gebhart/patrepeval huggingface dataset:
Schemi per il monitoraggio dei terreni golenali parzialmente saturi del fiume panaro nella valutazione dei processi di interazione del suolo con vegetazione ed atmosfera (2021)

Il monitoraggio della zona non satura riveste un ruolo cruciale nella comprensione e nell’analisi dei fenomeni di interazione terreno-vegetazione-atmosfera ed è, ad oggi, pratica piuttosto frequente quella di far uso di sensori per la valutazione, diretta o indiretta, di alcune variabili di stato del suolo quali suzione e contenuto d’acqua. Tali misurazioni in campo, insieme ai dati ottenuti in laboratorio, permettono infatti di sviluppare modelli numerici previsionali dettagliati e rappresentativi delle reali condizioni di sito. Una delle applicazioni di maggior interesse in tal senso è certamente rappresentata dai rilevati arginali, nei quali la variabilità spazio-temporale del livello di saturazione soprattutto a seguito ed in concomitanza di eventi di precipitazione e piena, ha forti implicazioni sulle condizioni di stabilità e filtrazione. In tale ambito, l’uso di dati di monitoraggio può essere dunque cruciale nella valutazione del rischio associato a fenomeni di rottura sia locali che globali. Nella presente nota verrà presentato lo schema di monitoraggio della zona non satura di un settore arginale del fiume Panaro ed il contesto di studio; l’area ricade sulla sponda lato fiume dell’argine, nella quale sono monitorate in continuo suzione, contenuto d’acqua e temperatura del suolo fino ad una profondità massima di circa 3 m dal piano campagna. Questi dati, associati alle condizioni climatiche, oltre che idrometriche, forniranno un utile riscontro al complesso sistema di interazioni terreno-vegetazione-atmosfera specifiche del sito, garantendo un riferimento per le analisi del bilancio idrologico ed indicazioni sulle caratteristiche di ritenzione idrica del suolo.
RFM and CLV: Using Iso-Value Curves for Customer Base Analysis (2005)

The authors present a new model that links the well-known RFM (recency, frequency, and monetary value) paradigm with customer lifetime value (CLV). Although previous researchers have made a conceptual link, none has presented a formal model with a well-grounded behavioral ”story.” Key to this analysis is the notion of ”iso-value” curves, which enable the grouping of individual customers who have different purchasing histories but similar future valuations. Iso-value curves make it easy to visualize the interactions and trade-offs among the RFM measures and CLV. The stochastic model is based on the Pareto/NBD framework to capture the flow of transactions over time and a gamma-gamma submodel for spend per transaction. The authors conduct several holdout tests to demonstrate the validity of the model's underlying components and then use it to estimate the total CLV for a cohort of new customers of the online music site CDNOW. Finally, the authors discuss broader issues and opportunities in the application of this model in actual practice.
Tough Hydrogel-Based Biocontainment of Engineered Organisms for Continuous, Self-Powered Sensing and Computation (2020)

ABSTRACT Genetically modified microorganisms (GMMs) can enable a wide range of important applications, including environmental sensing, precision therapeutics, and responsive materials. However, containment of GMMs to prevent environmental escape and satisfy regulatory requirements is a bottleneck for real-world use 1–7 . While biochemical strategies have been developed to restrict unwanted growth and replication of GMMs in the environment 8–12 , there is a need for deployable physical containment technologies to achieve redundant, multi-layered, and robust containment 2 . In addition, form factors that enable easy retrieval would be useful for environmental sensing. To address this challenge, we developed a hydrogel-based encapsulation system for GMMs that incorporates a biocompatible multilayer tough shell and an alginate-based core. This DEployable Physical COntainment Strategy (DEPCOS) allows no detectable GMM escape, bacteria to be protected against environmental insults including antibiotics and low pH, controllable lifespan, and easy retrieval of genetically recoded bacteria. To highlight the versatility of a DEPCOS, we demonstrate that robustly encapsulated cells can execute useful functions, including performing cell-cell communication with other encapsulated bacteria and sensing heavy metals in water samples from the Charles River. We envision that our multilayered physical and chemical containment strategy will facilitate the realization of a wide range of real-world applications for ‘living’ biosensors.
Computer-aided diagnosis of melanocytic lesions. (2006)

Image analysis has the potential to distinguish nevi and melanomas and to support the clinical diagnosis of melanocytic lesions by the general practitioner.
Male mice express spermatogenic cell‐specific triosephosphate isomerase isozymes (2013)

SUMMARY Triosephosphate isomerase 1 (TPI1) is a member of the glycolytic pathway, which is a critical source of energy for motility in mouse sperm. By immunoblotting, we detected two male, germ line‐specific TPI1 bands (M r 33,400 and 30,800) as well as the somatic‐type band (M r 27,700). Although all three bands were observed in spermatogenic cells, somatic‐type TPI1 disappeared from sperm during epididymal maturation. In vitro dephosphorylation analysis suggested that the two male, germ line‐specific TPI1 bands were not the result of phosphorylation of the 27,700 M r TPI1 band. The M r 33,400; 30,800; and 27,700 TPI1 bands corresponded to the respective sizes of the proteins predicted to use the first, second, and third possible initiation codons of the Tpi1 cDNA. We performed immunofluorescence on epididymal sperm and determined that TPI1 specifically localized in the principal piece. The antibody staining was stronger in cauda epididymal sperm than in caput epididymal sperm, a finding consistent with the identification of TPI1 as a cauda epididymal sperm‐enriched protein. Immunofluorescence with sodium dodecyl sulfate (SDS)‐insoluble flagellar accessory structures showed a strong TPI1 signal only in the principal piece, indicating that TPI1 is a component of the fibrous sheath. Northern blot hybridization detected longer Tpi1 transcripts (1.56 kb) in mouse testis, whereas somatic tissues had shorter transcripts (1.32 kb). As there is only one triosephosphate isomerase gene in the mouse genome, we conclude that the three variants we see in sperm result from the use of alternative translation start codons in spermatogenic cells. Mol. Reprod. Dev. 80: 862–870, 2013. © 2013 The Authors . Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
Bdellovibrio bacteriovorusStrains Produce a Novel Major Outer Membrane Protein during Predacious Growth in the Periplasm of Prey Bacteria (2004)

Bdellovibrio bacteriovorus is a predatory bacterium that is capable of invading a number of gram-negative bacteria. The life cycle of this predator can be divided into a nonreproductive phase outside the prey bacteria and a multiplication phase in their periplasm. It was suggested that during the reproduction phase, B. bacteriovorus reutilizes unmodified components of the prey's cell wall. We therefore examined the outer membranes of B. bacteriovorus strains HD100 (DSM 50701) and HD114 (DSM 50705) by using Escherichia coli, Yersinia enterocolitica, and Pseudomonas putida as prey organisms. The combined sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometric analyses revealed novel and innate major outer membrane proteins (OMPs) of B. bacteriovorus strains. An incorporation of prey-derived proteins into the cell wall of B. bacteriovorus was not observed. The corresponding genes of the B. bacteriovorus strains were elucidated by a reverse-genetics approach, and a leader peptide was deduced from the gene sequence and confirmed by Edman degradation. The host-independent mutant strain B. bacteriovorus HI100 (DSM 12732) growing in the absence of prey organisms possesses an OMP similar to the major OMPs of the host-dependent strains. The similarity of the primary structure of the OMPs produced by the three Bdellovibrio strains is between 67 and 89%. The leader peptides of all OMPs have a length of 20 amino acids and are highly conserved. The molecular sizes of the mature proteins range from 34.9 to 37.6 kDa. Secondary-structure predictions indicate preferential alpha-helices and little beta-barrel structures.
Soft information transfer for sequence detection with concatenated receivers (1996)

Concatenated encoders are found in many digital communication systems. A concatenated receiver for such a system consists of a chain of independently working estimators ended with an outer detector. Each stage of the receiver chain corresponds to a certain code in the system. Maximum likelihood sequence detection with a concatenated receiver requires soft information consisting of symbol aposteriori probabilities to be transferred between the receiver stages. In this paper the optimal inner estimator is derived and further simplified into a new asymptotically optimal one by imposing a tree structure on the inner code. By mapping several suboptimal inner estimators onto the tree structure and noting which approximations they make, a theoretical performance ranking is obtained. The asymptotical performance of the optimal concatenated detector at high signal-to-noise ratios (SNRs) is investigated. The decision variables underlying the pairwise error event probability are shown to be asymptotically Gaussian and consequently a free Euclidean distance can be found for the optimal concatenated detector.
WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains (2003)

WW domains mediate protein-protein interactions in a number of different cellular functions by recognizing proline-containing peptide sequences. We determined peptide recognition propensities for 42 WW domains using NMR spectroscopy and peptide library screens. As potential ligands, we studied both model peptides and peptides based on naturally occurring sequences, including phosphorylated residues. Thirty-two WW domains were classified into six groups according to detected ligand recognition preferences for binding the motifs PPx(Y/poY), (p/phi)P(p,g)PPpR, (p/phi)PPRgpPp, PPLPp, (p/xi)PPPPP, and (poS/poT)P (motifs according to modified Seefeld Convention 2001). In addition to these distinct binding motifs, group-specific WW domain consensus sequences were identified. For PPxY-recognizing domains, phospho-tyrosine binding was also observed. Based on the sequences of the PPx(Y/poY)-specific group, a profile hidden Markov model was calculated and used to predict PPx(Y/poY)-recognition activity for WW domains, which were not assayed. PPx(Y/poY)-binding was found to be a common property of NEDD4-like ubiquitin ligases.
A measurement of equal-loudness level contours for tone burst (2001)

We measured equal-loudness level contours for tone bursts lasting about 20ms. The results, which need to be confirmed, suggest that equal-loudness contours for tone bursts are similar to those in ISO226 for long-duration tones at frequencies below 6kHz but not at higher frequencies.
Enzyme-Doped Thin Films and Optical Fiber Sensors for Glutamate (2002)

Biomolecules encapsulated in porous silicate glass using the sol-gel process form optically transparent materials capable of biorecognition. We are working to design biosensors from these materials for the detection of glutamate, the major excitatory neurotransmitter in the central nervous system. Previously we demonstrated the ability of glutamate dehydrogenase (GDH)-doped sol-gel bulk materials to measure glutamate at varying concentrations. Here we show that GDH can be encapsulated in a thin film while retaining its enzymatic activity. The films are likely to be reaction limited rather than diffusion limited, as the reaction rate at saturating glutamate concentrations varies linearly with enzyme loading. At a given enzyme loading, the film reaction rate increases with increasing glutamate concentration, demonstrating its potential as a glutamate sensor material. In addition we have shown that the enzyme-doped sol-gel glass can be deposited onto the tip of an optical fiber. The fiber is active and responds to the presence of glutamate.
False Data Injection Detection for Phasor Measurement Units (2022)

Cyber-threats are becoming a big concern due to the potential severe consequences of such threats is false data injection (FDI) attacks where the measures data is manipulated such that the detection is unfeasible using traditional approaches. This work focuses on detecting FDIs for phasor measurement units where compromising one unit is sufficient for launching such attacks. In the proposed approach, moving averages and correlation are used along with machine learning algorithms to detect such attacks. The proposed approach is tested and validated using the IEEE 14-bus and the IEEE 30-bus test systems. The proposed performance was sufficient for detecting the location and attack instances under different scenarios and circumstances.
Role of HtrA in Surface Protein Expression and Biofilm Formation by Streptococcus mutans (2005)

The HtrA surface protease in gram-positive bacteria is involved in the processing and maturation of extracellular proteins and degradation of abnormal or misfolded proteins. Inactivation of htrA has been shown to affect the tolerance to thermal and environmental stress and to reduce virulence. We found that inactivation of Streptococcus mutans htrA by gene-replacement also resulted in a reduced ability to withstand exposure to low and high temperatures, low pH, and oxidative and DNA damaging agents. The htrA mutation affected surface expression of several extracellular proteins including glucan-binding protein B (GbpB), glucosyltransferases, and fructosyltransferase. In addition, htrA mutation also altered the surface expression of enolase and glyceraldehyde-3-phosphate dehydrogenease, two glycolytic enzymes that are known to be present on the streptococcal cell surface. As expected, microscopic analysis of in vitro grown biofilm structure revealed that the htrA deficient biofilms adopted a much more granular patchy appearance, rather than the relatively smooth confluent layer normally seen in the wild type. These results suggest that HtrA plays an important role in the biogenesis of extracellular proteins including surface associated glycolytic enzymes and in biofilm formation of S. mutans.
Characterization of moldable glass for imaging lenses in the shortwave infrared (SWIR) (2014)

The growing demand for short wave infrared (SWIR) sensors and cameras has focused attention on the need for lower cost optics in this infrared region. Traditional low Tg moldable glasses typically stop transmitting in the SWIR region. New low dispersion, moldable glasses have been found that transmit through 3 microns and in combination with Precision Glass Molding (PGM) can bring this enabling technology to SWIR optics. 
This investigation reviews the material performance for a potential moldable solution in the SWIR range. Specific attention is given toward glasses that achieve high yields during precision glass molding and are candidates for commercial success.
Simulation of non-resonant stellarator divertor (2021)

An efficient numerical method of studying nonresonant stellarator divertors was introduced in Boozer and Punjabi [Phys. Plasmas 25, 092505 (2018)]. This method is used in this paper to study a different magnetic field model of a nonresonant divertor. The most novel and interesting finding of this study is that diffusive magnetic field lines can be distinguished from lines that exit through the primary and the secondary turnstile, and that below some diffusive velocity, all lines exit through only the primary turnstile. The footprints of each family are stellarator symmetric and have a fixed location on the wall for all velocities. The probability exponent of the primary turnstile is d1 = 9/4 and that of the secondary turnstile is d2 = 3/2. This study also addresses the issues of an inadequate separation of the chamber walls from the outermost confining magnetic surface and a marginal step size of the numerical integrations that could compromise the interpretation of the earlier results [Boozer and Punjabi, Phys. Plasmas 25, 092505 (2018)]. The previous value of d1 = 2 is within the error bar of d1 = 9/4 estimated here.
PReS-FINAL-1007: Regulatory T cells functional specialization in JIA (2013)

Regulatory T cells (Treg) are important players in keeping the immune system in balance. In juvenile idiopathic arthritis (JIA), an autoimmune disease characterized by chronic inflammation of the joints, this balance is disturbed. Recently, different functional subsets of regulatory T cells (Treg) have been described in mice and human that mirror the T helper subsets. A lot remains unknown about the function and mechanism of action of Treg (subsets), especially in inflammatory environments.
Hot hole transport in a-Si/c-Si heterojunction solar cells (2014)

The transport behavior of photogenerated minority carriers in an a-Si/c-Si heterojunction solar cell is dependent on the energy distribution function (EDF) of the carriers impinging on the hetero-interface. The high field region at the interface results in a strongly non-Maxwellian distribution of holes incident on the surface, which has implications for current collection and a significant impact on the overall efficiency of the device. This work studies the effect of the high field transport on photogenerated carriers at the hetero-interface through a combination of Monte Carlo simulations and analysis of defect assisted transport. A three band warped non-parabolic band model is implemented to describe the valence band in order to accurately represent high energy photocarriers. Also, percolation path theory is applied to study defect assisted transport in the intrinsic amorphous region by considering mechanisms such as defect capture through tunneling, emission through Poole - Frenkel effect, and emission through tunneling.
Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples (2015)

Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.
Static and Experimental Analyses of the Pedaling with the Slider-Crank Mechanism (2007)

A slider-crank mechanism whose coupler curve is the approximate ellipse is designed so that the human may perform the pedaling of the elliptical motion of the foot. The set of the frame, the crank of the usual bicycle and the foot, the shank, the thigh of the man's leg to be pedaling composes the planar five-link mechanism with two degrees freedom. The set of the frame, moving links and the foot, the shank, the thigh in slider-crank pedaling composes the planar seven-link mechanism with two degrees freedom. Kinematic and static analyses of planar five and seven link mechanisms above-mentioned are possible to perform with given values of the angular displacement of the foot (the pedal angle) and ones of joint moments at the hip and the knee during a crank rotation. Then, a new procedure is proposed for analyzing motion, forces and moments of components in cases of ordinary pedaling (simple crank pedaling) and slider-crank pedaling and for evaluating their performance of pedaling. Simulation results of the pedal angle, the pedal force and the crank moment are verified experimentally.
Dectin-3 Deficiency Promotes Colitis Development due to Impaired Antifungal Innate Immune Responses in the Gut (2016)

Interactions between commensal fungi and gut immune system are critical for establishing colonic homeostasis. Here we found that mice deficient in Dectin-3 (Clec4d-/-), a C-type lectin receptor that senses fungal infection, were more susceptible to dextran sodium sulfate (DSS)-induced colitis compared with wild-type mice. The specific fungal burden of Candida (C.) tropicalis was markedly increased in the gut after DSS treatment in Clec4d-/- mice, and supplementation with C. tropicalis aggravated colitis only in Clec4d-/- mice, but not in wild-type controls. Mechanistically, Dectin-3 deficiency impairs phagocytic and fungicidal abilities of macrophages, and C. tropicalis-induced NF-κB activation and cytokine production. The conditioned media derived from Dectin-3-deficient macrophages were defective in promoting tissue repairing in colonic epithelial cells. Finally, anti-fungal therapy was effective in treating colitis in Clec4d-/- mice. These studies identified the role of Dectin-3 and its functional interaction with commensal fungi in intestinal immune system and regulation of colonic homeostasis.
Turboelectricand Hybrid Electric Aircraft Drive Key Performance Parameters (2018)

NASA has been investigating electrified aircraft propulsion as a means of furthering its goals of reducing fuel burn, emissions, and noise. However, the electric drive components required introduce weight and efficiency penalties at odds with these goals. The purpose of this paper is to propose electric drive specific power, electric drive efficiency, and electric propulsion fraction as the key performance parameters for fully turboelectric, partially turboelectric, and parallel hybrid electric aircraft power systems. The impact of these parameters on overall aircraft performance are investigated. Range equations for each aircraft type are described. The benefits and costs that may result from the electrified propulsion systems are enumerated. A breakeven analysis is conducted to find the minimum allowable electric drive specific power and efficiency, for a given electrical propulsion fraction and battery specific energy, that can preserve the range, payload weight, input energy, and ratio of operating empty weight to initial weight of the conventional aircraft.