Miracle-dz/UniFAR-FTUs huggingface dataset:
The genus Microcotyle in Mediterranean scorpaenoids (Teleostei), including the description of Microcotyle merche n. sp. from Helicolenus dactylopterus (Delaroche, 1809)

Abstract More than 65 species of the genus Microcotyle Van Beneden & Hesse, 1863, have been described to date, most of them infecting Perciformes. Among the scorpaenoids (Perciformes, formerly Scorpaeniformes) the species of the genus Microcotyle parasitize sebastids and scorpaenids worldwide. In this study, we provide new morphological and molecular data for Microcotyle spp. in sebastids and scorpaenids from the Western Mediterranean and north-east Atlantic. Specimens of Helicolenus dactylopterus (Delaroche, 1809) (n = 107) and Scorpaena spp. (n = 107) were examined and their microcotylid specimens morphologically and molecularly characterized. Microcotyle merche n. sp. ex H. dactylopterus and specimens of Microcotyle algeriensis Ayadi, Gey, Justine & Tazerouti, 2016 from a new host and locality (Scorpaena scrofa from the north-east Atlantic) are herein described. Both species are phylogenetically close, but their morphology is markedly different mostly because the anterior lobe of the haptor present in other Microcotyle species is almost absent in M. algeriensis. Findings of M. merche n. sp. in the Mediterranean also excludes the presence of Microcotyle sebastis in this sea, encouraging the review of the exceptionally large host range and geographical distribution of this species.
Review of Parameter Identification Procedures in Groundwater Hydrology: The Inverse Problem

The purpose of this survey is to review parameter identification procedures in groundwater hydrology and to examine computational techniques which have been developed to solve the inverse problem. Parameter identification methods are classified under the error criterion used in the formulation of the inverse problem. The problem of ill-posedness in connection with the inverse problem is addressed. Typical inverse solution techniques are highlighted. The review also includes the evaluation of methods used for computing the sensitivity matrix. Statistics which can be used to estimate the parameter uncertainty are outlined. Attempts have been made to compare and contrast representative inverse procedures, and direction for future research is suggested.
FDTD Modeling for Dispersive Media Using Matrix Exponential Method

This letter presents a finite-difference time-domain formulation to model electromagnetic wave propagation in dispersive media using matrix exponential method. The Maxwell's curl equations and the time domain relations between electric fields and auxiliary variables are formulated as a first order differential matrix system. The fundamental solution to such a system is derived in terms of matrix exponential and the update equations can be extracted conveniently from the solution. Numerical results show that this formulation yields higher accuracy compared to many other previous methods, without incurring additional auxiliary variable and complexity.
Inelastic Constitutive Modeling for Viscoplastcity Using Neural Networks

Up to now, a number of models have been proposed and discussed to describe a wide range of inelastic behaviors of materials. The fatal problem of using such models is however the existence of model errors, and the problem remains inevitably as far as a material model is written explicitly. In this paper, the authors define the implicit constitutive model and propose an implicit viscoplastic constitutive model using neural networks. In their modeling, inelastic material behaviors are generalized in a state space representation and the state space form is constructed by a neural network using input-output data sets. A technique to extract the input-output data from experimental data is also described. The proposed model was first generated from pseudo-experimental data created by one of the widely used constitutive models and was found to replace the model well. Then, having been tested with the actual experimental data, the proposed model resulted in a negligible amount of model errors indicating its superiority to all the existing explicit models in accuracy.
Compared With What? The Effects of Different Comparisons on Conceptual Knowledge and Procedural Flexibility for Equation Solving

Researchers in both cognitive science and mathematics education emphasize the importance of comparison for learning and transfer. However, surprisingly little is known about the advantages and disadvantages of what types of things are being compared. In this experimental study, 162 seventh- and eighth-grade students learned to solve equations (a) by comparing equivalent problems solved with the same solution method, (b) by comparing different problem types solved with the same solution method, or (c) by comparing different solution methods to the same problem. Students' conceptual knowledge and procedural flexibility were best supported by comparing solution methods and to a lesser extent by comparing problem types. The benefits of comparison are augmented when examples differ on relevant features, and contrasting methods may be particularly useful in mathematics learning.
Theory of mode locking with a slow saturable absorber

A closed-form solution is presented for the pulses of a homogeneously broadened laser mode locked by a saturable absorber of relaxation time much longer than the pulsewidth. With suitable approximations, the pulse shape is a secant hyperbolic. The system is described in terms of the linewidth omega C of the system, the saturation energies of the saturable absorber and the laser medium, the ratio of saturable-absorber loss to resonator loss, and the ratio of cavity round-trip time and laser-medium relaxation time. The energy and width of the pulse are obtained as functions of these parameters. Graphs are presented for the operating regimes as bounded by the choice of the preceding parameters. The theoretical predictions are compared with second-harmonic-generation (SHG) autocorrelation traces of mode-locked dye-laser pulses.
Molekulare Blutgruppenbestimmung

Zusammenfassung Die erste molekulare Analyse einer menschlichen Blutgruppe erfolgte 1983 mittels eines Restriktions-Fragment-Längen-Polymorphismus (RFLP) am System Xg. Seither wurden in unzähligen Studien die molekularen Ursachen für Blutgruppen und deren Antigene erforscht,und das resultierende Wissen für eine ständige Verbesserung der entsprechenden Analysemethoden verwendet. Die Untersuchung kausaler Punktmutationen (Single Nucleotide Polymorphism, SNP) aller 36 von der International Society for Blood Transfusion (ISBT) anerkannten Blutgruppensysteme erlaubt heute eine der Serologie ebenbürtige, exakte Vorhersage der Blutgruppenantigene. In Patienten wird die molekulare Blutgruppenbestimmung bevorzugt in Form von Einzelprobenanalytik für die Diagnose von RhD-Varianten eingesetzt, um damit transfusionsrelevante Entscheidungen bezüglich RhD zu treffen und um die Rh-Prophylaxe noch zielsicherer zu steuern. An Spenderproben und im Hochdurchsatz ermöglicht die Blutgruppen-Genotypisierung die Schaffung einer ausreichenden Anzahl von Spender-Datensätzen, um immunisierte Patienten bestverträglich zu transfundieren oder deren Immunisierung bereits im Ansatz zu vermeiden. Gleichzeitig werden heutzutage an den gleichen Proben zusätzlich eine Vielzahl weiterer SNPs zur Identifikation von Spendern mit seltener Negativität für hochfrequente Antigene getestet. Derartig umfassende Spender-Datensätze werden bereits ideal genutzt für „In-silico-Kreuzproben“ eingesetzt. Next Generation Sequencing (NGS) ist auch in der Transfusionsmedizin der „neue Stern am Horizont“ und wird vermutlich innert weniger Jahre eine wichtige Rolle in der Analyse kompletter Blutgruppengenome (chronischer) Empfänger spielen. Blutgruppenbestimmung als frühestes Beispiel echter personalisierter Medizin wird in ihrer molekularen Version mit dazu beitragen, den gebührenden Platz der Transfusionsmedizin in der modernen Medizin zu behaupten.
A Comparative Analysis of Hillary Clinton and John Mahama’s Concession Speeches in the 2016 US and Ghanaian Presidential Elections

Abstract Comparative research contributes to knowledge by providing a better understanding of how a phenomenon manifests in different socio-cultural contexts. In this present study, we examined the concession speeches of Hillary Clinton (United States, Democratic Party) and John Mahama (Ghana, National Democratic Congress, NDC) in the aftermath of their 2016 electoral defeats. Findings indicated that three similar frames emerged between the two candidates. Hillary Clinton’s frames included: acknowledging pain and acceptance, democracy, values and nationalism, and gratitude. John Mahama’s frames had: acceptance and concern, appreciation, unity, democracy, and nationhood. Both candidates accepted the electoral outcome, showed gratitude, and reaffirmed their belief in democracy and unity. However, there were slight differences. Hillary Clinton’s frame on acknowledging pain and acceptance had a more open, forthright recognition of being hurt in a way that enabled her to process the loss and pain. Findings from this study provide insights into recent concession speeches across two socio-cultural and continental divides, which builds on literature in framing and political communication.
Social responses to the COVID-19 pandemic

The COVID-19 pandemic has caused an immense impact on people and society (Alammary, Alshaikh, and Alhogail 2022; Chauhan et al. 2022; Law, Vostanis, and O’Reilly 2022). As a result, the COVID-19 pandemic has generated a strong demand for social responses to address the adverse effects of the COVID-19 pandemic (He, Zhang, and Li 2021; Kayis et al. 2021). Numerous people have been engaged in social media to share various information, such as health status, preventive behaviours, science and educational information, and community-related news (Nabity-Grover, Cheung, and Thatcher 2020; Riaz, Wang, and Guo 2021). When the COVID-19 pandemic broke out, numerous people expressed opinions on social media and sought to interact with others using social media. Many people rely on social media to obtain news about the pandemic and to share pandemic-related information with family and friends. Unfortunately, some of the information shared on social media is not inaccurate.
Understanding the solar system with numerical simulations and Levy flights

This thesis presents several investigations into the formation of planetary systems and the dynamical evolution of the small bodies left over from this process. We develop a numerical integration scheme with several optimizations for studying the late stages of planet formation: adaptive time steps, accurate treatment of close encounters between particles, and the ability to add non-conservative forces. Using this code, we simulate the phase of planet formation known as "oligarchic growth. " We find that when the dynamical friction from planetesimals is strong, the annular feeding zones of the protoplanets are inhabited by not one but several oligarchs on nearly the same semimajor axis. We systematically determine the number of co-orbital protoplanets sharing a feeding zone and the width of these zones as a function of the strength of dynamical friction and the total mass of the disk. The increased number of surviving protoplanets at the end of this phase qualitatively affects their subsequent evolution into full-sized planets. We also investigate the distribution of the eccentricities of the protoplanets in the runaway growth phase of planet formation. Using a Boltzmann equation, we find a simple analytic solution for the distribution function followed by the eccentricity. We show that this function is self-similar: it has a constant shape while the scale is set by the balance between mutual excitation and dynamical friction. The type of evolution described by this distribution function is known as a Levy flight. We use the Boltzmann equation framework to study the nearly circular orbits of Kuiper Belt binaries and the nearly radial orbits of comets during the formation of the Oort cloud. We calculate the distribution function of the eccentricity of Kuiper belt systems, like the moons of Pluto, given the stochastic perturbations caused by close encounters with other Kuiper belt objects. For Oort cloud comets, we find the distribution function of the angular momentum as it is excited by perturbations from passing stars in the Galaxy. Both systems evolve as Levy flights. This work unifies the effects of stochastic stellar encounters and the smooth torque from the Galactic potential on Oort cloud comets.
Tidal interactions in star cluster simulations

ABSTRA C T We describe the implementation of tidal circularization of binaries in an N-body code for star cluster simulations. The first part contains the theoretical framework for normal and chaotic tidal interactions, including capture from hyperbolic orbits. This formulation yields convenient expressions which are used to modify the binary elements. Stars are represented as polytropes, with a time-dependent effective polytropic index calculated for evolving stars. Stellar evolution is treated using a fast look-up table for stellar masses and radii. This gives a consistent astrophysical description of open clusters containing a significant proportion of primordial binaries with a wide range of masses and periods. An analytic expression for the chaos boundary for arbitrary mass ratio and polytropic indices is presented. We provide detailed correction procedures for tidal circularization and chaotic motion for perturbed binaries which are studied by the classical Kustaanheimo‐Stiefel two-body regularization method and also outline a similar treatment for multiple regularization of temporary subsystems involving 3‐6 members. Strong interactions in the latter lead to the formation of chaotic binaries and stable hierarchical systems in which the eccentricity of the inner binary may be subject to systematic changes on relatively short time-scales. Finally, we illustrate the effect of tidal circularization by presenting some results of a realistic cluster simulation involving 10 4 single stars and 500 primordial binaries.
A Rasch Hierarchical Measurement Model

In this article, a hierarchical measurement model is developed that enables researchers to measure a latent trait variable and model the error variance corresponding to multiple levels. The Rasch hierarchical measurement model (HMM) results when a Rasch IRT model and a one-way ANOVA with random effects are combined (Bryk & Raudenbush, 1992; Goldstein, 1987; Rasch, 1960). This model is appropriate for modeling dichotomous response strings nested within a contextual level. Examples of this type of structure include responses from students nested within schools and multiple response strings nested within people. Model parameter estimates of the Rasch HMM were obtained using the Bayesian data analysis methods of Gibbs sampling and the Metropolis-Hastings algorithm (Gelfand, Hills, Racine-Poon, & Smith, 1990; Hastings, 1970; Metropolis, Rosenbluth, Rosenbluth, Teller, & Teller, 1953). The model is illustrated with two simulated data sets and data from the Sloan Study of Youth and Social Development. The results are discussed and parameter estimates for the simulated data sets are compared to parameter estimates obtained using a two-step estimation approach.
Sequence-assignment validation in protein crystal structure models with checkMySequence

Sequence register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication I have shown that register shifts in cryo-EM models of proteins can be detected using a systematic re-assignment of short model fragments to the target sequence. Here, I show that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias corrected electron-density maps. I describe in detail five register shift errors detected using the method in models deposited in the PDB. Synopsis I show that checkMySequence, an automated method for validating sequence assignment in cryo-EM structures of proteins, can be used for validating crystal structure models.
Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry

The populations of the Angolan Namib Desert have been largely neglected in previous surveys of the genomic landscape of southern Africa. Although at present the Namib is culturally dominated by Southwest Bantu-speaking cattle-herders, the region exhibits an extraordinary ethnographic diversity which includes an array of semi-nomadic peoples whose subsistence strategies fall outside the traditional division between foraging and food production and can thus be referred to as “peripatetic”. Among these small-scale populations are the last speakers of the Kwadi branch of the Khoe-Kwadi language family associated with the introduction of pastoralism into southern Africa (Kwepe), as well as a range of groups whose origins remain enigmatic (Kwisi, Twa and Tjimba). Using genome-wide data from 208 individuals belonging to nine ethnically diverse groups from the Angolan Namib and adjacent areas (Kwepe, Kwisi, Twa, Tjimba, ! Xun, Kuvale, Himba, Nyaneka, Ovimbundu) in combination with published data from other regions of Africa, we reconstruct in detail the histories of contact emerging from pre-historic migrations to southern Africa and show that peripatetic groups from southwestern Angola stand out for exhibiting elevated levels of an unique, regionally-specific and highly divergent Pre-Bantu ancestry. These findings highlight the importance of the Namib for understanding the deep genetic structure of Africa.
Allergic Asthma Responses Are Dependent on Macrophage Ontogeny

The ontogenetic composition of tissue-resident macrophages following injury, environmental exposure, or experimental depletion can be altered upon re-establishment of homeostasis. However, the impact of altered resident macrophage ontogenetic milieu on subsequent immune responses is poorly understood. Hence, we assessed the effect of macrophage ontogeny alteration following return to homeostasis on subsequent allergic airway responses to house dust mites (HDM). Using lineage tracing, we confirmed alveolar and interstitial macrophage ontogeny and their replacement by bone marrow-derived macrophages following LPS exposure. This alteration in macrophage ontogenetic milieu reduced allergic airway responses to HDM challenge. In addition, we defined a distinct population of resident-derived interstitial macrophages expressing allergic airway disease genes, located adjacent to terminal bronchi, and reduced by prior LPS exposure. These findings support that the ontogenetic milieu of pulmonary macrophages is a central factor in allergic airway responses and has implications for how prior environmental exposures impact subsequent immune responses and the development of allergy.
A burns and COVID-19 shared stress responding gene network deciphers CD1C-CD141- DCs as the key cellular components in septic prognosis

Differential body responses to various stresses, infectious or noninfectious, govern clinical outcomes ranging from asymptoma to death. However, the common molecular and cellular nature of the stress responsome across different stimuli is not described. In this study, we compared the expression behaviors between burns and COVID-19 infection by choosing the transcriptome of peripheral blood from related patients as the analytic target since the blood cells reflect the systemic landscape of immune status. To this end, we identified an immune co-stimulator (CD86)-centered network, named stress-response core (SRC), which was robustly co-expressed in burns and COVID-19. The enhancement of SRC genes (SRCs) expression indicated favorable prognosis and less severity in both conditions. An independent whole blood single-cell RNA sequencing of COVID-19 patients demonstrated that the monocyte-dendritic cell (Mono-DC) wing was the major cellular source of SRC, among which the higher expression of the SRCs in the monocyte was associated with the asymptomatic COVID-19 patients, while the quantity-restricted and function-defected CD1C-CD141-DCs were recognized as the key signature which linked to bad consequences. Specifically, the proportion of the CD1C-CD141-DCs and their SRCs expression were step-wise reduced along with worse clinic conditions while the subcluster of CD1C-CD141-DCs from the critical COVID-19 patients was characterized of IFN signaling quiescence, high mitochondrial metabolism and immune-communication inactivation. Thus, our study identified an expression-synchronized and function-focused gene network in Mono-DC population whose expression status was prognosis-related and might serve as a new target of diagnosis and therapy.
Hsp70/Hsp90 organizing protein (HOP) maintains CRAF kinase activity and regulates MAPK signaling by enhancing Hsp90-CRAF association

The stability and activity of CRAF kinase are stringently regulated by heat shock protein 90 (Hsp90). Hsp90-mediated client folding and maturation is governed by its co-chaperones, but their functionality in chaperoning CRAF/Raf1 kinase to accomplish signaling under physiological conditions remains poorly understood. Here, we show that Hsp70/Hsp90 organizing protein (HOP) associates with CRAF kinase for maintaining its kinase activity and facilitates the activation of the MAPK pathway. Such activation is mediated by TPR2A-2B-DP2 domain of HOP and requires efficient binding to Hsp90. Being a recruiter of Hsp90, Cdc37 is unable to supplement the function of HOP/Sti1. Downregulation of HOP/Sti1 in yeast and in vitro cell culture significantly reduces the CRAF signaling. Our data suggest that Hsp90 is recruited to CRAF in two steps, separately initiated by co-chaperones HOP and Cdc37 respectively during CRAF folding/maturation, and again upon CRAF activation mediated by HOP during MAPK signaling. Therefore, HOP is a regulator of CRAF kinase during activation of MAPK pathway and serves as a sensor of growth signaling beyond its client folding and maturation function.
SOURSOP: A Python package for the analysis of simulations of intrinsically disordered proteins

Conformational heterogeneity is a defining hallmark of intrinsically disordered proteins and protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they control are associated with sequence-specific conformational ensembles. Simulations of conformational ensembles that are based on atomistic and coarse-grained models are routinely used to uncover the sequence-specific interactions that may contribute to IDR functions. These simulations are performed either independently or in conjunction with data from experiments. Functionally relevant features of IDRs can span a range of length scales. Extracting these features requires analysis routines that quantify a range of properties. Here, we describe a new analysis suite SOURSOP, an object-oriented and open-source toolkit designed for the analysis of simulated conformational ensembles of IDRs. SOURSOP implements several analysis routines motivated by principles in polymer physics, offering a unique collection of simple-to-use functions to characterize IDR ensembles. As an extendable framework, SOURSOP supports the development and implementation of new analysis routines that can be easily packaged and shared.