Miracle-dz/UniFAR-FTUs huggingface dataset:
Iron Opacity and the Pulsar of SN 1987A

Neutron stars formed in Type II supernovae are likely to be initially obscured by late-time fallback. Although much of the late-time fallback is quickly accreted via neutrino cooling, some material remains on the neutron star, forming an atmosphere that slowly accretes through photon emission. In this paper, we derive structure equations of the fallback atmosphere and present results of one-dimensional simulations of that fallback. The atmosphere remaining after neutrino cooling (Lν) becomes unimportant (Lν≲LEdd, e−, the Compton Eddington limit) is only a fraction of the total mass accreted (≲10-8 Macc=10−9 M☉). Recombined iron dominates the opacity in the outer regions, leading to an opacity 103-104 times higher than that of electron scattering alone. The resultant photon emission of the remnant atmosphere is limited to ≲10−3LEdd, e−. The late-time evolution of this system leads to the formation of a photon-driven wind from the accretion of the inner portion of the atmosphere, leaving, for most cases, a bare neutron star on timescales shorter than 1 yr. The degenerate remnant of 1987A may not be a black hole. Instead, the fallback material may have already accreted or blown off in the accretion-driven wind. If the neutron star has either a low magnetic field or a low rotational spin frequency, we would not expect to see the neutron star remnant of 1987A.
Polyphenolic Contents and Antioxidant Potential of Stem Bark Extracts from Jatropha curcas (Linn)

We assessed the polyphenolic contents and antioxidant potential of the aqueous, ethanol and methanol stem bark extracts of Jatropha curcas. The total phenol, flavonoids, flavonols and proanthocyanidin contents of the extracts were evaluated to determine their effect on the antioxidant property of this plant, using standard phytochemical methods. The antioxidant and free radical scavenging activity of ethanol, methanol and aqueous extracts of the plant were also assessed against 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), ferric reducing, nitric oxide (NO), superoxide anion, (O2−) and hydrogen peroxide (H2O2) using spectroscopic methods and results were compared with that of butylated hydroxyl toluene (BHT) and ascorbic acid as standards. The concentrations of different classes of phenolic compounds were higher in methanol and ethanol extracts compared to aqueous extracts. There was correlation between total phenol, total flavonoids, total flavonol and total proanthocyanidins (r = 0.996, 0.978, 0.908, and 0.985) respectively. There was correlations between the amount of phenolic compounds and percentage inhibition of DPPH radicals scavenging activity of the extract (r = 0.98). Findings from the present study indicated that J. curcas is a potential source of natural antioxidants and may be a good candidate for pharmaceutical plant based products.
Pretreatment with the Free Radical Scavenger Edaravone Prevents Cerebral Hyperperfusion after Carotid Endarterectomy

OBJECTIVE: Cerebral hyperperfusion syndrome after carotid endarterectomy (CEA) is a rare but potentially devastating complication. The purpose of the present study, which was not a randomized controlled trial but a case cohort study with historical control, was to determine whether pretreatment with a novel free radical scavenger, edaravone, could prevent occurrence of cerebral hyperperfusion after CEA. METHODS: Fifty patients with ipsilateral internal carotid artery stenosis (≥70%) underwent CEA with administration of edaravone before internal carotid artery clamping. Preoperative cerebral blood flow and cerebrovascular reactivity (CVR) to acetazolamide were assessed with single-photon emission computed tomography (SPECT). Cerebral blood flow also was measured immediately after CEA and on the 3rd postoperative day. RESULTS: Cerebral hyperperfusion (cerebral blood flow increase ≥100% compared with preoperative values) was revealed by SPECT performed immediately after CEA in only one patient (2%), who also exhibited reduced preoperative CVR. The incidence of post-CEA hyperperfusion as revealed by SPECT in the control group (51 CEA patients without administration of edaravone) was significantly higher (16%) (P = 0.0310, control versus treatment group). In addition, in a subgroup of patients with reduced preoperative CVR, the incidence of post-CEA hyperperfusion as revealed by SPECT in the edaravone group (7%) was significantly lower than that in the control group (67%) (P = 0.0029). Logistic regression analysis demonstrated that reduced preoperative CVR and absence of pretreatment with edaravone were significant independent predictors of post-CEA hyperperfusion as revealed by SPECT. CONCLUSION: Pretreatment with edaravone can prevent occurrence of cerebral hyperperfusion after CEA.
Parthenogenesis in Xenopus eggs requires centrosomal integrity

Xenopus eggs are laid arrested at second metaphase of meiosis lacking a functional centrosome. Upon fertilization, the sperm provides the active centrosome that is required for cleavage to occur. The injection of purified centrosomes mimics fertilization and leads to tadpole formation (parthenogenesis). In this work we show that the parthenogenetic activity of centrosomes is inactivated by urea concentrations higher than 2 M. The loss of activity is correlated with a progressive destruction of the centriolar cylinder and extraction of proteins. This shows that centrosomes are relatively sensitive to urea since complete protein unfolding and solubilization of proteins normally occurs at urea concentrations as high as 8-10 M. When present, the parthenogenetic activity is always associated with a pelletable fraction showing that it cannot be solubilized by urea. The parthenogenetic activity is progressively inactivated by salt concentrations higher than 2 M (NaCl or KCl). However, only a few proteins are extracted by these treatments and the centrosome ultrastructure is not affected. This shows that both parthenogenetic activity and centrosomal structure are resistant to relatively high ionic strength. Indeed, most protein structures held by electrostatic forces are dissociated by 2 M salt. The loss of parthenogenetic activity produced at higher salt concentrations, while the structure of the centrosome is unaffected, is an apparent paradox. We interpret this result as meaning that the native state of centrosomes is held together by forces that favor functional denaturation by high ionic strength. The respective effects of urea and salts on centrosomal structure and activity suggest that the centrosome is mainly held together by hydrogen and hydrophobic bonds. The in vitro microtubule nucleating activity of centrosomes can be inactivated at salt or urea concentrations that do not affect the parthenogenetic activity. Since egg cleavage requires the formation of microtubule asters, we conclude that the extracted or denatured microtubule nucleating activity of centrosomes can be complemented by components present in the egg cytoplasm. Both parthenogenetic and microtubule nucleating activities are abolished by protease treatments but resist nuclease action. Since we find no RNA in centrosomes treated by RNase, they probably do not contain a protected RNA. Taken together, these results are consistent with the idea that the whole or part of the centrosome structure acts as a seed to start the centrosome duplication cycle in Xenopus eggs.
Characterizing HIV transmission networks across the United States.

BACKGROUND Clinically, human immunodeficiency virus type 1 (HIV-1) pol sequences are used to evaluate for drug resistance. These data can also be used to evaluate transmission networks and help describe factors associated with transmission risk. METHODS HIV-1 pol sequences from participants at 5 sites in the CFAR Network of Integrated Clinical Systems (CNICS) cohort from 2000-2009 were analyzed for genetic relatedness. Only the first available sequence per participant was included. Inferred transmission networks ("clusters") were defined as ≥2 sequences with ≤1.5% genetic distance. Clusters including ≥3 patients ("networks") were evaluated for clinical and demographic associations. RESULTS Of 3697 sequences, 24% fell into inferred clusters: 155 clusters of 2 individuals ("dyads"), 54 clusters that included 3-14 individuals ("networks"), and 1 large cluster that included 336 individuals across all study sites. In multivariable analyses, factors associated with being in a cluster included not using antiretroviral (ARV) drugs at time of sampling (P < .001), sequence collected after 2004 (P < .001), CD4 cell count >350 cells/mL (P < .01), and viral load 10,000-100,000 copies/mL (P < .001) or >100,000 copies/mL (P < .001). In networks, women were more likely to cluster with other women (P < .001), and African Americans with other African Americans (P < .001). CONCLUSIONS Molecular epidemiology can be applied to study HIV transmission networks in geographically and demographically diverse cohorts. Clustering was associated with lack of ARV use and higher viral load, implying transmission may be interrupted by earlier diagnosis and treatment. Observed female and African American networks reinforce the importance of diagnosis and prevention efforts targeted by sex and race.
An introduced pentastomid parasite (Raillietiella frenata) infects native cane toads (Rhinella marina) in Panama

SUMMARY The pentastomid parasite, Raillietiella frenata, is native to Asia where it infects the Asian House gecko, Hemidactylus frenatus. This gecko has been widely introduced and recently R. frenata was found in introduced populations of cane toads (Rhinella marina) in Australia, indicating a host-switch from introduced geckos to toads. Here we report non-native adult R. frenata infecting the lungs of native cane toads in Panama. Eight of 64 toads were infected (median = 2·5, range = 1–80 pentastomids/toad) and pentastomid prevalence was positively associated with the number of buildings at a site, though further sampling is needed to confirm this pattern. We postulate that this pattern is likely due to a host shift of this parasite from an urban-associated introduced gecko. This is the first record of this parasite infecting cane toads in their native range, and the first instance of this parasite occurring in Central America.
Chronic lymphocytic leukemic B cells but not normal B cells are rescued from apoptosis by contact with normal bone marrow stromal cells.

The leukemic B lymphocytes from chronic lymphocytic leukemic (CLL) patients have a long survival in vivo, although ex vivo they rapidly die by apoptosis. To further investigate the mechanism of this, we have studied the influence of bone marrow stromal cells from normal subjects on apoptosis of B-CLL cells and normal umbilical cord blood (UCB) B lymphocytes. After 48 hours of incubation in medium alone, leukemic and normal B cells showed, respectively, 22 +/- 3% and 31 +/- 5% of apoptosis. Cocultures with stromal cells reduced the percentage of leukemic cells undergoing apoptosis (8 +/- 2%, P < . 0005) and prevented the loss of bcl-2 protein expression. In contrast, stromal cells slightly increased normal B-cell apoptosis (37 +/- 6%). Direct contact between leukemic cells and stromal cells was found to be essential for inhibition of leukemic cell apoptosis; indeed, separation of leukemic cells from stromal cells by microporous membrane increased spontaneous apoptosis, and comparable results were obtained with stromal cell conditioned medium. The difference in behavior observed between normal and leukemic B cells plated on stromal cells can be explained by the fact that only a few normal B cells adhere to stromal cells in comparison with B-CLL cells. B-CLL cell adhesion to stromal cells is mediated by beta1 and beta2 integrins acting simultaneously. Contact between B-CLL cells and bone marrow stromal cells seems to play a major role in the accumulation and survival of B-CLL cells in the bone marrow.
Energy dispersive x-ray spectroscopy for nanostructured thin film density evaluation

Abstract In this paper, we report on two fast and non-destructive methods for nanostructured film density evaluation based on a combination of energy dispersive x-ray spectroscopy for areal density measurement and scanning electron microscopy (SEM) for thickness evaluation. These techniques have been applied to films with density ranging from the density of a solid down to a few , with different compositions and morphologies. The high resolution of an electron microprobe has been exploited to characterize non-uniform films both at the macroscopic scale and at the microscopic scale.
Relative concentrations of haemostatic factors and cytokines in solvent/detergent-treated and fresh-frozen plasma.

BACKGROUND Indications, efficacy, and safety of plasma products are highly debated. We compared the concentrations of haemostatic proteins and cytokines in solvent/detergent-treated plasma (SDP) and fresh-frozen plasma (FFP). METHODS Concentrations of the following parameters were measured in 25 SDP and FFP samples: fibrinogen (FBG), factor (F) II, F V, F VII, F VIII, F IX, F X, F XIII, von Willebrand factor (vWF), D-Dimers, ADAMTS-13 protease, tumour necrosis factor-α (TNF-α), interleukin (IL)-1β, IL-6, IL-8, and IL-10. RESULTS Mean FBG concentrations in SDP and FFP were similar, but in FFP, the range was larger than in SDP (P<0.01). Mean F II, F VII, F VIII, F IX, and F XIII levels did not differ significantly. Higher concentrations of F V (P<0.01), F X (P<0.05), vWF (P<0.01), and ADAMTS-13 (P<0.01) were found in FFP. With the exception of F VIII and F IX, the range of concentrations for all of these factors was smaller (P<0.05) in SDP than in FFP. Concentrations of TNF-α, IL-8, and IL-10 (all P<0.01) were higher in FFP than in SDP, again with a higher variability and thus larger ranges (P<0.01). CONCLUSIONS Coagulation factor content is similar for SDP and FFP, with notable exceptions of less F V, vWF, and ADAMTS-13 in SDP. Cytokine concentrations (TNFα, IL-8, and IL-10) were significantly higher in FFP. The clinical relevance of these findings needs to be established in outcome studies.
Blaze: supporting two-phased call graph navigation in source code

Understanding source code is crucial for successful software maintenance. A particularly important activity to understand source code is navigating the call graph [4]. Programmers have developed distinct strategies for effective call graph exploration [3, 9]. We introduce Blaze, a source code exploration tool tailored closely to these strategies. In a study, we compare Blaze to Stacksplorer [2], a tool that visualizes the immediate neighborhood of the current method in the call graph, to a tool resembling the standard Call Hierarchy view in the Eclipse IDE, and to an unmodified Xcode installation. The call graph exploration tools significantly increased success rates in typical software maintenance tasks, and using Stacksplorer or Blaze significantly reduced task completion times compared to using the Call Hierarchy or Xcode.
Evolution of Limited-Feedback CoMP Systems from 4G to 5G: CoMP Features and Limited-Feedback Approaches

Coordinated multipoint (CoMP) transmission/reception has been adopted as a key technology to alleviate the intercell interference (ICI) in fourthgeneration (4G) mobile communication. This article reviews the state of the art in limited-feedback CoMP systems research. We first give an overview of recent related work in feedback-based coordinated transmission and then provide a performance analysis of typical feedback schemes and sensitivity to the channel state information (CSI) delay. To back up the discussion, we have validated the benefits of CoMP using field-test results from a CoMP trial network built at the Beijing University of Posts and Telecommunications (BUPT) campus. Furthermore, since mobile systems evolving to fifth generation (5G) have to bear a huge quantity of irregularly distributed wireless data traffic, cooperative communication will be more widely applied not only to address the ICI but also to improve the system resource utilization and data rate. We summarize the recent trend on 5G network architectures enabling the novel CoMP features, and we discuss the potential evolution directions of limited-feedback approaches motivated by CoMP development toward future 5G networks.
Fifty years of molecular (DNA/RNA) diagnostics.

As the journal Clinical Chemistry celebrates its 50th birthday and enters its 51st year, we reflect on recent advances in nucleic acid diagnostics. Although the structure of DNA was also described ∼50 years ago, only 20 years have past since a practical method of amplifying DNA for the clinical laboratory appeared, well known today as the PCR. Since the advent of PCR, growth in nucleic acid diagnostics has been extraordinary and is the fastest growing segment of many clinical laboratories. Clinical Chemistry is now subtitled The International Journal of Molecular Diagnostics and Laboratory Medicine in recognition of the importance of DNA/RNA diagnostics. In this review, we offer personal perspectives on five key advances in molecular diagnostics by some of the pioneers in the field. Russ Higuchi reviews real-time PCR, which is an elegant solution for nucleic acid quantification in research and the clinical laboratory. Carl Wittwer describes DNA melting analysis as a simple and surprisingly powerful tool that can be seamlessly appended to PCR. Tom Gingeras reviews the increasing power of array technology, with feature density rivaling microelectronics miniaturization. Progress on integrated devices that combine cell separation, sample preparation, amplification, and analysis is described by Larry Kricka. Finally, the field of circulating nucleic acids is reviewed by Dennis Lo, with a myriad of clinical applications enabled by a new understanding of the biology of extracellular DNA and RNA. Many early advances in molecular diagnostics have been highlighted in Clinical Chemistry . With DNA/RNA diagnostics becoming ever more important in the 21st century, the Journal serves as an advanced window into the future of molecular clinical chemistry. —Russ Higuchi When late in 1986 I joined Cetus, the birthplace of PCR, “closed-tube” PCR using a thermostable DNA polymerase had just been achieved (1)(2). Before this, the thermolabile polymerase had to …
Forging a Partnership to Achieve Competitive Advantage: The CIM Challenge

Computer-integrated manufacturing (CIM) could well become the most important application of information technology for achieving competitive advantage. Recent advances in manufacturing and information technologies present promising new strategic alternatives for designing business systems. CIM enables firms to respond quickly to market changes, achieve economies of scope, and manage the complexity of a multi-product environment. Attaining the strategic benefits of CIM requires decision support to integrate marketing with design, design with manufacturing, and manufacturing with strategic positioning. This emerging technology requires a partnership of executives in engineering, manufacturing, marketing, and MIS who share a common vision of how CIM makes possible new approaches to designing business systems.
Inhibition of both the apical sodium-dependent bile acid transporter and HMG-CoA reductase markedly enhances the clearance of LDL apoB Published, JLR Papers in Press, February 1, 2003. DOI 10.1194/jlr.M200482-JLR200

Discovery of the ileal apical sodium-dependent bile acid transporter (ASBT) permitted development of specific inhibitors of bile acid reabsorption, potentially a new class of cholesterol-lowering agents. In the present study, we tested the hypothesis that combining the novel ASBT inhibitor, SC-435, with the HMG-CoA reductase inhibitor, atorvastatin, would potentiate reductions in LDL cholesterol (LDL-C) and LDL apolipoprotein B (apoB). ApoB kinetic studies were performed in miniature pigs fed a typical human diet and treated with the combination of SC-435 (5 mg/kg/day) plus atorvastatin (3 mg/kg/day) (SC-435+A) or a placebo. SC-435+A decreased plasma total cholesterol by 23% and LDL-C by 40%. Multicompartmental analysis (SAAM II) demonstrated that LDL apoB significantly decreased by 35% due primarily to a 45% increase in the LDL apoB fractional catabolic rate (FCR). SC-435+A significantly decreased hepatic concentrations of free cholesterol and cholesteryl ester, and increased hepatic LDL receptor mRNA consequent to increased cholesterol 7α-hydroxylase expression and activity. In comparison, SC-435 (10 mg/kg/day) monotherapy decreased LDL apoB by 10% due entirely to an 18% increase in LDL apoB FCR, whereas atorvastatin monotherapy (3 mg/kg/day) decreased LDL apoB by 30% due primarily to a 22% reduction in LDL apoB production. We conclude that SC-435+A potentiates the reduction of LDL-C and LDL apoB due to complementary mechanisms of action.
Identification of broad-spectrum antiviral compounds and assessment of the druggability of their target for efficacy against respiratory syncytial virus (RSV)

The search for novel therapeutic interventions for viral disease is a challenging pursuit, hallmarked by the paucity of antiviral agents currently prescribed. Targeting of viral proteins has the inextricable challenge of rise of resistance. Safe and effective vaccines are not possible for many viral pathogens. New approaches are required to address the unmet medical need in this area. We undertook a cell-based high-throughput screen to identify leads for development of drugs to treat respiratory syncytial virus (RSV), a serious pediatric pathogen. We identified compounds that are potent (nanomolar) inhibitors of RSV in vitro in HEp-2 cells and in primary human bronchial epithelial cells and were shown to act postentry. Interestingly, two scaffolds exhibited broad-spectrum activity among multiple RNA viruses. Using the chemical matter as a probe, we identified the targets and identified a common cellular pathway: the de novo pyrimidine biosynthesis pathway. Both targets were validated in vitro and showed no significant cell cytotoxicity except for activity against proliferative B- and T-type lymphoid cells. Corollary to this finding was to understand the consequences of inhibition of the target to the host. An in vivo assessment for antiviral efficacy failed to demonstrate reduced viral load, but revealed microscopic changes and a trend toward reduced pyrimidine pools and findings in histopathology. We present here a discovery program that includes screen, target identification, validation, and druggability that can be broadly applied to identify and interrogate other host factors for antiviral effect starting from chemical matter of unknown target/mechanism of action.
Genistein, a tyrosine kinase inhibitor, blocks the "second window of protection" 48 h after ischemic preconditioning in the rabbit.

We have previously reported a delayed or "second window of protection" against infarction 24-72 h after ischemic preconditioning in the rabbit. This phenomenon has also been associated with the protein kinase C signalling pathway. In the present study, we expanded our investigation to ascertain whether protein tyrosine kinase was in any way associated with this phenomenon in the rabbit heart. We found that 48 h after ischemic preconditioning with 4x5 min coronary occlusions the percentage of myocardium infarcting within the risk zone following a 30-min coronary occlusion and 120-min reperfusion (I/R) was reduced from 39. 6+/-3.3% to 18.0+/-3.7% (P<0.01). However, an i.v. bolus administration of genistein (5 mg/kg), a tyrosine kinase inhibitor, 5 min before ischemic preconditioning stimulus, abolished this protection (I/R=39.0+/-3.4%). Genistein per se had no significant effect on infarction 48 h later. Risk zone volume after coronary ligation was not significantly different between intervention groups. There were no differences in hemodynamic parameters between groups throughout the experimental period. We conclude that the second window of protection, 48 h after preconditioning, is mediated by tyrosine kinase activation in the rabbit heart.