gebhart/patrepeval huggingface dataset:
Biomarkers in orthodontic tooth movement (2015)

Tooth movement by orthodontic treatment is characterized by remodeling changes in the periodontal ligament, alveolar bone, and gingiva. A reflection of these phenomenons can be found in the gingival crevicular fluid (GCF) of moving teeth, with significant elevations in the concentrations of its components like, cytokines, neurotransmitters, growth Factors, and a arachidonic acid metabolites. GCF arises at the gingival margin and can be described as a transudate or an exudate. Several studies have focused on the composition of GCF and the changes that occur during orthodontic tooth movement (OTM). GCF component analysis is a non-invasive method for studying the cellular response of the underlying periodontium. Clinically, GCF can be easily collected using platinum loops, filter paper strips, gingival washings, and micropipettes. A number of GCF biomarkers involve in bone remodeling during OTM. The data suggest that knowledge of all the biomarkers present in the GCF that can be used to mark the changes in tooth that is undergoing orthodontic treatment may be of clinical usefulness leading to proper choice of mechanical stress to improve and to shorten treatment time and avoid side effects.
Model order reduction for the transient vibro-acoustic simulation of acoustic guitars (2016)

Element-based modeling techniques such as the finite element method can be used to study the characteristics of a guitar design. While these element-based formulations are versatile enough to accurately describe the complex physical behavior of acoustic guitars, they are also computationally very demanding, especially for transient analysis where the system behavior has to be computed at a very large number of points in time. This paper proposes stability-preserving model order reduction techniques to facilitate the use of finite element models for the transient simulation of acoustic guitars. In this paper a Krylov subspace technique for model order reduction is paired with a fully coupled vibro-acoustic finite element model of a YAMAHA acoustic guitar. The resulting reduced-order model is small yet accurate and stable, and allows for auralization of the sound produced by the guitar model as well as the visualization of the full transient displacement and sound fields.
Ordering cancer mutational profiles of cross-sectional copy number alterations (2016)

Understanding the dynamical evolution of cancer, with the final goal of developing effective techniques for diagnosis, prediction and treatment is one of the main challenges of modern biosciences. In this paper we approach the temporal ordering reconstruction problem, which refers to the temporal sorting of a collection of static biological data. The solution of this problem may help in better understanding the key principles and properties of the disease progression. By using a previously proposed technique for extracting temporal progressions from cross-sectional cancer gene expression data, we develop a novel methodology to be applied to static cross-sectional copy number alterations, and we test it on patients diagnosed with colorectal cancer at different stages. To capture distinct aspects of this complex phenomenon, we define several measures of chromosomal alterations and filters targeting significant portions of chromosomes. Results obtained with various measures and filters highlight the best setting for the problem, the most relevant chromosomal alterations and emphasise the influence that copy number alterations hitting key genes may have on the development of the disease.
Organometallic Compounds as Sources of Carbanions (1986)

Alkanes, with their strong, low polarity C—C and C—H bonds, rarely participate in ionic reactions unless some heteroatom is present. The common heteroatoms such as halogen, oxygen and nitrogen are all more electronegative than carbon. The substituted carbon atoms are therefore cationoid and susceptible to nucleophilic attack; hence the predominance of SN reactions in aliphatic chemistry.
Research on Collision Detection Algorithm Based on OBB (2013)

To enhance the real-time and accuracy of collision detection in virtual environment, introduces oriented bounding box (OBB) technology of hierarchical bounding box collision detection algorithm:construction of bounding box, generation of bounding box tree, implementation of collision detection algorithm,overlap judgement of bounding box. Collision detection algorithm based on OBB in this article is applied to solve the problem of collision detection between rigid bodies.
An Efficient Method for the Regioselective Aminolysis of 2,3α‐Steroidal Epoxide. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Candida parapsilosis isolates carrying mutations outside FKS1 hotspot regions confer high echinocandin tolerance and facilitate the development of echinocandin resistance (2023)

Candida parapsilosis is a significant cause of candidemia worldwide. Echinocandin-resistant (ECR) and echinocandin-tolerant (ECT) C. parapsilosis isolates have been reported in various countries but are rare. Resistance and tolerance are predominantly caused by mutations related to the hotspot (HS) regions of the FKS1 gene. A relatively high proportion of clinical C. parapsilosis isolates carrying mutations outside the HS regions has been noted in some studies, but an association with echinocandin (EC) resistance or tolerance was not explored. Herein, CRISPR-Cas9 was used and the association between amino acid substitution in FKS1 outside HS 1/2 (V595I, S745L, M1328I, F1386S, and A1422G) with EC susceptibility profile was delineated. None of the mutations conferred EC resistance, but they resulted in a significantly higher level of EC tolerance than the parental isolate, ATCC 22019. When incubated on agar plates containing ECs, specifically caspofungin and micafungin, ECR colonies were exclusively observed among ECT isolates, particularly mutants carrying V595I, S745L, and F1386S. Additionally, mutants had significantly better growth rates in yeast extract peptone dextrose (YPD) and YPD containing agents inducing membrane and oxidative stresses. The mutants had a trivial fitness cost in the Galleria mellonella model relative to ATCC 22019. Collectively, this study supports epidemiological studies to catalog mutations occurring outside the HS regions of FKS1, even if they do not confer EC resistance. These mutations are important as they potentially confer a higher level of EC tolerance and a higher propensity to develop EC resistance, therefore unveiling a novel mechanism of EC tolerance in C. parapsilosis. The identification of EC tolerance in C. parapsilosis may have direct clinical benefit in patient management.
A Comparative Analysis of Characteristics of Mode Choice and Mode Transfer to Public Transit by Mode-Choice Class for the Effective Transportation Demand Management Implement (2013)

대도시를 중심으로 승용차 이용을 억제하고 대중교통의 수단분담률을 제고시키기 위한 다양한 교통수요관리방안이 추진되어 왔으나 승용차 통행량의 감소와 같은 정책적인 효과는 충분하다고 볼 수 없다. 이러한 원인의 하나로 대중교통 서비스의 향상을 통해 승용차로부터의 수단전환을 유도하는 정책들이 대중교통의 수단적 효용을 증가시키는 효과는 있었으나 모든 승용차 이용자에게 대중교통으로 전환할 정도는 아니었다는 것을 들 수 있다. 이에 본 연구에서는 교통수단선택 계층에 따라 교통수요관리 방안에 대한 인식의 차이가 있을 것으로 보고, 불특정 다수의 통행에서 승용차의 이용빈도를 기준으로 교통수단선택 계층(승용차 의존층, 승용차 선택층, 대중교통 선택층, 대중교통 의존층)을 분류하고 각 계층별로 수단선택 영향요인에 대한 인식 및 교통환경의 변화에 대한 통행행태의 차이를 비교 분석하였다. 그 결과로 승용차의 의존도가 높을수록 편리함이나 쾌적함과 같은 정성적 요인을 더 중요시 인식하고 있으며, 주차규제나 통행시간 및 비용의 증가와 같은 교통수요관리기법에 대해서는 승용차의 의존도가 낮을수록 대중교통으로 전환될 가능성이 높다는 것을 나타내었다. 또한 주차규제 정책 추진시 주변 도로의 주차단속이 병행되어야 하며, 경제적인 부담을 가중시키는 방법으로는 주차요금과 같이 승용차 이용시 선택적으로 발생되는 비용보다 연료비 인상과 같이 상시적인 비용부담이 가중될 수 있는 방법이 보다 효과적이라는 정책적인 시사점을 제시하였다. Various schemes of transportation demand management(TDM) to discourage the use of cars and enhance public transit performance have been implemented in large cities. Nevertheless, policy effects in reducing car have not been satisfactory. Car-dependent travelers who tend to keep driving cars regardless of the change of the trip circumstances as such increase of travel time and cost according to car use or improvement of public transit service may be due to not according to utility reflecting mode-specific impedance and their own socio-economic characteristics. In this study, travelers were classified into four groups by their choice frequency of private car and public transit in unspecified multiple trip(car-dependent, car-choice, public transit-choice, public transit-dependent class). And the characteristics of each group were comparative analyzed. The results show that the group of a higher car-dependent is a higher priority on convenience and comfortability of the car when making decisions and the group of a lower of car-dependent is likely to change to public transit.
Development and Evaluation of Motion-activated System for Improved Chest Drainage: Bench, In Vivo Results, and Pilot Clinical Use of Technology (2020)

<i>Objective</i>. The aim of this study was to evaluate a motion-activated system (MAS) that applies motion-activated energy (vibration) to prevent chest tube clogging and maintain tube patency. We performed chest tube blood flow analysis in vitro, studied MAS effects on intraluminal clot deposition in vivo, and conducted a pilot clinical test. <i>Background</i>. Chest tube clogging is known to adversely contribute to postoperative cardiac surgery outcomes. <i>Methods</i>. The MAS was tested in vitro with a blood-filled chest tube model for device acceleration and performance. In vivo acute hemothorax studies (n = 5) were performed in healthy pigs (48.0 ± 2 kg) to evaluate the drainage in MAS versus control (no device) groups. Using a high-speed camera (FASTCAM Mini AX200, 100 mm Zeiss lens) in an additional animal study (n = 1), intraluminal whole-blood activation imaging of the chest tube (32 Fr) was made. The pilot clinical study (n = 12) consisted of up to a 30 minutes device tolerance test. <i>Results</i>. In vitro MAS testing suggested optimal device performance. The 2-hour in vivo evaluation showed a longer incremental drainage in the MAS group versus control. The total drainage in the MAS group was significantly higher than that in the control group (379 ± 144 mL vs 143 ± 40 mL; <i>P</i> = .0097), indicating tube patency. The high-speed camera images showed a characteristic intraluminal blood "swirling" pattern. Clinical data showed no discomfort with the MAS use (pleural = 4; mediastinal = 8). <i>Conclusions</i>. The MAS showed optimal performance at bench and better drainage profile in vivo. The clinical trial showed patients' tolerance to the MAS and device safety.
Distortion of the Poisson Bracket by the Noncommutative Planck Constants (2009)

In this paper we introduce a kind of "noncommutative neighbourhood" of a semiclassical parameter corresponding to the Planck constant. This construction is defined as a certain filtered and graded algebra with an infinite number of generators indexed by planar binary leaf-labelled trees. The associated graded algebra (the classical shadow) is interpreted as a "distortion" of the algebra of classical observables of a physical system. It is proven that there exists a q-analogue of the Weyl quantization, where q is a matrix of formal variables, which induces a nontrivial noncommutative analogue of a Poisson bracket on the classical shadow.
Assessment of inflow boundary conditions for compressible turbulent boundary layers (2004)

A description of different inflow methodologies for turbulent boundary layers, including validity and limitations, is presented. We show that the use of genuine periodic boundary conditions, in which no alteration of the governing equations is made, results in growing mean flow and decaying turbulence. Premises under which the usage is valid are presented and explained, and comparisons with the extended temporal approach [T. Maeder, N. A. Adams, and L. Kleiser, “Direct simulation of turbulent supersonic boundary layers by an extended temporal approach,” J. Fluid Mech. 429, 187 (2001)] are used to assess the validity. Extending the work by Lund et al. [J. Comput. Phys. 140, 233 (1998)], we propose an inflow generation method for spatial simulations of compressible turbulent boundary layers. The method generates inflow by reintroducing a rescaled downstream flow field to the inlet of a computational domain. The rescaling is based on Morkovin’s hypothesis [P. Bradshaw, “Compressible turbulent shear layers,” Annu. Rev. Fluid Mech. 9, 33 (1977)] and generalized temperature–velocity relationships. This method is different from other existing rescaling techniques [S. Stolz and N. A. Adams, “Large-eddy simulation of high-Reynolds-number supersonic boundary layers using the approximate deconvolution model and a rescaling and recycling technique,” Phys. Fluids 15, 2398 (2003); G. Urbin and D. Knight, “Large-eddy simulation of a supersonic boundary layer using an unstructured grid,” AIAA J. 39, 1288 (2001)], in that a more consistent rescaling is employed for the mean and fluctuating thermodynamic variables. The results are compared against the well established van Driest II theory and indicate that the method is efficient and accurate.
The Rise of Hierarchical Nanostructured Materials from Renewable Sources: Learning from Nature (2018)

Mimicking Nature implies the use of bio-inspired hierarchical designs to manufacture nanostructured materials. Such materials should be produced from sustainable sources ( e.g., biomass) and through simple processes that use mild conditions, enabling sustainable solutions. The combination of different types of nanomaterials and the implementation of different features at different length scales can provide synthetic hierarchical nanostructures that mimic natural materials, outperforming the properties of their constitutive building blocks. Taking recent developments in flow-assisted assembly of nanocellulose crystals as a starting point, we review the state of the art and provide future perspectives on the manufacture of hierarchical nanostructured materials from sustainable sources, assembly techniques, and potential applications.
Diffusion Map-based Algorithm for Gain Function Approximation in the Feedback Particle Filter (2020)

Feedback particle filter (FPF) is a numerical algorithm to approximate the solution of the nonlinear filtering problem in continuous-time settings. In any numerical implementation of the FPF algorithm, the main challenge is to numerically approximate the so-called gain function. A numerical algorithm for gain function approximation is the subject of this paper. The exact gain function is the solution of a Poisson equation involving a probability-weighted Laplacian $\Delta_\rho$. The numerical problem is to approximate this solution using only finitely many particles sampled from the probability distribution $\rho$. A diffusion map-based algorithm was proposed by the authors in prior works [A. Taghvaei and P. G. Mehta, Gain function approximation in the feedback particle filter, in 2016 IEEE 55th Conference on Decision and Control (CDC), IEEE, 2016, pp. 5446--5452], [A. Taghvaei, P. G. Mehta, and S. P. Meyn, Error estimates for the kernel gain function approximation in the feedback particle filter, in American Control Conference (ACC), IEEE, 2017, pp. 4576--4582] to solve this problem. The algorithm is named as such because it involves, as an intermediate step, a diffusion map approximation of the exact semigroup $e^{\Delta_\rho}$. The original contribution of this paper is to carry out a rigorous error analysis of the diffusion map-based algorithm. The error is shown to include two components: bias and variance. The bias results from the diffusion map approximation of the exact semigroup. The variance arises because of finite sample size. Scalings and upper bounds are derived for bias and variance. These bounds are then illustrated with numerical experiments that serve to emphasize the effects of problem dimension and sample size. The proposed algorithm is applied to two filtering examples and comparisons provided with the sequential importance resampling (SIR) particle filter.
Plasma-cell-interaction: Expression of surface molecules on HaCaT keratinocytes after treatment with dielectric barrier discharge (DBD) plasma (2011)

Summary form only given. Non-thermal atmospheric-pressure plasmas have been developed that will be used for several indications, e.g. also in medicine. Here, living tissues and cells are in focus of plasma treatment, e.g. to improve wound healing or to induce apoptosis and growth arrest in tumour cells. Detailed investigations of plasma-cell interactions are strongly needed. The cell membrane with its embedded proteins is the first target of plasma treatment. Such cell surface molecules as integrins, cadherins or the epidermal growth factor receptor (EGFR) are of importance in wound healing and also for development of cancer metastasis. This study focused on measurement of cell surface molecules on human HaCaT keratinocytes promoting adhesion, migration and proliferation as one important feature of plasma-cell interactions. HaCaT keratinocytes were treated with plasma by a surface dielectric barrier discharge in air. Cell surface molecules were analyzed by flow cytometry 24h after plasma treatment. Besides a reduction of cell viability a significant down regulation of E-cadherin and the EGFR expression was observed. The influence on α <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> - and β <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -integrin was less pronounced and expression of ICAM-1 was not affected. The extent of effects depended on the treatment regimen and the exposure time of cells to the plasma. The two-dimensional culture of HaCaT keratinocytes are proved to be a suitable method of investigating plasma-cell interactions.
Breast tumor diagnosis system using three dimensional ultrasonic echography (1997)

This paper describes a breast tumor diagnosis system using three dimensional ultrasonic echographic images. Since a malignant tumor is characterized by the morphological surface roughness, it is significant for the diagnosis to extract the exact boundaries of the tumor and show the three dimensional structure of the tumors. The proposed system consists of three dimensional image capturing system and a fuzzy reasoning based algorithm for the extraction of breast tumors. The method the authors proposed in this paper classifies all the voxels as one of "tumor", "normal tissue" or "boundary" by employing fuzzy reasoning and relaxation techniques. In order to evaluate the surface roughness, the authors define a parameter of a ratio of the surface area over the volume of the extracted tumor. The results for the clinical cases of three malignant and two benign tumors are successfully obtained by the system using an ultrasonic mechanical sector scanning probe of 10 MHz. It is found that the differences in the surface roughness between both types of tumors are clearly evident using a rendered surface image of the extracted tumor, and the average value of the defined parameter for the above three malignant tumors is 9.6, and 3.8 for the benign tumours.
Altered proximal tubule glucose metabolism in X-linked hypophosphatemic mice. (1992)

In the present study we examined renal proximal tubule glucose metabolism in the X-linked hypophosphatemic (Hyp/Y) mouse. Compared to those in its normal (+/Y) littermate, Hyp/Y mouse proximal tubules showed a higher rate of glucose production when using glutamine or alpha-ketoglutarate as a substrate. The glucose production rate was not, however, different when using malate or fructose as the substrate. PTH stimulated glucose production in +/Y, but not Hyp/Y, mouse proximal tubules. The PTH resistance in Hyp/Y mouse involves steps at and post-cAMP formation, because in Hyp/Y mouse proximal tubules PTH effects a lesser stimulation of cAMP generation, and addition of 8-bromo-cAMP failed to increase the glucose production rate. The rate of glucose utilization as a whole was not different in the two groups, but the rate of glucose metabolized through the pentose cycle (PC) pathway was markedly lower in Hyp/Y mouse proximal tubules. The lower PC activity in Hyp/Y mouse proximal tubules did not result from a defect of PC enzymes, because both glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase enzyme activities were intact, and phenazine methosulfate was able to stimulate PC activity. The higher rate of glucose production and the lower rate of PC activities persisted in the in vitro cultured Hyp/Y mouse proximal tubular cells. These results suggest that the altered glucose metabolism in the Hyp/Y mouse proximal tubule is not maintained by external influences and may be an abnormality intrinsic to these cells.
Relationship Between Sensorineural Hearing Loss and Vestibular and Balance Function in Children (2008)

Similarities between the peripheral auditory and vestibular systems suggest that children with sensorineural hearing loss (SNHL) may demonstrate vestibular and balance impairments. This hypothesis was studied in 40 children with severe to profound SNHL and unilateral cochlear implants (CI). Vestibular function was assessed with caloric, rotational, and vestibular evoked myogenic potential (VEMP) testing; balance was assessed with standardized static and dynamic tests. Horizontal semicircular canal function was abnormal in 53% (17/32) with caloric, and 39% (14/36) with rotational stimulation. Saccular function was absent bilaterally in 5/26 (19%) and unilaterally in 5/26 (19%) with VEMP. Balance abilities were significantly poorer (μ=12.9±5(SD)) than normal hearing controls (μ=17±5(SD); p=0.0006) and correlated best with horizontal canal function from rotational stimulation (p=0.004;R2=0.24). SNHL from meningitis was associated with worse balance function than other etiologies. Vestibular and balance dysfunction occurred in &gt;1/3 of children with SNHL and CI, and is highly dependent on etiology.
Testosterone, androstenedione, dehydroepiandrosterone sulfate, and sex‐hormone‐binding globulin in pregnant alcohol abusers (1989)

We compared serum concentrations of total and free testosterone, androstenedione, dehydroepiandrosterone sulfate (DHEAS), and sex-hormone-binding globulin in 40 pregnant women exhibiting consistent alcohol abuse and in 20 abstinent pregnant controls. Sixteen drinkers gave birth to infants with fetal alcohol effects; the remaining 24 drinkers delivered healthy infants. Drinking patients with healthy infants had normal concentrations of total and free testosterone, sex-hormone-binding globulin, and DHEAS, but their levels of androstenedione increased between weeks 20-40 of pregnancy. Maternal drinking leading to fetal alcohol effects was accompanied by lowered concentrations of sex-hormone-binding globulin throughout pregnancy and by low total testosterone concentrations, although the latter difference reached statistical significance only at 16-20 weeks' gestation. In contrast, drinking leading to fetal damage was associated with higher free testosterone levels between weeks 16-20 of pregnancy and lowered concentrations of DHEAS between weeks 16-32 of gestation, whereas the androstenedione levels tended to be high throughout pregnancy. These changes in androgens can be explained in part by low sex-hormone-binding globulin concentrations, an insufficient supply of DHEAS by the adrenals, and reduced peripheral conversion of androstenedione to testosterone.