gebhart/patrepeval huggingface dataset:
Lysosomal killing of Mycobacterium mediated by ubiquitin-derived peptides is enhanced by autophagy (2007)

Mycobacterium tuberculosis parasitizes resting macrophages yet is killed by activated macrophages through both oxidative and nonoxidative mechanisms. Nonoxidative mechanisms are linked to the maturation of the bacteria-containing phagosome into an acidified, hydrolytically active compartment. We describe here a mechanism for killing Mycobacteria in the lysosomal compartment through the activity of peptides generated by the hydrolysis of ubiquitin. The induction of autophagy in infected macrophages enhanced the delivery of ubiquitin conjugates to the lysosome and increased the bactericidal capacity of the lysosomal soluble fraction. The accumulation of ubiquitinated proteins in the autophagolysosome provides one possible mechanism behind the antimicrobial activities observed for a range of pathogens in autophagous host cells.
Relationship between semen quality and seminal plasma total carnitine in infertile men (2003)

This study was designed to determine any correlation between infertility and semen quality with concentrations of total carnitine in human seminal plasma. Seminal plasma total carnitine concentrations were determined in 79 men. The seminal plasma of 65 infertile men and 14 men as a control group with proved fertility were investigated. The concentrations of total carnitine were reduced significantly in the infertile group compared to the control group (31.52 +/- 20.77 vs. 45.52 +/- 10.73 mg/l, P<0.05). The 65 infertile men were divided into five groups according to their sperm analysis: normospermia (n=42), oligospermia (n=23), asthenospermia (n=40), teratospermia (n=44) and oligoasthenospermia (n=10). Total seminal plasma carnitine concentration differed significantly between controls and the patient groups (P<0.05). There was a statistically significant positive correlation between seminal plasma total carnitine concentration with total sperm count and the percentage of normal forms (P<0.05 and P<0.01, respectively). Total carnitine concentration was found to be low in the asthenospermia group when compared with the group of patients, whose total motile sperm percentage was 51 (P<0.05). These findings suggest that the determination of seminal carnitine levels may be a useful test in evaluation of male infertility.
Vegetable Oils as Lubricants, Hydraulic Fluids, and Inks (2005)

Abstract Environmental concerns over the use of petroleum‐based products in various industries, such as forestry, farming, mining, boating, and others, has led to increased interest in the use of environmentally friendly fluids. The beneficial aspects of vegetable oils as lubricants are mainly their biodegradability and nontoxicity, which are not exhibited by conventional mineral base oils. Further, vegetable oils have superior solubilizing power for contaminants and additive molecules compared with mineral base fluids. Certain performance limitations of vegetable oil basestocks are poor oxidative stability due to bis‐allylic protons in the fatty acyl chain, deposit forming tendency, low‐temperature solidification, and low hydrolytic stability. Current research efforts are directed toward improving the thermal and low‐temperature stability of vegetable oils by chemical modification, blending with functional fluids and additive response studies.
Massive MIMO for 5G (2015)

• Massive MIMO has Many Extraordinary Benefits • High spectral efficiency: >20x gains over IMT-Advanced are foreseen • High SE per cell, but modest per user • Important: Fractional pilot reuse, pilots take up large part of coherence interval • High energy efficiency: Tens of Mbit/Joule are foreseen • Reduced transmit power per user and antenna, maybe not per cell • Circuit power dominates power consumption in urban scenarios • Important: Interference control, sharing circuit power between users • High hardware efficiency: High-grade hardware is not needed • Variance of distortion noise at BS can scale with number of antennas • Important: Quality of user device is the limiting factor
On Lu Ci (2003)

The conception Lu Ci given by Luo Di tends to exclude the various songs in music and literature history, thus making us more clearly aware of the songs' nature. Lii Ci refers to those rhythm song works or those possessing the rhythm rules. Songs since the Tang and Song Dynasty are called Lii Ci. One may think that it develops from a rhythm verse in the Tang Dynasty if viewing it only from a national literature form and not regarding it as musical literature, thus neglecting the certain cultural conditian of this song form' s being and even hiding its art' s quality. The appearance of Lii Ci doesn' t occur with the development of recent poem rhythm or the simple change of sentence structure. It's a new form musical literature with the popularity of New Yan - Yue in the Sui and Tang Dynasty. Songs in the Tang and Song Dynasty were performed according to notes. This doesn't weaken the original music with the appearance of Lii Ci, but in turn it brings Lii Ci music elements. The relation letween Lii Ci and music is not only a combination of songs and music system, but also a mixture of their forms, thus Lii Ci is the supreme state of China music literature.
Myocyte Turnover in the Aging Human Heart (2010)

The human heart is a highly dynamic organ regulated by a pool of resident hCSCs that modulate cardiac homeostasis and condition organ aging.
Ibrutinib-induced pneumonitis in patients with chronic lymphocytic leukemia (2015)

To the editor:

Chronic lymphocytic leukemia (CLL) is a B-cell lymphoproliferative disorder partly dependent on the B-cell receptor (BCR) signaling pathway. The novel BCR signal transduction inhibitor ibrutinib has emerged as an effective therapeutic agent for CLL.[1][1] Ibrutinib covalently binds
X-Linked Inhibitor of Apoptosis Protein-Mediated Attenuation of Apoptosis, Using a Novel Cardiac-Enhanced Adeno-Associated Viral Vector (2012)

Successful amelioration of cardiac dysfunction and heart failure through gene therapy approaches will require a transgene effective at attenuating myocardial injury, and subsequent remodeling, using an efficient and safe delivery vehicle. Our laboratory has established a well-curated, high-quality repository of human myocardial tissues that we use as a discovery engine to identify putative therapeutic transgene targets, as well as to better understand the molecular basis of human heart failure. By using this rare resource we were able to examine age- and sex-matched left ventricular samples from (1) end-stage failing human hearts and (2) nonfailing human hearts and were able to identify the X-linked inhibitor of apoptosis protein (XIAP) as a novel target for treating cardiac dysfunction. We demonstrate that XIAP is diminished in failing human hearts, indicating that this potent inhibitor of apoptosis may be central in protecting the human heart from cellular injury culminating in heart failure. Efforts to ameliorate heart failure through delivery of XIAP compelled the design of a novel adeno-associated viral (AAV) vector, termed SASTG, that achieves highly efficient transduction in mouse heart and in cultured neonatal rat cardiomyocytes. Increased XIAP expression achieved with the SASTG vector inhibits caspase-3/7 activity in neonatal cardiomyocytes after induction of apoptosis through three common cardiac stresses: protein kinase C-γ inhibition, hypoxia, or β-adrenergic receptor agonist. These studies demonstrate the potential benefit of XIAP to correct heart failure after highly efficient delivery to the heart with the rationally designed SASTG AAV vector.
Both the Lyt-2+ and L3T4+ T cell subsets are required for the transfer of diabetes in nonobese diabetic mice. (1988)

The nonobese diabetic mouse is a model of spontaneous type I diabetes mellitus. It is possible to induce diabetes in young, irradiated nonobese diabetic mice by using adoptive transfer of splenocytes or splenic T cells obtained from diabetic donors. This study demonstrates that the induction of diabetes in the adoptive transfer system is dependent on both the L3T4+ and Lyt-2+ subsets of T cells. Neither of these T cell subsets alone mediates the development of severe insulitis or diabetes when adoptively transferred to young, irradiated recipients. In addition, we show that both the L3T4+ and Lyt-2+ subsets must be obtained from diabetic donors in order to transfer diabetes; neither subset can be replaced with cells obtained from young, nondiabetic donors.
Inhibiting Ras prenylation increases the radiosensitivity of human tumor cell lines with activating mutations of ras oncogenes. (1998)

The influence of activated ras oncogenes on the sensitivity of human tumor cells to killing by radiation has been an unresolved question in radiobiology. We have examined this question by measuring the radiation sensitivity of human tumor cell lines with oncogenic mutations in their H- or K-ras genes after treatment with prenyltransferase inhibitors that prevent the posttranslational modification of ras required for its activity. Using two measures of clonogenic survival, we have demonstrated radiosensitization in cell lines with oncogenic H-ras mutations or with oncogenic K-ras mutations when ras processing was inhibited by prenyltransferase inhibitor treatment. In contrast, the inhibition of ras processing in cell lines expressing wild-type ras had no effect on radiation-induced cell death. The prenyltransferase inhibitors themselves inhibited clonogenic survival in some cases, but this inhibition did not correlate with ras mutational status. Although treatment with prenyltransferase inhibitors and radiation resulted in a greater reduction of clonogenicity than either treatment alone in cells with wild-type ras, treatment with both agents had a synergistic effect on cell killing in tumor cells with ras mutations. Our results demonstrate that the inhibition of oncogenic ras activity in human tumor cells can reduce the radiation survival of these cells, suggesting that oncogenic ras can contribute to radiation resistance in human tumors. These results further demonstrate the potential of using prenyltransferase inhibitors in combination with radiotherapy in the treatment of human malignancies.
Optimization of temporal filters for constructing robust features in speech recognition (2006)

Linear discriminant analysis (LDA) has long been used to derive data-driven temporal filters in order to improve the robustness of speech features used in speech recognition. In this paper, we proposed the use of new optimization criteria of principal component analysis (PCA) and the minimum classification error (MCE) for constructing the temporal filters. Detailed comparative performance analysis for the features obtained using the three optimization criteria, LDA, PCA, and MCE, with various types of noise and a wide range of SNR values is presented. It was found that the new criteria lead to superior performance over the original MFCC features, just as LDA-derived filters can. In addition, the newly proposed MCE-derived filters can often do better than the LDA-derived filters. Also, it is shown that further performance improvements are achievable if any of these LDA/PCA/MCE-derived filters are integrated with the conventional approach of cepstral mean and variance normalization (CMVN). The performance improvements obtained in recognition experiments are further supported by analyses conducted using two different distance measures.
Complete dielectric isolation by highly selective and self-stopping formation of oxidized porous silicon (1983)

Complete dielectric isolation of silicon regions 45 μm wide for microcircuits on silicon substrates is demonstrated by selective formation of oxidized porous silicon in heavily doped n-type regions. Anodic etching of n-type silicon in a hydrofluoric acid electrolyte exhibits a concentration-dependent voltage threshold. This voltage dependence allows the porous silicon formation process to be selective to heavily doped regions and self-stopping on lightly doped regions. Rapid oxidation of this porous silicon yields an oxide with dielectric properties approaching those of standard thermally grown silicon oxides. This process is an improvement over previously reported processes utilizing porous silicon in that wider regions (up to 300 μm) are dielectrically isolated by an oxide whose thickness is controllable and uniform so that stress and wafer warpage are minimized.
Enhanced De Novo Neurogenesis and Dopaminergic Neurogenesis in the Substantia Nigra of 1‐Methyl‐4‐phyenyl‐1,2,3,6‐Tetrahydropyridine‐Induced Parkinson's Disease‐Like Mice (2006)

Research reports on de novo neurogenesis, particularly dopaminergic (DA) neurogenesis in the adult mammalian substantia nigra (SN), remain very controversial. For this reason, we used the nestin second intron enhancer-controlled LacZ reporter transgenic mouse model coupled with the 1-methyl-4-phyenyl-1,2,3,6-tetrahydropyridine (MPTP) lesion system to investigate whether there are neurogenesis and DA neurogenesis in the SN of the adult normal and Parkinson's disease (PD)-like mice. First, we demonstrated the presence of neural progenitor cells (NPCs), basal levels of neurogenesis, and DA neurogenesis in the normal adult mouse SN. Second, we showed that there is not only a significant increase in the number of NPCs but also a dramatic increase of neurogenesis from the NPCs in the SN and the midline region adjacent to the SN of the PD-like mice compared with that of normal controls. More importantly, we also demonstrated that there is an increase of DA neurogenesis in the SN of the MPTP-lesioned mice. Third, we showed that the increased DA neurogenesis in the MPTP-lesioned mice was derived from the NPCs and 5-bromodeoxyuridine-positive cells, suggesting that multiple stem cell lineages may contribute to the enhanced neurogenesis in the adult SN. Taken together, these results establish that there are basal levels, albeit low, and increased levels of de novo neurogenesis and DA neurogenesis in the SN of the adult normal and PD-like mice, respectively. The increased NPCs in the MPTP-lesioned mice further suggest that experimental approaches to promote de novo neurogenesis may provide an effective therapy for PD by functional replacement of degenerated DA neurons.
The Magnetic Properties and Structure of the Hemochromogens and Related Substances (1936)

In the course of a general study of the structure of hemoglobin and its derivatives we have investigated the magnetic properties of ferriheme, ferroheme, several hemochromogens and nickel protoporphyrin. The results of this investigation and their structural interpretation are discussed in the following paragraphs.
Image Quality Affects Macular and Retinal Nerve Fiber Layer Thickness Measurements on Fourier-Domain Optical Coherence Tomography (2011)

Image quality metrics should be considered when evaluating thickness measurements derived from Fourier-domain OCT devices.
Fucoidan-Dependent Conformational Changes in Annexin II Tetramer (2000)

Fucoidan, a sulfated fucopolysaccharide, mimics the fucosylated glycans of glycoproteins and has therefore been used as a probe for investigating the role of membrane polysaccharides in cell-cell adhesion. In the present report we have characterized the interaction of fucoidan with the Ca(2+)- and phospholipid-binding protein annexin II tetramer (AIIt). AIIt bound to fucoidan with an apparent K(d) of 1.24 +/- 0.69 nM (mean +/- SD, n = 3) with a stoichiometry of 0.010 +/- 0.001 mol of fucoidan/mol of AIIt (mean +/- SD, n = 3). The binding of fucoidan to AIIt was Ca(2+)-independent. Furthermore, in the presence but not the absence of Ca(2+), the binding of fucoidan to AIIt caused a decrease in the alpha-helical content from 32% to 7%. A peptide corresponding to a region of the p36 subunit of AIIt, F(306)-S(313), which contains a Cardin-Weintraub consensus sequence for heparin binding, was shown to undergo a conformational change upon fucoidan binding. This suggests that heparin and fucoidan bound to this region of AIIt. The binding of fucoidan but not heparin by AIIt also inhibited the ability of AIIt to bind to and aggregate phospholipid liposomes. These results suggest that the binding of AIIt to the carbohydrate conjugates of certain membrane glycoproteins may have profound effects on the structure and biological activity of AIIt.
Electrostatic influence of local cysteine environments on disulfide exchange kinetics (1981)

The ionic strength dependence of the bimolecular rate constant for reaction of the negative disulfide 5,5'-dithiobis (2-nitrobenzoic acid) with cysteines in fragments of naturally occurring proteins was determined by stopped-flow spectroscopy. The Debye-Hückel relationship was applied to determine the effective charge at the cysteine and thereby determine the extent to which nearby neighbors in the primary sequence influence the kinetics. Corrections for the secondary salt effect on cysteine pKs were determined by direct spectrometric pH titration of sulfhydryl groups or by observation of the ionic strength dependence of kinetics of cysteine reaction with the neutral disulfide 2,2'-dithiodipyridine. Quantitative expressions was verified by model studies with N-acetyl-cystein. At ionic strengths equal to or greater than 20 mM, the net charge at the polypeptide cysteine site is the sum of the single negative charge of the thiolate anion and the charges of the amino acids immediately preceding and following the cysteine in the primary sequence. At lower ionic strengths, more distant residues influence kinetics. At pH 7.0, 23 degree C, and an ionic strength of 20 mM, rate constants for reaction of the negative disulfide with a cysteine having two positive neighbors, one positive and one neutral neighbor, or two neutral neighbors are 132000, 3350, and 367 s-1 M-1, respectively. This corresponds to a contribution to the activation energy of 0.65- 1.1 kcal/mol per ion pair involved in collision between the cysteine and disulfide regions. The results permit the estimation that cysteine local environments may provide a means of achieving a 10(6)-fold range in rate constants in disulfide exchange reactions in random-coil proteins. This range may prove useful in developing strategies for directing disulfide pairing in synthetic proteins.
Ueber neue organische Phosphorverbindungen II. Phosphazine (1919)

Fur die neuen Verbindungen schlagen wir den Namen
The Corynebacterium glutamicum aecD gene encodes a C-S lyase with alpha, beta-elimination activity that degrades aminoethylcysteine (1992)

S-(beta-Aminoethyl)-cysteine (AEC) resistance was achieved in Corynebacterium glutamicum by cloning a chromosomal 1.5-kb EcoRV-BglII DNA fragment on a multicopy plasmid. DNA sequence analysis of the 1.5-kb DNA fragment revealed an open reading frame (ORF326) which represents the AEC resistance gene, designated aecD. The aecD gene directs the synthesis of a 36-kDa protein which was visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The aecD gene is a nonessential gene and mediates AEC resistance only in an amplified state. C. glutamicum strains harboring an amplified aecD gene can utilize AEC as an alternative nitrogen source, indicating that the AEC resistance mechanism is due to AEC degradation. Since the AEC degradation products analyzed by high-pressure liquid chromatography were found to be pyruvate and aminoethanethiol (cysteamine), it was concluded that the aecD gene encodes a C-S lyase with alpha, beta-elimination activity. Besides AEC, the C-S lyase was also able to use cysteine, cystine, and cystathionine as substrates.
The Deubiquitylation Activity of Ubp8 Is Dependent upon Sgf11 and Its Association with the SAGA Complex (2005)

Covalent modifications of the histone tails and the cross talk between these modifications are hallmark features of gene regulation. The SAGA histone acetyltransferase complex is one of the most well-characterized complexes involved in these covalent modifications. The recent finding that the removal of the ubiquitin group from H2B is performed by a component of SAGA, Ubp8, is intriguing as it assigns two posttranslation modification processes to one complex. In this work, we characterize the association of Ubp8 with SAGA and the effect that acetylation and deubiquitylation have on one another in vitro and in vivo. We found not only that Ubp8 is a part of the SAGA complex, but also that its deubiquitylation activity requires Ubp8's association with SAGA. Furthermore, we found that the Ubp8 association with SAGA requires Sgf11 and that this requirement is reciprocal. We also found that the acetylation and deubiquitylation activities of SAGA are independent of one another. However, we found that preacetylating histone H2B inhibited subsequent deubiquitylation. Additionally, we found that increasing the ubiquitylation state of H2B inhibited the expression of the ARG1 gene, whose repression was previously shown to require the RAD6 ubiquitin ligase. Taken together, these data indicate that the expression of some genes, including ARG1, is regulated by a balance of histone H2B ubiquitylation in the cell.
CD38 functions are regulated through an internalization step. (1998)

The endocytosis of the human CD38 molecule has been investigated in normal lymphocytes and in a number of leukemia- and lymphoma-derived cell lines. CD38 internalization was followed using radioiodinated Abs in an acidic elution endocytosis assay to monitor the effects of cross-linking on internalization processes and to quantify the ratio of the internalized molecule. Second, conventional, confocal, and electron microscopies were used to evaluate the morphologic effects induced by ligation of the molecule with Abs mimicking the natural ligand(s). The results demonstrated that internalization is a reproducible phenomenon following CD38 ligation with both agonistic and nonagonistic specific Abs and involving only a fraction of the entire amount of the surface molecule. It is independent from signal transduction as can be inferred by the observation that 1) both agonistic and non agonistic Abs are effective and 2) the dynamic of internalization is much slower than that of cellular signaling. Morphologic studies demonstrated that endocytosis induced as a result of CD38 ligation presents a very specific pathway consisting of subcellular organelles fundamental to the processing of the complex. Our data indicate that down-regulation by endocytosis may be, in parallel with shedding, a regulatory element in activation and adhesion processes mediated by CD38. However, internalization seems not to be a key step in triggering intracellular signaling; more likely, it is a negative feedback control mechanism which interrupts signal transduction or cell-cell cross-talks mediated by membrane CD38.
Reduction of microtrenching and island formation in oxide plasma etching by employing electron beam charge neutralization (2001)

During plasma etching of oxide thin-film patterns, nonuniform charge buildup within etching features results in formation of microtrenches. Near the etch endpoint, the underlying film layer adjacent to the feature edges is exposed first, leaving an oxide island in the feature center and potentially causing underlayer damage before the endpoint is reached. Herein, a directional electron flux is added to the plasma ion flux incident on the etching substrate with the goal of minimizing microtrenching and oxide island formation. Scanning electron microscopic images of patterns etched with added electron irradiation show a reduction in microtrenching and oxide island formation as compared to patterns etched under identical conditions without electron irradiation. A computer simulation shows that the added electron irradiation reduces microtrenching by allowing more uniform ion flux to reach the feature bottom.