Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of irrigation water quality on the microbiological safety of fresh vegetables

The bacteriological quality of the irrigation canal from Loskop Dam, the two rivers that feed it and vegetables (broccoli and cauliflower) in Mpumalanga, SA, were investigated with respect to aerobic colony counts, aerobic sporeformers, anaerobic sporeformers and the presence of coliforms, faecal coliforms, Escherichia coli, Salmonella spp, Listeria monocytogenes, intestinal Enterococci and Staphylococcus aureus. Physico-chemical parameters determined for the surface water were pH, turbidity and chemical oxygen demand (COD). There were significant differences in the levels of COD and turbidity in the two rivers and the canal and the results of the three water samples were higher than WHO and SA water guidelines. Aerobic bacteria, aerobic spore bacteria and anaerobic spore bacteria in the two rivers, the canal and the vegetables followed the same trend. However, the level of aerobic bacteria (3–4 log10 cfu/g/ml), aerobic spore bacteria (1.6 log10 cfu/g/ml) and anaerobic spore bacteria (1.5 log10 cfu/g/ml) in both water and on vegetables during the period of sampling was low. Levels of faecal coliforms and E. coli were higher than the WHO standard. S. aureus, intestinal Enterococci, Salmonella, L. monocytogenes were recovered from the two rivers and the canal. Apart from L. monocytogenes that was not recovered from cauliflower, all bacterial pathogens recovered from the surface water were recovered from the vegetables. These results show that the rivers may contribute to the contamination in the irrigation canal and that may be a possible pre-harvest source of contamination of broccoli and cauliflower, which may in turn constitute a health risk to consumers.
The Intergenerational Transmission of War

We study whether war service by one generation affects service by the next generation in later wars, in the context of the major US theaters of the 20th century. To identify a causal effect, we exploit the fact that general suitability for service implies that how close to age 21 an individual’s father happened to be at a time of war is a key determinant of the father’s likelihood of participation. We find that a father’s war service experience has a positive and significant effect on his son’s likelihood of service. We estimate an intergenerational transmission parameter of approximately 0.1, across all wars, and that each individual war had a substantial impact on service in those that followed. We find evidence consistent with cultural transmission of war service from fathers to sons, and with the presence of substitutability between this direct transmission and oblique transmission (from society at large). In contrast, father’s war service increases sons’ educational achievement and actually reduces the likelihood of military service outside of wartime, suggesting that the results cannot be explained by material incentives or broader occupational choice. Taken together, our results indicate that a history of wars helps countries overcome the collective action problem of getting citizens to volunteer for war service.
Crop emergence date determination from spectral data

Estimating the emergence of a given crop, such as wheat or barley, is proposed using an analytic method which relies on the hypothesis that in the region (lambda = 0.70-1.35 microns) a given crop, after emergence, has a unique spectral profile in time. If the crop emerges early or late, relative to a reference standard determined for a given segment, the profile is displaced but has the same shape. Therefore, given the crop specific constants of the reference profile and a sufficient number of Landsat observations of reflectivity at specific times, the emergence date of a field can be determined.
Integrated modeling of long-term vegetation and hydrologic dynamics in Rocky Mountain watersheds

iii PREFACE iv TABLE OF CONTENTS ix LIST OF TABLES xvii LIST OF FIGURES xxi LIST OF ACRONYMS xxvii CHAPTER 1: An Index of Landscape Disturbance Connectivity for Vegetation Dynamics in Rocky Mountain Watersheds 1 ABSTRACT 2 2 INTRODUCTION 3 METHODS 7 STUDY AREA DESCRIPTION 7 SITE SELECTION 8 MODEL DESCRIPTION 8 MODEL DATA 12 VEGETATION CHARACTERIZATION 14 SIMULATION STRATEGY 15 COMPARISON OF SIMULATION SCENARIOS 16 Comparison of Disturbance Process Distributions 17 Comparison of Disturbed Area Proportions 19
HCNet: a database of heart and calcium functional network

SUMMARY The Heart and Calcium functional Network (HCNet) database is a collection of functional gene modules calculated from the microarray data compendium available from the GEO database. It is a specialized database designed to assist experimentalists for cardiac calcium signaling research by providing the pre-calculated gene clusters and their potential correlation network in heart. In the current release of HCNet, 57 functional modules from 786 target genes obtained by a bi-clustering analysis of 381 microarray datasets are available. Detailed information of the clusters such as expression profiles, network diagrams is provided in two categories, heart-specific genes and heart-specific genes along with calcium toolkit genes. Overrepresented gene ontological categories and transcription factors in each cluster are also provided to infer the biological implications of the detected functional modules. AVAILABILITY HCNet is available at http://sbrg2.gist. ac.kr/hcnet.
Bimanual coordination: electrophysiological and psychophysical study.

This work combines psychophysical studies in humans and monkeys with neural recordings from monkeys, in an attempt to study the mechanisms of coordination and execution of bimanual movements. The results of our study suggest that bimanual movement is a different entity from unimanual movement. The notion that bimanual movement is planned as a whole may explain the “bimanual coupling” paradigm and “bimanual specific activity”, found previously in our lab. In addition, it leads to a more holistic view of motor planning problem, its preferences and restrictions. Using the non-structured scribbling task in humans, we demonstrated that both hands are naturally coupled when special restrictions are not imposed. We advanced one step further by showing that non-symmetric bimanual movement is unexpectedly hard to perform and requires special learning. These simple experiments revealed the existence of a common plan for both hands. In the center-out task in both humans and monkeys we continued to study the dynamics of inter-arm coupling and found that it is high even before movement starts, and that it gradually decreases towards the end of the movement. This type of dynamics supports the notion that according to the brain original blueprint the two arms are coupled and that decoupling occurs due to a separate proprio-receptive negative feedback to each arm. As a possible neural correlate to this phenomenon, we found in monkeys that the LFP cross-correlations are high before movement starts and decrease as the movement is performed. The time scales for the inter-arm coupling decrease and the LFP cross-correlation decrease were very similar. In the same center-out task we compared bimanual performance with the unimanual movement from which it is composed and showed that the bimanual movement does not have a higher reaction time (RT) then the unimanual one. Furthermore we demonstrated in monkeys that the preparatory neural activity is significantly longer for unimanual non-dominant movements and equal for the bimanual and unimanual dominant movements. These findings support the notion that bimanual movement is not a combination of unimanual ones. Supplementary motor area (SMA) lesion study in monkeys revealed some transient changes in behavior; followed by some compensatory changes in primary motor cortex (MI). We found that MI activity in the absence of SMA is involved in the control of both sides of the body. The present study indicates that each hemisphere has information about both arms. Under normal conditions, this control is most likely obscured by the inhibition imposed by SMA on MI. A comparison of right and left MI reveals that there are functional differences between the two sides of the brain. These differences are small and further research with a larger monkey database is required to substantiate our conclusions.
Synaptic and intrinsic mechanisms underlying development of cortical direction selectivity

Modifications of synaptic inputs and cell-intrinsic properties both contribute to neuronal plasticity and development. To better understand these mechanisms, we undertook an intracellular analysis of the development of direction selectivity in the ferret visual cortex, which occurs rapidly over a few days after eye opening. We found strong evidence of developmental changes in linear spatiotemporal receptive fields of simple cells, implying alterations in circuit inputs. Further, this receptive field plasticity was accompanied by increases in near-spike-threshold excitability and input-output gain that resulted in dramatically increased spiking responses in the experienced state. Increases in subthreshold membrane responses induced by the receptive field plasticity and the increased input-output spiking gain were both necessary to explain the elevated firing rates in experienced ferrets. These results demonstrate that cortical direction selectivity develops through a combination of plasticity in inputs and in cell-intrinsic properties.
Community Structure of Montane forest along the Altitudinal Gradient in Garhwal Himalaya, India

The present study was done in sub-tropical and temperate Himalayan Forest of Saikot Reserve Forest, Kedarnath forest division in Chamoli district of Uttarakhand to understand the community structure and effect of altitudinal variation on structure and composition of the vegetation and to record the floristic diversity of the plants in the study area. The study area was categorized into four forest types on the basis of vegetation analysis, plant association or plant composition surveys, viz (1) Chir-Pine forest, (2) pine-oak forest (3) oak-pine-forest (4) oak-mixed forest. In the floristic study, a total of 58 species were recorded. Of the 58 plant species, 21 were tree, 11 shrubs and 26 herbs. The Quercus leucotrichophora forest was experiencing serious threat owing to human pressure and severe invasion of Pinus roxburghii which leads to loss of oak forest and development of pine forest.
A Cluster Randomized Trial Evaluating the Efficacy of Patient Navigation in Improving Quality of Diagnostic Care for Patients with Breast or Colorectal Cancer Abnormalities

Background: This study examines efficacy of a lay patient navigation (PN) program aimed to reduce time between a cancer abnormality and definitive diagnosis among racially/ethnically diverse and medically underserved populations of Tampa Bay, Florida. Methods: Using a cluster randomized design, the study consisted of 11 clinics (six navigated; five control). Patients were navigated from time of a breast or colorectal abnormality to diagnostic resolution, and to completion of cancer treatment. Using a generalized mixed-effects model to assess intervention effects, we examined: (i) length of time between abnormality and definitive diagnosis, and (ii) receipt of definitive diagnosis within the 6-month minimum follow-up period. Results: A total of 1,267 patients participated (588 navigated; 679 control). We also included data from an additional 309 chart abstractions (139 navigated arm; 170 control arm) that assessed outcomes at baseline. PN did not have a significant effect on time to diagnostic resolution in multivariable analysis that adjusted for race-ethnicity, language, insurance status, marital status, and cancer site (P = 0.16). Although more navigated patients achieved diagnostic resolution by 180 days, results were not statistically significant (74.5% navigated vs. 68.5% control, P = 0.07). Conclusions: PN did not impact the overall time to completion of diagnostic care or the number of patients who reached diagnostic resolution of a cancer abnormality. Further evaluation of PN programs applied to other patient populations across the cancer continuum is necessary to gain a better perspective on its effectiveness. Impact: PN programs may not impact timely resolution of an abnormality suspicious of breast or colorectal cancer. Cancer Epidemiol Biomarkers Prev; 21(10); 1664–72. ©2012 AACR.
Interpretation of geoid anomalies in the contact zone between the East European Craton and the Palaeozoic Platform—II: Modelling of density in the lithospheric mantle

SUMMARY We present analysis of lateral variations of density in the upper mantle in the area of contact of the precambrian East European Craton (EEC) and the Palaeozoic Platform (PP) in Poland, obtained by analysis of the gravimetric geoid undulations. A precise 3-D density model of the crust in the study area down to a depth of 50 km, discussed in the first part of this paper (Majdanski et al., in press) did not explain all features of the observed geoid. This suggests that these features can be due to density inhomogeneities in the upper mantle. To estimate them, we performed inversion of a residual between the observed geoid and undulations caused by the 3-D density distribution in the crust. Basing on the assumption of local isostatic compensation and Pratt–Hayford isostasy model, the density distribution in the upper mantle was parametrized as a 40-km-thick layer located above the assumed compensation depth of 140 km and subdivided into irregular blocks. The boundaries of the blocks were defined according to boundaries of major tectonic units in the study area and position and shape of the most pronounced anomalies in the residual geoid. A series of sensitivity tests calculated for such density heterogeneities in the upper mantle showed that they can produce geoid undulations of the order of several metres. The density values in each unit were taken as model parameters for the inversion procedure, and inverse problem was solved using global optimization with constraints. The density variations in the upper mantle in the final model correlate well with the surface heat flow. This suggests that these variations can be due to diversity in mantle temperature. The Trans-European Suture Zone (TESZ), which is a major suture separating the EEC from the PP, is not observed as a distinct unit in the mantle. Instead, our study suggests continuation of the lithosphere of the EEC beneath the PP and confirms subdivision of the TESZ into terranes with distinctly different evolution. A simple calculation shows that condition of local isostatic equilibrium is almost achieved at the assumed compensation depth, with the exception of several small-scale units. However, different loads and mass deficiencies in the lithosphere are compensated at different depth levels. This proves that the lithosphere is alternation of mechanically strong and weak layers, both in the crust and upper mantle, and that different loads can be compensated at different depth. However, the total compensation of all lithospheric loads occurs in the upper mantle.
Posterior propriety and computation for the Cox regression model with applications to missing covariates

In this paper, we carry out an in-depth theoretical investigation of Bayesian inference for the Cox regression model. We establish necessary and sufficient conditions for posterior propriety of the regression coefficient, β, in Cox's partial likelihood, which can be obtained as the limiting marginal posterior distribution of β through the specification of a gamma process prior for the cumulative baseline hazard and a uniform improper prior for β. We also examine necessary and sufficient conditions for posterior propriety of the regression coefficients, β, using full likelihood Bayesian approaches in which a gamma process prior is specified for the cumulative baseline hazard. We examine characterisation of posterior propriety under completely observed data settings as well as for settings involving missing covariates. Latent variables are introduced to facilitate a straightforward Gibbs sampling scheme in the Bayesian computation. A real dataset is presented to illustrate the proposed methodology. Copyright 2006, Oxford University Press.
Cryo-EM structure of amyloid fibril formed by α-synuclein familial A53E mutation

Synucleinopathies, including Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple systems atrophy (MSA) have the same hallmark pathologic feature of misfolded αsynuclein protein accumulation in the brain. PD patients who carry α-syn familial mutations usually have an earlier onset and more severe clinical symptoms and pathology than sporadic PD patients who carry wild-type (WT) α-syn. Therefore, revealing the structural effect of α-syn hereditary mutations on the wild-type fibril structure can help us understand synucleinopathies’ structural basis. Here, we present a 3.38 Å cryo-electron microscopy structure of α-synuclein fibrils containing the hereditary A53E mutation. The A53E fibril is composed of a symmetrical fibril, and the interaction interface between wild-type (WT) and A53E is different. In the mutant, only two residues, 59 and 60 form the interaction interface. Furthermore, ThT results and cell experiments also found that the A53E mutation delayed the formation of the fibril both in vitro and in vivo. This implies that the A53E mutation changes the aggregation mechanism of α-syn and therefore exhibits different pathological characteristics.
Estimated Future Salinity in the Arabian Gulf, the Mediterranean Sea and the Red Sea Consequences of Brine Discharge from Desalination

Seawater desalination constitutes an important source for water supply to the population bordering the Arabian Gulf, the Mediterranean Sea, and the Red Sea. The three regions represent about 11.8% of the world land area and the countries hosted approximately 9% of the world population in 1950 and 2008 and are projected to do so again in 2050. Population statistics for a 100-year period has been used including a prognosis from 2010 to 2050. Data on desalination plant capacity covering 12 years from 1996 to 2008 has been summarized and a prognosis of the increase in desalination for the three regions until 2050 developed. The results obtained for desalination capacity in the study area were 62%, 58%, and 60% of the world capacity for 1996, 2008, and 2050, respectively. The increase in the recovery ratio is considered an important factor in this study. In 1996 this ratio was about 30 to 35%, and in 2008 it was 40 to 45%, although in some plants it reached up to 50%. Brine discharge will increase the salinities of the Arabian Gulf, Mediterranean Sea, and Red Sea, by some extra 2.24, 0.81 and 1.16 g/l in the year 2050. (Less)
Icy rivers heating up : Modelling hydrological impacts of climate change in the (sub)arctic

The Arctic is considered to be particularly sensitive to global climate change. Global warming will seriously affect the components of the water balance in northern regions and changes in precipitation and temperature have immediate as well as long term effects on river systems. The main goal of this thesis was to assess the potential impact of climate change on the water balance and river discharge in the (sub)arctic Usa basin, East-European Russia on an annual, monthly and 5-daily basis. This enables the evaluation of 1) annual changes in the amount of river flow, 2) variations in timing and magnitude of discharge in various seasons, and 3) short-term responses in discharge to extreme events. To achieve these objectives a model is created with a monthly resolution for runoff simulation on seasonal scale (USAFLOW-1 and USAFLOW-2) and a model with a 5-daily resolution for the assessment of weekly runoff (USAFLOW-V). The models make optimal use of the available input data, have a model structure in which relevant processes are more adequately represented, and use parameters that are believed to be valid under present-day and future climate change conditions. The high sensitivity of the Arctic implies that impact of climate change and related environmental changes on river discharge can be considerable. The study shows that discharge in the Usa basin is highly sensitive to changes in precipitation and temperature. The effect of precipitation change is present throughout the year, while temperature changes affect discharge only in seasons when temperature fluctuates around the freezing point (April and October). Discharge is rather insensitive to changes in vegetation and permafrost. The impact study shows that annual discharge increases with up to 40% due to global warming. In case of a temperature increase of more than 8°C the (sub)arctic nival regime may give way to a pluvial discharge regime. The effects of climate change may be nonlinear and snowmelt runoff either increases or decreases depending on the amount of snowfall. In areas where the start of the snowmelt season is characterised by a rapid transition from temperatures far below the freezing point to far above the freezing point, snowmelt occurs far more rapidly, but timing of snowmelt runoff is only slightly affected. In areas where this transition is far more gradual, the snowmelt runoff peak shifts back in time, but snowmelt runoff may be extended over a longer period. In the Usa basin, the amount of snowfall is simulated to remain similar if climate changes, but in areas where snowmelt becomes more rapid peak flow could increase and consequently floods will be more abundant. The increase in discharge for the Usa basin will increase the availability of water for industrial and domestic purposes in seasons that have limited water available at present (for example the winter season). Furthermore, a more even distribution of discharge throughout the year will be beneficial for inland navigation.
Digested disorder

The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a “Digested Disorder” project and represent a series of reader’s digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.