gebhart/patrepeval huggingface dataset:
Homologous recombination in prokaryotes: enzymes and controlling sites (1989)

A common step in prokaryotic recombination appears to be the synapsis of the 3'-end of single-stranded DNA with duplex DNA to form a D-loop. The enzymatic mechanisms by which 3'-ends are produced and by which D-loops are converted into recombinant molecules are illustrated by proposed mechanisms of recombination by the Escherichia coli RecBCD pathway and the phage lambda Red pathway. The enzymes promoting recombination and the special DNA sites at which they act are emphasized. Recombination by other E. coli pathways and in other prokaryotes is compared with these mechanisms.
Properties of the Adeno-Associated Virus Assembly-Activating Protein (2012)

ABSTRACT Adeno-associated virus (AAV) capsid assembly requires expression of the assembly-activating protein (AAP) together with capsid proteins VP1, VP2, and VP3. AAP is encoded by an alternative open reading frame of the cap gene. Sequence analysis and site-directed mutagenesis revealed that AAP contains two hydrophobic domains in the N-terminal part of the molecule that are essential for its assembly-promoting activity. Mutation of these sequences reduced the interaction of AAP with the capsid proteins. Deletions and a point mutation in the capsid protein C terminus also abolished capsid assembly and strongly reduced the interaction with AAP. Interpretation of these observations on a structural basis suggests an interaction of AAP with the VP C terminus, which forms the capsid protein interface at the 2-fold symmetry axis. This interpretation is supported by a decrease in the interaction of monoclonal antibody B1 with VP3 under nondenaturing conditions in the presence of AAP, indicative of steric hindrance of B1 binding to its C-terminal epitope by AAP. In addition, AAP forms high-molecular-weight oligomers and changes the conformation of nonassembled VP molecules as detected by conformation-sensitive monoclonal antibodies A20 and C37. Combined, these observations suggest a possible scaffolding activity of AAP in the AAV capsid assembly reaction.
Amyloid Formation by Transthyretin: From Protein Stability to Protein Aggregation (2003)

In recent years the issues of protein stability, folding and aggregation have become central in several pathological conditions and in particular in amyloid diseases. Here, we review the recent developments on the molecular mechanisms of amyloid formation by transthyretin (TTR), in particular, in what concerns to protein conformational stability, protein folding and aggregation. Transthyretin has been implicated in pathologies such as senile systemic amyloidosis (SSA), familial amyloid polyneuropathy (FAP) and familial amyloid cardiomyopathy (FAC) which are characterized by extracellular deposition of insoluble amyloid fibrils. SSA is generally a mild disorder and affects predominantly individuals over 80 years of age. In contrast, FAP is an autossomal dominant lethal disease, characterized by peripheral neuropathy, which may affect individuals from their twenties. While in SSA WT-TTR and its fragments are the major constituents of the amyloid fibrils, in FAP and FAC the amyloid fibrils are mostly constituted by variants of TTR. Today, more than 80 TTR mutations throughout the TTR sequence are known. Transthyretin is a homotetrameric protein found in the plasma and in the cerebral-spinal fluid, it is synthesized in the liver and in the choroid plexus of the brain, it has a total molecular mass of 55kDa and a high percentage of β-sheet. Current views on amyloid fibril formation by TTR state that, depending on the protein variant or solution conditions, the native tetrameric protein might dissociate to non-native or partially unfolded monomeric (or even dimeric) species with a high tendency for ordered aggregation into soluble oligomers which grow into insoluble oligomers and eventually mature amyloid fibrils. Thus, issues such as dissociation thermodynamics and dissociation kinetics of the native tetrameric TTR and thermodynamic stability and conformational fluctuations of the non-native TTR molecular species are essential in determining the amyloidogenic potential of different TTR variants. In addition, several other cellular and tissue factors must be involved in modulating the penetrance and age of onset of amyloid pathologies by TTR. Keywords: transthyretin, amyloid, familial amyloidotic polyneuropathy, protein stability, protein aggregation, misfolding
ChemInform Abstract: Studies on Quinazolines. Part 6. Asymmetric Synthesis of (S)‐(+)‐ and ( R)‐(‐)‐3‐((4‐(2‐Methoxyphenyl)piperazin‐1‐yl)methyl)‐5‐methylthio‐2,3‐ dihydroimidazo(1,2‐c)quinazolines. (1996)

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.
Influence of Intron Length on Alternative Splicing of CD44 (1998)

Although the splicing of transcripts from most eukaryotic genes occurs in a constitutive fashion, some genes can undergo a process of alternative splicing. This is a genetically economical process which allows a single gene to give rise to several protein isoforms by the inclusion or exclusion of sequences into or from the mature mRNA. CD44 provides a unique example; more than 1,000 possible isoforms can be produced by the inclusion or exclusion of a central tandem array of 10 alternatively spliced exons. Certain alternatively spliced exons have been ascribed specific functions; however, independent regulation of the inclusion or skipping of each of these exons would clearly demand an extremely complex regulatory network. Such a network would involve the interaction of many exon-specific trans-acting factors with the pre-mRNA. Therefore, to assess whether the exons are indeed independently regulated, we have examined the alternative exon content of a large number of individual CD44 cDNA isoforms. This analysis shows that the downstream alternatively spliced exons are favored over those lying upstream and that alternative exons are often included in blocks rather than singly. Using a novel in vivo alternative splicing assay, we show that intron length has a major influence upon the alternative splicing of CD44. We propose a kinetic model in which short introns may overcome the poor recognition of alternatively spliced exons. These observations suggest that for CD44, intron length has been exploited in the evolution of the genomic structure to enable tissue-specific patterns of splicing to be maintained.
Long‐term culture of human trophoblast cells (1985)

A technique is presented for the preparation of cultures of replicating human trophoblast cells from term placentas. The adherent cells obtained were very slow growing (doubling time 12.5 days) as measured by the rate of increase in cell protein, [14C]-leucine uptake and cell number. Cells from individual placentas have been maintained in continuous culture for up to 1 year (10-12 passages) and have been successfully recultured after storage in liquid nitrogen. Cultured cells showed positive immunofluorescent staining for human placental lactogen, human chorionic gonadotrophin, transferrin and type IV collagen. The adenine nucleotide content indicated that energetically the cells were in balance even after prolonged culture.
Efficient Prediction Structures for Multiview Video Coding (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> An experimental analysis of multiview video coding (MVC) for various temporal and inter-view prediction structures is presented. The compression method is based on the multiple reference picture technique in the H.264/AVC video coding standard. The idea is to exploit the statistical dependencies from both temporal and inter-view reference pictures for motion-compensated prediction. The effectiveness of this approach is demonstrated by an experimental analysis of temporal versus inter-view prediction in terms of the Lagrange cost function. The results show that prediction with temporal reference pictures is highly efficient, but for 20% of a picture's blocks on average prediction with reference pictures from adjacent views is more efficient. Hierarchical B pictures are used as basic structure for temporal prediction. Their advantages are combined with inter-view prediction for different temporal hierarchy levels, starting from simulcast coding with no inter-view prediction up to full level inter-view prediction. When using inter-view prediction at key picture temporal levels, average gains of 1.4-dB peak signal-to-noise ratio (PSNR) are reported, while additionally using inter-view prediction at nonkey picture temporal levels, average gains of 1.6-dB PSNR are reported. For some cases, gains of more than 3 dB, corresponding to bit-rate savings of up to 50%, are obtained. </para>
The Effect of Overexpression of Pdx1 and Foxa2 on the Differentiation of Human Embryonic Stem Cells into Pancreatic Cells (2006)

Human embryonic stem cells (HESCs) are pluripotent cells that may serve as a source of cells for transplantation medicine and as a tool to study human embryogenesis. Using genetic manipulation methodologies, we have investigated the potential of HESCs to differentiate into the various pancreatic cell types. We initially created various HESCs carrying the enhanced green fluorescent protein (eGFP) reporter gene under the control of either the insulin promoter or the pancreatic and duodenal homeobox factor-1 (Pdx1) promoter. Our analysis revealed that during the differentiation of HESCs into embryoid bodies (EBs), we could detect green fluorescent cells when eGFP is regulated by Pdx1 promoter but not by insulin promoter. To examine whether we can induce differentiation into pancreatic cells, we have established human embryonic stem cell lines that constitutively express either Pdx1 or the endodermal transcription factor Foxa2. Following differentiation into EBs, the constitutive expression of Pdx1 enhanced the differentiation of HESCs toward pancreatic endocrine and exocrine cell types. Thus, we have demonstrated expression of several transcription factors that are downstream of Pdx1 and various molecular markers for the different pancreatic cell types. However, the expression of the insulin gene could be demonstrated only when the cells differentiated in vivo into teratomas. We conclude that although overexpression of Pdx1 enhanced expression of pancreatic enriched genes, induction of insulin expression may require additional signals that are only present in vivo.
Hyaluronan, CD44, and Cyclooxygenase-2 in Colon Cancer (2008)

Carcinomas arising from colon epithelia develop or progress in a stromal microenvironment that is elevated in hyaluronan; interactions between elevated hyaluronan and the CD44 receptors on epithelial tumor cells activate an HA-receptor tyrosine kinase-mediated cell survival pathway. In this review we provide evidence that the hyaluronan-ErbB2-PI3kinase/AKT-ss-catenin-COX-2 signaling axis leads to intestinal epithelial and colon tumor cell division and proliferation. This review includes a summary of the authors work over the past years as well as citations of specific reviews related to role of hyaluronan in the pathogenesis of colon cancer.
Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus : Characterization of a Coenzyme A- Dependent NAD(P)H Sulfur Oxidoreductase (2007)

The hyperthermophilic archaeon Pyrococcus furiosus uses carbohydrates as a carbon source and produces acetate, CO2, and H2 as end products. When S(0) is added to a growing culture, within 10 min the rate of H2 production rapidly decreases and H(2)S is detected. After 1 hour cells contain high NADPH- and coenzyme A-dependent S(0) reduction activity (0.7 units/mg, 85 degrees C) located in the cytoplasm. The enzyme responsible for this activity was purified to electrophoretic homogeneity (specific activity, 100 units/mg) and is termed NAD(P)H elemental sulfur oxidoreductase (NSR). NSR is a homodimeric flavoprotein (M(r), 100,000) and is encoded by PF1186. This designation was previously assigned to the gene encoding an enzyme that reduces coenzyme A disulfide, which is a side reaction of NSR. Whole-genome DNA microarray and quantitative PCR analyses showed that the expression of NSR is up-regulated up to sevenfold within 10 min of S(0) addition. This primary response to S(0) also involves the up-regulation (>16-fold) of a 13-gene cluster encoding a membrane-bound oxidoreductase (MBX). The cluster encoding MBX is proposed to replace the homologous 14-gene cluster that encodes the ferredoxin-oxidizing, H2-evolving membrane-bound hydrogenase (MBH), which is down-regulated >12-fold within 10 min of S(0) addition. Although an activity for MBX could not be demonstrated, it is proposed to conserve energy by oxidizing ferredoxin and reducing NADP, which is used by NSR to reduce S(0). A secondary response to S(0) is observed 30 min after S(0) addition and includes the up-regulation of genes encoding proteins involved in amino acid biosynthesis and iron metabolism, as well as two so-called sulfur-induced proteins termed SipA and SipB. This novel S(0)-reducing system involving NSR and MBX has been found so far only in the heterotrophic Thermococcales and is in contrast to the cytochrome- and quinone-based S(0)-reducing system in autotrophic archaea and bacteria.
Spatial multiuser access OFDM with antenna diversity and power control (2002)

The capacity can be dramatically increased by employing multiple antennas. However, in the multiple-user environment, the system performance is limited by cochannel interference. This paper describes a spatial multiuser access scheme using singular value decomposition (MU-SVD), associated with orthogonal frequency division multiplexing (OFDM) for an intersymbol interference channel. The proposed method can separate the transmission of interest in the space domain, without loss of antenna diversity, thus successfully isolating each source with a spatially distinct signature waveform. Moreover, power control for sub-channels is adopted to enhance the spectral and power efficiency. Simulations show MU-SVD with power allocation achieves a huge gain.
Selection of Primers for Polymerase Chain Reaction (2003)

One of the most important factors affecting the quality of polymerase chain reaction (PCR) is the choice of primers. Several rules should be observed when designing primers and, in general, the more DNA sequence information available, the better the chance of finding an "ideal" primer pair. Fortunately, not all primer selection criteria need be met in order to synthesize a clean, specific product, since the adjustment of PCR conditions (such as composition of the reaction mixture, temperature, and duration of PCR steps) may considerably improve the reaction specificity. Amplification of 200-400-bp DNA is the most efficient and, in these cases, one may design efficient primers simply by following a few simple rules described in this chapter. It is more difficult to choose primers for efficient amplification of longer DNA fragments, and use of an appropriate primer analysis software is worthwhile.
Histone deacetylases as therapeutic targets in hematologic malignancies (2002)

During the past 5 years, it has become increasingly apparent that deregulated transcriptional control is a root cause of hematologic malignancy. Chromosomal translocations yield novel fusion transcription factors that in turn either activate genes critical for cell growth or repress genes important for normal cellular differentiation. Many of the fusion proteins of myeloid leukemia are aberrant transcriptional repressors and share the property of recruiting histone deacetylases (HDACs) to target genes. HDACs, by acting on chromatin and on transcription factors themselves, can modulate gene regulation. HDACs also play major roles in the function of well-characterized tumor suppressors such as p53 and Rb. Thus, HDACs are a compelling therapeutic target for cancer therapy. Several classes of HDAC inhibitors induce differentiation and cell death in myeloid and lymphoid model systems. Some of these are now in clinical trials for hematologic malignancies. The nature of HDAC function, the classes of inhibitors available, and recent experimental and clinical data will be reviewed.
Acute graft versus host disease due to T lymphocytes recognizing a single HLA-DPB1*0501 mismatch. (1996)

Analysis of a large number of unrelated bone marrow transplantations (BMT) has shown that HLA-DP incompatibility did not detectably influence the risk for acute graft-versus-host disease (aGVHD). Accordingly, it was proposed that HLA-DP determinants did not function as transplantation antigens in the same way as HLA-A, -B, or -DR. We have previously shown that HLA-DP (as well as HLA-A, -B, -DQ, or -DR)-specific T cells could be isolated from skin biopsies of patients who developed an aGVHD after semiallogeneic BMT. Nevertheless, whether a single HLA-DP mismatched allele could induce a detectable allo-specific reaction in vivo after BMT remained to be established. To directly address this issue we studied one patient who presented aGVHD after receiving purified CD34+ bone marrow (BM) cells from an unrelated donor with a single HLA-DP mismatch in the GVHD direction. To characterize the immunological events associated with GVHD, we analyzed the peripheral T cell repertoire, the T cell receptor Vbeta diversity, and the specificity of T cells invading a skin biopsy at the onset of GVHD. Our results demonstrated that a large fraction of skin-infiltrating lymphocytes, which expressed diverse T cell receptors, were reactive against this single HLA-DPB1 *0501 mismatch and consequently that a single HLA-DP mismatch between BM donor and recipient can activate a strong T cell response in vivo.
[A case of mesenteric panniculitis of the transverse colon]. (1990)

A case of mesenteric panniculitis in a 55-year-old female was reported. Image diagnosis of this rare clinical entity, which is characterized by a nonspecific inflammatory process involving the adipose tissue of the mesentery, was considered. We treated this patient conservatively and this led to remission.
CANDI. Development of the automated nursing assessment tool. (1989)

This article describes the results of the first phase of an interdisciplinary project to develop an expert system to aid in nursing diagnosis. The overall system, called CANDI (Computer Aided Nursing Diagnosis and Intervention), is reviewed briefly, and development of the automated (computerized) assessment guide is described in detail. Lessons learned from initial evaluation of the system, and the resulting modifications, also are discussed along with preparations for the next phase--development of the knowledge base.
Th17 cells: from precursors to players in inflammation and infection (2009)

Upon activation, naive CD4(+) T cells differentiate into different lineages of effector T(h) subsets. Each subset is characterized by its unique cytokine profile and biological functions. T(h)17, a newly described T(h) subset that produces IL-17, IL-17F and IL-22 in preference to other cytokines, has been shown to play an important role in clearing specific pathogens and in inducing autoimmune tissue inflammations. Over the last 2-3 years, significant progress has been made to understand the development and biological functions of T(h)17 subset. Transforming growth factor beta (TGF) together with IL-6 or IL-21 initiates the differentiation while IL-23 stabilizes the generation of T(h)17 cells. The transcription factors of T(h)17 cells [retinoid-related orphan receptor (ROR) gammat, ROR-alpha and signal transducer and activator of transcription-3] have been described recently. Since TGF-beta is essential for the generation of both T(h)17 and regulatory T (T(reg)) cells from naive T cells, which suggests a developmental link between T(h)17 and T(reg) cells. Functions of these two subsets of T cells are, however, opposite to each other; T(h)17 cells are highly pathogenic during the inflammatory process while T(reg) cells are crucial for inhibiting tissue inflammation and maintaining self-tolerance. Here, we review the recent information on differentiation and effector functions of T(h)17 cells during inflammatory conditions.
Production of a Broad Spectrum Antimicrobial Substance byLactobacillus reuteri (1989)

Lactobacillus reuteri resides in the gastrointestinal tract of humans, swine, poultry and other animals. Resting cells of this species convert glycerol into a potent, broad-spectrum antimicrobial substance termed reuterin. Reuterin is a low molecular weight, neutral, water soluble compound, capable of inhibiting growth of species representing all bacterial genera tested thus far, including: Escherichia, Salmonella, Shigella, Proteus, Pseudomonas, Clostridium and Staphylococcus. Also affected, but to a lesser degree, are lactic acid bacteria belonging to the genera Streptococcus, Pediococcus, Leuconostoc, and Lactobacillus. In this report we describe a method to screen lactobacilli for production of unique antimicrobial substances and the discovery of reuterin.
Threaded Fusion Cages for Lumbar Interbody Fusions (1997)

Assuming that the fusion success, clinical outcome, and complication rates are sufficiently similar between these two techniques, the striking improvement in overall surgical and hospitalization costs, surgical time, and blood losses provided by the threaded fusion cage technique can be major decision points in method selection. Further, no threaded fusion cage case having a normal adjacent level preoperatively developed a fusion transition syndrome over a followup period from 3 to 29 months (averaging 24 months) that required a second fusion procedure, and no cage had to be removed because of instrumentation-associated pain, although each of these problems are known to occur in at lease 10% of pedicle screw implants. Ten of the 25 (40%) 360 degrees fusion cases in this study required subsequent instrumentation removal, although no case has required adjacent level surgery for transition syndrome.
Screening for Colorectal Cancer (1995)

In the past few years, knowledge of the clinical, biologic, and molecular genetic characteristics of colorectal cancer has greatly increased. Although the most cost-effective approach remains to be identified, screening for colorectal cancer can decrease mortality due to this disease by detecting cancers at earlier stages and allowing the removal of adenomas, thus preventing the subsequent development of cancer. Molecular studies that have helped define the genetic basis for this disease hold great promise for the development of better and more powerful methods to identify populations at risk. Individually, these technological, clinical, and basic-science advances are exciting; together, they promise to move us closer to the goal of substantially reducing mortality due to colorectal cancer.
Deep Packet Inspection as a Service (2014)

Middleboxes play a major role in contemporary networks, as forwarding packets is often not enough to meet operator demands, and other functionalities (such as security, QoS/QoE provisioning, and load balancing) are required. Traffic is usually routed through a sequence of such middleboxes, which either reside across the network or in a single, consolidated location. Although middleboxes provide a vast range of different capabilities, there are components that are shared among many of them.