Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic damage to single biomolecules in femtosecond X-ray imaging

Knowledge of the structure of large, complex molecules is of vital interest in understanding their function in biological systems. Standard X-ray crystallographic methods of structure determination are unsuitable for a large class of biomolecules for which it is difficult, or impossible to form high-quality crystals. The technique of coherent diffractive imaging (CDI) provides a route toward the determination of large molecular structures without crystallisation. CDI uses a Fourier transform mapping between fields in the sample and detector planes; this implies attainable resolution is limited by the angle to which signal can be measured. Unfortunately, biological molecules scatter weakly; in order to obtain signal to the required angle an extremely bright new source of X-rays is required. These new sources, the X-ray free-electron lasers (XFELs), have brightnesses approaching that sufficient to resolve biological molecules to atomic resolution. This increased brightness has an unfortunate side effect, the number of unwanted photoionisation events in the target molecule is vastly increased. This leads to an imbalance of charge that results in the eventual destruction of the molecule. In this thesis, I show that the intense illumination from an XFEL produces a time-dependent electron density in the target molecule. This effect targets the inner shell electrons in the molecule, and hence preferentially degrades the high-resolution information. I further show that the time-dependent electron density in the molecule can be treated as a partially coherent secondary source of X-rays, violating the coherence assumption inherent to CDI. This damage-induced degree of partial coherence is determined from simulated experimental conditions. It is demonstrated that this degree of partial coherence due to damage can be used to infer information about the physical processes underlying the interaction between the molecule and the X-ray field. This in-
Strengthening of Masonry Structures Using Epoxy-Bonded FRP Laminates

The present study presents a systematic analysis for the short-term strength of masonry walls, strengthened with externally bonded fiber reinforced polymer (FRP) laminates under monotonic out-of-plane bending, in-plane bending, and in-plane shear, all combined with axial load, within the framework of modern design codes (e.g., Eurocode 6). The results, which are presented in the form of both design equations and normalized interaction diagrams, show that: (1) when out-of-plane bending response dominates, as in the case of upper story levels, where axial loads are low, the increase in bending capacity is quite high; (2) in the (rather rare) case of in-plane bending, high area fractions of reinforcement placed near the highly stressed zones give considerable strength increases (regardless of the axial load), provided that premature peeling-off of the laminates is prevented; and (3) the in-plane shear capacity of FRP-strengthened walls can be quite high, too, especially in the case of low axial loads. The re.
Severe community-acquired pneumonia

Severe community-acquired pneumonia is the most life-threatening form of community-acquired pneumonia, characterised by intensive care unit admission and high morbidity and mortality. In this review article, we cover in depth six aspects of severe community-acquired pneumonia that are still controversial: use of PCR molecular techniques for microbial diagnosis; the role of biomarkers for initial management; duration of treatment, macrolides or quinolones in the initial empirical antibiotic therapy; the use of prediction scores for drug-resistant pathogens to modify initial empiric therapy; the use of noninvasive mechanical ventilation and high-flow nasal oxygen; and the use of corticosteroids as adjunctive therapy in severe community-acquired pneumonia. Severe community-acquired pneumonia is the most lethal form of community-acquired pneumonia. Mortality of these patients can reach 40%, which is unacceptable. Clinical and basic research has to be focused on this population to reduce mortality. https://bit.ly/3DXshSz
Influence of Fibre Type and Fibre Volume Fraction on Dynamic Properties of Slurry Infiltrated Fibre Concrete

The effect of fibre type and fibre amount on physico-mechanical properties of slurry infiltrated fibre concrete (SIFCON) at both quasi-static and dynamic load was evaluated experimentally. SIFCON is a special type of cement-based composite with high fibre volume fraction, extremely strong and ductile. Test specimens were prepared with 7 types of steel fibres (with different shape and mechanical parameters) in four volume fractions (7.5-15 vol. %). High performance fibre-reinforced concrete (HPFRC) has also been cast and tested for comparison purposes. The impact test has been carried out by using an in-house manufactured impact testing machine based on drop test principle. The test results revealed that SIFCON slab with 15 vol. % fibre content exhibits superior energy-absorption characteristics when compared to other slab specimens. Diameter of the fibres plays an important role for both strength and energy absorption capacity of SIFCON - using of low-diameter fibres with higher aspect ratio leads to the best results.
Applications of the Wei-Lachin Multivariate One-Sided Test for Multiple Outcomes on Possibly Different Scales

Many studies aim to assess whether a therapy has a beneficial effect on multiple outcomes simultaneously relative to a control. Often the joint null hypothesis of no difference for the set of outcomes is tested using separate tests with a correction for multiple tests, or using a multivariate T 2-like MANOVA or global test. However, a more powerful test in this case is a multivariate one-sided or one-directional test directed at detecting a simultaneous beneficial treatment effect on each outcome, though not necessarily of the same magnitude. The Wei-Lachin test is a simple 1 df test obtained from a simple sum of the component statistics that was originally described in the context of a multivariate rank analysis. Under mild conditions this test provides a maximin efficient test of the null hypothesis of no difference between treatment groups for all outcomes versus the alternative hypothesis that the experimental treatment is better than control for some or all of the component outcomes, and not worse for any. Herein applications are described to a simultaneous test for multiple differences in means, proportions or life-times, and combinations thereof, all on potentially different scales. The evaluation of sample size and power for such analyses is also described. For a test of means of two outcomes with a common unit variance and correlation 0.5, the sample size needed to provide 90% power for two separate one-sided tests at the 0.025 level is 64% greater than that needed for the single Wei-Lachin multivariate one-directional test at the 0.05 level. Thus, a Wei-Lachin test with these operating characteristics is 39% more efficient than two separate tests. Likewise, compared to a T 2-like omnibus test on 2 df, the Wei-Lachin test is 32% more efficient. An example is provided in which the Wei-Lachin test of multiple components has superior power to a test of a composite outcome.
HLA-G 3′UTR Polymorphisms Predict Drug-Induced G3-4 Toxicity Related to Folinic Acid/5-Fluorouracil/Oxaliplatin (FOLFOX4) Chemotherapy in Non-Metastatic Colorectal Cancer

Polymorphisms in drug-metabolizing enzymes might not completely explain inter-individual differences in toxicity profiles of patients with colorectal cancer (CRC) that receive folinic acid/5-fluorouracil/oxaliplatin (FOLFOX4). Recent data indicate that the immune system could contribute to FOLFOX4 outcomes. In light of the immune inhibitory nature of human leukocyte antigen-G (HLA-G), a non-classical major histocompatibility complex (MHC) class I molecule, we aimed to identify novel genomic markers of grades 3 and 4 (G3-4) toxicity related to FOLFOX4 therapy in patients with CRC. We retrospectively analyzed data for 144 patients with stages II-III CRC to identify HLA-G 3′ untranslated region (3′UTR) polymorphisms and related haplotypes and evaluate their impact on the risk of developing G3-4 toxicities (i.e., neutropenia, hematological/non-hematological toxicity, neurotoxicity) with logistic regression. The rs1610696-G/G polymorphism was associated with increased risk of G3-4 neutropenia (OR = 3.76, p = 0.015) and neurotoxicity (OR = 8.78, p = 0.016); rs371194629-Ins/Ins was associated with increased risk of neurotoxicity (OR = 5.49, p = 0.027). HLA-G 3′UTR-2, which contains rs1610696-G/G and rs371194629-Ins/Ins polymorphisms, was associated with increased risk of G3-4 neutropenia (OR = 3.92, p = 0.017) and neurotoxicity (OR = 11.29, p = 0.009). A bootstrap analysis confirmed the predictive value of rs1610696 and rs371194629, but the UTR-2 haplotype was validated only for neurotoxicity. This exploratory study identified new HLA-G 3′UTR polymorphisms/haplotypes as potential predictive markers of G3-4 toxicities in CRC.
Ultrastructure and Molecular Phylogenetic Position of Heteronema scaphurum: A Eukaryovorous Euglenid with a Cytoproct

Euglenids comprise a distinct clade of flagellates with diverse modes of nutrition, including phagotrophy, osmotrophy and phototrophy. Much of the previous research on euglenids has focused on phototrophic species because of their ecological abundance and significance as indicators for the health of aquatic ecosystems. Although largely understudied, phagotrophic species probably represent the majority of euglenid diversity. Phagotrophic euglenids tend to be either bacterivorous or eukaryovorous and use an elaborate feeding apparatus for capturing prey cells. We characterized the ultrastructure and molecular phylogenetic position of Heteronema scaphurum, a eukaryovorous euglenid collected in freshwater. This species was equipped with a distinct cytoproct through which waste products were eliminated in the form of faecal pellets; a cytoproct has not been reported in any other member of the Euglenida. Heteronema scaphurum also had a novel predatory mode of feeding. The euglenid ensnared and corralled several green algal prey cells (i.e. Chlamydomonas) with hook‐like flagella covered in mucous before engulfing the bundle of prey cells whole. Molecular phylogenetic analyses inferred from small subunit rDNA sequences placed this species with other eukaryovorous euglenids, which was consistent with ultrastructural features associated with the feeding apparatus, flagellar apparatus, extrusomes, and pellicle.
Tissue‐Carbon Incorporation Rates in Lizards: Implications for Ecological Studies Using Stable Isotopes in Terrestrial Ectotherms

Carbon stable isotope (δ13C) analysis can be used to infer the origin and to estimate the flow of nutrient resources through animals and across ecological compartments. These applications require knowledge of the rates at which carbon is incorporated into animal tissues and diet‐to‐tissue discrimination factors (Δ13C). Studies of carbon dynamics in terrestrial vertebrates to date have focused almost solely on endothermic animals; ectotherms such as reptiles have received little attention. Here we determined carbon incorporation rates and Δ13C in tissues of prairie lizards (Sceloporus undulatus consobrinus) and collared lizards (Crotaphytus collaris). The smaller lizard, S. undulatus, had carbon retention times of 25 and 61 d in plasma and red blood cells (RBC), respectively, compared with 44 and 311 d for the larger C. collaris. Liver, muscle, and skin carbon retention times for S. undulatus were 21, 81, and 94 d. Growth contributed 9%–19% of the carbon incorporated into these tissues. This contribution is similar to endotherms measured at comparable developmental stages. Mean Δ13C for plasma (−0.2‰ ± 0.4‰ Vienna Pee Dee Belemnite Standard) and RBCs (−1.3‰ ± 0.8‰) were similar to values reported for other vertebrates. Carbon incorporation rates for these ectotherms, however, are seven times slower than in similarly sized adult endotherms. Although a limited comparison with data for warm‐water fishes suggests comparable incorporation rates between aquatic and terrestrial ectotherms, this study highlights the lack of experimental data for isotope dynamics in ectotherms across a range of temperatures, body sizes, and developmental stages.
Mechanistic Approach for Relating Test Roller Penetration to Strength Properties of Bases and Subgrades

ABSTRACT Theoretical formulas that relate penetration depth of a test roller to strength properties of bases and subgrades are presented. The algebraic expressions, derived using the generalized bearing capacity formula employed regularly in geotechnical practice, specifically relate angle of internal friction and soil cohesion to the penetration depth of a towed, rigid wheel with a known force (weight) applied. The existence of such a relationship has the potential to reinvent test rolling as a quality assurance tool capable of providing a continuous record of in situ soil strength measurements along a roadway. Besides supplying a means for interpretation of test roller measurements, the proposed formulas provide a method for practitioners to investigate the influence of modifying test roller characteristics (such as reducing weight or changing wheel size) and to calibrate a test roller to be particularly sensitive to certain soils. The predictions show promising agreement with results from three-dimensional numerical simulation and experimental data.
IR Spectroscopy and Scanning Electron Microscopy Studies of Natural Ageing of Polypropylene

In the present work we are concerned in the study by IR Spectroscopy and Scanning Electron Microscopy of the effect of solar radiation in two different regions on the natural ageing of the polypropylene(PP). The first region of Mohammedia and the second region of Talsint-Figug. The analysis showed a marked degradation of the surface, which is mainly caused by the contamination of the superficial structure by oxygen. This study was conducted with the aid of three samples of PP: the first was new, the second sample (M) old was exposed about four months the region of Mohammedia; and third, sample (t) old was exposed four about months the region of Talsint-Figug. Spectral analysis indicates that, for new sample, oxygen establishes single bonds with carbon. However, through the ageing process, spectral changes essentially occur in the regions of -3400, -1712, and 1170 cm which correspond to hydroxyl and/or hydrogen peroxide groups, a carbonyl group, and C─O. The examin of the bands corresponding to a carbonyl group reveals the presence of a complicated mixture of oxidation products: aldehydes, ketones, esters, acids, peresters, and peracids. Spectral analysis also shows that the most favorable site for oxidation is at the methylene group. This result is a consequence of the increase of the reactivity of the reactions of oxidation which brings a breaking of the macromolecular skeleton of the formation of peroxide of under products which might act as catalysts of
Atherosclerosis revisited from a clinical perspective: still an inflammatory disease?

Summary Compelling experimental results have substantiated the immune-driven inflammatory nature of atherosclerosis. Most of the scientific advances over the past decades have been achieved by relying on transgenic animal models that have been employed with increasing levels of sophistication. However, recent failures in translating various anti-inflammatory therapeutic strategies for use in humans might raise some skepticism with regards to an inflammatory causality underlying human atherosclerosis. By applying a dialectical approach, this Perspective aims to challenge and deduce the nature of atherosclerosis by reviewing results exclusively derived from human studies and recent clinical trials, as “things may not always be, what they appear”. Note: The review process for this manuscript was fully handled by Gregory Y. H. Lip, Editor in Chief.
Plasmodium falciparum var Gene Expression Homogeneity as a Marker of the Host-Parasite Relationship under Different Levels of Naturally Acquired Immunity to Malaria

Acquired immunity to Plasmodium falciparum infection causes a change from frequent, sometimes life-threatening, malaria in young children to asymptomatic, chronic infections in older children and adults. Little is known about how this transition occurs but antibodies to the extremely diverse PfEMP1 parasite antigens are thought to play a role. PfEMP1 is encoded by a family of 60 var genes that undergo clonal antigenic variation, potentially creating an antigenically heterogeneous infecting population of parasites within the host. Previous theoretical work suggests that antibodies to PfEMP1 may play a role in “orchestrating” their expression within infections leading to sequential, homogeneous expression of var genes, and prolonged infection chronicity. Here, using a cloning and sequencing approach we compare the var expression homogeneity (VEH) between isolates from children with asymptomatic and clinical infections. We show that asymptomatic infections have higher VEH than clinical infections and a broader host antibody response. We discuss this in relation to the potential role of host antibodies in promoting chronicity of infection and parasite survival through the low transmission season.
Do Women Have a Choice? Care Providers’ and Decision Makers’ Perspectives on Barriers to Access of Health Services for Birth after a Previous Cesarean

BACKGROUND Repeat cesarean delivery is the single largest contributor to the escalating cesarean rate worldwide. Approximately 80 percent of women with a past cesarean are candidates for vaginal birth after a cesarean (VBAC), but in Canada less than one-third plan VBAC. Emerging evidence suggests that these trends may be due in part to nonclinical factors, including care provider practice patterns and delays in access to surgical and anesthesia services. This study sought to explore maternity care providers' and decision makers' attitudes toward and experiences with providing and planning services for women with a previous cesarean. METHODS In-depth, semi-structured interviews were conducted with family physicians, midwives, obstetricians, nurses, anesthetists, and health service decision makers recruited from three rural and two urban Canadian communities. Constructivist grounded theory informed iterative data collection and analysis. RESULTS Analysis of interviews (n = 35) revealed that the factors influencing decisions resulted from interactions between the clinical, organizational, and policy levels of the health care system. Physicians acted as information providers of clinical risks and benefits, with limited discussion of patient preferences. Decision makers serving large hospitals revealed concerns related to liability and patient safety. These stemmed from competing access to surgical resources. CONCLUSIONS To facilitate women's increased access to planned VBAC, it is necessary to address the barriers perceived by care providers and decision makers. Strategies to mitigate concerns include initiating decision support immediately after the primary cesarean, addressing the social risks that influence women's preferences, and managing perceptions of patient and litigation risks through shared decision making.
Oxytocin but Not Testosterone Modulates Behavioral Patterns in Autism Spectrum Disorders

Autism spectrum disorder (ASD) is a neurodevelopmental disorder of unknown etiology. Social deficits represent one of the core symptoms of the diagnosis. The aim was to reveal possible correlations among peripheral levels of oxytocin and testosterone with behavioral and symptom characteristics in patients with ASD. 8 children with ASD were recruited and underwent psychological profiling. Blood oxytocin and testosterone levels were analyzed using ELISA method. Oxytocin levels positively correlated with Adaptation to change category of CARS-2 (P = 0.008, R = 0.848) and Vineland-II maladaptive behavior scores (P = 0.004, R = 0.884). No significant correlations were found among testosterone levels and behavioral parameters. Higher oxytocin levels were connected with more severe adaptive behavior in ASD patients. Increased oxytocin levels in children with more severe phenotype could be a result of compensatory mechanism of impaired oxytocin signaling. Oxytocin seems to employ distinct mechanisms in regulating social behavior in autism and healthy population.
Episodic Future Thinking Following vmPFC Damage: Impaired Event Construction, Maintenance, or Narration?

Objective: Functional neuroimaging and lesion studies show that the ventromedial prefrontal cortex (vmPFC) is implicated in episodic future thinking (EFT), yet its role remains unclear. In this study, we sought to (a) confirm recent findings of impaired EFT in patients with lesions to the vmPFC (vmPFC patients) using a new task, and (b) investigate the influence of nonepisodic mechanisms, namely, narrative construction and working memory maintenance, on vmPFC patients’ EFT performance. Method: vmPFC patients and healthy participants imagined future events using pictures as cues, described pictures, or described pictures while maintaining them in working memory after an observation phase. Results: Compared with the controls, vmPFC patients produced less specific reports across all conditions, as indicated by fewer internal (episodic) but a similar number of external (semantic) details. However, controlling for description and working memory performance did not eliminate group differences in EFT. Moreover, vmPFC damage reduced the proportion of internal-to-total details for EFT only. Conclusions: These results indicate that EFT problems in vmPFC patients are not merely the reflection of problems in maintaining in working memory and narrating events, but, more likely, of an impairment upstream, in creating novel events.
Effect of material and fabrication technique on marginal fit and fracture resistance of adhesively luted inlays made of CAD/CAM ceramics and hybrid materials

Abstract This study evaluated the fracture resistance and marginal fit of CAD/CAM ceramic and composite inlays. Molars (N = 80) were prepared to receive Mesio-occlusal-distal (MOD) inlays and randomly divided into four groups to be restored depending on the materials: (a) HLD: heat-pressed lithium disilicate ceramic (IPS e.max Press), (b) CLD: CAD/CAM-fabricated lithium disilicate ceramic (IPS e.max CAD), (c) NC: CAD/CAM nano-ceramic resin (Lava Ultimate), (d) RC: Indirect resin composite (Filtek P60). Each group was randomly divided into two subgroups regarding the resin cement: (a) High-viscosity resin cement (Syntac, Variolink II), (b) Self-adhesive low-viscosity cement (RelyX Ultimate). After marginal gap and cement thickness measurements, specimens were loaded to fracture in a Universal Testing Machine (1 mm/min). Intact molars acted as the control group (n = 10). Data were analyzed using one-way and two-way ANOVA, Tukey’s tests (α = 0.05). Before cementation, CLD group showed significantly lower mean marginal gap (65 ± 22.4 μm) and after cementation, cement thickness was again the lowest with CLD (82.6 ± 24.6 μm) and the highest with HLD (108.4 ± 21.3 μm) (p < 0.001). The mean marginal gaps of inlays at the gingival margin were significantly higher than at the occlusal and the axial margins (p < 0.05). While material type significantly affected the mean fracture resistance (p < 0.001), the cement type had no effect on the results (p = 0.083). NC group (2486 ± 40 N) showed significantly higher mean fracture load compared to those of other three groups (1997.5 ± 60–2007 ± 30) (p < 0.05). The mean fracture resistance of control group with the intact teeth was significantly higher than those of all groups (p < 0.05) except for NC (p > 0.05).