gebhart/patrepeval huggingface dataset:
Analysis of Long Term File Reference Patterns for Application to File Migration Algorithms (1981)

In most large computer installations files are moved between on-line disk and mass storage (tape, integrated mass storage device) either automatically by the system and/or at the direction of the user. In this paper we present and analyze long term file reference data in order to develop a basis for the construction of algorithms for file migration. Specifically, we examine the use of the on-line user (primarily text editor) data sets at the Stanford Linear Accelerator Center (SLAC) computer installation through the analysis of 13 months of file reference data. We find that most files are used very few times. Of those that are used sufficiently frequently that their reference patterns may be examined, we find that: 1) about a third show declining rates of reference during their lifetime, 2) of the remainder, very few (about 5 percent) show correlated interreference intervals, and 3) interreference intervals (in days) appear to be more skewed than would occur with the Bernoulli process. Thus, about two-thirds of all suffi1ciently active files appear to be referenced as a renewal process with a skewed interreference distribution. A large number of other file reference statistics (file lifetimes, interference distributions, moments, means, number of uses/ file, file sizes, file rates of reference, etc.) are computed and presented. Throughout, statistical tests are described and explained. The results of our analysis of file reference patterns are applied in a companion paper to the development and comparative evaluation of file migration algorithms.
Amphiregulin Is a Critical Downstream Effector of Estrogen Signaling in ERα-Positive Breast Cancer (2015)

Estrogen stimulation promotes epithelial cell proliferation in estrogen receptor (ERα)-positive breast cancer. Many ERα target genes have been enumerated, but the identities of the key effectors mediating the estrogen signal remain obscure. During mouse mammary gland development, the estrogen growth factor receptor (EGFR) ligand amphiregulin acts as an important stage-specific effector of estrogen signaling. In this study, we investigated the role of amphiregulin in breast cancer cell proliferation using human tissue samples and tumor xenografts in mice. Amphiregulin was enriched in ERα-positive human breast tumor cells and required for estrogen-dependent growth of MCF7 tumor xenografts. Furthermore, amphiregulin levels were suppressed in patients treated with endocrine therapy. Suppression of EGF receptor signaling appeared necessary for the therapeutic response in this setting. Our findings implicate amphiregulin as a critical mediator of the estrogen response in ERα-positive breast cancer, emphasizing the importance of EGF receptor signaling in breast tumor pathogenesis and therapeutic response.
Bioactive Nanoparticle–Gelatin Composite Scaffold with Mechanical Performance Comparable to Cancellous Bones (2014)

Mechanical properties are among the most concerned issues for artificial bone grafting materials. The scaffolds used for bone grafts are either too brittle (glass) or too weak (polymer), and therefore composite scaffolds are naturally expected as the solution. However, despite the intensive studies on composite bone grafting materials, there still lacks a material that could be matched to the natural cancellous bones. In this study, nanosized bioactive particles (BP) with controllable size and good colloidal stability were used to composite with gelatin, forming macroporous scaffolds. It was found that the mechanical properties of obtained composite scaffolds, in terms of elastic modulus, compressive strength, and strain at failure, could match to that of natural cancellous bones. This is ascribed to the good distribution of particle in matrix and strong interaction between particle and gelatin. Furthermore, the incorporation of BPs endues the composite scaffolds with bioactivity, forming HA upon reacting with simulated body fluid (SBF) within days, thus stimulating preosteoblasts attachment, growth, and proliferation in these scaffolds. Together with their good mechanical properties, these composite scaffolds are promising artificial bone grating materials.
Crescent, a novel chick gene encoding a Frizzled-like cysteine-rich domain, is expressed in anterior regions during early embryogenesis (1997)

We describe the isolation of a novel chicken gene that we have termed crescent, based on the most distinctive stage of its highly dynamic expression pattern during early embryogenesis. Crescent encodes a protein that in its N-terminal half shows the characteristic invariant 9 cysteine residues of the cysteine-rich domain (CRD) found in the Frizzled family of proteins, in Smoothened and in Collagen XVIII. The CRD of several Frizzled proteins have recently been shown to bind to Wg. Unlike Frizzled proteins, crescent does not contain a transmembrane domain and thus can not function as a receptor. Crescent expression is first found at stage XII (E-G&K) in the center of the area pellucida. On primitive streak formation, expression is detected in the entire anterior half of the area pellucida in the hypoblast layer. At maximal streak extension, crescent transcripts are localized primarily to the germinal crescent, where the primordial germ cells reside. During head process and head fold stages, crescent labels the anteriormost endodermal cells which will give rise to prospective foregut. With the commencement of somitogenesis, crescent expression rapidly wanes.
Smart Cluster Network (SCnet): design of high performance communication system for SAN (1999)

Smart Cluster Network (SCnet) is a high performance Virtual Interface (VI) Architecture communication system for UNIX/sup TM/ systems connected with Fujitsu's Synfnity-0 System Area Network (SAN). It is the first UNIX/sup TM/ VI architecture system that achieves "FuIl Conformance", as defined by Intel Corp. The paper describes the design of SCnet, focusing on multiple Network Interface Card (NIC) support for load balance, inter-process protection, memory registration, and communication protocols. The paper presents the main problems faced and our solutions for them. We propose extensions needed to support the VI architecture effectively on current systems. We evaluated the SCnet performance experimentally using a two node cluster system connected with the Fujitsu's Synfinity-O SAN. Latency as low as 42 microseconds, and throughput as high as 108 MBytes/sec is achieved ruing a single NIC. When using 2 NICs per node, throughput of 210 MBytes/sec is achieved.
Identify the reference signal of scalp EEG recording (2013)

In [10] we proposed two methods to identify the reference signal under the key assumption that the reference signal is independent from EEG sources. This assumption may be true for intracranial EEG with a scalp reference. However, it may not be true for scalp sources with a scalp reference electrode. As such, this limits the application of our methods to the vast majority of scalp EEG with cephalic reference or non-cephalic reference such as earlobe. In this paper, we select the earlobe of one subject as the reference site, propose one special experimental method for the subject by taping the reference electrode about once every second and record scalp EEG for some time period. In this way we try to artificially produce the reference signal which may be independent from scalp sources so that the two methods in [10] can be successfully applied. As a result, for upcoming scalp EEG without taping the reference electrode, we propose two simulation methods to automatically identify the reference signal without taping in real time. Our simulation results show that the corrected scalp EEG after identifying the reference signal and removing it from the original scalp EEG by means of each of two simulation methods not only completely removes obvious common artifacts, but also involves much more brain neural activities than the corrected EEG after removing average reference (AR) from the original scalp EEG. Moreover, the identified reference signal during no-taping is indeed correlated with scalp sources.
Quantitative second-harmonic generation microscopy in collagen (2003)

The second-harmonic signal in collagen, even in highly organized samples such as rat tail tendon fascicles, varies significantly with position. Previous studies suggest that this variability may be due to the parallel and antiparallel orientation of neighboring collagen fibrils. We applied high-resolution second-harmonic generation microscopy to confirm this hypothesis. Studies in which the focal spot diameter was varied from approximately 1 to approximately 6 microm strongly suggest that regions in which collagen fibrils have the same orientation in rat tail tendon are likely to be less than approximately 1 microm in diameter. These measurements required accurate determination of the focal spot size achieved by use of different microscope objectives; we developed a technique that uses second-harmonic generation in a quartz reference to measure the focal spot diameter directly. We also used the quartz reference to determine a lower limit (dXXX > 0.4 pm/V) for the magnitude of the second-order nonlinear susceptibility in collagen.
Epitaxial growth of amorphous Ge films deposited on single-crystal Ge (1981)

The epitaxial growth of amorphous Ge films deposited onto 〈110〉 Ge substrate is demonstrated. Substrate cleaning prior to deposition involves only conventional chemical procedures. The growth appears to be a strong function of the interface cleanliness. Two different growth mechanisms are observed: (a) a direct transition from amorphous to single-crystalline layer and (b) the growth involving the transition of amorphous to polycrystals to single crystal.
Treatment of Experimental Nephrotic Syndrome with Artesunate (2007)

The present study was designed to test the therapeutic effect of a new antimalarial drug, artesunate in experimental model of nephrotic syndrome. To induce this experimental model, Adriamycin was given once by a single intravenous injection (7.5 mg/kg) through the tail vein. Six days after injection of Adriamycin, therapeutic protocol was developed by intraperitoneally (IP) administration of 5 mg/kg artesunate (ARS). Total of IP injections were 14, of which 5 injections were made every day and 9 injections were carried out at regular 48-h intervals. Therapeutic protocol was terminated on day 28 and animals were killed on day 49. The results showed that treatment with ARS caused a significant reduction in the level of proteinuria, urine urea and urine sodium compared with nontreated controls. In addition, decrease in serum triglyceride and increase in the level of serum albumin was significant in treated group with ARS compared with nontreated controls. Moreover, treatment with ARS significantly reduced glomerular polymorphonuclear (PMN) and mononuclear cells infiltration, hypercellularity, karyorrhexis, wire loops, and hydropic change in capillary network within the renal cortex, as well as decreased hyalin casts. On the other hand, healthy controls receiving ARS showed a significant decrease in amounts of serum triglyceride, urine urea, and urine sodium and potassium compared with normal group. These data suggest that artesunate therapy can ameliorate proteinuria, and suppress the progression of glomerular lesions in experimental model of nephrotic syndrome; it may also be recommended as a lipid-lowering drug.
Web content adaptation for mobile handheld devices (2007)

Creative technologies can help overcome the limitations of mobile handheld devices while maximizing their strengths.
Impaired thrombolysis: a novel cardiovascular risk factor in end-stage renal disease (2012)

Impaired endogenous thrombolysis is a novel risk factor in ESRD, strongly associated with cardiovascular events.
P6F-2 Piezoelectric Generator as Power Supply for RFID-Tags and Applications (2007)

A piezoelectric power generator or harvester can convert impact energy from various mechanical vibrations of daily life into electrical energy. It is an environmentally friendly power generating system. Recently, battery powered RFID tags have attracted attention as a new technology for commodity identification and management in the ubiquitous computer society. However, the need for periodic battery exchange is a major disadvantage of such active RFID-tags. This study describes possible applications of piezoelectric generators to active RFID-tags. As examples of RFID-tag applications enabled by a piezoelectric generator, we propose a safety system to monitor children going to and returning from school as well as a network system to monitor the utilization of a conference room. Experimental results are presented.
Discussion Addendum for: Applications of (2 <scp> <i>S</i> </scp> )‐(–)‐3‐ <i>exo</i> ‐Morpholinoisoborneol [(–) <scp>MIB</scp> ] in Organic Synthesis (2014)

Abstract Lupinine 2‐(2,5‐Dimethoxyphenyl)ethanamine 1,7,7‐Trimethylbicyclo[2.2.1]heptan‐2‐one Cyclohexyl[2‐(2‐hydroxyethyl)‐1‐piperidinyl]methanone (2S)‐(–)‐3‐exo‐morpholinoisoborneol Potassium tert ‐butoxide Isoamyl nitrite Lithium aluminium hydride Tetrahydrofuran 2‐Bromoethyl ether Triethylamine Dimethyl sulfoxide
Surface immunoglobulin-mediated B-cell activation in the absence of detectable elevations in intracellular ionized calcium: a model for T-cell-independent B-cell activation. (1989)

We recently showed that anti-immunoglobulin conjugated to high molecular weight dextran is 1000-fold more mitogenic for B cells than unconjugated anti-immunoglobulin. This system serves as a model for T-cell-independent type 2 antigens such as haptenated Ficoll, dextran, and bacterial polysaccharides, which can also stimulate B-cell proliferation and antibody production at low concentrations. We show here that conjugated anti-immunoglobulin, at concentrations that stimulate significant increases in expression of major histocompatibility complex class II molecules and incorporation of thymidine into DNA, does not induce detectable modulation of surface immunoglobulin. These results indicate that the facilitated T-cell-independent B-cell activation by polysaccharide antigens may result from inability to modulate surface immunoglobulin, possibly resulting in persistent and/or repetitive signaling. Early large increases in Ca2+ and breakdown of inositol phospholipids presently thought to be involved in transduction of the mitogenic signal are not detectable at low concentrations of conjugated anti-immunoglobulin, raising the possibility that these biochemical events may not in fact be central to this signaling pathway.
Fasting reduces plasma proprotein convertase, subtilisin/kexin type 9 and cholesterol biosynthesis in humans (2010)

Proprotein convertase, subtilisin/kexin type 9 (PCSK9), a key regulator of plasma LDL-cholesterol (LDL-c) and cardiovascular risk, is produced in liver and secreted into plasma where it binds hepatic LDL receptors (LDLR), leading to their degradation. PCSK9 is transcriptionally activated by sterol response element-binding protein (SREBP)-2, a transcription factor that also activates all genes for cholesterol synthesis as well as the LDLR. Here we investigated the relationship between plasma PCSK9 levels and the lathosterol-to-cholesterol ratio, a marker of cholesterol biosynthesis, in 18 healthy subjects during a 48 h fast. In all individuals, plasma PCSK9 levels declined steadily during the fasting period, reaching a nadir at 36 h that was ∼58% lower than levels measured in the fed state (P < 0.001). Similarly, the lathosterol-to-cholesterol ratio declined in parallel with plasma PCSK9 concentrations during the fast, reaching a nadir at 36 h that was ∼28% lower than that measured in the fed state (P = 0.024). In summary, fasting has a marked effect on plasma PCSK9 concentrations, which is mirrored by measures of cholesterol synthesis in humans. Inasmuch as cholesterol synthesis and PCSK9 are both regulated by SREBP-2, these results suggest that plasma PCSK9 levels may serve as a surrogate marker of hepatic SREBP-2 activity in humans.
A hepatitis A virus deletion mutant which lacks the first pyrimidine-rich tract of the 5' nontranslated RNA remains virulent in primates after direct intrahepatic nucleic acid transfection (1995)

Cell culture-adapted variants of hepatitis A virus (HAV) in which the first pyrimidine-rich tract (pY1; nucleotides 99 to 138) of the 5' nontranslated region has been deleted (delta 96-137 or delta 96-139) replicate as well as parental virus in cultured cells (D.R. Shaffer, E.A. Brown, and S.M. Lemon, J. Virol. 68:5568-5578, 1994). To determine whether viruses with such large deletion mutations are able to replicate and to produce acute hepatitis in primates, we reconstructed the delta 96-137 deletion in the genetic background of a virulent virus which differs from the wild type by only one mutation in the 2B-coding region (HM175/8Y). Full-length synthetic delta 96-137/8Y RNA was injected into the livers of two HAV-seronegative marmosets (Saguinus mystax). Both animals developed serum liver enzyme elevations and inflammatory changes in serial liver biopsies within 3 to 4 weeks of inoculation which were comparable in magnitude to those observed previously following intrahepatic inoculation of marmosets with HM175/8Y RNA. Sequencing of RNA from virus shed in feces demonstrated the presence of the delta 96-137 deletion. These results indicate that the pY1 sequence of HAV is not required for efficient viral replication in hepatocytes in situ or for production of acute hepatic injury following intrahepatic RNA transfection in primates.
Identification of a major QTL controlling the content of B-type starch granules in Aegilops (2011)

Starch within the endosperm of most species of the Triticeae has a unique bimodal granule morphology comprising large lenticular A-type granules and smaller near-spherical B-type granules. However, a few wild wheat species (Aegilops) are known to lack B-granules. Ae. peregrina and a synthetic tetraploid Aegilops with the same genome composition (SU) were found to differ in B-granule number. The synthetic tetraploid had normal A- and B-type starch granules whilst Ae. peregrina had only A-granules because the B-granules failed to initiate. A population segregating for B-granule number was generated by crossing these two accessions and was used to study the genetic basis of B-granule initiation. A combination of Bulked Segregant Analysis and QTL mapping identified a major QTL located on the short arm of chromosome 4S that accounted for 44.4% of the phenotypic variation. The lack of B-granules in polyploid Aegilops with diverse genomes suggests that the B-granule locus has been lost several times independently during the evolution of the Triticeae. It is proposed that the B-granule locus is susceptible to silencing during polyploidization and a model is presented to explain the observed data based on the assumption that the initiation of B-granules is controlled by a single major locus per haploid genome.
Effect of Recombinant Human Growth Hormone on Catabolic Hormones and Free Fatty Acids Following Thermal Injury (1992)

Severe burn injury elicits the release of catabolic hormones that contribute to negative nitrogen balance, protein wasting, and impaired wound healing. Previous studies have shown that burn patients receiving recombinant human growth hormone (rhGH) therapy have an increase in the rate of skin donor site healing and a shorter hospital stay. The mechanism by which rhGH exerts its effects, however, is not clearly understood. This study examines the effects of rhGH on circulating levels of catabolic hormones and nonesterified fatty acids in pediatric burn patients. Patients with greater than 40% total body surface area burn were randomly assigned to receive placebo (n = 8) or 0.2 mg/kg/day rhGH (n = 6) throughout their hospitalization. All patients had early morning blood samples assessed for catecholamines (CAT), cortisol, insulin, glucagon, and free fatty acid (FFA) levels during a period of hypermetabolism. No differences could be demonstrated in age, burn size, postburn day of evaluation, resting energy expenditure per kilogram, respiratory rate, heart rate, respiratory quotient, serum cortisol, and serum glucose between placebo- and rhGH-treated patients. The rhGH-treated group did show a significant elevation (p less than 0.05) in insulin-like growth factor-1 (55.9 +/- 14.5 vs. 168 +/- 23.7 mU/mL), total catecholamines (1,817 +/- 177 vs. 1,117 +/- 137 pg/mL), norepinephrine (1,257 +/- 121 vs. 867 +/- 113 pg/mL), epinephrine (385 +/- 175 vs. 147 +/- 36 pg/mL), insulin (32.8 +/- 3.3 vs. 25.0 +/- 3.0 mU/mL), glucagon (215 +/- 18 vs. 158 +/- 22 pg/mL), and free fatty acids (0.74 +/- 0.01 vs. 0.59 +/- 0.04 mEq/L) compared with the placebo group (data expressed as mean +/- SE).(ABSTRACT TRUNCATED AT 250 WORDS)
Connective Tissue Progenitors: Practical Concepts for Clinical Applications (2002)

Tissue engineering can be defined as any effort to create or induce the formation of a specific tissue in a specific location through the selection and manipulation of cells, matrices, and biologic stimuli. The biologic concepts and the biochemical and biophysical principles on which these efforts are based have become an exciting and rapidly evolving field of biomedical research. More importantly, tissue engineering is becoming a clinical reality in the practice of orthopaedic surgery, providing patients and physicians with an expanding set of practical tools for effective therapy. New and improved matrices and bioactive factors inevitably will play important roles in the evolution of orthopaedic tissue engineering. However, tissue engineering never can stray far from fundamental biologic principles, and one of these is that cells do all the work. No new tissue forms except through the activity of living cells. No bone graft, no matrix, no growth factor, no cytokine can contribute to the generation or integration of new tissue, except through the influence it has on the behavior of cells. The efficacy of all current clinical tools depends entirely on the cells in the grafted site, particularly the small subset of stem cells and progenitor cells that are capable of generating new tissue. The current authors review a series of key biologic concepts related to the rational design and selection of composites of cells and matrices in contemporary bone grafting and tissue engineering efforts. The functional paradigms of stem cell biology are reviewed, including self renewal, asymmetric and symmetric mitosis, and lineage restriction. Several potential sources for autogenous stem cells for connective tissues are discussed. Finally, a simple mathematical model is introduced as a tool for understanding the functional demands placed on stem cells and progenitors in a graft site and to provide a conceptual framework for the rational design of cell matrix composite grafts.