gebhart/patrepeval huggingface dataset:
Trastuzumab-DM1: A Review of the Novel Immuno-Conjugate for HER2- Overexpressing Breast Cancer (2009)

Trastuzumab is a monoclonal antibody targeted against the HER2 tyrosine kinase receptor. Although trastuzumab is a very active agent in HER2-expressing breast cancer, the majority of patients with metastatic HER2 overexpressing breast cancer who initially respond to trastuzumab develop resistance within one year of initiation of treatment, and in the adjuvant setting, progress despite trastuzumab-based therapy. The immuno-conjugate Trastuzumab-DM1 (T-DM1) was designed to combine the biological activity of trastuzumab with the targeted delivery of a highly potent antimicrotubule agent, DM1, a maytansine derivative, to HER2-expressing breast cancer cells. T-DM1 is the first immuno-conjugate with a non-reducible thioether linker in clinical trials. Here, we summarize evidence from pre-clinical studies, analyze clinical data, and discuss the potential clinical implications of T-DM1.
Evolution of the Haptophyta and the molecular clock and the origin of the secondary endosymbiosis. (2002)

The cell division cycle and the circadian clock represent two major cellular rhythms. These two periodic processes are coupled in multiple ways, given that several molecular components of the cell cycle network are controlled in a circadian manner. For example, in the network of cyclin-dependent kinases (Cdks) that governs progression along the successive phases of the cell cycle, the synthesis of the kinase Wee1, which inhibits the G2/M transition, is enhanced by the complex CLOCK-BMAL1 that plays a central role in the circadian clock network. Another component of the latter network, REV-ERBα, inhibits the synthesis of the Cdk inhibitor p21. Moreover, the synthesis of the oncogene c-Myc, which promotes G1 cyclin synthesis, is repressed by CLOCK-BMAL1. Using detailed computational models for the two networks we investigate the conditions in which the mammalian cell cycle can be entrained by the circadian clock. We show that the cell cycle can be brought to oscillate at a period of 24 h or 48 h when its autonomous period prior to coupling is in an appropriate range. The model indicates that the combination of multiple modes of coupling does not necessarily facilitate entrainment of the cell cycle by the circadian clock. Entrainment can also occur as a result of circadian variations in the level of a growth factor controlling entry into G1. Outside the range of entrainment, the coupling to the circadian clock may lead to disconnected oscillations in the cell cycle and the circadian system, or to complex oscillatory dynamics of the cell cycle in the form of endoreplication, complex periodic oscillations or chaos. The model predicts that the transition from entrainment to 24 h or 48 h might occur when the strength of coupling to the circadian clock or the level of growth factor decrease below critical values.
Stimulation of guanylate cyclase activity and reduction of adenylate cyclase activity by granulocyte-macrophage colony-stimulating factor in human blood neutrophils. (1988)

Human neutrophils were incubated with granulocyte-macrophage (GM)-CSF and examined for changes in second messenger systems. Twofold increases in cGMP but not cAMP were measured after 5 to 20 min with 100 U/ml GM-CSF. Guanylate cyclase activities in membrane and cytosol fractions were increased to the same extent whether measured in the presence of Mg2+ or Mn2+, or in the cytosol with Mg2+ + N-methyl-N'-nitro-N-nitroso-guanidine. Kinetic studies of the cytosol enzyme showed no changes in the Km values for Mg2+ and Mn2+dependent guanylate cyclase activities (0.91 and 0.022 mM, respectively), whereas Vm values were increased after treating intact cells with GM-CSF. Two peaks of guanylate cyclase activity were observed, one at 10 and another at 60 min after adding 100 U/ml GM-CSF, whereas only one peak at 5 min occurred with 1 U/ml. Adenylate cyclase activity was reduced by nearly 50% after adding 100 U/ml GM-CSF for 10 to 30 min. These effects were also seen in the presence of several hormonal and nonhormonal adenylate cyclase stimulators. In contrast, small increases in adenylate cyclase activity occurred after adding 1 U/ml GM-CSF. In experiments to examine the pathway of guanylate cyclase activation by GM-CSF, we observed no changes in inositol phosphates, intracellular calcium ion, or cytosolic protein kinase C. The augmentation of chemotactic peptide-induced superoxide production by GM-CSF concentrations, may be related to the effects of the higher levels of GM-CSF to stimulate late increases in guanylate cyclase or decreases in adenylate cyclase.
Synthesis, characterization, antimicrobial, insecticidal and anthelmintic screening of some new s-triazine derivatives of pyrazoline, pyrimidine, isoxazoline and isothiazoline moiety (2012)

1-(4-(4,6-Bis(4�-chlorophenylamino)-1,3,5-triazin-2-ylamino)-phenyl)-3-(aryl substituted) prop-2-en-1-one 3 has been used as precursor to synthesize some new pyrimidine, pyrazoline, isoxazoline and isothiazoline derivatives. Several derivatives have been synthesized and evaluated for their antimicrobial efficacy against Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae and Staphyllococcus aureus, antifungal activity against B. fragilis, B. vulgatus, F. oxysporum and T. viridae, insecticidal activity against Periplaneta americana and anthelmintic activity against Pheretima posthuma (Indian adult earthworm).
A survey of data provenance in e-science (2005)

Data management is growing in complexity as large-scale applications take advantage of the loosely coupled resources brought together by grid middleware and by abundant storage capacity. Metadata describing the data products used in and generated by these applications is essential to disambiguate the data and enable reuse. Data provenance, one kind of metadata, pertains to the derivation history of a data product starting from its original sources.In this paper we create a taxonomy of data provenance characteristics and apply it to current research efforts in e-science, focusing primarily on scientific workflow approaches. The main aspect of our taxonomy categorizes provenance systems based on why they record provenance, what they describe, how they represent and store provenance, and ways to disseminate it. The survey culminates with an identification of open research problems in the field.
1-Deoxy-d-xylulose 5-Phosphate Synthase Catalyzes a Novel Random Sequential Mechanism (2011)

Emerging resistance of human pathogens to anti-infective agents make it necessary to develop new agents to treat infection. The methylerythritol phosphate pathway has been identified as an anti-infective target, as this essential isoprenoid biosynthetic pathway is widespread in human pathogens but absent in humans. The first enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes the formation of DXP via condensation of D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate in a thiamine diphosphate-dependent manner. Structural analysis has revealed a unique domain arrangement suggesting opportunities for the selective targeting of DXP synthase; however, reports on the kinetic mechanism are conflicting. Here, we present the results of tryptophan fluorescence binding and kinetic analyses of DXP synthase and propose a new model for substrate binding and mechanism. Our results are consistent with a random sequential kinetic mechanism, which is unprecedented in this enzyme class.
Focal Nodular Hyperplasia (2012)

Focal nodular hyperplasia (FNH) is the second most common benign hepatic mass. The primary purpose of this article is to provide a relevant case study and offer a review of the recent literature related to FNH with a discussion of both the clinical and imaging findings of this classically benign hepatic lesion. Although magnetic resonance imaging is considered the gold standard of FNH imaging, the sonographic and computed tomography appearance also is offered in this article. Furthermore, contrast-enhanced ultrasound, which boasts a 96% success rate at differentiating FNH from other hepatic tumors, is analyzed. The historical treatment options, including medical and possible surgical intervention, are provided as well. Last, this article offers an analysis of the prognosis for the patient diagnosed with FNH.
Marine Microbiome as a Source of Antimalarials (2019)

It is important to discover novel antimalarial pharmacophores because of the widespread emergence of <i>Plasmodium falciparum</i> isolates resistant to the available drugs. Secondary metabolites derived from microbes associated with marine invertebrates are a valuable resource for the discovery of novel drug leads. However, the potential of marine microbes as a source of antimalarials has not been explored. We investigated the promise of marine microorganisms for the production of antimalarial activities by testing 2365 diverse microbial extracts using phenotypic screening of a multidrug resistant chloroquine resistant <i>P. falciparum</i> strain. We conducted counter screening against mammalian cells for the 317 active extracts that exhibited more than 70% inhibition at 1 µg/mL. The screen identified 17 potent bioactive leads from a broad range of taxa. Our results establish that the marine microbiome is a rich source of antiplasmodial compounds that warrants in depth exploration.
Altering the Emission Behavior with the Turn of a Thiophene Ring:  The Photophysics of Condensed Ring Systems of Alternating Benzenes and Thiophenes (2006)

Six aromatic compounds with embedded thiophenes differing in the number of rings (2-5) and thiophene orientation along the long axis of the molecule (syn, anti) were investigated. Photophysical properties, steady-state absorption, fluorescence, phosphorescence, lifetimes, quantum yields, and a comprehensive time-resolved spectroscopic analysis (femtosecond and nanosecond transient absorption spectroscopy) have been studied as a function of molecular structure.
Supplementary Materials and Methods from A Hyaluronidase-Responsive Nanoparticle-Based Drug Delivery System for Targeting Colon Cancer Cells (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
Offline Health Diagnosis of Power Device Based on Nonintrusive Inductively Coupled Approach (2018)

Understanding the causes of a power device's defect plays a crucial role in failure and reliability analyses, and hence, the need of health diagnosis. Health diagnosis involves the measurement of predefined electrical parameters of a power device under its usual operating condition and the analyses of their deviations from their norms. Instead of the conventional direct measurements of voltage and current waveforms in time domain, this paper proposes a nonintrusive measurement method that measures the ON-state impedance of a power device in frequency domain. The proposed method eliminates direct electrical contact with the device-under-test, and it has the ability to detect the deviation of the ON-state impedance from its norm for health diagnosis purpose.
Isolation and culture of human neuromicrovascular endothelial cells for the study of angiogenesis in vitro (1999)

Neovascularization in the adult central nervous system occurs as a response to several pathophysiological conditions such as ischemia, wound repair, or neoplasia. Endothelial cells from different blood vessel types, different organs, and different species are heterogeneous; therefore, the appropriate cell type should be used to study specific aspects of vascular pathology. We have developed a method to isolate human cerebral microvascular endothelial cells (CMECs) from small, freshly obtained specimens of normal brain adherent to human arteriovenous malformations (AVMs). The isolation procedure involves enzymatic digestions and gradient centrifugations, yielding over 95% pure primary cultures. Alternative isolation methods using magnetic beads, panning, or cloning were not superior with regard to cell purity or yield. CMECs were identified by their immunoreactivity for vWF, CD34, EN4, binding of Ulex europeus lectin, and uptake of DiI-Ac-LDL. They displayed ultrastructural features characteristic of blood-brain barrier endothelial cells and expressed GLUT-1. CMECs were subcultured; however, prolonged culture led to reduced culture purity. Vascular endothelial growth factor, basic fibroblast growth factor and hepatocyte growth factor/scatter factor stimulated the directional motility of CMECs, with dose-response profiles similar to human umbilical vein endothelial cells (HUVECs). In contrast, to stimulate proliferation, lower concentrations of growth factors tended to be necessary for CMECs than for the large vessel endothelial cells. CMECs formed capillary tube-like structures in an in vitro angiogenesis assay using matrigel. This study expands the spectrum of available tissue sources for the isolation of human neuromicrovascular endothelial cells, which are essential for the in vitro study of blood-brain barrier function and cerebral angiogenesis.
Suppression of Botrytis cinerea causing the grey mould disease of grape-vine by an aggressive mycoparasite, Pythium radiosum (1999)

Pythium radiosum Paul has been found to be an aggressive mycoparasite of Botrytis cinerea which causes grey mould disease on the grape-vine. The mycoparasitic fungus enters the host mycelium, coagulates its protoplasm, empties its contents and finally comes out producing numerous ramifications and sexual structures. When the infected mycelium of B. cinerea is applied to the leaves of the grape-vine, the characteristic grey mould symptoms fail to appear. Since P. radiosum causes no harm to the grape-vine, it can be used as a biological control agent against B. cinerea. A brief account of the mycoparasite and its antagonism towards B. cinerea is discussed here.
Electron transport chains of lactic acid bacteria - walking on crutches is part of their lifestyle (2009)

A variety of lactic acid bacteria contain rudimentary electron transport chains that can be reconstituted by the addition of heme and menaquinone to the growth medium. These activated electron transport chains lead to higher biomass production and increased robustness, which is beneficial for industrial applications, but a major concern when dealing with pathogenic lactic acid bacteria.
Potential sites of PI-3 kinase function in the endocytic pathway revealed by the PI-3 kinase inhibitor, wortmannin. (1996)

Previously we have shown that PDGF receptor mutants that do not bind PI-3 kinase internalize after ligand binding, but fail to downregulate and degrade. To define further the role of PI-3 kinase in trafficking processes in mammalian cells, we have investigated the effects of a potent inhibitor of PI-3 kinase activity, wortmannin. At nanomolar concentrations, wortmannin inhibited both the transfer of PDGF receptors from peripheral compartments to juxtanuclear vesicles, and their subsequent degradation. In contrast, the delivery of soluble phase markers to lysosomes, assessed by the accumulation of Lucifer yellow (LY) in perinuclear vesicles after 120 min of incubation, was not blocked by wortmannin. Furthermore, wortmannin did not affect the rate of transferrin uptake, and caused only a small decrease in its rate of recycling. Thus, the effects of wortmannin on PDGFr trafficking are much more pronounced than its effects on other endocytic events. Unexpectedly, wortmannin also caused a striking effect on the morphology of endosomal compartments, marked by tubulation and enlargement of endosomes containing transferrin or LY. This effect was somewhat similar to that produced by brefeldin A, and was also blocked by pre-treatment of cells with aluminum fluoride (AlF4-). These results suggest two sites in the endocytic pathway where PI-3 kinase activity may be required: (a) to sort PDGF receptors from peripheral compartments to the lysosomal degradative pathway; and (b) to regulate the structure of endosomes containing lysosomally directed and recycling molecules. This latter function could be mediated through the activation of AlFt4-)-sensitive GTP-binding proteins downstream of PI-3 kinase.
All-semiconductor room-temperature terahertz time domain spectrometer (2008)

We report what we believe to be the first demonstration of an all-semiconductor room-temperature terahertz time domain spectrometer. An optical Stark mode-locked vertical-external-cavity surface-emitting laser with 480 fs pulses at 1044 nm was used to illuminate low-temperature-grown photoconductive antennae with 5 mum-gap bow-tie-shaped electrodes. The coherently detected spectrum has a bandwidth close to 1 THz, in which water absorption lines at 0.555 and 0.751 THz can be resolved.
Gram-Negative Endocarditis Caused by Campylobacter fetus (1978)

Campylobacter fetus is a rare cause of endocarditis that is difficult to diagnose because of the fastidiousness of the organism. The source of infection is unknown and it may involve a normal or previously damaged aortic valve. The onset is insidious, and if there is a prior history of recent onset of fever, thrombophlebitis, and diarrhea, infection caused by this organism should be considered. Echocardiography may be useful. The organism is sensitive to a variety of antibiotics, including the combination of penicillin and streptomycin. The prognosis and survival are good.
Test and simulation of dynamic phase compensation from Mita-Teknik A/S (2004)

This report describes the test of a dynamic phase compensation unit or a wind turbine with directly connected induction generators. The compensation unit is based on thyristor switched capacitors, where conventional wind turbine compensations use mechanical contactors to switch the capacitors. The influence on power quality analysed, and influence on component lifetime is discussed. Besides, simulation models in Matlab/Simulink are presented, including a flickermeter model.
A method of reliability assessment on creep corrosion for immersion silver finished PCBs (2009)

This study focuses on a method of reliability assessment for creep corrosion on immersion silver-finished PCBs utilizing the mixed flow gas (MFG) test and clay test. Four kinds of locations were defined to conveniently describe the location from which the dendrite corrosion products were growing: IL refers to the location that corrosion products grew from a hole or pad edge with solder mask; IIL refers to the location that corrosion products grew from a hole or pad edge without solder mask; IIIL refers to the location that corrosion products grew on a hole or pad; and IVL refers to the location that corrosion products grew from solder mask. The IL dendrite corrosion product is a key factor to result in a short circuit. It is better to use the maximum length of the IL dendrite corrosion products as an assessment parameter. The failure criterion can be the distance (or half the distance) between the edges of two holes (or pads) or from one hole to another pad. The regression equation of the maximum length of the IL dendrite corrosion products and time can be used to predict remaining life. IVL dendrite corrosion products are potentially dangerous to result in a short circuit. The growth rate of corrosion products, which refers to the length that the corrosion products grow per unit of time, can also be an assessment parameter to describe the growth features of corrosion products. The thickness gain of copper for monitoring corrosion rate can be measured by cross-section method. Two cases show that the thickness gains conform to lognormal distribution.
Brain Representations of Affective Valence and Intensity in Sustained Pleasure and Pain (2023)

ABSTRACT Pleasure and pain are two opposites that compete and influence each other, implying the existence of brain systems that integrate them to generate modality-general affective experiences. Here, we examined the brain’s general affective codes (i.e., affective valence and intensity) across sustained pleasure and pain through an fMRI experiment ( n = 58). We found that the distinct sub-populations of voxels within the ventromedial and lateral prefrontal cortices, the orbitofrontal cortex, the anterior insula, and the amygdala were involved in decoding affective valence versus intensity, which was replicated in an independent test dataset ( n = 62). The affective valence and intensity models were connected to distinct large-scale brain networks—the intensity model to the ventral attention network and the valence model to the limbic and default mode networks. Overall, this study identified the brain representations of affective valence and intensity across pleasure and pain, promoting the systems-level understanding of human affective experiences.
A Parallel Method for Texture Reconstruction in Large-Scale 3D Automatic Modeling Based on Oblique Photography (2022)

Common methods of texture reconstruction first build a visual list for each triangular face, and then select the best image for each triangular face based on the graph-cut method. These methods have problems such as high memory consumption, and difficulties in large-area texture reconstruction. Hence, this paper proposes a parallel method for texture reconstruction in large-scale 3D automatic modeling. First, the hierarchical relationships between the texture reconstruction are calculated in accordance with the adjacency relationships between partitioning cells. Second, building contours are extracted based on the 3D mesh model, the tiles are divided into two categories (occlusion and non-occlusion), and the incorrect occlusion relationship is restored based on the occluded tiles. Then, the graph-cut algorithm is constructed to select the best-view label. Finally, the jagged labels between adjacent labels are smoothed to alleviate the problem of texture seams. Oblique photography data from an area of 10 km2 in Dongying, Shandong were used for validation. The experimental results reveal the following: (i) concerning reconstruction efficiency, the Waechter method can perform texture reconstruction only in a small area, whereas with the proposed method, the size of the reconstruction area is not restricted. The memory consumption is improved by factors of approximately 2–13. (ii) Concerning reconstruction results, the Waechter method incorrectly reconstructs the textures of partially occluded regions at the tile edges, while the proposed method can reconstruct the textures correctly. (iii) Compared to the Waechter method, the proposed approach has a 30% lower reduction in the number of texture fragments.