Miracle-dz/UniFAR-FTUs huggingface dataset:
Excess Nicotinamide Induces Reactive Oxygen Species Generation, Insulin Resistance, and Epigenetic Change in Rats and Humans

The implementation of grain fortification with niacin, commonly in the form of nicotinamide, has significantly increased niacin per capita consumption in U.S. from 1930s. Nicotinamide is the precursor of NAD and NADP, which participate in many biological reactions. Therefore, nicotinamide homeostasis is vitally important for the body. This study is to investigate the effects of excess nicotinamide on ROS generation, insulin resistance, and epigenetic change, which are hallmarks of type 2 diabetes. We found acute nicotinamide overload increased ROS generation, insulin resistance, and reduced muscle glycogen level in adult rats. Besides these effects, long-term nicotinamide overload led to oxidative stress in kidney and liver, increased their DNA damage, and decreased their global DNA methylation profile. We further demonstrated that decreasing nicotinamide degradation and excretion level was crucial for the ROS generation- and insulin resistance-inducing effects using an impaired skin detoxification rat model. Using oral glucose tolerance test (OGTT), we observed that in healthy volunteers, nicotinamide addition induced higher levels of ROS generation and insulin resistance in the early phase, followed by hypoglycemia in the late phase. Compared to controls, diabetic patients showed a disturbed nicotinamide degradation pattern, characterized by higher plasma N 1 -methylnicotinamide (NMN) levels and lower urinary degraded metabolite, N 1 -methyl-2-pyridone-5-carboxamide (2-Py). Mechanistically nicotinamide degradation process was associated with ROS generation; excess nicotinamide led to higher ROS generation causing kidney and liver damage. We also found that excess nicotinamide disturbed the monoamine neurotransmitters degradation and DNA methylation by competing for the biological methyl-donor, betaine in the body. In summary, our results indicate that excess nicotinamide may play an important role in type 2 diabetes. Disclosure Y. Zhou: None. N. Chen: None. D. Li: None. W. Sun: None. S. Zhou: None.
Anatomical response of wheat cultivars to drought stress

The study was carried out to investigate the responses of drought stress on wheat tissues. Five wheat cultivars Alta 84 (AL), Atila (AT), Cettia (CE), Norman Bourgluk 2008 (NB) and Seri M82 (SE) were cultivated. Four weeks after planting, healthy plants were subjected to four treatments viz- well-watered (D1), watered daily, drought stress (D2), one weekly watering, drought stress (D3), two weekly watering and drought stress (D4), and three weekly watering. The experiment was a factorial experiment conducted in a completely randomized design (CRD) with three replicates; Transverse section (TS) of the leaves collected were sectioned using microtome, stained and observed under compound microscope. Mesophyll cells, vascular bundles, bundle sheaths and xylem tissues were measured using ocular micrometer. Epidermal peels were prepared to determine the number of stomata and trichomes. When drought stress was imposed (D2, D3 and D4), wheat cultivar Cettia developed larger mesophyll cells, xylem tissues, vascular bundles and bundle sheaths than other cultivars. Thus, larger vascular bundles would facilitate faster movement of water and mineral salts up to the shoot from the root. Cultivar Atila developed higher number of trichomes during drought stress D2 than other cultivars which help to reduce the rate of transpiration of water out of the epidermal leaves. Wheat cultivars Cettia and Atila could be drought tolerant cultivars. Generally, wheat cultivars developed stable stomata number and stomata closure mechanism to cope with drought stress. There was an increase in number of trichomes at D2, D3 and D4 which revealed the ecologically adaptation of wheat plants to drought stress. Key words : Wheat Cultivars, Drought Stress, Anatomical Structures.
The interaction between the meningeal lymphatics and blood-brain barrier

Here we show the interaction between the meningeal lymphatic system and the blood-brain barrier (BBB) function. In normal state, the meningeal lymphatic vessels are invisible on optical coherent tomography (OCT), while during the opening of the BBB, meningeal lymphatic vessels are clearly visualized by OCT in the area of cerebral venous sinuses. These results give a significant impulse in the new application of OCT for the study of physiology of meningeal lymphatic system as well as sheds light on novel strategies in the prognosis of the opening of the BBB related with many central nervous system diseases, such as stroke, brain trauma, Alzheimers disease, etc.
Biophysical Principles of Lineage Factor PU.1 Binding Revealed by NextPBMs

Determining the biophysical principles that shape transcription factor (TF) binding in a cell-specific manner is key to quantitative models of gene expression. High-throughput (HT) in vitro methods measuring protein-DNA binding are invaluable for relating TF binding affinity to genome-wide binding; however, the impact of cell-specific post-translational modifications (PTMs) and cofactors are not routinely assessed. To address these limitations, we describe a new HT approach, called nextPBMs (nuclear extract protein-binding microarrays), to characterize TF binding that accounts for PTMs and endogenous cofactors. We use nextPBMs to examine the DNA binding of the lineage factor PU.1/Spi1 and IRF8 in human monocytes. We identify two binding modes for PU.1 in monocytes – autonomous binding unaffected by PTMs and cooperative binding with IRF8, and identify a single cooperative mode for IRF8. We characterize the DNA binding of PU.1:IRF8 complexes, and show how nextPBMs can be used to discover cell-specific cofactors and characterize TF cooperativity at single-nucleotide resolution. We show that chromatin state and cofactors both influence the affinity requirements for PU.1 binding sites. Furthermore, we find that the influences of cooperative (IRF8) and collaborative (C/EBPα) cofactors on PU.1-binding-site affinity are independent and additive.
The effect of intragastric and ad libitum administration of red wines (Cabernet Sauvignon, Merlot, Carménère and Cabernet Sauvignon/Nebbiolo) and alcohol in the cyto/genotoxicity evaluated in the peripheral blood of CD-1 mice

Se evaluo la cito/genotoxicidad en sangre periferica de ratones CD-1 expuestos a diferentes variedades de vino tinto ( Cabernet Sauvignon , Merlot , Carmenere y Cabernet Sauvignon/Nebbiolo ). Grupos de cinco organismos fueron tratados: a) con el vehiculo, b) vino tinto o etanol (diluidos al 75 y 10%, respectivamente) ad libitum , y c) vino tinto sin diluir o etanol diluido al 13.5% (dos dosis diarias-0.25 ml, via i.g.). La genotoxicidad se evaluo con los micronucleos (MN) y la citotoxicidad con la relacion entre eritrocitos policromaticos/normocromaticos (EPC/ENC) a las 0, 24, 48 y 72 h. Solo se observaron incrementos significativos en los MN con los tratamientos i.g de Cabernet Sauvignon , Merlot y etanol, siendo mayor para el etanol. La administracion ad libitum de los vinos tintos redujo los MN. Nuestros hallazgos sugieren que los efectos genotoxicos del vino tinto podrian estar relacionados con la biodisponibilidad, farmacodinamica y farmacocinetica del etanol. No se observaron efectos citotoxicos.
How familiarity warps representation in the face space

Recognition of familiar as compared to unfamiliar faces is robust and resistant to marked image distortion or degradation. Here we tested the flexibility of familiar face recognition with a morphing paradigm where the appearance of a personally familiar face was mixed with the appearance of a stranger (Experiment 1) and the appearance of one's own face with the appearance of a familiar face and the appearance of a stranger (Experiment 2). The aim of the two experiments was to assess how categorical boundaries for recognition of identity are affected by familiarity. We found a narrower categorical boundary for the identity of personally familiar faces when they were mixed with unfamiliar identities as compared to the control condition, in which the appearance of two unfamiliar faces was mixed. Our results suggest that familiarity warps the representational geometry of face space, amplifying perceptual distances for small changes in the appearance of familiar faces that are inconsistent with the structural features that define their identities.
Role of DDX RNA helicases in cancer cells

DEAD-BOX (DDX) RNA helicases are a large family of proteins characterized by the presence of a DEAD/H (Asp-Glu-Ala-Asp/His) motif. Their main function is to unwind double stranded RNA to promote downstream molecular events. They are involved in virtually all steps of RNA metabolism such as transcription, translation, RNA export and degradation, ribosome biogenesis and pre-mRNA splicing. The aim of my work was to investigate the functions of human DDX3X and DDX54 RNA helicases, particularly in in vitro cancer models. To provide insight into their molecular functions, I identified RNAs bound by DDX3X and DDX54 in breast cancer (MCF7) cells by performing iCLIP experiments. This generated two very distinct RNA binding profiles: DDX3X preferentially bound exonic regions of mRNAs encoding translational factors, whilst DDX54 preferentially bound non-coding RNAs and intronic regions of mRNAs encoding nuclear proteins. Further bioinformatic analysis identified a few discrete binding motifs within DDX3X target RNAs. One of these, within the human JUND transcript, was validated as a DDX3X binding site using electrophoretic mobility shift assays. Notably, the levels of proteins encoded by mRNAs bound by DDX3X were altered following knockdown of the helicase. These data highlight the importance of DDX3X in maintaining appropriate levels of certain proteins, which in turn may explain at least some of the changes in phenotype observed upon DDX3X knockdown. In this regard, I showed that knocking down DDX3X or DDX54 in MCF7 cells slowed cell proliferation by inducing a G1/S phase arrest. Furthermore, a CRISPR/Cas9 dropout screen in a leukaemia cell line (MLL-AF9) showed that both helicases are essential for growth of these cells. However, loss of DDX3X or DDX54 had little effect on proliferation of immortalized NIH3T3 cells indicating that their loss is not generally lethal. In subsequent CRISPR/Cas9 dropout screens in various other cancer cell lines, including some derived from solid tumours, DDX54 was found to be essential for growth of all cell lines. In contrast, DDX3X was required for proliferation of only a subset of these. Focusing on DDX3X, I identified that the integrity of the helicase's RNA binding domains is essential for growth and cell cycle progression of an acute myeloid leukaemia cell line (OCI-AML3). Overall, my findings shed mechanistic insight upon the role of DDX RNA helicases in cancer and identify DDX3X and DDX54 as potential targets for therapeutic intervention in certain cancers.
Tintinnina (Ciliophora) and Foraminifera in plankton of hypersaline Lagoon Bardawil (Egypt): spatial and temporal variability

Lagoon Bardawil, belonging to the few hypersaline lagoons in the Mediterranean Sea, is located in the middle of the Sinai coast. Composition, distribution, and seasonal dynamics of large planktonic tintinnids and foraminifera at 12 stations in the lagoon were studied in 2009 and 2010. Fifteen species of Ciliophora (Tintinnina) and two species of Foraminifera were identified. The occurrence of different species varied greatly in the study period: two species were found in 42% to 49% of all samples, two species in 21% to 23%, 4 species in 10% to 20%, and 10 species in 1% to 5%. Only three species were found throughout the year. The average total number of all recorded protozoa varied from 2333 ind. /m 3 " role="presentation"> 3 (spring) to 13,733 ind. /m 3 " role="presentation"> 3 (winter): Tintinnina from 1250 ind. /m 3 " role="presentation"> 3 (spring) to 12,867 ind. /m 3 " role="presentation"> 3 (winter) and Foraminifera from 200 ind. /m 3 " role="presentation"> 3 (autumn) to 1083 ind. /m 3 " role="presentation"> 3 (spring). The distribution of total abundance of tintinnids and foraminifers in the lagoon area was close to random in summer and spring; during autumn and winter, it was aggregated. Tintinnid and foraminifera studies in Lagoon Bardawil were carried out previously (1985-2010); summarizing all data, it was found that interannual differences may be explained by stochastic causes and nondirected climate fluctuations.
Clinical strains of mycobacterium tuberculosis induce strain-specific patterns of cytokine production, gene expression and pathway changes in pulmonary alveolar epithelial cells.

The M. tuberculosis F15/LAM4/KZN, F11, F28 and Beijing strain families have been associated with high transmission rates within the South African population. The current study focused on elucidating the cytokine/chemokine response induced by these strain families of M. tuberculosis in pulmonary epithelial cells. The A549 pulmonary epithelial cell line was infected with the F15/LAM4/KZN, F28, F11, Beijing, Unique and H37Rv strains and the supernatant harvested at 0, 24, 48 and 72 hr for cytokine/chemokine analysis using the Bio-Plex Pro Human Cytokine Group 27-Plex Assay. Among the 23 cytokines/chemokines that were detected, a significant production of anti-inflammatory and pro-inflammatory cytokines, as well as chemokines was observed at different time intervals. All strains induced a gradual increase in cytokines/chemokines that peaked mostly at either 48 or 72 hr post-infection. However, production of each cytokine/chemokine was observed to be strain and time specific. High cytokine levels were induced by the F28 strain at 48 hr and F15/LAM4/KZN strain at 72 hr for most analytes. Lower cytokine production was induced by the Beijing and Unique strains at alltime intervals, suggesting a higher virulence of these strains compared to other strain families. On the other hand, the F15/LAM4/KZN strain induced high protective cytokine production, suggesting a lower virulence for this strain. Cytokine/chemokine production by the laboratory H37Rv was variable with either a higher or lower concentration for some analytes compared to
Control of Silicon Nanowires Crystallinity using Metal Assisted Chemical Etching of Silicon and Porous Silicon Substrate

Control of crystallinity is a vital aspect while synthesizing silicon nanowires (SiNWs). Solar photovoltaic devices need a highly crystalline phase, while lithium-ion battery anodes require a highly amorphous phase. The possible solution lies in the choice of substrate, either a silicon or porous silicon. Metal-assisted chemical etching is a low-cost method used for fabricating silicon nanowires using an electrolyte solution (hydrofluoric acid, metal salt, and hydrogen peroxide) at room temperature. Various combinations of substrates and electrolyte compositions are studied to control the morphology of synthesized nanowires such as length, strain, hydrophobicity, and crystallinity. Microscopic and spectroscopic study of the synthesized nanowires is carried out to explain the presence of the amorphous phase and strain in the SiNWs. The Si+MII combination produces the highest crystallinity (i.e., 84.91%) and length of SiNWs (i.e., 23.3 μm), which is more suitable for solar cell application compared to other combinations. The PSi+MII combination results in the highest amorphous Si phases (i.e., 35.79%), suitable for lithium-ion battery anode.
Visual reconstruction from 2-photon calcium imaging suggests linear readout properties of neurons in mouse primary visual cortex

Deciphering the neural code, that is interpreting the responses of sensory neurons from the perspective of a downstream population, is an important step towards understanding how the brain processes sensory stimulation. While previous work has focused on classification algorithms to identify the most likely stimulus label in a predefined set of categories, fewer studies have approached a full stimulus reconstruction task. Outstanding questions revolve around the type of algorithm that is most suited to decoding (i.e. full reconstruction, in the context of this study), especially in the presence of strong encoding non-linearities, and the possible role of pairwise correlations. We present, here, the first pixel-by-pixel reconstruction of a complex natural stimulus from 2-photon calcium imaging responses of mouse primary visual cortex (V1). We decoded the activity of approximately 100 neurons from layer 2/3 using an optimal linear estimator and an artificial neural network. We also investigated how much accuracy is lost in this decoding operation when ignoring pairwise neural correlations. We found that a simple linear estimator is sufficient to extract relevant stimulus features from the neural responses, and that it was not significantly outperformed by a non-linear decoding algorithm. The importance of pairwise correlations for reconstruction accuracy was also limited. The results of this study suggest that, conditional on the spatial and temporal limits of the recording technique, V1 neurons display linear readout properties, with low information content in the joint distribution of their activity.
Use of Artificial Waterholes by Animals in the Southern Region of the Kruger National Park, South Africa

Artificial waterholes are a widely used, yet contested wildlife management practice in semi-arid environments. We evaluated wildlife water provisioning at four artificial waterholes in the southern region of the Kruger National Park. We documented daily waterhole visitation patterns of mammals during the wet and dry seasons using camera-traps. We recorded 26 mammal species at the waterholes, with African elephants (Loxodonta africana) and impalas (Aepyceros melampus) being the most abundant. We used generalized linear mixed models (GLMM) to determine which variables (season, time of day, water quality, and the presence of carnivores or elephants) would affect animal visitation. Waterhole visitation patterns differed according to time of day, but this effect remained relatively constant between seasons. More animals visited waterholes in the dry season compared to the wet season. Carnivore presence negatively affected impala abundance. Elephant presence did not affect impala and white rhinoceros (Ceratotherium simum) visits to waterholes. Water quality also appeared to play a role in determining animal abundance. Based on our results, though obtained from a limited sample size, we suggest some management practices to be considered when deciding which waterholes should be closed down or left open.
Neutralisation of toxins by probiotics during the transit into the gut: challenges and perspectives

Food contamination by toxins (both mycotoxins and bacterial toxins) represents a great challenge for their implications on health. Toxins could be removed during production, but many times, they enter the gut and act on the host. To some extents, a benefit of probiotics could be the removal/neutralisation of harmful compounds in the gut with an indirect health effect on the host. Some authors addressed the ability of yeasts and bacteria to remove mycotoxins and other toxins; however, to the best of our knowledge, there is not an overview on how and when mycotoxins and some other bacterial toxins (like cyanotoxins) can be removed by probiotics into the gut. Therefore, this topic is addressed in this paper. The manuscript is organised with an initial overview of the literature about probiotics, mycotoxins and cyanotoxins followed by a section on the ability of probiotics to remove toxins in vitro and in vivo.
Plant life history stage and nurse age change the development of ecological networks in an arid ecosystem

Understanding how ecological networks are organised over the course of an organism’s lifetime is crucial for predicting the dynamics of interacting populations and communities across temporal scales. However, most studies so far considered only one life history stage at a time, such as adult, when studying networks of interacting species. Therefore, knowledge about how multiple life history stages affect the development and stability of plant–plant association networks is lacking. We measured the understory adult plant community and the soil seed bank across a plant age gradient of the nurse shrub Retama sphaerocarpa in an arid ecosystem in Spain. Using a multilayer network approach, we built adult understory–nurse and seed bank–nurse networks and analysed how network nestedness, species’ role, and species specificity varied between them and with nurse plant age. We found that seed bank and adult understory networks changed depending on nurse plant age in two different ways. With increasing nurse plant age, adult understory networks became significantly more nested than seed bank networks. The nested architecture of seed bank networks was therefore a poor predictor of adult understory network nestedness. The contribution and specificity of species to network nestedness increased with increasing nurse plant age more in the adult understory than in seed bank networks, despite high species turnover. Our data show that life history and ontogeny affect the development of plant–plant association networks. Niche construction and environmental filtering along nurse ontogeny seem pivotal mechanisms structuring adult understory networks while the assembly of seed bank networks seems rather stochastic. We highlight the importance of mature plant communities for maintaining rare species populations and supporting the stability of ecological communities through time.
Densidade populacional de Tibraca limbativentris em arroz irrigado por inundação e plantas hospedeiras alternativas

The objective of this work were to evaluate the population dynamics of the rice stem bug ( Tibraca limbativentris ) around and in flood irrigated rice cultivation area, to quantify the insect population flow between crops and host plants, and to determine the effect of the species, the diameter of the plant, and the distance of the host plant from the border on the rice stem bug population. The work was conducted in the 2012/2013 harvest and in the off-season, with sampling of rice, Andropogom bicornis , and Andropogon lateralis plants in six cultivated areas, in order to count the number of insects. The population density of the rice stem bug in irrigated rice and alternative host plants presents spatial and temporal dependence. In the cultivated areas, the population density of the rice stem bug increases according to the evolution of the rice phenological stages, with the highest densities concentrated in regions close to the crop borders. The diameter and species of the host plant affect the rice stem bug population. Andropogon bicornis plants have higher population densities than A. lateralis , and plants with larger diameters show higher population densities of the rice stem bug. In the off-season, the greatest population of the rice stem bug on host plants is concentrated up to 45 m from the crop border, but it can disperse until 150 m.
Antibacterial and Antifungal Effect of Cinnamon

Cinnamon (Cinnamomum zeylanicum, and Cinnamon cassia), the eternal tree of tropical medicine, belongs to the Lauraceae family. Cinnamon is one of the most important spices used daily by people all over the world. Cinnamon primarily contains vital oils and other derivatives, such as cinnamaldehyde, cinnamic acid, and cinnamate. Traditional uses of Cinnamon throughout Asia, Africa, and Europe have been recorded, where it has been used as a medicine. Many researches were done to study the effect of cinnamon as antifungal and antibacterial cause skin, oral infection and foodborne bacteria. The antibacterial activity was certified to the presence of some phytochemicals in the extracts and recommended that it was possibly due to their major component cinnamaldehyde.