Miracle-dz/UniFAR-FTUs huggingface dataset:
A Causal Entropy Bound

The identiﬁcation of a causal-connection scale motivates us to propose a new covariant bound on entropy within a generic space-like region. This “causal entropy bound”, scaling as √ EV , and thus lying around the geometric mean of Bekenstein’s S/ER and holographic S/A bounds, is checked in various “critical” situations. In the case of limited gravity, Bekenstein’s bound is the strongest while naive holography is the weakest. In the case of strong gravity, our bound and Bousso’s holographic bound are stronger than Bekenstein’s, while naive holography is too tight, and hence typically wrong.
Improved detection of Zika virus RNA in human and animal specimens by a novel, highly sensitive and specific real‐time RT‐PCR assay targeting the 5′‐untranslated region of Zika virus

We developed and evaluated five novel real‐time RT‐PCR assays targeting conserved regions in the 5′‐untranslated region (5′‐UTR), envelope (E'), non‐structural protein 2A (NS2A), NS5 and 3′‐UTR of the ZIKV genome.
The Influence of Experimental Parameters and Specimen Geometry on the Mass Spectra of Copper During Pulsed-Laser Atom-Probe Tomography

Abstract We have studied the influence of experimental factors and specimen geometry on the quality of the mass spectra in copper (Cu) during pulsed-laser atom-probe tomography. We have evaluated the effects of laser pulse energy, laser pulse frequency, specimen base temperature, specimen tip radius, and specimen tip shank half-angle on the effects of mass resolving power, (m/Δm), at full-width at half-maximum and at full-width at tenth-maximum, the tail size after the major mass-to-charge state (m/n) ratio peaks, and the mass spectra. Our results indicate that mass resolving power improves with decreasing pulse energy between 40 and 80 pJ and decreasing base temperature between 20 and 80 K. The mass resolving power also improves with increasing tip radius and shank half-angle. A pulse frequency of 250 kHz slightly improves the mass resolving power relative to 100 or 500 kHz. The tail size decreases with increasing pulse energy. The mass resolving power improves when the cooling time is reduced, which is influenced by the thermal diffusivity of Cu and the specimen base temperature.
Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement.

BACKGROUND AND AIMS The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250-300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. METHODS Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. KEY RESULTS Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. CONCLUSIONS On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and Trimelopter. Each of these has a particular syndrome of morphological characters. As a result, 105 new combinations are made and two new names are proposed to accommodate the taxa studied in the new arrangement. A short morphological diagnosis, synonymy, details of distribution and an identification key are presented.
Lobe-generating centres in the simple leaves of Myriophyllum aquaticum: evidence for KN1-like activity.

BACKGROUND AND AIMS The mature morphology of most plants can usually be said to consist of three mutually exclusive organs: leaves, stems, and roots. The vast majority of mature morphologies may be easily grouped into one of these mutually exclusive categories. However, during very early stages of development and in many instances from inception, the division between organ categories becomes fuzzy due to the overlap in developmental processes that are shared between the aforementioned mutually exclusive categories. One such overlap has been described at the gene level where KNOXI homologues, transcription factors responsible for maintaining indeterminate cell fate, are expressed in the shoot apical meristem and during early stages of compound leaf development. This study characterizes the occurrence and spatial localization of mRNA of a KNOXI homologue, MaKN1, during the early stages of development in the simple leaves of Myriophyllum aquaticum, an aquatic angiosperm from the family Haloragaceae exhibiting pentamerous whorls of finely lobed leaves. METHODS A 300-bp KNOXI fragment was sequenced from M. aquaticum and used in an RNA localization study to determine the temporal and spatial expression of KNOXI during the early stages of leaf lobe development in M. aquaticum. The developmental sequence of leaves of M. aquaticum was also described using scanning electron microscopy. KEY RESULTS Lobe development of M. aquaticum occurs in two very distinct regions at the leaf base in an alternating fashion reminiscent of a distichous shoot system. It was discovered that MaKN1 expression is localized to both the shoot apical meristem and early stages of leaf primordia development (P1-P7). Initially, MaKN1 is expressed ubiquitously throughout primordia (P1-P3); however, as lobes develop, MaKN1 becomes localized to recently emerged lobe primordia, and disappears as lobes develop basipetally. CONCLUSIONS The pattern of gene expression is indicative of shared developmental processes during early development between shoots, compound leaves, highly lobed simple leaves and unifoliate simple leaves which lack KNOXI expression. These findings are supportive of Arber's less rigid 'partial shoot' theory, which conceptualizes compound leaves as having shoot-like elements.
Effect of cotrimoxazole prophylaxis on malaria occurrence among HIV‐infected adults in West Africa: the MALHIV Study

Cotrimoxazole (CTX) should be given to all HIV‐infected adults with mild or severe HIV‐disease or those with CD4 counts below 350/mm3 according to 2006 WHO guidelines. We assessed the impact of CTX prophylaxis on the risk of malaria episodes in HIV‐1‐infected adults from four West African countries with different patterns of malaria transmission.
Tests for inbreeding and outbreeding depression and estimation of population differentiation in the bird-pollinated shrub Grevillea mucronulata.

BACKGROUND AND AIMS Plants show patterns of spatial genetic differentiation reflecting gene flow mediated by pollen and seed dispersal and genotype × environment interactions. If patterns of genetic structure are determined largely by gene flow then they may be useful in predicting the likelihood of inbreeding or outbreeding depression but should be less useful if there is strong site-specific selection. For many Australian plants little is known about either their population genetics or the effects on mating systems of variation in pollen transfer distances. Experimental pollinations were used to compare the reproductive success of bird-adapted Grevillea mucronulata plants mated with individuals from a range of spatial scales. A hierarchical survey of microsatellite DNA variation was also conducted to describe the scale of population differentiation for neutral markers. METHODS The effects of four pollen treatments on reproductive performance were compared. These treatments were characterized by transfer of pollen from (a) neighbouring adults; (b) an adjacent cluster of adults (30-50 m distant); (c) a distant cluster (>5 km distant); and (d) open pollination. Sets of 17·9 ± 3·3 leaves from each of 15 clusters of plants were genotyped and spatial autocorrelation and F statistics were used to describe patterns of genetic structure. KEY RESULTS Grevillea mucronulata displayed evidence of both inbreeding and outbreeding depression, with 'intermediate' pollen producing consistently superior outcomes for most aspects of fitness including seed set, seed size, germination and seedling growth. Significant genotypic structuring was detected within clusters (spatial autocorrelation) and among adjacent clusters and clusters separated by >5 km distance (F(ST) = 0·07 and 0·10). CONCLUSIONS The superior outcome of intermediate pollen transfer and genetic differentiation of adjacent clusters suggests that G. mucronulata selection disfavours matings among closely and distantly related neighbours. Moreover, the performance of open-pollinated seedlings was poor, implying that current mating patterns are suboptimal.
Evaluation of the Pharmacokinetics of Two Recombinant Human Erythropoietin Preparations: Epoetin Zeta and Epoetin Alfa

Abstract The pharmacokinetic properties of a new recombinant erythropoietin preparation (epoetin zeta, CAS 604802-70-2) compared to a reference product (epoetin alfa, CAS 113427-24-0) were analyzed after a single intravenous bolus injection of 10,000 IU in a two-period crossover design in 24 healthy volunteers. Peripheral venous blood samples were obtained pre-dose, and 0:05, 0:20, 0:40, 1:00, 1:20, 1:40, 2:00, 3:00, 4:00, 6:00, 8:00, 12:00, 24:00, 36:00, 48:00, and 72:00 hours post dosing. Samples of 24 volunteers were analyzed by means of a specific immunoassay (ELISA). Three volunteers were excluded from statistical analysis due to a paravasal injection in one of both study periods with resulting low plasma levels of epoetin. Comparison of both preparations showed nearly identical pharmacokinetic properties after intravenous administration. The usual bioequivalence limits were fulfilled for all relevant pharmacokinetic parameters.
Effects of Oral Supplementation with Iron (III) Hydroxide Polymaltose Complex on the Hematological Profile of Adolescents with Varying Iron Status

Abstract Objective: To assess the effects of supplementation with oral iron(III) hydroxide polymaltose complex on the iron status of adolescents with and without iron deficiency and anemia. Method: Adolescents of both sexes with varying iron status were allocated to four treatment groups by using inclusion criteria. Three of the four groups received iron(III) hydroxide polymaltose complex (IPC, Maltofer®) containing100 mg of iron 6 days a week for 8 months. The fourth group was given a placebo. Hematological parameters were assessed at the baseline and after 4 and 8 months of supplementation. Results: IPC supplementation resulted in a significant increase in iron parameters in all the three supplemented groups including correction of iron deficiency and anemia along with improvement in storage iron after 8 months. No side effects were noted in any of the supplemented subjects. Conclusions: IPC supplementation im proved the iron status of adolescents with and without iron deficiency and anemia. These data provide evidence that IPC is an easy-to-administer and well tolerated compound which can improve and normalize the iron status of iron deficient and anemic patients.
Astrocytes facilitate melanoma brain metastasis via secretion of IL‐23

Melanoma is the leading cause of skin cancer mortality. The major cause of melanoma mortality is metastasis to distant organs, frequently to the brain. The microenvironment plays a critical role in tumourigenesis and metastasis. In order to treat or prevent metastasis, the interactions of disseminated tumour cells with the microenvironment at the metastatic organ have to be elucidated. However, the role of brain stromal cells in facilitating metastatic growth is poorly understood. Astrocytes are glial cells that function in repair and scarring of the brain following injury, in part via mediating neuroinflammation, but the role of astrocytes in melanoma brain metastasis is largely unresolved. Here we show that astrocytes can be reprogrammed by human brain‐metastasizing melanoma cells to express pro‐inflammatory factors, including the cytokine IL‐23, which was highly expressed by metastases‐associated astrocytes in vivo. Moreover, we show that the interactions between astrocytes and melanoma cells are reciprocal: paracrine signalling from astrocytes up‐regulates the secretion of the matrix metalloproteinase MMP2 and enhances the invasiveness of brain‐metastasizing melanoma cells. IL‐23 was sufficient to increase melanoma cell invasion, and neutralizing antibodies to IL‐23 could block this enhanced migration, implying a functional role for astrocyte‐derived IL‐23 in facilitating the progression of melanoma brain metastasis. Knocking down the expression of MMP2 in melanoma cells resulted in inhibition of IL‐23‐induced invasiveness. Thus, our study demonstrates that bidirectional signalling between melanoma cells and astrocytes results in the formation of a pro‐inflammatory milieu in the brain, and in functional enhancement of the metastatic potential of disseminated melanoma cells. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Functional Analysis of the Chloroplast Division Complex Using Schizosaccharomyces pombe as a Heterologous Expression System

Abstract Chloroplast division is driven by a macromolecular complex that assembles at the midplastid. The FtsZ ring (Z ring) is the central structure in this complex, and is composed of the functionally distinct cytoskeletal proteins FtsZ1 and FtsZ2. Recent studies in the heterologous Schizosaccharomyces pombe system showed that Arabidopsis FtsZ1 and FtsZ2 filaments have distinct assembly and turnover characteristics. To further analyze these FtsZs, we employed this system to compare the assembly and dynamic properties of FtsZ1 and FtsZ2 lacking their N- and/or C-termini with those of their full-length counterparts. Our data provide evidence that the N-terminus of FtsZ2 is critical for its structural dominance over FtsZ1, and that the N- and C-termini promote polymer bundling and turnover of both FtsZs and contribute to their distinct behaviors. We also assessed how ARC6 affects FtsZ2 filament dynamics, and found that it interacts with and stabilizes FtsZ2 filaments in S. pombe independent of its presumed Z-ring tethering function in planta. Finally, we generated FtsZ1-FtsZ2 coexpression constructs to facilitate reconstitution of more complex interaction networks. Our experiments yield new insight into factors influencing FtsZ behavior and highlight the utility of S. pombe for analyzing chloroplast FtsZs and their assembly regulators.
Reply: Prophylactic variceal ligation is not recommended for patients awaiting live donor liver transplant

We thank Wai and colleagues for their comment on our article. Their experience is consistent with ours and different from that reported by Jutabha et al. In all 3 studies, the patients were liver transplant candidates and thus constituted a particular subgroup of patients with cirrhosis, as underlined also by Boyer. In our opinion, this favors the use of beta-blockers instead of banding for primary prophylaxis for at least 2 reasons. The first, as underlined by Wai et al., is the short follow-up before liver transplantation. In fact, as shown in Fig. 2 of our study, patients treated by ligation can bleed during treatment but not after variceal eradication unless varices recur. In contrast, patients taking beta-blockers present the same risk of bleeding over the same time period. As a result, a possible advantage of banding can be seen only after a long follow-up, which is unlikely in patients awaiting liver transplant as usually this occurs within 1 year. The other reason is that this group of patients is followed up intensively, and this may increase compliance to therapy. The use of beta-blockers does require dose adjustment and trying to maximize the dose tolerated by the patient. The 2 bleeding episodes from postbanding ulcers reported by Wai et al. are added to several others that have taken place during prophylactic treatment, including 2 events described in our study. Globally, the reported cases number at least 15, some of which have been fatal. In contrast, beta-blockers for primary prophylaxis of variceal bleeding have not caused fatalities thus far. It is difficult to predict which patients are at risk for postbanding ulcer bleeding. Our patients bled 9 and 11 days after the first banding session, respectively. One was Child B7, and the other was Child C14. The patients treated by Wai et al. bled 8 and 9 days after the second prophylactic ligation. Shepke et al. reported 5 (7%) bleeding episodes from postbanding ulcers, 2 of them fatal. The latter happened 3 and 12 days after the first banding session, respectively. Triantos et al., treating patients unable to take betablockers, reported 3 cases of variceal bleeding, all between the first and second prophylactic banding sessions. As most bleeding occurs after the first banding session, we think that longer intervals between sessions, advocated by some authors to overcome this problem, would not reduce this risk. In addition and not to be discounted, we found that the costs are reduced to a third when beta-blockers are used with respect to banding for primary prophylaxis in these patients. Thus, nonselective beta-blockers remain the therapy of first choice for primary prophylaxis in liver transplant candidates.
Loss of keratin 19 favours the development of cholestatic liver disease through decreased ductular reaction

Keratins (K) are cytoprotective proteins and keratin mutations predispose to the development of multiple human diseases. K19 represents the most widely used marker of biliary and hepatic progenitor cells as well as a marker of ductular reaction that constitutes the basic regenerative response to chronic liver injury. In the present study, we investigated the role of K19 in biliary and hepatic progenitor cells and its importance for ductular reaction. K19 wild‐type (WT) and knockout (KO) mice were fed: (a) 3,5‐diethoxycarbonyl‐1,4‐dihydrocollidine (DDC); (b) cholic acid (CA); (c) a choline‐deficient, ethionine‐supplemented (CDE) diet; or (d) were subjected to common bile duct ligation (CBDL). The bile composition, liver damage, bile duct proliferation, oval cell content and biliary fibrosis were analysed. In untreated animals, loss of K19 led to redistribution of the K network in biliary epithelial cells (BECs) but to no obvious biliary phenotype. After DDC feeding, K19 KO mice exhibited (compared to WTs): (a) increased cholestasis; (b) less pronounced ductular reaction with reduced ductular proliferation and fewer oval cells; (c) impaired Notch 2 signalling in BECs; (d) lower biliary fibrosis score and biliary bicarbonate concentration. An attenuated oval cell proliferation in K19 KOs was also found after feeding with the CDE diet. K19 KOs subjected to CBDL displayed lower BEC proliferation, oval cell content and less prominent Notch 2 signal. K19 deficiency did not change the extent of CA‐ or CBDL‐induced liver injury and fibrosis. Our results demonstrate that K19 plays an important role in the ductular reaction and might be of importance in multiple chronic liver disorders that frequently display a ductular reaction. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Modeling of Infrared–Visible Sum Frequency Generation Microscopy Images of a Giant Liposome

Abstract The article explores the theory of infrared–visible sum frequency generation microscopy of phospholipid envelopes with dimensions larger than the wavelength of the nonlinear emission. The main part of the study concerns derivation and accounting for the contributions of effective nonlinear responses specific to sites on the surfaces of a bilayer envelope and their dependence on polarization condition and experimental geometry. The nonlinear responses of sites are mapped onto the image plane according to their emission directions and the numerical aperture of a sampling microscope objective. According to the simulation results, we discuss possible approaches to characterize the shape of the envelope, to extract molecular hyperpolarizabilities, and to anticipate possible heterogeneity in envelope composition and anisotropy of the environment proximal to the envelope. The modeling approach offers a promising analytic facility to assist connecting microscopy observations in engineered liposomes, cellular envelopes, and subcellular organelles of relatively large dimensions to molecular properties, and hence to chemistry and structure down to available spatial resolution.
Pancreatic pathophysiology in cystic fibrosis

The pancreas is one of the earliest, and most commonly affected, organs in patients with cystic fibrosis (CF). Studying the pathogenesis of pancreatic disease is limited in CF patients, due to its early clinical onset, co‐morbidities and lack of tissue samples from the early phases of disease. In recent years, several new CF animal models have been developed that have advanced our understanding of both CF exocrine and endocrine pancreatic disease. Additionally, these models have helped us to better define the influence of pancreatic lesions on CF disease progression in other organs, such as the gastrointestinal tract and lung. Copyright Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.