Miracle-dz/UniFAR-FTUs huggingface dataset:
Raman spectroscopy in microfluidics

Raman spectroscopy allows the identification of molecules and crystalline solids by their fingerprint-like, vibrational signature. This work contributes to three fields of applied Raman spectroscopy: Raman blood analysis, Spatially Offset Raman Spectroscopy (SORS) in microfluidics and Raman scattering in nanostructured dielectric metasurfaces. Inspired by the industry partner Radiometer, a microfluidic plasma fractionation scheme in whole blood flow is developed in this work which allows the optical inspection of instantaneously created blood plasma. The combination of this microfluidic chip with Raman spectroscopy is suitable for accelerated free hemoglobin quantification on whole blood at clinically relevant concentrations of hemolysis. Furthermore, the liquid in the microfluidic channel and the PDMS chip material are by design a twolayer system where the methodology of SORS can be applied. An alignment protocol is proposed in this thesis which allows consistent alignment of Raman optics with respect to the microfluidic chip for quantitative Raman concentration measurements of analyte in the microfluidic channel. Nanostructured dielectric metasurfaces are rich in optical properties. They show for example Mie-type resonances in the visible and near-infrared part of the optical spectrum. Here the effect of such resonances on the enhanced Raman scattered intensity is investigated. A tunable Raman setup has been established that allows scanning of the Raman excitation wavelength across both Mie-type and Fabry-Pérottype resonances.
Formulation and Characterization of Fenofibrate Loaded Solid Dispersion with Enhanced Dissolution Profile

Fenofibrate (FF) is an anti-hyperlipidaemic drug belonging to BCS class-II (low solubility, high permeability). Its bioavailability is limited by the dissolution rate. This study was aimed to enhance the rate of dissolution of poorly water soluble drug, FF. Initially, solid dispersions of fenofibrate (SDFs) were formulated with Carplex-80 or PEG-4000 or in combination at various weight ratios and were subjected to dissolution study. On the basis of drug release at various time intervals, the formulation producing maximum drug concentration was evaluated physicochemically using differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD), Fourier-transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). It was observed that the peak drug concentration was obtained at 120 min of dissolution by formulation SDF-7, which contains a mixture of Carplex-80 and PEG-4000 at weight ratio 1:5:6 of FF:PEG-4000:Carplex-80, respectively. Thus, the extent of drug release by SDF-7 was maximized by 2.5-fold than that of pure FF. Physicochemical characterization revealed the reason for this increased drug release as a conversion of crystalline FF to amorphous form and ensured the chemical compatibility among FF and carriers. The results specified the significant improvement of FF release using solid dispersion technique.
Cocrystals of 2-Aminopyrimidine with Boric Acid—Crystal Engineering of a Novel Nonlinear Optically (NLO) Active Crystal

Crystal engineering of novel materials for nonlinear optics (NLO) based on 2-aminopyrimidine yielded two molecular cocrystals with boric acid—trigonal (P3221 space group) 2-aminopyrimidine—boric acid (3/2) and monoclinic (C2/c space group) 2-aminopyrimidine—boric acid (1/2). In addition to crystal structure determination by single crystal X-ray diffraction, the cocrystals were characterized by powder X-ray diffraction and vibrational spectroscopy (FTIR and FT Raman). Large single crystals of the non-centrosymmetric cocrystal 2-aminopyrimidine—boric acid (3/2) were grown to study the optical properties and determine the second harmonic generation (SHG) efficiency (using 800 nm fundamental laser line) of powder samples.
How Accurately Can We Model Magma Reservoir Failure With Uncertainties in Host Rock Rheology?

Forecasting the onset of a volcanic eruption from a closed system requires understanding its stress state and failure potential, which can be investigated through numerical modeling. However, the lack of constraints on model parameters, especially rheology, may substantially impair the accuracy of failure forecasts. Therefore, it is essential to know whether large variations and uncertainties in rock properties will preclude the ability of models to predict reservoir failure. A series of two‐dimensional, axisymmetric models are used to investigate sensitivities of brittle failure initiation to assumed rock properties. The numerical experiments indicate that the deformation and overpressure at failure onset simulated by elastic models will be much lower than the viscoelastic models, when the timescale of pressurization exceeds the viscoelastic relaxation time of the host rock. Poisson's ratio and internal friction angle have much less effect on failure forecasts than Young's modulus. Variations in Young's modulus significantly affect the prediction of surface deformation before failure onset when Young's modulus is < 40 GPa. Longer precursory volcano‐tectonic events may occur in weak host rock (E < 40 GPa) due to well‐developed Coulomb failure prior to dike propagation. Thus, combining surface deformation with seismicity may enhance the accuracy of eruption forecast in these situations. Compared to large and oblate magma systems, small and prolate systems create far less surface uplift prior to failure initiation, suggesting that more frequent measurements are necessary.
PolSAR Image Classification via Learned Superpixels and QCNN Integrating Color Features

Polarimetric synthetic aperture radar (PolSAR) image classification plays an important role in various PolSAR image application. And many pixel-wise, region-based classification methods have been proposed for PolSAR images. However, most of the pixel-wise methods can not model local spatial relationship of pixels due to negative effects of speckle noise, and most of the region-based methods fail to figure out the regions with the similar polarimetric features. Considering that color features can provide good visual expression and perform well for image interpretation, in this work, based on the PolSAR pseudo-color image over Pauli decomposition, we propose a supervised PolSAR image classification approach combining learned superpixels and quaternion convolutional neural network (QCNN). First, the PolSAR RGB pseudo-color image is formed under Pauli decomposition. Second, we train QCNN with quaternion PolSAR data converted by RGB channels to extract deep color features and obtain pixel-wise classification map. QCNN treats color channels as a quaternion matrix excavating the relationship among the color channels effectively and avoiding information loss. Third, pixel affinity network (PAN) is utilized to generate the learned superpixels of PolSAR pseudo-color image. The learned superpixels allow the local information exploitation available in the presence of speckle noise. Finally, we fuse the pixel-wise classification result and superpixels to acquire the ultimate pixel-wise PolSAR image classification map. Experiments on three real PolSAR data sets show that the proposed approach can obtain 96.56%, 95.59%, and 92.55% accuracy for Flevoland, San Francisco and Oberpfaffenhofen data set, respectively. And compared with state-of-the-art PolSAR image classification methods, the proposed algorithm can obtained competitive classification results.
Constraining Crustal Properties Using Receiver Functions and the Autocorrelation of Earthquake‐Generated Body Waves

Passive seismic methods for imaging the discontinuity structure of Earth have primarily focused on differences in vertically and radially polarized energy in the coda of earthquake‐generated body waves (e.g., receiver functions). To convert the timing of scattered wave arrivals to depth, three parameters must be known or inferred: depth or layer thickness (H), P‐wave velocity (VP), and S‐wave velocity (VS). A common way to solve for these parameters is through H‐κ stacking analysis, in which layer thickness and the ratio between VP and VS (κ) is calculated while holding one of the velocity parameters constant. However, this assumption biases estimates of layer properties and leads to uncertainties that are not appropriately quantified. As these results are commonly used as starting models for more complex seismic or geodynamic analyses, these assumptions can propagate much further than the initial study. In this study, we introduce independent observations from body‐wave autocorrelations that can help constrain this underdetermined problem. P‐wave autocorrelation allows for the recovery of the Moho‐reflected P‐wave phase from teleseismic earthquakes, which is removed during deconvolution in the calculation of receiver functions. As the Moho‐reflected P‐wave is independent of VS, this constraint allows us to create a system of equations that better quantifies the thickness, VP, and VS of a layer and produces a more appropriate estimation of associated uncertainties. We apply this to 88 seismic stations that are spatially distributed throughout the United States to obtain a model of crustal variability that is unbiased by a priori assumptions of velocity structure.
Regional Influences on U.S. Monetary Policy : Some Implications for Europe

This paper looks at the monetary policy decisions of the U.S. Federal Reserve and asks whether those decisions have been influenced solely by national concerns, or whether regional factors have played a role. All of the Federal Reserve’s policymakers have some regional identity, i.e., either their positions explicitly carry some regional affiliation or their region of origin is a factor that must be considered in the selection process. This research is relevant for the Fed, and it may also be relevant for Europe’s fledgling central bank in Frankfurt. Critics have asserted that ECB policymakers have an incentive to base policy on national developments and respond to national political pressures. We find that Fed policymakers do take into account developments in regional unemployment when deciding monetary policy, and that these regional developments are more important for central bankers at the hub than in the spokes. These findings are robust to a variety of different specifications of the voting equation.
Interplay between hybridisation gaps and unusual magnetic orders in Kondo semiconductors CeT2Al10 (T = Ru and Os)

ABSTRACT Kondo semiconductors based on rare-earth elements possess a narrow gap in the renormalised density of states near the Fermi level. Their ground states remain nonmagnetic due to strong hybridisation of the 4f state with conduction bands. However, in the orthorhombic compounds CeT2Al10 (T = Ru, Os), opening of a hybridisation gap is followed by an antiferromagnetic (AFM) order at a rather high temperature TN ≅ 28 K. Our systematic studies of the effects of electron/hole doping on the magnetic and transport properties, electron tunnelling, and spin-gap formation revealed that the hybridisation gap is indispensable for the unusual AFM order. Under uniaxial pressure, TN increases linearly as the orthorhombic b-axis parameter is decreased. Our findings support the model that a kind of charge-density wave developing along the b axis in the presence of the hybridisation gap induces the AFM order in these systems.
The AMPK-TORC1 signalling axis regulates caffeine-mediated DNA damage checkpoint override and cell cycle effects in fission yeast

Caffeine, a widely consumed neuroactive compound, induces DNA damage checkpoint signalling override, and enhances sensitivity to DNA damaging agents. However, the precise underlying mechanisms have remained elusive. In fission yeast S. pombe, the Ataxia Telangiectasia Mutated (ATM) and Ataxia Telangiectasia mutated Related (ATR) orthologue Rad3 has been proposed as the cellular target of caffeine. Nevertheless, recent studies suggest that the Target of Rapamycin Complex 1 (TORC1) might be the main target. Caffeine mimics the effects of activating the Sty1-regulated stress response and the AMP-Activated Protein Kinase (AMPK) homologue Ssp1-Ssp2 pathways on cell cycle progression. Direct inhibition of TORC1 with the ATP-competitive inhibitor torin1, is sufficient to override DNA damage checkpoint signalling. It is, therefore, plausible, that caffeine modulates cell cycle kinetics by indirectly suppressing TORC1 through Ssp2 activation. Ssp1 and ssp2 deletion suppresses the effects of caffeine on cell cycle progression. In contrast, direct inhibition of TORC1 advances cell division in these mutants. These observations suggest that caffeine overrides DNA damage signalling, in part, via the indirect inhibition of TORC1 through Ssp2 activation. Alternatively, Ssp1 and Ssp2 may potentiate the effect of caffeine on Cdc25 activity. The AMPK-mTORC1 signalling axis plays an important role in aging and disease and presents a potential target for chemo- and radio-sensitization. Our results provide further insights of the underlying mechanisms by which caffeine modulates cell cycle progression in the context of Ssp1-AMPKαSsp2-TORC1 signalling activities and can potentially aid in the development of novel dietary regimens, therapeutics, and chemo-sensitizing agents.
Effective design and inference for cell sorting and sequencing based massively parallel reporter assays

The ability to measure the phenotype of millions of different genetic designs using Massively Parallel Reporter Assays (MPRAs) has revolutionised our understanding of genotype-to-phenotype relationships and opened avenues for data-centric approaches to biological design. However, our knowledge of how best to design these costly experiments and the effect that our choices have on the quality of the data produced is lacking. Here, we tackle this issue by developing FORE-CAST, a Python package that supports the accurate simulation of cell-sorting and sequencing based MPRAs and robust maximum like-lihood based inference of genetic design function from MPRA data. We use FORECAST’s capabilities to reveal rules for MPRA experimental design that help ensure accurate genotype-to-phenotype links and show how the simulation of MPRA experiments can help us better understand the limits of prediction accuracy when this data is used for training deep learning based classifiers. As the scale and scope of MPRAs grows, tools like FORECAST will help ensure we make informed decisions during their development and the most of the data produced.
Simulating the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics during walking

Walking balance is central to independent mobility, and falls due to loss of balance are a leading cause of death for people 65 years of age and older. Bipedal gait is typically unstable, but healthy humans use corrective torques to counteract perturbations and stabilize gait. Exoskeleton assistance could benefit people with neuromuscular deficits by providing stabilizing torques at lower-limb joints to replace lost muscle strength and sensorimotor control. However, it is unclear how applied exoskeleton torques translate to changes in walking kinematics. This study used musculoskeletal simulation to investigate how exoskeleton torques applied to the ankle and subtalar joints alter center of mass kinematics during walking. We first created muscle-driven walking simulations using OpenSim Moco by tracking experimental kinematics and ground reaction forces recorded from five healthy adults. We then used forward integration to simulate the effect of exoskeleton torques applied to the ankle and subtalar joints while keeping muscle excitations fixed based on our previous tracking simulation results. Exoskeleton torque lasted for 15% of the gait cycle and was applied between foot-flat and toe-off during the stance phase, and changes in center of mass kinematics were recorded when the torque application ended. We found that changes in center of mass kinematics were dependent on both the type and timing of exoskeleton torques. Plantarflexion torques produced upward and backward changes in velocity of the center of mass in mid-stance and upward and forward velocity changes near toe-off. Eversion and inversion torques primarily produced lateral and medial changes in velocity in mid-stance, respectively. Intrinsic muscle properties reduced kinematic changes from exoskeleton torques. Our results provide mappings between ankle plantarflexion and inversion-eversion torques and changes in center of mass kinematics which can inform designers building exoskeletons aimed at stabilizing balance during walking. Our simulations and software are freely available and allow researchers to explore the effects of applied torques on balance and gait.
Developmental issues in Chinese children's character acquisition

Measures of phonological processing, speech perception, and Chinese character recognition were administered to 109 Hong Kong Chinese 3- and 4-year-olds. A model predicting phonological awareness from vocabulary, verbal short-term memory, and speech perception was supported. Both phonological awareness and letter naming predicted unique variance in character recognition after controlling for other phonological processing and vocabulary skills, similar to previous studies of Western readers.
Age-related changes in “cortical” 1/f dynamics are linked to cardiac activity

The power of electrophysiologically measured cortical activity decays 1/fX. The slope of this decay (i.e. the spectral exponent) is modulated by various factors such as age, cognitive states or psychiatric/neurological disorders. Interestingly, a mostly parallel line of research has also uncovered similar effects for the spectral slope in the electrocardiogram (ECG). This raises the question whether these bodywide changes in spectral slopes are (in-)dependent. Focusing on well-established age-related changes in spectral slopes we analyzed a total of 1282 recordings of magnetoencephalography (MEG) resting state measurements with concurrent ECG in an age-diverse sample. We show that the aperiodic signal recorded using surface electrodes/sensors originates from multiple physiological sources. In particular, significant parts of age-related changes in aperiodic activity normally interpreted to be of neural origin can be explained by cardiac activity. Moreover, our results suggest that changes (flattening/steepening) of the spectral slope with age are dependent on the recording site and investigated frequency range. Our results highlight the complexity of aperiodic activity while raising concerns when interpreting aperiodic activity as “cortical” without considering physiological influences.
Rac1, Rac3 GTPases and TPC2 are required for axonal outgrowth and migration of cortical interneurons

Rho GTPases, among them Rac1 and Rac3, are major transducers of extracellular signals and are involved in multiple cellular processes. In cortical interneurons, the neurons that control excitation/inhibition balance of cortical circuits, Rac1 and Rac3 are essential for their development. Ablation of both, leads to a severe reduction in the numbers of mature interneurons found in the murine cortex, which is partially due to abnormal cell cycle progression of interneuron precursors and defective formation of their growth cones. Here we present new evidence that upon Rac1 and Rac3 ablation, centrosome, Golgi complex and lysosome positioning are significantly perturbed, thus affecting both interneuron migration and axon growth. Moreover, for the first time we provide evidence of altered expression and localization of the two-pore channel 2 (TPC2) voltage-gated ion channel that mediates Ca2+ release. Pharmacological inhibition of TPC2 negatively affected axonal growth and migration of interneurons. Our data taken together suggest that TPC2 contributes to the severe phenotype in axon growth initiation, extension and interneuron migration in the absence of Rac1 and Rac3. SUMMARY STATEMENT Rac1/3 severely affect cortical interneuron migration by affecting centrosome, Golgi and lysosome positioning. TPC2 likely contributes to the phenotype by decreasing axonogenesis and somatic migration.
Impacts of Sea Surface Temperature Improved by a High-Resolution Ocean Model on Summer Precipitation in a Dynamical Downscaling over Japan

We evaluated the impact of sea surface temperature (SST) improvement realized by increasing horizontal resolution of an ocean model on dynamical downscaling (DDS) over Japan, focusing on the effects of the Kuroshio on summer precipitation in Japan. Two sets of SSTs were simulated using a high-resolution North Pacific (NP) model and a low-resolution global (GLB) ocean model. Using these SSTs as the lower boundary conditions for the atmosphere, two DDS experiments were conducted (NPrun and GLB-run). In NP-run, summer precipitation increases over the Kuroshio and reduces over Pacific coastal areas of Japan compared with GLB-run. Due to weaker southerly winds north of the Kuroshio in NP-run, the water vapor flux transported to Japan is smaller than in GLB-run. Both the pressure adjustment and the vertical mixing mechanisms weaken the southerly winds, with the latter being slightly more effective. Increasing the horizontal resolution of the ocean model, so that the Kuroshio is more realistically reproduced, improves the accuracy of simulated precipitation over Japan. (Citation: Watanabe, S. I., H. Tsujino, A. Murata, and M. Ishii, 2019: Impacts of sea surface temperature improved by a high-resolution ocean model on summer precipitation in a dynamical downscaling over Japan. SOLA, 15, 183−188, doi:10.2151/ sola.2019-033.)
A hierarchical analysis of the niche relationships of four amphibians from forested habitats of northwestern California

A Hierarchical Analysis of the Niche Relationships of Four Amphibians from Forested Habitats of Northwestern California by Hartwell H. Welsh, Jr. Doctor of Philosophy in Wildland Resource Science University of California at Berkeley Professor Michael L. Morrison, Chair Knowledge of the habitat associations of the Del Norte salamander (Plethodon elongatus), the southern torrent salamander (Rhyacotriton variegatus), the tailed frog (Ascaphus truei), and the Pacific giant salamander (Dicamptodon tenebrosus) derives primarily from anecdotal and general literature accounts. These accounts are based on museum collections and a small number of studies, most from single localities, focused on natural history aspects other than habitat. Such sources are from few localities with a preponderance of sites near major roads where collectors tend to focus, which can result in a biased view of habitat relationships. I used stratified systematic sampling to quantify the habitat of these species across their ranges in northwestern California. Variables representing three spatial scales and up to 11 ecological components were examined. Using discriminant analysis and multiple regression techniques I found these species were restricted to specific habitat features and microclimatic conditions. The habitat of the terrestrial Del Norte salamander consists of older forests (>200 years) with large trees, closed, multi-storied canopy 2 comprised of both conifers and hardwoods, a cool, moist, and stable microclimate, a deep litter layer, and rocky substrates dominated by cobble-size pieces. The three aquatic species have niches consisting of a relatively narrow range of physical and microclimatic conditions associated with, cold, clear headwater to mid-order streams with loose, coarse substrates and low sedimentation, in older, more structurally complex forests. These results are consistent with earlier research indicating that these amphibians require conditions of microclimate and forest structure which are typically created, stabilized, and maintained within late seral stage forest ecosystems. These habitat conditions appear to be required for both survival and reproductive success and therefore indicate an ecological dependency by these species on late seral stage forest habitats.