Miracle-dz/UniFAR-FTUs huggingface dataset:
SgTiler: a fast method to design tiling sgRNAs for CRISPR/Cas9 mediated screening

Summary Screening of genomic regions of interest using CRISPR/Cas9 is getting increasingly popular. The system requires designing of single guide RNAs (sgRNAs) that can efficiently guide the Cas9 endonuclease to the targeted region with minimal off-target effects. Tiling sgRNAs is the most effective way to perturb regulatory regions, such as promoters and enhancers. sgTiler is the first tool that provides a fast method for designing tiling sgRNAs. Availability and Implementation sgTiler is a command line tool that requires only one command to execute. Its source code is freely available on the web at https://github.com/HansenHeLab/sgTiler. sgTiler is implemented in Python and supported on any platform with Python and Bowtie.
Correspondence: fMRI replicability depends upon sufficient individual-level data

The replicability of activations from functional magnetic resonance imaging (fMRI) data have increasingly been called into question. Concerns have been raised that historically, sample sizes have been insufficient to produce adequate power, leading to unreliable results. Recently, Turner and colleagues demonstrated that even with large sample sizes, the replicability of fMRI can be worryingly low. However, their datasets featured low amounts of data at the individual-level. Here, I demonstrate that replicability depends critically on sufficient individual-level sampling. I show that fMRI can have strong replicability even at modest sample sizes when individuals are adequately sampled, but that inadequate individual-level sampling leads to poor replicability. These data indicate that fMRI replicability cannot be judged solely on sample size, and that we must be mindful to design our studies to adequately sample at the individual-level.
Hyperparameter-free optimizer of stochastic gradient descent that incorporates unit correction and moment estimation

In the deep learning era, stochastic gradient descent is the most common method used for optimizing neural network parameters. Among the various mathematical optimization methods, the gradient descent method is the most naive. Adjustment of learning rate is necessary for quick convergence, which is normally done manually with gradient descent. Many optimizers have been developed to control the learning rate and increase convergence speed. Generally, these optimizers adjust the learning rate automatically in response to learning status. These optimizers were gradually improved by incorporating the effective aspects of earlier methods. In this study, we developed a new optimizer: YamAdam. Our optimizer is based on Adam, which utilizes the first and second moments of previous gradients. In addition to the moment estimation system, we incorporated an advantageous part of AdaDelta, namely a unit correction system, into YamAdam. According to benchmark tests on some common datasets, our optimizer showed similar or faster convergent performance compared to the existing methods. YamAdam is an option as an alternative optimizer for deep learning.
A cautionary tale for in situ fluorometric measurement of stream chlorophyll a: influences of light and periphyton biomass

The use of in situ fluorometry to estimate stream benthic chlorophyll a (Chl a) has the potential to substantially reduce sampling costs and increase the feasibility of spatial and temporal replication. We evaluated the utility of a bbe moldaenke BenthoTorch fluorometer by estimating stream benthic Chl a under different natural light scenarios and by comparing estimates to laboratory measurements. BenthoTorch Chl a increased after rocks measured under direct solar radiation were moved into the shade, but values generally plateaued within 20 to 30 min of being in the shade. A proposed in situ procedure to shade substrates prior to measurements showed mean Chl a estimates between 1.05 and 2.13× greater than when substrates were measured under midday solar radiation conditions. We used this proposed procedure to compare Chl a estimates between the BenthoTorch (Chl aBT) and established laboratory methods (Chl aLab) at 50 sites throughout a productive basin in northeastern Oregon. A positive relationship existed between reach-scale Chl aBT and Chl aLab (r2 = 0.51, p< 0.001), but this relationship was not 1∶1. Chl aBT was greater than Chl aLab when laboratory values were <2 µg Chl a/cm2, but when laboratory values were >4 µg Chl a/cm2, Chl aBT was always lower than Chl aLab estimates. The Chl aLab∶Chl aBT ratio was positively related to reach-scale periphyton ash-free dry mass (AFDM), indicating increasing discrepancies between methods with greater periphyton biomass (r2 = 0.68, p < 0.0001). Collectively, our findings suggest that: 1) light conditions typically encountered in natural field settings can substantially alter Chl a estimates when using the BenthoTorch, and 2) at productive sites, the BenthoTorch can underestimate Chl a because of greater periphyton mat thickness.
A Prototype Operational Earthquake Loss 2 Model for California Based on UCERF 3-ETAS 3 – A First Look at Valuation 4

We present a prototype operational loss model for California based on 6 UCERF3-ETAS, which represents the first earthquake forecast to relax fault 7 segmentation assumptions and to include multi-fault ruptures, elastic-rebound, 8 and spatiotemporal clustering, all of which seem important for generating realistic 9 and useful aftershock statistics. UCERF3-ETAS is nevertheless an approximation 10 of the system, however, so usefulness will vary and potential value needs to be 11 ascertained in the context of each application. We examine this question with 12 respect to statewide loss estimates, exemplifying how risk can be elevated by 13 orders of magnitude due to triggered events following various scenario 14 earthquakes. Two important considerations are the probability gains, relative to 15 loss likelihoods in the absence of main shocks, and the rapid decay of gains with 16 time. We hope this paper inspires similar analyses with respect to other risk 17 metrics to help determine whether operationalization of UCERF3-ETAS would be 18 worth the considerable resources required. 19
Perspectives into the value of genera, families and orders in classification

This paper briefly discusses the history of fungal taxonomy and contributes to the concepts and the importance of ranking genera, families and orders. We propose recommendations for introducing species into appropriate ranks such as genera, families and orders, as well as the rationale to maintain species in one genus or segregate one genus into several genera. Various ways to rank fungi have commonly been based on morphological and phylogenetic species concepts. More recently, the use of molecular clocks, coupled with estimates of divergence times, has provided insights into how to assign species and support their establishment at different taxonomic hierarchical levels. Case studies are given from the order Botryosphaeriales and Pleosporales, and the genera Camarosporium, Colletotrichum, Diaporthe, Pestalotiopsis, Lophiostoma and Agaricus to demonstrate taxonomic ambiguities and the subjectivity in classification of fungi.
Effect of Different Auxins on Rooting of Semi Hard and Soft Wood Cuttings of Guava (Psidium guajava L.) CV. Safeda

An experiment was conducted to investigate the effect of different auxin on rooting in soft and semi-hard wood stem cuttings of guava. The maximum 80.3% sprouting response was recorded after 32 days of planting when soft wood cuttings were treated with 100 mg IAA/100 g talcum powder. Comparatively IAA was stronger than IBA in sprouting for both types of cuttings. The maximum number of leaves (8) was recorded in soft wood cuttings treated with IBA. The number of leaves in soft wood cuttings treated with either IBA or IAA and NAA were greater than semi hard wood cuttings. The maximum number of roots (27.6) per cutting was recorded in soft wood cuttings treated with IAA. As compared to control, auxin treatment promoted rooting in both types of cuttings. The maximum number of roots per cutting ranged from 11 to 17.3 in semi hard wood cuttings, while in soft wood cutting it ranged from 15.6 to 27.6. Irrespective of cutting type, IAA and NAA seem to be the most efficient in promoting roots. By contrast, IBA was more effective only in soft wood cuttings. The ultimate plant survival is, however, the key in such studies. In overall experiment, maximum of 28% survival rate was recorded in soft wood cuttings when exposed to IAA at 100 mg per 100 g talcum powder combination.
Microbial transformation of mestanolone by Macrophomina phaseolina and Cunninghamella blakesleeana and anticancer activities of the transformed products

The microbial transformation of anabolic androgenic steroid mestanolone (1) with Macrophomina phaseolina and Cunninghamella blakesleeana has afforded seven metabolites. The structures of these metabolites were characterized as 17β-hydroxy-17α-methyl-5α-androsta-1-ene-3,11-dione (2), 14α,17β-dihydroxy-17α-methyl-5α-androstan-3,11-dione (3), 17β-hydroxy-17α-methyl-5α-androstan-1,14-diene-3,11-dione (4), 17β-hydroxy-17α-methyl-5α-androstan-3,11-dione (5), 11β,17β-dihydroxy-17α-methyl-5α-androstan-1-ene-3-one (6), 9α,11β,17β-trihydroxy-17α-methyl-5α-androstan-3-one (7), and 1β,11α,17β-trihydroxy-17α-methyl-5α-androstan-3-one (8). All the metabolites, except 5 and 6, were identified as new compounds. Substrate 1 (IC50 = 27.6 ± 1.1 μM), and its metabolites 2 (IC50 = 19.2 ± 2.9 μM) and 6 (IC50 = 12.8 ± 0.6 μM) exhibited moderate cytotoxicity against the HeLa cancer cell line (human cervical carcinoma). All metabolites were noncytotoxic to 3T3 (mouse fibroblast) and H460 (human lung carcinoma) cell lines. The metabolites were also evaluated for immunomodulatory activity, and all were found to be inactive.
Fast and simple comparison of semi-structured data, with emphasis on electronic health records

We present a locality-sensitive hashing strategy for summarizing semi-structured data (e.g., in JSON or XML formats) into ‘data fingerprints’: highly compressed representations which cannot recreate details in the data, yet simplify and greatly accelerate the comparison and clustering of semi-structured data by preserving similarity relationships. Computation on data fingerprints is fast: in one example involving complex simulated medical records, the average time to encode one record was 0.53 seconds, and the average pairwise comparison time was 3.75 microseconds. Both processes are trivially parallelizable. Applications include detection of duplicates, clustering and classification of semi-structured data, which support larger goals including summarizing large and complex data sets, quality assessment, and data mining. We illustrate use cases with three analyses of electronic health records (EHRs): (1) pairwise comparison of patient records, (2) analysis of cohort structure, and (3) evaluation of methods for generating simulated patient data.
A new phylogenetic tribal classification of the grape family (Vitaceae)

Vitaceae (the grape family) consist of 16 genera and ca. 950 species primarily distributed in tropical regions. The family is well‐known for the economic importance of grapes, and is also ecologically significant with many species as dominant climbers in tropical and temperate forests. Recent phylogenetic and phylogenomic analyses of sequence data from all three genomes have supported five major clades within Vitaceae: (i) the clade of Ampelopsis, Nekemias, Rhoicissus, and Clematicissus; (ii) the Cissus clade; (iii) the clade of Cayratia, Causonis, Cyphostemma, Pseudocayratia, Tetrastigma, and an undescribed genus “Afrocayratia”; (iv) the clade of Parthenocissus and Yua; and (v) the grape genus Vitis and its close tropical relatives Ampelocissus, Pterisanthes and Nothocissus, with Nothocissus and Pterisanthes nested within Ampelocissus. Based on the phylogenetic and morphological (mostly inflorescence, floral and seed characters) evidence, the new classification places the 950 species and 16 genera into five tribes: (i) tribe Ampelopsideae J.Wen & Z.L. Nie, trib. nov. (47 species in four genera; Ampelopsis, Nekemias, Rhoicissus and Clematicissus); (ii) tribe Cisseae Rchb. (300 species in one genus; Cissus); (iii) tribe Cayratieae J.Wen & L.M. Lu, trib. nov. (370 species in seven genera; Cayratia, Causonis, “Afrocayratia”, Pseudocayratia, Acareosperma, Cyphostemma and Tetrastigma); (iv) tribe Parthenocisseae J.Wen & Z.D. Chen, trib. nov. (ca. 16 spp. in two genera; Parthenocissus and Yua); and (v) tribe Viteae Dumort. (ca. 190 species in two genera; Ampelocissus and Vitis).
Productivity and quality of melon cultivated in a protected environment under different soil managements

The need to adapt agricultural crops to climate change and to develop more sustainable cultivation systems has been a major challenge for agriculture. In this study the effects of soil conservation practices were evaluated on production aspects of melon ( Cucumis melo ), cultivar BRS Araguaia, cultivated in a greenhouse under soil and climatic conditions of the Brazilian Cerrado. The adopted experimental design was of randomized blocks with three treatments (soil managements) and six replicates. We evaluated the following soil management systems: no-tillage (PD), minimum tillage (CM) and conventional tillage (PC) in two cycles. Increases in commercial productivity and average number of marketable fruits were observed for PD (61.5 and 61.2 t/ha; 56,000 and 44,300 fruits/ha in the first and second cycles, respectively) and CM (59.7 and 57.5 t/ha; 55,700 and 42,400 fruits/ha in the first and second cycles, respectively). No effects of management systems on fruit quality were observed. PD and CM were effective in increasing the production of melon under evaluated conditions.
Response of benthic fauna to experimental bottom fishing: A global meta‐analysis

Bottom‐contact fishing gears are globally the most widespread anthropogenic sources of direct disturbance to the seabed and associated biota. Managing these fishing disturbances requires quantification of gear impacts on biota and the rate of recovery following disturbance. We undertook a systematic review and meta‐analysis of 122 experiments on the effects‐of‐bottom fishing to quantify the removal of benthos in the path of the fishing gear and to estimate rates of recovery following disturbance. A gear pass reduced benthic invertebrate abundance by 26% and species richness by 19%. The effect was strongly gear‐specific, with gears that penetrate deeper into the sediment having a significantly larger impact than those that penetrate less. Sediment composition (% mud and presence of biogenic habitat) and the history of fishing disturbance prior to an experimental fishing event were also important predictors of depletion, with communities in areas that were not previously fished, predominantly muddy or biogenic habitats being more strongly affected by fishing. Sessile and low mobility biota with longer life‐spans such as sponges, soft corals and bivalves took much longer to recover after fishing (>3 year) than mobile biota with shorter life‐spans such as polychaetes and malacostracans (<1 year). This meta‐analysis provides insights into the dynamics of recovery. Our estimates of depletion along with estimates of recovery rates and large‐scale, high‐resolution maps of fishing frequency and habitat will support more rigorous assessment of the environmental impacts of bottom‐contact gears, thus supporting better informed choices in trade‐offs between environmental impacts and fish production.
A new scoring system to predict the incidence of new onset diabetes after transplantation (NODAT)

Background. We performed this study to develop a new scoring system to stratify different levels of risk of developing new onset diabetes after transplantation (NODAT) in patients who underwent renal transplantation. Many prognostic variables have been previously described but few efforts have been made to group them in order to enhance their individual predictive power. Material and methods. In a first phase, 100 patients were prospectively analysed to determine which factors were significantly associated with the development of NODAT. A risk score ranging from 0 to 10 points was developed using a multivariate analysis. In a second phase, such score was validated in a new sample of 100 patients. Results. BMI ≥ 23.5 kg/m2, age ≥ 38.5 years, fasting blood sugar at 1st post-operative day ≥ 159.5 mg/dL, fasting blood sugar at 5th post-operative day ≥ 122.5 mg/dL and HOMA-IR ≥ 2.5 were found as independent prognostic variables. A clear distinction was shown among categories of low, intermediate and high risk, defined according to the risk score. Conclusion. This new scoring framework is basic and simple to accomplish. It permits a generally excellent stratification of risk of developing NODAT in patients undergoing renal transplantation. They might be separated in three risk stratification cohorts, which could be of help in early identification of NODAT.
Is intensity of plant root mycorrhizal colonization a good proxy for plant growth rate, dominance and decomposition in nutrient poor conditions?

Questions: Mycorrhizae may be a key element of plant nutritional strategies and of carbon and nutrient cycling. Recent research suggests that in natural conditions, intensity of mycorrhizal colonization should be considered an important plant feature. How are inter-specific variations in mycorrhizal colonization rate, plant relative growth rate (RGR) and leaf litter decomposability related? Is (arbuscular) mycorrhizal colonization linked to the dominance of plant species in nutrient-stressed ecosystems? Location: Teberda State Biosphere Reserve, northwest Caucasus, Russia. Methods: We measured plant RGR under mycorrhizal limitation and under natural nutrition conditions, together with leaf litter decomposability and field intensity of mycorrhizal colonization across a wide range of plant species, typical for alpine communities of European mountains. We applied regression analysis to test whether the intensity of mycorrhizal colonization is a good predictor of RGR and decomposition rate, and tested how these traits predict plant dominance in communities. Results: Forb species with a high level of field mycorrhizal colonization had lower RGR under nutritional and mycorrhizal limitation, while grasses were unaffected. Litter decomposition rate was not related to the intensity of mycorrhizal colonization. Dominant species mostly had a higher level of mycorrhizal colonization and lower RGR without mycorrhizal colonization than subordinate species, implying that they were more dependent on mycorrhizal symbionts. There were no differences in litter decomposability. Conclusions: In alpine herbaceous plant communities dominated by arbuscular mycorrhizae, nutrient dynamics are to a large extent controlled by mycorrhizal symbiosis. Intensity of mycorrhizal colonization is a negative predictor for whole plant RGR. Our study highlights the importance of mycorrhizal colonization as a key trait underpinning the role of plant species in carbon and nutrient dynamics in nutrient-limited herbaceous plant communities.
Effect of exposure time on mass‐rearing production of the olive fruit fly parasitoid, Psyttalia lounsburyi (Hymenoptera: Braconidae)

Classical biological control programmes rely on mass production of high‐quality beneficial insects for subsequent releases into the field. Psyttalia lounsburyi (Silvestri) (Hymenoptera: Braconidae) is a koinobiont larval–pupal endoparasitoid of tephritid flies that is being reared to support a classical biological control programme for olive fruit fly in California. The mass‐rearing system for a P. lounsburyi colony, initiated with insects originally collected in Kenya, was evaluated with the goal of increasing production, while at the same time reducing time requirements for rearing in a quarantine facility. We tested the effect of exposure time of a factitious host Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), on parasitization, adult production, superparasitism, and sex ratio of P. lounsburyi and survival of the host. Parasitization rates were highest (31%) at 3‐ and 4‐hr exposure times, while adult production (i.e., emergence of wasp progeny) was highest (16%) at the 2‐hr exposure time. Superparasitism over the course of the study was 1.5% and did not appear to be a factor affecting parasitoid production. The sex ratio of wasp progeny was male‐biased and did not vary significantly over different exposure times. The rate of stings on host larvae increased with exposure time and was consistent with decreases in pupal eclosion from larvae and emergence rate of adult flies. When compared to current rearing procedures, the 2‐hr exposure time resulted in an overall 2.8‐fold increase in P. lounsburyi production when standardized for time.
Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat

In the first longitudinal study of bat microbiomes, we find that unlike the pattern described in humans and other mammals, the prominent dynamics in Egyptian fruit bats’ fur microbiomes are those of change over time at the level of the colony as a whole. Thus, on average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats’ ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats’ fur, but differs from the more individualized pattern found in the bats’ gut microbiome.
EpCAM- AN OLD CANCER ANTIGEN, TURNED ONCOGENIC RECEPTOR AND ITS TAGETING IMMUNOTHERAPY

EpCAM is a cell adhesion molecule. Its structure, its expression and the oncogenic potential, and its signaling network and target therapy were in concise reviewed. In recent advances,in addition to PI3K/akt and Raf/MAPK pathway involving in cell survival,anti-apoptosis and proliferation,and malignant initiation and progression(see figure by Zhu,1986-91), three distinct pathway are illustrated: EpCAM/E-cadherin-catenin-actin cytoskeleton, EpCAM/ wint-catenin signaling and its major EpCAM/ nuclear signaling presented by Maetzel D in 2009 and Munz M in 2004. Moreover, more accumulated data are needed in detail mechanism. The data may provide its cancer biology and clinical targeting therapy benefits. Google Scholar