gebhart/patrepeval huggingface dataset:
Gene Expression Profiling using Nanostring Digital RNA Counting to Identify Potential Target Antigens for Melanoma Immunotherapy (2013)

The application of Nanostring RNA counting technology was used to directly quantitate the gene expression levels of multiple potential tumor antigens. Analysis of cell lines, 59 tumors, and normal tissues identified seven potential immunotherapy targets for the treatment of melanoma that could increase the number of patients potentially eligible for adoptive immunotherapy.
New Technology for the Synthesis of Vancomycin‐Type Biaryl Ring Systems (1997)

A mild, NiO-promoted cyclization leads to the synthesis of rigid 12-membered peptide–biaryl ring systems (example on the right) of the type found in the glycopeptide antibiotic vancomycin. This synthetic method brings us a step closer to the total synthesis of vancomycin itself. Boc = tert-butoxycarbonyl; X, for example, O; R, for example, H.
ChemInform Abstract: Gel Precursor to Silicon Oxycarbide Glasses with Ultrahigh Ceramic Yield. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Total recall II: Query expansion revisited (2011)

Most effective particular object and image retrieval approaches are based on the bag-of-words (BoW) model. All state-of-the-art retrieval results have been achieved by methods that include a query expansion that brings a significant boost in performance. We introduce three extensions to automatic query expansion: (i) a method capable of preventing tf-idf failure caused by the presence of sets of correlated features (confusers), (ii) an improved spatial verification and re-ranking step that incrementally builds a statistical model of the query object and (iii) we learn relevant spatial context to boost retrieval performance. The three improvements of query expansion were evaluated on standard Paris and Oxford datasets according to a standard protocol, and state-of-the-art results were achieved.
Specificity profiling of CRISPR system reveals greatly enhanced off-target gene editing (2020)

To explore the editing specificity of CRISPR/Cpf1 system, effects of target mutation were systematically examined using a reporter activation assay, with a set of single-nucleotide mutated target site. Consistent with our previous study performed with CRISPR/Cas9, a "core" sequence region that is highly sensitive to target mutation was characterized. The region is of 4-nucleotide long, located from +4 to +7 position of the target site, and positioned within a positively charged central channel when assembled into Cpf1 endonuclease. Single-nucleotide mutation at the core sequence could abolish gene editing mediated by a however active sgRNA. With a great majority of the target sites, a kind of 'super' off-target gene editing was observed with both CRISPR/Cpf1 and CRISPR/Cas9. For a given target site, mutation at certain positions led to greatly enhanced off-target gene editing efficacy, even up to 10-fold of that of the fully-matched target. Study further found that these effects were determined by the identity of target nucleotide, rather than the nucleotide of crRNA. This likely suggests that the interactions between target nucleotide and the endonuclease are involved in this process.
Modulation of the cellular and humoral immune responses of tumor patients by mistletoe therapy. (1998)

There is evidence from recent data that mistletoe extracts exert immunostimulatory properties which could explain their therapeutic effects observed in some tumor patients. Aim of our study was, therefore, to investigate the effect of a subcutaneous 16-weeks therapy with a mistletoe extract (ABNOBAviscum Mali, AM) on the cellular and humoral immune responses in eight breast cancer patients. Mistletoe therapy induced a strong initial proliferation of peripheral blood mononuclear cells (PBMC) in all individuals, which, however, decreased in six patients during the observation period, indicating that not only activating but also inhibitory mechanisms have been induced. In all supernatants of AM-stimulated cell cultures TNF-alpha or IL-6 were found, indicating the activation of cells of the monocyte-/macrophage lineage by mistletoe extracts. Further analyses revealed, that AM induced in vitro also the release of low amounts of IFN-gamma and IL-4 with individual variations. At the end of the therapy, a shift to Th1- related cytokines could be observed in the in vitro cell culture system. All patients produced anti-mistletoe lectin 1 antibodies of the IgG-type during therapy and in four of them additionally antibodies of the IgE-type were found. It, therefore, seems that AM can influence the Th1/Th2 balance and, in case of a Th1 shift, this may favourably influence the tumor growth.
What Makes a Visualization Memorable? (2013)

An ongoing debate in the Visualization community concerns the role that visualization types play in data understanding. In human cognition, understanding and memorability are intertwined. As a first step towards being able to ask questions about impact and effectiveness, here we ask: 'What makes a visualization memorable?' We ran the largest scale visualization study to date using 2,070 single-panel visualizations, categorized with visualization type (e.g., bar chart, line graph, etc.), collected from news media sites, government reports, scientific journals, and infographic sources. Each visualization was annotated with additional attributes, including ratings for data-ink ratios and visual densities. Using Amazon's Mechanical Turk, we collected memorability scores for hundreds of these visualizations, and discovered that observers are consistent in which visualizations they find memorable and forgettable. We find intuitive results (e.g., attributes like color and the inclusion of a human recognizable object enhance memorability) and less intuitive results (e.g., common graphs are less memorable than unique visualization types). Altogether our findings suggest that quantifying memorability is a general metric of the utility of information, an essential step towards determining how to design effective visualizations.
A serine and a lysine residue implicated in the catalytic mechanism of the Escherichia coli leader peptidase. (1993)

We report that a thiol leader peptidase, produced by replacing the critical serine at position 90 with a cysteine residue, is enzymatically active. In contrast to the wild-type leader peptidase, the thiol enzyme can be inactivated with N-ethylmaleimide, a cysteine-specific reagent. This strongly suggests that the serine 90 is involved in catalysis and is located at the active site. Of the three conserved basic residues in the signal peptidase family, only lysine 145 appears to be critical for catalysis; when lysine 145 was mutated to an alanine residue, leader peptidase K145A protein was inactive both in vitro and in vivo. A control experiment showed that the K145A mutant competes with the wild-type leader peptidase for substrate binding, confirming that the K145A mutation did not cause a global conformational change. The data provides evidence that catalysis of leader peptidase is carried out by a serine-lysine dyad.
Generation of angiostatin-like fragments from plasminogen by prostate-specific antigen (1999)

Angiostatin, a potent inhibitor of angiogenesis, tumour growth and metastasis, is a biologically active fragment of plasminogen, containing the kringle domains 1-4. It is generated from plasminogen by limited proteolysis. We show that prostate-specific antigen (PSA), a serine proteinase secreted by human prostate and human prostate cancer cells, is able to convert Lys-plasminogen to biologically active angiostatin-like fragments, containing kringles 1-4, by limited proteolysis of peptide bond Glu439-Ala440 in vitro. In an in vitro morphogenesis assay, the purified angiostatin-like fragments inhibited proliferation and tubular formation of human umbilical vein endothelial cells with the same efficacy as angiostatin. This finding might help to understand growth characteristics of prostate cancer, which usually has low microvessel density and slow proliferation.
Assembly of Amphiphilic Phenylacetylene Macrocycles at the Air−Water Interface and on Solid Surfaces (1996)

The assembly of amphiphilic phenylacetylene macrocycles (PAMs), with molecular structures that vary in terms of the nature and orientation of their pendant functional groups, has been studied on a Langmuir−Blodgett trough and after transfer onto solid substrates. These monolayer films are of interest as two-dimensional host matrices and shape selective membranes whose two-dimensional organization should bring together shape selective compartments. The disk-like PAMs can, in principle, adopt orientations in which the plane of the macrocycle can range from perpendicular (edge-on) to parallel (face-on) at the interface. PAMs functionalized with six hydrophilic groups around the periphery do not prefer the face-on orientation and are most likely tilted, perhaps in a poorly organized state. PAMs that have spatially segregated hydrophilic and hydrophobic groups adopt the edge-on orientation when the hydrophilic moieties are carboxylate groups. In contrast, PAMs appended with acid moieties do not lead to stable monolayers, most likely because they engage in strong intermolecular hydrogen bonding interactions as evidenced by 1H NMR and vapor pressure osmometry of the solutions. Monolayers of the dicarboxylate PAMs were transferred onto fused silica and Si(100) surfaces and these were in turn characterized by contact angle, ellipsometry, absorption FTIR, and angle-resolved X-ray photoelectron spectroscopies. Taken together these characterization experiments strongly support the hypothesis that the dicarboxylate PAMs form a well-ordered and stable two-dimensional array and that they adopt the edge-on configuration with near-vertical orientation of the macrocycle plane.
Emerging Small Molecule Drugs (2014)

Dyslipidaemia is a major risk factor for cardiovascular diseases. Pharmacological lowering of LDL-C levels using statins reduces cardiovascular risk. However, a substantial residual risk persists especially in patients with type 2 diabetes mellitus. Because of the inverse association observed in epidemiological studies of HDL-C with the risk for cardiovascular diseases, novel therapeutic strategies to raise HDL-C levels or improve HDL functionality are developed as complementary therapy for cardiovascular diseases. However, until now most therapies targeting HDL-C levels failed in clinical trials because of side effects or absence of clinical benefits. This chapter will highlight the emerging small molecules currently developed and tested in clinical trials to pharmacologically modulate HDL-C and functionality including new CETP inhibitors (anacetrapib, evacetrapib), novel PPAR agonists (K-877, CER-002, DSP-8658, INT131 and GFT505), LXR agonists (ATI-111, LXR-623, XL-652) and RVX-208.
How music and computers work (1994)

How do computers enhance live musical performances or change what we hear in film and television? What is MIDI and how does one go about putting a MIDI system together? Erik Holsinger, multimedia expert, brings us the answers to these and many other questions. Includes an exciting CD that plays on either a CD player, or, for graphics and sound, on a multimedia computer. -- Audio CD-ROM contains over an hour of music examples, technology demonstrations, and interviews
Abstract 3819: Activation of toll-like receptor 5 on breast cancer cells by flagellin suppresses tumor development and growth (2010)

Abstract Toll-like receptors (TLRs) play key roles in both the innate and adaptive immune systems, particularly in inflammatory responses against pathogen infection. Recent evidence showed that functional TLRs are also expressed on a wide variety of tumor cells; however, their activation exhibits either antitumor or pro-tumor effects. In order to investigate the function of TLR signaling pathways in breast cancers, we analyzed the expression of TLRs and their functional status in breast cancer cells by RT-PCR and NF-κB reporter gene assays in response to synthetic ligands for these receptors. We found that only TLR5 signaling is highly responsive in breast cancer cells. The phosphorylation levels of IκB, ERK, and JNK after flagellin (an agonist of TLR5) stimulation were increased in tumor cells. Activation of TLR5 signaling in tumor cells by flagellin induces the secretion of various cytokines and chemokines including interleukin-6, interleukin-8, and TNF-α. Moreover, flagellin/TLR5 signaling in MCF-7 cells inhibits an anchorage-independent growth, a hallmark of tumorigenic transformation. In addition, the secretion of soluble factors induced by flagellin contributed to the growth-inhibitive activity in an autocrine fashion. The inhibitive activity was further confirmed in mouse xenografts of human breast cancer model. Administration of flagellin inhibits tumor growth and therefore prolongs the survival of tumor-bearing mice. These findings indicate that TLR5 activation by flagellin mediates innate immunity to elicit potent antitumor activity in breast cancers, which may serve as a novel therapeutic target for human breast cancer therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3819.
A novel, potent, and specific ephrinA1-based cytotoxin against EphA2 receptor–expressing tumor cells (2007)

We have previously shown that the EphA2 receptor tyrosine kinase is overexpressed in glioblastoma multiforme (GBM) and represents a novel, attractive therapeutic target for the treatment of brain tumors. Here, we have developed an EphA2-targeted agent, ephrinA1-PE38QQR, a novel cytotoxin composed of ephrinA1, a ligand for EphA2, and PE38QQR, a mutated form of Pseudomonas aeruginosa exotoxin A. EphrinA1-PE38QQR showed potent and dose-dependent killing of GBM cells overexpressing the EphA2 receptor in cell viability and clonogenic survival assays, with an average IC(50) of approximately 10(-11) mol/L. The conjugate was also highly effective in killing breast and prostate cancer cells overexpressing EphA2. The cytotoxic effect of ephrinA1-PE38QQR was specific, as it was neutralized by an excess of EphA2 ligands. Moreover, normal human endothelial cells and breast cancer cells that do not overexpress EphA2, as well as GBM cells that have down-regulated EphA2, were not susceptible to the cytotoxin. EphrinA1-PE38QQR-mediated cytotoxicity induced caspase-dependent apoptosis, which was, however, not responsible for cell death in response to the conjugate. In addition, the conjugate elicited no changes in the activity of survival pathways such as phosphoinositide 3-kinase, measured by AKT phosphorylation. This is the first attempt to create a cytotoxic therapy using any of the ephrin ligands of either class (A or B) conjugated to a bacterial toxin. EphrinA1-PE38QQR is very potent and specific, produces cell death that is caspase independent, and forms the basis for the further development of clinically applicable EphA2-targeted cytotoxins.
GTSE1 expression represses apoptotic signaling and confers cisplatin resistance in gastric cancer cells (2015)

Our study identifies GTSE1 as a biomarker for cisplatin resistance in gastric cancer cells. This study also suggests the repressive role of GTSE1 in cisplatin induced apoptosis and signifies its potential utility as a therapeutic target for better clinical management of gastric cancer patients.
A software development system for FPGA-based data acquisition systems (1996)

We present a compiler, debugger, linker, and hardware/software interface for data acquisition systems based on hardware that is reconfigurable by the end user. Unlike earlier work, we choose a source language which is software-oriented. Our goal is to make systems with reconfigurable hardware accessible to scientists and engineers who are competent programmers but are not hardware literate.
Successful vitrification of human amnion-derived mesenchymal stem cells (2008)

Our results suggest that vitrification is a reliable and effective method for cryopreservation of HAMs.
Buffer capacity of biologics—from buffer salts to buffering by antibodies (2013)

Controlling pH is essential for a variety of biopharmaceutical process steps. The chemical stability of biologics such as monoclonal antibodies is pH-dependent and slightly acidic conditions are favorable for stability in a number of cases. Since control of pH is widely provided by added buffer salts, the current study summarizes the buffer characteristics of acetate, citrate, histidine, succinate, and phosphate buffers. Experimentally derived values largely coincide with values calculated from a model that had been proposed in 1922 by van Slyke. As high concentrated protein formulations become more and more prevalent for biologics, the self-buffering potential of proteins becomes of relevance. The current study provides information on buffer characteristics for pH ranges down to 4.0 and up to 8.0 and shows that a monoclonal antibody at 50 mg/mL exhibits similar buffer capacity as 6 mM citrate or 14 mM histidine (pH 5.0-6.0). Buffer capacity of antibody solutions scales linearly with protein concentration up to more than 200 mg/mL. At a protein concentration of 220 mg/mL, the buffer capacity resembles the buffer capacity of 30 mM citrate or 50 mM histidine (pH 5.0-6.0). The buffer capacity of monoclonal antibodies is practically identical at the process relevant temperatures 5, 25, and 40°C. Changes in ionic strength of ΔI=0.15, in contrast, can alter the buffer capacity up to 35%. In conclusion, due to efficient self-buffering by antibodies in the pH range of favored chemical stability, conventional buffer excipients could be dispensable for pH stabilization of high concentrated protein solutions.
Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene (1993)

Biphenyl dioxygenase catalyzes the first step in the aerobic degradation of polychlorinated biphenyls (PCBs). The nucleotide and amino acid sequences of the biphenyl dioxygenases from two PCB-degrading strains (Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707) were compared. The sequences were found to be nearly identical, yet these enzymes exhibited dramatically different substrate specificities for PCBs. Site-directed mutagenesis of the LB400 bphA gene resulted in an enzyme combining the broad congener specificity of LB400 with increased activity against several congeners characteristic of KF707. These data strongly suggest that the BphA subunit of biphenyl dioxygenase plays an important role in determining substrate selectivity. Further alteration of this enzyme can be used to develop a greater understanding of the structural basis for congener specificity and to broaden the range of degradable PCB congeners.
The JPEG still picture compression standard (1991)

A dvances <>"e,the pa,t decade ,n many aspects <d d,g,tal 1<,< t,,l<,lOg~-~3Pe~,alldev,ces for ,n,,tqeacqulsltlon,data storage, and b!LrIlappedprlrltlng and dlsplayhave hrought about many .pphcatlons of d,g,tal ,mag,ng HcIwcver, these appbcat,ons tend to be speclabzed due to their relativelyhigh cost With the possible except,o" of facslmde, d,g,tal ,magez arc nor commonplace In general-purpose comput,ng systemsthe waytext and geometric graphics are The majority of modern b"s,ness and cons"mer usage (If photographs and otber types of ,mages takes place through more trad!tlonal analog means
Rapid and Sensitive p53 Alteration Analysis in Biopsies from Lung Cancer Patients Using a Functional Assay and A Universal Oligonucleotide Array (2004)

The versatility and sensitivity of this new array assay should allow additional development of mutation profiling arrays that could be applied to biological samples with a low tumor cell content such as bronchial aspirates, bronchoalveolar lavage fluid, or serum.
Molecular Analysis of a Novel Winged Helix Protein, WIN (1997)

We have cloned a novel winged helix factor, WIN, from the rat insulinoma cell line, INS-1. Northern blot analysis demonstrated that WIN is highly expressed in a variety of insulinoma cell lines and rat embryonic pancreas and liver. In adults, WIN expression was detected in thymus, testis, lung, and several intestinal regions. We determined the DNA sequences bound in vitro by baculovirus-expressed WIN protein in a polymerase chain reaction-based selection procedure. WIN was found to bind with high affinity to the selected sequence 5'-AGATTGAGTA-3', which is similar to the recently identified HNF-6 binding sequence 5'-DHWATTGAYTWWD-3' (where W = A or T, Y = T or C, H is not G, and D is not C). We have isolated human WIN cDNAs by library screening and 5'-rapid amplification of cDNA ends. Sequence analysis indicates that the carboxyl terminus of human WIN has been previously isolated as a putative phosphorylation substrate, MPM2-reactive phosphoprotein 2 (MPP2); WIN may be regulated by phosphorylation. Alignment of the rat and human WIN cDNAs and their comparison with mouse genomic sequence revealed that the WIN DNA binding domain is encoded by four exons, two of which (exons 4 and 6) are alternatively spliced to generate at least three classes of mRNA transcripts. These transcripts were shown by RNase protection assay to be differentially expressed in different tissues. Alternative splicing within the winged helix DNA binding domain might result in modulation of DNA binding specificity.
The pharmacokinetics of hyperpolarized xenon: Implications for cerebral MRI (1997)

In this work, a compartmental model to predict the concentration of hyperpolarized xenon (Xe) in the brain is developed based on the well established kinetics of Xe and estimated T1 values for the compartments. For the gaseous compartments, T1 was set to 12 seconds. For the tissue compartments, T1 was set to 6 seconds. Three gas delivery techniques were modeled: hyperventilation followed by breath-hold, continual breathing, and hyperventilation followed by continual breathing. Based on Xe CT, it is estimated that the maximum concentration of Xe that could be breathed is 80%. Based on this value and the estimated maximum polarization of 50%, the peak gray matter concentration of hyperpolarized Xe is calculated to be .036 mM. This leads to an estimated signal-to-noise ratio (SNR), at 2 T, for hyperpolarized Xe that is a factor of 50 lower than the SNR for proton MRI. The peak concentration of hyperpolarized Xe was also calculated over a wide range of gas and tissue T1 values. This model also predicts that the arterial blood will have a concentration of hyperpolarized Xe that is 10 times greater than the concentration in gray matter. An interactive version of the model can be found on the World Wide Web at http:(/)/ric.uthscsa.edu/staff /charlesmartinphd.html.
Chemistry of the elements (1984)

Origin of the elements, isotopes and atomic weights Chemical periodicity and the periodic table Hydrogen Lithium, sodium, potassium, rubidium, caesium and francium Beryllium, magnesium, calcium, strontium, barium and radium Boron Aluminium, gallium, indium and thallium Carbon Silicon Germanium, tin and lead Nitrogen Phosphorus Arsenic, antimony and bismuth Oxygen Sulfur Selenium, tellurium and polonium The halogens: fluorine, chlorine, bromine, iodine and astatine The noble gases: helium, neon, argon, krypton, xenon, and radon Coordination and organometallic compounds Scandium, yttrium, lanthanum and actinium Titanium, zirconium and hafnium Vanadium, niobium and tantalum Chromium, molybdenum and tungsten Manganese, technetium and rhenium Iron, ruthenium and osmium Cobalt, rhodium and iridium Nickel, palladium, and platinum Copper, silver and gold Zinc, cadmium and mercury The lanthanide elements The actinideand transactinide elements (Z=90-112).