Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the sustainability of deep groundwater as an arsenic-safe resource in the Bengal Basin

Tens of millions of people in the Bengal Basin region of Bangladesh and India drink groundwater containing unsafe concentrations of arsenic. This high-arsenic groundwater is produced from shallow (<100 m) depths by domestic and irrigation wells in the Bengal Basin aquifer system. The government of Bangladesh has begun to install wells to depths of >150 m where groundwater arsenic concentrations are nearly uniformly low, and many more wells are needed, however, the sustainability of deep, arsenic-safe groundwater has not been previously assessed. Deeper pumping could induce downward migration of dissolved arsenic, permanently destroying the deep resource. Here, it is shown, through quantitative, large-scale hydrogeologic analysis and simulation of the entire basin, that the deeper part of the aquifer system may provide a sustainable source of arsenic-safe water if its utilization is limited to domestic supply. Simulations provide two explanations for this result: deep domestic pumping only slightly perturbs the deep groundwater flow system, and substantial shallow pumping for irrigation forms a hydraulic barrier that protects deeper resources from shallow arsenic sources. Additional analysis indicates that this simple management approach could provide arsenic-safe drinking water to >90% of the arsenic-impacted region over a 1,000-year timescale. This insight may assist water-resources managers in alleviating one of the world's largest groundwater contamination problems.
Interferon Resistance of Hepatitis C Virus Genotype 1b: Relationship to Nonstructural 5A Gene Quasispecies Mutations

ABSTRACT A 40-amino-acid sequence located in the nonstructural 5A (NS5A) protein of hepatitis C virus genotype 1b (HCV-1b) was recently suggested to be the interferon sensitivity-determining region (ISDR), because HCV-1b strains with an ISDR amino acid sequence identical to that of the prototype strain HCV-J were found to be resistant to alpha interferon (IFN-α) whereas strains with amino acid substitutions were found to be sensitive (N. Enomoto, I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, N. Izumi, F. Marumo, and C. Sato, J. Clin. Invest. 96:224–230, 1995; N. Enomoto, I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, Y. Ogura, N. Izumi, F. Marumo, and C. Sato, N. Engl. J. Med. 334:77–81, 1996). We used single-strand conformation polymorphism (SSCP) analysis, combined with cloning and sequencing strategies, to characterize NS5A quasispecies in HCV-1b-infected patients and determine the relationships between pre- and posttreatment NS5A quasispecies mutations and the IFN-α sensitivity of HCV-1b. The serine residues involved in phosphorylation of NS5A protein were highly conserved both in the various patients and in quasispecies in a given patient, suggesting that phosphorylation is important in NS5A protein function. A hot spot for amino acid substitutions was found at positions 2217 to 2218; it could be the result of either strong selection pressure or tolerance to these amino acid replacements. The proportion of synonymous mutations was significantly higher than the proportion of nonsynonymous mutations, suggesting that genetic variability in the region studied was the result of high mutation rates and viral replication kinetics rather than of positive selection. Sustained HCV RNA clearance was associated with low viral load and low nucleotide sequence entropy, suggesting (i) that the replication kinetics when treatment is started plays a critical role in HCV-1b sensitivity to IFN-α and (ii) that HCV-1b resistance to IFN-α could be conferred by numerous and/or related mutations that could be patient specific and located at different positions throughout the viral genome and could allow escape variants to be selected by IFN-α-stimulated immune responses. No NS5A sequence appeared to be intrinsically resistant or sensitive to IFN-α, but the HCV-J sequence was significantly more frequent in nonresponder quasispecies than in sustained virological responder quasispecies, suggesting that the balance between NS5A quasispecies sequences in infected patients could have a subtle regulatory influence on HCV replication.
Seasonal Rearing Habitat in a Large Mediterranean‐Climate River: Management Implications at the Southern Extent of Pacific Salmon (Oncorhynchus spp.)

Pacific salmon (Oncorhynchus) use a variety of rearing environments prior to seaward migration, yet large river habitats and their use have not been well defined, particularly at the southernmost salmon range where major landscape‐level alterations have occurred. We explored juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) presence along the river continuum and in main‐channel and off‐channel habitats of a regulated California Mediterranean‐climate river. Over an 8‐year period, off‐channels of the lower Mokelumne River exhibited slower and warmer water than the main‐channel. Probability of salmonid presence varied by stream reach and habitat types. Steelhead and Chinook salmon both demonstrated transitional responses to the dry season, with juveniles leaving off‐channels by midsummer. This corresponded to flow recession, increasing water temperatures, salmonid growth and end of emigration period. Main‐channel steelhead observations continued until the following storm season, which brought cool flood flows to reconnect off‐channels and the next juvenile cohort of both species to the river. Within arid climates, low‐gradient off‐channels appear more transiently used than in cooler and more northern humid climate systems. Within a highly regulated Mediterranean‐climate river, off‐channel habitats become increasingly scarce, disconnected or temperature limiting in low‐gradient reaches both seasonally and due to anthropogenic modifications. These observations may provide guidance for future management within large salmon streams. Copyright © 2015 John Wiley & Sons, Ltd.
Diagnosing the Sensitivity of Local Land–Atmosphere Coupling via the Soil Moisture–Boundary Layer Interaction

AbstractThe inherent coupled nature of earth’s energy and water cycles places significant importance on the proper representation and diagnosis of land–atmosphere (LA) interactions in hydrometeorological prediction models. However, the precise nature of the soil moisture–precipitation relationship at the local scale is largely determined by a series of nonlinear processes and feedbacks that are difficult to quantify. To quantify the strength of the local LA coupling (LoCo), this process chain must be considered both in full and as individual components through their relationships and sensitivities. To address this, recent modeling and diagnostic studies have been extended to 1) quantify the processes governing LoCo utilizing the thermodynamic properties of mixing diagrams, and 2) diagnose the sensitivity of coupled systems, including clouds and moist processes, to perturbations in soil moisture. This work employs NASA’s Land Information System (LIS) coupled to the Weather Research and Forecasting (WRF) me.
Collision risk modeling of air traffic

Air Traffic Management (ATM) involves interactions between multiple human operators, procedures and technical systems, all of which are highly distributed. This yields that providing safety is more than making sure that each of the ATM elements functions properly safe; it is the complex interaction between them that determines safety. The assessment of isolated indicators falls short in covering the complex interactions between procedures, human operators and technical systems in safety-critical non-nominal situations. To improve this situation, this paper develops an approach towards the modelling and assessment of risk of mid-air collision between aircraft.
Reciprocal Responses in the Interaction between Arabidopsis and the Cell-Content-Feeding Chelicerate Herbivore Spider Mite1[W][OPEN]

Analysis of genome-wide Arabidopsis responses to spider mite identifies the secondary metabolites that limit the mite's ability to use Arabidopsis as a host. Most molecular-genetic studies of plant defense responses to arthropod herbivores have focused on insects. However, plant-feeding mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g. lepidopteran larvae or aphids). The two-spotted spider mite (Tetranychus urticae) is among the most significant mite pests in agriculture, feeding on a staggering number of plant hosts. To understand the interactions between spider mite and a plant at the molecular level, we examined reciprocal genome-wide responses of mites and its host Arabidopsis (Arabidopsis thaliana). Despite differences in feeding guilds, we found that transcriptional responses of Arabidopsis to mite herbivory resembled those observed for lepidopteran herbivores. Mutant analysis of induced plant defense pathways showed functionally that only a subset of induced programs, including jasmonic acid signaling and biosynthesis of indole glucosinolates, are central to Arabidopsis’s defense to mite herbivory. On the herbivore side, indole glucosinolates dramatically increased mite mortality and development times. We identified an indole glucosinolate dose-dependent increase in the number of differentially expressed mite genes belonging to pathways associated with detoxification of xenobiotics. This demonstrates that spider mite is sensitive to Arabidopsis defenses that have also been associated with the deterrence of insect herbivores that are very distantly related to chelicerates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.
Lipid Accumulation in an Oleaginous Yeast (Candida 107) Growing on Glucose Under Various Conditions in a One- and Two-Stage Continuous Culture

Lipid accumulation and fatty acid composition in Candida 107 have been studied using a two-stage continuous culture system in which the first vessel was run under carbon-limited conditions and then the entire output was passed into a second vessel, where lipid accumulation was stimulated by adding only glucose. Maximum lipid accumulation (28% of yeast [dry weight]) occurred for a volume ratio of vessel 1 to vessel 2 of 3:5, with 30 g of glucose per liter being added to vessel 2 operated at 25°C with an aeration rate of between 0.1 and 1.0 volume of air/volume of medium per min. Although the maximum specific rate of lipid formation (0.05 g of lipid/g of yeast per h) was higher than in a nitrogen-limited, single-stage system, the efficiency of lipid formation was much less and never exceeded 14 g of lipid produced per 100 g of glucose consumed. The fatty acid composition was not significantly altered in either the two-stage or single-stage culture (nitrogen-limited) systems by changes in growth temperature (from 19 to 33°C) or aeration rates (0.05 to 1.0 volume of air/volume of medium per min); or, in the two-stage system, by changes in the residence time of the yeast in the second vessel (from 3.2 to 24.4 h), or, in the single-stage system, by changes in pH (from 3.5 to 7.5). Only when the concentration of glucose entering vessel 2 of the two-stage system was less than 30 g/liter did significant changes in the fatty acids occur. Thus, although a two-stage continuous culture system allows lipid accumulation to be separated from the growth phase, it offers no practical advantages over a single-stage system as a means of producing microbial oils and fats.
Parallel development of orientation maps and spatial frequency selectivity in cat visual cortex

In an early stage of the postnatal development of cats, orientation maps mature and spatial frequency selectivity is consolidated. To investigate the time course of orientation map maturation associated with the consolidation of spatial frequency selectivity, we performed optical imaging of intrinsic signals in areas 17 and 18 of cats under the stimulation of drifting square‐wave gratings with different orientations and spatial frequencies. First, orientation maps for lower spatial frequencies emerged in the entire part of the lateral gyrus, which includes areas 17 and 18, and then these orientation maps in the posterior part of the lateral gyrus disappeared as orientation maps for higher spatial frequencies matured. Independent of age, an anteroposterior gradient of response strengths from lower to higher spatial frequencies was observed. This indicates that the regional distribution of spatial frequencies is innately determined. The size of iso‐orientation domains tended to decrease as the stimulus spatial frequency increased at every age examined. In contrast, orientation representation bias changed with age. In cats younger than 3 months, the cardinal (vertical and horizontal) orientations were represented predominantly over the oblique orientations. However, in young adult cats from 3 to 9 months old, the representation bias switched to predominantly oblique orientations. These age‐dependent changes in the orientation representation bias imply that orientation maps continue to elaborate within postnatal 1 year with the consolidation of spatial frequency selectivity. We conclude that both intrinsic and mutual factors lead to the development of orientation maps and spatial frequency selectivity.
Integrating 3D seismic curvature and curvature gradient attributes for fracture characterization: Methodologies and interpretational implications

ABSTRACTIn 3D seismic interpretation, curvature is a popular attribute that depicts the geometry of seismic reflectors and has been widely used to detect faults in the subsurface; however, it provides only part of the solutions to subsurface structure analysis. This study extends the curvature algorithm to a new curvature gradient algorithm and integrates both algorithms for fracture detection using a 3D seismic test data set over Teapot Dome (Wyoming). In fractured reservoirs at Teapot Dome formed by tectonic folding and faulting, curvature helps define the crestal portion of reservoirs that is associated with strong seismic amplitude and high oil productivity. In contrast, curvature gradient helps define the regional northwest-trending and the cross-regional northeast-trending lineaments that are associated with weak seismic amplitude and low oil productivity. In concert with previous reports from image logs, cores, and outcrops, an integrated seismic curvature and curvature gradient analysis suggests t.
Genetics of Arterial Prothrombotic Risk States

Coronary artery disease is a leading cause of death worldwide and the largest killer of men and women in the United States. The pathophysiology of myocardial infarction is multifactorial, and numerous physiologic systems converge to dictate the formation of the two fundamental lesions, thrombosis and atherosclerosis. In this review we address genetic aspects of arterial thrombosis and the key thrombotic factors that have been associated with the increased risk for its development. Specifically, we consider components of coagulation, fibrinolysis, and Platelet adhesive receptors, and we review the genetic epidemiology and in vitro laboratory data regarding their risk for the acute coronary syndromes. In combination with traditional risk factor assessment, in the near future these inherited markers can be used to manage patients with vascular disease through a better utilization of invasive or expensive diagnostic testing, as well as pharmacologic intervention.
Low-income Groups and Behaviour Change Interventions: A review of intervention content and effectiveness

This is the second paper in a series, Kicking Bad Habits, on how people can be encouraged to adopt healthy behaviour. Looking at interventions targeted specifically at low-income groups, this paper asks which interventions are effective in getting people to quit smoking, eat healthily and exercise. It reveals that the most frequently used techniques are providing information and encouraging people to set goals, which can be particularly effective at changing behaviour in disadvantaged groups.
Microleakage of different root canal obturation techniques

Summary Leakage examination was performed using fluid transport system measuring movement of an air bubble. Tested techniques were cold lat- eral condensation technique, Touchn Heat and Thermafil technique. Root canals were obturated with gutta-percha in combination with AH Plus and RoekoSeal sealers. After storing in saline solution, microleak- age was measured in intervals of one month, six months and one year. The minimum microleakage values were obtained in all intervals in canals obturated using cold lateral condensation technique, while max- imum values were obtained in Thermafil technique (p< 0.05). Signifi- cantly more leakage was found for all tested techniques in the interval of 12 months after obturation (p< 0.05). There was no difference between obturation quality between RoekoSeal and AH Plus, no mat- ter what obturation technique was used.
Biologically Unavoidable Sequences

A biologically unavoidable sequence is an infinite gender sequence which occurs in every gendered, infinite genealogical network satisfying certain tame conditions. We show that every eventually periodic sequence is biologically unavoidable (this generalizes Koenig's Lemma), and we exhibit some biologically avoidable sequences. Finally we give an application of unavoidable sequences to cellular automata.
Effect of Distillers Grains or Corn Supplementation Frequency on Forage Intake and Digestibility 1

Ten ruminally cannulated heifers (BW = 416 kg; SD = 24) were used to test the effect of the form and frequency of supplemental energy on forage DMI and digestibility. Five treatments were arranged in a replicated, 5 × 4 Latin rectangle (n = 8), and included no supplement (control), dry-rolled corn (DRC) fed daily, DRC fed on alternate days (DRC-A), dried distillers grains plus solubles (DDGS) fed daily, and DDGS fed on alternate days (DDGS-A). Supplements fed daily were fed at 0.40% of BW, whereas alternate day-fed supplements were fed at 0.80% of BW every other day. Chopped grass hay (8.2% CP) was fed to allow ad libitum DMI, and the intake pattern was measured. Control heifers had greater (P < 0.01) hay DMI than supplemented heifers (1.88 vs. 1.66% of BW daily, respectively), although total DMI was lower (P < 0.01) for control. Hay DMI did not differ (P = 0.45)
A Characterization of Quality-Adjusted Life-Years Under Cumulative Prospect Theory

Quality-adjusted life-years (QALYs) are the most common utility measure in medical decision analysis and economic evaluations of health care. This paper presents an axiomatization of QALYs under cumulative prospect theory (CPT), currently the most influential model for decision under uncertainty. Because the set of health states need not be endowed with a natural topology that is connected, we first show how existing CPT characterizations can be extended to a class of outcome sets for which no connected natural topology is given. We then characterize QALY models with linear, power, and exponential utility for duration. Finally, we define loss aversion for multiattribute utility theory and characterize the QALY models under general and constant loss aversion. The measurement of QALYs belongs to the general field of multiattribute utility theory. Hence, our results can be generalized to other multiattribute decision contexts and they thereby contribute to the development of multiattribute utility theory under cumulative prospect theory.
The representation of stimulus familiarity in anterior inferior temporal cortex.

1. The inferior temporal (IT) cortex plays an important role in both short- and long-term memory for visual patterns. Most previous studies of IT neurons have tested their responses in recency memory tasks, which require that the memory lasts only the length of a single behavioral trial, which may be < 1 s. To determine the role of IT neurons in longer lasting memories, we measured their responses to initially novel stimuli as the stimuli gradually became familiar to the animal. 2. Two rhesus monkeys were trained on a delayed matching to sample (DMS) task with several intervening stimuli between the sample and the final matching stimulus on each trial. The purpose of the task was to ensure that the animal attended to the stimuli and held them in memory, at least temporarily. Unlike in several previous studies, the focus was not on within-trial effects but rather on the incidental memories that built up across trials as the stimuli became familiar. Each cell was tested with a set of 20 novel stimuli (digitized pictures of objects) that the monkey had not seen before. These stimuli were used in a fixed order over the course of an hour-long recording session, and the number of intervening trials between repetitions of a given sample stimulus was varied. 3. The responses of about one-third of the cells recorded in anterior-ventral IT cortex declined systematically as the novel stimuli became familiar. After six to eight repetitions, responses reached a plateau that was approximately 40% of the peak response. Virtually all of these cells also showed selectivity for particular visual stimuli and thus were not "novelty detectors" in the sense of cells that respond to any novel stimulus. Rather, the responses of these cells were a joint function of familiarity and specific object features such as shape and color. A few cells showed increasing responses with repetition over the recording session, but these changes were accompanied by changes in baseline firing rate, suggesting that they were caused by nonspecific effects. 4. The decrement in response with familiarity was stimulus specific and bridged > 150 presentations of other stimuli, the maximum tested. For some cells the maximum decrement in response occurred for those stimuli that initially elicited the largest response. There was no significant change in response to stimuli that were already familiar. 5. The same cells that showed familiarity effects also showed reduced responses to the matching stimuli at the end of each trial, compared with the responses to the samples. (ABSTRACT TRUNCATED AT 400 WORDS)
Discrimination of fish populations using parasites: Random Forests on a ‘predictable’ host-parasite system

SUMMARY We address the effect of spatial scale and temporal variation on model generality when forming predictive models for fish assignment using a new data mining approach, Random Forests (RF), to variable biological markers (parasite community data). Models were implemented for a fish host-parasite system sampled along the Mediterranean and Atlantic coasts of Spain and were validated using independent datasets. We considered 2 basic classification problems in evaluating the importance of variations in parasite infracommunities for assignment of individual fish to their populations of origin: multiclass (2–5 population models, using 2 seasonal replicates from each of the populations) and 2-class task (using 4 seasonal replicates from 1 Atlantic and 1 Mediterranean population each). The main results are that (i) RF are well suited for multiclass population assignment using parasite communities in non-migratory fish; (ii) RF provide an efficient means for model cross-validation on the baseline data and this allows sample size limitations in parasite tag studies to be tackled effectively; (iii) the performance of RF is dependent on the complexity and spatial extent/configuration of the problem; and (iv) the development of predictive models is strongly influenced by seasonal change and this stresses the importance of both temporal replication and model validation in parasite tagging studies.