Miracle-dz/UniFAR-FTUs huggingface dataset:
Low phosphorus supply constrains plant responses to elevated CO2: A meta‐analysis

Phosphorus (P) is an essential macro‐nutrient required for plant metabolism and growth. Low P availability could potentially limit plant responses to elevated carbon dioxide (eCO2), but consensus has yet to be reached on the extent of this limitation. Here, based on data from experiments that manipulated both CO2 and P for young individuals of woody and non‐woody species, we present a meta‐analysis of P limitation impacts on plant growth, physiological, and morphological response to eCO2. We show that low P availability attenuated plant photosynthetic response to eCO2 by approximately one‐quarter, leading to a reduced, but still positive photosynthetic response to eCO2 compared to those under high P availability. Furthermore, low P limited plant aboveground, belowground, and total biomass responses to eCO2, by 14.7%, 14.3%, and 12.4%, respectively, equivalent to an approximate halving of the eCO2 responses observed under high P availability. In comparison, low P availability did not significantly alter the eCO2‐induced changes in plant tissue nutrient concentration, suggesting tissue nutrient flexibility is an important mechanism allowing biomass response to eCO2 under low P availability. Low P significantly reduced the eCO2‐induced increase in leaf area by 14.3%, mirroring the aboveground biomass response, but low P did not affect the eCO2‐induced increase in root length. Woody plants exhibited stronger attenuation effect of low P on aboveground biomass response to eCO2 than non‐woody plants, while plants with different mycorrhizal associations showed similar responses to low P and eCO2 interaction. This meta‐analysis highlights crucial data gaps in capturing plant responses to eCO2 and low P availability. Field‐based experiments with longer‐term exposure of both CO2 and P manipulations are critically needed to provide ecosystem‐scale understanding. Taken together, our results provide a quantitative baseline to constrain model‐based hypotheses of plant responses to eCO2 under P limitation, thereby improving projections of future global change impacts.
Excessive parallelism in protein evolution of Lake Baikal amphipod species flock.

Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistasic interactions underlying the dynamic nature of the amino acid preferences: the same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, while in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.
Recent developments in stunning and slaughter of poultry

A requirement under humane slaughter regulation is that stunning methods should induce immediate loss of consciousness and sensibility. If the onset of unconsciousness is not immediate, the induction of unconsciousness with a stunning method should not cause in animals avoidable anxiety, fear, pain, distress or suffering. The duration of unconsciousness induced by a stunning procedure must be longer than the sum of time that lapses between the end of stun and the time to onset of death. Since the effect of a stunning method is momentary, the onus of preventing resumption of consciousness thereafter relies on the efficiency of slaughter procedure; i.e. the prompt and accurate severance of blood vessels supplying oxygenated blood to the brain. Electrical water baths and gas or controlled atmospheres are commonly used for stunning poultry under commercial conditions. The electrical waveforms (sine wave alternating current or pulsed direct current) and frequencies (Hz) employed to stun poultry and the amount of current applied to individual birds in a water bath stunner widely varies. Rationalisation of electrical variables is urgently warranted. Varieties of gas mixtures have been proposed or used for stunning or killing poultry in crates or conveyors however the bird welfare implications have not been communicated effectively to facilitate progress. This review deals with the efficacy of electrical variables used in the water baths and of slaughter methods, and the relative merits of different gas mixtures used for stunning or killing broilers.
Efficacy of herbicides applied during the dry and wet seasons for Euphorbia heterophylla control in sugarcane

Objetivou-se estudar o efeito de herbicidas aplicados em pre e pos-emergencia, isolados e em combinacoes nas epocas seca e umida, para o controle de leiteiro (Euphorbia heterophylla) na cultura de cana-de-acucar. O experimento foi desenvolvido no periodo de agosto de 2008 a junho de 2009, em area de producao comercial de cana-de-acucar localizada no municipio de Jaboticabal-SP. O delineamento experimental foi o de blocos ao acaso, com quatro repeticoes, em esquema de parcela subdividida. Na epoca seca foram avaliados os herbicidas amicarbazone (1.400 g ha-1), imazapic (147 g ha-1) e sulfentrazone (900 g ha-1), aplicados em 1o/8/2008 apos a colheita da cana, e testemunha sem manejo previo das plantas daninhas. Os herbicidas utilizados na epoca umida foram: mesotrione isolado (192 g ha-1) e em mistura (120 g ha-1) com ametryn (1.500 gha-1), atrazine (1.500 gha-1) ou diuron + hexazinone (702 + 198 g ha-1), aplicados em 14/11/2008, alem de testemunha capinada e outra sem manejo das plantas daninhas. A aplicacao de imazapic na epoca seca foi eficaz no controle de E. heterophylla, dispensando a complementacao de manejo na epoca umida. No entanto, para os herbicidas amicarbazone e sulfentrazone houve necessidade da aplicacao de mesotrione, isolado ou em mistura com ametryn, atrazine ou diuron + hexazinone, para a manutencao do controle de E. heterophylla na epoca umida (de 105 a 230 dias apos a aplicacao na epoca seca). Quando nao foi realizada a aplicacao de herbicida na epoca seca, constatou-se melhor controle de E. heterophylla na epoca umida com o herbicida mesotrione associado a ametryn, atrazine ou diuron + hexazinone do que quando aplicado isoladamente. Apesar dos sintomas visuais de fitointoxicacao ocasionados pelos tratamentos mesotrione + ametryn e mesotrione + (diuron + hexazinone) pulverizados na epoca umida, nenhum dos manejos adotados ou combinacoes entre eles interferiu no numero de colmos viaveis por metro linear, no diâmetro e na altura de colmos de cana-de-acucar.
Planting conditions improve translocation success of the endangered terrestrial orchid Diuris fragrantissima (Orchidaceae)

By conducting reintroductions of the endangered terrestrial orchid Diuris fragrantissima D.L. Jones & M.A.Clem. we compared planting at the following three stages of the natural perennial growth cycle: as actively growing symbiotic plants in spring and autumn and as dormant tubers in summer. Plants reintroduced in spring and autumn were incorporated into randomised treatments involving soil aeration and addition of a mycorrhizal fungus. The addition of a mycorrhizal fungus and soil aeration together significantly increased survival and flowering of plants reintroduced in spring, whereas they had no significant effect on plants reintroduced in autumn. Addition of a fungus without soil aeration did not improve plant survival or flowering. Reintroducing actively growing plants was more successful than reintroducing dormant tubers, with 32.5% and 29.1% plants (reintroduced in spring and autumn, respectively) and 11.0% of tubers persisting after 4 years. Although survival of reintroduced plants declined at a rate of 16.9% per year for 4 years following reintroduction, survival of remnant plants remained relatively constant, ranging from 80.0 to 93.0%. Tuber size was positively correlated with survival and flowering of reintroduced plants for 2 years following reintroduction. A general trend was observed towards the increased likelihood of re-emergence and flowering of plants that flowered in previous seasons.
Proto-oncogene RTL4 promotes tumorigenesis and invasiveness of papillary thyroid cancer.

BACKGROUND Although the prognosis of papillary thyroid carcinoma (PTC) is good, its widespread prevalence still degrades the quality of life of tens of thousands of patients. PTC can even be life-threatening as a result of its aggressiveness and metastasis. METHODS Using complete transcriptome sequence analysis, cutting-edge research has revealed many tumor-associated genes. These related genes help us better understand the tumorigenesis and progression of PTC. We discovered that retrotransposon Gag like 4 (RTL4) is a novel potential PTC-associated gene. By Quantitative real-time polymerase chain reaction (qRT-PCR), we observed an obvious upregulation of RTL4 in PTC tissue. And, we validated the expression characteristics of RTL4 using data from the Cancer Genome Atlas (TCGA). Furthermore, we down-regulated RTL4 expression levels in relevant cell lines and studied the biological function of the RTL4 line in PTC by cell proliferation, colony formation, migration and invasion assays. RESULTS In the present study, high expression of RTL4 suggested lymph node metastasis (P = 0.028) and was associated with the pathological type (P = 0.001). RTL4 had the validity of distinguishing PTC tissues and normal tissues showed an AUC of 87.53% for the TCGA data set. The downregulation of RTL4 in the PTC cell lines distinctly inhibited cell colony formation, proliferation, migration, and invasion. CONCLUSIONS The result revealed RTL4 is closely related to the occurrence and development of PTC. RTL4 may participate in the HOTAIR-miR-206-ZCCHC16 ceRNA regulatory network and be regulated and play a role in the ceRNA regulatory network. It may be used as a target or indicator for the treatment and prognosis of PTC.
EFFECT OF SALICILYC ACID ON ASSIMILATORY PIGMENTS AND AMINOACIDS CONTENT IN SALT STRESSED WHEAT (TRITICUM AESTIVUM, CV. CRISANA) SEEDLINGS

Abiotic stress causes drastic yield reductions in most crops. Salinity is one of the major abiotic stresses and researchers are trying to find the most suitable substance to enhance plant tolerance to stress factors. One of these substances is Salicylic Acid (SA). It has a significant impact on the various aspects of the plant life. In this paper we study the effect of presoaking seeds in 0.05 or 0.1 mM SA solutions in pot experience, on some biochemical parameters modification like: assimilatory pigment contents, proline and other free aminoacid content in salt stressed wheat seedlngs. Salt stress was simulated by irrigation of the wheat seedlings with 0.2M NaCl solution. The highest enhancements of the tolerance to salinity on Triticum aestivum cultivar Crisana, plantlets were recorded in the case of treatments with 0.1 mM SA solution.
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing

Abstract Motivation Mining drug–disease association and related interactions are essential for developing in silico drug repurposing (DR) methods and understanding underlying biological mechanisms. Recently, large-scale biological databases are increasingly available for pharmaceutical research, allowing for deep characterization for molecular informatics and drug discovery. However, DR is challenging due to the molecular heterogeneity of disease and diverse drug–disease associations. Importantly, the complexity of molecular target interactions, such as protein–protein interaction (PPI), remains to be elucidated. DR thus requires deep exploration of a multimodal biological network in an integrative context. Results In this study, we propose BiFusion, a bipartite graph convolution network model for DR through heterogeneous information fusion. Our approach combines insights of multiscale pharmaceutical information by constructing a multirelational graph of drug–protein, disease–protein and PPIs. Especially, our model introduces protein nodes as a bridge for message passing among diverse biological domains, which provides insights into utilizing PPI for improved DR assessment. Unlike conventional graph convolution networks always assuming the same node attributes in a global graph, our approach models interdomain information fusion with bipartite graph convolution operation. We offered an exploratory analysis for finding novel drug–disease associations. Extensive experiments showed that our approach achieved improved performance than multiple baselines for DR analysis. Availability and implementation Source code and preprocessed datasets are at: https://github.com/zcwang0702/BiFusion.
Sustained acoustic medicine; sonophoresis for nonsteroidal anti-inflammatory drug delivery in arthritis

Background: Arthritis pain is primarily managed by nonsteroidal anti-inflammatory drugs (NSAIDs), such as diclofenac. Topical diclofenac gel is limited in efficacy due to its limited penetration through the skin. This study investigates the use of a multihour, wearable, localized, sonophoresis transdermal drug delivery device for the penetration enhancement of diclofenac through the skin. Materials & methods: A commercially available, sustained acoustic medicine (sam®) ultrasound device providing 4 h, 1.3 W, 132 mW/cm2, 3 MHz ultrasound treatment was evaluated for increasing the drug delivery of diclofenac gel through a human skin model and was compared with standard of care topical control diclofenac gel. Results: Sonophoresis of the diclofenac gel for 4 h increases diclofenac delivery by 3.8× (p < 0.01), and penetration by 32% (p < 0.01). Conclusion: Sustained acoustic medicine can be used as a transdermal drug-delivery device for nonsteroidal anti-inflammatory drugs.
High CO2 concentration and iron availability determine the metabolic inventory in an Emiliania huxleyi-dominated phytoplankton community.

Ocean acidification (OA), a consequence of anthropogenic carbon dioxide (CO2 ) emissions, strongly impacts marine ecosystems. OA also influences iron (Fe) solubility, affecting biogeochemical and ecological processes. We investigated the interactive effects of CO2 and Fe availability on the metabolome response of a natural phytoplankton community. Using mesocosms we exposed phytoplankton to ambient (390 μatm) or future CO2 levels predicted for the year 2100 (900 μatm), combined with ambient (4.5 nM) or high (12 nM) dissolved iron (dFe). By integrating over the whole phytoplankton community, we assigned functional changes based on altered metabolite concentrations. Our study revealed the complexity of phytoplankton metabolism. Metabolic profiles showed three stages in response to treatments and phytoplankton dynamics. Metabolome changes were related to the plankton group contributing respective metabolites, explaining bloom decline and community succession. CO2 and Fe affected metabolic profiles. Most saccharides, fatty acids, amino acids, and many sterols significantly correlated with the high dFe treatment at ambient pCO2 . High CO2 lowered the abundance of many metabolites irrespective of Fe. However, sugar alcohols accumulated, indicating potential stress. We demonstrate that not only altered species composition, but also changes in the metabolic landscape affecting the plankton community, may change as a consequence of future high-CO2 oceans. This article is protected by copyright. All rights reserved.
Complex Genetics in Pancreatitis

Supplemental digital content is available in the text. Objectives Chronic pancreatitis is the end stage of a pathologic inflammatory syndrome with multiple etiological factors, including genetic. We hypothesized that some pancreatitis etiology originates in pancreatic acinar or duct cells and requires both injury and compensatory mechanism failure. Methods One hundred pancreatitis patients were assessed using a DNA sequencing panel for pancreatitis. Cooccurrence of variants within and between genes was measured. Gene coexpression was confirmed via published single-cell RNA sequencing. Results One hundred and twenty-one variants were identified in 2 or more patients, 15 of which were enriched compared with reference populations. Single cell RNA-sequencing data verified coexpression of GGT1, CFTR, and PRSS1 in duct cells, PRSS1, CPA1, CEL, CTRC, and SPINK1 in acinar cells, and UBR1 in both. Multiple-risk variants with injury/stress effects (CEL, CFTR, CPA1, PRSS1) and impaired cell protection (CTRC, GGT1, SPINK1, UBR1) cooccur within duct cells, acinar cells, or both. Conclusions Pancreatitis is a complex disorder with genetic interactions across genes and cell types. These findings suggest a new, non-Mendelian genetic risk/etiology paradigm where a combination of nonpathogenic genetic risk variants in groups of susceptibility genes and injury/dysfunction response genes contribute to acquired pancreatic disease.
SEASONAL OCCURRENCE AND BIOLOGY OF GLOBE THISTLE CAPITULUM WEEVIL LARINUS ONOPORDI (F.) (COLEOPTERA: CURCULIONIDAE) IN NORTHEASTERN TURKEY

The biology of weevil species, Larinus onopordi (F.) living on globe thistle Echinops sphaerocephalus L. was described for the first time. The species is univoltine, adults overwinter under hiding object as aggregated. Eggs are inserted into the flowerhead; L. onopordi deposited eggs superficially, 1-23 (3.76) eggs each capitulum may be occur in one flowerhead, larvae develop in capitulum eating and destroying the seeds. In late summer, larvae complete their growth; prepare pupal case 1-4 (0.84) case in each flowerhead and pupation occurs in here. New generation adults emerge from flowerhead after waiting several days. Thus, this weevil has one generation per year in northeatern Turkey. A braconid wasp, Bracon facialis Thom. (Hymenoptera: Braconidae) reared from the pupal stage of L. onopordi.
Autocrine INSL5 promotes tumor progression and glycolysis via activation of STAT5 signaling

Metabolic reprogramming plays important roles in development and progression of nasopharyngeal carcinoma (NPC), but the underlying mechanism has not been completely defined. In this work, we found INSL5 was elevated in NPC tumor tissue and the plasma of NPC patients. Plasma INSL5 could serve as a novel diagnostic marker for NPC, especially for serum VCA‐IgA‐negative patients. Moreover, higher plasma INSL5 level was associated with poor disease outcome. Functionally, INSL5 overexpression increased, whereas knockdown of its receptor GPCR142 or inhibition of INSL5 reduced cell proliferation, colony formation, and cell invasion in vitro and tumorigenicity in vivo. Mechanistically, INSL5 enhanced phosphorylation and nuclear translocation of STAT5 and promoted glycolytic gene expression, leading to induced glycolysis in cancer cells. Pharmaceutical inhibition of glycolysis by 2‐DG or blockade of INSL5 by a neutralizing antibody reversed INSL5‐induced proliferation and invasion, indicating that INSL5 can be a potential therapeutic target in NPC. In conclusion, INSL5 enhances NPC progression by regulating cancer cell metabolic reprogramming and is a potential diagnostic and prognostic marker as well as a therapeutic target for NPC.
Clinical characteristics and social productivity levels of patients with malignant rheumatoid arthritis based on a nationwide clinical database in Japan: annual survey from 2003 to 2013

Abstract Objectives Malignant rheumatoid arthritis (MRA) is defined as rheumatoid arthritis (RA) with systemic vasculitis or other severe extra-articular manifestations. Japan has a nationwide database for MRA. We analyzed the characteristics of Japanese patients with MRA based on data from the Ministry of Health, Labour and Welfare (MHLW). Methods We were permitted to use data on 43,108 patients who were registered in the MHLW database from 2003 to 2013. Results Median age was 65 (interquartile range, 57–72) years. Patients consisted of 71% females. Proportions of patients who had or had experienced interstitial pneumonia and pleuritis were increased, episcleritis was stable, and other MRA manifestations were decreased over time. The number of positive symptoms per patient also decreased over time. The median dose of glucocorticoid, percentage of patients undergoing surgery, and use of non-steroidal anti-inflammatory drugs and apheresis decreased year by year. Steinbrocker stage and class improved over time. Median C-reactive protein levels and erythrocyte sedimentation rate also decreased. Regarding social productivity levels of patients with MRA, the proportion of patients who were working or working from home increased and the proportion of patients recuperating or hospitalized decreased. Conclusion In patients with MRA, disease activity decreased and social productivity improved from 2003 to 2013.
Propagule pressure in the presence of uncertainty: extending the utility of proxy variables with hierarchical models

Species invasions depend on the abundance and rate at which organisms are introduced to new localities, known as propagule pressure. Due to the challenges of measuring propagule pressure, proxy variables are often used; however, untested proxy variables may obscure the role of propagule pressure vs. ecological factors that facilitate invasion, leading to uncertainty about the invasion process and confounding management response. To generate absolute estimates of propagule pressure and facilitate meaningful comparison among pathways of species introduction, we extend proxy variables by combining ecological and global trade data with hierarchical statistical models. We derive absolute propagule pressure with probability distribution functions (propagule size: the probability of introducing n propagules per event; and overall propagule pressure: the probability of introducing n propagules per year) and, based on these projections, evaluate the performance of ballast water volume (m3) as a common proxy variable. Hindcast accuracy of ballast water volume was low but strongly scale‐dependent, exhibiting poor accuracy (R2 = 0·058) at small scales and only marginal accuracy at large scales (overall R2 = 0·169). As a result, conclusions about propagule pressure are likely to be biased based on the ballast volume proxy, as may be conclusions about species invasion when ballast water volume has been used. Irrespective of geographic pathway, estimated propagule sizes demonstrated extreme leptokurtosis and long right tails, with maximum values between 131‐fold and 2966‐fold greater than median values. These characteristics signify a subset of introduction events involving extreme propagule abundance that may provide opportunity to overcome Allee thresholds or marginal environmental conditions. Developing meaningful propagule supply functions is critical to resolve the role of propagule pressure within the invasion process and test hypotheses about species colonization at landscape scales. By joining absolute propagule pressure with existing theory about species extinction, the expected ecological outcome of environmental policy to manage propagule pressure can be estimated within a statistical framework.