Miracle-dz/UniFAR-FTUs huggingface dataset:
Tuning Cancer Fate: Tumor Microenvironment's Role in Cancer Stem Cell Quiescence and Reawakening

Cancer cell dormancy is a common feature of human tumors and represents a major clinical barrier to the long-term efficacy of anticancer therapies. Dormant cancer cells, either in primary tumors or disseminated in secondary organs, may reawaken and relapse into a more aggressive disease. The mechanisms underpinning dormancy entry and exit strongly resemble those governing cancer cell stemness and include intrinsic and contextual cues. Cellular and molecular components of the tumor microenvironment persistently interact with cancer cells. This dialog is highly dynamic, as it evolves over time and space, strongly cooperates with intrinsic cell nets, and governs cancer cell features (like quiescence and stemness) and fate (survival and outgrowth). Therefore, there is a need for deeper insight into the biology of dormant cancer (stem) cells and the mechanisms regulating the equilibrium quiescence-versus-proliferation are vital in our pursuit of new therapeutic opportunities to prevent cancer from recurring. Here, we review and discuss microenvironmental regulations of cancer dormancy and its parallels with cancer stemness, and offer insights into the therapeutic strategies adopted to prevent a lethal recurrence, by either eradicating resident dormant cancer (stem) cells or maintaining them in a dormant state.
Exploring Spiroplasma Biology: Opportunities and Challenges

Spiroplasmas are cell-wall-deficient helical bacteria belonging to the class Mollicutes. Their ability to maintain a helical shape in the absence of cell wall and their motility in the absence of external appendages have attracted attention from the scientific community for a long time. In this review we compare and contrast motility, shape determination and cytokinesis mechanisms of Spiroplasma with those of other Mollicutes and cell-walled bacteria. The current models for rod-shape determination and cytokinesis in cell-walled bacteria propose a prominent role for the cell wall synthesis machinery. These models also involve the cooperation of the actin-like protein MreB and FtsZ, the bacterial homolog of tubulin. However the exact role of the cytoskeletal proteins is still under much debate. Spiroplasma possess MreBs, exhibit a rod-shape dependent helical morphology, and divide by an FtsZ-dependent mechanism. Hence, spiroplasmas represent model organisms for deciphering the roles of MreBs and FtsZ in fundamental mechanisms of non-spherical shape determination and cytokinesis in bacteria, in the absence of a cell wall. Identification of components implicated in these processes and deciphering their functions would require genetic experiments. Challenges in genetic manipulations in spiroplasmas are a major bottleneck in understanding their biology. We discuss advancements in genome sequencing, gene editing technologies, super-resolution microscopy and electron cryomicroscopy and tomography, which can be employed for addressing long-standing questions related to Spiroplasma biology.
RESIVOZ: Dialogue System for Voice-based Information Registration in Eldercare

espanolRESIVOZ es un sistema de dialogo orientado a ayudar a gerontologos a registrar facilmente informacion sobre sus cuidados a los residentes. En comparacion con el uso tradicional de ordenadores instalados en puntos de control especificos para registrar la informacion, la naturaleza manos-libres y movil de RESIVOZ permite al personal gerontologico registrar sus actividades de forma natural, donde y cuando se necesite. Ademas del principal componente de sistema de dialogo hablado, el prototipo de sistema tambien incluye un panel de administracion y una aplicacion movil disenada para visualizar y editar la informacion de cuidados a residentes. EnglishRESIVOZ is a spoken dialogue system aimed at helping geriatric nurses easily register resident caring information. Compared to the traditional use of computers installed at specific control points for information recording, RESIVOZ's hands-free and mobile nature allows nurses to enter their activities in a natural way, when and where needed. Besides the core spoken dialogue component, the presented prototype system also includes an administration panel and a mobile phone App designed to visualise and edit resident caring information.
clusterTools: proximity searches for functional elements to identify putative biosynthetic gene clusters

Motivation: The low cost of DNA sequencing has accelerated research in natural product biosynthesis allowing us to rapidly link small molecules to the clusters that produce them. However, the large amount of data means that the number of putative biosynthetic gene clusters (BGCs) far exceeds our ability to experimentally characterize them. This necessitates the need for development of further tools to analyze putative BGCs to flag those of interest for further characterization. Results: Clustertools implements a framework to aid in the characterization of putative BGCs. It does this by or-ganizing genomic information on coding sequences in a way that enables directed, hypothesis-driven queries for functional elements in close physical proximity of each other. Genomic sequence databases can be constructed in clusterTools with an interface to the NCBI Genbank and Genomes databases, or from private sequence databases. clusterTools can be used either to identify interesting BGCs from a database of putative BGCs, or on databases of genomic sequences to identify and download regions of interest in the DNA for further processing and annotation in programs such as antiSMASH. We have used clusterTools to identify putative and known biosynthetic gene clus-ters involved in bacterial polyketide alkaoloid and tetronate biosynthesis. Availability and Implementation: Clustertools is implemented in Python and is available via the AGPL. Stand-alone versions of clusterTools are available for Macintosh, Windows, and Linux upon registration (https://goo.gl/forms/QRKTkpqiA0g31IWp1). The source-code is available at https://www.github. com/emzodls/clusterArch. Supplementary information: A manual describing the Python toolkit that powers clusterTools, as well as the HMMs constructed for the tetronate search is available online.
The Antinociceptive Effect of GW5074 in C57BL/6 Mice

Visceral pain is one of the most common type of pain in mammals, however its mechanisms of action has not clearly been understood. In common sense, prostaglandins are released depending on tissue damage to reduce the threshold of pain receptors. Thus, pharmacological inhibition of c-Raf kinase signaling which controls the expression of cytokines and other proinflammatory factors may increase the threshold of these receptors. In the present study, we aimed to investigate the possible antinociceptive effect of GW5074, a selective c-Raf inhibitor, in chemically induced pain model. Pretreatment with GW5074 (0.5 and 2 mg/kg) significantly reduced the number of abdominal contractions induced by acetic acid. Therefore, our results suggest the idea that c-Raf kinase signaling could be responsible in peripheral pain mechanisms.
EM-studies on Salviniaceae Megaspores from the Middle Miocene Fasterholt Flora, Denmark

AbstractReproductive organs of Salvinia and Azolla were found together with other small plant remains in the Middle Miocene Fasterholt flora, Denmark. They were examined by the use of SEM and TEM; this was done with the three species of Azolla for the first time. Salvinia is represented by one, or possibly two, species. The megaspore of S. cerebrata has a characteristic surface sculpture of irregular, rounded ridges. Some specimens differ from the typical S. cerebrata by having strongly developed verrucae or clavae. They are described as Salvinia sp. , but it is possible that they represent a variety of S. cerebrata. Azolla is represented by three species. A. nikitinii and A. ventricosa have nine floats in two tiers; massulae have not been found. A. tuganensis has three floats in one tier, massulae have anchor-shaped glochidia.
On lattice point counting in Δ-modular polyhedra

Let a polyhedron $P$ be defined by one of the following ways: (i) $P = \{x \in R^n \colon A x \leq b\}$, where $A \in Z^{(n+k) \times n}$, $b \in Z^{(n+k)}$ and $rank\, A = n$; (ii) $P = \{x \in R_+^n \colon A x = b\}$, where $A \in Z^{k \times n}$, $b \in Z^{k}$ and $rank\, A = k$. And let all rank order minors of $A$ be bounded by $\Delta$ in absolute values. We show that the short rational generating function for the power series $$ \sum\limits_{m \in P \cap Z^n} x^m $$ can be computed with the arithmetic complexity $ O\left(T_{SNF}(d) \cdot d^{k} \cdot d^{\log_2 \Delta}\right), $ where $k$ and $\Delta$ are fixed, $d = \dim P$, and $T_{SNF}(m)$ is the complexity to compute the Smith Normal Form for $m \times m$ integer matrix. In particular, $d = n$ for the case (i) and $d = n-k$ for the case (ii). The simplest examples of polyhedra that meet conditions (i) or (ii) are the simplicies, the subset sum polytope and the knapsack or multidimensional knapsack polytopes. We apply these results to parametric polytopes, and show that the step polynomial representation of the function $c_P(y) = |P_{y} \cap Z^n|$, where $P_{y}$ is parametric polytope, can be computed by a polynomial time even in varying dimension if $P_{y}$ has a close structure to the cases (i) or (ii). As another consequence, we show that the coefficients $e_i(P,m)$ of the Ehrhart quasi-polynomial $$ \left| mP \cap Z^n\right| = \sum\limits_{j = 0}^n e_i(P,m)m^j $$ can be computed by a polynomial time algorithm for fixed $k$ and $\Delta$.
EVALUATION OF RAPD AND SSR MOLECULAR MARKERS IN BREAD WHEATGENOTYPES

In this study was evaluated the molecular analysis of 10 bread wheat genotypes using RAPD and SSR markers. In RAPD with 6 primers and in SSR with 5 primers were detected 33 and 17 polymorphism allels for genotypes. The most Polymorphic Information Content (PIC) value and polymorphism percentage was detected by UBC 350 and UBC 109 markers with values 0.53 and 0.50 respectively in RAPDs. In SSRs, Xgwm 469-6D marker detected 14 bands with 5 polymorphic alleles but Xgwm120-2B had the most PIC with 57%. For both markers UPGMA was the best method of clustering. Although markers could show genotypes in 2 clusters but that was very different in molecular analysis. In final results RAPDs could detect more polymorphism alleles than SSRs.
The Temperature-Regulation of Pseudomonas aeruginosa cmaX-cfrX-cmpX Operon Reveals an Intriguing Molecular Network Involving the Sigma Factors AlgU and SigX

Pseudomonas aeruginosa is a highly adaptable Gram-negative opportunistic pathogen, notably due to its large number of transcription regulators. The extracytoplasmic sigma factor (ECFσ) AlgU, responsible for alginate biosynthesis, is also involved in responses to cell wall stress and heat shock via the RpoH alternative σ factor. The SigX ECFσ emerged as a major regulator involved in the envelope stress response via membrane remodeling, virulence and biofilm formation. However, their functional interactions to coordinate the envelope homeostasis in response to environmental variations remain to be determined. The regulation of the putative cmaX-cfrX-cmpX operon located directly upstream sigX was investigated by applying sudden temperature shifts from 37°C. We identified a SigX- and an AlgU- dependent promoter region upstream of cfrX and cmaX, respectively. We show that cmaX expression is increased upon heat shock through an AlgU-dependent but RpoH independent mechanism. In addition, the ECFσ SigX is activated in response to valinomycin, an agent altering the membrane structure, and up-regulates cfrX-cmpX transcription in response to cold shock. Altogether, these data provide new insights into the regulation exerted by SigX and networks that are involved in maintaining envelope homeostasis.
Stratification and diversity of beetles (Insecta, Coleoptera) in native elm forests of the Ussuri Nature Reserve, Russia

The vertical stratification of beetles (Coleoptera) in native elm forest in the Komarovka River valley (Primorsky Krai) was studied for the first time. The highest number of species was observed in the shrub stratum. Migration of beetles from the crown and the ground strata to the shrub stratum increases its taxonomic diversity. The trophic group plays a crucial role in vertical stratification of beetles. It was found by analyzing the features of vertical stratification of beetles in native elm forest that beetle species with a broader trophic spectrum (phytophages assemblages) are observed as one proceeds from the ground stratum to the upper canopy stratum, which is associated with the diversity of the vegetation. Furthermore, the abundance of phytopages rises, while that of zoophages, coprophages, and necrophages decreases. Thus, the proportion of phytophages in the ground and crown strata is 11.8% and 77.3%; the ratio between zoophages and necrophages is 52.9 and 32.4% in the ground stratum and 9.1 and 4.5% in the crown stratum, respectively. Keywords: Coleoptera - Diversity - Trophic groups - Elm - Valley forests - Primorsky Krai
Kepekaan Erythricium salmonicolor Penyebab Penyakit Jamur Upas pada Kemiri Sunan terhadap Suhu, Cahaya, dan Fungisida

A typical pink disease symptom appeared on stem of Reutealis trisperma in Bogor. The present study was aimed for confirming the causal pathogen and testing its sensitivity to temperature, light and fungicides. The fungus was identified based on its morphological characteristics. The fungal inoculum was obtained by tissue isolation of infected stem bark. For pathogenicity test, the fungus was inoculated onto sterilized pieces of woody R. trisperma branch, then fastened on the seedlings and incubated in the green house. The effect of temperatures on fungal growth was tested by planting the fungal colony onto potato dextrose agar (PDA) then incubated at 25–34 °C. The sensitivity of the fungus to light was tested by inoculating the fungus into flask with potato dextrose broth (PDB) medium on a shaker (60 rpm) exposing it to white light tube (400 luks) or in a dark condition for 15 days at 25 °C. The obtained fungal colonies were weighed. Efficacy of copper hydroxide and mancozeb against the fungal colony growth was tested by inoculating the fungus onto PDA amended with 100, 200, 300, 400, and 500 ppm, respectively, of tested fungicides. The results showed that the causal pathogen was Erythricium salmonicolor . In the pathogenicity test, cobwebs of E. salmonicolor were formed on inoculated seedlings 3 weeks after inoculation. The optimum temperature for growth of E. salmonicolor was 28 °C. There was no significant effect of light on fungal growth. Mancozeb suppressed colony of E. salmonicolor growth better than copper hydroxide.
Molecular Detection, Typing, and Quantification of Campylobacter spp. in Foods of Animal Origin.

The most frequently reported zoonosis and the main bacterial foodborne disease infection in humans is caused by Campylobacter spp. , and C. jejuni and C. coli are the most common types. These bacteria can be found in the intestinal tracts of cattle, dogs, cats, sheep, poultry and pigs. The isolation of this microorganism is laborious because it requires specific media and a low oxygen concentration for growth. Additionally, differentiation between species through conventional bacteriology is difficult, as there are few different biochemical characteristics among the various species. Molecular microbiological techniques have become more important and are now broadly applied to help overcome difficulties in the identification, differentiation, and quantification of this pathogen. To date, there have been advances in the development and use of molecular techniques for the identification of microorganisms in foodstuffs. Tools such as pulsed-field gel electrophoresis and multilocus sequence typing are the most commonly used for typing. For the identification and confirmation of species, polymerase chain reaction (PCR) is crucial. Quantification by real-time PCR has wide applicability. To identify strains and antimicrobial resistance genes, sequencing technologies have been applied. This review builds on the discussion about the main and most widely used molecular methods for Campylobacter, as well as methods showing better potential for the classification, identification, and quantification of this important pathogen.
Utilizing NMR to study RNA- and compound-binding mechanisms of Musashi-1, a stem/progenitor cell marker in various normal and cancer cells

Received: March 11, 2018; Accepted: March 29, 2018; Published: April 02, 2018 An RNA-binding protein, Musashi-1 (Msi1), is a posttranscriptional gene regulator that is involved in the regulation of stem cell self-renewal. Because of its high-level expression in neural stem cells (NSCs) and undifferentiated neural precursor cells [1], Msi1 is used as a cell marker for NSCs and progenitor cells in the central nervous system. Increasing evidence suggested that Mis1 acts as a critical regulator of the status of stem/progenitor cells in other tissues and organs [2,3], including the breast, eye, hair follicles, intestine, and stomach, in either embryonic or adult stages; thus, Msi1 may also be used as an effective marker for stem/progenitor cells in a wide range of tissues and organs.
Backward evolution from gene network dynamics

Gene expression is controlled by regulator genes that together with effector genes form gene regulatory networks. How mutation in the genes comprising gene regulatory networks influences cell population dynamics has not been adequately investigated. In this study, we develop mathematical models to study how a mutation in a regulator gene that reaches the effector gene with a time delay affects short-term and long-term population growth. Using theory and experiment, we find a paradoxical outcome of evolution where a mutation in a regulator gene leads to an interaction between gene regulatory network and population dynamics, causing in certain cases a permanent decrease in population fitness in a constant environment. Significance Statement The properties of a cell are largely the products of its proteins, synthesized at rates depending on the regulation of protein coding genes. Single-cell measurements show that genetically identical cells can differ radically in their protein levels, partially due to the random production and degradation of proteins. It is currently unknown how mutants arise and spread in populations affected by such biological variability. We use computer simulations and evolution experiments to study how a mutant spreads in a population that carries a synthetic drug resistance gene network. Our results show for the first time a paradoxical outcome of evolution, where an initially beneficial mutation can interact with gene regulatory network dynamics and cause a permanent decrease in population fitness in the same environment.
Induction of Male-Sterility by Controlling of Gibberellin Biosynthesis in Rice (Oryza sativa)

Gibberellins (GAs) are important hormones at every plant developmental stage including vegetative and reproductive. It is reported in many plant species that many dwarfism and male sterile mutants have defective GA biosynthesis genes. RNA interference (RNAi) technology can reduce expression of specific genes at the transcription level. Also, promoters can control the spatial and temporal expression of genes. Specific promoters containing the RNAi vector can control specific genes’ spatial and temporal expression at the transcriptional level. In this study, at first, five anther specific promoters were chosen and verified by examining their tissue specific expression using promoter::GUS transgenic analysis. RNAi vectors, which contain five anther specific promoters and one constitutive promoter fused to GA biosynthesis related genes, were constructed for controlling of GA biosynthesis in stem and floral tissue. OsAct1 promoter containing OsGA20ox1 and OsGA3ox2 RNAi T1 plants showed reduced gene expression and short plant height phenotype compare to wild type plant. OsGA20ox and OsGA3ox RNAi transformants also showed reduced fertility or sterile phenotype.
Relationship of Freshwater Fish Recruitment With Distinct Reproductive Strategies and Flood Attributes: A Long-Term View in the Upper Paraná River Floodplain

The flood pulse is the main driving force for communities' structure and functioning in river-floodplain systems. High synchrony exists between the hydrological cycle and reproductive cycle events for several fish species. However, species with different reproductive strategies can respond in different ways to the flood regime. Thus, this study intends to evaluate the relationship between the recruitment of different reproductive guilds of freshwater fish and flood attributes (flood duration, maximum annual water level, and delay of flood) from a time series of 20 years in the Upper Paraná River floodplain, Brazil. The abundance of four guilds was evaluated: (i) long-distance migratory with external fertilization and without parental care (LMEF); (ii) non-migratory or short-distance migratory with external fertilization and without parental care (NEFW); (iii) non-migratory or short-distance migratory with external fertilization and parental care (NEFP); and (iv) non-migratory or short-distance migratory with internal fertilization and without parental care (NIF). Multiple regression analyses were applied between flood attributes and abundance of young-of-the-year or juveniles for each reproductive guild. This study observed a consistent pattern of long-lasting flooding positively influencing the recruitment of all reproductive guilds, while water level intensity and the time of the onset of flooding also influenced some non-migratory strategies. We can conclude that the conservation of fish populations and the maintenance of ecosystem functions and services associated with them need to be considered in the operating protocols of upstream hydroelectric plants, since they are dependent on the flooding controlled by them.
Wound healing and antioxidant capacity of Musa paradisiaca Linn. peel extracts

Context: Musa paradisiaca has several biological activities within them wound healing, hypoglycemic, hepatoprotective, antimicrobial, antioxidant, among others. However, these properties in peel have been poorly explored. Aims: Evaluate the wound healing activity induced by an incision wound model using methanolic, hexanoic and chloroformic extracts from M. paradisiaca peel. Methods: Dehydrated M. paradisíaca peel was mixed with methanol, hexane, and chloroform. The presence of bioactive substances of the M. paradisiaca peel extracts was carried out by the Trease and Evans methods. Antioxidant capacity was evaluated by the 2,2-diphenyl-2-picrylhydrazyl (DPPH) method. Acute toxicity was realized according to up and down OECD procedure in BALB/c mice. Wound healing activity was evaluated in male Wistar rats. Histological analyses of tissues were made by microscopy using staining methods of hematoxylin and eosin and Masson-trichrome. Results: Treated groups with methanolic and hexanoic extracts of M. paradisiaca peel showed better wound healing activity in comparison with the group treated with chloroformic extract, with an inhibition of DPPH radical bleaching of 89-90%. It may be due to the presence of alkaloids, tannins, saponins and phenols as principal constituents by conferring antioxidant capacity. The extract did not induce any toxicity. Conclusions: The findings showed the wound healing and antioxidant capacity of M. paradisiaca peel extract. It was observed that depending on the extraction solvent; there is a variation in the antioxidant capacity that also affects the effectiveness of the restoration of tissue, suggesting that the antioxidant capacity could play a major role in the process of wound healing.