Miracle-dz/UniFAR-FTUs huggingface dataset:
The potential of copy number gains and losses, detected by array-based comparative genomic hybridization, for computational differential diagnosis of B-cell lymphomas and genetic regions involved in lymphomagenesis

The findings of this study suggest that data of copy number gains and losses obtained with array CGH might be employed for computational differential diagnosis of B-cell lymphomas. Background The differentiation of biologically and clinically different malignant lymphoma diseases or subtypes is crucial because it leads to better prognostication and therapeutic decision-making. Attempts have been made at subtype classification for diagnosing lymphomas on the basis of gene-expression profiling. Although array-based comparative genomic hybridization (array CGH) has identified a characteristic genomic alteration pattern for each disease entity, it has not been clear whether each patient with certain genomic alterations can be classified by array CGH data. Design and Methods Data on copy number gains and losses for 46 diffuse large B-cell lymphomas and 29 mantle cell lymphomas were used. The gene expressions of the diffuse large B-cell lymphomas cases were profiled and hierarchical clustering revealed that 28 of them were of the activated B-cell type and 18 were of the germinal center-B-cell type. Using these data, we developed a computer algorithm to classify lymphoma diseases or subtypes on the basis of copy number gains and losses. Results The method correctly classified 88% of the diffuse large B-cell lymphomas and mantle cell lymphomas, and 83% of the activated B-cell and germinal center-B-cell subtypes. These results demonstrate that copy number gains and losses detected by array CGH can be used for classifying lymphomas into biologically and clinically distinct diseases or subtypes. Conclusions Our computer algorithm based on array CGH data successfully classified diffuse large B-cell lymphomas and mantle cell lymphomas and activated B-cell and germinal center-B-cell subtypes with high accuracy. An important finding is that the regions automatically identified by the computer algorithm were located in the critical regions that are likely to be involved in the development of lymphoma.
Natural History of Human Respiratory Syncytial Virus Inferred from Phylogenetic Analysis of the Attachment (G) Glycoprotein with a 60-Nucleotide Duplication

ABSTRACT A total of 47 clinical samples were identified during an active surveillance program of respiratory infections in Buenos Aires (BA) (1999 to 2004) that contained sequences of human respiratory syncytial virus (HRSV) with a 60-nucleotide duplication in the attachment (G) protein gene. This duplication was analogous to that previously described for other three viruses also isolated in Buenos Aires in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003). Phylogenetic analysis indicated that BA sequences with that duplication shared a common ancestor (dated about 1998) with other HRSV G sequences reported worldwide after 1999. The duplicated nucleotide sequence was an exact copy of the preceding 60 nucleotides in early viruses, but both copies of the duplicated segment accumulated nucleotide substitutions in more recent viruses at a rate apparently higher than in other regions of the G protein gene. The evolution of the viruses with the duplicated G segment apparently followed the overall evolutionary pattern previously described for HRSV, and this genotype has replaced other prevailing antigenic group B genotypes in Buenos Aires and other places. Thus, the duplicated segment represents a natural tag that can be used to track the dissemination and evolution of HRSV in an unprecedented setting. We have taken advantage of this situation to reexamine the molecular epidemiology of HRSV and to explore the natural history of this important human pathogen.
Genome-wide investigation and expression analysis of AP2-ERF gene family in salt tolerant common bean

Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species' miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean.
Metschnikowia pulcherrima Influences the Expression of Genes Involved in PDH Bypass and Glyceropyruvic Fermentation in Saccharomyces cerevisiae

Previous studies reported that the use of Metschnikowia pulcherrima in sequential culture fermentation with Saccharomyces cerevisiae mainly induced a reduction of volatile acidity in wine. The impact of the presence of this yeast on the metabolic pathway involved in pyruvate dehydrogenase (PDH) bypass and glycerol production in S. cerevisiae has never been investigated. In this work, we compared acetic acid and glycerol production kinetics between pure S. cerevisiae culture and its sequential culture with M. pulcherrima during alcoholic fermentation. In parallel, the expression levels of the principal genes involved in PDH bypass and glyceropyruvic fermentation in S. cerevisiae were investigated. A sequential culture of M. pulcherrima/S. cerevisiae at an inoculation ratio of 10:1 produced 40% less acetic acid than pure S. cerevisiae culture and led to the enhancement of glycerol content (12% higher). High expression levels of pyruvate decarboxylase PDC1 and PDC5, acetaldehyde dehydrogenase ALD6, alcohol dehydrogenase ADH1 and glycerol-3-phosphate dehydrogenase PDC1 genes during the first 3 days of fermentation in sequential culture conditions are highlighted. Despite the complexity of correlating gene expression levels to acetic acid formation kinetics, we demonstrate that the acetic acid production pathway is altered by sequential culture conditions. Moreover, we show for the first time that the entire acetic acid and glycerol metabolic pathway can be modulated in S. cerevisiae by the presence of M. pulcherrima at the beginning of fermentation.
Bone Marrow Transplantation Alters the Tremor Phenotype in the Murine Model of Globoid-Cell Leukodystrophy

Tremor is a prominent phenotype of the twitcher mouse, an authentic genetic model of Globoid-Cell Leukodystrophy (GLD, Krabbe’s disease). In the current study, the tremor was quantified using a force-plate actometer designed to accommodate low-weight mice. The actometer records the force oscillations caused by a mouse’s movements, and the rhythmic structure of the force variations can be revealed. Results showed that twitcher mice had significantly increased power across a broad band of higher frequencies compared to wildtype mice. Bone marrow transplantation (BMT), the only available therapy for GLD, worsened the tremor in the twitcher mice and induced a measureable alteration of movement phenotype in the wildtype mice. These data highlight the damaging effects of conditioning radiation and BMT in the neonatal period. The behavioral methodology used herein provides a quantitative approach for assessing the efficacy of potential therapeutic interventions for Krabbe’s disease.
Fuzzy optimization of linear objective function subject to max-average relational inequality constraints

An optimization problem of a linear objective function subject to a system of fuzzy relational inequalities based on max-average composition and fuzzy inequality is presented. This problem is converted to a new one with ordinary inequalities by using linear membership functions and Bellman-Zadeh decision. Then, dimension of the last problem is reduced and an algorithm is presented to generate the optimal solution of the initial optimization problem. Two numerical examples are given to illustrate the steps of the algorithm. Some aspects of sensitivity analysis of the problem is investigated.
In vitro activity of bedaquiline against rapidly growing nontuberculous mycobacteria

Bedaquiline (BDQ) has been proven to be effective in the treatment of multidrug-resistant tuberculosis. We hypothesized that BDQ could be a potential agent to treat nontuberculous mycobacterial (NTM) infection. The objective of this study was to evaluate the in vitro activity of BDQ against rapidly growing mycobacteria by assessing the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) against 18 NTM strains. For MIC determination we performed the resazurin microtitre assay broth dilution, and for the MBC the c.f. u. was determined. BDQ exhibited a strong inhibitory effect against most NTM tested; however, for some NTM strains the MBC was significantly higher than the MIC. A new finding is that Mycobacterium flavescens has a mutation in the gene atpE associated with natural resistance to BDQ. These preliminary promising results demonstrate that BDQ could be potentially useful for the treatment of NTM.
Club cell 10-kDa protein attenuates airway mucus hypersecretion and inflammation

Bacterial lipopolysaccharide (LPS) and interleukin (IL)-13 increase mucus secretion and inflammatory cytokine production in normal human bronchial epithelial (NHBE) cells. We evaluated the effect of club cell 10-kDa protein (CC10), an anti-inflammatory protein produced by epithelial cells, on mucus secretion, cell morphology and inflammatory cytokine production. NHBE cells were cultured at an air–liquid interface with CC10 or vehicle and exposed to LPS on day 14. Mucin MUC5AC, IL-8 and granulocyte-macrophage colony-stimulating factor were measured in cell supernatants. MUC5AC and IL-8 mRNA expression were measured by real-time PCR. Western blotting was used to evaluate nuclear factor (NF)-&kgr;B and extracellular signal-regulated kinase (ERK) activation. Cells were evaluated histologically. Additionally, NHBE cells were exposed to IL-13 and CC10 for 14 days, and secretion of the mucins MUC5AC and MUC5B was measured. MUC5AC secretion stimulated either by LPS or by IL-13 was attenuated by CC10 at 20 ng·mL−1 (p<0.05). CC10 at 20 ng·mL−1 also attenuated IL-8 secretion (p<0.05). MUC5AC and IL-8 mRNA expression were also decreased by CC10 (p<0.05). CC10 attenuated phosphorylation of NF-&kgr;B (p<0.05) and ERK1/2 (p<0.05). CC10 attenuates LPS-induced mucus secretion in airway cells, in part due to inhibition of NF-&kgr;B and ERK phosphorylation. CC10 attenuates LPS-induced mucus secretion in airway cells and plays a role in decreasing airway inflammation http://ow.ly/v6TDe For editorial comments see page 831.
AB INITIO EQUATION OF STATE FOR HYDROGEN–HELIUM MIXTURES WITH RECALIBRATION OF THE GIANT-PLANET MASS–RADIUS RELATION

Using density functional molecular dynamics simulations, we determine the equation of state (EOS) for hydrogen–helium mixtures spanning density–temperature conditions typical of giant-planet interiors, ∼0.2–9 g cm−3 and 1000–80,000 K for a typical helium mass fraction of 0.245. In addition to computing internal energy and pressure, we determine the entropy using an ab initio thermodynamic integration technique. A comprehensive EOS table with 391 density–temperature points is constructed and the results are presented in the form of a two-dimensional free energy fit for interpolation. Deviations between our ab initio EOS and the semi-analytical EOS model by Saumon and Chabrier are analyzed in detail, and we use the results for initial revision of the inferred thermal state of giant planets with known values for mass and radius. Changes are most pronounced for planets in the Jupiter mass range and below. We present a revision to the mass–radius relationship that makes the hottest exoplanets increase in radius by ∼0.2 Jupiter radii at fixed entropy and for masses greater than ∼0.5 Jupiter mass. This change is large enough to have possible implications for some discrepant “inflated giant exoplanets. ”
Exploiting a Proximity-based Positional Model to Improve the Quality of Information Extraction by Text Segmentation

A large number of web pages contain information of entities in a form of lists of field values. Those implicit semi-structured records are often available in textual sources on the web such as advertisings of products, postal addresses, bibliographic information, etc. Harvesting information of those entities from such lists of field values is challenge task because the lists are manually generated, not written in a well-defined templates or may miss some information. In this paper, we introduce a proximity-based positional model (PPM) to improve the quality of extracting information by text segmentation. Our proposed model offers improvements over the fixed-positional model proposed in ONDUX, a current state-of-art method for information extraction by text segmentation (IETS) to revise the labels of text segments in an input list of field values. Different from fixed-positional model in previous work, the key idea of PPM is to define proximity heuristic for labels in an input list in a unified language model. Our proposed model is estimated based on propagated counts of labels through a proximity-based density function. We propose and study several density functions and experimental results on different domains show that PPM is effective to revise labels and helps to improve performance of current state-of-art method.
Influence of 340 mT static magnetic field on germination potential and mid‐infrared spectrum of wheat

In a number of studies, a static magnetic field was observed to positively influence the growing process of various plants; however, the effect has not yet been related to possible structural changes. We investigate if the static magnetic field that improves germination of wheat also alters wheat's near‐infrared spectrum. Two groups of seeds were exposed to 340 mT for 16 h cumulatively. The first group was exposed 8 days for 2 h per day, while the second group was exposed 4 h per day for 4 consecutive days. One half of each of the exposed seed groups as well as of the unexposed control groups was sown, and the other half was used for mid‐infrared spectra measurements. The sown seeds were monitored for 3 weeks after sowing. Germination of the groups exposed to the magnetic field was faster compared to corresponding non‐exposed groups that were grown under the same conditions. The magnetic field exposure caused the enhancement of one OH peak at 3,369 cm−1 and two CO peaks at 1,662 cm−1 and 1,740 cm−1 in the mid‐infrared spectrum. The effect was more pronounced for the 4 day, 4 h/day exposure. Bioelectromagnetics. 38:533–540, 2017. © 2017 Wiley Periodicals, Inc.
Two Alternating Motor Programs Drive Navigation in Drosophila Larva

When placed on a temperature gradient, a Drosophila larva navigates away from excessive cold or heat by regulating the size, frequency, and direction of reorientation maneuvers between successive periods of forward movement. Forward movement is driven by peristalsis waves that travel from tail to head. During each reorientation maneuver, the larva pauses and sweeps its head from side to side until it picks a new direction for forward movement. Here, we characterized the motor programs that underlie the initiation, execution, and completion of reorientation maneuvers by measuring body segment dynamics of freely moving larvae with fluorescent muscle fibers as they were exposed to temporal changes in temperature. We find that reorientation maneuvers are characterized by highly stereotyped spatiotemporal patterns of segment dynamics. Reorientation maneuvers are initiated with head sweeping movement driven by asymmetric contraction of a portion of anterior body segments. The larva attains a new direction for forward movement after head sweeping movement by using peristalsis waves that gradually push posterior body segments out of alignment with the tail (i.e., the previous direction of forward movement) into alignment with the head. Thus, reorientation maneuvers during thermotaxis are carried out by two alternating motor programs: (1) peristalsis for driving forward movement and (2) asymmetric contraction of anterior body segments for driving head sweeping movement.
B cells expressing CD11b effectively inhibit CD4+ T‐cell responses and ameliorate experimental autoimmune hepatitis in mice

Increasing evidence in recent years has suggested that B cells act as a crucial regulator in autoimmune diseases. However, little is known about their role in autoimmune hepatitis (AIH) and the underlying regulatory mechanisms. In this study, we show that B cells ameliorated experimental AIH (EAH) by suppressing CD4+ T‐cell responses and that CD11b expression on B cells was required for the regulatory function of B cells. In vitro studies reveal that the suppressive function of CD11b was mediated by the impairment of T‐cell antigen receptor (TCR) signaling transduction and the promotion of TCR down‐regulation. Moreover, we show that the increased CD11b expression on B cells was interleukin (IL)−10 dependent and that additional IL‐10 stimulation promoted CD11b expression on B cells, thereby enhancing B‐cell regulatory effects. Conclusion: These findings reveal a previously unrecognized role for CD11b in B‐cell regulatory function and its protective effect on EAH. (Hepatology 2015;62:1563–1575)
Agile Practices in Global Software Engineering - A Systematic Map

This paper presents the results of systematically reviewing the current research literature on the use of agile practices and lean software development in global software engineering (GSE). The primary purpose is to highlight under which circumstances they have been applied efficiently. Some common terms related to agile practices (e.g. scrum, extreme programming) were considered in formulating the search strings, along with a number of alternatives for GSE such as offshoring, outsourcing, and virtual teams. The results were limited to peer-reviewed conference papers/journal articles, published between 1999 and 2009. The synthesis was made through classifying the papers into different categories (e.g. research type, distribution). The analysis revealed that in most cases agile practices were modified with respect to the context and situational requirements. This indicates the need for future research on how to integrate all experiences and practices in a way to assist practitioners when setting up non-collocated agile projects.
Stiffness of Endodontically-treated Teeth Related to Restoration Technique

Endodontically-treated posterior teeth are susceptible to fracture; consequently, full-occlusal-coverage restorations are recommended. We designed this study to examine the potential for alternative restorative techniques for pulpless teeth, using strain gauges mounted on extracted maxillary second premolars to measure strains generated by nondestructive occlusal loading. Cuspal stiffness was evaluated on the following sequentially performed procedures: unaltered tooth, completion of all endodontic procedures, appropriate restorative preparation, and restoration. The restorative procedures evaluated were: (1) amalgam, (2) cast gold onlay, (3) composite restoration with enamel etch, and (4) composite restoration with enamel and dentin etch. Finally, all teeth were loaded to fracture. Cast gold was the strongest restorative material tested (2.11 relative stiffness, compared with that of the unaltered tooth at 1.00), and amalgam was the weakest (0.35 relative stiffness). Composite restoration and enamel plus dentin etch were almost as strong as the unaltered tooth (0.87 relative stiffness), while enamel-etch-only yielded lower stiffness (0.51).
Attenuation of lung cancer stem cell tumorigenesis and metastasis by cisplatin

ABSTRACT Purpose: To investigate the effect of cisplatin on the growth and metastasis abilities of lung cancer stem cells (CSCs) via molecular imaging. Materials and Methods: The expression changes of lung CSCs cell marker in A549-Luc-C8 human non-small-cell lung cancer (NSCLC) cell line with or without cisplatin treatment were detected by flow cytometry. The tumorigenesis and metastasis abilities of A549-Luc-C8 cells were monitored both in vitro and in vivo, and the mechanism was assessed by gene sequencing. Results: About 1%–2% of CSCs were detected in A549-Luc-C8 cells and decreased CSCs percentage was observed after cisplatin treatment. Attenuated tumorigenesis and metastasis abilities of A549-Luc-C8 cells were found in cisplatin treated group. Conclusions: Decreased percentage of CSCs in A549-Luc-C8 cells can be induced by cisplatin treatment, which may partly be attributed to the attenuated expression of growth factors.
Security Analysis and Improvements for IEEE 802.11i

This paper analyzes the IEEE 802.11i wireless networking standard with respect to data confidentiality, integrity, mutual authentication, and availability. Under our threat model, 802.11i appears to provide effective data confidentiality and integrity when CCMP is used. Furthermore, 802.11i may provide satisfactory mutual authentication and key management, although there are some potential implementation oversights that may cause severe problems. Since the 802.11i design does not emphasize availability, several DoS attacks are possible. We review the known DoS attacks on unprotected management frames and EAP frames, and discuss ways of mitigating them in 802.11i. The practicality of a DoS attack against Michael MIC Failure countermeasure is discussed and improvements are proposed. Two new DoS attacks and possible repairs are identified: RSN IE Poisoning and 4-Way Handshake Blocking. Finally some tradeoffs in failure-recovery strategies are discussed and an improved variant of 802.11i is proposed to address all the discussed vulnerabilities.