Miracle-dz/UniFAR-FTUs huggingface dataset:
Intra-Molecular Cross-Linking of Acidic Residues for Protein Structure Studies

Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would help to develop structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine (lysine, the amino terminus) selective reagents. Previous work using these cross-linkers has shown that for several proteins of known structure, the number of cross-links that can be obtained experimentally may be small compared to what would be expected from the known structure, due to the relative reactivity, distribution and solvent accessibility of the lysines in the protein sequence. To overcome these limitations, we have investigated the use of cross-linking reagents that can react with other reactive side chains in proteins. We used 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) to activate the carboxylic acid containing residues, aspartic acid (D), glutamic acid (E) and the carboxy terminus (O), for cross-linking reactions. Once activated, the DEO side chains can react to form “zero-length” cross-links with nearby primary amine containing residues, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO side chains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker arm of variable length. Using these reagents, we have found three new “zero-length” cross-links in ubiquitin consistent with its known structure (M1–E16, M1–E18 and K63–E64). Using the dihydrazide cross-linkers, we have identified two new cross-links (D21–D32 and E24–D32) unambiguously. Using a library of dihydrazide cross-linkers with varying arm length, we have shown that there is a minimum arm length required for the DEO–DEO cross-links of 5. 8Å. These results show that additional structural information can be obtained by exploiting new cross-linker chemistry, increasing the probability that the protein target will yield sufficient distance constraints to develop a structural model.
Early socioemotional competence, psychopathology, and latent class profiles of reparative prosocial behaviors from preschool through early adolescence

Abstract Children who have difficulty using reparative behaviors following transgressions display a wide range of poorer social and emotional outcomes. Despite the importance of reparative skills, no study has charted the developmental trajectory of these behaviors or pinpointed predictors of poorer reparative abilities. To address these gaps in the literature, this study applied growth mixture modeling to parent reports of children's reparative behaviors (N = 230) in a 9-year longitudinal data set spanning from preschool to early adolescence. Three distinct trajectories of reparative behaviors were found: a low-stable, moderate-stable, and high-stable latent class. Poorer emotion understanding, social withdrawal, social rejection, and maladaptive guilt in the preschool period predicted membership in a low-stable reparative trajectory. Externalizing diagnoses, particularly conduct disorder and oppositional defiant disorder, also predicted membership in a low-stable reparative trajectory. Preschool-onset depression predicted membership in a low-stable reparative trajectory through high levels of maladaptive guilt. The findings from this study suggest that socioemotional deficits in the preschool period set children on longstanding trajectories of impaired reparative responding. Thus, emotion understanding, social functioning, maladaptive guilt, and early psychiatric symptoms should be targeted in early preventive interventions.
Differential 12‐O‐Tetradecanoylphorbol‐13‐acetate‐induced activation of rat mammary carcinoma susceptibility Fbxo10 variant promoters via a PKC‐AP1 pathway

Rat mammary carcinoma susceptibility 5a1 (Mcs5a1), which is concordant to human MCS5A1 breast cancer risk locus, mediates susceptibility by a non‐mammary cell‐autonomous mechanism associated with T cell differential expression of F‐box protein 10 (Fbxo10). Human FBXO10, an evolutionarily conserved ubiquitin ligase gene, was shown to have a potential role in regulating cell death by controlling the degradation of Bcl‐2, a key protein involved in apoptosis. Breast cancer susceptibility is controlled by interactions between environmental and genetic factors; therefore, we sought to determine if breast cancer risk‐associated environmental chemicals interact with Mcs5a1 variants using luciferase reporter constructs containing 4.2 kb Fbxo10 promoters based on alleles of mammary cancer susceptible Wistar Furth (WF) and resistant Wistar Kyoto (WKY) rat strains. 12‐O‐Tetradecanoylphorbol‐13‐acetate (TPA) induced activation of a 4.2 kb WF Fbxo10 promoter region, but lower levels of activation of the homologous WKY Fbxo10 promoter region. Using general and specific protein kinase inhibitors, we identified a protein kinase C (PKC) pathway that mediated TPA activation. We narrowed the possible PKCs to a member of the atypical PKC isoforms, namely PKCµ. We also determined that activator protein 1 (AP1) family member c‐Fos mediated TPA activation of the 4.2 kb WF Fbxo10 promoter. TPA was shown to induce endogenous FBXO10 mRNA and FBXO10 protein in Jurkat cells, a human T cell line, with a maximal level of expression from 1.5 to 2.5 h after exposure. These results indicate that FBXO10/Fbxo10 expression is regulated by a PKC‐dependent pathway acting through c‐Fos, which binds AP1‐specific DNA elements in Mcs5a1. © 2013 Wiley Periodicals, Inc.
Coxsackievirus B3 Replication Is Reduced by Inhibition of the Extracellular Signal-Regulated Kinase (ERK) Signaling Pathway

ABSTRACT Coxsackievirus B3 (CVB3) is the most common human pathogen for viral myocarditis. We have previously shown that the signaling protein p21 ras GTPase-activating protein (RasGAP) is cleaved and that mitogen-activated protein kinases (MAPKs) ERK1/2 are activated in the late phase of CVB3 infection. However, the role of intracellular signaling pathways in CVB3-mediated myocarditis and the relative advantages of such pathways to host or virus remain largely unclear. In this study we extended our prior studies by examining the interaction between CVB3 replication and intracellular signaling pathways in HeLa cells. We observed that CVB3 infection induced a biphasic activation of ERK1/2, early transient activation versus late sustained activation, which were regulated by different mechanisms. Infection by UV-irradiated, inactivated virus capable of receptor binding and endocytosis triggered early ERK1/2 activation, but was insufficient to trigger late ERK1/2 activation. By using a general caspase inhibitor (zVAD.fmk) we further demonstrated that late ERK1/2 activation was not a result of CVB3-mediated caspase cleavage. Treatment of cells with U0126, a selective inhibitor of MAPK kinase (MEK), significantly inhibited CVB3 progeny release and decreased virus protein production. Furthermore, inhibition of ERK1/2 activation circumvented CVB3-induced apoptosis and viral protease-mediated RasGAP cleavage. Taken together, these data suggest that ERK1/2 activation is important for CVB3 replication and contributes to virus-mediated changes in host cells. Our findings demonstrate coxsackievirus takeover of a particular host signaling mechanism and uncover a prospective approach to stymie virus spread and preserve myocardial integrity.
Dividend taxation, ownership structure and payout policy: evidence from India

Despite the widespread criticism against double taxation of dividends, most countries follow the policy of taxing the same income twice – once when the corporations earn it and a second time when shareholders receive it. Critics of the double taxation policy clamor for its abolition citing the economic inefficiencies it engenders. In 1997, the Indian government eliminated double taxation of dividends by exempting dividend income from personal taxes but requiring the firms to pay a 10% tax on the amount of dividend distributed. Using this rule change as a natural experiment, we examine the impact of this rule change on firm valuation. We show that elimination of double taxation on dividends is not unambiguously beneficial to the stockholders of the firm. We find that tax status and ownership structure play a significant role in explaining the direction of observed changes in valuation. An interesting finding of this paper is that shareholders seem to value visibility. Visible firms are subject to the disciplining effect of more stringent disclosures in the financial press. We do find pervasive evidence that firms increased their dividends subsequent to rule change. We however, do not find any association between the change in dividends and ownership structure.
Women’s expectations of healthcare providers in the context of reproductive abuse in Australia

Abstract Reproductive abuse is a poorly understood form of violence against women. It is defined as a deliberate attempt to interfere with or control a women’s reproductive choices and is usually perpetrated by a male intimate partner. Reproductive abuse is associated with a range of poor health outcomes for women, increasing the likelihood that they will visit a healthcare provider. Despite this, there is a dearth of evidence to inform best practice in health settings, particularly research that highlights the voices of survivors. Qualitative studies to date have focused on intimate partner or sexual violence more broadly, yet it is likely that reproductive abuse presents its own nuance in terms of a supportive response. In this paper, we address this gap by reporting qualitative data from 14 women who self-identified as survivors of reproductive abuse. Findings suggest that healthcare providers have an important role to play in responding to reproductive abuse, focusing on taking the problem seriously, reinforcing that the behaviour is wrong, asking about other forms of violence and addressing women’s needs and priorities for contraception and reproductive autonomy. This study has important implications for the development of best practice guidelines for healthcare providers responding to reproductive abuse in female patients.
Chapter 5 Classifying Unstructured Textual Data Using the Product Score Model : An Alternative Text Mining Algorithm

Unstructured textual data such as students’ essays and life narratives can provide helpful information in educational and psychological measurement, but often contain irregularities and ambiguities, which creates difficulties in analysis. Text mining techniques that seek to extract useful information from textual data sources through identifying interesting patterns are promising. This chapter describes the general procedures of text classification using text mining and presents an alternative machine learning algorithm for text classification, named the product score model (PSM). Using the bag-of-words representation (single words), we conducted a comparative study between PSM and two commonly used classification models, decision tree and naïve Bayes. An application of these three models is illustrated for real textual data. The results showed the PSM performed the most efficiently and stably in classifying text. Implications of these results for the PSM are further discussed and recommendations about its use are given.
Efficacy and Safety of Tinefcon® Tablets in Subjects with Plaque Psoriasis: An Open Label, Non-Comparative, Multicenter, Phase IV Trial

Importance: This post-marketing surveillance study was conducted to evaluate real-world information about the efficacy and safety of oral Tinefcon? tablets (Sphaeranthus indicus based) in plaque psoriasis patients. Materials and Methods: Patients aged at least 18 years and older with clinical diagnosis of plaque psoriasis, were enrolled in this open label, non-comparative, multicenter trial. All eligible subjects received four 700 mg Tinefcon? tablets/day for 12 weeks. The primary outcome measure was percent change in Psoriasis Area Severity Index (PASI) score from baseline to week 12. The secondary outcome measures were Physician Global Assessment (PGA), Nail Psoriasis Severity Index (NAPSI), Psoriatic Arthritis Evaluation and Gene Expression Profiling and Immunohistochemistry. Results: After completion of Tinefcon? treatment at 12 weeks, more than half of subjects (52%) achieved PASI 50 response; PASI 75 response was attained in 68 (23%) subjects and PASI 90 response in 22 (7%) subjects. Five subjects with severe psoriasis achieved PASI 90 without receiving any concomitant medication. Reduction in severity as assessed by PGA was observed in more than half of patients with moderate disease. Histopathological evaluation revealed that epidermal thickness was considerably reduced in 66% of subjects. The expression of inflammatory marker S100A9 protein was(meaningfully reduced in 60% patients with non-significant reduction of Keratin 10 protein expression. Gene expression analysis showed increase down regulation of SERPINB4; PI3 and KRT16 genes after a 12-week treatment period in subjects with higher PASI scores. Conclusion: Oral Tinefcon? tablets showed good efficacy and had a favorable safety profile in plaque psoriasis patients.
Scene Regularity Interacts With Individual Biases to Modulate Perceptual Stability

Sensory input is inherently ambiguous but our brains achieve remarkable perceptual stability. Prior experience and knowledge of the statistical properties of the world are thought to play a key role in the stabilization process. Individual differences in responses to ambiguous input and biases toward one or the other interpretation could modulate the decision mechanism for perception. However, the role of perceptual bias and its interaction with stimulus spatial properties such as regularity and element density remain to be understood. To this end, we developed novel bi-stable moving visual stimuli in which perception could be parametrically manipulated between two possible mutually exclusive interpretations: transparently or coherently moving. We probed perceptual stability across three composite stimulus element density levels with normal or degraded regularity using a factorial design. We found that increased density led to the amplification of individual biases and consequently to a stabilization of one interpretation over the alternative. This effect was reduced for degraded regularity, demonstrating an interaction between density and regularity. To understand how prior knowledge could be used by the brain in this task, we compared the data with simulations coming from four different hierarchical models of causal inference. These models made different assumptions about the use of prior information by including conditional priors that either facilitated or inhibited motion direction integration. An architecture that included a prior inhibiting motion direction integration consistently outperformed the others. Our results support the hypothesis that direction integration based on sensory likelihoods maybe the default processing mode with conditional priors inhibiting integration employed in order to help motion segmentation and transparency perception.
Operon Concatenation Is an Ancient Feature That Restricts the Potential to Rearrange Bacterial Chromosomes

Abstract The last common ancestor of the Gammaproteobacteria carried an important 40-kb chromosome section encoding 51 proteins of the transcriptional and translational machinery. These genes were organized into eight contiguous operons (rrnB-tufB-secE-rpoBC-str-S10-spc-alpha). Over 2 Gy of evolution, in different lineages, some of the operons became separated by multigene insertions. Surprisingly, in many Enterobacteriaceae, much of the ancient organization is conserved, indicating a strong selective force on the operons to remain colinear. Here, we show for one operon pair, tufB-secE in Salmonella, that an interruption of contiguity significantly reduces growth rate. Our data show that the tufB-secE operons are concatenated by an interoperon terminator–promoter overlap that plays a significant role regulating gene expression. Interrupting operon contiguity interferes with this regulation, reducing cellular fitness. Six operons of the ancestral chromosome section remain contiguous in Salmonella (tufB-secE-rpoBC and S10-spc-alpha) and, strikingly, each of these operon pairs is also connected by an interoperon terminator–promoter overlap. Accordingly, we propose that operon concatenation is an ancient feature that restricts the potential to rearrange bacterial chromosomes and can select for the maintenance of a colinear operon organization over billions of years.
High-Throughput Microfluidic 3D Cytotoxicity Assay for Cancer Immunotherapy (CACI-IMPACT Platform)

Adoptive cell transfer against solid tumors faces challenges to overcome tumor microenvironment (TME), which plays as a physical barrier and provides immuno-suppressive conditions. Classical cytotoxicity assays are widely used to measure killing ability of the engineered cytotoxic lymphocytes as therapeutics, but the results cannot represent the performance in clinical application due to the absence of the TME. This paper describes a 3D cytotoxicity assay using an injection molded plastic array culture (CACI-IMPACT) device for 3D cytotoxicity assay to assess killing abilities of cytotoxic lymphocytes in 3D microenvironment through a spatiotemporal analysis of the lymphocytes and cancer cells embedded in 3D extra cellular matrix (ECM). Rail-based microfluidic design was integrated within a single 96-well and the wells were rectangularly arrayed in 2 × 6 to enhance the experimental throughput. The rail-based microstructures facilitate hydrogel patterning with simple pipetting so that hydrogel pre-solution aspirated with 10 μl pipette can be patterned in 10 wells within 30 s. To demonstrate 3D cytotoxicity assay, we patterned HeLa cells encapsulated by collagen gel and observed infiltration, migration and cytotoxic activity of NK-92 cells against HeLa cells in the collagen matrix. We found that 3D ECM significantly reduced migration of cytotoxic lymphocytes and access to cancer cells, resulting in lower cytotoxicity compared with 2D assays. In dense ECM, the physical barrier function of the 3D matrix was enhanced, but the cytotoxic lymphocytes effectively killed cancer cells once they contacted with cancer cells. The results implied ECM significantly influences migration and cytotoxicity of cytotoxic lymphocytes. Hence, the CACI-IMPACT platform, enabling high-throughput 3D co-culture of cytotoxic lymphocyte with cancer cells, has the potential to be used for pre-clinical evaluation of cytotoxic lymphocytes engineered for immunotherapy against solid tumors.
IKD: a knowledge-based tool for integrating a knowledge base and a database

In order to integrate a knowledge-based system (KBS) and relational database system (RDBS) more naturally and flexibly, it is necessary to work with these two systems cooperatively. The IKD system functions as an interface between the KBS and RDBS by representing their conceptual structures in frames. Two types of frames are distinguished from one another: one defines the data structure of an integrating database (DB) and the other represents conceptual objects dealing with a KBS. Several types of operations on the DB are processed based on message passing among frames. <<ETX>>
Ret‐PCP2 colocalizes with protein kinase C in a subset of primate ON cone bipolar cells

Purkinje cell protein 2 (PCP2), a member of the family of guanine dissociation inhibitors and a strong interactor with the G‐protein subunit Gαo, localizes to retinal ON bipolar cells. The retina‐specific splice variant of PCP2, Ret‐PCP2, accelerates the light response of rod bipolar cells by modulating the mGluR6 transduction cascade. All ON cone bipolar cells express mGluR6 and Gαo, but only a subset expresses Ret‐PCP2. Here we test the hypothesis that Ret‐PCP2 contributes to shaping the various temporal bandwidths of ON cone bipolar cells in monkey retina. We found that the retinal splice variants in monkey and mouse are similar and longer than the cerebellar variants. Ret‐PCP2 is strongly expressed by diffuse cone bipolar type 4 cells (DB4; marked with anti‐PKCα) and weakly expressed by midget bipolar dendrites (labeled by antibodies against Gαo, Gγ13, or mGluR6). Ret‐PCP2 is absent from diffuse cone bipolar type 6 (DB6; marked with anti‐CD15) and blue cone bipolar cells (marked with anti‐CCK precursor). Thus, cone bipolar cells that terminate in stratum 3 of the inner plexiform layer (DB4) express more Ret‐PCP2 than those that terminate in strata 3 + 4 (midget bipolar cells), and these in turn express more than those that terminate in stratum 5 (DB6 and blue cone bipolar cells). This expression pattern approximates the arborization of ganglion cells (GC) with different temporal bandwidths: parasol GCs stratifying near stratum 3 are faster than midget GCs stratifying in strata 3 + 4, and these are probably faster than the sluggish GCs that arborize in stratum 5. J. Comp. Neurol. 518:1098–1112, 2010. © 2009 Wiley‐Liss, Inc.
Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).