Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Response to Benthic Environment in Trench and Flat Seabed Sediments in Tokyo Bay, Japan

Abstract In order to elucidate microbial response to the benthic environment in trench and flat seabed sediments, dynamic changes in the sediment microbial community and the water quality of overlying water were evaluated during summer and autumn in Tokyo Bay, Japan. A large amount of nutrients accumulated in the trench during summer when stratification occurred, which stimulated the sediment microbial growth, resulting in higher microbial density compared to the flat seabed sediment. Additionally, predominant ubiquinone species in the two sediments were ubiquinone with 9 isoprene units (Q-9) and Q-8, respectively, while menaquinone with 6 isoprene units (MK-6) dominated. Hence, the different bottom shapes were expected to produce distinct microbial environments. In autumn, the convective mixing of seawater resulted in the disappearance of stratification and the deposition of nutrients onto the flat seabed sediment, which contributed to excessive microbial growth. During this transition period, Q-containing bacteria dominated with lag time instead of MK-containing bacteria. At the same time, the molar fraction of MK-6 that might correspond to sulfate-reducing bacteria also rapidly decreased. However, this microbial change was not observed in the trench since it kept anaerobic conditions longer. Multidimensional scaling analysis indicated that dissolved oxygen of the bottom water can drive microbial community shift.
Novel agents and strategies to treat herpes simplex virus infections

The quiet pandemic of herpes simplex virus (HSV) infection has plagued humanity since ancient times, causing mucocutaneous infection, such as herpes labialis and herpes genitalis. Disease symptoms often interfere with everyday activities and occasionally HSV infections are the cause of life-threatening or sight-impairing disease, especially in neonates and the immunocompromised patient population. After primary or initial infection the virus persists for life in a latent form in neurons of the host, periodically reactivating and often resulting in significant psychosocial distress for the patient. Currently, no cure is available. In the mid-1950s the first antiviral, idoxuridine, was developed for topical treatment of herpes disease and, in 1978, vidarabine was licensed for systemic use to treat HSV encephalitis. Acyclovir (Zovirax®), a potent, specific and tolerable nucleosidic inhibitor of the herpes DNA polymerase, was a milestone in the development of antiviral drugs in the late 1970s. In the mid-1990s, when acyclovir became a generic drug, valacyclovir (Valtrex®) and famciclovir (Famvir®), prodrugs of the gold standard and penciclovir (Denavir®, Vectavir®), a close analogue, were launched. Though numerous approaches and strategies were tested and considerable effort was expended in the search of the next generation of an antiherpetic therapy, it proved difficult to outperform acyclovir. Notable in this regard was the award of a Nobel Prize in 1988 for the elucidation of mechanistic principles which resulted in the development of new drugs such as acyclovir. Vaccines, interleukins, interferons, therapeutic proteins, antibodies, immunomodulators and small-molecule drugs with specific or nonspecific modes of action lacked either efficacy or the required safety profile to replace the nucleosidic drugs acyclovir, valacyclovir, penciclovir and famciclovir as the first choice of treatment. Recently though, new inhibitors of the HSV helicase-primase with potent in vitro antiherpes activity, novel mechanisms of action, low resistance rates and superior efficacy against HSV in animal models have been discovered. This review summarises the current therapeutic options, discusses the potential of preclinical or investigational drugs and provides an up-to-date interpretation of the challenge to establish novel treatments for herpes simplex disease.
Use of Inverse Reinforcement Learning for Identity Prediction

We adopt Markov Decision Processes (MDP) to model sequential decision problems, which have the characteristic that the current decision made by a human decision maker has an uncertain impact on future opportunity. We hypothesize that the individuality of decision makers can be modeled as differences in the reward function under a common MDP model. A machine learning technique, Inverse Reinforcement Learning (IRL), was used to learn an individual's reward function based on limited observation of his or her decision choices. This work serves as an initial investigation for using IRL to analyze decision making, conducted through a human experiment in a cyber shopping environment. Specifically, the ability to determine the demographic identity of users is conducted through prediction analysis and supervised learning. The results show that IRL can be used to correctly identify participants, at a rate of 68% for gender and 66% for one of three college major categories.
Cool‐skin and warm‐layer effects on sea surface temperature

To obtain bulk surface flux estimates approaching the ±10 W m−2 accuracy desired for the Tropical Ocean-Global Atmosphere Coupled Ocean-Atmosphere Response Experiment (COARE) program, bulk water temperature data from ships and buoys must be corrected for cool-skin and diurnal warm-layer effects. In this paper we describe two simple scaling models to estimate these corrections. The cool-skin model is based on the standard Saunders [1967] treatment, including the effects of solar radiation absorption, modified to include both shear-driven and convectively driven turbulence through their relative contributions to the near-surface turbulent kinetic energy dissipation rate. Shear and convective effects are comparable at a wind speed of about 2.5 m s−1. For the R/V Moana Wave COARE data collected in the tropical western Pacific, the model gives an average cool skin of 0.30 K at night and an average local noon value of 0.18 K. The warm-layer model is based on a single-layer scaling version of a model by Price et al. [1986]. In this model, once solar heating of the ocean exceeds the combined cooling by turbulent scalar heat transfer and net longwave radiation, then the main body of the mixed layer is cut off from its source of turbulence. Thereafter, surface inputs of heat and momentum are confined to a depth DT that is determined by the subsequent integrals of the heat and momentum. The model assumes linear profiles of temperature-induced and surface-stress-induced current in this “warm layer. ” The model is shown to describe the peak afternoon warming and diurnal cycle of the warming quite accurately, on average, with a choice of a critical Richardson number of 0.65. For a clear day with a 10-m wind speed of 1 m s−1, the peak afternoon warming is about 3.8 K with a warm-layer depth of 0.7 m, decreasing to about 0.2 K and 19 m at a wind speed of 7 m s−1. For an average over 70 days sampled during COARE, the cool skin increases the average atmospheric heat input to the ocean by about 11 W m−2; the warm layer decreases it by about 4 W m−2 (but the effect can be 50 W m−2 at midday).
The Effect of Shallow San Francisco Bay Sediments on Waveforms Recorded during the MW 4.6 Bolinas, California, Earthquake

To investigate the effect of the shallow, low-velocity sediments on the seismic wave field in the northern San Francisco Bay, we modeled tangential component displacement seismograms recorded during the 18 August 1999 M W 4.6 Bolinas, California, earthquake. The modeling indicates that the velocity structure of Pleistocene horizons in the San Francisco Bay is important for simulations of weak ground motions for Bay Area earthquakes. Models including the Pleistocene sediments generate the 1-sec-period surface waves observed at several stations. Modeling of Treasure and Yerba Buena Island records requires structures approximately an order of magnitude higher in spatial resolution than the current 3D velocity models for the region. This pair of sites, located only 2 km apart in the bay, records a sixfold difference in peak ground acceleration during the Bolinas earthquake. Three transects are forward modeled using 1D frequency-wavenumber integration and 2D finite-difference methods. Generally the ground motions are characterized by a direct shear wave ( S ), a midcrustal reflection ( S 1), a near-receiver multiple ( S 2), and surface waves. The direct S arrival at all six stations requires a faster model than GIL7, the model routinely used to estimate earthquake source parameters using the Berkeley Digital Seismic Network. In addition, the timing of S 1 indicates the possibility of a dipping midcrustal interface. S 2 can be matched with a single strong impedance contrast at 3 km depth. A thin (200-m) surface layer of weathered rock and sediments simulates the surface waves that follow S 2 at the Richmond Field Station site. However, the surface waves at Treasure Island and the Berkeley sites are longer in duration and higher amplitude than at Richmond and require 2D structure. A simple shallow uniform basin model for the San Francisco Bay consisting of stiff sediments (shear-wave velocity, β = 400 m/sec; thickness ∼100 m) over weathered rock ( β = 1.5 km/sec) of the Franciscan assemblage produces surface waves in the 0.02-2 Hz passband at Treasure Island and the Berkeley sites. Manuscript received 27 July 2001.
Urban detection using Decision Tree classifier: a case study

This work constitutes a first step towards the definition of a methodology for automatic urban extraction from medium spatial resolution Landsat data. Decision Tree is investigated as classification technique due to its ability in establishing which is the most relevant information to be used for the classification process and its capability of extracting rules that can be further ap-plied to other inputs. The attention was focused on the evaluation of parameters that better define the training set to be used for the learning phase of the classifier since its definition affects all the next steps of the process. Different training sets were created by combining different features, such as different level of radiometric pre-processing applied to the input images, the number of classes considered to train the classifier, the temporal extent of the training set and the use of different at-tributes (bands or spectral indexes). Different post-processing techniques were also evaluated. Classifiers, obtained by the generated training sets, were evaluated in two different areas of Pied-mont Region, where the official regional cartography at scale 1:10000 was used for validation. Accuracies round 81% in the Torino case study and around 96%-97% in Asti case study were reached, thanks to the use of indexes such as NDVI and NDBBBI and the use of post-processing such as majority filtering that allowed enhancing classifier performances
Routing Bandwidth Guaranteed Paths with Local Restoration in Label Switched Networks

The emerging Multi-Protocol Label Switching (MPLS) networks enable network service providers to route band-width guaranteed paths between customer sites [3, 2, 8, 5]. This basic Label Switched Path (LSP) routing is often enhanced using restoration routing which sets up alternate LSPs to guarantee uninterrupted connectivity in case network links or nodes along primary path fail. In this paper, we address the problem of distributed routing of restoration paths, which can be defined as follows: given a request for a bandwidth guaranteed LSP between two nodes, find a primary LSP and a set of backup LSPs that protect the links along the primary LSP. A routing algorithm that computes these paths must optimize the restoration latency and the amount of bandwidth used. In this paper, we introduce the concept of " backtrack-ing " to bound the restoration latency. We consider three different cases characterized by a parameter called back-tracking distance : (1) no backtracking (¼), (2) limited backtracking (), and (3) unlimited backtracking (½). We use a link cost model that captures band-width sharing among links using various types of aggregate link state information. We first show that joint optimization of primary and backup paths is NP-hard in all cases. We then consider algorithms that compute primary and backup paths in two separate steps. Using link cost metrics that capture bandwidth sharing, we devise heuristics for each case. Our simulation study shows that these algorithms offer a way to tradeoff bandwidth to meet a range of restoration latency requirements.
Reconstruction of holocene environmental changes in northern British Columbia using fossil midges

Lake sediments contain the remains of midge communities that may be used as biological proxies for inferring past environmental changes. Freshwater midges, including Chironomidae and Chaoboridae, from two alpine tarns (Pyramid Lake and Bullwinkle Lake) in the Cassiar Mountains of northern British Columbia were used to estimate Holocene palaeotemperature changes, and more specifically, to test for the presence of the Milankovitch thermal maximum, an early Holocene warm interval coinciding with peak Holocene summer solar insolation. Mean July air temperatures were reconstructed using midge-inference models developed via weighted averagingpartial least squares (WA-PLS) regression. Cold-tolerant midge taxa dominate the stratigraphies from both Pyramid and Bullwinkle Lakes; however, warm-adapted species are more common in Bullwinkle Lake. Early Holocene warming is apparent at both lakes, however it is unclear whether this is indicative of the Milankovitch thermal maximum. A decrease in temperature occurs from 8,700-7,900 cal. yr BP at Pyramid Lake, around the same time that the 8,200 cal. yr BP cooling event occurred in the northern hemisphere. During the middle Holocene, records from Pyramid Lake indicate an overall decrease in temperature, with a short period of warmer temperatures that peak at 5,100 cal. yr BP. Temperatures fluctuate little during this time at Bullwinkle Lake. A short warming phase is apparent at both lakes during the late Holocene. July temperatures are highest at 2,000 cal. yr BP (10.5°C) in Pyramid Lake and at 1,200 cal. yr BP (13°C) in Bullwinkle Lake. Thereafter, temperatures return to what they were before the warming occurred, and at Bullwinkle Lake, vary little throughout the remainder of the Holocene.
Space Research in Africa: Challenges and Opportunities

Africa has lost its glory as the pioneer of space research as evidenced by the ancient library of Alexandria in Egypt that housed the first space research centre more than two thousand years ago. Cave paintings in Olduvai Gorge in present day Tanzania showed how the first humans communicated millions of years ago. Early Africans used drum beats to alert of an impending danger or of festivities. The discovery of papyrus the material used as writing paper and the invention of words that make the alphabet all originated in Ancient Egypt. All of these examples show that at a certain stage in history, Africa was a leader in science and technology (Shibanda & Isabel, 2000). However in the 21st Century, Africa has lagged behind technologically compared to all the other continents. Space research and deployment of supporting technologies including remote sensing and Geospatial Information Systems (GIS) remain fundamental to bridge the technological gap between Africa and the rest of the world hence solving some of Africa’s challenges. This study analyses the challenges and opportunities that African countries face in harnessing space technologies to be used in natural disaster management, disease prevention, land use, agricultural productivity improvements and even in conflict resolution.
Applicability of phosphorus site indices to wastewater effluent-irrigated cropland

Phosphorus (P) indices, originally developed to assess the risk of P export to aquatic systems from agricultural fields receiving inorganic fertilizers and livestock manures, are being used for other P sources with different characteristics and methods of application. This study determined Pennsylvania P index scores for eleven crop fields of Penn State University's Living Filter system receiving 130 kg P2O5 ha−1 (115 lb P2O5 ac−1) in 2008 via sprinkler irrigation of municipal wastewater effluent. A baseline assessment of P index treated effluent irrigation as surface application of completely soluble P source material with maximum potential of runoff P loss. Three fields located ≤22 m (200 ft) from streams ranked high and very high in P loss rating under baseline assessment. Modified assessments involved changing the application method multiplier and P source coefficient to more accurately reflect the year-round intermittent application of P via sprinkler irrigation. All fields were ranked as having low risk of P export using the modified parameters. Site monitoring data from nearly 50 years of effluent irrigation show no evidence of excess P transport to groundwater or off-site surface water, suggesting that baseline assessment might be overestimating P loss rating of some fields. Results underscore the need to tailor P indexing tools to address the differential risk of P loss for specific P sources and application methods.
Modelling Investment When Relative Prices are Trending: Theory and Evidence for the United Kingdom

In recent work, Stacey Tevlin and Karl Whelan argue that aggregate econometric models fail to capture the US investment boom in plant and machinery in the second half of the 1990s, whereas a disaggregated approach does much better. In particular, they show that aggregate models do not capture the increase in replacement investment associated with compositional shifts in the capital stock towards high depreciation rate assets, such as computers. And aggregate models invariably find little or no role for the real user cost, so do not pick up the strong effects of relative price declines on investment in computers. In this paper, a data set for the United Kingdom is constructed in order to investigate the ability of different equations to account for the UK boom in plant and machinery investment in the second half of the 1990s. The findings are similar to those of Tevlin and Whelan, whose analysis is extended in two main ways. First, the failure of the aggregate equations is explained more formally in terms of misspecification when relative prices are trending downwards. Second, the econometric analysis is conducted in a formal cointegration framework. As in the United States, the paper shows that asset-level equations can explain the investment boom in plant and machinery in the second half of the 1990s in the United Kingdom, whereas the aggregate equation fails completely.
Allais Paradoxes Can be Reversed by Presenting Choices in Canonical Split Form

This paper tests Birnbaum’s (2004) theory that the constant consequence paradoxes of Allais are due to violations of coalescing, the assumption that when two branches lead to the same consequence, they can be combined by adding their probabilities. Rank dependent utility and cumulative prospect theory imply that the Allais paradoxes are due to violations of restricted branch independence, a weaker form of Savage’s sure thing axiom. This paper will analyze separately whether erroneous random response variation might be responsible for these two effects. When errors are factored out, violations of restricted branch independence also remain significant and opposite from the direction of Allais paradoxes, suggesting that models such as CPT that attribute Allais paradoxes to violations of restricted branch independence should be rejected.
Sediment source fingerprinting: Testing hypotheses about contributions from potential sediment sources

Techniques involving composite fingerprints and multivariate mixing models are being increasingly used in catchment studies to establish the relative contributions of potential sources to the suspended sediment output. Such information is important both for understanding the fine sediment dynamics of a catchment and for targeting remediation measures required to reduce sediment-related environmental problems. A multivariate mixing model algorithm, which compares the concentrations of a range of geochemical properties of the suspended sediment load with those of a number s of potential sources, is commonly used to provide estimates of the relative contributions (P 1 , P 2 ,., P s ) of those sources to the suspended sediment load. However, such models do not provide measures of the uncertainty associated with the P-values. This paper describes how the usual mixing model can be modified, such that the optimization procedure used to estimate the sediment proportions P 1 , P 2 . contributed by different sources also provides measures of their uncertainty. This approach allows hypotheses concerning the P values to be tested, such as: (i) whether the individual P-values differ significantly from zero, and (ii) whether the P-values change significantly between events. To calculate the uncertainty associated with a P-value, a statistical model which considers the correlation between the tracer variables is used. This approach has been tested using data from a small rural catchment in southern Brazil where a sediment source investigation is in progress. Sediment samples collected during 48 storm events were used to establish the source contributions.
Alcoholic liver cirrhosis increases the risk of left ventricular diastolic dysfunction.

OBJECTIVES The aim of this study was to prove that the incidence of the more unusual and largely under-researched cardiac dysfunction, i.e. diastolic, is more frequent in patients with alcoholic cirrhosis. Comparison of the incidence of left ventricular diastolic dysfunction in medical-ward patients with no prior history of cardiovascular disease to that of the patients with hepatic cirrhosis caused by alcohol abuse was carried out. The study is original from the point of view of examination of patients with cirrhosis of solely alcoholic aetiology in one Central-European university hospital. METHODS Three methods of echocardiographic examination were used: (i) pulse Doppler echocardiography to assess blood flow through the mitral valve and in the pulmonary veins, (ii) tissue Doppler imaging (TDI) to assess mitral annular motion, and (iii) colour M-mode Doppler echocardiography to assess blood flow from the left atrium into the left ventricle. RESULTS The results found confirmed that the incidence of left ventricular diastolic dysfunction in patients with alcohol-related liver cirrhosis, classified as Child-Pugh grade A and B, was significantly higher than in the controls without any prior liver disease. Furthermore, our research team has newly noticed how the severity of diastolic dysfunction affects the morbidity and mortality of patients undergoing such treatments as the transjugular intrahepatic portosystemic shunt (TIPS), liver transplantation and other surgical interventions resulting from different indications. CONCLUSION The high incidence of diastolic dysfunction in cirrhotic alcoholics should not be underestimated. Examination of diastolic dysfunction should be a standard procedure for making clinical decisions about these patients.