Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress.

BACKGROUND AND AIMS Genetic markers can be used in combination with ecophysiological crop models to predict the performance of genotypes. Crop models can estimate the contribution of individual markers to crop performance in given environments. The objectives of this study were to explore the use of crop models to design markers and virtual ideotypes for improving yields of rice (Oryza sativa) under drought stress. METHODS Using the model GECROS, crop yield was dissected into seven easily measured parameters. Loci for these parameters were identified for a rice population of 94 introgression lines (ILs) derived from two parents differing in drought tolerance. Marker-based values of ILs for each of these parameters were estimated from additive allele effects of the loci, and were fed to the model in order to simulate yields of the ILs grown under well-watered and drought conditions and in order to design virtual ideotypes for those conditions. KEY RESULTS To account for genotypic yield differences, it was necessary to parameterize the model for differences in an additional trait 'total crop nitrogen uptake' (Nmax) among the ILs. Genetic variation in Nmax had the most significant effect on yield; five other parameters also significantly influenced yield, but seed weight and leaf photosynthesis did not. Using the marker-based parameter values, GECROS also simulated yield variation among 251 recombinant inbred lines of the same parents. The model-based dissection approach detected more markers than the analysis using only yield per se. Model-based sensitivity analysis ranked all markers for their importance in determining yield differences among the ILs. Virtual ideotypes based on markers identified by modelling had 10-36 % more yield than those based on markers for yield per se. CONCLUSIONS This study outlines a genotype-to-phenotype approach that exploits the potential value of marker-based crop modelling in developing new plant types with high yields. The approach can provide more markers for selection programmes for specific environments whilst also allowing for prioritization. Crop modelling is thus a powerful tool for marker design for improved rice yields and for ideotyping under contrasting conditions.
Stem anteversion mismatch to the anatomical anteversion causes loss of periprosthetic bone density after THA

The short tapered-wedge stem is popular worldwide because it potentially preserves more bone stock during total hip arthroplasty (THA). However, stem version mismatch may affect physiological stress distribution. In this study, we analyzed the correlations between periprosthetic bone mineral density (BMD) changes and anteversion mismatch in patients who underwent THA using a short tapered-wedge stem. The study included 44 patients (44 joints) who underwent THA with a Tri-Lock stem. At baseline and at 6 and 24 months postoperatively, the BMDs in the seven Gruen zones were evaluated using dual-energy X-ray absorptiometry. BMD changes and stem alignment, that is, anteversion and stem anteversion mismatch to the anatomical canal anteversion, were analyzed. Significant negative correlations were found between BMD changes and absolute anteversion error in Gruen zones 1 and 7 at 6 and 24 months postoperatively (zone 1, 6M; RR= −0.48, p < 0.001) (zone 7, 6M; RR= −0.46, p = 0.002) (zone 1, 24M; RR= −0.47, p = 0.001) (zone 7, 24M; RR= −0.40, p = 0.007). We further demonstrated that excessive stem anteversion mismatch to the anatomical canal anteversion causes stem point contact with the cortical bone in the distal portion and affected proximal periprosthetic BMD loss after THA. We recommend that the native anatomical anteversion angle should be used as a reference for inserting the tapered-wedge stems.
Consolidation of soil under depth-dependent ramp load

This technical note presents a mathematical solution for the consolidation analysis of a soil layer with a change in vertical total stress that varies linearly with depth and time and then remains unchanged after a certain period of time. The solution is described in detail. Results are presented as figures and tables for practical applications.Key words: consolidation, pore-water pressure, average degree of consolidation, total stress, clay, soil.
Power exploration for embedded VLIW architectures

In this paper, we propose a system-level power exploration methodology for embedded VLIW architectures based on an instruction-level analysis. The instruction-level energy model targets a general pipeline scalar processor; several architectural parameters such as number and type of pipeline stages as well as average stall/latency cycles per instruction and inter-instruction effects are taken into account. The application of the proposed model to VLIW processors results intractable from the point of view of both spatial and temporal complexity (which grow exponentially w.r.t. the number of possible operations in the ISA). To reduce this complexity, the basic model has been extended by assuming that the energy associated with a long instruction is given by the sum of the energy associated with the single operations of the long instruction and the single pipeline stages. The instruction-level energy model has been applied to a simplified VLIW architecture to demonstrate the validity of the proposed approach.
Analysis of high‐throughput screening assays using cluster enrichment

In this paper, we describe the implementation and evaluation of a cluster‐based enrichment strategy to call hits from a high‐throughput screen using a typical cell‐based assay of 160,000 chemical compounds. Our focus is on statistical properties of the prospective design choices throughout the analysis, including how to choose the number of clusters for optimal power, the choice of test statistic, the significance thresholds for clusters and the activity threshold for candidate hits, how to rank selected hits for carry‐forward to the confirmation screen, and how to identify confirmed hits in a data‐driven manner. Whereas previously the literature has focused on choice of test statistic or chemical descriptors, our studies suggest that cluster size is the more important design choice. We recommend clusters to be ranked by enrichment odds ratio, not by p‐value. Our conceptually simple test statistic is seen to identify the same set of hits as more complex scoring methods proposed in the literature do. We prospectively confirm that such a cluster‐based approach can outperform the naive top X approach and estimate that we improved confirmation rates by about 31.5% from 813 using the top X approach to 1187 using our cluster‐based method. Copyright © 2012 John Wiley & Sons, Ltd.
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms

Kinases play central roles in signaling pathways and are promising therapeutic targets for many diseases. Designing selective kinase inhibitors is an emergent and challenging task, because kinases share an evolutionary conserved ATP-binding site. KIDFamMap (http://gemdock.life.nctu.edu.tw/KIDFamMap/) is the first database to explore kinase-inhibitor families (KIFs) and kinase-inhibitor-disease (KID) relationships for kinase inhibitor selectivity and mechanisms. This database includes 1208 KIFs, 962 KIDs, 55 603 kinase-inhibitor interactions (KIIs), 35 788 kinase inhibitors, 399 human protein kinases, 339 diseases and 638 disease allelic variants. Here, a KIF can be defined as follows: (i) the kinases in the KIF with significant sequence similarity, (ii) the inhibitors in the KIF with significant topology similarity and (iii) the KIIs in the KIF with significant interaction similarity. The KIIs within a KIF are often conserved on some consensus KIDFamMap anchors, which represent conserved interactions between the kinase subsites and consensus moieties of their inhibitors. Our experimental results reveal that the members of a KIF often possess similar inhibition profiles. The KIDFamMap anchors can reflect kinase conformations types, kinase functions and kinase inhibitor selectivity. We believe that KIDFamMap provides biological insights into kinase inhibitor selectivity and binding mechanisms.
A conserved open reading frame that overlaps the herpes simplex virus thymidine kinase gene is important for viral growth in cell culture

Of 18 mutants containing clustered point mutations within UL24 (an open reading frame that overlaps the herpes simplex virus thymidine kinase gene on the opposite strand), 15 formed small plaques and were substantially impaired for virus growth in cell culture. Mutations conferring the small plaque phenotype disrupt regions of UL24 that share considerable sequence similarity with open reading frames common to herpesviruses of mammals and birds. We infer that UL24 is expressed and important for virus growth in cell culture and suggest that possible effects on UL24 should be considered in studies of thymidine kinase-deficient mutants.
In Stent Restenosis Predictors after Carotid Artery Stenting

Purpose. The long-term efficacy of carotid artery stenting is debated. Predictors of stent restenosis are not fully investigated. Our aim was to assess the incidence of long term restenosis after CAS and to identify some predictors of restenosis. Methods. We retrospectively selected 189 treated patients and we obtained the survival Kaplan-Meier curves for overall survival, for freedom from stroke or death and from restenosis. To correlate clinical, radiological, and procedural variables to stent restenosis, an univariate analysis was performed while to determine independent predictors of restenosis, a multivariate analysis was applied. Results. At 1, 3, and 5 years, the cumulative overall survival rate was 98%, 94%, and 92% with a cumulative primary patency rate of 87%, 82.5%, and 82.5%. The percentage residual stenosis after CAS and multiple stents deployment were independent predictors of restenosis, while diabetes and tumors are suggestive but not significant predictors of restenosis. Conclusions. In our CAS experience, encouraging long-term results seem to derive from both neurological event free rate and restenosis incidence. Adequate recanalization of the treated vessel is important to limit the development of stent restenosis. Multiple stents deployment, and with less evidence, diabetes, or neoplasms has to be considered to facilitate restenosis.
Stochastic Convex Optimization with Bandit Feedback

This paper addresses the problem of minimizing a convex, Lipschitz function f over a convex, compact set χ under a stochastic bandit feedback model. In this model, the algorithm is allowed to observe noisy realizations of the function value f(x) at any query point x ∈ χ. We demonstrate a generalization of the ellipsoid algorithm that incurs O(poly (d) √T) regret. Since any algorithm has regret at least Ω(√T) on this problem, our algorithm is optimal in terms of the scaling with T.
Cytomegalovirus-induced mononucleosis in guinea pigs

The effects of cytomegalovirus (CMV) infection on hematopoietic and lymphoid tissues were studied in guinea pigs. Blood parameters, histopathology, and virus distribution in the bone marrow, spleen, lymph nodes, and thymus were assessed during primary nonlethal acute and chronic guinea pig CMV infection. Transient hematological changes comparable to those seen in human CMV mononucleosis were observed during acute infection. These included anemia and leukocytosis with atypical lymphocytes. Splenomegaly and stimulation of spleen and lymph node T- and B-cell areas were also noted. These changes occurred at the peak of virus recovery from all tissues tested, as well as from macrophages and B- and T- cell-enriched spleen subpopulations. Virus was cleared rapidly from blood and bone marrow; blood counts, spleen size, and histology returned to normal within 1 month after virus inoculation. However, guinea pigs failed to eliminate the virus completely from lymphoid tissues, since virus persisted in splenic macrophage and B-lymphocyte-enriched populations during chronic infection. The data suggest that CMV-infected mononuclear cells play a role in the establishment of generalized acute infection and virus persistence.
Soft-decision COVQ for Rayleigh-fading channels

A channel-optimized vector quantizer (COVQ) scheme that exploits the channel soft-decision information is proposed. The scheme is designed for stationary memoryless Gaussian and Gauss-Markov sources transmitted over BPSK-modulated Rayleigh-fading channels. It is demonstrated that substantial coding gains of 2-3 dB in channel signal-to-noise ratio (SNR) and 1-1.5 dB in source signal-to-distortion ratio (SDR) can be achieved over COVQ systems designed for discrete (hard-decision demodulated) channels.
Trends in sexually transmitted infections (other than HIV) in older people: analysis of data from an enhanced surveillance system

Objective: This study examines the distribution of selected sexually transmitted infections (STIs) in older people (aged ⩾45 years) attending genitourinary medicine (GUM) clinics in the West Midlands, UK. Methods: Analysis of data from the regional enhanced STI surveillance system for the period 1996–2003. Selected STIs were chlamydia, genital herpes, genital warts, gonorrhoea and syphilis. Results: Altogether, 4445 STI episodes were reported among older people during the study period. Between 1996 and 2003 older people accounted for 3.7% and 4.3%, respectively, of all GUM clinic attendances. The rate of STIs in older people more than doubled in 2003 compared with 1996 (p<0.0001). Rates for all five selected diagnoses were significantly higher in 2003 compared to 1996. A significantly increasing trend over time was seen overall (p<0.0001) and for each of the selected diagnoses. Overall, males and those aged 55–59 years of age were significantly more likely to be affected. Conclusions: This study provides evidence of significant increases in attendance at GUM clinics by older people. Although it is recognised that young people should remain the focus of sexual health programmes, the results indicate that sexual risk-taking behaviour is not confined to young people but also occurs among older people. There is therefore a need to develop and implement evidence-based multifaceted sexual health programmes that while aiming to reduce STI transmission among all age groups should include interventions aimed specifically at older people and address societal and healthcare attitudes, myths and assumptions about sexual activity among older people.
The influence of convection on the water isotopic composition of the TTL and tropical stratosphere

We present the first in situ measurements of HDO across the tropical tropopause, obtained by the ICOS and Hoxotope water isotope instruments during the CR-AVE and TC4 aircraft campaigns out of Costa Rica in winter and summer, respectively. We use these data to explore the role convection plays in delivering water to the tropical tropopause layer (TTL) and stratosphere. We find that isotopic ratios within the TTL are inconsistent with gradual ascent and dehydration by in-situ cirrus formation and suggest that convective ice lofting and evaporation play a strong role throughout the TTL. We use a convective influence model and a simple parameterized model of dehydration along back trajectories to demonstrate that the convective injection of isotopically heavy water can account for the predominant isotopic profile in the TTL. Air parcels with significantly enhanced water vapor and isotopic composition can be linked via trajectory analysis to specific convective events in the Western Tropical Pacific, Southern Pacific Ocean, and South America. Using a simple model of dehydration and hydration along trajectories we show that convection during the summertime TC4 campaign moistened the upper part of the TTL by as much as 2.0 ppmv water vapor. The results suggest that deep convection is significant for the moisture budget of the tropical near-tropopause region and must be included to fully model the dynamics and chemistry of the TTL and lower stratosphere. 1 School of Engineering and Applied Sciences, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, USA 2 NASA Ames Research Center, Moffett Field, CA, USA 3 BAERI, Sonoma, CA, USA 4 now at Geology and Planetary Sciences Division, California Institute of Technology, Pasadena, CA 5 now at NASA Goddard Space Flight Center, Greenbelt, MD 6 now at Department of Geophysical Sciences, University of Chicago, Chicago, IL
Analysis of load structures for current-mode logic

Integrated circuit technology allows load characteristics to be shaped to the requirements of a circuit. Because it is possible to claim advantages for a variety of loads, a computer-aided analysis is used to relate the transient characteristics of a current-mode logic circuit to its static load line. A variety of load lines have been studied and an integrated diode-clamped-type load structure appears to offer the best static and dynamic characteristics.
Automatic Configuration of Sequential Planning Portfolios

Sequential planning portfolios exploit the complementary strengths of different planners. Similarly, automated algorithm configuration tools can customize parameterized planning algorithms for a given type of tasks. Although some work has been done towards combining portfolios and algorithm configuration, the problem of automatically generating a sequential planning portfolio from a parameterized planner for a given type of tasks is still largely unsolved. Here, we present Cedalion, a conceptually simple approach for this problem that greedily searches for the pair of parameter configuration and runtime which, when appended to the current portfolio, maximizes portfolio improvement per additional runtime spent. We show theoretically that Cedalion yields portfolios provably within a constant factor of optimal for the training set distribution. We evaluate Cedalion empirically by applying it to construct sequential planning portfolios based on component planners from the highly parameterized Fast Downward (FD) framework. Results for a broad range of planning settings demonstrate that -- without any knowledge of planning or FD -- Cedalion constructs sequential FD portfolios that rival, and in some cases substantially outperform, manually-built FD portfolios.
Dissipation in the Baltic proper during winter stratification

[1] Profiles of dissipation rates and stratification between 10 and 120 m depth were measured with a loosely tethered profiler over a 9-day winter period in the Gotland Basin of the Baltic Sea. Supplementary measurements of current profiles were made with moored ADCPs. Temporal and spatial patterns of the stratification were observed by means of towed CTD. Shallow freshwater lenses in the surface mixed layer, mesoscale eddies, inertial oscillations, and inertial waves as part of the internal wave spectrum provided the marine physical environment for the small-scale turbulence. Two well-separated turbulence regimes were detected. The turbulence in the surface mixed layer was well correlated with the wind. The majority of the energy flux from the wind to the turbulent kinetic energy was dissipated within the surface mixed layer. A minor part of this flux was consumed by changes of the potential energy of the fresh water lenses. The penetration depth Hpen of the wind-driven turbulence into the weakly stratified surface mixed layer depended on the local wind speed (W10) as Hpen = cW103/2 Active erosion of the Baltic halocline by wind-driven turbulence is expected for wind speeds greater than 14 m/s. The turbulence in the strongly stratified interior of the water column was quite independent of the meteorological forcing at the sea surface. The integrated production of turbulent kinetic energy exceeded the energy loss of inertial oscillations in the surface layer suggesting additional energy sources which might have been provided by inertial wave radiation during geostrophic adjustment of coastal jets and mesoscale eddies. The averaged dissipation rate profile in the stratified part of the water column, best fitted by e ∝ EN, was different from the scaling of the dissipation in the thermocline of the ocean [Henyey et al., 1986]. The diapycnical mixing coefficient (Kv) was best fit by Kv = a0/N according to Stigebrandt [1987] with a0 ≈ 0.87 × 10−7 m2/s2. The diapycnal diffusivity estimated from the dissipation rate was lower than those estimated by the bulk method.
Seismic imaging of oceanic layer 2A between 9°30′N and 10°N on the East Pacific Rise from two‐ship wide‐aperture profiles

We analyze two-ship multichannel seismic wide aperture profiles (WAP) acquired on the East Pacific Rise (EPR) between 9°30′C and 10°N in May and June 1985. For offsets between 2 and 5 km, most of the WAP common depth point (CDP) gathers exhibit a strong retrograde, reflection-like seismic arrival that corresponds to rays turned within a very strong velocity gradient zone underlying the uppermost crustal layer 2A. Stacking of this postcritical arrival for hundreds of CDP gathers along the WAP lines yields remarkably clear, and virtually continuous, images of the bottom of layer 2A for several tens of kilometers along and across the EPR. An innovative combination of this image with others of the seafloor (SF) and of the axial magma chamber (AMC) provides an unusually clear composite picture of young upper crust. We combine these images with detailed seismic velocity information, also obtained from the CDP gathers, to achieve an accurate determination of the layer 2A thickness in the area. Along the EPR axis between 9°30°N and 10°N, layer 2A shows a relatively constant thickness between 100 and 150 m (80–120 ms two-way travel time). Across the axis, however, a line near 9°30′N indicates that layer 2A thickness rapidly increases by approximately a factor of 2 within 2–4 km of the axis and remains nearly constant afterwards. Thus the final thickness of layer 2A is attained before the development of large-scale tectonic faulting, strongly suggesting that the thickening of layer 2A away from the axis is due to successive episodes of volcanic activity increasing the thickness of the uppermost crustal section from the top, rather than tectonic fracturing lowering the uppermost crustal seismic velocities and pushing the bottom of layer 2A downwards as the crust moves away from the axis.
Differential feedback of MIMO channel correlation matrices based on geodesic curves

This paper proposes a differential quantization strategy to be used in the feedback link of a multi-input-multi-output (MIMO) communication system. This algorithm is applied to the channel correlation matrix exploiting geodesic curves and the intrinsic geometry of positive definite Hermitian matrices. Simulation results in the paper show that the proposed algorithm improves other techniques based on the direct quantization of the channel response matrix or the quantization of the subspace spanned by the strongest eigenmodes of the MIMO channel, i.e., Grassmannian based techniques. The main drawback of Grassmananian based algorithms is that the transmitter is constrained to apply a uniform power allocation among eigenmodes, which is not forced in the algorithm proposed in this paper.