Miracle-dz/UniFAR-FTUs huggingface dataset:
RSK2 phosphorylates T-bet to attenuate colon cancer metastasis and growth

Significance Many patients with colorectal cancer die because of metastases in distant organs such as the liver and lungs, rather than from the primary tumor. A better molecular understanding of colorectal cancer has allowed for improved patient prognosis and the launching of precision medicine for treating metastatic colorectal cancer. Here we demonstrate that a deficiency of ribosomal S6 kinase 2 (RSK2) can result in dramatically decreased IFNγ secretion through an inappropriate phosphorylation status of T-bet, a modulator of IFNγ expression. Decreased IFNγ levels can lead to immune suppression, accelerating colon cancer-mediated liver and lung metastasis. We found that RSK2-mediated phosphorylation of T-bet at serines 498 and 502 is required for the inhibition of colon cancer metastasis and growth, through a positive regulation of RSK2/T-bet/IFNγ signaling. Metastasis is a major cause of cancer-related deaths. Approximately 80% of patients with colorectal cancer develop liver metastasis and 20% develop lung metastasis. We found that at different stages of colon cancer, IFNγ secretion from peripheral blood mononuclear cells was decreased compared with healthy controls. The ribosomal S6 kinase (RSK) family of kinases has multiple cellular functions, and we examined their roles in this observed IFNγ decrease. Flow cytometry analysis of wild-type (WT) and RSK2 knockout (KO) mice revealed significantly lower levels of IFNγ in the RSK2 KO mice compared with the WT mice. Since IFNγ is a component of immunity, which contributes to protection against metastatic carcinomas, we conducted a colon cancer liver metastasis experiment. We found significantly greater metastasis in RSK2 KO mice compared with WT mice. Transcription factor T-bet can directly activate Ifnγ gene transcription. In vitro kinase assay results showed that RSK2 phosphorylated T-bet at serines 498 and 502. We show that phosphorylation of T-bet by RSK2 is required for IFNγ expression, because knockdown of RSK2 expression or overexpression of mutant T-bet reduces IFNγ mRNA expression. To verify the function of the phosphorylation sites, we overexpressed a constitutively active mutant T-bet (S498E/S502E) in bone marrow. Mutant T-bet restored the IFNγ mRNA levels and dramatically reduced the metastasis rate in these mice. Overall, these results indicate that phosphorylation of T-bet is required for the inhibition of colon cancer metastasis and growth through a positive regulation of RSK2/T-bet/IFNγ signaling.
Music Tweet Map: A browsing interface to explore the microblogosphere of music

In this demo paper, we present the “Music Tweet Map” interface for browsing music listening events on a global scale. These events have been extracted automatically from a large set of microblogs harvested from Twitter. We showcase the major functionalities offered by the interface, i.e., browsing music by time, specific locations, topic clusters learned from tag information, and music charts. Furthermore, music can be explored via artist similarity. To this end, we present a music similarity measure, based on co-occurrence analysis of items in users' listening histories.
Draft Genome Sequences of Two Novel Pseudomonas Strains Exhibiting Differential Hypersensitivity Reactions on Tobacco and Corn Seedlings

ABSTRACT Two novel Pseudomonas strains (S1E40 and S3E12) isolated from corn roots are antagonistic to Rhizoctonia solani and exhibit differential hypersensitivity reactions on tobacco and corn seedlings. We report here the draft genome sequences of strains S1E40 and S3E12, consisting of 6.98 and 7.06 Mb with 6,150 and 6,129 predicted protein-coding sequences, respectively.
Lithium-induced neuroprotection is associated with epigenetic modification of specific BDNF gene promoter and altered expression of apoptotic-regulatory proteins

Bipolar disorder (BD), one of the most debilitating mental disorders, is associated with increased morbidity and mortality. Lithium is the first line of treatment option for BD and is often used for maintenance therapy. Recently, the neuroprotective action of lithium has gained tremendous attention, given that BD is associated with structural and functional abnormalities of the brain. However, the precise molecular mechanism by which lithium exerts its neuroprotective action is not clearly understood. In hippocampal neurons, the effects of lithium (1 and 2 mM) on neuronal viability against glutamate-induced cytotoxicity, dendritic length and number, and expression and methylation of BDNF promoter exons and expression of apoptotic regulatory genes were studied. In rat hippocampal neurons, lithium not only increased dendritic length and number, but also neuronal viability against glutamate-induced cytotoxicity. While lithium increased the expression of BDNF as well as genes associated with neuroprotection such as Bcl2 and Bcl-XL, it decreased the expression of pro-apoptotic genes Bax, Bad, and caspases 3. Interestingly, lithium activated transcription of specific exon IV to induce BDNF gene expression. This was accompanied by hypomethylation of BDNF exon IV promoter. This study delineates mechanisms by which lithium mediates its effects in protecting neurons.
Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria. ” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
Effects of lavender straw on stress and travel sickness in pigs.

OBJECTIVE To observe pigs during road journeys in order to establish whether lavender straw was likely to decrease stress and incidence of travel sickness. SUBJECTS Forty 70-kg Large White pigs were transported by road for 2 hours, 20 animals each day, over a 2-day period. DESIGN On day 1, ample wheat straw was provided as bedding such that the floor of the vehicle was entirely covered (straw condition). On day 2, lavender straw was provided as bedding (lavender condition). During the journey, direct behavioral observations of the individually marked pigs were made by scanning every 10 minutes for incidence of standing and lying along with the less severe symptoms of travel sickness (foaming at the mouth and repetitive chomping). Incidences of retching and vomiting were noted as they occurred. A general activity index was also scored every 10 minutes (5 = high activity, 1 = low activity). Saliva samples were taken from each animal at different stages of the journey for analysis of cortisol. RESULTS Pigs stood more when in the straw condition, but were more active when standing in the lavender condition. Symptoms of travel sickness appeared to be less acute in the lavender condition, with more animals exhibiting the less severe symptom, foaming and chomping (a total of 3 in straw compared with 6 in lavender), but fewer animals showing the more severe symptoms of retching and vomiting (in straw, 3 retched, 6 vomited; in lavender 0 retched, 3 vomited). A total of 6 animals retched or vomited in the straw condition but only 3 in the lavender. There was a significant difference in mean concentrations of cortisol between conditions but this was due to a difference in mean baseline concentrations between groups. CONCLUSION Addition of lavender straw appeared to decrease incidence and severity of travel sickness but not overall levels of stress (as measured by concentrations of salivary cortisol).
Economic load dispatch using improved particle swarm optimization algorithms

The main objective of Economic Load Dispatch (ELD) problem is to schedule the connected generating units of plant outputs so as to fulfill load demands at minimum operating cost while satisfying all operational constraints. Recently particle swarm optimization algorithms inspired by collective behavior of swarm has been applied successfully to solve ELD problem. It is a population based stochastic optimization process driven by the simulation of a social psychological metaphor. In this paper three improved PSO algorithms- IPSO-A, IPSO-B and IPSO-C have been developed and implemented to solve ELD for IEEE 5, 14 and 30 bus systems. Conventional PSO (CPSO) using inertia weight and constriction factor individually as well as simultaneously have been also implemented to solve ELD problem. PSO algorithms have been compared for twenty trial runs. The best, worst, average fitness and their standard deviation for all the algorithms have been determined. The results show that proposed improved PSO techniques gives the optimum operating cost with consistent results in terms of diversity of results.
Positive autoregulation of the yeast transcription factor Pdr3p, which is involved in control of drug resistance

Simultaneous resistance to an array of drugs with different cytotoxic activities is a property of Saccharomyces cerevisiae, in which the protein Pdr3p has recently been shown to play a role as a transcriptional regulator. We provide evidence that the yeast PDR3 gene, which encodes a zinc finger transcription factor implicated in certain drug resistance phenomena, is under positive autoregulation by Pdr3p. DNase I footprinting analyses using bacterially expressed Pdr3p showed specific recognition by this protein of at least two upstream activating sequences in the PDR3 promoter. The use of lacZ reporter constructs, a mutational analysis of the upstream activating sequences, as well as band shift experiments enabled the identification of two 5'TC CGCGGA3' sequence motifs in the PDR3 gene as consensus elements for the binding of Pdr3p. Several similar sequence motifs can be found in the promoter of PDR5, a gene encoding an ATP-dependent drug pump whose Pdr3p-induced overexpression is responsible for drug resistance phenomena. Recently one of these sequence elements was shown to be the target of Pdr3p to elevate the level of PDR5 transcription. Finally, we provide evidence in the absence of PDR1 for a PDR3-controlled transcriptional induction of the drug pump by cycloheximide and propose a model for the mechanism governing the transcriptional autoregulation of Pdr3p.
Multiple markers and multiple individuals refine true seal phylogeny and bring molecules and morphology back in line

Despite decades of study, some aspects of Phocidae (Pinnipedia, Carnivora) phylogeny still remain unresolved. Using the largest novel dataset to date, including all extant phocids and comprising 15 nuclear and 13 mitochondrial genes, we illustrate the utility of including multiple individuals per species in resolving rapid radiations, and provide new insight into phocid phylogeny. In line with longstanding morphological views, Pusa is recovered as monophyletic for the first time with genetic data. The data are also used to explore the relationship between genetic distance and taxonomic rank. Intraspecific sampling also highlights the discrepancy between molecular and morphological rates of evolution within Phocidae.
META-STABLE BRANE CONFIGURATIONS BY HIGHER-ORDER POLYNOMIAL SUPERPOTENTIAL

We construct the type IIA nonsupersymmetric meta-stable brane configuration consisting of (2k+1) NS5-branes and D4-branes where the electric gauge theory superpotential has an order (2k+2) polynomial for the bifundamentals. We find a rich pattern of nonsupersymmetric meta-stable states as well as the supersymmetric stable ones. By adding the orientifold 4-plane to this brane configuration, we also describe the intersecting brane configuration of type IIA string theory corresponding to the meta-stable nonsupersymmetric vacua of corresponding gauge theory.
ProM: The Process Mining Toolkit

Process mining has been around for a decade, and it has proven to be a very fertile and successful research field. Part of this success can be contributed to the ProM tool, which combines most of the existing process mining techniques as plug-ins in a single tool. ProM6 removes many limitations that existed in the previous versions, in particular with respect to the tight integration between the tool and the GUI. ProM 6 has been developed from scratch and uses a completely redesigned architecture. The changes were driven by many real-life applications and new insights into the design of process analysis software. Furthermore, the introduction of XESame in this toolkit allows for the conversion of logs to the ProM native format without programming.
Hybrid Incompatibility in Arabidopsis Is Determined by a Multiple-Locus Genetic Network1[W][OA]

The cross between Arabidopsis thaliana and the closely related species Arabidopsis arenosa results in postzygotic hybrid incompatibility, manifested as seed death. Ecotypes of A. thaliana were tested for their ability to produce live seed when crossed to A. arenosa. The identified genetic variation was used to map quantitative trait loci (QTLs) encoded by the A. thaliana genome that affect the frequency of postzygotic lethality and the phenotypes of surviving seeds. Seven QTLs affecting the A. thaliana component of this hybrid incompatibility were identified by crossing a Columbia × C24 recombinant inbred line population to diploid A. arenosa pollen donors. Additional epistatic loci were identified based on their pairwise interaction with one or several of these QTLs. Epistatic interactions were detected for all seven QTLs. The two largest additive QTLs were subjected to fine-mapping, indicating the action of at least two genes in each. The topology of this network reveals a large set of minor-effect loci from the maternal genome controlling hybrid growth and viability at different developmental stages. Our study establishes a framework that will enable the identification and characterization of genes and pathways in A. thaliana responsible for hybrid lethality in the A. thaliana × A. arenosa interspecific cross.
Gender Detection using Machine Learning Techniques and Delaunay Triangulation

Data mining today is being used widely in diverse areas. For example: fraudulent systems, recommender systems, disease prediction, and numerous other applications. One such application is exploited in this article. This paper presents an approach to detect gender of a person through frontal facial image, using techniques of data mining and Delaunay triangulation. Gender prediction can prove to be a very useful technique in HCI (Human Computer Interaction) Systems. Classification, being a very power technique in data mining to group categorical data, is used here to classify a gender as either male, or female. Various classification algorithms such as Functional Trees, AdaBoost, J48, and few others are used to gauge the maximum accuracy. The model used in this paper is robust and attains accuracy level of 93.8283% along with relative scale invariance. Details of the prediction model and results are reported herein. General Terms Data mining, classification algorithms, WEKA tool, gender detection, Machine learning
Computing "Elo Ratings" of Move Patterns in the Game of Go

Move patterns are an essential method to incorporate do- main knowledge into Go-playing programs. This paper presents a new Bayesian technique for supervised learning of such patterns from game records, based on a generalization of Elo ratings. Each sample move in the training data is considered as a victory of a team of pattern features. Elo ratings of individual pattern features are computed from these victo- ries, and can be used in previously unseen positions to compute a prob- ability distribution over legal moves. In this approach, several pattern features may be combined, without an exponential cost in the number of features. Despite a very small number of training games (652), this algorithm outperforms most previous pattern-learning algorithms, both in terms of mean log-evidence ( 2.69), and prediction rate (34.9%). A 19◊ 19 Monte-Carlo program improved with these patterns reached the level of the strongest classical programs. and little domain expertise. This paper presents a new supervised pattern-learning algorithm, based on the Bradley-Terry model. The Bradley-Terry model is the theoretical basis of the Elo rating system. The principle of Elo ratings, as applied to chess, is that each player gets a numerical strength estimation, computed from the observation of past game results. From the ratings of players, it is possible to estimate a probability distribution over the outcome of future games. The same principle
Analyzing Exceptions in the Context of Test Data Generation Based on Symbolic Execution

Testing exception scenarios is a challenging task in the context of test data generation based on symbolic execution. In such a context, test data is generated based on constraints explicitly declared in the code. However, constraints required to activate specific exceptions may not be directly declared in the code. In such a case, implicit constraints have to be inferred from exception handling mechanisms. Given that exceptions can be raised in several situations, finding constraints to generate test data to exercise all possible faulty scenarios can significantly increase the number of paths and constraints, which can cause or aggravate path explosion issues. This paper reports on an investigation that we carried out to gauge the cost (i.e., number of path constraints) of four data generation approaches aimed at covering exception dependent paths.
Linguistic analysis of lone offender manifestos

The Internet and social media allow people to spread their views rapidly to a large group of people. While the right to freely express one's ideas and views is a cornerstone in a democratic society, in some cases the Internet can serve as a breeding ground for violent extremism and terrorism. Hence, in order to protect democracy, effective techniques of Internet surveillance are needed. Previous research has shown that there is a connection between word use and psychological states. The text analysis tool Linguistic Inquiry and Word Count (LIWC) counts words in psychologically meaningful categories. Based on the relative frequency of words from the different categories, conclusions can be drawn about the author of for instance a blog text. In this work, we have explored the characteristics of written communication produced by ten different lone offenders prior to their engagement in targeted violence. We found eight possible indicators of the drives and emotions that preceded their attacks.
Influence of size and CCD-angle of a short stem hip arthroplasty on strain patterns of the proximal femur - an experimental study.

PURPOSE The number of primary total hip arthroplasties (THA) is steadily increasing. Over the last decade numerous so-called short stem hip arthroplasties were introduced on the market. The aim of these implants with a predominantly metaphyseal anchorage is to reduce stress shielding and thereby the risk of aseptic loosening. One of the short stem arthroplasties with predominant metaphyseal fixation is the METHA® short stem (Aesculap, Tuttlingen, Germany). In order to reconstruct the biomechanics the METHA stem is available in different sizes with different centrum-collum-diaphysis-angles (CCD-angle). In this study, we want to address the research question of how the size of the implant and different CCD-angles influence the strain patterns of the proximal femur. METHODS Three different stem sizes (size 2, 3 and 4 - CCD-angle 130°) and three stems with different CCD-angles (size 3 - 120°, 130° and 135° CCD-angle) were successively implanted in a synthetic femur. Eight strain gauges monitored the corresponding strain patterns of the proximal femur. RESULTS Independent of stem size and CCD-angle only small changes in the strains were recorded around the distal part of the METHA stem when compared to the intact femur. However, all stems increased the strains in the region of the calcar. This was most pronounced by smaller CCD-angles and major sizes. CONCLUSION The stem size and CCD-angle primarily influence the region of the calcar. Greater sizes and smaller CCD-angles lead to increased strains at the calcar. The other regions are hardly influenced by the stem size and CCDangle of the femoral component.
Embedded vision-based nighttime driver assistance system

This study presents an effective method for detecting vehicles in front of the camera-assisted car during nighttime driving and implements it on an embedded system. The proposed method detects vehicles based on detecting and locating vehicle headlights and taillights using techniques of image segmentation and pattern analysis. Firstly, to effectively extract bright objects of interest, a segmentation process based on automatic multilevel thresholding applied on the grabbed road-scene images. Then the extracted bright objects are processed by to identify the vehicles by locating and analyzing their vehicle light patterns and to estimate their distances to the cameraassisted car by a rule-based procedure. Finally, we also implement the above vision-based techniques on a real-time system mounted in the host car. The proposed vision-based techniques are integrated and implemented on an ARMLinux embedded platform, as well as the peripheral devices, including image grabbing devices, voice reporting module, and other in-vehicle control devices, will be also integrated to accomplish an in-vehicle embedded vision-based nighttime driver assistance system.
Learning to type with the tip of the tongue: a performance study for a tongue-computer interface

This study is motivated by the need to know the characteristics of the learning processes in tongue-computer interaction and to obtain a useful insight to a better design of the tongue-computer interface for computer text input. Tongue-typing can be a good alternative to hand input methods for physically disabled individuals or tasks where hand-typing is not possible. In order to evaluate the process of typing with the tip of the tongue, eight volunteers participated in tip-of-tongue selectivity training experiments using an inductive tongue-computer interface. Performance data based on typing speed and accuracy fits a general learning model based on the power law of practice, which can be used to estimate further improvements of tongue-typing performance. Simulated expert typing rates predict a tongue-typing performance 8 times slower than normal QWERTY keyboard, but duplicate the performance of other alternative input interfaces. Our results encourage the use of a tongue-computer interface over other methods for physically disabled individuals.