Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast Nonnegative Matrix Factorization: An Active-Set-Like Method and Comparisons

Nonnegative matrix factorization (NMF) is a dimension reduction method that has been widely used for numerous applications, including text mining, computer vision, pattern discovery, and bioinformatics. A mathematical formulation for NMF appears as a nonconvex optimization problem, and various types of algorithms have been devised to solve the problem. The alternating nonnegative least squares (ANLS) framework is a block coordinate descent approach for solving NMF, which was recently shown to be theoretically sound and empirically efficient. In this paper, we present a novel algorithm for NMF based on the ANLS framework. Our new algorithm builds upon the block principal pivoting method for the nonnegativity-constrained least squares problem that overcomes a limitation of the active set method. We introduce ideas that efficiently extend the block principal pivoting method within the context of NMF computation. Our algorithm inherits the convergence property of the ANLS framework and can easily be extended to other constrained NMF formulations. Extensive computational comparisons using data sets that are from real life applications as well as those artificially generated show that the proposed algorithm provides state-of-the-art performance in terms of computational speed.
Meiotic nuclear movements in fission yeast are regulated by the transcription factor Mei4 downstream of a Cds1-dependent replication checkpoint pathway

In meiosis, the fission yeast nucleus displays an elongated morphology, moving back and forth within the cell; these nuclear movements continue for approximately 2 h before meiotic nuclear divisions. Meiotic DNA replication occurs in an early phase of the nuclear movements and is followed by meiotic prophase. Here we report that in mutants deficient in meiotic DNA replication, the duration of nuclear movements is strikingly prolonged to four to 5 h. We found that this prolongation was caused by the Cds1‐dependent replication checkpoint, which represses expression of the mei4+ gene encoding a meiosis‐specific transcription factor. In the absence of Mei4, nuclear movements persisted for more than 8 h. In contrast, overproduction of Mei4 accelerated termination of nuclear movements to approximately 30 min. These results show that Mei4 is involved in the termination of nuclear movements and that Mei4‐mediated regulatory pathways link a DNA replication checkpoint to the termination of nuclear movements.
Hyperinsulinemia and the Aldosterone and Pressor Responses to Angiotensin II

To determine whether hyperinsulinemia alters angiotensin II-medlated aldosterone secretion, the increase in plasma aldosterone after intravenous angiotensin II (5, 10, and 20 ng/kg/min for 15 minutes each) was measured before and after euglycemic hyperinsulinemia in seven chronically instrumented dogs. In a random sequence on 4 successive days, dogs received either 0, 2, 4, or 8 milllunits/kg/min insulin. Euglycemic hyperinsulinemia, at all insulin doses, resulted in a significantly greater (p < 0.01) change in the angiotensin U-stimulated increments of plasma aldosterone than was observed when angiotensin II was administered alone. However, there was no dose-dependence of insulin's effect on angiotensin H-stimulated aldosterone. The effect of weight gain on the angiotensin II response was also evaluated in five dogs. After weight gain, euglycemic hyperinsulinemia augmented angiotensin H-stimulated aldosterone to the same magnitude that was observed before weight gain. Possible mechanisms whereby insulin could increase angiotensin II-stimulated aldosterone production include: increased intracellular potassium, reduced plasma free fatty acids, and a direct action of insulin to induce increased adrenal steroidogenesis. In addition to altering the angiotensin II-aldosterone dose-response curve, hyperinsulinemia also increased the pressor action of angiotensin II. In contrast to the angiotensin II-aldosterone response, progressive hyperinsulinemia resulted in a progressive increase in the pressor response to angiotensin II. The increased pressor response is probably due to an increased activation of the sympathetic nervous system by insulin.
A Dynamic Prioritized Load Balanced Round Robin Elasticity Mechanism on Cloud Mobile Services

- Cloud mobile applications assure flexible services to several business customer requirements which are isolated from the infrastructure form. However, elastic application is not effective on the transparent use of cloud mobile resources where the components are rearranged based on the workload of business logic. While public cloud integrates all the resource strategies on scientific workloads, the CPU load is raised and is not effective in solving the optimization problem in various elasticity cloud applications. In this work to reduce the CPU load in the cloud elasticity environment, Dynamic Prioritized Load Balanced Round Robin (DP-LBRR) framework is constructed. The Load Balanced Round Robin (LBRR) algorithm in DP-LBRR framework mainly focused on distributing the load to the CPU aiming at balancing the CPU load rate. The CPU in turn executes different types of requests from various cloud mobile environments by allocating each virtual machine in a cyclic order with the objective of reducing the latency time. The LBRR algorithm added a Dynamic Priority Load Scheduler into the system for reducing the memory consumption and solves the optimization problem in the elasticity cloud services using priority value. The priority value in the Dynamic Prioritized Load Balanced Round Robin framework is evaluated based on the active priority concept aiming at reducing the memory consumption. The active priority finds the maximum and the next maximum priority nodes for easy scheduling in the cloud mobile environments and therefore improving the efficiency of scheduling the tasks in the elasticity cloud services. Experimental results demonstrate that the proposed framework achieves better performance by improving the scheduling efficiency and balances the CPU load rate compared to the state-of-the-art works.
Clinical Practice Guidelines for Pediatric Appendicitis Evaluation Can Decrease Computed Tomography Utilization While Maintaining Diagnostic Accuracy

Objectives The objective of this study was to compare usage of computed tomography (CT) scan for evaluation of appendicitis in a children’s hospital emergency department before and after implementation of a clinical practice guideline focused on early surgical consultation before obtaining advanced imaging. Methods A multidisciplinary team met to create a pathway to formalize the evaluation of pediatric patients with abdominal pain. Computed tomography scan utilization rates were studied before and after pathway implementation. Results Among patients who had appendectomy in the year before implementation (n = 70), 90% had CT scans, 6.9% had ultrasound, and 5.7% had no imaging. The negative appendectomy rate before implementation was 5.7%. In patients undergoing appendectomy in the postimplementation cohort (n = 96), 48% underwent CT, 39.6% underwent ultrasound, and 15.6% had no imaging. The negative appendectomy rate was 5.2%. We demonstrated a 41% decrease in CT use for patients undergoing appendectomy at our institution without an increase in the negative appendectomy rate or missed appendectomy. The results were even more striking when comparing the rate of CT scan use in the subset of patients undergoing appendectomy without imaging from an outside hospital. In these patients, CT scan utilization decreased from 82% to 20%, a 76% reduction in CT use in our facility after protocol implementation. Conclusions Implementation of a clinical evaluation pathway emphasizing examination, early surgeon involvement, and utilization of ultrasound as the initial imaging modality for evaluation of abdominal pain concerning for appendicitis resulted in a marked decrease in the reliance on CT scanning without loss of diagnostic accuracy.
Institute for Mathematical Physics Geometric Modular Action and Spacetime Symmetry Groups Geometric Modular Action and Spacetime Symmetry Groups

A condition of geometric modular action is proposed as a selection principle for physically interesting states on general space-times. This condition is naturally associated with transformation groups of partially ordered sets and provides these groups with projective representations. Under suitable additional conditions, these groups induce groups of point transformations on these space-times, which may be interpreted as symmetry groups. The consequences of this condition are studied in detail in application to two concrete space-times { four-dimensional Minkowski and three-dimensional de Sitter spaces { for which it is shown how this condition characterizes the states invariant under the respective isometry group. An intriguing new algebraic characterization of vacuum states is given. In addition, the logical relations between the condition proposed in this paper and the condition of modular covariance, widely used in the literature, are completely illuminated.
Rescaled Lotka–Volterra models converge to super-Brownian motion

We show that a sequence of stochastic spatial Lotka-Volterra models, suitably rescaled in space and time, converges weakly to super-Brownian motion with drift. The result includes both long range and nearest neighbor models, the latter for dimensions three and above. These theorems are special cases of a general convergence theorem for perturbations of the voter model.
Axiomatizing complete positivity

There are two ways to turn a categorical model for pure quantum theory into one for mixed quantum theory, both resulting in a category of completely positive maps. One has quantum systems as objects, whereas the other also allows classical systems on an equal footing. The former has been axiomatized using environment structures. We extend this axiomatization to the latter by introducing decoherence structures.
Finding Non-Arbitrary Form-Meaning Systematicity Using String-Metric Learning for Kernel Regression

Arbitrariness of the sign—the notion that the forms of words are unrelated to their meanings—is an underlying assumption of many linguistic theories. Two lines of research have recently challenged this assumption, but they produce differing characterizations of non-arbitrariness in language. Behavioral and corpus studies have conﬁrmed the validity of localized form-meaning patterns manifested in limited subsets of the lexicon. Meanwhile, global (lexicon-wide) statistical analyses instead ﬁnd diffuse form-meaning system-aticity across the lexicon as a whole. We bridge the gap with an approach that can detect both local and global form-meaning systematicity in language. In the kernel regression formulation we introduce, form-meaning relationships can be used to predict words’ distributional semantic vectors from their forms. Furthermore, we introduce a novel metric learning algorithm that can learn weighted edit distances that minimize kernel regression error. Our results suggest that the English lexicon exhibits far more global form-meaning systematicity than previously discovered, and that much of this systematicity is focused in localized form-meaning patterns.
Transient Outward Current Carried by Potassium and Sodium in Quiescent Atrioventricular Node Cells of Rabbits

Single atrioventricular node cells were dispersed by treating the rabbit heart with collagenase. In Tyrode's solution, the cells became rounded, and about 20% of them showed spontaneous activity, whereas the rest remained quiescent. When those quiescent cells were whole-cell clamped, depolarizing clamp pulses from the holding potential of −83 mV induced an outward current which decayed quickly, with a time course similar to that of the transient outward current in the Purkinje fiber. The amplitude of the current became larger when progressively more positive clamp pulses were given from a very negative holding potential. The inactivation time course of this current consisted of two exponential components. Single-channel current recordings from those cells revealed a class of channels that activated more frequently during the initial part of depolarizing pulses. Summation of those unitary currents reproduced activation and inactivation time courses of the macroscopic current well, suggesting that this channel corresponds to the transient outward current. The current-voltage relationship of the channel was linear with the slope conductance of 19.9 ± 1.8 pS (n = 7), and the reversal potential was near the resting potential of the atrioventricular node cell with 5.4 mM potassium chloride and 134.6 mw sodium chloride in the pipette. The channel was passing mainly potassium ions, but sodium ions also seemed to carry a fraction of the current. The possible role of the transient outward current in the quiescent node cell is discussed.
SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations

Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 104–106 RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (107–108 RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts.
Influenza Virus Reassortment Occurs with High Frequency in the Absence of Segment Mismatch

Reassortment is fundamental to the evolution of influenza viruses and plays a key role in the generation of epidemiologically significant strains. Previous studies indicate that reassortment is restricted by segment mismatch, arising from functional incompatibilities among components of two viruses. Additional factors that dictate the efficiency of reassortment remain poorly characterized. Thus, it is unclear what conditions are favorable for reassortment and therefore under what circumstances novel influenza A viruses might arise in nature. Herein, we describe a system for studying reassortment in the absence of segment mismatch and exploit this system to determine the baseline efficiency of reassortment and the effects of infection dose and timing. Silent mutations were introduced into A/Panama/2007/99 virus such that high-resolution melt analysis could be used to differentiate all eight segments of the wild-type and the silently mutated variant virus. The use of phenotypically identical parent viruses ensured that all progeny were equally fit, allowing reassortment to be measured without selection bias. Using this system, we found that reassortment occurred efficiently (88.4%) following high multiplicity infection, suggesting the process is not appreciably limited by intracellular compartmentalization. That co-infection is the major determinant of reassortment efficiency in the absence of segment mismatch was confirmed with the observation that the proportion of viruses with reassortant genotypes increased exponentially with the proportion of cells co-infected. The number of reassortants shed from co-infected guinea pigs was likewise dependent on dose. With 106 PFU inocula, 46%–86% of viruses isolated from guinea pigs were reassortants. The introduction of a delay between infections also had a strong impact on reassortment and allowed definition of time windows during which super-infection led to reassortment in culture and in vivo. Overall, our results indicate that reassortment between two like influenza viruses is efficient but also strongly dependent on dose and timing of the infections.
Reliability of cognitive tests of ELSA-Brasil, the brazilian longitudinal study of adult health

Cognitive function evaluation entails the use of neuropsychological tests, applied exclusively or in sequence. The results of these tests may be influenced by factors related to the environment, the interviewer or the interviewee. OBJECTIVES We examined the test-retest reliability of some tests of the Brazilian version from the Consortium to Establish a Registry for Alzheimer's disease. METHODS The ELSA-Brasil is a multicentre study of civil servants (35-74 years of age) from public institutions across six Brazilian States. The same tests were applied, in different order of appearance, by the same trained and certified interviewer, with an approximate 20-day interval, to 160 adults (51% men, mean age 52 years). The Intraclass Correlation Coefficient (ICC) was used to assess the reliability of the measures; and a dispersion graph was used to examine the patterns of agreement between them. RESULTS We observed higher retest scores in all tests as well as a shorter test completion time for the Trail Making Test B. ICC values for each test were as following: Word List Learning Test (0.56), Word Recall (0.50), Word Recognition (0.35), Phonemic Verbal Fluency Test (VFT, 0.61), Semantic VFT (0.53) and Trail B (0.91). The Bland-Altman plot showed better correlation of executive function (VFT and Trail B) than of memory tests. CONCLUSIONS Better performance in retest may reflect a learning effect, and suggest that retest should be repeated using alternate forms or after longer periods. In this sample of adults with high schooling level, reliability was only moderate for memory tests whereas the measurement of executive function proved more reliable.
Multi-armed bandit for LTE-U and WiFi coexistence in unlicensed bands

In order to cope with the phenomenal growth of mobile data traffic, unlicensed spectrum can be utilized by the Long Term Evolution (LTE) cellular systems. However, ensuring fair coexistence with Wi-Fi is a mandatory requirement. In one approach, periodically configurable transmission gaps can be used to facilitate a coexistence between WiFi and LTE. In this paper, a Multi-Armed Bandit (MAB) based dynamic duty cycle selection method is proposed for configuration of transmission gaps ensuring a better coexistence for both technologies. Then the concept is further strengthened with downlink power control mechanism using the same algorithm leading to a high energy efficiency and interference reduction. Performance results are given for different user equipment and WiFi station densities in which it is shown that significant improvements in overall throughput and energy efficiency can be achieved.
Variation in Resistance of Mycobacterium paratuberculosis to Acid Environments as a Function of Culture Medium

ABSTRACT Acid resistance of Mycobacterium paratuberculosis was examined as a function of growth conditions (i.e., in vitro growth medium and pH). M. paratuberculosis was cultured in either fatty acid-containing medium (7H9-OADC) or glycerol-containing medium (WR-GD or 7H9-GD) at two culture pHs (pHs 6.0 and 6.8). Organisms produced in these six medium and pH conditions were then tested for resistance to acetate buffer at pHs 3, 4, 5, and 6 at 20°C. A radiometric culture method (BACTEC) was used to quantify viable M. paratuberculosis cell data at various acid exposure times, and D values (decimal reduction times, or the times required to kill a 1-log10 concentration of bacteria) were determined. Soluble proteins of M. paratuberculosis grown under all six conditions were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to identify proteins that may be associated with acid resistance or susceptibility. The culture medium affected growth rate and morphology: thin floating sheets of cells were observed in 7H9-OADC versus confluent, thick, waxy, and wrinkled pellicles in WR-GD. Culture medium pH affected growth rate (which was highest at pH 6.0), but it had little or no effect on D values for M. paratuberculosis at any test pH. When grown in 7H9-OADC, M. paratuberculosis was more acid resistant at all test pHs (higher D values) than when grown in WR-GD. Glycerol appeared to be the culture medium component most responsible for lower levels of M. paratuberculosis acid resistance. When glycerol was substituted for OADC in the 7H9 medium, D values were significantly lower than those of 7H9-OADC-grown M. paratuberculosis and were approximately the same as those for M. paratuberculosis grown in WR-GD medium. Comparison of the SDS-PAGE protein profiles for M. paratuberculosis cultures grown in 7H9-OADC, WR-GD, or 7H9-GD medium revealed that increased expression of 34.2- and 14.0-kDa proteins was associated with higher levels of acid resistance of M. paratuberculosis grown in 7H9-OADC medium and that 56.6- and 41.3-kDa proteins were associated with lower levels of acid resistance. This is the first report showing that in vitro culture conditions significantly affect growth characteristics, acid resistance, and protein expression of M. paratuberculosis, and the results emphasize the importance of culture conditions for in vitro susceptibility studies.