Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Formation of Boxy and Disky Elliptical Galaxies

The origin of boxy and disky elliptical galaxies is investigated. The results of two collisionless N-body simulations of spiral-spiral mergers with mass ratios of 1 : 1 and 3 : 1 are discussed, and the projected properties of the merger remnants are investigated. It is shown that the equal-mass merger leads to an anisotropic, slowly rotating system with preferentially boxy isophotes and significant minor-axis rotation. The unequal-mass merger results in the formation of a rotationally supported elliptical galaxy with disky isophotes and small minor-axis rotation. The observed scatter in the kinematical and isophotal properties of both classes of elliptical galaxies can be explained by projection effects.
Motzkin Paths and Reduced Decompositions for Permutations with Forbidden Patterns

We obtain a characterization of (321, 3¯ permutations in terms of their canonical reduced decompositions. This characterization is used to construct a bijection for a recent result that the number of (321, 3¯ permutations of length n equals the n-th Motzkin number, due to Gire, and further studied by Barcucci, Del Lungo, Pergola, Pinzani and Guibert. Similarly, we obtain a characterization of (231, 4 ¯ permutations. For these two classes, we show that the number of descents of a permutation equals the number of up steps on the corresponding Motzkin path. Moreover, we find a relationship between the inversion number of a permutation and the area of the corresponding Motzkin path.
90 Part 1 Chapter # GENOME-WIDE CO-EXPRESSION PATTERNS OF HUMAN CIS-ANTISENSE GENE PAIRS

Motivation: To study possible mechanisms of cis-antisense regulation in human genome, we carried out a global microarray-based co-expression analysis of a large number of cis-antisense gene pairs. We focused on cis-antisense expression patterns in distinct breast cancer types. Results: We identified common positive co-regulation patterns which reproducibly expressed in the human breast cancer cells and specific positive co-expression patterns which uniquely associated with lowand in highly-aggressive types of breast cancer cells. The enrichment of co-regulation patterns of gene pairs in the same loci in compare to random gene pairs in different loci of the human genome and absence of other regulatory modalities allowed us to suggest that cis-antisense transcripts might be controlled by (i) distant mechanisms associated with chromatin remodeling and by (ii) local mechanisms due to mutual local de-repression of mRNA synthesis initiated by temporal triplexforming mRNA which can form DNA transcription bubbles.
Detection and prevention of changes in the DOM tree

The current generation of client-side Cross-Site Scripting filters are mostly browser-based tools and do not allow the web developers to control authorized or unauthorized modifications of the web page’s Document Object Model (DOM). In this thesis, we propose a policy-based and browser-based protection mechanism to detect and prevent unauthorized tampering with the DOM. To examine the efficiency and feasibility of our approach, we implement the proposed solution in an open source web browser, Chromium. Our proposed approach has little performance overhead and effectively detects malicious modifications of the DOM. We also conduct a thorough analysis of the current state-of-the-art policy-based MutationObserver API and uncover a set of limitations.
DNA Ligase III Promotes Alternative Nonhomologous End-Joining during Chromosomal Translocation Formation

Nonhomologous end-joining (NHEJ) is the primary DNA repair pathway thought to underlie chromosomal translocations and other genomic rearrangements in somatic cells. The canonical NHEJ pathway, including DNA ligase IV (Lig4), suppresses genomic instability and chromosomal translocations, leading to the notion that a poorly defined, alternative NHEJ (alt-NHEJ) pathway generates these rearrangements. Here, we investigate the DNA ligase requirement of chromosomal translocation formation in mouse cells. Mammals have two other DNA ligases, Lig1 and Lig3, in addition to Lig4. As deletion of Lig3 results in cellular lethality due to its requirement in mitochondria, we used recently developed cell lines deficient in nuclear Lig3 but rescued for mitochondrial DNA ligase activity. Further, zinc finger endonucleases were used to generate DNA breaks at endogenous loci to induce translocations. Unlike with Lig4 deficiency, which causes an increase in translocation frequency, translocations are reduced in frequency in the absence of Lig3. Residual translocations in Lig3-deficient cells do not show a bias toward use of pre-existing microhomology at the breakpoint junctions, unlike either wild-type or Lig4-deficient cells, consistent with the notion that alt-NHEJ is impaired with Lig3 loss. By contrast, Lig1 depletion in otherwise wild-type cells does not reduce translocations or affect microhomology use. However, translocations are further reduced in Lig3-deficient cells upon Lig1 knockdown, suggesting the existence of two alt-NHEJ pathways, one that is biased toward microhomology use and requires Lig3 and a back-up pathway which does not depend on microhomology and utilizes Lig1.
Noise-robust ASR by using distinctive phonetic features approximated with logarithmic normal distribution of HMM

Various approaches focused on noise-robustness have been investigated with the aim of using an automatic speech recognition (ASR) system in practical environments. We have previously proposed a distinctive phonetic feature (DPF) parameter set for a noise-robust ASR system, which reduced the effect of high-level additive noise[1]. This paper describes an attempt to replace normal distributions (NDs) of DPFs with logarithmic normal distributions (LNDs) in HMMs because DPFs show skew symmetry, or positive and negative skewness. The HMM with the LNDs was firstly evaluated in comparison with a standard HMM with NDs in an experiment using an isolated spoken-word recognition task with clean speech. Then noise robustness was tested with four types of additive noise. In the case of DPFs as an input feature vector set, the proposed HMM with the LNDs can outperform the standard HMM with the NDs in the isolated spoken-word recognition task both with clean speech and with speech contaminated by additive noise. Furthermore, we achieved significant improvements over a baseline system with MFCC and dynamic feature-set when combining the DPFs with static MFCCs and ∆ P.
Syntactic Disambiguation by Learning Weighted Government Patterns from a Large Corpus

A method of syntactic disambiguation based on proper prepositional phrase attachment, or, more generally, attachment of the clauses in specific grammatical cases, is described. The research was based on Spanish and Russian material. The data set built and used by the procedure is a kind of a syntactic government patterns dictionary. The algorithm requires a morphological and a syntactic parser and assigns probability weights to the variants built by the parser. No manual markup is required. At the training stage, the procedure works iteratively on a large text corpus, in alternating steps re-estimating the frequencies of individual government patterns and then the weights of the variants. The method is compatible with other methods of estimation of the variants. The data set built by the algorithm is useful for compilation of a combinatory dictionary for human readers. Some generalizations of the method are discussed.
MicroRNA-1 Downregulation Increases Connexin 43 Displacement and Induces Ventricular Tachyarrhythmias in Rodent Hypertrophic Hearts

Downregulation of the muscle-specific microRNA-1 (miR-1) mediates the induction of pathologic cardiac hypertrophy. Dysfunction of the gap junction protein connexin 43 (Cx43), an established miR-1 target, during cardiac hypertrophy leads to ventricular tachyarrhythmias (VT). However, it is still unknown whether miR-1 and Cx43 are interconnected in the pro-arrhythmic context of hypertrophy. Thus, in this study we investigated whether a reduction in the extent of cardiac hypertrophy could limit the pathological electrical remodeling of Cx43 and the onset of VT by modulating miR-1 levels. Wistar male rats underwent mechanical constriction of the ascending aorta to induce pathologic left ventricular hypertrophy (LVH) and afterwards were randomly assigned to receive 10mg/kg valsartan, VAL (LVH+VAL) delivered in the drinking water or placebo (LVH) for 12 weeks. Sham surgery was performed for control groups. Programmed ventricular stimulation reproducibly induced VT in LVH compared to LVH+VAL group. When compared to sham controls, rats from LVH group showed a significant decrease of miR-1 and an increase of Cx43 expression and its ERK1/2-dependent phosphorylation, which displaces Cx43 from the gap junction. Interestingly, VAL administration to rats with aortic banding significantly reduced cardiac hypertrophy and prevented miR-1 down-regulation and Cx43 up-regulation and phosphorylation. Gain- and loss-of-function experiments in neonatal cardiomyocytes (NCMs) in vitro confirmed that Cx43 is a direct target of miR-1. Accordingly, in vitro angiotensin II stimulation reduced miR-1 levels and increased Cx43 expression and phosphorylation compared to un-stimulated NCMs. Finally, in vivo miR-1 cardiac overexpression by an adenoviral vector intra-myocardial injection reduced Cx43 expression and phosphorylation in mice with isoproterenol-induced LVH. In conclusion, miR-1 regulates Cx43 expression and activity in hypertrophic cardiomyocytes in vitro and in vivo. Treatment of pressure overload-induced myocyte hypertrophy reduces the risk of life-threatening VT by normalizing miR-1 expression levels with the consequent stabilization of Cx43 expression and activity within the gap junction.
Visual recognition based on randomized visual dictionaries

In visual recognition, Bag-of-Visual-Word(BoVW) method has been widely used due to its excellent categorization performance. However, the conventional BoVW method has problems of visual word synonymy and ambiguity, meanwhile its time efficiency decreases along with visual data scaling up. Thus, this paper proposes a visual recognition method based on randomized visual dictionaries. Firstly, we introduce E2LSH(Exact Euclidean Locality Sensitive Hashing) to cluster local feature points of training video key frames and construct a group of scalable randomized visual dictionaries. Secondly, based upon these randomized visual dictionaries, we train a group of SVM classifiers for each visual concept. Finally, a voting strategy is utilized to integrate opinions of SVM classifiers, thus accomplishing visual recognition. Experimental results show that compared to traditional BoVW method, our method achieves higher visual recognition accuracy, meanwhile guaranteeing acceptable time efficiency.
A multi-agent system that facilitates scientific publications search

It is very difficult for beginners to define and find the most relevant literature in a research field. They can search on the web or look at the most important journals and conference proceedings, but it would be much better to receive suggestions directly from experts of the field. Unfortunately, this is not always possible and systems like CiteSeer and GoogleScholar become extremely useful for beginners (and not only). In this paper, we present an agent-based system that facilitates scientific publications search. Users interacting with their personal agents produce a transfer of knowledge about relevant publications from experts to beginners. Each personal agent observes how publications are used and induces behavioral patterns that are used to create more effective recommendations. Feedback exchange allows agents to share their knowledge and virtual communities of cloned experts can be created to support novice users. We present a set of experimental results, obtained using CiteSeer as a source of information, that show the effectiveness of our approach.
The controversial nature of the Weissella genus: technological and functional aspects versus whole genome analysis-based pathogenic potential for their application in food and health

Despite the use of several Weissella (W.) strains for biotechnological and probiotic purposes, certain species of this genus were found to act as opportunistic pathogens, while strains of W. ceti were recognized to be pathogenic for farmed rainbow trout. Herein, we investigated the pathogenic potential of weissellas based on in silico analyses of the 13 whole genome sequences available to date in the NCBI database. Our screening allowed us to find several virulence determinants such as collagen adhesins, aggregation substances, mucus-binding proteins, and hemolysins in some species. Moreover, we detected several antibiotic resistance-encoding genes, whose presence could increase the potential pathogenicity of some strains, but should not be regarded as an excluding trait for beneficial weissellas, as long as these genes are not present on mobile genetic elements. Thus, selection of weissellas intended to be used as starters or for biotechnological or probiotic purposes should be investigated regarding their safety aspects on a strain to strain basis, preferably also by genome sequencing, since nucleotide sequence heterogeneity in virulence and antibiotic resistance genes makes PCR-based screening unreliable for safety assessments. In this sense, the application of W. confusa and W. cibaria strains as starter cultures or as probiotics should be approached with caution, by carefully selecting strains that lack pathogenic potential.
Transient decrease in interleukin‐7 availability arrests B lymphopoiesis during pregnancy

In mice, B lymphopoiesis is transiently arrested during pregnancy, and this is thought to be due to depletion of a hormone‐sensitive bone marrow precursor. In this study, combining in vitro and in vivo approaches with detailed phenotypic and functional analysis of progenitor cells, we have investigated the effects of pregnancy on mouse B cell development. Recently, we characterized a BM progenitor called early progenitor with lymphoid and myeloid potential (EPLM) which, when cultured under B cell conditions, is the immediate precursor of pre‐B1 cells. Results obtained show that during late pregnancy, B cell development was blocked at the EPLM‐to‐pre‐B1 transition. This block was associated with a lack of IL‐7 due to a down‐regulation of IL‐7 gene transcription. Moreover, we established that exogenously administered IL‐7 could rescue B lymphopoiesis in pregnant mice. We conclude that during pregnancy, rather than directly depleting a hormone‐sensitive B cell precursor, hormones dampen BM B cell development by fine‐tuning IL‐7 availability.
Combining heterogeneous across-country data for prediction of enteric methane from proxies in dairy cattle

Large-scale measurement of enteric methane (CH4) from individual animals is a requisite for estimation of genetic parameters and prediction of breeding values. Direct measurement of individual CH4 emissions is logistically demanding and expensive, and correlated traits (proxies) or models can be used instead as a means to predict emissions. However, most predictive models tend to be specific and are valid mainly within the circumstances under which they were developed. Robust prediction models that work across countries and production environments may be built by combining heterogeneous data from several sources. However, combining heterogeneous individual animal observations on CH4 proxies from several sources is challenging and reports are scant in literature. The main objective of this study was to combine heterogeneous individual animal observations on CH4 proxies to develop robust enteric CH4 prediction models. Data on dairy cattle CH4 emissions and related proxies from 16 herds were made available by 13 research centers across 9 European countries within the Methagene EU COST Action FA1302 consortium on “Large-scale methane measurements on individual ruminants for genetic evaluations”. After a through edition and harmonization, the final dataset comprised 48,804 observations from 2,391 cows. Random Forest (RF) models were used to predict CH4 emissions and to estimate the relative importance of proxies for across-country predictions. Principal component analysis (PCA) was used to detect potential data stratifications. Milk yield, milk fat, DIM, BW, herd and country of origin appeared to be the most relevant proxies in the prediction model. An overall prediction accuracy of 0.81 was estimated from the combined heterogeneous data. This study is a first attempt to develop methods and approaches to combine heterogeneous individual animal data on proxies for CH4 to build robust models for prediction of CH4 emissions across diverse production systems and environments. The methodology outlined here can be extended to combining heterogeneous data, pedigree information and genome-wide dense marker information for estimation of genetic parameters and prediction of breeding values for traits related to dairy system CH4 emissions. Keywords: enteric methane, heterogeneous data, prediction accuracy, methane proxies, random forest, dairy cattle.
Comment on Pepino et al. Sucralose Affects Glycemic and Hormonal Responses to an Oral Glucose Load. Diabetes Care 2013;36:2530–2535

We are interested in the recent publication by Pepino et al. (1), given that the body of evidence supports the safe use of sucralose. Pepino et al. was a small, nonblinded, randomized, cross-over study in a select group of mostly female (15/17), predominantly African American (13/17), relatively young (mean age 35 years), morbidly obese (BMI 42.3 ± 1.6 kg/m2), insulin-sensitive subjects. The study evaluated the response to a 75-g oral glucose tolerance test (OGTT) conducted 10 min after consumption of 60 mL of either distilled water or an aqueous 2 mmol/L sucralose solution. OGTTs were conducted about 1 week apart in the morning after a self-reported overnight fast. While a statistically significant difference in peak plasma glucose …
p53 mutation in plasma DNA and its prognostic value in breast cancer patients.

PURPOSE Tumor-specific DNA has recently been detected in the plasma of lung, head and neck, breast, and colon cancer patients. Detection of tumor-specific genetic materials in cancer patients at sites distant from the tumor, such as in the blood, may provide a unique and valuable tumor marker for diagnosis and prognosis. EXPERIMENTAL DESIGN The present investigation was aimed at determining the presence of p53 mutations in the peripheral blood of breast cancer patients and its prognostic value in these patients. RESULTS In this study, we found that the mean concentration of plasma DNA in healthy women was 21 ng/ml, whereas in patients with breast cancer the mean concentration was 211 ng/ml (P < 0.01). p53 mutations were detected in the primary tumors of 46 of 126 (36.5%) breast cancer patients. Of these 46 patients, 30 (65.1%) were found to have p53 mutations in their plasma DNA. p53 mutations in plasma DNA were strongly correlated with clinical stage, tumor size, lymph node (LN) metastasis, and estrogen receptor status (P < 0.05). After a median follow-up of 29 months, univariate and multivariate analysis revealed that both primary tumor and plasma DNA p53 mutations were significant prognostic factors for both relapse-free and overall survival. Furthermore, we demonstrated that patients with both primary tumor and plasma p53 mutations have the worst survival. This outcome occurs in both LN-positive and LN-negative groups. Thirteen of the 22 (59%) patients with recurrence and/or metastasis later had detectable p53 mutations in their plasma DNA. CONCLUSIONS Detection of p53 mutations in plasma DNA may be used as a prognostic factor and an early marker to indicate recurrence or distant metastasis.
Recent prognostic factors in diffuse large B-cell lymphoma indicate NF-κB pathway as a target for new therapeutic strategies

The diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoid cancer. The classical chemotherapy regimen given to these patients was the CHOP (Cyclophosphamide, Hydroxydaunorubicin or Adriamycin, Oncovin or Vincristine, Prednisone or Prednisolone), but recently rituximab with CHOP (R-CHOP) increased the number of cases responding to first line therapy. DLBCL classification identified three principle subgroups. The first one, named germinal centre B cell-like (GCB), responds to both CHOP and R-CHOP treatment and it is mainly characterised by the expression of markers like Bcl-6 and CD10. The second, the activated B-cell like (ABC), has a worse prognosis in comparison with GCB, and is mainly characterised by the expression of IRF-4, PRDM1 and NF-κB. It is interesting to notice that IRF-4 and PRDM1 are under the transcriptional control of NF-κB, whose high activation level is associated with a worse prognosis. The third one, mediastinal large B-cell lymphoma (PMBCL) is an uncommon subtype characteristically found in young females. Gene expression profiling suggests that this disease resembles Hodgkin lymphoma more than other types of DLBCL. The impact of rituximab on the outcome of patients with PMBCL has still not been fully assessed. It was seen that rituximab inhibits NF-κB pathway in vitro. However, the clinical significance of this finding is still unknown, because both ABC and GCB DLBCL show a significant improvement of overall survival after R-CHOP treatment. In this review, the NF-κB pathway is suggested as a target for new chemotherapy strategies based on the association of CHOP with molecules more effective than rituximab in this pathway inhibition.
In Vitro Processing of Herpes Simplex Virus Type 1 DNA Replication Intermediates by the Viral Alkaline Nuclease, UL12

ABSTRACT Herpes simplex virus type 1 (HSV-1) DNA replication intermediates exist in a complex nonlinear structure that does not migrate into a pulsed-field gel. Genetic evidence suggests that the product of the UL12 gene, termed alkaline nuclease, plays a role in processing replication intermediates (R. Martinez, R. T. Sarisky, P. C. Weber, and S. K. Weller, J. Virol. 70:2075–2085, 1996). In this study we have tested the hypothesis that alkaline nuclease acts as a structure-specific resolvase. Cruciform structures generated with oligonucleotides were treated with purified alkaline nuclease; however, instead of being resolved into linear duplexes as would be expected of a resolvase activity, the artificial cruciforms were degraded. DNA replication intermediates were isolated from the well of a pulsed-field gel (“well DNA”) and treated with purified HSV-1 alkaline nuclease. Although alkaline nuclease can degrade virion DNA to completion, digestion of well DNA results in a smaller-than-unit-length product that migrates as a heterogeneous smear; this product is resistant to further digestion by alkaline nuclease. The smaller-than-unit-length products are representative of the entire HSV genome, indicating that alkaline nuclease is not inhibited at specific sequences. To further probe the structure of replicating DNA, well DNA was treated with various known nucleases; our results indicate that replicating DNA apparently contains no accessible double-stranded ends but does contain nicks and gaps. Our data suggest that UL12 functions at nicks and gaps in replicating DNA to correctly repair or process the replicating genome into a form suitable for encapsidation.