gebhart/patrepeval huggingface dataset:
Laminar and Columnar Organization of Ascending Excitatory Projections to Layer 2/3 Pyramidal Neurons in Rat Barrel Cortex (2005)

Excitatory synaptic projections to layer 2/3 (L2/3) pyramidal neurons in brain slices from the rat barrel cortex were measured using quantitative laser-scanning photostimulation (LSPS) mapping. In the barrel cortex, cytoarchitectonic "barrels" and "septa" in L4 define a stereotypical array of landmarks, allowing alignment and averaging of LSPS maps from multiple cells in different slices. We distinguished inputs to L2 and L3 neurons above barrels and septa. Average input maps revealed that barrel-related ascending projections (L4-->2/3barrel) interdigitated with a novel septum-related projection (L5A-->2septum). We also explored the functional organization of these projections by comparing the input maps of multiple cells in individual slices. L2/3 cells sharing the same barrel-related column showed strong correlations in their input maps, independent of their precise locations within the column; otherwise, correlations fell rapidly as a function of intersomatic separation. Our data indicate that barrel-related and septum-related columns are associated with distinct functional circuits. These projections are likely to mediate parallel processing of somatosensory signals within the barrel cortex, with L4-->2/3barrel and L5A-->2septum representing the intracortical continuations of, respectively, the subcortical lemniscal and paralemniscal systems conveying somatosensory information to the barrel cortex.
Relaxing Music Prevents Stress-Induced Increases in Subjective Anxiety, Systolic Blood Pressure, and Heart Rate in Healthy Males and Females (2001)

Previous research suggests that while subjective anxiety is reduced by relaxing music, the effect of music on physiological stress indices is less consistent. In the current study, the effect of relaxing music on participants' subjective and physiological response to stress was explored, with attention paid to methodological factors and mediating variables that might have contributed to inconsistencies in previous studies. Undergraduate students (43 females & 44 males) were exposed to a cognitive stressor task involving preparation for an oral presentation either in the presence of Pachelbel's Canon in D major, or in silence. Measures of subjective anxiety, heart rate, blood pressure, cortisol, and salivary IgA were obtained during rest and after presentation of the stressor. The stressor caused significant increases in subjective anxiety, heart rate, and systolic blood pressure in male and female controls. These stress-induced increases were each prevented by exposure to music, and this effect was independent of gender. Music also enhanced baseline salivary IgA levels in the absence of any stress-induced effects. These findings provide experimental support for claims that music is an effective anxiolytic treatment, the robustness of which is demonstrated by retention of the effect in the presence of a range of potentially mediating variables.
Three-dimensional optical data storage in refractive media by two-photon point excitation (1991)

What is to our knowledge the first high-density (>10(12) bits/cm(3)) optical recording of digital information in a multilayered, three-dimensional format is reported. Information is written as submicrometer volume elements of increased refractive index in a photopolymer by two-photon excitation of a photoinitiator at the waist of a highly focused beam from a colliding-pulse mode-locked laser. Quadratic dependence of two-photon excitation on intensity confines polymerization to the focal volume. Information is read with sufficient axial resolution by differential interference contrast microscopy. This write-once, read-many technique should increase the capacity of the spinning disk format by 100-fold.
Multiple drug-resistant human KB carcinoma cells independently selected for high-level resistance to colchicine, adriamycin, or vinblastine show changes in expression of specific proteins. (1986)

We have established four cell lines derived from the human KB carcinoma cell line which express high-level multiple drug resistance. One of these lines was selected for resistance to colchicine, one was selected for resistance to colchicine in the presence of the tumor promoter, mezerein, one for resistance to vinblastine, and one for resistance to adriamycin. All of these cell lines are cross-resistant to the other selective agents. The development of multidrug resistance in these cultured human carcinoma cells is associated with a limited number of specific protein alterations revealed by high resolution two-dimensional gel electrophoresis and Western blot analysis. These protein alterations in multidrug-resistant lines include the decreased prevalence of members of a family of proteins of molecular mass 70,000 to 80,000 daltons, pI 4.8-5.0, the increased synthesis of a protein of molecular mass 21,000 daltons, pI 5.0, in the colchicine-resistant cell lines only, and the increased expression of a 170,000-dalton protein in membrane preparations from all of the resistant cells. The loss of the 70,000- to 80,000-dalton proteins in the multidrug-resistant lines, which can also be demonstrated by immunoprecipitation of these proteins with specific antisera, is associated with a loss of translatable mRNA for these proteins. These studies suggest that only a limited number of protein changes occur in multidrug-resistant cell lines.
Substrate specificity of Fpg protein. Recognition and cleavage of oxidatively damaged DNA. (1994)

The 8-oxoguanine-DNA glycosylase of Escherichia coli, also known as formamidopyrimidine-DNA glycosylase (Fpg protein), has N-glycosylase and AP-lyase activities. This enzyme repairs oxidative DNA damage by efficiently removing formamidopyrimidine lesions and 8-oxoguanine residues from DNA. Defined oligodeoxynucleotides containing various 8-oxopurines were used to examine the substrate specificity of Fpg protein and to establish the role of functional groups in DNA on damage recognition and catalysis. Binding affinities of Fpg protein were established for duplex oligodeoxynucleotides containing 8-oxo-2'-deoxyguanine, 8-oxo-2'-deoxyadenine, 8-oxo-2'-deoxynebularine, 8-oxo-2'-deoxyinosine, abasic sites, and a ring-open adduct of C8-aminofluorene guanine. The C8 keto group of 8-oxodG:dC presents in the major groove and is correlated with tight binding (Kd = 8.9 nM). Binding is much weaker when the C8 keto functional group is in the minor groove, as in 8-oxodG:dA (Kd = 340 nM). Km and Vmax were determined for the cleavage reaction. Specificity constants (Kcat/Km) are consistently higher for oligodeoxynucleotide duplexes containing 8-oxopurines with C6 and C8 keto groups, as in 8-oxodG:dC and 8-oxodI:dC, where Kcat/Km are 9.3 and 18 min-1 nM x 10(-3), respectively. 8-oxodN:dC lacks the C6 keto group; the specificity constant is 0.024 min-1 nM x 10(-3). Taken together, our data suggest that the C8 keto group of 8-oxodeoxyguanine and the carbonyl moiety of formamidopyrimidine enable Fpg protein to recognize and bind duplex DNA containing these modified bases. An enzyme-catalyzed reaction involving the C6 keto group of the substrate leads to removal of these lesions. A mechanism involving protonation at O-6 of 8-oxoguanine is proposed to account for the N-glycosylase activity of this enzyme.
Measuring Oxidative mtDNA Damage and Repair Using Quantitative PCR (2003)

The human mitochondrial genome was completely sequenced in 1981 by Anderson and co-workers (1) and consists of a closed circular supercoiled DNA molecule of 16,569 base pairs. Mammalian cells characteristically contain a few hundred to several thousand mitochondria, each with 2-10 copies of the genome. The mitochondrial genome encodes 13 polypeptides, 22 transfer RNAs (tRNAs), and 2 rRNA. The 13 polypeptides encoded by the mitochondrial DNA (mtDNA) are essential subunits of the electron transport chain (ETC) and ATP synthase; cells lacking mtDNA are completely dependent on glycolysis for survival (2).
Test application time reduction for sequential circuits with scan (1995)

Scan designs alleviate the test generation problem for sequential circuits. However, scan operations substantially increase the total number of test clocks during test application stage. Classical methods used to solve this problem perform test compaction and obtain fewer test vectors. In this paper we show that such a strategy does not always reduce the test clocks or test application time. Our approach is to associate a scan strategy function with each test vector during test generation for circuits with full or partial scan. The paper presents two algorithms to generate test sequences that reduce the number of test clocks required to apply the test sequences. The algorithms are based on: (1) heuristics that determine the need for scan operations; and (2) controlling sequential test generation process by choosing an appropriate target fault. In this paper we define and investigate different scan strategies for full and partial scan designs. We propose approximate measures that can be used for selection of a target fault during sequential test generation. These concepts are integrated into the algorithms Test Application time Reduction for Full scan (TARF) and Test Application time Reduction for Partial scan (TARP). The algorithms are implemented, and their efficiencies are demonstrated by using them for a set of ISCAS sequential benchmark circuits. The experiments show that, in full scan designs, TARF generated vectors require 36% fewer test clocks compared to the vectors from COMPACTEST that produces near optimal test sets. Similarly for partial scan designs, TARP achieves over 30% cumulative test clock reduction compared to the results from FASTEST which produced generally fewer vectors than other ATPG systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis and antifouling activity of 3-isocyanotheonellin and its analogues (2002)

A new synthesis of 3-isocyanotheonellin, a marine sesquiterpene with potent antifouling activity against the larvae of the barnacle Balanus amphirite, and its analogues is described. The highlight of the synthetic strategy is the one-step construction of a tertiary isocyanide from an alcohol using trimethylsilyl cyanide and a silver salt. The antifouling activities of 3-isocyanotheonellin and its analogues are also reported.
A Comparative Study of Amphiphilic PAMAM Dendrimers at the Air−Water Interface with Different Hydrophobe Attachment Groups (2007)

Generation 0 through 5 polyamidoamine (PAMAM) dendrimers with three different types of groups connecting to hydrophobic C12 tails and one type of group connecting to C18 tails were synthesized and studied as monolayers at the air-water interface with a Langmuir trough. The molecular areas were significantly influenced by the size and the type of connecting group. Higher-generation (e.g., G4 and G5) amphiphilic PAMAMs with amide connecting groups were more responsive to changes in compression rate and subphase temperature and less stable than the corresponding opened epoxide- or ester-connected counterparts. Intramolecular (and possibly also intermolecular) attractive hydrogen-bond interactions between the amide connectors are proposed as the reason for this behavior.
Advanced Chronic Heart Failure: A Position Statement from the Study Group on Advanced Heart Failure of the Heart Failure Association of the European Society of Cardiology (2007)

Therapy has improved the survival of heart failure (HF) patients. However, many patients progress to advanced chronic HF (ACHF). We propose a practical clinical definition and describe the characteristics of this condition. Patients that are generally recognised as ACHF often exhibit the following characteristics: 1) severe symptoms (NYHA class III to IV); 2) episodes with clinical signs of fluid retention and/or peripheral hypoperfusion; 3) objective evidence of severe cardiac dysfunction, shown by at least one of the following: left ventricular ejection fraction<30%, pseudonormal or restrictive mitral inflow pattern at Doppler-echocardiography; high left and/or right ventricular filling pressures; elevated B-type natriuretic peptides; 4) severe impairment of functional capacity demonstrated by either inability to exercise, a 6-minute walk test distance<300 m or a peak oxygen uptake<12-14 ml/kg/min; 5) history of >1 HF hospitalisation in the past 6 months; 6) presence of all the previous features despite optimal therapy. This definition identifies a group of patients with compromised quality of life, poor prognosis, and a high risk of clinical events. These patients deserve effective therapeutic options and should be potential targets for future clinical research initiatives.
Endothelial Expression of a Mononuclear Leukocyte Adhesion Molecule During Atherogenesis (1991)

An inducible rabbit endothelial adhesion molecule that is selective for mononuclear leukocytes has been identified. This adhesion protein was expressed on the surface of activated cultured endothelium in two forms, 118 and 98 kilodaltons, the amino-terminal sequence of each being highly homologous to human VCAM-1. In dietary hypercholesterolemic and Watanabe heritable hyperlipidemic rabbit models of atherosclerosis, this adhesion molecule was found to be expressed in a localized fashion by aortic endothelium that overlies early foam cell lesions. This lesion-localized expression suggests a potential endothelium-dependent mechanism for mononuclear leukocyte recruitment during atherogenesis and may provide a molecular marker for early atherosclerosis.
Antiviral research: strategies in antiviral drug discovery. (2009)

Table of Contents 1. Antiherpesviral DNA Polymerase Inhibitors Donald M. Coen 2. Entry Inhibitors of Human Immunodeficiency Virus Masanori Baba 3. Human Immunodeficiency Virus Type 1 Non-Nucleoside Reverse Transcriptase Inhibitors Dirk Jochmans, Johan Vingerhoets, Eric Arnoult, Luc Geeraert, and Jerome Guillemont 4. Nucleoside Analogue Inhibitors of Human Immunodeficiency Virus Reverse Transcriptase Jerome Deval and Matthias Gotte 5. Integrase as a Novel Target for the Inhibition of Human Immunodeficiency Virus Type 1 Infection: Current Status and Future Perspectives Linos P.R. Vandekerckhove, Frauke Christ, Zeger Debyser, Andrew Owen, David Back, Arnout Voet, Jonathan Schapiro, and Dirk Vogelaers 6. Human Immunodeficiency Virus Type 1 Tat and Rev as Potential Targets for Drug Development Sergei Nekhai and Kuan-Teh Jeang 7. Inhibitors of the Human Immunodeficiency Virus Protease Jorge L. Martinez-Cajas and Mark A. Wainberg 8. Hepatitis C Virus RNA-Dependent RNA Polymerase as a Target for Antiviral Drug Intervention: Non-Nucleoside Inhibitors Yaya Liu, Yupeng He, and Akhteruzzaman Molla 9. Nucleoside Analog Inhibitors of Hepatitis C Viral Replication Steven S. Carroll and Robert L. LaFemina 10. Antiviral Targets in Orthopoxviruses Mark N. Prichard and Earl R. Kern 11. Influenza Virus Antiviral Targets Gillian M. Air and Wayne J. Brouillette 12. Developments in the Search for Small Molecule Inhibitors for Treatment of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) Dale L. Barnard and Yohichi Kumaki 13. Antiviral Treatment of Flaviviruses Justin G. Julander 14. Clinical Aspects of Hepatitis C Virus Infection David Durantel and Fabien Zoulim 15. Microbicides: Molecular Strategies for Prevention of Sexually Transmitted Viral Disease Raina N. Fichorova 16. Phenotypic Susceptibility Assays for Human Immunodeficiency Virus Type 1 Neil T. Parkin, Eoin Coakley, and Christos J. Petropoulos 17. Metabolism of Antiviral Nucleosides and Nucleotides Adrian S. Ray and Michael J. M. Hitchcock 18. Targeting the Interferon Response for Antiviral Therapy Michael D. Robek 19. Toll-Like Receptors: Novel Molecular Targets for Antiviral Immunotherapy Raymund R. Razonable, Albert J. Eid, and Martin Henault 20. New Herpes Simplex Virus Replication Targets Sandra K. Weller Afterword: Closing Thoughts Robert L. LaFemina
Activating mutations for the Met tyrosine kinase receptor in human cancer (1997)

Recently, mutations in the Met tyrosine kinase receptor have been identified in both hereditary and sporadic forms of papillary renal carcinoma. We have introduced the corresponding mutations into the met cDNA and examined the effect of each mutation in biochemical and biological assays. We find that the Met mutants exhibit increased levels of tyrosine phosphorylation and enhanced kinase activity toward an exogenous substrate when compared with wild-type Met. Moreover, NIH 3T3 cells expressing mutant Met molecules form foci in vitro and are tumorigenic in nude mice. Enzymatic and biological differences were evident among the various mutants examined, and the somatic mutations were generally more active than those of germ-line origin. A strong correlation between the enzymatic and biological activity of the mutants was observed, indicating that tumorigenesis by Met is quantitatively related to its level of activation. These results demonstrate that the Met mutants originally identified in human papillary renal carcinoma are oncogenic and thus are likely to play a determinant role in this disease, and these results raise the possibility that activating Met mutations also may contribute to other human malignancies.
Graded Infill Structure of Wind Turbine Blade Accounting for Internal Stress in Big Area Additive Manufacturing (2024)

In additively manufactured (AM) components, infill structure significantly affects the mechanical performance of the final printed part. However, mechanical stress induced by operation loads has been so far neglected for infill patterning. Most slicers currently available in the market provide infill patterns that are uniform in shape and size regardless of the operational loading. We develop a design approach for infill patterns that accounts for the induced stress. This approach differs from topology optimization as it focuses on the porous infill, which allows the external shape of the printed part to remain intact. The proposed approach uses a computational stress analysis to control the distribution of the local density of the infill pattern. We have applied the approach to a wind turbine blade core with infill densities optimized based on the structural loads. The blade core is fabricated in our big area additive manufacturing (BAAM) system. To ensure less warpage and better inter-layer bonding, fast layer deposition is critical in BAAM system. We have optimized the tool path sequences to minimize the deposition time via the solution to the Chinese Postman Problem (CPP). For the application of wind turbine infill, the deposition from the CPP method is twice faster than the deposition from conventional slicing.
White blood cells, C-reactive protein and erythrocyte sedimentation rate in pneumococcal pneumonia in children (1997)

We evaluated the applicability of C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), white blood cell count (WBC), and absolute neutrophil count (ANC), in the screening of pneumococcal (PNC) pneumonia in children. In 1981-1982, 161 children were treated for radiologically verified community-acquired pneumonia in the hospital during a period of 12 months. The Streptococcus pneumoniae aetiology of infection was studied by antigen, antibody and immune complex assays in acute and convalescent sera. In acute blood samples, CRP was measured by the immunonephelometric method, ESR by the Westergren method, WBC using an automatic cell counter, and thereafter the ANC was calculated after microscopic examination of peripheral smears. CRP and ESR were significantly higher in patients with alveolar (n=53) than in those with interstitial (n=108) pneumonia. CRP, ESR and ANC were significantly higher in PNC (n=29) than in viral (n=23) pneumonia. The values in mixed PNC and viral infections (n=17) were approximately midway between PNC and viral cases. All cases with serologic evidence of S. pneumoniae aetiology were combined (n=46) for calculation of diagnostic parameters. When a cut-off limit of 60 mg x L(-1) was used, CRP had a sensitivity of 26% and a specificity of 83% in the screening of PNC pneumonia. We conclude that C-reactive protein and erythrocyte sedimentation rate have a limited capacity to differentiate between pneumococcal and nonpneumococcal pneumonia. C-reactive protein is recommended as the first-line method of screening, and the value of 60 mg x L(-1) as the cut-off limit.
Lysyl oxidase expression and inhibition in uveal melanoma (2010)

Lysyl oxidase is a marker of poor prognosis in several malignancies and is hypothesized to promote a migratory phenotype in hypoxic breast carcinomas. This study aims to characterize the expression of the lysyl oxidase and lysyl oxidase-like proteins in human uveal melanoma cell lines and archival choroidal melanomas using immunohistochemistry. The transcriptional control of lysyl oxidase will also be investigated under simulated hypoxic conditions using cobalt chloride. Lastly, changes in cellular proliferation and invasion will be assessed after the treatment of cell lines with beta-aminopropionitrile, a lysyl oxidase catalytic inhibitor. Retrospective analysis of lysyl oxidase expression in primary human uveal melanoma showed 82% (27 of 33) of tumors being stained positive. High lysyl oxidase expression correlated with the aggressive epithelioid cell type and was associated with shorter metastasis-free survival. Simulated hypoxia resulted in a significant increase in lysyl oxidase mRNA expression. Inhibiting lysyl oxidase's catalytic activity significantly reduced cellular invasion but had no effect on cell proliferation. Our study is the first to show lysyl oxidase expression in primary choroidal melanomas. This protein may represent a potential therapeutic target that warrants further study in this malignancy.
Actin ‘purse string’ filaments are anchored by E-cadherin-mediated adherens junctions at the leading edge of the epithelial wound, providing coordinated cell movement (1998)

At the leading edge of healing embryonic epithelium, cables of actin filaments appear to extend from cell to cell, forming a ring around the wound circumference. It has been hypothesized that this actin filament cable functions as a contractile 'purse string' to facilitate wound closure. We have observed this cable in large, circular healing epithelial wounds in corneas of adult mice. To elucidate the role of the actin filament cable, we characterized the molecular components associated with the cell-cell junction where the actin filament cable inserts and with the actin filament cable itself, and we studied the effect of disruption of the cable using an E-cadherin function-blocking antibody, ECCD-1. Localization of E-cadherin and the direct association of catenins with actin filament cable at the cell-cell interface of the actin cable confirmed that the cell-cell junction associated with the actin filament cable is an adherens junction. The E-cadherin function-blocking antibody caused disruption of the actin filament cable and induction of prominent lamellipodial extensions on cells at the leading edge, leading to a ragged uneven epithelial wound margin. These data demonstrate that cell-to-cell associated E-cadherin molecules link the actin filament cable, forming a functional adherens junction, and that the actin filament cable plays a role in coordinating cell movement.