gebhart/patrepeval huggingface dataset:
Specific gene transfer mediated by lactosylated poly-L-lysine into hepatoma cells (1993)

Plasmid DNA/glycosylated polylysine complexes were used to transfer in vitro a luciferase reporter gene into human hepatoma cells by a receptor-mediated endocytosis process. HepG2 cells which express a galactose specific membrane lectin were efficiently and selectively transfected with pSV2Luc/lactosylated polylysine complexes in a sugar dependent manner: i) HepG2 cells which do not express membrane lectin specific for mannose were quite poorly transfected with pSV2Luc/mannosylated polylysine complexes, ii) HeLa cells which do not express membrane lectin specific for galactose were not transfected with pSV2Luc/lactosylated polylysine complexes. The transfection efficiency of HepG2 cells with pSV2Luc/lactosylated polylysine complexes was greatly enhanced either in the presence of chloroquine or in the presence of a fusogenic peptide. A 22-residue peptide derived from the influenza virus hemagglutinin HA2 N-terminal polypeptide that mimics the fusogenic activity of the virus, was selected. In the presence of the fusogenic peptide, the luciferase activity in HepG2 cells was 10 fold larger than that of cells transfected with pSV2Luc/lactosylated polylysine complexes in the presence of chloroquine.
Perforated monolayers: fabrication of calix[6]arene-based composite membranes that function as molecular sieves (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPerforated monolayers: fabrication of calix[6]arene-based composite membranes that function as molecular sievesMark D. Conner, Vaclav Janout, Ivo Kudelka, Petr Dedek, Jiayi Zhu, and Steven L. RegenCite this: Langmuir 1993, 9, 9, 2389–2397Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://doi.org/10.1021/la00033a022Request reuse permissionsArticle Views244Altmetric-Citations48LEARN 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 InReddit PDF (3 MB) Get e-Alertsclose Get e-Alerts
Deferred updates and data placement in distributed databases (2002)

Commercial distributed database systems generally support an optional protocol that provides loose consistency of replicas, allowing replicas to be inconsistent for some time. In such a protocol, each replicated data item is assigned a primary copy site. Typically, a transaction updates only the primary copies of data items, with updates to other copies deferred until after the transaction commits. After a transaction commits, its updates to primary copies are sent transactionally to the other sites containing secondary copies. We investigate the transaction model underlying the above protocol. We show that global serializability in such a system is a property of the placement of primary and secondary copies of replicated data items. We present a polynomial time algorithm to assign primary sites to data items so that the resulting topology ensures serializability.
Deep Learning based Radiomics (DLR) and its usage in noninvasive IDH1 prediction for low grade glioma (2017)

Deep learning-based radiomics (DLR) was developed to extract deep information from multiple modalities of magnetic resonance (MR) images. The performance of DLR for predicting the mutation status of isocitrate dehydrogenase 1 (IDH1) was validated in a dataset of 151 patients with low-grade glioma. A modified convolutional neural network (CNN) structure with 6 convolutional layers and a fully connected layer with 4096 neurons was used to segment tumors. Instead of calculating image features from segmented images, as typically performed for normal radiomics approaches, image features were obtained by normalizing the information of the last convolutional layers of the CNN. Fisher vector was used to encode the CNN features from image slices of different sizes. High-throughput features with dimensionality greater than 1.6*10<sup>4</sup> were obtained from the CNN. Paired t-tests and F-scores were used to select CNN features that were able to discriminate IDH1. With the same dataset, the area under the operating characteristic curve (AUC) of the normal radiomics method was 86% for IDH1 estimation, whereas for DLR the AUC was 92%. The AUC of IDH1 estimation was further improved to 95% using DLR based on multiple-modality MR images. DLR could be a powerful way to extract deep information from medical images.
Analysis, design, and iterative decoding of double serially concatenated codes with interleavers (1998)

A double serially concatenated code with two interleavers consists of the cascade of an outer encoder, an interleaver permuting the outer codeword bits, a middle encoder, another interleaver permuting the middle codeword bits, and an inner encoder whose input words are the permuted middle codewords. The construction can be generalized to h cascaded encoders separated by h-1 interleavers, where h>3. We obtain upper bounds to the average maximum likelihood bit-error probability of double serially concatenated block and convolutional coding schemes. Then, we derive design guidelines for the outer, middle, and inner codes that maximize the interleaver gain and the asymptotic slope of the error probability curves. Finally, we propose a low-complexity iterative decoding algorithm. Comparisons with parallel concatenated convolutional codes, known as "turbo codes", and with the proposed serially concatenated convolutional codes are also presented, showing that in some cases, the new schemes offer better performance.
Magic of the Occult? (1999)

The AIDS epidemic continues unabated, undaunted by researchers' attempts to develop a vaccine for this disease. Now a new, promising method for raising potentially effective antibodies to HIV is reported in this week's issue ([ LaCasse et al ][1].). In their Perspective, Montefiori and Moore describe the ambitious experiments that led to this discovery and the work that needs to be done before it is clear whether these results will pave the way to stemming the spread of AIDS.

 [1]: http://www.sciencemag.org/cgi/content/short/283/5400/357
HOMOLOGOUS RECOMBINATION IN MAMMALIAN CELLS (1989)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Sequence analysis of nephropathogenic infectious bronchitis virus strains of the Massachusetts genotype in Beijing (2001)

The first 440 nucleotides of the S1 part of the spike protein (S) gene of three nephropathogenic infection bronchitis virus (IBV) strains (BJ1, BJ2 and BJ3), isolated from three rural chicken farms of Beijing with outbreaks of avian infectious bronchitis, were sequenced after reverse transcriptasenested polymerase chain reaction amplification. The sequence data were analyzed and compared with the standard IBV strains M41, Beaudette, vaccine strain H120 and Chinese vaccine strain D41. The three IBV isolates and strain M41 showed more than 99.1 and 97.8% identity in nucleotide sequence and deduced amino acid sequence, respectively, suggesting that the three nephropathogenic IBV strains belonged to the Massachusetts genotype of IBV.
Tumor- and Neoantigen-Reactive T-cell Receptors Can Be Identified Based on Their Frequency in Fresh Tumor (2016)

Adoptive transfer of T cells with engineered T-cell receptor (TCR) genes that target tumor-specific antigens can mediate cancer regression. Accumulating evidence suggests that the clinical success of many immunotherapies is mediated by T cells targeting mutated neoantigens unique to the patient. We hypothesized that the most frequent TCR clonotypes infiltrating the tumor were reactive against tumor antigens. To test this hypothesis, we developed a multistep strategy that involved TCRB deep sequencing of the CD8(+)PD-1(+) T-cell subset, matching of TCRA-TCRB pairs by pairSEQ and single-cell RT-PCR, followed by testing of the TCRs for tumor-antigen specificity. Analysis of 12 fresh metastatic melanomas revealed that in 11 samples, up to 5 tumor-reactive TCRs were present in the 5 most frequently occurring clonotypes, which included reactivity against neoantigens. These data show the feasibility of developing a rapid, personalized TCR-gene therapy approach that targets the unique set of antigens presented by the autologous tumor without the need to identify their immunologic reactivity. Cancer Immunol Res; 4(9); 734-43. ©2016 AACR.
Transfer of oleic acid between albumin and phospholipid vesicles. (1986)

The net transfer of oleic acid between egg phosphatidylcholine unilamellar vesicles and bovine serum albumin has been monitored by 13C NMR spectroscopy and 90% isotopically substituted [1-13C]oleic acid. The carboxyl chemical shifts of oleic acid bound to albumin were different from those for oleic acid in phospholipid vesicles. Therefore, in mixtures of donor particles (vesicles or albumin with oleic acid) and acceptor particles (fatty acid-free albumin or vesicles), the equilibrium distribution of oleic acid was determined from chemical shift and peak intensity data without separation of donor and acceptor particles. In a system containing equal masses of albumin and phospholipid and a stoichiometry of 4-5 mol of oleic acid per mol of albumin, the oleic acid distribution was pH dependent, with greater than or equal to 80% of the oleic acid associated with albumin at pH 7.4; association was greater than or equal to 90% at pH 8.0. Decreasing the pH below 7.4 markedly decreased the proportion of fatty acid bound to albumin; at pH 5.4, less than or equal to 10% of the oleic acid was bound to albumin and greater than 90% was associated with vesicles. The distribution was reversible with pH and was independent of whether vesicles or albumin acted as a donor. These data suggest that pH may strongly influence the partitioning of fatty acid between cellular membranes and albumin. The 13C NMR method is also advantageous because it provides information about the structural environments of oleic acid bound to albumin or phospholipid, the ionization state of oleic acid in each environment, and the structural integrity of the vesicles. In addition, minimum and maximum limits for the exchange rates of oleic acid among different environments were obtained from the NMR data.
Guanosine regulates adenosine levels in the kidney (2014)

In cell culture, extracellular guanosine increases extracellular adenosine by attenuating the disposition of extracellular adenosine (American Journal of Physiology - Cell Physiology 304: C406-C421, 2013). The goal of this investigation was to determine whether this "guanosine-adenosine mechanism" is operative in an intact organ. Twenty-seven isolated, perfused mouse kidneys were subjected to metabolic poisons (iodoacetate plus 2,4-dinitrophenol) to cause energy depletion and thereby stimulate renal adenosine production. Adenosine levels in the renal venous perfusate increased from a baseline of 36 ± 8 to 499 ± 96, 258 ± 50, and 71 ± 13 nmol/L at 15, 30, and 60 min, respectively, after administering metabolic poisons (% of basal; 1366 ± 229, 715 ± 128, and 206 ± 33, respectively). Changes in renal venous levels of guanosine closely mirrored the time course of changes in adenosine: baseline of 15 ± 2 to 157 ± 13, 121 ± 8, and 50 ± 5 nmol/L at 15, 30, and 60 min, respectively (% of basal; 1132 ± 104, 871 ± 59, and 400 ± 51, respectively). Freeze-clamp experiments in 12 kidneys confirmed that metabolic poisons increased kidney tissue levels of adenosine and guanosine. In eight additional kidneys, we examined the ability of guanosine to reduce the renal clearance of exogenous adenosine; and these experiments revealed that guanosine significantly decreased the renal extraction of adenosine. Because guanosine is metabolized by purine nucleoside phosphorylase (PNPase), in another set of 16 kidneys we examined the effects of 8-aminoguanine (PNPase inhibitor) on renal venous levels of adenosine and inosine (adenosine metabolite). Kidneys treated with 8-aminoguanine showed a more robust increase in both adenosine and inosine in response to metabolic poisons. We conclude that in the intact kidney, guanosine regulates adenosine levels.
Beneficial Effects of Amiodarone and Dronedarone (SR 33589b), when Applied During Low-Flow Ischemia, on Arrhythmia and Functional Parameters Assessed during Reperfusion in Isolated Rat Hearts (2001)

The effects of short-term amiodarone and dronedarone treatments on action potential characteristics and arrhythmia (ventricular tachycardia ) induced by reperfusion after global low-flow ischemia were studied in rat hearts. The actions of amiodarone and SR on recovery of coronary flow and contractile function were also determined. Isolated hearts were stabilized for 40 min and were then submitted to 25-min global low-flow ischemia (constant coronary flow, 0.3 ml/min) followed by 30 min of reperfusion at constant pressure. Drugs were applied only during ischemia: consequently, action potential duration (APD) tended to widen. During reperfusion, APD tended to recover or shorten, and the more complete the recovery, the less the arrhythmia. Despite its ability to widen APD during ischemia, amiodarone facilitated APD recovery during reperfusion. Moreover, APD shortening and ventricular tachycardia suppression exhibit a bell-shaped concentration-response relation, implying that the drugs affect ventricular tachycardia by a class III-independent action. These results point to an anti-ischemic action supported by improvement in function and inhibition of reactive hyperemia.
Detailed FD-TD analysis of electromagnetic fields penetrating narrow slots and lapped joints in thick conducting screens (1988)

The physics of electromagnetic-wave transmission through narrow slots and tapped joints in thick conducting screens is examined in detail by applying numerical models to compute both field distributions within the slots and joints, and fields transmitted to the shadow region. The primary modeling tool is the finite-difference time-domain (FD-TD) method, using a Faraday's-law contour integral approach to modify the basic FD-TD algorithm to properly model the slot physics, even when the slot gap width is much less than one space lattice cell. Finely sampled method-of-moments (MM) models are used to validate the FD-TD tool for relatively simple straight slots; FD-TD is then used to explore properties of more complicated lapped joints which are widely used for shielding purposes at junctions of metal surfaces. It is found that previously reported slot resonances occur in a more general sense for lapped joints as path-length resonances. In addition to greatly enhanced power transmission, path-length resonances can result in total fields within the joint exceeding the incident fields by more than one order of magnitude. Sample field distributions for this case are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
qPCR Analysis and RNAi Define Pharyngeal Gland Cell-Expressed Genes of Heterodera glycines Required for Initial Interactions with the Host (2007)

Changes in transcript abundance of genes expressed in the three pharyngeal gland cells of Heterodera glycines after host invasion were monitored by quantitative polymerase chain reaction (qPCR) and the consequences of disrupting their expression studied by RNAi treatment prior to invasion. Two transcripts were known to be expressed in the two subventral gland cells (hg-pel and hg-eng-1), a further two in the single dorsal gland cell only (hg-gp and hg-syv46), and a fifth transcript (hg-cm) was expressed by both gland cell types. The qPCR study established that transcripts of hg-syv46 and hg-gp increased in abundance by 2 days postinfection (dpi), with the former remaining the most abundant. The hg-cm transcript level showed minor changes from 0 to 14 dpi but did fall by 21 dpi. In contrast, hg-eng-1 and hg-eng-2 messenger (m)RNA declined by 7 dpi and hg-pel by 14 dpi before it increased at 21 dpi. RNAi-targeting of hg-eng-1 reduced the number of females present on the plants at 10 days. Targeting of hg-gp, hg-cm, and hg-pel caused a change in sexual fate favoring male development on roots. Both effects were evident after targeting hg-syv46. Suppression of hg-eng-1 mRNA levels in second-stage juveniles (J2i) by RNAi was transient, with a recovery by 15 days of incubation in water after treatment. Presoaking H. glycines J2 with double-stranded RNA has value for studying gene function during the nematode's early interaction with a plant.
Inertial microfluidics (2009)

Despite the common wisdom that inertia does not contribute to microfluidic phenomena, recent work has shown a variety of useful effects that depend on fluid inertia for applications in enhanced mixing, particle separation, and bioparticle focusing. Due to the robust, fault-tolerant physical effects employed and high rates of operation, inertial microfluidic systems are poised to have a critical impact on high-throughput separation applications in environmental cleanup and physiological fluids processing, as well as bioparticle focusing applications in clinical diagnostics. In this review I will discuss the recent accelerated progress in developing prototype inertial microfluidic systems for a variety of applications and attempt to clarify the fundamental fluid dynamic effects that are being exploited. Finally, since this a nascent area of research, I will suggest some future promising directions exploiting fluid inertia on the microscale.
[Expression of 67kD laminin receptor in human hepatocellular carcinoma cells]. (2003)

The conflict of laminin binding activity and the expression of 67 LR in the three cell lines suggested SMMC-7721 HCC cells may express 67 LR with higher laminin affinity than L-02 hepatic cells, and other laminin receptors were involved in laminin binding.
A Synthesis of Nordihydroguaiaretic Acid (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Synthesis of Nordihydroguaiaretic AcidS. V. Lieberman, George P. Mueller, and Eric T. StillerCite this: J. Am. Chem. Soc. 1947, 69, 6, 1540–1541Publication Date (Print):June 1, 1947Publication History Published online1 May 2002Published inissue 1 June 1947https://pubs.acs.org/doi/10.1021/ja01198a513https://doi.org/10.1021/ja01198a513research-articleACS PublicationsRequest reuse permissionsArticle Views231Altmetric-Citations6LEARN 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
New Synthetic Technology for Efficient Construction of α-Hydroxy-β-amino Amides via the Passerini Reaction1 (2000)

[reaction: see text] The Passerini reaction of N-protected amino aldehydes, isonitriles, and TFA using pyridine-type bases proceeds under mild conditions and directly affords alpha-hydroxy-beta-amino amide derivatives in moderate to high yields. These adducts are readily hydrolyzed to alpha-hydroxy-beta-amino carboxylic acids. Application of these key intermediates to concise syntheses of P(1)-alpha-ketoamide protease inhibitors is illustrated.
Microstructure, thermal properties and susceptibility of the high amylose wheat starch to enzymatic hydrolysis: a new material for resistant starch (RSIII) production (2004)

Differential scanning calorimetry, optical (LM) and scanning electron (SEM) microscopy methods were used for studying the properties and structure of type III resistant starches obtained from high amylose (39.5% amylose) wheat starch. The susceptibility of RSIII starch to enzymatic hydrolysis was also studied. This study has shown that the structure of the investigated, laboratory-obtained preparation was highly influenced by the processing parameters - indicating changes typical of a repeated heating-cooling process. Thermal properties connected with the presence of amylose-lipid complexes, as well as ordered structure fragments in the preparations, were in high accordance to those reported in literature for RSIII preparations from normal wheat, high amylose barley and pea starches as well as commercial types - Novelose 330 or CrystaLean. It was shown that high amylose wheat is a promising raw material for processing bakery and extrusion food products with a reasonably high content of resistant starches without the addition of commercial resistant starches to meal or extrusion mixture.
Activation of Hepatocyte Growth Factor (HGF) by Endogenous HGF Activator Is Required for Metanephric Kidney Morphogenesis in Vitro (2001)

The interaction of hepatocyte growth factor (HGF) with c-Met has been implicated in morphogenesis of the kidney, lung, mammary gland, liver, placenta, and limb bud. HGF is secreted as an inactive zymogen and must be cleaved by a serine protease to initiate Met signaling. We show here that a serine protease specific for HGF, HGF activator (HGFA), is expressed and activated by the ureteric bud of the developing kidney in vivo and in vitro. Inhibition of HGFA activity with serine protease inhibitors reduced ureteric bud branching and inhibited glomerulogenesis and nephrogenesis. Activated HGF rescued developing kidneys from the effects of inhibitors. HGFA was localized around the tips of the ureteric bud in developing kidneys, while HGF was expressed diffusely throughout the mesenchyme. These data show that expression of HGF is not sufficient for development, but that its activation is also required. The localization of HGFA to the ureteric bud and the mesenchyme immediately adjacent to it suggests that HGFA creates a gradient of HGF activity in the developing kidney. The creation and shape of gradients of activated HGF by the localized secretion of HGF activators could play an important role in pattern formation by HGF responsive tissues.