Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural Taskonomy: Inferring the Similarity of Task-Derived Representations from Brain Activity

Convolutional neural networks (CNNs) trained for object recognition have been widely used to account for visually-driven neural responses in both the human and primate brains. However, because of the generality and complexity of the task of object classification, it is often difficult to make precise inferences about neural information processing using CNN representations from object classification despite the fact that these representations are effective for predicting brain activity. To better understand underlying the nature of the visual features encoded in different brain regions of the human brain, we predicted brain responses to images using fine-grained representations drawn from 19 specific computer vision tasks. Individual encoding models for each task were constructed and then applied to BOLD5000—a large-scale dataset comprised of fMRI scans collected while observers viewed over 5000 naturalistic scene and object images. Because different encoding models predict activity in different brain regions, we were able to associate specific vision tasks with each region. For example, within scene-selective brain regions, features from 3D tasks such as 3D keypoints and 3D edges explain greater variance as compared to 2D tasks—a pattern that replicates across the whole brain. Using results across all 19 task representations, we constructed a “task graph” based on the spatial layout of well-predicted brain areas from each task. We then compared the brain-derived task structure with the task structure derived from transfer learning accuracy in order to assess the degree of shared information between the two task spaces. These computationally-driven results—arising out of state-of-the-art computer vision methods—begin to reveal the task-specific architecture of the human visual system.
Aromatic property of cherry wine produced by malolactic fermentation of controlled and spontaneous on the bacterial evolution

ABSTRACT This work investigated the effect of controlled malolactic fermentation starters (Lactobacillus plantarum NoVA and Oenococcus oeni Oenos) and an un-inoculated culture on cherry wine’s physical, biochemical and sensory properties. NoVA promoted MLF most efficiently (15d), resulted in a large increase in the concentration of many esters and aromatic alcohols, and reinforced the cherry wine’s ‘fruity’ note and overall aroma. MLF carried out by Oenos lasted for 18 days, accompanied by the increase of many volatile compounds (with 2-phenylethyl acetate and benzaldehyde as major representatives) and several biogenic amines. With respect to spontaneous MLF, Tatumella, Pantoea, Lactococcus, and Lactobacillus were identified as the dominant genera, with a fermentation period of 25 d and the total biogenic amine amount 1.6-fold than that at the end of alcoholic fermentation. This study has proved that the use of Viniflora NoVA to conduct MLF is a worthwhile alternative to the traditional cherry wine-making.
A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination

Mycobacterium tuberculosis (Mtb), the causative infectious agent of tuberculosis (TB), kills more individuals per year than any other infectious agent. Granulomas, the hallmark of Mtb infection, are complex structures that form in lungs, composed of immune cells surrounding bacteria, infected cells, and a caseous necrotic core. While granulomas serve to physically contain and immunologically restrain bacteria growth, some granulomas are unable to control Mtb growth, leading to bacteria and infected cells leaving the granuloma and disseminating, either resulting in additional granuloma formation (local or non-local) or spread to airways or lymph nodes. Dissemination is associated with development of active TB. It is challenging to experimentally address specific mechanisms driving dissemination from TB lung granulomas. Herein, we develop a novel hybrid multi-scale computational model, MultiGran, that tracks Mtb infection within multiple granulomas in an entire lung. MultiGran follows cells, cytokines, and bacterial populations within each lung granuloma throughout the course of infection and is calibrated to multiple non-human primate (NHP) cellular, granuloma, and whole-lung datasets. We show that MultiGran can recapitulate patterns of in vivo local and non-local dissemination, predict likelihood of dissemination, and predict a crucial role for multifunctional CD8+ T cells and macrophage dynamics for preventing dissemination. Author Summary Tuberculosis (TB) is caused by infection with Mycobacterium tuberculosis (Mtb) and kills 3 people per minute worldwide. Granulomas, spherical structures composed of immune cells surrounding bacteria, are the hallmark of Mtb infection and sometimes fail to contain the bacteria and disseminate, leading to further granuloma growth within the lung environment. To date, the mechanisms that determine granuloma dissemination events have not been characterized. We present a computational multi-scale model of granuloma formation and dissemination within primate lungs. Our computational model is calibrated to multiple experimental datasets across the cellular, granuloma, and whole-lung scales of non-human primates. We match to both individual granuloma and granuloma-population datasets, predict likelihood of dissemination events, and predict a critical role for multifunctional CD8+ T cells and macrophage-bacteria interactions to prevent infection dissemination.
A cell-based evaluation of a non-essential amino acid formulation as a non-bioactive control for activation and stimulation of muscle protein synthesis using ex vivo human serum

Purpose The purpose of this study was to compare the effect of treating skeletal muscle cells with media conditioned by postprandial ex vivo human serum fed with either isonitrogenous NEAA or a whey protein hydrolysate (WPH) on stimulating MPS in C2C12 skeletal muscle cells. Methods Blood was taken from six young healthy males following overnight fast (fasted) and 60 min postprandial (fed) ingestion of either WPH or NEAA (0.33 g.kg-1 Body Mass). C2C12 myotubes were treated with media conditioned by ex vivo human serum (20%) for 4 h. Activation of MPS signalling (phosphorylation of mTOR, P70S6K and 4E-BP1) were determined in vitro by Western Blot and subsequent de novo MPS were determined in vitro by Western Blot and surface sensing of translation technique (SUnSET) techniques, respectively. Results Media conditioned by NEAA fed serum had no effect on protein signalling or MPS compared to fasted, whereas media conditioned by WPH fed serum significantly increased mTOR, P70S6K and 4E-BP1 phosphorylation (p<0.01, p<0.05) compared to fasted serum. Furthermore, the effect of media conditioned by WPH fed serum on protein signalling and MPS was significantly increased (p<0.01, p<0.05) compared to NEAA fed serum. Conclusion In summary, media conditioned by NEAA fed serum did not result in activation of MPS. Therefore, these in vitro findings suggest the use of isonitrogenous NEAA acts as an effective control for comparing bioactivity of different proteins on activation of MPS. These findings also confirm that activation of MPS in C2C12 myotubes treated with media conditioned by WPH-fed serum is primarily due to circulating EAA.
The Characteristics of Soil C, N, and P Stoichiometric Ratios as Affected by Geological Background in a Karst Graben Area, Southwest China

Understanding ecological stoichiometric characteristics of soil nutrient elements is crucial to guide ecological restoration and agricultural cultivation in karst rocky desertification region, but the information about the effect of the geological background on ecological stoichiometric ratios remains unknown. Soils from different landforms, including a basin, slope, and plateau, were sampled to investigate the spatial variance of the ecological stoichiometric characteristics of soil carbon (C), nitrogen (N), and phosphorus (P) under different rocky desertification grades (LRD: light rocky desertification; MRD: moderate rocky desertification; and SRD: severe rocky desertification) in a karst graben basin of Southwest China. Soil C:N ratio was not significantly influenced by rocky desertification grade, which was at a relatively stable level in the same landform, but soil C:P and N:P ratios increased with increasing rocky desertification grade. This change was consistent with increased soil organic carbon (SOC) and total nitrogen (TN) concentrations in the same geomorphic location along with the intensification of rocky desertification, but soil P concentration remained at a relatively stable level, indicating that P may be the limiting macronutrient for plant growth during vegetation restoration in a karst graben area. The soil C:N ratio of slope land was larger than that of the basin and plateau, while the soil C:P ratio and N:P ratio of the slope and plateau were significantly larger than that of the basin. The correlations between pH and C, N, and P stoichiometry decreased significantly when Ca was used as a control variable. In sharp contrast, the correlations between Ca and C, N, and P stoichiometry were highly significant no matter whether pH was used as a control variable, suggesting the important role of Ca in soil C, N, and P stoichiometry in karst graben basins.
TSG-6 in extracellular vesicles from canine mesenchymal stem/stromal is a major factor in relieving DSS-induced colitis

Mesenchymal stem/stromal cell (MSC)-derived extracellular vesicles (EV) have been reported to be beneficial against dextran sulfate sodium (DSS)-induced colitis in mice. However, the underlying mechanisms have not been fully elucidated. We hypothesize that the tumor necrosis factor-α-stimulated gene/protein 6 (TSG-6) in EVs is a key factor influencing the alleviation of colitis symptoms. DSS-induced colitis mice (C57BL/6, male, n = 6-8/group) were intraperitoneally administered EVs (100 ug/mice) on day 1, 3, and 5; colon tissues were collected on day 10 for histopathological, qRT-PCR, western blot, and immunofluorescence analyses. In mice injected with EV, inflammation was alleviated. Indeed, EVs regulated the levels of pro- and anti-inflammatory cytokines, such as TNF-α, IL-1β, IFN-γ, IL-6, and IL-10 in inflamed colons. However, when injected with TSG-6 depleted EV, the degree of inflammatory relief was reduced. Furthermore, TSG-6 in EVs plays a key role in increasing regulatory T cells (Tregs) in the colon. In conclusion, this study shows that TSG-6 in EVs is a major factor in the relief of DSS-induced colitis, by increasing the number of Tregs in the colon.
Effects of egg harvest on egg laying of Glaucous-winged Gulls Larus glaucescens

SCHAEFER, A.L. , BISHOP, M.A. & JURICA, K. 2019. Effects of egg harvest on egg laying of Glaucous-winged Gulls Larus glaucescens. Marine Ornithology 47: 179–183. Subsistence harvest of wild bird eggs is a traditional activity across many parts of Alaska. We examined the impact of egg collection on Glaucous-winged Gulls Larus glaucescens nesting on Alaska’s Copper River Delta by comparing egg laying patterns across two experimental plots. In one plot, we manually removed eggs from incomplete clutches and in the other we walked through the plot to create disturbance. Gulls in this study did not appear to increase the number of eggs laid to compensate for eggs experimentally removed from their nests, with only 10 % of gull pairs completing a full clutch following nest manipulation.
Mini-review: oomycete RXLR genes as effector-triggered immunity

Oomycetes are known to secrete a vast arsenal of effectors that modulate the host defense system as well as facilitate establishing a parasitic infection in plants. In recent years, tremendous progress has been made in the field of effectromics based on studies of oomycetes, especially the cytoplasmic family of RXLR effectors. Yet, the biology of the RXLR effector family is still poorly understood. There has been a consensus regarding the structure of the RXLR motif in the mycologist community. However, the function of the RXLR motif is still unclear. First, different models have suggested that the role of the RXLR motif is either in translocation to a target destination inside a host cell or in the cleavage of itself followed by secretion. Second, recent studies have suggested different functional models for the RXLR motif. According to a widely accepted model, the RXLR motif is directly involved in the translocation of effectors to target sites. In contrast, a new study has proposed that the RXLR motif is involved in secretion rather than translocation. Thus, this review is an attempt to summarize the recent advances made in the functional analysis of the N-terminal domain of RXLR effectors.
Chirp analyzer for estimating amplitude and latency of steady-state auditory envelope following responses

The envelope following response (EFR) is a scalp-recorded evoked potential elicited by carrier tones or noise, modulated in amplitude with a continuous sweep of modulation frequencies. This non-stationary response reflects the phase-locked neural activity of the auditory pathway to the temporal envelope of sounds and has been commonly assessed by fixed-frequency methods based on the discrete Fourier transform, such as the Fourier Analyzer (FA). In this work, we study the estimation of the EFR with the use of explicit time-frequency methods, which offer more information about the energy distribution of the recorded signal, such as the Short-Term Fourier Transform (STFT) and the Morlet Continuous Wavelet Transform (CWT). We further introduce the Chirp Analyzer (CA), which is similar to FA, but using as basis function the same linear chirp that amplitude-modulates the carrier stimulus. In a direct comparison using controlled simulated responses, the CA showed to be able to estimate the correct EFR amplitudes, without the typical bias offered by the estimation using STFT (equivalent to FA) and more robust to noise than the CWT method, although with higher sensitivity to the presence of a delay in the response with respect to the stimulus. For addressing the latter issue, we also propose here a novel methodology for estimating the apparent latency of the response. This method proved to be reliable when using the STFT and the CA methods, as assessed using simulated responses. The estimation of the EFR amplitude with any of the methods, but especially with CA, should be corrected by using the estimated delay when possible. An illustrative application of these methods to small datasets of a rat and a human newborn, suggested that all time-frequency methods can be used to study the EFR amplitudes in a wide range of modulation frequencies, but they should be interpreted in the light of the limitations shown in the simulation studies.
Dietary chia seeds (Salvia hispanica) improve acute dyslipidemia and steatohepatitis in rats.

Chia seeds (Salvia hispanica L.) are rich in omega fatty acids. Dyslipidemia and steatohepatitis are diseases that require effective treatments in obese and non-obese patients. The aim was to evaluate the effect of chia intake on acute tyloxapol (TI)-induced dyslipidemia, on acute carbon tetrachloride (TC)-induced steatohepatitis, and on mixed damage (TC+TI) in non-obese rats. Four experimental groups were fed for 4 weeks a diet with established rodent food (DE), and four groups were fed a diet with 15% added chia (DC). Plasma samples were analyzed for total cholesterol, triglycerides, glucose, biochemical liver damage markers, and tumor necrosis factor-α (TNF-α). Liver samples were used to quantify glycogen, catalase, lipid peroxidation, and TNF-α. A histopathological analysis was performed. DC intake partially or totally prevented steatohepatitis, and reduced lipids in the dyslipidemic groups. The hypolipidemic and hepatoprotective effects of chia may be correlated to its high content of α-linolenic acid (omega-3) and phenolics. PRACTICAL APPLICATIONS: Metabolic syndrome is associated with non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), which are currently the most common causes of chronic liver disease, cirrhosis, and hepatocellular carcinoma (HCC) worldwide. Dyslipidemia is a significant risk factor for NAFLD and NASH. Non-obese patients may have NAFLD or NASH. Metabolic syndrome and dyslipidemia are more strongly associated with NAFLD in non-obese than in obese patients. This is the first study evaluating the hypolipidemic and hepatoprotective effects of chia seed intake on acute dyslipidemia and/or steatohepatitis caused by the individual or combined administration of the inducers tyloxapol and carbon tetrachloride, respectively, in non-obese rats. The pharmacological effects of dietary chia are correlated to its high content of omega-3 and omega-6 (1:1), protein, dietary fiber, and phenolics. The results suggest that inclusion of chia in diets of non-obese patients with dyslipidemia and/or NAFLD/NASH may improve their health state and preventing cirrhosis or HCC.
Isolation, screening, identification and optimization of cultural conditions for selected local bacterial β-galactosidase producer.

Fifty two bacterial isolates were isolated from different sources (commercial cow milk "from markets present in Giza", commercial yoghurt "from markets present in Giza" and agricultural soil" presents in Giza and Kalubeia") and assessed for their β-galactosidase production. Results of this work showed that 24 of these isolates produced β-galactosidase. The most producer bacterial isolate was identified as Bacillus subtilis. In addition, some of nutritional and environmental conditions for production of the enzyme by the selected isolate were studied of modified media contain as. Lactose 5g/L, yeast extract 10g/L, pH of the medium 7.0 and the incubation temperature at 30°C for 48 hours was the most suitable conditions for the production of βgalactosidase.
Length-Weight relations and condition factor of roach Rutilus rutilus (Linnaeus, 1758) in Lake Volvi (Northern Greece)

Length-weight relations (LWRs) and different indices of condition factor for roach from Lake Volvi (Northern Greece) were estimated. Results showed that roach are heavier of a given length in Lake Volvi than in other areas worldwide, with females exhibited higher weight than males of the same length. Significant differences (P<0.05) of LWRs were also exhibited between sexes depending on month. CLARK condition factor peaked at the end of summer displaying no significant difference between sexes, whereas the other three estimated condition factors (Allometric, FULTON, LE CREN) peaked in winter. The estimation of different proxies of condition factor disaggregated by sex might reduce the uncertainty raised by the estimation of fish growth.
Poultry Farm and Poultry Products as Sources of Multiple Antimicrobial-Resistant Salmonella and S. aureus

Background: Poultry production is a key interface for the spread of novel zoonotic and antibiotic-resistant foodborne pathogens. Salmonella spp. and S. aureus isolates from 2 poultry production were tested for resistance to clinical antibiotics. Methods: One hundred 100 anal swab samples were aseptically collected from 2 small scale poultry farms located within Agulu, during the period of February 2016 to May 2016. The swab sticks were carefully transferred into the buffered peptone water and incubated at 37°C for 24hours and pre-enriched in sterile nutrient broth at 37°C for 24hours. After which, the culture was streaked on selective media Salmonella-shigella Agar and Mannitol Salt Agar using a sterile wire loop and further incubated at 37°C for 24 hours. S. aureus and Salmonella isolates were identified using standard microbiological identification techniques. The isolates were evaluated for antibiotic susceptibility, and for the expression of extended spectrum β-lactamase as well as vancomycin sensitivity. Results: One hundred bacterial isolates (44 S. aureus and 56 Salmonella spp.) were bacteriologically obtained from the poultry samples. Resistance pattern of the isolates to antibiotics was in the order of ceftazidime>cefuroxime>cloxacillin>augmentin®>ceftriaxone>erythromycin>gentamicin>ofloxacin for S. aureus while the Salmonella spp. had augmentin®>cefuroxime~ofloxacin>gentamicin>ceftazidime>ceftriaxone. Only 5.3% (3/56) Salmonella spp. was ESBL producers while 27.3% S. aureus were Vancomycin resistant. Conclusion: Our findings demonstrated that the poultry farm and poultry products could be a source of multiple antimicrobial-resistant Salmonella and S. aureus and may constitute a public health concern considering the circulation and consumption of livestock and their products, especially chickens and eggs.
Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and eight clades of trypanosomes, identifying parasite-specific informative features (including base-pairs and base mis-pairs) that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. These findings support a systems biology model in which combination chemotherapies that target multiple tRNA-synthetase interactions should be comparatively less prone to the emergence of resistance than conventional single drug therapies. Author Summary Trypanosome parasites pose a significant health risk worldwide. Conventional drug development strategies have proven challenging given the high conservation between humans and pathogens, with off-target toxicity being a common problem. Protein synthesis inhibitors have historically been an attractive target for antimicrobial discovery against bacteria, and more recently for eukaryotic pathogens. Here we propose that exploiting pathogen-specific tRNA-synthetase interactions offers the potential for highly targeted drug discovery. To this end, we improved tRNA gene annotations in trypanosome genomes, identified functionally informative trypanosome-specific tRNA features, and showed that these features are highly conserved over approximately 250 million years of trypanosome evolution. Highlighting the species-specific and broad-spectrum potential of our approach, we identified natural product inhibitors against the parasite translational machinery that have no effect on the homologous human enzyme.