Miracle-dz/UniFAR-FTUs huggingface dataset:
Diel changes in nitrogen and carbon resource status and use for growth in young plants of tomato (Solanum lycopersicum).

BACKGROUND AND AIMS Modellers often define growth as the development of plant structures from endogenous resources, thus making a distinction between structural (W(S)) and total (W) dry biomass, the latter being the sum of W(S) and the weight of storage compounds. In this study, short-term C and N reserves were characterized experimentally (forms, organ distribution, time changes) in relation to light and nutrition signals, and organ structural growth in response to reserve levels was evaluated. METHODS Tomato plants (Solanum lycopersicum) were grown hydroponically in a growth room with a 12-h photoperiod and an adequate supply of NO(3)(-) (3 mol m(-3)). Three experiments were carried out 18 d after sowing: [NO(3)(-)] was either maintained at 3 mol m(-3), changed to 0.02 mol m(-3) or to 0 mol m(-3). Plants were sampled periodically throughout the light/dark cycles over 24-48 h. Organ W(S) was calculated from W together with the amount of different compounds that act as C and N resources, i.e. non-structural carbohydrates and carboxylates, nitrate and free amino acids. KEY RESULTS With adequate nutrition, carbohydrates accumulated in leaves during light periods, when photosynthesis exceeded growth needs, but decreased at night when these sugars are the main source of C for growth. At the end of the night, carbohydrates were still high enough to fuel full-rate growth, as W(S) increased at a near constant rate throughout the light/dark cycle. When nitrate levels were restricted, C reserves increased, but [NO(3)(-)] decreased progressively in stems, which contain most of the plant N reserves, and rapidly in leaves and roots. This resulted in a rapid restriction of structural growth. CONCLUSIONS Periodic darkness did not restrict growth because sufficient carbohydrate reserves accumulated during the light period. Structural growth, however, was very responsive to NO(3)(-) nutrition, because N reserves were mostly located in stems, which have limited nitrate reduction capacity.
Oxide Wizard: An EELS Application to Characterize the White Lines of Transition Metal Edges

Abstract Physicochemical properties of transition metal oxides are directly determined by the oxidation state of the metallic cations. To address the increasing need to accurately evaluate the oxidation states of transition metal oxide systems at the nanoscale, here we present “Oxide Wizard. ” This script for Digital Micrograph characterizes the energy-loss near-edge structure and the position of the transition metal edges in the electron energy-loss spectrum. These characteristics of the edges can be linked to the oxidation states of transition metals with high spatial resolution. The power of the script is demonstrated by mapping manganese oxidation states in Fe3O4/Mn3O4 core/shell nanoparticles with sub-nanometer resolution in real space.
Recent advances in understanding the assembly and repair of photosystem II.

BACKGROUND Photosystem II (PSII) is the light-driven water:plastoquinone oxidoreductase of oxygenic photosynthesis and is found in the thylakoid membrane of chloroplasts and cyanobacteria. Considerable attention is focused on how PSII is assembled in vivo and how it is repaired following irreversible damage by visible light (so-called photoinhibition). Understanding these processes might lead to the development of plants with improved growth characteristics especially under conditions of abiotic stress. SCOPE Here we summarize recent results on the assembly and repair of PSII in cyanobacteria, which are excellent model organisms to study higher plant photosynthesis. CONCLUSIONS Assembly of PSII is highly co-ordinated and proceeds through a number of distinct assembly intermediates. Associated with these assembly complexes are proteins that are not found in the final functional PSII complex. Structural information and possible functions are beginning to emerge for several of these 'assembly' factors, notably Ycf48/Hcf136, Psb27 and Psb28. A number of other auxiliary proteins have been identified that appear to have evolved since the divergence of chloroplasts and cyanobacteria. The repair of PSII involves partial disassembly of the damaged complex, the selective replacement of the damaged sub-unit (predominantly the D1 sub-unit) by a newly synthesized copy, and reassembly. It is likely that chlorophyll released during the repair process is temporarily stored by small CAB-like proteins (SCPs). A model is proposed in which damaged D1 is removed in Synechocystis sp. PCC 6803 by a hetero-oligomeric complex composed of two different types of FtsH sub-unit (FtsH2 and FtsH3), with degradation proceeding from the N-terminus of D1 in a highly processive reaction. It is postulated that a similar mechanism of D1 degradation also operates in chloroplasts. Deg proteases are not required for D1 degradation in Synechocystis 6803 but members of this protease family might play a supplementary role in D1 degradation in chloroplasts under extreme conditions.
Variation of seed heteromorphism in Chenopodium album and the effect of salinity stress on the descendants.

BACKGROUND AND AIMS Chenopodium album is well-known as a serious weed and is a salt-tolerant species inhabiting semi-arid and light-saline environments in Xinjiang, China. It produces large amounts of heteromorphic (black and brown) seeds. The primary aims of the present study were to compare the germination characteristics of heteromorphic seeds, the diversity of plant growth and seed proliferation pattern of the resulting plants, and the correlation between NaCl stress and variation of seed heteromorphism. METHODS The phenotypic characters of heteromorphic seeds, e.g. seed morphology, seed mass and total seed protein were determined. The effects of dry storage at room temperature on dormancy behaviour, the germination response of seeds to salinity stress, and the effect of salinity on growth and seed proliferation with plants derived from different seed types were investigated. KEY RESULTS Black and brown seeds differed in seed morphology, mass, total seed protein, dormancy behaviour and salinity tolerance. Brown seeds were large, non-dormant and more salt tolerant, and could germinate rapidly to a high percentage in a wider range of environments; black seeds were salt-sensitive, and a large proportion of seeds were dormant. These characteristics varied between two populations. There was little difference in growth characteristics and seed output of plants produced from the two seed morphs except when plants were subjected to high salinity stress. Plants that suffered higher salinity stress produced more brown (salt-tolerant) seeds. CONCLUSIONS The two seed morphs of C. album exhibited distinct diversity in germination characteristics. There was a significant difference in plant development and seed proliferation pattern from the two types of seeds only when the parent plants were treated with high salinity. In addition, seed heteromorphism of C. album varied between the two populations, and such variation may be attributed, at least in part, to the salinity.
Constitutive activation of distinct NF‐κB signals in EBV‐associated nasopharyngeal carcinoma

As a distinct type of head and neck cancer, non‐keratinizing nasopharyngeal carcinoma (NPC) is closely associated with EBV infection and massive lymphoid infiltration. The unique histological features suggest that local inflammation plays an important role in NPC tumourigenesis. We comprehensively characterized NF‐κB signalling, a key inflammatory pathway which might contribute to the tumourigenesis of this EBV‐associated cancer. By EMSA, western blotting, and immunohistochemical staining, constitutive activation of distinct NF‐κB complexes, either p50/p50/Bcl3 or p50/RelB, was found in almost all EBV‐positive NPC tumours. siRNA or chemical inhibition of NF‐κB signalling significantly inhibited the growth of EBV‐positive NPC cells C666‐1. Gene expression profiling identified a number of NF‐κB target genes involved in cell proliferation, apoptosis, immune response, and transcription. We further confirmed that p50 signals modulate the expression of multiple oncogenes (MYB, BCL2), chemokines, and chemokine receptors (CXCL9, CXCL10, CX3CL1, and CCL20). The findings support a crucial role of these constitutively activated NF‐κB signals in NPC tumourigenesis and local inflammation. In addition to expression of the viral oncoprotein LMP1, genetic alteration of several NF‐κB regulators (eg TRAF3, TRAF2, NFKBIA, A20) also contributes to the aberrant NF‐κB activation in EBV‐associated NPC. Except for LMP1‐expressing C15 cells, all NPC tumour lines harbour at least one of these genetic alterations. Importantly, missense mutations of TRAF3, TRAF2, and A20 were also detected in 3/33 (9.1%) primary tumours. Taken together with the reported LTBR amplification in 7.3% of primary NPCs, genetic alterations in NF‐κB pathways occurred in at least 16% of cases of this cancer. The findings indicate that distinct NF‐κB signals are constitutively activated in EBV‐positive NPC cells by either multiple genetic changes or EBV latent genes. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Carcinoma of Stomach

of heparin is valueless with respect to the production of cloaring factor. ' Therefore the ideal dose of heparin is that which will just produce.the maximum amount of clearing factor and hence have a minimum anticoagulant action. We chose 2,000 units As our standard dose, bearing in mind the fact that a mere 400 units of heparin would produce measurable amounts of clearing factor,' but we do not know if this is the ideal dose. We have found by in vitro studies that clearing factor is produced by our method of treatment, and because of the small dose of-heparin we have not encountered haemorrhage at the fracture sites. -We are, etc., HAROLD COEN.
Macrophages from the synovium of active rheumatoid arthritis exhibit an activin A‐dependent pro‐inflammatory profile

Rheumatoid arthritis (RA) is a chronic inflammatory disease whose pathogenesis and severity correlates with the presence of macrophage‐derived pro‐inflammatory cytokines within the inflamed synovium. Macrophage‐derived cytokines fuel the pathological processes in RA and are targets of clinically successful therapies. However, although macrophage polarization determines cytokine production, the polarization state of macrophages in RA joints remains poorly defined. To dissect the molecular basis for the tissue‐damaging effects of macrophages in RA joints, we undertook the phenotypic and transcriptomic characterization of ex vivo isolated CD14+ RA synovial fluid (RA‐SF) macrophages. Flow cytometry and gene profiling indicated that RA‐SF macrophages express pro‐inflammatory polarization markers (MMP12, EGLN3, CCR2), lack expression of markers associated with homeostatic and anti‐inflammatory polarization (IGF1, HTR2B) and exhibit a transcriptomic profile that resembles the activin A‐dependent gene signature of pro‐inflammatory in vitro‐generated macrophages. In fact, high levels of Smad‐activating activin A were found in RA‐SF and, accordingly, the Smad signalling pathway was activated in ex vivo‐isolated RA‐SF macrophages. In vitro experiments on monocytes and macrophages indicated that RA‐SF promoted the acquisition of pro‐inflammatory markers (INHBA, MMP12, EGLN3, CCR2) but led to a significant reduction in the expression of genes associated with homeostasis and inflammation resolution (FOLR2, SERPINB2, IGF1, CD36), thus confirming the pro‐inflammatory polarization ability of RA‐SF. Importantly, the macrophage‐polarizing ability of RA‐SF was inhibited by an anti‐activin A‐neutralizing antibody, thus demonstrating that activin A mediates the pro‐inflammatory macrophage‐polarizing ability of RA‐SF. Moreover, and in line with these findings, multicolour immunofluorescence evidenced that macrophages within RA synovial membranes (RA‐SM) also express pro‐inflammatory polarization markers whose expression is activin A‐dependent. Altogether, our results demonstrate that macrophages from RA synovial fluids and membranes exhibit an MMP12+ EGLN3+ CCR2+ pro‐inflammatory polarization state whose acquisition is partly dependent on activin A from the synovial fluid. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
PART OF A SPECIAL ISSUE ON SEXUAL PLANT REPRODUCTION Identification and characterization of TcCRP1, a pollen tube attractant from Torenia concolor

† Background and Aims During sexual reproduction in higher angiosperms, the pollen tubes are directed to the ovules in the pistil to deliver sperm cells. This pollen tube attraction is highly species speciﬁc, and a group of small secreted proteins, TfCRPs, are necessary for this process in Torenia fournieri . † Methods A candidate pollen tube attractant protein in Torenia concolor , a related species of T. fournieri , was isolated and the attractant abilities between them were compared. † Key Results TcCRP1 , an orthologous gene of TfCRP1 from T. concolor , is expressed predominantly in the synergid cell. The gene product attracted pollen tubes in a concentration-dependent manner, but attracted fewer pollen tubes from the other species. † Conclusions The results indicated that this class of CRP proteins is a common pollen tube attractant in Torenia species. The sequence diversity of these proteins is important for species-speciﬁc pollen tube attraction.
Delayed Cardioprotective Effect of Ischemic Preconditioning is mediated by Heat Shock Protein in Cat Heart

Background:It is well known that ischemic preconditioning protects the heart against infarction or arrhythmias from a subsequent ischemic injury. Two phases of the effect of preconditioning has been explored, early protection and second window of protection at 24 hours. The late protection was seen in some animal model, but the precise mechanism is controversal. This study was designed to evaluate the late cardioprotective effect and role of HSP70 in ischemic preconditioning of cat heart. Methods:Two groups of cats were studied. Control animals were subjected to an episode of 40-min coronary artery occlusion followed by 30-min reperfusion. Experimental animals were subjected to ischemic preconditioning before the 40-min ishcemia/reperfusion. The preconditioning protocol was comprised of three 5-min episodes of ischemia interspersed by 10-min episodes of reperfusion. After sustained ischemia and reperfusion, left ventricular risk area and infart area were measured by injection of Evans blue bye and triphenyltetrazolium staining, and myocardial HSP70 mRNA was examined in risk (left ventricular anterior wall) and nonrisk (left ventricular posterior wall) area using northern blot hybridization. HSP70 mRNA expression was quantified as a percent of GAPDH. The late cardioprotective effects of ischemic preconditioning were determined by infarct size (% area at risk). Results: Infarct size was markedly limited by ischemic preconditioning when compared with the control group (18.5± 6.9% vs 38.5±11.1%;p<0.001). HSP70 mRNA expression in risk area was much higher in preconditioning group than control group (78±12% vs 41±11%;p<0.01). But, there was no significant difference of HSP70 mRNA expression in the posterior wall between control and ischemic preconditioning group. Conclusions: These data suggest that ischemic preconditioning have delayed myocardial protective effect from ischemia. The increase in myocardial HSP70 mRNA may be one of the contributing factors to the delayed cardioprotective effects of ischemic preconditioning in cats. (Korean Circulation J 2001;31(1):16-23)
Functional biscuits and coronary heart disease risk factors

Purpose – The purpose of this study is to biomedically assess biscuits designed to reduce selected risk factors for coronary heart disease, in particular serum homocysteine and glucose.Design/methodology/approach – In this study, one of the countries leading jam sandwhich biscuits was significantly modified, with particular attention being paid to sugar, fat and salt concentration. A traditional biscuit was converted to a functional food by the addition of vitamin B12, Folic Acid, Vitamin C and Prebiotic fibre, while reducing salt and sugar.Findings – The results obtained from a clinical trial demonstrated that serum homocysteine and blood glucose were significantly decreased (P < 0.05) when the modified product and the traditional biscuit were compared. These findings confirm that a health promoting biscuit can be produced commercially, and have similar organoleptic properties as the standard high fat, high sugar and salt product.Practical implications – These findings could have significant implications.
Vocal Development as a Guide to Modeling the Evolution of Language

Modeling of evolution and development of language has principally utilized mature units of spoken language, phonemes and words, as both targets and inputs. This approach cannot address the earliest phases of development because young infants are unable to produce such language features. We argue that units of early vocal development-protophones and their primitive illocutionary/perlocutionary forces-should be targeted in evolutionary modeling because they suggest likely units of hominin vocalization/communication shortly after the split from the chimpanzee/bonobo lineage, and because early development of spontaneous vocal capability is a logically necessary step toward vocal language, a root capability without which other crucial steps toward vocal language capability are impossible. Modeling of language evolution/development must account for dynamic change in early communicative units of form/function across time. We argue for interactive contributions of sender/infants and receiver/caregivers in a feedback loop involving both development and evolution and propose to begin computational modeling at the hominin break from the primate communicative background.
Paediatric and adult soft tissue sarcomas with NTRK1 gene fusions: a subset of spindle cell sarcomas unified by a prominent myopericytic/haemangiopericytic pattern

Neoplasms with a myopericytomatous pattern represent a morphological spectrum of lesions encompassing myopericytoma of the skin and soft tissue, angioleiomyoma, myofibromatosis/infantile haemangiopericytoma and putative neoplasms reported as malignant myopericytoma. Lack of reproducible phenotypic and genetic features of malignant myopericytic neoplasms have prevented the establishment of myopericytic sarcoma as an acceptable diagnostic category. Following detection of a LMNA–NTRK1 gene fusion in an index case of paediatric haemangiopericytoma‐like sarcoma by combined whole‐genome and RNA sequencing, we identified three additional sarcomas harbouring NTRK1 gene fusions, termed 'spindle cell sarcoma, NOS with myo/haemangiopericytic growth pattern'. The patients were two children aged 11 months and 2 years and two adults aged 51 and 80 years. While the tumours of the adults were strikingly myopericytoma‐like, but with clear‐cut atypical features, the paediatric cases were more akin to infantile myofibromatosis/haemangiopericytoma. All cases contained numerous thick‐walled dysplastic‐like vessels with segmental or diffuse nodular myxohyaline myo‐intimal proliferations of smooth muscle actin‐positive cells, occasionally associated with thrombosis. Immunohistochemistry showed variable expression of smooth muscle actin and CD34, but other mesenchymal markers, including STAT6, were negative. This study showed a novel variant of myo/haemangiopericytic sarcoma with recurrent NTRK1 gene fusions. Given the recent introduction of a novel therapeutic approach targeting NTRK fusion‐positive neoplasms, recognition of this rare but likely under‐reported sarcoma variant is strongly encouraged. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The fate of duplicated genes in a polyploid plant genome.

Polyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result in extensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally and evolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 million years ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutes a good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, we tested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested, approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only a small proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition, duplicated genes were often found in collinear blocks, and several blocks of duplicated genes were co-regulated, suggesting some type of epigenetic or positional regulation. We also found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.
The Aquilegia FRUITFULL-like genes play key roles in leaf morphogenesis and inflorescence development.

The APETALA1/FRUITFULL (AP1/FUL) MADS box transcription factors are best known for the role of AP1 in Arabidopsis sepal and petal identity, the canonical A function of the ABC model of flower development. However, this gene lineage underwent multiple duplication events during angiosperm evolution, providing different taxa with unique gene complements. One such duplication correlates with the origin of the core eudicots, and produced the euAP1 and euFUL clades. Together, euAP1 and euFUL genes function in proper floral meristem identity and repression of axillary meristem growth. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth and fruit development. To investigate the impact of the core eudicot duplication on the functional diversification of this gene lineage, we studied the role of pre-duplication FUL-like genes in columbine (Aquilegia coerulea). Our results show that AqcFL1 genes are broadly expressed in vegetative and reproductive meristems, leaves and flowers. Virus-induced gene silencing of the loci results in plants with increased branching, shorter inflorescences with fewer flowers, and dramatic changes in leaf shape and complexity. However, aqcfl1 plants have normal flowers and fruits. Our results show that, in contrast to characterized AP1/FUL genes, the AqcFL1 loci are either genetically redundant or have been decoupled from the floral genetic program, and play a major role in leaf morphogenesis. We analyze the results in the context of the core eudicot duplication, and discuss the implications of our findings in terms of the genetic regulation of leaf morphogenesis in Aquilegia and other flowering plants.