Miracle-dz/UniFAR-FTUs huggingface dataset:
Tissue-Specific Effects of Loss of Estrogen during Menopause and Aging

The roles of estrogens have been best studied in the breast, breast cancers, and in the female reproductive tract. However, estrogens have important functions in almost every tissue in the body. Recent clinical trials such as the Women’s Health Initiative have highlighted both the importance of estrogens and how little we know about the molecular mechanism of estrogens in these other tissues. In this review, we illustrate the diverse functions of estrogens in the bone, adipose tissue, skin, hair, brain, skeletal muscle and cardiovascular system, and how the loss of estrogens during aging affects these tissues. Early transcriptional targets of estrogen are reviewed in each tissue. We also describe the tissue-specific effects of selective estrogen receptor modulators (SERMs) used for the treatment of breast cancers and postmenopausal symptoms.
Transition from foreland-to piggyback-basin deposition, Plio-Pleistocene Upper Siwalik Group, Shinghar Range, NW Pakistan

Plio-Pleistocene synorogenic deposits of the Upper Siwalik Group in the Shinghar Range (Trans-Indus Salt Ranges) of north-western Pakistan record the transition from foreland-basin to piggyback-basin deposition on the hangingwall of the Salt Range thrust. The Siwalik and Upper Siwalik Groups are over 4 km thick in the Shinghar Range. The lower 3 km consists of the Miocene Siwalik Group, which was deposited by a south-flowing foreland trunk stream, the palaeo-Indus River. The upper 1·5 km consists of the Upper Siwalik Group, which is herein divided into three members. The lowest member includes deposits of the south-flowing palaeo-Indus River and is distinguished from the underlying Siwalik Group by the first appearance of conglomerate. The transition from the lower member to the middle member is interpreted as recording uplift on the Salt Range thrust. As the Salt Range thrust was active, the palaeo-Indus River was bifurcated to the east and west around the embryonic Shinghar Range and overbank and lacustrine deposition occurred, represented by the middle member. When the Shinghar Range achieved significant topography, the upper member was deposited by streams transporting gravel and sand that flowed north and west out of the range and into a piggyback basin that formed on the hangingwall of the Salt Range thrust. New and previously published palaeomagnetic stratigraphy and fission-track ages from volcaniclastic deposits within the Upper Siwalik Group provide tight constraints on the chronology of sedimentary-facies transitions and timing of uplift of the Shinghar Range. The integration of sedimentological and geochronological data indicates that motion on the Salt Range thrust and repositioning of the Indus River began at ∼1·0 Ma.
Signaling Interactions in the Adrenal Cortex

The major physiological stimuli of aldosterone secretion are angiotensin II (AII) and extracellular K+, whereas cortisol production is primarily regulated by corticotropin (ACTH) in fasciculata cells. AII triggers Ca2+ release from internal stores that is followed by store-operated and voltage-dependent Ca2+ entry, whereas K+-evoked depolarization activates voltage-dependent Ca2+ channels. ACTH acts primarily through the formation of cAMP and subsequent protein phosphorylation by protein kinase A. Both Ca2+ and cAMP facilitate the transfer of cholesterol to mitochondrial inner membrane. The cytosolic Ca2+ signal is transferred into the mitochondrial matrix and enhances pyridine nucleotide reduction. Increased formation of NADH results in increased ATP production, whereas that of NADPH supports steroid production. In reality, the control of adrenocortical function is a lot more sophisticated with second messengers crosstalking and mutually modifying each other’s pathways. Cytosolic Ca2+ and cGMP are both capable of modifying cAMP metabolism, while cAMP may enhance Ca2+ release and voltage-activated Ca2+ channel activity. Besides, mitochondrial Ca2+ signal brings about cAMP formation within the organelle and this further enhances aldosterone production. Maintained aldosterone and cortisol secretion are optimized by the concurrent actions of Ca2+ and cAMP, as exemplified by the apparent synergism of Ca2+ influx (inducing cAMP formation) and Ca2+ release during response to AII. Thus, cross-actions of parallel signal transducing pathways are not mere intracellular curiosities but rather substantial phenomena, which fine-tune the biological response. Our review focuses on these functionally relevant interactions between the Ca2+ and the cyclic nucleotide signal transducing pathways hitherto described in the adrenal cortex.
Improving ATR performance through distance metric learning

High resolution synthetic aperture radar images usually contain much redundant, noisy and irrelevant information. Eliminating these information or extracting only useful information can enhance ATR performance, reduce processing time and increase the robustness of the ATR systems. Most existing feature extraction methods are either computationally expensive or can only provide ad hoc solutions and have no guarantee of optimality. In this paper, we describe a new distance metric learning algorithm. The algorithm is based on the local learning strategy and is formulated as a convex optimization problem. The algorithm not only is capable of learning the feature significance and feature correlations in a high dimensional space but also is very easy to implement with guaranteed global optimality. Experimental results based on the MSTAR database are presented to demonstrate the effectiveness of the new algorithm.
Mapping wetlands using multi-temporal RADARSAT-1 data and a decision-based classifier

The purpose of this study was to determine the suitability of multi-temporal RADARSAT-1 data and a decision classifier for mapping the Lower Islands of the Paraná Delta wetland in Argentina. The information-extraction strategy was based on identification of the interaction mechanisms occurring between the radar signal and the canopy, considering different vegetation phenology and flood conditions. Such information was used in the design of a decision classifier to obtain a land cover map. In addition, results were compared with those obtained from an iterative optimization clustering procedure (ISODATA algorithm). The quality of the maps obtained was assessed by an error matrix evaluation. The decision classifier was able to discriminate among land cover types with an overall accuracy on the order of 85%, and ISODATA had an overall accuracy of 81%. Two of the available scenes were taken during the high flood of the El Niño event of 1998, and the results obtained also show that RADARSAT-1 data are quite effective not only in delineating the inundation area, but also in identifying the flood condition of each of the land cover types considered. Two main conclusions are derived from this research: (1) the need for multi-temporal SAR data acquired under different environmental conditions for mapping wetlands, and (2) the advantages and flexibility of physically based reasoning classifiers for synthetic aperture radar (SAR) data classification.
Regulatory T-cell impairment in cystic fibrosis patients with chronic pseudomonas infection.

RATIONALE Patients with cystic fibrosis (CF) lung disease have chronic airway inflammation driven by disrupted balance of T-cell (Th17 and Th2) responses. Regulatory T cells (Tregs) dampen T-cell activation, but their role in CF is incompletely understood. OBJECTIVES To characterize numbers, function, and clinical impact of Tregs in CF lung disease. METHODS Tregs were quantified in peripheral blood and airway samples from patients with CF and from lung disease control patients without CF and healthy control subjects. The role of Pseudomonas aeruginosa and CF transmembrane conductance regulator (CFTR) in Treg regulation was analyzed by using in vitro and murine in vivo models. MEASUREMENTS AND MAIN RESULTS Tregs were decreased in peripheral blood and airways of patients with CF compared with healthy controls or lung disease patients without CF and correlated positively with lung function parameters. Patients with CF with chronic P. aeruginosa infection had lower Tregs compared with patients with CF without P. aeruginosa infection. Genetic knockout, pharmacological inhibition, and P. aeruginosa infection studies showed that both P. aeruginosa and CFTR contributed to Treg dysregulation in CF. Functionally, Tregs from patients with CF or from Cftr(-/-) mice were impaired in suppressing conventional T cells, an effect that was enhanced by P. aeruginosa infection. The loss of Tregs in CF affected memory, but not naive Tregs, and manifested gradually with disease progression. CONCLUSIONS Patients with CF who have chronic P. aeruginosa infection show an age-dependent, quantitative, and qualitative impairment of Tregs. Modulation of Tregs represents a novel strategy to rebalance T-cell responses, dampen inflammation, and ultimately improve outcomes for patients with infective CF lung disease.
Blind channel estimation for Hankel space-time code

In this paper a new space-time code known as Hankel space-time code, is proposed, which can perform blind estimation on MIMO channels. The identifiability conditions are presented, which show that the mild requirements on the source signal can be easily satisfied. The proposed Hankel space-time code achieves high transmission rates. Simulation results are presented to demonstrate the performance of blind channel estimation algorithm for the proposed space-time code with various numbers of antennas, transmission rates and input packet sizes
Interpretação morfoestrutural com dados SRTM no auxílio à exploração petrolífera: um exemplo na bacia sedimentar do Amazonas

A disponibilidade de modelos digitais de elevacao gerados com pela SRTM abriu novas possibilidades para estudos de sensoriamento remoto geologico na regiao amazonica, uma vez que tais modelos realcam detalhes sutis da morfologia do terreno e da rede hidrografica, geralmente mascarados em imagens orbitais convencionais. Usando como estudo de caso uma area localizada na Bacia do Amazonas, o presente artigo discute uma abordagem para uso desses dados como subsidio a exploracao petrolifera na regiao. A analise da rede de drenagem extraida automaticamente daquele produto, aliada a informacao altimetrica, revelou varias anomalias de drenagem que podem indicar expressao em superficie de feicoes geologicas em profundidade. O campo de gas de Azulao esta situado exatamente nos limites de uma dessas anomalias de drenagem, sugerindo que ela deva representar a expressao morfologica das estruturas responsaveis pelo trapeamento dos hidrocarbonetos naquela area. A abordagem metodologica discutida neste artigo podera ser replicada em outras bacias sedimentares, especialmente nas Bacias do Amazonas e do Solimoes, com cerca de 1.000. 000 km2 cobertos pela floresta tropical.
Oligophrenin-1: the link between calcium-regulated exocytosis and compensatory endocytosis in neuroendocrine cells.

In neuroendocrine cells, hormones and neuropeptides are released from large-dense core vesicles (secretory granules) by calcium-regulated exocytosis. Following exocytosis, compensatory uptake of membrane is required to maintain membrane homeostasis and allow recycling of secretory vesicle membranes. How these cells initiate and regulate this compensatory endocytosis remains poorly understood. Our recent data suggests that oligophrenin-1 (OPHN1) is a link coupling calcium-regulated exocytosis to compensatory endocytosis of secretory granules in the adrenal chromaffin cells (Houy et al., 2015, J Neurosci. 2015, 35:11045-55). Here, we highlight the major evidence and discuss how OPHN1 could couple these two processes.
Cochlear Dummy Electrodes for Insertion Training and Research Purposes: Fabrication, Mechanical Characterization, and Experimental Validation

To develop skills sufficient for hearing preservation cochlear implant surgery, surgeons need to perform several electrode insertion trials in ex vivo temporal bones, thereby consuming relatively expensive electrode carriers. The objectives of this study were to evaluate the insertion characteristics of cochlear electrodes in a plastic scala tympani model and to fabricate radio opaque polymer filament dummy electrodes of equivalent mechanical properties. In addition, this study should aid the design and development of new cochlear electrodes. Automated insertion force measurement is a new technique to reproducibly analyze and evaluate the insertion dynamics and mechanical characteristics of an electrode. Mechanical properties of MED-EL's FLEX28, FLEX24, and FLEX20 electrodes were assessed with the help of an automated insertion tool. Statistical analysis of the overall mechanical behavior of the electrodes and factors influencing the insertion force are discussed. Radio opaque dummy electrodes of comparable characteristics were fabricated based on insertion force measurements. The platinum-iridium wires were replaced by polymer filament to provide sufficient stiffness to the electrodes and to eradicate the metallic artifacts in X-ray and computed tomography (CT) images. These low-cost dummy electrodes are cheap alternatives for surgical training and for in vitro, ex vivo, and in vivo research purposes.
Aberrant Brain Network Efficiency in Parkinson’s Disease Patients with Tremor: A Multi-Modality Study

The coordination of spontaneous brain activity is widely enhanced relative to compensation activity in Parkinson’s disease (PD) with tremor; however, the associated topological organization remains unclear. This study collected magnetic resonance imaging data from 36 participants [i.e., 16 PD patients and 20 matched normal controls (NCs)] and constructed wavelet-based functional and morphological brain networks for individual participants. Graph-based network analysis indicated that the information translation efficiency in the functional brain network was disrupted within the wavelet scale 2 (i.e., 0.063–0.125 Hz) in PD patients. Compared with the NCs, the network local efficiency was decreased and the network global efficiency was increased in PD patients. Network local efficiency could effectively discriminate PD patients from the NCs using multivariate pattern analysis, and could also describe the variability of tremor based on a multiple linear regression model (MLRM). However, these observations were not identified in the network global efficiency. Notably, the global and local efficiency were both significantly increased in the morphological brain network of PD patients. We further found that the global and local network efficiency both worked well on PD classifications (i.e., using MVPA) and clinical performance descriptions (i.e., using MLRM). More importantly, functional and morphological brain networks were highly associated in terms of network local efficiency in PD patients. This study sheds lights on network disorganization in PD with tremor and helps for understanding the neural basis underlying this type of PD.
3D Segmentation in the Clinic: A Grand Challenge

This paper describes the set-up of a segmentation competi- tion for automatic and semi-automatic extraction of the liver from com- puted tomography scans and the caudate nucleus from brain MRI data. This competition was held in the form of a workshop at the 2007 Medical Image Computing and Computer Assisted Intervention conference. The rationale for organizing the competition is discussed, the training and test data sets for both segmentation tasks are described and the scoring system used to evaluate the segmentation is presented.
An Evaluation of Surface Atmospheric Changes over the Arctic Ocean for 2000–09 Using Recent Reanalyses

AbstractThe authors examine five recent reanalysis products [NCEP Climate Forecast System Reanalysis (CFSR), Modern-Era Retrospective Analysis for Research and Applications (MERRA), Japanese 25-year Reanalysis Project (JRA-25), Interim ECMWF Re-Analysis (ERA-Interim), and Arctic System Reanalysis (ASR)] for 1) trends in near-surface radiation fluxes, air temperature, and humidity, which are important indicators of changes within the Arctic Ocean and also influence sea ice and ocean conditions, and 2) fidelity of these atmospheric fields and effects for an extreme event: namely, the 2007 ice retreat. An analysis of trends over the Arctic for the past decade (2000–09) shows that reanalysis solutions have large spreads, particularly for downwelling shortwave radiation. In many cases, the differences in significant trends between the five reanalysis products are comparable to the estimated trend within a particular product. These discrepancies make it difficult to establish a consensus on likely changes occur.
MalwareMonitor: An SDN-based Framework for Securing Large Networks

Large high-speed networks such as in campuses and enterprises teem with malware infections; current solutions are either incapable of coping with the high data rates, or lacking in effective and speedy threat detection and mitigation. This work presents an early architecture for MalwareMonitor, a security framework that leverages SDN technology to address these limitations. We propose elastically partitioning network traffic to enable distributing detection load across a range of detectors; further, a centralized SDN controller allows for network-wide threat correlation as well as speedy control of malicious flows.
Sprouty proteins regulate ureteric branching by coordinating reciprocal epithelial Wnt11, mesenchymal Gdnf and stromal Fgf7 signalling during kidney development

The kidney is a classic model for studying mechanisms of inductive tissue interactions associated with the epithelial branching common to many embryonic organs, but the molecular mechanisms are still poorly known. Sprouty proteins antagonize tyrosine kinases in the Egf and Fgf receptors and are candidate components of inductive signalling in the kidney as well. We have addressed the function of sprouty proteins in vivo by targeted expression of human sprouty 2 (SPRY2) in the ureteric bud, which normally expresses inductive signals and mouse sprouty 2 (Spry2). Ectopic SPRY2 expression led to postnatal death resulting from kidney failure, manifested as unilateral agenesis, lobularization of the organ or reduction in organ size because of inhibition of ureteric branching. The experimentally induced dysmorphology associated with deregulated expression of Wnt11, Gdnf and Fgf7 genes in the early stages of organogenesis indicated a crucial role for sprouty function in coordination of epithelial-mesenchymal and stromal signalling, the sites of expression of these genes. Moreover, Fgf7 induced Spry2 gene expression in vitro and led with Gdnf to a partial rescue of the SPRY2-mediated defect in ureteric branching. Remarkably, it also led to supernumerary epithelial bud formation from the Wolffian duct. Together, these data suggest that Spry genes contribute to reciprocal epithelial-mesenchymal and stromal signalling controlling ureteric branching, which involves the coordination of Ffg/Wnt11/Gdnf pathways.
A Distributed Power-Saving Topology Management Scheme in Green Internet

In a context of explosive development in Internet scale and excessive underutilization of a large number of network elements, the power consumption issues of the current Internet have become hot subjects extensively concerned by ICT (Information and Communication Technology) sector and research institutions in recent years, which even further lead to the severe economic issues and intractable environmental issues. On the basis of above circumstances, a Distributed Power-saving Topology Management Scheme (DPTMS) is devised to achieve power saving for current Internet in the paper. After introducing the network model and power model, we describe the design of DPTMS including four modules: traffic prediction module, information awareness model, distributed topology decision-making module and sleeping control module. In the simulation and evaluation, DPTMS is compared with GRiDA as for network power consumption and network performance, which shows it is feasible and effective for a power-saving topology management.
Molecular Profiling of Patient-Matched Brain and Extracranial Melanoma Metastases Implicates the PI3K Pathway as a Therapeutic Target

Purpose: An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Experimental Design: Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and quantitative analysis of protein expression and activation by reverse-phase protein array (RPPA) analysis were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors. Results: The status of 154 previously reported hotspot mutations, including driver mutations in BRAF and NRAS, were concordant in all evaluable patient-matched pairs of tumors. Overall patterns of CNV, mRNA expression, and protein expression were largely similar between the paired samples for individual patients. However, brain metastases demonstrated increased expression of several activation-specific protein markers in the PI3K/AKT pathway compared with the extracranial metastases. Conclusions: These results add to the understanding of the molecular characteristics of melanoma brain metastases and support the rationale for additional testing of the PI3K/AKT pathway as a therapeutic target in these highly aggressive tumors. Clin Cancer Res; 20(21); 5537–46. ©2014 AACR.
NITROGEN TRANFORMATIONS AND THE NITROGEN BUDGET OF A HYPERTROPHIC IMPOUNDMENT (HARTBEESPOORT DAM, SOUTH AFRICA)

SUMMARY The major components of the nitrogen balance of hypertrophic Hartbeespoort Dam were studied at weekly intervals from October 1980 to September 1984. The Crocodile River contributed over 80Z of the hydraulic load and over 97X of the annual total nitrogen load to the impoundment. More than 802 of this nitrogen load was composed of nitrate. Monthly measurements of nitrification and denitrification rates carried out within the impoundment over one annual cycle revealed that the rates of both processes were highest at the ammonia-oxygen chemocline during summer stratification and at the sediment-water interface during winter isothermy. Mass balance calculations showed that between 35 and 49% of the annual total nitrogen load were lost via denitrification each year; the data are compared with those in the literature. Conditions in the lake will favour a change in phytoplankton species composition from Microcystis to a nitrogen-fixing species if the present trend of decreasing inorganic nitrogen concentr.
An Improved Texture Synthesis Algorithm Using Morphological Processing with Image Analogy

Texture synthesis is an important technology for graphics a nd animation. This paper proposes a novel method based upon the multi-resolution neighborhood match ing technique pioneered by Wei and Levoy. Wei and Levoy’s simple but powerful method is effective at sy nthesizing a wide range of textures. However, it has a tendency to produce synthesis artifacts in textures containing distinctive structural elements with large degrees of irregularity, such as stones in a stone wall . We propose several improvements designed to overcome these artifacts: (1) Morphological operations to emphasize key aspects of structure such as edges followed by image analogy to undo the effects of morphology ( 2) Combining non-causal neighborhoods with causal neighborhoods (3) Appropriate weighting of the parent and current level in the multi-resolution pyramid. Experimental results demonstrate that these modi fications improve the quality of synthesis for textures containing irregularly structured components.