gebhart/patrepeval huggingface dataset:
A model explaining mRNA level fluctuations based on activity demands and RNA age (2021)

Cellular RNA levels typically fluctuate and are influenced by different transcription rates and RNA degradation rates. However, the understanding of the fundamental relationships between RNA abundance, environmental stimuli, RNA activities, and RNA age distributions is incomplete. Furthermore, the rates of RNA degradation and transcription are difficult to measure in transcriptomic experiments in living organisms, especially in studies involving humans. A model based on activity demands and RNA age was developed to explore the mechanisms of RNA level fluctuations. Using single-cell time-series gene expression experimental data, we assessed the transcription rates, RNA degradation rates, RNA life spans, RNA demand, accumulated transcription levels, and accumulated RNA degradation levels. This model could also predict RNA levels under simulation backgrounds, such as stimuli that induce regular oscillations in RNA abundance, stable RNA levels over time that result from long-term shortage of total RNA activity or from uncontrollable transcription, and relationships between RNA/protein levels and metabolic rates. This information contributes to existing knowledge.
Formation of orogenic gold deposits by progressive movement of a fault-fracture mesh through the upper crustal brittle-ductile transition zone (2022)

Orogenic gold deposits are comprised of complex quartz vein arrays that form as a result of fluid flow along transcrustal fault zones in active orogenic belts. Mineral precipitation in these deposits occurs under variable pressure conditions, but a mechanism explaining how the pressure regimes evolve through time has not previously been proposed. Here we show that extensional quartz veins at the Garrcon deposit in the Abitibi greenstone belt of Canada preserve petrographic characteristics suggesting that the three recognized paragenetic stages formed within different pressure regimes. The first stage involved the growth of interlocking quartz grains competing for space in fractures held open by hydrothermal fluids at supralithostatic pressures. Subsequent fluid flow at fluctuating pressure conditions caused recrystallization of the vein quartz and the precipitation of sulfide minerals through wall-rock sulfidation, with some of the sulfide minerals containing microscopic gold. These pressure fluctuations between supralithostatic to near-hydrostatic conditions resulted in the post-entrapment modification of the fluid inclusion inventory of the quartz. Late fluid flow occurred at near-hydrostatic conditions and resulted in the formation of fluid inclusions that have not been affected by post-entrapment modification as pressure conditions never returned to supralithostatic conditions. This late fluid flow is interpreted to have formed the texturally late, coarse native gold that occurs along quartz grain boundaries and in open spaces. The systematic evolution of the pressure regimes in orogenic gold deposits such as Garrcon can be explained by relative movement of fault-fracture meshes across the base of the upper crustal brittle-ductile transition zone. We conclude that early vein quartz in orogenic deposits is precipitated at near-lithostatic conditions whereas the paragenetically late gold is introduced at distinctly lower pressure.
Motion Adaptive Orientation Adjustment of a Virtual Teacher to Support Physical Task Learning (2012)

Watching a real teacher in a real environment from a good distance and with a clear viewing angle has a significant effect on learning physical tasks. This applies to physical-task learning in a mixed-reality environment as well. Observing and imitating body motion is important for learning some physical tasks, including spatial collaborative work. When people learn a task with physical objects, they want to try and practice the task with the actual objects. They also want to keep the referential behavior model close to them at all times. Showing the virtual teacher by using mixed-reality technology can create such an environment, and thus has been researched in this study. It is known that a virtual teacher-model's position and orientation influence (a) the number of errors, and (b) the accomplishment time in physical-task learning using mixed-reality environments. This paper proposes an automatic adjustment method governing the virtual teacher's horizontal rotation angle, so that the learner can easily observe important body motions. The method divides the whole task motion into fixed duration segments, and seeks the most important moving part of the body in each segment, and then rotates the virtual teacher to show the most important part to the learner accordingly. To evaluate the method, a generic physical-task learning experiment was conducted. The method was revealed to be effective for motions that gradually reposition the most important moving part, such as in some manufacturing and cooking tasks. This study is therefore considered likely to enhance the transference of physical-task skills.
Graphene stabilization of two-dimensional gallium nitride (2015)

The spectrum of two-dimensional (2D) materials beyond graphene offers a remarkable platform to study new phenomena in condensed matter physics. Among these materials, layered hexagonal boron nitride (hBN), with its wide bandgap energy (~5.0-6.0 eV), has clearly established that 2D nitrides are key to advancing novel devices1. A gap, however, remains between the theoretical prediction of 2D nitrides beyond hBN and experimental realization of such structures. Here we demonstrate the synthesis of 2D gallium nitride (GaN) via a novel migration-enhanced encapsulated growth (MEEG) technique utilizing epitaxial graphene. We theoretically predict and experimentally validate that the atomic structure of 2D GaN grown via MEEG is notably different from reported theory. Moreover, we establish that graphene plays a critical role in stabilizing the direct-bandgap (nearly 5.0 eV), 2D buckled structure. Our results provide a foundation for discovery and stabilization of novel 2D nitrides that are difficult to prepare via traditional synthesis.
Distribution and Taxonomy of Gomphocerinae (Orthoptera, Acrididae) Species in The Anatolian Black Sea Basin and Check List of Turkey Subfamily Fauna (2013)

This study was carried out especially between 2003 and 2006, at different altitudes and habitats, and 5244 Gomphocerinae specimens were collected in Black Sea Regions to determine subfamily species ranging between 200 meter and 2460 meter in 175 different localities in this area. These specimens were prepared according to standart methods in the laboratory, then researched and compared with present literature, acoustics characteristics, museum specimens determined before, and specimens researched. Finally, 52 species belonging to 17 genera of the Gomphocerinae subfamily along with present literature were indicated in the Black Sea Region. Eight of 52 Gomphocerinae subfamily species were collected for the first time from the Black Sea Region and with previous studies totaly 60 Gomphocerinae subfamily taxon are distributed in this area. In addition to these, Dociostaurus ( Kazakia ) tartarus has been given a new record for Turkey. Original description name, printed journal, distributions for world, and variations, if existed, were given for every genus and species. By checking over previous studies, check list for Gomphocerinae subfamily fauna of Turkey was prepared, and evaluated in terms of taxonomic, faunistics, and biogeographic terms.
Effect of the vertical earthquake component on permanent seismic displacement of soil slopes based on the nonlinear Mohr–Coulomb failure criterion (2017)

In the present study, a model is developed to calculate the upper bound of the seismic displacement of a slope based on the sliding rigid block model. In this model, it is assumed that the geotechnical materials satisfy the nonlinear Mohr–Coulomb (M–C) failure criterion, and the instantaneous shear strength parameters are introduced by the “external tangent method”. A sequential quadratic program, based on the nonlinear iteration procedure, is also employed to obtain the optimal solution for the objective function. Using the upper bound method and the Newmark sliding rigid block model, the effect of the vertical earthquake component on the permanent displacement of slopes is studied under the following two conditions: (1) It is assumed that the vertical acceleration is in phase with the horizontal acceleration; (2) Actual vertical ground motion records are used (i.e., the vertical and horizontal accelerations are mutually independent). The results show that the nonlinear parameter m significantly affects the permanent displacement of slopes, and that the effect of the vertical earthquake component on permanent displacement cannot be ignored. The impact of the vertical earthquake component on slope stability will be overestimated if the vertical acceleration is in phase with the horizontal acceleration.
Metadynamics simulations of ice nucleation and growth (2008)

The metadynamics method for accelerating rate events in molecular simulations is applied to the problem of ice freezing. We demonstrate homogeneous nucleation and growth of ice at 180 K in the isothermal-isobaric ensemble without the presence of external fields or surfaces. This result represents the first report of continuous and dynamic ice nucleation in a system of freely evolving density. Simulations are conducted using a variety of periodic simulation domains. In all cases the cubic polymorph ice I(c) is grown. The influence of boundary effects on estimates of the nucleation free energy barrier are discussed in relation to differences between this and earlier work.
Probing Spatial Organization of DNA Strands Using Enzyme-Free Hairpin Assembly Circuits (2012)

Catalyzed hairpin assembly (CHA) is a robust enzyme-free signal-amplification reaction that has a wide range of potential applications, especially in biosensing. Although most studies of the analytical applications of CHA have focused on the measurement of concentrations of biomolecules, we show here that CHA can also be used to probe the spatial organization of biomolecules such as single-stranded DNA. The basis of such detection is the fact that a DNA structure that brings a toehold and a branch-migration domain into close proximity can catalyze the CHA reaction. We quantitatively studied this phenomenon and applied it to the detection of domain reorganization that occurs during DNA self-assembly processes such as the hybridization chain reaction (HCR). We also show that CHA circuits can be designed to detect certain types of hybridization defects. This principle allowed us to develop a "signal on" assay that can simultaneously respond to multiple types of mutations in a DNA strand in one simple reaction, which is of great interest in genotyping and molecular diagnostics. These findings highlight the potential impacts of DNA circuitry on DNA nanotechnology and provide new tools for further development of these fields.
[The five-minute interview. A brief method for assessing expressed emotion status]. (1992)

The Camberwell Family Interview (CFI) has been developed to assess the expressed emotion status (EE), a measure of the attitudes and feelings that a relative expresses about a schizophrenic family member. The EE measure has shown to be a good predictor of relapses in the course of schizophrenia, and has proved valid in a number of different cultures. However, the extensive, semistructured CFI is so time-consuming, that it only has been employed in a few specialized research centers. Therefore a brief method for assessing the EE index has been developed on the basis of a 5-minute speech sample (FMSS), which showed a reasonable correspondence with EE ratings derived from the CFI. The present article describes the development of a German version of the FMSS. The correspondence between blind EE ratings derived from the FMSS and the CFI was investigated on a sample of 176 interviews of relatives of schizophrenics. The relationship between the procedures to assess the EE index was significantly close. These results show the validity of the FMSS as a brief EE screening procedure for German-speaking populations.
Monitoring Trends on Facebook (2011)

The public nature of user generated content on social media platforms offers the possibility for trend monitoring as an insight into the topics that attract the attention of a large fraction of users. While Google Trends and Twitter have already been recognized as a valuable source of trend information by the practitioners and scholars, at the moment there are no practical implementations or research efforts in the field of trend detection over Face book public posts. In this paper we present two contributions towards trend monitoring over Face book public posts. We propose and evaluate a system for trend detection based on the characteristics of the posts shared on Face book. Based on our results we propose three categories of trending topics: 'disruptive events', 'popular topics' and 'daily routines'. We analyze and compare the characteristics of the proposed categories in terms of distribution and information diffusion in order to increase the understanding of emerging trends on Face book. Finally we draw conclusions from our findings in terms of challenges and opportunities for future work in this direction.
Force tracking in impedance control (2002)

Two simple and computationally efficient schemes for force tracking using impedance control are presented. The schemes generate the reference position trajectory required to produce a desired contact force despite lack of knowledge of the environmental stiffness and location. The first scheme uses direct adaptive control to generate the reference position on-line as a function of the force tracking-error. The second scheme utilizes an indirect adaptive strategy in which the environmental parameters are estimated on-line, and the required reference position is computed based on these estimates. Simulation studies are presented for a 7-degrees-of-freedom (DOF) robotics research arm using full arm dynamics. It is shown that the adaptive schemes are able to compensate for uncertainties in both the environmental stiffness and location, so that the end-effector applies the desired contact force while exhibiting the specified impedance dynamics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Federated Clustering for Electricity Consumption Pattern Extraction (2022)

The wide popularity of smart meters enables the collection of massive amounts of fine-grained electricity consumption data. Extracting typical electricity consumption patterns from these data supports the retailers in their understanding of consumer behaviors. In this way, diversified services such as personalized price design and demand response targeting can be provided. Various clustering algorithms have been studied for electricity consumption pattern extraction. These methods have to be implemented in a centralized way, assuming that all smart meter data can be accessed. However, smart meter data may belong to different retailers or even consumers themselves who are not willing to share their data. In order to better protect the privacy of the smart meter data owners, this paper proposes two federated learning approaches for electricity consumption pattern extraction, where the k-means clustering algorithm can be trained in a distributed way based on two frequently used strategies, namely model-averaging and gradient-sharing. Numerical experiments on two real-world smart meter datasets are conducted to verify the effectiveness of the proposed method.
SYSTEMATICS, TAXONOMY AND CLASSIFICATION OF BACTERIA (2017)

РезюмеВ лекции представлены достижения последних лет по систематике микроорганизмов.Приведен терминологический словарь, приведены правила и порядок присвоения
Control of Virginia Creeper (Parthenocissus quinquefolia): Effects of Carrier Volume on Toxicity and Distribution of Triclopyr (1988)

The butoxyethyl ester of triclopyr {[(3,5,6-trichloro-2-pyridinyl)oxy] acetic acid} was more effective than either the triethylamine salt formulation or an equivalent combined rate of the butoxyethyl esters of triclopyr plus 2,4-D [(2,4-dichlorophenoxy)acetic acid] (1:2, w/w) for the control of Virginia creeper [ Parthenocissus quinquefolia (L.) Planch. # PRTQU]. Carrier volume did not affect 14 C-triclopyr absorption and distribution, but control generally was greater after high carrier-volume application (281 L/ha) because the dense Virginia creeper canopy was thoroughly penetrated. In orchards, Virginia creeper was controlled by triclopyr ester at 0.6 kg ae/ha through the second season after treatment if foliage was covered thoroughly.
Papulacandins - Synthesis and biological activity of papulacandin B derivatives. (1987)

A series of papulacandin B derivatives was synthesized and their in vitro and in vivo activity against Candida albicans and other fungi was established. The biological data have shown that some 10-alkyl ether and 11-acylamino derivatives exhibit an improved in vivo activity compared to papulacandin B whereas derivatization in other positions of the molecule led to less potent compounds.
Template-mediated synthesis and bio-functionalization of flexible lignin-based nanotubes and nanowires (2012)

Limitations of cylindrical carbon nanotubes based on the buckminsterfullerene structure as delivery vehicles for therapeutic agents include their chemical inertness, sharp edges and toxicological concerns. As an alternative, we have developed lignin-based nanotubes synthesized in a sacrificial template of commercially available alumina membranes. Lignin is a complex phenolic plant cell wall polymer that is generated as a waste product from paper mills and biorefineries that process lignocellulosic biomass into fuels and chemicals. We covalently linked isolated lignin to the inner walls of activated alumina membranes and then added layers of dehydrogenation polymer onto this base layer via a peroxidase-catalyzed reaction. By using phenolic monomers displaying different reactivities, we were able to change the thickness of the polymer layer deposited within the pores, resulting in the synthesis of nanotubes with a wall thickness of approximately 15 nm or nanowires with a nominal diameter of 200 nm. These novel nanotubes are flexible and can be bio-functionalized easily and specifically, as shown by in vitro assays with biotin and Concanavalin A. Together with their intrinsic optical properties, which can also be varied as a function of their chemical composition, these lignin-based nanotubes are expected to enable a variety of new applications including as delivery systems that can be easily localized and imaged after uptake by living cells.
Tunability improvement of a doubly resonant OPO for fast and high resolution gas spectroscopy (2018)

High resolution gas spectroscopy in the mid-infrared in a transportable device is a big challenge allowing to address numerous applications: air quality or industrial process monitoring, defense and security, medical diagnostics... Together with high tunability in the mid-infrared, spectral purity, narrow bandwidth, compactness and robustness are needed. Nested Cavity doubly resonant OPO (NesCOPO) fulfill all those requirements. This architecture is already commercialized (in the X-FLR8 portable gas analyzer from Blue Industry and Science) and allows to reach low threshold compatible with the use of compact micro-chip nanosecond YAG laser. A wide spectral range can be obtain (2 - 10 &mu;m). In the most mature version NesCOPO takes benefit of down-conversion of a laser radiation at 1.064 &mu;m in a PPLN bulk crystal and give rise to two secondary radiation around 1.5 &mu;m and between 3.2 and 4.25 &mu;m. This last radiation is used to probe rovibrational absorption lines of species of interest using absorption or transmission spectroscopy. Speed in the selection of the emitted wavelength can be an important requirement especially when security is involved. We use engineering of the crystal using fan-out configuration. Evolution of the bandwidth and phase shift between the three waves after reflection onto the end cavity mirror has to be managed to maintain high conversion efficiency. Experiment show more flexible behavior than expected with theory. This lead to fine wavelength control on the overall emission spectrum (over 1 &mu;m) without using crystal temperature tuning that slow down tuning speed.
Outcome of valve ablation in late‐presenting posterior urethral valves (2004)

PUV should be considered in boys presenting with voiding dysfunction. After valve ablation most patients improve dramatically. Despite surgery, enuresis, urinary frequency and poor bladder emptying persisted in some and required further treatment. The continued bladder dysfunction suggested that irreversible urinary tract damage may have occurred. Even in this apparently mildly affected group, long-term follow-up is essential.
Abstract P415: Weight Variation and Change in N-terminal Pro-brain Natriuretic Peptide (NT-proBNP) (2020)

Introduction: Natriuretic peptides (NPs) are biochemical markers of cardiac function and NTproBNP strongly predicts heart failure. NPs also have a role in the adipose tissue, stimulating lipolysis, mitochondrial biogenesis and browning of adipocytes. Cross-sectional studies have demonstrated that diabetes and higher levels of adiposity are paradoxically associated with lower levels of BNP and NT-proBNP, suggesting that NPs may protect against metabolic dysregulation. Methods: We hypothesized that increases in NT-proBNP over time would be associated with decreases in weight and a lower risk of obesity in a community-based population. We analyzed data from 10,093 participants from the Atherosclerosis Risk in Communities (ARIC) Study with measurements of NT-proBNP at two time points 6-years apart (visit 2, 1990-92 and visit 4, 1996-98). Multivariable regression models were used, and sensitivity analysis excluding patients with heart failure was performed. Results: Mean age at baseline (1990-1992) was 57 years (SD 6), 57% were women and 78% were white. The prevalence of obesity increased from 28% to 35% in the 6-year follow up period. Higher baseline levels of NT-proBNP were associated with reduced risk of obesity after adjustment for other risk factors ( Table ). There was an inverse association between change in NT-proBNP levels between the visits and weight change ( Figure ). Results were similar after excluding cases of heart failure. Conclusions: We found inverse associations of NT-proBNP levels with weight change and incidence of obesity. Our results suggest that NPs or their pathways may be potential targets in the treatment of obesity. Nonetheless, the molecular networks involving the natriuretic system are complex and additional work, especially intervention studies, are needed to address the clinical relevance of this finding.
Cation and Spin Ordering in the n = 1 Ruddlesden—Popper Phase La2Sr2LiRuO8. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
In-plane Raman scattering of (001)-Si/Ge superlattices: Theory and experiment (1994)

Using a micro-Raman setup, in-plane Raman scattering was performed on short-period (001)-Si/Ge superlattices, and the complete phonon spectrum (longitudinal and transverse, optical and acoustic modes) could be studied. In the relevant wave-vector range, the in-plane dispersion was found to affect the frequencies of folded-acoustic modes, while being negligible for confined optical modes. The comparison with theoretical spectra, calculated by means of first-principles interatomic force constants, shows that the observed deviations of ``unfolded'' confined optical modes from the bulk dispersions can be attributed to interface roughness and is well described by a simple alloy layer model (2--3 intermixed SiGe atomic layers at interfaces).