Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Structure and Genetic Diversity Within the Endangered Species Pityopsis ruthii (Asteraceae)

Pityopsis ruthii (Ruth’s golden aster) is a federally endangered herbaceous perennial endemic to the Hiwassee and Ocoee Rivers in southeastern Tennessee, United States. Comprehensive genetic studies providing novel information to conservationists for preservation of the species are lacking. Genetic variation and gene flow were evaluated for 814 individuals from 33 discrete locations using polymorphic microsatellites: seven chloroplast and twelve nuclear. A total of 198 alleles were detected with the nuclear loci and 79 alleles with the chloroplast loci. Gene flow was estimated, with the Hiwassee River (Nm = 2.16; FST = 0.15) showing higher levels of gene flow and lower levels of population differentiation than the Ocoee River (Nm = 1.28; FST = 0.19). Population structure was examined using Bayesian cluster analyses. Nuclear and chloroplast analyses were incongruent. From the chloroplast microsatellites, three clusters were identified; all were present in sampling sites at both rivers, indicating a lack of allele fixation along rivers. Nuclear markers revealed two clusters and separated by river. When the Hiwassee River locations were analyzed, four clusters were identified for both the chloroplast and nuclear microsatellites, though the individuals clustered differently. Analysis of the Ocoee River revealed two clusters for the chloroplast microsatellites and three for the nuclear microsatellites. We recommend P. ruthii be managed as four populations for the Hiwassee River and three populations for the Ocoee River. Our results provide critical genetic information for P. ruthii that can be used for species management decisions to drive future population augmentation/reintroduction and ex situ conservation efforts.
Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community

ABSTRACT Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of ∼106 cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.
Invariant transports of stationary random measures and mass-stationarity

We introduce and discuss balancing invariant transports of stationary random measures on a Polish Abelian group. The first main result is an associated fundamental invariance property of Palm measures, derived from a generalization of Neveu’s exchange formula. The second main result is a simple sufficient and necessary criterion for the existence of balancing invariant transports. We then introduce (in a non-stationary setting) the concept of mass-stationarity with respect to a random measure, formalizing the intuitive idea that the origin is a typical location in the mass. The third main result of the paper is that a measure is a Palm measure if and only if it is mass-stationary.
Control of cell proliferation

Much effort has gone into understanding the factors which regulate the growth of mammalian cells. Normal cells can exist in a proliferating state, or they can leave the cell division cycle and pass into a resting state, where they remain viable and functional for long periods. It is the switch between these alternative possibilities of cycling growth and quiescence that is of paramount importance in growth regulation. In the normal situation, there is a balance between cell proliferation and cell death. The movement of cells between the quiescent and growing state is under precise regulation in order to ensure the correct balance. In cancer this regulation is altered such that the rate of cell proliferation exceeds the rate of cell death. It is thus important to learn about the regulatory processes and how they are disrupted in the cancer cell. Evidence for alterations in these control events in tumor cells comes from in vitro experiments. Several culture conditions that are suboptimal for cell growth, as well as certain drugs, reversibly shift normal tissue culture cells into a quiescent state, whereas under the same culture conditions or in the presence of the same drugs certain transformed, tumor‐forming cells continue to traverse the cell cycle. This suggests a derangement of regulatory biochemical mechanisms. We are already in a position to take empirical advantage of these observations. In mice we are attempting to use “protective” drugs such as the ones which have been found to be effective in cell culture to shift reversibly and selectively the rapidly proliferating cells of the bone marrow, intestinal epithelium, and lymph nodes into a quiescent state. Such protective drugs would then protect these normal tissues, which are generally the most susceptible to the toxicity of anti‐cancer drugs, from the cytotoxicity of growth‐specific antineoplastic agents. The tumor cells, which would not be stopped by these protective drugs, would still be killed. This project is major, and full of uncertainties as to how all of the normal cells will respond and how each tumor type (which differs in its control characteristics, among other things) will respond. Studies of this sort should be applicable to the treatment of at least some tumors. As we apply these ideas, we will increasingly develop a stock of information on which to base further approaches to cancer chemotherapy.
Discourse Structure, Grounding, and Prosody in Task-Oriented Dialogue

This article explores the relationship between discourse structure, grounding, and prosody in interactive discourse through an empirical analysis of task-oriented dialogue (the Australian Map Task corpus). Our focus is on the role that prosody plays in the process of grounding-the attainment and acknowledgment of mutual knowledge by discourse participants (Clark, 1996). We investigate how patterns of prosodic boundary strengths, pitch contour, pausing, and overlap relate to the structuring of "common ground units" (Nakatani & Traum, 1999), collaborative units that capture the points in the discourse at which common ground is established. We also examine the distribution of dialogue acts (Jurafsky, Shriberg, & Biasca, 1997) within common ground units to add to the emerging model of dialogue structure that takes into account the "joint action" feature of interactive discourse. Our results show that responses belonging to different types of common ground units have different prosodic profiles. These results have implications for computational and psychological modeling of dialogue structure as well as our understanding of the functions of prosody in interaction.
REMOD: A Tool for Analyzing and Remodeling the Dendritic Architecture of Neural Cells

Dendritic morphology is a key determinant of how individual neurons acquire a unique signal processing profile. The highly branched dendritic structure that originates from the cell body, explores the surrounding 3D space in a fractal-like manner, until it reaches a certain amount of complexity. Its shape undergoes significant alterations under various physiological or neuropathological conditions. Yet, despite the profound effect that these alterations can have on neuronal function, the causal relationship between the two remains largely elusive. The lack of a systematic approach for remodeling neural cells and their dendritic trees is a key limitation that contributes to this problem. Such causal relationships can be inferred via the use of large-scale neuronal models whereby the anatomical plasticity of neurons is accounted for, in order to enhance their biological relevance and hence their predictive performance. To facilitate this effort, we developed a computational tool named REMOD that allows the structural remodeling of any type of virtual neuron. REMOD is written in Python and can be accessed through a dedicated web interface that guides the user through various options to manipulate selected neuronal morphologies. REMOD can also be used to extract meaningful morphology statistics for one or multiple reconstructions, including features such as sholl analysis, total dendritic length and area, path length to the soma, centrifugal branch order, diameter tapering and more. As such, the tool can be used both for the analysis and/or the remodeling of neuronal morphologies of any type.
Hallucinating faces

Faces often appear very small in surveillance imagery because of the wide fields of view that are typically used and the relatively large distance between the cameras and the scene. For tasks such as face recognition, resolution enhancement techniques are therefore generally needed. Although numerous resolution enhancement algorithms have been proposed in the literature, most of them are limited by the fact that they make weak, if any, assumptions about the scene. We propose an algorithm to learn a prior on the spatial distribution of the image gradient for frontal images of faces. We proceed to show how such a prior can be incorporated into a resolution enhancement algorithm to yield 4- to 8-fold improvements in resolution (i.e., 16 to 64 times as many pixels). The additional pixels are, in effect, hallucinated.
Performance of Coherent UWB Rake Receivers using Different Channel Estimators

The performance of DS-UWB and TH-UWB for a single-user link is compared for a data rate of 100 Mbps using the newly proposed, realistic UWB channel model from IEEE P802.15. The performance of suboptimal, fractionally spaced (FS), coherent Rake receivers with a pulse matched filter is evaluated with numerical simulations when different channel estimation algorithms, suitable for coherent detection, are used. The FS-Rake receiver is compared with pulse and symbol spaced Rake receivers and an optimal maximum-likelihood detector. Assuming perfect channel estimates, the FS-Rake receiver causes losses of 1 dB compared with the ML detector. For the FSRake receiver, the best evaluated channel estimation algorithm has a fractional loss compared with the perfect estimated channel. Using this algorithm, DS-UWB outperforms TH-UWB with 2 dB when the transmitter-receiver separation is 0 to 4 metre. Since TH-UWB is also more difficult to synchronize, the conclusion is that DS-UWB is more suitable for high-speed indoor links.
Robustly stabilizing MPC for perturbed PWL systems

This paper deals with robustly stable model predictive control (MPC) of the class of piecewise linear systems. A piecewise linear feedback controller, that stabilizes the nominal system, is derived from linear matrix inequalities. Further, an algorithm is designed for constructing a polyhedral robustly positively invariant set for the system. First, a minmax feedback MPC scheme with known mode, based on a dual-mode approach that stabilizes the system, is presented. The second robustly stable MPC scheme is based on a semi-feedback controller, but this time the mode of the system is unknown.
On products and powers of linear codes under componentwise multiplication

In this text we develop the formalism of products and powers of linear codes under componentwise multiplication. As an expanded version of the author's talk at AGCT-14, focus is put mostly on basic properties and descriptive statements that could otherwise probably not fit in a regular research paper. On the other hand, more advanced results and applications are only quickly mentioned with references to the literature. We also point out a few open problems. Our presentation alternates between two points of view, which the theory intertwines in an essential way: that of combinatorial coding, and that of algebraic geometry. In appendices that can be read independently, we investigate topics in multilinear algebra over finite fields, notably we establish a criterion for a symmetric multilinear map to admit a symmetric algorithm, or equivalently, for a symmetric tensor to decompose as a sum of elementary symmetric tensors.
Real or Imagined? A Study Exploring the Existence of Common Method Variance Effects in Road Safety Research

Common method variance (CMV) has received little attention within the field of road safety research despite a heavy reliance on self-report data. Two surveys were completed by 214 motorists over a two-month period, allowing associations between social desirability and key road safety variables and relationships between scales across the two survey waves to be examined. Social desirability was found to have a strong negative correlation with the Driver Behaviour Questionnaire (DBQ) sub-scales as well as age, but not with crashes and offences. Drivers who scored higher on the social desirability scale were also less likely to report aberrant driving behaviours as measured by the DBQ. Controlling for social desirability did not substantially alter the predictive relationship between the DBQ and the crash and offences variables. The strength of the correlations within and between the two waves were also compared with the results strongly suggesting that effects associated with CMV were present. Identification of CMV would be enhanced by the replication of this study with a larger sample size and comparing self-report data with official sources.
Development of Skeletal Muscle and Expression of Candidate Genes in Bovine Fetuses from Embryos Produced In Vivo or In Vitro1

Abstract The objectives of this study were to determine the effects of in vitro embryo production on histological development and gene expression in the skeletal muscle of bovine fetuses during late gestation. Blastocysts produced in vivo were obtained from superovulated Holstein cows. Blastocysts produced in vitro were obtained from oocytes of Holstein cows that were matured and fertilized in vitro. Single blastocysts were transferred into heifers at a synchronized estrous and fetuses were recovered at Day 222 of gestation (n = 12 each for in vivo and in vitro). Samples of semitendinosus muscle were obtained for histological analysis and assessment of gene expression. Individual muscle sections were stained for the assessment of primary muscle fibers, secondary muscle fibers, or total muscle fibers. Semiquantitative reverse transcription-polymerase chain reaction assays were performed for 5 different candidate genes. The ratio of secondary-to-primary fiber number was greater in fetuses from embryos produced in vitro compared with fetuses from embryos produced in vivo. Similarly, the ratio of secondary-to-primary fiber volume density tended to be greater in fetuses from embryos produced in vitro. The proportional volume of tissue present between myofibrils was greater in fetuses from embryos produced in vitro. The expression of mRNA for myostatin was decreased in skeletal muscle of fetuses in the in vitro group compared with controls. The expression of mRNA for glyceraldehyde-3-phosphate dehydrogenase tended to be increased in skeletal muscle of fetuses in the in vitro treatment group. There was no effect of treatment on the expression of mRNAs for myf-5, myoD, or myogenin. In conclusion, in vitro production of embryos resulted in fetuses with altered development of skeletal muscle fibers. Myostatin was identified as the candidate gene whose expression may contribute to the observed changes in muscle development of these fetuses.
On complexity of Shmoys-Swamy class of two-stage linear stochastic programming problems

We consider a class of two-stage linear stochastic programming problems, introduced by Shmoys and Swamy [4], motivated by a relaxation of a stochastic set cover problem. We show that the sample size required to solve this problem by the sample average approximation (SAA) method with a relative accuracy κ > 0 and confidence 1 − α is polynomial in κ, log(α−1), dimensions of the problem and a certain parameter λ. This implies that such problems can be solved in time polynomial in these parameters, the result obtained in [4] by a different method. ∗Georgia Institute of Technology, Atlanta, Georgia 30332, USA, nemirovs@isye.gatech. edu †Georgia Institute of Technology, Atlanta, Georgia 30332, USA, ashapiro@isye.gatech. edu. Research of this author was partly supported by the NSF grant DMS-0510324.
Systemic injection of an H4 receptor agonist induces a decrease in CREB and pCREB levels in the cerebellar vermis and prefrontal cortex in mice

Studies have shown that an injection with the histamine H4 receptor agonist VUF-8430 modulates emotional memory processes. In the present study, the aim was to verify if intraperitoneal (ip) injection of VUF-8430 (500 ng/kg) in mice affects the synthesis of proteins required for memory consolidation processes by activating the phosphorylation of CREB (pCREB) in classical structures linked to emotional memory (prefrontal cortex, amygdala, and hippocampus) and the cerebellar vermis, a structure that has also been recently implicated in emotional memory. The results obtained using western blot analysis demonstrated that VUF-8430 induced a decrease in CREB and pCREB levels in the cerebellar vermis and prefrontal cortex, suggesting that this dose impaired the activation of cell signaling pathways in these structures. There was no change in protein expression in the amygdala and hippocampus. Our results are preliminary, and further investigations are needed to investigate the role of the H4 receptors in the central nervous system.
Near Infrared Photoimmunotherapy in the Treatment of Disseminated Peritoneal Ovarian Cancer

Near infrared photoimmunotherapy (NIR-PIT) is a new cancer treatment that combines the specificity of intravenously injected antibodies for targeting tumors with the toxicity induced by photosensitizers after exposure to near infrared (NIR) light. Herein, we evaluate the efficacy of NIR-PIT in a mouse model of disseminated peritoneal ovarian cancer. In vitro and in vivo experiments were conducted with a HER2-expressing, luciferase-expressing, ovarian cancer cell line (SKOV-luc). An antibody–photosensitizer conjugate (APC) consisting of trastuzumab and a phthalocyanine dye, IRDye-700DX, was synthesized (tra-IR700) and cells or tumors were exposed to NIR light. In vitro PIT cytotoxicity was assessed with dead staining and luciferase activity in freely growing cells and in a three-dimensional (3D) spheroid model. In vivo NIR-PIT was performed in mice with tumors implanted in the peritoneum and in the flank and these were assessed by tumor volume and/or bioluminescence. In vitro NIR-PIT–induced cytotoxicity was light dose dependent. Repeated light exposures induced complete tumor cell killing in the 3D spheroid model. In vivo the antitumor effects of NIR-PIT were confirmed by significant reductions in both tumor volume and luciferase activity in the flank model (NIR-PIT vs. control in tumor volume changes at day 10, P = 0.0001; NIR-PIT vs. control in luciferase activity at day 4, P = 0.0237), and the peritoneal model (NIR-PIT vs. control in luciferase activity at day 7, P = 0.0037). NIR-PIT provided effective cell killing in this HER2-positive model of disseminated peritoneal ovarian cancer. Thus, NIR-PIT is a promising new therapy for the treatment of disseminated peritoneal tumors. Mol Cancer Ther; 14(1); 141–50. ©2014 AACR.
A Study of Data Locality in YARN

Co-locating the computation as close as possible to the data is an important consideration in the current data intensive systems. This is known as data locality problem. In this paper, we analyze the impact of data locality on YARN, which is the new version of Hadoop. We investigate YARN delay scheduler behavior with respect to data locality for a variety of workloads and configurations. We address in this paper three problems related to data locality. First, we study the trade-off between the data locality and the job completion time. Secondly, we observe that there is an imbalance of resource allocation when considering the data locality, which may under-utilize the cluster. Thirdly, we address the redundant I/O operations when different YARN containers request input data blocks on the same node. Additionally, we propose YARN Locality Simulator (YLocSim), a simulator tool that simulates the interactions between YARN components in a real cluster and reports the data locality percentages in real time. We validate YLocSim over a real cluster setup and use it in our study.
Multilingual Ontology Matching based on Wiktionary Data Accessible via SPARQL Endpoint

Interoperability is a feature required by the Semantic Web. It is provided by the ontology matching methods and algorithms. But now ontologies are presented not only in English, but in other languages as well. It is important to use an automatic translation for obtaining correct matching pairs in multilingual ontology matching. The translation into many languages could be based on the Google Translate API, the Wiktionary database, etc. From the point of view of the balance of presence of many languages, of manually crafted translations, of a huge size of a dictionary, the most promising resource is the Wiktionary. It is a collaborative project working on the same principles as the Wikipedia. The parser of the Wiktionary was developed and the machine-readable dictionary was designed. The data of the machine-readable Wiktionary are stored in a relational database, but with the help of D2R server the database is presented as an RDF store. Thus, it is possible to get lexicographic information (definitions, translations, synonyms) from web service using SPARQL requests. In the case study, the problem entity is a task of multilingual ontology matching based on Wiktionary data accessible via SPARQL endpoint. Ontology matching results obtained using Wiktionary were compared with results based on Google Translate API.