Miracle-dz/UniFAR-FTUs huggingface dataset:
SINE Retrotransposons Import Polyadenylation Signals to 3’UTRs in Dog (Canis familiaris)

Background Messenger RNA 3’ untranslated regions (3’UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3’UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy number. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may help terminate transcript in some dog genes. Results Dog 3’UTRs have several peaks of AATAAA PAS frequency within 40 bp of the 3’UTR end, including four bp-interval peaks at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. While density of antisense-oriented Can-SINEs in 3’UTRs is fairly constant with distances from 3’end, sense-oriented Can-SINEs are common at the 3’end but nearly absent farther upstream. There are nine Can-SINE sub-types in the dog genome and the consensus sequence sense strands (head to tail) all carry at least three PASs while antisense strands usually have none. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp for target site duplications (TSDs). We find that all Can-SINE types favor integration at TSDs beginning with A(4). The count of AATAAA PASs differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3’UTR ends are very likely to carry AATAAA on the mRNA sense strand while those farther upstream are not. We also identified loci where Can-SINE insertion has truncated or altered a dog 3’UTR compared to the human ortholog. Conclusion Dog Can-SINE activity has imported AATAAA PASs into gene transcripts and led to alteration of 3’UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3’UTR regions but are retained at the far downstream end of 3’UTRs, which we infer reflects their role as termination sequences for these transcripts.
Comments on the numerical simulations of electrolytes in periodic boundary conditions

Relying on the article of de Leeuw, Perram, and Smith [Proc. R. Soc. London, Ser. A 373, 27 (1980)] we justify the expression of the Hamiltonian actually used in the numerical simulations of electrolyte solutions in a periodic geometry. It involves the itinerant dipole moment Mi of the charges rather than the electric moment MB of the simulation box. The vector Mi is defined as the electric moment of the particles which were in the simulation box at t=0 and may have diffused away in the neighboring cells in the course of the simulation. Some comments on Stillinger–Lovett conditions are included.
Interactive Textbooks in School Informatics: A Case Study in Estonia

A move from printed to digital textbooks is often implemented on three different levels, while the highest level is interactive textbook that is able to check the learners' responses to learning tasks (incl. program code) and give personalised, automated feedback. Such interactive textbooks were developed in Estonia to support implementation of radically reformed national curriculum in informatics. This paper summarises a case study focusing on design, development and piloting of two online textbooks
Insights in the aerobic oxidation of aldehydes

The hydroformylation of olefins (oxo synthesis) is the most important process for the production of higher aldehydes (>C4). The liquid phase oxidation of the latter to carboxylic acids by molecular oxygen or air has been known for more than 150 years and is an industrially important process. However, in the recent literature, several different oxidizing reagents and catalytic processes have been reported for this oxidation but most of them have limitations as they use environmentally unacceptable reagents or unnecessarily sophisticated conditions. Herein, we re-evaluated the air oxidation of aldehydes. We show that under mild conditions (air or oxygen and non-optimized stirring), reactions are transfer limited and thus catalyst has no effect on reaction rate. Using efficient stirring (self-suction turbine), uncatalysed air oxidation of 0.8 M aldehyde is possible in 50 min at room temperature whereas less than 10 min was necessary with 10 ppm Mn(II). Thus, recommendations for avoiding common pitfalls that may rise during the evaluation of new catalysts are made.
Recombinant Fc-fusion vaccine of RBD induced protection against SARS-CoV-2 in non-human primate and mice

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to infect people globally. The increased COVID-19 cases and no licensed vaccines highlight the need to develop safe and effective vaccines against SARS-CoV-2 infection. Multiple vaccines candidates are under pre-clinical or clinical trails with different strengths and weaknesses. Here we developed a pilot scale production of a recombinant subunit vaccine (RBD-Fc Vacc) with the Receptor Binding Domain of SARS-CoV-2 S protein fused with the Fc domain of human IgG1. RBD-Fc Vacc induced SARS-CoV-2 specific neutralizing antibodies in non-human primates and human ACE2 transgenic mice. The antibodies induced in macaca fascicularis neutralized three divergent SARS-CoV2 strains, suggesting a broader neutralizing ability. Three times immunizations protected Macaca fascicularis (20ug or 40ug per dose) and mice (10ug or 20ug per dose) from SARS-CoV-2 infection respectively. These data support clinical development of SARS-CoV-2 vaccines for humans. RBD-Fc Vacc is currently being assessed in randomized controlled phase 1/II human clinical trails. Summary This study confirms protective efficacy of a SARS-CoV-2 RBD-Fc subunit vaccine.
White matter alterations in glaucoma and vision-deprived brains differ outside the visual system

The degree to which glaucoma has effects beyond the eye –in the brain– is unclear. We investigated white matter microstructure (WMM) alterations in 37 tracts of patients with glaucoma, monocular blindness and controls. We used reproducible methods and the advanced cloud computing platform brainlife.io. White matter tracts were subdivided into seven categories ranging from primarily involved in vision (the visual white matter) to primarily involved in cognition and motor control. WMM in both glaucoma and monocular blind subjects was lower than controls in the visual white matter, suggesting neurodegenerative mechanisms due to reduced sensory inputs. In glaucoma participants WMM differences from controls decreased outside the visual white matter. A test-retest validation approach was used to validate these results. The pattern of results was different in monocular blind participants, where WMM properties increased outside the visual white matter as compared to controls. The pattern of results suggests that whereas in the blind loss of visual input might promote white matter reorganization outside of the early visual system, such reorganization might be reduced or absent in glaucoma. The results provide indirect evidence that in glaucoma unknown factors might limit the brain plasticity effects that in other patient groups follow visual loss.
Palynological, physico-chemical and colour characterization of Moroccan honeys: I. River red gum (Eucalyptus camaldulensis Dehnh) honey

The melissopalynological, physico-chemical and colour characteristics of Eucalyptus honeys from Morocco were studied. It is generally accepted that a minimum content of 70% of Eucalyptus pollen is necessary to classify an Eucalyptus honey as unifloral. Twenty-eight physico-chemical and five colour parameters were measured, including the content of sugars and minerals, proline, water content, pH, acidity, hydroxymethylfurfural, diastase activity, ash, electrical conductivity, colour coordinates (L*, a*, b*), chroma (C* ab ) and hue angle (h ab ). Pollen analysis was included, and samples contained a mean of six pollen types (range 2-12). The majority of the samples (75%) contained more than 90% Eucalyptus pollen. The presence of Quercus, Plantago and Thymelaea pollen allows the differentiation of these honeys from those with a different geographical origin. Physico-chemical analysis showed that there was a low percentage of sucrose (x = 0.01%) and trisaccharides. Mineral analysis showed a low percentage of Mg (x = 25.99 ppm) and K (x = 205 ppm), while electrical conductivity (x = 721 pS cm -l ) and diastase activity (x = 39.05 °Gothe) showed medium-high values. The colour parameters lightness (L*) and chroma (C* ab ) showed relatively low values.
Residual heavy metal concentrations in sludge amended coastal plain soils. II. Predicting metal concentrations in tobacco from soil test information

Abstract The purpose of the research was to develop mathematical relationships which utilize soil test information to estimate the concentration of heavy metals (Zn, Cu, Mn, Ni and Cd) in tobacco grown in sludge‐amended soils. Regression analyses were performed on plant and soil metal concentration results obtained from investigations conducted in Maryland involving two sites amended with municipal sludge materials at several rates 12 and 8 years earlier, respectively. Soil test information consisted of pH, total and extractable metals utilizing three extractants (DTPA pH 7.3, Mehlich 1 and 3). Mathematical relationships were developed using linear regression, stepwise multiple regression, and General Linear Model (GLM) analysis procedures available through SAS. R2 values for Zn, Cu, Mn, Ni and Cd ranged from 0.65 to 0.95 depending on the extractant; however, equations for Fe and Pb were not presented because of low R2 (<0.5) values for all extractants.
The phonon-drag thermopower in Si:B and Si:Sb δ-doped samples

The thermal conductivity and the thermoelectric power of two dimensional hole and electron gases in B and Sb delta-doped Si structures have been measured for the first time. The temperature range was 1.4 K to 30 K, and carrier sheet densities were in the range 0.3 to 1.0×1014 cm-2. Kohn anomalies have been observed in all samples. The thermopower is dominated by the phonon drag contribution in each case. Calculations of the temperature dependence of the thermopower agree with experimental data when unscreened phonon scattering potentials are used for Si:B and Si:Sb.
Postnatal persistence of sex-dependent renal developmentally programmed structural and molecular changes in nonhuman primates

Background Poor nutrition during development programs kidney function. No studies on postnatal consequences of decreased perinatal nutrition exist in nonhuman primates (NHP) for translation to human renal disease. Our baboon model of moderate maternal nutrient restriction (MNR) produces intrauterine growth restricted (IUGR) and programs renal fetal phenotype. We hypothesized that the IUGR phenotype persists postnatally, influencing responses to a high-fat, high-carbohydrate, high-salt (HFCS) diet. Methods Pregnant baboons ate chow (Control; CON) or 70% of control intake (MNR) from 0.16 gestation through lactation. MNR offspring were IUGR at birth. At weaning, all offspring (CON and IUGR females and males, n=3/group) ate chow. At ~4.5 years of age, blood, urine, and kidney biopsies were collected before and after a 7-week HFCS diet challenge. Kidney function, unbiased kidney gene expression, and untargeted urine metabolomics were evaluated. Results IUGR female and male kidney transcriptome and urine metabolome differed from CON at 3.5 years, prior to HFCS. After the challenge, we observed sex-specific and fetal exposure-specific responses in urine creatinine, urine metabolites, and renal signaling pathways. Conclusions We previously showed mTOR signaling dysregulation in IUGR fetal kidneys. Before HFCS, gene expression analysis indicated that dysregulation persists postnatally in IUGR females. IUGR male offspring response to HFCS showed uncoordinated signaling pathway responses suggestive of proximal tubule injury. To our knowledge, this is the first study comparing CON and IUGR postnatal juvenile NHP and the impact of fetal and postnatal life caloric mismatch. Perinatal history needs to be taken into account when assessing renal disease risk.
The effect of polarity and surface states on the Fermi level at III-nitride surfaces

Surface states and their influence on the Fermi level at the surface of GaN and AlN are studied using x-ray photoelectron spectroscopy (XPS). The effect of polarity on surface electronic properties was studied. Accurate modeling of the valence band edge and comparison with XPS data revealed the presence of donor surface states at 1.4 eV and acceptor states at energies >2.7 eV from the valence band in GaN. Al polar AlN showed acceptor states at energies >3.3 eV. Density of acceptor surface states was estimated to be between 1013 and 1014 eV−1 cm−2 in both GaN and AlN. The shift in charge neutrality levels and barrier heights due to polarity and the density of surface states on AlN and GaN were estimated from XPS measurements. Theoretical modeling and comparison with XPS data implied full compensation of spontaneous polarization charge by charged surface states. Barrier height measurements also reveal a dependence on polarity with ϕmetal-polar > ϕnon-polar > ϕnitrogen-polar suggesting that the N-polar sur.
Comparison of porcine corneal decellularization methods and importance of preserving corneal limbus through decellularization

Background The aim of this study is to compare the three previously applied, conventional porcine corneal decellularization methods and to demonstrate the importance of preserving the corneal limbus through decellularization. Methods Fresh, wild-type (with or without) limbus porcine corneas were decellularized using three different methods, including (i) sodium dodecyl sulfate (SDS), (ii) hypertonic saline (HS), and (iii) N2 gas (NG). Post-treatment evaluation was carried out using histological, residual nuclear material, and ultrastructural analyses. Glycerol was used to help reduce the adverse effects of decellularization. The corneas were preserved for two weeks in cornea storage medium. Results All three decellularization methods reduced the number of keratocytes at different rates in the stromal tissue. However, all methods, except SDS, resulted in the retention of large numbers of cells and cell fragments. The SDS method (0.1% SDS, 48h) resulted in almost 100% decellularization in corneas without limbus. Low decellularization capacity of the NG method (<50%) could make it unfavorable. Although HS method had a more balanced damage-decellularization ratio, its decellularization capacity was lower than SDS method. Preservation of the corneoscleral limbus could partially prevent structural damage and edema, but it would reduce the decellularization capacity. Conclusion Our results suggest that SDS is a very powerful decellularization method, but it damages the cornea irreversibly. Preserving the corneoscleral limbus reduces the efficiency of decellularization, but also reduces the damage.
Seeding Growth for Size Control of 5−40 nm Diameter Gold Nanoparticles

Following a seeding growth approach, gold nanoparticles of diameters 5−40 nm were prepared with 10−15% standard deviation in diameter from 3.5 ± 0.7 nm gold particle seeds. Particle size can be controlled by varying the ratio of seed to metal salt, and thus any size in the range 5−40 nm can be prepared. The method can also be scaled up to produce 10−100 mg of gold nanoparticles.
Correlation between the Vibrational Frequencies of the Carboxylate Group and the Types of Its Coordination to a Metal Ion: An ab Initio Molecular Orbital Study

The structures and vibrational frequencies of the acetate ion interacting with a metal ion (Na+, Mg2+, and Ca2+) in the unidentate, bidentate, bridging, and pseudobridging forms are studied by ab initio molecular orbital calculations. Effects of a water molecule coordinating to either the acetate ion or the metal ion are also examined. The calculations are carried out by using the self-consistent reaction field method at the Hartree−Fock level with the 6-31+G** basis set. For the species interacting with a divalent metal cation, the lengths of the two CO bonds of the acetate ion are nearly equal in the bidentate form but are significantly different in the unidentate form. The frequency of the COO- antisymmetric stretch of the unidentate species is higher than that of the ionic species, which is in turn higher than that of the bidentate species. The reverse is the case for the COO- symmetric stretch. As a result, the frequency separations (Δνa-s) between the COO- antisymmetric and symmetric stretches for t.
Intramolecular synergism and bacterial lysis regulation can explain the complex multi-domain architecture of the bacteriophage endolysin PlySK1249

Endolysins are peptidoglycan hydrolases produced at the end of the bacteriophage (phage) replication cycle to lyse the host cell. Gram-positive phages endolysins come in a variety of multi-modular forms that combine different catalytic domains and may have evolved to adapt to their bacterial hosts. However, the reason why phage can adopt endolysin with such complex multidomain architecture is for the moment not well understood. We used the Streptococcus dysgalactiae phage endolysin PlySK1249 as a model to study the implication of multi-domain architecture in phage-induced bacterial lysis and lysis regulation. The activity of the enzyme relied on a bacteriolytic amidase (Ami), a non-bacteriolytic L-Ala-D-Ala endopeptidase (CHAP) acting as a de-chaining enzyme and central LysM cell wall binding domain (CBD). Ami and CHAP synergized for peptidoglycan digestion and bacteriolysis in the native enzyme or when expressed individually and reunified in vitro. This cooperation could be modulated by bacterial cell wall-associated proteases, which specifically cleaved the two linkers connecting the different domains. While both catalytic domains were observed to act coordinately to optimize bacterial lysis, the CBD is expected to delay diffusion of the enzyme until proteolytic inactivation is achieved. As for certain autolysins, PlySK1249 cleavage by bacterial cell wall associated proteases might be an example of dual phage-bacterial regulation and mutual coevolution. In addition, understanding more thoroughly the multidomain interplay of PlySK1249 opens new perspectives on the ideal architecture of therapeutic antibacterial endolysins.
The choice of a zeroth-order Hamiltonian for second-order perturbation theory with a complete active space self-consistent-field reference function

The choice of a zeroth‐order Hamiltonian, H0, for second‐order perturbation theory with a complete active space self‐consistent‐field (CASSCF) reference function is discussed in detail, in the context of the inclusion of the denominator shifts found to be important in recent single‐reference high‐spin open‐shell theories and the formulation of a computationally efficient method. Using projection operators and second quantization algebra, an operator is constructed which consists of the complete active space Hamiltonian in the active space and the Mo/ller–Plesset zeroth‐order Hamiltonian in the inactive and secondary spaces. This operator, designated CAS/A, has the reference as an eigenfunction without the necessity of projection, it naturally incorporates denominator shifts which appear in terms of active space Fock operators, it does not give rise to intruder states, and it costs little more than other CASSCF perturbation theories. The incorporation of the complete active space Hamiltonian introduces ad.
Lignin-Degrading Enzymes from Mycelial Cultures of Basidiomycete Fungi Isolated in Tanzania

This research involved field surveys in different geographical locations in Tanzania for collection of fungi species, identification of the isolates, and screening for lignin-degrading enzyme production. Out of 18 saprophytic fungi (both wood and non-wood inhabiting) isolates, 17 were positive in the rhemazol brilliant blue-R (RBBR) decolorization test; 15 of the isolates oxidized guaiacol while 7 and 12 oxidized α-naphthol and pyrogallol, respectively. The cultures with 1% glucose concentration showed the fastest growth of mycelia and highest MnP, LiP, and Lac activities. MnP was found to be dominant among the tested isolates and Laetiporus sulphurae had the highest LiP activity of 65.2 U/ml. Most of the fungi isolates produced more than two extracellular enzymes, suggesting that these isolates possess the ability to degrade lignin or related polyphenolic compounds, and thus they can be used in upgrading low quality animal feed. The selected fungi isolates reduced cellulose and hemicellulose contents in rice straw by an average of 10% and 35%, respectively, delignification ratio of 23% and increased its relative crude protein content by more than 50%.
In-situ study of the growth, structure and reactivity of Pt-Pd nanoalloys

Les proprietes catalytiques des nanoparticules metalliques peuvent etre ameliorees par effet d’alliages. La synthese en solution par voie colloidale permet de preparer des nanoalliages homogenes en taille, en forme et en composition chimique, de structure ordonnee, desordonnee ou cœur-coquille. La nucleation et la croissance des nanoalliages de Pt-Pd sont etudiees ici par microscopie electronique en transmission, en condition standard, puis in situ dans une cellule liquide formee par des feuilles d’oxyde de graphene. La cinetique de croissance des nanoalliages de Pt-Pd correspond a l’incorporation directe des monomeres en solution, compatible avec un processus limite par la reaction de surface, sans phenomene de coalescence, contrairement a la croissance du Pt pur. La structure theorique a l’equilibre des nanoalliages de Pt-Pd est determinee par des simulations Monte Carlo. La structure la plus probable correspond a une surface riche en Pd et a une sous couche atomique riche en Pt, stable a des temperatures elevees. L’effet de l’adsorption de gaz oxydants ou reducteurs sur la forme des nanoparticules, est etudie in situ par microscopie environnementale sous pression de quelques mbar, dans un porte objet environnemental. On observe des changements de formes sous oxygene, dus au developpement de facettes d’indices plus eleves. La reactivite des nanocubes de Pd@Pt est etudiee pour l’oxydation du CO en fonction du recouvrement de Pt a la surface. La reactivite maximale pour un faible recouvrement est interpretee par une baisse de l’energie d’adsorption du CO liee au desaccord parametrique entre le Pt et le Pd et a la modification de la structure electronique du Pt lie au Pd.