Miracle-dz/UniFAR-FTUs huggingface dataset:
The HCP 7T Retinotopy Dataset: Description and pRF Analysis

About a quarter of human cerebral cortex is dedicated mainly to visual processing. The large-scale organization of visual cortex can be measured with functional magnetic resonance imaging (fMRI) while subjects view spatially modulated visual stimuli, also known as ‘retinotopic mapping’. One of the datasets collected by the Human Connectome Project (HCP) involved ultra-high-field (7 Tesla) fMRI retinotopic mapping in 181 healthy young adults (1.6-mm resolution), yielding the largest freely available collection of retinotopy data. Here, we describe the experimental paradigm and the results of model-based analysis of the fMRI data. These results provide estimates of population receptive field position and size. Our analyses include both results from individual subjects as well as results obtained by averaging fMRI time-series across subjects at each cortical and subcortical location and then fitting models. Both the group-average and individual-subject results reveal robust signals across much of the brain, including occipital, temporal, parietal, and frontal cortex as well as subcortical areas. The group-average results agree well with previously published parcellations of visual areas. In addition, split-half analyses show strong within-subject reliability, further demonstrating the high quality of the data. We make publicly available the analysis results for individual subjects and the group average, as well as associated stimuli and analysis code. These resources provide an opportunity for studying fine-scale individual variability in cortical and subcortical organization and the properties of high-resolution fMRI. In addition, they provide a set of observations that can be compared with other HCP measures acquired in these same participants.
Altered sensitivity to motion of area MT neurons following long-term V1 lesions

The middle temporal area (MT) receives its main afferents from the striate cortex (V1). However, MT also receives direct thalamic projections, which have been hypothesized to play a crucial role in residual vision after V1 lesions. MT neurons continue to respond shortly after V1 lesions, but human clinical work has shown that lesion effects can take up to six months to stabilize, making it important to understand MT responses after long-term deprivation of V1 inputs. We recorded neuronal responses in MT to moving dot stimuli in adult marmoset monkeys, 7-11 months after unilateral V1 lesions. Fewer MT neurons were direction selective, including neurons whose locations corresponded to the intact parts of V1. Firing rates were higher and more variable, and increased with motion strength regardless of direction. These properties could be re-created by a network model with imbalanced inhibition and excitation, providing the first insights into functional implications of long-term plasticity in MT following V1 lesions.
Analyzing Hominin Phylogeny: Cladistic Approach

An understanding of the phylogenetic relationships among organisms is critical for evaluating the evolutionary history of their adaptations and biogeography as well as forming the basis for systematics. As the numbers of hominin fossils and hominin taxa have increased over the past 40 years, controversies over phylogeny have expanded and have become a hallmark of paleoanthropology. Concordant with the rise in taxonomic diversity, the increased use of phylogenetic systematics, or cladistics, has provided a valuable tool for reconstructing hominin phylogeny. Despite the widespread view that hominin phylogeny is a source of endless debate, there is a broad consensus regarding many aspects of hominin phylogeny.
Experimental evaluation of the robustness of the growth–stress tolerance trade‐off within the perennial grass Dactylis glomerata

1. A core tenet of functional ecology is that the vast phenotypic diversity observed in the plant kingdom could be partly generated by a trade-off between the ability of plants to grow quickly and acquire resources in rich environments vs. monitor the decrease in soil water content. Once a pot’s soil water con tent fell to around the wilting point, between 11.5% and 12.5% (27– 35 days later), plants were cropped at 3 cm and the pot was put back under irrigation, thus ending the severe drought. The plants were ir rigated during 15 days after which dehydration survival was measured. Plants that did not produce new shoots after 15 days were counted as dead. The survival rate was measured as the proportion of recovering plants vs. the number of pre- existing plants (plant survival; %).
DeepGS: Predicting phenotypes from genotypes using Deep Learning

Motivation Genomic selection (GS) is a new breeding strategy by which the phenotypes of quantitative traits are usually predicted based on genome-wide markers of genotypes using conventional statistical models. However, the GS prediction models typically make strong assumptions and perform linear regression analysis, limiting their accuracies since they do not capture the complex, non-linear relationships within genotypes, and between genotypes and phenotypes. Results We present a deep learning method, named DeepGS, to predict phenotypes from genotypes. Using a deep convolutional neural network, DeepGS uses hidden variables that jointly represent features in genotypic markers when making predictions; it also employs convolution, sampling and dropout strategies to reduce the complexity of high-dimensional marker data. We used a large GS dataset to train DeepGS and compare its performance with other methods. In terms of mean normalized discounted cumulative gain value, DeepGS achieves an increase of 27.70%~246.34% over a conventional neural network in selecting top-ranked 1% individuals with high phenotypic values for the eight tested traits. Additionally, compared with the widely used method RR-BLUP, DeepGS still yields a relative improvement ranging from 1.44% to 65.24%. Through extensive simulation experiments, we also demonstrated the effectiveness and robustness of DeepGS for the absent of outlier individuals and subsets of genotypic markers. Finally, we illustrated the complementarity of DeepGS and RR-BLUP with an ensemble learning approach for further improving prediction performance. Availability DeepGS is provided as an open source R package available at https://github.com/cma2015/DeepGS.
Genome-wide association analysis of lifetime cannabis use (N=184,765) identifies new risk loci, genetic overlap with mental health, and a causal influence of schizophrenia on cannabis use

Cannabis use is a heritable trait [1] that has been associated with adverse mental health outcomes. To identify risk variants and improve our knowledge of the genetic etiology of cannabis use, we performed the largest genome-wide association study (GWAS) meta-analysis for lifetime cannabis use (N=184,765) to date. We identified 4 independent loci containing genome-wide significant SNP associations. Gene-based tests revealed 29 genome-wide significant genes located in these 4 loci and 8 additional regions. All SNPs combined explained 10% of the variance in lifetime cannabis use. The most significantly associated gene, CADM2, has previously been associated with substance use and risk-taking phenotypes [2–4]. We used S-PrediXcan to explore gene expression levels and found 11 unique eGenes. LD-score regression uncovered genetic correlations with smoking, alcohol use and mental health outcomes, including schizophrenia and bipolar disorder. Mendelian randomisation analysis provided evidence for a causal positive influence of schizophrenia risk on lifetime cannabis use.
Metribuzin Absorption and Translocation in Two Barley (Hordeum vulgare) Cultivars

Root and foliar absorption and translocation of 14C-metribuzin [4-amino-6-(1,1-dimethylethyl)-3-(methylthio)-1,2,4-triazin-5(4H)-one] were determined in tolerant (‘Steptoe’) and susceptible (‘Morex’) barley (Hordeum vulgare L.) cultivars grown in nutrient solution culture under greenhouse conditions. Root-applied metribuzin toxicity to the two barley cultivars was also examined. A 50% reduction in growth occurred at 0.22 and 0.72 μM metribuzin for Morex and Steptoe, respectively. Root absorption was similar for both cultivars at 1 day, but Steptoe absorbed about two times more metribuzin 4 and 8 days after application than did Morex. Steptoe absorbed 19% of the total applied metribuzin by 8 days. Root absorption was positively correlated with water uptake (r≥ 0.87). Leaf absorption was three times greater for Morex than for Steptoe after 4 days. Transport to leaves from root application was rapid, and, by 1 and 8 days, leaves of Steptoe contained 71 and 82% and leaves of Morex 78 and 84% of the total absorbed 14C, respectively. Translocation was apoplastic following both root and leaf absorption and was similar for both cultivars. Differential tolerance could partially be accounted for by differences in foliar absorption but not by differences in root absorption.
In vivo study of the two-component signaling network in Escherichia coli

Microorganisms commonly use ‘two-component’ signaling systems for sensing environmental conditions, with members being present in nearly all bacterial and archaeal genomes in different numbers. Prototypical two-component systems are comprised of a sensory histidine kinase and a response regulator protein that is phosphorylated by the kinase. The regulator typically acts as a transcription factor regulating gene expression. Due to their prevalence in microorganisms, a basic understanding of the principles of two-component systems provides insights into mechanisms of prokaryotic signaling circuits. Apart from a few studies performed in vitro, the signaling properties of a whole bacterial two-component network in vivo remains largely unclear. Using a system level approach, we characterized the localization of signaling proteins and the interactions between pathways on different levels in the model bacterium Escherichia coli. We constructed a comprehensive library of fluorescent protein fusions to kinases and regulators from two-component systems, and applied fluorescence microscopy to analyze their spatial organization within the cell. We found that most of the sensors exhibit a intrinsic tendency for cluster formation, which might provide a scaffold for information processing and insulation against detrimental noise from other sources. We used in vivo FRET microscopy tools to study protein interactions in a systematic way. For kinases, we could confirm the formation of sensor dimers or higher order oligomers in vivo in most of the cases. For the sensor BaeS, we characterized the change of sensor confirmation upon stimulation. Additionally, we identified a few pathways exhibiting interconnections on the sensor level and between sensors and non-cognate regulators, providing an additional layer of information processing. We could confirm the physiological relevance of some of these pathway interconnections on the gene expression level, using flow cytometry measurements of a fluorescent promotor library. Moreover, using this library we found most of the reported stimuli not affecting two-component gene expression. Taken together, our data provide a deeper understanding of cellular organization within and interconnections between different two-component systems in E. coli. The results of this study can broaden the understanding of cell signaling principles in bacteria.
The inhibitory effect of traditional pomegranate molasses on S. typhimurium growth on parsley leaves and in mixed salad vegetables

Pomegranate (PG) molasses is an essential condiment that is commonly used in Middle Eastern cuisine in local and international gastronomic markets. There is scarce information on the inhibitory effect of PG molasses on Salmonella growth mainly under in situ conditions and in a food matrix. PG molasses in different dilution ratios of 1:1 and 1:7, combined with sodium chloride (2%, v/v), vinegar (2.4%, v/v), and in a dressing mix was tested against Salmonella enterica serovar Typhimurium LT2 on parsley and salad vegetables. The results showed significant log reductions in Salmonella on parsley treated with PG solutions for 15, 30, and 60 min, reaching a level of 2.55 log cfu/g. The addition of sodium chloride (2%, v/v) and vinegar (2.4%, v/v) to PG molasses did not exert a synergistic or antagonistic effect on its antibacterial activity. Additionally, the application of PG molasses dressing on salads contaminated with low (3 log cfu/g) and high (6 log cfu/g) inoculum levels resulted in 2–3 log reduction independent of temperature (p < .05) compared with 0.5–1 log reduction for thorough washing alone which may damage the leaf surfaces. This study showed that PG molasses has a great efficacy against S. typhimurium and the potential to enhance the microbial safety of ready‐to‐eat salads and parsley leaves. PRACTICAL APPLICATIONS: The implication of fresh‐cut vegetables in food poisoning are well documented, at the same time, the washing methods in restaurants or home settings are reportedly not effective enough to mitigate the risks of pathogens found in vegetables. This study shows that Pomegranate (PG) molasses has a greater efficacy than chlorine (200 ppm) against S. typhimurium and achieved comparable to greater log reduction values than organic acids. The storage temperature and food matrix did not alter the potency of PG. The present work showed that promoting the use of PG as a natural additive and condiment to ready‐to‐eat (RTE) vegetables offers a great potential to effectively reduce the risk of Salmonella contamination and to improve their microbial safety. Furthermore, this study provided preliminary data that serve as additional inputs in quantitative microbial risk assessment models for estimating the risk of Salmonella infection associated with consuming RTE salads served in Mediterranean cuisines.
Systematic investigation of the phase behavior in binary fluid mixtures. I. Calculations based on the Redlich–Kwong equation of state

The original Redlich–Kwong equation, together with the usual quadratic mixing rules, has been used to calculate phase diagrams for binary fluid mixtures and to classify them according to the system of van Konynenburg and Scott. Global phase diagrams (maps) showing the extent of the various phase diagram classes in the space of the Redlich–Kwong parameters are presented. While for molecules of equal size the results are very similar to those known for the van der Waals equation, the maps become topologically different for molecules of unequal sizes; some complicated phase diagram classes, which otherwise cover small domains on the maps or cannot be found at all, become quite important.
First report of twig blight of ban tulsi (Croton bonplandianus Bail.) caused by Choanephora cucurbitarum (Berk. & Ravenel) Thaxt. in India

In August 2015, twig blight disease of ban tulsi (Croton bonplandianus Bail.) caused by Choanephora cucurbitarum (Berk. & Ravenel) Thaxt. was observed for the first time, in the Gangetic alluvial region of West Bengal, India. A severe disease incidence (40–50%) showed twig blight symptoms starting with shoot apical meristem (SAM), leaf, and blossom blight symptoms. Typical symptoms were characterized by over-projecting black pin head like emerging sporangiola which formed mycelial cushion on the infected surface. The present report describes the identification of the causal pathogen as C. cucurbitarum based on its morphology and the internal transcribed spacer of its ribosomal DNA (rDNA – ITS) sequences with 100% identity of NCBI-GenBank published Choanephora database. Optimum temperatures, 28–30°C, coupled with high relative humidity (80–90%) during the monsoon season enhances the disease’s progress. To the best of our knowledge this is the first report of twig blight of C. bonplandianus, caused by C. cucurbitarum, in India as well as globally.
The roles of p53, p21, and RB in regulation of proliferation and apoptosis in hepatocytes

Precise control of proliferation and apoptosis is essential for the prevention of cancer. Pathways involving p53, p21, and RB are central to the regulation of these processes, and are dysregulated in almost all human cancers. This thesis describes an investigation into the effects of inactivating components of the p53-p21-RB pathway in order to better understand the mechanisms underlying its role in preventing cancer. Hepatocytes isolated from transgenic mice bearing mutations in p53, p21, Rb, and combinations of all three, were employed to provide insight into the pathways controlling hepatocyte proliferation and apoptosis. In the case of the Rb mutation, Cre/LoxP conditional gene targeting was used to overcome the problem of embryonic lethality of Rb knock-out. In vitro Rb gene deletion mediated by adenovirus-Cre was successfully developed and characterised. This revealed that adenovirus-Cre-mediated gene deletion is extremely efficient in hepatocytes and that adenoviral infection had no affect on cell viability or growth. Expression of Cre, however, stimulated DNA synthesis while expression of LacZ adversely affected viability at higher MOI. These findings underline the need for careful characterisation of gene deletion systems employing both adenovirus and Cre recombinase. Analysis of hepatocytes deficient in p53, Rb, and p21, revealed severe defects in proliferation accompanied by an increase in ploidy, and nuclear and mitotic abnormalities. Analysis of hepatocytes deficient in combinations of all three genes provided insight into the level of interdependency between these genes, suggesting that there are two major pathways regulating hepatocyte proliferation: a p21-RB pathway that operates independently of p53, and a p53-p21 pathway that operates independently of RB. The p53-p21-RB pathway is critically important in regulating cellular responses to stress. The role of p53, p21, and RB in regulation of hepatocyte responses to DNA damage was investigated. It was found that each of these proteins is required for the maintenance, but not initiation, of UV-induced arrest. Both p53dependent and -independent pathways of UV-induced apoptosis exist, and loss of Rb or p21 increased susceptibility to p53-independent, but not p53-dependent, apoptosis.
Prevalence, cytotoxicity and antibiotic susceptibility of Campylobacter species recovered from retail chicken meat in Mansoura, Egypt

This study was performed to determine the prevalence of Campylobacter species in retail chicken meat and chicken by-product, determine their in vitro cytotoxicity, as well as, examine their susceptibility to different antimicrobials. A total of 300 raw chicken meat samples were collected from different retail chicken meat outlets located at Mansoura city, Egypt classified into 120 thighs, 120 breasts, and 60 livers. All samples were subjected to conventional culture techniques and confirmed as Campylobacter jejuni by real time polymerase chain reaction (PCR). Antimicrobial susceptibility of Campylobacter species was determined using disc diffusion method to determine their susceptibility to 12 different antimicrobial agents. In addition, C. jejuni isolates were examined for their cytotoxicity against Vero cells. The overall prevalence of Campylobacter spp. was 10.3% (31/300) classified into 20 (18.2%) C. jejuni and 11 (10.7%) Campylobacter coli. Among C. jejuni isolates (n=20), 15 strains belonged to biotype I and 5 isolates belonged to biotype II. The isolation rate from chicken thighs, breasts and livers was 12.5, 10 and 6.6%, respectively. A total of 15 (75%) C. jejuni strains revealed cytopathic effect (CPE) against Vero cells. Campylobacter spp. displayed a high antimicrobial resistance against penicillin G, gentamicin, trimethoprim-sulfamethoxazole, cephalothin, erythromycin, and chloramphenicol. On the other hand, Campylobacter spp. displayed high sensitivity to ciprofloxacin and nalidixic acid. Multidrug resistance was observed in 85 and 81.82% of C. jejuni and C. coli isolates, respectively High frequency of cytotoxicity and multidrug resistance in Campylobacter spp. from chicken meat indicates an important epidemiological role of Campylobacter spp. in human infections which necessitate proper hygienic measures on poultry farms and control measures during carcass slaughtering and processing. Key words: Campylobacter; retail chickens meat, real time polymerase chain reaction (PCR), cytotoxicity, antimicrobial susceptibility.
Identification of unique microRNAs associated with pancreatic cancer radioresistance using deep sequencing

Background: Pancreatic cancer is the most aggressive tumor type and is characterized by a poor prognosis. The main cause of treatment failure is the presence of tumor cells resistant to conventional therapies. MicroRNAs (miRNAs) play important roles in modulating the development of pancreatic carcinoma (PC). Methods: In this study, we established radioresistant cell lines from the commonly used human PC parental cell lines. We used high throughput sequencing to screen miRNA expression in both radioresistant and parental cell lines. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to confirm the results. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological processes (BPs) were performed to analyze gene set enrichment. Results: In total, 242 differentially expressed miRNAs were identified between these two groups. Compared with the parental line, SW1990-R exhibited with 97 upregulated and 145 downregulated miRNAs. qRT-PCR confirmed five upregulated (miR-497-5p, miR-146b-3p, miR-181a-3p, miR-33a-3p, and miR-32-5p) and five downregulated (miR-7-5p, miR-30b-5p, miR-181a-5p, miR-296-5p, and miR-216a-5p) miRNAs. GO and KEGG enrichment analyses revealed that some of the differentially expressed miRNAs regulated classical functions and pathways, including signal transduction, global and overview map, and immune system. Conclusions: Differential expression of miRNAs in relation to radioresistance suggests that various miRNAs may be predictive biomarkers or therapeutic targets in PC.
Acquiring absolute pitch in adulthood is difficult but possible

Absolute pitch (AP) refers to the rare ability to name the pitch of a tone without external reference. It is widely believed that acquiring AP in adulthood is impossible, since AP is only for the selected few with rare genetic makeup and early musical training. In three experiments, we trained adults to name pitches for 12 to 40 hours. After training, 14% of the participants (6 out of 43) were able to name twelve pitches at 90% accuracy or above, with semitone errors considered incorrect. This performance level was comparable to that of real-world ‘AP possessors’. AP training showed classic characteristics of perceptual learning, including performance enhancement, generalization of learning and sustained improvement for at least one to three months. Exploratory extrapolation analyses suggest that 39.5% and 58.1% of the participants would acquire AP if the training lasted for 60 and 180 hours respectively, suggesting the potential for the majority of the participants to acquire AP. We demonstrate that AP continues to be learnable in adulthood. The extent to which one acquires AP may thus be better explained by the amount and type of perceptual experience.