gebhart/patrepeval huggingface dataset:
Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans (2009)

Neutrophils are the first line of defense at the site of an infection. They encounter and kill microbes intracellularly upon phagocytosis or extracellularly by degranulation of antimicrobial proteins and the release of Neutrophil Extracellular Traps (NETs). NETs were shown to ensnare and kill microbes. However, their complete protein composition and the antimicrobial mechanism are not well understood. Using a proteomic approach, we identified 24 NET-associated proteins. Quantitative analysis of these proteins and high resolution electron microscopy showed that NETs consist of modified nucleosomes and a stringent selection of other proteins. In contrast to previous results, we found several NET proteins that are cytoplasmic in unstimulated neutrophils. We demonstrated that of those proteins, the antimicrobial heterodimer calprotectin is released in NETs as the major antifungal component. Absence of calprotectin in NETs resulted in complete loss of antifungal activity in vitro. Analysis of three different Candida albicans in vivo infection models indicated that NET formation is a hitherto unrecognized route of calprotectin release. By comparing wild-type and calprotectin-deficient animals we found that calprotectin is crucial for the clearance of infection. Taken together, the present investigations confirmed the antifungal activity of calprotectin in vitro and, moreover, demonstrated that it contributes to effective host defense against C. albicans in vivo. We showed for the first time that a proportion of calprotectin is bound to NETs in vitro and in vivo.
Analysis of immunoglobulin glycosylation by LC‐ESI‐MS of glycopeptides and oligosaccharides (2008)

Two LC-ESI-MS methods for the analysis of antibody glycosylation are presented. In the first approach, tryptic glycopeptides are separated by RP chromatography and analyzed by ESI-MS. This "glycopeptide strategy" allows a protein- and subclass-specific quantitation of both neutral and sialylated glycan structures. Additional information about under- or deglycosylation and the protein backbone, e.g., termini, can be extracted from the same data. In the second LC-ESI-MS method, released oligosaccharides are separated on porous graphitic carbon (PGC). A complete structural assignment of neutral and sialylated oligosaccharides occurring on antibodies is thereby achieved in one chromatographic run. The two methods were applied to polyclonal human IgG, to commercial mAb expressed in CHO cells (Rituximab, Xolair, and Herceptin), in SP2/0 (Erbitux and Remicade) or NS0 cells (Zenapax) and the anti-HIV antibody 4E10 produced either in CHO cells or in a human cell line. Both methods require comparably little sample preparation and can be applied to SDS-PAGE bands. They both outperform non-MS methods in terms of reliability of peak assignment and MALDI-MS of underivatized glycans with regard to the recording of sialylated structures. Regarding fast and yet detailed structural assignment, LC-MS on graphitic carbon supersedes all other current methods.
Constellation Design for Improved Iterative LDPC Decoding (2008)

Recent advances in iteratively decoded channel codes such as low-density parity-check (LDPC) codes make it possible to operate close to channel capacity limits. The capacity of a coded modulation is therefore a very useful indicator when analyzing the performance of a near infinite-length code under maximum likelihood (ML) decoding. In this work, we analyze the behavior of LDPC codes of moderate lengths using belief propagation (BP) based decoding algorithms. We found that in many cases analyzing the capacity of the coded modulation is not enough to predict which constellation will yield the best error rate performance in a Gaussian noise channel. For the case of M-ary constellations with M=8 and 16 we show how a lower error rate can be achieved by making simple changes to constant envelope phase-shift keying (PSK) constellations. Modifying these constellations translates to an increase in the mean log-likelihood ratio of some of the received bits, resulting in an improvement in performance.
Intramolecular sensitization of americium luminescence in solution: shining light on short-lived forbidden 5f transitions (2016)

The photophysical properties and solution thermodynamics of water soluble trivalent americium (Am(III)) complexes formed with multidentate chromophore-bearing ligands, 3,4,3-LI(1,2-HOPO), Enterobactin, and 5-LIO(Me-3,2-HOPO), were investigated. The three chelators were shown to act as antenna chromophores for Am(III), generating sensitized luminescence emission from the metal upon complexation, with very short lifetimes ranging from 33 to 42 ns and low luminescence quantum yields (10(-3) to 10(-2)%), characteristic of Near Infra-Red emitters in similar systems. The specific emission peak of Am(III) assigned to the (5)D1 → (7)F1 f-f transition was exploited to characterize the high proton-independent stability of the complex formed with the most efficient sensitizer 3,4,3-LI(1,2-HOPO), with a log β110 = 20.4 ± 0.2 value. In addition, the optical and solution thermodynamic features of these Am(III) complexes, combined with density functional theory calculations, were used to probe the influence of electronic structure on coordination properties across the f-element series and to gain insight into ligand field effects.
Classification and Function Prediction of Proteins Using Diagnostic Amino Acid Patterns (1994)

Protein sequence similarities offer a convenient means for the classification and identification of protein families and superfamilies. Frequently, proteins descended from a common ancestor preserve their basic three-dimensional conformations even when they have accumulated large numbers of amino acid substitutions and short insertions or deletions. These may prohibit establishment of homology or evolutionary relationships by traditional global sequence alignment means. Limited regions of sequence similarity can also be the result of evolutionary convergence driven by a need for a common function. Regardless of whether divergent or convergent evolution played a role in the appearance of local sequence similarities, these confined regions of similarity can provide insight into structural and functional relationships of proteins that otherwise fail to show significant similarity by global alignment methods.
A Predictable Execution Model for COTS-Based Embedded Systems (2011)

Building safety-critical real-time systems out of inexpensive, non-real-time, COTS components is challenging. Although COTS components generally offer high performance, they can occasionally incur significant timing delays. To prevent this, we propose controlling the operating point of each shared resource (like the cache, memory, and interconnection buses) to maintain it below its saturation limit. This is necessary because the low-level arbiters of these shared resources are not typically designed to provide real-time guarantees. In this work, we introduce a novel system execution model, the Predictable Execution Model (PREM), which, in contrast to the standard COTS execution model, coschedules at a high level all active components in the system, such as CPU cores and I/O peripherals. In order to permit predictable, system-wide execution, we argue that real-time embedded applications should be compiled according to a new set of rules dictated by PREM. To experimentally validate our theory, we developed a COTS-based PREM testbed and modified the LLVM Compiler Infrastructure to produce PREM-compatible executables.
Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments (2017)

The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand-receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling.
Favorable Long-Term Outcome after Liver-Kidney Transplant for Recurrent Hemolytic Uremic Syndrome Associated with a Factor H Mutation (2006)

A male child initially presented with atypical hemolytic uremic syndrome (HUS) at the age of 4 months and progressed within weeks to end stage renal disease (ESRD). At the age of 2 years he received a live-related kidney transplant from his mother, which, despite initial good function, was lost to recurrent disease after 2 weeks. Complement factor H analysis showed low serum levels and the presence of two mutations on different alleles (c.2918G > A, Cys973Tyr and c.3590T > C, Val1197Ala). His survival on dialysis was at risk because of access failure and recurrent bacteremic episodes. Therefore, at the age of 5 years he received a combined liver-kidney transplant with pre-operative plasma exchange. Initial function of both grafts was excellent and this has been maintained for over 2 years. This report suggests that despite setbacks in previous experience, combined liver-kidney transplantation offers the prospect of a favorable long-term outcome for patients with HUS associated with complement factor H mutations.
모바일 웹 크롤링과 GPS를 이용한 지역 뉴스레이터 설계 및 구현 (2017)

본 논문은 지역에 관심이 많은 사용자들이 실시간으로 모바일 웹페이지 형태의 뉴스를 제공 받을 수 있는 시스템을 설계하고 이를 제작하였다. 사용자는 실시간으로 본인이 위치한 지역을 대상으로 종합되어지는 뉴스를 모바일 웹페이지 형태의 오브젝트로 제공받는다. 본 연구를 통해 지역 관심도 향상 및 지역 개발 촉진 및 관광시설 피드백 활성화 효과의 기대가 가능하다.
Spin accumulation in metallic nanoparticles (2007)

The rapid development of spin electronics has emphasized the importance of spin accumulation to transport properties and spin manipulation for quantum computing. The latter requires sufficiently long spin-relaxation times, that may be achieved in nanometric particles. Spin accumulation is then expected to take place and strongly affect the transport properties of the particles. The main transport phenomena occurring in nanoparticles will be reviewed, as well as their interplay with spin accumulation. Recent experimental results confirming the theoretical predictions will also be presented. They show clear evidence of the enhancement of the spin-relaxation time in nanometric particles and are promising for the development of spin-electronics devices.
Genome-wide analysis of gene expression in intestinal-type gastric cancers using a complementary DNA microarray representing 23,040 genes. (2002)

To shed light on mechanisms that underlie development and/or progression of intestinal-type gastric cancer, we compared expression profiles of cancer cells obtained by laser-capture microdissection of 20 intestinal-type gastric tumors with expression of genes in corresponding noncancerous mucosae, by a cDNA microarray consisting of 23,040 genes. We identified 61 genes that were commonly up-regulated and 63 that were commonly down-regulated in the cancer tissues. Altered expression of 12 of those genes was associated with lymph node metastasis. A "predictive score," based on expression profiles of five of the genes that were able to distinguish tumors with metastasis from node-negative tumors in our panel, correctly diagnosed the lymph node status of nine additional gastric cancers. This genome-wide information contributes to an improved understanding of molecular changes during the development of intestinal-type gastric cancers. It may help clinicians predict metastasis to lymph nodes and assist researchers in identifying novel therapeutic targets for this type of cancer.
Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium (2021)

Since its emergence in 2019, circulating populations of the new coronavirus (CoV) continuously acquired genetic diversity. At the end of 2020, a variant named 20I/501Y.V1 (lineage B.1.1.7) emerged and replaced other circulating strains in several regions. This phenomenon has been poorly associated with biological evidence that this variant and the original strain exhibit different phenotypic characteristics. Here, we analyze the replication ability of this new variant in different cellular models using for comparison an ancestral D614G European strain (lineage B1). Results from comparative replication kinetics experiments <i>in vitro</i> and in a human reconstituted bronchial epithelium showed no difference. However, when both viruses were put in competition in human reconstituted bronchial epithelium, the 20I/501Y.V1 variant outcompeted the ancestral strain. All together, these findings demonstrate that this new variant replicates more efficiently and may contribute to a better understanding of the progressive replacement of circulating strains by the severe acute respiratory CoV-2 (SARS-CoV-2) 20I/501Y.V1 variant. <b>IMPORTANCE</b> The emergence of several SARS-CoV-2 variants raised numerous questions concerning the future course of the pandemic. We are currently observing a replacement of the circulating viruses by the variant from the United Kingdom known as 20I/501Y.V1, from the B.1.1.7 lineage, but there is little biological evidence that this new variant exhibits a different phenotype. In the present study, we used different cellular models to assess the replication ability of the 20I/501Y.V1 variant. Our results showed that this variant replicates more efficiently in human reconstituted bronchial epithelium, which may explain why it spreads so rapidly in human populations.
Stable Gene Silencing in Human Monocytic Cell Lines Using Lentiviral-delivered Small Interference RNA (2004)

Studying mononuclear phagocyte cell biology through genetic manipulation by non-viral transfection methods has been challenging due to the dual problems of low transfection efficiency and the difficulty in obtaining stable transfection. To overcome this problem, we developed a system for mediating RNA interference in monocytic cells. The p110alpha isoform of phosphoinositide 3-kinases (PI3Ks) was silenced using a lentiviral vector expressing short hairpin RNA (shRNA). This resulted in the generation of stable THP-1 and U-937 monocytic cell lines deficient in p110alpha. Notably, p110alpha was silenced without affecting levels of either the other class I(A) PI3K catalytic subunits p110beta and p110delta, or the p85alpha regulatory subunit. The role of p110alpha in mediating cell adherence was examined. Monocyte adherence induced in response to either lipopolysaccharide (LPS) or 1alpha,25-dihydroxycholecalciferol (D(3)) was blocked by the PI3K inhibitor LY294002. However, although adherence induced in response to D(3) was sensitive to silencing of p110alpha, LPS-induced adherence was not. Expression of the monocyte differentiation marker CD11b was also induced by D(3) in a PI3K-dependent manner and gene silencing using shRNA showed that p110alpha was also required for this effect. Taken together, these findings demonstrate that LPS and D(3) use distinct isoforms of class I(A) PI3K to induce functional responses and that lentiviral-mediated delivery of shRNA is a powerful approach to study monocyte biology.
Immune Complex-Bearing Follicular Dendritic Cells Deliver a Late Antigenic Signal That Promotes Somatic Hypermutation (2008)

We reasoned that immune complex (IC)-bearing follicular dendritic cells (FDCs) promote somatic hypermutation (SHM). This hypothesis was tested in murine germinal center reactions induced in vitro by coculturing 6-day (4-hydroxy-3-nitrophenyl) acetyl-primed but unmutated lambda+ B cells, chicken gamma-globulin (CGG) memory T cells, FDCs, and ICs (anti-CGG plus NP-CGG). Mutations in primed lambda+ B cells were obtained only when both FDCs and immunogen were present. FDCs alone promoted B cell survival and Ab production but there were no mutations without more immunogen. Moreover, the mutation rate was enhanced when FDCs were activated. Trapped ICs ranged from 200 to 500 A apart on FDC membranes and this correlated with the periodicity known to optimally signal BCRs. FDCs are unique in their ability to retain ICs for months and a second signal mediated by FDC-ICs appeared to be needed a week or more after immunization by immunogen persisting on FDCs. However, the time needed to detect extensive SHM could be reduced to 7 days if ICs were injected together with memory T cells in vivo. In marked contrast, no mutations were apparent after 7 days in vivo if ICs were replaced by free Ag that would not load on FDCs until Ab was produced. The data suggest that specific Ab production leads to the following events: Ab encounters Ag and ICs are formed, ICs are trapped by FDCs, B cells are stimulated by periodically arranged Ag in ICs on FDCs, and this late antigenic signal promotes SHM.
Biological Variation Data Applied to the Selection of Serum Lipid Ratios Used as Risk Markers of Coronary Heart Disease (1992)

The biological variation of several relative lipid quantities, calculated as the ratios between the concentrations of various serum lipids and apolipoproteins, has been estimated over a one-year period. The medians of the within-subject biological coefficient of variation, separated by sex when significant differences exist, were 15.4% for [apolipoprotein A-I]/[apolipoprotein B], 6.8% for [high-density lipoprotein (HDL)-cholesterol]/[cholesterol], 10.5% and 17.6% (women and men, respectively) for [HDL2-cholesterol]/[HDL-cholesterol], 13.6% for [HDL2-cholesterol]/[HDL3-cholesterol], 10.6% for [low-density lipoprotein (LDL)-cholesterol]/[apolipoprotein B], 10.6% and 8.7% (women and men, respectively) for [LDL-cholesterol]/[cholesterol], and 6.3% for [LDL-cholesterol]/[HDL-cholesterol]. From these data, we have calculated the critical difference for significant change detection, the index of individuality, and the goal for the between-day imprecision. Concerning within-subject biological variation, the best ratios for the detection of risk of coronary heart disease and the monitoring of intervention are [LDL-cholesterol]/[HDL-cholesterol] and [HDL-cholesterol]/[cholesterol]. The index of individuality obtained in this study indicates that the use of population-based reference values is inadequate for interpreting the ratios studied.
Exenatide versus Insulin Glargine in Patients with Suboptimally Controlled Type 2 Diabetes (2005)

Exenatide and insulin glargine achieved similar improvements in overall glycemic control in patients with type 2 diabetes that was suboptimally controlled with oral combination therapy. Exenatide was associated with weight reduction and had a higher incidence of gastrointestinal adverse effects than insulin glargine.
Probabilistic Latent Semantic Analysis (2013)

Probabilistic Latent Semantic Analysis is a novel statistical technique for the analysis of two-mode and co-occurrence data, which has applications in information retrieval and filtering, natural language processing, machine learning from text, and in related areas. Compared to standard Latent Semantic Analysis which stems from linear algebra and performs a Singular Value Decomposition of co-occurrence tables, the proposed method is based on a mixture decomposition derived from a latent class model. This results in a more principled approach which has a solid foundation in statistics. In order to avoid overfitting, we propose a widely applicable generalization of maximum likelihood model fitting by tempered EM. Our approach yields substantial and consistent improvements over Latent Semantic Analysis in a number of experiments.
Introduction of liposome-encapsulated SV40 DNA into cells. (1980)

DNA, isolated from Simian virus 40 (SV40), has been encapsulated in large (0.4-micrometer diameter) unilamellar phospholipid vesicles. The procedure used for liposome preparation encapsulated the SV40 DNA at high efficiency (30 to 50% entrapment) and did not alter the physical or biological properties of the DNA molecules. The biological activity of the liposome-entrapped viral DNA was determined by plaque assays on a permissive monkey cell line. The infectivity of liposome-entrapped SV40 DNA was enhanced at least 100-fold over that of free naked DNA. Importantly, the infectivity of vesicle-entrapped DNA was resistant to DNase digestion, dependent on the amount of DNA encapsulated per vesicle and on the vesicle lipid composition. Liposomes composed of phosphatidylserine were the most efficient for delivery of DNA to cells (1.8 x 10(3) plaque-forming units/micrograms of DNA). Following the incubation of DNA-containing liposomes with cells, their infectivity could be enhanced an additional 10- to 200-fold by exposing the cells to high concentrations of polyethylene glycol or glycerol. Under these conditions the infectivity of liposome-encapsulated SV40 DNA (3 x 10(5) plaque-forming units/microgram) was comparable with values reported using the calcium phosphate method. In addition to providing a sensitive assay for monitoring and optimizing the delivery of vesicle contents to cells, the liposome-mediated delivery of nucleic acids may have potential for increasing the efficiency of DNA delivery to cells and for extending the number of cell types which can be transformed or transfected.
2-D Index Map Coding for HEVC Screen Content Compression (2015)

This paper introduces a 2-D index map coding of the palette mode in screen content coding extension of the High-Efficiency Video Coding (HEVC SCC) standard to further improve the compression performance. In contrast to the current 1-D search using RUN to represent the length of matched string, we bring the block width and height to describe the arbitrary rectangle shape. We also use the block vector displacement to signal the matched block distance efficiently. By enlarging the search range from current coding tree unit (CTU) to a small neighbor CTU window (i.e., 3×5 CTUs), it provides the coding efficiency comparable to the case that full-frame intra block copy is used. It is more practical to use the local search window in real life considering the trade-off between the coding efficiency and implementation cost.
Amidines. Part 41. Effects of substitution at the amidino carbon atom and at the imino nitrogen atom on the preferred configuration at the CN bond in the 13C NMR spectra of N 1,N 1-dimethyl-N 2-alkylamidines (2001)

A new approach, based on the correlation between the chemical shifts of carbon atoms directly bonded to the two nitrogen atoms, enabled the determination of the preferred configuration of the CN bond in N1,N1-dimethylamidines containing a CH2 group at the imino nitrogen atom. The 13C NMR chemical shifts of 40 N1,N1-dimethyl-N2-alkylamidines and 35 N1,N1-dimethyl-N2-benzylamidines of general formula Me2N–CR1NR2, each divided into seven series depending on the substituent R1, have been determined in CDCl3 solutions. The V-shaped relationship between the chemical shifts of carbon atoms bonded directly to the amino and the imino nitrogen atoms reveals that, in the case of N2-alkyl and N2-benzylamidines, the volume of the substituent (R1) at the amidino carbon atom determines the preferred isomer. For amidines where R1 is isopropyl, isobutyl, tert-butyl or cyclohexyl the Z configuration is the preferred one.