Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-Parametrical Canonical Analysis of Quality-Related Characteristics of Eggs of Different Varieties of Native Hens Compared to Laying Lineage

Simple Summary The development of new more productive lines of laying hens has displaced native breeds to second place; therefore, new lines of research that ensure the conservation of local breeds and biodiversity are increasingly necessary. The aim of the present study is to characterize the productive capability of Utrerana and to compare the relationships among parameters determining the internal and external quality of the egg, through canonical correlation analysis. We used a flock of 68 Utrerana hens with animals of each of its four varieties (white, black, Franciscan and partridge), and a group of 17 Leghorn hens as a control group. The breed and variety significantly affected egg characteristics. The external and internal quality parameters of the egg were evaluated and reported results providing consistent data for the characterization of the products from this breed. This productive characterization could benefit the conservation of the Utrerana breed, the establishment of livestock models that adapt to it and the search for a market in which this product could be used. Abstract The aim of the present study is to characterize the productive capability of Utrerana and to compare the relationships among parameters determining the internal and external quality of the egg, through canonical correlation analysis. A flock of 68 Utrerana hens and a control group of Leghorn hens (n = 17) were housed individually to allow individual identification of eggs and for the assessment of egg quality characteristics. Almost all variables showed differences when both breeds were compared, except for white height, yolk diameter, yolkL* and yolk pH (p > 0.05). Only minor diameter, white height, yolkL*, yolka*, and shell weight reported significant differences between laying age groups. White height, yolk color, and almost all yolk color coordinates were significantly different (p < 0.05) for period and month. Egg and white weight reached highest significantly different levels for the fourth and fifth time that the hens laid an egg. External quality-related traits are better predictors of internal quality-related traits than vice versa, enabling the implementation of an effective noninvasive method for internal quality determination and egg classification aimed at suiting the needs of consumers.
Estimation of the Knee Adduction Moment and Joint Contact Force during Daily Living Activities Using Inertial Motion Capture

Knee osteoarthritis is a major cause of pain and disability in the elderly population with many daily living activities being difficult to perform as a result of this disease. The present study aimed to estimate the knee adduction moment and tibiofemoral joint contact force during daily living activities using a musculoskeletal model with inertial motion capture derived kinematics in an elderly population. Eight elderly participants were instrumented with 17 inertial measurement units, as well as 53 opto-reflective markers affixed to anatomical landmarks. Participants performed stair ascent, stair descent, and sit-to-stand movements while both motion capture methods were synchronously recorded. A musculoskeletal model containing 39 degrees-of-freedom was used to estimate the knee adduction moment and tibiofemoral joint contact force. Strong to excellent Pearson correlation coefficients were found for the IMC-derived kinematics across the daily living tasks with root mean square errors (RMSE) between 3° and 7°. Furthermore, moderate to strong Pearson correlation coefficients were found in the knee adduction moment and tibiofemoral joint contact forces with RMSE between 0.006–0.014 body weight × body height and 0.4 to 1 body weights, respectively. These findings demonstrate that inertial motion capture may be used to estimate knee adduction moments and tibiofemoral contact forces with comparable accuracy to optical motion capture.
CLIMATE ANALOGUES OF CAPITAL CITIES IN THE WEST SOUTH AMERICA

By means of a recently customary nonparametric method future climate analogues were predictable for West South American capital cities. The nonparametric scheme showed in this research for identifying climate analogues can be applied for impact assessments under a changing climate. MRI-AGCM3.2H with a horizontal resolution of 60 km, three convection schemes, four sea surface temperature distributions, and two initial conditions and under scenario A1B of the Special Report on Emissions Scenarios were used. The total ensemble scope was 24, with a simulation period of 25 years. Utmost of the future analogues are at lower latitudes than their target cities. Estimated seasonal variations in surface air temperature and rainfall in Santiago de Chile City look similar to the present-day climate of Cape Town, located in South Africa and for La Paz City a climate analogue is found at Oruro in Bolivia.
Particulate Matter-Induced Aryl Hydrocarbon Receptor Regulates Autophagy in Keratinocytes

Particulate matter (PM), which refers to the mixture of particles present in the air, can have harmful effects. Damage to cells by PM, including disruption of organelles and proteins, can trigger autophagy, and the relationship between autophagy and PM has been well studied. However, the cellular regulators of PM-induced autophagy have not been well characterized, especially in keratinocytes. The Aryl Hydrocarbon Receptor (AhR) is expressed in the epidermis and is activated by PM. In this study, we investigated the role of the AhR in PM-induced autophagy in HaCaT cells. Our results showed that PM led to AhR activation in keratinocytes. Activation of the AhR-target gene CYP1A1 by PM was reduced by co-treatment with α-naphthoflavone (α-NF), an AhR inhibitor. We also evaluated activation of the autophagy pathway in PM-treated keratinocytes. In HaCaT cells, treatment with PM treatment led to the induction of microtubules-associated proteins light chain 3 (LC3) and p62/SQSTM1, which are essential components of the autophagy pathway. To study the role of the AhR in mediating PM-induced autophagy, we treated cells with α-NF or used an siRNA against AhR. Expression of LC3-ІІ induced by PM was decreased in a dose dependent manner by α-NF. Furthermore, knockdown of AhR with siAhR diminished PM-induced expression of LC3-ІІ and p62. Together, these results suggest that inhibition of the AhR decreases PM-induced autophagy. We confirmed these results using the autophagy-inhibitors BAF and 3-MA. Taken together, our results indicate that exposure to PM induces autophagy via the AhR in HaCaT keratinocytes.
P38 and JNK Mitogen-Activated Protein Kinases Interact With Chikungunya Virus Non-structural Protein-2 and Regulate TNF Induction During Viral Infection in Macrophages

Chikungunya virus (CHIKV), a mosquito-borne Alphavirus, is endemic in different parts of the globe. The host macrophages are identified as the major cellular reservoirs of CHIKV during infection and this virus triggers robust TNF production in the host macrophages, which might be a key mediator of virus induced inflammation. However, the molecular mechanism underneath TNF induction is not understood yet. Accordingly, the Raw264.7 cells, a mouse macrophage cell line, were infected with CHIKV to address the above-mentioned question. It was observed that CHIKV induces both p38 and JNK phosphorylation in macrophages in a time-dependent manner and p-p38 inhibitor, SB203580 is effective in reducing infection even at lower concentration as compared to the p-JNK inhibitor, SP600125. However, inhibition of p-p38 and p-JNK decreased CHIKV induced TNF production in the host macrophages. Moreover, CHIKV induced macrophage derived TNF was found to facilitate TCR driven T cell activation. Additionally, it was noticed that the expressions of key transcription factors involved mainly in antiviral responses (p-IRF3) and TNF production (p-c-jun) were induced significantly in the CHIKV infected macrophages as compared to the corresponding mock cells. Further, it was demonstrated that CHIKV mediated TNF production in the macrophages is dependent on p38 and JNK MAPK pathways linking p-c-jun transcription factor. Interestingly, it was found that CHIKV nsP2 interacts with both p-p38 and p-JNK MAPKs in the macrophages. This observation was supported by the in silico protein-protein docking analysis which illustrates the specific amino acids responsible for the nsP2-MAPKs interactions. A strong polar interaction was predicted between Thr-180 (within the phosphorylation lip) of p38 and Gln-273 of nsP2, whereas, no such polar interaction was predicted for the phosphorylation lip of JNK which indicates the differential roles of p-p38 and p-JNK during CHIKV infection in the host macrophages. In summary, for the first time it has been shown that CHIKV triggers robust TNF production in the host macrophages via both p-p38 and p-JNK/p-c-jun pathways and the interaction of viral protein, nsP2 with these MAPKs during infection. Hence, this information might shed light in rationale-based drug designing strategies toward a possible control measure of CHIKV infection in future.
The natural history of Get3‐like chaperones

Get3 in yeast or TRC40 in mammals is an ATPase that, in eukaryotes, is a central element of the GET or TRC pathway involved in the targeting of tail‐anchored proteins. Get3 has also been shown to possess chaperone holdase activity. A bioinformatic assessment was performed across all domains of life on functionally important regions of Get3 including the TRC40‐insert and the hydrophobic groove essential for tail‐anchored protein binding. We find that such a hydrophobic groove is much more common in bacterial Get3 homologs than previously appreciated based on a directed comparison of bacterial ArsA and yeast Get3. Furthermore, our analysis shows that the region containing the TRC40‐insert varies in length and methionine content to an unexpected extent within eukaryotes and also between different phylogenetic groups. In fact, since the TRC40‐insert is present in all domains of life, we suggest that its presence does not automatically predict a tail‐anchored protein targeting function. This opens up a new perspective on the function of organellar Get3 homologs in plants which feature the TRC40‐insert but have not been demonstrated to function in tail‐anchored protein targeting. Our analysis also highlights a large diversity of the ways Get3 homologs dimerize. Thus, based on the structural features of Get3 homologs, these proteins may have an unexplored functional diversity in all domains of life.
Apolipoprotein A-I Crosses the Blood-Brain Barrier through Clathrin-Independent and Cholesterol-Mediated Endocytosis

Recent studies suggest that apolipoprotein A-I (ApoA-I), the major protein constituent of high-density lipoprotein particles, plays a critical role in preserving cerebrovascular integrity and reducing Alzheimer’s risk. ApoA-I present in brain is thought to be primarily derived from the peripheral circulation. Although plasma-to-brain delivery of ApoA-I is claimed to be handled by the blood-cerebrospinal fluid barrier (BCSFB), a contribution by the blood-brain barrier (BBB), which serves as a major portal for protein delivery to brain, cannot be ruled out. In this study, we assessed the permeability–surface area product (PS) of radioiodinated ApoA-I (125I-ApoA-I) in various brain regions of wild-type rats after an intravenous bolus injection. The PS value at the cortex, caudate putamen, hippocampus, thalamus, brain stem, and cerebellum was found to be 0.39, 0.28, 0.28, 0.36, 0.69, and 0.76 (ml/g per second × 10−6), respectively. Solutes delivered into brain via the BCSFB are expected to show greater accumulation in the thalamus due to its periventricular location. The modest permeability for 125I-ApoA-I into the thalamus relative to other regions suggests that BCSFB transport accounts for only a portion of total brain uptake and thus BBB transport cannot be ruled out. In addition, we show that Alexa Flour 647-labeled ApoA-I (AF647-ApoA-I) undergoes clathrin-independent and cholesterol-mediated endocytosis in transformed human cerebral microvascular endothelial cells (hCMEC/D3). Further, Z-series confocal images of the hCMEC/D3 monolayers and Western blot detection of intact ApoA-I on the abluminal side demonstrated AF647-ApoA-I transcytosis across the endothelium. These findings implicate the BBB as a significant portal for ApoA-I delivery into brain.
Pulmonary Alveolar Proteinosis

Abstract The profoundly hypoxemic child presents an interesting set of diagnostic and management challenges in the pediatric emergency department. While common pathologies including pneumonia, asthma, bronchiolitis, and pneumothoraces are managed using evidence-based algorithms, more enigmatic pathologies may present the treating physician with less diagnostic and therapeutic clarity. We present the case of a profoundly hypoxemic 16-year-old girl who presented in minimal distress, with oxyhemoglobin saturation of 63% on room air.
Single-view cone-beam x-ray luminescence optical tomography based on Group_YALL1 method

Single-view cone beam x-ray luminescence optical tomography (CB-XLOT) has the merit of short data acquisition time, which is important for resolving fast biological processes in vivo. However, challenges remain in the reconstruction of single-view CB-XLOT. In our previous work, by using the sparsity-based reconstruction method, we have demonstrated the feasibility of single-view CB-XLOT. But, when the imaging conditions become complicated (e.g. multiple adjacent nanophosphors (NPs) contained in imaged object), it is difficult to resolve each NP by the previous method. To solve the problem, we hereby present a sparsity reconstruction method based on group information, termed Group_YALL1. The imaging performance of single-view CB-XLOT can be further improved by utilizing the group sparsity characteristic of NPs as a priori knowledge of reconstruction constraint. To assess the capability of the method, we used a customized CB-XLOT/XCT system to perform the numerical simulation and physical phantom experiments. The experimental results demonstrate that compared with the former sparse reconstruction method (e.g. YALL1), the proposed Group_YALL1 method can accurately resolve the NPs embedded in the object, even if they are close to each other. The acquired location error is less than 1 mm. Hence, this method has the potential to greatly reduce the data acquisition time while preserving a high imaging quality.
Diabetes-related events in adolescents and young adults: opportunities for psychosocial interventions

ABSTRACT This study was conducted to evaluate predictive factors of diabetes-related emergency room (ER) visits and hospitalizations among adolescents and young adults (AYA) with type 1 diabetes (T1D). Baseline demographic, medical, and psychosocial variables were collected for 177 AYA with T1D. Medical records were reviewed to identify ER visits and hospitalizations related to diabetes. Those with diabetes-related events had significantly higher hemoglobin A1c (A1c) values at baseline (p = 0.0001) and during an average 3.36 years of follow-up (p < 0.0001). Participants with events were more likely to have Medicaid or no insurance vs. private insurance (p = 0.0006) and were more likely to be on multiple daily injections vs. insulin pumps (p = 0.0159). Participants with events reported greater diabetes impact on their lives and their parents reported less autonomy in AYA with events (p = 0.0435). These results suggest that when participants were transferring from pediatric to adult care services, factors such as A1c, insurance status and diabetes treatment are associated with diabetes-related events. Further research is needed to elucidate a causative relationship and develop focused interventions to reduce diabetes-related events during this high-risk time. Autonomy should be further explored to determine its role in diabetes-related events during this transition period.
Canonical Correlation Analysis With L2,1-Norm for Multiview Data Representation

For many machine learning algorithms, their success heavily depends on data representation. In this paper, we present an <inline-formula> <tex-math notation="LaTeX">${\ell }_{2,1}$ </tex-math></inline-formula>-norm constrained canonical correlation analysis (CCA) model, that is, <inline-formula> <tex-math notation="LaTeX">$ {L}_{{2,1}}$ </tex-math></inline-formula>-CCA, toward discovering compact and discriminative representation for the data associated with multiple views. To well exploit the complementary and coherent information across multiple views, the <inline-formula> <tex-math notation="LaTeX">${\ell }_{{2,1}}$ </tex-math></inline-formula>-norm is employed to constrain the canonical loadings and measure the canonical correlation loss term simultaneously. It enables, on the one hand, the canonical loadings to be with the capacity of variable selection for facilitating the interpretability of the learned canonical variables, and on the other hand, the learned canonical common representation keeps highly consistent with the most canonical variables from each view of the data. Meanwhile, the proposed <inline-formula> <tex-math notation="LaTeX">${L}_{{2,1}}$ </tex-math></inline-formula>-CCA can also be provided with the desired insensitivity to noise (outliers) to some degree. To solve the optimization problem, we develop an efficient alternating optimization algorithm and give its convergence analysis both theoretically and experimentally. Considerable experiment results on several real-world datasets have demonstrated that <inline-formula> <tex-math notation="LaTeX">${L}_{{2,1}}$ </tex-math></inline-formula>-CCA can achieve competitive or better performance in comparison with some representative approaches for multiview representation learning.
Metformin Attenuates Early-Stage Atherosclerosis in Mildly Hyperglycemic Oikawa-Nagao Mice

Aim: Although metformin treatment has been reported to reduce the risk of cardiovascular events in patients with type 2 diabetes, the underlying mechanisms have not been elucidated fully. Here we assessed atherosclerotic lesion formation in newly established 2 mouse lines with different blood glucose levels (Oikawa-Nagao Diabetes-Prone [ON-DP] and -Resistant [ON-DR]) to evaluate the effect of metformin on early-stage atherosclerosis. Methods: Mildly hyperglycemic ON-DP and normoglycemic ON-DR female mice fed an atherogenic diet for 20 weeks (8–28 weeks of age). During the feeding period, one group of each mouse line received metformin in drinking water (0.1%), while another group received water alone as control. Atherosclerotic lesion formation in the aortic sinus was quantitively analyzed from the oil red O-stained area of the serial sections. Results: Metformin treatment did not affect food intake, body weight, and casual blood glucose levels within each mouse line during the 20-week feeding period. Nevertheless, metformin treatment significantly reduced atherosclerotic lesion formation in the ON-DP mice (59% of control), whereas no significant effect of metformin was observed in the lesion size of the ON-DR mice. Conclusion: Metformin can attenuate early-stage atherogenesis in mildly hyperglycemic ON-DP mice. Pleiotropic effects of metformin, beyond its glucose-lowering action, may contribute to the antiatherogenic property in the early-stage atherosclerosis.
A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia

Bats are implicated as natural reservoirs for a wide range of zoonotic viruses including SARS and MERS coronaviruses, Ebola, Marburg, Nipah, Hendra, Rabies and other lyssaviruses. Accordingly, many One Health surveillance and viral discovery programs have focused on bats. In this report we present viral metagenomic data from bats collected in the Kingdom of Saudi Arabia [KSA]. Unbiased high throughput sequencing of fecal samples from 72 bat individuals comprising four species; lesser mouse-tailed bat (Rhinopoma hardwickii), Egyptian tomb bat (Taphozous perforatus), straw-colored fruit bat (Eidolon helvum), and Egyptian fruit bat (Rousettus aegyptiacus) revealed molecular evidence of a diverse set of viral families: Picornaviridae (hepatovirus, teschovirus, parechovirus), Reoviridae (rotavirus), Polyomaviridae (polyomavirus), Papillomaviridae (papillomavirus), Astroviridae (astrovirus), Caliciviridae (sapovirus), Coronaviridae (coronavirus), Adenoviridae (adenovirus), Paramyxoviridae (paramyxovirus), and unassigned mononegavirales (chuvirus). Additionally, we discovered a bastro-like virus (Middle East Hepe-Astrovirus), with a genomic organization similar to Hepeviridae. However, since it shared homology with Hepeviridae and Astroviridae at ORF1 and in ORF2, respectively, the newly discovered Hepe-Astrovirus may represent a phylogenetic bridge between Hepeviridae and Astroviridae.
Quantitative analysis of the ThrbCRM1-centered gene regulatory network

ABSTRACT Enhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as close to an in vivo context as possible. Here we use electroporation of plasmid reporters to define critical parameters of a specific cis-regulatory element, ThrbCRM1, during retinal development. ThrbCRM1 is associated with cone photoreceptor genesis and activated in a subset of developing retinal cells that co-express the Otx2 and Onecut1 (OC1) transcription factors. Variation of reporter plasmid concentration was used to generate dose response curves and revealed an effect of binding site availability on the number and strength of cells with reporter activity. Critical sequence elements of the ThrbCRM1 element were defined using both mutagenesis and misexpression of the Otx2 and OC1 transcription factors in the developing retina. Additionally, these experiments suggest that the ThrbCRM1 element is co-regulated by Otx2 and OC1 even under conditions of sub-optimal binding of OC1. Summary: Systematic variation of the levels of a transcriptional reporter plasmid, its trans-acting factors and transcription factor binding sites reveals properties of a retinal enhancer during development.
Learning bioinspired joint geometry from motion capture data of bat flight

Bioinspired robotic systems are often designed by assuming that the kinematics of the biological system of interest are well approximated by an open kinematic chain subject to box constraints. These box-constrains are typically generated by designer interpretation of biomotion and anatomical studies or pragmatic fabrication constraints. In contrast to this standard design paradigm, this paper presents a methodology for learning joint geometry which restricts the range of motion of generic ball joints to only the reachable set observed during biomotion experiments. This reachable set is identified by constructing an analytical-empirical potential energy function over the experimental observations. The energy function effectively ‘pushes’ configurations close to the set of observations. This energy function is then thresholded to identify the zero-potential (ZP) configuration set, and joint geometry is constructed using the resulting contour. We construct an entire bat wing using this method, and demonstrate through motion capture experiments that the learned geometry successfully restricts motions to the ZP set.