Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient Growth and Optimal Excitation of Thermohaline Variability

The physical mechanisms of transient amplification of initial perturbations to the thermohaline circulation (THC), and of the optimal stochastic forcing of THC variability, are discussed using a simple meridional box model. Two distinct mechanisms of transient amplification are found. One such mechanism, with a transient amplification timescale of a couple of years, involves an interaction between the THC induced by rapidly decaying sea surface temperature anomalies and the THC induced by the slower-decaying salinity mode. The second mechanism of transient amplification involves an interaction between different slowly decaying salinity modes and has a typical growth timescale of decades. The optimal stochastic atmospheric forcing of heat and freshwater fluxes are calculated as well. It is shown that the optimal forcing induces low-frequency THC variability by exciting the salinity-dominated variability modes of the THC.
A systematic review of the management of acute pyogenic flexor tenosynovitis

Pyogenic flexor tenosynovitis (PFT) is an aggressive closed-space infection that can result in severe morbidity. Although surgical treatment of pyogenic flexor tenosynovitis has been widely described, the role of antibiotic therapy is inadequately understood. We conducted a literature review of studies reporting on acute pyogenic flexor tenosynovitis management. A total of 28 case series articles were obtained, all of which used surgical intervention with varied use of antibiotics. Inconsistencies among the studies limited summative statistical analysis. Our results showed that use of antibiotics as a component of therapy resulted in improved range of motion outcomes (54% excellent vs. 14% excellent), as did using catheter irrigation rather than open washout (71% excellent vs. 26% excellent). These studies showed benefits of early treatment of pyogenic flexor tenosynovitis and of systemic antibiotic use. As broad-spectrum antibiotics have changed the management of other infectious conditions, we must more closely evaluate consistent antibiotic use in pyogenic flexor tenosynovitis management. Level of Evidence: Therapeutic, Level III
Cytokine Removal during Continuous Renal Replacement Therapy: An Ex Vivo Comparison of Convection and Diffusion

Background and objectives It is unknown whether cytokine adsorption to the membrane during continuous renal replacement therapy is affected by the technique. Such knowledge might affect the choice of technique in vivo. Accordingly, we conducted an ex vivo study to test whether continuous veno-venous hemofiltration (CVVH) or continuous veno-venous hemodialysis (CVVHD) affect cytokine adsorption differently. Setting Laboratory attached to the Intensive Care Unit of a tertiary hospital Design Six healthy human volunteers donated blood, which was incubated with endotoxin. Control blood was left at room temperature, and treatment blood was recirculated for eight hours through closed circuits using polyacrylonitrile membranes (AN69). The effect of CVVH and CVVHD on cytokine removal from the circuits was compared. Measurements The concentrations of interleukins (IL)-1ß, 6, 8, 10 and TNF were measured in the control samples, pre-and post-filter and in the effluent at baseline and hourly thereafter. The clearances by adsorption, and filtration were calculated. Results Control cytokine concentrations remained the same or increased slightly. Adsorption was the major mechanism of removal for all cytokines with the exception of IL-1ß, but the effect was short-lived. Peak adsorption generally occurred at baseline before the start of CVVH and CVVHD, with clearances ranging from 43.7ml/min (for IL-8) to 7.6ml/min (for IL-10). The time-weighted average total clearances during CVVH were 23.3, 4.3, 3.8, –2.0, and 15ml/min for IL-8, IL-1ß, TNF, IL-6, and IL-10 respectively. The corresponding clearances during CVVHD were 19.0, 10.7, 2.7, 2.4, and 0.3ml/min. IL-10 clearances were greater during CVVH than CVVHD (p=0.03). Non adsorptive CVVH clearance of IL-1ß was greater than CVVHD clearance, but this advantage was outweighed by an increased tendency of the membrane to release IL-1ß into the circuit during HF. Conclusions The technique of solute removal had only a minor effect on the magnitude of cytokine adsorption, and neither technique had the advantage for all the measured cytokines.
IL-1&bgr; Inhibits Connexin 43 and Disrupts Decidualization of Human Endometrial Stromal Cells Through ERK1/2 and p38 MAP Kinase

Inflammation can interfere with endometrial receptivity. We examined how interleukin 1β (IL-1β) affects expression of the uterine gap junction protein connexin 43 (Cx43), which is known to be critical for embryonic implantation. We used an in vitro model of human endometrial stromal cells (ESCs), Western blotting, and a combination of validated, selective kinase inhibitors to evaluate five canonical IL-1β signaling pathways. Cx43 and two other markers of ESC differentiation (prolactin and VEGF) were inhibited predominantly via IL-1β-activated ERK1/2 and p38 MAP kinase cascades. The findings were corroborated using small interfering RNA to silence critical genes in either pathway. By contrast, upregulation of endogenous pro-IL-1α and pro-IL-1β following recombinant IL-1β treatment was mediated via the Jun N-terminal kinase pathway. The clinicopharmacological significance of our findings is that multiple signaling cascades may need to be neutralized to reverse deleterious effects of IL-1β on human endometrial function.
Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs

A high-throughput peptide array approach reveals insight into kinase substrates and specificity. Exploring Kinase Selectivity Kinases are master regulators of cellular behavior. Because of the large number of kinases and the even larger number of substrates, approaches that permit global analysis are valuable tools for investigating kinase biology. Mok et al. identified the phosphorylation site selectivity for 61 of the 122 kinases in Saccharomyces cerevisiae by screening a miniaturized peptide library. By integrating these data with other data sets and structural information, they revealed information about the relationship between kinase catalytic residues and substrate selectivity. They also identified and experimentally verified substrates for kinases, including one for which limited functional information was previously available, showing the potential for this type of analysis as a launching point for the exploration of the biological functions of kinases. Phosphorylation is a universal mechanism for regulating cell behavior in eukaryotes. Although protein kinases target short linear sequence motifs on their substrates, the rules for kinase substrate recognition are not completely understood. We used a rapid peptide screening approach to determine consensus phosphorylation site motifs targeted by 61 of the 122 kinases in Saccharomyces cerevisiae. By correlating these motifs with kinase primary sequence, we uncovered previously unappreciated rules for determining specificity within the kinase family, including a residue determining P−3 arginine specificity among members of the CMGC [CDK (cyclin-dependent kinase), MAPK (mitogen-activated protein kinase), GSK (glycogen synthase kinase), and CDK-like] group of kinases. Furthermore, computational scanning of the yeast proteome enabled the prediction of thousands of new kinase-substrate relationships. We experimentally verified several candidate substrates of the Prk1 family of kinases in vitro and in vivo and identified a protein substrate of the kinase Vhs1. Together, these results elucidate how kinase catalytic domains recognize their phosphorylation targets and suggest general avenues for the identification of previously unknown kinase substrates across eukaryotes.
Bipartite graph structures for efficient balancing of heterogeneous loads

This paper considers large scale distributed content service platforms, such as peer-to-peer video-on-demand systems. Such systems feature two basic resources, namely storage and bandwidth. Their efficiency critically depends on two factors: (i) content replication within servers, and (ii) how incoming service requests are matched to servers holding requested content. To inform the corresponding design choices, we make the following contributions. We first show that, for underloaded systems, so-called proportional content placement with a simple greedy strategy for matching requests to servers ensures full system efficiency provided storage size grows logarithmically with the system size. However, for constant storage size, this strategy undergoes a phase transition with severe loss of efficiency as system load approaches criticality. To better understand the role of the matching strategy in this performance degradation, we characterize the asymptotic system efficiency under an optimal matching policy. Our analysis shows that -in contrast to greedy matching- optimal matching incurs an inefficiency that is exponentially small in the server storage size, even at critical system loads. It further allows a characterization of content replication policies that minimize the inefficiency. These optimal policies, which differ markedly from proportional placement, have a simple structure which makes them implementable in practice. On the methodological side, our analysis of matching performance uses the theory of local weak limits of random graphs, and highlights a novel characterization of matching numbers in bipartite graphs, which may both be of independent interest.
Chaotic Multidirectional Associative Memory with adaptive scaling factor of refractoriness

The association ability of neural networks composed of chaotic neuron models or chaotic neuron-based models are very sensitive to chaotic neuron parameters such as scaling factor of refractoriness α and damping factor k and so on. And, in these models, appropriate parameters have to determined by trial and error. In this research, a Chaotic Multidirectional Associative Memory with adaptive scaling factor of refractoriness which can realize one-to-many associations and whose parameters can be determined automatically is proposed. In this model, scaling factor of refractoriness α varies depends on time and internal states of neurons. We examined one-to-many associations ability of the proposed model and the Chaotic Multidirectional Associative Memory with variable scaling factor of refractoriness. And, we confirmed that one-to-many association ability of the proposed model is almost equal to that of well-tuned Chaotic Multidirectional Associative Memory with variable scaling factor of refractoriness.
Impact of selected inborn errors of metabolism on prenatal and neonatal development

In general, data regarding maturational processes of different metabolic pathways in the very vulnerable fetal and neonatal period are rare. This review is to substantiate the impact of selected inborn errors of metabolism on this critical period of life and their clinical manifestation. Significant adaptation of mitochondrial/energy‐, carbohydrate‐, lysosomal‐, and amino acid‐metabolism occurs during early prenatal and neonatal development. In utero, metabolic environment has an impact on the development of the fetus as well as fetal organ maturation. Defects of distinct metabolic pathways could therefore already be of significant relevance in utero and for clinical manifestations in the early fetal and neonatal period. Disturbances of these pathways may influence intrauterine growth and health. Production of a toxic intrauterine milieu, energy‐deficiency, modification of membrane function, or disturbance of the normal intrauterine expression of genes may be responsible for fetal compromise and developmental disorders. Three categories of metabolic disorders will be discussed: the “intoxication type” (classical galactosemia, ornithine transcarbamylase deficiency, and “maternal phenylketonuria”), the “storage type” (Morbus Niemann Pick type C), and the “energy deficient type” (including long‐chain fatty acid oxidation disorders, pyruvate dehydrogenase deficiency, and respiratory chain defects). For these disorders, the pathophysiology of early manifestation, special aspects regarding the prenatal and neonatal period, and diagnostic as well as therapeutic options are presented. © 2010 IUBMB IUBMB Life, 62(6): 403–413, 2010
Simple Syntactic and Morphological Processing Can Help English-Hindi Statistical Machine Translation

In this paper, we report our work on incorporating syntactic and morphological information for English to Hindi statistical machine translation. Two simple and computationally inexpensive ideas have proven to be surprisingly effective: (i) reordering the English source sentence as per Hindi syntax, and (ii) using the suffixes of Hindi words. The former is done by applying simple transformation rules on the English parse tree. The latter, by using a simple suffix separation program. With only a small amount of bilingual training data and limited tools for Hindi, we achieve reasonable performance and substantial improvements over the baseline phrase-based system. Our approach eschews the use of parsing or other sophisticated linguistic tools for the target language (Hindi) making it a useful framework for statistical machine translation from English to Indian languages in general, since such tools are not widely available for Indian languages currently.
Mixed-Mode Fracture of Uniaxial Fiber Reinforced Composites.

Abstract : Mixed-mode matrix fracture in notched off-axis undirectional composite is investigated. First the problem is treated by an exact formulation based on elastic fracture mechanics. It is then simulated by a finite element model. Correlation with experiment suggests a fracture criterion based on total strain energy release rate as the fracture parameter. Keywords: Composite material, Graphite epoxy, Mixed mode fracture matrix cracking, Singular integral equation, Finite element simulation, Experiment analysis correlation.
Construction of invariant families of sets for linear systems with delay

Synthesis methods for the construction of invariant sets for delay difference equations (DDEs) suffer either from computational complexity, i.e., those based on the Krasovskii approach, or come with considerable conservatism, i.e., those based on the Razumikhin approach. This paper utilizes the concepts of vector Lyapunov functions and set-dynamics in order to introduce a novel notion of invariance for linear DDEs, termed the invariant family of sets. The proposed concept of an invariant family of sets allows for a suitable trade-off between computational simplicity and conceptual generality. In addition, it reduces the stability analysis for a DDE to the stability analysis for a relatively simple comparison system. The practical implementation for families of ellipsoidal sets proposed in this paper leads to synthesis algorithms that can be realized by solving a sequence of linear matrix inequalities.
Sewage sludge nutrient solubilization using a single-stage microwave treatment

The effects of an advanced oxidation process combining microwave, hydrogen peroxide and acid hydrolysis in a single stage (MW/H2O2/H+-AOP) on the process efficiency of sewage sludge treatment and nutrient recovery were investigated. At lower temperature regimes (60–80°C), the soluble phosphate was substantially higher in a two-stage process than in a single stage MW/H2O2/H+-AOP process. However, higher soluble phosphate concentration was obtained for single-stage treatment at the higher operating temperature regimes (100–120°C). With the addition of an inorganic acid, a very high yield of soluble phosphate was obtained in the solution at 120°C. In tests with acid addition, soluble ammonia increased as temperature increased. For single stage MW/H2O2/H+-AOP, maximum soluble ammonia was obtained at 120°C. Significant concentrations of soluble COD were also obtained in this treatment. A threshold temperature of 80°C was observed, at which all of the COD could be solubilized. However, at higher temperatures (100–120°C), further oxidation processes occurred to form carbon dioxide, resulting in decreased amounts of soluble COD in the solution.
Burden of acute gastroenteritis and healthcare-seeking behaviour in France: a population-based study

SUMMARY In France surveillance underestimates the true burden of acute gastroenteritis (AG). We conducted a population-based, retrospective cross-sectional telephone survey between May 2009 and April 2010 in order to obtain more accurate estimates of the incidence and the burden of AG and to describe healthcare-seeking behaviour for AG. Of the 10 080 persons included in the survey, 260 respondents reported 263 episodes of AG. The incidence rate of AG was estimated at 0·33 cases/person-year (95% CI 0·28–0·37). It was highest in children aged <5 years and declined with age. Thirty-three percent (95% CI 27–40) of the AG cases consulted a physician and 76% (95% CI 70–82) used medication. Our results indicate that there are more than 21 million episodes of AG each year in France. These results allow a more accurate interpretation of the data derived from existing AG surveillance systems.
Pain Assessment of Children with Autism Spectrum Disorders

Objective: Pain assessment of individuals with autism spectrum disorder (ASD) is largely unexplored. The core deficits of ASD may interfere with this population's ability to effectively use traditional pain assessment tools. Accurate pain assessment is essential to providing quality care. The objective was to illuminate barriers to pain assessment in children with an ASD, describe novel methods to communicate about their pain experience, and identify vocabularies that hold meaning with respect to pain to better understand pain from their context. Methods: Qualitative descriptive study using semistructured interviews including interactive electronic technology to enhance communication. Subjects included children aged 6 to 17 years with ASD experiencing acute pain after a surgical procedure at a large urban tertiary children's hospital. Results: Based on the analysis of 40 interviews, participants consisted of 34 (85%) male, 29 (72.5%) non-Hispanic white with mean age 11.75 ± 3.36 years (range: 6–17). All subjects were able to describe and locate their pain but required a variety of approaches. Assessment preferences included minimal time spent focusing on pain and simplistic language and actions using terms familiar to each subject. Notably, subjects were able to reliably demonstrate understanding of graded response and seriation. Parent involvement was essential, both in helping interpret the child's needs and providing trusted support. Conclusions: Some children with ASD require an alternate interactive approach to pain assessment. Individualized consideration and estimation of pain assessment methods for use in this population may provide more meaningful interactions, ultimately guiding better pain management interventions.
Rapid Multi-Locus Sequence Typing Using Microfluidic Biochips

Background Multiple locus sequence typing (MLST) has become a central genotyping strategy for analysis of bacterial populations. The scheme involves de novo sequencing of 6–8 housekeeping loci to assign unique sequence types. In this work we adapted MLST to a rapid microfluidics platform in order to enhance speed and reduce laboratory labor time. Methodology/Principal Findings Using two integrated microfluidic devices, DNA was purified from 100 Bacillus cereus soil isolates, used as a template for multiplex amplification of 7 loci and sequenced on forward and reverse strands. The time on instrument from loading genomic DNA to generation of electropherograms was only 1.5 hours. We obtained full-length sequence of all seven MLST alleles from 84 representing 46 different Sequence Types. At least one allele could be sequenced from a further 15 strains. The nucleotide diversity of B. cereus isolated in this study from one location in Rockville, Maryland (0.04 substitutions per site) was found to be as great as the global collection of isolates. Conclusions/Significance Biogeographical investigation of pathogens is only one of a panoply of possible applications of microfluidics based MLST; others include microbiologic forensics, biothreat identification, and rapid characterization of human clinical samples.
Idiotypic–anti‐idiotypic complexes and their in vivo metabolism

Different strategies can be used to improve the tumor:non‐tumor ratio of radiolabeled antibodies in immunotargeting. One approach is to use secondary antibodies to clear out redundant, circulating primary antibodies. In the current study, the in vitro complex formation and in vivo clearing capabilities and metabolism of the monoclonal antibody TS1 and its monoclonal anti‐idiotype, αTS1, were studied.
Effect of Acetate on Molecular and Physiological Aspects of Clostridium beijerinckii NCIMB 8052 Solvent Production and Strain Degeneration

ABSTRACT The addition of sodium acetate to chemically defined MP2 medium was found to increase and stabilize solvent production and also increase glucose utilization by Clostridium beijerinckii NCIMB 8052. RNA and enzyme analyses indicated that coenzyme A (CoA) transferase was highly expressed and has higher activity in C. beijerinckiiNCIMB 8052 grown in MP2 medium containing added sodium acetate than in the microorganism grown without sodium acetate. RNA analysis suggested the existence of a sol operon and confirmed the presence of a ptb-buk operon in C. beijerinckii NCIMB 8052. In addition to CoA transferase, C. beijerinckii NCIMB 8052 grown in MP2 medium containing added acetate demonstrated higher acetate kinase- and butyrate kinase-specific activity than when the culture was grown in MP2 medium containing no added acetate. Southern blot analysis with chromosomal DNA isolated from solventogenic and degenerated C. beijerinckii NCIMB 8052 indicated thatC. beijerinckii NCIMB 8052 strain degeneration does not involve loss of the CoA transferase genes. The addition of acetate to MP2 medium may induce the expression of the sol operon, which ensures solvent production and prevents strain degeneration inC. beijerinckii NCIMB 8052.
Semantic Data Caching and Replacement

We propose a semantic model for client-side caching and replacement in a client-server database system and compare this approach to page caching and tuple caching strategies. Our caching model is based on, and derives its advantages from, three key ideas. First, the client maintains a semantic description of the data in its cache,which allows for a compact specification, as a remainder query, of the tuples needed to answer a query that are not available in the cache. Second, usage information for replacement policies is maintained in an adaptive fashion for semantic regions, which are associated with collections of tuples. This avoids the high overheads of tuple caching and, unlike page caching, is insensitive to bad clustering. Third, maintaining a semantic description of cached data enables the use of sophisticated value functions that incorporate semantic notions of locality, not just LRU or MRU, for cache replacement. We validate these ideas with a detailed performance study that includes traditional workloads as well as a workload motivated by a mobile navigation application.
Efficient scan chain design for power minimization during scan testing under routing constraint

Scan-based architectures, though widely used in modern designs, are expensive in power consumption. In this paper, we present a new technique that allows to design power-optimized scan chains under a given routing constraint. The proposed technique is a three-phase process based on clustering and reordering of scan cells in the design. It allows to reduce average power consumption during scan testing. Owing to this technique, short scan connections in scan chains are guaranteed and congestion problems in the design are avoided.