Miracle-dz/UniFAR-FTUs huggingface dataset:
The immunoglobulin A isotype of the Arabian camel (Camelus dromedarius) preserves the dualistic structure of unconventional single-domain and canonical heavy chains

Evolutionary processes of adaptive immunity in Camelidae and some cartilaginous fishes resulted in the concurrent expression of classic heavy-light chain heterotetrameric antibodies together with unconventional heavy chain-only homodimeric antibodies of the IgG class. Heavy chain-only IgG bears a single variable domain and lacks the constant heavy (CH) γ1 domain required for the covalent pairing with the light chain. It has so far not been reported whether this distinctive feature of IgG is also observed in the IgA isotype. Therefore, gene-specific primers were used to generate a library of IgA heavy chain cDNA derived from RNA extracted from the third eyelid of the dromedary where isolated lymphoid follicles and plasma cells abound at inductive and effector sites, respectively. Majority of the cDNA clones revealed the hallmarks of heavy chain-only antibodies, i.e. camelid-specific amino acid substitutions in framework region 1 and 2, broad length distribution of complementarity determining region 3, and the absence of the CHα1 domain. In a few clones, however, the cDNA of canonical IgA heavy chain was amplified which included the CHα1 domain, analogous to CHγ1 domain in dromedary IgG1 subclass. Moreover, we noticed a short, proline-rich hinge, similar to that in human IgA2, and, at the N-terminal end of the CHα3 domain, a unique, camelid-specific pentapeptide consisting of serine, glutamic acid, aspartic acid, alanine or threonine, and isoleucine, of undetermined function, designated as the inter-α region. Immunoblots using rabbit anti-camel IgA antibodies raised against CHα2 and CHα3 domains as well as the inter-α region revealed the expression of a ∼52 kDa and a ∼60 kDa IgA species, corresponding to unconventional and canonical IgA heavy chain, respectively, in tissue extracts of the third eyelid, trachea, small and large intestine. In contrast, the leporine anti-CHα1 antibody detected canonical, but not unconventional IgA heavy chain, in all the examined tissues, milk, and serum, in addition to another hitherto unexplored species of ∼45 kDa in milk and serum. Immunohistology using anti-CHα domain antibodies confirmed the expression of both variants of IgA heavy chains in plasma cells in the third eyelid’s lacrimal gland, and in the lamina propria of conjunctiva, bronchial and intestinal mucosa. We conclude that in the dromedary, the IgA isotype has expanded the immunoglobulin repertoire by co-expressing single-domain unconventional as well as canonical IgA heavy chains, comparable to the IgG class, thus underscoring the crucial role of heavy chain-only antibodies in immune defense not only in circulation but also at the mucosal frontiers.
Statistical Downscaling Using Kernel Quantile Regression to Predict Extreme Rainfall

Rainfall is one of climate elements with diverse intensity. In extreme circumtances it is necessary to study extreme rainfall to minimize impacts that may occur. Statistical downscaling is a method that can be used to predict rainfall, which is utilizing Global Circurlation Model (GCM) output data. The characteristics of GCM output data is curse of dimensionality which causes multicollinearity. Kernel trick is one method that can be used to overcome this problem by transforming GCM output data into a high-dimensional feature space. The transformation results are modeled with kernel quantile regression. This paper presents the use of kernel quantile regression to predict extreme rainfall, compared to kernel quantile regression with principal components. The result showed that based on the RMSEP values and the correlations, both models gave relatively similiar prediction.
Generative design approach to combine architected Voronoi foams with porous collagen scaffolds to create a tunable composite biomaterial

Regenerative biomaterials for musculoskeletal defects must address multi-scale mechanical challenges. We are developing biomaterials for craniomaxillofacial bone defects that are often large and irregularly shaped. These require close conformal contact between implant and defect margins to aid healing. While we have identified a mineralized collagen scaffold that promotes mesenchymal stem cell osteogenic differentiation in vitro and bone formation in vivo, its mechanical performance is insufficient for surgical translation. We report a generative design approach to create scaffold-mesh composites by embedding a macro-scale polymeric Voronoi mesh into the mineralized collagen scaffold. The mechanics of architected foam reinforced composites are defined by a rigorous predictive moduli equation. We show biphasic composites localize strain during loading. Further, planar and 3D mesh-scaffold composites can be rapidly shaped to aid conformal fitting. Voronoi-based composites overcome traditional porosity-mechanics relationship limits while enabling rapid shaping of regenerative implants to conformally fit complex defects unique for individual patients.
Bordetella Filamentous hemagglutinin (FhaB) and Adenylyl cyclase toxin (ACT) interactions on the bacterial surface are consistent with FhaB-mediated delivery of ACT to phagocytic cells

Bordetella species that cause respiratory infections in mammals include B. pertussis, which causes human whooping cough, and B. bronchiseptica, which infects nearly all mammals. Both bacterial species produce filamentous hemagglutinin (FhaB) and adenylyl cyclase toxin (ACT), prominent surface-associated and secreted virulence factors that contribute to persistence in the lower respiratory tract by inhibiting clearance by phagocytic cells. FhaB and ACT proteins interact with themselves, each other, and host cells. Using immunoblot analyses, we showed that ACT binds to FhaB preferentially on the bacterial surface before being released into the extracellular environment. We showed that SphB1, a surface protease identified based on its ability to cleave FhaB, also cleaves ACT, and we showed that the presence of ACT blocks SphB1-dependent and independent cleavage of FhaB, but the presence of FhaB does not block SphB1-dependent cleavage of ACT. SphB1-dependent cleavage of ACT occurs proximally to ACT’s active site, and hence is predicted to inactivate ACT. We also showed that FhaB-bound ACT can intoxicate host cells producing CR3, the receptor for ACT. In addition to increasing our understanding of FhaB, ACT, and ACT interactions on the Bordetella surface, our data support a model in which FhaB functions as a novel toxin delivery system by binding to ACT and allowing its release upon binding of ACT to its receptor, CR3, on phagocytic cells. AUTHOR SUMMARY Bacteria need to control the variety, abundance, and conformation of proteins on the cellular surface to survive. Members of the Gram-negative bacterial genus Bordetella include B. pertussis, which causes whooping cough in humans, and B. bronchiseptica, which causes respiratory infections in a broad range of mammals. These extremely closely related species produce two prominent virulence factors, the two-partner secretion (TPS) effector FhaB and Adenylyl cyclase toxin (ACT), that interact with themselves, each other, and host cells. In this work, we showed that ACT binds preferentially to FhaB on the bacterial surface before being released into the extracellular environment. We showed that the exoprotease SphB1, which cleaves FhaB, also cleaves ACT. We showed that ACT that is bound to FhaB can be delivered to CR3+ host cells. Our data support a model in which FhaB functions to deliver ACT specifically to phagocytic cells, and not epithelial cells. This is the first report of a TPS system facilitating delivery of a separate polypeptide toxin to target cells and expands our understanding of how these systems contribute to bacterial pathogenesis.
PENGARUH VOID PADA PENAMPANG TIANG FONDASI TERHADAP P-Y CURVE

Analisa daya dukung lateral merupakan aspek penting dalam perancangan fondasi untuk mengantisipasi kegagalan fondasi tiang. Salah satu metodenya adalah p-y curve yang merupakan pengembangan dari metode Balok pada Fondasi Winkler. Metode p-y curve memodelkan tanah sebagai pegas non-linier. Metode ini diperkenalkan oleh McClelland dan Focht pada tahun 1956 dalam bentuk kurva hubungan reaksi tanah dengan defleksi akibat beban lateral. Metode p-y curve lebih umum digunakan karena tahap pengerjaannya yang tidak rumit jika dibandingkan dengan metode lainnya dan hasilnya dapat diandalkan. Akan tetapi, metode p-y curve tidak memperhitungkan pengaruh bentuk penampang karena tiang disederhanakan menjadi model tiang satu dimensi dengan pendekatan empiris. Penelitian ini membandingkan pengaruh lubang pada penampang spun pile dan tiang baja tubular terhadap p-y curve menggunakan metode yang diusulkan oleh Georgiadis (2010) dengan p-y curve yang dibentuk dengan program LPILE. Hasil dari penelitian ini menunjukkan bahwa p-y curve untuk tiang dengan penampang solid lebih kaku daripada tiang dengan penampang void.
Detecting shifts in the mode of chromosomal speciation across the cosmopolitan plant lineage Carex

Recent studies of angiosperm diversification have focused on the role of polyploidy as a driver of diversification. However, we know far less about the effects of single changes in chromosome number—dysploidy, which can mediate lineage diversification by affecting recombination rates, linkage, and/or reproductive isolation. Modeling the effects of dysploidy on diversification is mathematically and computationally challenging because many states and parameters are required to track changes in individual chromosomes, especially in lineages that have high variability in chromosome number. Additionally, we expect the processes of diversification and dysploidy to vary across clades, which requires modeling process variation to disentangle the effects of the observed trait (chromosome number) from the effects of unobserved traits on diversification. In this work, we propose a new state-dependent diversification model of chromosome evolution that includes numerous character states and explicitly models heterogeneity in the diversification process. Our model includes parameters that functionally link diversification rates to dysploidy rates and differentiate between anagenetic and cladogenetic changes. We apply this model to Carex (Cyperaceae), a model lineage for understanding dysploidy and diversification, leveraging chromosome number information and the most recent time-calibrated phylogenetic tree for over 700 species and subspecies. We recover distinct modes of chromosomal speciation across Carex. In one mode, dysploidy occurs very frequently and drives faster diversification rates. In the other mode, dysploidy is rare and diversification is driven by other factors, unmeasured in our analysis. This study is the first to demonstrate that dysploidy drives diversification in plants while considering unmeasured factors affecting diversification. Significance Statement Evolutionary genomic rearrangements via the gain and/or loss of chromosomes without losing DNA may cause new species to form, but how this process plays out over a millions-of-years timescale is unclear. We test if there is a detectable effect of chromosome gains/losses on the rate of species formation in a large, diverse group of plants. We demonstrate decisively for the first time that these rearrangements sometimes drive the formation of new species through two evolutionary modes. In one mode, rearrangements happen rapidly and sometimes cause new species to form. In the other mode, rearrangements happen less frequently and are not associated with new species formation; instead, other factors—unmeasured in our analysis—likely drive the formation of new species.
MAGPIE: an interactive tool for visualizing and analyzing many simultaneous protein interactions with a binding partner

Summary: We present MAGPIE, a tool for analyzing thousands of protein-ligand interactions at once. MAGPIE generates an interactive 3D visualization from a set of protein complex structures that share a target ligand, as well as sequence logo-style frequency graphs that show all the amino acids from the set of protein binders that interact with user-selected target ligand positions. MAGPIE is compatible with small molecule or protein ligands. Availability and implementation: MAGPIE is implemented in Python 3 and is freely available with two dataset/usage examples and a helper script to prepare MAGPIE inputs at https://github.com/glasgowlab/MAGPIE. Additional documentation is in the Supplementary data online.
Aplication of Interferometric Radiometry to Earth Observation

La tesis contiene en primer lugar un estudio de las técnicas de interferometria radiometrica, con énfasis en las causas de error y su impacto en las características del sensor. A continuación se proponen y comparan varias técnicas de calibracion basadas en la inyección de ruido.Un aspecto notable de la tesis consiste en el desarrollo de técnicas de reconstrucción de la imagen radiometrica adaptadas a la geometría del sensor miras propuesto por la agencia espacial europea (esa). La tesis incluye tambien el diseño de un prototipo a escala reducida de radiometro interferometrico que se ha utilizado para verificar los resultados teóricos y simulados.En resumen se trata de un trabajo muy completo y riguroso, con numerosas aportaciones originales, que han sido contrastadas experimentalmente.
Mobile Communication Log Time Series to Detect Depressive Symptoms

Major Depressive Disorder (MDD) is highly prevalent and characterized by often debilitating behavioral and cognitive symptoms. MDD is poorly understood, likely due to considerable heterogeneity and self-report-driven symptomatology. While researchers have been exploring the ability of machine learning to screen for MDD, much less attention has been paid to individual symptoms. We posit that understanding the relationship between objective data streams and individual depression symptoms is important for understanding the considerable heterogeneity in MDD. Thus, we conduct a comprehensive comparative study to explore the ability of machine learning to predict nine self-reported depressive symptoms with call and text logs. We created time series from the logs of over 300 participants by aggregating communication attributes– average length, count, or contacts– every 4, 6, 12, or 24 hours. We were most successful predicting movement irregularities with a balanced accuracy of 0.70. Further, we predicted suicidal ideation with a balanced accuracy of 0.67. Outgoing texts proved to be the most useful log type. This study provides valuable insights for future mobile health research aimed at personalizing assessment and intervention for MDD.
The Mechanism and Predictability of an Elevated Convection Initiation Event in a Weak-Lifting Environment in Central-Eastern China

An elevated convection initiation (CI) of a quasi-linear mesoscale convective system (MCS) that occurred in a weak-lifting environment in the early morning on 23 June 2016 in central-eastern China was investigated using observational analysis and convection-permitting numerical simulations. This MCS gradually developed into a surface-based MCS and eventually produced a strong supercell that spawned an EF4 tornado in Yancheng City of Jiangsu Province and killed 98 people. This elevated MCS was initiated ahead of a surface front without identifiable boundaries at the surface. An elevated moist absolutely unstable layer (MAUL) was found to be conducive to the CI. The MAUL provided negligible convective inhibition and contributed to CI without strong-lifting mechanisms. Numerical simulation results showed that the formation of the elevated MAUL was mainly attributed to adiabatic cooling by weak vertical ascent and sufficient horizontal moisture transport near the terminus of a low-level jet. The weak vertical ascent before the CI was sloping and was likely to be relevant to the layer-lifting process associated with the realization of potential instability. The results showed that the MAUL in this weak-lifting environment was characterized by a shallower depth, a weaker lapse rate, and a longer sustaining period than the conditions in a strong-lifting environment. The predictability of this elevated CI case was examined using a 10-member ensemble forecast. A total of 80% of the ensemble members captured the CI. Rather than a difference in lifting, whether having an elevated MAUL or not was the major difference between CI and non-CI members in the present case.
Curcumin/Fusidic Acid Bitherapy Loaded Mixed Micellar Nanogel for Acne Vulgaris Treatment: In Vitro and In Vivo Studies

The combination of herbal drugs with a topical antibacterial for managing a chronic disease like acne vulgaris has emerged lately to settle side effects and bacterial multidrug resistance. Mixed micelles (MMs) incorporated into nanogel were explored for hybrid delivery of curcumin (Cur) and fusidic acid (FA) combination presenting a multi-strategic treatment. Curcumin-fusidic acid–loaded mixed micelles (Cur-FA-MMs) were assessed for size, surface charge, compatibility, in vitro release, and encapsulation. The selected formula was further loaded into nanogel and investigated for viscosity, ex vivo permeation, and in vivo potential. Cur-FA-MMs exhibited uniform nanosized spherical morphology, and negative surface charge affording high encapsulation for both drugs with a biphasic in vitro release over a period of 48h and good colloidal stability. The attained Cur-FA-MM-loaded nanogel had optimum viscosity with remarkable permeation coefficient values nearly 2-fold that related to plain nanogel. The pharmacodynamic effect of Cur on FA was pronounced by the significant improvement of the skin’s degree of inflammation, epidermal hypertrophy, and congestion in animals treated with Cur-FA-MM-loaded nanogel. In conclusion, micellar nanogel could enable the progressive effect of Cur (an antioxidant with reported antibiotic activity) on FA (antibiotic) and decrease the risk of emerging antibiotic resistance by enhancing the solubility and permeation of Cur.
The Role of the Customer’s Perception of Service Quality (CPSQ) in the Relationship between Information Technology Competence (ITC) and Customer Satisfaction (CS), A field study applied on government sector

the present research aimed to test the significant relationship between information technology Competence represented in two dimensions: IT knowledge and IT skills on the one hand and customer satisfaction represented in two dimensions: on employees and on services on the other hand, as well as the Mediating role of customers' perception of service quality represented in four dimensions: reliability, assurance responsiveness, and empathy in this relation, the relationships between the variables are suggested by a theoretical framework deriving four hypotheses examined through structural equation modeling applied to a sample of 308 clients in the government sector, the findings pointed to the direct relationship between information technology competence and customer satisfaction, supported the direct relationship between information technology competence and customer perception of service quality, As well as the findings showed a positive correlation between customer perception of service quality on the one hand and customer satisfaction on the other hand, the results also showed an improvement in the strength of the relationship between information technology competence and customer's satisfaction through the mediating role of customer perception of service quality as intermediate variables. finally, the government sector should not only provide the facilities that enable employees to perform the tasks assigned to them but should also improve their competence in doing so which lowers customer concerns about possible paper and document loss or disabling their services.
Statistical Foundations of Econometric Modelling

This textbook provides an introduction to econometrics through a grounding in probability theory and statistical inference. The emphasis is on the concepts and ideas underlying probability theory and statistical inference, and on motivating the learning of them both at a formal and an intuitive level. It encourages the mastering of fundamental concepts and theoretical perspectives which guide the formulation and solution of problems in econometric modelling. This makes it an ideal introduction to empirical econometric modelling and the more advanced econometric literature. It is recommended for use on courses giving students a thorough grounding in econometrics at undergraduate or graduate level.
Does Pension Funds' Fiduciary Duty Prohibit the Integration of Environmental Responsibility Criteria in Investment Processes?: A Realistic Prudent Investment Test

Pension funds have recently developed an increasing interest in environmental, social or governance (ESG) criteria, but critics claim that the integration of any of these non-financial criteria into pension fund investment processes conflicts with fiduciary duties. On this matter, the 2005 Freshfields report concluded that pension funds’ fiduciary duties (e.g. prudent action for proper purpose) only permit the consideration of an ESG criterion, if this process has no detrimental financial effects. While a body of research exists on the general relationship between ESG criteria and financial performance/risk management, no study has yet investigated the financial and risk implications of integrating any ESG criterion into an investment process from the perspective of pension funds, whose unique financial and legal characteristics require a specialised research design (e.g. a prudent, very large scale investment process). To study this effect, we develop a test of the prudent integration of ESG criteria in realistic and synthetic pension fund investment processes. We analyse over 1,500 firms from 26 developed countries over a 77 months period using aggregated and disaggregated corporate environmental responsibility ratings supplied by EIRIS. Our results are twofold. First, we find zero indications that the integration of aggregated or disaggregated corporate environmental responsibility ratings into pension fund investment processes has any detrimental financial effect. Second, findings from our risk analysis even support integrating corporate environmental criteria into pension fund investment processes, as the downside volatility is substantially lower. Robustness tests for temporal consistency and industry controls for sector bias confirm these findings. Hence, we conclude that pension funds’ fiduciary duties do not appear to prohibit the integration of environmental responsibility criteria into their investment processes. Future research might want to investigate the effect of integrating other ESG criteria into a realistic prudent pension fund investment process.