gebhart/patrepeval huggingface dataset:
Exploration of the Catalytic and Kinetic Mechanism of ATP Hydrolysis by Bacteriophage T4 Rad50 (2015)

DNA double‐strand breaks are among the most harmful forms of DNA damage and unless correctly repaired they may lead to the development of cancer. A well‐conserved protein complex, Mre11/Rad50, plays a primary role in the initial steps of DNA double‐strand break repair. Rad50 is a member of the ABC protein super‐family, which is defined by six conserved motifs that make up the two ATP active sites that are shared across subunits of the protein dimer. The identity of the catalytic base has been controversial and the kinetic mechanism for only a small number of super‐family members has been determined. We have used a combination of steady state and pre‐steady kinetics, along with site‐directed mutagenesis, solvent isotope and viscosity effects, and pH rate profiles to probe the kinetic and catalytic mechanism of this important ABC protein super‐family member. The results suggest that the catalytic mechanism of Rad50 proceeds thru a dissociative‐like, asymmetric transition state and that enzyme chemistry is the rate‐limiting step of the catalytic cycle. Mutations of the Walker B glutamate and the H‐loop histidine suggest that although these two residues are likely involved in the positioning of the attacking water molecule, neither act to abstract a proton during the transition state of the reaction. In addition, mutation of these residues results in a substantial loss of ATP cooperativity, which when combined with previous results from our laboratory, suggests two routes of communication between ATP active sites. While there does not appear to be a single unifying theme for the rate‐limiting step of the reaction, our conclusions for Rad50 regarding the catalytic mechanism and cooperativity are expected to apply more broadly to the ABC protein super‐family.
The configurational statistics of a polymeric chain confined by impenetrable barriers (1976)

General expressions, applicable to any chain distribution function, are developed for the configurational statistics of a polymeric chain which is confined by any number of impenetrable barriers. The reflection principle, or method of images, is employed for this purpose. The procedure for obtaining approximate, analytical equations from these general expressions is then illustrated using the statistics of a real polymeric chain, to the order N−1, for the cases of: a loop (a chain with both ends attached to the same wall), a cilia (a chain with one end attached to a wall and the other end free), and a bridge (a chain with its ends attached to opposite walls), all between two walls.
Aggressive Forms of Follicular-derived Thyroid Carcinoma (2003)

Although most follicular-derived thyroid carcinomas are well differentiated and have an excellent prognosis, certain forms of thyroid carcinoma behave in a clinically more aggressive fashion. We present a case of a 27-year-old woman who presented with a palpable, 3.0-cm right thyroid nodule. Fine needle aspiration showed a cellular lesion with many crowded groups of small follicular cells with scant cytoplasm, clumped chromatin, moderate nuclear pleomorphism, and mitotic activity. Surgical resection of the thyroid gland revealed an insular carcinoma with classic nested architecture arising within a microfollicular thyroid neoplasm. Two years later, the patient developed multiple liver nodules detected by computed tomography, and fine needle aspiration showed metastatic insular carcinoma. Insular carcinoma, in particular, as well as certain subtypes of papillary carcinoma, such as the tall cell, columnar cell, and diffuse sclerosing variants, is considered to be an aggressive form of follicular-derived carcinoma. Its clinical behavior is between that of well differentiated thyroid carcinoma and of anaplastic carcinoma, the most highly aggressive follicular-derived malignancy arising within the thyroid gland. Cytologic and histologic recognition of these aggressive variants of thyroid carcinoma is important because the specific diagnosis may impact the clinical management of these patients.
Enhanced Mechanical Properties of Epoxy Nanocomposites by Mixing Noncovalently Functionalized Boron Nitride Nanoflakes (2013)

The influence of surface modifications on the mechanical properties of epoxy-hexagonal boron nitride nanoflake (BNNF) nanocomposites is investigated. Homogeneous distributions of boron nitride nanoflakes in a polymer matrix, preserving intrinsic material properties of boron nitride nanoflakes, is the key to successful composite applications. Here, a method is suggested to obtain noncovalently functionalized BNNFs with 1-pyrenebutyric acid (PBA) molecules and to synthesize epoxy-BNNF nanocomposites with enhanced mechanical properties. The incorporation of noncovalently functionalized BNNFs into epoxy resin yields an elastic modulus of 3.34 GPa, and 71.9 MPa ultimate tensile strength at 0.3 wt%. The toughening enhancement is as high as 107% compared to the value of neat epoxy. The creep strain and the creep compliance of the noncovalently functionalized BNNF nanocomposite is significantly less than the neat epoxy and the nonfunctionalized BNNF nanocomposite. Noncovalent functionalization of BNNFs is effective to increase mechanical properties by strong affinity between the fillers and the matrix.
Two-step integral imaging for orthoscopic three-dimensional imaging with improved viewing resolution (2002)

We present a two-step integral imaging system to obtain 3-D orthoscopic real images. By adopting a nonstationary micro-optics tech- nique, we demonstrate experimentally the potential usefulness of two- step integral imaging. © 2002 Society of Photo-Optical Instrumentation Engineers.
<i>Pseudomonas aeruginosa</i> and other predictors of mortality and morbidity in young children with cystic fibrosis (2002)

We conducted a registry-based study to determine prognostic indicators of 8-year mortality and morbidity in young children with cystic fibrosis (CF). Patients ages 1-5 years from the 1990 U.S. Cystic Fibrosis Foundation (CFF) National Patient Registry served as the study cohort (N = 3,323). Registry data provided information on baseline characteristics in 1990, 8-year mortality, and clinical outcomes in 1998.P. aeruginosa respiratory infection was found to be a major predictor of morbidity and mortality. The 8-year risk of death was 2.6 times higher in patients who had respiratory cultures positive for P. aeruginosa in 1990 (95% confidence interval 1.6, 4.1) than in children without P. aeruginosa in their respiratory cultures. Culture-positive patients in 1990 also had a significantly lower percent predicted forced expiratory volume in 1 sec (FEV(1)) and weight percentile at follow-up, and they had an increased risk of continued P. aeruginosa respiratory infection and hospitalization for acute respiratory exacerbation in 1998. Among the other predictors of increased morbidity and mortality were lower baseline weight percentiles and number of CF-related hospitalizations during the baseline year.These findings confirm reports from previous smaller studies of outcomes among young children with CF, and highlight the potential to decrease the morbidity and mortality of young patients with CF through early intervention.
Hemodynamic Changes in Patients with Portal Venous Obstruction (1983)

Splanchnic and systemic hemodynamics were evaluated in five adult patients with portal hypertension due to portal venous obstruction and were compared with those of patients with cirrhosis and those of a control group. In patients with portal venous obstruction, the gradient between wedged and free hepatic venous pressures ranged from 2 to 3 mm Hg, as in the control group, and was significantly lower than in patients with cirrhosis. Hepatic blood flow averaged 0.521 +/- 0.127 liter per min per m2 (mean +/- S.D.) and was significantly lower than that measured in cirrhotic and normal patients. Cardiac index averaged 3.788 +/- 0.629 liters per min per m2; this high value for cardiac index was not significantly different from that measured in cirrhotic patients, but was significantly higher than in patients of the control group. It is suggested that a hyperkinetic circulatory state may result from the development of portal-systemic venous collateral circulation in patients with portal venous obstruction having normal liver and hepatic venous pressures.
A Comparison Framework for Reactor Anti-Neutrino Detectors in Near-Field Nuclear Safeguards Applications (2017)

Electron anti-neutrino ( e) detectors can support nuclear safeguards, from reactor monitoring to spent fuel characterization. In recent years, the scientific community has developed multiple detector concepts, many of which have been prototyped or deployed for specific measurements by their respective collaborations. However, the diversity of technical approaches, deployment conditions, and analysis techniques complicates direct performance comparison between designs. We have begun development of a simulation framework to compare and evaluate existing and proposed detector designs for nonproliferation applications in a uniform manner. This report demonstrates the intent and capabilities of the framework by evaluating four detector design concepts, calculating generic reactor antineutrino counting sensitivity, and capabilities in a plutonium disposition application example.
Structural requirements for inducing <i>in vitro</i> B lymphocyte activation by chemically synthesized derivatives related to the nonreducing D‐glucosamine subunit of lipid A (1986)

Mitogenic and polyclonal B cell activation (PBA) activities of 16 synthetic compounds related to the nonreducing D-glucosamine (GlcN-II) subunit of lipid A were investigated. Among compounds possessing the GlcN backbone, a 4-O-phosphorylated GlcN derivative carrying N-linked 3-tetradecanoyloxytetradecanoyl [C14-O-(C14)] and 3-O-linked tetradecanoyl (C14) groups, GLA-27, expressed the highest degree of both activities. Omission of the 3-O-linked C14 group from GLA-27 and transfer of the C14 group to the C-6 position induced critical changes in expression of activities. Both 4-O-phosphorylated compounds carrying an N-linked C14 or 3-hydroxytetradecanoyl (C14OH) group instead of the C14-O-(C14) group in GLA-27 showed no detectable activity. Substituting a 3-O-linked C14 group in GLA-27 for the C14-O-(C14) group also markedly decreased mitogenic and PBA activities. Change of phosphorylation site from the C-4 to the C-6 position and bisphosphorylation at the C-4 and C-6 positions induced somewhat weak depression. Much weaker activities were observed in a compound carrying N-linked 3-dodecanoyloxydodecanoyl [C12-O-(C12)] and 3-O-dodecanoyl (C12) as fatty acid substituents. No detectable activity was seen in a compound carrying N-linked 3-hexadecanoyloxyhexadecanoyl [C16-O-(C16)] and 3-O-hexadecanoyl (C16), indicating that the most suitable carbon chain length for expressing the activities is C14. Regarding structural change of the GlcN backbone, a 1-deoxy derivative of GLA-27 exhibited stronger activity than did GLA-27 itself. Mitogenic and PBA activity of GLA-27 were stronger than those of lipid X, which corresponds to the reducing D-GlcN (GlcN-I) subunit of Escherichia coli lipid A and is a 1-O-phosphorylated GlcN derivative carrying N- and 3-O-linked C14OH groups. These results indicate that N-linked acyloxyacyl and 3-O-linked acyl groups and phosphorylation are critical for expressing both mitogenic and PBA activities.
Terminations: The Death of the Lion. the Coxon Fund. the Middle Years. the Altar of the Dead (1895)

Long been considered one of the literary giants of his age, Henry James is an exquisite stylist who questioned the mores and stereotypes of the Gilded Age
Comparison of Thermal and Non-Thermal Ablation of Tumor Using Focused Short Pulse Laser Beam (2007)

For last few decades laser-induced tumor ablation has attracted significant attention of researchers. The accessibility of tumors located deep inside the body organ using fiber-optic probe without any major surgical resection has made this method an alternative for conventional surgical resection. Various minimally invasive techniques have been developed are used to ablate the tumor successfully with minimum collateral damages [1, 2]. All these techniques utilize the photo-thermal mechanism where conversion of laser energy (mainly from CW or long pulsed laser source) to heat energy leads to necrosis of the tissue through photocoagulation. Since, the necrosis of tumor is achieved by volumetric heating of the whole tumor there remains a significant chance of heat spreading out of the tumor volume damaging surrounding healthy tissue. Therefore, precise control of treatment parameters (laser pulse width, laser power, and irradiation time) is required to restrict the heat spread to the healthy tissue surrounding the tumor.
Viable<i>Borrelia burgdorferi</i>Enhances Interleukin-10 Production and Suppresses Activation of Murine Macrophages (2007)

Although it is capable of eliciting strong innate and adaptive immune responses, Borrelia burgdorferi often evades immune clearance through largely unknown mechanisms. Our previous studies determined that infected interlukin-10-/- (IL-10-/-) mice show significantly lower B. burgdorferi levels than wild-type (B6) mice and that IL-10 inhibits innate immune responses critical for controlling B. burgdorferi infection. To determine whether virulent B. burgdorferi preferentially enhances IL-10 production, we developed an in vitro coculture medium (RPMI.B) in which both B. burgdorferi and primary macrophages (Mphis) remain viable. B. burgdorferi grew at similar rates and was able to regulate expression of immunoreactive proteins with similar kinetics in RPMI.B and in traditional BSK medium; in contrast, B. burgdorferi cultured in conventional tissue culture medium (RPMI) rapidly lost viability. Coculture of viable B. burgdorferi in RPMI.B with Mphis resulted in more rapid and significant increases in IL-10 transcripts and secreted proteins than coculture with nonviable B. burgdorferi in RPMI, which corresponded with decreased production of proinflammatory cytokines. Addition of live B. burgdorferi to Mphis in RPMI.B also elicited substantially higher IL-10 levels than heat-killed bacteria elicited, confirming that increased IL-10 production was not inherent to coculture in RPMI.B. Transfer of supernatants from B. burgdorferi-stimulated Mphis into naïve Mphi cultures resulted in suppressed activation upon subsequent stimulation with different bacterial agonists, and this suppression was obviated by IL-10-specific antibody. In vivo analyses determined that murine skin samples exhibited substantial upregulation of IL-10 within 24 h of injection of B. burgdorferi. Together, these results suggest that viable B. burgdorferi can suppress early Mphi responses during infection by causing increased release of IL-10.
Multiscale permutation entropy analysis of EEG recordings during sevoflurane anesthesia (2010)

Electroencephalogram (EEG) monitoring of the effect of anesthetic drugs on the central nervous system has long been used in anesthesia research. Several methods based on nonlinear dynamics, such as permutation entropy (PE), have been proposed to analyze EEG series during anesthesia. However, these measures are still single-scale based and may not completely describe the dynamical characteristics of complex EEG series. In this paper, a novel measure combining multiscale PE information, called CMSPE (composite multi-scale permutation entropy), was proposed for quantifying the anesthetic drug effect on EEG recordings during sevoflurane anesthesia. Three sets of simulated EEG series during awake, light and deep anesthesia were used to select the parameters for the multiscale PE analysis: embedding dimension m, lag tau and scales to be integrated into the CMSPE index. Then, the CMSPE index and raw single-scale PE index were applied to EEG recordings from 18 patients who received sevoflurane anesthesia. Pharmacokinetic/pharmacodynamic (PKPD) modeling was used to relate the measured EEG indices and the anesthetic drug concentration. Prediction probability (P(k)) statistics and correlation analysis with the response entropy (RE) index, derived from the spectral entropy (M-entropy module; GE Healthcare, Helsinki, Finland), were investigated to evaluate the effectiveness of the new proposed measure. It was found that raw single-scale PE was blind to subtle transitions between light and deep anesthesia, while the CMSPE index tracked these changes accurately. Around the time of loss of consciousness, CMSPE responded significantly more rapidly than the raw PE, with the absolute slopes of linearly fitted response versus time plots of 0.12 (0.09-0.15) and 0.10 (0.06-0.13), respectively. The prediction probability P(k) of 0.86 (0.85-0.88) and 0.85 (0.80-0.86) for CMSPE and raw PE indicated that the CMSPE index correlated well with the underlying anesthetic effect. The correlation coefficient for the comparison between the CMSPE index and RE index of 0.84 (0.80-0.88) was significantly higher than the raw PE index of 0.75 (0.66-0.84). The results show that the CMSPE outperforms the raw single-scale PE in reflecting the sevoflurane drug effect on the central nervous system.
Energetics of Metal−Ligand Multiple Bonds. A Combined Solution Thermochemical and ab Initio Quantum Chemical Study of MO Bonding in Group 6 Metallocene Oxo Complexes (1998)

In this paper, we report a synthetic, molecular structure, thermochemical, and ab initio Hartree−Fock/Moller−Plesset level study of bonding and bonding energetics in the group 6 metallocene oxo series Cp2Mo/(MeCp)2MO, M = Cr, Mo, W. Efficient, high-yield syntheses of the pairs Cp2MH2/(MeCp)2MH2, Cp2MCl2/(MeCp)2MCl2, and Cp2MO/(MeCp)2MO where M = Mo or W are reported. The molecular structure of (MeCp)2WO features a “bent sandwich” geometry with a WO distance of 2.04(1) Å and an average WC(Cp) distance of 2.371(8) Å. Thus, WC(Cp) exhibits a ∼0.07 Å elongation over the corresponding distance in typical Cp2WX2 complexes and a WO distance which appears to be elongated versus what might be expected for a formal triple bond. D(MO) values obtained from (MeCp)2MO silanolytic (Me3SiCl, Me3SiI) batch titration calorimetry are very large: 110(11) kcal/mol (M = Mo) and 132(10) kcal/mol (M = W). The corresponding D(WOTMS) value is determined to be 65(18) kcal/mol. Ab initio relativistic core potential calculations reveal significantly weakened MCp bonding versus that in the corresponding Cp2MCl2 compounds, weakened MO bonding due to population of MO π antibonding levels, and a pronounced accumulation of negative charge on the oxo ligand (consistent with observed nucleophilicity of these complexes). Calculated Cp2MCl2 and Cp2MO molecular geometries and D(MO) values at the MP2 level are in favorable agreement with experiment. The D(MO) and D(MO) data provide significant insight into the chemistry of Cp2MO complexes, especially in regard to constraints on oxo transfer as well as oxametallacycle formation and scission processes.
Neutron Radii of Calcium Isotopes from Pion Total Cross Section Measurements (1977)

Measurements of the total cross section differences ${\ensuremath{\sigma}}_{T}(^{48}\mathrm{Ca})\ensuremath{-}{\ensuremath{\sigma}}_{T}(^{40}\mathrm{Ca})$ and ${\ensuremath{\sigma}}_{T}(^{44}\mathrm{Ca})\ensuremath{-}{\ensuremath{\sigma}}_{T}(^{40}\mathrm{Ca})$ are reported for positive and negative pions. Optical-model calculations are used to extract values of the rms neutron radius difference for each isotope pair. For $^{48}\mathrm{Ca}$-$^{40}\mathrm{Ca}$ the deduced radius difference agrees with the results of recent $\ensuremath{\alpha}$-particle and proton scattering experiments but is smaller than values predicted from Hartree-Fock calculations.
Attachment and bonding: A new synthesis. (2005)

Attachment and bonding are evolved processes; the mechanisms that permit the development of selective social bonds are assumed to be very ancient, based on neural circuitry rooted deep in mammalian evolution, but the nature and timing of these processes and their ultimate and proximate causes are only beginning to be understood. In this Dahlem Workshop Report, scientists from different disciplines -- including anthropology, psychology, psychiatry, and behavioral biology -- come together to explore the concepts of attachment and bonding from diverse perspectives. In their studies they seek to understand the causes or the consequences of attachment and bonding in general and their different qualities in individual development in particular. They address such questions as biobehavioral processes in attachment and bonding; early social attachment and its influences on later patterns of behavior; bonding later in life; and adaptive and maladaptive (or pathological) outcomes. The studies confirm that social bonds have consequences for virtually all aspects of behavior and may be protective in the face of both physical and emotional challenges.
Bilateral diffuse uveal melanocytic proliferation: Case report and literature review (2017)

Bilateral diffuse uveal melanocytic proliferation (BDUMP) is a rare paraneoplastic intraocular disease that causes progressive visual loss in patients driven by an IgG factor associated with an underlying malignancy. Characteristic ocular findings include exudative retinal detachment, rapid cataract formation and uveal melanocytic tumours. The awareness and documentation of BDUMP has increased during the past decade, and the increasing amount of data collected demonstrates the effect of treatment with plasmapheresis and the value of diagnostic tools in BDUMP such as genetic and immunologic investigations. The literature of BDUMP has not been reviewed since 2003, and there is a growing need for an updated review on diagnosis and management of BDUMP. We review the literature and report a case of BDUMP with a white ciliary body tumour, iris rubeosis, increased iris pigmentation and cataract.
In Situ Soil Treatments to Reduce the Phyto‐ and Bioavailability of Lead, Zinc, and Cadmium (2004)

A study was established near a former Zn and Pb smelter to test the ability of soil amendments to reduce the availability of Pb, Zn, and Cd in situ. Soil collected from the field was amended in the lab with P added as 1% P-H3PO4, biosolids compost added at 10% (referred to hereafter as "compost"), and a high-Fe by-product (referred to hereafter as "Fe") + P-triple superphosphate (TSP) (2.5% Fe + 1% P-TSP) and incubated under laboratory conditions at a constant soil pH. Changes in Pb bioavailability were measured with an in vitro test and a feeding study with weanling rats. Field-amended and incubated soils using these plus additional treatments were evaluated using the in vitro extraction and tall fescue (Festuca arundinacea Schreb. cv. Kentucky-31) metal concentration. Reductions were observed across all parameters but were not consistent. In the feeding study, the 1% P-H3PO4 and compost treatments resulted in a decrease of 26% in rat tissue Pb concentration compared with the control soil. The 2.5% Fe + 1% P-TSP showed a 39% decrease. The 1% P-H3PO4 treatment caused the greatest reduction in in vitro extractable Pb from field samples (pH 2.2) with a measured reduction of 66%, while the compost treatment had a 39% reduction and the 2.5% Fe + 1% P-TSP treatment a 50% reduction. The in vitro extraction (pH 1.5) run on field samples showed no reduction in the compost or Fe treatments. The 1% P-H3PO4 treatment was the most effective at reducing plant Pb, Zn, and Cd.