Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous inhibition of glioma angiogenesis, cell proliferation, and invasion by a naturally occurring fragment of human metalloproteinase-2.

Angiogenesis, tumor cell proliferation, and migration are the hallmarks of solid tumors, such as gliomas. This study demonstrates that a fragment derived from the autocatalytic digestion of matrix metalloproteinase (MMP)-2, called PEX, acts simultaneously as an inhibitor of glioma angiogenesis, cell proliferation, and migration. PEX is detected in the cultured medium of various human glioma, endothelial, breast, and prostate carcinoma cell lines. PEX is purified from the medium of glioma cell lines by chromatography, where PEX is constitutively expressed as a free and a TIMP-2-bound form. In human glioma tissue, PEX expression correlates with histological subtype and grade and with alpha v beta 3 integrin expression to which it is bound. Systemic administration of PEX to s.c. and intracranial human glioma xenografts results in a 99% suppression of tumor growth with no signs of toxicity. Thus, PEX is a very promising candidate for the treatment of human malignant gliomas.
Analysis of Conserved Hydrophobic Cores in Proteins and Supramolecular Complexes

The conserved hydrophobic core is an important feature of a family of protein domains. We suggest a procedure for finding and the analysis of conserved hydrophobic cores. The procedure is based on using an original program called CluD (http://monkey.belozersky.msu.ru/CluD/cgi-bin/hftri.pl). Conserved hydrophobic cores of several families including homeodomains and interlock-containing domains are described. Hydrophobic clusters on some protein-DNA and protein-protein interfaces were also analyzed.
ZOT! to Wikipedia Vandalism - Lab Report for PAN at CLEF 2010

This vandalism detector uses features primarily derived from a word-preserving differencing of the text for each Wikipedia article from before and after the edit, along with a few metadata features and statistics on the before and after text. Features computed from the text difference are then a combination of statistics such as length, markup count, and blanking along with a selected number of TFIDF values for words and bigrams. Our training set was expanded from that supplied for the shared task to include the 5K vandalism edit corpus from West et al. Vandalism edits in the training set that were classiﬁed as “regular” by a classiﬁer trained on all the data were removed from the training set used for the ﬁnal classiﬁer. Classiﬁcation was performed using bagging of the Weka J48graft (C4.5) decision tree [3] which resulted in an evaluation score of 0.84340 AUC. It is unclear whether the expanded vandalism data improved or degraded performance because that changed the ratio of regular to vandalism edits in the training set and we did not make any adjustment for that when training the classiﬁer.
Syntax in language and music: what is the right level of comparison?

It is often claimed that music and language share a process of hierarchical structure building, a mental “syntax. ” Although several lines of research point to commonalities, and possibly a shared syntactic component, differences between “language syntax” and “music syntax” can also be found at several levels: conveyed meaning, and the atoms of combination, for example. To bring music and language closer to one another, some researchers have suggested a comparison between music and phonology (“phonological syntax”), but here too, one quickly arrives at a situation of intriguing similarities and obvious differences. In this paper, we suggest that a fruitful comparison between the two domains could benefit from taking the grammar of action into account. In particular, we suggest that what is called “syntax” can be investigated in terms of goal of action, action planning, motor control, and sensory-motor integration. At this level of comparison, we suggest that some of the differences between language and music could be explained in terms of different goals reflected in the hierarchical structures of action planning: the hierarchical structures of music arise to achieve goals with a strong relation to the affective-gestural system encoding tension-relaxation patterns as well as socio-intentional system, whereas hierarchical structures in language are embedded in a conceptual system that gives rise to compositional meaning. Similarities between music and language are most clear in the way several hierarchical plans for executing action are processed in time and sequentially integrated to achieve various goals.
Spanish-to-Basque MultiEngine Machine Translation for a Restricted Domain

We present our initial strategy for Spanish-to-Basque MultiEngine Machine Translation, a language pair with very different structure and word order and with no huge parallel corpus available. This hybrid proposal is based on the combination of three different MT paradigms: Example-Based MT, Statistical MT and Rule- Based MT. We have evaluated the system, reporting automatic evaluation metrics for a corpus in a test domain. The first results obtained are encouraging.
Roles and post-translational regulation of cardiac class IIa histone deacetylase isoforms

Cardiomyocyte hypertrophy is an integral component of pathological cardiac remodelling in response to mechanical and chemical stresses in settings such as chronic hypertension or myocardial infarction. For hypertrophy to ensue, the pertinent mechanical and chemical signals need to be transmitted from membrane sensors (such as receptors for neurohormonal mediators) to the cardiomyocyte nucleus, leading to altered transcription of the genes that regulate cell growth. In recent years, nuclear histone deacetylases (HDACs) have attracted considerable attention as signal‐responsive, distal regulators of the transcriptional reprogramming that in turn precipitates cardiomyocyte hypertrophy, with particular focus on the role of members of the class IIa family, such as HDAC4 and HDAC5. These histone deacetylase isoforms appear to repress cardiomyocyte hypertrophy through mechanisms that involve protein interactions in the cardiomyocyte nucleus, particularly with pro‐hypertrophic transcription factors, rather than via histone deacetylation. In contrast, evidence indicates that class I HDACs promote cardiomyocyte hypertrophy through mechanisms that are dependent on their enzymatic activity and thus sensitive to pharmacological HDAC inhibitors. Although considerable progress has been made in understanding the roles of post‐translational modifications (PTMs) such as phosphorylation, oxidation and proteolytic cleavage in regulating class IIa HDAC localisation and function, more work is required to explore the contributions of other PTMs, such as ubiquitination and sumoylation, as well as potential cross‐regulatory interactions between distinct PTMs and between class IIa and class I HDAC isoforms.
Dynamic Network Coding for Multiple Sessions Based on Flow Gain

This paper proposes a dynamic coding policy (MSNC) which allows network coding applied across multiple sessions and develops a necessary condition for MSNC by denoting the benefit gaining from coding. With MSNC, intermediate nodes can independently judge whether the coding operation is appropriate and easily decide which packet to transmit among the incoming flows. To make the network coding feasible in practic, a control mechanism for an intermediate node is presented, which illustrates the operations for the incoming packet flows. Simulation results demonstrate the advantage of MSNC in terms of both throughput and fairness.
Functional electrical stimulation changes dynamic resources in children with spastic cerebral palsy.

BACKGROUND AND PURPOSE Children with cerebral palsy (CP) often are faced with difficulty in walking. The purpose of this experiment was to determine the effects of functional electrical stimulation (FES) applied to the gastrocnemius-soleus muscle complex on the ability to produce appropriately timed force and reduce stiffness (elastic property of the body) and on stride length and stride frequency during walking. SUBJECTS AND METHODS Thirteen children with spastic CP (including 4 children who were dropped from the study due to their inability to cooperate) and 6 children who were developing typically participated in the study. A crossover study design was implemented. The children with spastic CP were randomly assigned to either a group that received FES for 15 trials followed by no FES for 15 trials or a group that received no FES for 15 trials followed by FES for 15 trials. The children who were having typical development walked without FES. Kinematic data were collected for the children with CP in each walking condition and for the children who were developing typically. Impulse (force-producing ability) and stiffness were estimated from an escapement-driven pendulum and spring system model of human walking. Stride length and stride frequency also were measured. To compare between walking conditions and between the children with CP and the children who were developing typically, dimensional analysis and speed normalization procedures were used. RESULTS Nonparametric statistics showed that there was no significant difference between the children with CP in the no-FES condition and the children who were developing typically on speed-normalized dimensionless impulse. In contrast, the children with CP in the FES condition had a significantly higher median value than the children who were developing typically. The FES significantly increased speed-normalized dimensionless impulse from 10.02 to 16.32 when comparing walking conditions for the children with CP. No significant differences were found between walking conditions for stiffness, stride length, and stride frequency. DISCUSSION AND CONCLUSION The results suggest that FES is effective in increasing impulse during walking but not in decreasing stiffness. The effect on increasing impulse does not result in more typical spatiotemporal gait parameters.
A proposed structural basis for picrotoxinin and picrotin binding in the glycine receptor pore

Picrotoxin, an antagonist of structurally‐rated GABAA receptors (GABAARs) and glycine receptors (GlyRs), is an equimolar mixture of picrotoxinin (PTXININ) and picrotin (PTN). These compounds share a common structure except that PTN contains a slightly larger dimethylmethanol in place of the PTXININ isopropenyl group. Although the homomeric α1 GlyR is equally sensitive to both compounds, we show here that homomeric α2 and α3 GlyRs, like most GABAARs, are selectively inhibited by PTXININ. As conservative mutations to pore‐lining 6′ threonines equally affect the sensitivity of the α1 GlyR to both compounds, we conclude that PTXININ and PTN bind to 6′ threonines by hydrogen bonding with exocyclic oxygens common to both molecules. In contrast, substitution of the 2′ pore‐lining glycine by serine selectively reduces PTN sensitivity, whereas the introduction of 2′ alanines selectively increases PTXININ sensitivity. These results define the orientation of PTXININ and PTN binding in the α1 GlyR pore and allow us to conclude that the relatively reduced sensitivity of PTN at GABAARs and α2 and α3 GlyRs is due predominantly to its larger size and reduced ability to form hydrophobic interactions with 2′ alanines.
In vivo expression of neurotrophins and neurotrophin receptors is conserved in adult porcine retina in vitro.

PURPOSE To characterize and compare the expression of neurotrophins (NTs) and their receptors within adult porcine retinal ganglion cells (RGCs) in vivo and in vitro. METHODS The distribution of nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3) and -4 (NT-4), and their high-affinity receptors TrkA, TrkB, TrkC and low-affinity receptor p75, was analyzed in adult porcine retinal sections by immunohistochemistry. In addition, adult porcine retinas were dissociated and cultured in four different conditions: control, semipure RGCs, supplemented with BDNF, or seeded on Müller glia feeder layers. Double immunostaining was performed with antibodies to NTs or their receptors combined with neurofilament antibody to identify RGCs in culture. RESULTS In vivo, immunolabeling of NGF was very faint, BDNF was especially prominent in RGCs and inner nuclear layer cells, NT-3 stained widespread nuclei, and NT-4 was undetectable. TrkA immunoreactivity was visible in the nerve fiber layer, TrkB staining was within RGC bodies, TrkC was undetectable, and p75 was widely expressed across the retina, within the Müller glia. Expression of neurotrophins and their receptors was maintained in all four models of adult RGCs in vitro, showing that expression was not influenced by substrate or culture conditions. We observed prominent staining of TrkA within growth cones, and a clear expression of p75 within a subpopulation of RGCs in vitro. CONCLUSIONS These findings demonstrate that the expression of NTs and their receptors within adult porcine RGCs is maintained in vitro, under conditions of limited interaction with neighboring neurons and deprived of afferent inputs and target tissue. TrkA may be involved in regeneration of nerve terminals.
A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes

The genes that determine the development of the male or female sex are known in Caenorhabditis elegans, Drosophila, and most mammals. In many other organisms the existence of sex-determining factors has been shown by genetic evidence but the genes are unknown. We have found that in the fish medaka the Y chromosome-specific region spans only about 280 kb. It contains a duplicated copy of the autosomal DMRT1 gene, named DMRT1Y. This is the only functional gene in this chromosome segment and maps precisely to the male sex-determining locus. The gene is expressed during male embryonic and larval development and in the Sertoli cells of the adult testes. These features make DMRT1Y a candidate for the medaka male sex-determining gene.
Questions Unanswered , and Questions Not Yet

J.M. Bower (ed.), 20 Years of Computational Neuroscience, Springer Series in Computational Neuroscience 9, DOI 10.1007/978-1-4614-1424-7_12, © Springer Science+Business Media New York 2013 Abstract I have been asked to review the progress that computational neuroscience has made over the past 20 years in understanding how vision works. In refl ecting on this question, I come to the conclusion that perhaps the most important advance we have made is in gaining a deeper appreciation of the magnitude of the problem before us. While there has been steady progress in our understanding—and I will review some highlights here—we are still confronted with profound mysteries about how visual systems work. These are not just mysteries about biology, but also about the general principles that enable vision in any system whether it be biological or machine. I devote much of this chapter to examining these open questions, as they are crucial in guiding and motivating current efforts. Finally, I shall argue that the biggest mysteries are likely to be ones we are not currently aware of, and that bearing this in mind is important as it encourages a more exploratory, as opposed to strictly hypothesis-driven, approach.
The granule-bound starch synthase (GBSSI) gene in the Rosaceae: multiple loci and phylogenetic utility.

We sampled the 5' end of the granule-bound starch synthase gene (GBSSI or waxy) in Rosaceae, sequencing 108 clones from 18 species in 14 genera representing all four subfamilies (Amygdaloideae, Maloideae, Rosoideae, and Spiraeoideae), as well as four clones from Rhamnus catharticus (Rhamnaceae). This is the first phylogenetic study to use the 5' portion of this nuclear gene. Parsimony and maximum-likelihood analyses of 941 bases from seven complete and two partial exons demonstrate the presence of two loci (GBSSI-1 and GBSSI-2) in the Rosaceae. Southern hybridization analyses with locus-specific probes confirm that all four Rosaceae subfamilies have at least two GBSSI loci, even though only one locus has been reported in all previously studied diploid flowering plants. Phylogenetic analyses also identify four clades representing four loci in the Maloideae. Phylogenetic relationships inferred from GBSSI sequences are largely compatible with those from chloroplast (cpDNA: ndhF, rbcL) and nuclear ribosomal internal transcribed spacer (nrITS) DNA. Large clades are marked by significant intron variation: a long first intron plus no sixth intron in Maloideae GBSSI-1, a long fourth intron in Rosoideae GBSSI-1, and a GT to GC mutation in the 5' splice site of the fourth intron in all GBSSI-2 sequences. Our data do not support the long-held hypothesis that Maloideae originated from an ancient hybridization between amygdaloid and spiraeoid ancestors. Instead, Spiraeoideae genera (Kageneckia and Vauquelinia) are their closest relatives in all four GBSSI clades.
Joint friction identification for robots using TSK fuzzy system based on subtractive clustering

In this paper, the joint friction of a robotic manipulatoris identified by using subtractive clustering based Takagi-Sugeno-Kang (TSK) fuzzy logic system (FLS). The proposed approach can provide accurate prediction of the joint friction despite the nonlinearity of the friction and measurement uncertainty. Simulation results show the effectiveness and convenience of the method.
High serum levels of norovirus genotype-specific blocking antibodies correlate with protection from infection in children.

BACKGROUND Norovirus is a common cause of acute gastroenteritis in children. Serum immunoglobulin G (IgG) antibodies have been implicated in protection against norovirus-associated gastroenteritis, but the level, specificity, and functionality necessary for protection remain to be elucidated. METHODS Norovirus-specific IgG antibodies to genogroup II (GII)-4-2010 New Orleans (NO), GII-4-1999, GII-12-1998, GI-1-2001, and GI-3-2002 virus-like particles (VLPs) were determined by enzyme-linked immunosorbent assay in serum samples collected from children who presented to the hospital because of acute norovirus gastroenteritis in 2009-2011. The blocking activity of the antibodies was tested in a surrogate neutralization assay. RESULTS Most norovirus infections (62.8%) in the study population were caused by a GII-4 NO variant. Children who acquired GII-4 NO infection had a low preexisting type-specific IgG level and blocking activity of the sera, in contrast to children infected with other GII genotypes. Following GII-4 NO infection, genotype-specific seroconversion and a corresponding increase in blocking antibody potential was observed. Although seroconversion to the heterologous GII-4-1999 variant was observed, there was no corresponding increase in the specific blocking antibody titer. There was no concomitant seroconversion against GI VLPs, indicating a highly genogroup-specific antibody response. CONCLUSIONS High preexisting norovirus genotype-specific serum IgG titers and blocking activity in children indicate protection from norovirus infection in a strain-specific manner.
Journal of Theoretical and Applied Information Technology E-democracy in Middle East: Hard to Approach

The paper will explore the key benefits and challenges in advancing e-Government for democratic participation and social inclusion, particularly from a Middle Eastern regional perspective (i.e., Hashemite Kingdom of Jordan). The use of online Internet services for applying e-democracy is studied with many clarifying comments and obstacles. The authors suggest that the implementation of e-Democracy requires an environment of confidence that must be created. In addition, a transition period of " real democracy " must be implemented first for some time. Some of the problems with implementing of e-Democracy in the Middle East are presented. In addition, many observations and examples are given to verify the notes of the authors.
texturebook submitted to World Scientific : 14/04/08 : 10.15 1/11 MULTI-RESOLUTION CLUSTERING OF TEXTURE IMAGES

The focus of this paper is mainly on texture synthesis rather than analysis. We describe a new method for analysis/synthesis of textures using a non-parametric multi-resolution approach. In the analysis step the new technique clusters together structural features with the same visual appearance from an input texture using a standard pyramid-based decomposition. The synthesis is obtained through a sampling procedure constraining the distribution of the spatial characteristics at lower resolution. This is realized through a new data structure called frequency tree that implicitly describes the texture itself. Experimental results show the effectiveness of such approach: it is capable to reproduce efficiently the generative stochastic process of a wide class of real texture images. The proposed method achieves a greater computational efficiency than other approach known in the literature.
Cancer Therapy : Clinical A Randomized Phase II Presurgical Trial of Transdermal 4-Hydroxytamoxifen Gel versus Oral Tamoxifen in Women with Ductal Carcinoma In Situ of the Breast

Purpose: Local transdermal therapy to the breast may achieve effective target-organ drug delivery, while diminishing systemic effects. We conducted a randomized, double-blind, placebo-controlled phase II trial comparing transdermal 4-hydroxytamoxifen gel (4-OHT) to oral tamoxifen (oral-T) in women with ductal carcinoma in situ (DCIS). Methods: Twenty-seven preand postmenopausal women were randomized to 4-OHT (4 mg/day) or oral-T (20mg/day) for 6 to 10 weeks before surgery. Plasma, nipple aspirate fluid, and breast adipose tissue concentrations of tamoxifen and itsmajormetabolites were determined by liquid chromatography/tandem mass spectrometry. The primary endpoint was Ki67 labeling in DCIS lesions, measured by immunohistochemistry. In plasma, insulin-like growth factor-1 (IGFI), sex hormone–binding globulin (SHBG), and coagulation protein concentrations were determined. Results: Posttherapy Ki67 decreased by 3.4% in the 4-OHT and 5.1% in the oral-T group (P 0.03 in both, between-group P 1⁄4 0. 99). Mean plasma 4-OHT was 0.2 and 1.1 ng/mL in 4-OHT and oral groups, respectively (P1⁄4 0.0003), whereasmean breast adipose tissue concentrations of 4-OHTwere 5.8 ng/g in the 4-OHT group and 5.4 ng/g in the oral group (P 1⁄4 0.88). There were significant increases in plasma SHBG, factor VIII, and von Willebrand factor and a significant decrease in plasma IGFI with oral-T, but not with 4-OHT. The incidence of hot flashes was similar in both groups. Conclusions: The antiproliferative effect of 4-OHT gel applied to breast skin was similar to that of oral-T, but effects on endocrine and coagulation parameters were reduced. These findings support the further evaluation of local transdermal therapy for DCIS and breast cancer prevention. Clin Cancer Res; 20(14);
TTAF: TCP Timeout Adaptivity Based on Fast Retransmit over MANET

Transmission Control Protocol (TCP) is one of the most widely deployed transport layer protocols. It responds to all packet losses, either due to congestion or link breakages, by invoking various congestion control mechanisms. All these mechanisms imply a reduction in the amount of transmitted data. Computing a proper value of the retransmission timeout (RTO) is a challenge for TCP. In mobile ad hoc networks (MANET), mobility and bit error cause a lot of packet losses which degrades TCP throughput. In this paper we introduce an adaptation of TCP Ne wReno in order to improve its performance during the fast recovery phase. Our adapted algorithm, which we called TTAF, does not rely only on round trip time samples but also takes into consideration fast retransmit events in tuning the value of RTO. A set of experiments have been conducted to evaluate the effect of TTAF over MANET with various mobility speed, traffic load, and bit error rates. Results have shown an improvement in TTAF throughput compared with that of TCP NewReno.