Miracle-dz/UniFAR-FTUs huggingface dataset:
Escholarship@umms Program in Gene Function and Expression Publications and Presentations Program in Gene Function and Expression an Improved Predictive Recognition Model for Cys2-his2 Zinc Finger Proteins Repository Citation an Improved Predictive Recognition Model for Cys2-his2 Zinc Finger Proteins

An improved predictive recognition model for Cys2-His2 zinc finger proteins" (2014). Program in Gene Function and Expression Publications and Presentations. Paper 236. improved predictive recognition model for Cys2-His2 zinc finger proteins. ABSTRACT Cys 2-His 2 zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukary-otes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
EFFICACY OF SYSTEMIC INSECTICIDES AGAINST THE CITRUS MEALYBUG, PLANOCOCCUS CITRI, AND PESTICIDE MIXTURES AGAINST THE WESTERN FLOWER THRIPS, FRANKLINIELLA OCCIDENTALIS, IN PROTECTED ENVIRONMENTS

Protected environments, such as greenhouses and interior plantscapes provide optimal conditions for arthropod (insect and/or mite) pests to survive, develop, and reproduce. Two commonly encountered insect pests in protected environments include the citrus mealybug (CMB), Planococcus citri, and the western flower thrips (WFT), Frankliniella occidentalis. It is difficult to mitigate CMB and WFT populations due to the behavioral characteristics of the insects and few pesticides that are registered for use in protected environments. This research involved two distinctly different studies. The objectives of the first study were to determine the efficacy and residual activity of systemic insecticides registered for use against CMB and to quantify CMB feeding locations. The objectives of the second study were to determine the compatibility and efficacy of commonly used binary pesticide mixtures against the WFT under both laboratory and greenhouse conditions. To determine the efficacy of systemic insecticides against CMB, greenhouse experiments were conducted in which coleus, Solenstemon scutellarioides, plants were artificially infested with CMB. Drench applications of each designated treatment were applied to each plant. Results associated with drench applications of the systemic insecticides against CMB indicated minimal CMB mortality (<30%) for both preventative and curative drench applications of azadirachtin and spirotetramat. Thiamethoxam, a neonicotinoid-based insecticide, at the labeled and twice the labeled rate provided the highest CMB mortality; however, not until 21 days after treatment was this observed, and CMB mortality was <80%. In all cases, significantly more CMB were located on the stem of green coleus plants compared to the leaf top and bottom. Pesticide mixture compatibility was determined using jar tests. In addition, phytotoxicity and efficacy of pesticide mixtures against WFT was determined through a series of laboratory and greenhouse experiments for each individual pesticide, and the mixtures to determine synergism, antagonism, or no effect. Results associated with the jar tests indicated that all the mixtures were compatible. Furthermore, the mixtures were not phytotoxic to the horticultural plant species evaluated. Laboratory results indicated that mixtures containing spinosad + bifenazate were antagonistic against WFT. Greenhouse experiments demonstrated significantly reduced efficacy associated with the abamectin + azadirachtin mixtures; however, each binary mixture provided approximately 80% mortality of WFT.
Recognizing induced emotions of movie audiences: Are induced and perceived emotions the same?

Predicting the emotional response of movie audiences to affective movie content is a challenging task in affective computing. Previous work has focused on using audiovisual movie content to predict movie induced emotions. However, the relationship between the audience's perceptions of the affective movie content (perceived emotions) and the emotions evoked in the audience (induced emotions) remains unexplored. In this work, we address the relationship between perceived and induced emotions in movies, and identify features and modelling approaches effective for predicting movie induced emotions. First, we extend the LIRIS-ACCEDE database by annotating perceived emotions in a crowd-sourced manner, and find that perceived and induced emotions are not always consistent. Second, we show that dialogue events and aesthetic highlights are effective predictors of movie induced emotions. In addition to movie based features, we also study physiological and behavioural measurements of audiences. Our experiments show that induced emotion recognition can benefit from including temporal context and from including multimodal information. Our study bridges the gap between affective content analysis and induced emotion prediction.
(E)-4-Methoxy-2-[3-(trifluoromethyl)phenyliminomethyl]phenol

The title compound, C15H12F3NO2, adopts the phenol–imine tautomeric form, with the H atom attached to oxygen rather than to nitrogen. There are two independent molecules aligned nearly parallel in the asymmetric unit with their trifloramethyl groups pointing in opposite directions. The dihedral angles between the aromatic rings are 40.43 (1)° in the first molecule and 36.12 (1)° in the second. Strong intramolecular O—H⋯N hydrogen bonding generates S(6) ring motifs. Weak intermolecular C—H⋯O hydrogen bonds link the independent molecules separately into sheets normal to [010]. In addition, C—H⋯π interactions are also observed. The F atoms of the trifluoromethyl groups are disordered over two sets of sites with refined site occupancies of 0.59 (2)/0.41 (2) and 0.62 (3)/0.38 (3), respectively.
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction. Results: We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods. Availability: Our programs can be freely downloaded from http://compbio.mit.edu/ranger-dtl/. Contact: mukul@csail.mit.edu; manoli@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Synth-tax: Modification of BERT Syntax Representations via Structural Probes

Large, pretrained, ‘black-box’ language models like BERT have recently risen to prominence, and we seek to understand how they represent linguistic information by causally relating models’ predictions to their internal representations. In particular, we provide a careful framework of assumptions and causality, and we manipulate BERT’s purported sentence-syntactic representations provided by the structural probe [1] to examine whether the resulting predictions of subject-verb number agreement changes. While our evidence is inconclusive, we find that BERT likely does not encode syntax in exactly the manner structural probe’s success suggests, either capturing syntax poorly or also conflating it with other linguistic information like number. In addition, we find evidence that BERT performs worse on subjectverb number agreement tasks when words are broken into separate wordpieces.
The role of LKB1 in the pathogenesis of Osteosarcoma

Osteosarcoma (OS) is a rare malignant mesenchymal neoplasm, but the third most common cancer in adolescents. Understanding the molecular pathogenesis of this disease is essential to design new, effective therapeutic strategies to improve patient survival. The recent report that LKB1-deficient mice develop bone-forming tumours begs the question whether loss of this tumour suppressor gene plays a role in human OS pathogenesis. We found that LKB1 protein expression was reduced in 20 of 26 (77%) human OS cases by Western blot and 153 of 259 (59%) by immunohistochemistry. Downstream, the mTOR pathway was activated in 137 of 158 cases (87%) and this activation was correlated to LKB1 loss, providing new insights into potential treatments. No copy number loss of the LKB1 region was identified in 93 OS cases by interphase fluorescent in situ hybridization. Four of 12 informative cases had concomitant loss of one parental allele at the locus of one single nucleotide polymorphism and reduced protein expression; one of them possessed only one LKB1 copy by qPCR. Direct sequencing of 21 cases failed to detect LKB1 mutations and all these cases expressed similarly high levels of LKB1 mRNA by qRT-PCR, irrespective of their protein expression. It suggested that LKB1 is regulated post-transcriptionally in OS. In silico analysis of our OS microRNA data showed that this cannot be accounted for by microRNA directly targeting LKB1 mRNA and a preliminary study could not exclude the involvement of SIRT1. The knock-down of LKB1 by shRNA in the osteoblast cell line HOB had only subtle effects on cell proliferation and survival. Its role in OS pathogenesis was confirmed by knock-in in LKB1-deficient OS cell lines, which induced reduced cell proliferation. To conclude, LKB1 protein expression is reduced in a subset of OS by a post-transcriptional mechanism, leading to increased cell proliferation in the tumour.
Prevalence of Root Caries among Patients Attending RAKCODS Hospital

Root caries is one of the most significant dental problems among older adults. In order to prevent tooth loss due to root caries, the risk factors must be identified. The objectives of the study were to evaluate the prevalence of root caries and the associated risk factors among patients attending Ras Al-Khaimah College of Dental Sciences (RAKCODS) hospital. Cross-sectional descriptive study was done in RAKCODS based on random sampling using 212 participants, both genders with age 35 and above, during 6 months period, the risk factor associated with root caries were analyzed by multiple regression assay. The prevalence of root caries was 39.6% among the tested patient. Among the independent factors age, educational qualification, fluoride-containing toothpaste, smoking habit, dry mouth syndrome, plaque index and number of missing teeth showed a statistically significant influence on root caries Prevalence. According to the result of our study root caries is one of the significant oral health problems among patients attending RAKCODS hospital and the above mentioned factors play an important role in root caries prevalence. Clinical article (J Int Dent Med Res 2020; 13(1): 295-300)
Human Herpesvirus 8 Seroprevalence, China

To summarize the seroprevalence of human herpesvirus 8 (HHV-8) in mainland China, we conducted a systematic review and meta-analysis based on available literature. Data show that differences in HHV-8 prevalence vary considerably among different ethnic groups and geographic regions. Blood-borne transmission could be a potential route for HHV-8 infection in China.
Survey of Ontario Bulk Tank Raw Milk for Food-Borne Pathogens.

Raw (unpasteurized) milk can be a source of food-borne pathogens. Raw milk consumption results in sporadic disease outbreaks. Pasteurization is designed to destroy all bacterial pathogens common to raw milk, excluding spore-forming bacteria and possibly Mycobacterium paratuberculosis , but some people continue to drink raw milk, believing it to be safe. Current methods for assessing the bacteriological quality of raw milk, such as aerobic plate counts, are not usually designed to detect specific pathogens. The objective of this study was to estimate the proportion of pick-ups (loads of raw milk from a single farm bulk tank) from Ontario farm bulk tanks that contained Listeria monocytogenes . Salmonella spp. , Campylobacter spp. , and/or verotoxigenic Escherichia coli (VTEC). Samples from 1,720 pick-ups of raw milk were tested for the presence of these pathogens, and 47 L. monocytogenes , three Salmonella spp. , eight Campylobacter spp. , and 15 VTEC isolates were detected, representing 2.73, 0.17, 0.47, and 0.87% of milk samples, respectively. Estimates of the proportion of theoretical tanker truck loads of pooled raw milk contaminated with pathogens ranged from a low of 0.51 % of tankers containing raw milk from 3 bulk tanks being contaminated with Salmonella spp. to a high of 34.41 % of tankers containing raw milk from 10 bulk tanks being contaminated with at least one of the pathogens. Associations between the presence of pathogens and raw milk sample characteristics were investigated. The mean somatic cell count was higher among VTEC- or L. monocytogenes -positive samples, and the mean aerobic plate count was found to be higher among L. monocytogenes -positive samples. These results confirm the presence of bacterial food pathogens in raw milk and emphasize the importance of continued diligence in the application of hygiene programs within dairies and the separation of raw milk from pasteurized milk and milk products.
Editorial of E-Book on Action and Language Integration

Increasing theoretical and experimental research on action and language processing in humans and animals clearly demonstrates the strict interaction and co-dependence between language and action. This has been extensively demonstrated in neuroscientific investigations (e.g., Rizzolatti and Arbib, 1998; Cappa and Perani, 2003; Pulvermuller, 2003), psychology experiments (e.g., Glenberg and Kaschak, 2002; Pecher and Zwaan, 2005; Barsalou, 2008), evolutionary psychology (e.g., Corballis, 2002), and computational modeling (e.g., Cangelosi and Parisi, 2004; Massera et al., 2007; Cangelosi, 2010). All these studies have important implication both for the understanding of the action basis of cognition in natural and artificial cognitive systems, as well as for the design of cognitive and communicative capabilities in robots (Cangelosi et al., 2010). The journal “Frontiers in Neurorobotics” published a collection of articles on the topic of action and language integration both in natural cognitive systems (e.g., humans and animals) and in artificial cognitive agents (robots and simulated agents). These articles are now collected in an e-book, for wider dissemination. This set of chapters provides an up to date overview of current advances in the grounding of language into sensorimotor knowledge. The first chapters primarily focus on experimental evidence from cognitive psychology (Symes et al., 2010), cognitive neuroscience studies (Borghi et al., 2010), and comparative experimental/simulation studies (Greco and Caneva, 2010). Two chapters then use neural network simulation for motor chains for sentence processing (Chersi et al., 2010) and a computational model of gaze planning in word recognition and reading (Ferro et al., 2010). Finally, four chapters use cognitive systems and robotics methodologies to investigate general principles of action–language grounding (Parisi, 2010), teleological representations of action and language for human–robot interaction experiments (Lallee et al., 2010), verbal and non-verbal communication in neurorobotics models (Bicho et al., 2010), and action bases of action words (Marocco et al., 2010).
Empathy matters: ERP evidence for inter-individual differences in social language processing

When an adult claims he cannot sleep without his teddy bear, people tend to react surprised. Language interpretation is, thus, influenced by social context, such as who the speaker is. The present study reveals inter-individual differences in brain reactivity to social aspects of language. Whereas women showed brain reactivity when stereotype-based inferences about a speaker conflicted with the content of the message, men did not. This sex difference in social information processing can be explained by a specific cognitive trait, one’s ability to empathize. Individuals who empathize to a greater degree revealed larger N400 effects (as well as a larger increase in γ-band power) to socially relevant information. These results indicate that individuals with high-empathizing skills are able to rapidly integrate information about the speaker with the content of the message, as they make use of voice-based inferences about the speaker to process language in a top-down manner. Alternatively, individuals with lower empathizing skills did not use information about social stereotypes in implicit sentence comprehension, but rather took a more bottom-up approach to the processing of these social pragmatic sentences.
GITR Activation Induces an Opposite Effect on Alloreactive CD4+ and CD8+ T Cells in Graft-Versus-Host Disease

Glucocorticoid-induced tumor necrosis factor receptor family-related gene (GITR) is a member of the tumor necrosis factor receptor (TNFR) family that is expressed at low levels on unstimulated T cells, B cells, and macrophages. Upon activation, CD4+ and CD8+ T cells up-regulate GITR expression, whereas immunoregulatory T cells constitutively express high levels of GITR. Here, we show that GITR may regulate alloreactive responses during graft-versus-host disease (GVHD) after allogeneic bone marrow transplantation (BMT). Using a BMT model with major histocompatibility complex class I and class II disparity, we demonstrate that GITR stimulation in vitro and in vivo enhances alloreactive CD8+CD25− T cell proliferation, whereas it decreases alloreactive CD4+CD25− proliferation. Allo-stimulated CD4+CD25− cells show increased apoptosis upon GITR stimulation that is dependent on the Fas–FasL pathway. Recipients of an allograft containing CD8+CD25− donor T cells had increased GVHD morbidity and mortality in the presence of GITR-activating antibody (Ab). Conversely, recipients of an allograft with CD4+CD25− T cells showed a significant decrease in GVHD when treated with a GITR-activating Ab. Our findings indicate that GITR has opposite effects on the regulation of alloreactive CD4+ and CD8+ T cells.
Dissecting primary resistance to anti-EGFRs in RAS and BRAF wt metastatic colorectal cancer (mCRC): A case-control study.

11508Background: Almost half of RAS and BRAFwt mCRC patients do not respond to anti-EGFRs. Different molecular alterations suggested as predictors of resistance have not been validated. Methods: We conducted a case-control study to prospectively demonstrate the negative predictive impact of HER-2 amplification or mutations (mut), MET amplification, NTRK/ROS1/ALK/RET rearrangements, and mut activating MAPKs or PI3K/Akt axis. Patients with RAS and BRAFwt mCRC clearly resistant (cases) or clearly sensitive (controls) to anti-EGFRs were selected. Hypothesizing a prevalence of candidate alterations of 0% and 15% among controls and cases, 47 cases and 47 controls were needed to be able to reject the null hypothesis of equally prevalent alterations, with a- and b- error 0.05 and 0.20. Since hypermutated tumors may hardly rely on a single pathway for their growth, we also evaluated the impact of microsatellite instability. Results: 47 cases and 47 controls were included. Primary endpoint was met: mentioned altera.
Injecting drug use is associated with a more rapid CD4 cell decline among treatment naïve HIV-positive patients in Indonesia

It remains unclear whether the natural course of human immunodeficiency virus (HIV) differs in subjects infected through injecting drug use (IDU) and no data have been published from low‐ or middle‐income countries. We addressed this question in an urban cohort in Indonesia, which is experiencing a rapidly growing HIV epidemic strongly driven by IDU.
UvA-DARE (Digital Academic Repository) Brand content diffusion on Social Networking Sites: Exploring the triadic relationship between the brand, the individual, and the community

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Discovery of catalytically active orthologues of the Parkinson's disease kinase PINK1: analysis of substrate specificity and impact of mutations

Missense mutations of the phosphatase and tensin homolog (PTEN)-induced kinase 1 (PINK1) gene cause autosomal-recessive Parkinson's disease. To date, little is known about the intrinsic catalytic properties of PINK1 since the human enzyme displays such low kinase activity in vitro. We have discovered that, in contrast to mammalian PINK1, insect orthologues of PINK1 we have investigated—namely Drosophila melanogaster (dPINK1), Tribolium castaneum (TcPINK1) and Pediculus humanus corporis (PhcPINK1)—are active as judged by their ability to phosphorylate the generic substrate myelin basic protein. We have exploited the most active orthologue, TcPINK1, to assess its substrate specificity and elaborated a peptide substrate (PINKtide, KKWIpYRRSPRRR) that can be employed to quantify PINK1 kinase activity. Analysis of PINKtide variants reveal that PINK1 phosphorylates serine or threonine, but not tyrosine, and we show that PINK1 exhibits a preference for a proline at the +1 position relative to the phosphorylation site. We have also, for the first time, been able to investigate the effect of Parkinson's disease-associated PINK1 missense mutations, and found that nearly all those located within the kinase domain, as well as the C-terminal non-catalytic region, markedly suppress kinase activity. This emphasizes the crucial importance of PINK1 kinase activity in preventing the development of Parkinson's disease. Our findings will aid future studies aimed at understanding how the activity of PINK1 is regulated and the identification of physiological substrates.