Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving a global model from the boundary layer: Total turbulent energy and the neutral limit Prandtl number

Model intercomparisons have identified important deficits in the representation of the stable boundary layer by turbulence parametrizations used in current weather and climate models. However, detrimental impacts of more realistic schemes on the large‐scale flow have hindered progress in this area. Here we implement a total turbulent energy scheme into the climate model ECHAM6. The total turbulent energy scheme considers the effects of Earth's rotation and static stability on the turbulence length scale. In contrast to the previously used turbulence scheme, the TTE scheme also implicitly represents entrainment flux in a dry convective boundary layer. Reducing the previously exaggerated surface drag in stable boundary layers indeed causes an increase in southern hemispheric zonal winds and large‐scale pressure gradients beyond observed values. These biases can be largely removed by increasing the parametrized orographic drag. Reducing the neutral limit turbulent Prandtl number warms and moistens low‐latitude boundary layers and acts to reduce longstanding radiation biases in the stratocumulus regions, the Southern Ocean and the equatorial cold tongue that are common to many climate models.
Nonuniform muscle hypertrophy: its relation to muscle activation in training session.

PURPOSE Muscle hypertrophy in response to resistance training has been reported to occur nonuniformly along the length of the muscle. The purpose of the present study was to examine whether the regional difference in muscle hypertrophy induced by a training intervention corresponds to the regional difference in muscle activation in the training session. METHODS Twelve young men participated in a training intervention program for the elbow extensors with a multijoint resistance exercise for 12 wk (3 d · wk(-1)). Before and after the intervention, cross-sectional areas of the triceps brachii along its length were measured with magnetic resonance images. A series of transverse relaxation time (T2)-weighted magnetic resonance images was recorded before and immediately after the first session of training intervention. The T2 was calculated for each pixel within the triceps brachii. In the images recorded after the session, the number of pixels with a T2 greater than the threshold (mean + 1 SD of T2 before the session) was expressed as the ratio to the whole number of pixels within the muscle and used as an index of muscle activation (percent activated area). RESULTS The percent activated area of the triceps brachii in the first session was significantly higher in the middle regions than that in the most proximal region. Similarly, the relative change in cross-sectional area induced by the training intervention was also significantly greater in the middle regions than the most proximal region. CONCLUSION The results suggest that nonuniform muscle hypertrophy after training intervention is due to the region-specific muscle activation during the training session.
Intracellular Ca2+ stores in chicken Purkinje neurons: differential distribution of the low affinity-high capacity Ca2+ binding protein, calsequestrin, of Ca2+ ATPase and of the ER lumenal protein, Bip

To identify intracellular Ca2+ stores, we have mapped (by cryosection immunofluorescence and immunogold labeling) the distribution in the chicken cerebellar cortex of an essential component, the main low affinity-high capacity Ca2+ binding protein which in this tissue has been recently shown undistinguishable from muscle calsequestrin (Volpe, P., B. H. Alderson-Lang, L. Madeddu, E. Damiani, J. H. Collins, and A. Margreth. 1990. Neuron. 5:713-721). Appreciable levels of the protein were found exclusively within Purkinje neurons, distributed to the cell body, the axon, and the elaborate dendritic tree, with little labeling, however, of dendritic spines. At the EM level the protein displayed a dual localization: within the ER (rough- and smooth-surfaced cisternae, including the cisternal stacks recently shown [in the rat] to be highly enriched in receptors for inositol 1,4,5-triphosphate) and, over 10- fold more concentrated, within a population of moderately dense, membrane-bound small vacuoles and tubules, identified as calciosomes. These latter structures were widely distributed both in the cell body (approximately 1% of the cross-sectional area, particularly concentrated near the Golgi complex) and in the dendrites, up to the entrance of the spines. The distribution of calsequestrin was compared to those of another putative component of the Ca2+ stores, the membrane pump Ca2+ ATPase, and of the ER resident lumenal protein, Bip. Ca2+ ATPase was expressed by both calciosomes and regular ER cisternae, but excluded from cisternal stacks; Bip was abundant within the ER lumena (cisternae and stacks) and very low within calciosomes (average calsequestrin/Bip immunolabeling ratios were approximately 0.5 and 36.5 in the two types of structure, respectively). These results suggest that ER cisternal stacks do not represent independent Ca2+ stores, but operate coordinately with the adjacent, lumenally continuous ER cisternae. The ER and calciosomes could serve as rapidly exchanging Ca2+ stores, characterized however by different properties, in particular, by the greater Ca2+ accumulation potential of calciosomes. Hypotheses of calciosome biogenesis (directly from the ER or via the Golgi complex) are discussed.
The NIE Approach to Economic Development An Analytic Primer

The objectives of the Forum Series are to help USAID make its donor assistance more effective and sustainable by incorporating insights from the New Institutional Economics into USAID's programming and delivery of development assistance. Services for the Forum Series are provided by the Center for Institutional Reform and the Informal Sector (IRIS) and its consultants. The views and interpretations represented in this paper belong solely to its author and should not be attributed to USAID or to IRIS. Abstract The aim of this paper is to introduce the reader involved in foreign assistance to some ways in which NIE can provide insights that help in the design of reform programs. This is not meant to be an exhaustive review of NIE and development. The paper is organized as follows: I begin by describing Williamson's hierarchy of institutions: social structure and human motivations that take centuries or millennia to evolve, political institutions that take decades to gel, legal institutions that take years to be legislated, and the use of law by private parties that can be established over much shorter periods. Within this discussion I introduce several conceptual ideas and theoretical insights from NIE: • Transactions costs and the components of transactions costs (informational asymmetries and the administrative costs of reducing informational asymmetries). • The incomplete contracts problem, which refers to how to design contracts when important varia bles cannot be observed. • The principal-agent problem, which refers to how a principal who cannot observe the agent's action, can induce the agent to take the right action. • The adverse selection problem, which refers to the problem of creating markets where the quality of the goods or the trustworthiness of the participants is in question. • The collective action problem, which refers to how any rational agent alone would undersupply effort or resources to resolve group problems. The paper discusses the following insights: Aligning the incentives of agents with the interests of principals, and improving information flows about actions and outputs can improve outcomes. This applies to principal agent relationships in both the political sphere (voter-prime minister-civil servant) and the economic sphere (creditor-debtor, shareholder-manager). It also applies to clear property rights, which give private agents sharp incentives to minimize on costs while maintaining quality; and to solutions for collective actions like rewarding citizens who detect defectors. The paper also points out the limitations of NIE: Incentives are at times not appropriate; …
Aberrant LPL Expression, Driven by STAT3, Mediates Free Fatty Acid Metabolism in CLL Cells

While reviewing chronic lymphocytic leukemia (CLL) bone marrow slides, we identified cytoplasmic lipid vacuoles in CLL cells but not in normal B cells. Because lipoprotein lipase (LPL), which catalyzes hydrolysis of triglycerides into free fatty acids (FFA), is aberrantly expressed in CLL, we investigated whether LPL regulates the oxidative metabolic capacity of CLL cells. We found that unlike normal B cells, CLL cells metabolize FFAs. Because STAT3 is constitutively activated in CLL cells and because we identified putative STAT3 binding sites in the LPL promoter, we sought to determine whether STAT3 drives the aberrant expression of LPL. Transfection of luciferase reporter gene constructs driven by LPL promoter fragments into MM1 cells revealed that STAT3 activates the LPL promoter. In addition, chromatin immunoprecipitation confirmed that STAT3 binds to the LPL promoter. Furthermore, transfection of CLL cells with STAT3-shRNA downregulated LPL transcripts and protein levels, confirming that STAT3 activates the LPL gene. Finally, transfection of CLL cells with LPL-siRNAs decreased the capacity of CLL cells to oxidize FFAs and reduced cell viability. Implications: Our study suggests that CLL cells adopt their metabolism to oxidize FFA. Activated STAT3 induces LPL, which catalyzes the hydrolysis of triglycerides into FFA. Therefore, inhibition of STAT3 is likely to prevent the capacity of CLL cells to utilize FFA. Mol Cancer Res; 13(5); 944–53. ©2015 AACR.
Data Mining Using MLC a Machine Learning Library in C++

Data mining algorithms including machine learning, statistical analysis, and pattern recognition techniques can greatly improve our understanding of data warehouses that are now becoming more widespread. In this paper, we focus on classification algorithms and review the need for multiple classification algorithms. We describe a system called MLC++, which was designed to help choose the appropriate classification algorithm for a given dataset by making it easy to compare the utility of different algorithms on a specific dataset of interest. MLC++ not only provides a workbench for such comparisons, but also provides a library of C++ classes to aid in the development of new algorithms, especially hybrid algorithms and multi-strategy algorithms. Such algorithms are generally hard to code from scratch. We discuss design issues, interfaces to other programs, and visualization of the resulting classifiers.
The evolutionary basis of human social learning

Humans are characterized by an extreme dependence on culturally transmitted information. Such dependence requires the complex integration of social and asocial information to generate effective learning and decision making. Recent formal theory predicts that natural selection should favour adaptive learning strategies, but relevant empirical work is scarce and rarely examines multiple strategies or tasks. We tested nine hypotheses derived from theoretical models, running a series of experiments investigating factors affecting when and how humans use social information, and whether such behaviour is adaptive, across several computer-based tasks. The number of demonstrators, consensus among demonstrators, confidence of subjects, task difficulty, number of sessions, cost of asocial learning, subject performance and demonstrator performance all influenced subjects' use of social information, and did so adaptively. Our analysis provides strong support for the hypothesis that human social learning is regulated by adaptive learning rules.
The Scurfy mutation of FoxP3 in the thymus stroma leads to defective thymopoiesis

The Scurfy mutation of the FoxP3 gene (FoxP3 sf) in the mouse and analogous mutations in human result in lethal autoimmunity. The mutation of FoxP3 in the hematopoietic cells impairs the development of regulatory T cells. In addition, development of the Scurfy disease also may require mutation of the gene in nonhematopoietic cells. The T cell–extrinsic function of FoxP3 has not been characterized. Here we show that the FoxP3sf mutation leads to defective thymopoiesis, which is caused by inactivation of FoxP3 in the thymic stromal cells. FoxP3 mutation also results in overexpression of ErbB2 in the thymic stroma, which may be involved in defective thymopoiesis. Our data reveal a novel T cell–extrinsic function of FoxP3. In combination, the T cell–intrinsic and –extrinsic defects provide plausible explanation for the severity of the autoimmune diseases in the scurfy mice and in patients who have immunodysregulation, polyendocrinopathy, enteropathy, and X-linked syndrome.
Stochastic sampling of the RNA structural alignment space

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the ‘structural alignment’ space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The ‘best’ centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc. rochester.edu.
Magnesium deficiency induces joint cartilage lesions in juvenile rats which are identical to quinolone-induced arthropathy

Quinolones accumulate in cartilage, and because they form chelate complexes with divalent cations, they possess the potential to induce a deficiency of functionally available magnesium. To test the hypothesis that quinolone-induced arthropathy is caused (or aggravated) by magnesium deficiency in cartilage, we induced magnesium deficiency by feeding juvenile rats a magnesium-deficient diet for 9 days and treated the rats with single oral doses of ofloxacin (0, 100, 300, 600, or 1,200 mg/kg of body weight) during this period. Additional groups of juvenile rats on a normal diet were treated with ofloxacin correspondingly. Typical cartilage lesions (e.g., swollen matrix, cleft formation) were found in knee joints of all magnesium-deficient rats, including those without ofloxacin treatment. Lesions in these groups were not distinguishable from lesions induced by a single dose of 600 mg of ofloxacin per kg of body weight or higher in rats on a normal diet. Ofloxacin levels in plasma after 600 mg/kg of body weight were approximately 10-fold higher than those in humans during therapy with this quinolone. Lesions in rats treated with ofloxacin plus magnesium deficiency were more pronounced than those in rats with normal magnesium concentrations. After intake of a magnesium-deficient diet for 9 days, the magnesium concentration in serum (mean +/- standard deviation) was 0.18 +/- 0.05 mmol/liter (control on normal diet, 0.82 +/- 0.10 mmol/liter). Magnesium concentrations in bone (femur) and cartilage (processus xiphoideus) samples were 64.7 +/- 10.5 and 14.3 +/- 3.9 mmol/kg of dry weight, respectively, which corresponded to approximately 50% of the concentrations measured in controls on a normal diet. It was concluded that quinolone-induced arthropathy is probably caused by a deficit of available magnesium in joint cartilage due to the formation of quinolone-magnesium chelate complexes. If juvenile patients must be treated with quinolones for serious infections, it seems prudent to ensure that these patients do not have a disturbed magnesium balance.
Diagnostic Methods for Platelet Bacteria Screening: Current Status and Developments

Bacterial contamination of blood components and the prevention of transfusion-associated bacterial infection still remains a major challenge in transfusion medicine. Over the past few decades, a significant reduction in the transmission of viral infections has been achieved due to the introduction of mandatory virus screening. Platelet concentrates (PCs) represent one of the highest risks for bacterial infection. This is due to the required storage conditions for PCs in gas-permeable containers at room temperature with constant agitation, which support bacterial proliferation from low contamination levels to high titers. In contrast to virus screening, since 1997 in Germany bacterial testing of PCs is only performed as a routine quality control or, since 2008, to prolong the shelf life to 5 days. In general, bacterial screening of PCs by cultivation methods is implemented by the various blood services. Although these culturing systems will remain the gold standard, the significance of rapid methods for screening for bacterial contamination has increased over the last few years. These new methods provide powerful tools for increasing the bacterial safety of blood components. This article summarizes the course of policies and provisions introduced to increase bacterial safety of blood components in Germany. Furthermore, we give an overview of the different diagnostic methods for bacterial screening of PCs and their current applicability in routine screening processes.
Evaluating the effect of therapeutic gardens

Sometimes the visitors to therapeutic gardens do not necessarily experience the garden the way the designers intended. A postoccupancy evaluation (POE) can reveal discrepancies between the designer's intentions and use of the environment by the actual visitors. A POE is a user-oriented assessment that elicits the opinions of the visitors to a building, facility, or environment. This paper describes a POE of therapeutic gardens at a multilevel care facility for the aged. The population included patients at various stages of Alzheimer's disease progression.
Comparison of Cross-Sectional Hardness and Transverse Microradiography of Artificial Carious Enamel Lesions Induced by Different Demineralising Solutions and Gels

The aims of this study were: (1) to correlate surface (SH) and cross-sectional hardness (CSH) with microradiographic parameters of artificial enamel lesions; (2) to compare lesions prepared by different protocols. Fifty bovine enamel specimens were allocated by stratified randomisation according to their initial SH values to five groups and lesions produced by different methods: MC gel (methylcellulose gel/lactic acid, pH 4.6, 14 days); PA gel (polyacrylic acid/lactic acid/hydroxyapatite, pH 4.8, 16 h); MHDP (undersaturated lactate buffer/methyl diphosphonate, pH 5.0, 6 days); buffer (undersaturated acetate buffer/fluoride, pH 5.0, 16 h), and pH cycling (7 days). SH of the lesions (SH1) was measured. The specimens were longitudinally sectioned and transverse microradiography (TMR) and CSH measured at 10- to 220-μm depth from the surface. Overall, there was a medium correlation but non-linear and variable relationship between mineral content and √CSH. √SH1 was weakly to moderately correlated with surface layer properties, weakly correlated with lesion depth but uncorrelated with integrated mineral loss. MHDP lesions showed the highest subsurface mineral loss, followed by pH cycling, buffer, PA gel and MC gel lesions. The conclusions were: (1) CSH, as an alternative to TMR, does not estimate mineral content very accurately, but gives information about mechanical properties of lesions; (2) SH should not be used to analyse lesions; (3) artificial caries lesions produced by the protocols differ, especially considering the method of analysis.
On the Syntax and Semantics of Architectural Principles

This paper illustrates why architectural principles are important for IT management and how the principles can be used. By analyzing architectural principles at an enterprise, knowledge is gained on how to formulate principles so that they are an effective steering tool. This knowledge is transformed into a framework for formulating architectural principles. The analysis of the architectural principles has been performed from two different angles; have we got the principles right (syntax) and have we got the right principles (semantics). The industrial case is complemented with examples from literature.
GlcNAc-6P Levels Modulate the Expression of Curli Fibers by Escherichia coli

ABSTRACT Curli are extracellular surface fibers that are produced by many members of the Enterobacteriaceae and contribute to biofilm formation. The environmental cues that promote biofilm formation are poorly understood. We found that deletion of the N-acetylglucosamine-6-phosphate (GlcNAc-6P) deacetylase gene, nagA, resulted in decreased transcription from the curli-specific promoters csgBA and csgDEFG and a corresponding decrease in curli production in Escherichia coli. nagA is in an operon that contains nagB, nagC, nagD, and nagE, whose products are required for utilization of GlcNAc as a carbon source. NagC is a repressor of the nagBACD and nagE genes in the absence of intracellular GlcNAc-6P. We found that nagC mutants were also defective in curli production. Growth of a wild-type strain on media containing additional GlcNAc reduced curli gene transcription to a level similar to the level observed when nagA was deleted. The defect in curli production in nagA or nagC mutants was alleviated by deletion of the GlcNAc transporter gene, nagE. Curli-producing ΔnagA suppressor mutants whose cells were unable to take up GlcNAc were isolated. These results suggest that elevated levels of intracellular GlcNAc-6P signal cells to down-regulate curli gene expression.
Rules Transparency and Political Accountability

Allocative and redistributive rules in the public sector are often less contingent on available information than normative theory would suggest. This paper offers a political economy explanation. Under different rules, even if the observable outcomes of policies remain the same, the informational content which can be extracted by these observations is different. Simpler rules are more transparent because they allow citizens to gain more information on politicians. Since there are limits to what voters can observe, this may be a relevant insight into the functioning of the political system.