gebhart/patrepeval huggingface dataset:
Perspectives on the mechanism of pyroptosis after intracerebral hemorrhage (2022)

Intracerebral hemorrhage (ICH) is a highly harmful neurological disorder with high rates of mortality, disability, and recurrence. However, effective therapies are not currently available. Secondary immune injury and cell death are the leading causes of brain injury and a poor prognosis. Pyroptosis is a recently discovered form of programmed cell death that differs from apoptosis and necrosis and is mediated by gasdermin proteins. Pyroptosis is caused by multiple pathways that eventually form pores in the cell membrane, facilitating the release of inflammatory substances and causing the cell to rupture and die. Pyroptosis occurs in neurons, glial cells, and endothelial cells after ICH. Furthermore, pyroptosis causes cell death and releases inflammatory factors such as interleukin (IL)-1β and IL-18, leading to a secondary immune-inflammatory response and further brain damage. The NOD-like receptor protein 3 (NLRP3)/caspase-1/gasdermin D (GSDMD) pathway plays the most critical role in pyroptosis after ICH. Pyroptosis can be inhibited by directly targeting NLRP3 or its upstream molecules, or directly interfering with caspase-1 expression and GSDMD formation, thus significantly improving the prognosis of ICH. The present review discusses key pathological pathways and regulatory mechanisms of pyroptosis after ICH and suggests possible intervention strategies to mitigate pyroptosis and brain dysfunction after ICH.
Nondestructive Defect Characterization of Saw-Damage-Etched Multicrystalline Silicon Wafers Using Scanning Electron Acoustic Microscopy (2012)

Defects in multicrystalline silicon wafers after saw-damage etch (SDE) for different etch durations are characterized nondestructively using scanning electron acoustic microcopy (SEAM). SEAM is shown to be able to detect both surface and subsurface defects, as well as crystallographic imperfections such as grain boundaries in mc-Si wafers. The capabilities of the SEAM imaging are further extended for investigations of the structural properties of the saw-damage-induced defects and optimization of the SDE process. It is established that SEAM could be effective in determining the optimal SDE etch duration required for the minimization or complete removal of the saw-damage layer. In addition, it also confirms that the SDE process itself does not create new line-like defects.
Peri-Implant Sulcus Fluid (PISF) Matrix Metalloproteinase (MMP) -8 Levels in Peri-Implantitis (2016)

MMP-8 levels increase in peri-implantitis affected implants both in non-periodontitis and periodontitis patients, but levels still after treatment of the condition reflect intensified host response around implants and indicate challenges of controlling peri-Implantitis with any treatment modality.
Figure S1 Full Protocol from Randomized Phase II Trial of Carboplatin–Paclitaxel Compared with Carboplatin–Paclitaxel–Trastuzumab in Advanced (Stage III–IV) or Recurrent Uterine Serous Carcinomas that Overexpress Her2/Neu (NCT01367002): Updated Overall Survival Analysis (2023)

&lt;p&gt;Full Protocol&lt;/p&gt;
ChemInform Abstract: Synthesis, Molecular Modeling, 2‐D NMR, and Biological Evaluation of ILV Mimics as Potential Modulators of Protein Kinase C. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
MORBIDITY AND MORTALITY OF HAWAIIAN GEESE (BRANTA SANDVICENSIS) AND LAYSAN ALBATROSS (PHOEBASTRIA IMMUTABILIS) ASSOCIATED WITH RETICULOENDOTHELIOSIS VIRUS (2022)

Only one virus, Avipox, has been documented previously in wild birds in Hawaii. Using immunohistochemistry and PCR, we found that two native threatened Hawaiian Geese (Branta sandvicensis), one with multicentric histiocytoma and the other with toxoplasmosis, and one Laysan Albatross (Phoebastria immutabilis) with avian pox were infected with reticuloendotheliosis virus (REV). The virus was isolated from one of the geese by cell culture. Surveys of other Hawaiian geese with various pathologies, avian pox cases, and pox viral isolates using PCR failed to reveal REV, suggesting that the virus is uncommon, at least in samples examined. The full genome of the Gag, Pol, and Env genes were sequenced for all three infected birds and revealed geographic divergence of the Pol gene, suggesting it to be under strong selective pressure. Our finding of REV in Hawaii makes this only the second virus documented in native Hawaiian birds associated with pathology. Moreover, the presence of REV in a pelagic seabird is unusual. Future surveys should seek the reservoir of the virus in efforts to trace its origins.
Myeloid Acyl-CoA:Cholesterol Acyltransferase 1 Deficiency Reduces Lesion Macrophage Content and Suppresses Atherosclerosis Progression (2016)

Acyl-CoA:cholesterol acyltransferase 1 (Acat1) converts cellular cholesterol to cholesteryl esters and is considered a drug target for treating atherosclerosis. However, in mouse models for atherosclerosis, global Acat1 knockout (Acat1(-/-)) did not prevent lesion development. Acat1(-/-) increased apoptosis within lesions and led to several additional undesirable phenotypes, including hair loss, dry eye, leukocytosis, xanthomatosis, and a reduced life span. To determine the roles of Acat1 in monocytes/macrophages in atherosclerosis, we produced a myeloid-specific Acat1 knockout (Acat1(-M/-M)) mouse and showed that, in the Apoe knockout (Apoe(-/-)) mouse model for atherosclerosis, Acat1(-M/-M) decreased the plaque area and reduced lesion size without causing leukocytosis, dry eye, hair loss, or a reduced life span. Acat1(-M/-M) enhanced xanthomatosis in apoe(-/-) mice, a skin disease that is not associated with diet-induced atherosclerosis in humans. Analyses of atherosclerotic lesions showed that Acat1(-M/-M) reduced macrophage numbers and diminished the cholesterol and cholesteryl ester load without causing detectable apoptotic cell death. Leukocyte migration analysis in vivo showed that Acat1(-M/-M) caused much fewer leukocytes to appear at the activated endothelium. Studies in inflammatory (Ly6C(hi)-positive) monocytes and in cultured macrophages showed that inhibiting ACAT1 by gene knockout or by pharmacological inhibition caused a significant decrease in integrin β 1 (CD29) expression in activated monocytes/macrophages. The sparse presence of lesion macrophages without Acat1 can therefore, in part, be attributed to decreased interaction between inflammatory monocytes/macrophages lacking Acat1 and the activated endothelium. We conclude that targeting ACAT1 in a myeloid cell lineage suppresses atherosclerosis progression while avoiding many of the undesirable side effects caused by global Acat1 inhibition.
Eavesdropping on the Arctic: Automated bioacoustics reveal dynamics in songbird breeding phenology (2018)

Bioacoustic networks could vastly expand the coverage of wildlife monitoring to complement satellite observations of climate and vegetation. This approach would enable global-scale understanding of how climate change influences phenomena such as migratory timing of avian species. The enormous data sets that autonomous recorders typically generate demand automated analyses that remain largely undeveloped. We devised automated signal processing and machine learning approaches to estimate dates on which songbird communities arrived at arctic breeding grounds. Acoustically estimated dates agreed well with those determined via traditional surveys and were strongly related to the landscape's snow-free dates. We found that environmental conditions heavily influenced daily variation in songbird vocal activity, especially before egg laying. Our novel approaches demonstrate that variation in avian migratory arrival can be detected autonomously. Large-scale deployment of this innovation in wildlife monitoring would enable the coverage necessary to assess and forecast changes in bird migration in the face of climate change.
Quantitative Aspect of Leucophyllum frutescens Fraction before and after Encapsulation in Polymeric Nanoparticles (2017)

The interest on plants has been focalized due to their biological activities. Extracts or fractions from plants in biodegradable polymeric nanoparticles (NP) provide many advantages on application studies. The encapsulation of the extract or fraction in NP is determined for the establishment of the test dose. HPLC method is an alternative to calculate this parameter. An analytical method based on HPLC for quantification of a hexane fraction from <i>L. frutescens</i> was developed and validated according to ICH. Different concentrations of the hexane fraction from leaves (HFL) were prepared (100-600 <i>μ</i>g/mL). Linearity, limit of detection, limit of quantification, and intra- and interday precision parameters were determined. HFL was encapsulated by nanoprecipitation technique and analyzed by HPLC for quantitative aspect. The method was linear and precise for the quantification of the HFL components. NP size was 190 nm with homogeneous size distribution. Through validation method, it was determined that the encapsulation of components (1), (2), (3), and (4) was 44, 74, 86, and 97%, respectively. A simple, repeatable, and reproducible methodology was developed for the propose of quantifying the components of a vegetable material loaded in NP, using as a model the hexane fraction of <i>L. frutescens</i> leaves.
Early Transcription Controls after Induction of Prophage (1970)

Temperate bacteriophage λ is one of the viruses most extensively studied both genetically and biochemically (Dove, 1968; Echols and Joyner, 1968; Radding, 1969; Calendar, 1970). The λ chromosome can code for about 40 or 50 average size proteins. More than 30 genes have been identified, of which about 20 are involved in post-replicative functions such as lysis (genes S and R), head formation (genes A through F) and tail formation (genes Z through J). All these late genes except for S and R are localized on the GC rich half of the chromosome (Fig. 1). Early genes, in contrast, are clustered on the AT rich half. Besides replication genes (O and P) and several genes involved in integration, excision and recombination (β, exo, xis, int, and perhaps some genes from the b2 region) the early region includes at least six regulatory genes: CI CII, CIII, cro, N, and Q. Viral...
Secret Sharing and Error Correcting (2009)

The goal of this paper is to present a survey on certain recent developments in the theory of unconditional Multi Party Computation (MPC) and Secret Sharing Schemes (SSS) related to Error Correcting Codes.
Optimizing power consumption in networked devices (2012)

As networked devices have become less expensive and more capable, the market for these devices has exploded. Further, users are demanding greater speeds, better performance, and seamless operation from these devices. User demand for better QoS and better device interoperability is driving the development of devices with multiple network interfaces, and standards for integrating multiple interfaces into a single logical network. Proliferation of devices and multiple network interfaces means that power consumption at the networking layer becomes an increasingly relevant concern for device owners and operators. In this paper, we present methods and review approaches for reducing power consumption in four domains: in a single network interface in a single device; in a single network across all devices sharing that network; in a single device with multiple network interfaces connected to different media types; and across the union of devices with multiple network interfaces connected to different media types.
Synthesis of real-world driving cycles using stochastic process and statistical methodology (2011)

This paper proposes a procedure for synthesising real-world driving cycles to reproduce naturalistic driving patterns for arbitrary driving distances. The procedure combines stochastic processes and statistical methodologies. Vehicle dynamics equations are investigated and two states, velocity and acceleration, are selected to represent real-world driving behaviour with the Markov chain. Then, the information is extracted from the naturalistic driving data measured in Southeast Michigan in a form of transition probability matrices (TPMs). Statistical methods are utilised to guarantee the representativeness of synthesised cycles. Results demonstrate the ability to capture features of a whole category of naturalistic data with a single synthetic cycle.
High-Throughput Five Minute Microwave Accelerated Glycosylation Approach to the Synthesis of Nucleoside Libraries (2006)

The Vorbrüggen glycosylation reaction was adapted into a one-step 5 min/130 degrees C microwave assisted reaction. Triethanolamine in acetontrile containing 2% water was determined to be optimal for the neutralization of trimethylsilyl triflate allowing for direct MPLC purification of the reaction mixture. When coupled with a NH3/methanol deprotection reaction, a high-throughput method of nucleoside library synthesis was enabled. The method was demonstrated by examining the ribosylation of 48 nitrogen containing heteroaromatic bases that included 25 purines, four pyrazolopyrimidines, two 8-azapurines, one 2-azapurine, two imidazopyridines, two benzimidazoles, three imidazoles, three 1,2,4-triazoles, two pyrimidines, two 3-deazapyrimidines, one quinazolinedione, and one alloxazine. Of these, 32 yielded single regioisomer products, and six resulted in separable mixtures. Seven examples provided inseparable regioisomer mixtures of -two to three compounds (16 nucleosides), and three examples failed to yield isolable products. For the 45 single isomers isolated, the average two-step overall yield +/- SD was 26 +/- 16%, and the average purity +/- SD was 95 +/- 6%. A total of 58 different nucleosides were prepared of which 15 had not previously been accessed directly from glycosylation/deprotection of a readily available base.
Photophysical and Electrochemical Properties of New Bacteriochlorins and Characterization of Radical Cation and Radical Anion Species (2002)

The synthesis, photophysical, and photochemical properties of a series of stable bacteriochlorins containing a fused six-member anhydride or an imide ring are discussed. The Qy band (a1u → egx transition) in the near-infrared region (NIR) lies between 788 and 831 nm depending upon the macrocycle substituents. Compounds with such a long-wavelength absorption are highly promising for their potential use in photodynamic therapy. Fluorescence maxima are also observed in the long-wavelength region of the spectrum, between 804 and 842 nm, and have lifetimes between 1.1 and 1.4 ns. The phosphorescence maxima are red-shifted to 840−870 nm. The triplet−triplet transient absorption spectra are observed to have maxima between 570 and 640 nm with lifetimes between 72 and 150 μs. The triplet excited states are efficiently quenched by oxygen to produce singlet oxygen. The quantum yields of the generated singlet oxygen were determined to be in the range of 0.33−0.55. The bacteriochlorin derivatives are easy to oxidize by one electron, and reversible half-wave potentials range between 0.65 and 0.82 V vs SCE in benzonitrile containing 0.1 M tetra-n-butylammonium perchlorate (TBAP). The second oxidation is irreversible and occurs at a rather constant potential of 1.17−1.22 V independent of the macrocycle substituents. The bacteriochlorin derivatives are also easy to reduce, and the reversible first and second one-electron reduction potentials range between −0.53 and −0.80 V and between −0.95 and −1.28 V vs SCE, respectively. Spectroelectrochemical measurements reveal the expected π radical cation and π radical anion marker bands of the bacteriochlorin derivatives. The electron spin resonance (ESR) spectra of the radical cations and radical anions produced by the chemical oxidation and reduction are reported, and the experimental and calculated spin densities are compared to each other.
Assignment of side‐chain conformation using adiabatic energy mapping, free energy perturbation, and molecular dynamic simulations (1999)

NMR spectroscopic analysis of the C-terminal Kunitz domain fragment (alpha3(VI)) from the human alpha3-chain of type VI collagen has revealed that the side chain of Trp21 exists in two unequally populated conformations. The major conformation (M) is identical to the conformation observed in the X-ray crystallographic structure, while the minor conformation (m) cannot structurally be resolved in detail by NMR due to insufficient NOE data. In the present study, we have applied: (1) rigid and adiabatic mapping, (2) free energy simulations, and (3) molecular dynamic simulations to elucidate the structure of the m conformer and to provide a possible pathway of the Trp21 side chain between the two conformers. Adiabatic energy mapping of conformations of the Trp21 side chain obtained by energy minimization identified two energy minima: One corresponding to the conformation of Trp21 observed in the X-ray crystallographic structure and solution structure of alpha3(VI) (the M conformation) and the second corresponding to the m conformation predicted by NMR spectroscopy. A transition pathway between the M and m conformation is suggested. The free-energy difference between the two conformers obtained by the thermodynamic integration method is calculated to 1.77+/-0.7 kcal/mol in favor of the M form, which is in good agreement with NMR results. Structural and dynamic properties of the major and minor conformers of the alpha3(VI) molecule were investigated by molecular dynamic. Essential dynamics analysis of the two resulting 800 ps trajectories reveals that when going from the M to the m conformation only small, localized changes in the protein structure are induced. However, notable differences are observed in the mobility of the binding loop (residues Thr13-Ile18), which is more flexible in the m conformation than in the M conformation. This suggests that the reorientation of Trp2 might influence the inhibitory activity against trypsin, despite the relative large distance between the binding loop and Trp21.
Interleukin-4 and interferon-γ discordantly regulate collagen biosynthesis by functionally distinct lung fibroblast subsets (1996)

Pulmonary fibrosis is a potentially fatal consequence of treatments for malignancy and is an increasing problem in bone marrow transplant patients and in cases of allogenic lung transplant. The fibrotic response is characterized by increases in lung fibroblast number and collagen synthesis. This laboratory previously isolated stable, functionally distinct, murine lung fibroblast subsets (Thy-1+ and Thy-1-) to study the contribution of fibroblast subpopulations in lung fibrosis. The fibroblast fibrotic response may be induced by cytokines secreted by infiltrating cells such as T lymphocytes and mast cells. In the current study two key regulatory cytokines, interferon-gamma (IFN-gamma) and interleukin-4 (IL-4), were investigated for their effects on the collagen synthesis of murine lung fibroblast subsets. IL-4 and IFN-gamma are putatively characterized as fibrogenic and anti-fibrogenic cytokines, respectively, and are found in repairing lung tissue. Stimulation with recombinant IL-4 induced a100% increase in total collagen production only by Thy-1+ fibroblasts. Types I and III collagen mRNA were increased in the Thy-1+ fibroblasts, unlike the Thy-1- subset. In contrast, IFN-gamma decreased constitutive collagen production by more than 50% in Thy-1+ and Thy-1- fibroblasts. Interestingly, the two subsets utilized their collagen production machinery (collagenase, tissue inhibitors of metalloproteinases) differently to further regulate collagen turnover in response to IL-4 and IFN-gamma. Overall, our data support the hypothesis that IL-4 is fibrogenic and IFN-gamma is anti-fibrogenic. Moreover, selective expansion of IL-4 responsive fibroblasts (e.g., Thy-1+) may be important in the transition from repair to chronic fibrosis. In addition, these data suggest that an inflammatory response dominated by IL-4-producing Th2 lymphocytes and/or mast cells will promote fibrosis development.
Cytochemical and biochemical evidence of cathepsin B in malignant, transformed and normal breast epithelial cells (1987)

Human breast cancer cell lines, as well as transformed mammary epithelial cells (HBL-100) and growth-stimulated normal breast epithelial cells showed positive cytochemical reaction with the proteinase substrate 2-(N-benzyloxycarbonyl-L-arginyl-L-arginylamido)-4-methoxynapht halene, in the presence of 5-nitrosalicylaldehyde. The reaction product, small fluorescent granules, was distributed throughout the cytoplasm, in the perinuclear zone, in some cytoplasmic projections, and at the cell surface. Using a panel of various proteinase inhibitors, we found that the formation of the reaction product was an enzymic function of a cysteine proteinase. Using the substrate 7-(N-benzyloxycarbonyl-L-arginyl-L-arginylamido)-4-methylcoumarin, we evaluated some biochemical properties of the cysteine proteinase, including pH-activity profile, pH stability, apparent relative molecular mass and sensitivity toward various proteinase inhibitors. We found that the proteinase from the studied breast epithelial cells exhibited characteristics of a mature form of cathepsin B. Taken together, the cytochemical and biochemical data provide evidence that human breast epithelial cells of cancer origin, as well as in the transformed or growth-stimulated state express active cathepsin B and compartmentalize it into specific subcellular sites.
Potent antiviral effect of reverset in HIV-1-infected adults following a single oral dose. (2004)

Reverset (2',3'-didehydro-2',3'-dideoxy-5-fluorocytidine, RVT) is a potent inhibitor of HIV-1 replication in cell culture, with a 90% effective concentration at or below 1 microM. In vitro, RVT retains its activity against isolates harbouring mutations in the reverse transcriptase (RT) gene that otherwise confer resistance to lamivudine and/or zidovudine. The pharmacokinetics and safety of single oral doses of RVT (10-200 mg) were evaluated in an initial Phase I clinical trial. The viral load changes were determined on 18 HIV-1-infected antiretroviral therapy-naive subjects that were randomized into three cohorts, each cohort consisting of three study periods. The subjects received up to two oral doses of active drug and one placebo dose with a 1-week washout period separating the three study periods. Quantification of viral RNA was performed on the pre-dose, 12, 24 and 48 h post-dose plasma samples. A single oral dose of RVT to antiretroviral-naive subjects significantly reduced plasma viral load by 0.45 +/- 0.10 log10 copies/ml (P=0.0003). A mean drop of 0.37 +/- 0.12 log10 copies/ml (P=0.001) was obtained at the lowest dose of 10 mg. Sequence analysis of the HIV-1 RT gene performed before and after RVT dosing detected no genotypic changes in this short-term study. The viral RT gene of one subject had at predose the following genotype: L41 + N103 + C181 + W210 + D215, indicating prior exposure to zidovudine and non-nucleoside analogues, and anticipating high-level resistance against these agents. A single 10 mg RVT dose resulted in a viral load drop of 0.61 +/- 0.05 log10 providing evidence that a viral strain with the indicated genotype is susceptible to RVT.