We present a new digital elevation model (DEM) of the Antarctic ice
sheet and ice shelves based on 2.5×108 observations
recorded by the CryoSat-2 satellite radar altimeter between
July 2010 and ...July 2016. The DEM is formed from spatio-temporal fits
to elevation measurements accumulated within 1, 2, and 5 km
grid cells, and is posted at the modal resolution of
1 km. Altogether, 94 % of the grounded ice sheet and
98 % of the floating ice shelves are observed, and the remaining
grid cells north of 88∘ S are interpolated using ordinary
kriging. The median and root mean square difference between the DEM
and 2.3×107 airborne laser altimeter measurements
acquired during NASA Operation IceBridge campaigns are −0.30 and
13.50 m, respectively. The DEM uncertainty rises in regions
of high slope, especially where elevation measurements were
acquired in low-resolution mode; taking this into account, we
estimate the average accuracy to be 9.5 m – a value that is
comparable to or better than that of other models derived from
satellite radar and laser altimetry.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Compared to other ions, protons (H+) and hydroxide ions (OH-) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural ...diffusion'-the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH- can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH- hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from ...an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and ¹H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Chromosomes are the physical realization of genetic information and thus form the basis for its readout and propagation. Here we present a high-resolution chromosomal contact map derived from a ...modified genome-wide chromosome conformation capture approach applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of contact density and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, whereas active domains reach out of the territory to form remote intra- and interchromosomal contacts. Moreover, we systematically identify specific long-range intrachromosomal contacts between Polycomb-repressed domains. Together, these observations allow for quantitative prediction of the Drosophila chromosomal contact map, laying the foundation for detailed studies of chromosome structure and function in a genetically tractable system.
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► High-resolution genome-wide chromosomal contact map of the Drosophila genome ► Genome partitioning into physically and epigenetically defined domains ► Contacts between domains are hierarchical and depend on their epigenetic context ► Specific distal contacts suggest functional associations of Polycomb domains
A genome-wide chromosomal contact map of the Drosophila genome at kilobase resolution shows that the genome is partitioned into physical domains and that contact between domains is dependent upon their epigenetic profile.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of ...introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently developed colored noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequency-optimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nosé-Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogen-in-palladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a near-optimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations.
Summary
Cryoinjury is a consequence of cryopreservation and may have a negative impact on sperm quality regarding motility, morphology, and viability. This study was designed to identify potential ...proteomic changes in human sperm cells throughout the cryopreservation process. Comparisons made within this study included the detection of the sperm proteomic changes induced by incubation of the sperm cells with a protein‐free cryoprotectant (with and without CryoSperm), and the proteomic changes induced by freezing, thawing, and subsequent after‐thawing incubation at two different temperatures (0 °C vs. 23 °C). Tandem Mass Tag (TMT) peptide labeling coupled with LC‐MS/MS was used for protein quantification. LC‐MS/MS resulted in the identification of 769 quantifiable proteins. The abundance of 105 proteins was altered upon CryoSperm incubation. Freezing and thawing also induced substantial protein changes. However, fewer changes were observed when semen was thawed and then maintained after‐thawing at approximately 0 °C than when it was maintained after‐thawing at 23 °C, with 60 and 99 differential proteins detected, respectively, as compared to unfrozen semen incubated in CryoSperm. Collectively, these differences indicate that substantial changes occur in the sperm proteome at every stage of the cryopreservation process which may ultimately impair the sperm fertilizing capability. This is the first study to compare protein levels in fresh and cryopreserved semen using the TMT technology coupled to LC‐MS/MS.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
Equivalence of laboratory tests over time is important for longitudinal studies. Even a small systematic difference (bias) can result in substantial misclassification.
We selected 200 Atherosclerosis ...Risk in Communities Study participants attending all 5 study visits over 25 years. Eight analytes were remeasured in 2011-2013 from stored blood samples from multiple visits: creatinine, uric acid, glucose, total cholesterol, HDL cholesterol, LDL cholesterol, triglycerides, and high-sensitivity C-reactive protein. Original values were recalibrated to remeasured values with Deming regression. Differences >10% were considered to reflect substantial bias, and correction equations were applied to affected analytes in the total study population. We examined trends in chronic kidney disease (CKD) pre- and postrecalibration.
Repeat measures were highly correlated with original values Pearson r > 0.85 after removing outliers (median 4.5% of paired measurements), but 2 of 8 analytes (creatinine and uric acid) had differences >10%. Original values of creatinine and uric acid were recalibrated to current values with correction equations. CKD prevalence differed substantially after recalibration of creatinine (visits 1, 2, 4, and 5 prerecalibration: 21.7%, 36.1%, 3.5%, and 29.4%, respectively; postrecalibration: 1.3%, 2.2%, 6.4%, and 29.4%). For HDL cholesterol, the current direct enzymatic method differed substantially from magnesium dextran precipitation used during visits 1-4.
Analytes remeasured in samples stored for approximately 25 years were highly correlated with original values, but 2 of the 8 analytes showed substantial bias at multiple visits. Laboratory recalibration improved reproducibility of test results across visits and resulted in substantial differences in CKD prevalence. We demonstrate the importance of consistent recalibration of laboratory assays in a cohort study.
Mussels are filter-feeders living in a bacteria-rich environment. We have previously found that numerous bacterial species are naturally present within the cell-free hemolymph, including several of ...the
Vibrio genus, whereas the intra-cellular content of hemocytes was sterile. When bacteria were injected into the circulation of the mussel, the number of living intra-hemocyte bacteria dramatically increased in less than an hour, suggesting intense phagocytosis, then gradually decreased, with no viable bacteria remaining 12
h post-injection for
Micrococcus lysodeikticus, 24
h for
Vibrio splendidus and more than 48
h for
V ibrio anguillarum. The total hemocyte count (THC) was dramatically lowered by the bacterial injections, as quantified by flow cytometry.
V. splendidus induced the strongest decreases with −66% 9
h post-injection of living bacteria and −56% 3
h post-injection of heat-killed bacteria. Flow cytometry was used to identify three main sub-populations of hemocytes, namely hyalinocytes, small granulocytes and large granulocytes. When THC was minimal, i.e. within the first 9
h post-injection, proportions of the three cell categories varied dramatically, suggesting differential involvement according to the targets, but small granulocytes remained the majority. According to a decrease in their number followed by an increase (+90% at 12
h with living
V. splendidus), hyalinocytes also appeared to be involved as cellular effectors of antibacterial immunity, despite possessing little capacity for phagocytosis and not containing antimicrobial peptides.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
In the present paper, the complex mechanical behaviour of the surfaces joining two differentbodies is analysed by a cohesive-frictional interface constitutive model. The kinematical behaviouris ...characterized by the presence of discontinuous displacement fields, that take place at the internalconnecting surfaces, both in the fully cohesive phase and in the delamination one. Generally, in order tocatch discontinuous displacement fields, internal connecting surfaces (adhesive layers) are modelled bymeans of interface elements, which connect, node by node, the meshes of the joined bodies, requiringthe mesh to be conforming to the geometry of the single bodies and to the relevant connecting surface.In the present paper, the Extended Finite Element Method (XFEM) is employed to model, both fromthe geometrical and from the kinematical point of view, the whole domain, including the connectedbodies and the joining surface. The joining surface is not discretized by specific finite elements, butit is defined as an internal discontinuity surface, whose spatial position inside the mesh is analyticallydefined. The proposed approach is developed for two-dimensional composite domains, formed by twoor more material portions joined together by means of a zero thickness adhesive layer. The numericalresults obtained with the proposed approach are compared with the results of the classical interfacefinite element approach. Some examples of delamination and frictional contact are proposed withlinear, circular and curvilinear adhesive layer.
Sarcopenic obesity is a clinical and functional condition characterized by the coexistence of excess fat mass and sarcopenia. Currently, different definitions of sarcopenic obesity exist and its ...diagnostic criteria and cut-offs are not universally established. Therefore, the prevalence and sensitivity of this condition for any disease risk prediction is affected significantly.
This work was conducted under the auspices of the European Society for Clinical Nutrition and Metabolism (ESPEN) and the European Association for the Study of Obesity (EASO). An international expert panel performed a systematic review as an initial step to analyze and summarize the available scientific literature on the definitions and the diagnostic criteria for sarcopenic obesity proposed and/or applied in human studies to date.
The present systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The search was conducted in April 2018 in three databases (PubMed, Scopus, Web of Science). Human studies conducted in both sexes, irrespective of ethnicity, and published from 2007 to 2018 were included; cohorts of individuals with obesity and acute or chronic conditions and treatments reported to negatively influence skeletal muscle mass and function independently of obesity were excluded from final analyses. The quality of the studies was evaluated using the Newcastle–Ottawa Scale (NOS) adapted for cross sectional studies.
The electronic search retrieved 2335 papers of which 75 met the eligibility criteria. A marked heterogeneity in definitions and approaches to diagnose sarcopenic obesity was observed. This was mainly due to differences in the definitions of obesity and sarcopenia, in the methodologies used to assess body composition and physical function, and in the reference values for the variables that have been used (different cut-offs, interquartile analysis, diverse statistical stratification methods). This variability may be attributable, at least in part, to the availability of the methodologies in the different settings, to the variability in specialties and backgrounds of the researcher, and to the different settings (general population, clinical settings, etc.) where studies were performed.
The results of the current work support the need for consensus proposals on: 1) definition of sarcopenic obesity; 2) diagnostic criteria both at the level of potential gold-standards and acceptable surrogates with wide clinical applicability, and with related cut-off values; 3) methodologies to be used in actions 1 and 2. First steps should be aimed at reaching consensus on plausible proposals that would need subsequent validation based on homogeneous studies and databases, possibly based on analyses of existing cohorts, to help define the prevalence of the condition, its clinical and functional relevance as well as most effective prevention and treatment strategies.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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