gebhart/patrepeval huggingface dataset:
The Learnability of Optimality Theory: An Algorithm and Some Basic Complexity Results (1995)

If Optimality Theory (Prince &amp; Smolensky 1991, 1993) is correct, Universal Grammar provides a set of universal constraints which are highly general, inherently conflicting, and consequently rampantly violated in the surface forms of languages. A language’s grammar ranks the universal constraints in a dominance hierarchy, higher-ranked constraints taking absolute priority over lower-ranked constraints, so that violations of a constraint occur in well-formed structures when, and only when, they are necessary to prevent violation of higher-ranked constraints. Languages differ principally in how they rank the universal constraints in their language-specific dominance hierarchies. The surface forms of a given language are structural descriptions of inputs which are optimal in the following sense: they satisfy the universal constraints, or, when these constraints are brought into conflict by an input, they satisfy the highest-ranked constraints possible. This notion of optimality is partly language-specific, since the ranking of constraints is language-particular, and partly universal, since the constraints which evaluate well-formedness are (at least to a considerable extent) universal. In many respects, ranking of universal constraints in Optimality Theory plays a role analogous to parameter-setting in principles-and-parameters theory.
Modification of the Curd Firmness Test for Cottage Cheese (1966)

studied, one would expect 65 to 90% of the acids reported in Table 1 to exist in the salt form.This would affect the aroma resulting from volatile short-chain acids and the contribution to flavor made by long-chain acids.Unfortunately, it is not possible to determine experimentally the ratio of a given acid to its salt in cheese.
SICTA: a 0.693 contention tree algorithm using successive interference cancellation (2005)

Contention tree algorithms have provable stability properties, and are known to achieve stable throughput as high as 0.487 for the infinite population Poisson model. A common feature in all these random access protocols is that collided packets at the receive-node are always discarded. In this paper, we derive a novel tree algorithm (TA) that we naturally term SICTA because it relies on successive interference cancellation to resolve collided packets. Performance metrics including throughput and delay are analyzed to establish that SICTA outperforms existing contention tree algorithms reaching 0.693 in stable throughput.
Cooperative and individualistic functions of the microRNAs in the miR-23a~27a~24-2 cluster and its implication in human diseases (2010)

The small RNA molecules of about 19-22 nucleotides in length, aptly called microRNAs, perform the task of gene regulation in the cell. Interestingly, till the early nineties very little was known about them but eventually, the microRNAs have become forefront in the area of research. The huge number of microRNAs plus each one of them targeting a vast number of related as well as unrelated genes makes them very interesting molecules to study. To add to the mystery of miRNAs is the fact that the same miRNA can have antagonizing role in two different cell types i.e. in one cell type; the miRNA promotes proliferation whereas in another cell type the same miRNA inhibits proliferation. Another remarkable aspect of the microRNAs is that many of them exist in clusters. In humans alone, out of 721 microRNAs known, 247 of them occur in 64 clusters at an inter-miRNA distance of less than 5000 bp. The reason for this clustering of miRNAs is not fully understood but since the miRNA clusters are evolutionary conserved, their significance cannot be ruled out. The objective of this review is to summarize the recent progress on the functional characterization of miR-23a~27a~24-2 cluster in humans in relation to various health and diseased conditions and to highlight the cooperative effects of the miRNAs of this cluster.
Optimization of the hölder image descriptor using a genetic algorithm (2010)

Local image features can provide the basis for robust and invariant recognition of objects and scenes. Therefore, compact and distinctive representations of local shape and appearance has become invaluable in modern computer vision. In this work, we study a local descriptor based on the Hölder exponent, a measure of signal regularity. The proposal is to find an optimal number of dimensions for the descriptor using a genetic algorithm (GA). To guide the GA search, fitness is computed based on the performance of the descriptor when applied to standard region matching problems. This criterion is quantified using the F-Measure, derived from recall and precision analysis. Results show that it is possible to reduce the size of the canonical Hölder descriptor without degrading the quality of its performance. In fact, the best descriptor found through the GA search is nearly 70% smaller and achieves similar performance on standard tests.
Screening effects on branched upward leaders (2012)

A qualitative model of a branched, positive upward leader is discussed that explains observations of the current cutoff of base current before the end of leader structure development and the fast recovery of nearby electric fields. Screening of cloud electric fields by branching is a powerful mechanism to influence branch cutoffs a well as the birth of recoil leaders on old dead channels. The analysis is based on well established physics principles of leader behavior in thunderstorms like the theory of Kasemir [2] on leader charge relation to environmental potential and [3] the formation of static charges by the streamer process.
Crystal Growth of Cyclodextrin-based Metal-organic Framework for Carbon Dioxide Capture and Separation (2016)

Crystalline cyclodextrin-based metal-organic framework (CD-MOF) was synthesized by vapor diffusion of methanol into a KOH solution of -cyclodextrin (-CD). Its CO2 adsorption behaviors were evaluated both qualitatively and quantitatively. The adsorption behaviors of CD-MOF to separate and capture CO2 have been tested by using thermogravimetric analysis in the multiple adsorption-desorption process. The chemical sorption of CO2 was found to be caused by the formation of reversible carbonic acid. The adsorption amount of CO2 was tested in pure CO2 gas and 25vol% CO2 in Ar gas. As a result, there is no difference of the adsorption amount against the CO2 concentration and the saturated adsorption amount was 24 mg-CO2/g-CD-MOF at 30oC.
Generation of aroE overexpression mutant of Bacillus megaterium for the production of shikimic acid (2015)

This will add up a new organism in the armory for the fermentation based production which is better over plant based extraction and chemical synthesis of shikimic acid.
The molecular yo-yo method: Live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions (2013)

By monitoring multiple molecular transitions, force-clamp, and trap-position-clamp methods have led to precise determinations of the free energies and free energy landscapes for molecular states populated in equilibrium at the same or similar forces. Here, we present a powerful new elaboration of the force-clamp and force-jump methods, applicable to transitions far from equilibrium. Specifically, we have implemented a live jump detection and force-clamp algorithm that intelligently adjusts and maintains the force on a single molecule in response to the measured state of that molecule. We are able to collect hundreds of individual molecular transitions at different forces, many times faster than previously, permitting us to accurately determine force-dependent lifetime distributions and reaction rates. Application of our method to unwinding and rewinding the nucleosome inner turn, using optical tweezers reveals experimental lifetime distributions that comprise a statistically meaningful number of transitions, and that are accurately single exponential. These measurements significantly reduce the error in the previously measured rates, and demonstrate the existence of a single, dominant free energy barrier at each force studied. A key benefit of the molecular yo-yo method for nucleosomes is that it reduces as far as possible the time spent in the tangentially bound state, which minimizes the loss of nucleosomes by dissociation.
A singular values approach in helicopter gas turbine engines flight testing analysis (2020)

The process of empirical models evaluation is at the core business of experimental flight-testing data analysis. Accurate and convenient flight-testing of helicopter engine(s) available power is crucial for predicting the total helicopter performance. Common practice in estimation of in-flight helicopter gas turbine engine power consists of a reduction of flight-test data into simplistic single-variable analysis approach. While such an approach is convenient for practical use, it often results in unrealistic predictions of the available engine(s) power. A novel approach for the helicopter available power problem is the so-called Multivariable Polynomial Optimization under Constraints method. In this method, 18 regressors, constructed from the engine non-dimensional parameters, are used to define empirical polynomial models. This paper is intended to complement the Multivariable Polynomial Optimization under Constraints method and answer the question of which multivariable polynomial can be generally used in representing helicopter gas-turbine engine performance? In this sense, a variety of seven gas-turbine engines installed on different helicopters are analyzed, each one giving 512 possible polynomial models to be used for available-power calculations. While conventional statistical methods of hypothesis-testing failed in providing the answer to the question stated above of which the best general empirical model for representing engine performance is, an alternative approach based on the Singular-Value-Decomposition theorem, was proven successful in providing the answer. Moreover, this approach presented in the paper yielded a short list of 10 simple and convenient multivariable polynomials, best representing the performance of all seven engines analyzed as a group.
Phlegmasia Cerulea Dolens: Therapeutic Considerations (1988)

Phlegmasia cerulea dolens (PCD) is a rare venous disorder that continues to be a major therapeutic challenge. We reviewed 16 cases of PCD treated during the past 15 years; 11 of the patients were male, and the average age of all the patients was 59 years. Malignant disease was the most common underlying condition (seven patients). Venous gangrene (VG) was present in seven extremities. Three treatment methods were used alone or in combination--intravenous heparin, venous thrombectomy, and thrombolytic therapy. Heparin was used initially in 13 patients; it yielded a successful result in seven (53%) patients, none of whom had VG. Venous thrombectomy was done in six patients; in three it was the primary procedure, in two it followed failure of heparin, and in one it followed failure of both heparin and thrombolytic therapy. Venous thrombectomy was successful in three (50%) patients, one of whom had early VG. Thrombolytic therapy was used on one occasion in conjunction with both heparin and venous thrombectomy, without benefit. Five patients died, all with VG, three after heparin only, one after heparin and venous thrombectomy, and one after all three treatment methods. Review of the 38 cases reported in the recent literature shows comparable results. These data suggest that nongangrenous forms of PCD respond well to systemic anticoagulation. Combination therapy using venous thrombectomy and heparin is indicated for severe ischemia, early VG, or failure of PCD to improve after six to 12 hours of heparin therapy. Phlegmasia cerulea dolens with VG is the lethal form of the entity and responds poorly to established therapy. Future therapeutic trials need to consider aggressive use of thrombolysis with or without thrombectomy.
SCR Device Fabricated With Dummy-Gate Structure to Improve Turn-On Speed for Effective ESD Protection in CMOS Technology (2005)

Turn-on speed is the main concern for an on-chip electrostatic discharge (ESD) protection device, especially in the nanoscale CMOS processes with ultrathin gate oxide. A novel dummy-gate-blocking silicon-controlled rectifier (SCR) device employing a substrate-triggered technique is proposed to improve the turn-on speed of an SCR device for using in an on-chip ESD protection circuit to effectively protect the much thinner gate oxide. The fabrication of the proposed SCR device with dummy-gate structure is fully process-compatible with general CMOS process, without using an extra mask layer or adding process steps. From the experimental results in a 0.25-/spl mu/m CMOS process with a gate-oxide thickness of /spl sim/50 /spl Aring/, the switching voltage, turn-on speed, turn-on resistance, and charged-device-model ESD levels of the SCR device with dummy-gate structure have been greatly improved, as compared to the normal SCR with shallow trench isolation structure.
Measurement of islet cell antibodies in the Type 1 Diabetes Genetics Consortium: efforts to harmonize procedures among the laboratories (2010)

Modifications in the assays are needed to improve comparability of results expressed as WHO units/mL across laboratories. It will be essential to retain high intra- and inter-assay precision, sensitivity and specificity and to confirm the accuracy of harmonized methods.
Benefits of a roundabout (2010)

The signal-to-noise ratio for room-temperature readout of individual qubits can be substantially improved by taking an indirect route through intermediate energy levels.
Yap, a Novel Family of Eight bZIP Proteins in Saccharomyces cerevisiae with Distinct Biological Functions (1997)

Saccharomyces cerevisiae contains eight members of a novel and fungus-specific family of bZIP proteins that is defined by four atypical residues on the DNA-binding surface. Two of these proteins, Yap1 and Yap2, are transcriptional activators involved in pleiotropic drug resistance. Although initially described as AP-1 factors, at least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position ±2 from the optimal AP-1 site (TGACTCA); further, a Yap-like derivative of the AP-1 factor Gcn4 (A239Q S242F) binds efficiently to the Yap recognition sequence. Molecular modeling suggests that the Yap-specific residues make novel contacts and cause physical constraints at the ±2 position that may account for the distinct DNA-binding specificities of Yap and AP-1 proteins. To various extents, Yap1, Yap2, Yap3, and Yap5 activate transcription from a promoter containing a Yap recognition site. Yap-dependent transcription is abolished in strains containing high levels of protein kinase A; in contrast, Gcn4 transcriptional activity is stimulated by protein kinase A. Interestingly, Yap1 transcriptional activity is stimulated by hydrogen peroxide, whereas Yap2 activity is stimulated by aminotriazole and cadmium. In addition, unlike other yap mutations tested, yap4 (cin5) mutations affect chromosome stability, and they suppress the cold-sensitive phenotype of yap1 mutant strains. Thus, members of the Yap family carry out overlapping but distinct biological functions.
Topically Applied Etamsylate: A New Orphan Drug for HHT-Derived Epistaxis (Antiangiogenesis through FGF Pathway Inhibition) (2019)

Hereditary hemorrhagic telangiectasia (HHT) is a vascular dysplasia characterized by recurrent and spontaneous epistaxis (nose bleeds), telangiectases on skin and mucosa, internal organ arteriovenous malformations, and dominant autosomal inheritance. Mutations in <i>Endoglin</i> and <i>ACVRL1</i> / <i>ALK1</i> , genes mainly expressed in endothelium, are responsible in 90% of the cases for the pathology. These genes are involved in the transforming growth factor-β(TGF-β) signaling pathway. Epistaxis remains as one of the most common symptoms impairing the quality of life of patients, becoming life-threatening in some cases. Different strategies have been used to decrease nose bleeds, among them is antiangiogenesis. The two main angiogenic pathways in endothelial cells depend on vascular endothelial growth factor and fibroblast growth factor (FGF). The present work has used etamsylate, the diethylamine salt of the 2,5-dihydroxybenzene sulfonate anion, also known as dobesilate, as a FGF signaling inhibitor. In endothelial cells, in vitro experiments show that etamsylate acts as an antiangiogenic factor, inhibiting wound healing and matrigel tubulogenesis. Moreover, etamsylate decreases phosphorylation of Akt and ERK1/2. A pilot clinical trial (EudraCT: 2016-003982-24) was performed with 12 HHT patients using a topical spray of etamsylate twice a day for 4 weeks. The epistaxis severity score (HHT-ESS) and other pertinent parameters were registered in the clinical trial. The significant reduction in the ESS scale, together with the lack of significant side effects, allowed the designation of topical etamsylate as a new orphan drug for epistaxis in HHT (EMA/OD/135/18).
Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton (2022)

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a "genome shock", leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (<i>Gossypium hirsutum</i> and <i>Gossypium barbadense</i>, AADD) and its extant AA (<i>Gossypium arboreum</i>) and DD (<i>Gossypium raimondii</i>) progenitors. We observed distinct DHS distributions between <i>G. arboreum</i> and <i>G. raimondii</i>. In contrast, the DHSs of the two subgenomes of <i>G. hirsutum</i> and <i>G. barbadense</i> showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids <i>Gossypium darwinii</i> and <i>G. hirsutum</i> var. <i>yucatanense</i>, but absent from a resynthesized hybrid of <i>G. arboreum</i> and <i>G. raimondii</i>, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative <i>cis</i>-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.
Cost-Effective Surface Modification for Metallic Bipolar Plates (2006)

Presented at the 2006 DOE Hydrogen, Fuel Cells & Infrastructure Technologies Program Annual Merit Review in Washington, D.C., May 16-19, 2006.
Quantized Consensus (2006)

We study the distributed averaging problem on arbitrary connected graphs, with the additional constraint that the value at each node is an integer. This discretized distributed averaging problem models averaging in a network with finite capacity channels (and in this form has applications to distributed detection in sensor networks) and load balancing in a processor network. We describe simple randomized distributed algorithms which achieve consensus to the extent that the discrete nature of the problem permits.
Experimental determination of shift-less aberration bases for sensorless adaptive optics in nonlinear microscopy (2021)

Adaptive optics can improve the performance of optical systems and devices by correcting phase aberrations. While in most applications wavefront sensing is employed to drive the adaptive optics correction, some microscopy methods may require sensorless optimization of the wavefront. In these cases, the correction is performed by describing the aberration as a linear combination of a base of influence functions, optimizing an image quality metric as a function of the coefficients. The influence functions base is generally chosen to either efficiently represent the adaptive device used or to describe generic wavefronts in an orthogonal fashion. A rarely discussed problem is that most correction bases have elements which introduce, together with a correction of the aberration, a shift of the imaging field of view in three dimensions. While simple methods to solve the problem are available for linear microscopy methods, nonlinear microscopy techniques such as multiphoton or second harmonic generation microscopy require non-trivial base determination. In this paper, we discuss the problem, and we present a method for calibrating a shift-less base on a spatial light modulator for two-photon microscopy.
Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System (2016)

In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.
Dispersive Liquid–Liquid Microextraction (DLLME) (2017)

Approaches for analytical-scale extraction are developing rapidly as new strategies are implemented to improve sample throughput, to minimize material use in laboratory methods, and to develop on-site capabilities. In this contribution, definitions and recommendations for symbols for the terms used in analytical extraction are presented. Exhaustive, microextraction, elevated temperature, microwave- and ultrasound-assisted, parallel batch, flow through systems, and membrane extraction approaches are discussed. An associated tutorial titled “Extraction” provides a detailed introduction to the topic.