bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.
Authors: Zhang Hongyi , Deng Wenjing , Lu Changhua , He Mengling , Yan Hanjing 
Published: February 2022

Background
Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil.

Methods
To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads.

Results
In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” and “monoterpene biosynthesis”. Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in P. cablin.
Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study
Authors: Tandy Corinne B. , Odoi Agricola 
Published: February 2022

Background
In the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida.

Methods
Vaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions.

Results
Total exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high median income (p = 0.001), high percentage of Hispanic population (p = 0.046), and low percentage of population with a college education (p = 0.013). A predictor of high risk of non-medical vaccination exemptions was high percentage of White population (p = 0.045). However, predictors of low risks of non-medical exemptions were high percentages of population: living in rural areas (p = 0.023), with college education (p = 0.013), with high school education (p = 0.009), and with less than high school education (p < 0.001).

Conclusions
There is evidence of county-level geographic disparities in both total and non-medical vaccination exemption risks in Florida. These disparities are explained by differences in county-level socioeconomic and demographic factors. Study findings are important in guiding resource allocation for health planning aimed at improving vaccination rates and reducing incidence of vaccine-preventable diseases.
Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition
Authors: Zang Wenli , Liu Junchao , Geng Fengxue , Liu Dongjuan , Zhang Shuwei , Li Yuchao , Pan Yaping 
Published: February 2022

Background
Oral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism.

Methods
Two OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography.

Results
Our results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment.

Conclusions
Our study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis.
Preliminary Investigation of the Relationship of Ivymount Social Cognition Instructional Package (IvySCIP) to Similar Assessment Tools and Impact on Students with High Functioning Autism
Authors: Müller Eve , Wood Caitlin , Childress Deb , Cannon Lynn , Dardick William 
Published: February 2022

Abstract
Ivymount Social Cognition Instructional Project (IvySCIP) supports teachers and related service providers to implement data-driven social and emotional learning (SEL) instruction for their kindergarten through 5th grade students with social cognition challenges, especially those with high functioning autism spectrum disorders (HF-ASD). Based on comprehensive assessment of students’ SEL strengths and needs, IvySCIP identifies instructional priority areas, generates individualized education plan (IEP) goal recommendations, and enables SEL progress monitoring. In order to begin establishing the psychometric properties of the IvySCIP strengths and needs assessment, we examined correlations between participants’ scores on IvySCIP and their scores on similar tools. As predicted, strong correlations emerged between IvySCIP and other tools. We also examined the impact of using IvySCIP over a 20 week period to facilitate SEL in students with HF-ASD. IvySCIP was piloted with 53 instructor/student pairs broken into two groups. The first group received 20 weeks of access to IvySCIP and the latter received 10 weeks of access. While pilot study outcomes suggested that there were no significant differences between the groups, all students made significant SEL progress over the course of the 20 week study as measured by IvySCIP and similar tools. Social validation surveys indicated that instructors perceived IvySCIP to be innovative, valuable, and an effective means of improving SEL instruction for students.
Implantable left ventricular assist systems (LVAS): Recent results. A report from a series of meetings sponsored by the Study Group on Advanced Heart Failure of the Working Group on Heart Failure
Authors: Mohacsi Paul , Deng Mario C. , Murphy Richard , Bergh Claes‐Håkan , Gronda Edoardo , Komajda Michel , Pacher Richard , Spinar Jindrich , Swedberg Karl , Cleland John F. 
Published: July 2002

AbstractImplantable left ventricular assist systems (LVAS) consist of implantable pumps with small control consoles and power sources that can be worn externally. These systems provide far greater patient mobility and independence than external pumps with bulky control consoles. Patients with implantable LVAS can be discharged from hospital and are able to return to work and resume active sports. Most patients have received these systems as a bridge to heart transplantation. Clinical status and quality of life improve dramatically after device implantation and survival on support (60–70% after approx. 100 days of support) is acceptable compared with transplant candidates on medical therapy. Patient selection and adverse events, primarily bleeding, thromboembolism and infection, are important issues with LVAS. In the future, long‐term support and bridging to myocardial recovery may become important indications for LVAS.
Intravenous inotropic agents in the intensive therapy unit: do they really make a difference?
Authors: Opasich Cristina , Russo Alessandra , Mingrone Renato , Zambelli Mara , Tavazzi Luigi 
Published: July 2002

AbstractPart of the management of refractory heart failure is treatment aimed at preventing organ damage due to inadequate oxygen delivery, improving hemodynamics, and maximizing cardiac output while maintaining only mildly elevated ventricular filling pressures The aim of this paper is to review the most updated indications on intravenous inotropic agents, and to compare their cardiac and peripheral effects. Finally, clinical implications of their use (alone or in combination) are reviewed.
Supercritical Fluids Are Superior Media for Catalysis by Cross‐Linked Enzyme Microcrystals of Subtilisin Carlsberg
Authors: Fontes Nuno , Almeida M. Conceição , Garcia Silvia , Peres Célia , Partridge Johann , Halling Peter J. , Barreiros Susana 
Published: July 2002

AbstractWe report on the performance of cross‐linked enzyme microcrystals (CLECs) of subtilisin Carlsberg in supercritical fluids (SC‐fluids). The catalytic activity of CLECs in SC‐ethane was found to be 2‐ to 10‐fold greater than in hexane under the same conditions, using CLECs dried by propanol washing. Air‐dried CLECs and lyophilized powders showed much lower activities, reflecting the same hydration hysteresis effects as in organic solvents. Reaction rates were much lower in SC‐CO2, especially at higher water activity, probably as a result of acid‐base effects of carbonic acid on the enzyme.
Interobserver variability of sonographically determined second‐trimester nuchal skinfold thickness measurements
Authors: Donnenfeld A. E. , Meister D. , Allison J. , Brennan K. , Ludomirsky A. , Rightmire D. 
Published: July 2002

AbstractTwenty physicians experienced in fetal sonographic evaluation obtained fetal nuchal skinfold thickness measurements in each of five pregnant women between 16 and 18 weeks' gestation. A random effects analysis of variance model was used to explore the sources of variation in the set of measurements, to determine the interobserver variability of sonographically measured second‐ trimester nuchal skinfold thickness. It was possible to obtain 96 measurements. Four measurements (all in the same patient) were deemed unobtainable due to fetal position. All recorded measurements were between 1.7 and 4.5 mm. The means (and ranges) for the five patients were 2.7 (1.7–3.6), 2.9 (2.0–4.5), 2.7 (2.0–4.0), 3.3 (2.2–4.0), and 2.7 (1.8–4.0) mm. The standard deviation for interobserver variability, caused by the combined effect of physician and machine imprecision, was 0.56 mm and the overall coefficient of variation was 19.8%. Inter patient differences were statistically significant (p = 0.004). Interphysician differences were not (p = 0.11). We conclude that experienced physician sonographers using high‐resolution ultrasound equipment are able to obtain second‐trimester nuchal skinfold thickness measurements within 1.1 mm of the estimated true value with 95% probability. Copyright © 1995 International Society of Ultrasound in Obstetrics and Gynecology
Theory of potential distributions in abrupt heterojunction crystalline semiconductor devices: Treatment of Schottky barriers and rectifiers
Authors: Mohammad S. Noor 
Published: July 2002

A theoretical method for potential distribution in abrupt heterojunctions (HJs) made of uniformly doped degenerate semiconductors has been developed. The method reduces automatically to that in HJs from nondegenerate semiconductors in the limits of low carrier concentrations. For the development of the method the rigid band approximation of degenerate semiconductors has been considered to be valid. The transport equations of Marshak and Van Vliet [Solid-State Electron. 21, 417 (1978)] and an analytical approximation for the Fermi–Dirac
integral of order half by the present author [Solid-State Electron. 30, 713 (1987)] have been employed for the formulation. The average of the scattered experimental data for band-gap narrowing of n-Si, n-Ge, p-GaAs, and n-InP have been fitted to the same form as that for the Fermi–Dirac integral of order 1/2 to ease this formulation. Local electrostatic field and local electrostatic potentials obtained from the formulation reduce to those of Chatterjee and Marshak [Solid-State Electron. 24, 1111 (1981)], Cserveny [Int. J. Electron. 25, 65 (1968)], and Kroemer [J. Appl. Phys. 52, 873 (1981)] under special conditions. It is noted that band-gap narrowing and consideration of Fermi–Dirac statistics represent opposite effects for effective intrinsic carrier concentration and local electrostatic field. At some critical concentration belonging to the degenerate limit of a semiconductor, these two effects cancel the influence of each other on effective intrinsic carrier concentration of the semiconductor and on transition region properties of an HJ. Below this critical concentration, band-gap narrowing rather than a consideration of Fermi–Dirac statistics dominantly influences the device properties. However, above this critical concentration, consideration of Fermi–Dirac statistics dominates over the other. Applications of electrostatic field and electrostatic potential to isotype and anisotype HJs have been discussed. On the basis of present formulas a general form for potential distribution in Schottky barriers has been derived. The relation reduces to that of Gummel and Scarfetter [J. Appl. Phys. 38, 2148 (1967)] under special conditions. Theoretical reasons underlying the lack of rectification in various n-N HJs have been analyzed. In light of this analysis, a theoretical model in terms of many-body electron-electron and electron-donor interactions, and in terms of lowering of band edge in the vicinity of transition region, has been proposed. Numerical results obtained from this model for n-GaAs agree remarkably with observations from experimental measurements.
Phenomenologies of ferromagnetism in metals (invited) (abstract)
Authors: Arrott A. S. , Heinrich B. 
Published: July 2002

Magnetism remains mysterious 100 years after Ewing made his initial models of interacting compasses. Many aspects are seen clearly, but at each step from the spinning electron to the rotor of a motor complexity obscures. At the macroscopic level the difficulties in ferromagnetism start with magnetostatics, which in principle calls for the evaluation of sixfold integrals. At the quantum level one needs fully relativistic spin-polarized calculations that remain beyond the current state of the art in order to have a full description of the ground state of a homogeneous piece of material with periodic boundary conditions. While it is known in principle how to carry out such calculations, in practice an experimentalist relies on phenomenology for the interpretation of
data. The role of phenomenology is to create molds into which the experimental data is pressed. Theoretical analyses of critical phenomena are among the triumphs of modern magnetism. The picture is beautiful as long as one ignores anisotropies, dipole–dipole interactions, magnetostriction, and dynamic effects, all of which are the heart of micromagnetics, not to mention imperfections, inhomogeneities, and surface effects. Studies of the response, static and dynamic, of nearly perfect single crystals of Fe, grown from the decomposition of FeCl2 in the form of whiskers, provide examples where the
experiments attempt to approach the neatness of the theories. Interpretation of data requires understanding of the dominant magnetostatics, the underlying micromagnetics and the resulting magnetization patterns, and the major role of eddy currents in obscuring intrinsic loss effects. One combines these aspects of Maxwell’s equations with parametric formulations of the equation of state and the Landau–Lifshitz equations of motion to extract magnetizations, susceptibilities, anisotropies, and damping parameters as functions of internal fields and frequency. The micromagnetics of the ideally soft ferromagnetic material serves as a foundation for the phenomenology. Fifty years of progress
in understanding of phase transitions provides the critical phenomenology. The Landau–Lifshitz equations of motion developed for feromagnetism also describe the dynamic response in the transition from paramagnetism to ferromagnetism when allowance is made for the frequency, field, and temperature dependence of the damping. When the phenomenology and the data are not in full accord it is difficult to assign the source of the misfit. Yet one rejoices in the fact that they fit, sort of.
Correlation functions of the X
Y model (abstract)
Authors: Bonner J. C. , Müller G. , Parkinson J. B. 
Published: July 2002

Recently an elegant and quite powerful finite-system approach to determine the exponents ηx and ηz from simple spectral properties has been proposed. For critical systems, the two exponents can be expressed in terms of finite-size spectral gaps as follows: η(N)x=2ΔE01(N)/ΔE(N), η(N)z=2ΔE00(N)/ΔE(N). Here ΔE(N) is the finite-size gap between the ground state (SzT=0,k=0) and the lowest excitation at k=2π/N; ΔE01(N) is the gap to the lowest ‖SzT‖=1 excitations (at k=π), and ΔE00(N) is the gap to the next lowest SzT=0 excited state. The η(N) sequence is then extrapolated to N→∞. For XY models, differences between s=1/2 and s≥1 appear. For s=1/2, the excitations which determine ΔE00(N) and ΔE(N) are degenerate, which implies that ηz=1/2, in agreement with the exact analytic result. For spin-1, however, the next lowest SzT=0 state is located at k=2π/N instead of k=π, and is therefore identical to the state which determines the gap ΔE.
The resulting equality ΔE=ΔE00 implies ηz=2, as in the spin-1/2 case. In fact, our result corresponds to power-law decay for all s, and hence we differ from Schulz and Ziman, who claim the out-of-plane correlation function decays exponentially for s&gt;1/2. For the in-plane correlation function, the spectral gap method again agrees with the exact result ηx=0.5 for s=1/2. The consensus of this and other numerical methods for s=1 gives a value ηx≂0.20, considerably different from the case of s=1/2. Hence it is tempting to conjecture that ηx is s dependent, implying that XY models belong to different universality classes for different s. However, a finite-size study of the conformal anomaly produces the result that c=1, independent of s. This situation is further discussed.
Electrohydrodynamical study of the instability of a thin liquid metal film: Application to planar liquid metal ion sources
Authors: Miskovsky N. M. , He J. , Cutler P. H. , Chung M. 
Published: July 2002

Liquid metal ion sources are of interest in diverse areas of technology since they provide a high brightness, quasipoint source of ions and droplets for microfabrication, surface analysis, ultrathin film deposition, and other potential applications. N. M. Miskovsky, M. Chung, P. H. Cutler, T. E. Feuchtwang, and E. Kazes [J. Vac. Sci. Technol. A 6, 2992 (1988)] have developed an electrohydrodynamic capillary wave theory for ion and droplet emission in electrically stressed conducting viscous fluids based on a mathematical formalism introduced by J. R. Melcher and C. V. Smith [Phys. Fluids 12, 778 (1969)] and S. Grossmann and A. Muller [Z. Phys. B 57, 161 (1984)]. As the simplest analytical application of this theory they chose a model consisting of a planar fluid of thickness ‘‘a’’ supported on a rigid electrode. A parallel planar counter electrode is at a distance ‘‘b’’ from the unperturbed surface. The Navier–Stokes equation was solved subject to a dynamical Laplace–Young stress boundary condition (which includes the frictional tensor) to obtain the dispersion relation used to investigate the stability of the system.
In earlier work the effect of viscosity and gravity on the spectrum of unstable wavelengths for the case of a thick film (i.e., λ≫a) was investigated within the planar surface capillary wave model. In this limit, it was found that viscosity plays a significant role in determining the growth rate and the dominant mode, suggesting that it should be included in studies of the instabilities in liquid metal ion sources. It was also found that the local electric field is much larger than the average field of the perturbed fluid surface, implying that nonlinear effects can be important. In the present study the same formalism is used to investigate the case of a thin (i.e., λ&lt;a) liquid metal film. For thin films, that is, &lt;1 μm, the effect of the boundary conditions at the supporting electrode can produce significant changes in the maximum growth rate (∼20%), the dominant mode (∼10%), and the maximum value of Re(ω2) (∼40%). For both the thick- and thin-film regimes viscous damping is found to have an important role increasing the stability of the fluid film. In addition, an increase in viscosity shifts the most unstable mode to longer wavelengths. This shift competes with the effect of decreasing the film thickness.