Miracle-dz/UniFAR-FTUs huggingface dataset:
Root system size and precision in nutrient foraging: responses to spatial pattern of nutrient supply in six herbaceous species

1 An experiment was carried out to test the hypotheses that in heterogeneous environments: (i) the size of species’ root systems will be negatively correlated with their ability to place roots precisely in nutrient‐rich patches; (ii) precision of root placement will be less affected by distance to nutrient patches in species with large root systems; (iii) species with greater precision in root placement will show greater variation in biomass (sensitivity) in response to heterogeneity in nutrient supply; and (iv) plants will be less precise in root placement, and will invest more biomass in above‐ground structures or in fitness‐related attributes, when in association with mycorrhizas. 2 Single plants of six herbaceous species (Arrhenatherum elatius, Festuca ovina, Plantago lanceolata, Campanula rotundifolia,Papaver rhoeas and Sonchus oleraceus) were grown in pots with mycorrhizas either present or absent. The same amount of nutrients was supplied either homogeneously or heterogeneously at different distances from the plants. Pots received the same quantity of nutrients in all treatments. 3 There was a significant negative correlation between species’ root system biomass and precision. Several species, including some with large root systems, showed small but highly significant differences in precision between the various treatments. Only the high‐precision species Papaver and the low‐precision species Campanula exhibited sensitivity in biomass produced in response to different patterns of heterogeneity. 4 The precision with which roots were placed in nutrient‐rich patches was affected by distance from patches in Papaver, the smallest‐rooted species used in the experiment, and in Plantago, one of the larger‐rooted species. There was no evidence to support the hypothesis that precision would be affected more by distance from nutrient patches in small‐rooted species than in large‐rooted species. 5 The presence of mycorrhizas did not affect precision of root placement in any species. However, allocation of biomass to roots was significantly lower in Arrhenatherum, and allocation to reproductive structures was significantly higher in Campanula, when mycorrhizas were present. 6 This study confirms that there are differences between species in precision of nutrient foraging that are related to root system size. It also shows that there is variation in precision within species in response to the location of nutrient‐rich patches, and that the ability of a species to display precision in nutrient foraging is dependent on its environmental setting.
Neither fixed nor random: weighted least squares meta‐regression

Our study revisits and challenges two core conventional meta‐regression estimators: the prevalent use of ‘mixed‐effects’ or random‐effects meta‐regression analysis and the correction of standard errors that defines fixed‐effects meta‐regression analysis (FE‐MRA). We show how and explain why an unrestricted weighted least squares MRA (WLS‐MRA) estimator is superior to conventional random‐effects (or mixed‐effects) meta‐regression when there is publication (or small‐sample) bias that is as good as FE‐MRA in all cases and better than fixed effects in most practical applications. Simulations and statistical theory show that WLS‐MRA provides satisfactory estimates of meta‐regression coefficients that are practically equivalent to mixed effects or random effects when there is no publication bias. When there is publication selection bias, WLS‐MRA always has smaller bias than mixed effects or random effects. In practical applications, an unrestricted WLS meta‐regression is likely to give practically equivalent or superior estimates to fixed‐effects, random‐effects, and mixed‐effects meta‐regression approaches. However, random‐effects meta‐regression remains viable and perhaps somewhat preferable if selection for statistical significance (publication bias) can be ruled out and when random, additive normal heterogeneity is known to directly affect the ‘true’ regression coefficient. Copyright © 2016 John Wiley & Sons, Ltd.
The Conversion of a Peer Teaching Course in the Puncture of Peripheral Veins for Medical Students into an Interprofessional Course

Objective: There is a great interest on both a national and international level in promoting cooperation between different occupational groups within the healthcare professions through interprofessional education (IPE) [1], [2], [3]. Within this project, a peer teaching course on the puncture of peripheral veins was therefore converted from a course for medical students into an IPE learning unit. Students from different occupational groups were to learn within the context of this course, according to the definition from the World Health Organisation (WHO), with and from each other [1]. Project description: This course constituted a small group class in the peer teaching format. The didactic principle was based on the idea that the students were to practice the respective practical skills in pairs and give each other reciprocal feedback. Together with the Department for Health at the Bern University of Applied Sciences (BUAS) and the Bern Center of Higher Education of Nusing (BCHEN), the course, which was conducted by the Institute of Medical Education at the University of Bern (IME), was converted into a voluntary IPE pilot project. Students from all three institutions were represented in terms of participants as well as tutors. Results: The course was evaluated very positively by participants, peer tutors and the participating institutions. By means of an OSCE, it could be proven that the course content had been successfully imparted. On the basis of these results, it was determined that the course should be compulsory in the future for students at all three institutions. Discussion: The evaluation results show the successful conversion of the course into an IPE format within the context of the pilot project. The interactive format of the course created the prerequisite that the students from different professional groups learned with and from each other in actuality, and did not just study the same objectives at the same time as with multiprofessional learning. Cooperation between the three institutions is a cornerstone for the development of a research structure which may examine the effect of IPE in the future.
Acute hepatitis B virus infection in humanized chimeric mice has multiphasic viral kinetics

Chimeric urokinase type plasminogen activator (uPA)/severely severe combined immunodeficiency (SCID) mice reconstituted with humanized livers are useful for studying hepatitis B virus (HBV) infection in the absence of an adaptive immune response. However, the detailed characterization of HBV infection kinetics necessary to enable in‐depth mechanistic studies in this in vivo HBV infection model is lacking. To characterize HBV kinetics post‐inoculation (p.i.) to steady state, 42 mice were inoculated with HBV. Serum HBV DNA was frequently measured from 1 minute to 63 days p.i. Total intrahepatic HBV DNA, HBV covalently closed circular DNA (cccDNA), and HBV RNA was measured in a subset of mice at 2, 4, 6, 10, and 13 weeks p.i. HBV half‐life (t1/2) was estimated using a linear mixed‐effects model. During the first 6 hours p.i. , serum HBV declined in repopulated uPA/SCID mice with a t1/2 = 62 minutes (95% confidence interval [CI] = 59‐67). Thereafter, viral decline slowed followed by a 2‐day lower plateau. Subsequent viral amplification was multiphasic with an initial mean doubling time of t2 = 8 ± 3 hours followed by an interim plateau before prolonged amplification (t2 = 2 ± 0.5 days) to a final HBV steady state of 9.3 ± 0.3 log copies (cps)/mL. Serum HBV and intrahepatic HBV DNA were positively correlated (R2 = 0.98). Conclusion: HBV infection in uPA/SCID chimeric mice is highly dynamic despite the absence of an adaptive immune response. Serum HBV t1/2 in humanized uPA/SCID mice was estimated to be ∼1 hour regardless of inoculum size. The HBV acute infection kinetics presented here is an important step in characterizing this experimental model system so that it can be effectively used to elucidate the dynamics of the HBV life cycle and thus possibly reveal effective antiviral drug targets. (Hepatology 2018).
Tensile forces drive a reversible fibroblast-to-myofibroblast transition during tissue growth in engineered clefts

Fibroblasts transition into myofibroblasts in a highly tensed growth front and revert back to fibroblasts as the tissue matures. Myofibroblasts orchestrate wound healing processes, and if they remain activated, they drive disease progression such as fibrosis and cancer. Besides growth factor signaling, the local extracellular matrix (ECM) and its mechanical properties are central regulators of these processes. It remains unknown whether transforming growth factor–β (TGF-β) and tensile forces work synergistically in up-regulating the transition of fibroblasts into myofibroblasts and whether myofibroblasts undergo apoptosis or become deactivated by other means once tissue homeostasis is reached. We used three-dimensional microtissues grown in vitro from fibroblasts in macroscopically engineered clefts for several weeks and found that fibroblasts transitioned into myofibroblasts at the highly tensed growth front as the microtissue progressively closed the cleft, in analogy to closing a wound site. Proliferation was up-regulated at the growth front, and new highly stretched fibronectin fibers were deposited, as revealed by fibronectin fluorescence resonance energy transfer probes. As the tissue was growing, the ECM underneath matured into a collagen-rich tissue containing mostly fibroblasts instead of myofibroblasts, and the fibronectin fibers were under reduced tension. This correlated with a progressive rounding of cells from the growth front inward, with decreased α–smooth muscle actin expression, YAP nuclear translocation, and cell proliferation. Together, this suggests that the myofibroblast phenotype is stabilized at the growth front by tensile forces, even in the absence of endogenously supplemented TGF-β, and reverts into a quiescent fibroblast phenotype already 10 μm behind the growth front, thus giving rise to a myofibroblast-to-fibroblast transition. This is the hallmark of reaching prohealing homeostasis.
Lactobacillus rhamnosus GG Protects against Non-Alcoholic Fatty Liver Disease in Mice

Objective Experimental evidence revealed that obesity-associated non-alcoholic fatty liver disease (NAFLD) is linked to changes in intestinal permeability and translocation of bacterial products to the liver. Hitherto, no reliable therapy is available except for weight reduction. Within this study, we examined the possible effect of the probiotic bacterial strain Lactobacillus rhamnosus GG (LGG) as protective agent against experimental NAFLD in a mouse model. Methods Experimental NAFLD was induced by a high-fructose diet over eight weeks in C57BL/J6 mice. Fructose was administered via the drinking water containing 30% fructose with or without LGG at a concentration resulting in approximately 5×107 colony forming units/g body weight. Mice were examined for changes in small intestinal microbiota, gut barrier function, lipopolysaccharide (LPS) concentrations in the portal vein, liver inflammation and fat accumulation in the liver. Results LGG increased beneficial bacteria in the distal small intestine. Moreover, LGG reduced duodenal IκB protein levels and restored the duodenal tight junction protein concentration. Portal LPS (P≤0.05) was reduced and tended to attenuate TNF-α, IL-8R and IL-1β mRNA expression in the liver feeding a high-fructose diet supplemented with LGG. Furthermore liver fat accumulation and portal alanine-aminotransferase concentrations (P≤0.05) were attenuated in mice fed the high-fructose diet and LGG. Conclusions We show for the first time that LGG protects mice from NAFLD induced by a high-fructose diet. The underlying mechanisms of protection likely involve an increase of beneficial bacteria, restoration of gut barrier function and subsequent attenuation of liver inflammation and steatosis.
Child Abuse Experiences and Perceived Need for Care and Mental Health Service Use among Members of the Canadian Armed Forces

Objective: Child abuse is associated with poor mental health outcomes in adulthood. However, little is known about how a history of child abuse may be related to perceived need for care (PNC) and mental health service use (MHSU) among Canadian military personnel. The objectives of this study were to determine 1) the relationship between child abuse history and PNC and 2) the relationship between child abuse history and MHSU in the Canadian military. Method: Data were drawn from the 2013 Canadian Forces Mental Health Survey (n = 6692 Regular Force personnel between the ages of 18 and 60 years). Logistic regression was used to examine the relationships between individual child abuse types and PNC and MHSU while adjusting for sociodemographic variables, the presence of mental disorders, deployment-related variables, and other types of child abuse. Population attributable fractions (PAFs) were calculated to estimate the proportion of PNC and MHSU that may be attributable to child abuse. Results: Each individual child abuse type was associated with increased odds of PNC and MHSU after adjusting for all covariates (adjusted odds ratio ranging from 1.26 to 1.80). PAFs showed that if any child abuse did not occur, PNC and MHSU among Regular Force personnel may be reduced by approximately 14.3% and 11.3%, respectively. Conclusions: This study highlights that preenlistment factors, such as a history of child abuse, have an independent association with PNC and MHSU and hence need to be considered when assessing the mental health service needs of the Canadian Regular Force personnel.
Effect of Mold Temperature on Morphology and Mechanical Properties of Injection Molded HDPE Structural Foams

In this study, HDPE structural foams are produced by injection molding under different mold temperatures to study the effect of this variable on average cell dimension, cell density, and skin thickness ratio. Samples are also produced by setting independently the temperature of the fixed and moving plate of the mold to detect the sensitivity of foam structure to a temperature gradient in processing. The resulting foams are also characterized in terms of mechanical properties including impact and flexural tests. It has been found that for homogeneous mold temperatures, symmetrical skin thicknesses are obtained, which increase with decreasing mold temperature. On the other hand, by keeping one mold face at a constant temperature and varying the second one, asymmetric skin thicknesses are obtained. The degree of asymmetry is found to increase as the temperature difference between both molds increased. Furthermore, decreasing mold temperature produces a small increase in average cell sizes and reduced cell density. In general, both impact strength and flexural moduli of the structural foams increase with increasing skin thickness. For the particular case of asymmetric foams, the flexural moduli are slightly higher when the load is applied on the thicker skin; while much higher impact strength is obtained when the falling weight strikes the samples on the face having the smaller skin thickness.
Effect ofFecBGene on Body Weight in Black Bengal Goat

FecB gene is first described gene which has been found to increase ovulation rate and litter size in sheep. But, work related to genetic mechanism and genetic markers for caprine proliferation has not been done so much. The present study was aimed to screen Black Bengal goat population for polymorphism of FecB gene and to study its effect on body weight at different growth stages. DNA samples from 96 animals were isolated and subjected to PCR. Amplified fragments obtained were allowed for polyacrylamide gel electrophoresis for the detection of single strand conformational polymorphism (SSCP) variants. Among all samples, three different SSCP variants were found which were marked as AA, AB and BB. The highest genotype frequency was observed for AB (0.38), which was followed by BB (0.33) and AA (0.29). Least-square analysis of variance showed significant (P<0.01) effect of genotype on body weight at birth only. The least square mean of body weights at birth for genotype BB (01.17±00.03 kg) was significantly lower than that of genotype AA (01.43±00.03 kg) and genotype AB (01.36±00.02 kg). It was also observed that genotype had non-significant effect on body weight at 4-week, 8-week, 12-week, 24-week, 36-week and 48-week of age. These results indicate that effect of FecB on body weight was limited at birth only. No significant effects were found on growth rate at later stage of life. FecB gene was hitherto linked to prolificacy. So, the effect of FecB gene on other traits has important bearing if the research is continued further with more number of species specific primers at other loci.
Bions: A Family of Biomimetic Mineralo-Organic Complexes Derived from Biological Fluids

Mineralo-organic nanoparticles form spontaneously in human body fluids when the concentrations of calcium and phosphate ions exceed saturation. We have shown previously that these mineralo-organic nanoparticles possess biomimetic properties and can reproduce the whole phenomenology of the so-called nanobacteria—mineralized entities initially described as the smallest microorganisms on earth. Here, we examine the possibility that various charged elements and ions may form mineral nanoparticles with similar properties in biological fluids. Remarkably, all the elements tested, including sodium, magnesium, aluminum, calcium, manganese, iron, cobalt, nickel, copper, zinc, strontium, and barium form mineralo-organic particles with bacteria-like morphologies and other complex shapes following precipitation with phosphate in body fluids. Upon formation, these mineralo-organic particles, which we term bions, invariably accumulate carbonate apatite during incubation in biological fluids; yet, the particles also incorporate additional elements and thus reflect the ionic milieu in which they form. Bions initially harbor an amorphous mineral phase that gradually converts to crystals in culture. Our results show that serum produces a dual inhibition-seeding effect on bion formation. Using a comprehensive proteomic analysis, we identify a wide range of proteins that bind to these mineral particles during incubation in medium containing serum. The two main binding proteins identified, albumin and fetuin-A, act as both inhibitors and seeders of bions in culture. Notably, bions possess several biomimetic properties, including the possibility to increase in size and number and to be sub-cultured in fresh culture medium. Based on these results, we propose that bions represent biological, mineralo-organic particles that may form in the body under both physiological and pathological homeostasis conditions. These mineralo-organic particles may be part of a physiological cycle that regulates the function, transport and disposal of elements and minerals in the human body.
SPECIATION OF J UNIPERUS CEDRUS AND J. MADERENSIS IN THE ARCHIPELAGOS OF CANARIES AND MADEIRA BASED ON TERPENOIDS AND nrDNA AND petN-psbM SEQUENCES.

Analyses of nrDNA and petN-PsbM sequence data, combined with leaf terpenes data, revealed that putative J. cedrus from Madeira is as distinct from J. cedrus of the Canary Islands as it is from J. oxycedrus. These data support the recognition of the Madeira juniper at the specific level, J. maderensis (Menezes) R. P. Adams comb. et stat. nov. Phytologia 92(1): 44-55 (April, 2010).
A C-terminal “Tail” Region in the Rous Sarcoma Virus Integrase Provides High Plasticity of Functional Integrase Oligomerization during Intasome Assembly*

The retrovirus integrase (IN) inserts the viral cDNA into the host DNA genome. Atomic structures of five different retrovirus INs complexed with their respective viral DNA or branched viral/target DNA substrates have indicated these intasomes are composed of IN subunits ranging from tetramers, to octamers, or to hexadecamers. IN precursors are monomers, dimers, or tetramers in solution. But how intasome assembly is controlled remains unclear. Therefore, we sought to unravel the functional mechanisms in different intasomes. We produced kinetically stabilized Rous sarcoma virus (RSV) intasomes with human immunodeficiency virus type 1 strand transfer inhibitors that interact simultaneously with IN and viral DNA within intasomes. We examined the ability of RSV IN dimers to assemble two viral DNA molecules into intasomes containing IN tetramers in contrast to one possessing IN octamers. We observed that the last 18 residues of the C terminus (“tail” region) of IN (residues 1–286) determined whether an IN tetramer or octamer assembled with viral DNA. A series of truncations of the tail region indicated that these 18 residues are critical for the assembly of an intasome containing IN octamers but not for an intasome containing IN tetramers. The C-terminally truncated IN (residues 1–269) produced an intasome that contained tetramers but failed to produce an intasome with octamers. Both intasomes have similar catalytic activities. The results suggest a high degree of plasticity for functional multimerization and reveal a critical role of the C-terminal tail region of IN in higher order oligomerization of intasomes, potentially informing future strategies to prevent retroviral integration.
Similarity estimation techniques from rounding algorithms

(MATH) A locality sensitive hashing scheme is a distribution on a family $\F$ of hash functions operating on a collection of objects, such that for two objects <i>x,y</i>, <b>Pr</b><sub><i>h</i></sub>εF[<i>h</i>(<i>x</i>) = <i>h</i>(<i>y</i>)] = sim(<i>x,y</i>), where <i>sim</i>(<i>x,y</i>) ε [0,1] is some similarity function defined on the collection of objects. Such a scheme leads to a compact representation of objects so that similarity of objects can be estimated from their compact sketches, and also leads to efficient algorithms for approximate nearest neighbor search and clustering. Min-wise independent permutations provide an elegant construction of such a locality sensitive hashing scheme for a collection of subsets with the set similarity measure <i>sim</i>(<i>A,B</i>) = \frac{|A &Pgr; B|}{|A &Pgr B|}. (MATH) We show that rounding algorithms for LPs and SDPs used in the context of approximation algorithms can be viewed as locality sensitive hashing schemes for several interesting collections of objects. Based on this insight, we construct new locality sensitive hashing schemes for:<ol><li>A collection of vectors with the distance between → \over <i>u</i> and → \over <i>v</i> measured by Ø(→ \over <i>u</i>, → \over <i>v</i>)/π, where Ø(→ \over <i>u</i>, → \over <i>v</i>) is the angle between → \over <i>u</i>) and → \over <i>v</i>). This yields a sketching scheme for estimating the cosine similarity measure between two vectors, as well as a simple alternative to minwise independent permutations for estimating set similarity. </li><li>A collection of distributions on <i>n</i> points in a metric space, with distance between distributions measured by the Earth Mover Distance (<b>EMD</b>), (a popular distance measure in graphics and vision). Our hash functions map distributions to points in the metric space such that, for distributions <i>P</i> and <i>Q</i>, <b>EMD</b>(<i>P,Q</i>) &xie; <b>E</b><sub>hε\F</sub> [<i>d</i>(<i>h</i>(<i>P</i>),<i>h</i>(<i>Q</i>))] &xie; <i>O</i>(log <i>n</i> log log <i>n</i>). <b>EMD</b>(<i>P, Q</i>). </li></ol>.