Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Clusters of Neurons in Layer 6 of Macaque V1

Layer 6 appears to perform a very important role in the function of macaque primary visual cortex, V1, but not enough is understood about the functional characteristics of neurons in the layer 6 population. It is unclear to what extent the population is homogeneous with respect to their visual properties or if one can identify distinct subpopulations. Here we performed a cluster analysis based on measurements of the responses of single neurons in layer 6 of primary visual cortex in male macaque monkeys (Macaca fascicularis) to achromatic grating stimuli that varied in orientation, direction of motion, spatial and temporal frequency, and contrast. The visual stimuli were presented in a stimulus window that was also varied in size. Using the responses to parametric variation in these stimulus variables, we extracted a number of tuning response measures and used them in the cluster analysis. Six main clusters emerged along with some smaller clusters. Additionally, we asked whether parameter distributions from each of the clusters were statistically different. There were clear separations of parameters between some of the clusters, particularly for f1/f0 ratio, direction selectivity, and temporal frequency bandwidth, but other dimensions also showed differences between clusters. Our data suggest that in layer 6 there are multiple parallel circuits that provide information about different aspects of the visual stimulus. SIGNIFICANCE STATEMENT The cortex is multilayered and is involved in many high-level computations. In the current study, we have asked whether there are subpopulations of neurons, clusters, in layer 6 of cortex with different functional tuning properties that provide information about different aspects of the visual image. We identified six major functional clusters within layer 6. These findings show that there is much more complexity to the circuits in cortex than previously demonstrated and open up a new avenue for experimental investigation within layers of other cortical areas and for the elaboration of models of circuit function that incorporate many parallel pathways with different functional roles.
Symptom clusters in newly diagnosed glioma patients: which symptom clusters are independently associated with functioning and global health status?

Abstract Background Symptom management in glioma patients remains challenging, as patients suffer from various concurrently occurring symptoms. This study aimed to identify symptom clusters and examine the association between these symptom clusters and patients’ functioning. Methods Data of the CODAGLIO project was used, including individual patient data from previously published international randomized controlled trials (RCTs) in glioma patients. Symptom prevalence and level of functioning were assessed with European Organisation for Research and Treatment of Cancer (EORTC) quality of life QLQ-C30 and QLQ-BN20 self-report questionnaires. Associations between symptoms were examined with Spearman correlation coefficients and partial correlation networks. Hierarchical cluster analyses were performed to identify symptom clusters. Multivariable regression analyses were performed to determine independent associations between the symptom clusters and functioning, adjusted for possible confounders. Results Included in the analysis were 4307 newly diagnosed glioma patients from 11 RCTs who completed the EORTC questionnaires before randomization. Many patients (44%) suffered from 5–10 symptoms simultaneously. Four symptom clusters were identified: a motor cluster, a fatigue cluster, a pain cluster, and a gastrointestinal/seizures/bladder control cluster. Having symptoms in the motor cluster was associated with decreased (≥10 points difference) physical, role, and social functioning (betas ranged from −11.3 to −15.9, all P < 0.001), independent of other factors. Similarly, having symptoms in the fatigue cluster was found to negatively influence role functioning (beta of −12.3, P < 0.001), independent of other factors. Conclusions Two symptom clusters, the fatigue and motor cluster, were frequently affected in glioma patients and were found to independently have a negative association with certain aspects of patients’ functioning as measured with a self-report questionnaire.
A machine learning approach predicts essential genes and pharmacological targets in cancer

Loss-of-function (LoF) screenings have the potential to reveal novel cancer-specific vulnerabilities, prioritize drug treatments, and inform precision medicine therapeutics. These screenings were traditionally done using shRNAs, but with the recent emergence of CRISPR technology there has been a shift in methodology. However, recent analyses have found large inconsistencies between CRISPR and shRNA essentiality results. Here, we examined the DepMap project, the largest cancer LoF effort undertaken to date, and find a lack of correlation between CRISPR and shRNA LoF results; we further characterized differences between genes found to be essential by either platform. We then introduce ECLIPSE, a machine learning approach, which combines genomic, cell line, and experimental design features to predict essential genes and platform specific essential genes in specific cancer cell lines. We applied ECLIPSE to known drug targets and found that our approach strongly differentiated drugs approved for cancer versus those that have not, and can thus be leveraged to identify potential cancer repurposing opportunities. Overall, ECLIPSE allows for a more comprehensive analysis of gene essentiality and drug development; which neither platform can achieve alone.
Changes in decomposition rate and litterfall in riparian zones with different basal area of exotic Eucalyptus in south-eastern Brazil

Exotic species in riparian environments can influence the quantity and quality of litterfall in the ecological system. The objective of this study was to evaluate the influence of Eucalyptus leaves on litterfall and terrestrial and aquatic leaf decomposition in a riparian forest in São Paulo state, Brazil. Three riparian zones were evaluated, and they were designated as areas of low (L), medium (M) and high (H) Eucalyptus basal area, respectively. Each riparian area was evaluated by surveying its structure and floristic composition. The amount of litterfall was evaluated over one year, and leaves were collected in terrestrial and vertical collectors. We evaluated the rates of aquatic and terrestrial decomposition of Eucalyptus and native leaves within litterbags. In general, area H had lower species richness, a higher edge effect and high Eucalyptus litterfall. Area L had higher species diversity (H′, Shannon– Wiener index), higher Pielou’s equitability index (J′), and smaller amounts of Eucalyptus litterfall. Eucalyptus leaves had higher extractive and lignin content compared with that of native trees. Eucalyptus leaves had a lower decomposition rate, except for the aquatic environment in area M. Our results show that the presence of Eucalyptus in riparian zones can increase litterfall and reduce the rate of leaf decomposition, but more studies are needed to evaluate any changes in ecosystem function from Eucalyptus presence.
Taking DBpedia Across Borders: Building the Serbian Chapter

—With the emergence of Linked Data, DBpedia has steadily grown to become one of the largest and most important structured knowledge sources we know of today. Adopting Wikipedia’s practice of entrusting the community with most of the work, the DBpedia internationalization committee has made a major step towards the move from unstructured to structured knowledge on the Web. Still, with new languages come new challenges. In this paper, we inspect some common obstacles that need to be tackled in order to add one more language to this popular data hub, but also some that haven’t been encountered before in this domain. More specifically, we explore the digraphic nature of the Serbian language, analyze the state of the DBpedia Extraction Framework with respect to its support for languages that use multiple scripts, and propose solutions towards overcoming this problem. Finally, we deploy the first digraphic DBpedia edition, taking the leading position amongst all DBpedia versions in the percentage of all covered Wikipedia templates, and all template occurrences in Wikipedia that are mapped, while adding a valuable new chapter to the DBpedia project and enriching the Linked Open Data Cloud even further. 
Lead bioaccumulation, subcellular distribution and chemical form in sugarcane and its potential for phytoremediation of lead-contaminated soil

Abstract Sugarcane is a promising species for lead (Pb) phytoextraction due to its large biomass and high tolerance toward Pb content. To understand the mechanisms involved in Pb tolerance and detoxification and its potential for phytoremediation in sugarcane, the bioaccumulation, subcellular distribution, and chemical forms of Pb in different tissues were investigated through pot cultivation sugarcane with increasing Pb concentrations in the present study. Results showed that sugarcane could tolerate high concentrations of Pb (up to 1250.0–1750.0 mg/kg); the Pb content in roots and shoots increased with increasing Pb concentration. A large amount of Pb content was stored in roots. The subcellular distribution of Pb in sugarcane revealed that the majority of Pb was bound to the cell wall. Meanwhile, the greatest amount of Pb was extracted by 2.0% acetic acid and 0.6 mol/L HCl, which indicated that most of Pb was combined with undissolved phosphate and oxalate. These results implied that the Pb formation of undissolved salts and compartmentalization in the cell wall may be a key strategy for Pb detoxicity and tolerance in sugarcane.
The antioxidant activity and active sites of delphinidin and petunidin measured by DFT, in vitro chemical-based and cell-based assays.

A computational DFT B3LYP method with 6-311G (d,p) basis set, the in vitro chemical-based and cellular antioxidant activity (CAA) assays were applied in this study to explain the structure-antioxidant activity relationships of delphinidin and petunidin. The compound molecular structures, spectral properties, frontier orbital energy, and transition state of delphinidin and petunidin were compared. In transition state, the result of the active site (O21-H32 and O22-H33) was consistent with the result of bond length. The frontier orbital theory results indicated that the probable antioxidant activity order was petunidin (0.09126 a.u.) > delphinidin (0.09175 a.u.), which agreed well with the cell-based antioxidant activity determined by CAA. However, the order of ABTS•+ and DPPH radical scavenging activity was delphinidin > petunidin. Our study could help to provide a rational approach for the investigation of antioxidant activity of phytochemicals. PRACTICAL APPLICATIONS: As anthocyanins, delphinidin and petunidin with great antioxidant activity are widely found in various fruits and vegetables. However, there are many kinds of methods used to measure their antioxidant activity and the antioxidant mechanism which are not concrete and clear. Therefore, it is crucial to study the antioxidant actvity of anthocyanins utilizing the DFT method combined with in vitro chemical-based and cell-based assays. Our study could contribute not only to the elucidation of chemical mechanism of antioxidants and exploration the structural features in essence, but also to promote the further development of phytochemicals in the field of food chemistry and pharmacy.
AN APPLICATION OF THE EFFECT OF GPR DATA PROCESSING IN HIGH-ORDER STATISTICS

This paper introduces a method for studying the effect based on high-order statistics of GPR data.The basic idea of this method is the utilization of high-order statistical parameters in signal recognition and detection for processing and reconstruction of different models for GPR records.The model test shows that there are different high-order statistical features in different models,and the high-order statistics show obvious effect on suppressing background noise and multiple reflection of GPR data.
Artificial Rearing and Nutritional Physiology of the Planthoppers and Leafhoppers (Hemiptera: Delphacidae and Deltocephalidae) on a Holidic Diet

Among the planthoppers and leafhoppers, some species, Sl\Ch as Nilaparvata lugens Stal and Sogatella furcif era Horvath, have been considered to come to Japan from foreign countries every year because they are unable to hibernate in Japan, while other species like Laodelphax striatellus Fallen and N ephotettix cincticeps Uhler are able to hibernate in Japan. In spite of heavy damage of rice crop caused by them, many aspects of basic problems such as their nutritional requirements or growth physiology have not been clarified yet. With the purpose of making clear the nutritional requirements of these insects, we have developed a method of artificial rearing on a synthetic diet which consists of only
NMR reveals light-induced changes in the dynamics of a photoswitchable fluorescent protein

The availability of fluorescent proteins with distinct phototransformation properties is crucial for a wide range of applications in advanced fluorescence microscopy and biotechnology. To rationally design new variants optimized for specific applications, a detailed understanding of the mechanistic features underlying phototransformation is essential. At present, little is known about the conformational dynamics of fluorescent proteins at physiological temperature, and how these dynamics contribute to the observed phototransformation properties. Here, we apply high-resolution NMR spectroscopy in solution combined with in-situ sample illumination at different wavelengths to investigate the conformational dynamics of rsFolder, a GFP-derived protein that can be reversibly switched between a green fluorescent state and a non-fluorescent state. Our results add a dynamic view to the static structures obtained by X-ray crystallography. Including NMR into the analytical toolbox used for fluorescent protein research provides new opportunities for investigating the effect of mutations or changes in the environmental conditions on the conformational dynamics of phototransformable fluorescent proteins, and their correlation with the observed photochemical and photophysical properties. Significance Photo-transformable Fluorescent Proteins (PTFPs) are essential tools for super-resolution (SR) microscopy. In practical applications, however, researchers often encounter problems when using PTFPs in a particular cellular context, because the environmental conditions (pH, temperature, redox potential, oxygen level, viscosity, …) affect their brightness, photostability, phototransformation kinetics, etc. Rational fluorescent protein engineering exploits the mechanistic information available from structural studies, mainly X-ray crystallography, in order to design new PTFP variants with improved properties for particular applications. Here we apply NMR spectroscopy in solution to investigate the light-induced changes in conformational dynamics of rsFolder, a reversibly switchable fluorescent protein. The dynamic view offered by NMR highlights protein regions that comprise potentially interesting mutation points for future mutagenesis campaigns.
Cohesin removal reprograms gene expression upon mitotic entry

Entering mitosis, the genome is restructured to facilitate chromosome segregation, accompanied by dramatic changes in gene expression. However, the mechanisms that underlie mitotic transcriptional regulation are unclear. In contrast to transcribed genes, centromere regions retain transcriptionally active RNA Polymerase II (RNAPII) in mitosis. Here, we demonstrate that chromatin-bound cohesin is sufficient to retain RNAPII at centromeres while WAPL-mediated removal of cohesin during prophase is required for RNAPII dissociation from chromosome arms. Failure to remove cohesin from chromosome arms results in a failure to release elongating RNAPII and nascent transcripts from mitotic chromosomes and dramatically alters gene expression. We propose that prophase cohesin removal is the key step in reprogramming gene expression as cells transition from G2 to mitosis, and is temporally coupled with chromosome condensation to coordinate chromosome segregation with changes in gene expression. Highlights Mitotic centromere transcription requires cohesin Cohesin removal releases elongating RNA Pol II and nascent RNA from chromatin The prophase pathway reprograms gene expression during mitosis
The use of bromelain as a feed additive in fish diets: Growth performance, intestinal morphology, digestive enzyme and immune response of juvenile Sterlet (Acipenser ruthenus)

Bromelain is a proteolytic enzyme extracted from Ananas comosus and has great potential to affect several physiological functions. The current study examined the effect of bromelain added to commercial feed at concentrations of 0 g (control), 10 g (B1) and 20 g (B2) per kg diet on growth, feed utilization, intestinal morphology, digestive enzyme and immune response of juvenile Sterlet (Acipenser ruthenus) for 56 days. At the end of this experiment, the highest final body weight was detected in fish fed diet of B2 compared to control. The protein content of whole fish was higher in fish fed diet of B1 and B2, but the content of calcium, iron, copper and zinc was noted lower in fillets of fish fed diet of B1 and B2. Supplementation with bromelain significantly increased the height of mucosal folds, enterocytes and the supranuclear zone of the epithelial cells compared to control diet. The enzymatic activity of lipase and pepsin was significantly (p 0.05) difference was found in ceruloplasmin, metabolic activity of spleen macrophages and potential killing activity of spleen phagocytes between different treatments.
First report of Trichogrammadanausicida and Trichogrammacacaeciae reared from Thaumatotibialeucotreta eggs in Israel

Abstract The egg parasitpoids Trichogrammadanausicida (Nagaraja) and Trichogrammacacaeciae (Marchal) (Hymenoptera: Trichogrammatidae), are reported for the first time in Israel. Moreover, our discovery of T.danausicida is the first report of this parasitoid species outside of India. The occurrence of those trichogrammatids was first discovered and documented in May 2016 during a survey of egg parasitoids of the False codling moth Thaumatotibialeucotreta (Lepidoptera: Tortricidae). The field survey was conducted on castor bean fruits (Ricinuscommunis) in the Israeli central coastal plain. The identity of the parasitoids was revealed by means of sequencing a portion of the cytochrome oxidase I gene (COI) of the studied parasitoids.
The value of contrast-enhanced ultrasonography to detect the sacroiliac joint for predicting relapse after discontinuation of anti-tumor necrosis factor therapy in patients with ankylosing spondylitis.

Background Ankylosing spondylitis (AS) is a chronic inflammatory disease characterized by high relapse. Therefore, the present study aimed to investigate the ultrasonographic features of contrast-enhanced ultrasonography (CEUS) in the sacroiliac joint (SIJ) in patients with AS in remission after discontinuation of anti-tumor necrosis factor (TNF) therapy, and also examined the role of CEUS in predicting relapse. Methods In this prospective observational study, 130 SIJs in 65 patients with AS (according to modified New York criteria) satisfying Ankylosing Spondylitis Disease Activity Score (ASDAS) inactive disease after discontinuation of anti-TNF therapy were investigated on color Doppler ultrasonography (CDUS) and CEUS. Vascularization and the resistive index (RI) of the SIJ were observed and measured. We defined no blood flow, high RI of arterial blood flow (RI ≥0.7), the reversed phase in the diastolic phase or venous blood flow in the bilateral SIJs, as negative CDUS/CEUS; meanwhile, low RI of arterial blood flow (RI <0.7) in the unilateral or bilateral SIJs was defined as positive CDUS/CEUS. All the patients were followed up for 52 weeks until relapse. Relapse was defined as an increase of two or more items in comparison with the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) at the time of anti-TNF withdrawal. Results After 52 weeks, 46 of the 65 patients (70.8%) had relapse. The mean time to relapse was 31.4 weeks (±8.4 weeks, range 20 to 52). After discontinuation of anti-TNF therapy, positive CEUS accounted for 61.5%; this was significantly more than positive CDUS (13.8%). The vascularization detected by CEUS for patients of relapse was significantly different from that of patients with remission (P<0.05). In addition, patients with negative CEUS had a longer duration of remission than the patients with positive CEUS (P=0.005). A Cox proportional hazards regression analysis found that the disease duration could also be regarded as a factor predictive of relapse in patients with AS. Conclusions The use of CEUS distinctly improved the detection of vascularization in the SIJ in patients with AS in remission after anti-TNF withdrawal. The presence of vascularization in the SIJ detected by CEUS at the time of anti-TNF withdrawal could yield a valuable predictor of relapse in patients with AS. A significant limit of this study is the lack of magnetic resonance imaging (MRI) as the standard reference.
Facilitators to Accessibility of HIV/AIDS-Related Health Services among Transgender Women Living with HIV in Yogyakarta, Indonesia

The study aimed to explore facilitators or enabling factors that enhance accessibility (defined as the opportunity to be able to use) to HIV/AIDS-related health services among HIV positive transgender women, also known as Waria in Yogyakarta, Indonesia. A qualitative study employing one-on-one in-depth interviews was conducted from December 2017 to February 2018. Participants were HIV positive Waria recruited using purposive and snowball sampling techniques. Data were analysed using the framework analysis for qualitative research. The findings showed that participants' knowledge of HIV/AIDS and the availability of HIV/AIDS-related health services were enablers to the services accessibility. Emotional support from fellow Waria displayed in various ways, such as kind and caring attention, attentive listening, and encouraging words, was an important social support that played a role in supporting Waria's accessibility to the services. HIV/AIDS-related health service information shared personally or jointly by fellow Waria and instrumental support including helping each other to collect antiretroviral (ARV) from hospitals or community health centres, contacting ambulance in emergency situations, accompanying each other to health service facilities, and helping those without the health insurance to receive free health services were also the social support enabling accessibility to the services among the study participants. Appraisal support such as providing constructive feedback and affirmation was another enabling factor to Waria's accessibility to the services. The findings indicate the needs to broadly disseminate information and educate Waria populations and their significant others about HIV/AIDS and related health services to raise their awareness of HIV/AIDS and acceptance of HIV/AIDS positive individuals. Educating and broadly disseminating this information in other settings in the country will also increase accessibility to the HIV/AIDS services among Waria, their families, and communities addressing the currently existing inequities in health. The findings also reinforce the importance of the establishment of Waria peer-support groups within Waria communities and the involvement of Waria in HIV/AIDS activities and programs, which may increase their awareness of HIV/AIDS, and accessibility to HIV/AIDS-related health services.