julilili42/papers huggingface dataset:
Evaluation of Biochars and Activated Carbons for In Situ Remediation Of Sediments Impacted With Organics, Mercury, And Methylmercury
2013-10-29

In situ amendment of activated carbon (AC) to sediments can effectively reduce the bioavailability of hydrophobic organic contaminants. While biochars have been suggested as low-cost and sustainable alternatives to ACs, there are few comparative sorption data especially for mercury (Hg) and methylmercury (MeHg) at the low porewater concentrations in sediments. Here we compare the ability of a wide range of commercially available and laboratory synthesized ACs and biochars to sorb PAHs, PCBs, DDTs, inorganic Hg, and MeHg at environmentally relevant concentrations. Compared to natural organic matter, sorption capacity for most organic compounds was at least 1-2 orders of magnitude higher for unactivated biochars and 3-4 orders of magnitude higher for ACs which translated to sediment porewater PCB concentration reductions of 18-80% for unactivated biochars, and >99% for ACs with 5% by weight amendment to sediment. Steam activated carbons were more effective than biochars in Hg sorption and translated to modeled porewater Hg reduction in the range of 94-98% for sediments with low native Kd and 31-73% for sediments with high native Kd values for Hg. Unactivated biochars were as effective as the steam activated carbons for MeHg sorption. Predicted reductions of porewater MeHg were 73-92% for sediments with low native Kd and 57-86% for sediment with high native K(d). ACs with high surface areas therefore are likely to be effective in reducing porewater concentrations of organics, Hg, and MeHg in impacted sediments. Unactivated biochars had limited effectiveness for organics and Hg but can be considered when MeHg exposure is the primary concern.
Expression of stromal cell-derived factor-1 receptors CXCR4 and CXCR7 on circulating platelets of patients with acute coronary syndrome and association with left ventricular functional recovery
2013-10-29

These findings indicate that platelet surface expression of CXCR4 and CXCR7 might differentially contribute to SDF-1-mediated effects on regenerative mechanisms following ACS. Studies are warranted to further evaluate the regulatory mechanisms of CXCR4/-7 expression and its prognostic impact on CAD.
Genetic Basis for the Biosynthesis of the Pharmaceutically Important Class of Epoxyketone Proteasome Inhibitors
2013-10-29

The epoxyketone proteasome inhibitors are an established class of therapeutic agents for the treatment of cancer. Their unique α',β'-epoxyketone pharmacophore allows binding to the catalytic β-subunits of the proteasome with extraordinary specificity. Here, we report the characterization of the first gene clusters for the biosynthesis of natural peptidyl-epoxyketones. The clusters for epoxomicin, the lead compound for the anticancer drug Kyprolis, and for eponemycin were identified in the actinobacterial producer strains ATCC 53904 and Streptomyces hygroscopicus ATCC 53709, respectively, using a modified protocol for Ion Torrent PGM genome sequencing. Both gene clusters code for a hybrid nonribosomal peptide synthetase/polyketide synthase multifunctional enzyme complex and homologous redox enzymes. Epoxomicin and eponemycin were heterologously produced in Streptomyces albus J1046 via whole pathway expression. Moreover, we employed mass spectral molecular networking for a new comparative metabolomics approach in a heterologous system and discovered a number of putative epoxyketone derivatives. With this study, we have definitively linked epoxyketone proteasome inhibitors and their biosynthesis genes for the first time in any organism, which will now allow for their detailed biochemical investigation.
Vibrotactile Discrimination in the Rat Whisker System is Based on Neuronal Coding of Instantaneous Kinematic Cues
2013-10-29

Which physical parameter of vibrissa deflections is extracted by the rodent tactile system for discrimination? Particularly, it remains unclear whether perception has access to instantaneous kinematic parameters (i.e., the details of the trajectory) or relies on temporally integration of the movement trajectory such as frequency (e.g., spectral information) and intensity (e.g., mean speed). Here, we use a novel detection of change paradigm in head-fixed rats, which presents pulsatile vibrissa stimuli in seamless sequence for discrimination. This procedure ensures that processes of decision making can directly tap into sensory signals (no memory functions involved). We find that discrimination performance based on instantaneous kinematic cues far exceeds the ones provided by frequency and intensity. Neuronal modeling based on barrel cortex single units shows that small populations of sensitive neurons provide a transient signal that optimally fits the characteristic of the subject's perception. The present study is the first to show that perceptual read-out is superior in situations allowing the subject to base perception on detailed trajectory cues, that is, instantaneous kinematic variables. A possible impact of this finding on tactile systems of other species is suggested by evidence for instantaneous coding also in primates.
Tensile and shear strength of porous dust\\n agglomerates
2013-10-29

\\n Context. Within the sequential accretion scenario of planet formation,\\n planets are built up through a sequence of sticking collisions. The outcome of collisions\\n between porous dust aggregates is very important for the growth from very small dust\\n particles to planetesimals. In this work we determine the necessary material properties of\\n dust aggregates as a function of porosity.\\n Aims. Continuum models such as SPH that are capable of simulating\\n collisions of macroscopic dust aggregates require a set of material parameters. Some of\\n them, such as the tensile and shear strength, are difficult to obtain from laboratory\\n experiments. The aim of this work is to determine these parameters from ab initio\\n molecular dynamics simulations.\\n Methods. We simulated the behavior of porous dust aggregates using a\\n detailed micro-physical model of the interaction of spherical grains that includes\\n adhesion forces, rolling, twisting, and sliding. Using different methods of preparing the\\n samples, we studied the strength behavior of our samples with varying porosity and\\n coordination number of the material.\\n Results. For the tensile strength, we can reproduce data from laboratory\\n experiments very well. For the shear strength, there are no experimental data available.\\n The results from our simulations differ significantly from previous theoretical models,\\n which indicates that the latter might not be sufficient to describe porous dust\\n aggregates.\\n Conclusions. We have provided the functional behavior of tensile and\\n shear strength of porous dust aggregates as a function of the porosity, which can be\\n directly applied to continuum simulations of these objects in planet formation\\n scenarios.\\n
SIL1 mutations and clinical spectrum in patients with Marinesco-Sjögren syndrome
2013-10-30

Marinesco-Sjögren syndrome is a rare autosomal recessive multisystem disorder featuring cerebellar ataxia, early-onset cataracts, chronic myopathy, variable intellectual disability and delayed motor development. More recently, mutations in the SIL1 gene, which encodes an endoplasmic reticulum resident co-chaperone, were identified as the main cause of Marinesco-Sjögren syndrome. Here we describe the results of SIL1 mutation analysis in 62 patients presenting with early-onset ataxia, cataracts and myopathy or combinations of at least two of these. We obtained a mutation detection rate of 60% (15/25) among patients with the characteristic Marinesco-Sjögren syndrome triad (ataxia, cataracts, myopathy) whereas the detection rate in the group of patients with more variable phenotypic presentation was below 3% (1/37). We report 16 unrelated families with a total of 19 different SIL1 mutations. Among these mutations are 15 previously unreported changes, including single- and multi-exon deletions. Based on data from our screening cohort and data compiled from the literature we found that SIL1 mutations are invariably associated with the combination of a cerebellar syndrome and chronic myopathy. Cataracts were observed in all patients beyond the age of 7 years, but might be missing in infants. Six patients with SIL1 mutations had no intellectual disability, extending the known wide range of cognitive capabilities in Marinesco-Sjögren syndrome to include normal intelligence. Modestly constant features were somatic growth retardation, skeletal abnormalities and pyramidal tract signs. Examination of mutant SIL1 expression in cultured patient lymphoblasts suggested that SIL1 mutations result in severely reduced SIL1 protein levels irrespective of the type and position of mutations. Our data broaden the SIL1 mutation spectrum and confirm that SIL1 is the major Marinesco-Sjögren syndrome gene. SIL1 patients usually present with the characteristic triad but cataracts might be missing in young children. As cognitive impairment is not obligatory, patients without intellectual disability but a Marinesco-Sjögren syndrome-compatible phenotype should receive SIL1 mutation analysis. Despite allelic heterogeneity and many families with private mutations, the phenotype related to SIL1 mutations is relatively homogenous. Based on SIL1 expression studies we speculate that this may arise from a uniform effect of different mutations on protein expression.
Aminothiazole-Featured Pirinixic Acid Derivatives As Dual 5-Lipoxygenase and Microsomal Prostaglandin E2Synthase-1 Inhibitors with Improved Potency and Efficiency in Vivo
2013-10-30

Dual inhibition of microsomal prostaglandin E2 synthase-1 (mPGES-1) and 5-lipoxygenase (5-LO) is currently pursued as potential pharmacological strategy for treatment of inflammation and cancer. Here we present a series of 26 novel 2-aminothiazole-featured pirinixic acid derivatives as dual 5-LO/mPGES-1 inhibitors with improved potency (exemplified by compound 16 (2-[(4-chloro-6-{[4-(naphthalen-2-yl)-1,3-thiazol-2-yl]amino}pyrimidin-2-yl)sulfanyl]octanoic acid) with IC50 = 0.3 and 0.4 μM, respectively) and bioactivity in vivo. Computational analysis presumes binding sites of 16 at the tip of the 5-LO catalytic domain and within a subpocket of the mPGES-1 active site. Compound 16 (10 μM) hardly suppressed cyclooxygenase (COX)-1/2 activities, failed to inhibit 12/15-LOs, and is devoid of radical scavenger properties. Finally, compound 16 reduced vascular permeability and inflammatory cell infiltration in a zymosan-induced mouse peritonitis model accompanied by impaired levels of cysteinyl-leukotrienes and prostaglandin E2. Together, 2-aminothiazole-featured pirinixic acids represent potent dual 5-LO/mPGES-1 inhibitors with an attractive pharmacological profile as anti-inflammatory drugs.
Modelling accretion in transitional disks
2013-10-30

Transitional disks are protoplanetary disk around young stars that display\\ninner holes in the dust distribution within a few AU, which is accompanied\\nnevertheless by some gas accretion onto the central star. These cavities could\\npossibly be created by the presence of one or more massive planets. If the gap\\nis created by planets and gas is still present in it, then there should be a\\nflow of gas past the planet into the inner region. It is our goal to study the\\nmass accretion rate into the gap and in particular the dependency on the\\nplanet's mass and the thermodynamic properties of the disk. We performed 2D\\nhydro simulations for disks with embedded planets. We added radiative cooling\\nfrom the disk surfaces, radiative diffusion in the disk midplane, and stellar\\nirradiation to the energy equation to have more realistic models. The mass flow\\nrate into the gap region depends, for given disk thermodynamics,\\nnon-monotonically on the mass of the planet. Generally, more massive planets\\nopen wider and deeper gaps which would tend to reduce the mass accretion into\\nthe inner cavity. However, for larger mass planets the outer disk becomes\\neccentric and the mass flow rate is enhanced over the low mass cases. As a\\nresult, for the isothermal disks the mass flow is always comparable to the\\nexpected mass flow of unperturbed disks M_d, while for more realistic radiative\\ndisks the mass flow is very small for low mass planets (&lt;= 4 M_jup) and about\\n50% for larger planet masses. For the radiative disks that critical planet mass\\nfor the disk to become eccentric is much larger that in the isothermal case.\\nMassive embedded planets can reduce the mass flow across the gap considerably,\\nto values of about an order of magnitude smaller than the standard disk\\naccretion rate, and can be responsible for opening large cavities. The\\nremaining mass flow into the central cavity is in good agreement with the\\nobservations.\\n
A Prospective Experimental Study to Investigate the Peritoneal Adhesion Formation of Argon Plasma Coagulation (APC) Versus a Novel Aerosol Plasma in a Rat Model
2013-10-30

Background. This is a prospective, randomized, controlled, single-blinded study to investigate peritoneal adhesion formation of standard argon plasma coagulation (APC) versus aerosol plasma coagulation in a rat model. Methods. Bilateral lesions were created on the abdominal wall of 16 female Wistar rats with standard and aerosol plasma coagulation APC energy in a standard fashion. After 10 days, the rats were killed humanely to evaluate the peritoneal trauma sites. Adhesion incidence, quantity, and quality were scored 10 days postoperatively and studied histopathologically. Results. Average energy intake was 97.7 ± 3.1 J for APC and 93.8 ± 4.2 J for aerosol plasma coagulation. Incidence of adhesion formation was 74.2% for standard APC and 16.1% for aerosol plasma coagulation ( P &lt; .0001). Standard APC mainly results in dense adhesions. Histological evaluation revealed no significant difference with regard to the average depth of lesions created by APC and aerosol plasma coagulation ( P = 0.21) at day 10; both groups showed an identical morphology of necrosis and granulation tissue formation. Conclusions. This study compares adhesion formation of standard APC versus aerosol plasma coagulation in a rat model. Standard APC produced significantly more adhesions. Aerosol plasma coagulation creates fewer adhesions, which are of lower grade, which seems to be achieved mainly by improved peritoneal conditioning in this animal model.
Novel surgical methods in Descemet’s membrane endothelial keratoplasty
2013-10-30

Endothelial keratoplasty is continually evolving both in surgical technique and clinical outcomes. The latest development of posterior lamellar surgery represents Descemet’s membrane endothelial keratoplasty (DMEK) introduced by Melles from Rotterdam. This leaves a secure eye with less postoperative astigmatism, a faster visual rehabilitation and better optical quality when compared with other posterior keratoplasty techniques. Despite the recent advances in posterior lamellar surgery techniques, the preparation of the Descemet’s membrane (DM) and the unfolding in the anterior chamber in DMEK still poses a risk of complication during surgery. Today, despite the fact that the availability of donor tissues prepared by a steadily increasing number of eye banks worldwide should have boosted the feasibility of DMEK in many endothelial disorders, yet membrane dissection and intraoperative graft unfolding difficulties hinder the implementation of the aforesaid technique. Therefore, further efforts are needed for improving current surgical techniques of donor preparation, insertion and unfolding. In this review, surgical methods of DM’s preparation and unfolding techniques in the anterior chamber are summarized.
Faculty Opinions recommendation of Nonarteritic anterior ischemic optic neuropathy and obstructive sleep apnea.
2013-10-30

BACKGROUND: To evaluate the obstructive sleep apnea syndrome (OSAS) in patients with nonarteritic anterior ischemic optic neuropathy (NAION).METHODS: We recruited 27 patients with NAION and 27 age-matched and sex-matched controls who also were similar for systemic risk factors such as diabetes mellitus, hypertension, and hypercholesterolemia. All patients and controls underwent overnight polysomnography for the diagnosis of OSAS and calculation of apnea-hypopnea index (AHI).RESULTS: Patients and controls were statistically similar in terms of age, sex, gender, smoking, systemic risk factors, neck circumference, and body mass index. The subjects with AHI ≥ 20 were accepted as OSAS. Fifteen of 27 patients (55.6%) with NAION and 6 of 27 controls (22.2%) had OSAS (P < 0.05).CONCLUSION: The prevalence of OSAS was higher in patients with NAION, and the difference between patient and control groups was statistically significant (P < 0.05). This result supports prior series suggesting the association between NAION and OSAS. PMID: 23719289
APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories
2013-10-31

APL@Voro is a new program developed to aid in the analysis of GROMACS trajectories of lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a GROMACS index file to create a two-dimensional geometric representation of a bilayer. Voronoi diagrams and Delaunay triangulations--generated for different selection models of lipids--support the analysis of the bilayer. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. The application of the developed software is discussed for three example systems simulated with GROMACS. The program is written in C++, is open source, and is available free of charge.
Rapidly rotating neutron stars in scalar-tensor theories of gravity
2013-10-31

We present the field equations governing the equilibrium of rapidly rotating neutron stars in scalar-tensor theories of gravity, as well as representative numerical solutions. The conditions for the presence of a nontrivial scalar field and the deviations from the general relativistic solutions are studied. Two examples of scalar-tensor theories are examined - one case that is equivalent to the Brans-Dicke theory and a second case, that is perturbatively equivalent to Einstein's General Relativity in the weak field regime, but can differ significantly for strong fields. Our numerical results show that rapidly rotating neutron star models with a nontrivial scalar field exist in both cases and that the effect of the scalar field is stronger for rapid rotation. If we consider values of the coupling parameters in accordance with current observations, only the second example of scalar-tensor theories has significant influence on the neutron star structure. We show that scalarized, rapidly rotating neutron stars exist for a larger range of the parameters than in the static case, since a nontrivial scalar field is present even for values of the coupling constant , and that these solutions are energetically more favorable than the general relativistic ones. In addition, the deviations of the rapidly rotating scalar-tensor neutron stars from the general-relativistic solutions is significantly larger than in the static case.
The more the merrier: Multi-species experiments in ecology
2013-10-31

A major objective in ecology is to find general patterns, and to establish the rules and underlying mechanisms that generate those patterns. Nevertheless, most of our current insights in ecology are based on case studies of a single or few species, whereas multi-species experimental studies remain rare. We underline the power of the multi-species experimental approach for addressing general ecological questions, e.g. on species environmental responses or on patterns of among- and within-species variation. We present simulations that show that the accuracy of estimates of between-group differences is increased by maximizing the number of species rather than the number of populations or individuals per species. Thus, the more species a multi-species experiment includes, the more powerful it is. In addition, we discuss some inevitable methodological challenges of multi-species experiments. While we acknowledge the value of single- or few-species experiments, we strongly advocate the use of multi-species experiments for addressing ecological questions at a more general level.
Prospective analysis of intrinsic and extrinsic risk factors on the development of Achilles tendon pain in runners
2013-10-31

There are currently no generally accepted, consistent results that clearly characterize factors causing A chilles tendon pain ( AT ) in runners. Therefore, we carried out a prospective study to evaluate the multifactorial influence of clinical, biomechanical (isometric strength measurements and three‐dimensional kinematics) and training‐related risk factors on the development of AT . Two hundred sixty‐nine uninjured runners were recruited and underwent an initial examination. One hundred forty‐two subjects completed their participation by submitting training information on a weekly basis over a maximal period of 1 year. Forty‐five subjects developed an overuse injury, with 10 runners suffering from AT . In an uninjured state, AT runners already demonstrated decreased knee flexor strength and abnormal lower leg kinematics (sagittal knee and ankle joint) compared with a matched control group. A relationship between years of running experience or previous overuse injuries and the development of new symptoms could not be established. The interrelationship of biomechanical and training‐specific variables on the generation of AT is evident. A combination of alterations in lower leg kinematics and higher impacts caused by fast training sessions might lead to excessive stress on the A chilles tendon during weight bearing and thus to AT in recreational runners.
Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands
2013-10-31

B-Lymphotropic Polyomavirus (LPyV) serves as a paradigm of virus receptor binding and tropism, and is the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). LPyV infection depends on sialic acid on host cells, but the molecular interactions underlying LPyV-receptor binding were unknown. We find by glycan array screening that LPyV specifically recognizes a linear carbohydrate motif that contains α2,3-linked sialic acid. High-resolution crystal structures of the LPyV capsid protein VP1 alone and in complex with the trisaccharide ligands 3'-sialyllactose and 3'-sialyl-N-acetyl-lactosamine (3SL and 3SLN, respectively) show essentially identical interactions. Most contacts are contributed by the sialic acid moiety, which is almost entirely buried in a narrow, preformed cleft at the outer surface of the capsid. The recessed nature of the binding site on VP1 and the nature of the observed glycan interactions differ from those of related polyomaviruses and most other sialic acid-binding viruses, which bind sialic acid in shallow, more exposed grooves. Despite their different modes for recognition, the sialic acid binding sites of LPyV and SV40 are half-conserved, hinting at an evolutionary strategy for diversification of binding sites. Our analysis provides a structural basis for the observed specificity of LPyV for linear glycan motifs terminating in α2,3-linked sialic acid, and links the different tropisms of known LPyV strains to the receptor binding site. It also serves as a useful template for understanding the ligand-binding properties and serological crossreactivity of HPyV9.