gebhart/patrepeval huggingface dataset:
Modeling TCP latency (2002)

Several analytic models describe the steady-state throughput of bulk transfer TCP flows as a function of round trip time and packet loss rate. These models describe flows based on the assumption that they are long enough to sustain many packet losses. However, most TCP transfers across today's Internet are short enough to see few, if any, losses and consequently their performance is dominated by startup effects such as connection establishment and slow start. This paper extends the steady-state model proposed in Padhye et al. (1998), in order to capture these startup effects. The extended model characterizes the expected value and distribution of TCP connection establishment and data transfer latency as a function of transfer size, round trip time, and packet loss rate. Using simulations, controlled measurements of TCP transfers, and live Web measurements we show that, unlike earlier steady-state models for TCP performance, our extended model describes connection establishment and data transfer latency under a range of packet loss conditions, including no loss.
Comparison of morphology and mechanical properties of PLGA bioscaffolds (2008)

In this study, bioscaffolds using poly(DL-lactide-co-glycolide) acid (PLGA) were fabricated and studied. The gas foaming/salt leaching technique in a batch foaming setup was employed, and the effects of material composition of PLGA on the morphology and mechanical properties using this process were investigated. Two material compositions of PLGA 50/50 and 85/15 were used, and characterization of scaffolds fabricated with these materials showed that a lower relative density can be achieved with an increasing poly(DL-lactide) acid (PDLLA) content; however, higher open-cell porosity was obtained with lower PDLLA content. Furthermore, the effect of PLGA composition on modulus of the scaffolds was minor.
Current Limitations to Protein Threading Approaches (1997)

A short review of the threading approach to protein structure prediction, including presentation of some open statistical problems. Also discussed is one of the likely sources of the current limited success, that being the form of the pairwise potentials used in most threading approaches.
Measurement of the band gap of GexSi1−x/Si strained-layer heterostructures (1985)

We have used photocurrent spectroscopy to measure the optical absorption spectra of coherently strained layers of GexSi1−x grown on 〈001〉 Si by molecular beam epitaxy. A dramatic lowering of the indirect band gap, relative to that of unstrained bulk Ge-Si alloys, is observed. Our results for 0≤x≤0.7 are in remarkably good agreement with recent calculations of the effects of misfit strain on the band edges of coherently strained Ge-Si heterostructures. At x=0.6, the gap is lower than that of pure Ge.
T1, T2 relaxation and magnetization transfer in tissue at 3T (2005)

T1, T2, and magnetization transfer (MT) measurements were performed in vitro at 3 T and 37 degrees C on a variety of tissues: mouse liver, muscle, and heart; rat spinal cord and kidney; bovine optic nerve, cartilage, and white and gray matter; and human blood. The MR parameters were compared to those at 1.5 T. As expected, the T2 relaxation time constants and quantitative MT parameters (MT exchange rate, R, macromolecular pool fraction, M0B, and macromolecular T2 relaxation time, T2B) at 3 T were similar to those at 1.5 T. The T1 relaxation time values, however, for all measured tissues increased significantly with field strength. Consequently, the phenomenological MT parameter, magnetization transfer ratio, MTR, was lower by approximately 2 to 10%. Collectively, these results provide a useful reference for optimization of pulse sequence parameters for MRI at 3 T.
Sequencing RNA by a combination of exonuclease digestion and uridine specific chemical cleavage using MALDI-TOF (1998)

The determination of DNA sequences by partial exonuclease digestion followed by Matrix-Assisted Laser Desorption Time of Flight Mass Spectrometry (MALDI-TOF) is a well established method. When the same procedure is applied to RNA, difficulties arise due to the small (1 Da) mass difference between the nucleotides U and C, which makes unambiguous assignment difficult using a MALDI-TOF instrument. Here we report our experiences with sequence specific endonucleases and chemical methods followed by MALDI-TOF to resolve these sequence ambiguities. We have found chemical methods superior to endonucleases both in terms of correct specificity and extent of sequence coverage. This methodology can be used in combination with exonuclease digestion to rapidly assign RNA sequences.
Model Studies of the Effect of Orthophospho-l-serine on Biological Mineralization (2001)

The effect of phospho-l-serine in supersaturated solutions of calcium phosphate was investigated at plethostatic conditions. Phospho-l-serine inhibited the crystal growth of hydroxyapatite {Ca5OH(PO4)3, HAP} by blocking the crystal growth centers through adsorption. Complete inhibition was attained with a phospho-l-serine concentration of 4 × 10-4 M. Analysis of the kinetics and adsorption isotherm results showed a Langmuir-type adsorption. The amount of phospho-l-serine adsorbed on HAP decreased as pH increased from 7.4 to 10.4. The adsorbed species of phospho-l-serine, which in the pH range 7.4−10.4 are mainly the monoprotonated species (HL2-), are located in the inner Helmholtz plane (IHP) of the double layer at the HAP/electrolyte interface, interacting with the surface of HAP with both electrostatic and chemical interactions. The location of the negatively charged HL2- species at the IHP caused a shift of the ζ-potential to more negative values. Finally, a model was established for the adsorption of phospho-l-serine onto the HAP surface at pH 7.4, according to which an ion pair forms between the protonated amino group of one HL2- species and one negative site of the surface of HAP, i.e., the phosphate or hydroxyl group. Due to electrostatic repulsion, the negatively charged deprotonated carboxyl and phosphate groups of the adsorbed HL2- species are oriented in a manner ensuring the maximum possible distance from the negatively charged surface of HAP.
Radical Cystectomy for Stages TA, TIS and T1 Transitional Cell Carcinoma of the Bladder (1994)

Between January 1969 and January 1990, 531 patients underwent bilateral pelvic lymph node dissection and radical cystectomy for the management of transitional cell carcinoma of the bladder. Of these procedures 220 were performed for clinical stage Ta (31 patients), Tis (23) or T1 (166) disease, which was either high grade or recalcitrant to transurethral resection and/or intravesical chemotherapy. This subgroup of patients was studied to evaluate the outcome of recurrent or chemotherapy resistant superficial transitional cell carcinoma of the bladder after radical cystectomy. The operative mortality rate for the group was 2.3% and the overall complication rate was 20.4%. The pelvic recurrence rate was 5.9%. The 5-year cancer-specific survival rates for patients with pathological stage Ta (11), Tis (19), T0 (43) and T1 (91) disease were 88%, 100%, 80% and 76%, respectively. The 10-year cancer-specific survival rates were 75%, 92%, 66% and 62%, respectively. A total of 74 patients received preoperative radiation therapy (2,000 rad) but they had no better 5-year cancer-specific survival rates than did nonirradiated patients. Transurethral resection and/or preoperative radiation therapy resulted in a pathological status of T0 in 43 patients but this did not confer a survival advantage. Although bladder preservation is preferable, low operative mortality and pelvic recurrence rates, as well as new methods of continent urinary diversion continue to make radical cystectomy the definitive form of therapy for patients with superficial disease recalcitrant to transurethral therapy.
A Novel Gene Encoding Xanthan Lyase of Paenibacillus alginolyticus Strain XL-1 (2000)

Xanthan-modifying enzymes are powerful tools in studying structure-function relationships of this polysaccharide. One of these modifying enzymes is xanthan lyase, which removes the terminal side chain residue of xanthan. In this paper, the cloning and sequencing of the first xanthan lyase-encoding gene is described, i. e., the xalA gene, encoding pyruvated mannose-specific xanthan lyase of Paenibacillus alginolyticus XL-1. The xalA gene encoded a 100, 823-Da protein, including a 36-amino-acid signal sequence. The 96, 887-Da mature enzyme could be expressed functionally in Escherichia coli. Like the native enzyme, the recombinant enzyme showed no activity on depyruvated xanthan. Compared to production by P. alginolyticus, a 30-fold increase in volumetric productivity of soluble xanthan lyase was achieved by heterologous production in E. coli. The recombinant xanthan lyase was used to produce modified xanthan, which showed a dramatic loss of the capacity to form gels with locust bean gum.
Influenza Vaccination with a Live Attenuated Vaccine (2009)

Influenza is a highly contagious, acute respiratory illness with a long history of outbreaks dating back several centuries. Although immunization is an effective means of protection against influenza, vaccination rates have been suboptimal, especially among certain high-risk groups, including children and health care personnel. This article reviews basic information about influenza and immunization, discusses the relevance of children as vectors of disease, and highlights current information on FluMist, an intranasally administered, live attenuated influenza vaccine, including studies of its use compared with trivalent inactivated vaccine and in children.
Mass separation of metallic and semiconducting single‐wall carbon nanotubes using agarose gel (2009)

Abstract Metallic and semiconducting single‐wall carbon nanotubes (SWCNTs) were separated using agarose gel. When the SWCNTs isolated with sodium dodecyl sulfate (SDS) were embedded in agarose gel, the metallic SWCNTs were eluted from the gel by applying electronic field or mechanical stress, for example, centrifugation etc., and semiconducting SWCNTs remained in the gel. The purities for metallic and semiconducting SWCNTs were ∼70% and ∼95%, respectively. One of the simplest methods was freeze, thaw and squeeze the SWCNTs containing gel. These methods can separate various kinds of SWCNTs. By using centrifugation method, we could separate about 10 mg of SWCNTs with a 500 ml bottle.
Specific HIV gp120-cleaving Antibodies Induced by Covalently Reactive Analog of gp120 (2003)

We report the results of efforts to strengthen and direct the natural nucleophilic activity of antibodies (Abs) for the purpose of specific cleavage of the human immunodeficiency virus-1 coat protein gp120. Phosphonate diester groups previously reported to form a covalent bond with the active site nucleophile of serine proteases (Paul, S., Tramontano, A., Gololobov, G., Zhou, Y. X., Taguchi, H., Karle, S., Nishiyama, Y., Planque, S., and George, S. (2001) J. Biol. Chem. 276, 28314-28320) were placed on Lys side chains of gp120. Seven monoclonal Abs raised by immunization with the covalently reactive analog of gp120 displayed irreversible binding to this compound (binding resistant to dissociation with the denaturant SDS). Catalytic cleavage of biotinylated gp120 by three monoclonal antibodies was observed. No cleavage of albumin and the extracellular domain of the epidermal growth factor receptor was detected. Cleavage of model peptide substrates occurred on the C-terminal side of basic amino acids, and Km for this reaction was approximately 200-fold greater than that for gp120 cleavage, indicating Ab specialization for the gp120 substrate. A hapten phosphonate diester devoid of gp120 inhibited the catalytic activity with exceptional potency, confirming that the reaction proceeds via a serine protease mechanism. Irreversible binding of the hapten phosphonate diester by polyclonal IgG from mice immunized with gp120 covalently reactive analog was increased compared with similar preparations from animals immunized with control gp120, indicating induction of Ab nucleophilicity. These findings suggest the feasibility of raising antigen-specific proteolytic antibodies on demand by covalent immunization.
Functional dyspepsia, delayed gastric emptying, and impaired quality of life (2005)

In patients with functional dyspepsia selected for a clinical trial programme, gastric emptying did not usefully stratify them symptomatically. Quality of life of patients with functional dyspepsia enrolled in this clinical trial programme was significantly impaired but this was not explained by delayed gastric emptying.
Muscular atrophy of caveolin-3–deficient mice is rescued by myostatin inhibition (2006)

Caveolin-3, the muscle-specific isoform of caveolins, plays important roles in signal transduction. Dominant-negative mutations of the caveolin-3 gene cause autosomal dominant limb-girdle muscular dystrophy 1C (LGMD1C) with loss of caveolin-3. However, identification of the precise molecular mechanism leading to muscular atrophy in caveolin-3-deficient muscle has remained elusive. Myostatin, a member of the muscle-specific TGF-beta superfamily, negatively regulates skeletal muscle volume. Here we report that caveolin-3 inhibited myostatin signaling by suppressing activation of its type I receptor; this was followed by hypophosphorylation of an intracellular effector, Mad homolog 2 (Smad2), and decreased downstream transcriptional activity. Loss of caveolin-3 in P104L mutant caveolin-3 transgenic mice caused muscular atrophy with increase in phosphorylated Smad2 (p-Smad2) as well as p21 (also known as Cdkn1a), a myostatin target gene. Introduction of the myostatin prodomain, an inhibitor of myostatin, by genetic crossing or intraperitoneal administration of the soluble type II myostatin receptor, another inhibitor, ameliorated muscular atrophy of the mutant caveolin-3 transgenic mice with suppression of p-Smad2 and p21 levels. These findings suggest that caveolin-3 normally suppresses the myostatin-mediated signal, thereby preventing muscular atrophy, and that hyperactivation of myostatin signaling participates in the pathogenesis of muscular atrophy in a mouse model of LGMD1C. Myostatin inhibition may be a promising therapy for LGMD1C patients.
The anti-inflammatory effect of combined complement and CD14 inhibition is preserved during escalating bacterial load (2015)

Combined inhibition of complement and CD14 is known to attenuate bacterial-induced inflammation, but the dependency of the bacterial load on this effect is unknown. Thus, we investigated whether the effect of such combined inhibition on Escherichia coli- and Staphylococcus aureus-induced inflammation was preserved during increasing bacterial concentrations. Human whole blood was preincubated with anti-CD14, eculizumab (C5-inhibitor) or compstatin (C3-inhibitor), or combinations thereof. Then heat-inactivated bacteria were added at final concentrations of 5 × 10(4) -1 × 10(8) /ml (E. coli) or 5 × 10(7) -4 × 10(8) /ml (S. aureus). Inflammatory markers were measured using enzyme-linked immunosorbent assay (ELISA), multiplex technology and flow cytometry. Combined inhibition of complement and CD14 significantly (P < 0.05) reduced E. coli-induced interleukin (IL)-6 by 40-92% at all bacterial concentrations. IL-1β, IL-8 and macrophage inflammatory protein (MIP)-1α were significantly (P < 0.05) inhibited by 53-100%, and the effect was lost only at the highest bacterial concentration. Tumour necrosis factor (TNF) and MIP-1β were significantly (P < 0.05) reduced by 80-97% at the lowest bacterial concentration. Monocyte and granulocyte CD11b were significantly (P < 0.05) reduced by 63-91% at all bacterial doses. Lactoferrin was significantly (P < 0.05) attenuated to the level of background activity at the lowest bacterial concentration. Similar effects were observed for S. aureus, but the attenuation was, in general, less pronounced. Compared to E. coli, much higher concentrations of S. aureus were required to induce the same cytokine responses. This study demonstrates generally preserved effects of combined complement and CD14 inhibition on Gram-negative and Gram-positive bacterial-induced inflammation during escalating bacterial load. The implications of these findings for future therapy of sepsis are discussed.
Amino Acid Difference Formula to Help Explain Protein Evolution (1974)

A formula for diference between amino acids combines properties that correlate best with protein residue substitution frequencies: composition, polarity, and molecular volume. Substitution frequencies agree much better with overall chemical difference between exchanging residues than with minimum base changes between their codons. Correlation coefficients show that fixation of mutations between dissimilar amino acids is generally rare.
Leptin Immunoreactivity Is Localized to Neurons in Rat Brain (2002)

Leptin is secreted from adipocytes and is thought to enter the brain to regulate and coordinate metabolism, feeding behaviour, energy balance and reproduction. It is now clear that there are many additional sites of leptin production, including human placenta, ovary, stomach, skeletal muscle, mammary gland, pituitary gland and brain. In the present work, we employed double-label immunofluorescent histochemistry to establish the neuronal localization of leptin immunoreactivity (IR). To accomplish this, we used the neuron-specific marker NeuN to label cells in the arcuate nucleus (ARC), piriform cortex and hippocampus. In the supraoptic nucleus (SON) and paraventricular nucleus (PVN), we used antisera to oxytocin and vasopressin as neuronal markers. Double labelling revealed leptin IR in neurons of the ARC and piriform cortex. Leptin IR was confined to the nucleus and to distinct perinuclear sites. In contrast, neurons in the CA 2/CA 3 region of the hippocampus showed little nuclear staining. Leptin IR was clustered around the nucleus in these cells. Neurons of the dentate gyrus exhibited both nuclear and perinuclear localization of leptin IR. In the SON/PVN, most oxytocin- and vasopressin-IR neurons also contained leptin IR, often in perinuclear sites. In conclusion, the neuronal, perinuclear localization of leptin IR in rat brain corresponds closely to that of leptin receptor (OB-R) IR, which has also been detected intracellularly. Our observation of leptin IR associated with cell nuclei suggests the existence of an OB-R distinct from the well-described membrane forms.
A 126 dB linear switched-capacitor delta-sigma modulator (2002)

Low-frequency measurement applications where low power, high dynamic range and high linearity are important naturally migrate toward oversampling converters. Measuring seismic activity is one such application that requires at least 120 dB S/D. The switched-capacitor delta-sigma modulator presented in this paper achieves the above goals with single-ended linearity in excess of 120 dB. Various distortion mechanisms in switched-capacitor topologies are explained along with solutions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Investigation of the structure of lipid A from Actinobacillus actinomycetemcomitans strain Y4 and human clinical isolate PO 1021‐7 (1991)

The lipopolysaccharides of Actinobacillus actinomycetemcomitans strain Y4 and a human clinical isolate PO 1021-7 were examined by SDS/PAGE, deoxycholate/PAGE and mass spectrometry. PAGE analysis revealed an electrophoretic pattern similar to the SR-type lipopolysaccharide (LPS) of Salmonella. Deoxycholate/PAGE indicated the LPS of A. actinomycetemcomitans to consist of short sugar chains. Chemical analysis revealed the presence of thiobarbituric-acid-positive material (3-deoxy-D-manno-octulosonic acid equivalents) and four neutral sugars: glucose, galactose, D-glycero-D-manno-heptose and L-glycero-D-manno-heptose. Phosphate, glucosamine, glycine, and the fatty acids, 3-hydroxymyristic acid, myristic acid and palmitic acid, comprised the remainder of the molecule. The structure of the free lipid A revealed it to consist of a 1,6-glucosamine disaccharide esterified at C4' by a phosphomonoester. The hydroxyl group at C3 and the amide group of the non-reducing glucosamine were both acylated by 3-myristoylmyristic acid; analogous sites on the reducing glucosamine were acylated by 3-hydroxymyristic acid. Hydroxyl groups at C4 and C6' in the free lipid A were unsubstituted, with C6 being the proposed attachment site of the polysaccharide moiety. Chemical analysis revealed the presence of glycine in the intact LPS; its exact location in the A. actinomycetemcomitans LPS is still to be determined. Both intact LPS and free lipid A were highly lethal to galactosamine-sensitized mice, comparable to that of Salmonella.
Regulation of adiponectin and its receptors in response to development of diet-induced obesity in mice (2006)

Adiponectin and its receptors play an important role in energy homeostasis and insulin resistance, but their regulation remains to be fully elucidated. We hypothesized that high-fat diet would decrease adiponectin but increase adiponectin receptor (AdipoR1 and AdipoR2) expression in diet-induced obesity (DIO)-prone C57BL/6J and DIO-resistant A/J mice. We found that circulating adiponectin and adiponectin expression in white adipose tissue are higher at baseline in C57BL/6J mice compared with A/J mice. Circulating adiponectin increases at 10 wk but decreases at 18 wk in response to advancing age and high-fat feeding. However, adiponectin levels corrected for visceral fat mass and adiponectin mRNA expression in WAT are affected by high-fat feeding only, with both being decreased after 10 wk in C57BL/6J mice. Muscle AdipoR1 expression in both C57BL/6J and A/J mice and liver adipoR1 expression in C57BL/6J mice increase at 18 wk of age. High-fat feeding increases both AdipoR1 and AdipoR2 expression in liver in both strains of mice and increases muscle AdipoR1 expression in C57BL/6J mice after 18 wk. Thus advanced age and high-fat feeding, both of which are factors that predispose humans to obesity and insulin resistance, are associated with decreasing adiponectin and increasing AdipoR1 and/or AdipoR2 levels.
cDNA and deduced amino acid sequence of a mouse DNA repair enzyme (APEX nuclease) with significant homology to Escherichia coli exonuclease III. (1991)

We purified a mouse DNA repair enzyme having apurinic/apyrimidinic endonuclease, DNA 3'-phosphatase, 3'-5'-exonuclease and DNA 3' repair diesterase activities, and designated the enzyme as APEX nuclease. A cDNA clone for the enzyme was isolated from a mouse spleen cDNA library using probes of degenerate oligonucleotides deduced from the N-terminal amino acid sequence of the enzyme. The complete nucleotide sequence of the cDNA (1.3 kilobases) was determined. Northern hybridization using this cDNA showed that the size of its mRNA is about 1.5 kilobases. The complete amino acid sequence for the enzyme predicted from the nucleotide sequence of the cDNA (APEX nuclease cDNA) indicates that the enzyme consists of 316 amino acids with a calculated molecular weight of 35,400. The predicted sequence contains the partial amino acid sequences determined by a protein sequencer from the purified enzyme. The coding sequence of APEX nuclease was cloned into pUC18 SmaI and HindIII sites in the control frame of the lacZ promoter. The construct was introduced into BW2001 (xth-11, nfo-2) strain cells of Escherichia coli. The transformed cells expressed a 36.4-kDa polypeptide (the 316 amino acid sequence of APEX nuclease headed by the N-terminal decapeptide of beta-galactosidase) and were less sensitive to methyl methanesulfonate than the parent cells. The fusion product showed priming activity for DNA polymerase on bleomycin-damaged DNA and acid-depurinated DNA. The deduced amino acid sequence of mouse APEX nuclease exhibits a significant homology to those of exonuclease III of E. coli and ExoA protein of Streptococcus pneumoniae and an intensive homology with that of bovine AP endonuclease 1.