gebhart/patrepeval huggingface dataset:
Human Serum Processing and Analysis Methods for Rapid and Reproducible N-Glycan Mass Profiling (2010)

Glycans constitute a new class of compounds for biomarker discovery. Glycosylation is a common post-translational modification and is often associated with transformation to malignancy. To analyze glycans, they are released from proteins, enriched, and measured with mass spectrometry. For biomarker discovery, repeatability at every step of the process is important. Locating and minimizing the process variability is key to establishing a robust platform stable enough for biomarker discovery. Understanding the variability of the measurement devices helps understand the variability associated with the chemical processing. This report explores the potential use of methods expediting the enzymatic release of glycans such as a microwave reactor and automation of the solid-phase extraction with a robotic liquid handler. The study employs matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry but would be suitable with any mass spectrometry method. Methods for system-wide data analysis are examined because proper metrics for evaluating the performance of glycan sample preparation procedures are not well established.
Axonal regeneration and limited functional recovery following hippocampal deafferentation (1995)

Although central neurons do not naturally recover following injury, damaged adult septal neurons can regenerate when nerve growth factor (NGF) is provided along with a suitable cellular substrate. This study investigates the outgrowth of axotomized septal neurons grafted with primary fibroblasts genetically modified to produce NGF. Confocal microscope images of double staining for neuritic markers (neurofilament or low-affinity NGF receptor) and the astrocytic marker glial fibrillary acidic protein (GFAP) demonstrated that regenerating neurites crossed dense buildups of astrocytic processes at the edges of NGF-producing grafts and were in apposition with astrocytic processes within NGF-producing grafts. Immunoreactivity for acetylcholinesterase and low-(p75) and high-affinity (TrkA) NGF receptors was dense in NGF-producing grafts but absent in control grafts. NGF-grafted rats exhibited significantly increased hippocampal density of p75-immunoreactive fibers and significantly decreased ectopic hippocampal sympathetic ingrowth as compared to control-grafted rats. Rats with unilateral fimbria-fornix lesions and NGF-producing grafts exhibited ameliorated performance on a simple memory task. These findings demonstrate that implantation of NGF-producing grafts to the lesion cavity allows axotomized septal cholinergic neurons to reinnervate the hippocampus, and that rats receiving these grafts show a partial recovery of function.
Macromol. Rapid Commun. 17/2010 (2010)

Back Cover: The image presents the synthesis and characterization of aggregates and intracellular distribution of fluorescently labeled P(HPMA)-b-P(LLA) block copolymers. The reactive precursor polymer P(PFMA)-b-P(LLA) enables the incorporation of various functionalities, while the biodegradable PLLA block can be used to encapsulate bioactive agents. More details can be found in the article by M. Barz, F. K. Wolf, F. Canal, K. Koynov, M. J. Vicent, H. Frey, and R. Zentel* on page 1492.
Understanding the function of acculturation and prejudicial attitudes among Asian Americans. (1999)

This study examined the theoretical and measurement issues involved in the current study of Asian American ethnic identity development and acculturation. Specifically, an attempt was made to investigate the influence of acculturation in predicting prejudicial social attitudes. A total of 289 college students from 2 universities were given the Asian and Anglo Acculturation Scale, the Suinn-Lew Asian Self-Identity Acculturation Scale, and the Quick Discrimination Index. Results suggest that students who were more acculturated and who were Asian identified tended to have less prejudicial attitudes. Results also suggested that Asian American women tended to have less prejudicial attitudes than did Asian American men. Implications for counseling are discussed.
Grain boundary compositions in Cu(InGa)Se2 (2007)

A microchemical analysis study is reported comparing the grain and grain boundary chemistries of Cu(In,Ga)Se2 (CIGS) films deposited by three different laboratories by different processes. An analysis of a GaAs wafer is described to provide a calibration of the accuracy and precision of the energy dispersive spectroscopy nanoprobe analysis as applied in the current instruments. When averaged over many measurements the precision of the instrument is ±0.1at.% and the accuracy is ±1.0at.% for individual points. The analysis of the CIGS shows less than 0.5at.% composition difference for each constituent element between grain and grain boundary compositions when averaged over hundreds of data points for most samples. One sample deposited at 400°C as a bilayer shows different grain and grain boundary compositions with grain boundaries being In deficient and Se rich. Both grain and grain boundary data in this sample scatter along a line between the Cu(In,Ga)Se2 and CuSe2 phases, which is a nonequilibrium behavior. The scatter in individual analyses is significantly greater than the noise in the analysis technique indicating real composition differences at different points within both grains and grain boundaries. No evidence was found for other substitutional impurities such as O or Na in the grain boundaries. The results suggest that the grain boundaries are self-passivating without a chemistry change.
Microarray analysis of differentially expressed genes regulating lipid metabolism during melanoma progression. (2015)

A new hallmark of cancer involves acquisition of a lipogenic phenotype which promotes tumorigenesis. Little is known about lipid metabolism in melanomas. Therefore, we used BRB (Biometrics Research Branch) class comparison tool with multivariate analysis to identify differentially expressed genes in human cutaneous melanomas, compared with benign nevi and normal skin derived from the microarray dataset (GDS1375). The methods were validated by identifying known melanoma biomarkers (CITED1, FGFR2, PTPRF, LICAM, SPP1 and PHACTR1) in our results. Eighteen genes regulating metabolism of fatty acids, lipid second messengers and gangliosides were 2-9 fold upregulated in melanomas of GDS-1375. Out of the 18 genes, 13 were confirmed by KEGG pathway analysis and 10 were also significantly upregulated in human melanoma cell lines of NCI-60 Cell Miner database. Results showed that melanomas upregulated PPARGC1A transcription factor and its target genes regulating synthesis of fatty acids (SCD) and complex lipids (FABP3 and ACSL3). Melanoma also upregulated genes which prevented lipotoxicity (CPT2 and ACOT7) and regulated lipid second messengers, such as phosphatidic acid (AGPAT-4, PLD3) and inositol triphosphate (ITPKB, ITPR3). Genes for synthesis of pro-tumorigenic GM3 and GD3 gangliosides (UGCG, HEXA, ST3GAL5 and ST8SIA1) were also upregulated in melanoma. Overall, the microarray analysis of GDS-1375 dataset indicated that melanomas can become lipogenic by upregulating genes, leading to increase in fatty acid metabolism, metabolism of specific lipid second messengers, and ganglioside synthesis.
Inducible and Reversible Gene Expression with the rtTA System for the Study of Memory (1998)

To obtain rapidly inducible and reversible expression of transgenes in the forebrain of the mouse, we have combined the reverse tetracycline-controlled transactivator (rtTA) system with the CaMKIIalpha promoter. We show that doxycycline induces maximal gene expression in neurons of the forebrain within 6 days and that this expression can be reversed by removal of doxycycline. Using calcineurin as a test transgene, we show that doxycycline-induced expression impairs both an intermediate form of LTP (I-LTP) in the hippocampus and the storage of spatial memory. The reversibility of the rtTA system in turn allowed us to examine the effects of the transgene on memory retrieval after normal storage had occurred. This examination suggests that retrieval requires some of the same molecular components required for storage.
The Coördination of Silver Ion with Unsaturated Compounds (1938)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Coördination of Silver Ion with Unsaturated CompoundsSaul Winstein and Howard J. LucasCite this: J. Am. Chem. Soc. 1938, 60, 4, 836–847Publication Date (Print):April 1, 1938Publication History Published online1 May 2002Published inissue 1 April 1938https://pubs.acs.org/doi/10.1021/ja01271a021https://doi.org/10.1021/ja01271a021research-articleACS PublicationsRequest reuse permissionsArticle Views677Altmetric-Citations210LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Guanylin, Uroguanylin, and Heat-stable Euterotoxin Activate Guanylate Cyclase C and/or a Pertussis Toxin-sensitive G Protein in Human Proximal Tubule Cells (2002)

Membrane guanylate cyclase C (GC-C) is the receptor for guanylin, uroguanylin, and heat-stable enterotoxin (STa) in the intestine. GC-C-deficient mice show resistance to STa in intestine but saluretic and diuretic effects of uroguanylin and STa are not disturbed. Here we describe the cellular effects of these peptides using immortalized human kidney epithelial (IHKE-1) cells with properties of the proximal tubule, analyzed with the slow-whole-cell patch clamp technique. Uroguanylin (10 or 100 nm) either hyperpolarized or depolarized membrane voltages (V(m)). Guanylin and STa (both 10 or 100 nm), as well as 8-Br-cGMP (100 microm), depolarized V(m). All peptide effects were absent in the presence of 1 mm Ba(2+). Uroguanylin and guanylin changed V(m) pH dependently. Pertussis toxin (1 microg/ml, 24 h) inhibited hyperpolarizations caused by uroguanylin. Depolarizations caused by guanylin and uroguanylin were blocked by the tyrosine kinase inhibitor, genistein (10 microm). All three peptides increased cellular cGMP. mRNA for GC-C was detected in IHKE-1 cells and in isolated human proximal tubules. In IHKE-1 cells GC-C was also detected by immunostaining. These findings suggest that GC-C is probably the receptor for guanylin and STa. For uroguanylin two distinct signaling pathways exist in IHKE-1 cells, one involves GC-C and cGMP as second messenger, the other is cGMP-independent and connected to a pertussis toxin-sensitive G protein.
Marginal adaptation of a restorative resin polymerized at reduced rate (1991)

The aim of this study was to investigate the effect of reduced rate of polymerization on the marginal adaptation of a composite resin inserted in dentin cavities treated with a simplified Gluma system. The effect on bonding strength to dentin and compressive strength was also investigated. The light intensity of the polymerization unit was lowered by the use of a transformer, and thus the rate of polymerization of the composite resin. When the resin was irradiated for 30 s at 110 V followed by 30 s at 220 V, the marginal adaptation was significantly improved. This condition resulted in acceptable values of bonding strength to dentin and diametral compressive strength. It is suggested that the reduced rate of polymerization may allow for increased flow of the material, decreasing the contraction stress in the filling.
Solder joint fatigue life model methodology for 63Sn37Pb and 95.5Sn4Ag0.5Cu materials (2004)

A tluee-dimensional finite elcincnt analysis methodolob?. which explores global. sub-structure_ and sub-inodeling solution options using both slice and syniinetry models has been developed and applied for the purpose of deriving life prediction equations that detenninc the fatibwe respoiise of inicmclectronic package structures using both eutectic (63Sn37Pb) and lead-free (95.SSnlAgO.5Cu) solder materials. The sub-structure and sub-modeling nictliodologies provide a means to iiiiprove siinulation run times for standard single die package structures alulc facilitating tlie development and execution of larger models rcquired for non-syimiietrical multi-die package structures. The study focuses on printed circuit board (PCB) level solder joint fatigue life under accelerated tcinpcrature ?cling couditions. Time-dependent plasticity (i.e. creep) and time-independent plasticity solder inaterid properties are simultaneously accounted for in Uie prcscnted finite element simulation methodolog. Thus, it is believed that the methodology and resulting life prediction equations can also be applied to board level bend cycling. power cycling, and drop shock solder fatigue. However. this point requires fuflhcr study and verification. The solder structures accoiiuuodate llie bulk of tlie total plastic strain that is generated during accelemted tempemiure cycling due to the thermal expansion mismatch behveen the wious iiiaterials that encompass the ovemll structures of microelectronic packages. Since the total plastic strain (i.e. crcep and timeindcpendcnt plasticity) is a donunant parameter that influences solder Fatigue, it was used as a basis for evaluation of solder joint structural integrity. The paper discusses the analysis methodolog? ‘aud results as implemented using the ANSYS finite element simulation sofhwre tool.
A Synopsis on the Role of Tyrosine Hydroxylase in Parkinson’s Disease (2012)

Parkinson's disease (PD) is a common chronic progressive neurodegenerative disorder in elderly people. A consistent neurochemical abnormality in PD is degeneration of dopaminergic neurons in substantia nigra pars compacta, leading to a reduction of striatal dopamine (DA) levels. As tyrosine hydroxylase (TH) catalyses the formation of L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of DA, the disease can be considered as a TH-deficiency syndrome of the striatum. Problems related to PD usually build up when vesicular storage of DA is altered by the presence of either α-synuclein protofibrils or oxidative stress. Phosphorylation of three physiologically-regulated specific sites of N-terminal domain of TH is vital in regulating its kinetic and protein interaction. The concept of physiological significance of TH isoforms is another interesting aspect to be explored further for a comprehensive understanding of its role in PD. Thus, a logical and efficient strategy for PD treatment is based on correcting or bypassing the enzyme deficiency by the treatment with L-DOPA, DA agonists, inhibitors of DA metabolism or brain grafts with cells expressing a high level of TH. Neurotrophic factors are also attracting the attention of neuroscientists because they provide the essential neuroprotective and neurorestorative properties to the nigrostriatal DA system. PPAR-γ, a key regulator of immune responses, is likewise a promising target for the treatment of PD, which can be achieved by the use of agonists with the potential to impact the expression of pro- and anti-inflammatory cytokines at the transcriptional level in immune cells via expression of TH. Herein, we review the primary biochemical and pathological features of PD, and describe both classical and developing approaches aimed to ameliorate disease symptoms and its progression.
PREDICTION OF THE PERSISTENCE OF THE TRIAZINE HERBICIDES ATRAZINE, CYANAZINE, AND METRIBUZIN IN REGINA HEAVY CLAY (1989)

The persistence of the herbicides cyanazine, metribuzin, and atrazine was studied at different controlled temperature and moisture contents in Regina Heavy Clay soil. Degradation of the herbicides approximated first-order kinetics at temperatures in the range 5–30 °C and at moistures of above 20%. The breakdown of cyanazine was faster than metribuzin, which, in turn, was more rapid than atrazine. The breakdown of the three herbicides under field conditions, following June applications of 1.0 kg ha −1 , was measured. Over 90% of the applied cyanazine had dissipated within 56 d, while the metribuzin and atrazine were more persistent, with approximately 30% of the initial treatment remaining at the end of the growing season. In all cases, there was no leaching of the chemicals below 10 cm. The laboratory data were used in conjunction with meteorological records in a computer program to simulate the dissipation pattern for the herbicides. There was good agreement between the observed and predicted residue levels for cyanazine, and a reasonable agreement for atrazine. For metribuzin, the model underestimated the rate of loss. Key words: Herbicides, atrazine, cyanazine, metribuzin, predicted field persistence
Chaperone-Assisted Protein Folding in the Cell Cytoplasm (2001)

Folding of polypeptides in the cell typically requires the assistance of a set of proteins termed molecular chaperones. Chaperones are an essential group of proteins necessary for cell viability under both normal and stress conditions. There are several chaperone systems which carry out a multitude of functions all aimed towards insuring the proper folding of target proteins. Chaperones can assist in the efficient folding of newly-translated proteins as these proteins are being synthesized on the ribosome and can maintain pre-existing proteins in a stable conformation. Chaperones can also promote the disaggregation of preformed protein aggregates. Many of the identified chaperones are also heat shock proteins. The general mechanism by which chaperones carry out their function usually involves multiple rounds of regulated binding and release of an unstable conformer of target polypeptides. The four main chaperone systems in the Escherichia coli cytoplasm are as follows. (1) Ribosome-associated trigger factor that assists in the folding of newly-synthesized nascent chains. (2) The Hsp 70 system consisting of DnaK (Hsp 70), its cofactor DnaJ (Hsp 40), and the nucleotide exchange factor GrpE. This system recognizes polypeptide chains in an extended conformation. (3) The Hsp 60 system, consisting of GroEL (Hsp 60) and its cofactor GroES (Hsp 10), which assists in the folding of compact folding intermediates that expose hydrophobic surfaces. (4) The Clp ATPases which are typically members of the Hsp 100 family of heat shock proteins. These ATPases can unfold proteins and disaggregate preformed protein aggregates to target them for degradation. Several advances have recently been made in characterizing the structure and function of all of these chaperone systems. These advances have provided us with a better understanding of the protein folding process in the cell.
Dose escalation in chemoradiation for anal cancer: preliminary results of RTOG 92-08. (2006)

Numerical increases in radiotherapy dose over those used in conventional chemotherapy regimens for anal cancers do not appear to increase local control when given in split-course fashion. For higher radiotherapy doses (> 50 Gy) to increase local control, radiation may have to be given in continuous fashion, which almost certainly means that our threshold of acceptable acute toxicity, particularly dermal toxicity, may have to be raised.
Metastable phase formation in titanium-silicon thin films (1985)

The formation of TiSi2 thin films on silicon substrates has been investigated with several transmission electron microscope techniques. For films formed either by reacting titanium with a silicon substrate or by sintering a codeposited (Ti+Si) mixture, electron diffraction patterns show that a metastable phase—TiSi2 (C49 or ZrSi2 structure)—forms prior to the equilibrium phase—TiSi2 (C54 structure). High-resolution images indicate that the metastable TiSi2-silicon interface is atomically sharp, with no ‘‘glassy membrane’’ layer present. The annealing temperature required to transform the metastable TiSi2 to the low resistivity, equilibrium TiSi2 increases as the thin-film impurity content increases. Previous studies of TiSi2 formation are discussed in light of these results.
Temporal and Triggered Evolution of Host–Guest Characteristics in Amphiphilic Polymer Assemblies (2016)

An amphiphilic polymer with cleavable side chain and main chain functional groups has been designed and synthesized. Specific cleavage of either of its functional groups was found to have an effect on the morphology of the assembly. Degradation of the main chain is shown to cause morphology of the supramolecular assembly to evolve with time from a micelle-like assembly to a vesicular assembly. On the other hand, stimulus-induced cleavage of the side chains causes these nanoassemblies to disassemble. These temporal (main chain) and triggered (side chain) degradation processes have implications in the design of degradable polymers as supramolecular scaffolds for biological applications.
Anti-Jo-1 positive inclusion body myositis with a marked and sustained clinical improvement after oral prednisone (2001)

The three major categories of the idiopathic inflammatory myopathies are dermatomyositis, polymyositis, and inclusion body myositis.1 The most important clinical feature distinguishing inclusion body myositis from dermatomyositis and polymyositis is the lack of responsiveness to immunosuppressive treatment.1 2 Yet, it is the experience of many clinicians that a small subgroup of patients with inclusion body myositis show at least a partial response to immunosuppressive treatment. There are no specific characteristics which can identify this subgroup. In this report we present an anti-Jo-1 positive patient with inclusion body myositis who showed a marked and sustained clinical improvement after treatment with oral prednisone.

A 74 year old man, with no relevant medical history, presented with a slowly progressive proximal muscle weakness of the lower limbs. On presentation there were no complaints of muscle weakness of the upper limbs, dysphagia, myalgia, arthralgia, or feelings of general malaise. He denied any sensory symptoms. His family history was negative for neuromuscular or rheumatic disorders and he did not use any myotoxic drugs.

Physical examination showed asymmetric proximal and distal muscle weakness (muscle strength in MRC grades: neck flexors 3, right and left triceps 4, right and left iliopsoas 4, right and left gluteus maximus 4, right quadriceps 4, left quadriceps 2.5, right and left hamstrings …
A Convenient Strategy for the Synthesis of 4,5-Bis(o-haloaryl)isoxazoles (2000)

A series of new 1,2-bis(o-haloaryl)ethanones is efficiently prepared and applied to the synthesis of 4,5-bis(o-haloaryl)isoxazoles. Isolation of intermediate hydroxyisoxazolines, which are structurally examined, provides a definitive proof for a heterocyclization mechanism based on an amine exchange process. The isolation and X-ray crystallographic studies of significant side products such as benzamides and triarylpropionitriles are also described.