gebhart/patrepeval huggingface dataset:
Ultra-High Expression of a Thermally Responsive Recombinant Fusion Protein in E. coli (2006)

Elastin-like polypeptides (ELPs) are recombinant peptide-based biopolymers that contain repetitive sequences enriched in glycine, valine, proline, and alanine. Because of the unusually large fraction of these amino acids in ELPs as compared to other cellular proteins, we hypothesized that intracellular pools of these amino acids can be selectively depleted and limit protein yields during expression. In this study, we examined how culture conditions and individual medium components affect protein yields by monitoring cell growth and protein expression kinetics of E. coli expressing an ELP tagged with a green fluorescent protein (GFP). By determining the underlying principles of superior fusion protein yields generated by the hyperexpression protocol, we further improved protein yields through the addition of glycerol and certain amino acids such as proline and alanine and found that amino acid concentrations and the type of basal medium used strongly influenced this beneficial effect. Surprisingly, amino acids other than those that are abundant in ELPs, for example, asparagine, aspartic acid, glutamine, and glutamic acid, also enhanced protein yields even in a nutrient-rich medium. Compared to commonly used Luria-Bertani medium, the protein yield was improved by 36-fold to the remarkable level of 1.6 g/L in shaker flask cultures with a modified medium and optimized culture conditions, which also led to a 8-fold reduction in the cost of the fusion protein. To our knowledge, this is the highest yield of an ELP-fusion protein purified from E. coli cultured in shaker flasks. This study also suggests a useful strategy to improve the yields of other ELP fusion proteins and repetitive polypeptides.
Enhanced luminescence of Y3Al5O12:Ce3+ nanophosphor for white light-emitting diodes (2006)

Results pertaining to the development of highly dispersible stand-alone particles of Ce3+-doped Y3Al5O12 nanophosphor and their luminescence are presented. The yellow light-emitting nanophosphor was produced as a result of a single-step auto-combustion process, which requires no auxiliary annealing treatments prior to any practical application. The structure, photoluminescence, and chromaticity of the powder nanophosphor samples with the compositions Y(3−x)Al5O12:xCe3+ (x=0.01–1) are featured in the letter. The nanophosphor absorbs light efficiently in the visible region of 400–500nm, and shows single broadband emission peaking at ∼560nm. The luminescence yield is almost analogous to the samples made from other conventional methods. Hence, it could be an apt candidate for generating white light when coupled to a blue light-emitting diode (λem=450nm).
Controlled growth of highly uniform, axial/radial direction-defined, individually addressable InP nanowire arrays (2005)

We report on the systematically controlled growth of InP nanowire arrays by catalyst-free selective area metalorganic vapour phase epitaxy on partially masked InP(111)A substrates. The length, diameter, shape and position of the nanowires were precisely controlled by careful choice of the growth conditions and mask patterning. Manipulation of the growth conditions also enabled us to deliberately define the nanowire growth along either the axial or the radial direction, which has significant potential for the realization of novel nanostructures. Transmission electron microscopy studies revealed that the InP nanowires grown were single-crystalline with wurtzite crystal structure and the photoluminescence studies carried out at 4 K on InP nanowire arrays revealed a single intense emission peak with a significant blueshift. The controlled fabrication thus enabled the nanowires to be realized in a highly uniform manner as reproducibly identical structures and with perfect positioning in predetermined configurations, making them highly suitable for practical integration into nanodevices.
Docetaxel and Paclitaxel in the Treatment of Breast Cancer: A Review of Clinical Experience (2004)

In the 10 years since their initial licensing in Europe, the taxanes, paclitaxel and docetaxel, have emerged as fundamental drugs in the treatment of breast cancer. Clinically meaningful benefits were first shown in the metastatic setting, and large-scale exploration of their roles in the adjuvant therapy of early-stage disease is ongoing. Benefits have been seen in the neoadjuvant setting as well, mainly with docetaxel. This paper reviews the current roles of the taxanes in the treatment of metastatic and early-stage breast cancer. Also addressed are outstanding issues involving optimal dosing and sequencing, as well as a discussion of the relative merits of each agent in this setting. Clinicians should choose a taxane-based regimen for their patients with breast cancer based on consideration of the pharmacokinetics, clinical activity, and dosing schedule that best meets the patients' needs. At the current time, the pharmacokinetic profile, consistent positive clinical results, and convenience of an intermittent, short-infusion schedule have made docetaxel the preferred taxane for many clinicians treating patients with breast cancer.
Molecular beacons attached to glass beads fluoresce upon hybridisation to target DNA (2000)

Molecular beacons attached to glass beads have been synthesised which are non-fluorescent until exposed to a complementary target nucleic acid, whereupon they fluoresce, indicating hybridisation.
Liver-specific gene expression in mesenchymal stem cells is induced by liver cells (2005)

The results indicate that (1) rat MSC from bone marrow can differentiate towards hepatocytic lineage in vitro, and (2) that the microenvironment plays a decisive role for the induction of hepatic differentiation of rMSC.
Evaluating the IHS Criteria for Cluster Headache – a Comparison between Patients Meeting all Criteria and Patients Failing One Criterion (2006)

Cluster headache (CH) is diagnosed according to criteria of the International Headache Society (IHS), but, in clinical practice, these criteria seem too restrictive. As part of a nation-wide study, we identified a group of patients who met all criteria minus one (IHS-CH-1), and assessed in which way they differed from CH patients meeting all criteria (IHS-CH). We performed a nation-wide questionnaire study for CH and CH-like syndromes, including questions based on the IHS criteria, and additional features such as restlessness during attacks, nocturnal onset of attacks, circadian rhythmicity of attacks and response to treatment. IHS-CH and IHS-CH-1 patients were compared. Of 1452 responders to two questionnaires, 1163 were IHS-CH and 289 were IHS-CH-1. The majority of the IHS-CH-1 patients were classified as such because their attacks exceeded 3 h (64%, median attack duration: 5 h), or came in a frequency of less than 1 per 2 days (16%). Age at onset was similar between the groups. The male to female ratio was 3.7 : 1 in the IHS-CH group and around 1.6 : 1 in the IHS-CH-1 groups (P < 0.005). Patients with attacks exceeding 3 h less often reported a circadian rhythmicity (IHS-CH-1: 49%, IHS-CH: 64%), episodic periodicity (IHS-CH-1: 65%, IHS-CH: 78%), nocturnal attacks (IHS-CH-1: 67%, IHS-CH: 78%), smoking (IHS-CH-1: 90%, IHS-CH: 80%) and restlessness during attacks (IHS-CH-1: 64%, IHS-CH: 76%) than IHS-CH patients (P < 0.005). Photo- or phono-phobia (IHS-CH-1: 67%, IHS-CH: 54%) and nausea (IHS-CH-1: 38%, IHS-CH: 27%) were more frequently reported by patients who reported to have attacks exceeding 3 h (P < 0.005). Similar proportions reported effect of verapamil on their attacks (IHS-CH-1: 54%, IHS-CH 61%). We conclude that average attack duration exceeding 3 h was frequently the reason for not fulfilling IHS CH criteria. Symptoms often accompanying CH such as restlessness, nocturnal attacks and an episodic attack pattern were relatively frequently present in IHS-CH-1 patients with longer attacks. These patients may therefore be diagnosed with CH. Attack frequency may not be a useful criterion for the diagnosis of CH. The upper limit of 3 h should be increased in future diagnostic criteria.
Structure-Function Relationships in a Type I Antifreeze Polypeptide (1998)

Several analogs of an alanine-rich, alpha-helical type I antifreeze polypeptide from the winter flounder were synthesized and studied to evaluate the role of threonine residues on antifreeze activity. In this series, the four Thr residues in the wild type polypeptide were substituted with from one to four Ser, allo-Thr, or Val residues. Circular dichroism studies determined that these substitutions did not significantly diminish alpha-helicity. Thermal hysteresis data showed that substitution of Thr by Ser resulted in moderate to complete loss of antifreeze activity, depending on the number and position of the substituted Thr residue(s). Replacement by Val, in confirmation of other recent reports, or by allo-Thr had a much less detrimental effect on activity though there were qualitative differences in activity between the mutants and the wild type AFP. Based on these results, we propose that both the methyl and hydroxyl groups of Thr, particularly of the central two Thr residues, Thr13 and Thr24, play key roles in the ice-binding properties of the antifreeze peptide. Specifically, the methyls participate in hydrophobic interactions with ice, which provide the driving force for binding and stability, whereas the hydroxyls and other polar residues control binding specificity and impart additional stability through hydrogen bonding.
Herpes Simplex Virus and Toll-Like Receptors (2005)

The earliest interactions between viruses and host cells are critical to determining the outcome of infections. The interactions between a virus and its host cells that lead to the production of inflammatory cytokines are essential to the development of T cells and antibodies that provide long-term defense against the invaders. At the same time, however, these same cytokines (or sometimes other mediators or chemokines) stimulate inflammation, which may lead to localized tissue damage and/or systemic circulatory collapse and death. This review focuses on the interaction between Toll-like receptors, a critical component of the innate immune system of mammals, and their role in herpes simplex pathogenesis and immunity.
The phosphorylation state of the FIGQY tyrosine of neurofascin determines ankyrin-binding activity and patterns of cell segregation (1997)

Cell-cell recognition and patterning of cell contacts have a critical role in mediating reversible assembly of a variety of transcellular complexes in the nervous system. This study provides evidence for regulation of cell interactions through modulation of ankyrin binding to neurofascin, a member of the L1CAM family of nervous system cell adhesion molecules. The phosphorylation state of the conserved FIGQY tyrosine in the cytoplasmic domain of neurofascin regulates ankyrin binding and governs neurofascin-dependent cell aggregation as well as cell sorting when neurofascin is expressed in neuroblastoma cells. These findings suggest a general mechanism for the patterning of cell contact based on external signals that regulate tyrosine phosphorylation of L1CAM members and modulate their binding to ankyrin.
Modernizing the Nonhomologous End-Joining Repertoire: Alternative and Classical NHEJ Share the Stage (2013)

DNA double-strand breaks (DSBs) are common lesions that continually threaten genomic integrity. Failure to repair a DSB has deleterious consequences, including cell death. Misrepair is also fraught with danger, especially inappropriate end-joining events, which commonly underlie oncogenic transformation and can scramble the genome. Canonically, cells employ two basic mechanisms to repair DSBs: homologous recombination (HR) and the classical nonhomologous end-joining pathway (cNHEJ). More recent experiments identified a highly error-prone NHEJ pathway, termed alternative NHEJ (aNHEJ), which operates in both cNHEJ-proficient and cNHEJ-deficient cells. aNHEJ is now recognized to catalyze many genome rearrangements, some leading to oncogenic transformation. Here, we review the mechanisms of cNHEJ and aNHEJ, their interconnections with the DNA damage response (DDR), and the mechanisms used to determine which of the three DSB repair pathways is used to heal a particular DSB. We briefly review recent clinical applications involving NHEJ and NHEJ inhibitors.
[Treatment of spasmodic torticollis by local injections of botulinum toxin]. (1990)

Injections of botulinum toxin into the main cervical muscles responsible for abnormal posture and movements in spasmodic torticollis reduced pain and attenuated dystonia for a period of 2 months on average. After several sessions 9 out of 36 patients (25 p. 100) felt they had improved by at least 50 percent, 16 (44 p.100) by 50 to 75 percent, and 6 (17 p. 100) by more than 75 percent. There were six failures.
Serum Leptin Levels in Wild and Captive Populations of Baboons (Papio): Implications for the Ancestral Role of Leptin (2001)

Leptin has emerged as the major lipostat, regulating adiposity by affecting feeding behavior and thermogenesis. Leptin levels in normal-weight Western humans and in captive rodents are 5-15 ng/ml. But evidence suggests that these levels are abnormally high and that leptin may have evolved as a more general metabolic signal, with its most robust effects at lower levels. If this is true, then wild, healthy animal populations should have lower levels of leptin than captive populations and Western Man. We examined leptin levels in wild, East African populations of baboons (Papio anubis, P. hamadryas, and anubis/hamadryas hybrids). Serum leptin levels averaged less than 1 ng/ml, and no differences occurred in leptin levels among the species. In wild baboons, serum leptin levels were highest in the youngest baboons, with a trend toward an inverse relation between dental age and serum leptin levels. In comparison, captive baboons had levels about three times higher than wild baboons, with a clear inverse relation between age and leptin levels. These results support the view that leptin evolved to be effective at low levels.
Leptin and Aging: Correlation with Endocrine Changes in Male and Female Healthy Adult Populations of Different Body Weights (2000)

Aging is associated with changes in plasma levels of several hormones. There are conflicting reports on whether circulating leptin levels change during aging, the possible explanation for which is that alterations in adiposity and body mass index (BMI) also occur. In this study we measured plasma leptin and other hormonal parameters known to influence leptin in 150 men and 320 women of a wide age (18-77 yr) and BMI (18.5-61.1 kg/m2) range. Subjects of each gender were separated into 2 groups of similar BMI, i.e. nonobese (BMI, <30) and obese (BMI, >30), and treated separately. Statistical analysis was performed, treating each group of subjects as a whole population or divided into age groups (<30, 30-50, and >50 yr). BMI-adjusted leptin levels were progressively lower with increasing age in women, with a consistent fall after menopause (-21%; P < 0.001); in men, leptin levels also tended to be lower in subjects more than 50 yr of age, but the reduction was not significant. Multiple linear regression analysis, performed on subjects treated either as a whole population or divided into obese and nonobese, showed that in both genders BMI and age were independent contributors of leptin levels, and there was an inverse relationship between leptin and age in both obese (standardized coefficient beta = -0.25 in women and -0.23 in men; P < 0.01) and nonobese (-0.22 in women and -0.20 in men; P < 0.05) subjects. The correlation of leptin and age with plasma levels of sex and thyroid hormones, GH, insulin-like growth factor I, PRL, and insulin was also evaluated. The variables that correlated with leptin were included in a multiple regression model that included BMI and age. Testosterone in men (-0.43 in nonobese and -0.19 in obese; P < 0.05) and estradiol in women (0.22 in nonobese and 0.24 in obese; P < 0.05) were important contributors to leptin levels; also, dehydroepiandrosterone sulfate in obese women (-0.16) and sex hormone-binding globulin in obese subjects of both genders (0.15 in women and 0.19 in men) were significant determinants in the model. However, none of the hormonal parameters abolished the negative correlation between leptin and age or the gender difference in leptin levels. In conclusion, our data show that in adult humans of different body weight, serum leptin gradually declines during aging; leptin reduction is higher in women than in men, but it is independent from BMI and other age-related endocrine changes.
c-Jun-mediated anticancer mechanisms of tylophorine (2013)

Tylophorine, a phenanthroindolizidine alkaloid, is the major medicinal constituent of herb Tylophora indica. Tylophorine treatment increased the accumulation of c-Jun protein, a component of activator protein 1 (AP1), in carcinoma cells. An in vitro kinase assay revealed that the resultant c-Jun phosphorylation was primarily mediated via activated c-Jun N-terminal protein kinase (JNK). Moreover, flow cytometry indicated that ectopically overexpressed c-Jun in conjunction with tylophorine significantly increased the number of carcinoma cells that were arrested at the G1 phase. The tylophorine-mediated downregulation of cyclin A2 protein levels is known to be involved in the primary G1 arrest. Chromatin immunoprecipitation and reporter assays revealed that tylophorine enhanced the c-Jun downregulation of the cyclin A2 promoter activity upon increased binding of c-Jun to the deregulation AP1 site and decreased binding to the upregulation activating transcription factor (ATF) site in the cyclin A2 promoter, thereby reducing cyclin A2 expression. Further, biochemical studies using pharmacological inhibitors and RNA silencing approaches demonstrated that tylophorine-mediated elevation of the c-Jun protein level occurs primarily via two discrete prolonged signaling pathways: (i) the NF-κB/PKCδ_(MKK4)_JNK cascade, which phosphorylates c-Jun and increases its stability by slowing its ubiquitination, and (ii) the PI3K_PDK1_PP2A_eEF2 cascade, which sustains eukaryotic elongation factor 2 (eEF2) activity and thus c-Jun protein translation. To the best of our knowledge, this report is the first to demonstrate the involvement of c-Jun in the anticancer activity of tylophorine and the release of c-Jun translation from a global translational blockade via the PI3K_PDK1_eEF2 signaling cascade.
Image Compression in Face Recognition - a Literature Survey (2008)

Recent Advances in Face Recognition 2 performing face recognition directly in the compressed domain. We shall try to link the surveyed research hypotheses and conclusions to some real world scenarios as frequently as possible. We shall mostly concentrate on JPEG (Wallace, 1991) and JPEG2000 We feel that common image compression standards such as JPEG and JPEG2000 have the highest potential for actual usage in real life, since the image will always have to decompressed and presented to a human at some point. From that perspective it seems reasonable to use a well-known and commonly implemented compression format that any device can decompress. The rest of this chapter comprises of four sections. In section 2 we shall give an overview of research in spatial (pixel) domain, mainly focusing on the influence that degraded image quality (due to compression) has on recognition accuracy. In section 3 we shall follow the same lines of thought for the transform (compressed) domain research, also covering some research that is well connected to the topic even though the actual experiments in the surveyed papers were not performed with face recognition scenarios. We feel that the presented results from other research areas will give potential future research directions. In section 4 we review the presented material and try to pinpoint some future research directions.
Anti-human tumor antibodies induced in mice and rabbits by "internal image" anti-idiotypic monoclonal immunoglobulins. (1987)

MBr1 is a murine monoclonal antibody, defining a saccharidic epitope [CaMBr1] of a human tissue-specific, tumor-associated globoside, present on the mammary carcinoma cell line MCF-7. The same epitope is shared by glycoproteins present on normal and neoplastic mammary epithelial cells, and by mucins from some ovarian cyst fluids. We have used MBr1 as the monoclonal antitumor antibody in an idiotypic sequence of immunizations in order to obtain and characterize "internal images" of the original epitope to be used as substitutes of the nominal antigen in serologic immunoassays. Two monoclonal anti-idiotypic antibodies (beta-1 and beta-2), which reacted with paratope-related idiotopes on MBr1, were obtained. The analysis of the antigenic and immunogenic properties of these molecules by both "antigen" and "antibody" competition assays provided evidence that both beta-1 and beta-2 bear "internal images" of the MBr1-defined epitope. Moreover, when injected in mice and rabbits both beta-1 and beta-2 induced anti anti-idiotypic antibodies, which mimicked MBr1 in binding MCF-7 as well as normal and neoplastic mammary gland epithelial cells. These data are discussed in terms of their possible application to the production of tumor-associated antigen substitutes and their use in serologic immunoassays.
Diffusion in Brain Extracellular Space (2008)

Diffusion in the extracellular space (ECS) of the brain is constrained by the volume fraction and the tortuosity and a modified diffusion equation represents the transport behavior of many molecules in the brain. Deviations from the equation reveal loss of molecules across the blood-brain barrier, through cellular uptake, binding, or other mechanisms. Early diffusion measurements used radiolabeled sucrose and other tracers. Presently, the real-time iontophoresis (RTI) method is employed for small ions and the integrative optical imaging (IOI) method for fluorescent macromolecules, including dextrans or proteins. Theoretical models and simulations of the ECS have explored the influence of ECS geometry, effects of dead-space microdomains, extracellular matrix, and interaction of macromolecules with ECS channels. Extensive experimental studies with the RTI method employing the cation tetramethylammonium (TMA) in normal brain tissue show that the volume fraction of the ECS typically is approximately 20% and the tortuosity is approximately 1.6 (i.e., free diffusion coefficient of TMA is reduced by 2.6), although there are regional variations. These parameters change during development and aging. Diffusion properties have been characterized in several interventions, including brain stimulation, osmotic challenge, and knockout of extracellular matrix components. Measurements have also been made during ischemia, in models of Alzheimer's and Parkinson's diseases, and in human gliomas. Overall, these studies improve our conception of ECS structure and the roles of glia and extracellular matrix in modulating the ECS microenvironment. Knowledge of ECS diffusion properties is valuable in contexts ranging from understanding extrasynaptic volume transmission to the development of paradigms for drug delivery to the brain.