gebhart/patrepeval huggingface dataset:
DNA Sequencing Protocols (1993)

The purpose of DNA Sequencing Protocols is to provide detailed practical procedures for the widest range of DNA sequencing meth­ ods, and we believe that all the vanguard techniques now being applied in this fast-evolving field are comprehensively covered. Sequencing technology has advanced at a phenomenal rate since the original methods were first described in the late 1970s and there is now a huge variety of strategies and methods that can be employed to determine the sequence of any DNA of interest. More recently, a large number of new and innovative sequencing techniques have been developed, including the use of such novel polymerases as Tag poly­ merase and Sequenase, the harnessing of PCR technology for linear amplification (cycle) sequencing, and the advent of automated DNA sequencers. DNA sequencing is surely one of the most important techniques in the molecular biology laboratory. Sequence analysis is providing an increasingly useful approach to the characterization of biological systems, and major multinational projects are already underway to map and sequence the entire genome of organisms, such as Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, and Homo sapiens. Most scientists recognize the importance of DNA sequence data and perceive DNA sequencing as a valuable and indispensable aspect of their work. Recent technological advances, especially in the area of automated sequencing, have removed much of the drudg­ ery that was formerly associated with the technique, whereas innova­ tive computer software has greatly simplified the analysis and manipulation of sequence data
Synthesis and Spectroscopic Properties of Fused‐Ring‐Expanded Aza‐Boradiazaindacenes (2011)

A series of fused-ring-expanded aza-boradiazaindacene (aza-BODIPY) dyes have been synthesized by reacting arylmagnesium bromides with phthalonitriles or naphthalenedicarbonitriles. An analysis of the structure-property relationships has been carried out based on X-ray crystallography, optical spectroscopy, and theoretical calculations. Benzo and 1,2-naphtho-fused 3,5-diaryl aza-BODIPY dyes display markedly red shifted absorption and emission bands in the near-IR region (>700 nm) due to changes in the energies of the frontier MOs relative to those of 1,3,5,7-tetraaryl aza-BODIPYs. Only one 1,2-naphtho-fused aza-BODIPY of the three possible isomers is formed due to steric effects, and 2,3-naphtho-fused compounds could not be characterized because the final BF(2) complexes are unstable in solution. The incorporation of a -N(CH(3))(2) group at the para-positions of a benzo-fused 3,5-diaryl aza-BODIPY quenches the fluorescence in polar solvents and results in a ratiometric pH response, which could be used in future practical applications as an NIR "turn-on" fluorescence sensor.
Heparin-Induced Hyperkalemia: Report of a Case (1980)

A 77-year-old diabetic man with a creatinine clearance of 23--27 ml/min developed hyperkalemia while receiving heparin for peripheral arterial insufficiency. Discontinuation of this agent led to resolution of hyperkalemia as the plasma aldosterone concentration multiplied by sixfold. Renal insufficiency may have predisposed this patient to the development of hyperkalemia when heparin therapy suppressed aldosterone synthesis.
The role of left prefrontal cortex in language and memory (1998)

This article reviews attempts to characterize the mental operations mediated by left inferior prefrontal cortex, especially the anterior and inferior portion of the gyrus, with the functional neuroimaging techniques of positron emission tomography and functional magnetic resonance imaging. Activations in this region occur during semantic, relative to nonsemantic, tasks for the generation of words to semantic cues or the classification of words or pictures into semantic categories. This activation appears in the right prefrontal cortex of people known to be atypically right-hemisphere dominant for language. In this region, activations are associated with meaningful encoding that leads to superior explicit memory for stimuli and deactivations with implicit semantic memory (repetition priming) for words and pictures. New findings are reported showing that patients with global amnesia show deactivations in the same region associated with repetition priming, that activation in this region reflects selection of a response from among numerous relative to few alternatives, and that activations in a portion of this region are associated specifically with semantic relative to phonological processing. It is hypothesized that activations in left inferior prefrontal cortex reflect a domain-specific semantic working memory capacity that is invoked more for semantic than nonsemantic analyses regardless of stimulus modality, more for initial than for repeated semantic analysis of a word or picture, more when a response must be selected from among many than few legitimate alternatives, and that yields superior later explicit memory for experiences.
A comparative study of linked list sorting algorithms (1996)

Carraway recently published an article [2] describing a sorting algorithm (the sediment sort) for doubly linked lists. He claimed that the sediment sort is one of the fastest and most efficient sorts for linked list, and planned to determine its complexity. In this article, a comparative study will be presented to show that the sediment sort is only a minor variation of the bubble sort which has been known to the computer science community for more than three decades and that the sediment sort is perhaps the slowest algorithm for sorting linked lists.
Epitaxial lift-off and its applications (1993)

In this paper the authors will give an overview of the epitaxial lift-off (ELO) technique and its applications. This first part will describe the basic technology, which includes chemical lift-off, handling bonding, stress, alignment, etc. The second part will give an overview of device results obtained with ELO (LED and lasers on Si, MESFETs on InP, OEICs etc).
Therapeutic bispecific antibodies: The selection of stable single-chain fragments to overcome engineering obstacles. (2010)

The clinical success of mAbs continues to reinforce antibody engineering as an essential tool for the development of biologics. Research focused on discovering the next generation of therapeutics has prompted a revisiting of the concept of bispecific antibodies (bsAbs). Recently, clinical programs investigating combinations of mAb therapies have renewed interest in the applications of bsAbs. However, because of challenges with production, efforts directed toward the development of bsAbs have yet to yield a product approved by the FDA. The current status of these proteins implies that the strategies for constructing therapeutic bsAbs will likely require a highly refined design plan at the outset of the engineering process. Antibody fragments are attractive building blocks for the assembly of bsAbs. Of the recombinant antibody fragments, single-chain variable fragments (scFvs) offer the advantage of expression as a single polypeptide, thereby greatly simplifying production. However, issues with stability have plagued these proteins and limit the application of scFvs as therapeutics. Recent advances in selection processes using display platforms have been reported that facilitate the 'evolution' of scFvs to obtain stabilities comparable with those of mAbs. The timely advances in scFv engineering parallel the resurgence of bsAbs and enable the construction of dual-targeting proteins that can be manufactured as therapeutics.
Clinical aspects of coal workers' pneumoconiosis and silicosis. (1993)

Coal workers' pneumoconiosis and silicosis are two important respiratory disorders that result from the inhalation of respirable particles in mining. This chapter focuses on the clinical aspects of these disorders, including their pathogenesis and pathology, and approaches to their evaluation and management.
Modulation-doped n-type Si/SiGe with inverted interface (1994)

We report the growth of n-type modulation-doped Si/SiGe with the doped SiGe supply layer underneath the strained Si channel. The mobility and charge density are measured in samples with 2- and 3-nm-thick spacers using gated Hall measurements. A peak room temperature mobility of 2200 cm2/V s is measured at a sheet density of 2.5×1012 cm−2. The measurements indicate a clear mobility modulation especially near threshold. Our layer design allows the gate to induce a sheet charge density of up to 3.2×1012 cm−2, before any significant reduction in the mobility is observed.
A novel subset of B7-H3+CD14+HLA-DR−/lowmyeloid-derived suppressor cells are associated with progression of human NSCLC (2015)

Myeloid-derived suppressor cells (MDSC) potently inhibit antitumor immune responses, and thereby promoti tumor progression and metastasis. However, the nature of human tumor-infiltrating MDSC remains poorly characterized. Here, we find B7-H3 is exclusively expressed on a subset of intratumoral CD14<sup>+</sup>HLA-DR<sup>-/low</sup> MDSC but absent from adjacent normal lung tissues of patients with non-small cell lung carcinoma (NSCLC). Cytokine analysis revealed that B7-H3<sup>+</sup>CD14<sup>+</sup>HLA-DR<sup>-/low</sup> MDSC (B7-H3<sup>+</sup>MDSC) produced higher levels of IL-10 and TNFα but lower levels of IL-1β and IL-6 when compared with B7-H3<sup>-</sup>CD14<sup>+</sup>HLA-DR<sup>-/low</sup> myeloid-derived suppressor cells (B7-H3<sup>-</sup>MDSC). In a murine lung cancer model, B7-H3<sup>+</sup>MDSCs were found only in the tumor microenvironment and their frequencies increased during tumor progression. Clinical data analysis indicated that a higher frequency of B7-H3<sup>+</sup>MDSCs was associated with reduced recurrence-free survival in patients with NSCLC. Taken together, we identify a novel subset of MDSCs within the tumor microenvironment that fosters tumor progression.
Grass genomes (1998)

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that insert between genes. These retroelements are less abundant in smaller genome plants, including rice and sorghum. Although 5- to 200-kb blocks of methylated, presumably heterochromatic, retrotransposons flank most maize genes, rice and sorghum genes are often adjacent. Similar genes are commonly found in the same relative chromosomal locations and orientations in each of these three species, although there are numerous exceptions to this collinearity (i.e., rearrangements) that can be detected at the levels of both the recombinational map and cloned DNA. Evolutionarily conserved sequences are largely confined to genes and their regulatory elements. Our results indicate that a knowledge of grass genome structure will be a useful tool for gene discovery and isolation, but the general rules and biological significance of grass genome organization remain to be determined. Moreover, the nature and frequency of exceptions to the general patterns of grass genome structure and collinearity are still largely unknown and will require extensive further investigation.
Therapy of Patients with T-cell Lymphomas and Leukemias Using an Anti-CD7 Monoclonal Antibody-Rich a Chain Immunotoxin (1997)

Anti-CD7-dgA, DA7, consists of deglycosylated ricin A chain coupled to a mouse monoclonal anti-human CD7 antibody. This study determined the maximally tolerated dose (MTD) of this immunotoxin administered as a one hour infusion over five days to 11 patients with T-cell lymphoma (>30% CD7+ malignant cells). The MTD was 0.2 mg/kg/day or 1 mg/kg/120 hours (maximal toxicity grade 3) with vascular leak syndrome (VLS) as dose-limiting toxicity (DLT). Predictors of severe VLS included age and absence of circulating lymphoma cells. Two partial responses and one minimal response were seen. Patients with minimal lymphoma burden or T-cell large granular lymphocyte (LGL) leukemia showed the best responses. The mean maximal serum concentration of immunotoxin at the MTD was 2.5 ug/ml. The mean alpha-phase half-life was 1.5 hours and the mean beta-phase half-life was 8 hours. Repeated dosing had minimal effects on either peak serum immunotoxin concentrations or serum half-lives. While human antimouse antibodies were observed, they were low in concentration (<55 ng/ml). Human anti-ricin antibody was elevated in one patient (190 ng/ml). VLS presented with hypoalbuminemia, dyspnea, pulmonary edema, aphasia, and peripheral edema and cleared over a two week period. Serum fibronectin levels were measured in three patients and were very low in one patient who developed VLS. No specific binding of DA7 immunotoxin was seen with vascular endothelium in various human tissues.
ROMP Reactivity of endo- and exo-Dicyclopentadiene (2002)

The activation parameters for the ring-opening metathesis polymerization (ROMP) of endo- (1) and exo-dicyclopentadiene (2), endo-1,2-dihydrodicylopentadiene (3), and norbornene (4) in the presence of Grubbs' catalyst were determined using in situ NMR. The exo isomer of DCP was found to be more than an order of magnitude more reactive than the endo isomer. endo-DCP was found to have reactivity similar to its partially saturated counterpart 3, suggesting that the cause of the rate difference between the two isomers of DCP is primarily steric in nature. This interaction is shown to be predominantly entropic and is suspected to originate from an interaction of the penultimate repeat unit and the incoming monomer. Additionally, the alkylidene generated during the polymerization of endo-DCP was found to form an intramolecular complex, but this complex only affects the rate slightly.
Site-Specific Recombinases for Manipulation of the Mouse Genome (2009)

Site-specific recombination systems are widespread and popular tools for all scientists interested in manipulating the mouse genome. In this chapter, we focus on the use of site-specific recombinases (SSR) to unravel the function of genes of the mouse. In the first part, we review the most commonly used SSR, Cre and Flp, as well as the newly developed systems such as Dre and PhiC31, and we present the inducible SSR systems. As experience has shown that these systems are not as straightforward as expected, particular attention is paid to facts and artefacts associated with their production and applications to study the mouse genome. In the next part of this chapter, we illustrate new applications of SSRs that allow engineering of the mouse genome with more and more precision, including the FLEX and the RMCE strategies. We conclude and suggest a workflow procedure that can be followed when using SSR to create your mouse model of interest. Together, these strategies and procedures provide the basis for a wide variety of studies that will ultimately lead to the analysis of the function of a gene at the cellular level in the mouse.
In silico screening for tumour‐specific expressed sequences in human genome (2001)

A computer-based differential display tool named HsAnalyst has been developed and successfully used for the comparison of expression patterns in a set of tumours versus a set of normal tissues. A list of EST clusters highly represented in tumours and rarely observed in normal tissues has been developed as a resulting output file of the program. These differentially expressed EST clusters (genes) can be useful for developing new tumour markers and prognostic indicators for a wide set of human malignancies. Tumour-specific protein-coding genes may be considered a manifestation of tumour-specific gene expression.
Advances in the genetics of endometriosis (2010)

Endometriosis is a gynecological disease characterized by implantation of endometrial tissue outside of the uterus. Early familial aggregation and twin studies noted a higher risk of endometriosis among relatives. Studies on the roles of the environment, genetics and aberrant regulation in the endometrium and endometriotic lesions of women with endometriosis suggest that endometriosis arises from the interplay between genetic variants and environmental factors. Elucidating the hereditary component has proven difficult because multiple genes seem to produce a susceptibility to developing endometriosis. Molecular techniques, including linkage and genome-wide analysis, have identified candidate genes located near known loci related to development and regulation of the female reproductive tract. As new candidate genes are discovered and hereditary pathways identified using technologies such as genome-wide analysis, the possibility of prevention and treatment becomes more tangible for millions of women affected by endometriosis. Here, we discuss the advances of genetic research in endometriosis and describe technologies that have contributed to the current understanding of the genetic variability in endometriosis, variability that includes regulatory polymorphisms in key genes.
Atomic layer epitaxy growth of titanium dioxide thin films from titanium ethoxide (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAtomic layer epitaxy growth of titanium dioxide thin films from titanium ethoxideMikko Ritala, Markku Leskela, and Eero RauhalaCite this: Chem. Mater. 1994, 6, 4, 556–561Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/cm00040a035https://doi.org/10.1021/cm00040a035research-articleACS PublicationsRequest reuse permissionsArticle Views842Altmetric-Citations92LEARN 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
Monocyte enrichment from leukapheresis products by using the Elutra cell separator (2007)

These results indicate that the Elutra cell separator allows for fast and easy enrichment of monocytes within a closed system. Furthermore, these monocytes can be differentiated into functionally mature DCs. Compared to plastic adherence and immunomagnetic selection methods, the elutriation procedure is inexpensive, efficient, and very effective.
Tyrosine kinase inhibitor–induced CD70 expression mediates drug resistance in leukemia stem cells by activating Wnt signaling (2015)

In chronic myelogenous leukemia (CML), oncogenic BCR-ABL1 activates the Wnt pathway, which is fundamental for leukemia stem cell (LSC) maintenance. Tyrosine kinase inhibitor (TKI) treatment reduces Wnt signaling in LSCs and often results in molecular remission of CML; however, LSCs persist long term despite BCR-ABL1 inhibition, ultimately causing disease relapse. We demonstrate that TKIs induce the expression of the tumor necrosis factor (TNF) family ligand CD70 in LSCs by down-regulating microRNA-29, resulting in reduced CD70 promoter DNA methylation and up-regulation of the transcription factor specificity protein 1. The resulting increase in CD70 triggered CD27 signaling and compensatory Wnt pathway activation. Combining TKIs with CD70 blockade effectively eliminated human CD34(+) CML stem/progenitor cells in xenografts and LSCs in a murine CML model. Therefore, targeting TKI-induced expression of CD70 and compensatory Wnt signaling resulting from the CD70/CD27 interaction is a promising approach to overcoming treatment resistance in CML LSCs.
Amino acid residues that affect interaction of tissue-type plasminogen activator with plasminogen activator inhibitor 1. (1990)

Fibrinolysis is regulated in part by the interaction between tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor 1 (PAI-1, a serine protease inhibitor of the serpin family). It is known from our earlier work that deletion of a loop of amino acids (residues 296-302) from the serine protease domain of t-PA suppresses the interaction between the two proteins without altering the reactivity of t-PA towards its substrate, plasminogen. To define more precisely the role of individual residues within this loop, we have used site-directed mutagenesis to replace Lys-296, Arg-298, and Arg-299 with negatively charged glutamic residues. Replacement of all three positively charged amino acids generates a variant of t-PA that associates inefficiently with PAI-1 and is highly resistant to inhibition by the serpin. Two t-PAs with point mutations (Arg-298----Glu and Arg-299----Glu) are partially resistant to inhibition by PAI-1 and associate with the serpin at intermediate rates. Other point mutations (Lys-296----Glu, His-297----Glu, and Pro-301----Gly) do not detectably affect the interaction of t-PA with PAI-1. None of these substitutions has a significant effect on the rate of catalysis by t-PA or on the affinity of the enzyme for its substrate, plasminogen. On the basis of these results, we propose a model in which positively charged residues located in a surface loop near the active site of t-PA form ionic bonds with complementary negatively charged residues C-terminal to the reactive center of PAI-1.
CAD/CAM transtibial prosthetic sockets from central fabrication facilities: How accurate are they? (2007)

This research compares transtibial prosthetic sockets made by central fabrication facilities with their corresponding American Academy of Orthotists and Prosthetists (AAOP) electronic shape files and assesses the central fabrication process. We ordered three different socket shapes from each of 10 manufacturers. Then we digitized the sockets using a very accurate custom mechanical digitizer. Results showed that quality varied considerably among the different manufacturers. Four of the companies consistently made sockets within +/-1.1% volume (approximately 1 sock ply) of the AAOP electronic shape file, while six other companies did not. Six of the companies showed consistent undersizing or oversizing in their sockets, which suggests a consistent calibration or manufacturing error. Other companies showed inconsistent sizing or shape distortion, a difficult problem that represents a most challenging limitation for central fabrication facilities.