Miracle-dz/UniFAR-FTUs huggingface dataset:
Stromal retinoic acid receptor β promotes mammary gland tumorigenesis

Retinoic acid is a potent differentiation and antiproliferative agent of breast cancer cells, and one of its receptors, retinoic acid receptor β (RARβ), has been proposed to act as a tumor suppressor. In contrast, we report herein that inactivation of Rarb in the mouse results in a protective effect against ErbB2-induced mammary gland tumorigenesis. Strikingly, tissue recombination experiments indicate that the presence of Rarb in the stromal compartment is essential for the growth of mammary carcinoma. Ablation of Rarb leads to a remodeling of the stroma during tumor progression that includes a decrease in angiogenesis, in the recruitment of inflammatory cells, and in the number myofibroblasts. In agreement with this finding, we observed that a markedly reduced expression of chemokine (C-X-C motif) ligand 12 (Cxcl12) in the stroma of Rarb-null mice is accompanied by a decrease in the CXCL12/chemokine C-X-C receptor 4 (CXCR4)/ErbB2 signaling axis in the tumors. Relevance to the human disease is underlined by the finding that gene-expression profiling of the Rarb-deficient mammary stromal compartment identified an ortholog RARβ signature in human microdissected breast tissues that differentiates tumor from normal stroma. Our study thus implicates RARβ in promoting tumorigenesis and suggests that retinoid-based approaches for the prevention and treatment of breast cancer should be redesigned.
Simple valves on a pdms microchip bonded via patterned oxygen plasma

The simplest form of microfluidic valve is proposed with detailed working mechanism. Conventional on-chip valves are requiring a multiple layers of microchip with complicated fluidic pattern and/or complicated external control system. In contrast, our developed valve can be fabricated in a bilayer microchip with a simple pattern, two channels and a wall separating them. Our valve fabrication was based on a plasma patterning method with a sacrificial aluminum layer, which shield the oxygen plasma activation only in the aimed position of the substrate. This approach is more robust than the conventional "plasma deactivation" approach based on the chemical patterning via micro-contact printing. For the valve regulation, no external control line is necessary but a weak pressure to the injection channel. Although our valve has no simpler structure than that of the hydrophobic valve which has ever been the simplest, our valve has a significant advantage in the repeatable utility. Due to its simplicity, moreover, long term injection more than 120 min was easily and precisely carried out. These highest simplicity and performance are quite suitable for the large integration and mass production of complicated lab-on-a-chip system for the application to biological research.
Multiple Scale Music Segmentation Using Rhythm, Timbre, and Harmony

The segmentation of music into intro-chorus-verse-outro, and similar segments, is a difficult topic. A method for performing automatic segmentation based on features related to rhythm, timbre, and harmony is presented, and compared, between the features and between the features and manual segmentation of a database of 48 songs. Standard information retrieval performance measures are used in the comparison, and it is shown that the timbre-related feature performs best.
Simultaneous Targeting of Multiple Gene Homeologs to Alter Seed Oil Production in Camelina sativa

The ability to transform Camelina sativa easily with biosynthetic enzymes derived from other plants has made this oil seed crop an ideal platform for the production of unusual lipids valuable for different applications. However, in addition to expressing transgenic enzymes, the suppression of endogenous enzyme activity to reduce competition for common substrates or cofactors is also required to enhance the production of target compounds. As camelina possesses a relatively undifferentiated hexaploid genome, up to three gene homeologs can code for any particular enzymatic activity, complicating efforts to alter endogenous biosynthetic pathways. New genome editing technologies, such as that offered by the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system, offer the capability to introduce mutations into specifically targeted genomic sites. Here, by using a carefully designed guide RNA identical to all three homeologs, we demonstrate the ability of the CRISPR/Cas genome editing system to introduce mutations in all three CsDGAT1 or CsPDAT1 homeologous genes important for triacylglycerol (TAG) synthesis in developing seeds. Sequence analysis from transgenic T1 plants revealed that each CsDGAT1 or each CsPDAT1 homeolog was altered by multiple mutations, resulting in a genetic mosaic in the plants. Interestingly, seed harvested from both CsDGAT1- and CsPDAT1-targeted lines was often shrunken and wrinkled. Further, lipid analysis revealed that many lines produced seed with reduced oil content and altered fatty acid composition, consistent with the role of the targeted genes in seed oil biosynthesis. The CRISPR/Cas system therefore represents a useful method to alter endogenous biosynthetic pathways efficiently in polyploid species such as camelina.
Object-Oriented Parallel Parsing for Context-Free Grammars

This paper describes a new parallel parsing scheme for context-free grammars and our experience of implementing this scheme, and it also reports the result of our simulation for running the parsing program on a massive parallel processor.In our basic parsing scheme, a set of context free grammar rules is represented by a network of processor-like computing agents each having its local memory. Each computing agent in the network corresponds to an occurrence of a non-terminal or terminal symbol appearing in the grammar rules. Computing agents in the network work concurrently and communicate with one another by passing messages which are partial parse trees.This scheme is shown to be fast (0(n*h) time for the first complete parse tree, where n is the length of an input sentence and h is the height of the parse tree) and useful in various modes of parsing such as on-line parsing, overlap parsing, on-line unparsing, pipe-lining to semantics processing, etc. Performance evaluation for implementing this scheme on a massive parallel machine is conducted by distributed event simulation using the Time Warp mechanism/Jefferson85/. Our parsing scheme is implemented in a programming language called ABCL/1 which is designed for object-oriented concurrent programming and used for various concurrent programming /Yonezawa86/. The program is currently runing on standard single-cpu machines such as SUN3s and Symbolics Lisp machines (by simulated parallelism). In our experiment and simulation, a set of about 250 context-free grammar rules specifying a subset of English is represented by the corresponding network of objects (i.e., computing agents) and about 1100 concurrently executable objects are involved.
Anticipatory Anxiety Disrupts Neural Valuation during Risky Choice

Incidental negative emotions unrelated to the current task, such as background anxiety, can strongly influence decisions. This is most evident in psychiatric disorders associated with generalized emotional disturbances. However, the neural mechanisms by which incidental emotions may affect choices remain poorly understood. Here we study the effects of incidental anxiety on human risky decision making, focusing on both behavioral preferences and their underlying neural processes. Although observable choices remained stable across affective contexts with high and low incidental anxiety, we found a clear change in neural valuation signals: during high incidental anxiety, activity in ventromedial prefrontal cortex and ventral striatum showed a marked reduction in (1) neural coding of the expected subjective value (ESV) of risky options, (2) prediction of observed choices, (3) functional coupling with other areas of the valuation system, and (4) baseline activity. At the same time, activity in the anterior insula showed an increase in coding the negative ESV of risky lotteries, and this neural activity predicted whether the risky lotteries would be rejected. This pattern of results suggests that incidental anxiety can shift the focus of neural valuation from possible positive consequences to anticipated negative consequences of choice options. Moreover, our findings show that these changes in neural value coding can occur in the absence of changes in overt behavior. This suggest a possible pathway by which background anxiety may lead to the development of chronic reward desensitization and a maladaptive focus on negative cognitions, as prevalent in affective and anxiety disorders.
Bit allocation strategy among users in coordinated multi-cell systems with limited feedback

In this paper, we propose a novel bit allocation strategy in coordinated multi-cell systems with limited feedback. Multi-cell cooperation technique is an effective way to improve the system throughput and especially the performance of the cell edge users. In a Coordinated Multi-Point (CoMP) system, the rate loss caused by quantization error of Channel State Information (CSI) is minimized considering two aspects of the channels. Firstly, as the physical conditions and constraints of different users are not identical, appropriately allocating feedback bits to users based on their channels can achieve higher throughput. Secondly, in a Coordinated Beamforming/Coordinated Scheduling (CB/CS) system, each user has a serving channel to the serving base station and an interfering channel to the coordinated base station. The user needs to partition its available bits between the two channels. Thus, we study a global bit allocation strategy that can minimize the rate loss from that of the full CSI circumstance. From our simulation results, we prove that the proposed bit allocation strategy achieves higher per-cell sum-rate compared with the equal bit allocation strategy.
The statistical crisis in science

What can we say about the statistical crisis in science that has not already been said? Eminent scientists like Paul Meehl, Jakob Cohen and John Ioannidis have already done a great job pinpointing the problems with P-values, null hypothesis significance testing, nonreplicable research, sloppy statistics and fishing expeditions. At the other end of the spectrum journalists at The Atlantic, The New Yorker, FiveThirtyEight and The New York Times have done a surprisingly good job of translating these issues to a lay audience. What is left?
THE INCOMPATIBILITY OF RAPID ROTATION WITH NARROW PHOTOSPHERIC X-RAY LINES IN EXO 0748−676

X-ray observations of EXO 0748−676 during thermonuclear bursts revealed a set of narrow (Δλ/λ = 0.018) absorption lines that potentially originate from the stellar photosphere. The identification of these lines with particular atomic transitions led to the measurement of the surface gravitational redshift of the neutron star and to constraints on its mass and radius. However, the recent detection of 552 Hz oscillations at 15% rms amplitude revealed the spin frequency of the neutron star and brought into question the consistency of such a rapid spin with the narrow width of the absorption lines. Here, we calculate the amplitudes of burst oscillations and the width of absorption lines emerging from the surface of a rapidly rotating neutron star for a wide range of model parameters. We show that no combination of neutron star and geometric parameters can simultaneously reproduce the narrowness of the absorption lines, the high amplitude of the oscillations, and the observed flux at the time the oscillations were detected. We, therefore, conclude that the observed absorption lines are unlikely to originate from the surface of this neutron star.
The Comprehension of Metaphorical Expressions by Jordanian EFL Learners

This study explores the ability of Jordanian learners of English as a foreign language (EFL) to comprehend metaphorical expressions in English and investigates whether the use of their first language (L1) conceptual and linguistic knowledge may facilitate the comprehension of these expressions. For this purpose, the study adopts a contrastive model developed by Charteris-Black, which consists of six types of metaphor to compare and contrast in both English and Arabic. On the basis of this model, the researcher designed a multiple-choice test to assess the participants’ recognition of English metaphorical expressions. The results reveal that the participants’ receptive knowledge of metaphors varied on the basis of the six types of metaphor. The study provides evidence of the possibility that EFL learners display general conceptualizing capacity regardless of their language, which hints, possibly, at the potential universality of conceptual metaphor. It also proposes some pedagogical implications that may assist EFL learners in acquiring metaphorical expressions in English.
Decarceration and its possible effects on inmates, staff, and communities

Few current criminal justice scholars, practitioners, and politicians expected to witness the phenomenon of decreasing correctional populations. Yet, there is evidence at local, state, and regional levels of significant declines in the growth of incarceration and even decreases in the size of prisoner populations. In this article we delineate the extent of decarceration and examine the context in which it has occurred. We then explore possible positive and negative outcomes resulting from decarceration and conclude with an agenda for advancing a decarceration movement.
Application of Collective Movement in Real Life Scenarios: Overview of Current Flocking Solutions

Today more and more attention is given to collective movement of dynamic nodes, called flocking. The main problem is how to control the nodes to behave as a group and make them move together to destinations (and moreover complete some tasks such as sensing, transporting, etc.). Currently there are many works, which attempt to solve the flocking problem, but very few of them are suitable for real world use. This is because most of the algorithms are overlooking crucial physical limitations or the used model is not detailed enough. In this paper we survey the existing flocking algorithms, including a review of the most important requirements for real application scenarios.
Clinical outcomes after open locked intramedullary nailing of closed femoral shaft fractures for adult patients in a Nigerian Hospital

Background: Femoral shaft fractures are common injuries in adults. Closed locked intramedullary nailing is the recommended treatment for femoral shaft fractures due to its high union rate. Objective: The objective of this study is to determine the outcome of management of closed femoral shaft fractures in adult patients, using open locked intramedullary nailing. Patients and Methods: This is a prospective study which was carried out on all adult patients aged 16 years and above who presented within 2 weeks of sustaining closed femoral shaft fractures to the accident and emergency unit of a University Teaching Hospital in Nigeria from January 2013 to December 2013. Pathological fractures were excluded from the study. The procedure was carried out using standard techniques, and each patient was followed up for a minimum of 1 year. Results: Forty-three patients were recruited into the study. They had a mean age of 36.9 ± 11.7 years, with a male to female ratio of 2.9:1. The most common cause of closed femoral shaft fractures was road traffic crashes (95.3%), with motorcycle-related injuries found to be the highest type (56.1%). The rate of union in the study was 95.3%. The average time to radiological union was 14.0 ± 1.2 weeks while the mean time to painless full weight bearing was 14.2 ± 1.2 weeks. Among the complications encountered were broken nails (4.7%), infection, loosening of the distal screw, and limb length discrepancy (2.3% each). Using Thoresen's criteria, excellent results were obtained in 93% and poor results in 4.7% of patients. Conclusion: Open locked intramedullary nailing gives excellent clinical outcomes with high union and low complication rates in the management of closed femoral shaft fractures in adult patients.
Effects of Valproic Acid Coadministration on Plasma Efavirenz and Lopinavir Concentrations in Human Immunodeficiency Virus-Infected Adults

ABSTRACT Valproic acid (VPA) has the potential to benefit patients suffering from human immunodeficiency virus (HIV)-associated cognitive impairment. The purpose of this study was to determine if VPA affects the plasma concentration of efavirenz (EFV) or lopinavir. HIV type 1 (HIV-1)-infected patients receiving EFV or lopinavir-ritonavir (LPV/r) had 9 or 10 blood samples drawn over 8 to 24 h of a dosing interval at steady state before and after receiving 250 mg of VPA twice daily for 7 days. VPA blood samples drawn before (C0) and 8 h after the morning dose (8 h) were compared to blood samples from a group of HIV-1-infected subjects who were taking either combined nucleoside reverse transcriptase inhibitors alone or had discontinued antiretroviral therapy. Pharmacokinetic parameters were calculated by noncompartmental analysis, and tests of bioequivalence were based on 90% confidence intervals (CIs) for ratios or differences. The geometric mean ratio (GMR) (90% CI) of the areas under the concentration-time curve from 0 to 24 h (AUC0-24s) of EFV (n = 11) with and without VPA was 1.00 (0.85, 1.17). The GMR (90% CI) of the AUC0-8s of LPV (n = 8) with and without VPA was 1.38 (0.98, 1.94). The differences (90% CI) in mean C0 and 8-h VPA concentrations versus the control (n = 11) were −1.0 (−9.4, 7.4) μg/ml and −2.1 (−11.1, 6.9) μg/ml for EFV (n = 10) and −5.0 (−13.2, 3.3) μg/ml and −6.7 (−17.6, 4.2) μg/ml for LPV/r (n = 11), respectively. EFV administration alone is bioequivalent to EFV and VPA coadministration. LPV concentrations tended to be higher when the drug was combined with VPA. Results of VPA comparisons fail to raise concern that coadministration with EFV or LPV/r will significantly influence trough concentrations of VPA.
Identifying the clinical needs and patterns of health service use of adolescent girls and women with autism spectrum disorder

Girls and women in the general population present with a distinct profile of clinical needs and use more associated health services compared to boys and men; however, research focused on health service use patterns among girls and women with Autism Spectrum Disorder (ASD) is limited. In the current study, caregivers of 61 adolescent girls and women with ASD and 223 boys and men with ASD completed an online survey. Descriptive analyses were conducted to better understand the clinical needs and associated service use patterns of girls and women with ASD. Sex/gender comparisons were made of individuals’ clinical needs and service use. Adolescent girls and women with ASD had prevalent co‐occurring mental and physical conditions and parents reported elevated levels of caregiver strain. Multiple service use was common across age groups, particularly among adolescent girls and women with intellectual disability. Overall, few sex/gender differences emerged, although a significantly greater proportion of girls and women accessed psychiatry and emergency department services as compared to boys and men. Though the current study is limited by its use of parent report and small sample size, it suggests that girls and women with ASD may share many of the same high clinical needs and patterns of services use as boys and men with ASD. Areas for future research are discussed to help ensure appropriate support is provided to this understudied population. Autism Res 2017, 10: 1558–1566. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
Re: Incidence of discrepant results between QF‐PCR and karyotype testing in chorion villus samples: UK experience

The recent article by Holgado et al. reported an audit of discrepant results for chromosomal aneuploidy between quantitative fluorescence polymerase chain reaction (QF-PCR) and cultured karyotype testing in chorion villus samples (CVS) over a 7-year period (2002–2009). A similar audit of all UK laboratories providing the same dual CVS testing was conducted in 2007 following reports of discrepancies between test results. Changes in the preparation and selection of villus tissue for QF-PCR testing were recommended and adopted by all UK NHS laboratories in Best Practice Guidelines (ACC/CMGS). Recently, all UK laboratories were invited to re-audit their data to see whether these changes have resulted in a reduction in discrepancies. The results of this audit cycle (including details of the discrepancies and acknowledgement of data sources) will be published (manuscript in preparation). In the meantime, in the light of the relatively high incidence (0.12%) of complete CVS discrepancies reported by Holgado et al. it is informative to compare and contrast this data with overall UK CVS data from our re-audit. The Holgado et al. data set appears to be atypical: the overall UK incidence of this rare but clinically important class of discrepancies (for trisomy 13, 18 and 21) is considerably lower (0.02%) (see table). These data demonstrate an apparent sixfold difference in the incidence of complete discrepancies for the clinically important autosomal trisomies when comparing recent (re-audit) experience elsewhere in the UK (column 3) with directly comparable data reported by Holgado et al. (column 4). Since 2007/2008, UK laboratories have adopted a common approach to the preparation of CVS (mincing of combined villi/ enzymatic digestion) which differs from either of the two preparative methods described by Holgado et al. Further investigation seems warranted into the possibility that the ‘glass bead’ preparative method described by Holgado et al. is inadvertently contributing to preferential enrichment of embryologically remote cytotrophoblast DNA for QF-PCR aneuploidy testing. This could account for the increased incidence of discrepancies reported in their CVS cohort.
Pseudomonas aeruginosa invasion of and multiplication within corneal epithelial cells in vitro

Pseudomonas aeruginosa is usually considered an extracellular pathogen. Using assays to determine intracellular survival in the presence of gentamicin, we have previously demonstrated that P. aeruginosa is able to invade corneal cells during infectious keratitis in mice. In vitro, P. aeruginosa was found to enter the following cells: human corneal cells removed by irrigation; epithelial cells in the cornea of rats, mice, and rabbits; and primary corneal epithelial cells cultured from rat and rabbit eyes. The level of invasion was related to the level of adherent or associated bacteria. In general, invasion was more efficient with cultured epithelial cells than with cells tested in situ. Invasion did not occur when assays were performed at 4 degrees C. Cytochalasin D but not colchicine inhibited bacterial invasion, suggesting that bacterial entry was an endocytic process dependent on actin microfilaments but not microtubules. Bacteria that invaded cultured corneal epithelial cells were found to multiply within cells. The ability of P. aeruginosa to invade and multiply within corneal epithelial cells may contribute to the virulence of this organism during infectious keratitis, since intracellular bacteria can evade host immune effectors and antibiotics commonly used to treat infection.