Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of microbial loads present in two Western Cape rivers used for irrigation of vegetables

Agriculture in the Western Cape is not only one of the most important economic sectors but also provides many job opportunities. Over the last few years the sustainability of this successful industry has become threatened by the faecal pollution of rivers used to irrigate produce that will be consumed raw or after minimal processing. This situation not only poses an enormous risk to the health of the consumer but also to farmers who stand to lose their export licenses. The purpose of this study was to determine the microbial types and loads in river water, irrigation water and on irrigated produce. A baseline study was done on four sites in two Western Cape rivers. These sites were chosen to allow for the sampling of river water, irrigation water and irrigated produce so as to determine whether a link between the use of contaminated irrigation water and the microbial population found on irrigated produce exists. The physico-chemical analyses used in the study consisted of: pH, alkalinity, water temperature, conductivity and chemical oxygen demand. The microbial monitoring included the aerobic colony counts (ACC) and the enumeration of the total coliforms, faecal coliforms, staphylococci, enterococci, and aerobic and anaerobic sporeformers present in the water samples. The presence or absence of the potential pathogens like E. coli, Listeria and Salmonella, was also determined. During the baseline study faecal coliform counts as high as 160 000 organisms.100 mL were noted in the Plankenburg River, while counts as high as 460 000 organisms.100 mL were found in the Mosselbank River. Apart from this, high numbers of staphylococci and intestinal enterococci were often found, while E. coli, Listeria and Salmonella were present in samples from both of these rivers. Based on the results of the baseline study on the two rivers it was decided to do a more intensive study on the microbial load of the river and irrigation water as well as irrigated produce from the Mosselbank site. Lettuce and cabbages from a commercial farmer’s fields were chosen as the irrigated produce. During the warmer summer months, ACC counts in the river samples peaked at 12 8000 000 cfu.mL, while faecal coliform counts of 1 600 000 organisms.100 mL were found. The three potential pathogens (E. coli, Listeria and Salmonella) were present in all the river samples taken during this period. While the counts of indicator bacteria in the irrigation water was often lower, faecal coliform counts as high as 1 600 000 organisms.100 mL and several other potential pathogens were found on the irrigated lettuce and cabbage. This could indicate a possible
Edinburgh Explorer A Bayesian framework for word segmentation: Exploring the effects (cid:9)of context

Since the experiments of Saﬀran et al. (1996a), there has been a great deal of interest in the question of how statistical regularities in the speech stream might be used by infants to begin to identify individual words. In this work, we use computational modeling to explore the eﬀects of diﬀerent assumptions the learner might make regarding the nature of words – in particular, how these assumptions aﬀect the kinds of words that are segmented from a corpus of transcribed child-directed speech. We develop several models within a Bayesian ideal observer framework, and use them to examine the consequences of assuming either that words are independent units, or units that help to predict other units. We show through empirical and theoretical results that the assumption of independence causes the learner to undersegment the corpus, with many two- and three-word sequences (e.g. what’s that , do you , in the house ) misidentiﬁed as individual words. In contrast, when the learner assumes that words are predictive, the resulting segmentation is far more accurate. These results indicate that taking context into account is important for a statistical word segmentation strategy to be successful, and raise the possibility that even young infants may be able to exploit more subtle statistical patterns than have usually been considered. statistically independent, (alternatively) by a learner well predictive of later this by developing two diﬀerent Bayesian models of word segmentation incorporating each of these two diﬀerent assumptions. These models can be seen as ideal learners : they are designed to behave optimally given the available input data, in this case a corpus of phonemically transcribed child-directed speech.Using our ideal learning approach, we ﬁnd in our ﬁrst set of simulations that the learner who assumes that words are statistically independent units tends to undersegment the corpus, identifying commonly co-occurring sequences of words as single words. These results seem to conﬂict with those of several earlier models (Brent, 1999; Venkataraman, 2001; Batchelder, 2002), where systematic undersegmentation was not found even when words were assumed to be independent. However, we argue here that these previous results are misleading. Although each of these learners is based on a probabilistic model that deﬁnes an optimal solution to the segmentation problem, we provide both empirical and analytical evidence that the segmentations found by these learners are not the optimal ones. Rather, they are the result of limitations imposed by the particular learning algorithms employed. Further mathematical analysis shows that undersegmentation is the optimal solution to the learning problem for any reasonably deﬁned model that assumes statistical independence between words.
Microsoft Word-10186605-file00

Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan (Y.K.); Daiichi College of Pharmaceutical Sciences, Fukuoka 815-8511, Japan (K.H.); School of Pharmaceutical Sciences and Global Center of Excellence (COE) Program, University of Shizuoka, Shizuoka 422-8526, Japan (Y.I., F.A., T.Y., S.Y., M.D.); Faculty of Pharmaceutical Sciences, Health Science University of Hokkaido, Hokkaido 061-0293, Japan (T.E.) and Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka 814-0198, Japan (N.K.) DMD Fast Forward. Published on December 29, 2009 as doi:10.1124/dmd.109. 031153
Self-reported infections in the German National Cohort (GNC) in the context of the current research landscape

Max J Hassenstein1,2, Ghazal Aarabi3, Peter Ahnert4,5,6, Heiko Becher7, Claus-Werner Franzke8, Julia Fricke9, Gérard Krause1,10,11, Stephan Glöckner1,10, Cornelia Gottschick12, André Karch13, Yvonne Kemmling1, Tobias Kerrinnes1,10, Berit Lange1,10, Rafael Mikolajczyk12, Alexandra Nieters14,15, Jördis J Ott1,10, Wolfgang Ahrens16,17, Klaus Berger13, Claudia MeinkeFranze18, Sylvia Gastell19, Kathrin Günther16, Karin Halina Greiser20, Bernd Holleczek21, Johannes Horn12, Lina Jaeschke22, Annika Jagodzinski23,24,25, Lina Jansen26, Carmen Jochem27, Karl-Heinz Jöckel28, Rudolf Kaaks29, Lilian Krist9, Oliver Kuss30, Susan Langer12, Nicole Legath13, Michael Leitzmann27, Wolfgang Lieb31, Markus Loeffler4,5, Nina Mangold32,33, Karin B. Michels8, Christa Meisinger34,35, Nadia Obi7, Tobias Pischon22,36,37,38, Tamara Schikowski39, Sabine Schipf18, Matthias B. Schulze19, Andreas Stang28, Sabina Waniek31, Kerstin Wirkner4,5, Stefan N. Willich9, Stefanie Castell1,10
Reduced transmission of human schistosomiasis after restoration of a native river prawn that preys on the snail intermediate host

Significance Reinfection after treatment is a problem that plagues efforts to control parasites with complex transmission pathways, such as schistosomiasis, which affects at least 220 million people worldwide and requires an obligate snail intermediate host. Our study highlights a potential ecological solution to this global health problem: We show that a species of river prawn indigenous to the west coast of Africa, Macrobrachium vollenhovenii, could offer a low-cost, sustainable form of snail control that, when used in synergy with existing drug distribution campaigns, could reduce or locally eliminate the parasite. Biological conservation does not always benefit human health, but our results show that where it does, it could provide a win-win outcome for humans and nature. Eliminating human parasitic disease often requires interrupting complex transmission pathways. Even when drugs to treat people are available, disease control can be difficult if the parasite can persist in nonhuman hosts. Here, we show that restoration of a natural predator of a parasite’s intermediate hosts may enhance drug-based schistosomiasis control. Our study site was the Senegal River Basin, where villagers suffered a massive outbreak and persistent epidemic after the 1986 completion of the Diama Dam. The dam blocked the annual migration of native river prawns (Macrobrachium vollenhoveni) that are voracious predators of the snail intermediate hosts for schistosomiasis. We tested schistosomiasis control by reintroduced river prawns in a before-after-control-impact field experiment that tracked parasitism in snails and people at two matched villages after prawns were stocked at one village’s river access point. The abundance of infected snails was 80% lower at that village, presumably because prawn predation reduced the abundance and average life span of latently infected snails. As expected from a reduction in infected snails, human schistosomiasis prevalence was 18 ± 5% lower and egg burden was 50 ± 8% lower at the prawn-stocking village compared with the control village. In a mathematical model of the system, stocking prawns, coupled with infrequent mass drug treatment, eliminates schistosomiasis from high-transmission sites. We conclude that restoring river prawns could be a novel contribution to controlling, or eliminating, schistosomiasis.
The transmembrane protein golden goal regulates retinal axon guidance in Drosophila

Deutsche Zusammenfassung Während der Entwicklung des visuellen Systems von Drosophila selektieren Photorezeptor (R) Axone ihre Zielzellen Schritt für Schritt. Dabei treffen R Axone mit unterschiedlichen Identitäten ganz spezifische Entscheidungen zu bestimmten Zeitpunkten während der Entwicklung des visuellen Systems. Das kürzlich identifizierte Transmembranprotein Golden Goal (Gogo) wird dynamisch in allen R Axonen expremiert und lokalisiert vornehmlich in den Wachstumskegeln von auswachsenden Axonen. Gogo wird dort für die Steuerung der wachsenden Axone während der Entwicklung des visuellen Systems benötigt. In gogo Mutanten weisen R1-R6 Axone Fehlprojektionen während der Bildung der Lamina Cartridges auf. Dies läßt darauf schließen, daß Gogo für die Wahl der post-synaptischen Partner benötigt wird. Zusätzlich konnte eine sehr spezifische Funktion von Gogo in R8 Axonen gezeigt werden. Gogo wirkt in diesen Axonen an zwei unterschiedlichen Zeitpunkten während ihrer Entwicklung: Gogo reguliert Axon-Axon Interaktionen und Axon-Zielzellen Interaktionen. Der Gogo Mutanten Phenotyp in Larven suggeriert, daß Gogo abstoßende Axon-Axon Interaktionen zwischen R8 Axonen vermittelt und dadurch angemessene Abstände zwischen den Axonen bewirkt. Während den Puppenstadien hat Gogo eine andere Funktion. Hier reguliert es die Erkennung der temporären Zwischenschicht und die Aufrechterhaltung dieser axonalen Position bis zum zeitlich regulierten Weiterwachsen der Axone. Der Phenotyp bei Verlust der Gogo Funktion läßt darauf schließen, daß Axone nicht mehr richtig mit ihrer temporären Schicht interagieren können und dass diese Interaktion Voraussetzung dafür ist, daß R8 Axone in ihre korrekten Zielsäulen einwachsen können und ihre richtige Zielschicht zu innervieren. Die Überexpression von Gogo hingegen führt dazu, daß R8 Axone permanent an der eigentlich nur temporären Zwischenschicht verankert werden. Die beobachteten Überexpressionsphenotypen und dedektierten Proteinlevel in Antikörperfärbungen lassen darauf schließen, daß Gogo nach der temporären Zwischenphase aus den Axonen verschwinden muss und dadurch erst der letzte Auswachsschritt zur finalen Zielschicht M3 initiert werden kann. Einzelzell-Mosaik-Analysen haben in Kombination mit Rettungsexperimenten gezeigt, daß Gogo autonom in R Axonen benötigt wird. Eine detailierte Untersuchung der funktionellen Domänen läßt darauf schließen, daß Gogo als Rezeptor fungiert, der an einen bislang unidentifizierten Liganden über die Tsp1 and GOGO Domäne bindet. Bei dem kurzen konservierten zytoplasmatischen Tripeptidmotif, daß allen identifizierten Gogo Orthologen gemeinsam ist, könnte es sich um eine vermeintliche
Discovery of the distant lunar sodium tail and its enhancement following the Leonid Meteor Shower of 1998

Night‐time measurements using a bare CCD all‐sky imaging system have detected the presence of an extensive region of neutral sodium emission (589.1 nm) in the direction of the anti‐solar/lunar points. The emission was observed to occur during the nights of 21–22 August and 18–20 November, 1998 UT, centered on the new Moon period. The Moon is the most likely source of the neutral sodium, making this the first detection of the lunar sodium tail out to a distance of hundreds of lunar radii. The greater brightness of the emission feature on 19 November is attributed to the Leonid meteor shower which peaked on 17 November, 1998, less than two days before new Moon.
Remote sensing and measurement of the thickness of oil films on the sea surface using reflectivity contrast

Contrast in the reflectivity between pure and contaminated sea surfaces is the result of two effects, namely (1) differing reflectivities of pure sea water and oil on water and (2) damping effect of the oil film on the sea waves. The problem is to estimate their separate contributions to total contrast so that the substance effect can be isolated. Its magnitude provides assessment of the oil film thickness which can be obtained for sufficiently large averaging scales. The spectral behavior and film thickness dependence of contrast have been calculated for an undisturbed sea surface. The estimate of the damping effect has been made using the Cox- Munk distributions for pure and contaminated surfaces. The method chosen has been verified during a series of tests conducted in situ from an aircraft carrying a CO2 laser sensor operating at 10.6 micrometers .
Near-term Health Benefits of Greenhouse Gas Reductions: A Proposed Assessment Method and Application in Two Energy Sectors of China

This is a study of projected near-term health benefits associated with greenhouse (GHG) reductions resulting from changes in energy efficiency and structure of energy use in the power and household sectors of China. The work was commissioned by the former Office of Global and Integrated Environmental Health at WHO, in order to explore the scope for modelling in the assessment of such short-term health benefits. China was selected as an appropiate case study for this work, as it fulfilled most of the criteria required, including the fact that it is a large country, with data sets available on air pollution and health, and with information on projected trends in the consumption of fossil fuels
A reply to Carter and Davidson's “an evaluation of the contribution of soil micromorphology to the study of ancient arable agriculture”

In this current issue of Geoarchaeology, Carter and Davidson (535-547) have assessed published literature on soil micromorphological studies of ancient agriculture. Their "combative" arguments and final assertion that soil micromorphology cannot be used to identify ancient agriculture is challenged. It is also argued that, without confidence in this technique, it will be difficult for Carter and Donaldson to carry out the kinds of researches that they advocate. As well as challenging their view, the author provides an example of one way to collect and present data more accurately and convincingly from soil micromorphological studies of experiments in ancient agriculture. Readers can arrive at their own conclusions. © 1998 John Wiley & Sons, Inc.
A standardized head-fixation system for performing large-scale , in-1 vivo physiological recordings in mice 2 3

12 The Allen Institute recently built a set of high-throughput experimental pipelines to 13 collect comprehensive in vivo surveys of physiological activity in the visual cortex of awake, 14 head-fixed mice. Developing these large-scale, industrial-like pipelines posed many scientific, 15 operational, and engineering challenges. Here we describe our strategies for collecting 16 standardized, multi-modal in vivo datasets across many instrumental platforms over long 17 periods of time. Our goal of creating a cross-platform reference space to which all pipeline 18 datasets were mapped required development of 1) a robust headframe, 2) a reproducible 19 clamping system, and 3) data-collection systems that are built, and maintained, around precise 20 alignment with a reference artifact. When paired with our pipeline clamping system, the Allen 21 Brain Observatory headframe exceeded deflection and reproducibility requirements. All 22 headframe, surgical tooling, and clamp design documentation have been made freely available 23 as an open resource to the scientific community. 24
Unilateral Neglect : Clinical and Experimental Studies

Section A: What is Neglect? P. Halligan, J. Marshall, The Nature and Natural History of Neglect. G. Valler, The Anatomical Basis of Spatial Hemineglect in Humans. Section B: Neuropsychological Processes Underlying Neglect. G. Gainotti, The Role of Spontaneous Eye Movements in Orienting Attention and in Unilateral Neglect. G. Rizzolatti, A. Berti, Neural Mechanisms of Spatial Neglect. M. Kinsbourne, Orientational Bias Model of Unilateral Neglect: Evidence from Attentional Gradients within Hemispace. M.J. Farah, M.A. Wallace, S.P. Vecera, "What" and "Where" in Visual Attention: Evidence from the Neglect Syndrome. G.W. Humphries, M.J. Riddoch, Interactive Attentional Systems and Unilateral Visual Neglect. I. Robertson, The Relationship between Lateralised and Non-Lateralised Attentional Deficits in Unilateral Left Neglect. L.C. Robertson, M. Eglin, Attentional Search in Unilateral Visual Neglect. E. Ladevas, Shifts of Attention in Patients with Visual Neglect. R. Werth, Shifts and Omissions in Spatial Reference in Unilateral Neglect. A.W. Ellis, A.W. Young, B.M. Flude, Neglect and Visual Language. J. Marshall, P. Halligan, I. Robertson, A Critical Review of Contemporary Theories. Section C: Rehabilitation of Neglect. L. Diller, The Behavioural Management of Neglect. I. Robertson, P. Halligan, J. Marshall, Prospects for the Rehabilitation of Unilateral Neglect.
Discrete confidence levels revealed by sequential decisions

Whether humans are optimal decision makers is still a debated issue in the realm of perceptual decisions. Taking advantage of the direct link between an optimal decision-making and the confidence in that decision, we offer a new dual-decisions method of inferring such confidence without asking for its explicit valuation. Our method circumvents the well-known miscalibration issue with explicit confidence reports as well as the specification of the cost-function required by ‘opt-out’ or post-decision wagering methods. We show that observers’ inferred confidence in their first decision and its use in a subsequent decision (conditioned upon the correctness of the first) fall short of both the ideal Bayesian strategy, as well as of an under-sampling approximation or a modified Bayesian strategy augmented with an additional bias term to accommodate global miscalibration of confidence. The observed data are instead significantly better fitted by a model positing that observers use only few confidence levels or states, at odds with the continuous confidence function of stimulus level prescribed by a normative behavior. These findings question the validity of normative-Bayesian accounts of subjective confidence and metaperceptual judgments.
What do hydrologists mean when they use the term flushing?

*Correspondence to: Doug Burns, Watersheds Research Section, US Geological Survey, 425 Jordan Road, Troy, NY 12180-8349, USA. E-mail: daburns@usgs.gov The term ‘flushing’ appears commonly in the hydrological literature. The term has been used in an engineering sense to describe releases of water from dams or through sewer systems and the resulting effects on sediment transport (Kondolf and Wilcock, 1996; Campisano and Modica, 2003), but here I focus on the use of the term flushing to describe natural processes in catchments. In a recent search of ‘hydrological flushing’ on google.scholar. com, the term appeared in 2030 references. Of the 100 most cited references containing the term, only two predate 1997 and 73 have appeared since 2000, which indicates increasing recent use of the term in the peerreviewed literature. Given the increasing use of the term in the literature, it seems prudent to explore how the term is currently used and understood, how use of the term has evolved, and how our understanding of hydrological flushing is likely to evolve in the future. Webster’s Collegiate Dictionary defines flush as ‘4. to become cleaned, washed, or emptied out with a sudden flow of water’. In the hydrological literature, the term typically refers to the movement of a solute to a stream during snowmelt or a rain event. Early work identified flushing associated with the behaviour of dissolved organic carbon (DOC) during snowmelt in a stream in the Rocky Mountains (Hornberger et al., 1994; Boyer et al., 1997). However, the term has since been applied to describe the behaviour of many solutes, including: nitrate, silica, base cations, phosphorus, sulphate, and pesticides (Creed et al., 1996; Burns et al., 1998; Evans et al., 2000; Scanlon et al., 2001; Warren et al., 2001). Flushing refers to a hydrological process, and is generally used without consideration of the biogeochemical processes that act to retain solutes in catchments; however, use of a generic term such as flushing to describe the behaviour of all solutes can lead to confusion. Flushing behaviour has been identified for a large number of solutes that are controlled by biogeochemical processes, which range from passive with little surface interaction (such as those that control chloride and nitrate) to solutes that are held tightly by adsorption or released only through dissolution or redox reactions (such as phosphorus and sulphate). Are there certain behaviours or patterns displayed by all of these solutes that we can agree upon? How does the flushing behaviour of these solutes differ? The common thread is that these solutes undergo a period of accumulation,