Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal pressure-driven flows between superhydrophobic grooved surfaces: Large effective slip in the narrow-channel limit

The gross ampliﬁcation of the ﬂuid velocity in pressure-driven ﬂows due to the introduction of superhydrophobic walls is commonly quantiﬁed by an eﬀective slip length. The canonical duct-ﬂow geometry involves a periodic structure of longitudinal shear-free stripes at either one or both of the bounding walls, corresponding to ﬂat-meniscus gas bubbles trapped within a periodic array of grooves. This grating conﬁguration is characterized by two geometric parameters, namely the ratio κ of channel width to microstructure period and the areal fraction ∆ of the shear-free stripes. For wide channels, κ (cid:29) 1, this geometry is known to possess an approximate solution where the dimensionless slip length λ , normalized by the duct semi-width, is small, indicating a weak superhydrophobic eﬀect. We here address the other extreme of narrow channels, κ (cid:28) 1, iden-tifying large O ( κ − 2 ) values of λ for the symmetric conﬁguration, where both bounding walls are superhydrophobic. This velocity enhancement is associated with an unconventional Poiseuille-like ﬂow proﬁle where the parabolic velocity variation takes place in a direction parallel (rather than perpendicular) to the boundaries. Use of matched asymptotic expansions and conformal-mapping techniques provides λ up to O ( κ − 1 ), establishing the approximation which is in excellent agreement with a semi-analytic solution of the dual equations governing the respective coeﬃcients of a Fourier-series representation of the ﬂuid velocity. No similar singularity occurs in the corresponding asymmetric conﬁguration, where only one of the bounding walls is superhydrophobic; in that geometry, a Hele-Shaw approximation shows that
Increased ADAMTS‐13 proteolytic activity in rat hepatic stellate cells upon activation in vitro and in vivo

Summary. Introduction: ADAMTS‐13 is a member of ADisintegrin And Metalloprotease with ThromboSpondin type 1 repeats (ADAMTS) family, primarily synthesized in hepatic stellate cells (HSCs), one of the major cell types transdifferentiating into myofibroblasts during liver fibrosis. However, the association between ADAMTS‐13 expression and HSC activation or liver fibrosis is not known. Methods: In this study, we determined the ADAMTS‐13 mRNA, protein, and activity in isolated primary HSCs upon activation on a plastic dish and in liver after administration of carbon tetrachloride (CCl4) in rats. Results: We showed that ADAMTS‐13 antigen and proteolytic activity in the activated rat HSCs were dramatically increased, whereas ADAMTS‐13 mRNA in these cells was only minimally altered. Similarly, the ADAMTS‐13 antigen and proteolytic activity in rat liver after CCl4 injury were also significantly increased, whereas the ADAMTS‐13 mRNAs in these liver tissues were only slightly increased compared with normal. Surprisingly, despite the dramatic up‐regulation of ADAMTS‐13 protein synthesis in the activated HSCs after CCl4 administration, the plasma levels of ADAMTS‐13 protease in rats did not increase concordantly. Conclusion: We conclude that the up‐regulation of ADAMTS‐13 protein expression in rat HSCs during activation in vitro and in vivo suggests the possibility of ADAMTS‐13 proteolysis, an important part of function of the activated HSCs, perhaps through modulation of liver regeneration or formation of liver fibrosis after various injuries. The data also suggest the minimal contribution of the activated HSCs in regulation of plasma levels of ADAMTS‐13 protease.
QUMA: quantification tool for methylation analysis

Bisulfite sequencing, a standard method for DNA methylation profile analysis, is widely used in basic and clinical studies. This method is limited, however, by the time-consuming data analysis processes required to obtain accurate DNA methylation profiles from the raw sequence output of the DNA sequencer, and by the fact that quality checking of the results can be influenced by a researcher's bias. We have developed an interactive and easy-to-use web-based tool, QUMA (quantification tool for methylation analysis), for the bisulfite sequencing analysis of CpG methylation. QUMA includes most of the data-processing functions necessary for the analysis of bisulfite sequences. It also provides a platform for consistent quality control of the analysis. The QUMA web server is available at http://quma.cdb. riken.jp/.
Expansion of cytokine-producing CD4-CD8- T cells associated with abnormal Fas expression and hypereosinophilia

The mechanisms of sustained overproduction of eosinophils in the idiopathic hypereosinophilic syndrome and in some human immunodeficiency virus (HIV)-1-infected individuals are largely unknown. We hypothesized that T cells may release soluble products that regulate eosinophilia in these patients, as has been previously shown in bronchial asthma. We identified one patient with idiopathic hypereosinophilic syndrome and one HIV-1-infected individual with associated hypereosinophilia who demonstrated high numbers of CD4-CD8- T cells in peripheral blood. CD4-CD8- T cells from both patients, although highly activated, did not express functional Fas receptors. In one case, the lack of functional Fas receptors was associated with failure of Fas mRNA and protein expression, and in another, expression of a soluble form of the Fas molecule that may have antagonized normal signaling of Fas ligand. In contrast to the recently described lymphoproliferative/autoimmune syndrome, which is characterized by accumulation of CD4-CD8- T cells and mutations within the Fas gene, this study suggests somatic variations in Fas expression and function quite late in life. Both genetic and somatic abnormalities in regulation of the Fas gene are therefore associated with failures to undergo T cell apoptosis. Furthermore, the expanded population of CD4- CD8- T cells from both patients elaborated cytokines with antiapoptotic properties for eosinophils, indicating a major role of these T cells in the development of eosinophilia. Thus, this study demonstrates a sequential dysregulation of apoptosis in different cell types.
Cache bursts: A new approach for eliminating dead blocks and increasing cache efficiency

Data caches in general-purpose microprocessors often contain mostly dead blocks and are thus used inefficiently. To improve cache efficiency, dead blocks should be identified and evicted early. Prior schemes predict the death of a block immediately after it is accessed; however, these schemes yield lower prediction accuracy and coverage. Instead, we find that predicting the death of a block when it just moves out of the MRU position gives the best tradeoff between timeliness and prediction accuracy/coverage. Furthermore, the individual reference history of a block in the L1 cache can be irregular because of data/control dependence. This paper proposes a new class of dead-block predictors that predict dead blocks based on bursts of accesses to a cache block. A cache burst begins when a block becomes MRU and ends when it becomes non-MRU. Cache bursts are more predictable than individual references because they hide the irregularity of individual references. When used at the L1 cache, the best burst-based predictor can identify 96% of the dead blocks with a 96% accuracy. With the improved dead-block predictors, we evaluate three ways to increase cache efficiency by eliminating dead blocks early: replacement optimization, bypassing, and prefetching. The most effective approach, prefetching into dead blocks, increases the average L1 efficiency from 8% to 17% and the L2 efficiency from 17% to 27%. This increased cache efficiency translates into higher overall performance: prefetching into dead blocks outperforms the same prefetch scheme without dead-block prediction by 12% at the L1 and by 13% at the L2.
Using witness trees to assess forest change in southeastern Ohio

In 1787, the U.S. Congress authorized the sale of the "Ohio Company Purchase", ca. 5000 km2 in Appalachian Ohio. The land was surveyed using a township and range system shortly thereafter. Data on >5600 witness trees were transcribed from the survey records, and witness tree locations were plotted on a digital map. This information was used to evaluate presettlement forest composition and structure and to investigate vegetation-site relationships before widespread alteration of the forests had taken place. Presettlement conditions were compared with present conditions using forest inventory and analysis (FIA) data. Two hundred years ago, the forests of southeastern Ohio were dominated by large individuals of Quercus alba L. , Carya Nutt. spp. , Quercus velutina Lam. , and Fagus grandifolia Ehrh. These four taxa accounted for 74% of all witness trees. Although almost 70% of the region is forested today, the second-growth forest has witnessed a decrease in Quercus and Carya and an increase in Acer saccharum Ma.
Electroosmotic Flow and DNA Electrophoretic Transport in Micro/Nano Channels

In Micro/nano fluidic systems, electrokinetic transport is a convenient method to move materials, such as water, ions and particles for fast, high-resolution and low-cost analysis and synthesis. It has wide applications to drug delivery and its control, DNA and biomolecular sensing, manipulation, the manufacture laboratories on a microchip (lab-ona-chip) and many other areas. In the present work, electrokinetically driven fluid flow and particle transport in micro/nanoscale channels/pores with heterogeneous surface potential or converging shape are investigated theoretically and numerically. A step change in wall potential is found to induce a recirculation region in the bulk electroosmotic flow and interesting flow structures can be achieved by manipulating the surface heterogeneous patterns. Most of the previous work on this problem is based on the Debye-Huckel approximation and the validity of Boltzmann distribution for ionic species. In the present work, ionic species distributions in the electric double layers are found to be different from the Boltzmann distribution and this deviation is more noticeable for higher applied electric field. A mathematical model is developed to simulate the electroosmotic flow (EOF) and the transport of embedded particles in micro/nano nozzles/diffusers. Results can be used to estimate the mass transport of charged/uncharged species in micro/nano nozzles/diffusers which has a potential application in transdermal drug delivery. The model is extended to investigate the DNA electrophoretic transport through a converging nanopore for the ii purpose of DNA sequencing. The flow field, the resistive forces acting on the DNA, the DNA velocity and the ionic current through the nanopore are calculated numerically based on the Poisson-Boltzmann theory and the lubrication approximation. It is found that the electroosmotic flow inside the nanopore plays an important role in the DNA translocation process and the resulting viscous drag decreases the effective driving force acting on the DNA substantially. Entropic forces, used to be considered as the main resistive forces in previous works, are found to be small and negligible. Modeling and simulations are validated by the good agreement with the experimental data for the tethering force and the DNA velocity.
Angiotensin II Type 1 Receptor Blockers Reduce Urinary Oxidative Stress Markers in Hypertensive Diabetic Nephropathy

We tested the hypothesis that blockade of angiotensin II type 1 receptors reduces oxidative stress markers in parallel with urinary albumin and type IV collagen excretions. Sixty-six diabetic patients with nephropathy were randomly assigned to either the angiotensin II receptor blocker (ARB; n=33) or trichlormethiazide (n=33) group. The majority of patients had been treated with angiotensin-converting enzyme inhibitors or calcium channel blockers for ≥1 year before the present study. Reduction of blood pressure was not different between the 2 groups, and HbA1c levels did not change over the study period (8 weeks). Treatment with ARB (candesartan 8 mg/day, n=11 or valsartan 80 mg/day, n=22) for 8 weeks reduced the levels of plasma monocyte chemoattractant protein 1, interleukin 6, urinary 8-epi-prostaglandin F2&agr;, 8-hydroxydeoxyguanosine, albumin, and type IV collagen, whereas the levels of these markers were not altered with trichlormethiazide (2 mg/day). Significant correlation was observed between the reduction of the urinary 8-epi- prostaglandin F2&agr; and 8-hydroxydeoxyguanosine and those of the urinary albumin and type IV collagen. Subjects with large oxidative stress had large reduction rates because of ARB administration and showed large urinary albumin suppression. These results suggest that ARBs reduce oxidative stress and inflammation in diabetic patients independent of their effects on blood pressure. In addition, increases in oxidative stress caused by angiotensin II may play an important role in the progression of diabetic nephropathy. Our results may help to explain the clinical observation that ARB reduces urinary albumin excretion very efficiently in some patients but not in others.
Relationship between balance and abnormalities in cerebral magnetic resonance imaging in older adults.

BACKGROUND Falling is a major cause of disability and morbidity among older adults. Because poor balance is a major reason for frequent falls, assessment of balance and its risk factors are important. In this study, we postulated that cerebral changes identified on magnetic resonance (MR) imaging are related to balance, and that older adults with balance problems would have significantly greater prevalence of such brain abnormalities than older adults without balance problems. DESIGN AND MEASUREMENTS Several measures of balance were examined in more than 700 community-dwelling older men and women, blacks and whites. Balance measures included dynamic posturography, functional reach, Romberg and 1-foot stand tests, tandem stand, and 1-foot stand. Cerebral MR imaging assessments included ventricular size, sulcal widening, white matter disease, and ischemic infarctions. Cardiovascular disease and hypertension were determined and controlled for in the analyses. RESULTS A summary of the balance measures was significantly related to each of the 4 MR imaging measures, with those with poorer balance having more disease. The strongest associations with balance were seen for white matter disease and ventricular size. All but the ischemic infarction variable remained significantly associated with balance after adjustments for sex, race, age, cardiovascular disease, and hypertension. CONCLUSION Cerebral changes identified by MR imaging are associated with poorer balance among older adults.
Development and uncertainty analysis of a high-resolution NH 3 emissions inventory and its implications with precipitation over the Pearl River Delta region, China

Abstract. Detailed NH 3 emission inventories are important to understand various atmospheric processes, air quality modeling studies, air pollution management, and related environmental and ecological issues. A high-resolution NH 3 emission inventory was developed based on state-of-the-science techniques, up-to-date information, and advanced expert knowledge for the Pearl River Delta region, China. To provide model-ready emissions input, this NH 3 emissions inventory was spatially allocated to 3 km × 3 km grid cells using source-based spatial surrogates with geographical information system (GIS) technology. For NH 3 emissions, 9 source categories and 45 subcategories were identified in this region, and detailed spatial and temporal characteristics were investigated. Results show that livestock is by far the most important NH 3 emission source by contributing about 61.7% of the total NH 3 emissions in this region, followed by nitrogen fertilizer applications (~23.7%) and non-agricultural sources (~14.6%). Uncertainty analysis reveals that the uncertainties associated with different sources vary from source to source and the magnitude of the uncertainty associated with a specific source mainly depends on the degree of accuracy of the emission factors and activity data as well as the technique used to perform the estimate. Further studies should give priority to the hog, broiler, goose subsectors of the livestock source and N fertilizer application source in order to reduce uncertainties of ammonia emission estimates in this region. The validity of the NH 3 emissions inventory is justified by the trend analysis of local precipitation compositions, such as pH values, the Ca 2+ +NH 4 + /SO 4 2− + NO 3 − ratios, and NH 4 + concentrations which are directly or indirectly related to NH 3 emissions.
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome

For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1) assessing the performance of three different assembly tools (2) using both single and multiple k-mer (MK) approaches (3) examining the influence of the number of reads used in the assembly (4) merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck). We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT) and CEGMA (Core Eukaryotic Genes Mapping Approach) provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of MK in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi. org/10.6084/m9.figshare. 1032613.
Concurrent, object-oriented natural language parsing: the ParseTalk model

Abstract The ParseTalk model of concurrent, object-oriented natural language parsing is introduced. It builds upon the complete lexical distribution of grammatical knowledge and incorporates inheritance mechanisms in order to express generalizations over sets of lexical items. The grammar model integrates declarative well-formedness criteria constraining linguistic relations between heads and modifiers, and procedural specifications of the communication protocol for establishing these relations. The parser's computation model relies upon the actor paradigm, with concurrency entering through asynchronous message passing. We consider various extensions of the basic actor model as required for distributed natural language understanding and elaborate on the semantics of the actor computation model in terms of event type networks (a graph representation for actor grammar specifications) and event networks (graphs which represent the actor parser's behavior). Besides theoretical claims, we present an interactive grammar/parser workbench, a graphical development environment with various types of browsers, tracers, inspectors and debuggers, that has been adapted to the requirements of large-scale grammar engineering in a distributed, object-oriented specification and programming framework.
Effects of the Histone Deacetylase Inhibitor ITF2357 in Autoinflammatory Syndromes

We explored the effects of the oral histone deacetylase (HDAC) Inhibitor ITF2357 In patients with autoinflammatory syndrome. In this prospective open-label pilot study, eight patients were enrolled; one patient with tumor necrosis factor receptor-associated periodic syndrome (TRAPS), three patients with hyper-IgD and periodic fever syndrome (HIDS) and four patients with Schnitzler syndrome were closely followed during 90 d of ITF2357 treatment. Three patients with Schnitzler syndrome and one TRAPS patient experienced a partial remission. In four patients, there was no effect. In HIDS patients, there was a tendency toward a higher attack frequency and increasing attack severity. In two patients (one TRAPS and one HIDS), we observed a decrease of acute-phase response without signs of clinical improvement. One patient with Schnitzler syndrome showed a partial response despite an ongoing acute-phase response. In conclusion, ITF2357 monotherapy was able to induce partial response only in patients with Schnitzler syndrome and no response in patients with HIDS.
Elephant Herding Optimization

In this paper, a new kind of swarm-based metaheuristic search method, called Elephant Herding Optimization (EHO), is proposed for solving optimization tasks. The EHO method is inspired by the herding behavior of elephant group. In nature, the elephants belonging to different clans live together under the leadership of a matriarch, and the male elephants will leave their family group when they grow up. These two behaviors can be modelled into two following operators: clan updating operator and separating operator. In EHO, the elephants in each clan are updated by its current position and matriarch through clan updating operator. It is followed by the implementation of the separating operator which can enhance the population diversity at the later search phase. To demonstrate its effectiveness, EHO is benchmarked by fifteen test cases comparing with BBO, DE and GA. The results show that EHO can find the better values on most benchmark problems than those three metaheuristic algorithms.
A critical role for the Sp1-binding sites in the transforming growth factor-β-mediated inhibition of lipoprotein lipase gene expression in macrophages

Increasing evidence suggests that the cytokine transforming growth factor-β (TGF-β) inhibits the development of atherosclerosis. The lipoprotein lipase (LPL) enzyme expressed by macrophages has been implicated in the pathogenesis of atherosclerosis by stimulating the uptake of lipoprotein particles. Unfortunately, the action of TGF-β on the expression of LPL in macrophages remains largely unclear. We show that TGF-β inhibits LPL gene expression at the transcriptional level. Transient transfection assays reveal that the −31/+187 sequence contains the minimal TGF-β-responsive elements. Electrophoretic mobility shift assays show that Sp1 and Sp3 interact with two regions in the −31/+187 sequence. Mutations of these Sp1/Sp3 sites abolish the TGF-β-mediated suppression whereas multimers of the sequence impart the response to a heterologous promoter. TGF-β has no effect on the binding or steady-state polypeptide levels of Sp1 and Sp3. These results, therefore, suggest a novel mechanism for the TGF-β-mediated repression of LPL gene transcription that involves regulation of the action of Sp1 and Sp3.