the similarity of the fully mature virions appearing in the intercellular space. However, each subfamily of retroviruses can be readily differentiated from one another when each morphologic stage of virus replication is examined by electron microscopy.
Transient Blood-Brain Barrier Permeability following Profound Temporary Global Ischaemia: An Experimental Study Using 14C-AIB (1989)

The influence of reperfusion after profound incomplete forebrain ischaemia on blood-brain barrier (BBB) permeability to a small protein tracer was studied in male Sprague-Dawley rats. The mean cortical blood to brain transfer constant (Ki) for 14C-amino isobutyric acid (AIB) was significantly greater at 3 and 6 h of reperfusion, 2.5 times the mean values of controls (p less than 0.05) (2.5 microliter g-1 min-1 and 1.0 microliters g-1 min-1 respectively), but had returned to control values after reperfusion for 24 h. Analysis of distribution of Ki values showed that following 15 min and 30 min of profound ischaemia, there was a significant increase in transfer of AIB across the blood-brain barrier (BBB) after recirculation for up to 6 h, though there was no evidence of protein extravasation as assessed by Evans Blue (EB) dye. After 24 h of reperfusion, the BBB to AIB was restored, and Ki values had returned to control values. It is concluded that following transient global ischaemia, the BBB may recover rapidly.
Synthesis and Antibacterial Activity of Some Imidazo(1,2-a)pyrimidine Derivatives. (1992)

A series of 75 imidazo[1,2-a]pyrimidine derivatives were synthesized. The "in vitro" antibacterial activity of these compounds and their corresponding alpha-bromoketones against a variety of gram (+), gram (-) bacteria and Mycobacterium species is reported. Some of the prepared derivatives exhibited potent antimicrobial activity.