gebhart/patrepeval huggingface dataset:
Herpes Simplex Virus Latency-Associated Transcript Encodes a Protein Which Greatly Enhances Virus Growth, Can Compensate for Deficiencies in Immediate-Early Gene Expression, and Is Likely To Function during Reactivation from Virus Latency (1999)

Herpes simplex virus types 1 and 2 (HSV1 and HSV2) enter and reactivate from latency in sensory neurons, although the events governing these processes are little understood. During latency, only the latency-associated transcripts (LATs) are produced. However, although the LAT RNAs were described approximately 10 years ago, their function remains ambiguous. Mutations affecting the LATs have minimal effects other than a small reduction in establishment of and reactivation from latency in some cases. Mutations in putative LAT-contained open reading frames (ORFs) have so far shown no effect. The LATs consist of a large species from which smaller (approximately 2 kb), nuclear, nonlinear LATs which are abundant during latency are spliced. Thus, translation of ORFs in these smaller LATs would not usually be expected to be possible, and if expressed at all, their expression might be tightly regulated. Here we show that deregulated expression of the largest HSV1 2-kb LAT-contained ORF in various cells of neuronal and nonneuronal origin greatly enhances virus growth in a manner specific to HSV1-the HSV1 LAT ORF has no effect on the growth of HSV2. Similar results of enhanced growth were found when the HSV1 LAT ORF was constitutively expressed from within the HSV1 genome. The mechanism of LAT ORF action was strongly suggested to be by substituting for deficiencies in immediate-early (IE) gene expression (particularly ICP0), because deregulated LAT ORF expression, as well as enhancing wild-type virus growth, was also found to allow efficient growth of viruses with mutations in ICP0 or VMW65. Such viruses otherwise exhibit considerable growth defects. IE gene expression deficiencies are often the block to productive infection in nonpermissive cells and are also evident during latency. These results, which we show to be protein- rather than RNA-mediated effects, strongly suggest a function of the tightly regulated expression of a LAT ORF-encoded protein in the reactivation from HSV latency.
Twist1 Induces CCL2 and Recruits Macrophages to Promote Angiogenesis (2013)

The transcription factor Twist1 induces epithelial-mesenchymal transition and extracellular matrix degradation to promote tumor metastasis. Although Twist1 also plays a role in embryonic vascular development and tumor angiogenesis, the molecular mechanisms that underlie these processes are not as well understood. Here, we report a novel function for Twist1 in modifying the tumor microenvironment to promote progression. We found that expression of Twist1 in human mammary epithelial cells potently promoted angiogenesis. Surprisingly, Twist1 expression did not increase the secretion of the common proangiogenic factors VEGF and basic fibroblast growth factor but rather induced expression of the macrophage chemoattractant CCL2. Attenuation of endogenous Twist1 in vivo blocked macrophage recruitment and angiogenesis, whereas exogenous CCL2 rescued the ability of tumor cells lacking Twist1 to attract macrophages and promote angiogenesis. Macrophage recruitment also was essential for the ability of Twist1-expressing cells to elicit a strong angiogenic response. Together, our findings show that how Twist1 recruits stromal macrophages through CCL2 induction to promote angiogenesis and tumor progression. As Twist1 expression has been associated with poor survival in many human cancers, this finding suggests that anti-CCL2 therapy may offer a rational strategy to treat Twist1-positive metastatic cancers.
Advanced Windows: The Developer's Guide to the WIN32 API for Windows NT 3.5 and Windows 95 (1995)

To create programs for the Windows 95 or Windows NT operating systems, programmers need to know the art of 32-bit programming. Richter presents the first truly advanced book on programming for Windows that concentrates on advanced topics and advanced material on core topics, and provides a stepping stone to the next release of Microsoft Windows. Disk includes sample code and applications.
Electrochemical Approach to and the Physical Consequences of Preparing Nanostructures from Gold Nanorods with Smooth Ends (2008)

We have developed a method to smooth the end sections of nanowires and nanograps generated via the On-Wire Lithography process and studied these rods with optical spectroscopies and theoretical modeling (Discrete Dipole Approximation). The first step of the smoothing process is a reductive one aimed at controlling the diffusion and migration of metal ions to the growing nanorod surface by adjusting the applied potential and concentration of the metal ions in the growth solution. A second oxidative smoothing step, based in part on the energetic differences between topologically rough and smooth surfaces, is used to further smooth the nanorod. The RMS roughness can be reduced over five fold to approximately 5 nm. The properties of these smoothed rods were investigated by empirical and theoretical methods, where it was found the smoothed rods have sharper plasmon resonances and decreased SERS intensity.
In VivoElectroporation of Minicircle DNA as a Novel Method of Vaccine Delivery To Enhance HIV-1-Specific Immune Responses (2013)

DNA vaccines offer advantage over conventional vaccines, as they are safer to use, easier to produce, and able to induce humoral as well cellular immune responses. Unfortunately, no DNA vaccines have been licensed for human use for the difficulties in developing an efficient and safe in vivo gene delivery system. In vivo electroporation (EP)-based DNA delivery has attracted great attention for its potency to enhance cellular uptake of DNA vaccines and function as an adjuvant. Minicircle DNA (a new form of DNA containing only a gene expression cassette and lacking a backbone of bacterial plasmid DNA) is a powerful candidate of gene delivery in terms of improving the levels and the duration of transgene expression in vivo. In this study, as a novel vaccine delivery system, we combined in vivo EP and the minicircle DNA carrying a codon-optimized HIV-1 gag gene (minicircle-gag) to evaluate the immunogenicity of this system. We found that minicircle-gag conferred persistent and high levels of gag expression in vitro and in vivo. The use of EP delivery further increased minicircle-based gene expression. Moreover, when delivered by EP, minicircle-gag vaccination elicited a 2- to 3-fold increase in cellular immune response and a 1.5- to 3-fold augmentation of humoral immune responses compared with those elicited by a pVAX1-gag positive control. Increased immunogenicity of EP-assisted minicircle-gag may benefit from increasing local antigen expression, upregulating inflammatory genes, and recruiting immune cells. Collectively, in vivo EP of minicircle DNA functions as a novel vaccine platform that can enhance efficacy and immunogenicity of DNA vaccines.
Intermittent pneumatic leg compressions acutely upregulate VEGF and MCP-1 expression in skeletal muscle (2010)

Application of intermittent pneumatic compressions (IPC) is an extensively used therapeutic strategy in vascular medicine, but the mechanisms by which this method works are unclear. We tested the hypothesis that acute application (150 min) of cyclic leg compressions in a rat model signals upregulation of angiogenic factors in skeletal muscle. To explore the impact of different pressures and frequency of compressions, we divided rats into four groups as follows: 120 mmHg (2 s inflation/2 s deflation), 200 mmHg (2 s/2 s), 120 mmHg (4 s/16 s), and control (no intervention). Blood flow and leg oxygenation (study 1) and the mRNA expression of angiogenic mediators in the rat tibialis anterior muscle (study 2) were assessed after a single session of IPC. In all three groups exposed to the intervention, a modest hyperemia (approximately 37% above baseline) between compressions and a slight, nonsignificant increase in leg oxygen consumption (approximately 30%) were observed during IPC. Compared with values in the control group, vascular endothelial growth factor (VEGF) and monocyte chemotactic protein-1 (MCP-1) mRNA increased significantly (P < 0.05) only in rats exposed to the higher frequency of compressions (2 s on/2 s off). Endothelial nitric oxide synthase, matrix metalloproteinase-2, and hypoxia-inducible factor-1alpha mRNA did not change significantly following the intervention. These findings show that IPC application augments the mRNA content of key angiogenic factors in skeletal muscle. Importantly, the magnitude of changes in mRNA expression appeared to be modulated by the frequency of compressions such that a higher frequency (15 cycles/min) evoked more robust changes in VEGF and MCP-1 compared with a lower frequency (3 cycles/min).
Nonsurgical Uterotubal Insemination in the Mare (1998)

Uterotubal insemination with a low number of spermatozoa serves as a possible assisted reproductive procedure for achieving pregnancy in mares. The procedure requires a minimal amount of fluid and a suboptimal number of progressively motile, morphologically normal sperm, and it bypasses the uterine phase of sperm transport and selection. Authors’ address: Veterinary Medical Teaching Hospital (Vazquez and Medina) and Dept. of Population Health and Reproduction (all other authors), School of Veterinary Medicine, University of California at Davis, Davis, CA 95616. r 1998 AAEP.
Homeodomain proteins and eukaryotic translation initiation factor 4E (eIF4E): an unexpected relationship. (2005)

The central role of post-transcriptional modification of the expression of several genes involved in tumorigenesis implicates eIF4E as a pivotal factor in the regulation of cell survival, growth and proliferation. Overexpression of eIF4E leads to malignant transformation in vitro and induces tumor formation in vivo. Furthermore, upregulated expression of eIF4E has been reported in a variety of human malignancies. Consequently, studies over the last ten years have sought to better characterize the molecular mechanisms and cellular factors that control eIF4E activity. These efforts have revealed a role for eIF4E in diverse biological processes including embryonic development, cell cycle progression, synaptic plasticity and cancer. In this review we focus on several members of the homeodomain protein family, which have recently been identified as a novel class of eIF4E regulators.
Phosphoinositide 3-kinase activity is essential for all-trans-retinoic acid-induced granulocytic differentiation of HL-60 cells. (1999)

Phosphoinositide 3-kinase (PI 3-K) activity increases in HL-60 cells that are induced to granulocytic differentiation by all-trans-retinoic acid. Immunochemical and immunocytochemical analyses by confocal microscopy also reveal an increase in the amount of the enzyme, which is particularly evident at the nuclear level. Inhibition of PI 3-K activity by nanomolar concentrations of wortmannin and of its expression by transfection with an antisense fragment of p85alpha prevented the differentiative process. The data obtained indicate that PI 3-K activity plays an essential role in promoting granulocytic differentiation.
FOOD HABITS AND DIETARY OVERLAP OF NONGAME INSECTIVOROUS FISHES IN FLINT CREEK, OKLAHOMA, A WESTERN OZARK FOOTHILLS STREAM (1985)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Strategies for cancer therapy using carcinoembryonic antigen vaccines (2000)

Advances in molecular biology and immunology have renewed interest in the development of vaccines for the treatment or prevention of cancer. Research over the past 10 years has focused on the identification of suitable tumour antigens to use as targets for a variety of vaccine strategies. Carcinoembryonic antigen (CEA) was one of the first tumour antigens described, and is commonly expressed by a wide range of adenocarcinomas. Recent studies have identified several human-leukocyte-antigen-restricted epitopes (short peptides) within the CEA protein that can be recognised by human T lymphocytes (T cells). Although CEA-expressing tumour cells are generally weakly recognised by the immune system, several new strategies have been used to enhance immune responses against CEA. This includes using antibodies directed against CEA; inserting the CEA gene into recombinant viruses and bacteria as viral and bacterial vaccines; pulsing the CEA protein, peptides, DNA or RNA onto dendritic cells (specialised antigen-presenting cells); and combining CEA vaccines with cytokines or co-stimulatory molecules to increase vaccine effectiveness. Other factors that might be important in establishing systemic immunity against CEA are the dose, route, timing, and choice of vector and adjuvants for vaccine administration. Further research in understanding the fundamental processes involved in tumour-cell recognition by the immune system, better animal models, and improved clinical trial designs will help to define the full potential of CEA as a target for cancer vaccine development.
Hahb‐4, a homeobox‐leucine zipper gene potentially involved in abscisic acid‐dependent responses to water stress in sunflower* (2002)

Abstract Homeodomain‐leucine zipper proteins constitute a family of transcription factors found only in plants. We have characterized a full‐length cDNA encoding the sunflower homeobox‐leucine zipper protein Hahb‐4 ( Helianthus annuus h omeo b ox‐4). The complete cDNA is 674 base pairs long and contains an open reading frame of 177 amino acids that belongs to the Hd‐Zip I subfamily. Northern blot and RNAse A protection analysis show that the expression of Hahb‐4 is rapidly, strongly and reversibly induced by water deficit in whole seedlings, roots, stems and leaves. A similar fast induction of Hahb‐4 expression is observed when seedlings are subjected to a treatment with the hormone abscisic acid (ABA). Nuclei prepared from seedlings treated with ABA or subjected to water stress show a significant increase of protein(s) that specifically bind the sequence 5′‐CAAT(A/T)ATTG‐3′, recognized in vitro by Hahb‐4, suggesting that an active protein is synthesized in response to these treatments. The promoter region of the Hahb‐4 gene contains sequences that fit the consensus for a G‐box present in some AB A r esponsive e lements (ABREs). We propose that Hahb‐4 may function in signalling cascade(s) that control(s) a subset of the ABA‐mediated responses of sunflower to water stress.
Diversity of Bacterial Populations on the Tongue Dorsa of Patients with Halitosis and Healthy Patients (2003)

The primary purpose of the present study was to compare the microbial profiles of the tongue dorsa of healthy subjects and subjects with halitosis by using culture-independent molecular methods. Our overall goal was to determine the bacterial diversity on the surface of the tongue dorsum as part of our ongoing efforts to identify all cultivable and not-yet-cultivated species of the oral cavity. Tongue dorsum scrapings were analyzed from healthy subjects with no complaints of halitosis and subjects with halitosis, defined as an organoleptic score of 2 or more and volatile sulfur compound levels greater than 200 ppb. 16S rRNA genes from DNA isolated from tongue dorsum scrapings were amplified by PCR with universally conserved bacterial primers and cloned into Escherichia coli. Typically, 50 to 100 clones were analyzed from each subject. Fifty-one strains isolated from the tongue dorsa of healthy subjects were also analyzed. Partial sequences of approximately 500 bases of cloned inserts from the 16S rRNA genes of isolates were compared with sequences of known species or phylotypes to determine species identity or closest relatives. Nearly complete sequences of about 1,500 bases were obtained for potentially novel species or phylotypes. In an analysis of approximately 750 clones, 92 different bacterial species were identified. About half of the clones were identified as phylotypes, of which 29 were novel to the tongue microbiota. Fifty-one of the 92 species or phylotypes were detected in more than one subject. Those species most associated with healthy subjects were Streptococcus salivarius, Rothia mucilaginosa, and an uncharacterized species of Eubacterium (strain FTB41). Streptococcus salivarius was the predominant species in healthy subjects, as it represented 12 to 40% of the total clones analyzed from each healthy subject. Overall, the predominant microbiota on the tongue dorsa of healthy subjects was different from that on the tongue dorsa of subjects with halitosis. Those species most associated with halitosis were Atopobium parvulum, a phylotype (clone BS095) of Dialister, Eubacterium sulci, a phylotype (clone DR034) of the uncultivated phylum TM7, Solobacterium moorei, and a phylotype (clone BW009) of STREPTOCOCCUS: On the basis of our ongoing efforts to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species that colonize the oral cavity, there are now over 600 species.
RNA Guanine Quadruplex Invasion by Complementary and Homologous PNA Probes (2005)

Guanine quadruplexes are gaining increasing attention due to their suspected roles in regulating gene expression at the transcriptional and translational levels. This paper describes the ability of short peptide nucleic acid (PNA) probes to disrupt a stable RNA quadruplex and hybridize to their target sequence. In one case, the PNA probe is complementary to the target, resulting in formation of a Watson-Crick base-paired duplex. In the second case, the PNA probe is homologous to the target and forms a hybrid quadruplex structure. The hybrid duplex is formed in a 1:1 stoichiometry, as expected based on the constraints imposed by Watson-Crick pairing. However, the hybrid quadruplex is formed in a PNA2:RNA stoichiometry, due to the ability of the short PNA to hybridize with both halves of the original RNA quadruplex.
查尔斯·艾夫斯和他的音乐(上) (1989)

《七月四日》艾夫斯回忆道:“1897至1913年,我创造了一套管弦乐曲叫《假日》。这四首曲子,即《假日交响曲》的四个乐章,演奏时间约需一小时;虽然它们最初被合称为交响曲,但它们又是各自独立的乐曲,可以这样看待和演出。”四首曲子仿效维瓦尔第(Vivaldi)的《四季》。它们是《华盛顿的诞辰》(冬);《阵亡战士纪念日》(春)①;《七月四日》(夏)②;和《感恩节》(秋)③。艾夫斯称这作品为“一个男孩对他在康涅狄格州小镇上度过的假日的回忆。”但是,对于每一位意味深长的艺术家来说,这种
Influence of abomasal infusion of high levels of lysine or methionine, or both, on ruminal fermentation, eating behavior, and performance of lactating dairy cows. (2000)

Four multiparous late-lactation Holstein cows were fed a basal ration designed to be co-limiting in intestinally absorbable supplies of methionine and lysine. Cows were supplemented with no amino acids, lysine by abomasal infusion to 140% of the calculated intestinally absorbable requirement, methionine by abomasal infusion to 140% of requirement, or both amino acids in a 4 x 4 Latin square design with 28-d periods. Unsupplemented cows consumed 23.8 kg/d of dry matter and produced 36.9 kg/d of milk containing 3.70% fat, 3.22% protein, and 4.82% lactose. Cows ate less dry matter and produced less milk and milk lactose, and tended (P = .06 or .08) to produce less milk protein when abomasally infused with methionine alone or together with lysine. Infusion of lysine alone resulted in production values numerically between those of unsupplemented cows and those cows supplemented with methionine alone or together with lysine. Evaluation of the results with two metabolic models of dairy cows indicated that performance of unsupplemented cows may have been limited by delivery of metabolizable or digestible protein, or intestinally absorbable lysine, isoleucine, or histidine, depending on the metabolic model used to evaluate animal performance. Regardless, results are consistent with those using nonruminant species, which have shown that imbalanced profiles of intestinally absorbable amino acids are associated with reduced dry matter intake and animal performance. Results also show that negative effects on performance of lactating dairy cows can occur if methionine is supplied at levels substantially in excess of calculated intestinally absorbable requirements, either alone or together with lysine.
The use of genomic microarrays to study chromosomal abnormalities in mental retardation (2005)

Mental retardation affects 2 to 3% of the US population. It is defined by broad criteria, including significantly subaverage intelligence, onset by age 18, and impaired function in a group of adaptive skills. A myriad of genetic and environmental causes have been described, but for approximately half of individuals diagnosed with mental retardation the molecular basis remains unknown. Genomic microarrays, also called array comparative genomic hybridization (array CGH), represent one of several novel technologies that allow the detection of chromosomal abnormalities, such as microdeletions and microduplications, in a rapid, high throughput fashion from genomic DNA samples. In one early application of this technology, genomic microarrays have been used to characterize the extent of chromosomal changes in a group of patients diagnosed with one particular type of disorder that causes mental retardation, such as deletion 1p36 syndrome. In another application, DNA samples from individuals with idiopathic mental retardation have been assayed to scan the entire genome in attempts to identify chromosomal changes. Genomic microarrays offer both a genome-wide perspective of chromosomal aberrations as well as higher resolution (to the level of approximately one megabase) compared to alternative available technologies.
Ultrasonic fingerprint sensor using a piezoelectric micromachined ultrasonic transducer array integrated with complementary metal oxide semiconductor electronics (2015)

This paper presents an ultrasonic fingerprint sensor based on a 24 × 8 array of 22 MHz piezoelectric micromachined ultrasonic transducers (PMUTs) with 100 μm pitch, fully integrated with 180 nm complementary metal oxide semiconductor (CMOS) circuitry through eutectic wafer bonding. Each PMUT is directly bonded to a dedicated CMOS receive amplifier, minimizing electrical parasitics and eliminating the need for through-silicon vias. The array frequency response and vibration mode-shape were characterized using laser Doppler vibrometry and verified via finite element method simulation. The array's acoustic output was measured using a hydrophone to be ∼14 kPa with a 28 V input, in reasonable agreement with predication from analytical calculation. Pulse-echo imaging of a 1D steel grating is demonstrated using electronic scanning of a 20 × 8 sub-array, resulting in 300 mV maximum received amplitude and 5:1 contrast ratio. Because the small size of this array limits the maximum image size, mechanical scanning was used to image a 2D polydimethylsiloxane fingerprint phantom (10 mm × 8 mm) at a 1.2 mm distance from the array.
Purification of a protein from Agrobacterium tumefaciens strain A348 that binds phenolic compounds (1997)

In order to induce tumours on dicotyledonous plants, the bacterium Agrobacterium tumefaciens needs to be able to sense signal molecules, i.e. phenolic compounds. In order to identify putative chemoreceptors or environmental sensors involved in vir gene induction, we undertook the purification of a phenol-binding protein by affinity chromatography on a syringamide Ultrogel A4 column equilibrated at pH 5.6. A mild extraction of bacterial proteins with a Tris/HCl buffer at pH 9.0 led to the purification of a 39 kDa protein (Pbp39) with a pl of 4.3 after specific elution of the affinity matrix with sodium syringate. When the affinity chromatography was performed at neutral pH, barely any protein was isolated, indicating the importance of an acidic pH for optimal affinity. A microplate binding experiment revealed that both syringlyl biotinylated-BSA and sinapyl-biotinylated-BSA bound at pH 5.6 to the plate coated with Pbp39.