Miracle-dz/UniFAR-FTUs huggingface dataset:
Supernumerary Asymmetric Dic(15;15) With Secondary Mosaic Formation in One of Two Developmentally Retarded Twins

Abstract Two male twins born after IVF therapy were investigated for 9 years. Lymphocyte culture at the age of 1 and 9 years revealed that one twin (P1) carried a supernumerary asymmetric dic(15;15) which was present in 100% of cells. In buccal mucosa, however, the derivative 15 (der(15)) was lost in 12% of cells. The der(15) was maternal in origin and was determined to be a meiosis I abnormality. The asymmetric structure of the der(15), as demonstrated by GTG banding and microarray analysis, resulted in a tetrasomy for the region 15q11q13.2 and trisomy for 15q13.2q13. 3. Both regions were interrupted by a disomic fragment of 514 kb; this region has been published as a CNV. Monosomy for this CNV was confirmed in the mother, along with a second CNV in the distal breakpoint region in 15q13.3. The patient had a second structural aberration, namely an almost complete deletion of one of the two centromeres in the der(15), such that it was not detected by metaphase or interphase FISH with the DNA probe D15Z4. The conventional karyotypes of the parents and the second twin (P2) were normal. The second twins retardation was obviously caused by an infection at the age of 4 weeks, followed by multiple organ failure. Twin P1 received special support from birth to the age of 9 years and has developed better than was to be expected from findings in the literature, while his twin brother failed to show developmental progress.
MovieTweetings: a movie rating dataset collected from twitter

Public rating datasets, like MovieLens or Netflix, have long been popular and widely used in the recommmender systems domain for experimentation and comparison. More and more however they are becoming outdated and fail to incorporate new and relevant items. In our work, we tap into the vast availability of social media and construct a new movie rating dataset ‘MovieTweetings’ based on public and well-structured tweets. With currently over 60,000 ratings and the addition of around 500 new ratings per day we believe this dataset can show to be very useful as an always up-to-date and natural rating dataset for movie recommenders.
Revisiting criteria for plant miRNA annotation in the era of big data

MicroRNAs (miRNAs) are ~21 nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential post-transcriptional regulators of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of post-transcriptional regulation). Next-generation DNA sequencing methods have yielded extensive datasets of plant small RNAs, resulting in many miRNA annotations, occasionally inaccurately curated. The sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of “big data” from DNA sequencing. The updated criteria emphasize replication, the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.
RESEARCH ARTICLE Towards Trajectory Anonymization: a Generalization-Based Approach

Trajectory datasets are becoming more and more popular due to the massive usage of GPS and other location-based devices and services. In this paper, we address privacy issues regarding the identification of individuals in static trajectory datasets. We provide privacy protection by defining trajectory k-anonymity, meaning every released information refers to at least k users/trajectories. We propose a novel generalization-based approach that applies to trajectories and sequences in general. We also suggest the use of a simple random reconstruction of the original dataset from the anonymization, to overcome possible drawbacks of generalization approaches. We present a utility metric that maximizes the probability of a good representation and propose trajectory anonymization techniques to address time and space sensitive applications. The experimental results over synthetic trajectory datasets show the effectiveness of the proposed approach.
Taxonomic and functional ant diversity along a secondary successional gradient in a tropical forest

The taxonomic diversity (TD) of tropical flora and fauna tends to increase during secondary succession. This increase may be accompanied by changes in functional diversity (FD), although the relationship between TD and FD is not well understood. To explore this relationship, we examined the correlations between the TD and FD of ants and forest age in secondary forests at the α‐ and β‐diversity levels using single‐ and multi‐trait‐based approaches. Our objectives were to understand ant diversity patterns and to evaluate the role of secondary forests in the conservation of biodiversity and in the resilience of tropical forests. Ant assemblages were sampled across a chronosequence in the Lacandon region, Mexico. All species were characterized according to 12 functional ecomorphological traits relevant to their feeding behavior. We found that TD and FD were related to forest age at the alpha level, but not at the beta level. α‐functional richness and divergence increased linearly with species richness and diversity, respectively. Also, the relationship between taxonomic and functional turnover was linear and positive. Our results indicated that functional traits were complementary across the chronosequence. The increase in FD was mainly driven by the addition of rare species with relevant traits. The older secondary forests did not recover all of the functions of old growth forest but did show a tendency to recovery. Because older successional stages support more TD and FD, we suggest developing agriculture and forestry management practices that facilitate rapid post‐agricultural succession and thereby better preserve the functionality of tropical forests.
Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Each individual cell produces its own set of transcripts, which is the combined result of genetic variation, transcription regulation and post-transcriptional processing. Due to this combinatorial nature, obtaining the exhaustive set of full-length transcripts for a given species is a never-ending endeavor. Yet, each RNA deep sequencing experiment produces a variety of transcripts that depart from the reference transcriptome and should be properly identified. To address this challenge, we introduce a k-mer-based software protocol for capturing local RNA variation from a set of standard RNA-seq libraries, independently of a reference genome or transcriptome. Our software, called DE-kupl, analyzes k-mer contents and detects k-mers with differential abundance directly from the raw data files, prior to assembly or mapping. This enables to retrieve the virtually complete set of unannotated variation lying in an RNA-seq dataset. This variation is subsequently assigned to biological events such as differential lincRNAs, antisense RNAs, splice and polyadenylation variants, introns, expressed repeats, and SNV-harboring or exogenous RNA. We applied DE-kupl to public RNA-seq datasets, including an Epythelial-Mensenchymal Transition model and different human tissues. DE-kupl identified abundant novel events and showed excellent reproducibility when applied to independent deep sequencing experiments. DE-kupl is a new paradigm for analyzing differential RNA-seq data with no preconception on target events, which can also provide fresh insights into existing RNA-seq repositories.
Considerações sobre a degradação da fibra em forragens tropicais associada com suplementos energéticos ou nitrogenados

The carbohydrates constitute between 70 and 80 % of ruminant’s diet and are fundamental for your demands by energy, synthesis of microbial protein, milk components and maintenance of the animal health. The tropical forage grass present, normally, lower contents of crude protein, which are associated with highest fiber contents that can represent around 60 % of the forage dry matter. The fiber represents the carbohydrate fraction of slow digestion or nondegradable that occupies space in gastrointestinal system and, in function of his concentration and digestibility, imposes limitations to the nutrients voluntary intake, dry matter and energy. The energy or nitrogenous supplements can supply the needs in energy and protein of the microorganisms and of the ruminant, providing favorable conditions to the rumen environment, maximizing the microbial growth and the utilization of the forage fibrous compounds. The synchronization between carbohydrates and protein sources can maximize the microbial efficiency and the diminution of the loss of nitrogen as ammonia and the carbohydrates energy, promoting improvement dry matter digestion, especially forage fibrous fraction. In this paper are analyzed the effects of energy and/or protein supplementation about the degradation and fiber voluntary intake of the tropical forage grasses.
Design, Implementation & Testing of Positioning Techniques in Mobile Networks

This paper illustrates two techniques for improved estimation of the location of Mobile Stations (MS) in cellular Networks. The first approach is the statistical method in which signal properties are treated as random variables which are statistically dependent on the location of the transmitter and the receiver. Location estimation for a set of observed signal strengths at a specific location is done as an inference problem. In the second approach, Database Correlation, signal information seen by an MS is stored in the form of fingerprints. To estimate the location, difference between the measurement and the database fingerprints is calculated using a correlation algorithm. Database fingerprints with least difference are selected as the nearest fingerprints for the location to be estimated. The two techniques have been tested through extensive measurements in two environments, urban and sub urban, to verify their performances. Two different implementations have been developed and presented for the statistical technique examined through simulations in the literature. In the implementation of database correlation method, different correlation algorithms and measurement conditions are proposed, implemented and tested. In addition, the accuracies of two techniques have been presented compared to the simple geometrical method for position estimation.
Flight-deck automation: promises and problems

Modern microprocessor technology and display systems make it entirely feasible to automate many of the flight-deck functions previously performed manually. There are many benefits to be derived from automation; the question today is not whether a function can be automated, but whether it should be, due to various human factors issues. It is highly questionable whether total system safety is always enhanced by allocating functions to automatic devices rather than human operators, and there is some reason to believe that flight-deck automation may have already passed its optimum point. This is an age-old question in the human factors profession, and there are few guidelines available to the system designer. This paper presents the state-of-the-art in human factors in flight-deck automation, identifies a number of critical problem areas, and offers broad design guidelines. Some automation-related aircraft accidents and incidents are discussed as examples of human factors problems in automated flight.
Investigation the Distributions and Pharmacokinetics of Five Rhubarb Anthraquinones in Rabbits and Rats

The main effective components of Rhubarb are anthraquinones (AQs), most of which are glycoside and others are free. The concentrations of AQs derivatives (rhein, aloe-emodin, emodin and chrysophanol) in plasma and homogenate were assayed with a high performance liquid chromatography (HPLC) method. The pharmacokinetic parameter and distributions of rhubarb AQs in rabbits or rats were obtained after given different formulas respectively. The elimination of AQs was fit to a two-compartment model in rats and rabbits. There were no significant differences in the main pharmacokinetic parameters between with rhein and AQs in rats. AQs were distributed in kidney, liver, blood, heart progressively. The AQs were mainly existed as rhein in vivo and excreted by kidney. To the formulas containing rhubarb, rhein could be used as a probe for pharmacokinetic study of Rhubarb AQs in vivo.
Topographic mapping: a new approach

A new scheme for reconstructing scene topography using both interferometric phase and backscattering intensity is presented. The authors use the framework of Bayesian theory and look for the scene topography which best explains the observed data. They iteratively improve the estimation changing the topography and simulate, in the Lambertian approximation, a SAR image to be compared to the real one. The fidelity to the observed interferogram is expressed in terms of the phase-difference between the simulated and the observed phase. The regularity of the scene topography is expressed as a Gibbs random field. This allows the authors to obtain an energy to be minimized. The solution of this optimization problem is obtained by a relaxation method.
Características del paisaje y su relación con la diversidad y estructura de la vegetación ribereña del sureste de México

Antecedentes y Objetivos: El cambio de uso del suelo generado por actividades humanas, ha fragmentado los corredores ribereños causando cambios en la diversidad y estructura de su vegetación. El objetivo de este estudio fue comparar la diversidad, estructura y similitud florística en cinco sitios del río Tacotalpa en Tabasco, México, relacionando las variables de vegetación con métricas del paisaje. Métodos: Se realizó un muestreo en cinco sitios del río Tacotalpa: Tapijulapa (s1), Arroyo Chispa (s2), Nuevo Madero (s3), Mexiquito (s4) y Oxolotán (s5). En cada sitio se establecieron 20 unidades de muestreo de 10 × 10 m. Los árboles y arbustos con un DAP≥1 cm fueron censados. La diversidad y estructura se comparó con un ANOVA de un factor. La similitud florística entre sitios se comparó con un cluster Bray-Curtis correlación de Pearson y ACP entre las variables de vegetación y métricas del paisaje, usando PAST y SPSS.Resultados clave: Se registraron 2589 individuos en 38 familias, 92 géneros y 119 especies. La diversidad 0D del s2 fue estadísticamente menor que en s1 y s3, mientras que 1D fue similar en los cinco sitios. La densidad de árboles del s1 fue significativamente mayor que s2, s3 y s5. Los promedios del DAP y altura del s1 fueron bajos, mostrando significancia con el s2 (p<0.05). La similitud florística osciló entre 0.41 a 0.58. La diversidad orden 0D, las especies arbustivas y la densidad de árboles se correlacionaron positivamente con algunas de las métricas del paisaje. La diversidad 1D y especies arbóreas se correlacionaron positivamente con la distancia de carretera pavimentada, y la altura con la de terracería. Conclusiones: Las diferencias entre los sitios sugieren que existen diferentes niveles de perturbación en el río Tacotalpa. Las correlaciones positivas entre las variables de vegetación y métricas del paisaje indican que las infraestructuras cercanas a la ribera modifican la diversidad y estructura de la vegetación ribereña.
Primary Neuroendocrine Tumor of Breast: Report of a Rare Case with Review of Literature

A case of 52 years woman with a lump in her right breast. She was evaluated for surgery and modified radical mastectomy (MRM) was done. Grossing of specimen showed two tumors in retro areolar and lower outer quadrant respectively. Histopathology revealed neuroendocrine tumor of the breast. All eighteen lymph nodes showed reactive lymphoid hyperplasia. Immunohistochemical report showed cells were positive for synaptophysin, chromogranin, neuron specific enolase (NSE) and Ki67 (60-70%). The estrogen receptor, progesterone receptor and HER-2Neu were negative. No mucin production was seen in this patient.
Mechanistic studies on MGP-deficient mice: A model for keutel syndrome

Matrix Gla protein (MGP) is an extracellular matrix (ECM) protein with a potent anti-mineralization function, it is highly expressed in chondrocytes and vascular smooth muscle cells (VSMCs). Genetic mutations in MGP lead to Keutel syndrome, a rare autosomal disorder hallmarked by ectopic cartilage calcification, midface hypoplasia, peripheral pulmonary stenosis and vascular calcification. The Mgp-/- mice recapitulate the phenotypic traits of Keutel syndrome, albeit with a more severe vascular calcification phenotype. Although MGP is one of the most potent inhibitors of ectopic calcification in vivo, the molecular mechanisms of its mode of action are still unknown. Here, we investigated the epistatic effects of several genetic regulators of ECM mineralization on the vascular calcification phenotype of Mgp-/- mice. We show that transgenic augmentation of circulating fibroblast growth factor 23 (FGF23), a phosphaturic hormone, prevents the vascular calcification caused by MGP deficiency. Using a humanized mouse model, we showed that a 40% reduction of medial content of elastin, a protein abundant in the arterial media, completely prevented vascular calcification in Mgp-/- mice until 3 weeks of age. These findings demonstrate that the severity of medial calcification in MGP-deficient mice depends on the serum phosphate levels and the elastin content in the arterial walls. Also, we observed a progressive loss of body weight in Mgp-/- mice. Considering the paradigm linking metabolic regulators of energy metabolism and body mass to that of bone remodeling, we studied the bone volume in Mgp-/- mice. We noticed a decrease of bone volume in Mgp-/- mice caused by an impaired osteoblast function. We examined whether the prevention of arterial calcification in Mgp-/- mice could correct the low bone mass phenotype. The bone mass of two different genetic models: Mgp-/-;SM22-Mgp and Mgp-/-;Eln+/- mice were examined. In the former strain, vascular calcification was fully rescued by transgenic restoration of Mgp in the VSMCs, while in the latter, elastin haploinsufficiency significantly impeded the deposition of minerals in the arterial walls. In both models, the low bone mass phenotype seen in Mgp-/- mice was rescued. Our data support the hypothesis that the arterial calcification, not MGP deficiency itself, is the primary cause of the low bone mass phenotype in Mgp-/- mice, and provides evidence that arterial calcification affects bone remodeling. Lastly, we studied the craniofacial phenotype in Mgp-/- mice. Our comparative cephalometric analyses revealed a severe midface hypoplasia in Mgp-/- mice. In vivo reporter studies demonstrated that the Mgp promoter is highly active at the cranial sutures, cranial base synchondroses and nasal septum. We found the nasal septum to be abnormally mineralized and shortened in Mgp-/- mice. Transgenic restoration of Mgp expression in chondrocytes fully corrected the craniofacial anomalies caused by MGP deficiency, suggesting a local role for MGP in the developing nasal septum. Of note, systemic…
Complemented palindrome small RNAs first discovered from SARS coronavirus

In this study, we reported for the first time the existence of complemented palindrome small RNAs (cpsRNAs) and proposed cpsRNAs and palindrome small RNAs (psRNAs) as a novel class of small RNAs. The first discovered cpsRNA UCUUUAACAAGCUUGUUAAAGA from SARS coronavirus named SARS-CoV-cpsR-22 contained 22 nucleotides perfectly matching its reverse complementary sequence. Further sequence analysis supported that SARS-CoV-cpsR-22 originated from bat betacoronavirus. The results of RNAi experiments showed that one 19-nt segment of SARS-CoV-cpsR-22 significantly induced cell apoptosis. These results suggested that SARS-CoV-cpsR-22 could play a role in SARS-CoV infection or pathogenicity. The discovery of psRNAs and cpsRNAs paved the way to find new markers for pathogen detection and reveal the mechanisms in the infection or pathogenicity from a different point of view. The discovery of psRNAs and cpsRNAs also broaden the understanding of palindrome motifs in animal of plant genomes.
On-line versus memory-based orientations and self-report validity

A partial replication of a study by Nisbett and Bellows (1977) to which a memorization condition was added showed that subjects did not have introspective access to the determinants of their judgments, but did so only in the impression-formation condition. In the memorization condition, the subjects' self-reports matched the observed experimental effects. An analysis of the results showed that this was probably because the subjects' judgments in the latter condition were based on causal theories. ©1997 John Wiley & Sons, Ltd.
New Mining Concessions Could Severely Decrease Biodiversity and Ecosystem Services in Ecuador

Ecuador has among the world’s highest biodiversity, despite being a tiny fraction of the world’s land area. The threat of extinction for some of this biodiversity has dramatically increased since April 2016, during which time the Ecuadorian government has opened around 13% of the country to mining exploration, with many of the concessions in previously protected forests. Herein, we describe the system of protected lands in Ecuador, their mining laws, and outline the scale of threat by comparing the mammals, amphibians, reptiles, birds, and orchids from several now threatened protected areas, classed as “Bosques Protectores,” in the northwestern montane cloud forests. Together, these reserves form a buffer and a southern corridor for the still-protected Cotacachi-Cayapas Ecological Reserve, which is otherwise now surrounded by mining concessions. We gathered published literature, “gray literature,” information from reserve records and websites, and our previously unpublished observations to make comparative species tables for each reserve. Our results reveal the potential losses that mining could cause: eight critically endangered species, including two primates (brown-headed spider monkey and white-fronted capuchin), 37 endangered species, 153 vulnerable, 89 near threatened, and a large number of less threatened species. Our data show that each reserve protects a unique subset of taxa in this region of highly localized endemics and the reserves also generate sustainable income for local people. The short-term national profits from mining will not compensate for the permanent biodiversity losses, and the long-term ecosystem service and economic losses at the local and regional level.
Error Correction of Automatic Testing Systems for Hall Effect Current Sensors

In this paper an error correction method is proposed for improving the measuring accuracy of automatic testing systems for Hall Effect current sensors. The errors of the original testing system are determined by a reference sensor or a reference resistor. These error values are saved as corrections into a data matrix in the testing system. The systematic errors of the testing system are corrected by using the correction data matrix. In this way a conventional measuring system can be enhanced into a precise measuring system. The proposed method can be used in all automatic testing systems.