Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal complementary matrices in systems with overlapping decomposition: A computational approach

The paper deals with linear quadratic (LQ) optimal control of linear time-invariant (LTI) systems which are decomposed into overlapped subsystems. A mathematical framework (inclusion principle) is available to formalize different structural properties and relations between the initial and the expanded systems, in which the so called complementary matrices play an important role. Up to now, only the structure and conditions on these matrices have been studied in the literature, but not the way to obtain their numerical values systematically. This paper presents a computational approach to select complementary matrices, which can be useful for a practical use of overlapping decompositions. The specific objective is to obtain the complementary matrices such that the quadratic performance for the expanded optimal control problem is minimum. An example is supplied to illustrate the use of the proposed algorithm
Economías de escala en la producción de algodón: relaciones capitalistas y políticas públicas para el agro santafesino

El 75% de las unidades productivas de algodon en Santa Fe se encuadran en la categoria de PyMEs. Esto condiciona la incorporacion de tecnologias vinculadas a la escala y tiene a su vez impacto sobre costos e ingresos debido a que los costos fijos y algunos costos variables representan proporciones crecientes del ingreso y llevan a situaciones de estrechez financiera o de quebranto, incluso frente a similares niveles de precios y rendimientos. El objetivo del presente trabajo es determinar la diferencia en los resultados economicos obtenidos en las grandes empresas algodoneras con respecto de las pequenas, analizando las causas. Para eso se construyeron dos modelos representativos de gran empresa y de pequena empresa familiar del norte santafesino, obtenidos ambos en base a entrevistas abiertas y a la determinacion de grupos focalizados. Los resultados senalan que la gran empresa desarrolla la actividad con la posibilidad de obtener mejores margenes netos, pero esto no es debido al sesgo tecnologico inherente al tamano, sino a un mejor desarrollo de estrategias ajenas a la produccion en si: compra de insumos a menores precios, mayor precio del producto, baja inmovilizacion de capital en activos fijos y una fuerte tercerizacion del trabajo.
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform1[W]

With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
The cell wall is a real drag

Martiniere et al. (1), at long last, take a critical look at the general mobility of proteins in the plant plasma membrane. Hundreds of studies looking at the active or diffusion-limited transport of proteins in the animal cell plasma membrane paint a complex picture. There are mammalian proteins that wander the membrane aimlessly, proteins corralled into pens by the cytoskeleton, proteins that become stuck in a cholesterol-rich mud, and even proteins that anchor themselves to the ECM (2). From these broader findings, it appears clear that animal cells exploit the restriction of proteins to a 2D lipid plane for complex outcomes. At issue in plant cells is almost every property that has ever been ascribed to the transport of a plasma membrane protein in a cellular system. A systematic study of how different classes of membrane proteins move within the plant plasma membrane simply has not been done.
Niche construction, sources of selection and trait coevolution

Organisms modify and choose components of their local environments. This ‘niche construction’ can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.
Highly accurate data value prediction

Data dependences (data flow constraints) present a stubborn resistance to the amount of instruction-level parallelism that can be exploited from a program. Recent work has suggested that the limits imposed by data dependences can be overcome to some extent with the use of data value prediction. That is, when an instruction is fetched, its result can be predicted so that subsequent instructions that depend on the result can use this predicted value. When the correct result becomes available, all instructions that are data-dependent on that prediction can be validated. This paper investigates a variety of techniques to carry out highly accurate data value predictions. The first technique investigates the potential of using correlation in data value predictions. The second technique investigates the potential of monitoring the strides by which the results produced by different instances of an instruction change. The third technique investigates the potential of pattern-based two-level prediction schemes. The paper also presents the results from a simulation study that we conducted to verify the potential of the investigated prediction schemes. The results show that highly accurate data valve predictions are possible with two of the investigated schemes.
From Concept to Practice: The Recent History of Preterm Delivery Prevention. Part II: Subclinical Infection and Hormonal Effects

Under the new cervical insufficiency postulate, the final common pathway theoretically may be influenced by multiple interventions including not only cerclage, but also antibiotics, anti-inflammatory drugs, or progesterone. Since the late 1970s, accumulating evidence has implicated intrauterine infection as a cause of preterm labor. The use of antimicrobial therapy for the prevention of preterm delivery (PTD), although plausible and appealing, has remained largely ineffective so far. A decade of antimicrobial intervention trials to prevent infection-mediated PTD has had disappointing results. Several randomized clinical trials have assessed the role of bacterial vaginosis (BV) treatment in prevention of PTD. The inconsistent results of these trials suggest that other processes, possibly immunomodulation, may be important. Additional factors, still unidentified, pertaining to infectious agent virulence or host immune response modulation, may be responsible for the increased risk of PTD in only a small subset of pregnant women with BV. Even a particular genetic susceptibility was proposed as an intervening factor in the correlation between BV and PTD. Autocrine, paracrine, and endocrine processes in the fetal-placental-uterine unit may contribute to the premature activation of parturitional mechanisms. Progesterone has been used in an attempt to prevent PTD since the 1970s, but the evidence accumulated until the 1990s was fraught by mixed results, and was based mostly on underpowered studies with variable eligibility criteria, including history of spontaneous abortion as an indication for treatment. Two recent randomized, controlled clinical trials restimulated the interest in progesterone supplementation, suggesting that progesterone treatment may influence favorably the rate of preterm delivery, as well as perinatal mortality and morbidity. A major impediment in accepting progesterone as the magic bullet in the prevention of PTD is that its mechanism of action is less well understood than that of all the other prophylactic measures discussed in this review. The optimal formulation, route of administration, dose, and gestational age at initiation have yet to be established. Our ability to quantify prospectively the risk of PTD in a given patient is limited. Moreover, there are limited evidence-based strategies available for prevention of PTD, reflecting our incomplete understanding of the nature of preterm labor. Although an effective instrument in PTD prevention is still elusive, the studies conducted so far have led to a shift in our understanding of cervical insufficiency, infection-mediated PTD, and hormonal influences in human parturition.
Distributed and parallel algorithms and systems for inference of huge phylogenetic trees based on the maximum likelihood method

The computation of large phylogenetic (evolutionary) trees from DNA sequence data based on the maximum likelihood criterion is most probably NP-complete. Furthermore, the computation of the likelihood value for one single potential tree topology is computationally intensive. This thesis introduces a number of algorithmic and technical solutions which for the first time enable parallel inference of large phylogenetic trees comprising up to 10.000 organisms with maximum likelihood. The algorithmic part includes a technique to accelerate the computation of likelihood values, as well as novel search-space heuristics which significantly accelerate the tree inference process and yield better final trees at the same time. The technical part covers technical solutions for the acquisition of the enormous amount of required computational resources such as parallel MPI-based and distributed seti@home-like implementations of the basic sequential algorithm. Finally, the program has been used to compute a biologically significant initial small "tree of life" containing 10.000 representative organisms from the three domains: Bacteria, Eukarya, and Archaea based on data from the ARB database.
FZD7 regulates BMSCs-mediated protection of CML cells

Inspite of effective treatment with imatinib (IM), chronic myeloid leukemia (CML) is still an incurable disease. Some patients became refractory because of IM resistance. Bone marrow mesenchymal stem cells (BMSCs) have been implicated a role in promoting CML cells' resistance against IM treatment. The detailed molecular mechanisms, however, remain largely unknown. In this study, we found that BMSCs increased the expression of FZD7 and activated Wnt/β-catenin signaling pathway in CML cells. BMSCs from CML patients showed increased efficiency to accelerate CML cell proliferation, enhance the drug resistance of K562 cells and up-regulate the expression of FZD7. Antagonism of FZD7 expression by shRNA significantly suppressed proliferation and increased IM sensitivity of CML cells co-cultured with BMSCs cells. Our findings suggest that FZD7, involved in canonical Wnt signaling pathway, plays a critical role in mediating BMSCs-dependent protection of CML cells, and potentially provide a novel therapeutic target for CML.
Detecting breast cancer from infrared images by asymmetry analysis

Infrared imaging of the breast (also called thermography) has shown effective results in both risk assessment and prognostic determination of breast cancer. This paper proposes an automated approach to detect asymmetric abnormalities in thermograms. Canny edge detector is first used to derive the edges from the original image. Hough transform is then applied to the edge image to recognize the four feature curves, which include the left and the right body boundary curves, and the two parabolic curves indicating the lower boundaries of the breasts. Segmentation is conducted based on the intersection of the two parabolic curves and the body boundaries. Bezier histogram is then derived from each segment. Curvature information is finally computed from the histogram to be used to easily indicate the asymmetry.
C‐kit immunopositive interstitial cells (Cajal‐type) in human myometrium

Previous reports describing Cajal‐like interstitial cells in human uterus are contradictory in terms of c‐kit immunoreactivity: either negative (but vimentin‐positive) in pregnant myometrium, or positive, presumably in the endometrium. The aim of this study was to verify the existence of human myometrial Cajal‐like interstitial cells (m‐CLIC). Six different, complementary approaches were used: 1) methylene‐blue supravital staining of tissue samples (cryosections), 2) methylene blue and Janus green B vital staining (m‐CLIC and mitochondrial markers, respectively), and 3) extracellular single‐unit electrophysiological recordings in cell cultures, 4) non‐conventional light microscopy on glutaraldehyde/osmium fixed, Epon‐embedded semi‐thin sections (less than 1μm) stained with toluidine blue (TSM), 5) transmission electron microscopy (TEM), and 6) immunofluorescence (IF). We found m‐CLIC in myometrial cryosections and in cell cultures. In vitro, m‐CLIC represented ∼7% of the total cell number. m‐CLIC had 2–3 characteristic processes which were very long (∼ 60 μm), very thin (±0.5μm) and moniliform. The dilated portions of processes usually accomodated mitochondria. In vitro, m‐CLIC exhibited spontaneous electrical activity (62.4 ± 7.22 mV field potentials, short duration: 1.197 ± 0.04ms). Moreover, m‐CLIC fulfilled the usual TEM criteria, the so‐called ‘gold’ or ‘platinum’ standards (e.g. the presence of discontinuos basal lamina, caveolae, endoplasmic reticulum, and close contacts between each other, with myocytes, nerve fibers and/or capillaries etc.). IF showed that m‐CLIC express CD117/c‐kit, sometimes associated with CD34 and with vimentin along their processes.
Estimating aboveground tree biomass and leaf area index in a mountain birch forest using ASTER satellite data

Biomass and leaf area index (LAI) are important variables in many ecological and environmental applications. In this study, the suitability of visible to shortwave infrared advanced spaceborne thermal emission and reflection radiometer (ASTER) data for estimating aboveground tree and LAI in the treeline mountain birch forests was tested in northernmost Finland. The biomass and LAI of the 128 plots were surveyed, and the empirical relationships between forest variables and ASTER data were studied using correlation analysis and linear and non‐linear regression analysis. The studied spectral features also included several spectral vegetation indices (SVI) and canonical correlation analysis (CCA) transformed reflectances. The results indicate significant relationships between the biomass, LAI and ASTER data. The variables were predicted most accurately by CCA transformed reflectances, the approach corresponding to the multiple regression analysis. The lowest RMSEs were 3.45 t ha−1 (41.0%) and 0.28 m2m−2 (37.0%) for biomass and LAI respectively. The red band was the band with the strongest correlation against the biomass and LAI. SR and NDVI were the SVIs with the strongest linear and non‐linear relationships. Although the best models explained about 85% of the variation in biomass and LAI, the undergrowth vegetation and background reflectance are likely to affect the observed relationships.
Single-feed, compact, GPS patch antenna using metasurface

This paper proposes a single-feed, compact, metasurface-based antenna with circularly-polarized (CP) radiation for the Global Positioning System (GPS) receivers. The antenna consists of a square patch on the metasurface, which is a periodic lattice of 4 × 4 square metallic patches arranged on a grounded dielectric substrate. The CP radiation is obtained by truncating corners of the patch radiator. The truncated-cotner square patch on the metasurface structure is used to achieve an antenna miniaturization. The final design, with a size of 60 × 60 × 4.0 mm<sup>3</sup> (0.315λ<inf>o</inf> × 0.315λ<inf>o</inf> × 0.021λ<inf>o</inf> at the GPS L1 frequency) yields a bandwidth for |S<inf>11</inf>| < −10 dB of 1.562–1.733 GHz (171 MHz) and 3-dB axial ratio (AR) bandwidth of 1.570–1.592 GHz (22 MHz). At 1.58 GHz, the proposed antenna yielded a gain of 2.75 dBic and a 3 dB AR beamwidth of 138º and 144º in the x-z and y-z planes, respectively.
Future Cascadia megathrust rupture delineated by episodic tremor and slip

A suite of 15 episodic tremor and slip events imaged between 1997 and 2008 along the northern Cascadia subduction zone suggests future coseismic rupture will extend to 25 km depth, or ∼60 km inland of the Pacific coast, rather than stopping offshore at 15 km depth. An ETS‐derived coupling profile accurately predicts GPS‐measured interseismic deformation of the overlying North American plate, as measured by ∼50 continuous GPS stations across western Washington State. When extrapolated over the 550‐year average recurrence interval of Cascadia megathrust events, the coupling model also replicates the pattern and amplitude of coseismic coastal subsidence inferred from previous megathrust earthquakes here. For only the Washington State segment of the Cascadia margin, this translates into an Mw = 8.9 earthquake, with significant moment release close to its metropolitan centers.
Doxycycline in the management of sexually transmitted infections

Doxycycline is a second-generation tetracycline, available worldwide for half a century. It is an inexpensive broad-spectrum antimicrobial agent largely used in the management of several bacterial infections, particularly involving intracellular pathogens, as well as in the treatment of acne or for the prophylaxis of malaria. Physicochemical characteristics of doxycycline (liposolubility) allow a high diffusion in the tissues and organs. It has high bioavailability and a long elimination half-life allowing oral administration of one or two daily doses. Over the last decade, the prevalence of bacterial sexually transmitted infections (STIs) (syphilis, chlamydiosis, gonorrhoea and Mycoplasma genitalium infections) has increased in most countries, mainly in MSM, many of whom are infected with HIV. In light of increasing prevalence of resistance towards first-line regimens of some STI agents and recently updated recommendations for STI management, doxycycline appears to be an attractive option compared with other available antibiotics for the treatment of some STIs due to its efficacy, good tolerability and oral administration. More recently, indications for doxycycline in STI prophylaxis have been evaluated. Considering the renewed interest of doxycycline in STI management, this review aims to update the pharmacology of, efficacy of, safety of and resistance to doxycycline in this context of use.
N-acetylcysteine in the prevention of contrast-induced nephropathy.

BACKGROUND AND OBJECTIVES Contrast-induced nephropathy (CIN) is a common clinical problem that is growing in importance as an increasing number of tests and procedures that utilize contrast media are performed. DESIGN, SETTING, PARTICIPANTS, AND MEASUREMENTS The biological and pharmacological properties of n-acetylcysteine (NAC) are reviewed, as well as the current literature relevant to the ability of NAC to prevent CIN. RESULTS After publication of a seminal study by Tepel et al. in 2000, there has been a surge in interest regarding the ability of NAC to reduce the risk for CIN. Since then a large number of studies, mostly with relatively small sample sizes, have been published. CONCLUSIONS The results have been remarkably varied with some studies finding great efficacy with NAC but most finding no significant benefit.
Monochloramine Inactivation of Bacterial Select Agents

ABSTRACT Seven species of bacterial select agents were tested for susceptibility to monochloramine. Under test conditions, the monochloramine routinely maintained in potable water would reduce six of the species by 2 orders of magnitude within 4.2 h. Bacillus anthracis spores would require up to 3.5 days for the same inactivation with monochloramine.
Necrotizing Enterocolitis in Small-for-Gestational-Age Neonates: A Matched Case-Control Study

Background: Small for gestational age (SGA) neonates are at increased risk of mortality and morbidity, including necrotizing enterocolitis (NEC), but detailed information on the incidence and risk factors of NEC in SGA neonates is lacking. Objective: This study aims to estimate the incidence of NEC in a large cohort of SGA neonates, compared to appropriate for gestational age (AGA) neonates. Methods: We included all SGA neonates without congenital malformations admitted to our neonatal nursery between 2004 and 2013. Neonates in the SGA group were matched for gestational age with a control group of AGA neonates admitted during the same study period. We recorded the occurrence of NEC and studied the association with SGA and other potential risk factors. Results: A total of 475 SGA neonates were matched for gestational age at birth to 475 control AGA neonates. The incidence of NEC in the SGA group was 3.2% (15/475) versus 1.3% (6/475) in the AGA group (OR 2.55, 95% CI 0.98-6.63, p = 0.047). The incidence of NEC in the subgroups with mild, moderate and severe SGA was 2.3% (5/215), 4.7% (5/1.07) and 3.2% (5/153), respectively (p = 0.531). Conclusions: The risk of development of NEC is more than twofold increased in SGA neonates compared to AGA neonates. We found no association between the severity of SGA and NEC.
Redundância de dados para uma Solução de Voz Sobre IP

O tema principal deste projeto visa a resolucao de determinados tipos de limitacao que ocorrem num sistema multi-site de processamento de chamadas de voz sobre IP que lida com sistemas de bases de dados relacionais. Tais limitacoes surgem devido ao mecanismo de replicacao de dados utilizado para transportar a informacao contida nas bases de dados de um site para outro, geograficamente disperso.A metodologia de trabalho adotada passou pela analise a determinados produtos de gestao de bases de dados, bem conhecidos no mercado, e posterior avaliacao de pros e contras da migracao dos atuais sistemas. Apos esta fase, iniciou-se a construcao de uma nova arquitetura de replicacao com base num plugin aplicado nas bases de dados pre-existentes, e noutras modificacoes que se mostraram necessarias.Atraves deste novo mecanismo, preve-se que os atuais sistemas em producao possam beneficiar de uma atualizacao e eliminar completamente as limitacoes de servico existentes em determinados casos. Futuramente, outros componentes do produto poderao beneficiar de uma solucao semelhante para fazer face a problemas identicos.