Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural features underlying antigen presentation by the non-classical MHC class Ib molecule

Blocking of the NKG2A receptor expressed on NK cells and CD8 + T cells with an anti-NKG2A antibody for elicitation of cytolytic activity, is a promising immune checkpoint in cancer immunotherapy. EXX1, a novel TCR-like antibody with specificity for the NKG2A ligand, Qa-1 b - a murine non-classical MHC class Ib ortholog of HLA-E - has been assessed in tumor models in vitro. The antibody only engages with Qa-1 b when it presents the dominant peptide Qdm, derived from the leader sequence of the classical MHC class Ia H-2D. This raises questions about the structural features of antigen presentation by Qa-1 b , and the molecular parameters driving the specificity of the TCR-like antibody. The purpose of this study is to determine and compare the crystal structures of Qa-1 b in complex with Qdm (AMAPRTLLL) and peptide 001 (AQAERTPEL). The Qa-1 b heavy chain and mouse beta-2 microglobulin were recombinantly expressed in E.coli , refolded in the presence of respective peptide, purified using size exclusion chromatography and crystallized with the hanging drop vapor diffusion method. Thermal stability of the MHC/peptide complexes was assessed with nano differential scanning fluorimetry, implying a higher stability of Qa-1 b /001. Crystals of the Qa-1 b /Qdm and Qa-1 b /001 were obtained with 8% PEG4000, 10 mM NiCl 2 , 0.1 M sodium acetate at pH 5.7, and 10% PEG4000, 10mM NiCl 2 and 0.1 M sodium acetate at pH 6.0, respectively. The structure of Qa-1 b /001 was obtained by molecular replacement at 2.43 Å. The presence of negatively charged side chains that protrude from the binding groove, may imply that differences in electrostatic interactions between Qdm and 001 will determine antibody-binding. Further structural characterizations, of Qa-1 b complexes with bound EXX1 are of great interest.
Influence of lowland aquifers and anthropogenic impacts on the isotope hydrology of contrasting mesoscale catchments

We examined the isotope hydrology of eight, contrasting mesoscale (104–488 km2) catchments characterized by a systematic change in the relative importance of upland and lowland areas that reflects the relative distribution of metamorphic and sedimentary rocks. Precipitation and stream water were monitored over a 12‐month period, and stable isotopes were used to examine spatial variations in the hydrometric and tracer dynamics of the catchments. Isotopic tracers were used to examine the temporal dynamics of different runoff sources, and geochemical tracers (alkalinity) were used to identify the geographic sources of runoff. Input–output relationships of isotopic tracers were explored using a gamma function to fit a transit time distribution, which was used to test the hypothesis that the length of mean transit times increased systematically with the cover of sandstone aquifers in the catchments. However, in three catchments, the increased influence of anthropogenic factors, notably reservoir storage, urban runoff and agricultural abstraction for irrigation, prevented reliable transit time estimation. For sites where tentative mean transit time estimates were possible, these varied from around 1.6 years in upland catchments dominated by metamorphic rocks (>75%) and responsive soils to around 4 years in catchments with 34% sandstone cover and freely draining soils. These preliminary results were consistent with inferences of geochemical tracers on the increased role of sedimentary aquifers as runoff sources in lowland areas, but observation from a larger number of sites is needed to confirm this. Copyright © 2012 John Wiley & Sons, Ltd.
Ecohydrological controls on soil moisture and hydraulic conductivity within a pinyon‐juniper woodland

The impact of pinyon‐juniper woodland encroachment on rangeland ecosystems is often associated with a reduction of streamflow and recharge and an increase in soil erosion. The objective of this study is to investigate vegetational control on seasonal soil hydrologic properties along a 15‐m transect in pinyon‐juniper woodland with biocrust. We demonstrate that the juniper tree controls soil water content (SWC) patterns directly under the canopy via interception, and beyond the canopy via shading in a preferred orientation, opposite to the prevailing wind direction. The juniper also controls the SWC and unsaturated hydraulic conductivity measured close to water saturation (K(h)) under the canopy by the creation of soil water repellency due to needle drop. We use this information to refine the hydrologic functional unit (HFU) concept into three interacting hydrologic units: canopy patches, intercanopy patches, and a transitional unit formed by intercanopy patches in the rain shadow of the juniper tree. Spatial autoregressive state‐space models show the close relationship between K(h) close to soil water saturation and SWC at medium and low levels, integrating a number of influences on hydraulic conductivity.
Prediction of Postoperative Delirium After Cardiac Surgery with A Quick Test of Cognitive Speed, Mini-Mental State Examination and Hospital Anxiety and Depression Scale

Purpose: To evaluate if preoperative assessment with A Quick Test of Cognitive Speed (AQT) could increase the accuracy of predicting delirium after cardiac surgery compared to Mini-Mental State Examination (MMSE), and examine if a composite of variables, including cognitive function and depressive symptoms, could be useful to predict delirium. Patients and Methods: Cardiac surgery was performed in 218 patients (mean age 72 years). Preoperative evaluation involved AQT, MMSE and Hospital Anxiety And Depression Scale (HADS). Postoperative delirium was assessed using Nursing Delirium Screening Scale (Nu-DESC) and Confusion Assessment Method-ICU (CAM-ICU). Logistic regression was performed to detect predictors of postoperative delirium and receiver operator characteristic curves (ROC) with area under the curve (AUC) to determine the accuracy. Results: Postoperative delirium occurred in 47 patients (22%) who had lower MMSE scores (median (range), 27 (19–30) vs 28 (20– 30), p =0.009) and slower AQT (median (range), 76 (48–181) vs 70 (40–182) seconds, p =0.030) than patients without delirium. Predictive power measured as AUC (95% CI) was 0.605 (0.51–0.70) for AQT and 0.623 (0.53–0.72) for MMSE. Logistic regression (OR, 95% CI) showed MMSE <27 points (2.72, 1.27–5.86), AQT >70 sec (2.26, 1.03–4.95), HADS-D >4 points (2.60, 1.21–5.58) and longer cardiopulmonary bypass-time (1.007, 1.002–1.013) to be associated with postoperative delirium. Combining these parameters yielded an AUC of 0.736 (0.65–0.82). Conclusion: The ability of predicting delirium using AQT was similar to MMSE, and only slightly higher by combining AQT and MMSE. Adding HADS-D and cardiopulmonary bypass-time to MMSE and AQT increased the predictive power to a borderline acceptable discriminatory value. Preoperative cognitive tests and screening for depressive symptoms may help identify patients at risk of postoperative delirium. Yet, there is still a need to establish useful preoperative tests. and the combination of AQT and MMSE marginally increased the predictive power measured by AUC. A composite of MMSE, AQT, HADS-D and cardiopulmonary bypass time further increased the predictive accuracy to an AUC of 0.736, which is a borderline acceptable discriminatory value in clinical practice. Our results confirm the association of impaired
How climate How climate-smart is farmer-managed natural regeneration (FMNR) as a restoration practice? Assessing the resilience of West African parklands using a trait-based approach

Recently, widespread regreening of some parts of the Sahel took place because farmers have allowed the regeneration of young trees in their fields, a practice known as farmer managed natural regeneration (FMNR). FMNR is seen as a promising method to restore degraded landscapes while improving rural livelihoods, yet little is known about the factors influencing the regeneration dynamics and diversity of woody species on which FMNR practices depend. Insight from the field of functional ecology could help to guide the restoration of agroecosystems that are resilient in the face of erratic climate conditions. In an agricultural landscape of Burkina Faso, I evaluated changes in species composition, diversity and functional properties (weighted-mean trait values and functional diversity) between the established and the regenerating tree community. Using the same parameters, I also explored the response of the regenerating vegetation to different land use types and farming practices. My results show that regeneration is dominated mainly by drought tolerant shrub species at the expanse of large tree species that characterize the established community. Higher land use intensity had a negative effect on regeneration diversity and favored drought tolerant vegetation. Diversity of the regenerating vegetation was affected positively by fire and selective tree cutting but negatively by livestock. My findings highlight that current land use management in west African parklands hampers diversification of the regenerating vegetation and by relying solely on the natural regeneration of trees, FMNR alone might not be able to restore multifunctional and resilient ecosystems. The maintenance of land units that promote the regeneration of multiple species, in particular those of socio-economic value for local communities, should be a priority. When natural regeneration is failing, enrichment planting and domestication of key species should be considered.
Combined physiological effects of bronchodilators and hyperoxia on exertional dyspnea in normoxic COPD

Background : Studies examining the physiological interactions of oxygen (O 2 ) and bronchodilators (BD) during exercise in COPD should provide new insights into mechanisms of exercise intolerance. We examined the effects of O 2 and BD, alone and in combination, on dyspnea, ventilation (V E ), breathing pattern, operating lung volumes and exercise endurance. Methods : In a randomized, double-blind, crossover study, 16 patients with COPD (FEV 1 =43(3) %predicted; mean(SEM)) performed pulmonary function tests and an incremental exercise test, then completed four visits in which they received either nebulized BD (ipratropium 0.5 mg + salbutamol 2.5 mg) or placebo (PL) with either 50% O 2 or room air (RA). At 90-105 minutes post-dose, patients performed pulmonary function tests then breathed RA or O 2 during symptom-limited constant-load exercise at 75% peak work rate. Results : With BD, inspiratory capacity (IC) increased 0.3(0.1) L (p<0.05) at rest and during exercise permitting greater tidal volume (V T ) expansion during exercise and a greater peak V E . With O 2 , V E decreased during exercise as a result of decreased breathing frequency ( F ), with no significant change in IC. During exercise with BD+O 2 , IC and V T increased, F decreased, and V E did not change. Dyspnea decreased with all interventions at a standardized time during exercise compared with PL+RA (p<0.05). Endurance time was significantly (p<0.05) greater with BD+O 2 (10.4(1.6) min) than with O 2 (8.5(1.4) min), BD (7.1(1.3) min) and PL+RA (5.4(0.9) min). Conclusion As our analysis of dyspnea-V E slopes suggests, dyspnea relief during O 2 is mainly linked to reduced ventilatory demand. The benefits following O 2 and combined O 2 and BD were most pronounced in those with the most severe disease and these individuals showed greater reduction in operating lung volumes during exercise than patients with less severe COPD. The physiological interactions of combining BD and O 2 culminated in impressive improvements in exertional symptoms and exercise endurance, thus underscoring the incremental benefits of reducing neural drive and improving dynamic ventilatory mechanics. Finally, this study provides a physiological rationale for the recommendation of O 2 therapy as an adjunct to exercise reconditioning for patients with more advanced, normoxic COPD who remain incapacitated by dyspnea despite optimization of bronchodilators.
40Ar/ 39Ar and K–Ar geochronological age constraints for the inception and early evolution of the Izu–Bonin – Mariana arc system

K–Ar and 40Ar/39Ar dates are presented for locations in the Izu–Bonin – Mariana (IBM) forearc (Ocean Drilling Program (ODP) sites 786 & 782, Chichijima, Deep Sea Drilling Program (DSDP) sites 458 & 459, Saipan), and Palau on the remnant arc of the Kyushu–Palau Ridge. For a number of these locations, the 40Ar/39Ar plateau and 36Ar/40Ar versus 39Ar/40Ar isochrons give older ages than the K–Ar results. The most important results are: (i) at site 786, initial construction of the proto‐IBM (now forearc) basement occurred at least by ca 47–45 Ma, consistent with the age of the immediately overlying sediments (middle Eocene nannofossil Zone CP13c); the younger pulse of construction dated at ca 35 Ma by K–Ar could not be confirmed by 40Ar/39Ar analysis; (ii) 40Ar/39Ar ages for the initial construction of the Mariana portion of the IBM system are as old as those of the Izu–Bonin portion, for example at site 458, initial construction commenced at least by ca 49 Ma and at ca 47 Ma at Saipan (Sankakayuma Formation); and (iii) a combination of K–Ar and 40Ar/39Ar ages indicate continued boninite magmatism in the Izu–Bonin forearc (and remnant arc at Palau) until ca 35 Ma. Subduction inception including boninite series rocks along most of the exposed length of the IBM system, clearly preceded by some 5 million years the Middle Eocene (ca 43.5 Ma) change in Pacific plate motion. Boninitic series magmatism persisted at locations now exposed in the forearc for ∼ 15 million years after arc inception concurrently with low‐K tholeiitic series eruptions from a subaerial arc system, established at ≥ 40 Ma, on the Kyushu–Palau Ridge. For the Mariana portion of the IBM system, reconstruction of the proto‐arc places this activity adjacent to the concurrent but orthogonally spreading Central Basin Ridge of the West Philippine Basin. It is possible that a combination of subduction of a young North New Guinea Plate beneath newly created back‐arc basin crust may account for some of the features of the Mariana system. It is clear, however, that the understanding of the processes of subduction initiation and early IBM arc development is incomplete.
Southern ocean warming, sea level and hydrological change during the Paleocene-Eocene thermal maximum

Abstract. A brief (~150 kyr) period of widespread global average surface warming marks the transition between the Paleocene and Eocene epochs, ~56 million years ago. This so-called "Paleocene-Eocene thermal maximum" (PETM) is associated with the massive injection of 13C-depleted carbon, reflected in a negative carbon isotope excursion (CIE). Biotic responses include a global abundance peak (acme) of the subtropical dinoflagellate Apectodinium. Here we identify the PETM in a marine sedimentary sequence deposited on the East Tasman Plateau at Ocean Drilling Program (ODP) Site 1172 and show, based on the organic paleothermometer TEX86, that southwest Pacific sea surface temperatures increased from ~26 °C to ~33°C during the PETM. Such temperatures before, during and after the PETM are >10 °C warmer than predicted by paleoclimate model simulations for this latitude. In part, this discrepancy may be explained by potential seasonal biases in the TEX86 proxy in polar oceans. Additionally, the data suggest that not only Arctic, but also Antarctic temperatures may be underestimated in simulations of ancient greenhouse climates by current generation fully coupled climate models. An early influx of abundant Apectodinium confirms that environmental change preceded the CIE on a global scale. Organic dinoflagellate cyst assemblages suggest a local decrease in the amount of river run off reaching the core site during the PETM, possibly in concert with eustatic rise. Moreover, the assemblages suggest changes in seasonality of the regional hydrological system and storm activity. Finally, significant variation in dinoflagellate cyst assemblages during the PETM indicates that southwest Pacific climates varied significantly over time scales of 103 – 104 years during this event, a finding comparable to similar studies of PETM successions from the New Jersey Shelf.
Landscape Dynamics of the Spread of Sudden Oak Death

plant community structure (Ristaino and Gumpertz, 2000; Sudden Oak Death is caused by a newly discovered virulent Lundquist and Klopfenstein, 2001). pathogen (Phytophthora ramorum) that is killing thousands We present a landscape-scale study of the spatio-temporal of native oak trees in California. We present a landscape-scale dynamics of SuddenOak Death (SOD), analarming disease that study on the spatio-temporal dynamics of oak mortality. is killing thousands of native oak trees and tanoaks in the Coast Second-order spatial point-pattern analysis techniques Ranges of California and southwestern Oregon (McPherson et (Ripley’s K) were applied to the distribution of dead tree al., 2000; Garbelotto et al., 2001). Considerable progress has crowns (derived from high-resolution imagery) in Marin been made in the past year identifying host species and underCounty, California to determine the existence and scale of standing how this disease is related to other tree-killing dismortality clustering in two years (2000 and 2001). Both years showed clustering patterns between 100 and 300 m. A eases (Davidson et al., 2001; Davidson et al., 2002; Rizzo et al., classification tree model was developed to predict spatial 2002). However, we still do not know how the disease extends patterns of risk for oak mortality based on several landscape- its range across California’s landscape, and we have no ability scale variables. Proximity to forest edge was the most important to predictwhich stands of treesare at highrisk of infection.The explanatory factor, followed by topographic moisture index, objectives of this research are to proximity to trails, abundance of Umbellularia californica, and ● Determine the distribution and rate of oak mortality in the potential summer solar radiation. This research demonstrates study area; the utility of integrating remotely sensed imagery analysis with ● Determine the scale and extent to which the oak mortality is geographic information systems and spatial modeling for spatially clustered;
Properties of jets measured from tracks in proton-proton collisions at center-of-mass energy sqrt(s) = 7 TeV with the ATLAS detector

Jets are identified and their properties studied in center-of-mass energy sqrt(s) = 7 TeV proton-proton collisions at the Large Hadron Collider using charged particles measured by the ATLAS inner detector. Events are selected using a minimum bias trigger, allowing jets at very low transverse momentum to be observed and their characteristics in the transition to high-momentum fully perturbative jets to be studied. Jets are reconstructed using the anti-kt algorithm applied to charged particles with two radius parameter choices, 0.4 and 0.6. An inclusive charged jet transverse momentum cross section measurement from 4 GeV to 100 GeV is shown for four ranges in rapidity extending to 1.9 and corrected to charged particle-level truth jets. The transverse momenta and longitudinal momentum fractions of charged particles within jets are measured, along with the charged particle multiplicity and the particle density as a function of radial distance from the jet axis. Comparison of the data with the theoretical models implemented in existing tunings of Monte Carlo event generators indicates reasonable overall agreement between data and Monte Carlo. These comparisons are sensitive to Monte Carlo parton showering, hadronization, and soft physics models.
reduced prefrontal activation during verbal fluency task in chronic insomnia disorder: a multichannel near-infrared spectroscopy study

Purpose: Daytime complaints such as memory and attention deficits and failure to accomplish daily tasks are common in insomnia patients. However, objective psychological tests to detect cognitive impairment are equivocal. Neural function associated with cognitive performance may explain the discrepancy. The aim of this study was to investigate the hemodynamic response patterns of patients with chronic insomnia disorder (CID) using the noninvasive and low-cost functional neuroimaging technique of multichannel near-infrared spectroscopy (NIRS) in order to identify changes of neural function associated with cognitive performance. Patients and methods: Twenty-four CID patients and twenty-five healthy controls matched for age, right-hand dominance, educational level, and gender were examined during verbal fluency tasks (VFT) using NIRS. A covariance analysis was conducted to analyze differences of oxygenated hemoglobin (oxy-Hb) changes in prefrontal cortex (PFC) between the two groups and reduce the influence of the severity of depression. Pearson correlation coeffcients were calculated to examine the relationship between the oxy-Hb changes, with the severity of insomnia and depressive symptoms assessed by the Pittsburgh Sleep Quality Index (PSQI) and the Hamilton Rating Scale for Depression (HAMD). Results: The number of words generated during the VFT in CID groups showed no statistical differences with healthy controls. CID patients showed hypoactivation in the PFC during the cognitive task. In addition, we found that the function of left orbitofrontal cortex (OFC) during the VFT was significantly negatively correlated with the PSQI scores and the function of right dorsolateral PFC (DLPFC) was significantly negatively correlated with the HAMD scores. Conclusion: The present study detected dysfunctions in PFC in spite of intact performance which indicates the role of PFC in the neurophysiological underpinnings. Left OFC function is associated with insomnia symptoms and right DLPFC function is associated with depressive symptoms.
Tropical Pacific Ocean and the Madden-Julian Oscillation: Role of wind and buoyancy forcing

[1] A global ocean circulation model is used to examine the dynamical response of the tropical Pacific Ocean to forcing associated with the Madden-Julian Oscillation (MJO). Model sensitivity experiments first reveal that MJO-related changes in sea level are caused primarily by changes in wind stress. Further, the MJO-related changes in sea surface temperature (SST) are mainly caused by buoyancy (heat) flux in the Indian Ocean, by wind stress in the central tropical Pacific, and by both buoyancy flux and wind stress in the eastern tropical Pacific. Additional model sensitivity studies quantify the tropical Pacific Ocean response to MJO wind forcing. The simulations reveal that the subsurface temperature variations associated with the MJO propagate eastward along the thermocline and rise to the surface in the eastern Pacific. Zonal advection plays a dominant role in SST variation in the central Pacific; vertical advection plays an important role in the evolution of subsurface and surface temperatures in the eastern Pacific. Finally, it is shown that MJO wind forcing can rectify SST variations through nonlinear interactions of the intraseasonal variations of the zonal currents and the zonal SST gradient.