gebhart/patrepeval huggingface dataset:
Comparative 2D NMR studies of human insulin and despentapeptide insulin: sequential resonance assignment and implications for protein dynamics and receptor recognition (1991)

The solution structure and dynamics of human insulin are investigated by 2D 1H NMR spectroscopy in reference to a previously analyzed analogue, des-pentapeptide(B26-B30) insulin (DPI; Hua, Q.X., & Weiss, M.A. (1990) Biochemistry 29, 10545-10555). This spectroscopic comparison is of interest since (i) the structure of the C-terminal region of the B-chain has not been determined in the monomeric state and (ii) the role of this region in binding to the insulin receptor has been the subject of long-standing speculation. The present NMR studies are conducted in the presence of an organic cosolvent (20% acetic acid), under which conditions both proteins are monomeric and stably folded. Complete sequential assignment of human insulin is obtained and leads to the following conclusions. (1) The secondary structure of the insulin monomer (three alpha-helices and B-chain beta-turn) is similar to that observed in the 2-Zn crystal state. (2) The folding of DPI is essentially the same as the corresponding portion of intact insulin, in accord with the similarities between their respective crystal structures. However, differences between insulin and DPI are observed in the extent of conformational broadening of amide resonances, indicating that the presence or absence of residues B26-B30 influences the overall dynamics of the protein on the millisecond time scale. (3) Residues B24-B28 adopt an extended configuration in the monomer and pack against the hydrophobic core as in crystallographic dimers; residues B29 and B30 are largely disordered. This configuration differs from that described in a more organic milieu (35% acetonitrile; Kline, A.D., & Justice, R.M., Jr. (1990) Biochemistry 29, 2906-2913), suggesting that the conformation of insulin in the latter study may have been influenced by solvent composition. (4) The insulin fold is shown to provide a model for collective motions in a protein with implications for the mechanism of protein-protein recognition. To our knowledge, this paper describes the first detailed analysis of a protein NMR spectrum under conditions of extensive conformational broadening. Such an analysis is made possible in the present case by comparative study of an analogue (DPI) with more tractable spectroscopic properties.
Tumor Lymphangiogenesis as a Potential Therapeutic Target (2012)

Metastasis the spread of cancer cells to distant organs, is the main cause of death for cancer patients. Metastasis is often mediated by lymphatic vessels that invade the primary tumor, and an early sign of metastasis is the presence of cancer cells in the regional lymph node (the first lymph node colonized by metastasizing cancer cells from a primary tumor). Understanding the interplay between tumorigenesis and lymphangiogenesis (the formation of lymphatic vessels associated with tumor growth) will provide us with new insights into mechanisms that modulate metastatic spread. In the long term, these insights will help to define new molecular targets that could be used to block lymphatic vessel-mediated metastasis and increase patient survival. Here, we review the molecular mechanisms of embryonic lymphangiogenesis and those that are recapitulated in tumor lymphangiogenesis, with a view to identifying potential targets for therapies designed to suppress tumor lymphangiogenesis and hence metastasis.
Relation of the mineralogical and chemical composition to the fertilizer requirements of North Carolina soils (1914)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Latent Space Sparse Subspace Clustering (2013)

We propose a novel algorithm called Latent Space Sparse Subspace Clustering for simultaneous dimensionality reduction and clustering of data lying in a union of subspaces. Specifically, we describe a method that learns the projection of data and finds the sparse coefficients in the low-dimensional latent space. Cluster labels are then assigned by applying spectral clustering to a similarity matrix built from these sparse coefficients. An efficient optimization method is proposed and its non-linear extensions based on the kernel methods are presented. One of the main advantages of our method is that it is computationally efficient as the sparse coefficients are found in the low-dimensional latent space. Various experiments show that the proposed method performs better than the competitive state-of-the-art subspace clustering methods.
Evaluating the Potential for Shared Log Truck Resources in Middle Georgia (2006)

Abstract This study evaluates the potential gains from shared log trucking resources in a region with unconsolidated logging activities. This effort tracked 18 log trucks from three independent logging companies and six logging sites to 15 destinations over 5 days. We simulated a centralized dispatch system using actual inventory and loading/unloading data from the field study and incorporating constraints to manage hours worked and truck flows per tract. Results indicated the same volume of wood could be delivered with 0.92 fewer hours (55 minutes) per truck per day and 36 fewer miles driven per truck per day, with estimated daily cost savings for the 18-truck system of $500–750/day.
Comparative studies of human FcRIII-positive and negative natural killer cells. (1989)

In the present study we have identified and characterized three subpopulations of peripheral blood NK cells based on the surface expression of CD56 and CD16. We have designated these subsets CD16neg, CD16dim, and CD16bright according to the relative surface density of CD16. The CD16bright subset comprised about 10% to 15% of PBL, whereas the CD16dim and CD16neg subsets comprise less than 1% of the total lymphocytes. A detailed characterization of these subsets revealed both similarities and differences. The three subsets shared a great deal of phenotypic similarity, expressing CD2, CD7, CD11b, CD38, CD45R, CD18, and the p75 IL-2R on the majority of the cells in each subset. There were, however, several prominent phenotypic differences, particularly in the expression of CD57, CD11c, CD44, CD25, Leu-8, L263, and L265. The CD16neg cells were morphologically large agranular lymphocytes and demonstrated low levels of non-MHC restricted cytolysis of NK-sensitive tumor lines. The CD16dim and CD16bright subsets were large granular lymphocytes and revealed potent cytotoxicity against NK-sensitive targets. All subsets demonstrated IL-2-dependent activation and proliferation; however, the CD16dim and CD16neg subsets were preferentially responsive to very low concentrations of rIL-2. Although rIL-4 effectively inhibited the IL-2-induced cytolytic activation of all three NK cell subsets, only the CD16bright cells showed rIL-4 inhibition of IL-2 dependent proliferation. Cytokine transcription was also differentially regulated in the NK cell subsets after rIL-2 activation. Although TNF-alpha was equally transcribed in each subsets, IFN-gamma and serine protease-HF were preferentially transcribed in the CD16bright NK cells. Based on these results, we propose that these NK cell subsets represent portions of the NK cell differentiation pathway present in the peripheral blood.
The Application of High-Content Analysis in the Study of Targeted Particulate Delivery Systems for Intracellular Drug Delivery to Alveolar Macrophages (2011)

With an ever increasing number of particulate drug delivery systems being developed for the intracellular delivery of therapeutics a robust high-throughput method for studying particle-cell interactions is urgently required. Current methods used for analyzing particle-cell interaction include spectrofluorimetry, flow cytometry, and fluorescence/confocal microscopy, but these methods are not high throughput and provide only limited data on the specific number of particles delivered intracellularly to the target cell. The work herein presents an automated high-throughput method to analyze microparticulate drug delivery system (DDS) uptake byalveolar macrophages. Poly(lactic-co-glycolic acid) (PLGA) microparticles were prepared in a range of sizes using a solvent evaporation method. A human monocyte cell line (THP-1) was differentiated into macrophage like cells using phorbol 12-myristate 13-acetate (PMA), and cells were treated with microparticles for 1 h and studied using confocal laser scanning microscopy (CLSM), spectrofluorimetry and a high-content analysis (HCA). PLGA microparticles within the size range of 0.8-2.1 μm were found to be optimal for macrophage targeting (p < 0.05). Uptake studies carried out at 37 °C and 4 °C indicated that microparticles were internalized in an energy dependent manner. To improve particle uptake, a range of opsonic coatings were assessed. Coating PLGA particles with gelatin and ovalbumin was found to significantly increase particle uptake from 2.75 ± 0.98 particles per cell for particles coated with gelatin. Opsonic coating also significantly increased particle internalization into primary human alveolar macrophages (p < 0.01) with a 1.7-fold increase in uptake from 4.19 ± 0.48 for uncoated to 7.53 ± 0.88 particles per cell for coated particles. In comparison to techniques such as spectrofluorimetry and CLSM, HCA provides both qualitative and quantitative data on the influence of carrier design on cell targeting that can be gathered in a high-throughput format and therefore has great potential in the screening of intracellularly targeted DDS.
Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota (2007)

Most mucosal surfaces of the mammalian body are colonized by microbial communities ("microbiota"). A high density of commensal microbiota inhabits the intestine and shields from infection ("colonization resistance"). The virulence strategies allowing enteropathogenic bacteria to successfully compete with the microbiota and overcome colonization resistance are poorly understood. Here, we investigated manipulation of the intestinal microbiota by the enteropathogenic bacterium Salmonella enterica subspecies 1 serovar Typhimurium (S. Tm) in a mouse colitis model: we found that inflammatory host responses induced by S. Tm changed microbiota composition and suppressed its growth. In contrast to wild-type S. Tm, an avirulent invGsseD mutant failing to trigger colitis was outcompeted by the microbiota. This competitive defect was reverted if inflammation was provided concomitantly by mixed infection with wild-type S. Tm or in mice (IL10(-/-), VILLIN-HA(CL4-CD8)) with inflammatory bowel disease. Thus, inflammation is necessary and sufficient for overcoming colonization resistance. This reveals a new concept in infectious disease: in contrast to current thinking, inflammation is not always detrimental for the pathogen. Triggering the host's immune defence can shift the balance between the protective microbiota and the pathogen in favour of the pathogen.
The relationship between human papillomavirus L1 capsid protein and cervical lesions: a meta-analysis (2014)

Objective To investigate the relationship between human papillomavirus(HPV) L1 capsid protein and cervical lesions.Methods A meta-analysis of published data was performed to analyze the correlation of HPV L1 capsid protein expression with cervical lesion classification and prognosis by RevMan5.2 software.The effects of these outcomes were measured by OR and 95％CI.Results Fourteen reports were included to analyze the relationship between HPV L1 capsid protein and cervical lesion classification.The pooled OR with 95％CI of cervical intraepithelial neoplasia(CIN) Ⅰ vs CIN Ⅱ,CIN Ⅱ vs CINⅢ,CIN Ⅲvs squamous cell carcinoma(SCC) were 3.83 (95％CI:3.00-4.88),3.01 (95％CI:1.85-4.89) and 4.44(95％CI:2.09-9.43) in HPV L1 capsid protein expression,respectively.Four reports were included to analyze the relationship between HPV L1 capsid protein and the development of cervical lesions.The OR with 95％CI of HPV L1 capsid protein negative vs positive in 3 subgroups of lesion regression,lesion stable and lesion deterioration were 0.20 (95％CI:0.06-0.64,P＜0.05),1.1 1 (95％CI:0.78-1.58,P＞0.05) and 4.68 (95％CI:2.55-8.56,P＜0.01) respectively.Conclusions The expression of HPV L1 capsid protein is closely related to cervical lesions progression,and may be associated with the prognosis and outcome of cervical lesions.The patients with HPV L1 capsid protein positive are more likely to get improved,while the negative ones are more likely to develop to higher grade CIN,even SCC.

Key words: 
Papillomavirus infections;  L1 capsid protein;  Cervical lesions;  Cervical cancer;  Meta-analysis
Phenotypic and functional characteristics of CD4<sup>+</sup>CD39<sup>+</sup> FOXP3<sup>+</sup> and CD4<sup>+</sup>CD39<sup>+</sup>FOXP3<sup>neg</sup> T‐cell subsets in cancer patients (2012)

Human CD4(+) CD39(+) regulatory T (Treg) cells hydrolyze exogenous adenosine triphosphate (ATP) and participate in immunosuppressive adenosine production. They contain two T-cell subsets whose role in mediating suppression is not understood. Frequencies of both CD4(+) CD39(+) subsets were evaluated in peripheral blood lymphocytes of 57 cancer patients and in tumor infiltrating lymphocytes (TILs) of 6 patients. CD4(+) CD39(+) and CD4(+) CD39(neg) T cells isolated using immunobeads and cell sorting were cultured under various conditions. Their conversion into CD39(+) FOXP3(+) CD25(+) or CD39(+) FOX(neg) CD25(neg) cells was monitored by multiparameter flow cytometry. Hydrolysis of exogenous ATP was measured in luminescence assays. Two CD4(+) CD39(+) cell subsets differing in expression of CD25, FOXP3, CTLA-4, CD121a, PD-1, latency associated peptide (LAP), glycoprotein A repetitions predominant (GARP), and the cytokine profile accumulated with equal frequencies in the blood and tumor tissues of cancer patients. The frequency of both subsets was significantly increased in cancer. CD39 expression levels correlated with the subsets' ability to hydrolyze ATP. Conventional CD4(+) CD39(neg) T cells incubated with IL-2 + TGF-β expanded to generate CD4(+) CD39(+) FOXP3(+) Treg cells, while CD4(+) CD39(+) FOXP3(neg) CD25(neg) subset cells stimulated via the TCR and IL-2 converted to FOXP3(+) CTLA4(+) CD25(+) TGF-β-expressing Treg cells. Among CD4(+) CD39(+) Treg cells, the CD4(+) CD39(+) FOXP3(neg) CD25(neg) subset serves as a reservoir of cells able to convert to Treg cells upon activation by environmental signals.
Mutant NADH dehydrogenase subunit 4 gene delivery to mitochondria by targeting sequence-modified adeno-associated virus induces visual loss and optic atrophy in mice. (2012)

Due to the UGA codon at amino acid 16, mutant G11778A ND4 was translated only in the mitochondria where its expression led to significant loss of visual function, loss of retinal ganglion cells, and optic nerve degeneration recapitulating the hallmarks of human LHON.
Adhesion Failure of PVD Films Caused by Repeated Bending of Substrates (1981)

A method to evaluate the adhesion of PVD films was devised. Bi, Al and SiO films of various thicknesses were thermally evaporated onto copper or mild steel substrates. The substrate was subjected to repeated plastic bending. The adhesion failure life (bending cycles until the film-peeling) was taken as a measure of the adhesion. It was found that this method gave a result analogous to that obtained from the conventional method using adhesives. It was further confirmed that this method was applicable when the adhesion was so strong that the conventional method failed.
Phase I/II trial of paclitaxel by 1-hour infusion, carboplatin, and gemcitabine in the treatment of patients with advanced nonsmall cell lung carcinoma (1999)

This three-drug regimen is active and has acceptable toxicity in patients with advanced nonsmall cell lung carcinoma. Myelosuppression, particularly thrombocytopenia, is increased in comparison to the paclitaxel/carboplatin regimen. Fatigue also may be increased, but other nonhematologic toxicities are not altered substantially by adding gemcitabine. Although the response rate and median survival are improved modestly compared with our previous experience with paclitaxel/carboplatin, definitive conclusions regarding the efficacy of this regimen await the completion of randomized trials.
Acoustic Biosensors Coated With Phosphorylcholine Groups for Label-Free Detection of Human C-Reactive Protein in Serum (2015)

Mass-sensitive biosensor devices based on surface acoustic waves (SAWs) were coated with commercially available 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer for label-free detection of the inflammatory marker C-reactive protein (CRP) in human serum. Owing to the phosphorylcholine groups, the MPC polymer coating enables both binding of CRP and reduction of nonspecific adsorption of other proteins. Hence, MPC offers a simple and economic method to prepare CRP-specific biosensing layers without the use of additional capture molecules. Direct detection and a binding inhibition assay test format were used, where the latter was applied to minimize effects from the serum sample matrix. MPC polymer coated SAW biosensors could be used with both test formats to differentiate CRP serum concentrations in the normal range (i.e., 10 mg/L and below) from significantly increased serum concentrations which would indicate bacterial infection, tissue injury, and inflammation.
Riding the Internet highway (1993)

With a disk containing software, this book is the ideal starter kit for PC users. It focuses on the new Internet users' problems of accessing and communicating on the Internet. -- Teaches readers how to access the Internet from communications services such as CompuServe, Delphi, and America Online -- A resource for e-mail etiquette and procedures, Netnews topics, as well as reference materials -- Disk includes WinNET 2.0, a graphical interface to Internet newsgroups and e-mail
Grape Antioxidant Dietary Fiber Stimulates <i>Lactobacillus</i> Growth in Rat Cecum (2012)

Grape antioxidant fiber combines nutritional and physiological properties of dietary fiber and natural antioxidants from grapes. Grape antioxidant fiber could be used as an ingredient for functional foods and as a dietary supplement to increase the intake of dietary fiber and bioactive compounds.
A purely flexible lightweight membrane-type acoustic metamaterial (2015)

This paper proposes a purely flexible lightweight membrane-type acoustic structure, wherein one kind of flexible lightweight rubber material takes the roles of mass and stiffness and another type of lightweight flexible EVA (ethylene–vinyl acetate copolymer) or plastic material functions as the localized stiffness for each unit. Because both the scatterers and base are constituted by the same material, this type of structure breaks the limitation that the metamaterials and phononic crystals need different materials with relatively large density and elasticity modulus ratios to play the roles of the scatterers and base respectively. Based on the band structures with different units, mass block shapes and size parameters, it is suggested that the shapes of the mass block can significantly affect the band structure. In addition, this type of structure could not only open a full band gap in the low-frequency range below 500 Hz, but also obtain an ultra-low-frequency bending wave band gap in the range below 100 Hz. Finally, we take into account the semi-infinite medium as a component, and calculate the sound transmission loss (STL) to evaluate the interaction between the structure and air. An experimental validation employing the cylindrical mass structure was developed to directly support the simulation results. Since the structures proposed in this study have achieved a purely flexible lightweight design, there exists an important promotion effect to realize the engineering applications of the acoustic metamaterials in practice.
Gaussian Process Models for Indoor and Outdoor Sensor-Centric Robot Localization (2008)

This paper presents an approach to building a map from a sparse set of noisy observations, taken from known locations by a sensor with no obvious geometric model. The basic approach is to fit an interpolant to the training data, representing the expected observation, and to assume additive sensor noise. This paper takes a Bayesian view of the problem, maintaining a posterior over interpolants rather than simply the maximum-likelihood interpolant, giving a measure of uncertainty in the map at any point. This is done using a Gaussian process (GP) framework. The approach is validated experimentally both in an indoor office environment and an outdoor urban environment, using observations from an omnidirectional camera mounted on a mobile robot. A set of training data is collected from each environment and processed offline to produce a GP model. The robot then uses that model to localize while traversing each environment.
Effective text retrieval based on combining evidence from the corpus and users (1995)

The author surveys the representation, query processing and retrieval techniques used in the Inquery system. By combining evidence about relevance from the corpus, individual documents and users, Inquery achieves effective overall recall and precision evaluation while avoiding occasional major failures.
Gradients of transgene expression directed by the human myoglobin promoter in the developing mouse heart. (1993)

Prior studies using transient transfection assays in cultured avian and murine skeletal myotubes indicate that the proximal 2-kb segment of the 5' flanking region of the human myoglobin gene contains transcriptional control elements sufficient to direct muscle-specific and developmentally regulated expression of reporter genes. To examine the function of the human myoglobin gene promoter during development of skeletal and cardiac myocytes in the intact animal, a 2.0-kb myoglobin gene upstream fragment was fused to an Escherichia coli lacZ reporter gene and injected into fertilized mouse oocytes. beta-Galactosidase (beta-gal) activity was detected selectively in cardiac and skeletal myocytes of fetal and adult transgenic mice. A distinctive spatial pattern of myoglobin promoter activity was observed in fetal hearts: beta-gal staining was more pronounced within the left ventricular subendocardium than within the subepicardium and was essentially undetectable in the ventricular trabeculae or atria. Expression of endogenous myoglobin mRNA and protein, assessed by in situ hybridization and immunohistochemistry, demonstrated a similar spatial pattern. In contrast, hearts from adult transgenic mice demonstrated essentially homogeneous expression of beta-gal and of endogenous myoglobin mRNA and protein throughout the myocardium, including the trabeculae and atria. These data indicate that the 2.0-kb upstream region of the human myoglobin gene includes cis-acting regulatory elements sufficient to direct transgene expression during murine cardiac development that is myocyte-specific and responsive to positional cues in a similar manner to the endogenous myoglobin gene.
Ultrafast low-energy electron diffraction in transmission resolves polymer/graphene superstructure dynamics (2014)

Two-dimensional systems such as surfaces and molecular monolayers exhibit a multitude of intriguing phases and complex transitions. Ultrafast structural probing of such systems offers direct time-domain information on internal interactions and couplings to a substrate or bulk support. We have developed ultrafast low-energy electron diffraction and investigate in transmission the structural relaxation in a polymer/graphene bilayer system excited out of equilibrium. The laser-pump/electron-probe scheme resolves the ultrafast melting of a polymer superstructure consisting of folded-chain crystals registered to a free-standing graphene substrate. We extract the time scales of energy transfer across the bilayer interface, the loss of superstructure order, and the appearance of an amorphous phase with short-range correlations. The high surface sensitivity makes this experimental approach suitable for numerous problems in ultrafast surface science.