Miracle-dz/UniFAR-FTUs huggingface dataset:
Aerophytic cyanoprokaryotes from the Atlantic rainforest region of São Paulo State, Brazil: Chroococcales and Oscillatoriales

Puisque les algues sont principalement aquatiques, il semble presque paradoxal qu'il existe une flore du sol relativement diversifiee ou les cyanoprokaryotes aerophiles sont particulierement abondantes. Cependant, les etudes dans ce domaine ne sont pas tres nombreuses. Le present article se propose de contribuer a la connaissance taxonomique de la flore des cyanoprocaryotes chroococcales et oscillatoriales dans les regions tropicales. Des echantillons de cyanoprokaryotes ont ete preleves dans une foret ombrophile de l'etat de Sao Paulo, Bresil. Les donnees sur le type et la couleur de la masse des cyanoprokaryotes, le type de substrat, la temperature et l'humidite de la masse et de l'air, le pH et les irradiances absolue et relative ont aussi ete enregistrees. L'etude a montre la presence de 24 especes appartenant aux ordres des Chroococcales et Oscillatoriales (12 especes chacun). Aphanothece (quatre especes) etait le genre le plus riche en especes. En general, la resolution taxonomique sur la base de donnees morphologiques et morphometriques peut parfois demeurer problematique.
Modeling the Potential Productivity of Urban Agriculture and Its Impacts on Soil Quality Through Experimental Research on Scale-Appropriate Systems

Urban agriculture could play a central role in local and regional food sovereignty in developed countries, but in many cities, a lack of space and competition with other land uses limit production. Options for meaningfully advancing food sovereignty goals include sustainable intensification of existing urban farms and gardens; (2) expansion of production into interstitial and other underutilized spaces undevelopable for other purposes; and (3) expansion of production in protected environments. Observational studies suggest that–like smallholder agriculture in the Global South–urban home, community, and market gardens in the developed world can be highly productive–but often are not. Research on scale-appropriate systems and outreach to urban agriculturalists are needed to help them grow more food, more sustainably. This replicated, long-term trial is addressing this need—and a dearth of experimental, normative research on urban agriculture—by evaluating the yield performance and impact on soil quality of four different systems of small-scale food production in Rhode Island, the second most densely populated state in the United States and a potential model for the development of sustainable urban food systems. Systems are modeled on vernacular systems in Providence, RI and Chicago, IL and on the scholarly and gray literature on sustainable intensification. They differ in soil management practices and nutrient sources. Results from the first 3 years of data collection indicate all four systems can be highly productive, with varying tradeoffs in terms of their sustainability and impacts on soil quality. While total marketable food yields were relatively modest compared to those reported in the gray literature for biointensive agriculture−2.22–2.96 kg m−2 averaged over three summer growing seasons compared to 4.64 kg m−2 for the “low end” of biointensive production—yields for individual crops generally exceeded—and often far exceeded—regional averages and, for most crops and systems, national averages, without a loss in soil quality. In addition to demonstrating the high productivity of small-scale systems compared to commercial farms, the study establishes a framework for conducting normative, experimental research that can help to guide practice. It also offers more reliable yield estimates for modeling the production potential of cities than do observational studies and agronomic experiments on monocultures.
The Acquisition of Clause Chaining in Nungon

The clause chain is an under-investigated complex sentence type, found in hundreds of languages. In a clause chain, as many as 20 or more ‘medial’ clauses with under-specified verbal predicates combine with a single ‘final’ clause with fully-specified verbal predicate. Clause chains are of interest for three main reasons: (a) the special syntactic relationship between clauses, which is neither textbook subordination nor coordination; (b) the potential extreme length of a single chain; and (c) switch-reference marking in clause chains of some languages could require speakers to plan at least one clause ahead as they speak. Research on child production of complex sentences has largely overlooked clause chains. Longitudinal data for three children aged 1;1 to 3;3 acquiring the Papuan language Nungon show that Nungon-speaking children begin producing clause chains around the age of 2;4, with a marked increase in rate of use around age 2;11. Chain length is limited to two clauses until age 3;1. Different-subject marking in medial clauses is used by all three children early, but is first attested in one-clause, ‘root medial’ contexts, rather than in chains. Bayesian statistical models confirm the strong tendency for children to use root medials in expressions of desires and commands. Children’s production of three types of complex sentences—clause chains, subordinated final clauses, and coordinated final clauses—is shown to be subject to the same type of developmental constraint; but once development reaches an adequate level for increased complex sentence production, children acquiring Nungon produce many more clause chains than complex sentences involving subordinated or coordinated final clauses.
Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns

Some cell lines exhibit transcriptomic, epigenomic, and mutational signatures of a different cancer type than originally annotated. Cell lines are commonly used as cancer models. The tissue of origin provides context for understanding biological mechanisms and predicting therapy response. We therefore systematically examined whether cancer cell lines exhibit features matching the presumed cancer type of origin. Gene expression and DNA methylation classifiers trained on ~9000 tumors identified 35 (of 614 examined) cell lines that better matched a different tissue or cell type than the one originally assigned. Mutational patterns further supported most reassignments. For instance, cell lines identified as originating from the skin often exhibited a UV mutational signature. We cataloged 366 “golden set” cell lines in which transcriptomic and epigenomic profiles strongly resemble the cancer type of origin, further proposing their assignments to subtypes. Accounting for the uncertain tissue of origin in cell line panels can change the interpretation of drug screening and genetic screening data, revealing previously unknown genomic determinants of sensitivity or resistance.
Single-dose mRNA therapy via biomaterial-mediated sequestration of overexpressed proteins

Nanostructured mineral coatings delivering chemically modified or unmodified therapeutic mRNA improve diabetic wound healing. Nonviral mRNA delivery is an attractive therapeutic gene delivery strategy, as it achieves efficient protein overexpression in vivo and has a desirable safety profile. However, mRNA’s short cytoplasmic half-life limits its utility to therapeutic applications amenable to repeated dosing or short-term overexpression. Here, we describe a biomaterial that enables a durable in vivo response to a single mRNA dose via an “overexpress and sequester” mechanism, whereby mRNA-transfected cells locally overexpress a growth factor that is then sequestered within the biomaterial to sustain the biologic response over time. In a murine diabetic wound model, this strategy demonstrated improved wound healing compared to delivery of a single mRNA dose alone or recombinant protein. In addition, codelivery of anti-inflammatory proteins using this biomaterial eliminated the need for mRNA chemical modification for in vivo therapeutic efficacy. The results support an approach that may be broadly applicable for single-dose delivery of mRNA without chemical modification.
Transgenic Cotton (Gossypium hirsutum L.) to Combat Weed Vagaries: Utility of an Apical Meristem-Targeted in planta Transformation Strategy to Introgress a Modified CP4-EPSPS Gene for Glyphosate Tolerance

Weeds burden plant growth as they compete for space, sunlight, and soil nutrients leading to 25–80% yield losses. Glyphosate [N-(phosphonomethyl)glycine] is a widely used broad spectrum non-selective herbicide that controls weeds by inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme and interfering with the shikimate biosynthesis pathway. Cotton (Gossypium hirsutum L.) is one of the most important commercial crops grown worldwide for its fiber. We have developed herbicide tolerant transgenic cotton (cv. P8-6) by introgression of a codon-optimized and modified EPSPS gene (CP4-EPSPS) possessing an N-terminal chloroplast targeting peptide from Petunia hybrida. Because of the recalcitrant nature of cotton, a genotype-independent non-tissue culture-based apical meristem-targeted in planta transformation approach was used to develop transformants. Although in planta transformation methodologies are advantageous in developing a large number of transgenic plants, effective screening strategies are essential for initial identification of transformants. In the present study, the use of a two-level rigorous screening strategy identified 2.27% of T1 generation plants as tolerant to 800 and 1,500 mg/L of commercially available glyphosate (Roundup). Precise molecular characterization revealed stable integration, expression, and inheritance of CP4-EPSPS in advanced generations of the promising transgenic events. Further, superiority of selected transgenic plants in tolerating increasing levels of glyphosate (500–4,000 mg/L) was ascertained through reduced accumulation of shikimate. This report is the first of its kind where cotton transformants tolerating high levels of glyphosate (up to 4,000 mg/L) and accumulating low levels of shikimate have been identified. This study not only reiterated the genotype-independent nature of the transformation strategy but also reiterated the translational utility of the CP4-EPSPS gene in management of weeds.
hiPSC-Based Model of Prenatal Exposure to Cannabinoids: Effect on Neuronal Differentiation

Phytocannabinoids are psychotropic substances ofcannabis with the ability to bind endocannabinoid (eCB) receptors that regulate synaptic activity in the central nervous system (CNS). Synthetic cannabinoids (SCs) are synthetic analogs of Δ9-tetrahydrocannabinol (Δ9-THC), the psychotropic compound of cannabis, acting as agonists of eCB receptor CB1. SC is an easily available and popular alternative to cannabis, and their molecular structure is always changing, increasing the hazard for the general population. The popularity of cannabis and its derivatives may lead, and often does, to a child’s exposure to cannabis both in utero and through breastfeeding by a drug-consuming mother. Prenatal exposure to cannabis has been associated with an altered rate of mental development and significant changes in nervous system functioning. However, the understanding of mechanisms of its action on developing the human CNS is still lacking. We investigated the effect of continuous exposure to cannabinoids on developing human neurons, mimicking the prenatal exposure by drug-consuming mother. Two human induced pluripotent stem cells (hiPSC) lines were induced to differentiate into neuronal cells and exposed for 37 days to cannabidiol (CBD), Δ9-THC, and two SCs, THJ-018 and EG-018. Both Δ9-THC and SC, at 10 μM, promote precocious neuronal and glial differentiation, while CBD at the same concentration is neurotoxic. Neurons exposed to Δ9-THC and SC show abnormal functioning of voltage-gated calcium channels when stimulated by extracellular potassium. In sum, all studied substances have a profound impact on the developing neurons, highlighting the importance of thorough research on the impact of prenatal exposure to natural and SC.
Petunidin-Based Anthocyanin Relieves Oxygen Stress in Lactobacillus plantarum ST-III

Application of probiotics in the food industry has been hampered by their sensitivity to challenging conditions that reduce their vitality in food matrices. A lot of attempts have been made to promote the growth of these probiotics in the aspect of nutrition demands. Among the other adverse conditions, oxygen stress can restrict the growth of probiotics and has not yet been paid enough attention to. In this study, the effect of a petunidin-based anthocyanin (ACN) on the growth of probiotic Lactobacillus plantarum ST-III was investigated under oxygen stress. The growth of ST-III was analyzed through spot assay on agar plates as well as plating-based enumeration of the viable cells in the liquid culture. Results indicated that ACN could efficiently improve the growth of ST-III under oxygen stress, whereas no effect was observed in the absence of oxygen stress. Further investigations indicated that ACN reduced the oxido-reduction potential of the culture; meanwhile, it exerted a positive transcriptional regulation on the thioredoxin system of ST-III, leading to a decrease in reactive oxygen species accumulation within the cells. Moreover, ACN enabled the growth of ST-III in reconstituted skim milk and promoted the formation of milk clots. These results revealed the role of a petunidin-based ACN in oxygen stress relief and highlighted its potential in manufacture and preservation of L. plantarum-based dairy products.
Characterization of an endopolygalacturonase produced by the apple scab fungus, Venturia inaequalis

Secretion of a constitutive endopectinase was detected in cultures of Venturia inaequalis grown in complex and defined media. Pectinylase or pectinesterase activity was not present. The attainable level of extracellular pectinase was present after 5–10 d post inoculation, when only about 5–10% of mycelial mass had developed. Time course culture experiments with conidial and mycelial inoculum indicated that enzyme secretion did not depend on physiological effects within or shortly after conidial germination. Cellulosic substrates did not affect pectinase production. Catabolite repression or repression by glucose was not detected and there was no stimulation of enzyme production in media supplemented with pectic substrates. Inhibition of enzyme activity by galacturonic acid was not detected. Nineteen isolates of V. inaequalis were tested, all of which displayed constitutive pectinase production. All isolates were able to grow in the defined media with galacturonic acid or the pectic substrates as the sole carbon source. Mycelial pectinolytic activity was only detectable in substantial quantities when the fungus was grown in media supplemented with 1% pectin. The pectinase preparations displayed a long-term stability at temperatures up to 20 °C and within a pH-range of 5–7·5. Activity was very low at 5 and 10° and there was a distinct increase at 15 and 20°. Enzyme activity was highest at pH 4 and decreased with increasing pH. Time course viscometric assays and hplc analyses of liberated galacturonic acid indicated an endo-type degradation of pectin and polygalacturonic acid. Di- and trigalacturonic acid were released from pectin with high enzyme concentration and long incubation. Pectin with a degree of esterification of 93% showed reduced degradability. Pectinase preparations had a macerating activity on solvent extracted apple leaves and caused galacturonic acid release. Isoelectric focusing followed by a zymogram technique revealed a single activity band at pl 10. The pectinase preparations from culture filtrates or mycelia of 19 isolates did not show any differences in characteristics of degradative activity or the activity band detected after isoelectric focusing.
Interrelation between the relative fat mass index and other obesity indices in predicting clinical severity and prognosis of acute myocardial infarction

1Institute for Cardiovascular Prevention and Rehabilitation, Zagreb, Croatia 2School of Dental Medicine, University of Zagreb, Zagreb, Croatia 3School of Medicine, University of Zagreb, Zagreb, Croatia 4Faculty of Kinesiology, University of Zagreb, Zagreb, Croatia 5Coronary Care Unit, Department of Cardiology, Internal Medicine Clinic, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia 6Department of Emergency Medicine, Internal Medicine Clinic, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand KITLG/SCF and Gene-By-Air-Pollution Interaction

Baseline lung function is a standard diagnostic criterion used by clinicians to detect lung diseases. It is a complex trait significantly influenced by both genetics and environmental factors. Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV1), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV1 on chromosome 12 in 867 African American children with asthma (P = 1.26 × 10−8, β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV1. Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with KITLG (KIT ligand, also known as SCF), and their minor alleles were associated with increased expression of the KITLG gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure (P = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV1, possibly mediated through KITLG, in African American children with asthma. This is the first study that has identified a genetic association between lung function and KITLG, which has established a role in orchestrating allergic inflammation in asthma.
Isolation and characterization of sixteen microsatellite loci for the rudderfish Kyphosus elegans (Centrarchiformes: Kyphosidae) from Easter Island, discovered with Next Generation Sequencing

The rudderfish of the genus Kyphosus inhabits rocky environments and coral reefs in warm waters worldwide (Sakai and Nakabo, 2014). In the Pacific, Kyphosus elegans (Peters, 1869), formerly Pimelepterus sandwicensis Sauvage (1880) [please see Knudsen and Clements (2013) for revision), have an antitropical distribution in the central and western Pacific (Randall and Cea, 2010; ]. On Easter Island, K. elegans is an herbivorous species that feeds on macroalgae, such as Lobophora variegata and Sargassum and often occur in schools
Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1

Integrator is a key regulator of NEAT1 isoform switching and, thereby, paraspeckles biogenesis and chemosensitivity. RNA 3′ end processing provides a source of transcriptome diversification which affects various (patho)-physiological processes. A prime example is the transcript isoform switch that leads to the read-through expression of the long non-coding RNA NEAT1_2, at the expense of the shorter polyadenylated transcript NEAT1_1. NEAT1_2 is required for assembly of paraspeckles (PS), nuclear bodies that protect cancer cells from oncogene-induced replication stress and chemotherapy. Searching for proteins that modulate this event, we identified factors involved in the 3′ end processing of polyadenylated RNA and components of the Integrator complex. Perturbation experiments established that, by promoting the cleavage of NEAT1_2, Integrator forces NEAT1_2 to NEAT1_1 isoform switching and, thereby, restrains PS assembly. Consistently, low levels of Integrator subunits correlated with poorer prognosis of cancer patients exposed to chemotherapeutics. Our study establishes that Integrator regulates PS biogenesis and a link between Integrator, cancer biology, and chemosensitivity, which may be exploited therapeutically.
Experimental evolution of nascent multicellularity: Recognizing a Darwinian transition in individuality

Major evolutionary transitions in individuality, at any level of the biological hierarchy, occur when groups participate in Darwinian processes as units of selection in their own right. Identifying transitions in individuality can be problematic because apparent selection at one level of the biological hierarchy may be a by-product of selection occurring at another level. Here we discuss approaches to this “levels-of-selection” problem and apply them to a previously published experimental exploration of the evolutionary transition to multicellularity. In these experiments groups of the bacterium Pseudomonas fluorescens were required to reproduce via life cycles involving soma- and germline-like phases. The rate of transition between the two cell types was a focus of selection, and might be regarded as a property of groups, cells, or even genes. By examining the experimental data under several established philosophical frameworks, we argue that in the Pseudomonas experiments, bacterial groups acquired Darwinian properties sufficient to allow the evolution of traits adaptive at the group level.
Xenogenization of tumor cells by fusogenic exosomes in tumor microenvironment ignites and propagates antitumor immunity

Reinforcing danger signal by delivering viral antigens on cancer cells with fusogenic exosomes enhances anti-tumor immunity. Many cancer patients not responding to current immunotherapies fail to produce tumor-specific T cells for various reasons, such as a lack of recognition of cancer cells as foreign. Here, we suggest a previously unidentified method for xenogenizing (turning self to non-self) tumors by using fusogenic exosomes to introduce fusogenic viral antigens (VSV-G) onto the tumor cell surface. We found that xenogenized tumor cells were readily recognized and engulfed by dendritic cells; thereby, tumor antigens were efficiently presented to T lymphocytes. Moreover, exosome–VSV-G itself acts as a TLR4 agonist and stimulates the maturation of dendritic cells, leading to CD8+ T cell cross-priming. The administration of these exosomes in multiple tumor mouse models xenogenized tumor cells, resulting in tumor growth inhibition. The combinatorial treatment with anti–PD-L1 exhibited complete tumor regression (30%) and better long-term overall survival. These results suggest that tumor xenogenization by fusogenic exosomes provides a previously unidentified novel strategy for cancer immunotherapy.