Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface plasmon propagation in metal nanowires

Plasmonic circuitry is considered as a promising solution-effectivetechnology for miniaturizing and integrating the next generation ofoptical nano-devices. The realization of a practical plasmonic circuitry strongly depends on the complete understanding of the propagation properties of two key elements: surface plasmons and electrons. The critical part constituting the plasmonic circuitry is a waveguide which can sustain the two information-carriers simultaneously. Therefore, we present in this thesis the investigations on the propagation of surface plasmons and the co-propagation of surface plasmons and electrons in single crystalline metal nanowires. This thesis is therefore divided into two parts. In the first part, we investigate surface plasmons propagating in individual thick penta-twinned crystalline silver nanowires using dual-plane leakage radiation microscopy. The effective index and the losses of the mode are determined by measuring the wave vector content of the light emitted in the substrate. Surface plasmon mode is determined by numerical simulations and an analogy is drawn with molecular orbitals compound with similar symmetry. Leaky and bound modes selected by polarization inhomogeneity are demonstrated. We further investigate the effect of wire geometry (length, diameter) on the effective index and propagation losses. On the basis of the results obtained during the first part, we further investigate the effect of an electron flow on surface plasmon properties. We investigate to what extend surface plasmons and current-carrying electrons interfere in such a shared circuitry. By synchronously recording surface plasmons and electrical output characteristics of single crystalline silver and gold nanowires, we determine the limiting factors hindering the co-propagation of electrical current and surface plasmons in these nanoscale circuits. Analysis of wave vector distributions in Fourier images indicates that the effect of current flow on surface plasmons propagation is reflected by the morphological change during the electromigration process. We further investigate the possible crosstalk between co-propagating electrons and surface plasmons by applying alternating current bias
A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae.

A genome-wide screen of 4168 homozygous diploid yeast deletion strains has been performed to identify nonessential genes that participate in the bipolar budding pattern. By examining bud scar patterns representing the sites of previous cell divisions, 127 mutants representing three different phenotypes were found: unipolar, axial-like, and random. From this screen, 11 functional classes of known genes were identified, including those involved in actin-cytoskeleton organization, general bud site selection, cell polarity, vesicular transport, cell wall synthesis, protein modification, transcription, nuclear function, translation, and other functions. Four characterized genes that were not known previously to participate in bud site selection were also found to be important for the haploid axial budding pattern. In addition to known genes, we found 22 novel genes (20 are designated BUD13-BUD32) important for bud site selection. Deletion of one resulted in unipolar budding exclusively from the proximal pole, suggesting that this gene plays an important role in diploid distal budding. Mutations in 20 other novel BUD genes produced a random budding phenotype and one produced an axial-like budding defect. Several of the novel Bud proteins were fused to green fluorescence protein; two proteins were found to localize to sites of polarized cell growth (i.e., the bud tip in small budded cells and the neck in cells undergoing cytokinesis), similar to that postulated for the bipolar signals and proteins that target cell division site tags to their proper location in the cell. Four others localized to the nucleus, suggesting that they play a role in gene expression. The bipolar distal marker Bud8 was localized in a number of mutants; many showed an altered Bud8-green fluorescence protein localization pattern. Through the genome-wide identification and analysis of different mutants involved in bipolar bud site selection, an integrated pathway for this process is presented in which proximal and distal bud site selection tags are synthesized and localized at their appropriate poles, thereby directing growth at those sites. Genome-wide screens of defined collections of mutants hold significant promise for dissecting many biological processes in yeast.
A new modified thrombin binding aptamer containing a 5′–5′ inversion of polarity site

The solution structure of a new modified thrombin binding aptamer (TBA) containing a 5′–5′ inversion of polarity site, namely d(3′GGT5′-5′TGGTGTGGTTGG3′), is reported. NMR and CD spectroscopy, as well as molecular dynamic and mechanic calculations, have been used to characterize the 3D structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT and TT loops. d(3′GGT5′-5′TGGTGTGGTTGG3′) is characterized by an unusual folding, being three strands parallel to each other and only one strand oriented in opposite manner. This led to an anti-anti-anti-syn and syn-syn-syn-anti arrangement of the Gs in the two tetrads. The thermal stability of the modified oligonucleotide is 4°C higher than the corresponding unmodified TBA. d(3′GGT5′-5′TGGTGTGGTTGG3′) continues to display an anticoagulant activity, even if decreased with respect to the TBA.
A predictive science approach to aid understanding of electrospray ionisation tandem mass spectrometric fragmentation pathways of small molecules using density functional calculations.

RATIONALE Tandem mass spectrometry (MS/MS) dissociation pathways can vary markedly between compound classes and can result in challenging and time-consuming interpretation of the data. Compound, class and substructure specific fragmentation rules for protonated molecules require refinement to aid the structural elucidation process. METHODS The application of a predictive science approach using density functional theory (DFT) calculations has been investigated to estimate the abundances of first-generation product ions observed using an ion trap mass spectrometer. This has been achieved by application of Boltzmann population theory to electrospray ionisation (ESI)-MS and MS/MS data. RESULTS Tandem ESI-MS data for this preliminary study were used to investigate the internal stabilities of protonated species and their product ions. The calculated relative abundances of 11.3%, 96.5%, and 1.1% for the product ion (m/z 192) of three quinazoline structural isomers are compared with the experimental values of 16%, 90% and 0% observed in the first-generation product ion mass spectra. CONCLUSIONS Close correlation between calculated and experimental data has been demonstrated for these initial data. Applying this approach and establishing fragmentation rules, based on structure specific and common fragmentation behaviour, would improve and expedite the structural elucidation process.
Hearing Impairment in Congenitally Hypothyroid Patients

Objective Thyroid hormone is necessary for normal development of the auditory system. The aim of this study was to investigate the rate of hearing impairment in congenitally hypothyroid (CH) patients, and its relation with factors such as CH severity and age at starting treatment, during CH screening program in Isfahan. Methods Hearing acuity was assessed in two groups of children with (94 patients aged 4 months – 3 years) and without CH (450), between 2000-2006. Otoacostic emission (OAE) was performed by a two step method. After two tests without OAE signals bilaterally, they were referred for auditory brainstem response (ABR) test. Subjects with both OAE and ABR abnormal test results were considered to have hearing problem. Obtained data was compared in case and control group and also CH patients with and without hearing impairment. Findings Three (3.2%) of patients and 1 of control group (0.2%) were diagnosed with sensorineural hearing loss. The rate of hearing loss was not different significantly in two studied groups (P>0.05). There was no difference between age of starting treatment and first T4 and TSH level in CH patients with and without hearing loss (P>0.05). CH neonates with hearing impairment had thyroid dyshormonogenesis according to the follow up results. Conclusion The rate of hearing loss was low among our studied CH patients. It may be due to proper management of CH patients. In view of the fact that all CH neonates were dyshormonogentic and considering the relation between certain gene mutations and hearing impairment in CH patients, further studies with larger sample size, with regard to different etiologies of CH should be investigated to indicate the possible gene mutations related to hearing loss in CH.
BRDF Measurement Modelling using Wavelets for Efficient Path Tracing

Physically based rendering needs numerical models from real measurements, or analytical models from material definitions, of the Bidirectional Reflectance Distribution Function (BRDF). However, measured BRDF data sets are too large and provide no functionalities to be practically used in Monte Carlo path tracing algorithms. In this paper, we present a wavelet‐based generic BRDF model suitable for both physical analysis and path tracing. The model is based on the separation of spectral and geometrical aspect of the BRDF and allows a compact and efficient representation of isotropic, anisotropic and/or spectral BRDFs. After a brief survey of BRDF and wavelet theory, we present our software architecture for generic wavelet transform and how to use it to model BRDFs. Then, modelling results are presented on real and virtual BRDF measurements. Finally, we show how to exploit the multiresolution property of the wavelet encoding to reduce the variance by importance sampling in a path tracing algorithm.
Second-order correction to the Bloch-Nordsieck sum rule.

As shown many years ago by Bloch and Nordsieck [Phys. Rev. 52, 54 (1937)] and Nordsieck [Phys. Rev. 52, 59 (1937)], the cross section for scattering with the emission of an arbitrary number of soft photons is finite and can be expressed in terms of the cross section for scattering in the absence of the radiation field. The model used by Bloch and Nordsieck included only soft-photon modes of the field, with maximum frequency ${\mathrm{\ensuremath{\omega}}}_{\mathit{s}}$. They argued that corrections to their sum rule would be expressed in terms of two small parameters, ${\mathit{r}}_{0}$${\mathrm{\ensuremath{\omega}}}_{\mathit{s}}$/c and \ensuremath{\Elzxh}${\mathrm{\ensuremath{\omega}}}_{\mathit{s}}$/\ensuremath{\nu}, where ${\mathit{r}}_{0}$ is the classical electron radius and \ensuremath{\nu} is the scattering energy. Corrections of first order were obtained previously by the author [Phys. Rev. A 21, 1939 (1980)], in the context of a nonrelativistic formulation of the scattering problem. Here all corrections of second order are derived. As in the earlier versions, the corrected cross section for scattering in the radiation field, summed over final states of the field, is determined from a knowledge of the field-free cross section. Use of the unitarity property (the optical theorem) is found to be a simplifying technical device for this calculation, as indicated by the cancellation of divergences in the scattering amplitude in the forward direction. It is shown that in the dipole approximation the term in the electron-field interaction that is quadratic in the vector potential, while contributing to an energy-level shift, has no effect, to second order, on the final form of the sum rule.
Measuring movement and location of the gastroesophageal junction: research and clinical implications

Abstract Understanding the physiology of gastroesophageal junction (GEJ) is important as failure of its function is associated with reflux disease, hiatus hernia, and cancer. In recent years, there have been impressive developments in high resolution technologies allowing measurement of luminal pressure, pH, and impedance. One obvious deficiency is the lack of technique to monitor the movement and location of the GEJ over a prolonged period of time. Proximal movement of the GEJ during peristalsis and transient lower esophageal sphincter relaxations (TLESRs) is due to shortening of the longitudinal muscle of the esophagus. Techniques for measuring shortening include fluoroscopic imaging of mucosal clip, high-frequency intraluminal ultrasound, and high resolution manometry, but these techniques have limitations. Short segment reflux is recently found to be more common than traditional reflux and may account for the high prevalence of intestinal metaplasia and cancer seen at GEJ. While high resolution pHmetry is available, there is no technique that can reliably and continuously measure the position of the squamocolumnar junction. A new technique is recently reported allowing a precise and continuous measurement of the GEJ based on the principle of Hall effect. Reported studies have validated its accuracy both on the bench and against the gold standard, fluoroscopy. It has been used alongside high resolution manometry in studying the behavior of the GEJ during TLESRs and swallows. While there are challenges associated with this new technique, there are promising ongoing developments. There is exciting time ahead in research and clinical applications for this new technique.
Severe dental fluorosis and jowar consumption in Karnataka, India.

INTRODUCTION Dental fluorosis is a major public health problem in 17 states of India. Earlier studies have reported that Jowar (a type of millet) consumption interacts with fluoride (F) in the body and enhances fluorosis. We conducted this study to determine the association between jowar consumption and severity of dental fluorosis. METHODS A community based case control study was carried out in villages having different F levels (low, medium, and high) in drinking water in North Karnataka, India. 352 school Children (12-15 years, male 58%) with severe dental fluorosis classified by Thylstrup & Fejerskov Index (1988) were selected as cases. 428 school children (12-15 years, male 48.8%) with no dental fluorosis were selected randomly from the same area as controls. Exposure ascertainment of jowar consumption was done by 24-h diet recall and food frequency questionnaire. Ion selective electrode method was used to estimate the F level in spot urine samples of subjects and in drinking water. Multiple logistic regression analysis was done using SPSS V. 11.01 RESULTS Children who consumed jowar had 2.67 times more chance of getting severe dental fluorosis compared to those who did not [Odds Ratio (OR) 2.67, CI 1.98-3.62]. Children from high F level villages (OR 1.91, CI 1.27-2.85) had higher odds of severe dental fluorosis compared to children from medium and low F level villages. Daily jowar consumers (OR 2.14, CI 1.64-3.09) and weekly consumers (OR 1.68, CI 1.31-3.45) had higher risk for dental fluorosis compared to non jowar consumers. Children who started consuming jowar before 8 years of age had significantly higher proportion of severe dental fluorosis compared to their counterparts. Urinary F excretion among jowar consumers was significantly lower than non-jowar consumers. CONCLUSIONS Jowar consumption was positively associated with severity of dental fluorosis in this population.
Signal processing methodology to study the cutaneous vasodilator response to a local external pressure application detected by laser Doppler flowmetry

The existence of a cutaneous pressure-induced vasodilation (PIV) has recently been reported. This paper proposes a signal processing methodology to improve PIV knowledge. Temporal variations of laser Doppler signals rhythmic activities are first analyzed on anesthetized rats. The results lead to a method that provides a better PIV understanding.
Non-Invasive Brain-to-Brain Interface (BBI): Establishing Functional Links between Two Brains

Transcranial focused ultrasound (FUS) is capable of modulating the neural activity of specific brain regions, with a potential role as a non-invasive computer-to-brain interface (CBI). In conjunction with the use of brain-to-computer interface (BCI) techniques that translate brain function to generate computer commands, we investigated the feasibility of using the FUS-based CBI to non-invasively establish a functional link between the brains of different species (i.e. human and Sprague-Dawley rat), thus creating a brain-to-brain interface (BBI). The implementation was aimed to non-invasively translate the human volunteer’s intention to stimulate a rat’s brain motor area that is responsible for the tail movement. The volunteer initiated the intention by looking at a strobe light flicker on a computer display, and the degree of synchronization in the electroencephalographic steady-state-visual-evoked-potentials (SSVEP) with respect to the strobe frequency was analyzed using a computer. Increased signal amplitude in the SSVEP, indicating the volunteer’s intention, triggered the delivery of a burst-mode FUS (350 kHz ultrasound frequency, tone burst duration of 0.5 ms, pulse repetition frequency of 1 kHz, given for 300 msec duration) to excite the motor area of an anesthetized rat transcranially. The successful excitation subsequently elicited the tail movement, which was detected by a motion sensor. The interface was achieved at 94.0±3.0% accuracy, with a time delay of 1.59±1.07 sec from the thought-initiation to the creation of the tail movement. Our results demonstrate the feasibility of a computer-mediated BBI that links central neural functions between two biological entities, which may confer unexplored opportunities in the study of neuroscience with potential implications for therapeutic applications.
Dendritic and Axonal Targeting of Type 5 Metabotropic Glutamate Receptor Is Regulated by Homer1 Proteins and Neuronal Excitation

The physiological actions of neurotransmitter receptors are intimately linked to their proper neuronal compartment localization. Here we studied the effect of the metabotropic glutamate receptor (mGluR)-interacting proteins, Homer1a, b, and c, in the targeting of mGluR5 in neurons. We found that mGluR5 was exclusively localized in cell bodies when transfected alone in cultured cerebellar granule cells. In contrast, mGluR5 was found also in dendrites when coexpressed with Homer1b or Homer1c, and in both dendrites and axons when cotransfected with Homer1a. In dendrites, cotransfected mGluR5 and Homer1b/c formed clusters that colocalized with the synaptic marker synaptophysin. Interestingly when transfected alone, the Homer proteins were also translocated to neurites but did not form such clusters. Depolarization of the neurons with a mixture of ionotropic glutamate receptor agonists, NMDA and kainate, or potassium channel blockers, tetraethylammonium and 4-aminopyridine, induced transient expression of endogenous Homer1a and persistent neuritic localization of transfected mGluR5 even long after degradation of Homer1a. These results suggest that Homer1a/b/c proteins are involved in the targeting of mGluR5 to dendritic synaptic sites and/or axons and that this effect can be regulated by neuronal activity. Because the activity-dependent effect of endogenous Homer1a was also long-lasting, the axonal targeting of mGluR5 by this protein is likely to play an important role in synaptic plasticity.
Fenofibrate Metabolism in the Cynomolgus Monkey using Ultraperformance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry-Based Metabolomics

Fenofibrate, widely used for the treatment of dyslipidemia, activates the nuclear receptor, peroxisome proliferator-activated receptor α. However, liver toxicity, including liver cancer, occurs in rodents treated with fibrate drugs. Marked species differences occur in response to fibrate drugs, especially between rodents and humans, the latter of which are resistant to fibrate-induced cancer. Fenofibrate metabolism, which also shows species differences, has not been fully determined in humans and surrogate primates. In the present study, the metabolism of fenofibrate was investigated in cynomolgus monkeys by ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS)-based metabolomics. Urine samples were collected before and after oral doses of fenofibrate. The samples were analyzed in both positive-ion and negative-ion modes by UPLC-QTOFMS, and after data deconvolution, the resulting data matrices were subjected to multivariate data analysis. Pattern recognition was performed on the retention time, mass/charge ratio, and other metabolite-related variables. Synthesized or purchased authentic compounds were used for metabolite identification and structure elucidation by liquid chromatographytandem mass spectrometry. Several metabolites were identified, including fenofibric acid, reduced fenofibric acid, fenofibric acid ester glucuronide, reduced fenofibric acid ester glucuronide, and compound X. Another two metabolites (compound B and compound AR), not previously reported in other species, were characterized in cynomolgus monkeys. More importantly, previously unknown metabolites, fenofibric acid taurine conjugate and reduced fenofibric acid taurine conjugate were identified, revealing a previously unrecognized conjugation pathway for fenofibrate.
ROBUSTNESS-STRENGTH PERFORMANCE OF HIERARCHICAL ALPHA-HELICAL PROTEIN FILAMENTS

An abundant trait of biological protein materials are hierarchical nanostructures, ranging through atomistic, molecular to macroscopic scales. By utilizing the recently developed Hierarchical Bell Model, here we show that the use of hierarchical structures leads to an extended physical dimension in the material design space that resolves the conflict between disparate material properties such as strength and robustness, a limitation faced by many synthetic materials. We report materiomics studies in which we combine a large number of alpha-helical elements in all possible hierarchical combinations and measure their performance in the strength-robustness space while keeping the total material use constant. We find that for a large number of constitutive elements, most random structural combinations of elements (> 98%) lead to either high strength or high robustness, reflecting the so-called banana-curve performance in which strength and robustness are mutually exclusive properties. This banana-curve type behavior is common to most engineered materials. In contrast, for few, very specific types of combinations of the elements in hierarchies (< 2%) it is possible to maintain high strength at high robustness levels. This behavior is reminiscent of naturally observed material performance in biological materials, suggesting that the existence of particular hierarchical structures facilitates a fundamental change of the material performance. The results suggest that biological materials may have developed under evolutionary pressure to yield materials with multiple objectives, such as high strength and high robustness, a trait that can be achieved by utilization of hierarchical structures. Our results indicate that both the formation of hierarchies and the assembly of specific hierarchical structures play a crucial role in achieving these mechanical traits. Our findings may enable the development of self-assembled de novo bioinspired nanomaterials based on peptide and protein building blocks.