Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional characterization and architecture of recombinant yeast SWR1 histone exchange complex

Abstract We have prepared recombinant fourteen subunit yeast SWR1 complex from insect cells using a modified MultiBac system. The 1.07 MDa recombinant protein complex has histone-exchange activity. Full exchange activity is realized with a single SWR1 complex bound to a nucleosome. We also prepared mutant complexes that lack a variety of subunits or combinations of subunits and these start to reveal roles for some of these subunits as well as indicating interactions between them in the full complex. Complexes containing a series of N-terminally and C-terminally truncated Swr1 subunits reveal further details about interactions between subunits as well as their binding sites on the Swr1 subunit. Finally, we present electron microscopy studies revealing the dynamic nature of the complex and a 21 Å resolution reconstruction of the intact complex provides details not apparent in previously reported structures, including a large central cavity of sufficient size to accommodate a nucleosome.
Evaluating the Potential of Q-Band ESR Spectroscopy for Dose Reconstruction of Fossil Tooth Enamel

The potential of Q-band Electron Spin Resonance (ESR) for quantitative measurements has been scarcely evaluated in the literature and its application for dose reconstruction of fossil tooth enamel with dating purposes remains still quite unknown. Hence, we have performed a comparative study based on several Early to Middle Pleistocene fossil tooth samples using both X- and Q-band spectroscopies. Our results show that Q-band offers a significant improvement in terms of sensitivity and signal resolution: it allows not only to work with reduced amounts of valuable samples (< 4 mg), but also to identify different components of the main composite ESR signal. However, inherent precision of the ESR intensity measurements at Q-band is clearly lower than that achieved at X-band, highlighting the necessity to carry out repeated measurements. All dose values derived from X- and Q-band are nevertheless systematically consistent at either 1 or 2 sigma. In summary, our results indicate that Q-band could now be considered as a reliable tool for ESR dosimetry/dating of fossil teeth although further work is required to improve the repeatability of the measurements.
Corrosion Process and Mechanisms of Corrosion‐Induced Cracks in Reinforced Concrete identified by AE Analysis

Abstract: Concrete structures could suffer from the corrosion of reinforcing steel bars (rebars) because of the penetration of chloride ions. For crack detection and damage evaluation in concrete, acoustic emission (AE) techniques have been extensively applied to concrete and concrete structures. In the corrosion process of reinforced concrete, it is demonstrated that continuous AE monitoring is available to identify the onset of corrosion and the nucleation of concrete cracking because of the expansion of corrosion products. At the latter stage, the expansion of corrosion products generates corrosion‐induced cracks in concrete. The generating mechanisms of these cracks are studied in accelerated corrosion tests of reinforced concrete beams. Kinematics of microcracks are identified by SiGMA (Simplified Green’s functions for Moment tensor Analysis) analysis of AE. It is demonstrated that AE activity at the onset of corrosion and at the nucleation of corrosion‐induced cracks is in remarkable agreement with the phenomenological model of the corrosion process in steel. Then, mechanisms of corrosion‐induced cracks are visually and quantitatively investigated by the SiGMA analysis.
Cross-domain collaboration recommendation

Interdisciplinary collaborations have generated huge impact to society. However, it is often hard for researchers to establish such cross-domain collaborations. What are the patterns of cross-domain collaborations? How do those collaborations form? Can we predict this type of collaborations? Cross-domain collaborations exhibit very different patterns compared to traditional collaborations in the same domain: 1) sparse connection: cross-domain collaborations are rare; 2) complementary expertise: cross-domain collaborators often have different expertise and interest; 3) topic skewness: cross-domain collaboration topics are focused on a subset of topics. All these patterns violate fundamental assumptions of traditional recommendation systems. In this paper, we analyze the cross-domain collaboration data from research publications and confirm the above patterns. We propose the Cross-domain Topic Learning (CTL) model to address these challenges. For handling sparse connections, CTL consolidates the existing cross-domain collaborations through topic layers instead of at author layers, which alleviates the sparseness issue. For handling complementary expertise, CTL models topic distributions from source and target domains separately, as well as the correlation across domains. For handling topic skewness, CTL only models relevant topics to the cross-domain collaboration. We compare CTL with several baseline approaches on large publication datasets from different domains. CTL outperforms baselines significantly on multiple recommendation metrics. Beyond accurate recommendation performance, CTL is also insensitive to parameter tuning as confirmed in the sensitivity analysis.
Spectral measure of large random Hankel, Markov and Toeplitz matrices

We study the limiting spectral measure of large symmetric random matrices of linear algebraic structure. For Hankel and Toeplitz matrices generated by i.i. d. random variables {X k } of unit variance, and for symmetric Markov matrices generated by i.i. d. random variables {X ij } j>i of zero mean and unit variance, scaling the eigenvalues by √n we prove the almost sure, weak convergence of the spectral measures to universal, nonrandom, symmetric distributions γ H , γ M and γ T of unbounded support. The moments of γ H and γ T are the sum of volumes of solids related to Eulerian numbers, whereas γ M has a bounded smooth density given by the free convolution of the semicircle and normal densities. For symmetric Markov matrices generated by i.i. d. random variables {X iy } y>i of mean m and finite variance, scaling the eigenvalues by n we prove the almost sure, weak convergence of the spectral measures to the atomic measure at -m. If m = 0, and the fourth moment is finite, we prove that the spectral norm of M n scaled by √2n log n converges almost surely to 1.
Predominant Involvement of Ipsilateral Anterior and Posterior Circulations in Moyamoya Disease

Background and Purpose— We encountered several patients with childhood onset of moyamoya disease in whom the ipsilateral anterior and posterior circulations were predominantly involved. This study investigated whether this is an angiographic characteristic of this disease. Methods— We evaluated steno-occlusive lesions on angiograms of 85 patients with pediatric onset of moyamoya disease, using two 4-stage angiographic classification scales for the internal carotid artery and posterior cerebral artery systems (ICA and PCA staging, respectively) and determined whether lesions with more advanced ICA and PCA stages were on ipsilateral sides. Results— When positive laterality was defined as the presence of a difference by ≥1 stage between the stages on both sides, lateralities in the ICA stages and in the PCA stages were present in 40 (47%) and 27 patients (32%), respectively. Lesions with more advanced ICA and PCA stages were on the same side, with significant probability (P =0.024, Fisher’s exact test). Lateralities in both ICA and PCA lesions were found in 17 patients. In 14 (82%) of the 17 patients, the more advanced side of ICA lesions was the same as that of PCA lesions, while it was contralateral in 3 patients (18%). Conclusions— In pediatric-onset moyamoya disease, asymmetrical involvement of bilateral ICAs and PCAs was common, and the ipsilateral ICA and PCA tended to be predominantly involved.
An Isbell duality theorem for type refinement systems

Any refinement system (= functor) has a fully faithful representation in the refinement system of presheaves, by interpreting types as relative slice categories, and refinement types as presheaves over those categories. Motivated by an analogy between side effects in programming and context effects in linear logic, we study logical aspects of this ‘positive’ (covariant) representation, as well as of an associated ‘negative’ (contravariant) representation. We establish several preservation properties for these representations, including a generalization of Day's embedding theorem for monoidal closed categories. Then, we establish that the positive and negative representations satisfy an Isbell-style duality. As corollaries, we derive two different formulas for the positive representation of a pushforward (inspired by the classical negative translations of proof theory), which express it either as the dual of a pullback of a dual or as the double dual of a pushforward. Besides explaining how these constructions on refinement systems generalize familiar category-theoretic ones (by viewing categories as special refinement systems), our main running examples involve representations of Hoare logic and linear sequent calculus.
Validation of energy requirement references for exclusively breast-fed infants

In paediatric practice, mean reference energy requirements for groups are often used to predict individual infant energy requirements. References from the FAO/WHO/United Nations University are based on infants not fed according to the current infant feeding recommendations. The objective of the present study was to measure total energy expenditure (TEE) and determine energy requirements using criterion methods, and validate the use of TEE prediction equation and mean energy requirement references for predicting individual TEE and energy requirements, respectively, in infants who were exclusively breast-fed (EBF) to 6 months of age. EBF infants were included from Greater Glasgow for measurements at 3·5 (n 36) and 6 (n 33) months of age. TEE was measured using doubly labelled water and energy requirements were determined using the factorial approach. TEE and energy requirements were also predicted using equations based on body weight. Relationships between criterion methods and predictions were assessed using correlations. Paired t tests and Bland–Altman plots were used to assess agreement. At the population level, predicted and measured TEE were similar. The energy requirement reference significantly underestimated energy requirements by 7·2 % at 3·5 months at the population level, but there was no bias at 6 months. Errors at individual levels were large and energy requirements were underestimated to a larger extent for infants with higher energy requirements. This indicates that references presently used in clinical practice to estimate energy requirements may not fully account for the different growth pattern of EBF infants. More studies in infants EBF to 6 months of age are needed to understand how growth of EBF infants influences energy requirements.
Sex- and Age-related Differences in Morphine Requirements for Postoperative Pain Relief

Background:Sex-related differences in the perception of pain and susceptibility to opioids remain a matter of debate. Intravenous morphine titration used to obtain pain relief in the immediate postoperative period is a unique clinical model for assessing the effect of sex on reported pain. Because of the wide variation in dose requirements for pain management, the authors conducted a prospective study in a large population and also assessed the effect of aging. Methods:Intravenous morphine titration was administered as a bolus of 2 (body weight ≪ 60 kg) or 3 mg (body weight > 60 kg) during the immediate postoperative period. The interval between each bolus was 5 min. The visual analog pain scale (VAS) threshold required to administer morphine was 30, and pain relief was defined as a VAS score of 30 or less. Data are expressed as mean ± SD. Results:Data from 4,317 patients were analyzed; 54% of the patients were male, and 46% were female. The mean morphine dose required to obtain pain relief was 11.9 ± 6.8 mg or 0.173 ± 0.103 mg/kg. Women had a higher initial VAS score (74 ± 19 vs. 71 ± 19; P < 0.001) and required a greater dose of morphine (0.183 ± 0.111 vs. 0.165 ± 0.095 mg/kg; P < 0.001). In contrast, no significant difference was noted in elderly (aged > 75 yr) patients (0.163 ± 0.083 vs. 0.157 ± 0.085 mg/kg). Conclusion:Women experienced more severe postoperative pain and required a greater dose (+11%) of morphine than men in the immediate postoperative period. This sex-related difference disappeared in elderly patients.
Genetically modified yolk proteins precipitate in the adult Drosophila fat body

Ultrastructural and genetic studies were carried out on the fat body of a female sterile mutant fs(1)1163 to ascertain why yolk protein 1 (YP1) is not secreted from this tissue. Earlier molecular studies demonstrated that (a) normally yolk protein is synthesized in the fat body, secreted into the hemolymph and taken up by the ovary, (b) the 1163 mutation causes a single amino acid substitution in YP1, and (c) females homozygous for the mutation, or heterozygous females raised at 29 degrees C, retain YP1 in the fat body. Ultrastructural analysis in this paper shows that the fat body of these females contains masses of electron-dense material deposited in the subbasement membrane space. This subbasement membrane material (SBMM), which occasionally has a crystalline-like, fibrous component, is found in females whose genotypes include at least one copy of the mutant 1163 gene. These strains include a deletion strain that is hemizygous for the 1163 gene and two strains that are transgenic for the mutant gene. Immunogold studies indicate that SBMM contains yolk protein. We propose that the mutant protein is secreted into the subbasement membrane space, but because of the amino acid substitution in YP1, the oligomers containing YP1 condense into SBMM, which cannot penetrate the basement membrane. The similarity of SBMM and deoxyhemoglobin S fibers is discussed.
Polymeric liquids and networks : dynamics and rheology

1 Monomeric Liquid Dynamics 2 Linear Viscoelasticity 3 Stress Response to Shear Deformation 4 Stress-Deformation Relationships 5 Experimental Aspects 6 Flexible-Chain Dynamics 7 Entangled Chain Dynamics 8 Entangled Solution Dynamics 9 Dynamics of Non-linear Chains 10 Polydispersity Effects
The Forehead Zygomatic-Orbital Artery-Based Island Flap

This article describes an original forehead flap arterialized on the zygomatic-orbital artery. The idea became reality during the harvesting of a routine flap, when the discovery of an increased-caliber zygomatic-orbital artery and a small frontal branch of the superficial temporal artery prompted surgeons to try switching the arterial supply. This case demonstrates both the viability and the mobility of this flap used in the reconstruction of the lower third of the face. The second part of the article examines the anatomy of the zygomatic-orbital artery and its variants and relationships with the superficial temporal artery. To confirm the potential of this alternative flap and to improve current knowledge of the artery, the vascular anatomy of 50 frontotemporal zygomatic territories was investigated by ultrasonography. The three aspects verified were incidence, course constancy, and relationship with the frontal branch of the superficial temporal artery. The study suggests that the zygomatic-orbital artery could be a suitable replacement for the frontal artery when the latter is small, absent, or positioned too high to ensure maintenance of an adequate lateral flow to the forehead.
Repeatability of exhaled nitric oxide measurements in patients with COPD

The assessment of the presence of eosinophilic airway inflammation may help in predicting the steroid response in subjects with respiratory symptoms. Unlike patients with asthma, only a subset of patients with chronic obstructive pulmonary disease (COPD) benefits from steroid treatment. Fractional exhaled nitric oxide (FENO) is a useful surrogate marker for eosinophilic airway inflammation, but data on the repeatability of FENO measurements in COPD needed for the assessment of significant change are insufficient. The aim of this study was to assess the short‐term repeatability of FENO measurement in subjects with moderate to very severe chronic airway obstruction compared to that in healthy subjects. We studied 20 patients with stable COPD and 20 healthy subjects, and determined FENO (flow rate 50 ml s−1) three times: at baseline, 10 min and 24 h after baseline. Spirometry was performed on the first study day after the FENO measurements. The median FENO concentration in patients with COPD was 15·6 ppb, and in healthy subjects, 15·2 ppb. The coefficient of variation (CoV) for 24‐h measurements was 12·4% in COPD patients, and 15·9% in healthy subjects. Among COPD patients with global initiative for chronic obstructive lung disease stage 2 disease, the CoV was 13·7%, and among those with stage 3–4 disease, 10·5%. The findings indicate that the short‐term repeatability of FENO measurement in patients with moderate to very severe COPD is equally good as in healthy subjects. A change in FENO exceeding 24% is likely to reflect a minimum measurable change in COPD.
A relative basis for mixed Tate motives over the projective line minus three points

In a previous work, the author have built two families of distinguished algebraic cycles in Bloch-Kriz cubical cycle complex over the projective line minus three points. The goal of this paper is to show how these cycles induce well-defined elements in the $\HH^0$ of the bar construction of the cycle complex and thus generated comodules over this $\HH^0$, that is a mixed Tate motives as in Bloch and Kriz construction. In addition, it is shown that out of the two families only ones is needed at the bar construction level. As a consequence, the author obtains that one of the family gives a basis of the tannakian coLie coalgebra of mixed Tate motives over $\ps$ relatively to the tannakian coLie coalgebra of mixed Tate motives over $\Sp(\Q)$. This in turns provides a new formula for Goncharov motivic coproduct, which arise explicitly as the coaction dual to Ihara action by special derivations.
Visual and optical performance of diffractive multifocal intraocular lenses with different haptic designs: 6 month follow-up

Purpose To evaluate and compare the visual acuity outcomes and optical performances of eyes implanted with two diffractive multifocal intraocular lens (IOL) models with either a plate haptic design or a modified-C design. Methods This retrospective study comprised cataract patients who were implanted with either a plate haptic multifocal IOL model (AcrivaUD Reviol BB MFM 611 [VSY Biotechnology, Amsterdam, the Netherlands], group 1) or a modified-C haptic multifocal IOL model (AcrivaUD Reviol BB MF 613 [VSY Biotechnology, Amsterdam, the Netherlands], group 2) between June 2012 and May 2013. The 6 month postoperative visual acuity, refraction, defocus curve, contrast sensitivity, and wave-front aberration were evaluated and compared between these eyes, using different IOL models. Results One hundred fifty-eight eyes of 107 patients were included in this study. Significant improvement in visual acuities and refraction was found in both groups after cataract surgery (P<0.01). The visual acuity and contrast sensitivity were statistically better in group 1 than in group 2 (P<0.01). No statistically significant difference in the corneal higher-order aberrations was found between the two groups (P>0.05). However, the ocular higher-order aberrations in group 2 were significantly greater than in group 1 (P<0.05). Conclusion At 6 months postoperatively, both AcrivaUD Reviol BB MFM 611 IOL and AcrivaUD Reviol BB MF 613 IOL achieved excellent visual and refractive outcomes. The multifocal IOL model with plate haptic design resulted in better optical performances than that with the modified-C haptic design.
Ex Vivo Cytokine mRNA Levels Correlate with Changing Clinical Status of Ethiopian TB Patients and their Contacts Over Time

There is an increasing body of evidence which suggests that IL-4 plays a role in the pathogenesis of TB, but a general consensus on its role remains elusive. We have previously published data from a cohort of Ethiopian TB patients, their contacts, and community controls suggesting that enhanced IL-4 production is associated with infection with M. tuberculosis, rather than overt disease and that long-term protection in infected community controls is associated with co-production of the IL-4 antagonist IL-4d2, alongside elevated IL-4. Here, for the first time, we compare data on expression of IFN-γ, IL-4 and IL-4δ2 over time in TB patients and their household contacts. During the follow-up period, the TB patients completed therapy and ceased to display TB-like symptoms. This correlated with a decrease in the relative amount of IL-4 expressed. Over the same period, the clinical status of some of their contacts also changed, with a number developing TB-like symptoms or clinically apparent TB. IL-4 expression was disproportionately increased in this group. The findings support the hypothesis that elevated IL-4 production is generally associated with infection, but that TB disease is associated with a relatively increased expression of IL-4 compared to IFN-γ and IL-4δ2. However, the data also suggest that there are no clear-cut differences between groups: the immune response over time appears to include changes in the expression of IFN-γ, IL-4 and IL-4δ2, and it is the relative, not absolute levels of cytokine expression that are characteristic of clinical status.
The Influence of Sucralose on Bacterial Metabolism

Sucralose (1',4',6' trideoxy-trichloro-galactosucrose) is a nontoxic, intensely sweet sucrose derivative that has been shown to be non-cariogenic in experimental animals. The purpose of this study was to determine whether certain oral bacteria could utilize sucralose. Sucralose, as a sole carbon source, was unable to support growth of ten strains of oral bacteria and dental plaque. When sucralose was incorporated into a liquid medium containing glucose or sucrose, all organisms tested displayed similar pH falls, compared with controls. The incorporation of 126 mmol/L sucralose into glucose agar medium caused total inhibition of growth of Streptococcus sobrinus 6715-17, Streptococcus sanguis 10904, Streptococcus sanguis Challis, Streptococcus salivarius, and Actinomyces viscosus WVU627. Sucralose had no effect on IPS production. Sucralose was not bound to, nor taken up by, cells. Sucralose inhibited the formation of glucan and fructan polymers in proportion to the sucralose-to-enzyme ratio, but independent of the sucrose concentration in the assay mixture. No radioactive polymer was formed from 14C-U-sucralose added to mixtures containing glucosyltransferase (GTF) or fructosyltransferase (FTF). Inhibition of GTF and FTF by sucralose was removed following dialysis of the enzyme/sucralose mixture. These results show that sucralose was not utilized by the oral bacteria tested and that the inhibitory effect of sucralose on GTF and FTF was non-competitive and reversible. The results further support the concept that sucralose is non-cariogenic.