Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic dictionary learning strategies for sparse representation based hyperspectral image enhancement

This paper introduces four new dynamic dictionary learning methods to sparse representation based hyperspectral resolution enhancement. The impact of the type and size of the dynamic dictionary on the reconstruction quality is investigated for the recently proposed sparse representation based multiresolution image fusion method J-SparseFI-HM. Low resolution hyperspectral and high resolution multispectral input images are simulated from recently acquired airborne HySpex data. Experiments reveal that fusion products can be substantially improved by changing the dictionary type from the currently used nearest neighbor selection to a modified dissimilarity based dynamic dictionary.
Using Xenopus to understand human disease and developmental disorders

Model animals are crucial to biomedical research. Among the commonly used model animals, the amphibian, Xenopus, has had tremendous impact because of its unique experimental advantages, cost effectiveness, and close evolutionary relationship with mammals as a tetrapod. Over the past 50 years, the use of Xenopus has made possible many fundamental contributions to biomedicine, and it is a cornerstone of research in cell biology, developmental biology, evolutionary biology, immunology, molecular biology, neurobiology, and physiology. The prospects for Xenopus as an experimental system are excellent: Xenopus is uniquely well‐suited for many contemporary approaches used to study fundamental biological and disease mechanisms. Moreover, recent advances in high throughput DNA sequencing, genome editing, proteomics, and pharmacological screening are easily applicable in Xenopus, enabling rapid functional genomics and human disease modeling at a systems level.
Brief report: successful pregnancies but a higher risk of preterm births in patients with systemic sclerosis: an Italian multicenter study.

OBJECTIVE To assess fetal and maternal outcomes in women with systemic sclerosis (SSc). METHODS Prospectively collected data on 99 women with SSc from 25 Italian centers were analyzed retrospectively. Women with SSc were observed during 109 pregnancies (from 2000 to 2011), and outcomes were compared to those in the general obstetric population (total of 3,939 deliveries). The maternal age at conception was a mean ± SD 31.8 ± 5.3 years, and the median disease duration at conception was 60 months (range 2-193 months). RESULTS SSc patients, compared to the general obstetric population, had a significantly increased frequency of preterm deliveries (25% versus 12%) and severe preterm deliveries (<34 weeks of gestation) (10% versus 5%), intrauterine growth restriction (6% versus 1%), and babies with very-low birth weight (5% versus 1%). Results of multivariable analysis showed that corticosteroid use was associated with preterm deliveries (odds ratio [OR] 3.63, 95% confidence interval [95% CI] 1.12-11.78), whereas the use of folic acid (OR 0.30, 95% CI 0.10-0.91) and presence of anti-Scl-70 antibodies (OR 0.26, 95% CI 0.08-0.85) were protective. The disease remained stable in most SSc patients, but there were 4 cases of progression of disease within 1 year from delivery, all in anti-Scl-70 antibody-positive women, 3 of whom had a disease duration of <3 years. CONCLUSION Women with SSc can have successful pregnancies, but they have a higher-than-normal risk of preterm delivery, intrauterine growth restriction, and babies with very-low birth weight. Progression of the disease during or after pregnancy is rare, but possible. High-risk multidisciplinary management should be standard for these patients, and pregnancy should be avoided in women with severe organ damage and postponed in women with SSc of recent onset, particularly if the patient is positive for anti-Scl-70 antibodies.
Assessment of Yield Characteristics of Gas Pipeline Materials by Observing Surface-Local Deformation

A combination of the instrumented indentation and 3D morphology measurement has been tried in order to perform a real-time property measurement of degraded materials in gas pipelines; three-dimensional indent morphologies were recorded using a reflective laser scanner after a series of insturmented indentations on three metallic specimens. Dimensions of the permanent deformation zone and contact boundary were analyzed from the cross-sectional profile over an remnant indent and used for estimating yield strength and hardness, respectively. Estimated yield strength was comparable with that from uniaxial tensile test and actual hardness implying material pile-up effects was lower than the calculated value from indentation curve by . It means that this 3D image analysis can explain the material pile-up effects on the contact properties. Additionally, a combined system of indentation and laser sensor was newly designed by modifying a shape of the indentation loading fixture.
Chromosome Pairing in Hybrid Progeny between Triticum aestivum and Elytrigia elongata

In this study, the intergeneric hybrids F1, F2, BC1F1, BC1F2, and BC2F1 from Elytrigia elongata and Triticum aestivum crosses were produced to study their chromosome pairing behavior. The average E. elongata chromosome configuration of the two F1 hybrids agreed with the theoretical chromosome configuration of 21I+7II, indicating that the genomic constitution of this F1 hybrid was ABDStStEeEbEx. Compared with the BC1F1 generation, the BC2F1 generation showed a rapid decrease in the number of E. elongata chromosomes and the BC1F2 generation showed a more extensive distribution of E. elongata chromosomes. In addition, pairing between wheat and E. elongata chromosomes was detected in each of the wheat-E. elongata hybrid progenies, albeit rarely. Our results demonstrated that genomic in situ hybridization (GISH) using an E. elongata genomic DNA probe offers a reliable approach for characterizing chromosome pairing in wheat and E. elongata hybrid progenies.
UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing

Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better performance compared with earlier developed algorithms such as TopHat and MapSplice. To improve detection of splice junctions, TrueSight uses information on statistical patterns of nucleotide ordering in intronic and exonic DNA. This line of research led to yet another new algorithm, UnSplicer, designed for eukaryotic species with compact genomes where functional alternative splicing is likely to be dominated by splicing noise. Genome-specific parameters of the new algorithm are generated by GeneMark-ES, an ab initio gene prediction algorithm based on unsupervised training. UnSplicer shares several components with TrueSight; the difference lies in the training strategy and the classification algorithm. We tested UnSplicer on RNA-Seq data sets of Arabidopsis thaliana, Caenorhabditis elegans, Cryptococcus neoformans and Drosophila melanogaster. We have shown that splice junctions inferred by UnSplicer are in better agreement with knowledge accumulated on these well-studied genomes than predictions made by earlier developed tools.
Immune reconstitution after potent antiretroviral therapy in AIDS patients with progressive multifocal leukoencephalopathy

Neurological disease is the initial manifestation of acquired immunodeficiency syndrome (AIDS) in 10–20% of patients with HIV infection. Progressive multifocal leukoencephalopathy (PML) predominantly involves the cerebral hemispheres, with a small subset of patients having lesions predominantly or exclusively confined to the cerebellum. The radiological features of PML are typically non-inflammatory. As a result of potent antiretroviral therapy (ART), however, inflammatory lesions are becoming more common in HIV-infected individuals and are due, in part, to immune reconstitution that occurs in recipients of potent ART. In the majority of such cases, the clinical outcome of immune reconstitution PML has been beneficial to the host, although several case reports have described worsening or fatal outcomes in PML patients as a result of potent ART. The following 2 cases of immune reconstitution PML described in this report illustrate the varied radiological manifestations and clinical outcomes that can develop in AIDS patients with PML receiving potent ART. Moreover, these cases highlight the inflammatory changes observed on neuroimaging in AIDS patients with immune reconstitution PML receiving potent ART and to our knowledge are the first reports of immune reconstitution isolated to the cerebellum in such patients.
Production of Outer Membrane Vesicles and Outer Membrane Tubes by Francisella novicida

ABSTRACT Francisella spp. are highly infectious and virulent bacteria that cause the zoonotic disease tularemia. Knowledge is lacking for the virulence factors expressed by Francisella and how these factors are secreted and delivered to host cells. Gram-negative bacteria constitutively release outer membrane vesicles (OMV), which may function in the delivery of virulence factors to host cells. We identified growth conditions under which Francisella novicida produces abundant OMV. Purification of the vesicles revealed the presence of tube-shaped vesicles in addition to typical spherical OMV, and examination of whole bacteria revealed the presence of tubes extending out from the bacterial surface. Recently, both prokaryotic and eukaryotic cells have been shown to produce membrane-enclosed projections, termed nanotubes, which appear to function in cell-cell communication and the exchange of molecules. In contrast to these previously characterized structures, the F. novicida tubes are produced in liquid as well as on solid medium and are derived from the OM rather than the cytoplasmic membrane. The production of the OMV and tubes (OMV/T) by F. novicida was coordinately regulated and responsive to both growth medium and growth phase. Proteomic analysis of purified OMV/T identified known Francisella virulence factors among the constituent proteins, suggesting roles for the vesicles in pathogenesis. In support of this, production of OM tubes by F. novicida was stimulated during infection of macrophages and addition of purified OMV/T to macrophages elicited increased release of proinflammatory cytokines. Finally, vaccination with purified OMV/T protected mice from subsequent challenge with highly lethal doses of F. novicida.
Group Rights and Discrimination in International Law

Group hatred, disregard for the collective aspirations of religious, ethnic or cultural minorities, genocide, ethnic cleansing, apartheid, and anti-Semitism have been at the roots of the greatest tragedies of our time and are a source of internal and international conflict. This work studies this wide range of problems from the perspective of modern human rights law, with special emphasis on racism and religious intolerance. Also dealt with are measures adopted, or to be taken, for the protection of specific groups, including indigenous populations and migrant workers, as well as the present situation regarding the conventions against genocide, discrimination in education and labour, and the steps and declarations for the strengthening of group identity and their advancement. Special areas such as slavery, affirmative action, and modern models to preserve the collective personality are also discussed, including protective penal measures.
The benefits of R&D and breadth in innovation strategies: a comparison of Finnish service and manufacturing firms

This empirical study compares the determinants of innovation in manufacturing and services through descriptive and regression analyses of sales from innovative products and services. A particular focus is on the effects of R&D investments and breadth in knowledge sourcing and innovation objectives. The results suggest that, contrary to earlier research, R&D investments play a statistically and economically significant role in service innovation. We suggest that this results from the growing engagement of service firms in regular R&D activity. Both service and manufacturing firms also benefit from breadth in external knowledge sourcing strategies. In contrast, breadth in terms of pursuing parallel innovation objectives appears to have detrimental effects on innovation in service industries. We interpret the latter results through reference to service firms' R&D management capabilities: Managing multiple innovation projects is challenging, and some service firms may not have accumulated the requisite managerial processes and capabilities to benefit from these strategies. The available data provide support for this conjecture. The detrimental effects of breadth in innovation objectives are significantly mitigated by regular R&D activities. Copyright 2012 The Author 2012. Published by Oxford University Press on behalf of Associazione ICC. All rights reserved. , Oxford University Press.
Self‐reported history of infections and the risk of non‐Hodgkin lymphoma: An InterLymph pooled analysis

We performed a pooled analysis of data on self‐reported history of infections in relation to the risk of non‐Hodgkin lymphoma (NHL) from 17 case–control studies that included 12,585 cases and 15,416 controls aged 16–96 years at recruitment. Pooled odds ratios (OR) and 95% confidence intervals (95% CI) were estimated in two‐stage random‐effect or joint fixed‐effect models, adjusting for age, sex and study centre. Data from the 2 years before diagnosis (or date of interview for controls) were excluded. A self‐reported history of infectious mononucleosis was associated with an excess risk of NHL (OR = 1.26, 95% CI = 1.01–1.57 based on data from 16 studies); study‐specific results indicate significant (I2 = 51%, p = 0.01) heterogeneity. A self‐reported history of measles or whooping cough was associated with an approximate 15% reduction in risk. History of other infection was not associated with NHL. We find little clear evidence of an association between NHL risk and infection although the limitations of data based on self‐reported medical history (particularly of childhood illness reported by older people) are well recognized.
A Note on the Estimation of the Gini Index

This article provides a statistical decision-making framework for the Gini index through the introduction of practically usable confidence intervals for this index. The resultant intervals enable hypothesis testing with the Gini index as well as providing a mechanism for studying the reliability of its estimates. The article presents these confidence intervals and demonstrates their prospective uses with an illustrative example to officially published estimates for the index from 24 countries. JEL Classification: C02, C13
Soluble Triggering Receptor Expressed on Myeloid Cells-1 (sTREM-1) as a Diagnostic Marker of Ventilator-Associated Pneumonia

OBJECTIVE: To determine the utility of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) levels in bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC) samples from patients who underwent bronchoscopy for a clinical suspicion of ventilator-associated pneumonia (VAP), to categorize patients as VAP positive and VAP negative, when compared to quantitative culture results of BALF. METHODS: Observational study conducted on admitted patients in the trauma-surgical, medical-cardiac, burn, and neurosurgical ICUs of Harborview Medical Center between March 2009 and May 2010. BALF and EBC samples were obtained from 45 patients with clinically suspected VAP. Bronchoscopy was performed on the day of clinically suspected VAP. sTREM-1 levels in EBC and BAL fluid were measured using quantikine human TREM-1 immunoassay. VAP was diagnosed by quantitative cultures of BALF. RESULTS: The concentrations of sTREM-1 in BALF and EBC did not correlate with VAP status. sTREM-1 levels did not discriminate VAP positive from VAP negative patients, when compared to quantitative cultures of BALF as the gold standard. Using a cutoff value of 204 pg/mL for BALF sTREM-1 levels resulted in a sensitivity of 79% and a specificity of 23%. A cutoff value of 10 pg/mL for EBC sTREM-1 levels resulted in a sensitivity of 42% and a specificity of 50%. CONCLUSIONS: EBC and BALF sTREM-1 levels did not effectively categorize patients as VAP positive or VAP negative when using direct bronchoscopic quantitative culture samples as the comparison standard.
Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing.

SV40 early pre-mRNA is alternatively spliced to produce large T and small t mRNAs by use of different 5'-splice sites and a shared 3'-splice site. The large T splicing pathway uses multiple lariat branch sites, whereas small t splicing, constrained by its small intron size, can use only one. We exploited this situation to test the hypothesis that RNA-RNA base pairing between U2 snRNA and the branch site sequence is important in mammalian pre-mRNA splicing by constructing and analyzing several mutations in the small t pre-mRNA branch site (UUCUAAU). All of the mutations resulted in substantial decreases in small t splicing relative to large T. To test whether these effects resulted from decreased base pairing with U2 snRNA, compensatory mutations were introduced at the appropriate positions (nucleotides 34-36) in a cloned human U2 gene. All branch site mutations tested (four separate single base substitutions and two triple mutations) were suppressed (i.e., small t splicing was increased) by the appropriate U2 mutations. These results establish that recognition of the poorly conserved mammalian pre-mRNA branch site sequence by U2 snRNP can involve base-pairing.
Task-related training improves performance of seated reaching tasks after stroke. A randomized controlled trial.

BACKGROUND AND PURPOSE After stroke, the ability to balance in sitting is critical to independence. Although impairments in sitting balance are common, little is known about the effectiveness of rehabilitation strategies designed to improve it. The purpose of this randomized placebo-controlled study was to evaluate the effect of a 2-week task-related training program aimed at increasing distance reached and the contribution of the affected lower leg to support and balance. METHODS Twenty subjects at least 1 year after stroke were randomized into an experimental or control group. The experimental group participated in a standardized training program involving practice of reaching beyond arm's length. The control group received sham training involving completion of cognitive-manipulative tasks within arm's length. Performance of reaching in sitting was measured before and after training using electromyography, videotaping, and two force plates. Variables tested were movement time, distance reached, vertical ground reaction forces through the feet, and muscle activity. Subjects were also tested on sit-to-stand, walking, and cognitive tasks. Nineteen subjects completed the study. RESULTS After training, experimental subjects were able to reach faster and further, increase load through the affected foot, and increase activation of affected leg muscles compared with the control group (P < .01). The experimental group also improved in sit-to-stand. The control group did not improve in reaching or sit-to-stand. Neither group improved in walking. CONCLUSIONS This study provides strong evidence of the efficacy of task-related motor training in improving the ability to balance during seated reaching activities after stroke.
RUFINO at SemEval-2017 Task 2: Cross-lingual lexical similarity by extending PMI and word embeddings systems with a Swadesh’s-like list

The RUFINO team proposed a non-supervised, conceptually-simple and low-cost approach for addressing the Multilingual and Cross-lingual Semantic Word Similarity challenge at SemEval 2017. The proposed systems were cross-lingual extensions of popular monolingual lexical similarity approaches such as PMI and word2vec. The extensions were possible by means of a small parallel list of concepts similar to the Swadesh’s list, which we obtained in a semi-automatic way. In spite of its simplicity, our approach showed to be effective obtaining statistically-significant and consistent results in all datasets proposed for the task. Besides, we provide some research directions for improving this novel and affordable approach.
Wavelet-based ECG compression using dynamic vector quantization with tree codevectors in single codebook

In this paper, we propose a novel vector quantizer (VQ) in the wavelet domain for the compression of electrocardiogram (ECG) signals. A vector called tree vector (TV) is formed first in a novel structure, where wavelet transformed (WT) coefficients in the vector are arranged in the order of a hierarchical tree. Then, the TVs extracted from various WT subbands are collected in one single codebook. This feature is an advantage over traditional WT-VQ methods, where multiple codebooks are needed and are usually designed separately because numerical ranges of coefficient values in various WT subbands are quite different. Finally, a distortion-constrained codebook replenishment mechanism is incorporated into the VQ, where codevectors can be updated dynamically, to guarantee reliable quality of reconstructed ECG waveforms. With the proposed approach both visual quality and the objective quality in terms of the percent of root-mean-square difference (PRD) are excellent even in a very low bit rate. For the entire 48 records of Lead II ECG data in the MIT/BIH database, an average PRD of 7.3% at 146 b/s is obtained. For the same test data under consideration, the proposed method outperforms many recently published ones, including the best one known as the set partitioning in hierarchical trees.
Personal Best Marathon Time and Longest Training Run, Not Anthropometry, Predict Performance in Recreational 24-Hour Ultrarunners

Knechtle, B, Knechtle, P, Rosemann, T, and Lepers, R. Personal best marathon time and longest training run, not anthropometry, predict performance in recreational 24-hour ultrarunners. J Strength Cond Res 25(8): 2212-2218, 2011—In recent studies, a relationship between both low body fat and low thicknesses of selected skinfolds has been demonstrated for running performance of distances from 100 m to the marathon but not in ultramarathon. We investigated the association of anthropometric and training characteristics with race performance in 63 male recreational ultrarunners in a 24-hour run using bi and multivariate analysis. The athletes achieved an average distance of 146.1 (43.1) km. In the bivariate analysis, body mass (r = −0.25), the sum of 9 skinfolds (r = −0.32), the sum of upper body skinfolds (r = −0.34), body fat percentage (r = −0.32), weekly kilometers ran (r = 0.31), longest training session before the 24-hour run (r = 0.56), and personal best marathon time (r = −0.58) were related to race performance. Stepwise multiple regression showed that both the longest training session before the 24-hour run (p = 0.0013) and the personal best marathon time (p = 0.0015) had the best correlation with race performance. Performance in these 24-hour runners may be predicted (r2 = 0.46) by the following equation: Performance in a 24-hour run, km) = 234.7 + 0.481 (longest training session before the 24-hour run, km) - 0.594 (personal best marathon time, minutes). For practical applications, training variables such as volume and intensity were associated with performance but not anthropometric variables. To achieve maximum kilometers in a 24-hour run, recreational ultrarunners should have a personal best marathon time of ∼3 hours 20 minutes and complete a long training run of ∼60 km before the race, whereas anthropometric characteristics such as low body fat or low skinfold thicknesses showed no association with performance.