Miracle-dz/UniFAR-FTUs huggingface dataset:
Community structure (niche limitation and guild proportionality) in relation to the effect of spatial scale, in a Nothofagus forest sampled with a circular transect

A Nothofagus-dominated rainforest in eastern Fiordland, New Zealand, was sampled by shoot frequency in contiguous 1 x 1 m quadrats, along a topologically-circular transect. The data were analysed at five scales up to 5 x 1 m, to search for assembly rules, i.e., generalised restrictions on species cooccurrences. There was no evidence of niche limitation in terms of the whole community, at any scale examined. Rather, variance in species richness was greater than expected from a null model, suggesting environmental heterogeneity. This conclusion was confirmed by using a patch-model. Guild structure was examined in terms of synusiae, based on vertical stratification. The proportion of species in a quadrat that were from the Herb guild was significantly more constant than expected under the null model. However, using a patch-model this effect was reduced, and no longer significant. This suggests pools of species adapted to different micro-environments, but with parallel guild composition. Liane guild proportions were more variable than predicted by the null model; although this effect was not significant, it parallels reports from other South Island forests. The work confirms conclusions from previous work, that plant assembly rules are to be found only at small spatial scales. Processes leading to high and low variance in species richness and in guild proportions are discussed. Selection of a uniform site in the present work, and use of a patch-model, make it less likely that effects are due to environmental or historical effects. The use of guild proportionality as the criterion eliminates the effect of limitation on the number of individuals that can cooccur locally.
Prognostic impact of cytogenetic and interphase fluorescence in situ hybridization‐defined chromosome 13 deletion in multiple myeloma: early results of total therapy II

Summary. Cytogenetic abnormalities of chromosome 13 (CA 13) and those detected by fluorescence in situ hybridization (FISH 13) have both been associated with poor prognosis in multiple myeloma (MM) patients. The prognostic implications of CA, FISH 13 and other standard laboratory parameters were examined in the first 231 patients enrolled in Total Therapy II, an intensive cytotoxic chemotherapy programme with tandem autotransplants. Three‐year projections of event‐free survival (EFS) and overall survival (OS) were 71% and 77% respectively. CA 13 was detected in 14% and significantly correlated with FISH 13 (present in 51%), tumour burden, proliferative activity and lactic dehydrogenase (LDH). Both EFS and OS were significantly shorter in patients with CA 13, FISH 13, LDH ≥ 190 U/l, β2 microglobulin ≥ 4 mg/l and C reactive protein ≥ 4·0 mg/l; other CA was an additional risk factor for OS. Two‐thirds of CA 13 patients were identified by FISH 13 and plasma‐cell‐labelling index (PCLI) ≥ 0·4%; however, PCLI failed to identify additional risk groups in FISH subsets. Although present in considerably fewer patients, CA 13 imparted more rapid relapse (61% at 3 years) and death (43% at 3 years) than FISH 13 (38% and 35%; P = 0·02 and 0·1 respectively) and should be part of the initial work‐up of patients with MM.
The Src Family Kinase Hck Interacts with Bcr-Abl by a Kinase-independent Mechanism and Phosphorylates the Grb2-binding Site of Bcr*

bcr-abl, the oncogene causing chronic myeloid leukemia, encodes a fusion protein with constitutively active tyrosine kinase and transforming capacity in hematopoietic cells. Various intracellular signaling intermediates become activated and/or associate by/with Bcr-Abl, including the Src family kinase Hck. To elucidate some of the structural requirements and functional consequences of the association of Bcr-Abl with Hck, their interaction was investigated in transiently transfected COS7 cells. Neither the complex formation of Hck kinase with Bcr-Abl nor the activation of Hck by Bcr-Abl was dependent on the Abl kinase activity. Both inactivating point mutations of Hck and dephosphorylation of Hck enhanced its complex formation with Bcr-Abl, indicating that their physical interaction was negatively regulated by Hck (auto)phosphorylation. Finally, experiments with a series of kinase negative Bcr-Abl mutants showed that Hck phosphorylated Bcr-Abl and induced the binding of Grb2 to Tyr177 of Bcr-Abl. Taken together, our results suggest that Bcr-Abl preferentially binds inactive forms of Hck by an Abl kinase-independent mechanism. This physical interaction stimulates the Hck tyrosine kinase, which may then phosphorylate the Grb2-binding site in Bcr-Abl.
Activation of the Low Molecular Weight Protein Tyrosine Phosphatase in Keratinocytes Exposed to Hyperosmotic Stress

Herein, we provide new contribution to the mechanisms involved in keratinocytes response to hyperosmotic shock showing, for the first time, the participation of Low Molecular Weight Protein Tyrosine Phosphatase (LMWPTP) activity in this event. We reported that sorbitol-induced osmotic stress mediates alterations in the phosphorylation of pivotal cytoskeletal proteins, particularly Src and cofilin. Furthermore, an increase in the expression of the phosphorylated form of LMWPTP, which was followed by an augment in its catalytic activity, was observed. Of particular importance, these responses occurred in an intracellular milieu characterized by elevated levels of reduced glutathione (GSH) and increased expression of the antioxidant enzymes glutathione peroxidase and glutathione reductase. Altogether, our results suggest that hyperosmostic stress provides a favorable cellular environment to the activation of LMWPTP, which is associated with increased expression of antioxidant enzymes, high levels of GSH and inhibition of Src kinase. Finally, the real contribution of LMWPTP in the hyperosmotic stress response of keratinocytes was demonstrated through analysis of the effects of ACP1 gene knockdown in stressed and non-stressed cells. LMWPTP knockdown attenuates the effects of sorbitol induced-stress in HaCaT cells, mainly in the status of Src kinase, Rac and STAT5 phosphorylation and activity. These results describe for the first time the participation of LMWPTP in the dynamics of cytoskeleton rearrangement during exposure of human keratinocytes to hyperosmotic shock, which may contribute to cell death.
Measuring temporal compositions of urban morphology through spectral mixture analysis: toward a soft approach to change analysis in crowded cities

This paper reports on preliminary results from a study applying the technique of spectral mixture analysis (SMA) to the measurement of temporal changes in the composition of urban morphology in the metropolitan area of Greater Cairo, Egypt, between 1987 and 1998. Although several remote sensing techniques have been used successfully for urban change analysis, most of these focus on change ‘between’ classes measured in a discrete, crisp way through which each pixel is assigned to a label indicating either a change or no change in the class to which the pixel originally belonged. In many major cities, such as Cairo, change also occurs within classes (e.g. vertical growth of buildings, increase in housing density, decrease in open spaces) and is reflected by an aggregation of land cover and urban materials. None of these materials may seem important in isolation. Rather, the significance of these urban land covers arises from the way they interweave with each other to structure the morphology of the urban place. In this paper, a ‘soft’ approach is presented to identify and measure the composition of changing morphology from multi‐temporal, multi‐spectral satellite images. SMA is demonstrated to be capable of deriving spatially continuous variables quantified at the sub‐pixel level. These variables represent measures that can be compared across urban places and at different time periods. They can be integrated readily into a wide range of applications and models concerned with physical, economic and/or socio‐demographic phenomena in the city.
Development and Stem Cells Research Article

INTRODUCTION Many tissues and organs contain self-renewing stem cell populations that are crucial for their maintenance. Improper control of stem and progenitor cell populations may underlie tissue degeneration and cancer. Two general mechanisms for stem cell renewal by cell proliferation are: (1) strict asymmetric divisions, in which one cell retains stem cell fate while the other cell or its progeny differentiate; and (2) renewal at the population level, whereby the sum total of asymmetric and/or symmetric divisions (symmetric in the sense that a cell division yields two stem or two non-stem cells) maintains the population. Two additional, not necessarily mutually exclusive, mechanisms of renewal are dedifferentiation and renewal by facultative division of Often, stem cells are associated with an anatomically distinct niche. The niche communicates with stem cells via cell-cell signaling to direct stem cell fate, survival and proliferation potential (see Drummond-Barbosa, 2008; Voog and Jones, 2010). Arduous cell-autonomy and lineage-tracing studies are required to rigorously define renewal mechanisms. Ideally, lineally labeled cells are followed with non-invasive long-term imaging in both wild-type and informative mutant cell contexts. However, even when lineage information is available, the influence of anatomical constraints is difficult to assess in conjunction with signaling and cell division. Although lineage tracing is not currently feasible for many tissue types, anatomical, molecular and cell cycle information from static samples is often available. We reasoned
Plant species composition

The aim of the study was to assess plant species composition and its relation with soil seed bank as a basis for forest restoration through natural regeneration in Zaraninge and Mbwebwe coastal forests, Bagamoyo District Tanzania. Eighteen sample plots of size 0.07 ha were established systematically along transect in each of the two forests. Soil samples were collected within each plot at 0-10cm, 10-20cm and 20-30cm depths. The analysis was based on IVI computed from the average of relative basal area, density and frequency. Soil samples were analyzed for seed density of different plant species at the different depths. 62 and 50 plant species were identified in Zaraninge and Mbwebwe forests respectively. Out of 62 vascular plants identified in Zaraninge three species were rare plants, 35 common species and seven endemic to coastal forests. Mbwebwe forest had three rare plants, 26 common species and five endemic to coastal forests. The Shannon-Winner and Simpson Diversity Indices were 2.843, 0.093 and 2.5, 0.12 for Zaraninge and Mbwebwe forests respectively showing that the forests have high species diversity.
Synthesis of fatty acid ethyl esters in mammalian tissues after ethanol exposure: a systematic review of the literature

Abstract The ability to undergo non-oxidative metabolism from ethanol to fatty acid ethyl esters (FAEEs) varies greatly among tissues and organs. To gain a greater understanding of non-oxidative ethanol metabolism to FAEE, we aimed to collect all published data on FAEE synthesis in mammalian organs and tissues to identify all tissues, organs, and enzymes that are known to, or likely possess FAEE-synthetic activity. A systematic search for relevant papers was performed and two independent reviewers examined potentially relevant abstracts (articles on FAEEs that pertain to ethanol exposure) to determine whether they met the inclusion criteria. Information on FAEE synthesis was retrieved from papers meeting the inclusion/exclusion criteria and summarized by organ/tissue/matrix examined. The systematic search through four databases yielded 78 articles that investigated FAEE synthesis by tissues, tissue fractions and cell lines, and 29 articles that attempted to purify and/or characterize the enzymes involved in FAEE synthesis. Two enzyme activities have been studied: FAEE synthase (FAEES, which conjugates ethanol and free fatty acid) and acyl-CoA: ethanol O-acyltransferase (AEAT, which conjugates ethanol and fatty acyl-CoA). Both activities are expressed by a variety of different enzymes. FAEES activity is the most widely studied and has been purified from several tissues and shown to be associated with several well-known enzymes, while the identity of enzymes possessing AEAT activity remains unknown. The organs and tissues that have been shown to synthesize FAEEs are discussed, with special emphasis on the studies that attempted to elucidate the enzymology of FAEE synthesis in those tissues.
Concentration dependence of vibrational properties of bioprotectant/water mixtures by inelastic neutron scattering

Neutron scattering has been demonstrated to be a powerful tool for characterizing the structure and dynamics of biological molecules and for investigating the physical and chemical mechanisms of biophysical processes. The aim of the present work is to investigate by inelastic neutron scattering (INS) the vibrational behaviour of a class of bioprotectant systems, such as homologous disaccharides, trehalose, maltose and sucrose, in water mixtures. INS measurements have been performed on trehalose/H2O, maltose/H2O and sucrose/H2O mixtures at very low temperature as a function of concentration by using the thermal original spectrometer with cylindrical analyzers (TOSCA) spectrometer at the ISIS Facility (DRAL, UK). The findings allow the analyses of the vibrational features of the INS spectra in order to study the effect of disaccharides on the H2O hydrogen-bonded tetrahedral network. The obtained neutron scattering findings point out that disaccharides, and in particular trehalose, have a destructuring effect on the water tetrahedral network, as emphasized by the analysis of the librational modes region from 50 to 130 meV energy transfer. On the other hand, the analysis of the bending modes region (130–225 meV) shows a locally ordered structure in the disaccharide/H2O mixtures. Finally, the observed experimental evidences are linked to the different bioprotective effectiveness of disaccharides as a function of concentration.
Genome Analysis A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis 1 [ W ] [ OA ]

Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.
Crystal Structure of the “PhoU-Like” Phosphate Uptake Regulator from Aquifex aeolicus

ABSTRACT The phoU gene of Aquifex aeolicus encodes a protein called PHOU_AQUAE with sequence similarity to the PhoU protein of Escherichia coli. Despite the fact that there is a large number of family members (more than 300) attributed to almost all known bacteria and despite PHOU_AQUAE's association with the regulation of genes for phosphate metabolism, the nature of its regulatory function is not well understood. Nearly one-half of these PhoU-like proteins, including both PHOU_AQUAE and the one from E. coli, form a subfamily with an apparent dimer structure of two PhoU domains on the basis of their amino acid sequence. The crystal structure of PHOU_AQUAE (a 221-amino-acid protein) reveals two similar coiled-coil PhoU domains, each forming a three-helix bundle. The structures of PHOU_AQUAE proteins from both a soluble fraction and refolded inclusion bodies (at resolutions of 2.8 and 3.2Å, respectively) showed no significant differences. The folds of the PhoU domain and Bag domains (for a class of cofactors of the eukaryotic chaperone Hsp70 family) are similar. Accordingly, we propose that gene regulation by PhoU may occur by association of PHOU_AQUAE with the ATPase domain of the histidine kinase PhoR, promoting release of its substrate PhoB. Other proteins that share the PhoU domain fold include the coiled-coil domains of the STAT protein, the ribosome-recycling factor, and structural proteins like spectrin.
Volumetry: an alternative to assess therapy response for malignant pleural mesothelioma?

The purpose of our study was to assess robustness of volumetric measurement of malignant pleural mesothelioma (MPM) before and after chemotherapy to modified RECIST (response evaluation criteria in solid tumours) criteria. 30 patients with digitally available chest computed tomography (CT) scans before and after three cycles of chemotherapy were included. Three readers independently assessed tumour response using two different methods: 1) the modified RECIST criteria; and 2) the tumour volumetric approach using dedicated software (Myrian®; Intrasense, Paris, France). Inter-rater reliability of unidimensional and volumetric measurements was assessed using intraclass correlation. Tumour response classification for modified RECIST was compared to the volumetric approach applying unidimensional RECIST volumetric equivalent criteria. The determination of unidimensional tumour measurement (RECIST) revealed a low inter-rater reliability (0.55) and a low interobserver agreement for tumour response classification (general &kgr; 0.33). Only 14 patients were classified equally. A high inter-rater reliability (0.99) and interobserver agreement (general &kgr; 0.9) were found for absolute tumour volumes (volumetric measurements). 27 cases were classified equally. The number of cases classified as “stable disease” was higher for the volumetric approach using tumour-equivalent criteria compared to modified RECIST. Volumetric measurement of MPM on CT using Myrian® software is a reliable, reproducible and sensitive method to measure tumour volume and, thus, therapy response after induction chemotherapy.
Nature of calcification in codiacean algae

Two re-entrants or troughs extending from the Arctic basin into the northern Kara Sea, an epicontinental sea on the Eurasian continental shelf, were sampled during the summer of 1965. The program was limited to depths exceeding 100 fm. Distinct sedimentary zones exist in the westernmost trough which is open toward the southwest. These zones are expressed most strongly by the chlorite-kaolinite clay-group distribution which reflects a mixture from two distinct sources. The chloritic clays enter from the southwest and are dispersed northward along the eastern margin. The sedimentary zones depend more on the bottom relief, currents, and source than on the absolute water depth. The zones trend north-south, paralleling the dominant currents which consist of a north-flowing near-surface current on the east side and a southflowing bottom current on the west. The zonation is shown on maps of clay-group facies, water content, insoluble residue, and organic carbon. Similar zonation is suggested by the distribution of the grain size, the composition of the sand-size clastic grains, and foraminiferal populations. In terms of relative amounts, the easternmost zone or slope is characterized by a low water content, and abundant chloritic clays, sand, and Foraminifera. The deposits at the foot of the slope have a high water and organic-carbon content, little chloritic material, and the greatest amounts of soluble material, though they contain few Foraminifera. The trough-floor sediments are characterized by an intermediate water content, low amounts of organic carbon, a very low chloritic content, and varying amounts of soluble material. The easternmost trough, which is open only to the Arctic, does not contain distinct sedimentary zones, nor does it have a recognizable current pattern.
What You Get Is What You See: A Visual Markup Decompiler

Building on recent advances in image caption generation and optical character recognition (OCR), we present a general-purpose, deep learning-based system to decompile an image into presentational markup. While this task is a well-studied problem in OCR, our method takes an inherently different, data-driven approach. Our model does not require any knowledge of the underlying markup language, and is simply trained end-to-end on real-world example data. The model employs a convolutional network for text and layout recognition in tandem with an attention-based neural machine translation system. To train and evaluate the model, we introduce a new dataset of real-world rendered mathematical expressions paired with LaTeX markup, as well as a synthetic dataset of web pages paired with HTML snippets. Experimental results show that the system is surprisingly effective at generating accurate markup for both datasets. While a standard domain-specific LaTeX OCR system achieves around 25% accuracy, our model reproduces the exact rendered image on 75% of examples.