Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasticity of rhizosphere hydraulic properties as a key for efficient utilization of scarce resources.

BACKGROUND It is known that the soil near roots, the so-called rhizosphere, has physical and chemical properties different from those of the bulk soil. Rhizosphere properties are the result of several processes: root and soil shrinking/swelling during drying/wetting cycles, soil compaction by root growth, mucilage exuded by root caps, interaction of mucilage with soil particles, mucilage shrinking/swelling and mucilage biodegradation. These processes may lead to variable rhizosphere properties, i.e. the presence of air-filled gaps between soil and roots; water repellence in the rhizosphere caused by drying of mucilage around the soil particles; or water accumulation in the rhizosphere due to the high water-holding capacity of mucilage. The resulting properties are not constant in time but they change as a function of soil condition, root growth rate and mucilage age. SCOPE We consider such a variability as an expression of rhizosphere plasticity, which may be a strategy for plants to control which part of the root system will have a facilitated access to water and which roots will be disconnected from the soil, for instance by air-filled gaps or by rhizosphere hydrophobicity. To describe such a dualism, we suggest classifying rhizosphere into two categories: class A refers to a rhizosphere covered with hydrated mucilage that optimally connects roots to soil and facilitates water uptake from dry soils. Class B refers to the case of air-filled gaps and/or hydrophobic rhizosphere, which isolate roots from the soil and may limit water uptake from the soil as well water loss to the soil. The main function of roots covered by class B will be long-distance transport of water. OUTLOOK This concept has implications for soil and plant water relations at the plant scale. Root water uptake in dry conditions is expected to shift to regions covered with rhizosphere class A. On the other hand, hydraulic lift may be limited in regions covered with rhizosphere class B. New experimental methods need to be developed and applied to different plant species and soil types, in order to understand whether such dualism in rhizosphere properties is an important mechanism for efficient utilization of scarce resources and drought tolerance.
Oncogenic S1P signalling in EBV‐associated nasopharyngeal carcinoma activates AKT and promotes cell migration through S1P receptor 3

Undifferentiated nasopharyngeal carcinoma (NPC) is a cancer with high metastatic potential that is consistently associated with Epstein–Barr virus (EBV) infection. In this study, we have investigated the functional contribution of sphingosine‐1‐phosphate (S1P) signalling to the pathogenesis of NPC. We show that EBV infection or ectopic expression of the EBV‐encoded latent genes (EBNA1, LMP1, and LMP2A) can up‐regulate sphingosine kinase 1 (SPHK1), the key enzyme that produces S1P, in NPC cell lines. Exogenous addition of S1P promotes the migration of NPC cells through the activation of AKT; shRNA knockdown of SPHK1 resulted in a reduction in the levels of activated AKT and inhibition of cell migration. We also show that S1P receptor 3 (S1PR3) mRNA is overexpressed in EBV‐positive NPC patient‐derived xenografts and a subset of primary NPC tissues, and that knockdown of S1PR3 suppressed the activation of AKT and the S1P‐induced migration of NPC cells. Taken together, our data point to a central role for EBV in mediating the oncogenic effects of S1P in NPC and identify S1P signalling as a potential therapeutic target in this disease. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The Definition of Alcoholism

To establish a more precise use of the term alcoholism , a 23-member multidisciplinary committee of the National Council on Alcoholism and Drug Dependence and the American Society of Addiction Medicine conducted a 2-year study of the definition of alcoholism in the light of current concepts. The goals of the committee were to create by consensus a revised definition that is (1) scientifically valid, (2) clinically useful, and (3) understandable by the general public. Therefore, the committee agreed to define alcoholism as a primary, chronic disease with genetic, psychosocial, and environmental factors influencing its development and manifestations. The disease is often progressive and fatal. It is characterized by impaired control over drinking, preoccupation with the drug alcohol, use of alcohol despite adverse consequences, and distortions in thinking, most notably denial. Each of these symptoms may be continuous or periodic. ( JAMA . 1992;268:1012-1014)
MYC drives overexpression of telomerase RNA (hTR/TERC) in prostate cancer

Telomerase consists of at least two essential elements, an RNA component hTR or TERC that contains the template for telomere DNA addition and a catalytic reverse transcriptase (TERT). While expression of TERT has been considered the key rate‐limiting component for telomerase activity, increasing evidence suggests an important role for the regulation of TERC in telomere maintenance and perhaps other functions in human cancer. By using three orthogonal methods including RNAseq, RT‐qPCR, and an analytically validated chromogenic RNA in situ hybridization assay, we report consistent overexpression of TERC in prostate cancer. This overexpression occurs at the precursor stage (e.g. high‐grade prostatic intraepithelial neoplasia or PIN) and persists throughout all stages of disease progression. Levels of TERC correlate with levels of MYC (a known driver of prostate cancer) in clinical samples and we also show the following: forced reductions of MYC result in decreased TERC levels in eight cancer cell lines (prostate, lung, breast, and colorectal); forced overexpression of MYC in PCa cell lines, and in the mouse prostate, results in increased TERC levels; human TERC promoter activity is decreased after MYC silencing; and MYC occupies the TERC locus as assessed by chromatin immunoprecipitation (ChIP). Finally, we show that knockdown of TERC by siRNA results in reduced proliferation of prostate cancer cell lines. These studies indicate that TERC is consistently overexpressed in all stages of prostatic adenocarcinoma and that its expression is regulated by MYC. These findings nominate TERC as a novel prostate cancer biomarker and therapeutic target. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Alcohol Screening in the Acute Care Hospital

&NA; Many people admitted to the acute care hospital routinely use alcohol. Their patterns of drinking may vary widely from being low risk to hazardous. It is known that alcohol plays a part in the etiology of some illnesses and adds risk of further morbidity with the development of withdrawal symptoms. Conducting alcohol screening on patients admitted to the hospital cues the nurse to identify those patients in jeopardy of alcohol withdrawal syndrome. Nurses can be proactive in planning interventions for their patients. Early recognition and a timely response can facilitate healing and form an environment that is caring, protective and respectful of the patient's needs.
Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii.

BACKGROUND AND AIMS Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of spruce with similar morphology, Picea wilsonii, P. neoveitchii and P. morrisonicola. Picea wilsonii and P. neoveitchii occur from central to north-west China, where they have overlapping distributions. Picea morrisonicola, however, is restricted solely to the island of Taiwan and is isolated from the other two species by a long distance. METHODS Sequence variations were examined in 18 DNA fragments for 22 populations, including three fragments from the chloroplast (cp) genome, two from the mitochondrial (mt) genome and 13 from the nuclear genome. KEY RESULTS In both the cpDNA and the mtDNA, P. morrisonicola accumulated more species-specific mutations than the other two species. However, most nuclear haplotypes of P. morrisonicola were shared by P. wilsonii, or derived from the dominant haplotypes found in that species. Modelling of population genetic data supported the hypothesis that P. morrisonicola derived from P. wilsonii within the more recent past, most probably indicating progenitor-derivative speciation with a distinct bottleneck, although further gene flow from the progenitor to the derivative continued. In addition, the occurrence was detected of an obvious mtDNA introgression from P. neoveitchii to P. wilsonii despite their early divergence. CONCLUSIONS The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species.
Recent advances and opportunities in proteomic analyses of tumour heterogeneity

Solid tumour malignancies comprise a highly variable admixture of tumour and non‐tumour cellular populations, forming a complex cellular ecosystem and tumour microenvironment. This tumour heterogeneity is not incidental, and is known to correlate with poor patient prognosis for many cancer types. Indeed, non‐malignant cell populations, such as vascular endothelial and immune cells, are known to play key roles supporting and, in some cases, driving aggressive tumour biology, and represent targets of emerging therapeutics, such as antiangiogenesis and immune checkpoint inhibitors. The biochemical interplay between these cellular populations and how they contribute to molecular tumour heterogeneity remains enigmatic, particularly from the perspective of the tumour proteome. This review focuses on recent advances in proteomic methods, namely imaging mass spectrometry, single‐cell proteomic techniques, and preanalytical sample processing, that are uniquely positioned to enable detailed analysis of discrete cellular populations within tumours to improve our understanding of tumour proteomic heterogeneity. This review further emphasizes the opportunity afforded by the application of these techniques to the analysis of tumour heterogeneity in formalin‐fixed paraffin‐embedded archival tumour tissues, as these represent an invaluable resource for retrospective analyses that is now routinely accessible, owing to recent technological and methodological advances in tumour tissue proteomics. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Kombinationstherapie bei Epilepsie

Zusammenfassung Eine Monotherapie ist Standard der medikamentösen Epilepsie-Therapie, führt jedoch nur bei ca. 65 % der Patienten zu Anfallsfreiheit. Daher werden bis zu 50 % der Epilepsiepatienten zumindest zeitweilig mit einer Kombinationstherapie behandelt. Eine Kombination von Antiepileptika kann bei einem kleinen Prozentsatz von Patienten, die auf eine Monotherapie nicht angesprochen haben, zur Anfallsfreiheit führen. Monotherapie und Kombinationstherapie sind nicht immer Gegensätze, viele Substanzen haben mehrere Wirkmechanismen und stellen eine Art Kombinationstherapie in einer Substanz dar. Die Kombination von Substanzen mit unterschiedlichem Wirkungsmechanismus wird als „rationale Polypharmazie“ bezeichnet. Die Überlegenheit solcher Kombinationen gegenüber Kombinationen von Antiepileptika mit gleichem oder ähnlichem Wirkungsmechanismus ist bisher nicht durch randomisierte Studien bewiesen worden. Hinweise auf eine überlegene Verträglichkeit und Wirksamkeit bei Kombinationen mit verschiedenen Wirkmechanismen ergeben sich jedoch bei der Add-on-Gabe von Lacosamid zu Nicht-Natrium-Kanalblockern und bei der Kombination von Lamotrigin und Valproinsäure. Beim Einsatz einer Antiepileptika-Kombination sollten vor allem Wirksamkeit, Nebenwirkungsspektrum, Interaktionen und Kosten der gewählten Substanzen berücksichtigt werden, außerdem eventuell vorliegende Begleitkrankheiten.
Das pseudophakiebedingte zystoide Makulaödem

Zusammenfassung Das pseudophakiebedingte zystoide Makulaödem bleibt trotz der enormen Fortschritte in der modernen Kataraktchirurgie aufgrund der hohen Anzahl an jährlichen Operationen weiterhin ein Krankheitsbild mit immenser klinischer Relevanz, da auch nach unkomplikativer Operation eine bedeutsame und permanente Visusreduktion auftreten kann. Pathophysiologisch spielen in der Entstehung 4 intraokuläre Vorgänge eine entscheidende Rolle: 1. die operationsbedingte intraokuläre Freisetzung verschiedener Entzündungsmediatoren in die vordere Augenkammer; 2. die Entfernung der linsenbedingten Barriere mit einer konsekutiven Erhöhung der Diffusion zwischen vorderem und hinterem Augenabschnitt; 3. die Entstehung eines zystoiden Makulaödems durch die lokale Wirkung der Entzündungsmediatoren auf die Makula und 4. die vitreoretinale Traktion durch den nach anterior ziehenden Glaskörper. Zur Prävention werden die optimale präoperative Einstellung von systemischen und okulären Grunderkrankungen sowie die Risikobewertung des einzelnen Patienten empfohlen. Eine möglichst atraumatische Operationstechnik kann zusätzlich das Risiko des Auftretens eines postoperativen Makulaödems deutlich reduzieren. Zur Diagnostik des pseudophakiebedingten zystoiden Makulaödems stehen neben der subjektiven Beschwerdesymptomatik des Patienten die Durchführung von Funduskopie, Fluoreszenzangiografie und optischer Kohärenztomografie zur Verfügung. Präventive und therapeutische medikamentöse Leitlinien der Fachgesellschaften gibt es aktuell noch nicht. In einer Zusammenschau der Literatur wird für die Therapie ein Stufenschema, welches verschiedene Kombinationen aus medikamentösen und chirurgischen Therapieoptionen vorschlägt, empfohlen. Hier spielen die topische Gabe von nicht steroidalen Antiphlogistika, Kortikosteroiden und Karboanhydrasemmern sowie chirurgische Interventionsmöglichkeiten im Rahmen einer Vitrektomie eine wichtige Rolle.
ULTRAPETALA1 and LEAFY pathways function independently in specifying identity and determinacy at the Arabidopsis floral meristem.

BACKGROUND AND AIMS The morphological variability of the flower in angiosperms, combined with its relatively simple structure, makes it an excellent model to study cell specification and the establishment of morphogenetic patterns. Flowers are the products of floral meristems, which are determinate structures that generate four different types of floral organs before terminating. The precise organization of the flower in whorls, each defined by the identity and number of organs it contains, is controlled by a multi-layered network involving numerous transcriptional regulators. In particular, the AGAMOUS (AG) MADS domain-containing transcription factor plays a major role in controlling floral determinacy in Arabidopsis thaliana in addition to specifying reproductive organ identity. This study aims to characterize the genetic interactions between the ULTRAPETALA1 (ULT1) and LEAFY (LFY) transcriptional regulators during flower morphogenesis, with a focus on AG regulation. METHODS Genetic and molecular approaches were used to address the question of redundancy and reciprocal interdependency for the establishment of flower meristem initiation, identity and termination. In particular, the effects of loss of both ULT1 and LFY function were determined by analysing flower developmental phenotypes of double-mutant plants. The dependency of each factor on the other for activating developmental genes was also investigated in gain-of-function experiments. KEY RESULTS The ULT1 and LFY pathways, while both activating AG expression in the centre of the flower meristem, functioned independently in floral meristem determinacy. Ectopic transcriptional activation by ULT1 of AG and AP3, another gene encoding a MADS domain-containing flower architect, did not depend on LFY function. Similarly, LFY did not require ULT1 function to ectopically determine floral fate. CONCLUSIONS The results indicate that the ULT1 and LFY pathways act separately in regulating identity and determinacy at the floral meristem. In particular, they independently induce AG expression in the centre of the flower to terminate meristem activity. A model is proposed whereby these independent contributions bring about a switch at the AG locus from an inactive to an active transcriptional state at the correct time and place during flower development.
Sustainable intensification in agricultural systems.

BACKGROUND Agricultural systems are amended ecosystems with a variety of properties. Modern agroecosystems have tended towards high through-flow systems, with energy supplied by fossil fuels directed out of the system (either deliberately for harvests or accidentally through side effects). In the coming decades, resource constraints over water, soil, biodiversity and land will affect agricultural systems. Sustainable agroecosystems are those tending to have a positive impact on natural, social and human capital, while unsustainable systems feed back to deplete these assets, leaving fewer for the future. Sustainable intensification (SI) is defined as a process or system where agricultural yields are increased without adverse environmental impact and without the conversion of additional non-agricultural land. The concept does not articulate or privilege any particular vision or method of agricultural production. Rather, it emphasizes ends rather than means, and does not pre-determine technologies, species mix or particular design components. The combination of the terms 'sustainable' and 'intensification' is an attempt to indicate that desirable outcomes around both more food and improved environmental goods and services could be achieved by a variety of means. Nonetheless, it remains controversial to some. SCOPE AND CONCLUSIONS This review analyses recent evidence of the impacts of SI in both developing and industrialized countries, and demonstrates that both yield and natural capital dividends can occur. The review begins with analysis of the emergence of combined agricultural-environmental systems, the environmental and social outcomes of recent agricultural revolutions, and analyses the challenges for food production this century as populations grow and consumption patterns change. Emergent criticisms are highlighted, and the positive impacts of SI on food outputs and renewable capital assets detailed. It concludes with observations on policies and incentives necessary for the wider adoption of SI, and indicates how SI could both promote transitions towards greener economies as well as benefit from progress in other sectors.
Identification of the Arabidopsis RAM/MOR signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization.

BACKGROUND AND AIMS The RAM/MOR signalling network of eukaryotes is a conserved regulatory module involved in co-ordination of stem cell maintenance, cell differentiation and polarity establishment. To date, no such signalling network has been identified in plants. METHODS Genes encoding the bona fide core components of the RAM/MOR pathway were identified in Arabidopsis thaliana (arabidopsis) by sequence similarity searches conducted with the known components from other species. The transcriptional network(s) of the arabidopsis RAM/MOR signalling pathway were identified by running in-depth in silico analyses for genes co-regulated with the core components. In situ hybridization was used to confirm tissue-specific expression of selected RAM/MOR genes. KEY RESULTS Co-expression data suggested that the arabidopsis RAM/MOR pathway may include genes involved in floral transition, by co-operating with chromatin remodelling and mRNA processing/post-transcriptional gene silencing factors, and genes involved in the regulation of pollen tube polar growth. The RAM/MOR pathway may act upstream of the ROP1 machinery, affecting pollen tube polar growth, based on the co-expression of its components with ROP-GEFs. In silico tissue-specific co-expression data and in situ hybridization experiments suggest that different components of the arabidopsis RAM/MOR are expressed in the shoot apical meristem and inflorescence meristem and may be involved in the fine-tuning of stem cell maintenance and cell differentiation. CONCLUSIONS The arabidopsis RAM/MOR pathway may be part of the signalling cascade that converges in pollen tube polarized growth and in fine-tuning stem cell maintenance, differentiation and organ polarity.
Large-scale gene expression profiling data for the model moss Physcomitrella patens aid understanding of developmental progression, culture and stress conditions.

The moss Physcomitrella patens is an important model organism for studying plant evolution, development, physiology and biotechnology. Here we have generated microarray gene expression data covering the principal developmental stages, culture forms and some environmental/stress conditions. Example analyses of developmental stages and growth conditions as well as abiotic stress treatments demonstrate that (i) growth stage is dominant over culture conditions, (ii) liquid culture is not stressful for the plant, (iii) low pH might aid protoplastation by reduced expression of cell wall structure genes, (iv) largely the same gene pool mediates response to dehydration and rehydration, and (v) AP2/EREBP transcription factors play important roles in stress response reactions. With regard to the AP2 gene family, phylogenetic analysis and comparison with Arabidopsis thaliana shows commonalities as well as uniquely expressed family members under drought, light perturbations and protoplastation. Gene expression profiles for P. patens are available for the scientific community via the easy-to-use tool at https://www.genevestigator. com. By providing large-scale expression profiles, the usability of this model organism is further enhanced, for example by enabling selection of control genes for quantitative real-time PCR. Now, gene expression levels across a broad range of conditions can be accessed online for P. patens.
An Update on the Genetics of Paraganglioma, Pheochromocytoma, and Associated Hereditary Syndromes

Abstract Pheochromocytomas (PCCs) and paragangliomas (PGLs) are catecholamine-secreting tumors of neural crest origin. Once collectively known as the ‘10% tumor’, based on the frequency of inherited forms of the disease, they are now referred to as the ‘10-gene tumor’, based on the number of susceptibility genes identified to date. Most familial cases of pheochromocytoma and/or paraganglioma and 10–20% sporadic cases carry germline mutations in VHL, RET, NF1, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, or MAX. The finding of somatic mutations in VHL and RET in an additional 10–15% of tumors has brought the proportion of all patients with PCC and/or PGL due to a genetic disruption in these genes to approximately one half. These findings impact on the clinical management of patients. The diversity in the genetic etiology has transcription correlates, which are reflected in the 2 main transcription signatures underlying these mutations: a pseudohypoxic cluster (VHL and SDH gene mutation carriers) and a cluster rich in kinase receptor signaling and protein translation pathways (RET, NF1, TMEM127 and MAX mutation carriers). Recognition of these clusters offers clues to better understand tumor pathogenesis as well as a rationale for the development of targeted therapies. In this report we provide an overview of the transcription-based classification of PCCs and PGLs, an update on the more recently identified susceptibility genes and an outline of current gaps in this research field as well as challenges for the coming years.