Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets.

UNLABELLED Neuroendocrine prostate cancer (NEPC) is an aggressive subtype of prostate cancer that most commonly evolves from preexisting prostate adenocarcinoma (PCA). Using Next Generation RNA-sequencing and oligonucleotide arrays, we profiled 7 NEPC, 30 PCA, and 5 benign prostate tissue (BEN), and validated findings on tumors from a large cohort of patients (37 NEPC, 169 PCA, 22 BEN) using IHC and FISH. We discovered significant overexpression and gene amplification of AURKA and MYCN in 40% of NEPC and 5% of PCA, respectively, and evidence that that they cooperate to induce a neuroendocrine phenotype in prostate cells. There was dramatic and enhanced sensitivity of NEPC (and MYCN overexpressing PCA) to Aurora kinase inhibitor therapy both in vitro and in vivo, with complete suppression of neuroendocrine marker expression following treatment. We propose that alterations in Aurora kinase A and N-myc are involved in the development of NEPC, and future clinical trials will help determine from the efficacy of Aurora kinase inhibitor therapy. SIGNIFICANCE We report on the largest in-depth molecular analysis of NEPC and provide new insight into molecular events involved in the progression of prostate cancer.
LMP4 regulates Tbx5 protein subcellular localization and activity

The limb- and heart-specific Tbx5 transcription factor coexpresses with and directly binds to the novel PDZ-LIM domain protein, LMP4. LMP4 is distributed in the cytoplasm associated with the actin cytoskeleton. In the presence of LMP4, Tbx5 shuttles dynamically between the nucleus and cytoplasm and, in a complex with LMP4, localizes to actin filaments. Nuclear and cytoplasmic Tbx5 distribution in developing chicken wings suggests the functional significance of the LMP4–Tbx5 interaction. In primary epicardial cells, we demonstrate that Tbx5 protein subcellular relocalization can be stimulated by external signals that induce cell differentiation. To test whether the relocalization from nuclear to cytoplasmic sites interferes with downstream gene expression, we used limb-specific Fgf10 and heart-specific Anf promoter-luciferase reporters and demonstrate that LMP4 acts as a repressor of Tbx5 activity. These studies reveal a previously unknown mechanism for Tbx transcription factor regulation in vertebrate limb and heart development and provide a better understanding of the molecular basis of hand/heart birth defects associated with Tbx5 mutations.
Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase

Observations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacterium Pseudomonas fluorescens SBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation in carB that decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a pre-existing but hitherto unrecognised phenotypic switch. Genetic components surrounding bifurcation of UTP flux towards DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses – and based on a combination of genetics, transcriptomics, biochemistry and mathematical modelling – we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a feed-forward regulator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a programme that determines stochastic entry into the semi-quiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.
Ballistics: Theory and Design of Guns and Ammunition

Interior Ballistics Introductory Concepts Physical Foundation of Interior Ballistics Analytic and Computational Ballistics Ammunition Design Practice Weapon Design Practice Exterior Ballistics Introductory Concepts Dynamics Review Trajectories Linearized Aeroballistics Mass Asymmetries Lateral Throwoff Swerve Motion Non-Linear Aeroballistics Terminal Ballistics Introductory Concepts Penetration Theories Shock Physics Introduction to Explosive Effects Shaped Charges Wound Ballistics Appendix Glossary Gas Tables
A COMPARISON OF THE AFTERGLOWS OF SHORT- AND LONG-DURATION GAMMA-RAY BURSTS

We present a comparative study of the observed properties of the optical and X-ray afterglows of short- and long-duration γ-ray bursts (GRBs). Using a large sample of 37 short and 421 long GRBs, we find a strong correlation between the afterglow brightness measured after 11 hr and the observed fluence of the prompt emission. Both the optical (R band) and X-ray flux densities (FR and FX) scale with the γ-ray fluence, Fγ. For bursts with a known redshift, a tight correlation exists between the afterglow flux densities at 11 hr (rest frame) and the total isotropic γ-ray energy, Eγ,ISO: FR,X ∝ Eγ,ISOα, with α ≃ 1. The constant of proportionality is nearly identical for long and short bursts, when Eγ,ISO is obtained from the Swift data. Additionally, we find that for short busts with Fγ ≳ 10−7 erg cm−2, optical afterglows are nearly always detected by reasonably deep early observations. Finally, we show that the ratio FR/FX has very similar values for short and long bursts. These results are difficult to explain in the framework of the standard scenario, since they require that either (1) the number density of the surrounding medium of short bursts is typically comparable to, or even larger than the number density of long bursts; (2) short bursts explode into a density profile, n(r) ∝ r−2; or (3) the prompt γ-ray fluence depends on the density of the external medium. We therefore find it likely that either basic assumptions on the properties of the circumburst environment of short GRBs or else the standard models of GRB emission must be re-examined. We believe that the most likely solution is that the ambient density surrounding typical short bursts is higher than has generally been expected: a typical value of ∼1 cm−3 is indicated. We discuss recent modifications to the standard binary merger model for short bursts which may be able to explain the implied density.
Hawth ’ s Tools extension to ESRI ARCGIS : Beyer 2004 ; HRT extension for ESRI ARCGIS :

Wildlife tracking data management: a new vision Ferdinando Urbano1,2,*, Francesca Cagnacci2, Clément Calenge3, Holger Dettki4, Alison Cameron5 and Markus Neteler2 Via Fratelli Pozzi 7, 20127 Milan, Italy Research and Innovation Centre, Environment and Natural Resources Area, Edmund Mach Foundation, Via Mach 1, 38010 San Michele all’Adige, Trento, Italy Office National de la Chasse et de la Faune Sauvage, Direction des Etudes et de la Recherche, Saint Benoist, 78610 Auffargis, France Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Skogsmarksgränd, 901 83 Umea, Sweden Max Planck Institute for Ornithology, Vogelwarte Radolfzell, Schloß Möggingen, Schloßallee 2, 78315 Radolfzell, Germany
Fine needle aspiration.

Objective: To compare the recently proposed Milan System for Reporting Salivary Gland Cytopathology (MSRSGC) with the four-tiered reporting system (FTRS) followed at our institute. Methods: Parotid gland fine-needle aspirates reported over a period of 5 years were analysed. These aspirates had been placed into 4 categories according to the FTRS: unsatisfactory (UNS), no evidence of malignancy/negative (NEG), inconclusive for malignancy (INC), and diagnostic for malignancy/positive (POS). Aspirates with follow-up histopathology were then categorized according to the MSRSGC as follows: non-diagnostic, non-neoplastic, atypia of undetermined significance (AUS), neoplasm, suspicious for malignancy, and malignant. The risk of malignancy (ROM) was calculated. Results: A total of 893 parotid region aspirates were evaluated and histopathology was available for 190 cases (21%). ROM in MSRSGC groups, namely non-diagnostic, nonneoplastic, AUS, neoplasm, suspicious for malignant neoplasm, and malignant, was 44, 8, 0, 12, 81 and 100%, respectively. ROM in FTRS groups, namely UNS, NEG, INC, and POS, was 45, 13, 67 and 100%, respectively. Conclusions: MSRGC and FTRS are comparable with respect to the ROM across groups. Compared to FTRS, the further subcategorisation of the non-malignant group, the use of specific nomenclature, and the reproducibility of MSRGC provide proper risk stratification, thereby guiding better management and resulting in improved patient care. © 2018 S. Karger AG, Basel
Th1 and Th2 responses: what are they?

Cytokines are the hormonal messengers responsible for most of the biological effects in the immune system, such as cell mediated immunity and allergic type responses. Although they are numerous, cytokines can be functionally divided into two groups: those that are proinflammatory and those that are essentially anti-inflammatory but that promote allergic responses. T lymphocytes are a major source of cytokines. These cells bear antigen specific receptors on their cell surface to allow recognition of foreign pathogens. They can also recognise normal tissue during episodes of autoimmune diseases. There are two main subsets of T lymphocytes, distinguished by the presence of cell surface molecules known as CD4 and CD8. T lymphocytes expressing CD4 …
IN CHILDREN’S MENTAL HEALTH

This article presents a framework to be used in studying public policy development and implementation in children’s mental health. It particularly focuses on policy related to the establishment of community-based systems of care. The framework is based on a review of the literature on policy development and implementation, and focuses on four dimensions: the stages of policy development and implementation; the relationship between different levels of government; the relationship between different service sectors; and variables that affect the likelihood that a policy will achieve its intended effect. PAGE–1 Conceptual Framework for Effective Policy A CONCEPTUAL FRAMEWORK FOR DEVELOPING AND IMPLEMENTING EFFECTIVE POLICY IN CHILDREN’S MENTAL HEALTH Robert M. Friedman Research and Training Center for Children’s Mental Health Department of Child and Family Studies Louis de la Parte Florida Mental Health Institute University of South Florida
Incorporating Punctuation Into the Sentence Grammar: A Lexicalized Tree Adjoining Grammar Perspective

INCORPORATING PUNCTUATION INTO THE SENTENCE GRAMMAR A LEXICALIZED TREE ADJOINING GRAMMAR PERSPECTIVE Christine D Doran Supervisor Aravind K Joshi Punctuation helps us to structure and thus to understand texts Many uses of punctuation straddle the line between syntax and discourse because they serve to combine multiple propositions within a single orthographic sentence They allow us to insert discourse level relations at the level of a single sentence Just as people make use of information from punctuation in processing what they read computers can use information from punctuation in processing texts automatically Most cur rent natural language processing systems fail to take punctuation into account at all losing a valuable source of information about the text Those which do mostly do so in a super cial way again failing to fully exploit the information conveyed by punctuation To be able to make use of such information in a computational system we must rst characterize its uses and nd a suitable representation for encoding them The work here focuses on extending a syntactic grammar to handle phenomena occurring within a single sentence which have punctuation as an integral compo nent Punctuation marks are treated as full edged lexical items in a Lexicalized Tree Adjoining Grammar which is an extremely well suited formalism for encoding punctuation in the sentence grammar Each mark anchors its own elementary trees and imposes constraints on the surrounding lexical items I have analyzed data rep resenting a wide variety of constructions and added treatments of them to the large English grammar which is part of the XTAG system The advantages of using LTAG are that its elementary units are structured trees of a suitable size for stating the constraints we are interested in and the derivation histories it produces contain in formation the discourse grammar will need about which elementary units have used and how they have been combined I also consider in detail a few particularly inter esting constructions where the sentence and discourse grammars meet appositives reported speech and uses of parentheses My results con rm that punctuation can
Descriptions of two new Pseudophacopteron species (Hemiptera:Psylloidea: Phacopteronidae) inducing galls on Aspidosperma(Apocynaceae) in Brazil

Two new species of the large pantropical jumping plant-louse genus Pseudophacopteron Enderlein, 1921 (Hemiptera: Psylloidea: Phacopteronidae) are described from dry woodland habitats in the Midwest, Southeast and South of Brazil. Pseudophacopteron aspidospermi sp. nov. is associated with Aspidosperma australe, P. longicaudatum sp. nov. has been found on Aspidosperma macrocarpon and A. tomentosum (Apocynaceae). Both species induce intralaminar lenticular galls on the leaves of their host trees which have been the subject of several structural, histochemical and ecological publications. Adult males and females, fifth instar immatures and galls are illustrated including diagnostic morphological details, and compared with other Neotropical and Old World species of Pseudophacopteron and Phacopteronidae. The distribution of Pseudophacopteron in the Neotropical Region is briefl y discussed.
Babesiosis: Field assessment of protection in cattle immunized with a mixture of Babesia bovis recombinant proteins Babesiosis bovina: Evaluación en campo de la protección de bovinos inmunizados con una mezcla de proteínas recombinantes de Babesia bovis

The aim of the present research was to assess the immunogenicity and protective capability of a combination of the B. bovis recombinant proteins MSA-1, MSA-2c and 12D3 in cattle exposed to Babesia infection transmitted by ticks under natural conditions. The immunization phase of the study was conducted at CENID-Parasitología Veterinaria in Jiutepec, Morelos, and the challenge phase was carried out in an experimental station in Pichucalco, Chiapas, Mexico. Eighteen steers were randomly distributed into three groups of six animals each. Animals were treated on days 0 and 14 as follows: Group 1 (G1), control, with the adjuvant Montanide 70 (M70) + PBS; Group 2 (G2) with a mixture of the Babesia bovis recombinant proteins MSA-1, MSA-2c and 12D3 admixed in M70; Group 3 (G3) with a live attenuated mixed vaccine against bovine babesiosis (day 0 only). Immunization of cattle with a combination of recombinant proteins from B. bovis induced specific IgG antibodies that recognized the corresponding antigens of B. bovis by three immunological assays: Indirect fluorescent antibody test (IFAT), Enzyme-linked immunosorbent assay (ELISA) and Immunolotting (IB). However, the combination of the B. bovis recombinant proteins MSA-1, MSA-2c and 12D3 did not produce an adequate protection. Three animals in GII group were in need of treatment with specific babesiacide, indicating that the specific immune response evoked by these steers, was not necessarily protective (50% protection), as compared to the protection evoked by the attenuated vaccine (only 1 G3 steer required treatment, >80% protection). The immunization of cattle with a combination of recombinant proteins of B. bovis induced specific antibodies that recognized the corresponding antigens when analyzed by immunological assays. The combined use of B. bovis recombinant proteins MSA-1, MSA-2c, and 12D3 does not produce an adequate immune protection to ticktransmitted Babesia parasites as evidenced by the presence of severe signs of babesiosis in the experimental animals. The results, however, are encouraging and support the idea of finding a more suitable combination of recombinant proteins for successful protection of cattle facing a natural challenge with the parasite transmitted in the field by Rhipicephalus (Boophilus)
Group theoretical methods in machine learning

This thesis explores applications of non-commutative harmonic analysis to machine learning. In particular, we address learning on groups and learning in a way that is invariant to a group. The former arises in learning rankings and matchings, in both cases, the group being the symmetric group. The application we explore in detail is the identity management problem in multi-object tracking. The latter arises in many contexts, none more immediate than invariance to translation, rotation, scaling, etc., in computer vision. In this domain we derive a new system of translation and rotation invariant features for images, and introduce a new system of invariants applicable to any compact group, which we call the skew spectrum. The ideas behind harmonic analysis (commutative or non-commutative) run very deep, and one of the main messages of the thesis is that algebra can unravel structure in data which might otherwise be overlooked. All this would not be of much use to practitioners, however, were it not for a family of recently developed algorithms, chief amongst them fast Fourier transforms, which are finally starting to make it possible to scale up algebraic methods to the size of real-world problems. Much of our work revolves around carefully tailoring fast Fourier transforms to solve specialized tasks demanded by applications. The thesis includes background material in both machine learning and algebra, so it can serve as a primer for researchers familiar with one field but not the other.
Study on Changes of Hydrological Characteristics of Ebinur Lake Basin in Xinjiang

The paper presented the basic situation and the characteristics of Ebinur Lake Bbasin in Xinjiang. According to hydrology statistical data from various hydrologic stations in the Ebinur Lake Basin and the results of actual hydrologic investigation in recent years, it analyzed the temperature, evaporation, precipitation, glaciers, annual runoff and seasonal runoff, silt, ice sentiment, water quality, so as to study changes of hydrological characteristics in the Ebinur Lake Basin in Xinjiang. The research conclusion have an important value for protecting the ecological environment and allocating water resources in Ebinur Lake Basin.
Physical activity duration but not energy expenditure differs between daily compared with intermittent breakfast consumption in adolescent girls: a randomized crossover trial

1 Background: It is not known whether breakfast frequency affects physical activity (PA) in 2 children or adolescents. Objective: This study examined the effect of daily compared with 3 intermittent breakfast consumption on estimated PA energy expenditure (PAEE) in adolescent 4 girls. Methods: Using a randomized crossover design, 27 girls (age 12.4 ± 0.5 y, body mass 5 index 19.3 ± 3.0 kg∙m -2 ) completed two, 7-day conditions. A standardized breakfast (~1674 6 kJ) was consumed every day before 09:00 in the daily breakfast consumption (DBC) 7 condition. The standardized breakfast was consumed on only three days before 09:00 in the 8 intermittent breakfast consumption (IBC) condition alternating with breakfast omission on the 9 remaining four days (i.e., only water consumed before 10:30). Combined heart rate- 10 accelerometry was used to estimate PAEE throughout each condition. Statistical analyses 11 were completed using condition by time of day repeated measures analysis of variance. The 12 primary outcome was PAEE and the secondary outcome was time spent in PA. Results: Daily 13 estimated PAEE from sedentary, light, moderate and vigorous intensities and total PAEE 14 were not significantly different between the conditions. The condition by time of day 15 interaction for sedentary time ( P = 0.05) indicated that the girls spent 11.5 min/d more time 16 sedentary in IBC compared with DBC during 15:30-bedtime ( P = 0.04). Light PA was 19.8 17 min/d higher during DBC compared with IBC ( P = 0.05), which was accumulated during 18 wake-10:30 ( P = 0.04) and 15:30-bedtime ( P = 0.03). There were no significant differences in 19 time spent in MPA or VPA between the conditions. Conclusions: Adolescent girls spent 20 more time in light PA before 10:30 and after school and spent less time sedentary after school 21 when a standardized breakfast was consumed daily compared with intermittently across seven 22 days. However, breakfast manipulation did not affect estimated daily PAEE.
Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean

The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose‐5‐phosphate and the amino acid precursor erythrose‐4‐phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron‐rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world.
Performance Comparison of Digital microRNA Profiling Technologies Applied on Human Breast Cancer Cell Lines

MicroRNA profiling represents an important first-step in deducting individual RNA-based regulatory function in a cell, tissue, or at a specific developmental stage. Currently there are several different platforms to choose from in order to make the initial miRNA profiles. In this study we investigate recently developed digital microRNA high-throughput technologies. Four different platforms were compared including next generation SOLiD ligation sequencing and Illumina HiSeq sequencing, hybridization-based NanoString nCounter, and miRCURY locked nucleic acid RT-qPCR. For all four technologies, full microRNA profiles were generated from human cell lines that represent noninvasive and invasive tumorigenic breast cancer. This study reports the correlation between platforms, as well as a more extensive analysis of the accuracy and sensitivity of data generated when using different platforms and important consideration when verifying results by the use of additional technologies. We found all the platforms to be highly capable for microRNA analysis. Furthermore, the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS and RT-qPCR. Based on these findings we propose new guidelines and considerations when performing microRNA profiling.