Non-negative matrix factorization

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Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Single-cell RNA-Sequencing (scRNA-Seq) is a fast-evolving technology that enables the understanding of biological processes at an unprecedentedly high resolution. However, well-suited bioinformatics tools to analyze the data generated from this new technology are still lacking. Here we investigate the performance of non-negative matrix factorization (NMF) method to analyze a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic stem cells to human glioblastoma data. In comparison to other unsupervised clustering methods including K-means and hierarchical clustering, NMF has higher accuracy in separating similar groups in various datasets. We ranked genes by their importance scores (D-scores) in separating these groups, and discovered that NMF uniquely identifies genes expressed at intermediate levels as top-ranked genes. Finally, we show that in conjugation with the modularity detection method FEM, NMF reveals meaningful protein-protein interaction modules. In summary, we propose that NMF is a desirable method to analyze heterogeneous single-cell RNA- Seq data. The NMF based subpopulation detection package is available at: https: //github.com/lanagarmire/NMFEM.
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Analysis of trends in seasonal electrical energy consumption via non-negative tensor factorization

Analysis of trends in seasonal electrical energy consumption via non-negative tensor factorization

This study explores and evaluates the performance of a supervised single- channel source separation approach based on multi-way array (tensor) factor- ization for electrical source modeling regarding load disaggregation at long- term using a real dataset from an household. Multi-way arrays are a natural representation for multi-dimensional data and have been widely used in a variety of applications ranging from signal analysis neuroscience to source separation [4, 5, 6]. In a previous work, [7], we proposed a method for energy disaggregation STMF (Source Separation via Tensor and Matrix Factoriza- tion) where the data source model is obtained via non-negative factorization of a tensor composed by the collected consumption data of each electrical de- vice for a given house (prior measurements). The learned source models are used to predict the power consumption of each device over a period of time where only the whole-home electrical consumption signal (aggregated signal) is measured. The number of active appliances in a household depends on the time of day, weekday and season as wells as on personal needs, since every person has different routine habits concerning appliances’ usage. Although the electrical demand of appliances changes in accordance to consumer’s be- havior, user’s electrical consumption is strongly related to the type of the season of the year. Hence, as STMF is a supervised method, i.e. prior data is required to train the source models, its assessment on how to achieve load disaggregation for different seasons is relevant to be explored. The perfor- mance evaluation in [7] considers a real-world dataset comprising data for several households gathered during a few months. In this work instead we look at the seasonal trends in electrical consumption analysing data from only one household over a longer period of time.
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Contribution of residential wood combustion and other sources to hourly winter aerosol in Northern Sweden determined by positive matrix factorization

Contribution of residential wood combustion and other sources to hourly winter aerosol in Northern Sweden determined by positive matrix factorization

PMF is a powerful multivariate least-squares technique that constraints the solution to be non-negative and takes into account the uncertainty of the observed data (Paatero and Tapper, 1994). This method relies on the time-invariance of the source profiles and, thus, requires the emission par- ticle size distributions to be stable in the atmosphere be- tween the sources and the receptor site. According to Zhou et al. (2004), after some initial size distribution changes in the vicinity of the sources (due to coagulation and dry deposi- tion), it is reasonable to expect that particle size distributions will become relatively stable when sampling at some appro- priate distance from the emission sources.
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Rev. adm. empres.  vol.55 número5

Rev. adm. empres. vol.55 número5

Bank failures afect owners, employees, and customers, possibly causing large-scale economic dis- tress. Thus, banks must evaluate operational risks and develop early warning systems. This study investigates bank failures in the Organization for Economic Co-operation and Development, the North America Free Trade Area (NAFTA), the Association of Southeast Asian Nations, the European Union, newly industrialized countries, the G20, and the G8. We use inancial ratios to analyze and explore the appropriateness of prediction models. Results show that capital ratios, interest income compared to interest expenses, non-interest income compared to non-interest expenses, return on equity, and provisions for loan losses have signiicantly negative correlations with bank failure. However, loan ratios, non-performing loans, and ixed assets all have signiicantly positive correlations with bank failure. In addition, the accuracy of the logistic model for banks from NAFTA countries provides the best prediction accuracy regarding bank failure.
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CROSS-COUNTRY STUDY ON THE DETERMINANTS OF BANK FINANCIAL DISTRESS

CROSS-COUNTRY STUDY ON THE DETERMINANTS OF BANK FINANCIAL DISTRESS

Bank failures afect owners, employees, and customers, possibly causing large-scale economic dis- tress. Thus, banks must evaluate operational risks and develop early warning systems. This study investigates bank failures in the Organization for Economic Co-operation and Development, the North America Free Trade Area (NAFTA), the Association of Southeast Asian Nations, the European Union, newly industrialized countries, the G20, and the G8. We use inancial ratios to analyze and explore the appropriateness of prediction models. Results show that capital ratios, interest income compared to interest expenses, non-interest income compared to non-interest expenses, return on equity, and provisions for loan losses have signiicantly negative correlations with bank failure. However, loan ratios, non-performing loans, and ixed assets all have signiicantly positive correlations with bank failure. In addition, the accuracy of the logistic model for banks from NAFTA countries provides the best prediction accuracy regarding bank failure.
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Edema agudo pulmonar associado à obstrução das vias aéreas: relato de caso.

Edema agudo pulmonar associado à obstrução das vias aéreas: relato de caso.

ry of smoking 20 cigarettes a day for more than 10 years and allergy to sulfa. Physical exam, laboratory tests and chest X- ray were normal. Upon admission to the hospital there were no changes from the pre-anesthetic evaluation. In the ope- rating room, an 18G catheter was used for venipuncture in the upper limb and monitoring with pulse oximeter, non-in- vasive blood pressure and continuous electrocardiogram (EKG) on DII was initiated. Anesthesia was induced with midazolam (3 mg), fentanyl (100 µg) and propofol (100 mg). Tracheal intubation with a 7.5 ETT was facilitated by using atracurium (25 mg). Mechanical controlled ventilation was instituted with a tidal volume of 400 mL and respiratory rate adjusted by capnography. Anesthesia was maintained with 100% oxygen and enflurane. Intravenous ondansetron (4 mg) and cephalothin (1 g) were also administered. After confir- mation of moderate endometriosis the areas of endome- triosis were treated with electrofulguration and the adnexal mass was removed. The procedure lasted 3 hours without intercurrences. The patient was hydrated with Ringer’s lactate (1,500 mL) and final urine output was of 330 mL. Dypirone (2 g) and tramadol (50 mg) were administered for postoperative analgesia, 15 minutes before the end of the surgery. At the end, after reversion of the neuromuscular blockade with 0.75 mg of atropine and 1.5 mg of neostig- mine, the patient was allowed to breathe spontaneously for 5 minutes and extubated afterwards. Shortly after extubation the patient developed respiratory distress and obstruction of the airways with severe inspiratory effort and reduction in oxygen saturation to 80%. A diagnosis of laryngeal spasm was made, an oropharyngeal cannula was inserted and 100% oxygen was administered under pressure with a face mask. After the patient was stable she was transferred to the post-anesthesia recovery unit (PACU) where she received 5 L.min -1 of oxygen with a face mask and monitored with pul-
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Rev. Bras. Cir. Plást.  vol.27 número3

Rev. Bras. Cir. Plást. vol.27 número3

Background: Burn patients are initially treated with volume replacement and, impor- tantly, subsequent excision and early grafting of their injuries. These first aid measures improve the progress and survival rates of burned individuals. However, this treatment creates a new challenge in reparative surgery with regard to the management of burn sequelae, which mainly include contractures. In this study, we aimed to assess the effect of artificial dermal matrix application and negative pressure therapy on the treatment of burn sequelae. Methods: Ten patients with burn contractures were selected for this study and underwent scar contracture release, wound coverage with an artificial dermal matrix (Integra ® ), and negative pressure dressing according to the standard procedures.
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Identification and Detection of Methicillin Resistance in Non-Epidermidis Coagulase-Negative Staphylococci

Identification and Detection of Methicillin Resistance in Non-Epidermidis Coagulase-Negative Staphylococci

CTGGAACTTGTT GAGCAGAG [21]. Subsequently, 2 µL of bacterial DNA was added to the PCR tube, followed by 23 µL mixture containing 0.2 mM of each of the deoxynucleoside triphosphates (dNTPs), 1 X PCR buffer [20 mM Tris-HCl, 50 mM KCl (pH 8,4)], 1.0 U of Taq polymerase (Invitrogen, Carlsbad, USA), 1.5 mM MgCl 2 ; and 0.2 µM/µL of each primer. PCR was performed under the following conditions: initial denaturation for 2 min at 95°C, followed by 35 cycles of amplification: denaturation at 95°C for 20s, annealing at 53°C for 30s, extension at 72°C for 40s and a final extension step at 72° for 10 min, using a PTC 200 thermocycler (MJ Research, GMI, Minnesota, USA). A positive result was indicated by the presence of a 310-bp amplified DNA fragment when compared with a 100-bp DNA ladder (Invitrogen, Carlsbad, USA). The DNA fragment was revealed by electrophoresis on 1.5% agarose gel, staining with ethidium bromide, and visualization under ultraviolet light. Quality control was performed with S. aureus ATCC 25923 (mecA-negative) and S. aureus ATCC 33591 (mecA positive).
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Comprehensive factorization and I-central extensions

Comprehensive factorization and I-central extensions

Recall that a category E is regular [ 1] when regular epimorphisms are stable under pullbacks and any effective equivalence relation (i.e. which is the kernel equivalence relation of some map) admits a quotient. Regular categories are also characterized by the existence of a pullback-stable (regular epimorphism, monomorphism) factorization system. Let us begin by recalling a well-known theorem:

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Frames and factorization of graph Laplacians

Frames and factorization of graph Laplacians

Continuing earlier work [13,17,19–22,28] on analysis and spectral theory of infinite connected network-graphs G = (V, E), V for vertices, and E for edges, we study here a new factorization for the associated graph Laplacians. Our starting point is a fixed conductance function c for G. It is known that, to every prescribed conductance function c on the edges E of G, there is an associated pair (H E , ∆) where H E in an

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The influence of foreign equity and board membership on corporate strategy and management of internal costs in Portuguese banks

The influence of foreign equity and board membership on corporate strategy and management of internal costs in Portuguese banks

consequently, improvements in organizational structure and operational efficiency. Unlike foreign equity, foreign board membership has a positive influence on total costs. One possible explanation is that foreign board members may be more costly to hire. Furthermore, most of the foreign board member variables are negatively related to interest margin and positively related to non-interest margin. This supports the idea that foreign directors bring new perspectives to the domestic banking activity reducing their dependence on traditional areas of business as they seek other sources of business. Finally, our results indicate that presence of a foreign president
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Arq. Bras. Cardiol.  vol.90 número3

Arq. Bras. Cardiol. vol.90 número3

Thus, it seems clear that in women, in patients with no structural heart disease, and in those who were not taking negative chronotropic medication, the 3-second cut-off point is appropriate. In these individuals, the cardioinhibitory response to CSM was a specific finding for the etiologic diagnosis of syncope or falls in the preceding year (Table 3).

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Phenotypes of non-attached Pseudomonas aeruginosa aggregates resemble surface attached biofilm.

Phenotypes of non-attached Pseudomonas aeruginosa aggregates resemble surface attached biofilm.

To test whether the increased tolerance of aggregates is reversible (e.g. caused by physiology in the aggregate), we treated the aggregates with tobramycin for 24-h and subsequently disrupted the aggregates (Figure 6) mechanically prior to a second, 24-h antibiotic treatment. The second round of antibiotic treatment killed all bacteria from the disrupted aggregates in a time dependent manner (Cuzick’s test of trend p ,0.0001), e.g. extended periods of mixing/biofilm-disruption increased the extent of antibiotic tobramycin mediated killing. We found the increased killing to be significant (Kruskal-Wallis with Dunn’s post test: P ,0.05 when compared to 0 seconds) after 30 seconds of whirly mix. These results indicate that the capacity of the aggregates to cope with exposure to tobramycin treatment is reversible and thus likely to be caused by the immediate physiological state and/or the presence of particular matrix components in the aggregates rather than being caused by mutations leading to resistance. This is not surprising, since penetration of tobramycin into P. aeruginosa colony biofilms has been shown to be impeded and that breaking up of the biofilm cells restored their antibiotic sensitivity [28]. This emphasizes the apparent similarities between surface attached biofilms and aggregates. On the other hand, mechanical disruption of the Figure 1. SEM survey of different P. aeruginosa cultures. SEM of A – Aggregate harvested from a 48-h old stationary culture. B – Details of a 3- day old biofilm grown in flow-cell. C – Details of 48-h old stationary aggregate. D – Planktonic cells (OD 600 = 0.5). Note that the single planktonic cells
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Influência do diabetes tipo 1 no reparo de lesões produzidas por implantes intraperitoneais e subcutâneos em ratos wistar

Influência do diabetes tipo 1 no reparo de lesões produzidas por implantes intraperitoneais e subcutâneos em ratos wistar

Implantation of synthetic matrices and biomedical devices in diabetic individuals has become a common procedure to repair and/or replace biological tissues. However, an adverse foreign body reaction that invariably occurs adjacent to implant devices impairing their function is poorly characterized in the diabetic environment. We investigated the influence of this condition on the abnormal tissue healing response in implants placed subcutaneously in normglycemic and streptozotocin-induced diabetes in rats. In polyether-polyurethane sponge discs removed 10 days after implantation, the components of the fibrovascular tissue (angiogenesis, inflammation, fibrogenesis, and apoptosis) were assessed. Intra-implant levels of hemoglobin and vascular endothelial growth factor were not different after diabetes when compared with normglycemic counterparts. However, there were a lower number of vessels in the fibrovascular tissue from diabetic rats when compared with vessel numbers in implants from non-diabetic animals. Overall, the inflammatory parameters (neutrophil accumulation - myeloperoxidase activity, tumor necrosis factor alpha, and monocyte chemotactic protein-1 levels and mast cell counting) increased in subcutaneous implants after diabetes induction. However, macrophage activation (N-acetyl- β-D-glucosaminidase activity) was lower in implants from diabetic rats when compared with those from normoglycemic animals. All fibrogenic markers (transforming growth factor beta 1 levels, collagen deposition, fibrous capsule thickness, and foreign body giant cells) decreased after diabetes, whereas apoptosis (TUNEL) increased. Our results showing that hyperglycemia down regulates the main features of the foreign body reaction induced by subcutaneous implants in rats may be relevant in understanding biomaterial integration and performance in diabetes.
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Adaptation to High Grain Diets Proceeds Through Minimal Immune System Stimulation and Differences in Extracellular Matrix Protein Expression in A Model of Subacute Ruminal Acidosis in Non-lactating Dairy Cows

Adaptation to High Grain Diets Proceeds Through Minimal Immune System Stimulation and Differences in Extracellular Matrix Protein Expression in A Model of Subacute Ruminal Acidosis in Non-lactating Dairy Cows

Although many disorders affecting cattle are well characterized, the biochemical pathways responsible for the various etiologies are not. By studying these pathways, we can better understand the biochemical and perhaps the genetic factors that lead to disorders such as SARA. Currently it is not known whether changes in rumen integrity are the result of immune- mediated events or due to other changes in gene expression. However, it has been known for some time that increases in grain intake lead to a large and sudden increase in ruminal gram negative bacterial load (Motoi et al., 1993). The harder to digest saccharides derived from cellulose-based HF diets is a less preferred substrate than the more bioavailable sugars derived from fermentable HG diets for bacteria. As obligate anaerobes, gram negative bacteria such as E. coli thrive under these conditions. As a result, lipopolysaccharide (LPS) levels, derived and shed from the cell walls of such bacteria, significantly increase both in the rumen and in the systemic circulation (Motoi et al., 1993). Increases in acidity, coupled with LPS work together to damage the rumen, cause the initial local inflammatory reaction (Gozho et al., 2005) and initiate an immune-mediated cascade that will eventually lead to antigen clearance, ruminal wound healingand the reestablishment of metabolic homeostasis (Thibault et al., 2010).
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Toward the Application of Three-Dimensional Approach to Few-body Atomic Bound States

Toward the Application of Three-Dimensional Approach to Few-body Atomic Bound States

Abstract. The first step toward the application of an effective non partial wave (PW) numerical approach to few-body atomic bound states has been taken. The two-body transition amplitude which appears in the kernel of three-dimensional Faddeev-Yakubovsky integral equations is calculated as function of two-body Jacobi momen- tum vectors, i.e. as a function of the magnitude of initial and final momentum vectors and the angle between them. For numerical calculation the realistic interatomic interactions HFDHE2, HFD-B, LM2M2 and TTY are used. The angular and momentum dependence of the fully off-shell transition amplitude is studied at negative energies. It has been numerically shown that, similar to the nuclear case, the transition amplitude exhibits a characteristic angular behavior in the vicinity of 4 He dimer pole.
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Life History Strategy and Young Adult Substance Use

Life History Strategy and Young Adult Substance Use

Our study contained several skewed variables that violated the normality assumption of our imputation model. While this isn’t ideal in theory, the methods literature indicates that in the context of ordinal variables and skew, multiple imputation under a normal model preserves important characteristics of the data set as a whole (e.g., variances) and makes use of all possible information (Enders, 2010; von Hippel, 2013). The idea is that although the imputed values do not look like the observed values, the imputed variable behaves like the observed variable in the analysis. One strategy that has been recommended for satisfying the normality assumption of imputation models is the transformation of skewed variables prior to imputation. However, research suggests this actually hurts the imputation of variables that are linearly related because it introduces non-linearity and residual non- normality (von Hippel, 2013). Although transformations help match variables’ marginal distributions to th e imputation model’s assumptions, they create problems with the effects between variables and can skew residuals, which together lead to imputed values that bias estimates in the analysis phase. In this study, we chose multiple imputation under a normal model and imputed skewed variables as they were, given that this method is robust to departures from normality assumptions and produces reasonably unbiased parameter estimates that reflect the uncertainty associated with estimating missing data (Enders, 2010; Little and Rubin, 2002; von Hippel, 2013).
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An algorithm for SDV representation of 2D Behaviors

An algorithm for SDV representation of 2D Behaviors

It is a well-known fact that every 2D L-polynomial matrix can be factored as a product of three matrices: a factor right prime matrix by a square non-singular matrix by a factor left prime matrix. We will show that SDV-representable behaviors are exactly the ones for which this decomposition of its kernel representations yields factorizations where the factor right matrix is indeed a zero right prime and the square matrix has cw-unital determinant. This result provides a way of deciding whether or not a kernel behavior is SDV- representable using any of its kernel representations.
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Luis Felipe Reis, Túlio Galvão Ventura, Sônia Oliveira Souza, Arturo Arana- Pino, Marcelo Pelajo-Machado, Mario José S Pereira, Henrique Leonel Lenzi, Maria José Conceição, Christina Maeda Takiya

Luis Felipe Reis, Túlio Galvão Ventura, Sônia Oliveira Souza, Arturo Arana- Pino, Marcelo Pelajo-Machado, Mario José S Pereira, Henrique Leonel Lenzi, Maria José Conceição, Christina Maeda Takiya

Liver fibrosis is a complex process due to in- creased synthesis and deposition of extra cellular matrix components (Schuppan et al. 1993). Our re- sults demonstrate that PTX, despite its negative effect on extracellular matrix protein synthesis, re- duction of hepatic stellate cells (Pinzani et al. 1996) myofibroblast proliferation (Windmeier & Gressner 1996), and inhibition of platelet-derived growth fac- tor-driven proliferation of fibroblats (Peterson 1993), did not affect collagen deposition inside murine hepatic S. mansoni granulomas. This lack of effect on collagen synthesis is probably due, in part, to the fact that the drug was administered after granu- lomas elicitation, when immune competent cells were already stimulated. The decrease in the total number of hepatic granulomas could be due to some toxic effect of the drug on egg release and/or adult worm fecundity (the effect of PTX on adult worm morphology and fecundity is being analyzed). Fur- thermore, the decrease in the number of involutive granulomas could be paradoxically explained by PTX collagenase stimulation, an aspect already demonstrated by Berman and Duncan (1990), ac- celerating the time of granuloma disappearance. In fact, PTX can also markedly reduce the expression of the tissue inhibitor of metalloproteinase 1 (TIMP- 1) mRNA (Romanelli et al. 1997). According to these authors, the antifibrogenic action of PTX on hu- man hepatic stellate cells in response to transform- ing growth factor-beta 1 (TGF β1) is mainly medi- ated by extracellular collagen degradation rather than by a reduction of collagen synthesis.
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A Parallel Processing Algorithms for Solving Factorization and Knapsack Problems

A Parallel Processing Algorithms for Solving Factorization and Knapsack Problems

Quantum and Evolutionary computation are new forms of computing by their unique paradigm for designing algorithms.The Shor’s algorithm is based on quantum concepts such as Qubits, sup[r]

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