Miracle-dz/UniFAR-FTUs huggingface dataset:
Inducing Structural Prototypes for the Classification of Semi-Structured Data

The internet has evolved from a network of documents into a network of heterogeneous web applications. Semi-structured data offers enough structural flexibility, while providing the necessary semantic annotation to transfer information between those applications. Today the XML Data Model is the de facto standard meta-model for semi-structured data on the internet. Due to its generic nature, XML has become the foundation of numerous domain specific formats, causing an abundance of XML data that holds considerable potential for data analysis. This paper presents a case-based reasoning framework for classifying semi-structured data. It supports the extraction of a prototype tree from a cluster of data trees, as well as the classification of a data tree, based on its similarity to a set of prototype trees. By representing each cluster with only one prototype, an acceptable runtime of the classification can be maintained, even if the data clusters keep on growing.
An alternative technique for the long-term satellite tracking of leatherback turtles

The satellite transmitter fixed on a harness was, until a short time ago, the commonly used attachment technique to follow oceanic movements of the soft-shelled leatherback turtle Dermo- chelys coriacea. However, harnesses have recently been reported to have a potential welfare impact during long-term deployments in this species. Here, we present the first long-term (3 mo) monitoring of 2 leatherback turtles tracked with satellite transmitters directly attached to the carapace and compare tracking data with 3 other turtles, that were concurrently satellite-tracked with traditional harnesses. There were significantly more good quality locations recorded for carapace-equipped turtles than for turtles with harnesses, which suggests that the satellite transmitter is better directly fixed to the carapace. The mean locomotor travel rate (i.e. turtle's own motion taking potential current drift into account) for turtles with harnesses was 16% slower (0.50 ± 0.01 and 0.59 ± 0.02 m s -1 , respec- tively) and dives were 12% shorter (23.2 ± 0.8 and 26.3 ± 0.8 min, respectively) than for carapace- equipped turtles, but all were to a similar depth (87.0 ± 3.1 and 80.7 ± 2.9 m, respectively). Despite our small sample sizes, these first results suggest a marked hydrodynamic impact of the harness on the leatherback's swimming and diving capabilities, and stress the need for further developments to improve long-term monitoring while reducing hydrodynamic constraints for this species.
A highly automated method for simulating airfoil characteristics at low Reynolds number using a RANS-transition approach

The paper presents a novel procedure that highly automates subsonic airfoil simulations using a volume resolving Reynolds-Averaged Navier-Stokes approach (RANS). The procedure is designed to minimize human interaction to what is known from 2D panel schemes like XFOIL. Natural transition effects are captured with the -Re model, which makes the approach especially suited to low Reynolds number flows. The new procedure combines existing geometry and simulation software and completely automates the setup from mesh generation to solving and post-processing. Manual interaction is reduced to specifying airfoil shapes and flow parameters. A variety of validation cases is presented comparing the novel approach to wind tunnel measurements and respective XFOIL calculations. Airfoil lift, drag, moment and transition location show very good accuracy. The novel procedure shows superior performance for critical cases that involve large laminar separation bubbles when compared to XFOIL. It greatly enhances the ability to use RANS airfoil simulations in aerodynamic research or aircraft design.
Cross-Architecture Automatic Critical Path Detection For In-Core Performance Analysis

The creation of performance models is an essential part of optimizing scientific software. To run static performance analyses on code snippets, it is crucial to obtain an accurate in-core execution time prediction, which is highly dependent on the micro-architecture of the chip. Our previously developed Open Source Architecture Code Analyzer (OSACA) tool is a static performance analyzer for predicting the execution time of sequential loops. It previously supported only x86 (Intel and AMD) micro-architectures and simple, full-throughput prediction. We heavily extended its functionality by the detection of dependencies within and across assembly loops to identify the critical path and loop-carried dependencies. This enables a much improved runtime prediction in steady state execution. Furthermore, we enhanced the throughput prediction and added support for ARM-based micro-architectures, which turns OSACA into a versatile cross-architecture modeling tool. While its throughput and loop-carried dependency analysis give a lower bound runtime prediction, its critical path analysis can function as an upper bound for the execution time. We evaluate the quality of the analysis for code on Intel Cascade Lake, AMD Zen, and Marvell ThunderX2 micro-architectures based on machine models from available documentation and semi-automatic benchmarking. The predictions are compared with measurements and the analysis results from the related tools Intel Architecture Code Analyzer (IACA) and LLVM Machine Code Analyzer (LLVM-MCA). The comparison shows that OSACA is to date the most capable and versatile in-core runtime prediction tool available.
Bacteriochlorophyll a in the ocean: Is anoxygenic bacterial photosynthesis important?

Some groups of marine bacteria within the Α‐proteobacteria are capable of anoxygenic photosynthesis in oxic environments. Their primary photosynthetic pigment is bacteriochlorophyll a (BacChl a). The impact of these bacteria on flows of energy and carbon in the ocean has been difficult to ascertain in the past. Recently, however, Kolber et al. (2001) reported that such bacteria are abundant in the upper ocean and that these might contribute significantly to photosynthetically driven electron transport since measured and inferred ratios of BacChl a and chlorophyll a (Chl a) were about 0.8% in coastal environments and as high as 10% in the Eastern Tropical North Pacific. The authors suggested that the globally averaged BacChl a/Chl a ratio could be as high as 5 to 10%. To determine whether such high values are representative of other marine environments, concentrations of BacChl a were measured in samples collected in eutrophic nearshore and mesotrophic and oligotrophic offshore environments off Southern California. The average BacChl a/Chl a ratio was 1.1% in nearshore and 0.5% in mesotrophic shelf and oligotrophic offshore environments. Assuming that rates of photosynthesis scale with concentrations of photosynthetic pigments, these data suggest that the contribution of BacChl a driven anoxygenic bacterial photosynthesis to energy production in coastal eutrophic and offshore oligotrophic areas of the California current system is small, substantially smaller than the suggested global average of 5 to 10%.
The Validation of the ATRIA and CHA2DS2-Vasc Scores in Predicting Atrial Fibrillation after Coronary Artery Bypass Surgery

Objective The aim of this study was to evaluate the value of CHA2DS2-VASc and Anticoagulation and Risk Factors in Atrial Fibrillation (ATRIA) risk scores for prediction of postoperative atrial fibrillation (AF) development in patients undergoing coronary artery bypass grafting (CABG) operation. Methods The population of this observational study consisted of 370 patients undergoing CABG operation. CHA2DS2-VASc and ATRIA risk scores were calculated for all patients and their association with postoperative AF (AF episode lasting > 5 min) were evaluated. Predictors of postoperative AF were determined by multiple logistic regression analysis. Results During follow-up, 110 patients (29.7%) developed postoperative AF. With multiple logistic regression analysis, risk factors for postoperative AF were determined: ATRIA risk score (odds ratio [OR] 1.23; 95% confidence interval [CI] 1.11-1.36; P<0.001), fasting glucose level (OR 1.006; 95% CI 1.004-1.009; P<0.001), and 24-hour drainage amount (OR 1.002; 95% CI; 1.001-1.004; P<0.001). Receiver operating characteristic curve analyses showed that CHA2DS2-VASc and ATRIA risk scores were signiﬁcant predictors for new-onset AF (C-statistic 0.648; 95% CI 0.59-0.69; P<0.001; and C-statistic 0.664; 95% CI 0.61-0.71; P<0.001, respectively). Conclusion CHA2DS2-VASc and ATRIA risk scores predict new AF in patients undergoing CABG.
Gaussian Processes for Plume Distribution Estimation with UAVs

Recent scientific work explored the possibility to use mobile robots for environmental monitoring. This includes for example the estimation of ozone concentrations or locating the source of a pollutant plume. So far the modeling of the complete spatial distribution of a plume (which has different spatial characteristics compared to the ozone concentrations) has not been done. In this work existing methods of Bayesian optimization, namely global optimization (GO) and the distance based upper confidence bound (DUCB), were evaluated on this task. Also, a new method – plume distance based upper confidence bound (PDUCB) – and an extension to multiple robots is proposed. All methods were tested in simulations using the QRSim quadrotor simulator. The existing methods were not able to solve the task satisfyingly, whereas the PDUCB method was able to approximate plume distributions with noisy measurements reasonably well.
Seasonal patterns of soil respiration in intact and clear-cut northern hardwood forests

The flux of CO2 from forest soils is controlled by the respiration of plant roots and soil microorganisms, the rates of which are likely to change following forest harvesting. Root respiration should decrease, whereas microbial respiration should increase, in response to warmer soil temperatures and greater soil C availability following removal of the overstory. We investigated the influence of forest harvesting on seasonal patterns of soil respiration in two different northern hardwood ecosystems. One ecosystem was dominated in the overstory by Acersaccharum Marsh, and Quercusrubra L. , and the other by A. saccharum and Tiliaamericana L. ; two stands were studied in each ecosystem type. We measured daily rates of soil respiration using the soda-lime technique. Averaged across ecosystems, daily rates of soil respiration did not significantly differ between intact and clear-cut plots, nor did they differ between ecosystems or sites nested within ecosystems. Peak daily rates ranged from 2.75 to 3.00 g CO2-C•m.
Levels in Stabilization of Cell Differentiation and Its Experimental Transformation

Summary Ideas concerning the mechanism of cell phenotype and differentiation, i.e., the stability of the differentiated state, are considered. It is suggested that cell differentiation is based on a continuous reprogramming of nuclear function, including the coding both for substances specific to the terminal differentiation and for the programming factors themselves. A system of barriers prevents extrinsic programming factors from being predominant over the intrinsic ones. Cell differentiation can be altered by removing the barriers and thus allowing new programming factors to become prevalent. Examples of the artificial transformation of cell differentiation and its close relation to embryonic induction are discussed.
Crown architecture of the ginger Alpinia scabra (Zingiberaceae) in a tropical submontane forest, Indonesia Alpinia scabra

Crown architecture of a ginger, Alpinia scabra (Zingiberaceae), was studied on Mount Halimun in a tropical submontane forest in West Java, Indonesia. An aboveground shoot of A. scabra consists of one pseudostem and many leaves distributed along the pseudostem. The pseudostem is up to ca. 2 m long. The number of nodes per pseudostem increases, up to 25, with increasing pseudostem length. Pseudostems of smaller A. scabra stand vertically, while those of larger A. scabra bend. On the contrary, the leaf surface is horizontally oriented, irrespective of the pseudostem angle at each node. The horizontal orientation of leaf surface is thought to be effective for capturing the most light per unit leaf area. The internode length decreases from the base of the pseudostem to the tip, i.e., the internode length decreases with increasing pseudostem length, accompanied with stem bending. The ontogenic changes of leaf size in large individuals of A. scabra show that leaf size increases from the base of the pseudostem to the mid-point of pseudostem, and levels off or slightly decreases thenceforth. Thus, leaves were small near the base, where pseudostems stood vertically, and increased in size with pseudostem bending. The combination of an erect pseudostem and small leaves near the base contributes to less vertical overlap of leaves there. The results of this study suggest that A. scabra distributes leaves for efficient light capture by adjusting the internode length, leaf angle, pseudostem angle, and leaf size along the pseudostem.
KGBuilder: A System for Large-Scale Scientiﬁc Domain Knowledge Graph Building

With constantly booming, Knowledge Graphs (KGs) are attracting more attention. Based on various criteria, they can be divided into different categories. For example, if a KG is used to describe linguistic knowledge in some language (like the lexical database for English, WordNet[Miller, 1995]), it can be called the language one. Then, others can be called fact one, like Freebase[Bollacker et al., 2008]. Here, we adopt the open and specific domain one, focusing on the microbiology KG. So what is it like?
The Casuarina glauca metallothionein I promoter in nodulated transgenic hairy roots of the actinorhizal plant Datisca glomerata.

The activity of the promoter of a metallothionein gene expressed in actinorhizal nodules of Casuarina glauca Sieber ex Spreng. , CgMT1, has previously been analysed in Casaurinaceae and in tobacco (Nicotiana tabacum L.), Arabidopsis and rice. In all these plants, the promoter showed high activity in the root cortex and epidermis, making it a useful tool for the expression of transgenes. Therefore, its activity was now analysed in transgenic root systems of Datisca glomerata (C. Presl) Baill, an actinorhizal plant from a different phylogenetic group than C. glauca, using the same CgMT1::GUS fusion as in previous studies. However, in contrast with all other plant species examined previously, the CgMT1::GUS construct showed no activity at all in D. glomerata hairy roots: the expression pattern in nodules resembled that found in C. glauca nodules. This is probably due to the changed hormone balance in hairy roots since experiments on the CgMT1::GUS construct in transgenic Arabidopsis showed that CgMT1 promoter activity was repressed by auxin or cytokinin, respectively. Yet, in hairy roots of the model legume Lotus japonicus L. induced by the same Agrobacterium rhizogenes strain, the CgMT1 promoter was active in roots and not in nodules. These results indicate that although the expression of pRi T-DNA genes leads to changes in root hormone balance, these changes do not abolish the differences in phytohormone levels or sensitivity between plant species. Therefore, gene expression data obtained using transgenic hairy root systems have to be viewed with care, not only due to the disturbed hormone balance, but also because the effects of the pRI-T-DNA genes can differ between species.
Fermentative and nutritive quality of banana by-product silage for goats

This study was carried out to ascertain the ensiling capacity of fresh banana packaging industries by-products and the chemical composition and fermentative characteristics of the silage. Ensilability parameters were analysed in five different combinations [100% green banana (GB), 100% bunch (b), 30% GB–70% b, 50% GB–50% b and 100% ripe banana (RB)]. Subsequently, according to ensilability results, three combinations were selected [100% GB, 50% GB–50% b, 50% GB–50% b + additives, 10% molasses and 7% beet pulp] in order to assess the quality and stability over time of the experimental banana microsilages. The 50% GB–50% b combination showed the acceptable silage characteristics but requires certain additives to improve the fermentative process. The combination with better results, when assessed for quality and stability during the preservation process, was 50% GB–50% b + additives allowing to increase the initial dry matter (DM) and soluble sugars. This combination showed a good aptitude for ensilage, having a pleasant smell and good visual characteristics. The banana by-product showed moderate silage DM (20–30%) and organic matter (85–94%) content and low protein and fibre values. The chemical composition did not vary significantly along the conservation process. The three combinations of banana by-product silage studied presented a moderate DM content and a low protein value, with lower values in the 50% GB–50% b.
HOW MANY ANIMALS REALLY DO THE LÉVY WALK

Levy walks (LW) are superdiffusive and scale-free random walks that have recently emerged as a new conceptual tool for modeling animal search paths. They have been claimed to be more efficient than the "classical" random walks, and they also seem able to account for the actual search patterns of various species. This suggests that many animals may move using a LW process. LW patterns look like the actual search patterns displayed by animals foraging in a patchy environment, where extensive and intensive searching modes alternate, and which can be generated by a mixture of classical random walks. In this context, even elementary composite Brownian walks are more efficient than LW but may be confounded with them because they present apparent move-length-heavy tail distributions and superdiffusivity. The move-length "survival" distribution (i.e., the cumulative number of moves greater than any given threshold) appears to be a better means to highlight a LW pattern. Even once such a pattern has been clearly identified, it remains to determine how it was actually generated, because a LW pattern is not necessarily produced by a LW process but may emerge from the way the animal interacted with the environment structure through more classical movement processes. In any case, emergent movement patterns should not be confused with the processes that gave rise to them.
At‐line Monitoring of Bioprocess‐Relevant Marker Genes

The efficiency of an industrial bioprocess depends above all on the physiology of the host organism. Therefore, a rapid and direct analysis of the host's physiology during fermentation processes would be a worthwhile tool to improve the control of such bioprocesses in the future. This could be achieved by monitoring process‐relevant marker genes, the expression of which indicates unfavorable growth conditions. Recently it was shown that electrical DNA‐chips in combination with a magnetic bead‐based sandwich hybridization (BBSH) assay are a suitable alternative technique for a fast analysis of gene expression by monitoring the respective mRNA. In the present study, an improved protocol was established that allows for a shorter but still sensitive detection of specific mRNAs. The presented optimized BBSH protocol in combination with an electrochemical readout system was successfully applied for the analysis of Bacillus licheniformis marker genes indicating glucose‐ (acoA), nitrogen‐ (glnA) and phosphate‐ (phy, pstS) starvation. The expression profiles determined for all marker genes corresponded with the respective real‐time RT‐PCR measurements. Thus, the optimized protocol, in combination with the electrical chip, could provide the basis for a continuous at‐line monitoring of such biomarkers during bioprocesses.
Peroxidation of erythrocytes: FTIR spectroscopy studies of extracted lipids, isolated membranes, and intact cells

Fourier transform infrared (FTIR) spectroscopy was used to directly monitor peroxidative damage to membrane phospholipid acyl chains in erythrocyte membranes. Samples were suspended in a mixed 2H2O/H2O buffer system, thereby producing a “spectral window” in the C-H stretching region of the infrared spectrum. A decrease in the number of acyl chain CC bonds upon erythrocyte peroxidation was quantitated directly from the spectra of isolated membranes. Second-derivative spectroscopy permitted the conformationally sensitive membrane acyl chain methylene stretching modes to be separated from the protein (mostly hemoglobin) vibrations that dominate the spectra of intact cells. The sensitivity of these modes in erythrocytes was then determined in a series of thermotropic experiments. The effect of peroxidation upon the membrane acyl chain conformational order was monitored in isolated membranes and intact cells. No change in conformational order was detected upon peroxidation in intact cell and ghost spectra. In contrast, experiments with pure unsaturated phospholipids demonstrated that decreasing the CC bond population results in increased conformational order. The finding of identical results for peroxidation versus control samples in isolated membranes (“ghosts”) validates the results observed for intact cells. FTIR technology permits the direct monitoring of conformational order in the acyl chains of intact cells. © 1995 John Wiley & Sons, Inc.
Medizinische Versorgung

Mit der Einführung der Gesundheitskarte für Geflüchtete in Thüringen am 01.01. 2017 müssen nur noch sehr wenig medizinische Leistungen vom Sozialamt genehmigt werden (siehe Leistungsbereich C im Anhang der Rahmenvereinbarung [3]). Zuständig für die Gesundheitsversorgung sind die Sozialämter. In der Praxis besteht allerdings immer noch ein uneinheitliches Vorgehen der Sozialämter. Es werden nicht alle erforderlichen medizinischen Leistungen gewährt. Ein ungehinderter Zugang zu medizinischer Versorgung ist daher dringend notwendig.
Effect of Gama Irradiation of Bioethanol Producing Microorganisms on Bioethanol Formation from Sugarcane Bagasse and Potato Peels

HE PRESENT work was designed to investigate the production . of bioethanol from agriculture feedstock (sugarcane bagasse and potato peels) using Saccharomyces cerevisiae ATCC 7754 and Zymomonas mobilis ATCC 29191, exposed to different doses of gamma irradiation (0, 100, 300, 500, 1000 and 1500 Gy). The effect of different hydrolysis pretreatments of feedstock on resulting sugars (initial sugars), which were later fermented to bioethanol, was also tested and compared to non-hydrolyzed feedstock. Hydrolysis of sugarcane bagasse and potato peels was conducted with dilute sulphuric acid (2 and 6 % v/v), running at 100 and 120 ̊C for 30 and 60 min of retention time. The highest bioethanol concentration obtained from sugarcane bagasse was 10.3 gL -1 , which was produced by Sacch. cerevisiae ATCC 7754 irradiated at 300 Gy from hydrolysate of 2 % (v/v) H2SO4 at 120°C for 60 min treatment. From the same treatment, the highest bioethanol concentration obtained by Z. mobilis ATCC 29191 was 4.4 gL -1 , when irradiated at 100 Gy. This acid treatment produced 23.7 gL -1 of sugars from the feedstock. The highest bioethanol concentration obtained from potato peels was 7.5 gL -1 , produced by Sacch. cerevisiae ATCC 7754 irradiated at 300 Gy from hydrolysate of 6 % (v/v) H2SO4 at 100°C for 60 min treatment, followed by 5.7 gL -1 produced by Z. mobilis ATCC 29191 irradiated at 100 Gy. This treatment produced 24 gL -1 of sugars from the feedstock.