Quantifying chain reptation in entangled polymer melts: Topological and dynamical mapping of atomistic simulation results onto the tube model

The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability ?? (s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed ?? (s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic properties such as the zero shear rate viscosity and the spectra of storage and loss moduli obtained on the basis of the obtained ?? (s,t) curves for three different polymer melts (polyethylene, cis-1,4-polybutadiene, and trans-1,4-polybutadiene) are consistent with experimental rheological data and in qualitative agreement with the double reptation and dual constraint models. The new methodology is general and can be routinely applied to analyze primitive path dynamics and chain reptation in atomistic trajectories (accumulated through long MD simulations) of other model polymers or polymeric systems (e.g., bidisperse, branched, grafted, etc.); it is thus believed to be particularly useful in the future in evaluating proposed tube models and developing more accurate theories for entangled systems.open342

Giant Gravitons - with Strings Attached (III)

We develop techniques to compute the one-loop anomalous dimensions of operators in the ${\cal N}=4$ super Yang-Mills theory that are dual to open strings ending on boundstates of sphere giant gravitons. Our results, which are applicable to excitations involving an arbitrary number of open strings, generalize the single string results of hep-th/0701067. The open strings we consider carry angular momentum on an S$^3$ embedded in the S$^5$ of the AdS$_5\times$S$^5$ background. The problem of computing the one loop anomalous dimensions is replaced with the problem of diagonalizing an interacting Cuntz oscillator Hamiltonian. Our Cuntz oscillator dynamics illustrates how the Chan-Paton factors for open strings propagating on multiple branes can arise dynamically.Comment: 66 pages; v2: improved presentatio

Systematic investigation of organochlorine pesticides and polychlorinated biphenyls blood levels in Greek children from the Rhea birth cohort suggests historical exposure to DDT and through diet to DDE

Data availability: Data will be made available on request.Supplementary data are available online at: https://www.sciencedirect.com/science/article/pii/S0160412024002721#s0090:~:text=Appendix%20A.-,Supplementary%20data,-Data%20availability .The blood levels of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) have been thoroughly investigated in Greek children from the Rhea birth cohort study. This investigation aimed to assess exposure levels, explore their possible relationship with children's age and sex, and indicate potential sources of exposure. Exposure patterns and common sources of PCBs and OCPs were analyzed using bivariate and multivariate statistics. A total of 947 blood samples from study participants were analyzed for OCP and PCB exposure, with 375 samples collected at 4 years old, 239 at 6.5 years old, and 333 at 11 years old. Elevated levels of DDE were observed in 6.5-year-old children compared to corresponding levels in other European countries. Higher levels of DDE were found in 4-year-old children, with the lowest concentrations in the 11-year-old group. The DDT/DDE ratio was consistently less than 1 among all the examined subjects. These results indicate exposure to DDT and DDE both in utero and through breastfeeding and dietary intake. For the entire cohort population, the highest concentration was determined for PCB 28, followed by PCBs 138, 153, and 180. The sum of the six indicator PCBs implied low exposure levels for the majority of the cohort population. Spearman correlations revealed strong associations between PCBs and OCPs, while principal component analysis identified two different groupings of exposure. DDE exhibited a correlation with a series of PCBs (153, 156, 163, 180), indicating a combined OCP-PCB source, and an anticorrelation with others (52, 28, 101), implying a separate and competing source.Hellenic Ministry of Health and the General Secretariat for Research and Innovation

2'-O-methoxyethyl splice-switching oligos correct splicing from IVS2-745 β-thalassemia patient cells restoring HbA production and chain rebalance

\u3b2-thalassemia is a disorder caused by altered hemoglobin protein synthesis and affects individuals worldwide. Severe forms of the disease, left untreated, can result in death before the age of 3 years (1). The standard of care consists of chronic and costly palliative treatment by blood transfusion combined with iron chelation. This dual approach suppresses anemia and reduces iron-related toxicities in patients. Allogeneic bone marrow transplant is an option, but limited by the availability of a highly compatible HSC donor. While gene therapy is been explored in several trials, its use is highly limited to developed regions with centers of excellence and well-established healthcare systems (2). Hence, there remains a tremendous unmet medical need to develop alternative treatment strategies for \u3b2-thalassemia (3). Occurrence of aberrant splicing is one of the processes that affects \u3b2-globin synthesis in \u3b2-thalassemia. The (C>G) IVS-2-745 is a splicing mutation within intron 2 of the \u3b2-globin gene. It leads to an aberrantly spliced mRNA that incorporates an intron fragment. This results in an in-frame premature termination codon that inhibits \u3b2-globin production. Here, we propose the use of uniform 2'-O-methoxyethyl (2'-MOE) splice switching oligos (SSOs) to reverse this aberrant splicing in the pre-mRNA. With these lead SSOs we show aberrant to wild type splice switching. This switching leads to an increase of adult hemoglobin (HbA) up to 80% in erythroid cells from patients with the IVS-2-745 mutation. Furthermore, we demonstrate a restoration of the balance between \u3b2-like- and \u3b1-globin chains, and up to an 87% reduction in toxic \u3b1-heme aggregates. While examining the potential benefit of 2'-MOE-SSOs in a mixed sickle-thalassemic phenotypic setting, we found reduced HbS synthesis and sickle cell formation due to HbA induction. In summary, 2'-MOE-SSOs are a promising therapy for forms of \u3b2-thalassemia caused by mutations leading to aberrant splicing

Fish Farms at Sea: The Ground Truth from Google Earth

In the face of global overfishing of wild-caught seafood, ocean fish farming has augmented the supply of fresh fish to western markets and become one of the fastest growing global industries. Accurate reporting of quantities of wild-caught fish has been problematic and we questioned whether similar discrepancies in data exist in statistics for farmed fish production. In the Mediterranean Sea, ocean fish farming is prevalent and stationary cages can be seen off the coasts of 16 countries using satellite imagery available through Google Earth. Using this tool, we demonstrate here that a few trained scientists now have the capacity to ground truth farmed fish production data reported by the Mediterranean countries. With Google Earth, we could examine 91% of the Mediterranean coast and count 248 tuna cages (circular cages >40 m diameter) and 20,976 other fish cages within 10 km offshore, the majority of which were off Greece (49%) and Turkey (31%). Combining satellite imagery with assumptions about cage volume, fish density, harvest rates, and seasonal capacity, we make a conservative approximation of ocean-farmed finfish production for 16 Mediterranean countries. Our overall estimate of 225,736 t of farmed finfish (not including tuna) in the Mediterranean Sea in 2006 is only slightly more than the United Nations Food and Agriculture Organization reports. The results demonstrate the reliability of recent FAO farmed fish production statistics for the Mediterranean as well as the promise of Google Earth to collect and ground truth data

Characterization of Polar Organic Components in Fine Aerosols in the Southeastern United States: Identity, Origin, and Evolution

Filter samples of fine aerosols collected in the Southeastern United States in June 2004 were analyzed for the characterization of polar organic components. Four analytical techniques, liquid chromatography –mass spectrometry, ion trap mass spectrometry, laser desorption ionization mass spectrometry, and high-resolution mass spectrometry, were used for identification and quantification. Forty distinct species were detected, comprising on average 7.2% and 1.1% of the total particulate organic mass at three inland sites and a coastal site, respectively. The relative abundance of these species displays a rather consistent distribution pattern in the inland region, whereas a different pattern is found at the coastal site. Chemical and correlation analyses suggest that the detected species are secondary in nature and originate from terpene oxidation, with possible participation of NOx and SO2. It is estimated that polar, acidic components in fine aerosols in the Southeastern United States cover a molecular weight range of 150–400 Da and do not appear to be oligomeric. Other components with MW up to 800 Da may also be present. The detected polar organic species are similar to humic-like substances (HULIS) commonly found in fine aerosols in other rural areas. We present the first, direct evidence that atmospheric processing of biogenic emissions can lead to the formation of certain HULIS species in fine aerosols, and that this may be a typical pathway in the background atmosphere in continental regions; nevertheless, a natural source for HULIS, such as from aquatic and/or terrestrial humic/fulvic acids and their degradation products, cannot be precluded

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Neuroprotection by leptin in a rat model of permanent cerebral ischemia: effects on STAT3 phosphorylation in discrete cells of the brain

In addition to its effects in the hypothalamus to control body weight, leptin is involved in the regulation of neuronal function, development and survival. Recent findings have highlighted the neuroprotective effects of leptin against ischemic brain injury; however, to date, little is known about the role performed by the signal transducer and activator of transcription (STAT)-3, a major mediator of leptin receptor transduction pathway in the brain, in the beneficial effects of the hormone. Our data demonstrate that systemic acute administration of leptin produces neuroprotection in rats subjected to permanent middle cerebral artery occlusion (MCAo), as revealed by a significant reduction of the brain infarct volume and neurological deficit up to 7 days after the induction of ischemia. By combining a subcellular fractionation approach with immunohistofluorescence, we observe that neuroprotection is associated with a cell type-specific modulation of STAT3 phosphorylation in the ischemic cortex. The early enhancement of nuclear phospho-STAT3 induced by leptin in the astrocytes of the ischemic penumbra may contribute to a beneficial effect of these cells on the evolution of tissue damage. In addition, the elevation of phospho-STAT3 induced by leptin in the neurons after 24 h MCAo is associated with an increased expression of tissue inhibitor of matrix metalloproteinases-1 in the cortex, suggesting its possible involvement to the neuroprotection produced by the adipokine