Miracle-dz/UniFAR-FTUs huggingface dataset:
Geofold: Topology‐based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability

Protein unfolding is modeled as an ensemble of pathways, where each step in each pathway is the addition of one topologically possible conformational degree of freedom. Starting with a known protein structure, GeoFold hierarchically partitions (cuts) the native structure into substructures using revolute joints and translations. The energy of each cut and its activation barrier are calculated using buried solvent accessible surface area, side chain entropy, hydrogen bonding, buried cavities, and backbone degrees of freedom. A directed acyclic graph is constructed from the cuts, representing a network of simultaneous equilibria. Finite difference simulations on this graph simulate native unfolding pathways. Experimentally observed changes in the unfolding rates for disulfide mutants of barnase, T4 lysozyme, dihydrofolate reductase, and factor for inversion stimulation were qualitatively reproduced in these simulations. Detailed unfolding pathways for each case explain the effects of changes in the chain topology on the folding energy landscape. GeoFold is a useful tool for the inference of the effects of disulfide engineering on the energy landscape of protein unfolding. Proteins 2011. © 2012 Wiley Periodicals, Inc.
The Effect of Surface Soil Moisture on Heat Balance at a Bare Soil Surface

Surface soil moisture content, surface heat fluxes and meteorological data were measured simultaneously on a bare field to investigate the effect of surface soil moisture on the heat balance at a bare soil surface. A simple heat balance model for a bare soil surface was constructed, including empirical expressions of parameters (albedo, atmospheric emissivity, ratio G to Rn, aerodynamic resistance and soil resistance) which were determined from the measured data at 9 a.m., as it is difficult to evaluate the effect directly from the measured data. By calculation using this model, the relationship between the volumetric soil moisture content within the top 2cm layer and the surface heat balance under a given meteorological condition was clarified.
Monitoring and modeling primary production in coastal waters: Monitoring and modeling primary production in coastal waters: studies in Massachusetts Bay 1992-1994 studies in Massachusetts Bay 1992-1994

During 1992-1994, we made shipboard incubations su~table for determining rates of primary production in water from Boston Harbor, Massachusetts Bay, and Cape Cod Bay (Massachusetts, USA). These measurements were part of an extensive baseline monitoring program to characterize water quahty prior to divel-s~on of effluent from Boston Harbor directly into Massachusetts Bay via a sub-marine outfall diffuser. Production (P) was measured using whole-water samples exposed to irradiance (0 levels from -5 to 2000 pE m-' S-' P-Iincubations were performed on 6 surveys a year, spaced to capture principal features of the annual production cycle. The number of stations and depths examined varied between years. There were 10 stations and 2 depths sampled in 1992-1993. In 1994. we performed in-depth studies at 2 stations (Boston Harbor's edge and western Massachusetts Bay) hy sampling 4 depths. Using depth-intensive 1994 data a simple empirical regression model, using information on chlorophyll biomass, incident daily light, and the depth of the photic zone, predicted integrated primary production rates derived from P-lincubations. The regression model was virtually the same as described for other coastal waters, giv~ng confidence in general use of the model as an extrapolation tool. Using the 1994-based empirical model. \41e obtained favorable comparisons with production rates modeled from 1992-1993 P-I incubations. Combining the regression model with data on chlorophyll, light, and the photic zone collected on frequent hydrographic surveys (up to 16 y r ' ) , annual primary production was estimated for 1992-1994. Primary production in an intensively studied region of western Massachusetts Bay (21 hydrographic profile stations in an area -100 km2) ranged from 386 to 468 g C m-2 y r ' For a station at the edge of Boston Harbor near Deer Island extrapolations suggested production rates of 263 to 546 g C m-2 yr-' Based on 2 stat~ons in central Cape Cod Bay (1992-1993 only), model extrapolations suggested an annual production of 527 to 613 g C m-' )rr-' Analyses uslng ~ncubation and modeling results suggested that product~on variability was strongly related to fluctuations in incident irradiance, especially at daily to seasonal time scales. Chlorophyll variability secondarily influenced production, especially at seasonal to annual time scales. Finally, we provide a case where equ~valent production was achieved in environments 1~1th contrasting water quality (nutrient and chlorophyll concentrations) because of var~ations In the depth of the photic zone (controlled by both chlorophyll and non-chlorophyll turbidity). Con~parative analyses showed that our study estimates of primary production were consistent with the literature on nutrient-rich shelf environments. In conclusion, our study validated an empirical modeling approach to determining primary production in coastal marlne waters.
Advances in the Study of Evapotranspiration of Regional Land Surface Based on Remote Sensing Technology

The development of remote sensing technology provides a new means for the inversion and estimation of widespread land surface evapotranspiration(ET). Researchers both in China and abroad have already studied the theories and techniques of this field.The principle of energy balance is the basic theory of estimating land surface ET,which has led to the formulation of a lot of models and algorithms of remote sensing ET.Based on an analysis of basic principles as well as merits and shortcomings of several models,the authors expound the adaptability and progress of different methods,point out the existing problems of the study of remote sensing ET,and finally prospect the development trend of remote sensing ET.
EVALUATION OF THE SHEAR STRENGTH OF BEAM-COLUMN JOINTS OF REINFORCED CONCRETE FRAMES SUBJECTED TO EARTHQUAKE LOADING

Since 1967, when Hanson and Conner [1967] carried out the first seismic loading test on a beamcolumn joint of a reinforced concrete moment resisting frame, the importance of the design of beam-column joints has been recognised in the seismic design recommendations in different building standards. Recent earthquakes have strengthened the need for properly reinforcing beamcolumn joints to avoid partial or total structural collapse in large events and to avoid irreparable damage in moderate events. It is interesting to note that 30 years after the first test, and after a great deal of experimental work, recommendations for the design of beam-column joints in different design standards still have many discrepancies. This difference can be partly attributed to the difficulties in identifying the main parameters that affect the behaviour of joints.
Periprostatic fat tissue transcriptome reveals a signature diagnostic for 1 high-risk prostate cancer 2

1 Australian Prostate Cancer Research Centre Epworth, Richmond, Victoria, Australia 5 2 Department of Surgery, The University of Melbourne, Parkville, Victoria, Australia 6 3 Centre for Neural Engineering, Department of Computing and Information Systems, The University of 7 Melbourne, Parkville, Victoria, Australia 8 Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom 9 5 Diagnostic Genomics, NICTA, Victoria Research Laboratory, The University of Melbourne, Parkville, 10 Victoria, Australia 11 Division of Bioinformatics, Walter and Eliza Hall Institute, Parkville, Victoria, Australia 12 7 Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia 13 8 Department of Urology, Frankston Hospital, Frankston, Victoria, Australia 14 †These authors contributed equally to this work. 15 *Corresponding author 16 17 Corresponding Author 18 Dr Niall Corcoran 19 Department of Surgery, University of Melbourne, 5th Floor Clinical Sciences Building, 20 Royal Melbourne Hospital, Grattan Street, Parkville, Victoria, Australia. 21 Phone: 61-3-9342-7294 22 Fax: 61-3-9342-8928 23 E-mail: niallmcorcoran@gmail.com 24 25 26 Page 1 of 26 Accepted Preprint first posted on 28 March 2018 as Manuscript ERC-18-0058
Octrees for faster isosurface generation

The large size of many volume data . sets often prevent s visualization algorithms from providing interactive rendering . The use of hierarchical data str uctures can ameliorate this problem by storing summary information to prevent useless exploration of regions of' little o r no interest. within the volume . This extended abstract , discusses research into the use of the octree hierarchical data structure for this purpose . We introduc e a new space-efficient design for octree representation s of volumes whose dimensions are not conveniently a power of two : branch-on-need octrees (130NOs) . Usin g the application of octrees to isosurface generation as a focus, we present space and time comparisons for octreebased versus more traditional "marching" methods . A separate report gives details about the work stun marize d here [NV VG90a] . Octrees are hierarchical data structures based on recursive decomposition of space into (normally) eigh t subvolumes, where the root of the octree refers to the entire volume [\iea80, Sri81, Mea82, _ltea8d, MKIi'N87 . Sam90b, Sam90a] . They are a natural generalization o f quadtrees [KD76, War69], and have been found useful i n other 3-1) applications [1Vl\'V88, Wat89] . Bentley studied a generalization to k dimensions [Ben75j . Octrees are particularly appropriate for representing sampl e
A novel technique to incorporate structural prior information into multi-modal tomographic reconstruction

In this study, we aim to reconstruct single-photon emission computed tomography images using anatomical information from magnetic resonance imaging as a priori knowledge about the activity distribution. The trade-off between anatomical and emission data is one of the main concerns for such studies. In this work, we propose an anatomically driven anisotropic diffusion filter (ADADF) as a penalized maximum likelihood expectation maximization optimization framework. The ADADF method has improved edge-preserving denoising characteristics compared to other smoothing penalty terms based on quadratic and non-quadratic functions. The proposed method has an important ability to retain information which is absent in the anatomy. To make our approach more stable to the noise-edge classification problem, robust statistics have been employed. Comparison of the ADADF method is performed with a successful anatomically driven technique, namely, the Bowsher prior (BP). Quantitative assessment using simulated and clinical neuroreceptor volumetric data show the advantage of the ADADF over the BP. For the modelled data, the overall image resolution, the contrast, the signal-to-noise ratio and the ability to preserve important features in the data are all improved by using the proposed method. For clinical data, the contrast in the region of interest is significantly improved using the ADADF compared to the BP, while successfully eliminating noise. (Some figures may appear in colour only in the online journal)
The Natural History of Preclinical Diastolic Dysfunction: A Population-Based Study

Background—Preclinical diastolic dysfunction (PDD) has been broadly defined as subjects with left ventricular diastolic dysfunction, without the diagnosis of congestive heart failure (HF) and with normal systolic function. Our objective was to determine the risk factors associated with the progression from PDD (stage B) HF to symptomatic (stage C) HF. Methods and Results—Using the resources of the Rochester Epidemiology Project, all residents of Olmsted County, MN, who underwent echocardiography between January 1, 2004, and December 31, 2005, and had grade 2–4 diastolic dysfunction and ejection fraction ≥50% were identified. Patients with a diagnosis of HF before or within 30 days of the echocardiogram were excluded. Patients were also excluded if they had a diagnosis of atrial fibrillation or severe mitral or aortic valve regurgitation at the time of the echocardiogram. A total of 388 patients met the inclusion criteria. The mean age of the cohort was 67±12 years, with a female (57%) predominance. Prevalence of renal insufficiency (estimated glomerular filtration rate <60 mL/min per 1.73 m2) was 34%. The 3-year cumulative probabilities of development of (stage C) HF, development of atrial fibrillation, cardiac hospitalization, and mortality were 11.6%, 14.5%, 17.7%, and 10.1% respectively. In multivariable Cox proportional hazard regression analysis, we determined that age, renal dysfunction, and right ventricular systolic pressure were independently associated with the development of HF. Conclusions—This population-based study demonstrated that in PDD (stage B) HF, there was a moderate degree of progression to symptomatic (stage C) HF over 3 years, and renal dysfunction was associated with this progression independent of age, sex, hypertension, coronary disease, and ejection fraction.
4 Artificial Neural Networks for Material Identification , Mineralogy and Analytical Geochemistry Based on Laser-Induced Breakdown Spectroscopy

Artificial Neural Networks (ANN) are used nowadays in a broad range of areas such as pattern recognition, finances, data mining, battle scene analysis, process control, robotics, etc. Application of ANN in the field of spectroscopy has generated a long-standing interest of scientists, engineers and application specialists. The ANN’ capability of producing fast, reliable and accurate spectral data processing has become, in many cases, a bridging mechanism between science and application. A particular example of how ANN can transform plasma emission spectroscopy, that is quit challenging to model, into a turnkey ready to use device is described in this Chapter. Laser-Induced Breakdown Spectroscopy (LIBS) is a material-composition analytical technique gaining increased interest last decade in various application fields, such as geology, metallurgy, pharmaceutical, bio-medical, environmental, industrial process control and others (Cremer & Radziemski, 2006; Miziolek et al., 2006). It is in essence a spectroscopic analysis of light emitted by the hot plasma created on a sample by the laser-induced breakdown. LIBS offers numerous advantages as compared to the standard elemental analysis techniques (X-ray fluorescence or X-ray diffraction spectroscopy, inductively coupled plasma spectroscopy, etc.), such as: capability of remote analysis in the field, compact instrumentation, detection of all elements and high spatial resolution. Such features as minimum or no sample preparation requirement and dust mitigation using “cleaning“ laser shots are especially important for field geology and remotely operated rover-based instruments. As result, LIBS instruments have been selected as payloads for the 2011 Mars Science Laboratory mission led by the National Aeronautics and Space Administration (Lanza et al., 2010) and the ExoMars mission on Mars planned for 2018 and led by European Space Agency (Escudero-Sanz et al., 2008). Despite of the advantages, the main challenge is still the retrieval of accurate information from measured spectra. LIBS spectral signals, composed mostly of narrow emission lines, are complex nonlinear functions of concentrations of measured constituents and instrument
Scientific Papers of the University of Pardubice, Series D: Faculty of Economics and Administration

Community property is used primarily to carry out its tasks, this includes things belonging to the municipality and the property rights community. Of the Municipal System Act clearly discloses the fundamental principles governing the use of community assets, respectively. dealing with it. Each community has nurtured the assets, and enhance their overall value to maintain substantially unabated. These are the basic rules that must be met to ensure proper management of municipal property.
APPLICATION OF GREY SYNERGISTIC MODEL IN THE APPRAISAL OF REGIONAL WATER USE FOR INDUSTRY

Understanding the dynamic regular patterns of development of industry water use systems for different regions and the correlated relationships among them is the key step to realize water-saving society construction and sustainable utilization of water resource.Currently,the two-section linear models were usually employed to analyze the coordination of regional industry water use systems.However,it may not fit for describing the nonlinear structure of the regional industry water use systems.Hence,a grey synergistic model,which is well adaptive to nonlinear characteristic of the industry water use system,was established based on the theory of grey.The model was applied to the industry water use system in Shanghai from 1997 to 2005.The results showed that coordination degree of industry water use system of shanghai is basically favorable.But there still exists some space for promotion of water use system in Shanghai area,especially for the agriculture sub-system to which more attention should be paid to when planning the industry water use in the future.
Case Study: Application of the HEC-6 MOdel for the Main Stem of the Kankakee River in Illinois

This case study paper presents results on the application of the HEC-6 model to the main stem of the Kankakee River in Illinois, a distance of about 39.3 km. Modeling was performed to develop comprehensive plans for enhancing the aquatic habitats and also to forecast future sedimentation problems if specific management practices are implemented. The paper concentrates on the modeling aspects of this research. The extent of the model was from the Stateline Bridge to Kankakee Dam in Kankakee. The HEC-6 model, originally developed by the Hydrologic Engineering Center (HEC) of the U.S. Army Corps of Engineers, was adapted for this application. The model was run, calibrated, and verified for both the hydraulic and sediment components. The hydraulic component was calibrated through comparison of measured yearly hydrographs with computed values for three gauging stations on the river. The hydrologic component was verified for the same three gauging stations for two yearly hydrographs for 2 additional water years. The sediment component was calibrated with river cross-sectional data collected by the Illinois State Water Survey in 1980 and 1999. The calibrated and verified hydraulic and calibrated sediment components then were used to predict future changes in water surface elevations and thalweg elevations for a 20-year period beginning in 1999, the last date for which river cross-sectional data are available.
Association Between Years of Experience and Ankle Joint Disorder in Male Student Basketball Players Based on Ultrasonography

Inversion sprain of the ankle joint occurs frequently in basketball players and lateral ligament injuries of the ankle joint account for 45 % of all traumas in basketball [1, 2]. Of these injuries, the incidence of anterior talofibular ligament injury is the highest [3], and this is the primary cause of lateral instability of the ankle joint, for which concomitant occurrence of osteochondral injury in the talocrural joint region is of concern [4–6]. McKay reported the rate of ankle injury and risk factors of ankle injuries in basketball players. The chronic ankle symptoms were as high as 74 % [7]. Turner et al. reported physical activity levels in college students who have chronic ankle instability were decreased in comparison to the healthy group [8]. It is important to prevent these pathological conditions from developing, so children should be trained correctly from a young age [8, 9]. The repair process of osteochondral injury and impacts between bones in the talocrural joint due to frequent sprains promote osteophyte formation and may cause pain and restriction of the range of motion [10–12]. Persistence of this condition may induce osteoarthrosis of the ankle and markedly reduce ADL. It has also recently been reported that ankle joint sprain may be a risk factor for anterior cruciate ligament injury of the knee [13]. Therefore, prevention of this pathological condition is important because it may trigger a disorder-trauma chain in athletes. However, understanding of the actual state of ankle joint disorder and its prevention is insufficient in student players. Moreover, medical care for student players is limited compared to that for professional and national sports teams. Thorough medical checkups of the joint should be performed for student players who are immature physically, and this may promote the development of promising players with reduced disorders. With this background, we used a team approach including an orthopedist expert in ultrasonography diagnosis for musculoskeletal sports injuries, athletic trainers and physical therapists for Original Article
SCIENTIFIC PAPERS OF THE UNIVERSITY OF PARDUBICE

Environmental Management Accounting (EMA) is considered to be a system providing information to support decision-making mainly within the framework of environmental management. EMA includes also Environmental Cost Accounting which uses an extensive range of methods. Of major significance for the management of corporate processes are primarily the methods based on material and energy flows. The paper focuses on Material Flow Cost Accounting (MFCA). It characterizes MFCA not only as a tool of environmental management, but mainly as a tool for the management of material flows and points out the
Technological Change and the Environment Robert N. Stavins the Handbook of Environmental Economics Technological Change and the Environment

Environmental policy discussions increasingly focus on issues related to technological change. This is partly because the environmental consequences of social activity are frequently affected by the rate and direction of technological change, and partly because environmental policy interventions can themselves create constraints and incentives that have significant effects on the path of technological progress. This paper, prepared as a chapter draft for the forthcoming Handbook of Environmental Economics (North-Holland/Elsevier Science), summarizes current thinking on technological change in the broader economics literature, surveys the growing economic literature on the interaction between technology and the environment, and explores the normative implications of these analyses. We begin with a brief overview of the economics of technological change, and then examine theory and empirical evidence on invention, innovation, and diffusion and the related literature on the effects of environmental policy on the creation of new, environmentally friendly technology. We conclude with suggestions for further research on technological change and the environment.