Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Assessment of Single-Molecule Protein Sequencing

A single-molecule protein sequencer, which labels only 2 out of 20 amino acids and uses single-molecule TIRF microscopy to measure the order of these fingerprints, opens the door to identify proteins with high fidelity using only a small quantity of sample. From the fingerprint, a key challenge is to detect which protein was measured. We present a first tool that efficiently retrieves the protein sequences by just comparing the fingerprints, even in the presence of a high error rate. A clustering method is first employed to reduce the redundancy of the database. Given a fingerprint, our algorithm employs an efficient filtering strategy to identify potential matches and a dynamic programming to verify the matches found. These matches are then mapped back to the original fingerprint database to get the final proteins. We analyzed the detection behavior on simulated data and investigated how the use of additional information may improve the performance. In addition, we tested whether the fingerprint information is sufficient to solve other problems, such as distinguishing whether a human cell sample contains bacterial or viral proteins.
Examining the relationship between Latinos’ English proficiency, educational degree, language preferences, and their perceptions on the Americans

Using data from the 2018 National Survey of Latinos that was conducted by The Pew Hispanic Center/Kaiser Family Foundation, the researcher in the present study reports on the perceptions of Latinos on English and their educational degrees as well as their language preferences. This non-experimental quantitative study is considered one of the first ones focusing on Latinos’ language preferences conducted all over the United States. A highly randomly stratified 2,288 Latino adults (1,041 males and 1,091 females) who are 18 years old or older identified themselves as Latinos in this study. These participants were from 48 states in total. The results indicated that there was a positive relationship between the last degree attended and participants’ English proficiency; however, there was no association between participants’ preference of English over Spanish and their perceptions on the friendliness/closeness of American individuals. The implications and future direction are recommended at the end of the study based on these results.
Human neural stem cell therapy in a primate model for Parkinson's disease

Neural stem cells derived from various sources have shown considerable promise for the treatment of parkinsonian symptoms in a variety of animal models; however, the long- term potential of human neural stem cells to engraft, differentiate into dopamine neurons, and restore function in the dopamine-depleted non-human primate brain remains unknown. This dissertation describes a clinically relevant paradigm for transplantation of undifferentiated human fetal subventricular-zone derived NSC in the parkinsonian primate, including gene therapy enhancement with GDNF. Chapter 1 reviews literature regarding functional properties of NSC that make them a candidate for cellular transplantation in neurodegenerative disorders, the potent neurotrophic effects of GDNF, as well as the rationale for utilizing large animals to adequately test stem cell therapeutics. Chapter 2 describes a novel culturing system to overcome cellular senescence and efficiently expand large-scale human fetal NSC long-term without aberration. Included are clinically pertinent techniques to produce and deliver hfNSC into both the rodent and primate brain, as well as new advances in radiological tracking and imaging utilizing FDA-approved supra-magnetic iron-oxide particles. Chapter 3 demonstrates the first reported evidence that undifferentiated hfNSC differentiate into some TH-ir neurons and restore functional deficits in parkinsonian non-human primates. Normalization of dopamine -levels and nigrostriatal circuitry argue for neuroprotective effects of endogenous cells rather than direct cell replacement. To allow for morphological analysis of donor grafts, reporter hfNSC were created (Ch.2) for long-term studies. Chapter 4 presents a new paradigm in which hfNSC are homotopically transplanted concomitantly with striatal AAV-GDNF to enhance graft survival and promote axonal outgrowth. Transplanted cells engrafted for up to 11-months and differentiated extensively congruent with host circuitry, demonstrating for the first time that undifferentiated hfNSC retain developmentally relevant programs of differentiation and respond to host signals in the dopamine-depleted primate brain. Further, evidence supports the standing argument that fetal subventricular-zone derived NSC do not significantly differentiate into mature A9-subtype midbrain dopamine neurons in-vivo, even in a GDNF-rich environment. Chapter 5 discusses the significance of these findings to cellular transplantation in the adult CNS and the future application of stem cell transplantation with regards to Parkinson's disease
Ambush or active life: foraging mode influences haematocrit levels in snakes

The rate at which organisms acquire resources is a critical trait and foraging mode can vary from sit-and-wait tactics to being highly mobile and active. Snakes provide a robust opportunity to examine the physiological correlates of contrasted foraging strategies. In this context, haematocrit (Hct), a proxy of blood oxygen carrying capacity, should be a reliable indicator of aerobic activity levels. We used phylogenetically informed models to examine the relationship between foraging mode and Hct in 80 snake species. After accounting for clade and habitat effects, we found a significant relationship of Hct with foraging mode; Hct is lower in snakes that ambush prey compared to active foragers across habitats. Species using both foraging tactics had marginally lower Hct than active foragers. Ambush foraging tactics are widespread in snakes, notably among low-energy specialists that usually display low feeding frequency, as well as limited activity and daily movements. Because Hct influences blood viscosity, low levels may thus be advantageous by reducing maintenance and locomotory costs. Further studies are required to better understand the implication of foraging mode on blood characteristics and other aspects of snake physiology. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 636–645.
Pallid sturgeon size structure, condition, and growth in the Missouri River Basin

Summary We synthesized wild and stocked pallid sturgeon Scaphirhynchus albus capture data collected in four recovery areas of the Missouri River during 1998–2007, providing the first basin-wide analysis of size structure, growth, and condition. Proportional size distribution (PSD) values ranged from 20 to 33 and were indicative of past stockings given the continued lack of natural recruitment. A new weight-length regression derived from 2268 captured wild (8%), hatchery-stocked (75%), and unknown origin (16%) pallid sturgeon had a significantly lower slope and intercept from a previously published model that used only 214 wild fish and a truncated size range. Relative condition (Kn) declined after stocking throughout the basin but stabilized at 0.94 within 3 years. Spatially, Kn of juvenile pallid sturgeon (330–629 mm) was generally highest in the reaches of the Missouri River with large tributaries. In accordance with the latitudinal counter gradient growth hypothesis, similar absolute growth increments (both length and weight) of tagged age-1 pallid sturgeon in the Upper and Lower Missouri River indicated upstream fish grew at faster rates given the 1.3 fold difference in growing season length. From North to South, von Bertalanffy growth coefficients (k) showed a latitudinal increase while L∞ decreased, providing additional support of the latitudinal counter gradient growth hypothesis. However, growth rates of tagged juvenile pallid sturgeon aged 2–6 years were highest at the two most downstream reaches showing an increased influence of growing season length. In the Missouri River, pallid sturgeon (≤ ages 1–9 or 10 years) exhibited linear growth in the two most upstream reaches (Montana and North Dakota), exhibited logistic growth in the inter-reservoir reach in South Dakota/Nebraska while a power function best described growth downstream of the lowermost dam (Nebraska, Iowa, Kansas, and Missouri). Differing growth models among reaches highlights the confounding affect of habitat fragmentation by dams in the Missouri River on growth as well as potential latitudinal affects on sexual maturation. Relative condition and growth of pallid sturgeon appears adequate throughout the Missouri River indicating success of past stocking efforts to forestall extirpation.
Long‐term demographic consequences of eavesdropping for sagebrush

1. There are now approximately 10 examples of plants that use volatile cues emitted by damaged neighbours to adjust their defences against herbivores. For two of these examples, preliminary evidence suggested that plants may experience net benefits from such eavesdropping, although eavesdropping was uncommon in one case and estimates of plant fitness were ambiguous in the other case.
A Very Simple Closed-Form Expression for Pull-In Voltage and Fundamental Frequency of Fixed-Fixed Beam

In this paper, a very simple closed-form expression for pull-in voltage and fundamental frequency of a fixed-fixed beam is presented with appropriate accuracy. We propose a model incorporating all know factors including effects of partial electrode configuration, axial stress, nonlinear stiffening, charge redistribution, and the fringing field effects. For the first time we express an analytic formulation for the pull-in deflection as a function of beam specification. We make an extensive comparison between the results of pull-in voltage obtained by our new expression and well-known approaches proposed in the literature. To do this, we calculate pull-in voltage with our expression for a wide range of beam specification and compare it with numerical, experimental and also other reported expressions. The pull-in voltage model has an average error of %1.29 in comparison to the experimental data for beams with a complete electrode, and %3.37 as compared to the 3D-coupled FEM simulation results for beams with partial electrode. Moreover, we show that the calculated fundamental frequency using proposed model is in good agreement with the experimental result from zero to near the pull-in voltages.
The complete mitochondrial genome of black sea bass, Centropristis striata

Abstract The complete mitochondrial genome was sequenced from the marine teleost fish Black Sea Bass, Centropristis striata. The genome sequence is 16,986 bp in size and has a base composition of A (26.65%), T (26.44%), C (28.63%), and G (18.28%). The phylogenetic analysis showed that C. striata belongs to Serranidae family and is most closely related to Hypoplectrus. The complete mitochondrial genome sequences provided here was the first one in Centropristis, which would be useful for further understanding the evolution and conservation genetics of C. striata.
Natura 2000 Areas and Sites of National Interest (SNI): Measuring (un)Integration between Naturalness Preservation and Environmental Remediation Policies

The Natura 2000 network was established as a tool to preserve the biological diversity of the European territory with particular regard to vulnerable habitats and species. According to recent studies, a relevant percentage of Natura 2000 sites are expected to be lost by the end of this century and there is widespread evidence that biodiversity conservation policies are not fully effective in relation to the management plans of the protected areas. This paper addresses the issue by analyzing a specific case in which there is a problem of integration between different competences and sectoral policies that leads to the lack of a monitoring system of territorial management performances. The study area, located in the Basilicata Region (Southern Italy), includes a Site of National Interest (SNI), for which several reclamation projects are still in the submission/approval phase, and a partially overlapping Natura 2000 network site. The tool used to monitor biodiversity in the study area is the degradation map obtained through the “habitat quality and degradation” InVEST tool which is used to assess the current trend and thus define a baseline for comparison with two medium and long-term scenarios applicable to the SNI’s procedure of partial and total remediation. The proposed methodology is intended to be a part of a larger and more complex monitoring system that, developed within the framework of ecosystem services, allows for the overcoming of the limits related to fragmentation and contradictions that are present in land management by offering a valuable support to decision makers and the competent authorities in biodiversity conservation policy design.
Impact of Subgrid Variation of Water Vapor on Longwave Radiation in a General Circulation Model

Most general circulation models compute radiation fluxes by assuming that water vapor is uniform within individual grid layers, which leads to an underestimation of satellite‐observed longwave (LW) cloud radiative forcing (LWCF). To fix this problem, we calculated water vapor content separately for clear and cloudy portions and used them to compute LW radiation. The impacts of this modification were examined by comparing two global simulations with and without the modification (NEW and OLD, respectively). Global‐annual mean LWCF from NEW was 1.8 W m−2 higher than that of OLD, thus remedying a long‐standing negative bias of LWCF. This improvement is a combined result of more clear‐sky and less all‐sky upward LW flux at the top of the atmosphere than OLD. Large increases in LWCF and clear‐sky LW flux occurred in the tropical deep convection and midlatitude storm track regions where upper‐ and middle‐level clouds are abundant. Although only the LW radiation scheme was modified, global‐annual mean shortwave cloud radiative forcing also increased, particularly in the vicinity of the eastern subtropical marine stratocumulus decks through radiative feedback processes. With this improved treatment, it may be possible to tune general circulation models in a more flexible and physical way without introducing compensating errors.
Machine Learning for Asset Managers (Chapter 1)

Successful investment strategies are specific implementations of general theories. An investment strategy that lacks a theoretical justification is likely to be false. Hence, an asset manager should concentrate her efforts on developing a theory rather than on backtesting potential trading rules. The purpose of this Element is to introduce machine learning (ML) tools that can help asset managers discover economic and financial theories. ML is not a black box, and it does not necessarily overfit. ML tools complement rather than replace the classical statistical methods. Some of ML's strengths include (1) a focus on out-of-sample predictability over variance adjudication; (2) the use of computational methods to avoid relying on (potentially unrealistic) assumptions; (3) the ability to â€œlearnâ€ complex specifications, including nonlinear, hierarchical, and noncontinuous interaction effects in a high-dimensional space; and (4) the ability to disentangle the variable search from the specification search, robust to multicollinearity and other substitution effects.
Dégradation d'un composé xénobiotique récalcitrant : métabolisme du méthyl tert-butyl éther (MTBE) par mycobacterium austroafricanum IFP 2012

Afin d'obtenir le niveau requis d'indice d'octane et de limiter les rejets en monoxyde de carbone, les ethers carburants, principalement le methyl tert-butyl ether (MTBE), sont incorpores dans les essences. A la suite de fuites, le MTBE est apparu comme un polluant majeur des nappes aquiferes en raison de sa tres faible biodegradabilite. L'objectif de ce travail a ete d'etudier la degradation du MTBE par Mycobacterium austroafricanum IFP 2012. La voie metabolique a ete partiellement elucidee par l'identification de plusieurs intermediaires (tert-butyl formiate (TBF), tert-butyl alcool (TBA), acide -hydroxyisobutyrique et acetone) et activites enzymatiques (MTBE/TBA mono-oxygenase non-hemique et inductible, TBF esterase, 2-propanol : NDMA oxydoreductase et une mono-oxygenase impliquee dans la degradation de l'acetone). Le role du TBF et la necessite de cobalt ont ete proposes pour expliquer la faible biodegradation du MTBE ; le role de la liaison methoxy semblant limite.
Large-Eddy Simulation of Conditionally Neutral Boundary Layers: A Mesh Resolution Sensitivity Study

Large-eddy simulation (LES) is used to model turbulent winds in a nominally neutral atmospheric boundary layer at varying mesh resolutions. The boundary layer is driven by wind shear with zero surface heat flux and is capped by a stable inversion. Because of entrainment the boundary layer is in a weakly stably stratified regime. The simulations use meshes varying from 1282 × 64 to 10242 × 512 grid points in a fixed computational domain of size (2560, 2560, 896) m. The subgrid-scale (SGS) parameterizations used in the LES vary with the mesh spacing. Low-order statistics, spectra, and structure functions are compared on the different meshes and are used to assess grid convergence in the simulations. As expected, grid convergence is primarily achieved in the middle of the boundary layer where there is scale separation between the energy-containing and dissipative eddies. Near the surface second-order statistics do not converge on the meshes studied. The analysis also highlights differences between one-dimensional and two-dimensional velocity spectra; differences are attributed to sampling errors associated with aligning the horizontal coordinates with the vertically veering mean wind direction. Higher-order structure functions reveal non-Gaussian statistics on all scales, but are highly dependent on the mesh resolution. A generalized logarithmic law and a k−1 spectral scaling regime are identified with mesh-dependent parameters in agreement with previously published results.
Small-signal parameters extraction and noise analysis of CNTFETs

The use of carbon nanotube (CNT) field-effect transistors (FETs) in microwave circuit design requires an appropriate, immediate and efficient description of their performance. This work describes a technique to extract the parameters of an electrical equivalent circuit for CNTFETs. The equivalent circuit is used to model the dynamic and noise performance at low- and high-frequency of different CNTFET technologies, considering extrinsic and intrinsic device parameters as well as the contact resistance. The estimation of the contact resistance at the metal/CNTs interfaces is obtained from a Y-function based extraction method. The noise model includes four noise sources: thermal noise, thermal channel noise, shot channel noise and flicker noise. The proposed model is compared with a compact model calibrated to hysteresis-free experimental data from a high-frequency multi-tube (MT)-CNTFET technology. Additionally, it has been applied to experimental data from another fabricated MT-CNTFET technology. The comparison in both cases shows a good agreement between reference data (simulation and experimental) and results from the proposed model. Low- and high-frequency noise projections of the fabricated reference device are further studied. Noise results from both studied technologies show that shot noise mainly contributes to the total noise due to the presence of Schottky barriers at contacts and along the channel.
Implement Using KY Converter for Hybrid Renewable Energy Applications: Design, Analysis, and Implementation

This chapter mainly focuses on meeting the energy demand and methodologies of renewable energy. Nowadays, researchers are mainly focusing on renewable energy from the sun, wind, biomass, etc. due to energy crises and the lack of non-renewable energy. The potential for solar energy is high and this demand can best be met with hybrid systems, which can provide an uninterruptible power supply. This chapter looks at the performance metrics of hybrid energy as well as the methodologies and various control techniques connected with power management. The chapter also defines the photovoltaic (PV)-based, novel, dual KY boost converter. Dual PV sources act as input for the dual KY boost converter to generate as much energy as possible from the dual PV system, using the inverter module to produce single-phase alternating current output. A dual KY boost converter can provide higher maximum power, a faster response, and smaller voltage ripple. KY boost converters are designed to generate stable output values according to various conditions because of various control techniques and the maximum power point tracking control algorithm.
Student Pharmacist Perspectives on Factors That Influence Wellbeing During Pharmacy School

Objective. To explore first-year student pharmacist perspectives on the influence of individual, educational system, and health care system factors on their wellbeing during pharmacy school. Methods. As part of a required course, first-year student pharmacists were required to submit reflective essays detailing the factors that most significantly contributed to their wellbeing since starting pharmacy school. Reflections from students who consented to participate during the study period from February 2019 to July 2019 were included for analysis. Qualitative thematic analysis was performed using open and axial coding, hierarchical categorization, and representative theme determination through a process of iterative review and deliberation. Coders developed a codebook with operational definitions for each emergent code. Coders met biweekly with lead researchers to ensure consistency and reliability of data analysis and to address minor discrepancies in coding. All team members discussed and revised themes until consensus regarding final representative themes was achieved. Results. Forty-nine students (36.8% of the first-year class) submitted reflective essays for analysis. Five themes emerged for the factors most influential on student pharmacist wellbeing: workload; learning environment culture and values; meaningful pharmacy school experiences; relationships; and personal factors. Student pharmacists did not consistently identify health care system factors as influencing their wellbeing. Conclusion. Student pharmacists identified both education system and individual factors as influencing their wellbeing. Education systems should prioritize implementation of systematic strategies that address curricular and learning climate factors, maximize student engagement in meaningful experiences, optimize social connectedness, and provide individual student support.