Miracle-dz/UniFAR-FTUs huggingface dataset:
Orbital Energy-Based Reaction Analysis of SN2 Reactions

An orbital energy-based reaction analysis theory is presented as an extension of the orbital-based conceptual density functional theory. In the orbital energy-based theory, the orbitals contributing to reactions are interpreted to be valence orbitals giving the largest orbital energy variation from reactants to products. Reactions are taken to be electron transfer-driven when they provide small variations for the gaps between the contributing occupied and unoccupied orbital energies on the intrinsic reaction coordinates in the initial processes. The orbital energy-based theory is then applied to the calculations of several S N2 reactions. Using a reaction path search method, the Cl− + CH3I → ClCH3 + I− reaction, for which another reaction path called “roundabout path” is proposed, is found to have a precursor process similar to the roundabout path just before this SN2 reaction process. The orbital energy-based theory indicates that this precursor process is obviously driven by structural change, while the successor SN2 reaction proceeds through electron transfer between the contributing orbitals. Comparing the calculated results of the SN2 reactions in gas phase and in aqueous solution shows that the contributing orbitals significantly depend on solvent effects and these orbitals can be correctly determined by this theory.
Baf60c is a component of the neural progenitor‐specific BAF complex in developing retina

Remodeling of the chromatin network plays an important role regulating embryonic development as well as differentiation. The SWI/SNF complex is an ATP‐dependent chromatin‐remodeling complex. It consists of several proteins, including an ATPase subunit, either Brg1 or Brm. Two subunits of this complex, Baf53a and Baf45, have been previously identified as being neural progenitor‐specific. In this study, we show that Baf60c, another important part of this large complex, acts in a similar neural progenitor–specific manner. We show that during development Baf60c is expressed in neural progenitors in human retinas as well as mouse retina, cortex and spinal cord. Baf60c expression is lost during neural differentiation and its overexpression keeps the progenitors in a proliferative state through its interaction with the Notch pathway. Finally, we show that Baf60c is re‐expressed in the Müller glial cells that re‐enter the cell cycle after neurotoxic damage. Developmental Dynamics 237:3016–3023, 2008. © 2008 Wiley‐Liss, Inc.
Distinct mechanisms in the processing of English past tense morphology : A view from L 2 processing *

According to the Dual-Mechanism Model (Pinker & Prince, 1988), the processing of language is based upon two fundamentally different components: a rule component and an associative memory. The aim of this study was to analyze whether the theoretical tenets of the Dual-Mechanism Model, which has originally been established as a model of L1 processing, can be extended to the processing of L2 morphological processing. For this purpose, 49 adult Turkish learners of L2 English at two distinct proficiency levels and 8 adult native speakers of English participated in an elicited English past tense production task that tested their regular and irregular past tense formation behaviors on real and nonce verbs. The results display that L2 subjects behave quite similar to L1 subjects and compute regular and irregular past tense forms in qualitatively distinct ways, as proposed by the Dual-Mechanism Model. A second question that the study tried to approach is related to whether L2 learners at low proficiency levels lack a rule-system and initially compute regular and irregular forms exclusively over the associative memory until a certain proficiency level is reached as proposed by Zobl (1998). The results of the present study show that both low and high proficiency L2 learners were able to implement the past tense rule that adds the default past tense suffix “-ed” to stem forms and did not rely on the associative memory only. The results thus suggest that the two distinct mechanisms posited by the Dual-Mechanism Model are in use from early stages of interlanguage development on.
Regulation of mitochondrial dynamics and distribution by synapse position and neuronal activity in the axon

Proper distribution of axonal mitochondria is critical for multiple neuronal functions. To understand the underlying mechanisms for population behavior, quantitative characterisation of elemental dynamics on multiple time scales is required. Here we investigated the stability and transport of axonal mitochondria using live‐cell imaging of cultured mouse hippocampal neurons. We first characterised the long‐term stability of stationary mitochondria. At a given moment, about 10% of the mitochondria were in a state of transport and the remaining 90% were stationary. Among these stationary mitochondria, 40% of them remained in the same position over several days. The rest of the mitochondria transited to mobile state stochastically and this process could be detected and quantitatively analysed by time‐lapse imaging with intervals of 30 min. The stability of axonal mitochondria increased from 2 to 3 weeks in culture, was decreased by tetrodotoxin treatment, and was higher near synapses. Stationary mitochondria should be generated by pause of moving mitochondria and subsequent stabilisation. Therefore, we next analysed pause events of moving mitochondria by repetitive imaging at 0.3 Hz. We found that the probability of transient pause increased with field stimulation, decreased with tetrodotoxin treatment, and was higher near synapses. Finally, by combining parameters obtained from time‐lapse imaging with different time scales, we could estimate transition rates between different mitochondrial states. The analyses suggested specific developmental regulation in the probability of paused mitochondria to transit into stationary state. These findings indicate that multiple mitochondrial behaviors, especially those regulated by neuronal activity and synapse location, determine their distribution in the axon.
Advanced Diffusion MRI Tractography

The emergence of new neuroimaging techniques combined with sophisticated computational models and algorithms allows to non-invasively probe the structure of the brain in-vivo. Diffusion magnetic resonance imaging (dMRI) is a compelling tool for investigating the structure and geometry of brain tissue based on indirect measurement of the diffusion anisotropy of water. Tractography algorithms are able to reveal global fiber constructs by estimating continuous streamline connections based on the local diffusion information. These techniques contribute to a better understanding of neurological and neuropsychiatric disorders. However, tractograms are biased by algorithmic parameters, affected by partial voluming of different fiber populations or various tissue types and thus it is difficult to reliably extract biologically meaningful and quantitative measures. Furthermore, the adaptation into clinical research practice is challenging due to time constraints during the acquisition and the difficulty in standardizing diffusion datasets for group comparison. In this thesis, a flexible and modular software framework is proposed to perform various evaluations and analysis on subjectand group-level, in order to incorporate recent innovations and simplify the processing of structural diffusion MRI datasets. The quality assessment and monitoring is particularly important in patient populations and
A New Algorithm for the Satellite-Based Retrieval of Solar Surface Irradiance in Spectral Bands

Accurate solar surface irradiance data is a prerequisite for an efficient planning and operation of solar energy systems. Further, it is essential for climate monitoring and analysis. Recently, the demand on information about spectrally resolved solar surface irradiance has grown. As surface measurements are rare, satellite derived information with high accuracy might fill this gap. This paper describes a new approach for the retrieval of spectrally resolved solar surface irradiance from satellite data. The method combines a eigenvector-hybrid look-up table approach for the clear sky case with satellite derived cloud transmission (Heliosat method). The eigenvector LUT approach is already used to retrieve the broadband solar surface irradiance of data sets provided by the Climate Monitoring Satellite Application Facility (CM-SAF). This paper describes the extension of this approach to wavelength bands and the combination with spectrally resolved cloud transmission values derived with radiative transfer corrections of the broadband cloud transmission. Thus, the new approach is based on radiative transfer modeling and enables the use of extended information about the atmospheric state, among others, to resolve the effect of water vapor and ozone absorption bands. The method is validated with spectrally resolved measurements from two sites in Europe and by comparison with radiative transfer calculations. The validation results demonstrate the ability of the method to retrieve accurate spectrally resolved irradiance from satellites. The accuracy is in the range of the uncertainty of surface measurements, with exception of the UV and NIR ( ≥ 1200 nm) part of the spectrum, where higher deviations occur.
Retrospective Long-term Evaluation of Dental Implants in Totally and Partially Edentulous Patients. Part I: Survival and Marginal Bone Loss

Purpose:This retrospective longitudinal study aims to assess long-term outcomes of osseointegrated dental implants in partially and totally edentulous patients. Materials and Methods:Patients willing to sign the informed consent and attend a check-up were included. Implant failures were recorded, and marginal bone level and bone loss were evaluated on intraoral radiographs. Univariate and multivariate statistical analyses were conducted to determine the influence of various factors. Complications and patient satisfaction were recorded. Results:One hundred five patients who received 342 implants were included. Mean follow-up was 13.19 ± 3.70 years. 9.4% of implants were lost, and 78.1% of patients retained all implants placed. Mean marginal bone loss was 0.77 ± 1.10 mm, being greater than 3 mm in 2.5% of analyzed implants. Factors with possible influence on implant survival and marginal bone loss were smoking, osteopenia or osteoporosis, check-up frequency, implant surface, length and position, and type of prosthesis. 24.8% of patients remained free of complications. Patient satisfaction was high. Conclusions:In our sample, which included both totally and partially edentulous patients, long-term implant survival was more than 90% with a mean marginal bone loss of 0.77 mm and an implant survival at patient level of 78%; patient satisfaction was high despite the fact that complications were frequent.
Comparison of head nurses and practicing nurses in nurse competence assessment

BACKGROUND: Nurses play a crucial role in patient-care. Therefore, assessing nurses’ clinical competence is essential to achieve qualified and safe care. The aim of this study was to determine and compare the competence assessments made by head nurses and practicing nurses in a university hospital in Iran in 2009. METHODS: A cross-sectional survey was conducted to make comparisons of both self-assessment of nurse competence as well as assessment made by their respective head nurses working in a university hospital setting in Iran. The instrument employed for data collection was Nurse Competence Scale (NCS), whose reliability and validity have been previously confirmed. The clinical competence of the nurses in 73 skills under 7 categories was determined based on a Visual Analogue Scale (VAS) (0 to 100). They were also asked to indicate the extent to which their competence was actually used in clinical practice on a four-point scale of Likert. The data was analyzed through descriptive and inferential statistics. RESULTS: Comparison of self-assessment (87.03 ± 10.03) and the assessment done by head nurses (80.15 ± 15.54) showed a significant difference but no precise differences were found between the assessment methods for the frequency of using these competencies. CONCLUSIONS: The results of this study indicated no consensus between the nurses owns assessment and their head nurse assessment. Therefore, it is necessary to use a combination of nurses’ competence assessment methods in order to reach a more valid and precise conclusion.
Drugged Drivers Blood Concentrations in England and Wales Prior to the Introduction of Per Se Limits.

This report details the blood concentration of drugs found in motorists suspected of driving under the influence of drugs from 2010 to 2012 in England and Wales. This study was carried out as new legislation has come into place, setting fixed blood concentration limits for drugs in motorists. These include a cannabis (Δ9-THC) blood concentration of 2 µg/L, amphetamine 250 µg/L, benzoylecgonine (BZE) 50 µg/L, cocaine 10 µg/L, 6-monoacetylmorphine 5 µg/L, morphine 80 µg/L, diazepam 550 µg/L and methadone 500 µg/L. Samples were screened for opiates, methadone, benzodiazepines, cannabinoids, cocaine, amphetamines and methamphetamine. Cannabinoids were the most prevalent drug group (29.7%) followed by benzodiazepines (22.7%), opiates (18.8%), cocaine (16.3%), amphetamine (7%) and methadone (5.6%). The analytical results are compared with the new per se limits to give a reference of drug concentrations prior to this legislation coming into effect. Our studies show that 64.9% of the cannabis samples, 59.1% of the cocaine samples and 94.6% of the BZE samples would be above the new per se limits set under Section 5a of the Road Traffic Act. In contrast, the medicinal drugs such as benzodiazepines and opiates (morphine) were predominantly detected at concentrations below the new per se limit. Given its medical applications, amphetamines appear to have been grouped with the medicinal type drugs, with our data showing that 25.2% of the amphetamine positive samples would exceed the new specified limit. These data show that samples containing medicinal and prescription drugs are likely to be detected below the new legal limits, while illicit drugs were typically found at concentrations above the new specified limits.
GIPC: Glycosyl Inositol Phospho Ceramides, the major sphingolipids on earth

ABSTRACT What are the most abundant sphingolipids on earth? The answer is Glycosyl Inositol Phosphoryl Ceramides (GIPCs) present in fungi and the green lineage. In this review, we discuss the putative role of plant GIPCs in the lipid bilayer asymmetry, in the lateral organization of membrane rafts and in the very long chain fatty acid inter-leaflet coupling of lipids in the plant plasma membrane (PM). A special focus on the structural similarities -and putative functions- of GIPCs is discussed by comparison with animal gangliosides, structural homologs of plant GIPCs.
Systems Kinomics Demonstrates Congo Basin Monkeypox Virus Infection Selectively Modulates Host Cell Signaling Responses as Compared to West African Monkeypox Virus

Monkeypox virus (MPXV) is comprised of two clades: Congo Basin MPXV, with an associated case fatality rate of 10%, and Western African MPXV, which is associated with less severe infection and minimal lethality. We thus postulated that Congo Basin and West African MPXV would differentially modulate host cell responses and, as many host responses are regulated through phosphorylation independent of transcription or translation, we employed systems kinomics with peptide arrays to investigate these functional host responses. Using this approach we have demonstrated that Congo Basin MPXV infection selectively down-regulates host responses as compared with West African MPXV, including growth factor- and apoptosis-related responses. These results were confirmed using fluorescence-activated cell sorting analysis demonstrating that West African MPXV infection resulted in a significant increase in apoptosis in human monocytes as compared with Congo Basin MPXV. Further, differentially phosphorylated kinases were identified through comparison of our MPXV data sets and validated as potential targets for pharmacological inhibition of Congo Basin MPXV infection, including increased Akt S473 phosphorylation and decreased p53 S15 phosphorylation. Inhibition of Akt S473 phosphorylation resulted in a significant decrease in Congo Basin MPXV virus yield (261-fold) but did not affect West African MPXV. In addition, treatment with staurosporine, an apoptosis activator resulted in a 49-fold greater decrease in Congo Basin MPXV yields as compared with West African MPXV. Thus, using a systems kinomics approach, our investigation demonstrates that West African and Congo Basin MPXV differentially modulate host cell responses and has identified potential host targets of therapeutic interest.
Susceptibility factors to ozone-related mortality: a population-based case-crossover analysis.

RATIONALE Acute effects of ozone on mortality have been extensively documented in clinical and epidemiological research. However, only a few studies have focused on subgroups of the population especially vulnerable to these effects. OBJECTIVES To estimate the association between exposure to ozone and cause-specific mortality, and to evaluate whether individual sociodemographic characteristics or chronic conditions confer greater susceptibility to the adverse effects of ozone. METHODS A case-crossover analysis was conducted in 10 Italian cities. Data on mortality were collected for the period 2001 to 2005 (April-September) for 127,860 deceased subjects. Information was retrieved on cause of death, sociodemographic characteristics, chronic conditions from previous hospital admissions, and location of death. Daily ozone concentrations were collected from background fixed monitors. MEASUREMENTS AND MAIN RESULTS We estimated a 1.5% (95% confidence interval [CI], 0.9-2.1) increase in total mortality for a 10 microg/m(3) increase in ozone (8-h, lag 0-5). The effect lasted several days for total, cardiac and respiratory mortality (lag 0-5), and it was delayed for cerebrovascular deaths (lag 3-5). In the subgroup analysis, the effect was more pronounced in people older than 85 years of age (3.5%; 95% CI, 2.4-4.6) than in 35- to 64-year-old subjects (0.8%; 95% CI, -0.8 to 2.5), in women (2.2%; 95% CI, 1.4-3.1) than in men (0.8%; 95% CI, -0.1 to 1.8), and for out-of-hospital deaths (2.1%; 95% CI, 1.0-3.2), especially among patients with diabetes (5.5%; 95% CI, 1.4-9.8). CONCLUSIONS A greater vulnerability of elderly people and women was indicated; subjects who died at home and had diabetes emerged as especially affected.
Not All Inner Ears are the Same: Otolith Matrix Proteins in the Inner Ear of Sub‐Adult Cichlid Fish, Oreochromis Mossambicus, Reveal Insights Into the Biomineralization Process

The fish ear stones (otoliths) consist mainly of calcium carbonate and have lower amounts of a proteinous matrix. This matrix consists of macromolecules, which directly control the biomineralization process. We analyzed the composition of this proteinous matrix by mass spectrometry in a shotgun approach. For this purpose, an enhanced protein purification technique was developed that excludes any potential contamination of proteins from body fluids. Using this method we identified eight proteins in the inner ear of Oreochromis mossambicus. These include the common otolith matrix proteins (OMP‐1, otolin‐1, neuroserpin, SPARC and otoconin), and three proteins (alpha tectorin, otogelin and transferrin) not previously localized to the otoliths. Moreover, we were able to exclude the occurrence of two matrix proteins (starmaker and pre‐cerebellin‐like protein) known from other fish species. In further analyses, we show that the absence of the OMP starmaker corresponds to calcitic otoliths and that pre‐cerebellin‐like protein is not present at any stage during the development of the otoliths of the inner ear. This study shows O. mossambicus does not have all of the known otolith proteins indicating that the matrix proteins in the inner ear of fish are not the same across species. Further functional studies of the novel proteins we identified during otolith development are required. Anat Rec, 299:234–245, 2016. © 2015 Wiley Periodicals, Inc.
Breastfeeding rates among hyperphenylalaninemic infants

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The Human Splice Variant Δ16HER2 Induces Rapid Tumor Onset in a Reporter Transgenic Mouse

Several transgenic mice models solidly support the hypothesis that HER2 (ERBB2) overexpression or mutation promotes tumorigenesis. Recently, a HER2 splice variant lacking exon-16 (Δ16HER2) has been detected in human breast carcinomas. This alternative protein, a normal byproduct of HER2, has an increased transforming potency compared to wild-type (wt) HER2 receptors. To examine the ability of Δ16HER2 to transform mammary epithelium in vivo and to monitor Δ16HER2-driven tumorigenesis in live mice, we generated and characterized a mouse line that transgenically expresses both human Δ16HER2 and firefly luciferase under the transcriptional control of the MMTV promoter. All the transgenic females developed multifocal mammary tumors with a rapid onset and an average latency of 15.11 weeks. Immunohistochemical analysis revealed the concurrent expression of luciferase and the human Δ16HER2 oncogene only in the mammary gland and in strict correlation with tumor development. Transgenic Δ16HER2 expressed on the tumor cell plasma membrane from spontaneous mammary adenocarcinomas formed constitutively active homodimers able to activate the oncogenic signal transduction pathway mediated through Src kinase. These new transgenic animals demonstrate the ability of the human Δ16HER2 isoform to transform “per se” mammary epithelium in vivo. The high tumor incidence as well as the short latency strongly suggests that the Δ16HER2 splice variant represents the transforming form of the HER2 oncoprotein.
Modeling GATAD1-Associated Dilated Cardiomyopathy in Adult Zebrafish

Animal models have played a critical role in validating human dilated cardiomyopathy (DCM) genes, particularly those that implicate novel mechanisms for heart failure. However, the disease phenotype may be delayed due to age-dependent penetrance. For this reason, we generated an adult zebrafish model, which is a simpler vertebrate model with higher throughput than rodents. Specifically, we studied the zebrafish homologue of GATAD1, a recently identified gene for adult-onset autosomal recessive DCM. We showed cardiac expression of gatad1 transcripts, by whole mount in situ hybridization in zebrafish embryos, and demonstrated nuclear and sarcomeric I-band subcellular localization of Gatad1 protein in cardiomyocytes, by injecting a Tol2 plasmid encoding fluorescently-tagged Gatad1. We next generated gatad1 knock-out fish lines by TALEN technology and a transgenic fish line that expresses the human DCM GATAD1-S102P mutation in cardiomyocytes. Under stress conditions, longitudinal studies uncovered heart failure (HF)-like phenotypes in stable KO mutants and a tendency toward HF phenotypes in transgenic lines. Based on these efforts of studying a gene-based inherited cardiomyopathy model, we discuss the strengths and bottlenecks of adult zebrafish as a new vertebrate model for assessing candidate cardiomyopathy genes.