Miracle-dz/UniFAR-FTUs huggingface dataset:
Plastome Sequences of Lygodium japonicum and Marsilea crenata Reveal the Genome Organization Transformation from Basal Ferns to Core Leptosporangiates

Previous studies have shown that core leptosporangiates, the most species-rich group of extant ferns (monilophytes), have a distinct plastid genome (plastome) organization pattern from basal fern lineages. However, the details of genome structure transformation from ancestral ferns to core leptosporangiates remain unclear because of limited plastome data available. Here, we have determined the complete chloroplast genome sequences of Lygodium japonicum (Lygodiaceae), a member of schizaeoid ferns (Schizaeales), and Marsilea crenata (Marsileaceae), a representative of heterosporous ferns (Salviniales). The two species represent the sister and the basal lineages of core leptosporangiates, respectively, for which the plastome sequences are currently unavailable. Comparative genomic analysis of all sequenced fern plastomes reveals that the gene order of L. japonicum plastome occupies an intermediate position between that of basal ferns and core leptosporangiates. The two exons of the fern ndhB gene have a unique pattern of intragenic copy number variances. Specifically, the substitution rate heterogeneity between the two exons is congruent with their copy number changes, confirming the constraint role that inverted repeats may play on the substitution rate of chloroplast gene sequences.
The relationship between early maladaptive schemas and sexual self-esteem in female sex workers

Introduction: The present study aimed to investigate the relationship between early maladaptive schemas and sexual self-esteem in female sex workers. Materials and Methods: In this descriptive-correlational study conducted in February 2015, 108 female sex workers residing in Toos women's care center in Mashhad were selected through convenience sampling method. For data collection, Young Early Maladaptive Schema Questionnaire-Short Form (YSQ-SF) and Sexual Self-Esteem Inventory for Women-Short Form (SSEI-W-SF) were applied. Data analysis was performed using Pearson's correlation coefficient, stepwise regression and independent t-test by SPSS-22 software. Results: There was an inverse relationship between the scores of most of the early maladaptive schemas and sexual self-esteem in female sex workers (P<0.05). Three schemas of emotional deprivation, abandonment/instability and mistrust/abuse were significant predictors of sexual self-esteem in female sex workers (P<0.05). Scores of the schemas of social isolation/alienation, defectiveness/shame, failure, insufficient self-control/self-discipline, and unrelenting standards/hypercriticalness in female sex workers who have been living with their parents were lower than the scores of those female sex workers who lived with non-parents (P<0.05). Furthermore, the rate of sexual self-esteem in female sex workers who have been living with parents was higher relative to the female sex workers living with non-parents (P=0.017). Conclusion: The higher the rate of early maladaptive schemas in female sex workers, the lower the level of their sexual self-esteem will be. Not living with parents in the stages of development has a major role in the formation of early maladaptive schemas and thus reduced sexual self-esteem.
A One-shot Dynamic Coordination Algorithm for Distributed Sensor Networks

This paper presents a simple, fast coordination algorithm for the dynamic reorganization of agents in a distributed sensor network. Dynamic reorganization is a technique for adapting to the current local problemsolving situation that can both increase expected system performance and decrease the variance in performance. We compare our dynamic organization algorithm to a static algorithm with lower overhead. 'Oneshot' refers to the fact that the algorithm only uses one meta-level communication action. The other theme of this paper is our methodology for analyzing complex control and coordination issues without resorting to a handful of single-instance examples. Using a general model that we have developed of distributed sensor network environments [Decker and Lesser, 1993a], we present probabilistic performance bounds for our algorithm given any number of agents in any environment that fits our assumptions. This model also allows us to predict exactly in what situations and environments the performance benefits of dynamic reorganization outweigh the overhead.
Importance of tumor-specific cytotoxic CD8+ T-cells in eradication of a large subcutaneous MOPC-315 tumor following low-dose melphalan therapy.

We have previously demonstrated that depletion of CD8+ T-cells by the use of a monoclonal anti-Lyt-2.2 antibody abolishes the curative effectiveness of low-dose melphalan (L-phenylalanine mustard; L-PAM) therapy for BALB/c mice bearing a large (greater than or equal to 20 mm) s.c. MOPC-315 tumor and extensive metastases (Mokyr et al., Cancer Res., 49: 4597-4606, 1989). Here we show that as a consequence of low-dose L-PAM therapy, CD8+ T-cells accumulate in the s.c. tumor nodules of MOPC-315 tumor bearers. Specifically, an 80-fold increase in the number of CD8+ T-cells was seen within 5 days after the chemotherapy. Treatment of MOPC-315 tumor bearers with low-dose L-PAM in conjunction with monoclonal anti-Thy-1.2 or anti-Lyt-2.2 antibody, in contrast to treatment with monoclonal anti-L3T4 antibody, prevented the appearance of the massive CD8+ T-cell infiltrate in the s.c. tumor nodules. Fresh CD8+ T-cells derived from s.c. MOPC-315 tumor nodules that were regressing as a consequence of low-dose L-PAM therapy exhibited a potent direct lytic activity against the MOPC-315 plasmacytoma in a short-term in vitro assay. The specificity of the lytic activity exhibited by the CD8+ T-cells was illustrated not only by the inability of the CD8+ T-cells to lyse two antigenically unrelated thymomas (the WEHI 22.1 and the EL-4) and a natural killer-sensitive lymphoma (the YAC-1), but also by their relatively weak lytic activity against an antigenically related plasmacytoma (the MOPC-104E). Thus, CD8+ T-cells that infiltrate the s.c. tumor nodules of MOPC-315 tumor bearers following low-dose L-PAM therapy most likely exploit a CTL-type lytic mechanism to eradicate at least part of the large tumor burden not eliminated by the direct antitumor effects of the drug.
Langerhans Cell Histiocytosis: Radiographic Images in Pediatrics

A 24-month-old female infant had been well and developing normally until approximately 12 months of age when she began to have frequent ear infections and severe diaper rash. Between 12 months and 24 months she had 9 different antibiotic treated episodes of otitis media. Multiple antibiotics were given including Omnicef (cefdinir), amoxicillin, and Augmentin (amoxicillin clavulanate). However, when the antibiotics were discontinued, the infection returned. At the time of evaluation for the most recent ear infection, the child was found to be anemic with a hemoglobin level of 7.6 g/dL and mean corpuscular volume of 58. She was started on oral iron. However, after several weeks the parents noted swelling of the gums and bilateral proptosis. The child had skull films (Figure 1), a skeletal survey (Figure 2), chest and abdomen computed tomography (CT) scan (Figure 3), and head magnetic resonance imaging (MRI) scan performed (Figure 4).
Natural language interaction with semantic web ontologies

The Semantic Web is an effort to establish standards and mechanisms that will allow computers to reason more easily about the semantics of the Web resources (documents, data etc.). Ontologies play a central role in this endeavor. An ontology provides a conceptualization of a knowledge domain (e.g., consumer electronics) by defining the classes and subclasses of the domain entities, the types of possible relations between them etc. The current standard to specify Semantic Web ontologies is OWL, a formal language based on description logics and RDF, with OWL 2 being the latest OWL standard. Given an OWL ontology for a knowledge domain, one can publish on the Web machine-readable data pertaining to that domain (e.g., catalogues of products, their features etc.), with the data having formally defined semantics based on the conceptualization of the ontology. Several OWL syntaxes have been developed, but people unfamiliar with formal knowledge representation often have difficulties understanding them. This thesis considered methods that allow end-users to view ontology-based knowledge representations of the Semantic Web in the form of automatically generated texts in multiple natural languages. The first part of the thesis improved NaturalOWL, a Natural Language Generation system for OWL ontologies previously developed at AUEB. The system was modified to support OWL 2 and to be able to produce higher quality texts. Experiments showed that the texts generated by the new version of NaturalOWL are indeed of high quality and significantly better than texts generated by simpler systems, often called ontology
Adolescent Secure-Base Use and Parental Secure-Base Support: Relations with Adolescent Attachment Security

Title of Thesis: ADOLESCENT SECURE-BASE USE AND PARENTAL SECURE-BASE SUPPORT: RELATIONS WITH ADOLESCENT ATTACHMENT SECURITY Degree candidate: Matthew Jason Dykas Degree and year: Master of Arts, 2003 Thesis directed by: Professor Jude Cassidy Department of Psychology The goal of this investigation was to examine whether adolescent (AAI) attachment security could be linked to adolescents’ secure-base use and parents’ securebase support while discussing the adolescent’s developmentally salient task of leaving home after finishing high school. Results indicated that secure adolescents were more likely than insecure adolescents to use their mothers and their fathers as secure bases. Results also indicated that fathers of secure adolescents were more likely than fathers of insecure adolescents to support their adolescents’ secure-base behavior. There was no evidence, however, that mothers of insecure adolescents differed from mothers of secure adolescents in their amounts of secure-base support. Results also indicated that dyadic open communication was greatest in secure adolescent-mother and secure adolescent-father discussions. Secure adolescents were also more likely than insecure adolescents to use at least one parent as a secure-base and to have open dyadic communication with at least one parent.
The effects of obstructive jaundice on the pharmacodynamics of propofol: does the sensitivity of intravenous anesthetics change among icteric patients?

Background Some studies suggest that certain clinical symptoms of cholestasis, such as fatigue and pruritus, result from altered neurotransmission. Patients with obstructive jaundice also have labile blood pressure and heart rate. In the present study, the authors investigated whether obstructive jaundice affects a patient's sensitivity to hypnotics and the haemodynamic profile of propofol.
Balancing HPC applications through smart allocation of resources in MT processors

Many studies have shown that load imbalancing causes significant performance degradation in high performance computing (HPC) applications. Nowadays, multi-threaded (MT1) processors are widely used in HPC for their good performance/energy consumption and performance/cost ratios achieved sharing internal resources, like the instruction window or the physical register. Some of these processors provide the software hardware mechanisms for controlling the allocation of processor's internal resources. In this paper, we show, for the first time, that by appropriately using these mechanisms, we are able to control the tasks speed, reducing the imbalance in parallel applications transparently to the user and, hence, reducing the total execution time. Our results show that our proposal leads to a performance improvement up to 18% for one of the NAS benchmark. For a real HPC application (much more dynamic than the benchmark) the performance improvement is 8.1%. Our results also show that, if resource allocation is not used properly, the imbalance of applications is worsened causing performance loss.
hMOF Histone Acetyltransferase Is Required for Histone H4 Lysine 16 Acetylation in Mammalian Cells

ABSTRACT Reversible histone acetylation plays an important role in regulation of chromatin structure and function. Here, we report that the human orthologue of Drosophila melanogaster MOF, hMOF, is a histone H4 lysine K16-specific acetyltransferase. hMOF is also required for this modification in mammalian cells. Knockdown of hMOF in HeLa and HepG2 cells causes a dramatic reduction of histone H4K16 acetylation as detected by Western blot analysis and mass spectrometric analysis of endogenous histones. We also provide evidence that, similar to the Drosophila dosage compensation system, hMOF and hMSL3 form a complex in mammalian cells. hMOF and hMSL3 small interfering RNA-treated cells also show dramatic nuclear morphological deformations, depicted by a polylobulated nuclear phenotype. Reduction of hMOF protein levels by RNA interference in HeLa cells also leads to accumulation of cells in the G2 and M phases of the cell cycle. Treatment with specific inhibitors of the DNA damage response pathway reverts the cell cycle arrest caused by a reduction in hMOF protein levels. Furthermore, hMOF-depleted cells show an increased number of phospho-ATM and γH2AX foci and have an impaired repair response to ionizing radiation. Taken together, our data show that hMOF is required for histone H4 lysine 16 acetylation in mammalian cells and suggest that hMOF has a role in DNA damage response during cell cycle progression.
An Adaptation of Topic Modeling to Sentences

Advances in topic modeling have yielded effective methods for characterizing the latent semantics of textual data. However, applying standard topic modeling approaches to sentence-level tasks introduces a number of challenges. In this paper, we adapt the approach of latent-Dirichlet allocation to include an additional layer for incorporating information about the sentence boundaries in documents. We show that the addition of this minimal information of document structure improves the perplexity results of a trained model.
Carbon Nanotube Based Aqueous Ion and pH Sensor

Page 1 G  Abstract— This study characterizes the response of carbon nanotube (CNT) based biosensor FET chips to concentrations of aqueous electrical ions and pH of buffer solutions. The present scheme is distinguished from other CNT sensing methods as it uses a gate oxide overlayer on top of the CNTs. The sensor chips were exposed to varying concentrations of sodium chloride (NaCl) and standard buffers of different pH. The resulting data were analyzed using a custom-written program to quantify the response and sensitivity of the biosensors.
Analysis of the impact of DG on distribution network reconfiguration using OpenDSS

The integration of distributed energy resources into low and medium voltage networks will have profound impact on distribution network reconfiguration. In this paper, the impact of DG on distribution network reconfiguration is analyzed in both normal operation and post-fault scenarios with different load levels. Distribution system simulation is performed with the Open Distribution Simulator Software (OpenDSS). Due to the intrinsic nonlinear and non-differentiable mixed-integer nature of the problem, simulated annealing is used as the optimization algorithm. Using the proposed method, a case study of IEEE 33-bus system gives positive conclusions: in normal operation, the integration of DG increases the number of distribution network reconfiguration feasible solutions and reduces the total network loss of the optimal solution; while in post-fault condition, feasible solution can emerge with the integration of DG where there isn't any feasible solution originally. The integration of DG helps to ensure network power supply.
Promoting Non-Strict Programming — Draft —

In a non-strict functional programming language functions that yield the same result for all total arguments can still differ for partial arguments, that is, they differ in their strictness. Here a Haskell library is presented that enables the programmer to easily check whether a given function is least-strict; if it is not least-strict, then the tool suggests how to make it less strict.
The emergence of shared attention: Using robots to test developmental theories

The capacity for shared attention is a cornerstone of human social intelligence. Recent accounts attribute the emergence of shared attention to multiple cognitive mechanisms. Current behavioral data support an alternative dynamic systems model, but many questions remain. To answer these questions and test alternative theories, robotic models will play a critical role. Robotic models reduce the scope of the modeling task, permit comparison of empirically supported theories, and encourage parsimonious models of complex behaviors. Current efforts to model the emergence of shared attention are described.
In vitro selection of bacteria resistant to LY146032, a new cyclic lipopeptide

Isolates of Streptococcus pneumoniae, Enterococcus faecalis, Enterococcus faecium, and coagulase-positive and -negative staphylococci were investigated for their abilities, in vitro, to develop resistance to LY146032. Exposure of the organisms to incremental concentrations of LY146032 resulted in MICs 8- to 32-fold higher than those for the original isolates. After three passages on antibiotic-free medium, the high MICs were maintained for the coagulase-negative staphylococci and pneumococci, with a twofold decrease observed for the enterococci and a fourfold decrease observed for Staphylococcus aureus. The frequency of spontaneous emergence of resistance was highest with S. pneumoniae (1.2 X 10(-6) at 16 times the original MIC) and lowest with S. aureus (7.0 X 10(-10) at 8 times the original MIC). For bacteria For bacteria surviving time-kill studies MICs were also higher than were those for the original isolates. Exposure to LY146032 in vitro selected for strains with decreased susceptibilities to the antimicrobial agent. However, the emergence of resistance in vivo is unpredictable and can be evaluated only after prolonged clinical use of the drug.
Haploinsufficiency of the c-myc transcriptional repressor FIR, as a dominant negative-alternative splicing model, promoted p53-dependent T-cell acute lymphoblastic leukemia progression by activating Notch1

FUSE-binding protein (FBP)-interacting repressor (FIR) is a c-myc transcriptional suppressor. A splice variant of FIR that lacks exon 2 in the transcriptional repressor domain (FIRΔexon2) upregulates c-myc transcription by inactivating wild-type FIR. The ratio of FIRΔexon2/FIR mRNA was increased in human colorectal cancer and hepatocellular carcinoma tissues. Because FIRΔexon2 is considered to be a dominant negative regulator of FIR, FIR heterozygous knockout (FIR+/−) C57BL6 mice were generated. FIR complete knockout (FIR−/−) was embryonic lethal before E9.5; therefore, it is essential for embryogenesis. This strongly suggests that insufficiency of FIR is crucial for carcinogenesis. FIR+/− mice exhibited prominent c-myc mRNA upregulation, particularly in the peripheral blood (PB), without any significant pathogenic phenotype. Furthermore, elevated FIRΔexon2/FIR mRNA expression was detected in human leukemia samples and cell lines. Because the single knockout of TP53 generates thymic lymphoma, FIR+/−TP53−/− generated T-cell type acute lymphocytic/lymphoblastic leukemia (T-ALL) with increased organ or bone marrow invasion with poor prognosis. RNA-sequencing analysis of sorted thymic lymphoma cells revealed that the Notch signaling pathway was activated significantly in FIR+/−TP53−/− compared with that in FIR+/+TP53−/− mice. Notch1 mRNA expression in sorted thymic lymphoma cells was confirmed using qRT-PCR. In addition, flow cytometry revealed that c-myc mRNA was negatively correlated with FIR but positively correlated with Notch1 in sorted T-ALL/thymic lymphoma cells. Moreover, the knockdown of TP53 or c-myc using siRNA decreased Notch1 expression in cancer cells. In addition, an adenovirus vector encoding FIRΔexon2 cDNA increased bleomycin-induced DNA damage. Taken together, these data suggest that the altered expression of FIRΔexon2 increased Notch1 at least partially by activating c-Myc via a TP53-independent pathway. In conclusion, the alternative splicing of FIR, which generates FIRΔexon2, may contribute to both colorectal carcinogenesis and leukemogenesis.
Index Compression Using Fixed Binary Codewords

Document retrieval and web search engines index large quantities of text. The static costs associated with storing the index can be traded against dynamic costs associated with using it during query evaluation. Typically, index representations that are effective and obtain good compression tend not to be efficient, in that they require more operations during query processing. In this paper we describe a scheme for compressing lists of integers as sequences of fixed binary codewords that has the twin benefits of being both effective and efficient. Experimental results are given on several large text collections to validate these claims.
A Stigmergy Approach for Open Source Software Developer Community Simulation

The stigmergy collaboration approach provides a hypothesized explanation about how online groups work together. In this research, we presented a stigmergy approach for building an agent based open source software (OSS) developer community collaboration simulation. We used group of actors who collaborate on OSS projects as our frame of reference and investigated how the choices actors make in contribution their work on the projects determinate the global status of the whole OSS projects. In our simulation, the forum posts and project codes served as the digital pheromone and the modified Pierre-Paul Grasse pheromone model is used for computing developer agent behaviors selection probability.
The human T-lymphotropic virus type I tax gene can cooperate with the ras oncogene to induce neoplastic transformation of cells

Epidemiologic studies have linked infection by the human T-lymphotropic virus type I (HTLV-I) with the development of adult T-cell leukemia. The low penetrance of the virus and the long latency for disease manifestation are factors that obscure the role of HTLV-I infection in oncogenesis. We have used an in vitro transformation assay system to determine directly whether the HTLV-I tax gene has transformation potential. Transfection of the tax gene alone into early-passage rat embryo fibroblasts did not induce morphological alterations. However, cotransfection of tax with the selectable marker plasmid pRSVneo gave rise to G418-resistant colonies that could be established as immortalized cell lines. Cotransfection of tax with the ras oncogene into rat embryo fibroblasts gave rise to foci of transformed cells that were highly tumorigenic in nude mice. These data represent a direct demonstration of the oncogenic potential of the tax gene in nonlymphoid cells and establish HTLV-I as a transforming virus.