Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription*

Aberrant androgen receptor (AR)-dependent transcription is a hallmark of human prostate cancers. At the molecular level, ligand-mediated AR activation is coordinated through spatial and temporal protein-protein interactions involving AR-interacting proteins, which we designate the “AR-interactome. ” Despite many years of research, the ligand-sensitive protein complexes involved in ligand-mediated AR activation in prostate tumor cells have not been clearly defined. Here, we describe the development, characterization, and utilization of a novel human LNCaP prostate tumor cell line, N-AR, which stably expresses wild-type AR tagged at its N terminus with the streptavidin-binding peptide epitope (streptavidin-binding peptide-tagged wild-type androgen receptor; SBP-AR). A bioanalytical workflow involving streptavidin chromatography and label-free quantitative mass spectrometry was used to identify SBP-AR and associated ligand-sensitive cytosolic proteins/protein complexes linked to AR activation in prostate tumor cells. Functional studies verified that ligand-sensitive proteins identified in the proteomic screen encoded modulators of AR-mediated transcription, suggesting that these novel proteins were putative SBP-AR-interacting proteins in N-AR cells. This was supported by biochemical associations between recombinant SBP-AR and the ligand-sensitive coatomer protein complex I (COPI) retrograde trafficking complex in vitro. Extensive biochemical and molecular experiments showed that the COPI retrograde complex regulates ligand-mediated AR transcriptional activation, which correlated with the mobilization of the Golgi-localized ARA160 coactivator to the nuclear compartment of prostate tumor cells. Collectively, this study provides a bioanalytical strategy to validate the AR-interactome and define novel AR-interacting proteins involved in ligand-mediated AR activation in prostate tumor cells. Moreover, we describe a cellular system to study how compartment-specific AR-interacting proteins influence AR activation and contribute to aberrant AR-dependent transcription that underlies the majority of human prostate cancers.
Hypoxia-Driven Gene Expression Is an Independent Prognostic Factor in Stage II and III Colon Cancer Patients

Purpose: Hypoxia is considered a major microenvironmental factor influencing cancer behavior. Our aim was to develop a hypoxia-based gene score that could identify high and low risk within stage II and III colon cancer patients. Experimental Design: Differential gene expression of CaCo-2 colon cancer cells cultured in chronic hypoxia versus normoxia was tested for correlation with prognostic variables in published microarray datasets. These datasets were further used to downsize and optimize a gene score, which was subsequently determined in paraffin-embedded material of 126 patients with colon cancer treated in our center. Results: In the CaCo-2 cells, 923 genes with a 2-fold change and Limma corrected P ≤ 0.0001 were found differentially expressed in hypoxia versus normoxia. We identified 21 genes with prognostic value and overlapping in three different training sets and (n = 224). With a fourth published dataset (n = 177), the six-gene Colon Cancer Hypoxia Score (CCHS) was developed. Patients with low CCHS showed a significant better disease-free survival at three years (77.3%) compared with high CCHS patients (46.4%; log-rank, P = 0.006). This was independently confirmed in an external patient cohort of 90 stage II patients (86.9% vs. 52.2%; P = 0.001). Conclusions: Hypoxia-driven gene expression is associated with high recurrence rates in stage II and III colon cancer. A six-gene score was found to be of independent prognostic value in these patients. Our findings require further validation and incorporation in the current knowledge on molecular classification of colon cancer. Clin Cancer Res; 20(8); 2159–68. ©2014 AACR.
Separating Active and Passive Influences on Stomatal Control of Transpiration[OPEN]

Stomatal closure during water stress in the conifer Metasequoia glyptostroboides transitions from being entirely passive under moderate water stress to predominantly active, mediated by the level of foliar ABA, under more severe water stress. Motivated by studies suggesting that the stomata of ferns and lycophytes do not conform to the standard active abscisic acid (ABA) -mediated stomatal control model, we examined stomatal behavior in a conifer species (Metasequoia glyptostroboides) that is phylogenetically midway between the fern and angiosperm clades. Similar to ferns, daytime stomatal closure in response to moderate water stress seemed to be a passive hydraulic process in M. glyptostroboides immediately alleviated by rehydrating excised shoots. Only after prolonged exposure to more extreme water stress did active ABA-mediated stomatal closure become important, because foliar ABA production was triggered after leaf turgor loss. The influence of foliar ABA on stomatal conductance and stomatal aperture was highly predictable and additive with the passive hydraulic influence. M. glyptostroboides thus occupies a stomatal behavior type intermediate between the passively controlled ferns and the characteristic ABA-dependent stomatal closure described in angiosperm herbs. These results highlight the importance of considering phylogeny as a major determinant of stomatal behavior.
A Screening of UNF Targets Identifies Rnb, a Novel Regulator of Drosophila Circadian Rhythms

Behavioral circadian rhythms are controlled by multioscillator networks comprising functionally different subgroups of clock neurons. Studies have demonstrated that molecular clocks in the fruit fly Drosophila melanogaster are regulated differently in clock neuron subclasses to support their specific functions (Lee et al., 2016; Top et al., 2016). The nuclear receptor unfulfilled (unf) represents a regulatory node that provides the small ventral lateral neurons (s-LNvs) unique characteristics as the master pacemaker (Beuchle et al., 2012). We previously showed that UNF interacts with the s-LNv molecular clocks by regulating transcription of the core clock gene period (per) (Jaumouillé et al., 2015). To gain more insight into the mechanisms by which UNF contributes to the functioning of the circadian master pacemaker, we identified UNF target genes using chromatin immunoprecipitation. Our data demonstrate that a previously uncharacterized gene CG7837, which we termed R and B (Rnb), acts downstream of UNF to regulate the function of the s-LNvs as the master circadian pacemaker. Mutations and LNv-targeted adult-restricted knockdown of Rnb impair locomotor rhythms. RNB localizes to the nucleus, and its loss-of-function blunts the molecular rhythms and output rhythms of the s-LNvs, particularly the circadian rhythms in PDF accumulation and axonal arbor remodeling. These results establish a second pathway by which UNF interacts with the molecular clocks in the s-LNvs and highlight the mechanistic differences in the molecular clockwork within the pacemaker circuit. SIGNIFICANCE STATEMENT Circadian behavior is generated by a pacemaker circuit comprising diverse classes of pacemaker neurons, each of which contains a molecular clock. In addition to the anatomical and functional diversity, recent studies have shown the mechanistic differences in the molecular clockwork among the pacemaker neurons in Drosophila. Here, we identified the molecular characteristics distinguishing the s-LNvs, the master pacemaker of the locomotor rhythms, from other clock neuron subtypes. We demonstrated that a newly identified gene Rnb is an s-LNv-specific regulator of the molecular clock and essential for the generation of circadian locomotor behavior. Our results provide additional evidence to the emerging view that the differential regulation of the molecular clocks underlies the functional differences among the pacemaker neuron subgroups.
Ingestas recomendadas de energía y nutrientes

Para que la dieta sea adecuada y nutricionalmente equilibrada tienen que estar presentes en ella la energía y todos los nutrientes en cantidad y calidad adecuadas y suficientes para cubrir las necesidades del hombre y conseguir un óptimo estado de salud. Unos nutrientes se necesitan en mayores cantidades que otros (Tabla 1), pero todos son igualmente importantes desde el punto de vista nutricional. Según esto, el esquema general y teórico de la nutrición es muy sencillo: se trata, por un lado, de conocer las necesidades de energía y nutrientes de un individuo y por otro su ingesta real (Varela, 1982) (Figura 1). El enfrentamiento de ambos componentes puede servir de base para la planificación dietética y para la valoración del estado nutricional juzgado por la dieta, tanto en individuos como en grupos.
Cherry leaf roll virus - an Emerging Virus in Finland?

Cherry leaf roll virus, CLRV, is a plant pathogen that infects a variety of deciduous trees and shrubs in temperate regions. Little is known about its occurrence at high latitudes and especially in Finnish birch species. Still, symptoms that seemed to be associated with CLRV such as vein banding, leaf roll and decline have been observed in birch trees throughout the country since the summer of 2002. Six different birch species, subspecies or varieties, i.e. Betula pubescens subsp. pubescens (downy birch), B. pendula (silver birch), B. nana (dwarf birch), B. pubescens var. appressa (Kiilopaa birch), B. pubescens subsp. czerepanovii (mountain birch) and B. pendula var. carelica (curly birch) originating from all over Finland were assessed by immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR) for CLRV infection. It was shown that CLRV is widely distributed in B. pendula and B. pubescens throughout the country. Furthermore, dwarf birch, mountain birch, Kiilopaa birch and curly birch were confirmed to be previously unkown hosts of CLRV. Genetic analysis of virus sequence variants originating from Finnish birch trees revealed atypical phylogenetic relationships. In contrast to CLRV isolates from birches growing in the United Kingdom and Germany which clustered exclusively within group A, Finnish CLRV isolates belonged either to group B, D or E. Thus, virus population structure in Finnish birches seems to be more variable and host plant dependency seems not to apply for Finnish CLRV isolates.
Density Estimation on Delaunay Triangulations

Density Estimation is a very popular method to compute global illumination solutions in a complex virtual scene. After simulating the re ection paths of a large number of photons in the scene, the illumination at a surface point is approximated by estimating the density of photon hits in the point's surrounding. In this paper we describe a novel approach to compute such a density approximation based on Delaunay triangulation and mesh modi cation techniques.
An improved GA for identifying susceptibility genes in the presence of epistasis

Identifying the epistasis models between single nucleotide polymorphisms (SNPs) in several genes can explain the susceptibility to diseases. The statistical methods have been used to identify the significant epistasis models according to the related statistical values, including odds ratio (OR), chi-square test (χ2), p-value, etc. However, the high calculations limit the statistic to identify the high-order epistasis. In this study, we proposed an lsGA algorithm, genetic algorithm based on local search algorithm, to identify the significant epistasis model amongst the large SNP combinations. Two disease models were used to simulate the large data sets considering the minor allele frequency (MAF), number of SNP, and number of sample. The 3-order epistasis models were identified by chi-square test (χ2) for evaluating the significance (P-value <; 0.05). lsGA was compared with GA to analyze the improvement in the search abilities, and results showed that lsGA provided higher chi-square test values than that of GA.
Cytotoxic antibodies to cultured lymphoblasts unrelated to epstein‐barr virus

A micro‐51chromium‐release assay was used to examine the possible relationship between antibodies cytotoxic to lymphoid cells and EBV infections of the donors. No correlation was found between sera capable of killing lymphoid cells pre‐labelled with51 chromium and the presence or absence of antibodies to the viral capsid antigen (anti‐VCA). Sera obtained from patients with infectious mononucleosis, Burkitt's lymphoma, nasopharyngeal carcinoma and Hodgkin's disease known to have elevated titers to anti‐VCA showed cytotoxicity similar to control values. There appeared to be both heat‐stable and heat‐labile complement‐dependent cytotoxic antibodies.
Multiple Sound Source Location Estimation in Wireless Acoustic Sensor Networks Using DOA Estimates: The Data-Association Problem

In this paper, we consider the data-association problem for the localization of multiple sound sources in a wireless acoustic sensor network, where each node is a microphone array, using direction of arrival (DOA) estimates. The data-association problem arises because the central node that receives the multiple DOA estimates from the nodes cannot know to which source they belong. Hence, the DOAs from the different nodes that correspond to the same source must be found in order to perform accurate localization. We present a method to identify the correct association of DOAs to the sources and thus accurately estimate their locations. Our method results in high association and localization accuracy in realistic scenarios with missed detections, reverberation, noise, and moving sources and outperforms other recently proposed methods. It also incorporates a bitrate reduction scheme in order to keep the amount of information that needs to be transmitted in the network at low levels without affecting performance.
Rainbow OS: A distributed STM for in-memory data clusters

Making parallel programming safe and intuitive still remains a major challenge in view of the fact that the exploitation of parallelism is not only desirable for multicore architectures but also for distributed systems such as clusters and grids. We claim that Software Transactional Memory (STM) is one of the more promising approaches to simplify the parallel programmer's job. Our Rainbow OS offers a streamlined in-memory data facility, accommodating many distributed application scenarios using a lean and teachable STM approach. The paper gives an overview and then focuses on memory management strategies and how Rainbow OS can host multiple, coexisting, custom-tailored memory consistency models within its transactional environment. We explain the benefits of our cluster-wide STM for distributed programming, for consistent memory image checkpointing and for system-level recompilation with on-the-fly code replacement. We also describe how the transactional programming paradigm can be used inside the operating system, particularly for device driver development.
SOM-based hand gesture recognition for virtual interactions

In nowadays, hand gestures can be used as a more natural and convenient way for human computer interaction. The direct interface of hand gestures provides us a new way for communicating with the virtual environment. In this paper, we propose a new hand gesture recognition method using self-organizing map (SOM) with datagloves. The SOM method is a type of machine learning algorithm. It deals with the raw data sampled from datagloves as input vectors, and builds a mapping between these uncalibrated data and gesture commands. The results show the average recognition rate and time efficiency when using SOM for dataglove-based hand gesture recognition. A series of tasks in virtual house illustrate the performance of our interaction method based on hand gesture recognition.
Point cloud registration by combining shape and intensity contexts

Co-registration of point clouds is critical when a scene is measured several times. We present a novel feature based solution, where features are described by combining local shape context and local intensity (or image) context. The Euclidean distances of such shape and intensity combined context descriptors are used to identify candidate correspondences, which are then used as input to the final (co-)registration with the random sample consensus method. The proposed approach is embedded in the concepts of point cloud pyramid and local shape context. The use of pyramid allows for robustness to noise, whereas the new feature descriptor takes into account both local geometry and reflectivity. Tests with three point clouds: one airborne, one terrestrial, and one image derived, demonstrate an automated and robust registration at a precision of 1.4-1.7 times the point spacing, which is sufficient for many applications and can lead to a convergence for further refinement.
Irxl1 mutant mice show reduced tendon differentiation and no patterning defects in musculoskeletal system development

Irxl1 (Iroquois‐related homeobox like‐1) is a newly identified three amino‐acid loop extension (TALE) homeobox gene, which is expressed in various mesoderm‐derived tissues, particularly in the progenitors of the musculoskeletal system. To analyze the roles of Irxl1 during embryonic development, we generated mice carrying a null allele of Irxl1. Mice homozygous for the targeted allele were viable, fertile, and showed reduced tendon differentiation. Skeletal morphology and skeletal muscle weight in Irxl1‐knockout mice appeared normal. Expression patterns of several marker genes for cartilage, tendon, and muscle progenitors in homozygous mutant embryos were unchanged. These results suggest that Irxl1 is required for the tendon differentiation but dispensable for the patterning of the musculoskeletal system in development. genesis, 2011. © 2010 Wiley‐Liss, Inc.
Duplication of the Massa Intermedia in a Child

Accessible online at: www.karger. com/pne We report a 14-month-old female patient with DandyWalker variant and duplication of the massa intermedia (MI) (fig. 1). No other imaging anomalies were found intracranially. The child had no other medical or surgical history. Interestingly, in a postmortem examination of adult human brains, Malobabic et al. [1] report one case in which this structure was duplicated, although no illustrations or descriptions of this patient’s anatomy were provided. To our knowledge, our report represents the first documented incidence of duplication of the MI in a pediatric patient. The MI (interthalamic adhesion, middle, gray, soft commissure) is a bridge of gray tissue between the left and right thalami with an obscure function. When present, it generally traverses the third ventricle at about its midpoint, posterior to the posterior margin of the foramen of Monro. This tissue is first found between weeks 13 and 14 of fetal development [2]. Rosales et al. [2], in a study of 100 cerebra from birth to the 9th decade, found that the MI was absent in 17% of specimens. These same authors also found that following the 3rd decade of life, the MI undergoes increasing atrophy, and in older individuals, it may disappear. Brain, or for that matter diencephalic size, does not seem to influence the mass of the MI. Clinically, the MI has been misdiagnosed as a midline cyst in cases of hydrocephalus where it is stretched and hence dilated [3]. One must also entertain the possibility Fig. 1. T1-weighted axial MRI of the brain demonstrating the duplication of the MI posterior to the normally located MI within the third ventricle.
A PTCH1 Homolog Transcriptionally Activated by p53 Suppresses Hedgehog Signaling*

Background: p53 activates transcription of downstream target genes that contribute to tumor suppression. Results: The expression of PTCH53, a structural and functional homolog of PTCH1, is highly responsive to p53 in diverse cells and tissues. Conclusion: p53 can suppress canonical Hedgehog signaling via induction of PTCH53. Significance: PTCH53 is a new mediator by which p53 can suppress oncogenic Hedgehog signals. The p53-mediated responses to DNA damage and the Hedgehog (Hh) signaling pathway are each recurrently dysregulated in many types of human cancer. Here we describe PTCH53, a p53 target gene that is homologous to the tumor suppressor gene PTCH1 and can function as a repressor of Hh pathway activation. PTCH53 (previously designated PTCHD4) was highly responsive to p53 in vitro and was among a small number of genes that were consistently expressed at reduced levels in diverse TP53 mutant cell lines and human tumors. Increased expression of PTCH53 inhibited canonical Hh signaling by the G protein-coupled receptor SMO. PTCH53 thus delineates a novel, inducible pathway by which p53 can repress tumorigenic Hh signals.
Successful breast reconstruction using acellular dermal matrix can be recommended in healthy non-smoking patients.

INTRODUCTION We present Scandinavia's first series of immediate alloplastic breast reconstructions with an acellular dermal matrix. MATERIAL AND METHODS Data were collected retrospectively in 76 cases of immediate breast reconstruction using an acellular dermal matrix (ADM) and an implant. RESULTS A total of 59 women were reconstructed between June 2011 and January 2013. Cases included 42 unilateral and 17 bilateral reconstructions. A large number of patients had adjuvant therapy, hormone therapy (34), radiation therapy (27) or chemotherapy (38). The median age was 51 years (30-70 years) and the median follow-up period was 326 days (68-624 days). The co-morbidity factors included hypertension (n = 11), diabetes (n = 2) and 19 patients were smokers. Unsuccessful reconstructions counted ten cases (13%), eight of these due to necrosis and/or wound dehiscence (10%) and two due to infection (3%). The failure rate in non-smokers was 2/52 (4%) compared with 8/24 (33%) in smokers, p = 0.001. In hypertensive patients, the failure rate was 6/12 (50%) compared with 4/64 (6%)in normotensive patients, p = 0.001. 70% of the failed reconstructions occurred in patients older than 65 years of age. CONCLUSION Immediate alloplastic breast reconstruction using an ADM can be recommended to healthy non-smoking patients. FUNDING not relevant. TRIAL REGISTRATION not relevant.
On the stereochemical nanostructure-based mechanisms of electrical behavior of polymer insulators

The aim of this paper is to highlight the determining factor of some normal stereochemical nanostructures, especially the mmmr and mmmmrx, termini of isotactic sequence, on the ability of PVC, hydrogenated PVC (as a precursor of PE) and PP to accumulate, release and transport space charges. The correlations found for these polymers by using TSM, TSDC and IDC methods, provide an original interpretation of the space charge behavior of these insulators and open new prospects in the field of property/nanostructures relationships and performances.