gebhart/patrepeval huggingface dataset:
Ultra-low-loss optical fiber nanotapers (2004)

Optical fiber tapers with a waist size larger than 1microm are commonplace in telecommunications and sensor applications. However the fabrication of low-loss optical fiber tapers with subwavelength diameters was previously thought to be impractical due to difficulties associated with control of the surface roughness and diameter uniformity. In this paper we show that very-long ultra-low-loss tapers can in fact be produced using a conventional fiber taper rig incorporating a simple burner configuration. For single-mode operation, the optical losses we achieve at 1.55microm are one order of magnitude lower than losses previously reported in the literature for tapers of a similar size. SEM images confirm excellent taper uniformity. We believe that these low-loss structures should pave the way to a whole range of fiber nanodevices.
The Sorghum bicolor genome and the diversification of grasses (2009)

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
A molecular classifier for predicting future graft loss in late kidney transplant biopsies (2010)

Kidney transplant recipients that develop signs of renal dysfunction or proteinuria one or more years after transplantation are at considerable risk for progression to renal failure. To assess the kidney at this time, a "for-cause" biopsy is performed, but this provides little indication as to which recipients will go on to organ failure. In an attempt to identify molecules that could provide this information, we used microarrays to analyze gene expression in 105 for-cause biopsies taken between 1 and 31 years after transplantation. Using supervised principal components analysis, we derived a molecular classifier to predict graft loss. The genes associated with graft failure were related to tissue injury, epithelial dedifferentiation, matrix remodeling, and TGF-beta effects and showed little overlap with rejection-associated genes. We assigned a prognostic molecular risk score to each patient, identifying those at high or low risk for graft loss. The molecular risk score was correlated with interstitial fibrosis, tubular atrophy, tubulitis, interstitial inflammation, proteinuria, and glomerular filtration rate. In multivariate analysis, molecular risk score, peritubular capillary basement membrane multilayering, arteriolar hyalinosis, and proteinuria were independent predictors of graft loss. In an independent validation set, the molecular risk score was the only predictor of graft loss. Thus, the molecular risk score reflects active injury and is superior to either scarring or function in predicting graft failure.
Performance characteristics of a new monoclonal antibody test for bladder cancer: ImmunoCyt trade mark. (1997)

Transitional carcinoma of the bladder, an important tumor in both men and women, has traditionally been diagnosed and monitored using either or both of two different methodologies. Urinary cytology is highly specific, but has poor sensitivity. Cystoscopy with biopsy is highly accurate, but invasive. A newly developed immuno cytochemical test, ImmunoCyt trade mark (DiagnoCure Inc.), uses three monoclonal antibodies directed against transitional cell carcinoma antigens in exfoliated cells. This study involved 102 asymptomatic controls, and 198 patients with confirmed bladder cancer, in an assessment of the performance characteristics of ImmunoCyt. Combining this test with conventional urinary cytology improves accuracy. Depending on the cutoff level used in the interpretation of a positive result, the highest sensitivity of the test was 95%, with a corresponding specificity of 76.5%. This procedure offers the possibility of non-invasive diagnosis and monitoring of bladder cancer, with acceptable performance characteristics.
A Fast-Acting Reagent for Accurate Analysis of RNA Secondary and Tertiary Structure by SHAPE Chemistry (2007)

Selective 2‘-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry allows local nucleotide flexibility to be quantitatively assessed at single nucleotide resolution in any RNA. SHAPE chemistry exploits structure-based gating of the nucleophilic reactivity of the ribose 2‘-hydroxyl group by the extent to which a nucleotide is constrained or flexible. SHAPE chemistry was developed using N-methylisatoic anhydride (NMIA), which is only moderately electrophilic and requires tens of minutes to form ribose 2‘-O-adducts. Here, we design and evaluate a significantly more useful, fast-acting, reagent for SHAPE chemistry. Introduction of a nitro group para to the reactive carbonyl to form 1-methyl-7-nitroisatoic anhydride (1M7) yields a reagent that both reacts significantly more rapidly with RNA to form 2‘-O-adducts and is also more labile toward advantageous, self-limiting, hydrolysis. With 1M7, the single nucleotide resolution interrogation of the RNA structure is complete in 70 s. SHAPE analysis performed with 1M7 accurately reports the secondary and tertiary structure of the RNase P specificity domain and allows the secondary structure of this RNA to be predicted with up to 91% accuracy.
Intrapulmonary pharmacokinetics of azithromycin in healthy volunteers given five oral doses (1996)

The intrapulmonary pharmacokinetics of oral azithromycin were studied in 25 healthy volunteers, each of whom received an initial dose of 500 mg and then 250 mg once daily for four additional doses. Bronchoscopy, bronchoalveolar lavage, and venipuncture were performed 4, 28, 76, 124, 172, 244, 340, and 508 h after the first dose was administered. Azithromycin concentrations in epithelial lining fluid (ELF), alveolar macrophages, peripheral blood monocytes, and serum were measured by high-performance liquid chromatography. Azithromycin was extensively concentrated in cells and ELF. Drug concentrations in AMs (peak mean +/- standard deviation, 464 +/- 65 micrograms/ml) exceeded 80 micrograms/ml up to 508 h (21 days) following the first dose, while concentrations in PBMs (peak, 124 +/- 28 micrograms/ml) exceeded 20 micrograms/ml up to 340 h (14 days). Azithromycin concentrations in ELF peaked at 124 h (3.12 +/- 0.93 micrograms/ml) and were detectable up to 172 h (7 days), when they were 20 times the concurrent serum concentrations. Although the clinical significance of antibiotic concentrations in these compartments is nuclear, the sustained lung tissue penetration and extensive phagocytic accumulation demonstrated in this study support the proven efficacy of azithromycin administered on a 5-day dosage schedule in the treatment of extracellular or intracellular pulmonary infections.
Systematic analysis and modeling of integrated inductors and transformers in RF IC design (2000)

An efficient modeling technique and a novel CAD tool for the accurate prediction of the performance of integrated inductors and transformers is presented. This generic and process-independent approach generates lumped-element models that easily plug into the RF IC design flow. Their accuracy is established through comparisons with measurements of numerous fabricated inductor structures. This paper intends to provide answers to vital questions in regard to existing limits and future expectations of the performance of on-chip inductors using comprehensive nomographs and quantitative analysis of spiral inductor families. An LNA design paradigm depicts how first-time-working silicon can be achieved when on-chip inductors' coupling is taken into account during the layout design process, minimizing risk, time, and cost.
Effects of 4-nonylphenol on oxidant/antioxidant balance system inducing hepatic steatosis in male rat (2015)

An emerging literature suggests that early life exposure to 4-nonylphenol (4-NP), a widespread endocrine disrupting chemical, may increase the risk of metabolic syndrome. In this study, we investigated the hypothesis that intraperitoneal administration of 4-NP induces hepatic steatosis in rat. 24 male Sprague-Dawley rats were administered with 4-NP (0, 2, 10 and 50 mg/kg b.wt) in corn oil for 30 days. Liver histology, biochemical analysis and gene expression profiling were examined. After treatment, abnormal liver morphology and function were observed in the 4-NP-treated rat, and significant changes in gene expression an indicator of hepatic steatosis and apoptosis were observed compared with controls. Up-regulated genes involved in apoptosis, hepatotoxity and oxidative stress, increased ROS and decrease of antioxidant enzyme were observed in the 4-NP exposed rat. Extensive fatty accumulation in liver section and elevated serum GOT, GPT, LDH and γ-GT were also observed. Incidence and severity of liver steatosis was scored and taken into consideration (steatosis, ballooning and lobular inflammation). Hepatocytes apoptosis could promote NAFLD progression; Fas/FasL, TNF-α and Caspase-9 mRNA activation were important contributing factors to hepatic steatosis. These findings provide the first evidence that 4-NP affects the gene expression related to liver hepatotoxicity, which is correlated with hepatic steatosis.
Effects of thymidine and hydroxyurea on the metabolism and cytotoxicity of 1-B-D arabinofuranosylcytosine in highly resistant human leukemia cells (1991)

We have examined the effect of the ribonucleotide reductase inhibitors thymidine (dThd) and hydroxyurea (HU) on the metabolism and cytotoxicity of high concentrations (10 to 100 mumol/L) of cytosine arabinoside (Ara-C) in a deoxycytidine kinase-deficient, highly Ara-C- resistant human promyelocytic leukemic cell subline (HL-60/Ara-C). Administration of dThd or HU (0.5 to 3 mmol/L) in conjunction with high concentrations of Ara-C either sequentially or simultaneously lead to enhanced (and in some cases a supra-additive) inhibition of HL-60/Ara-C suspension culture growth and soft agar colony formation. In addition, exposure of cells to 0.5 mmol/L dThd or HU for 48 hours significantly increased the percentage of HL-60/Ara-C in S-phase. In contrast to previous studies involving low-dose Ara-C administration, we were unable to detect dThd- or HU-mediated increments in Ara-CTP formation in HL-60/Ara-C cells treated with high-dose Ara-C despite reductions in intracellular dCTP pools as great as 65%. However, dThd or HU did increase Ara-C incorporation into newly synthesized DNA. These studies show that administration of dThd or HU in conjunction with high concentrations of Ara-C results in an enhanced antiproliferative effect of Ara-C against Ara-C-resistant leukemic cells deficient in deoxycytidine kinase.
Ras-Induced Activation of Raf-1 Is Dependent on Tyrosine Phosphorylation (1996)

Although Rafs play a central role in signal transduction, the mechanism(s) by which they become activated is poorly understood. Raf-1 activation is dependent on the protein's ability to bind Ras, but Ras binding is insufficient to activate Raf-1 tyrosine phosphorylation to this Ras-induced activation, in the absence of an over-expressed tyrosine kinase. We demonstrate that Raf-1 purified form Sf9 cells coinfected with baculovirus Ras but not Src could be inactivated by protein tyrosine phosphatase PTP-1B. 14-3-3 and Hsp90 proteins blocked both the tyrosine dephosphorylation and inactivation of Raf-1, suggesting that Raf-1 activity is phosphotyrosine dependent. In Ras-transformed NIH 3T3 cells, a minority of Raf-1 protein was membrane associated, but essentially all Raf-1 activity and Raf-1 phosphotyrosine fractionated with plasma membranes. Thus, the tyrosine-phosphorylated and active pool of Raf-1 constitute a membrane-localized subfraction which could also be inactivated with PTP-1B. By contrast, B-Raf has aspartic acid residues at positions homologous to those of the phosphorylated tyrosines (at 340 and 341) of Raf-1 and displays a high basal level of activity. B-Raf was not detectably tyrosine phosphorylated, membrane localized, or further activated upon Ras transformation, even though B-Raf has been shown to bind to Ras in vitro. We conclude that tyrosine phosphorylation is an essential component of the mechanism by which Ras activates Raf-1 kinase activity and that steady-state activated Ras is insufficient to activate B-Raf in vivo.
Thermally Produced Biodegradable Scaffolds for Cartilage Tissue Engineering (2004)

A novel process was developed to fabricate biodegradable polymer scaffolds for tissue engineering applications, without using organic solvents. Solvent residues in scaffolds fabricated by processes involving organic solvents may damage cells transplanted onto the scaffolds or tissue near the transplantation site. Poly(L-lactic acid) (PLLA) powder and NaCl particles in a mold were compressed and subsequently heated at 180 degrees C (near the PLLA melting temperature) for 3 min. The heat treatment caused the polymer particles to fuse and form a continuous matrix containing entrapped NaCl particles. After dissolving the NaCl salts, which served as a porogen, porous biodegradable PLLA scaffolds were formed. The scaffold porosity and pore size were controlled by adjusting the NaCl/PLLA weight ratio and the NaCl particle size. The characteristics of the scaffolds were compared to those of scaffolds fabricated using a conventional solvent casting/particulate leaching (SC/PL) process, in terms of pore structure, pore-size distribution, and mechanical properties. A scanning electron microscopic examination showed highly interconnected and open pore structures in the scaffolds fabricated using the thermal process, whereas the SC/PL process yielded scaffolds with less interconnected and closed pore structures. Mercury intrusion porosimetry revealed that the thermally produced scaffolds had a much more uniform distribution of pore sizes than the SC/PL process. The utility of the thermally produced scaffolds was demonstrated by engineering cartilaginous tissues in vivo. In summary, the thermal process developed in this study yields tissue-engineering scaffolds with more favorable characteristics, with respect to, freedom from organic solvents, pore structure, and size distribution than the SC/PL process. Moreover, the thermal process could also be used to fabricate scaffolds from polymers that are insoluble in organic solvents, such as poly(glycolic acid). Cartilage tissue regenerated from thermally produced PLLA scaffold.
Patterning Sub-50 nm features with near-field embedded-amplitude masks (2002)

Sub-50 nm lines, holes, and posts have been patterned photolithographically using near-field embedded-amplitude masks and an exposing wavelength of 220 nm generated by an arc-lamp source. Interference in the optical near field is utilized to produce the fine patterns. In some cases, the feature sizes on the mask are more than six times larger than the size of the smallest features patterned on the substrate. Numerical simulations support the experimental results.
Follicular Bisection in Hair Transplantation Surgery: An in Vitro Model (1998)

The aim of this study was to evaluate, in an in vitro model, the survival and growth rates of transversely sectioned human hair follicles to assess experimentally the soundness of this approach as a future possible method for "duplicating" available donor hair grafts in hair transplantation procedures. A total of 300 human anagen hair follicles was obtained from 10 healthy male patients. Follicles were thus randomly assigned to one of the following groups: group A (control; n = 100 follicles), cultured intact as dissected, and group B (experimental; n = 200 follicles), transversely transected, parallel to the epidermal surface and immediately below the bulge area, to obtain 200 lower-half follicles and 200 upper-half follicles. Isolated hair follicles from both groups were maintained in culture for 10 days. The length of each follicle was measured immediately following isolation and at the end of the 10-day culture period. No statistically significant differences were found between the growth rate of intact follicles (mean 10-day growth rate = 2.71 mm) and of lower-half follicles (mean 10-day growth-rate = 2.64 mm), whereas a statistically significant difference was found between the growth rate of follicles from the two above-mentioned groups and the growth rate of the "upper-half" follicles (mean 10-day growth rate = 1.07 mm). Histologic analysis demonstrated that both intact and lower-half follicles maintained a normal histologic appearance, whereas in upper-half follicle sections we invariably detected a region of intense cell proliferation, reminiscent of a regenerated follicular papilla, surrounding the lowermost part of the follicle. In our opinion, the reported in vitro survival rate of transected human hair follicles might represent an interesting starting point in striving to augment the number of donor hairs available during a hair transplantation procedure.
AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA (2007)

Classical molecular dynamics (MD) simulations are useful for characterizing the structure and dynamics of biological macromolecules, ultimately, resulting in elucidation of biological function. The AMBER force field is widely used and has well-defined bond length, bond angle, partial charge, and van der Waals parameters for all the common amino acids and nucleotides, but it lacks parameters for many of the modifications found in nucleic acids and proteins. Presently there are 107 known naturally occurring modifications that play important roles in RNA stability, folding, and other functions. Modified nucleotides are found in almost all transfer RNAs, ribosomal RNAs of both the small and large subunits, and in many other functional RNAs. We developed force field parameters for the 107 modified nucleotides currently known to be present in RNA. The methodology used for deriving the modified nucleotide parameters is consistent with the methods used to develop the Cornell et al. force field. These parameters will improve the functionality of AMBER so that simulations can now be readily performed on diverse RNAs having post-transcriptional modifications.
Dimeric erythropoietin fusion protein with enhanced erythropoietic activity in vitro and in vivo (2001)

High doses of recombinant human erythropoietin (rhEpo) are required for the treatment of chronic anemia. Thus, it is clear that therapy for chronic anemia would greatly benefit from an erythropoietin derivative with increased erythropoietic activity rather than the native endogenous hormone. In this report, the activity of a human Epo-Epo dimer protein, obtained by recombinant technology, is described and compared with its Epo monomer counterpart produced under identical conditions. Although monomer Epo and dimer Epo-Epo had similar pharmacokinetics in normal mice, the increase in hematocrit value was greater with the dimer than with the monomer. Moreover, in clonogenic assays using CD34(+) human hematopoietic cells, the human dimer induced a 3- to 4-fold-greater proliferation of erythroid cells than the monomer. Controlled secretion of dimeric erythropoietin was achieved in beta-thalassemic mice by in vivo intramuscular electrotransfer of a mouse Epo-Epo plasmid containing the tetO element and of a plasmid encoding the tetracycline controlled transactivator tTA. Administration of tetracycline completely inhibited the expression of the mEpo dimer. On tetracycline withdrawal, expression of the Epo-Epo dimer resumed, thereby resulting in a large and sustained hematocrit increase in beta-thalassemic mice. No immunologic response against the dimer was apparent in mice because the duration of the hematocrit increase was similar to that observed with the monomeric form of mouse erythropoietin. (Blood. 2001;97:3776-3782)
Intercellular Adhesion Molecule 1 Is Critical for Activation of CD28-Deficient T Cells (2000)

Presentation of Ag to T lymphocytes in the absence of the requisite costimulatory signals leads to an Ag-specific unresponsiveness termed anergy, whereas Ag presentation in conjunction with costimulation leads to clonal expansion. B7/CD28 signaling has been shown to provide this critical costimulatory signal and blockade of this pathway may inhibit in vitro and in vivo immune responses. Although T cells from CD28-deficient mice are lacking in a variety of responses, they nonetheless are capable of various primary and secondary responses without the induction of anergy expected in the absence of costimulation. This suggests that there may be alternative costimulatory pathways that can replace CD28 signaling under certain circumstances. In this paper, we show that ICAM-1becomes a dominant costimulatory molecule for CD28-deficient T cells. ICAM-1 costimulates anti-CD3-mediated T cell proliferation and IL-2 secretion in CD28-deficient murine T cells. Furthermore, splenocytes from ICAM-1-deficient mice could not activate CD28-deficient T cells and splenocytes lacking both ICAM and CD28 fail to proliferate in response to anti-CD3-induced T cell signals. This confirms that not only can ICAM-1 act as a CD28-independent costimulator, but it is the dominant, requisite costimulatory molecule for the activation of T cells in the absence of B7/CD28 costimulation.
A novel approach to active listening room compensation for wave field synthesis using wave-domain adaptive filtering (2004)

Wave field synthesis is an auralization technique which allows the entire wave field to be controlled within the entire listening area. However, reflections in the listening room interfere with the auralized wave field and may impair the spatial reproduction. Active listening room compensation aims at reducing these impairments by using the playback system. Due to the high number of playback channels used for wave field synthesis, the existing approaches to room compensation are not applicable. A novel approach to active room compensation overcomes these problems by a transformation from the space-time to the wave domain and application of wave-domain adaptive filtering.
Hybrid image-/model-based gaze-contingent rendering (2007)

A nonisotropic hybrid image-/model-based gaze-contingent rendering technique utilizing ray casting on a GPU is discussed. Empirical evidence derived from human subject experiments indicates an inverse relationship between a peripherally degraded scene's high-resolution inset size and mean search time, a trend consistent with existing image- and model- based techniques. In addition, the data suggest that maintaining a target's silhouette edges decreases search times when compared to targets with degraded edges. Benefits of the hybrid technique include simplicity of design and parallelizability, both conducive to GPU implementation.