gebhart/patrepeval huggingface dataset:
Th2 Cytokines and Atopic Dermatitis (2011)

Atopic dermatitis (AD), a chronic relapsing inflammatory skin disease, is increasing in prevalence around the world. Intensive research is ongoing to understand the mechanisms involved in the development of AD and offer new treatment options for patients suffering from AD. In this review, we highlight the importance of allergic Th2 responses in the development of the disease and summarize relevant literature, including genetic studies, studies of human skin and mechanistic studies on keratinocytes and mouse models of AD. We discuss the importance of the skin barrier and review recent findings on the pro-Th2 cytokines TSLP, IL-25, and IL-33, notably their ability to polarize dendritic cells and promote Th2 responses. After a brief update on the contribution of different T-cell subsets to AD, we focus on Th2 cells and the respective contributions of each of the Th2 cytokines (IL-4, IL-13, IL-5, IL-31, and IL-10) to AD. We conclude with a brief discussion of the current gaps in our knowledge and technical limitations.
Ber-H2 (CD30) immunohistochemical staining in malignant melanoma. (1999)

Malignant melanoma can be included in the differential diagnosis of Hodgkin's disease, anaplastic large cell lymphoma, or embryonal carcinoma These malignancies express CD30, a marker of diagnostic value. A retrospective immunohistochemical study was undertaken to determine the frequency of immunoreactivity of Ber-H2 (anti-CD30 monoclonal antibody) in malignant melanoma Archival paraffin-embedded tissue from 24 primary and metastatic lesions was used. No Ber-H2 labeling was observed in the majority of the studied cases. Variable weak cytoplasmic staining was present in only one case. The findings are compared with the previous reports claiming frequent CD30 expression in malignant melanoma. We discuss issues pertaining to the interpretation of the Ber-H2 IHC staining in formalin-fixed, paraffin-embedded tissue.
Aqueous Humor Flow in Unilateral Carotid Stenosis (1996)

Our purpose was to study the relationship between carotid artery occlusive disease and aqueous flow in human subjects. Aqueous humor flow was measured by fluorophotometry in seven patients with unilateral carotid artery disease documented by oculoplethysmography. The mean (+/- SD) flow was 2.03 +/- 0.38 microliter/min in the affected eyes, 2.44 +/- 0.66 microliter/min in the unaffected contralateral eyes, and 2.56 +/- 0.61 microliter/min in a group of 14 age-matched controls. A statistically significant difference (p < 0.05) in the aqueous flow rate was seen between the affected and unaffected eyes and between the affected and control eyes. Aqueous flow in the unaffected and control eyes was not statistically different. The anterior chamber volumes and intraocular pressures were also not significantly different among groups. Severe carotid artery disease may reduce aqueous humor formation by lowering ciliary body blood flow to a point beyond which the eye cannot compensate.
A phase‐sensitive method of flip angle mapping (2008)

A radiofrequency (RF) excitation scheme is presented in which flip angle is encoded in the phase of the resulting excitation. This excitation is implemented with nonselective hard pulses, and is used to give flip angle maps over three-dimensional volumes. This phase-sensitive B1 mapping excitation can be combined with various acquisition methods such as gradient recalled echo (GRE) and echo-planar (EP) readouts. Imaging time depends primarily on the readout method, and is roughly equivalent to the imaging time of conventional double-angle techniques for three-dimensional acquisition. The phase-sensitive method allows imaging over a much wider range of flip angles than double-angle methods. Phantom and in vivo results are presented comparing the phase-sensitive method with the conventional double-angle method, demonstrating the ability of the phase-sensitive method to measure a wider range of flip angles than double-angle methods.
A next-generation antimicrobial wound dressing: a real-life clinical evaluation in the UK and Ireland (2016)

The authors are all employed by ConvaTec Ltd. but have no other conflict of interest to declare. Dressings were provided to the clinicians free of charge.
MIME-based Secure Peer-to-Peer Business Data Interchange over the Internet (2002)

This document describes how to exchange structured business data securely using SMTP transport for Electronic Data Interchange, (EDI - either the American Standards Committee X12 or UN/EDIFACT, Electronic Data Interchange for Administration, Commerce and Transport), XML or other data used for business to business data interchange. The data is packaged using standard MIME content-types. Authentication and privacy are obtained by using Cryptographic Message Syntax (S/MIME) or OpenPGP security body parts. Authenticated acknowledgements make use of multipart/signed replies to the original SMTP message.
Cytokine Gene Expression: Analysis using Northern Blotting, Polymerase Chain Reaction and in situ Hybridization (1991)

We describe here the use of northern blotting, PCR and in situ hybridization for the analysis of cytokine gene expression. These techniques, each with their advantages and disadvantages, have been used to monitor cytokine gene expression in sites of immune reactivity and in the developing thymus. Whilst expression of a gene usually correlates well with protein production from that gene, this may not always be the case. The development of methods to analyze protein production in situ, for instance by immunohistochemistry, together with analysis of mRNA expression will allow us to begin to understand the role of cytokines within the immune system of the intact animal.
Molecular Characterization of a Novel Human Hybrid-type Receptor That Binds the α2-Macroglobulin Receptor-associated Protein (1996)

The 39-40-kDa receptor-associated protein (RAP) binds to the members of the low density lipoprotein receptor gene family and functions as a specialized endoplasmic reticulum/Golgi chaperone. Using RAP affinity chromatography, we have purified a novel approximately 250-kDa brain protein and isolated the corresponding cDNA. The gene, designated SORL1, maps to chromosome 11q 23/24 and encodes a 2214-residue type 1 receptor containing a furin cleavage site immediately preceding the N terminus determined in the purified protein. The receptor, designated sorLA-1, has a short cytoplasmic tail containing a tyrosine-based internalization signal and a large external part containing (from the N-terminal): 1) a segment homologous to domains in the yeast vacuolar protein sorting 10 protein, Vps10p, that binds carboxypeptidase Y, 2) five tandemly arranged YWTD repeats and a cluster of 11 class A repeats characteristic of the low density lipoprotein receptor gene family receptors, and 3) six tandemly arranged fibronectin type III repeats also found in certain neural adhesion proteins. sorLA-1 may therefore be classified as a hybrid receptor. Northern blotting revealed specific mRNA transcripts in brain, spinal cord, and testis but not in several major organs. Both RAP and an antibody against a synthetic peptide derived from a sequence determined in the mature protein detected sorLA-1 in crude human brain extracts. The domain structure suggests that sorLA-1 is an endocytic receptor possibly implicated in the uptake of lipoproteins and of proteases.
Corkscrew point spread function for far-field three-dimensional nanoscale localization of pointlike objects (2011)

We describe the corkscrew point spread function (PSF), which can localize objects in three dimensions throughout a 3.2 μm depth of field with nanometer precision. The corkscrew PSF rotates as a function of the axial (z) position of an emitter. Fisher information calculations show that the corkscrew PSF can achieve nanometer localization precision with limited numbers of photons. We demonstrate three-dimensional super-resolution microscopy with the corkscrew PSF by imaging beads on the surface of a triangular polydimethylsiloxane (PDMS) grating. With 99,000 photons detected, the corkscrew PSF achieves a localization precision of 2.7 nm in x, 2.1 nm in y, and 5.7 nm in z.
Magmatic processes under mid‐ocean ridges: A detailed mineralogic study of lavas from East Pacific Rise 9°30′N, 10°30′N, and 11°20′N (2003)

Detailed petrologic study has been made for lavas from the northern East Pacific Rise (EPR) 9°30′N, 11°20′N, and 10°30′N. 9°30′N and 11°20′N have robust magma supply and a shallow melt lens while 10°30′N has nonrobust magma supply and no shallow melt lens. Lavas from all three localities are sparsely phyric and glassy, containing plagioclase ± olivine ± pyroxene. Typically, the lavas contain several to many (up to seven) distinct chemical groups of plagioclase that are not always distinct texturally. The lavas may also contain up to three chemically distinct groups of olivine and two groups of pyroxene. The lavas contain both individual crystals and groups comprising reticulate and dendritic clots that we interpret to represent bits of crystal networks forming in mushy zones of an axial magma chamber. 21 of the 23 samples studied in detail have diverse crystal compositions and require mixing, which most likely occurs when mostly liquid magma passes through mushy zones. We find no significant systematic differences between robust and nonrobust segments in terms of their crystal content, proportion of texturally distinct xenocrysts, crystal size, aspect ratio, roundness, modal abundance, magma residence time, number of diverse mineral‐chemical groups, and characteristics of mixing like the total range of composition of disequilibrium minerals present, and the magnitude of the chemical gaps between disequilibrium and equilibrium compositions. This unexpected and remarkable similarity suggests that the presence or absence of a seismically imaged shallow melt lens has essentially no effect on the mineralogy of erupted lavas. We conclude that the fundamentally important magmatic process under mid‐ocean ridges, from slow to fast, is the formation of crystal networks and their subsequent compaction; the seismically detected shallow melt lenses likely contain highly evolved magma, formed by expelled interstitial melt during crystal network compaction, and play very little role in crustal accretion. Our conclusion implies that the thick (&gt;3 km) low velocity zone near the base of the crust produces the thin (&lt;30 m) shallow melt lenses, not the other way around.
Fluorescence Probes for Structure (1972)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays (2004)

The effect of locked nucleic acid (LNA) modification position upon representative DNA polymerase and exonuclease activities has been examined for potential use in primer extension genotyping applications. For the 3'-->5' exonuclease activities of four proofreading DNA polymerases (Vent, Pfu, Klenow fragment and T7 DNA polymerase) as well as exonuclease III, an LNA at the terminal (L-1) position of a primer is found to provide partial protection against the exonucleases of the two family B polymerases only. In contrast, an LNA residue at the penultimate (L-2) position generates essentially complete nuclease resistance. The polymerase active sites of these enzymes also display a distinct preference. An L-1 LNA modification has modest effects upon poly merization, but an L-2 LNA group slows dTTP incorporation somewhat while virtually abolishing extension with ddTTP or acyTTP terminators, even with A488L Vent DNA polymerase engineered for terminator incorporation. These observations on active site preference have been utilized to demonstrate two novel assays: exonuclease-mediated single base extension (E-SBE) and proofreading allele-specific extension (PRASE). We show that a model PRASE genotyping reaction with L-2 LNA primers offers greater specificity than existing non-proofreading assays, whether or not the non-proofreading reaction employs LNA-modified primers.
Safety and immunologic correlates of Melanoma GVAX, a GM-CSF secreting allogeneic melanoma cell vaccine administered in the adjuvant setting (2015)

NCT01435499.
The Addition of a Tramadol Infusion to Morphine Patient-Controlled Analgesia After Abdominal Surgery: A Double-Blinded, Placebo-Controlled Randomized Trial (2002)

In this study, we determined whether adding a second pain-killing drug, tramadol, could improve pain relief after major surgery in patients receiving morphine patient-controlled analgesia. We found that patients receiving tramadol had significantly better opinions of their pain relief and used significantly less morphine with no increase in side effects.
Acute coronary reocclusion after thrombolysis with recombinant human tissue-type plasminogen activator: prevention by a maintenance infusion. (1986)

Twenty-nine patients with acute myocardial infarction were treated with recombinant human tissue-type plasminogen activator (rt-PA). The incidence of acute coronary reocclusion and its prevention by a maintenance infusion of rt-PA were studied. Intravenous rt-PA was given at a rate of 0.4 to 0.75 mg/kg over 60 to 120 min after angiographic documentation of complete coronary occlusion. Reperfusion was accomplished within 1 hr in 24 of 29 patients (83%) and was associated with a decrease of the plasma fibrinogen level by 20%. In a first group of 13 patients, 11 of whom were successfully reperfused, prevention of reocclusion was attempted with heparin anticoagulation. However, acute reocclusion within 1 hr after cessation of rt-PA was demonstrated angiographically in five of these patients (45%). Quantitative angiographic analysis indicated that acute reocclusion only occurred in patients with 80% or greater residual stenosis. In patients with less than 80% residual stenosis, heparin anticoagulation was sufficient to maintain patency during the hospital stay in four of five patients. In a second group of patients (n = 16), 13 of whom underwent reperfusion with intravenous rt-PA, seven demonstrated a residual stenosis of 80% or greater. These patients were given heparin and, in addition, 10 mg of rt-PA per hour for 4 hr. None developed acute angiographic reocclusion or clinical signs of reocclusion during the hospital stay. Repeat angiography at 10 to 14 days confirmed persistent patency in six of the seven patients. The maintenance infusion resulted in only a moderate additional drop in fibrinogen, while a steady-state plasma rt-PA level of 750 +/- 250 ng/ml was maintained.(ABSTRACT TRUNCATED AT 250 WORDS)
Random Insertional Mutagenesis Identifies Genes Associated with Virulence in the Wheat Scab Fungus Fusarium graminearum (2005)

ABSTRACT Fusarium graminearum is an important pathogen of small grains and maize in many areas of the world. To better understand the molecular mechanisms of F. graminearum pathogenesis, we used the restriction enzyme-mediated integration (REMI) approach to generate random insertional mutants. Eleven pathogenicity mutants were identified by screening 6,500 hygromycin-resistant transformants. Genetic analyses indicated that the defects in plant infection were tagged by the transforming vector in six of these mutants. In mutant M8, the transforming plasmid was integrated 110-bp upstream from the start codon of the cystathionine betalyase gene (CBL1). Gene replacement mutants deleted for CBL1 and the methionine synthase gene MSY1 were also obtained. Both the cbl1 and msy1 deletion mutants were methionine auxotrophic and significantly reduced in virulence on corn silks and wheat heads. We also identified genes disrupted by the transforming DNA in three other REMI mutants exhibiting reduced virulence. In mutants M68, the transforming vectors were inserted in the NADH: ubiquinone oxidoreductase. The putative b-ZIP transcription factor gene and the transducin beta-subunit-like gene disrupted in mutants M7 and M75, respectively, had no known homologs in filamentous fungi and were likely to be novel fungal virulence factors.
Antitumor and anti-intoxication activities of fumaric acid in cultured cells. (1981)

Fumaric acid, isolated as the active component of Capsella bursa-pastoris herb for inhibiting the solid growth of Ehrlich tumor in mice, was found to reduce markedly the growth and viability of Ehrlich, MH134, and L1210 mouse tumor cells in culture at concentration of 0.3 approximately 1.2 mg/ml. In contrast, fumaric acid at these concentrations in the culture medium had no deleterious effect on the monolayer development of mouse and chick embryo cells but exhibited activity to enhance the recovery of the cells from the toxic effects of mitomycin C, aflatoxin B1, N-methyl-N'-nitro-N-nitrosoguanidine, and potassium 1-methyl-7-[2-(5-nitro-2-furyl) vinyl]-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylate.
High‐level production of human type I collagen in the yeast Pichia pastoris (2001)

Four human genes, two of them encoding the proalpha1 and proalpha2 chains of type I procollagen and two of them the two types of subunit of prolyl 4-hydroxylase (4-PH), were integrated into the genome of Pichia pastoris. The proalpha1 and proalpha2 chains expressed formed type I procollagen molecules with the correct 2:1 chain ratio, and the 4-PH subunits formed an active enzyme tetramer that fully hydroxylated the proalpha chains. Chains lacking their N but not C propeptides formed pCcollagen molecules with the 2:1 chain ratio and, surprisingly, the expression levels of pCcollagen were 1.5-3-fold relative to those of procollagen. Both types of molecule could be converted by pepsin treatment to collagen molecules that formed native-type fibrils in vitro. The expression levels obtained for the pCcollagen using only single copies of each of the four genes and a 2 l fermenter ranged up to 0.5 g/l, indicating that it should be possible to optimize this system for high-level production of recombinant human type I collagen for numerous medical applications.
Cutting Edge: IRF8 Regulates Bax Transcription In Vivo in Primary Myeloid Cells (2011)

A prominent phenotype of IRF8 knockout (KO) mice is the uncontrolled expansion of immature myeloid cells. The molecular mechanism underlying this myeloproliferative syndrome is still elusive. In this study, we observed that Bax expression level is low in bone marrow preginitor cells and increases dramatically in primary myeloid cells in wt mice. In contrast, Bax expression level remained at a low level in primarymyeloid cells in IRF8 KO mice. However, in vitro IRF8 KO bone marrow-differentiated myeloid cells expressed Bax at a level as high as that in wild type myeloid cells. Furthermore, we demonstrated that IRF8 specifically binds to the Bax promoter region in primary myeloid cells. Functional analysis indicated that IRF8 deficiency results in increased resistance of the primary myeloid cells to Fas-mediated apoptosis. Our findings show that IRF8 directly regulates Bax transcription in vivo, but not in vitro during myeloid cell lineage differentiation.
Readings in Machine Learning (1991)

From the Publisher:
The ability to learn is a fundamental characteristic of intelligent behavior. Consequently, machine learning has been a focus of artificial intelligence since the beginnings of AI in the 1950s. The 1980s saw tremendous growth in the field, and this growth promises to continue with valuable contributions to science, engineering, and business.

Readings in Machine Learning collects the best of the published machine learning literature, including papers that address a wide range of learning tasks, and that introduce a variety of techniques for giving machines the ability to learn. The editors, in cooperation with a group of expert referees, have chosen important papers that empirically study, theoretically analyze, or psychologically justify machine learning algorithms. The papers are grouped into a dozen categories, each of which is introduced by the editors.
Synthetic application of biotransformations: absolute stereochemistry and Diels–Alder reactions of the (1S,2R)-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylic acid from Pseudomonas putida (1995)

1,cis-2-Dihydroxycyclohexa-3,5-diene-1-carboxylic acid, 2, produced by Pseudomonas putide, U103, was shown via X-ray analysis of its p-bromobenzoylmethyl ester to have (1S 2R) absolute stereochemistry. The stereo- and regio-selectivity of a series of cycloadditions of the methyl ester 3(R = Me) the methyl ester acetonide 5 and the hydroxymethylacetonide 6(R = H) with singlet oxygen, 4-phenyl-4,5-dihydro-3H-1,2,4-triazole-3,5-dione, N-phenylmaleimide and nitrosobenzene have been established. The stereochemistry of the oxygen adduct 7 of 5 was unambiguously assigned by X-ray analysis of 7. The acetonides 5 and 6(R = H) were attacked by the dienophiles anti to the acetonide group. The diol ester 3 underwent attack on the face syn to the diol groups. The regiochemistry of the addition of nitrosobenzene was predominantly with the N–phenyl group distal to the ester function in 3 and 5, but proximal to the hydroxymethyl group in 6(R = H).
General model of oil shale pyrolysis (1983)

A mathematical model for pyrolysis of Green River oil shale is developed from previous experiments on oil, water, and gas evolution and oil cracking over a wide range of pyrolysis conditions. Reactions included are evolution of 5 gas species, oil, and water from kerogen, clay dehydration, oil coking and cracking, and evolution of H/sub 2/ and CH/sub 4/ from char. Oil is treated in eleven boiling-point fractions in order to treat the competition between oil coking and evaporation, and to evaluate the effect of oil cracking on the boiling point distribution of the oil. The kinetics and product yields calculated by the model are compared to experimental results for pyrolysis conditions ranging from isothermal fluid-bed to high-pressure slow-heating-rate retorting.
DNA origami nanopores: developments, challenges and perspectives (2014)

DNA nanotechnology has enabled the construction of DNA origami nanopores; synthetic nanopores that present improved capabilities for the area of single molecule detection. Their extraordinary versatility makes them a new and powerful tool in nanobiotechnology for a wide range of important applications beyond molecular sensing. In this review, we briefly present the recent developments in this emerging field of research. We discuss the current challenges and possible solutions that would enhance the sensing capabilities of DNA origami nanopores. Finally, we anticipate novel avenues for future research and highlight a range of exciting ideas and applications that could be explored in the near future.