gebhart/patrepeval huggingface dataset:
RESOLVING PHYLOGENETIC AND TAXONOMIC CONFLICT IN BEGONIA (2022)

Begonia is the world’s fastest-growing genus and a focus of intense taxonomic research. To support this, a stable and useful sectional classification is needed. This paper reviews the feasibility and challenges of creating an infrageneric classification for Begonia based on phylogenetic data, and how to overcome phylogenetic and taxonomic conflict. In particular, it (i) tests genus-wide patterns of incongruence between phylogenies based on the nuclear, chloroplast and mitochondrial genomes; (ii) explains organelle inheritance and its contribution to phylogenetic incongruence, and (iii) presents a manifesto for a workable and stable subgeneric classification in light of the above and lays the foundation for a collaborative Begonia Phylogeny Group.
Spectral properties of molecular iodine in absorption cells filled to specified saturation pressure (2014)

We present the results of measurement and evaluation of spectral properties of iodine absorption cells filled at certain saturation pressure. A set of cells made of borosilicate glass instead of common fused silica was tested for their spectral properties in greater detail with special care for the long-term development of the absorption media purity. The results were compared with standard fused silica cells and the high quality of iodine was verified. A measurement method based on an approach relying on measurement of linewidth of the hyperfine transitions is proposed as a novel technique for iodine cell absorption media purity evaluation. A potential application in laser metrology of length is also discussed.
Data set for diffusion coefficients and relative creep rate ratios of 26 dilute Ni-X alloy systems from first-principles calculations (2018)

The development of future generations of Ni-base superalloys will depend on a systematic understanding of how each alloying element affects the fundamental properties of Ni-base superalloys, particularly with respect to their creep behavior. First, this article presents the temperature-dependent data of all factors entering into dilute impurity diffusion for 26 Ni-X alloy systems, including atomic jump frequencies, thermodynamic parameters, and diffusivity plots. Second, this article presents the data used to calculate the relative creep rate ratios showing the effect of each of the 26 alloying elements, X, on the dilute Ni-X alloy. The dataset refers to "A comprehensive first-principles study of solute elements in dilute Ni alloys: Diffusion coefficients and their implications to tailor creep rate" by Hargather et al. [1].
Introduction: Notes on ‘The Fetus in the womb’ by Leonardo da Vinci (2020)

This work must begin with the conception of man, and describe the nature of the womb and how the foetus lives in it, up to what stage it resides there, and in what way it quickens into life and feeds.Also, its growth and what interval there is between one stage of growth and another.What it is that forces it out from the body of the mother, and for what reasons it sometimes comes out of the mother's womb before the due time.-Leonardo da Vinci.
The Translational Value of Psychophysiology Methods and Mechanisms: Multilevel, Dynamic, Personalized (2018)

Individuals' subjective and expressive experience of change does not always align with their physiological reactivity. Thus, behavior change may be best understood when concurrently assessed across multiple biobehavioral levels. Further, behavior is initiated in the moment, often before conscious deliberation, suggesting that multilevel behavior change research may benefit from real-time methodological designs. Last, substance use trajectories vary widely, suggesting that different MOBCs are more or less active in individuals depending on their personal constituency and the functional need that their substance use serves; thus, methods that are amenable to personalized modeling approaches are important.
Expression of interleukins 1, 3, 6, stem cell factor and their receptors in acute leukemia blast cells and in normal peripheral lymphocytes and monocytes (1993)

Reverse transcriptase-polymerase chain reaction amplification (RT-PCR) and Southern blot analysis were used to evaluate ligand and receptor expression of interleukin 1 alpha (IL-1 alpha), interleukin 3 (IL-3), interleukin 6 (IL-6) and stem cell factor (SCF) in peripheral blood lymphocytes and monocytes and in several acute leukemia blast cell populations. Resting peripheral lymphocytes and monocytes expressed both ligand and receptor of the four cytokines at considerable levels. The leukemic blast cells of the M1-M4 phenotypes are characterized by almost complete lack of expression of IL-1 alpha, IL-3 and IL-6 and the constant and usually high expression of SCF. On the other hand, these myeloid blast cells express generally high levels of the four cytokine receptors. The data suggest that the regulation of the expression of IL-1 alpha, IL-3 and IL-6, at least in our limited number of leukemic cell populations studied, is independent of that of SCF. The results indicate that, at least in most of the leukemic myeloid blasts cells, the expression of SCF and its receptor, the c-kit oncogene, may permit an autocrine regulation of cell cycling.
Cul4A targets p27 for degradation and regulates proliferation, cell cycle exit, and differentiation during erythropoiesis (2006)

As erythroid progenitors differentiate into precursors and finally mature red blood cells, lineage-specific genes are induced, and proliferation declines until cell cycle exit. Cul4A encodes a core subunit of a ubiquitin ligase that targets proteins for ubiquitin-mediated degradation, and Cul4A-haploinsufficient mice display hematopoietic dysregulation with fewer multipotential and erythroid-committed progenitors. In this study, stress induced by 5-fluorouracil or phenylhydrazine revealed a delay in the recovery of erythroid progenitors, early precursors, and normal hematocrits in Cul4A(+/-) mice. Conversely, overexpression of Cul4A in a growth factor-dependent, proerythroblast cell line increased proliferation and the proportion of cells in S phase. When these proerythroblasts were induced to terminally differentiate, endogenous Cul4A protein expression declined 3.6-fold. Its enforced expression interfered with erythrocyte maturation and cell cycle exit and, instead, promoted proliferation. Furthermore, p27 normally accumulates during erythroid terminal differentiation, but Cul4A-enforced expression destabilized p27 and attenuated its accumulation. Cul4A and p27 proteins coimmunoprecipitate, indicating that a Cul4A ubiquitin ligase targets p27 for degradation. These findings indicate that a Cul4A ubiquitin ligase positively regulates proliferation by targeting p27 for degradation and that Cul4A down-regulation during terminal erythroid differentiation allows p27 to accumulate and signal cell cycle exit.
CEACAM1 Promotes Melanoma Cell Growth through Sox-2 (2014)

The prognostic value of the carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1) in melanoma was demonstrated more than a decade ago as superior to Breslow score. We have previously shown that intercellular homophilic CEACAM1 interactions protect melanoma cells from lymphocyte-mediated elimination. Here, we study the direct effects of CEACAM1 on melanoma cell biology. By employing tissue microarrays and low-passage primary cultures of metastatic melanoma, we show that CEACAM1 expression gradually increases from nevi to metastatic specimens, with a strong dominance of the CEACAM1-Long tail splice variant. Using experimental systems of CEACAM1 knockdown and overexpression of selective variants or truncation mutants, we prove that only the full-length long tail variant enhances melanoma cell proliferation in vitro and in vivo. This effect is not reversed with a CEACAM1-blocking antibody, suggesting that it is not mediated by intercellular homophilic interactions. Downstream, CEACAM1-Long increases the expression of Sox-2, which we show to be responsible for the CEACAM1-mediated enhanced proliferation. Furthermore, analysis of the CEACAM1 promoter reveals two single-nucleotide polymorphisms (SNPs) that significantly enhance the promoter's activity compared with the consensus nucleotides. Importantly, case-control genetic SNP analysis of 134 patients with melanoma and matched healthy donors show that patients with melanoma do not exhibit the Hardy-Weinberg balance and that homozygous SNP genotype enhances the hazard ratio to develop melanoma by 35%. These observations shed new mechanistic light on the role of CEACAM1 in melanoma, forming the basis for development of novel therapeutic and diagnostic technologies.
Constraints on dark matter models from a Fermi LAT search for high-energy cosmic-ray electrons from the Sun (2011)

During its first year of data taking, the Large Area Telescope (LAT) onboard the Fermi Gamma-Ray Space Telescope has collected a large sample of high-energy cosmic-ray electrons and positrons (CREs). We present the results of a directional analysis of the CRE events, in which we searched for a flux excess correlated with the direction of the Sun. Two different and complementary analysis approaches were implemented, and neither yielded evidence of a significant CRE flux excess from the Sun. We derive upper limits on the CRE flux from the Sun's direction, and use these bounds to constrain two classes of dark matter models which predict a solar CRE flux: (1) models in which dark matter annihilates to CREs via a light intermediate state, and (2) inelastic dark matter models in which dark matter annihilates to CREs.
Cost-Efficient RAA Technology for Development of the High-Gain Steerable Antennas for mmWave Communications (2020)

For the future millimeter wave wireless systems the high gain steerable antennas are the key technology to overcome large path loss and support users’ mobility and reconfigurable backhauling. This paper introduces a specially designed reflect-array antenna (RAA), integrating single phased antenna array (PAA) module (as a feed source) and flat reflecting surface. The RAA provides high antenna gain by focusing the beam in vertical plane, but, at the same time, supporting beamsteering capability in the horizontal plane. The RAA technology allows creation of the very larger aperture antennas with simplified light-weight design. Two RAA prototypes with different feed source mounting demonstrated reliable multi-gigabit IEEE 802.11ad link 2.3–4.62 Gbps at distances 100–150m. These properties of the RAAs make them suitable for both millimeter-wave mobile access and reconfigurable backhauling applications.
Management of Hallux Valgus Deformity in Patients with Metatarsus Adductus (2016)

Category: Bunion Introduction/Purpose: Metatarsus adductus (MA) is a congenital condition in which there is persistent adduction of the metatarsals, which has been shown to increase the risk of recurrence of hallux valgus in patients undergoing surgery. The rate of recurrence varies with the magnitude of the adductus, perhaps correlating with the type of surgery performed, ie. the treatment of the adductus deformity and not just the hallux valgus. The goal of this study was to further analyze a cohort of patients with severe MA and identify clinical/surgical factors that are associated with a lower rate of recurrent deformity. Methods: An IRB approved retrospective review between 2002-2012 was completed. All patients undergoing hallux valgus surgery were identified. Patients were included if adequate radiographic information /clinical records were available and if the MAA was greater than 31° (normal values for the MA angle are &lt; 20°). Clinical information collected included associated diagnoses, the presence of arthritis of the tarsometatarsal joints, the presence and degree of lesser toe valgus deformities and surgical procedures completed. Radiographic recurrence was defined as a postoperative HVA &gt; 20° (at most recent follow up). Results: A total of 19 patients with severe MA/hallux valgus were identified. The average age of patients in this group was 55 years (51-60). Eight patients had associated tarsometatarsal arthritis and ten patients had severe valgus lesser toe deformities. Nine patients were treated with a modified Lapidus procedure and 10 patients underwent a distal first metatarsal osteotomy. Of the 9 patients who were treated with a modified Lapidus procedure, 5 patients underwent simultaneous realignment arthrodesis of the 2nd/3rd TMT joints for management of simultaneous midfoot arthritis. One of these patients had radiographic recurrence of deformity. Of the 7 patients who underwent a distal first metatarsal osteotomy without realignment arthrodesis of the 5 had recurrence of deformity. When evaluating patients for treatment of lesser toe deformity, 11 patients who were treated with simultaneous distal metatarsal realignment osteotomies, did not have recurrence of hallux valgus. Conclusion: Based on our findings, the use of a modified Lapidus arthrodesis led to a lower rate of HV deformity recurrence in comparison to isolated distal first metatarsal osteotomies but only when performed in conjunction with realignment arthrodesis of the 2nd/3rd TMT joints and distal lesser metatarsal osteotomies. If the patient does not have arthritis of the lesser TMT joints proximal metatarsal osteotomies are sufficient for correction. Treatment of lesser toe deformity with distal osteotomies was associated with lower recurrence of HV deformity and should be included as part of the treatment algorithm.
Peripheral authentication for autonomous vehicles (2016)

We propose a peripheral authentication scheme for autonomous vehicles. A mutual authentication protocol is required to secure every peripheral device access to a vehicle. Specifically, we present a vehicle to peripheral device authentication scheme. In addition, our three way handshake scheme for vehicle to keyfob authentication scheme based on generalized peripheral authentication scheme has been proposed. The vehicle to keyfob authentication scheme is adapted and improved with an additional attribute verification of the keyfob holder. Conventionally, vehicle to keyfob authentication is realized through a challenge-response verification protocol. An authentic coupling between the vehicle identity and the keyfob avoids any illegal access to the vehicle. However, these authentication messages can be relayed by an active adversary, thereby, can amplify the actual distance between the authentic vehicle and the keyfob. Eventually, through this malicious relaying an adversary can possibly get access to the vehicle, without any effort to generate or decode the crypto credentials. Our solution is a two party, three way handshake scheme with proactive and reactive commitment verification. Conceptually, our solution is different than the distance bounding protocols that requires multiple rounds of round trip delay measurement.
Mortality prediction in idiopathic pulmonary fibrosis: evaluation of computer-based CT analysis with conventional severity measures (2016)

Computer-based computed tomography (CT) analysis can provide objective quantitation of disease in idiopathic pulmonary fibrosis (IPF). A computer algorithm, CALIPER, was compared with conventional CT and pulmonary function measures of disease severity for mortality prediction.CT and pulmonary function variables (forced expiratory volume in 1 s, forced vital capacity, diffusion capacity of the lung for carbon monoxide, transfer coefficient of the lung for carbon monoxide and composite physiologic index (CPI)) of 283 consecutive patients with a multidisciplinary diagnosis of IPF were evaluated against mortality. Visual and CALIPER CT features included total extent of interstitial lung disease, honeycombing, reticular pattern, ground glass opacities and emphysema. In addition, CALIPER scored pulmonary vessel volume (PVV) while traction bronchiectasis and consolidation were only scored visually. A combination of mortality predictors was compared with the Gender, Age, Physiology model.On univariate analyses, all visual and CALIPER-derived interstitial features and functional indices were predictive of mortality to a 0.01 level of significance. On multivariate analysis, visual CT parameters were discarded. Independent predictors of mortality were CPI (hazard ratio (95% CI) 1.05 (1.02-1.07), p<0.001) and two CALIPER parameters: PVV (1.23 (1.08-1.40), p=0.001) and honeycombing (1.18 (1.06-1.32), p=0.002). A three-group staging system derived from this model was powerfully predictive of mortality (2.23 (1.85-2.69), p<0.0001).CALIPER-derived parameters, in particular PVV, are more accurate prognostically than traditional visual CT scores. Quantitative tools such as CALIPER have the potential to improve staging systems in IPF.
Influence of the bluff body shear layers on the wake of a square prism in a turbulent flow (2016)

The influence of freestream turbulence on the transitional characteristics of a 2D square prism shear layer was considered experimentally. Bypass transition was observed to cause intermittent shear layer reattachment; this event has a cascading influence downstream, altering the formation of the von-K\'arm\'an street.
Acoustic holography with a concentric rigid and open spherical microphone array (2009)

We present a new method and performance data related to volumetric acoustic intensity imaging using a spherical microphone array (SMA) consisting of a dual, concentric rigid and open SMA. The dual, concentric array was designed to improve the frequency range of a standard SMA. We apply standard techniques associated with interior spherical near-field acoustic holography (NAH) and, in particular, consider issues related to the optimal use of information from both arrays for NAH projection and the advantages that thus accrue from utilising a dual, concentric SMA.
Microstructure, Solidification Texture, and Thermal Stability of 316 L Stainless Steel Manufactured by Laser Powder Bed Fusion (2018)

This article overviews the scientific results of the microstructural features observed in 316 L stainless steel manufactured by the laser powder bed fusion (LPBF) method obtained by the authors, and discusses the results with respect to the recently published literature. Microscopic features of the LPBF microstructure, i.e., epitaxial nucleation, cellular structure, microsegregation, porosity, competitive colony growth, and solidification texture, were experimentally studied by scanning and transmission electron microscopy, diffraction methods, and atom probe tomography. The influence of laser power and laser scanning speed on the microstructure was discussed in the perspective of governing the microstructure by controlling the process parameters. It was shown that the three-dimensional (3D) zig-zag solidification texture observed in the LPBF 316 L was related to the laser scanning strategy. The thermal stability of the microstructure was investigated under isothermal annealing conditions. It was shown that the cells formed at solidification started to disappear at about 800 °C, and that this process leads to a substantial decrease in hardness. Colony boundaries, nevertheless, were quite stable, and no significant grain growth was observed after heat treatment at 1050 °C. The observed experimental results are discussed with respect to the fundamental knowledge of the solidification processes, and compared with the existing literature data.
Fast Automated Inspection of Mechanical Assemblies using a combined 2D/3D vision approach (2012)

International audience
Lateral Pressure and VAS Pain Score Analysis for the Lateral Lumbar Interbody Fusion Procedure (2015)

In awake volunteers, the pressure at the iliac crest or greater trochanter at the break of the bed increases by increasing the bed angle. Women with a lower BMI had high VAS pain scores when their greater trochanter was at maximal bed break. Men with higher BMI had high VAS pain scores when their iliac crest was at maximal bed break. An awareness of the iliac crest or greater trochanter at the break of the bed should be considered to prevent pain and increased pressure based on the patient's sex and BMI.
Software cost estimation with incomplete data (2001)

The construction of software cost estimation models remains an active topic of research. The basic premise of cost modeling is that a historical database of software project cost data can be used to develop a quantitative model to predict the cost of future projects. One of the difficulties faced by workers in this area is that many of these historical databases contain substantial amounts of missing data. Thus far, the common practice has been to ignore observations with missing data. In principle, such a practice can lead to gross biases and may be detrimental to the accuracy of cost estimation models. We describe an extensive simulation where we evaluate different techniques for dealing with missing data in the context of software cost modeling. Three techniques are evaluated: listwise deletion, mean imputation, and eight different types of hot-deck imputation. Our results indicate that all the missing data techniques perform well with small biases and high precision. This suggests that the simplest technique, listwise deletion, is a reasonable choice. However, this will not necessarily provide the best performance. Consistent best performance (minimal bias and highest precision) can be obtained by using hot-deck imputation with Euclidean distance and a z-score standardization.
Computer-Aided Analysis of Nonlinear Systems (2020)

In general, the method of analysis applied to any nonlinear system depends to a large extent on the structure of the model representation. The combination of qualitative and numerical techniques has provided a useful, and more importantly flexible, methodology for the analysis of nonlinear systems. In control studies, the augmentation of the system model with one or more parameters enables the study of the system’s behavior over a specified range of parameter values. The stability of a model, both absolute and structural, is dependent on the location and distribution of degenerate singularities on the solution manifold of that system. The advantage of the parameterized cell map approach is that it combines the qualitative aspects of dynamical systems theory with the global aspect afforded by the unraveling algorithm. The dynamical systems approach is attractive in that it provides information on the very type of qualitative behavior the nonlinear model was constructed to emulate.
Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers (2012)

We determine the closest diploid progenitors of the triploid 'Cavendish' and 'Gros Michel' subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. 'Cavendish', 'Plantain' and 'Mutika-Lujugira'), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.