Constraints on Dark Matter Properties from Observations of Milky Way Satellite Galaxies.

We perform a comprehensive study of Milky Way (MW) satellite galaxies to constrain the fundamental properties of dark matter (DM). This analysis fully incorporates inhomogeneities in the spatial distribution and detectability of MW satellites and marginalizes over uncertainties in the mapping between galaxies and DM halos, the properties of the MW system, and the disruption of subhalos by the MW disk. Our results are consistent with the cold, collisionless DM paradigm and yield the strongest cosmological constraints to date on particle models of warm, interacting, and fuzzy dark matter. At 95% confidence, we report limits on (i) the mass of thermal relic warm DM, m_{WDM}>6.5 keV (free-streaming length, λ_{fs}≲10h^{-1} kpc), (ii) the velocity-independent DM-proton scattering cross section, σ_{0}<8.8×10^{-29} cm^{2} for a 100 MeV DM particle mass [DM-proton coupling, c_{p}≲(0.3 GeV)^{-2}], and (iii) the mass of fuzzy DM, m_{ϕ}>2.9×10^{-21} eV (de Broglie wavelength, λ_{dB}≲0.5 kpc). These constraints are complementary to other observational and laboratory constraints on DM properties.

Detection of CMB-Cluster Lensing using Polarization Data from SPTpol.

We report the first detection of gravitational lensing due to galaxy clusters using only the polarization of the cosmic microwave background (CMB). The lensing signal is obtained using a new estimator that extracts the lensing dipole signature from stacked images formed by rotating the cluster-centered Stokes QU map cutouts along the direction of the locally measured background CMB polarization gradient. Using data from the SPTpol 500 deg^{2} survey at the locations of roughly 18 000 clusters with richness λ≥10 from the Dark Energy Survey (DES) Year-3 full galaxy cluster catalog, we detect lensing at 4.8σ. The mean stacked mass of the selected sample is found to be (1.43±0.40)×10^{14}M_{⊙} which is in good agreement with optical weak lensing based estimates using DES data and CMB-lensing based estimates using SPTpol temperature data. This measurement is a key first step for cluster cosmology with future low-noise CMB surveys, like CMB-S4, for which CMB polarization will be the primary channel for cluster lensing measurements.

Cosmological Constraints from Multiple Probes in the Dark Energy Survey.

The combination of multiple observational probes has long been advocated as a powerful technique to constrain cosmological parameters, in particular dark energy. The Dark Energy Survey has measured 207 spectroscopically confirmed type Ia supernova light curves, the baryon acoustic oscillation feature, weak gravitational lensing, and galaxy clustering. Here we present combined results from these probes, deriving constraints on the equation of state, w, of dark energy and its energy density in the Universe. Independently of other experiments, such as those that measure the cosmic microwave background, the probes from this single photometric survey rule out a Universe with no dark energy, finding w=-0.80_{-0.11}^{+0.09}. The geometry is shown to be consistent with a spatially flat Universe, and we obtain a constraint on the baryon density of Ω_{b}=0.069_{-0.012}^{+0.009} that is independent of early Universe measurements. These results demonstrate the potential power of large multiprobe photometric surveys and pave the way for order of magnitude advances in our constraints on properties of dark energy and cosmology over the next decade.

The CUPIC algorithm: an accurate model for the prediction of sustained viral response under telaprevir or boceprevir triple therapy in cirrhotic patients.

Triple therapy using boceprevir or telaprevir remains the reference treatment for genotype 1 chronic hepatitis C in countries where new interferon-free regimens have not yet become available. Antiviral treatment is highly required in cirrhotic patients, but they represent a difficult-to-treat population. We aimed to develop a simple algorithm for the prediction of sustained viral response (SVR) in cirrhotic patients treated with triple therapy. A total of 484 cirrhotic patients from the ANRS CO20 CUPIC cohort treated with triple therapy were randomly distributed into derivation and validation sets. A total of 52.1% of patients achieved SVR. In the derivation set, a D0 score for the prediction of SVR before treatment initiation included the following independent predictors collected at day 0: prior treatment response, gamma-GT, platelets, telaprevir treatment, viral load. To refine the prediction at the early phase of the treatment, a W4 score included as additional parameter the viral load collected at week 4. The D0 and W4 scores were combined in the CUPIC algorithm defining three subgroups: 'no treatment initiation or early stop at week 4', 'undetermined' and 'SVR highly probable'. In the validation set, the rates of SVR in these three subgroups were, respectively, 11.1%, 50.0% and 82.2% (P < 0.001). By replacing the variable 'prior treatment response' with 'IL28B genotype', another algorithm was derived for treatment-naïve patients with similar results. The CUPIC algorithm is an easy-to-use tool that helps physicians weigh their decision between immediately treating cirrhotic patients using boceprevir/telaprevir triple therapy or waiting for new drugs to become available in their country.

Wide-Field Lensing Mass Maps from Dark Energy Survey Science Verification Data.

We present a mass map reconstructed from weak gravitational lensing shear measurements over 139 deg2 from the Dark Energy Survey science verification data. The mass map probes both luminous and dark matter, thus providing a tool for studying cosmology. We find good agreement between the mass map and the distribution of massive galaxy clusters identified using a red-sequence cluster finder. Potential candidates for superclusters and voids are identified using these maps. We measure the cross-correlation between the mass map and a magnitude-limited foreground galaxy sample and find a detection at the 6.8σ level with 20 arc min smoothing. These measurements are consistent with simulated galaxy catalogs based on N-body simulations from a cold dark matter model with a cosmological constant. This suggests low systematics uncertainties in the map. We summarize our key findings in this Letter; the detailed methodology and tests for systematics are presented in a companion paper.

α-helix to ß-hairpin transition of human amylin monomer.

The human islet amylin polypeptide is produced along with insulin by pancreatic islets. Under some circumstances, amylin can aggregate to form amyloid fibrils, whose presence in pancreatic cells is a common pathological feature of Type II diabetes. A growing body of evidence indicates that small, early stage aggregates of amylin are cytotoxic. A better understanding of the early stages of the amylin aggregation process and, in particular, of the nucleation events leading to fibril growth could help identify therapeutic strategies. Recent studies have shown that, in dilute solution, human amylin can adopt an α-helical conformation, a ß-hairpin conformation, or an unstructured coil conformation. While such states have comparable free energies, the ß-hairpin state exhibits a large propensity towards aggregation. In this work, we present a detailed computational analysis of the folding pathways that arise between the various conformational states of human amylin in water. A free energy surface for amylin in explicit water is first constructed by resorting to advanced sampling techniques. Extensive transition path sampling simulations are then employed to identify the preferred folding mechanisms between distinct minima on that surface. Our results reveal that the α-helical conformer of amylin undergoes a transformation into the ß-hairpin monomer through one of two mechanisms. In the first, misfolding begins through formation of specific contacts near the turn region, and proceeds via a zipping mechanism. In the second, misfolding occurs through an unstructured coil intermediate. The transition states for these processes are identified. Taken together, the findings presented in this work suggest that the inter-conversion of amylin between an α-helix and a ß-hairpin is an activated process and could constitute the nucleation event for fibril growth.

The effect of propofol on patient reaction time and its relationship with loss of verbal contact before induction of anaesthesia.

Increasing the calculated plasma concentration of propofol has been shown to increase choice reaction time and visual and auditory response times. We studied the relationship of reaction to a vibrating handset as the effect-site target-controlled propofol concentration was incrementally increased in 20 patients during sedation, before induction of general anaesthesia. The reaction time increased, initially slowly and then more rapidly, as the calculated effect-site concentration of propofol increased, until the reaction to the vibrating handset was lost at a mean (SD) propofol effect-site concentration of 2.0 (0.6) µg.ml(-1) . The loss of response to verbal contact occurred at a propofol effect-site concentration of 2.4 (0.5) µg.ml(-1) . Reaction time may be of use clinically to warn of impending loss of verbal contact.

Patient-maintained propofol sedation using reaction time monitoring: a volunteer safety study.

Previous volunteer studies of an effect-site controlled, patient-maintained sedation system using propofol have demonstrated a risk of over-sedation. We have incorporated a reaction-time monitor into the handset of the patient-maintained sedation system to add an individualised patient-feedback mechanism. This study assessed if such reaction-time feedback modification would reduce the risk of over-sedation in 20 healthy volunteers deliberately attempting to over-administer themselves propofol. All the volunteers successfully sedated themselves without reaching any unsafe endpoints. All volunteers maintained verbal contact throughout, in accordance with the definition of conscious sedation. The mean (SD) lowest S(p) O(2) was 97 (1.7) % when breathing room air and no volunteer required supplementary oxygen. The mean (SD) maximum effect-site propofol concentration reached was 1.7 (0.4) µg.ml(-1) . The present system was found to be safer than its predecessors, allowing conscious sedation, but preventing over-sedation.

Reaction time-monitored patient-maintained propofol sedation: a pilot study in oral surgery patients.

Previous volunteer studies of an effect-site controlled patient-maintained sedation system using propofol have demonstrated a risk of oversedation. We have incorporated a reaction time monitor into the handset to add an individualised patient-feedback mechanism. This pilot study assessed if the reaction time-feedback modification would prove safe and effective in 20 healthy patients receiving sedation while undergoing oral surgery. All patients successfully sedated themselves without reaching any unsafe endpoints. All 20 maintained verbal contact throughout. The mean (SD) lowest peripheral blood oxygen saturation was 98.0 (2.1)% breathing room air. No patient required supplementary oxygen. The mean (SD) maximum effect-site propofol concentration reached was 1.6 (0.5) µg.ml(-1). The present system was found to be safe and effective, allowing oral surgery treatment under conscious sedation, but preventing oversedation.

Effect of trehalose on the interaction of Alzheimer's Aß-peptide and anionic lipid monolayers.

The interaction of amyloid ß-peptide (Aß) with cell membranes is believed to play a central role in the pathogenesis of Alzheimer's disease. In particular, recent experimental evidence indicates that bilayer and monolayer membranes accelerate the aggregation and amyloid fibril formation rate of Aß. Understanding that interaction could help develop therapeutic strategies for treatment of the disease. Trehalose, a disaccharide of glucose, has been shown to be effective in preventing the aggregation of numerous proteins. It has also been shown to delay the onset of certain amyloid-related diseases in a mouse model. Using Langmuir monolayers and molecular simulations of the corresponding system, we study several thermodynamic and kinetic aspects of the insertion of Aß peptide into DPPG monolayers in water and trehalose subphases. In the water subphase, the insertion of the Aß peptide into the monolayer exhibits a lag time which decreases with increasing temperature of the subphase. In the presence of trehalose, the lag time is completely eliminated and peptide insertion is completed within a shorter time period compared to that observed in pure water. Molecular simulations show that more peptide is inserted into the monolayer in the water subphase, and that such insertion is deeper. The peptide at the monolayer interface orients itself parallel to the monolayer, while it inserts with an angle of 50° in the trehalose subphase. Simulations also show that trehalose reduces the conformational change that the peptide undergoes when it inserts into the monolayer. This observation helps explain the experimentally observed elimination of the lag time by trehalose and the temperature dependence of the lag time in the water subphase.

Structural effects and translocation of doxorubicin in a DPPC/Chol bilayer: the role of cholesterol.

We use molecular dynamics simulations to characterize the influence of cholesterol (Chol) on the interaction between the anticancer drug doxorubicin (DOX) and a dipalmitoyl phosphatidylcholine/Chol lipid bilayer. We calculate the potential of mean force, which gives us an estimate of the free energy barrier for DOX translocation across the membrane. We find free energy barriers of 23.1 ± 3.1 k(B)T, 36.8 ± 5.1 k(B)T, and 54.5 ± 4.7 k(B)T for systems composed of 0%, 15%, and 30% Chol, respectively. Our predictions agree with Arrhenius activation energies from experiments using phospholipid membranes, including 20 k(B)T for 0% Chol and 37.2 k(B)T for 20% Chol. The location of the free energy barrier for translocation across the bilayer is dependent on composition. As Chol concentration increases, this barrier changes from the release of DOX into the water to flip-flop over the membrane center. The drug greatly affects local membrane structure by attracting dipalmitoyl phosphatidylcholine headgroups, curving the membrane, and allowing water penetration. Despite its hydrophobicity, DOX facilitates water transport via its polar groups.

2DIR spectroscopy of human amylin fibrils reflects stable ß-sheet structure.

The aggregation of human amylin to form amyloid contributes to islet ß-cell dysfunction in type 2 diabetes. Studies of amyloid formation have been hindered by the low structural resolution or relatively modest time resolution of standard methods. Two-dimensional infrared (2DIR) spectroscopy, with its sensitivity to protein secondary structures and its intrinsic fast time resolution, is capable of capturing structural changes during the aggregation process. Moreover, isotope labeling enables the measurement of residue-specific information. The diagonal line widths of 2DIR spectra contain information about dynamics and structural heterogeneity of the system. We illustrate the power of a combined atomistic molecular dynamics simulation and theoretical and experimental 2DIR approach by analyzing the variation in diagonal line widths of individual amide I modes in a series of labeled samples of amylin amyloid fibrils. The theoretical and experimental 2DIR line widths suggest a "W" pattern, as a function of residue number. We show that large line widths result from substantial structural disorder and that this pattern is indicative of the stable secondary structure of the two ß-sheet regions. This work provides a protocol for bridging MD simulation and 2DIR experiments for future aggregation studies.

GNNQQNY--investigation of early steps during amyloid formation.

Protein aggregation has been implicated in the pathology of several neurodegenerative diseases, and a better understanding of how it proceeds is essential for the development of therapeutic strategies. Recently, the amyloidogenic heptapeptide GNNQQNY has emerged as a molecule of choice for fundamental studies of protein aggregation. A number of experimental and computational studies have examined the structure of the GNNQQNY aggregate. Less work, however, has been aimed at understanding its aggregation pathway. In this study, we present a detailed computational analysis of such a pathway. To that end, transition path sampling Monte Carlo simulations are used to examine the dimerization process. A statistical analysis of the reaction pathways shows that the dimerization reaction proceeds via a zipping mechanism, initiated with the formation of distinct contacts at the third residue (N). Asparagine residues are found to play a key role in the early stages of aggregation. And, contrary to previous belief, it is also shown that the tyrosine terminal group is not required to stabilize the dimer. In fact, an asparagine residue leads to faster aggregation of the peptide.

Stable and metastable states of human amylin in solution.

Patients with type II diabetes exhibit fibrillar deposits of human amylin protein in the pancreas. It has been proposed that amylin oligomers arising along the aggregation or fibril-formation pathways are important in the genesis of the disease. In a step toward understanding these aggregation pathways, in this work we report the conformational preferences of human amylin monomer in solution using molecular simulations and infrared experiments. In particular, we identify a stable conformer that could play a key role in aggregation. We find that amylin adopts three stable conformations: one with an α-helical segment comprising residues 9-17 and a short antiparallel ß-sheet comprising residues 24-28 and 31-35; one with an extended antiparallel ß-hairpin with the turn region comprising residues 20-23; and one with no particular structure. Using detailed calculations, we determine the relative stability of these various conformations, finding that the ß-hairpin conformation is the most stable, followed by the α-helical conformation, and then the unstructured coil. To test our predicted structure, we calculate its infrared spectrum in the amide I stretch regime, which is sensitive to secondary structure through vibrational couplings and linewidths, and compare it to experiment. We find that theoretically predicted spectra are in good agreement with the experimental line shapes presented herein. The implications of the monomer secondary structures on its aggregation pathway and on its interaction with cell membranes are discussed.

Solution structures of rat amylin peptide: simulation, theory, and experiment.

Amyloid deposits of amylin in the pancreas are an important characteristic feature found in patients with Type-2 diabetes. The aggregate has been considered important in the disease pathology and has been studied extensively. However, the secondary structures of the individual peptide have not been clearly identified. In this work, we present detailed solution structures of rat amylin using a combination of Monte Carlo and molecular dynamics simulations. A new Monte Carlo method is presented to determine the free energy of distinct biomolecular conformations. Both folded and random-coil conformations of rat amylin are observed in water and their relative stability is examined in detail. The former contains an alpha-helical segment comprised of residues 7-17. We find that at room temperature the folded structure is more stable, whereas at higher temperatures the random-coil structure predominates. From the configurations and weights we calculate the alpha-carbon NMR chemical shifts, with results that are in reasonable agreement with experiments of others. We also calculate the infrared spectrum in the amide I stretch regime, and the results are in fair agreement with the experimental line shape presented herein.

2D IR line shapes probe ovispirin peptide conformation and depth in lipid bilayers.

We report a structural study on the membrane binding of ovispirin using 2D IR line shape analysis, isotope labeling, and molecular dynamics simulations. Ovispirin is an antibiotic polypeptide that binds to the surfaces of membranes as an alpha-helix. By resolving individual backbone vibrational modes (amide I) using 1-(13)C=(18)O labeling, we measured the 2D IR line shapes for 15 of the 18 residues in this peptide. A comparison of the line shapes reveals an oscillation in the inhomogeneous line width that has a period equal to that of an alpha-helix (3.6 amino acids). The periodic trend is caused by the asymmetric environment of the membrane bilayer that exposes one face of the alpha-helix to much stronger environmental electrostatic forces than the other. We compare our experimental results to 2D IR line shapes calculated using the lowest free energy structure identified from molecular dynamics simulations. These simulations predict a periodic trend similar to the experiment and lead us to conclude that ovispirin lies in the membrane just below the headgroups, is tilted, and may be kinked. Besides providing insight into the antibiotic mechanism of ovispirin, our procedure provides an infrared method for studying peptide and protein structures that relies on the natural vibrational modes of the backbone. It is a complementary method to other techniques that utilize line shapes, such as fluorescence, NMR, and ESR spectroscopies, because it does not require mutations, the spectra can be quantitatively simulated using molecular dynamics, and the technique can be applied to difficult-to-study systems like ion channels, aggregated proteins, and kinetically evolving systems.

Immune reconstitution following rabbit antithymocyte globulin.

Depletional induction therapies are routinely used to prevent acute rejection and improve transplant outcome. The effects of depleting agents on T-cell subsets and subsequent T-cell reconstitution are incompletely defined. We used flow cytometry to examine the effects of rabbit antithymocyte globulin (rATG) on the peripheral T-cell repertoire of pediatric and adult renal transplant recipients. We found that while rATG effectively depleted CD45RA+CD27+ naïve and CD45RO+CD27+ central memory CD4+ T cells, it had little effect on CD45RO+CD27- CD4+ effector memory or CD45RA+CD31-, CD45RO+CD27+ and CD45RO+CD27- CD8+ T cell subsets. When we performed a kinetic analysis of CD31+ recent thymic emigrants and CD45RA+/RO+ T cells, we found evidence for both thymopoiesis and homeostatic proliferation contributing to immune reconstitution. We additionally examined the impact of rATG on peripheral CD4+Foxp3+ T cells. We found that in adults, administration of rATG-induced peripheral expansion and new thymic emigration of T cells with a Treg phenotype, while CD4+Foxp3+ T cells of thymic origin predominated in children, providing the first evidence that rATG induces Treg in vivo. Collectively our data indicate that rATG alters the balance of regulatory to memory effector T cells posttransplant, providing an explanation for how it positively impacts transplant outcome.

Silencing of tissue factor by antisense deoxyoligonucleotide mitigates thioacetamide-induced liver injury.

BACKGROUND: Retinoid receptors (RRs), RAR-α and RXR-α, work as transcription factors that regulate cell growth, differentiation, survival, and death. Hepatic stellate cells (HSCs) store retinoid and release its RRs as lipid droplets upon their activation. PURPOSE: We test the hypothesis that loss of retinoid receptors RAR-α and RXR-α from HSCs is dependent on tissue factor (TF) during thioacetamide (TAA)-induced liver injury. METHODS: Liver toxicity markers, TF, fibrin, cleaved caspase-3, and cyclin D1 as well as histopathology were investigated. RESULTS: Increased TF, fibrin, cleaved caspase-3, and cyclin D1 protein expression is seen in zone of central vein after TAA injection compared with vehicle-treated mice. A strong downregulation of RAR-α and RXR-α is seen in TAA-induced liver injury. In addition, histopathological obliteration and pericentral expression of cleaved caspase 3 and cyclin D1 are observed after TAA injection compared with the normal vehicle-treated mice. No changes have been seen in TAA/TF-sense (SC) in whole parameters compared with TAA-treated animals. TAA/TF-antisense (AS)-treated mice show normal expression of all parameters and normal histopathological features when compared with the control mice. In conclusion, this study declares that the strong downregulation of RAR-α and RXR-α may cause liver injury and particularly activation of HSCs in TAA-induced toxicity. TF-AS treatment not only downregulates TF protein expression but also alleviates loss of liver RAR-α and RXR-α and suppresses the activated apoptosis signals in TAA-induced liver toxicity. Finally, TF and RAR-α/RXR-α are important regulatory molecules in TAA induced acute liver injury.

Effect of trehalose on amyloid beta (29-40)-membrane interaction.

A growing body of experimental evidence indicates that the interaction between amyloid beta peptide and lipid bilayer membranes plays an important role in the development of Alzheimer disease. Recent experimental evidence also suggests that trehalose, a simple disaccharide, reduces the toxicity of amyloid beta peptide. Molecular simulations are used to examine the effect of trehalose on the conformational stability of amyloid beta peptide in aqueous solution and its effect on the interaction between amyloid beta peptide and a model phospholipid bilayer membrane. It is found that, in aqueous solution, the peptide exhibits a random coil conformation but, in the presence of trehalose, it adopts an alpha helical conformation. It is then shown that the insertion of amyloid beta peptide into a membrane is more favorable when the peptide is folded into an alpha-helix than in a random coil conformation, thereby suggesting that trehalose promotes the insertion of alpha-helical amyloid beta into biological membranes.

Folding of polyglutamine chains.

Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a beta-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded beta-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable beta-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.