Miracle-dz/UniFAR-FTUs huggingface dataset:
Prolactin Receptor Expression is an Independent Favorable Prognostic Marker in Human Breast Cancer

Prolactin (PRL) hormone plays an important role in the development of the mammary gland and terminal differentiation of the mammary epithelial cells. While initial studies suggested that PRL may contribute to the development of breast cancer through PRL/prolactin receptor (PRLR) autocrine function, mounting evidence indicate a different role for PRL, highlighting this hormone as a regulator of epithelial plasticity and as a potential tumor suppressor. To gain further insights into the role of PRL in human breast carcinogenesis, immunohistochemistry analyses of PRLR protein expression levels using tissue microarray of 102 cases were done in comparison with various clinical/pathologic parameters and molecular subtypes. In addition, gene expression level of PRLR was also evaluated in relation to intrinsic molecular subtypes, tumor grade, and patient outcome using GOBO database for 1881 breast cancer patients. Interestingly, PRLR expression was found to be significantly downregulated in invasive breast cancer (21.4%) in comparison with normal/benign (80%) and in situ carcinoma (60%) (P=0.003498). Moreover, PRLR expression was associated with lymph node negativity and low-grade well-differentiated tumors. PRLR expression was strongest in luminal A subtype, and was virtually undetectable in the worse prognosis triple-negative breast cancer subtype (P=0.00001). Furthermore, PRLR expression was independent of ER, PR, HER-2, and P53 status. Finally, PRLR expression was significantly (P<0.01) associated with prolonged distant metastasis–free survival in breast cancer patients. In conclusion, our results highlight PRLR as an independent predictor of favorable prognosis in human breast cancer.
Mycobacterium salmoniphilum infection in farmed Atlantic salmon, Salmo salar L.

Multiple greyish-white visceral nodules containing abundant rapidly growing and acid-fast bacteria, subsequently identified as Mycobacterium salmoniphilum, were detected in moribund and newly dead market-sized fish during a period of increased mortality in an Atlantic salmon, Salmo salar, farm in western Norway. Isolates cultured from diseased fish were phenotypically consistent with Mycobacterium sp. previously isolated from Atlantic salmon [MT 1890 (= NCIMB13533), MT1892, MT1900 and MT1901] in the Shetland Isles, Scotland. Partial sequences of 16S rDNA, ribosomal RNA internal transcribed spacer (ITS1), 65-kDa heat-shock protein (Hsp65) and β subunit of RNA polymerase (rpoB) revealed 97-99% similarity with M. salmoniphilum type strain ATCC 13758(T) . The source of infection was not confirmed. Koch's postulates were fulfilled following experimental challenge of Atlantic salmon with field isolate NVI6598 (FJ616988). Mortality was recorded in experimentally infected fish; however, the infection remained subclinical in the majority of affected fish over the 131-day challenge period.
Swirling astrophysical flows – efficient amplifiers of Alfvén waves!?

We show that a helical shear flow of a magnetized plasma may serve as an efficient amplifier of Alfven waves. We find that even when the flow is purely ejectional (i.e., when no rotation is present) Alfven waves are amplified through the transient, shear-induced, algebraic amplification process. Series of transient amplifications, taking place sequentially along the flow, may result in a cascade amplification of these waves. However, when a flow is swirling or helical (i.e., some rotation is imposed on the plasma motion), Alfven waves become subject to new, much more powerful shear instabilities. In this case, depending on the type of differential rotation, both usual and parametric instabilities may appear. We claim that these phenomena may lead to the generation of large amplitude Alfven waves and the mechanism may account for the appearance of such waves in the solar atmosphere, in accretion-ejection flows and in accretion columns. These processes may also serve as an important initial (linear and nonmodal) phase in the ultimate subcritical transition to MHD Alfvenic turbulence in various kinds of astrophysical shear flows.
Differential Roles for the Interferon-Inducible IFI16 and AIM2 Innate Immune Sensors for Cytosolic DNA in Cellular Senescence of Human Fibroblasts

The IFN-inducible IFI16 and AIM2 proteins act as innate immune sensors for cytosolic double-stranded DNA (dsDNA). On sensing dsDNA, the IFI16 protein induces the expression of IFN-β whereas the AIM2 protein forms an inflammasome, which promotes the secretion of IL-1β. Given that the knockdown of IFI16 expression in human diploid fibroblasts (HDF) delays the onset of cellular senescence, we investigated the potential roles for the IFI16 and AIM2 proteins in cellular senescence. We found that increased IFI16 protein levels in old (vs. young) HDFs were associated with the induction of IFN-β. In contrast, increased levels of the AIM2 protein in the senescent (vs. old) HDFs were associated with increased production of IL-1β. The knockdown of type I IFN-α receptor subunit, which reduced the basal levels of the IFI16 but not of the AIM2, protein delayed the onset of cellular senescence. Accordingly, increased constitutive levels of IFI16 and AIM2 proteins in ataxia telangiectasia mutated (ATM) HDFs were associated with the activation of the IFN signaling and increased levels of IL-1β. The IFN-β treatment of the young HDFs, which induced the expression of IFI16 and AIM2 proteins, activated a DNA damage response and also increased basal levels of IL-1β. Interestingly, the knockdown of AIM2 expression in HDFs increased the basal levels of IFI16 protein and activated the IFN signaling. In contrast, the knockdown of the IFI16 expression in HDFs decreased the basal and dsDNA-induced activation of the IFN signaling. Collectively, our observations show differential roles for the IFI16 and AIM2 proteins in cellular senescence and associated secretory phenotype. Mol Cancer Res; 9(5); 589–602. ©2011 AACR.
IGBT junction temperature estimation via gate voltage plateau sensing

A method for in-situ high bandwidth junction temperature estimation of Insulated Gate Bipolar Transistors (IGBTs) is introduced. The method is based on the acquisition of the gate voltage plateau during turn-on, which can be directly related to the junction temperature. This allows fast over temperature protection of the power device and thus enables operation at the boundary of the device safe operation area. Firstly, this paper discusses the underlying physical mechanisms. Secondly, the temperature sensitivity and the impact of interferences over the entire operation range of an IGBT. Finally, a sensing circuitry is presented, which allows accurate gate voltage plateau sensing every switching period as well as an easy integration into the gate driver. The performance of the proposed method is experimentally demonstrated over a wide range of temperatures and currents.
Influence of dietary protein level, amino acid supplementation, and dietary energy levels on growing-finishing pig performance and carcass composition.

Two experiments were conducted to determine the effects of feeding reduced-CP, AA-supplemented diets at two ambient temperatures (Exp. 1) or three levels of dietary NE (Exp. 2) on pig performance and carcass composition. In Exp. 1, 240 mixed-sex pigs were used to test whether projected differences in heat increment associated with diet composition affect pig performance. There were 10 replications of each treatment with four pigs per pen. For the 28-d trial, average initial and final BW were 28.7 kg and 47.5 kg, respectively. Pigs were maintained in a thermoneutral (23 degrees C) or heat-stressed (33 degrees C) environment and fed a 16% CP diet, a 12% CP diet, or a 12% CP diet supplemented with crystalline Lys, Trp, and Thr (on an as-fed basis). Pigs gained at similar rates when fed the 16% CP diet or the 12% CP diet supplemented with Lys, Trp, and Thr (P > 0.10). Pigs fed the 12% CP, AA-supplemented diet had a gain:feed similar to pigs fed the 16% CP diet when housed in the 23 degrees C environment but had a lower gain:feed in the 33 degrees C environment (diet x temperature, P < 0.01). In Exp. 2, 702 gilts were allotted to six treatments with nine replicates per treatment. Average initial and final BW were 25.3 and 109.7 kg, respectively. Gilts were fed two levels of CP (high CP with minimal crystalline AA supplementation or low CP with supplementation of Lys, Trp, Thr, and Met) and three levels of NE (high, medium, or low) in a 2 x 3 factorial arrangement. A four-phase feeding program was used, with diets containing apparent digestible Lys levels of 0.96, 0.75, 0.60, and 0.48% switched at a pig BW of 41.0, 58.8, and 82.3 kg, respectively. Pigs fed the low-CP, AA-supplemented diets had rates of growth and feed intake similar to pigs fed the high-CP diets. Dietary NE interacted with CP level for gain:feed (P < 0.06). A decrease in dietary NE from the highest NE level decreased gain:feed in pigs fed the high-CP diet; however, gain:feed declined in pigs fed the low-CP, AA-supplemented diet only when dietary NE was decreased to the lowest level. There was a slight reduction in longissimus area in pigs fed the low-CP diets (P < 0.08), but other estimates of carcass muscle did not differ (P > 0.10). These data suggest that pigs fed low-CP, AA-supplemented diets have performance and carcass characteristics similar to pigs fed higher levels of CP and that alterations in dietary NE do not have a discernible effect on pig performance or carcass composition.
Induced pluripotent stem cells: opportunities and challenges

Somatic cells have been reprogrammed into pluripotent stem cells by introducing a combination of several transcription factors, such as Oct3/4, Sox2, Klf4 and c-Myc. Induced pluripotent stem (iPS) cells from a patient's somatic cells could be a useful source for drug discovery and cell transplantation therapies. However, most human iPS cells are made by viral vectors, such as retrovirus and lentivirus, which integrate the reprogramming factors into the host genomes and may increase the risk of tumour formation. Several non-integration methods have been reported to overcome the safety concern associated with the generation of iPS cells, such as transient expression of the reprogramming factors using adenovirus vectors or plasmids, and direct delivery of reprogramming proteins. Although these transient expression methods could avoid genomic alteration of iPS cells, they are inefficient. Several studies of gene expression, epigenetic modification and differentiation revealed the insufficient reprogramming of iPS cells, thus suggesting the need for improvement of the reprogramming procedure not only in quantity but also in quality. This report will summarize the current knowledge of iPS generation and discuss future reprogramming methods for medical application.
Proprioceptive Navigation, Slip Estimation and Slip Control for Autonomous Wheeled Mobile Robots

For a two-wheeled differentially driven mobile robot a navigation and slip control algorithm is developed. The presented concept for purely proprioceptive navigation combines state estimation via extended Kalman filter from inertial sensor data (i.e. gyro and acceleration sensors) and odometric measurements (i.e. wheel angular encoders). The advantages of both types of sensors are exploited by selective mixing. Tangential slip detection and side-slip angle measurement enable slip control by transiently overriding a pre-planned trajectory. Experimental results demonstrating the performance of the proposed system are presented
WHO Group 5 Drugs and Difficult Multidrug-Resistant Tuberculosis: a Systematic Review with Cohort Analysis and Meta-Analysis

ABSTRACT It is often necessary to include WHO group 5 drugs in the treatment of extensively drug-resistant tuberculosis (XDR-TB) and fluoroquinolone-resistant multidrug-resistant tuberculosis (MDR-TB). As clinical evidence about the use of group 5 drugs is scarce, we conducted a systematic review using published individual patient data. We searched PubMed and OvidSP through 7 April 2013 for publications in English to assemble a cohort with fluoroquinolone-resistant MDR-TB treated with group 5 drugs. Favorable outcome was defined as sputum culture conversion, cure, or treatment completion in the absence of death, default, treatment failure, or relapse. A cohort of 194 patients was assembled from 20 articles involving 12 geographical regions. In descending order of frequency, linezolid was used in treatment of 162 (84%) patients, macrolides in 84 (43%), clofazimine in 65 (34%), amoxicillin with clavulanate in 56 (29%), thioridazine in 18 (9%), carbapenem in 16 (8%), and high-dose isoniazid in 16 (8%). Cohort analysis with robust Poisson regression models and random-effects meta-analysis similarly suggested that linezolid use significantly increased the probability (95% confidence interval) of favorable outcome by 57% (10% to 124%) and 55% (10% to 121%), respectively. Defining significant associations by risk ratios ≥ 1.2 or ≤ 0.9, neither cohort analysis nor meta-analysis demonstrated any significant add-on benefit from the use of other group 5 drugs with respect to outcome for patients treated with linezolid, although selection bias might have led to underestimation of their effects. Our findings substantiated the use of linezolid in the treatment of XDR-TB or fluoroquinolone-resistant MDR-TB and call for further studies to evaluate the roles of other group 5 drugs.
Improved coupled resonator filter performance using a carbon-doped oxide de-coupling layer

We describe a newly developed de-coupling material SiOCH for coupled resonator filter applications. The SiOCH films belong to a general class of low-k dielectrics often referred to as carbon-doped oxides (CDO). In this work, CDO replaces SiLK, significantly improving the performance of the resulting filters. In contrast to the spin-on and curing process used to deposit SiLK, the CDO films are deposited using plasma enhanced chemical vapor deposition. The resulting films possess a low acoustic impedance that can be varied over a range greater than 2∶1 through a choice of deposition conditions. The new filters possess several key advantages over the SiLK-based devices reported previously, including decreased filter insertion loss, a passband free of spurious notches, and a dramatically lower temperature coefficient of frequency.
Identification of regions of Ail required for the invasion and serum resistance phenotypes

Yersinia enterocolitica is an enteric pathogen that has served as a model system for the study of microbial pathogenesis. Numerous virulence gene have been identified both on the virulence plasmid and on the chromosome. One of the chromosomal genes that is highly correlated with virulence is ail, a gene identified along with inv in a screen for Y. enterocolitica genes that could confer an invasive phenotype to Escherichia coli. Ail also promotes serum resistance in both E. coli and Y. enterocolitica. Several virulence factors homologous to Ail have been identified in other pathogens, yet very little is known about what constitutes the functional domain(s) of these proteins. Proteins in this family are predicted to consist of eight transmembrane β‐sheets and four cell surface‐exposed loops. We constructed and characterized a number of insertion, deletion and point mutations in the regions of ail predicted to encode the cell surface loops. The results from the analysis of these mutants indicate that cell surface loops one and four do not directly promote invasion or serum resistance, whereas mutations in loop three appear to modulate both phenotypes. Analysis of mutations in loop 2 suggests that this surface‐exposed loop contains sequences required for serum resistance and invasion. In addition, a peptide derived from the sequence of loop 2 was able specifically to inhibit Ail‐mediated invasion in a dose‐dependent manner. These results suggest that Ail directly promotes invasion and that loop 2 contains an active site, perhaps a receptor‐binding domain. Analyses of the mutations also suggest that the serum resistance and invasion phenotypes may be separable, because there are numerous mutations that affect one phenotype but not the other.
ANXIOUS FORMS OF DEPRESSION

Previous research has described distinctive features for anxious and nonanxious forms of major depression. The concept of “mixed anxiety depression disorder” (MADD) refers to a milder degree of the anxious form of depression, since the depressive symptoms fall short of the number required for a diagnosis of major depression. It is argued that this can be thought of as a subclinical form of anxious depression, rather than a separate disorder in its own right. In view of its substantial prevalence in general medical settings, its associated disability and its public health importance, it deserves to be recognized, and seen as being continuous with the more severe forms of anxious depression. It will therefore be included in the Field Trials of the version of the ICD‐11 (where ICD is the International Classification of Disease) intended for primary care. It is argued that current anxiety, depression (without anxiety), and anxious depression would cover most of the psychologically distressed patients seen in general medical settings, using a pseudodimensional system.
DRAW: Deep Networks for Recognizing Styles of Artists Who Illustrate Children's Books

This paper is motivated from a young boy's capability to recognize an illustrator's style in a totally different context. In the book "We are All Born Free" [1], composed of selected rights from the Universal Declaration of Human Rights interpreted by different illustrators, the boy was surprised to see a picture similar to the ones in the "Winnie the Witch" series drawn by Korky Paul (Figure [1]). The style was noticeable in other characters of the same illustrator in different books as well. The capability of a child to easily spot the style was shown to be valid for other illustrators such as Axel Scheffler and Debi Gliori. The boy's enthusiasm let us to start the journey to explore the capabilities of machines to recognize the style of illustrators. We collected pages from children's books to construct a new illustrations dataset consisting of about 6500 pages from 24 artists. We exploited deep networks for categorizing illustrators and with around 94% classification performance our method over-performed the traditional methods by more than 10%. Going beyond categorization we explored transferring style. The classification performance on the transferred images has shown the ability of our system to capture the style. Furthermore, we discovered representative illustrations and discriminative stylistic elements.
How does landscape structure influence landscape connectivity

We investigated the impact of landscape structure on landscape connectivity using a combination of simulation and empirical experiments. In a previous study we documented the movement behaviour of a specialized goldenrod beetle (Trirhabda borealis Blake) in three kinds of patches: habitat (goldenrod) patches and two types of matrix patch (cut vegetation and cut vegetation containing camouflage netting as an impediment to movement). In the current study, we used this information to construct simulation and experimental landscapes consisting of mosaics of these three patch types, to study the effect of landscape structure on landscape connectivity, using the T. borealis beetle as a model system. In the simulation studies, landscape connectivity was based on movements of individual beetles, and was measured in six different ways. The simulations revealed that the six measures of landscape connectivity were influenced by different aspects of landscape structure, suggesting that: (1) landscape connectivity is a poorly defined concept, and (2) the same landscape may have different landscape connectivity values when different measures of landscape connectivity are used. There were two general predictions that held over all measures of landscape connectivity: (1) increasing interpatch distance significantly decreased landscape connectivity and (2) the influence of matrix elements on landscape connectivity was small in comparison to the influence of habitat elements. Empirical mark-release-resight experiments using Trirhabda beetles in experimental landscapes supported the simulation results.
Effects of Sensory Behavioral Tasks on Pain Threshold and Cortical Excitability

Background/Objective Transcutaneous electrical stimulation has been proven to modulate nervous system activity, leading to changes in pain perception, via the peripheral sensory system, in a bottom up approach. We tested whether different sensory behavioral tasks induce significant effects in pain processing and whether these changes correlate with cortical plasticity. Methodology/Principal Findings This randomized parallel designed experiment included forty healthy right-handed males. Three different somatosensory tasks, including learning tasks with and without visual feedback and simple somatosensory input, were tested on pressure pain threshold and motor cortex excitability using transcranial magnetic stimulation (TMS). Sensory tasks induced hand-specific pain modulation effects. They increased pain thresholds of the left hand (which was the target to the sensory tasks) and decreased them in the right hand. TMS showed that somatosensory input decreased cortical excitability, as indexed by reduced MEP amplitudes and increased SICI. Although somatosensory tasks similarly altered pain thresholds and cortical excitability, there was no significant correlation between these variables and only the visual feedback task showed significant somatosensory learning. Conclusions/Significance Lack of correlation between cortical excitability and pain thresholds and lack of differential effects across tasks, but significant changes in pain thresholds suggest that analgesic effects of somatosensory tasks are not primarily associated with motor cortical neural mechanisms, thus, suggesting that subcortical neural circuits and/or spinal cord are involved with the observed effects. Identifying the neural mechanisms of somatosensory stimulation on pain may open novel possibilities for combining different targeted therapies for pain control.
Entropy-based parametric estimation of spike train statistics

We consider the evolution of a network of neurons, focusing on the asymptotic behavior of spikes dynamics instead of membrane potential dynamics. The spike response is not sought as a deterministic response in this context, but as a conditional probability : "Reading out the code" consists of inferring such a probability. This probability is computed from empirical raster plots, by using the framework of thermodynamic formalism in ergodic theory. This gives us a parametric statistical model where the probability has the form of a Gibbs distribution. In this respect, this approach generalizes the seminal and profound work of Schneidman and collaborators. A minimal presentation of the formalism is reviewed here, while a general algorithmic estimation method is proposed yielding fast convergent implementations. It is also made explicit how several spike observables (entropy, rate, synchronizations, correlations) are given in closed-form from the parametric estimation. This paradigm does not only allow us to estimate the spike statistics, given a design choice, but also to compare different models, thus answering comparative questions about the neural code such as : "are correlations (or time synchrony or a given set of spike patterns, .) significant with respect to rate coding only ? " A numerical validation of the method is proposed and the perspectives regarding spike-train code analysis are also discussed.