Miracle-dz/UniFAR-FTUs huggingface dataset:
An improved protein decoy set for testing energy functions for protein structure prediction

We have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on sidechains and minimizing clashes. The new set consists of 1,400 model structures for 78 different and diverse protein targets and provides a challenging set for the testing and evaluation of scoring functions. We evaluated the extent to which a variety of all‐atom energy functions could identify the native and close‐to‐native structures in the new decoy sets. Of various implicit solvent models, we found that a solvent‐accessible surface area–based solvation provided the best enrichment and discrimination of close‐to‐native decoys. The combination of this solvation treatment with Lennard Jones terms and the original Rosetta energy provided better enrichment and discrimination than any of the individual terms. The results also highlight the differences in accuracy of NMR and X‐ray crystal structures: a large energy gap was observed between native and non‐native conformations for X‐ray structures but not for NMR structures. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Electronic textiles: a platform for pervasive computing

The invention of the Jacquard weaving machine led to the concept of a stored "program" and "mechanized" binary information processing. This development served as the inspiration for C. Babbage's analytical engine-the precursor to the modern-day computer. Today, more than 200 years later, the link between textiles and computing is more realistic than ever. In this paper, we look at the synergistic relationship between textiles and computing and identify the need for their "integration" using tools provided by an emerging new field of research that combines the strengths and capabilities of electronics and textiles into one: electronic textiles, or e-textiles. E-textiles, also called smart fabrics, have not only "wearable" capabilities like any other garment, but also have local monitoring and computation, as well as wireless communication capabilities. Sensors and simple computational elements are embedded in e-textiles, as well as built into yarns, with the goal of gathering sensitive information, monitoring vital statistics, and sending them remotely (possibly over a wireless channel) for further processing. The paper provides an overview of existing efforts and associated challenges in this area, while describing possible venues and opportunities for future research.
Are Animals Stuck in Time or Are They Chronesthetic Creatures?

Although psychologists study both the objective (behavior) and the subjective (phenomenology) components of cognition, we argue that an overemphasis on the subjective drives a wedge between psychology and other closely related scientific disciplines, such as comparative studies of cognition and artificial intelligence. This wedge is particularly apparent in contemporary studies of episodic recollection and future planning, two related abilities that many have assumed to be unique to humans. We shall challenge this doctrine. To do so, we shall adopt an ethological approach to comparative cognition and this necessitates two requirements. The first is that memory and planning need to be characterized in terms of objectively defined properties as opposed to purely phenomenological ones; the ability to remember what happened, where, and how long ago is a critical behavioral criterion for episodic memory. The second requirement is the identification of an ethological context in which these memories would confer a selective advantage. As a consequence, we turn this debate into an empirical evaluation in nonlinguistic animals and one embodied in synthetic creatures. Indeed, our behavioral conception of flexibly deployable information about "what, where, and when" has so far supported a comparative cognition in animals as diverse as corvids and primates. We argue that this approach may clarify and challenge ideas that have been based solely on research with human subjects, without the need to be constrained by phenomenological assumptions based on human-centric ways of thinking.
Overexpression of Guanylate Cyclase Activating Protein 2 in Rod Photoreceptors In Vivo Leads to Morphological Changes at the Synaptic Ribbon

Guanylate cyclase activating proteins are EF-hand containing proteins that confer calcium sensitivity to retinal guanylate cyclase at the outer segment discs of photoreceptor cells. By making the rate of cGMP synthesis dependent on the free intracellular calcium levels set by illumination, GCAPs play a fundamental role in the recovery of the light response and light adaptation. The main isoforms GCAP1 and GCAP2 also localize to the synaptic terminal, where their function is not known. Based on the reported interaction of GCAP2 with Ribeye, the major component of synaptic ribbons, it was proposed that GCAP2 could mediate the synaptic ribbon dynamic changes that happen in response to light. We here present a thorough ultrastructural analysis of rod synaptic terminals in loss-of-function (GCAP1/GCAP2 double knockout) and gain-of-function (transgenic overexpression) mouse models of GCAP2. Rod synaptic ribbons in GCAPs−/− mice did not differ from wildtype ribbons when mice were raised in constant darkness, indicating that GCAPs are not required for ribbon early assembly or maturation. Transgenic overexpression of GCAP2 in rods led to a shortening of synaptic ribbons, and to a higher than normal percentage of club-shaped and spherical ribbon morphologies. Restoration of GCAP2 expression in the GCAPs−/− background (GCAP2 expression in the absence of endogenous GCAP1) had the striking result of shortening ribbon length to a much higher degree than overexpression of GCAP2 in the wildtype background, as well as reducing the thickness of the outer plexiform layer without affecting the number of rod photoreceptor cells. These results indicate that preservation of the GCAP1 to GCAP2 relative levels is relevant for maintaining the integrity of the synaptic terminal. Our demonstration of GCAP2 immunolocalization at synaptic ribbons at the ultrastructural level would support a role of GCAPs at mediating the effect of light on morphological remodeling changes of synaptic ribbons.
Proteomics-Informed Identi ﬁ cation of Luminal Targets For In Situ Diagnosis of In ﬂ ammatory Bowel Disease

In ﬂ ammatory bowel disease (IBD) is a chronic condition resulting in impaired intestinal homeostasis. Current practices for diagnosis of IBD are challenged by invasive, demanding procedures. We hypothesized that proteomics analysis could provide a powerful tool for identifying clinical biomarkers for non-invasive IBD diagnosis. Here, the global intestinal proteomes from commonly used in vitro and in vivo models of IBD were analyzed to identify apical and luminal proteins that can be targeted by orally delivered diagnostic agents. Global proteomics analysis revealed upregulated plasma membrane proteins in intestinal segments of proximal-and distal colon from dextran sulfate sodium-treated mice and also in in ﬂ amed human intestinal Caco-2 cells pretreated with pro-in ﬂ ammatory agents. The upregulated colon proteins in mice were compared to the proteome of the healthy ileum, to ensure targeting of diagnostic agents to the in ﬂ amed colon. Promising target proteins for future investigations of non-invasive diagnosis of IBD were found in both systems and included Tgm2/TGM2, Icam1/ICAM1, Ceacam1/CEACAM1, and Anxa1/ANXA1. Ultimately, these ﬁ ndings will guide the selection of appropriate antibodies for surface functionalization of imaging agents aimed to target in ﬂ ammatory biomarkers in situ . © 2020 The Authors. Published by Elsevier Inc. on behalf of the American Pharmacists Association ® . This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
The Effect of Leadership and Work Environment on Employee Performance Mediated by Work Motivation in Class III Airport Management Unit Employees (UPBU)

The purpose of this study was to examine the influence of leadership and the work environment, which have a positive and significant effect on employee performance. Work motivation mediates positively and significantly the influence of leadership and the work environment on employee performance. The phenomenon that is the main focus of this research is the insufficient performance condition of class III Okaba UPBU employees, Merauke Regency, based on Passenger and Baggage Inspection, Check-In Services, and Departure Waiting Room Services. Methods of data processing and data analysis in this study using descriptive and quantitative analysis. The population in this study was 35 class III Okaba UPBU employees, Merauke Regency. The sampling technique uses a census technique that takes all employees as samples. Data analysis techniques in this study use path analysis. Collecting data in this study using a questionnaire. The results of the analysis in this study show that: 1). Leadership has a positive (28.8%) and significant (0.009 <0.05) effect on employee performance, 2). The work environment has a positive (49.9%) and significant (0.001 <0.05) effect on employee performance, 3). Work motivation mediates a positive (17.2%) and significant (t-count of 2.233 > t-table of 2.039) effect of leadership on employee performance, and 4). Work motivation mediates a positive (20.1%) and significant (t-count of 2.610 > t-table of 2.039) effect of the work environment on the performance of Class III Okaba Airport Operations Unit (UPBU) employees, Merauke Regency.
Quantum Technologies a Hermeneutic Technology Assessment Approach

This paper develops a hermeneutic technology assessment of quantum technologies. It offers a “vision assessment” of quantum technologies that can eventually lead to socio-ethical analysis. Section 2 describes this methodological approach and in particular the concept of the hermeneutic circle applied to technology. Section 3 gives a generic overview of quantum technologies and their impacts. Sections 4 and 5 apply the hermeneutic technology assessment approach to the study of quantum technologies. Section 5 proposes distinguishing three levels in the analysis of the creation and communication of social meanings to quantum technologies: (a) fictions, (b) popularization, and (c) scientific journal-ism. Section 6 analyzes the results and defines some lines of action to increase social acceptance and trust in quantum technologies. The aim of this paper is to contribute to the debate on quantum technologies by enhancing the reflection on them and their potential, as well as illustrating the complexity of technological innovation and the need to shape it.
Measles history and atopic diseases: a population-based cross-sectional study.

CONTEXT Many recent cross-sectional studies have suggested that lack of early exposure to communicable diseases, including measles, in affluent countries may have increased rates of atopic disease. OBJECTIVE To study the association between natural measles infection and atopy. DESIGN AND SETTING Cross-sectional nationwide study in Finland using data gathered between November 1, 1982, and June 30, 1986. SUBJECTS A total of 547910 individuals aged 14 months to 19 years who at the time of measles-mumps-rubella (MMR) vaccination had relevant information collected on the occurrence of measles and allergic rhinitis, eczema, and asthma. MAIN OUTCOME MEASURES Lifetime occurrence of atopic manifestations in subjects who had had measles compared with those who had not, expressed as age-specific and age-adjusted prevalence ratios. RESULTS The age-adjusted prevalence ratio of atopic manifestations among those who had had measles (n = 20 690) compared with those who had not (n = 527 220) was 1.32 (95% confidence interval [CI], 1.27-1.36) for eczema, 1.41 (95% CI, 1.33-1.49) for rhinitis, and 1.67 (95% CI, 1.54-1.79) for asthma. The positive association between measles and atopy was evident at all ages, in both urban and rural dwellers, and among subjects with many or few contacts at home or in day care. CONCLUSIONS Based on our data, measles and atopy occur more frequently together than expected, which does not support the hypothesis that experiencing natural measles infection offers protection against atopic disease.
NC2α Interacts with BTAF1 and Stimulates Its ATP-Dependent Association with TATA-Binding Protein

ABSTRACT Transcriptional activity of the TATA-binding protein (TBP) is controlled by a variety of proteins. The BTAF1 protein (formerly known as TAFII170/TAF-172 and the human ortholog of Saccharomyces cerevisiae Mot1p) and the NC2 complex composed of NC2α (DRAP1) and NC2β (Dr1) are able to bind to TBP directly and regulate RNA polymerase II transcription both positively and negatively. Here, we present evidence that the NC2α subunit interacts with BTAF1. In contrast, the NC2β subunit is not able to associate with BTAF1 and seems to interfere with the BTAF1-TBP interaction. Addition of NC2α or the NC2 complex can stimulate the ability of BTAF1 to interact with TBP. This function is dependent on the presence of ATP in cell extracts but does not involve the ATPase activity of BTAF1 nor phosphorylation of NC2α. Together, our results constitute the first evidence of the physical cooperation between BTAF1 and NC2α in TBP regulation and provide a framework to understand transcription functions of NC2α and NC2β in vivo.
Coin Betting and Parameter-Free Online Learning

In the recent years, a number of parameter-free algorithms have been developed for online linear optimization over Hilbert spaces and for learning with expert advice. These algorithms achieve optimal regret bounds that depend on the unknown competitors, without having to tune the learning rates with oracle choices. We present a new intuitive framework to design parameter-free algorithms for \emph{both} online linear optimization over Hilbert spaces and for learning with expert advice, based on reductions to betting on outcomes of adversarial coins. We instantiate it using a betting algorithm based on the Krichevsky-Trofimov estimator. The resulting algorithms are simple, with no parameters to be tuned, and they improve or match previous results in terms of regret guarantee and per-round complexity.
Perspectives on: Cyclic nucleotide microdomains and signaling specificity: Cyclic AMP compartments and signaling specificity: Role of cyclic nucleotide phosphodiesterases

Introduction The concept that cAMP has restricted access to different pools of intracellular effectors was articulated more than 30 years ago. Observations made by Corbin et al. (1977) demonstrated that the two isoenzymes of the major intracellular cAMP target, PKA I and II, are located in different cell compartments. PKA II was recovered predominantly in the particulate fraction of heart extracts, whereas PKA I was mostly soluble. Epinephrine activates the holoenzyme present in the particulate fraction and causes its translocation to the cytosol. In the same vein, Hayes et al. (1979) and Buxton and Brunton (1983) demonstrated that different hormones increase cAMP in cardiac myocytes, but only the -adrenergic agonists affect heart contractility, providing functional evidence for the selectivity of cAMP action. These findings led to the enunciation of a set of rules describing this unexpected property of cAMP signaling (Steinberg and Brunton, 2001). Although a small diffusible molecule, Steinberg and Brunton (2001) predicted that cAMP does not have equal access to all PKAs present in a cell, implying an uneven cAMP concentration or the presence of compartments of signaling. The demonstration that local -adrenergic activation does not elicit Ca currents measured at opposite ends of a frog cardiac myocyte provided experimental confirmation of constraints on the spread of the cAMP signal (Jurevicius and Fischmeister, 1996). At about the same time and using unrelated approaches, a field of cell biology was developed that supports the critical role of PKA targeting to different subcellular structures through A kinase anchoring protein (AKAP) scaffolds (Wong and Scott, 2004; Dodge-Kafka et al., 2006). Disruption of these complexes by several means provided additional compelling evidence that physiological cAMP signaling requires PKA anchoring. All of these findings support the conclusion that, functionally, cAMP does not behave as
The ectonucleotidase ENTPD1/CD39 limits biliary injury and fibrosis in mouse models of sclerosing cholangitis

The pathogenesis of primary sclerosing cholangitis (PSC) and the mechanistic link to inflammatory bowel disease remain ill‐defined. Ectonucleoside triphosphate diphosphohydrolase‐1 (ENTPD1)/clusters of differentiation (CD) 39, the dominant purinergic ecto‐enzyme, modulates intestinal inflammation. Here, we have explored the role of CD39 in biliary injury and fibrosis. The impact of CD39 deletion on disease severity was studied in multidrug resistance protein 2 (Mdr2)–/– and 3,5‐diethoxycarbonyl‐1,4‐dihydrocollidine mouse models of sclerosing cholangitis and biliary fibrosis. Antibody‐mediated CD8+ T‐cell depletion, selective gut decontamination, experimental colitis, and administration of stable adenosine triphosphate (ATP) agonist were performed. Retinoic acid‐induced gut imprinting on T cells was studied in vitro. Over half of Mdr2–/–;CD39–/– double mutants, expected by Mendelian genetics, died in utero. Compared to Mdr2–/–;CD39+/+, surviving Mdr2–/–;CD39–/– mice demonstrated exacerbated liver injury, fibrosis, and ductular reaction. CD39 deficiency led to a selective increase in hepatic CD8+ T cells and integrin α4β7, a T‐cell gut‐tropism receptor. CD8+ cell depletion in Mdr2–/–;CD39–/– mice diminished hepatobiliary injury and fibrosis. Treatment with antibiotics attenuated, whereas dextran sulfate sodium‐induced colitis exacerbated, liver fibrosis in Mdr2–/– mice. Colonic administration of αβ‐ATP into CD39‐sufficient Mdr2–/– mice triggered hepatic CD8+ cell influx and recapitulated the severe phenotype observed in Mdr2–/–;CD39–/– mice. In vitro, addition of ATP promoted the retinoic acid‐induced imprinting of gut‐homing integrin α4β7 on naive CD8+ cells. CD39 expression was relatively low in human normal or PSC livers but abundantly present on immune cells of the colon and further up‐regulated in samples of patients with inflammatory bowel disease. Conclusion: CD39 deletion promotes biliary injury and fibrosis through gut‐imprinted CD8+ T cells. Pharmacological modulation of purinergic signaling may represent a promising approach for the treatment of PSC. (Hepatology Communications 2017;1:957–972)
Matching Component Analysis for Microtexture Region Segmentation

Microtexture regions (MTR) are collections of grains with similar crystallographic orientation; their presence in aerospace components can signiﬁcantly impact compoent life. Thus, a method to detect and characterize MTR is needed. A potential solution is to fuse information from multiple nondestructive evaluation techniques that are sensitive to local crystallographic changes in titianum. In this work, we introduce a technique that combines a variant of the matching component analysis algorithm with level-set inversion in order to determine MTR boundaries using multiple sets of nondestructive evaluation data. Although this method is agnostic to the type of nondestructive evaluation data, here it is used to combine information from multiple rotations of an asymmetric eddy current coil. The method is successfully demonstrated on simulated eddy current data of a real titainum specimen.
Phosphorylation of human keratin 18 serine 33 regulates binding to 14‐3‐3 proteins

Members of the 14‐3‐3 protein family bind the human intermediate filament protein keratin 18 (K18) in vivo, in a cell‐cycle‐ and phosphorylation‐dependent manner. We identified K18 Ser33 as an interphase phosphorylation site, which increases its phosphorylation during mitosis in cultured cells and regenerating liver, and as an in vitro cdc2 kinase phosphorylation site. Comparison of wild‐type versus K18 Ser33→Ala/Asp transfected cells showed that K18 Ser33 phosphorylation is essential for the association of K18 with 14‐3‐3 proteins, and plays a role in keratin organization and distribution. Mutation of another K18 major phosphorylation site (Ser52) or K18 glycosylation sites had no effect on the binding of K18 to 14‐3‐3 proteins. The K18 phospho‐Ser33 motif is different from several 14‐3‐3‐binding phosphomotifs already described. Antibodies that are specific to K18 phospho‐Ser33 or phospho‐Ser52 show that although Ser52 and Ser33 phosphorylated K18 molecules manifest partial colocalization, these phosphorylation events reside predominantly on distinct K18 molecules. Our results demonstrate a unique K18 phosphorylation site that is necessary but not sufficient for K18 binding to 14‐3‐3 proteins. This binding is likely to involve one or more mitotic events coupled to K18 Ser33 phosphorylation, and plays a role in keratin subcellular distribution. Physiological Ser52 or Ser33 phosphorylation on distinct K18 molecules suggests functional compartmentalization of these modifications.
Screening of Bacterial Pathogens Attached to Invertebrate Bodies and Biocontrol of Pathogenic Aermonas hydrophila in Marsupenaeus japonicus Culture

Microbes play crucial role in aquaculture systems. In the present study, screening of the bacterial communities of Aeromonas sp . , Vibrio sp. , Staphylococcus sp . , E. coli sp. and Salmonella sp. associated with shrimp, bivalves and sea cucumber revealed that Aeromonas sp. was the dominant pathogen in shrimp representing 6.33% and 11.25% of the total heterotrophic bacteria associated with shrimp surface and body, respectively. Antibacterial activity of different extracts of the invertebrate bodies and chitosan in addition to eleven attached bacterial isolates were tested. The marine bacterial isolate which was identified as Vibrio alginolyticus by using 16S rDNA sequence analysis, was superior in its antibacterial activity, recording the highest activity unit of 10.24 ± 3.15 AU against A. hydrophila. The impact of probiotic V. alginolyticus S10 in improving the water quality of A. hydrophila infected Marsupenaeus japonicus culture was investigated. The histopathological study of M. japonicus tissues showed limited tissue damages observed in treatments using probiotic bacteria. Three stages of infection have been defined in infected hepatopancreas according to vacuolation, and hemolytic aggregation while intensity of infections in muscle and heart tissues was determined according to bacterial doses and hemolytic aggregation.
Enhancing Antifungal Activity of Itraconazole by Mesoporous Silica Nanoparticles

Mesoporous silica nanoparticles (MCM-41) have an ability to increase the solubility of poorly soluble drugs. In this study, MCM-41 was synthesized. Afterward, Itraconazole (ITZ) was loaded into MCM-41 and then was wrapped by chitosan. The synthesized nanoparticles were characterized. Controlled release of ITZ from the MSN-ITZ and MSN-ITZ-CHI was evaluated in hydrochloride acid buffer (pH: 1.2) and phosphate buffer saline (pH: 7.4). Antifungal and cytotoxic activities of MSN-ITZ and MSN-ITZ-CHI were evaluated. Amount of loaded ITZ into MCM-41 was determined 85%. The properties of MCM-41 and loading procedure revealed high performance of the drug loading and release studies. The release profiles of MSN-ITZ were 60% in HCl medium and 40% in PBS medium. Data demonstrated more efficient and rapid release of ITZ from MSN-ITZ. Minimum inhibitory concentrations of MSN-ITZ and MSN-ITZ-CHI, on Candida albicans and Aspergillus fumigatus showed 0.25 and 0.5 µg/ml with low concentration and more inhibitory effects in comparison to the ITZ. MSN-ITZ and MSN-ITZ-CHI revealed lower toxicity in comparison to the pure drug on the cell viability of TC1 cell line (P<0.05). It could be concluded that the MSN-ITZ and MSN-ITZ-CHI nanoparticles have promising advantages for enhancing antifungal effects and drug delivery studies of itraconazole.