Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of the 1990 winter/spring bloom in Chesapeake Bay

The winterkpring bloom of 1990 in Chesapeake Bay. USA, was prolonged and well developed, relative to other recent years, along the axis of the Bay. However, the bloom did not occur uniformly along the axis of the Bay, but rather developed and dissipated at different times in different regions of the Bay. The peak of the bloom progressed northward and was observed in late March in South Bay, early April in Mid Bay, and not until mid May in North Bay. We measured biomass and nutrient concentrations and the rates of carbon, nitrogen, phosphorus, and silicon utilization during the development and dissipation of the bloom, and compared ratios of these rates to the elemental ratios of the incoming nutrients and the resulting particulate material. In North Bay, bloom development was probably delayed due to light limitation of carbon uptake. Nitrogen was delivered and utilized in excess of stoichiometric proportions in the northern part of the Bay, eventually leading to phosphorus and/or silicon limitation. In the mid portion of the Bay, the mean stoichiometric proportions of the particulate nutrients were similar to Redfield proportions, but ratios of uptake of nitrogen and phosphorus exceeded Redfield proportions by more than 20-fold, reflecting both the high uptake rates of nitrogen and low uptake rates of phosphorus in that region. However, only at the peak of the bloom in mid April did transient phosphorus limitation of growth occur at Mid Bay. In contrast, ratios of nitrogen to phosphorus uptake rates in South Bay were considerably below Redfield proportions, primarily due to the low availability and low uptake rates of nitrogen. Concentrations of Si(OH), in South Bay were also extremely low through the bloom period, and thus Si(OH), and nitrogen, as well as pod3-, limited growth there. In addition, temperature appeared to play a key role in the collapse of the diatom assemblage in mid May. During the early stages of the bloom in South Bay, No3+ NOzcontributed >60% of the total nitrogen utilized, but by the end of the spring bloom period in May, over 50% of the nitrogen uthzed was urea alone. These data underscore the need to understand how freshwater flow, ambient nutrient concentrations, temperature, and light dlffer along the axis of the Bay to understand the differential timing and magnitude of bloom development in different regions of the Bay.
Increasing the power of tumour control and normal tissue complication probability modelling in radiotherapy: recent trends and current issues

The release of a homogeneous high dose to the tumour region has been one of the cornerstones of radiotherapy (RT) treatment since its early days. According to the organ type and to the cancer histology, different doses are required in order to inactivate malignant cells, thus stopping proliferation. However, radiation-induced cell killing is a stochastic process. Tumour control probability (TCP) models have been developed in order to assign a success rate to a given RT treatment. At the same time, there is the need to keep the risks of normal tissue toxicity at an acceptable level. Normal tissue complication probability (NTCP) models provide a means of doing this. Traditionally, TCP and NTCP models combine clinical outcomes with dosimetric information in terms of dose-volume histograms (DVH). Model parameters are derived by mathematical fits to clinical observations and are subsequently used to estimate the risk of tumour relapse or toxicity. In both types of models, all of the patient dosimetric information is condensed into the DVHs, which represents a potential limitation on their descriptive and predictive power. This choice, related to historical and practical reasons, does not allow the full complexity of the 3D dose distribution in the patient to be taken into account. Neglecting these aspects might be relevant in a modern RT setting, which often includes the presence of high dose gradient regions. This has motivated research on ‘advanced’ TCP and NTCP models, able to tackle the problem by looking at a different scale, e.g. in tumour sub-regions or at the single voxel level. This is relevant not only from the purely dosimetric point of view. Increasing evidence is reported on the heterogeneity of cancer tissues, suggesting that non-uniform dose distributions could result in improved survival, for instance if targeted to take into account sub volumes with high clonogen density or hypoxic radioresistant regions. Similarly, radiation-induced side effects are part of a complex biological response, which depends not only on cell killing, but also on the inflammatory response and in some cases on the interplay among different organs. Obviously, conventional NTCP models cannot describe this scenario, and the development of more advanced mathematical tools is needed. This review will be focused on the discussion of recent studies showing possible directions for moving the field of TCP and NTCP modelling forward. Without diminishing the role and usefulness of available models, the aim is to shed light on the benefits that might be achieved by ‘enhanced’ modelling. This could represent an important step in the gradual transition of radiation therapy towards a form of precision medicine.
Technical Note: Reanalysis of upper troposphere humidity data from the MOZAIC programme for the period 1994 to 2009

Abstract. In situ observational data on the relative humidity (RH) in the upper troposphere and lowermost stratosphere (UT/LS), or tropopause region, collected aboard civil passenger aircraft in the MOZAIC (Measurements of OZone, water vapour, carbon monoxide and nitrogen oxides by in-service AIrbus airCraft) programme were reanalysed for the period 2000 to 2009. Previous analyses of probability distribution functions (PDFs) of upper troposphere humidity (UTH) data from MOZAIC observations from year 2000 and later indicated a bias of UTH data towards higher RH values compared to data of the period 1994 to 1999. As a result, the PDF of UTH data show a substantial fraction of observations above 100% relative humidity with respect to liquid water. Such supersaturations, however, do not occur in the atmosphere because there is always a sufficient number of condensation nuclei available, that trigger condensation as soon as liquid saturation is slightly exceeded. An in-depth reanalysis of the data set identified a coding error in the calibration procedure from year 2000 on. The error did not affect earlier data from 1994 to 1999. The full data set for 2000–2009 was reanalysed applying the corrected calibration procedure. Applied correction schemes and a revised error analysis are presented along with the reanalysed PDF of relative humidity with respect to liquid water (RHliquid) and ice (RHice).
SPECTROSCOPIC ORBITAL PERIODS FOR 29 CATACLYSMIC VARIABLES FROM THE SLOAN DIGITAL SKY SURVEY

We report follow-up spectroscopy of 29 cataclysmic variables from the Sloan Digital Sky Survey (SDSS), 22 of which were discovered by SDSS and seven of which are previously known systems that were recovered in SDSS. The periods for 16 of these objects were included in the tabulation by Gänsicke et al. While most of the systems have periods less than 2 hr, only one has a period in the 80–86 minutes “spike” found by Gänsicke et al., and 11 have periods longer than 3 hr, indicating that the present sample is skewed toward longer-period, higher-luminosity objects. Seven of the objects have spectra resembling dwarf novae, but have apparently never been observed in outburst, suggesting that many cataclysmics with relatively low variability amplitude remain to be discovered. Some of the objects are notable. SDSS J07568+0858 and SDSS J08129+1911 were previously known to have deep eclipses; in addition to spectroscopy, we use archival data from the Catalina Real Time Transient Survey to refine their periods. We give a parallax-based distance of 195 (+54, −39) pc for LV Cnc (SDSS J09197+0857), which at Porb = 81 m has the shortest orbital period in our sample. SDSS J08091+3814 shows both the spectroscopic phase offset and phase-dependent absorption found in SW Sextantis stars. The average spectra of SDSS J08055+0720 and SDSS J16191+1351 show contributions from K-type secondaries, and SDSS J080440+0239 shows a contribution from an early M star. We use these to constrain the distances. SDSS J09459+2922 has characteristics typical of a magnetic system. SDSS11324+6249 may be a novalike variable, and if so, its orbital period (99 minutes) is unusually short for that subclass.
Experimental Study of the Crush Evolution and its Effect on the Expanded Clay Behavior

Abstract: Granular materials forming part of the structural elements for civil engineering, structures such as road embankments, the base of pavement and foundations. Among these materials, there are those where the grains have a brittle behavior: «crushing » It is, therefore important to study the crushing phenomenon of granular materials, because we need to better understand the behavior of this type of materials and provide information on the crushing evolution. The current work is an experimental study of the granular materials behavior subjected to crushing phenomenon. The expanded clay was chosen as a model material thanks to its brittle crushing behavior toward compressive forces. The study of this phenomenon can be very helpful to understand the soil’s behavior toward several types of loading. Uniaxial and triaxial compression tests were made to understand the effect of crushing on the grain size distribution, soil’s frictional properties and mechanical behavior
Real Time Object Tracking with Sparse Prototypes

Sparse representation (compressive sampling) has achieved impressive results in object tracking by looking for the best candidate with minimum reconstruction error using the target template. However, it may fail in some circumstances such as illumination changes, scale changes, the object color is similar with the surrounding region, and occlusion etc., in addition, high computational cost is required due to numerous calculations for solving an l1 norm related minimization problems. In order to resolve above problems, a novel method is introduced by exploiting an accelerated proximal gradient approach which aims to make the tracker runs in real time; moreover, both classic principal component analysis algorithm and sparse representation schemes are adapted for learning effective observation model and reduces the influence of appearance change. Both qualitative and quantitative evaluation demonstrate that the proposed tracking algorithm has favorably better performance than several state-of-the-art trackers using challenging benchmark image sequences, and significantly reduces the computing cost.
Microscopy techniques applied to the study of cell death in bacteria from freshwater ecosystems

T.P. Silva, J.P. Gamalier, N.S. Resende, N.O. Barros and R.C. N. Melo Laboratory of Cellular Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, MG, 36036-900, Juiz de Fora, MG, Brazil 2 Laboratory of Aquatic Ecology, Institute of Biological Sciences, Federal University of Juiz de Fora, MG, 36036-900, Juiz de Fora, MG, Brazil * Corresponding author: rossana.melo@ufjf.edu. br
CHAPTER 4 Immunological aspects of Y . pestis and vaccines

Plaque vaccines have been used since 1896 and have been found to reduce the incidence and severity of bubonic plague resulting from the bite of infected fleas. Both viable and nonviable plague vaccines have been associated with mild to severe side effects. In the mid-1900's, a formalinkilled whole cell vaccine was licensed and sold as "Plague Vaccine", USP in the U.S.A. An effective vaccine against pneumonic plague is yet to be developed. New approaches to effective vaccine development without side effects involve development of purified proteins such as the F1 capsular antigen and the V (LcrV) protein at the tip of the injectisome. The development of avirulent recombinant surrogate bacterial vaccines such as Salmonella harboring these Y. pestis proteins has been investigated, in addition to the use of plant and viral vector vaccines.
A Model of an Optimum Currency Area ip

This paper develops a two-country model to investigate the circumstances under which it is beneficial to participate in a currency area. It captures both the real and monetary arguments suggested by the optimum currency area literature in a simple monetary model of trade with nominal rigidities. The net benefits that one country expects from participation in a currency union increase with: the correlation of real shocks between countries; the degree of international labor mobility; the degree of adjustment provided by a fiscal tool; the difference between the inflationary bias of the domestic authority and the inflationary bias of the authority of the currency union; the variability of domestic monetary shocks; the extent of the deadweight and efficiency gains deriving from the adoption of a single currency. The same net benefits decrease with: the variability of real shocks; the variability of foreign monetary shocks; and the correlation of monetary shocks between countries. The effect of the degree of openness on the net benefits is ambiguous. This last result contrasts with the usual argument that the more open economies are the better candidates they make for a currency area.
The Role of E2 Proteins in Papillomavirus DNA Replication

Papillomaviruses are small, nonenveloped, double-stranded DNA viruses, which infect a wide variety of vertebrate species and induce proliferative lesions in their host. The viruses are species-specific and to date, more than 150 different types of papillomaviruses have been identified; each virus infects a specific region of cutaneous or internal mucosal epithelium in its host (McLaughlin-Drubin and Munger, 2009). Papillomaviruses are widely spread in nature and in most cases, papillomavirus infections are cleared by the host immune system, however, sometimes papillomaviruses establish persistent infections. Papillomavirus classification is based on nucleotide sequence homology (de Villiers et al., 2004). Human papillomavirus (HPV) types that infect the genital epithelia belong to subgroup A (alphapapillomaviruses), and are classified into highor low-risk types, depending upon their oncogenic potential. Persistent infection with high-risk HPVs (HPV16, 18, 31, 33, 45) can lead to cervical cancer, the second most common cancer in women (Durst et al., 1983; zur Hausen, 2000). Low-risk HPVs, such as HPV6 and 11, can infect genital tract as well as oral sites where they are generally associated with benign papillomas. The second major group of HPVs, supergroup B, also known as beta-papillomaviruses, infect skin epithelia and may develop skin cancers at the site of HPV infection (McLaughlin-Drubin and Munger, 2009).
CR-39 SAMPLING OF INDOOR RADON IN SOUTHERN ROMANIA

The new Solid State Nuclear Track Detector (SSNTD) Indoor Radon Laboratory of the Applied Nuclear Physics Department at the Horia Hulubei National Institute of Physics and Nuclear Engineering (IFIN) employs CR-39 plastic detectors and a Radosys set-up [1]. It is mainly aimed at the regional coverage of the necessities of indoor radon measurements especially in the Southern part of Romania, but also to become a reliable member of a National Radon network. The implementation of this technique brought along a series of tests for the better understanding of this already well established method, and was doubled by indoor sampling measurements at various sites. The geographical region covered by our study was expected to be of reasonably low impact, compared to radon prone areas in the country (e.g. Crucea in Moldova, Stei in Transylvania), however, as to our present knowledge, the statistic of existing measurements for this region is low and any new data are welcome. Radon originates from the U Ra natural decay series and escapes into air easily from the material in which it is formed (be it soil, rocks, water or building materials). The air we inhale (outdoors or indoors) contains radon. Average radon
The use of touch-screen tablets at home and pre-school to foster emergent literacy

Young children living in technology-based communities are using touch-screen tablets (e.g. iPads) to engage with the digital world at an early age. The intuitive touch-screen interface, easily downloadable apps (applications) and mobility of tablets drive their increasing popularity with pre-schoolers. This review examines research to date on tablets, apps and emergent literacy in young children in the home and at pre-school. Evidence is building that suggests tablets have the potential to foster emergent writing and letter knowledge. Although the impact of tablets on emergent literacy is not yet fully known, developing themes highlight potential benefits and hindrances of tablets for emergent literacy. Two important considerations are the quality of emergent literacy apps and the importance of scaffolding young children's use of tablets at home and pre-school to support emergent literacy development. Directions for future research and recommendations for parents and teachers are discussed.
Detection of Invalid Response Patterns on the California Psychological Inventory

When faced with the task of responding to a per sonality questionnaire, an individual may respond with a number of strategies or test-taking attitudes. Among these, deceptive (fake) and disengaged (random) atti tudes are of particular interest, for these can poten tially mislead and misinform test users. A two-stage model was devised to detect deceptive and disengaged protocols on the California Psychological Inventory. Using parameters from signal detection theory, this model is found to be highly sensitive in detecting in- validity. Index terms: California Psychological In ventory, expected utility, faking on personality inven tories, personality assessment, random response patterns, signal detection theory.
DIFFERENT IDENTIFICATION METHODS WITH APPLICATION TO A DC MOTOR

Neural networks and fuzzy inference systems are becoming wellrecognized tools of designing an identifier / controller capable of perceiving the operating environment and human operator with high performance. The purpose of this paper is to identify different models for a DC-servo system using the previous identification methods and linear identification methods as ARX, ARMAX and state space models. The paper compares between these methods and presents the practical results for the application these methods.
GEOCHEMISTRY OF VOLCANIC ASH LAYERS FROM LEG 87 A , NANKAI TROUGH ( SOUTH JAPAN ) 1

In the Leg 87A holes, 45 ash layers were sampled in Recent to upper Pliocene strata. The main volcanogenic deposits came from single eruptions or subcontemporaneous eruptions of cognate volcanoes. Some of them are mixed ashes produced from multiple eruptions and accumulated in reworked sediments. The petrographic and geochemical patterns indicate rhyolitic and dacitic compositions; andesitic glasses are scarce. We infer a magmatic affinity with calc-alkaline sources and a possible origin from the volcanic arc of southwestern Japan. A few samples may originate from the alkaline volcanism of southwestern Japan or the area south of Korea and the Sea of Japan.
Temporal Concurrent Planning with Stressed Actions

Temporal stress is something that humans have to face nearly every day. Humans have to handle situations, where there is not much time left for a specific task. Most robotic systems, on the other hand, are not able to act in such temporally unstructured environments. For that reason, we present the novel Temporal Stressing Fast Downward (TSFD)planning system based on Temporal Fast Downward (TFD), which solves temporal problems using a modified heuristic forward search. With this planner, we introduce the novel concept of stressed actions for temporally bounded problems. Stressed actions enable a robot to accelerate or decelerate actions under consideration of an action-specific temporal cost function and the available time for plan execution. We further introduce an improved decision epoch search that allows complete planning with temporal gaps. Our evaluation in benchmark domains and on the real humanoid robot ARMAR-III shows that TSFD has the ability to produce plans of better makespan than TFD and is able to solve problems that could not be handled before. Furthermore, TSFD performs better in typical service robotics tasks than baseline approaches. Finally, we show that stressed actions greatly increase the possibility of finding feasible solutions in temporally bounded tasks.
In vitro functional characterization of genes mediating breast cancer metastasis to the brain

1 – Summary The aggressive behavior of tumor metastasis and the lack of effective treatments are conditions that warrant the study of basic mechanisms of metastasis. The brain is one of the sites where breast cancer often forms metastasis. A model of spontaneous breast cancer brain metastasis has been previously generated in the laboratory and a gene expression profile has been determined. From the microarray analysis a list of genes with potential clinical relevance for breast cancer metastasis to the brain has been identified, based on their correlation with reduced BMFS (Brain Metastasis-Free Survival) parameter as determined by bioinformatic analysis of breast cancer gene expression data bases. The aim of this project was to functionally characterize a subset of these up-regulated genes previously identified in genome-wide screening to mediate spontaneous experimental breast cancer metastasis to the brain, in order to understand the biological implications of these selected genes. Here we provide evidence that the Cx31 protein promotes cell proliferation, resistance to apoptosis and stem cell self-renewal potential. In addition, the EDN1 peptide provides a pro-migratory pattern, promoting effects of resistance to apoptosis and stem cell self-renewal potential. Further findings are a pro-migratory activity of CTGF and a promoting stem cell self-renewal potential of IL1R2. In short, results obtained from this project are expected to contribute to a better understanding of the mechanism of breast cancer metastasis to the brain and to identify novel therapeutic approaches.