Miracle-dz/UniFAR-FTUs huggingface dataset:
Refining physical aspects of soil quality and soil health when exploring the effects of soil degradation and climate change on biomass production: an Italian case study

Abstract. This study focuses on soil physical aspects of soil quality and health with the objective to define procedures with worldwide rather than only regional applicability, reflecting modern developments in soil physical and agronomic research and addressing important questions regarding possible effects of soil degradation and climate change. In contrast to water and air, soils cannot, even after much research, be characterized by a universally accepted quality definition and this hampers the internal and external communication process. Soil quality expresses the capacity of the soil to function. Biomass production is a primary function, next to filtering and organic matter accumulation, and can be modeled with soil–water–atmosphere–plant (SWAP) simulation models, as used in the agronomic yield-gap program that defines potential yields (Yp) for any location on earth determined by radiation, temperature and standardized crop characteristics, assuming adequate water and nutrient supply and lack of pests and diseases. The water-limited yield (Yw) reflects, in addition, the often limited water availability at a particular location. Actual yields (Ya) can be considered in relation to Yw to indicate yield gaps, to be expressed in terms of the indicator (Ya/Yw)×100. Soil data to calculate Yw for a given soil type (the genoform) should consist of a range of soil properties as a function of past management (various phenoforms) rather than as a single representative dataset. This way a Yw-based characteristic soil quality range for every soil type is defined, based on semipermanent soil properties. In this study effects of subsoil compaction, overland flow following surface compaction and erosion were simulated for six soil series in the Destra Sele area in Italy, including effects of climate change. Recent proposals consider soil health, which appeals more to people than soil quality and is now defined by separate soil physical, chemical and biological indicators. Focusing on the soil function biomass production, physical soil health at a given time of a given type of soil can be expressed as a point (defined by a measured Ya) on the defined soil quality range for that particular type of soil, thereby defining the seriousness of the problem and the scope for improvement. The six soils showed different behavior following the three types of land degradation and projected climate change up to the year 2100. Effects are expected to be major as reductions of biomass production of up to 50 % appear likely under the scenarios. Rather than consider soil physical, chemical and biological indicators separately, as proposed now elsewhere for soil health, a sequential procedure is discussed, logically linking the separate procedures.
Weak Convergence and Uniform Normalization in Infinitary Rewriting

We study infinitary term rewriting systems containing finitely many rules. For these, we show that if a weakly convergent reduction is not strongly convergent, it contains a term that reduces to itself in one step (but the step itself need not be part of the reduction). Using this result, we prove the starkly surprising result that for any orthogonal system with finitely many rules, the system is weakly normalizing under weak convergence if{f} it is strongly normalizing under weak convergence if{f} it is weakly normalizing under strong convergence if{f} it is strongly normalizing under strong convergence. As further corollaries, we derive a number of new results for weakly convergent rewriting: Systems with finitely many rules enjoy unique normal forms, and acyclic orthogonal systems are confluent. Our results suggest that it may be possible to recover some of the positive results for strongly convergent rewriting in the setting of weak convergence, if systems with finitely many rules are considered. Finally, we give a number of counterexamples showing failure of most of the results when infinite sets of rules are allowed.
A time-invariant principle of genome evolution

Uncovering general principles of genome evolution that are time-invariant and that operate in germ and somatic cells has implications for genome-wide association studies (GWAS), gene therapy, and disease genomics. Here we investigate the relationship between structural alterations (e.g., insertions and deletions) and single-nucleotide substitutions by comparing the following genomes that diverged at different times across germ- and somatic-cell lineages: (i) the reference human and chimpanzee genome (in million years), (ii) the reference human and personal genomes (in tens of thousands of years), and (iii) structurally altered regions in cancer and genetically engineered cells (in days). At the species level, genes with structural alteration in nearby regions show increased single-nucleotide changes and tend to evolve faster. In personal genomes, the single-nucleotide substitution rate is higher near sites of structural alteration and decreases with increasing distance. In human cancer cell populations and in cells genetically engineered using zinc-finger nucleases, single-nucleotide changes occur frequently near sites of structural alterations. We present evidence that structural alteration induces single-nucleotide changes in nearby regions and discuss possible molecular mechanisms that contribute to this phenomenon. We propose that the low fidelity of nonreplicative error-prone repair polymerases, which are used during insertion or deletion, result in break-repair-induced single-nucleotide mutations in the vicinity of structural alteration. Thus, in the mutational landscape, structural alterations are linked to single-nucleotide changes across different time scales in both somatic- and germ-cell lineages. We discuss implications for genome evolution, GWAS, disease genomics, and gene therapy and emphasize the need to investigate both types of mutations within a single framework.
Análisis multitemporal (1937-2010) de la línea de costa de la isla de manzanillo, bahía de Cartagena - Colombia

El proposito de este estudio consistio en determinar y describir la tasa de avance\retroceso actual de la linea de costa de la Isla de Manzanillo, partiendo de datos obtenidos por sensores remotos, durante el periodo comprendido entre los anos 1937 y 2010, donde se evidencio un retroceso moderado de la linea de costa, con un lento erosivo y de accion constante. Para este analisis se debio establecer, comparar y evaluar las variaciones a traves de imagenes aereas. Se utilizaron programas digitales, que facilitaron el procesamiento de estas imagenes, las cuales admiten la comparacion de la linea de costa con un minimo grado de error. Se desarrollo con un eje tematico sobre procesos costeros y en concordancia con el estudio “Analisis multitemporal (1937-2010) de la linea de costa de la Isla de Manzanillo, por efecto de oleaje y procesos antropicos” (Bahia de Cartagena - Colombia). Palabras clave: Acrecion, Erosion, Aerofotografia, Linea de costa, Georreferenciacion. Abstract: The purpose of this study consisted on determining and describing the coast line advance and retreat rates of Manzanillo Island, using remote sensors data within 1937 and 2010, where a moderate setback of the coast line was evidenced, with a slow erosive process of constant action. To get this analysis were compared and evaluated the variations using aerial images. Digital programs were used to facilitate the procedure of these images; they admit the comparison of the coast line with a minimum degree of error. It was developed with a thematic axis on coastal process and in agreement with the “Multitemporal Analysis (1937-2010) of Manzanillo Island coast line, due to wave and anthropic effects”. Key words: Accretion, Erosion, Airphotography, Coastline, Geographic references.
UV and optical emission lines from the z∼ 2.6 radio galaxy 0828+193: spatially resolved measurements

We present an investigation into the spatial variation of the rest-frame ultraviolet (UV) and optical line and continuum emission along the radio axis of the z ∼ 2.6 radio galaxy 0828+193, using long-slit spectra from the Keck II and Subaru telescopes. Line brightnesses, line ratios and electron temperatures are examined, and their relationship with the arm-length asymmetry of the radio source is also investigated. We find that on the side of the nucleus with the shortest radio lobe, the gas covering factor is higher, and the ionization parameter is lower. The contrasts in environmental density required to explain the asymmetries in the line brightness and the radio arm-length asymmetries are in fair agreement with each other. These results add further weight to the conclusion of McCarthy, van Breugel & Kapahi ‐ lobe distance asymmetries in powerful radio sources are the result of an asymmetry in the environmental density. We also note that the brightness of both the UV and optical continuum emission shows a similar spatial asymmetry to that shown by the line emission. While the UV continuum asymmetry can be wholly explained by the expected asymmetry in the nebular continuum, the optical continuum asymmetry cannot. We argue that, at least at optical wavelengths, the starlight and/or the scattered light must also be strongly spatially asymmetric.
Mutations in PEX10 are a cause of autosomal recessive ataxia

Peroxisomal biogenesis disorders typically cause severe multisystem disease and early death. We describe a child and an adult of normal intelligence with progressive ataxia, axonal motor neuropathy, and decreased vibration sense. Both patients had marked cerebellar atrophy. Peroxisomal studies revealed a peroxisomal biogenesis disorder. Two mutations in PEX10 were found in the child, c.992G>A (novel) and c. 764_765insA, and in the adult, c.2T>C (novel) and c.790C>T. Transfection with wild‐type PEX10 corrected the fibroblast phenotype. Bile acid supplements and dietary restriction of phytanic acid were started. Peroxisomal biogenesis disorders should be considered in the differential diagnosis of autosomal recessive ataxia. ANN NEUROL 2010;68:259–263
Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases as Assessed in a Cell-Free Fluorescence-Based Enzyme Inhibition Assay

Neuraminidase is a key enzyme in the life cycle of influenza viruses and is present in some bacterial pathogens. We here assess the inhibitory potency of plant tannins versus clinically used inhibitors on both a viral and a bacterial model neuraminidase by applying the 2′-(4-methylumbelliferyl)-α-d-N-acetylneuraminic acid (MUNANA)-based activity assay. A range of flavan-3-ols, ellagitannins and chemically defined proanthocyanidin fractions was evaluated in comparison to oseltamivir carboxylate and zanamivir for their inhibitory activities against viral influenza A (H1N1) and bacterial Vibrio cholerae neuraminidase (VCNA). Compared to the positive controls, all tested polyphenols displayed a weak inhibition of the viral enzyme but similar or even higher potency on the bacterial neuraminidase. Structure–activity relationship analyses revealed the presence of galloyl groups and the hydroxylation pattern of the flavan skeleton to be crucial for inhibitory activity. The combination of zanamivir and EPs® 7630 (root extract of Pelargonium sidoides) showed synergistic inhibitory effects on the bacterial neuraminidase. Co-crystal structures of VCNA with oseltamivir carboxylate and zanamivir provided insight into bacterial versus viral enzyme-inhibitor interactions. The current data clearly indicate that inhibitor potency strongly depends on the biological origin of the enzyme and that results are not readily transferable. The therapeutic relevance of our findings is briefly discussed.
A Support Tool for Writing Multilingual Instructions

Multilingual instructions generation has been the object of many studies recently, motivated by the increased need to produce multilingual manuals coupled with the cost of technical writing and translating. These studies concentrate on the automatic generation of instructions, leaving technical writers out of the loop. In many cases, however it is not possible to dispense with human intervention entirely, for at least two reasons. First, the system must be provided with a semantic knowledge base from which the instructions can be generated. Second, it is the technical writers who have the expertise necessary for producing instructions appropriate for a specific product or company, and it is not necessarily an easy task to make this expertise available to a system. The results of a requirement analysis study confirm the view that the most useful tool is not a stand-alone writing tool but rather one that supports technical writers in their task. In this paper, we describe such a support tool, which we developed based on the results of our user requirement analysis.
Is it feasible to reconstruct body segment 3-D position and orientation using accelerometric data?

The analysis of the mechanics of the musculo-skeletal system during the execution of a motor task requires the determination of the instantaneous position and orientation of the body segments involved in relation to an inertial system of reference. By using adequately assembled uniaxial accelerometric sensors, an easy-to-manage measurement system can be obtained that estimates the three-dimensional position and orientation (P&O) of a body segment through an appropriate analytical model. However, the extent to which experimental errors, in particular accelerometers (ACs) assembly inaccuracies, affect such estimation has never been systematically investigated. This paper systematically analyzes the sensitivity of analytical models of body segment P&O reconstruction through a six-AC system and a nine-AC system to different sources of experimental error. We simulated and statistically assessed the performance of these models in the case of body segment motions typical of movements under muscular control. The results obtained indicated that the inaccuracy in the orientation of the individual AC's active axes and the offset error in the AC responses were the major sources of P&O estimation errors. In particular, no accurate estimation of position was possible with the analytical models analyzed. Under the motion conditions simulated in this study, no substantial advantages were found in using a nine-AC system rather than a six-AC system. Considering that the magnitudes of the simulated experimental errors were quite low (/spl les/0.1 deg: AC's orientation; /spl les/10/sup -4/ m: uncertainty of the distance between two ACs; /spl les/10/sup -2/ ms/sup -2/: random error; 0.5/spl middot/10/sup -2/ ms/sup -2/: offset error), the results indicate that none of the two ACs systems analyzed is suitable for body segment P&O estimation in routine biomechanical applications.
Consumer Prior Expectations and Analytic Categorization

The two common strategies for learning categories can be characterized as holistic categorization and analytic categorization. In holistic categorization, which is also called exemplar-based categorization, people rely on global similarity between items across all or most of their attributes. In analytic categorization, which is also called rule-based categorization, people learn to identify the key features that distinguish between items from different categories and rely on rules that are based on these discriminating features (Hutchison and Alba, 1991).
Low-Dose Topiramate in Alcohol Dependence: A Single-Blind, Placebo-Controlled Study

Introduction Topiramate (TOP) and anticonvulsants in general are considered safe and effective drugs for the treatment of alcohol dependence, even though TOP-induced adverse events are quite common, especially for high initial doses or if titration to 300 mg/d is too rapid. The aim of the present study was to assess the efficacy and tolerability profile of low-dose TOP for relapse prevention. Methods After detoxification, 52 patients were randomized into 2 groups as follows: 26 patients received 100 mg of TOP (oral, twice daily), titrated over 2 weeks, and 26 patients received placebo (PLA). Both groups underwent rehabilitation twice a week. Results After 6 weeks of treatment, compared with the PLA group, patients receiving TOP showed the following: (1) fewer drinking days (P < 0.05); (2) less daily alcohol consumption (P < 0.05); (3) more days of treatment (P < 0.05); (4) reduced levels of craving (Obsessive-Compulsive Drinking Scale) and withdrawal symptoms (Clinical Institute Withdrawal Assessment for Alcohol–Revised); and (5) improvement of anxiety, depression, and obsessive-compulsive symptom severity (Symptom Check List 90 Revised). Conclusions Despite the small sample size and the short follow-up period, the present PLA-controlled study demonstrated the potential usefulness of TOP, even when administered at a dosage of 100 mg/d, for the treatment of detoxified alcohol-dependent subjects, confirming results from previous studies testing higher doses of TOP.
Frame and Segment Level Recurrent Neural Networks for Phone Classification

We introduce a simple and efficient frame and segment level RNN model (FS-RNN) for phone classification. It processes the input at frame level and segment level by bidirectional gated RNNs. This type of processing is important to exploit the (temporal) information more effectively compared to (i) models which solely process the input at frame level and (ii) models which process the input on segment level using features obtained by heuristic aggregation of frame level features. Furthermore, we incorporated the activations of the last hidden layer of the FS-RNN as an additional feature type in a neural higherorder CRF (NHO-CRF). In experiments, we demonstrated excellent performance on the TIMIT phone classification task, reporting a performance of 13.8% phone error rate for the FSRNN model and 11.9% when combined with the NHO-CRF. In both cases we significantly exceeded the state-of-the-art performance.
The UL48 Tegument Protein of Pseudorabies Virus Is Critical for Intracytoplasmic Assembly of Infectious Virions

ABSTRACT The pseudorabies virus (PrV) homolog of the tegument protein encoded by the UL48 gene of herpes simplex virus type 1 (HSV-1) was identified by using a monospecific rabbit antiserum against a bacterial fusion protein. UL48-related polypeptides of 53, 55, and 57 kDa were detected in Western blots of infected cells and purified virions. Immunofluorescence studies demonstrated that the PrV UL48 protein is predominantly localized in the cytoplasm but is also found in the nuclei of infected cells. Moreover, it is a constituent of extracellular virus particles but is absent from primary enveloped perinuclear virions. In noncomplementing cells, a UL48-negative PrV mutant (PrV-ΔUL48) exhibited delayed growth and significantly reduced plaque sizes and virus titers, deficiencies which were corrected in UL48-expressing cells. RNA analyses indicated that, like its HSV-1 homolog, the PrV UL48 protein is involved in regulation of immediate-early gene expression. However, the most salient effect of the UL48 gene deletion was a severe defect in virion morphogenesis. Late after infection, electron microscopy of cells infected with PrV-ΔUL48 revealed retention of newly formed nucleocapsids in the cytoplasm, whereas enveloped intracytoplasmic or extracellular complete virions were only rarely observed. In contrast, capsidless particles were produced and released in great amounts. Remarkably, the intracytoplasmic capsids were labeled with antibodies against the UL36 and UL37 tegument proteins, whereas the capsidless particles were labeled with antisera directed against the UL46, UL47, and UL49 tegument proteins. These findings suggested that the UL48 protein is involved in linking capsid and future envelope-associated tegument proteins during virion formation. Thus, like its HSV-1 homolog, the UL48 protein of PrV functions in at least two different steps of the viral life cycle. The drastic inhibition of virion formation in the absence of the PrV UL48 protein indicates that it plays an important role in virion morphogenesis prior to secondary envelopment of intracytoplasmic nucleocapsids. However, the UL48 gene of PrV is not absolutely essential, and concomitant deletion of the adjacent tegument protein gene UL49 also did not abolish virus replication in cell culture.
Immunotherapy for Prostate Cancer: Lessons from Responses to Tumor-Associated Antigens

Prostate cancer (PCa) is the most common cancer in men and the second most common cause of cancer-related death in men. In recent years, novel therapeutic options for PCa have been developed and studied extensively in clinical trials. Sipuleucel-T is the first cell-based immunotherapeutic vaccine for treatment of cancer. This vaccine consists of autologous mononuclear cells stimulated and loaded with an immunostimulatory fusion protein containing the prostate tumor antigen prostate acid posphatase. The choice of antigen might be key for the efficiency of cell-based immunotherapy. Depending on the treatment strategy, target antigens should be immunogenic, abundantly expressed by tumor cells, and preferably functionally important for the tumor to prevent loss of antigen expression. Autoimmune responses have been reported against several antigens expressed in the prostate, indicating that PCa is a suitable target for immunotherapy. In this review, we will discuss PCa antigens that exhibit immunogenic features and/or have been targeted in immunotherapeutic settings with promising results, and we highlight the hurdles and opportunities for cancer immunotherapy.
Cr(VI) Sorption/Desorption on Pine Sawdust and Oak Wood Ash

The objective of this work was to study Cr(VI) sorption/desorption on two by-products from the wood industry: pine sawdust and oak wood ash. The retention/release experiments were carried out using standard batch-type trials. In the sorption-phase experiments, pine sawdust showed 23% sorption when a concentration of 100 mg Cr(VI)·L−1 was added, whereas sorption on oak wood ash was 17%. In the desorption-phase, chromium release was clearly higher from pine sawdust than from oak wood ash (98% and 66%, respectively). Sorption curves were well fitted to the Freundlich and Lineal models. In view of the results, both materials can be considered of very limited value to remove Cr from polluted soil and water, which can be of relevance regarding its appropriate use as biosorbents and recycled by-products.