Miracle-dz/UniFAR-FTUs huggingface dataset:
Virus-like particles in the tracheal mite Acarapis woodi (Rennie)

Summary &mdash; Tracheal mite infected honey bees were collected from Scotland and from California. The lyzed cells of the body cavity of tracheal mites in the honey bees collected from Scotland harboured numerous 27 nm isometric virus-like particles. These virus-like particles were formed in a crystalline array and were arranged in a hexagonal pattern. No virus-like particles were observed in the tracheal mites of the honey bees collected from California. The significance of these observa- tions in relation to the honey bee tracheal mite resistance is discussed.
The chemokine SDF-1 (cid:97) triggers CXCR4 receptor dimerization and activates the JAK/STAT pathway

The chemokine stromal cell-derived factor (SDF-1 (cid:97) ), the ligand for the CXCR4 receptor, induces a wide variety of effects that include calcium mobilization, chemotactic responses, bone marrow myelopoiesis, neuronal patterning, and prevention of HIV-1 infection. Nonetheless, little is known of the biochemical pathways required to achieve this variety of responses triggered after receptor–chemo-kine interaction. We developed a set of monoclonal antibodies that speciﬁcally recognize the CXCR4 receptor and used them to identify the signaling pathway activated after SDF-1 (cid:97) binding in human T cell lines. Here we demonstrate that SDF-1 (cid:97) activation promotes the physical association of G (cid:97) i with the CXCR4. Furthermore, within seconds of SDF-1 (cid:97) activation, the CXCR4 receptor becomes tyrosine phosphorylated through the activation and association with the receptor of JAK2 and JAK3 kinases. After SDF-1 (cid:97) binding, JAK2 and JAK3 associate with CXCR4 and are activated, probably by transphospho-rylation, in a G (cid:97) i -independent manner. This activation enables the recruitment and tyrosine phosphorylation of several members of the STAT family of transcription factors. Finally, we have also observed SDF-1 (cid:97) -induced activation and association of the the CXCR4 a -dependent manner. mechanisms cytokines. —Vila-Coro,
G ENE FLOW FROM FOREIGN PROVENANCES INTO LOCAL PLANT POPULATIONS : F ITNESS CONSEQUENCES AND IMPLICATIONS FOR BIODIVERSITY RESTORATION 1

Long-distance transplantation of seed material as done in restoration programs has raised concerns about the risks associated with the introduction of maladapted genotypes that may hybridize with neighboring native conspeciﬁ cs and decrease local population ﬁ tness (outbreeding depression). We studied the consequences of gene ﬂ ow from foreign provenances into local populations in the common grassland species Plantago lanceolata (Plantaginaceae). Three generations of intraspeciﬁ c hybrids (F 1 , F 2 , and backcross to the local plants) were produced by controlled crossings between local plants and plants from geographically or envi- ronmentally distant populations. Their performance was compared to that of within-population crosses in a ﬁ eld experiment. Early growth in some interpopulation hybrids was signiﬁ cantly reduced, and this decrease in performance was higher in progeny of crosses with the local population from a different habitat than with geographically distant populations. At the end of the growing season, most ﬁ tness-related traits of the interpopulation hybrids were close to the average of their parents. Crosses with low-per- forming foreign parents therefore resulted in reduced ﬁ tness of the hybrids compared to the local plants and dilution of local adaptation. We conclude that the introduction of maladapted populations from distant or ecologically distinct environments might, at least temporarily, decrease the ﬁ tness of neighboring local plants. random effect due to block, and the following covariates: seed mass for the dependent variable size-at-planting, size at planting for the dependent variables biomass and seed production. Vegetative biomass and seed production were square-root transformed to meet the assumptions of normality and homoscadesticity. Because the covariate size-at-planting was highly signiﬁ cant, only plants that were not replaced just after planting were included in the analysis; however, removing the covariate from the model and including all plants did not change the results. Dead plants ( N = 2) were excluded from the analysis. We calculated a series of a priori contrasts within signiﬁ cant origin effects to test for deviation from additive gene action. The performance of the F 1 and F 2 hybrids was compared to the mean performance (Pf) of their parents (midparent value: 1/2 ⋅ Pf CH1 + 1/2 ⋅ Pf Foreign ). Expected values for backcrosses were calcu- lated as 3/4 ⋅ Pf CH1 + 1/4 ⋅ Pf Foreign ( Etterson et al., 2007 ). For each hybrid generation, we calculated an overall contrast comparing the hybrids with their parents for all three origins (1 contrast with df = 3 for each generation). If this overall contrast was signiﬁ cant, we tested the hybrid vs. parental generation separately for each origin (3 contrasts with df = 1). The weightings for the contrasts as-sume additive gene action, i.e., they test whether heterotic (dominance) effects outweigh the breakdown of positive allele combinations due to hybridization.
The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function

Family 45 glycoside hydrolases (GH45) are endoglucanases that are integral to cellulolytic secretomes, and their ability to break down cellulose has been successfully exploited in textile and detergent industries. In addition to their industrial relevance, understanding the molecular mechanism of GH45-catalyzed hydrolysis is of fundamental importance because of their structural similarity to cell wall modifying enzymes such as bacterial lytic transglycosylases (LTs) and expansins present in bacteria, plants, and fungi. Our understanding of the catalytic itinerary of GH45s has been incomplete because a crystal structure with substrate spanning the –1 to +1 subsites is currently lacking. Here, we constructed and validated a putative Michaelis complex in silico and used it to elucidate the hydrolytic mechanism in a GH45, Cel45A from the fungus Humicola insolens, via unbiased simulation approaches. molecular that the active-site architecture in a lack of coordination for the hydroxymethyl group of the at the subsite. lack of coordination mobility the suggests the of a non-hydrolytic reaction when the catalytic base aspartic some LTs transglycosylase A and expansins. We calculated reaction free energies and demonstrate the thermodynamic feasibility of the hydrolytic and non-hydrolytic reaction mechanisms. Our results provide molecular insights into the hydrolysis with possible implications for elucidating the elusive catalytic mechanism in LTs and expansins.
Effects of Different Types of Burn Wounds and its Dressings on Millimeter-Wave Images

Abstract Millimeter-wave imaging is a promising technology for diagnosing skin burns, that may make it easier to assess and determine the burn depth in the near future. However, up to now, it has not yet been brought to clinical use due to the lack of clinical trails on patients and a millimeter-wave-aided classification of skin burns. In this paper, in a preliminary step, ex-vivo burned porcine skin is utilized to visualize and quantify skin that has been burned in different ways, and to access its effect on millimeter-wave images. For the first time, a 24 hour study of in-vivo human skin visualizes the effect of wound dressings using a fast imaging system operating at frequencies from 70 to 80 GHz. For validation, the effective relative permittivity of the skin and the dressings are measured using a open-ended coaxial probe. An analytical model is applied to calculate the reflection coefficient which are compared to the intensity of the millimeter-wave images to validate the model.
Development of multi-axis laser micromachining system suitable for machining non-linear contoured surfaces

DEVELOPMENT OF MULTI-AXIS LASER MICROMACHINING SYSTEM SUITABLE FOR MACHINING NON-LINEAR CONTOURED SURFACES Serhat Kerimoğlu M.Sc. in Mechanical Engineering Advisor: Melih Çakmakcı August 2016 In recent years, studies on manufacturing systems have proved the importance of cooperation of positioning systems with laser cutting technology. The performance of the manufacturing system can be improved by utilizing both laser and positioning systems together. In this study, design and development of a micromachining system which can perform on non-linear contoured surfaces is presented. Laser micromachining system is designed and assembled including a nanosecond Q-switched pulsed fiber laser, a 6-DOF hexapod manipulator, a granite table in order to absorb vibrations and an external cabin system to isolate the whole system for safety and health issues. Performance characteristics of micromachining devices mainly determined by precision and characteristics of each individual components of the system. Therefore, the studies to improve the performance of the laser micromachining system are related with laser, isolation and positioning systems. A dynamic model of the positioning system is derived to obtain the control parameters for the actual positioning system. By using these parameters, the performance of the laser micromachining system on nonlinear contoured surface is improved and discussed in detail. The simulation environment MATLAB/SimMechanics is used to model the dynamics of the positioning system. With the kinematic and dynamic model of the manipulation system simulations, significant performance enhancements are obtained on non-linear contoured surfaces.
Validation of a Mobile, Sensor-based Neurobehavioral Assessment With Digital Signal Processing and Machine-learning Analytics

Background: The Miro Health Mobile Assessment Platform consists of self-administered neurobehavioral and cognitive assessments that measure behaviors typically measured by specialized clinicians. Objective: To evaluate the Miro Health Mobile Assessment Platform’s concurrent validity, test–retest reliability, and mild cognitive impairment (MCI) classification performance. Method: Sixty study participants were evaluated with Miro Health version V.2. Healthy controls (HC), amnestic MCI (aMCI), and nonamnestic MCI (naMCI) ages 64–85 were evaluated with version V.3. Additional participants were recruited at Johns Hopkins Hospital to represent clinic patients, with wider ranges of age and diagnosis. In all, 90 HC, 21 aMCI, 17 naMCI, and 15 other cases were evaluated with V.3. Concurrent validity of the Miro Health variables and legacy neuropsychological test scores was assessed with Spearman correlations. Reliability was quantified with the scores’ intraclass correlations. A machine-learning algorithm combined Miro Health variable scores into a Risk score to differentiate HC from MCI or MCI subtypes. Results: In HC, correlations of Miro Health variables with legacy test scores ranged 0.27–0.68. Test–retest reliabilities ranged 0.25–0.79, with minimal learning effects. The Risk score differentiated individuals with aMCI from HC with an area under the receiver operator curve (AUROC) of 0.97; naMCI from HC with an AUROC of 0.80; combined MCI from HC with an AUROC of 0.89; and aMCI from naMCI with an AUROC of 0.83. Conclusion: The Miro Health Mobile Assessment Platform provides valid and reliable assessment of neurobehavioral and cognitive status, effectively distinguishes between HC and MCI, and differentiates aMCI from naMCI.
Social support mediates the effect of morningness on changes in subjective well‐being over 6 months

Studies show that morningness is positively associated with subjective well‐being. Our previous research investigated factors that could underlie this relationship, finding that the association between morningness–eveningness and subjective well‐being can be partially attributed to the higher levels of perceived social support received by morning‐oriented individuals. In the present study, we examine the longitudinal effects of perceived social support in mediating the relationship between morningness–eveningness and subjective well‐being. Our results show that this mediating effect remains significant with respect to changes in well‐being over a 6‐month period. It seems that the causal effect of morningness on well‐being may be partially mediated by the causal effect of social support. The findings provide further support for the conclusion that perceived social support is an important contributing factor to the greater well‐being reported by morning‐oriented individuals. Additionally, our results provide seminal evidence for the causal effect of morningness on well‐being.
Individual Differences in Implicit Bias Can Be Measured Reliably by Administering the Same Implicit Association Test Multiple Times

The use of the Implicit Association Test (IAT) as a measure of individual differences is stymied by insufficient test–retest reliability for assessing trait-level constructs. We assess the degree to which the IAT measures individual differences and test a method to improve its validity as a “trait” measure: aggregating across IATs. Across three studies, participants (total n = 960) completed multiple IATs in the same session or across multiple sessions. Using latent-variable models, we found that half of the variance in IAT scores reflects individual differences. Aggregating across multiple IATs approximately doubled the variance explained with explicit measures compared with a single IAT D-score. These findings show that IAT scores contain considerable noise and that a single IAT is inadequate to estimate trait bias. However, aggregation across multiple administrations can correct this and better estimate individual differences in implicit attitudes.
Estimation of glomerular filtration rate for drug dosing in patients with very high or low body mass index

An accurate estimated glomerular filtration rate (eGFR) is essential in drug dosing. This study demonstrates the limitations of indexed (ml/min/1.73 m2) and de‐indexed (ml/min) eGFR based drug dosing in patients with obesity or underweight. This systematic study aimed to determine the most appropriate approach to estimate the GFR for standardized eGFR based drug dosing in these patients. (Raw) data of 12 studies were selected to investigate the accuracy and bias of both the indexed and de‐indexed estimations of the Modification of Diet in Renal Disease (MDRD) study equation and the Chronic Kidney Disease Epidemiology Collaboration equation (CKD‐EPI), and of the Cockcroft–Gault (CG) in patients with obesity or underweight. Accuracy was calculated as the proportion of eGFR values within 30% of the measured GFR (P30) using an inert tracer (e.g., iohexol, inulin, 51Cr‐EDTA, or iothalamate clearance). An accuracy of at least 80% was considered acceptable. GFR values estimated with the CG, MDRD, and CKD‐EPI differ significantly within a patient with obesity or underweight regardless of whether it is indexed or de‐indexed. All studies, with two exceptions, show that all three equations are inaccurate for patients with underweight or class II obesity (P30: 55%–94%). De‐indexing eGFR improves not or modestly the accuracy, and mostly remains below the 80% (P30: 62%–100%). CG was highly inaccurate in obese and underweight patients (P30: 7%–82%). Although these results show that CG is obsolete, the accuracy of MDRD and CKD‐EPI is low in patients with obesity or underweight and de‐indexing is not the solution. Better education and more accurate methods for appropriate drug dosing (e.g., measured GFR with inert tracer, therapeutic drug monitoring, or 24‐h creatinine clearance) are recommended.
Research on Streamlining Seismic Safety Evaluation of Underground Reinforced Concrete Duct-Type Structures in Nuclear Power Plant Stations - Part-5. Analytical Simulation by Sophisticated Effective Stress Soil Model and Simple RC Macro-model

In this study, numerical simulation of large shaking table test on the underground RC structure in dry sand layer was performed by the non-linear effective stress analysis method developed by the authors considering the dilatancy characteristic of the ground based on the elasto-plasticity theory. Through the analysis, it was demonstrated that the amplification characteristics of the vertical motion induced in the ground were well simulated by appropriately evaluating the dilatancy characteristic of the ground and that the dilatancy of the ground did not exert a substantial effect on the shear deformation of the structure which was deeply buried in the dry sand layer.
Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

By their paternal transmission, Y‐chromosomal haplotypes are sensitive markers of population history and male‐mediated introgression. Previous studies identified biallelic single‐nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y‐chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y‐chromosomal variants from whole‐genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present‐day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male‐mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo‐Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y‐chromosomal variants for reconstructing the history of domestic species with a wide geographical range.
In-silico discovery of inhibitors against human papillomavirus E1 protein

Abstract High-risk (HR) Human papillomavirus (e.g. HPV16 and HPV18) causes approximately two-thirds of all cervical cancers in women. Although the first and second-generation vaccines confer some protection against individuals, there are no approved drugs to treat HR-HPV infections to-date. The HPV E1 protein is an attractive drug target because the protein is highly conserved across all HPV types and is crucial for the regulation of viral DNA replication. Hence, we used the Random Forest algorithm to construct a Quantitative-Structure Activity Relationship (QSAR) model to predict the potential inhibitors against the HPV E1 protein. Our QSAR classification model achieved an accuracy of 87.5%, area under the receiver operating characteristic curve of 1.00, and F-measure of 0.87 when evaluated using an external test set. We conducted a drug repurposing campaign by deploying the model to screen the Drugbank database. The top three compounds, namely Cinalukast, Lobeglitazone, and Efatutazone were analyzed for their cell membrane permeability, toxicity, and carcinogenicity. Finally, these three compounds were subjected to molecular docking and 200 ns-long Molecular Dynamics (MD) simulations. The predicted binding free energies for the candidates were calculated using the MM-GBSA method. The binding free energies for Cinalukast, Lobeglitazone, and Efatutazone were −37.84 kcal/mol, −25.30 kcal/mol, and −29.89 kcal/mol respectively. Therefore, we propose their chemical scaffolds for future rational design of E1 inhibitors. Communicated by Ramaswamy H. Sarma
Splicing factor 3B subunit 1 (SF3B1) mutation in the context of therapy‐related myelodysplastic syndromes

Splicing factor 3B subunit 1 (SF3B1) somatic mutation in the context of therapy‐related myelodysplastic syndromes (t‐MDS) has not been well defined. In a large cohort of patients with MDS, those with known SF3B1 somatic mutation were compared as de novo MDS (n = 289) and t‐MDS with mutant SF3B1 (SF3B1mut; n = 31). Baseline characteristics, concomitant mutations, and acute myeloid leukaemia (AML) transformation were similar between the two groups. The median overall survival (OS) of de novo MDS SF3B1mut was significantly longer compared to t‐MDS SF3B1mut but not significantly different when adjusted for comorbidities. Comparing t‐MDS wild‐type SF3B1 (SF3B1WT; n = 241) to t‐MDS SF3B1mut (n = 31), complex cytogenetics were seen in 37.4% versus 10.3% (p = 0.009), tumour protein p53 (TP53) mutation was 36.1% versus 10% (p = 0.004), and AML transformation was 34.4% compared to 12.9% (p = 0.016) respectively. OS was significantly shorter in SF3B1WT versus SF3B1mut. When applying the International Working Group for Prognosis of MDS (IWG‐PM) proposed SF3B1 criteria, OS was significantly shorter in SF3B1mut t‐MDS compared to de novo MDS SF3B1mut with no significance in AML transformation. Survival was compared between t‐MDS SF3B1mut who met the new proposed IWG‐PM criteria to t‐MDS SF3B1mut who did not meet criteria to survival of SF3B1WT t‐MDS. OS was 53 versus 22 and 18 months respectively (p = 0.006). AML transformation was 0%, 26.7% and 32.3% (p = 0.021). Leukaemia‐free survival was not reached among the three.
Do sclero‐embolization procedures have advantages over surgical ligature in treating varicocele in children, adolescents and adults? Results from a systematic review and meta‐analysis

We aimed to systematically review complications, and recurrence rate of varicocele treatment by comparing the surgical ligature versus sclero‐embolization techniques in children, adolescents and adults. The secondary outcomes were the evaluation of semen parameters and spontaneous pregnancy rate in adults. The review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses framework. Continuous variables were pooled using the inverse variance of the mean difference (MD) with a fixed effect, and 95% confidence interval (CI). The incidences of complications were pooled using the Cochran–Mantel–Haenszel Method with the random effect model and reported as Odds Ratio (OR), and 95% CI. Statistical significance was set two‐tail p‐value < 0.05. Twenty studies were included. Incidence of postoperative hydrocele was significantly higher in the surgical ligation group (OR 3.06 95% CI 1.06–8.88, p = 0.04). Incidence of postoperative orchiepidydimitys was significantly higher in sclero‐embolization group (OR 0.26 95% CI 0.08–0.85, p = 0.02). Presence of normal spermatozoa was significantly higher sclero‐embolization group compared with the surgical ligature group (MD 2.54% 95% CI 0.43–4.65, p = 0.02). No difference was found in overall complications, wound infection, testis pain, surgical site hematoma, total sperm count, sperm motility, pregnancy and recurrence rate. This review confirms that current data does still not support the superiority of one type of treatment over other ones.
Translational Significance of the LINE-1 Jumping Gene in Skeletal Muscle

Long INterspersed Element 1 (L1) is a mobile genetic element that is involved with muscle aging. However, exercise can downregulate this mechanism. Retrotransposons are gene segments that proliferate in the genome, and the Long INterspersed Element 1 (LINE-1 or L1) retrotransposon is active in humans. Although older mammals show enhanced skeletal muscle L1 expression, exercise generally reverses this trend. We hypothesize skeletal muscle L1 expression influences muscle physiology, and additional innovative investigations are needed to confirm this hypothesis.