Miracle-dz/UniFAR-FTUs huggingface dataset:
Sleeping site selection and presleep behavior in wild pigtailed macaques

Several factors are likely to control sleeping site selection and presleep behavior in nonhuman primates, including predation risk and location of food resources. We examined the effects of these factors on the sleeping behavior of northern pigtailed macaques (Macaca leonina). While following a troop living in the surroundings of the Visitor Center of Khao Yai National Park (Thailand), we recorded the physical characteristics and location of each sleeping site, tree, the individuals' place in the tree, posture, and behavior. We collected data for 154 nights between April 2009 and November 2010. The monkeys preferred tall sleeping trees (20.9 ± SD 4.9 m) and high sleeping places (15.8 ± SD 4.3 m), which may be an antipredator strategy. The choice of sleeping trees close to the last (146.7 ± SD 167.9 m) or to the first (150.4 ± SD 113.0 m) feeding tree of the day may save energy and decrease predation risk when monkeys are searching for food. Similarly, the choice of sleeping sites close to human settlements eases the access to human food during periods of fruit scarcity. Finally, the temporal pattern of use of sleeping sites, with a preference for four of the sleeping sites but few reuses during consecutive nights, may be a trade‐off between the need to have several sleeping sites (decreasing detection by predators and travel costs to feeding sites), and the need to sleep in well‐known sites (guaranteeing a faster escape in case of predator attack). Am. J. Primatol. 73:1222–1230, 2011. © 2011 Wiley Periodicals, Inc.
Association between social support and depression in the general population: the HUNT study, a cross-sectional survey.

AIM The aim was to investigate the associations between perceived social support and depression in a general population in relation to gender and age. BACKGROUND Social support is seen as one of the social determinants for overall health in the general population. Studies have found higher probability of experiencing depression among people who have a lack of social support; evidence from the general population has been more limited. Subjective perception that support would be available if needed may reduce and prevent depression and unnecessary suffering. DESIGN A cross-sectional survey with self-reported health was used. METHOD A total of 40,659 men and women aged 20-89 years living in Nord-Trøndelag County of Norway with valid ratings of depression subscale of the Hospital Anxiety and Depression Scale in the The Nord-Trøndelag Health Study 3 were used. Logistic regression was used to quantify associations between two types of perceived support (emotional and tangible) and depression. Gender, age and interaction effects were controlled for in the final model. RESULTS The main finding was that self-rated perceived support was significantly associated with Hospital Anxiety and Depression Scale-defined depression, even after controlling for age and gender; emotional support (OR = 3·14) and tangible support (OR = 2·93). The effects of emotional and tangible support differ between genders. Interaction effects were found for age groups and both emotional and tangible support. CONCLUSION Self-rated perceived functional social support is associated with Hospital Anxiety and Depression Scale-defined depression. In the group of older people who have a lack of social support, women seem to need more emotional support and men tangible support. RELEVANCE TO CLINICAL PRACTICE Health care providers should consider the close association between social support and depression in their continuing care, particularly in the older people.
In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis.

Thousands of untested chemicals in the environment require efficient characterization of carcinogenic potential in humans. A proposed solution is rapid testing of chemicals using in vitro high-throughput screening (HTS) assays for targets in pathways linked to disease processes to build models for priority setting and further testing. We describe a model for predicting rodent carcinogenicity based on HTS data from 292 chemicals tested in 672 assays mapping to 455 genes. All data come from the EPA ToxCast project. The model was trained on a subset of 232 chemicals with in vivo rodent carcinogenicity data in the Toxicity Reference Database (ToxRefDB). Individual HTS assays strongly associated with rodent cancers in ToxRefDB were linked to genes, pathways, and hallmark processes documented to be involved in tumor biology and cancer progression. Rodent liver cancer endpoints were linked to well-documented pathways such as peroxisome proliferator-activated receptor signaling and TP53 and novel targets such as PDE5A and PLAUR. Cancer hallmark genes associated with rodent thyroid tumors were found to be linked to human thyroid tumors and autoimmune thyroid disease. A model was developed in which these genes/pathways function as hypothetical enhancers or promoters of rat thyroid tumors, acting secondary to the key initiating event of thyroid hormone disruption. A simple scoring function was generated to identify chemicals with significant in vitro evidence that was predictive of in vivo carcinogenicity in different rat tissues and organs. This scoring function was applied to an external test set of 33 compounds with carcinogenicity classifications from the EPA's Office of Pesticide Programs and successfully (p = 0.024) differentiated between chemicals classified as "possible"/"probable"/"likely" carcinogens and those designated as "not likely" or with "evidence of noncarcinogenicity. " This model represents a chemical carcinogenicity prioritization tool supporting targeted testing and functional validation of cancer pathways.
Bile Acid Signal-induced Phosphorylation of Small Heterodimer Partner by Protein Kinase Cζ Is Critical for Epigenomic Regulation of Liver Metabolic Genes*

Background: Small heterodimer partner (SHP) is a key mediator of bile acid signaling. Results: Bile acid signal-induced phosphorylation at Thr-55 by protein kinase Cζ is important for SHP-mediated recruitment of chromatin modifiers and histone modifications. Conclusion: Thr-55 phosphorylation is critical for epigenomic regulation of liver metabolic genes. Significance: SHP Thr-55 phosphorylation may potentially provide a therapeutic target for bile acid-related diseases. Bile acids (BAs) are recently recognized key signaling molecules that control integrative metabolism and energy expenditure. BAs activate multiple signaling pathways, including those of nuclear receptors, primarily farnesoid X receptor (FXR), membrane BA receptors, and FXR-induced FGF19 to regulate the fed-state metabolism. Small heterodimer partner (SHP) has been implicated as a key mediator of these BA signaling pathways by recruitment of chromatin modifying proteins, but the key question of how SHP transduces BA signaling into repressive histone modifications at liver metabolic genes remains unknown. Here we show that protein kinase Cζ (PKCζ) is activated by BA or FGF19 and phosphorylates SHP at Thr-55 and that Thr-55 phosphorylation is critical for the epigenomic coordinator functions of SHP. PKCζ is coimmunopreciptitated with SHP and both are recruited to SHP target genes after bile acid or FGF19 treatment. Activated phosphorylated PKCζ and phosphorylated SHP are predominantly located in the nucleus after FGF19 treatment. Phosphorylation at Thr-55 is required for subsequent methylation at Arg-57, a naturally occurring mutation site in metabolic syndrome patients. Thr-55 phosphorylation increases interaction of SHP with chromatin modifiers and their occupancy at selective BA-responsive genes. This molecular cascade leads to repressive modifications of histones at metabolic target genes, and consequently, decreased BA pools and hepatic triglyceride levels. Remarkably, mutation of Thr-55 attenuates these SHP-mediated epigenomic and metabolic effects. This study identifies PKCζ as a novel key upstream regulator of BA-regulated SHP function, revealing the role of Thr-55 phosphorylation in epigenomic regulation of liver metabolism.
Structural Mechanism for the Specific Assembly and Activation of the Extracellular Signal Regulated Kinase 5 (ERK5) Module

Background: ERK5 have distinct signaling roles compared with ERK2. Results: New crystal structures of ERK5 reveal the structural basis for ERK5 versus ERK2 signaling. Conclusion: Assembly of the ERK5 signaling cascade requires a unique cooperation between a linear binding motif and a modular protein-protein interaction domain. Significance: Molecular principles underlying ERK-specific activation suggest how to interfere with their signaling pathways. Mitogen-activated protein kinase (MAPK) activation depends on a linear binding motif found in all MAPK kinases (MKK). In addition, the PB1 (Phox and Bem1) domain of MKK5 is required for extracellular signal regulated kinase 5 (ERK5) activation. We present the crystal structure of ERK5 in complex with an MKK5 construct comprised of the PB1 domain and the linear binding motif. We show that ERK5 has distinct protein-protein interaction surfaces compared with ERK2, which is the closest ERK5 paralog. The two MAPKs have characteristically different physiological functions and their distinct protein-protein interaction surface topography enables them to bind different sets of activators and substrates. Structural and biochemical characterization revealed that the MKK5 PB1 domain cooperates with the MAPK binding linear motif to achieve substrate specific binding, and it also enables co-recruitment of the upstream activating enzyme and the downstream substrate into one signaling competent complex. Studies on present day MAPKs and MKKs hint on the way protein kinase networks may evolve. In particular, they suggest how paralogous enzymes with similar catalytic properties could acquire novel signaling roles by merely changing the way they make physical links to other proteins.
Direct Expression and Validation of Phage-selected Peptide Variants in Mammalian Cells*

Background: Phage display technology is commonly used to improve peptide and protein affinities. Results: A system circumventing a key bottleneck in this technology is used to improve a peptide inhibitor of HIV-1 entry. Conclusion: This system enables integration of sensitive and functional assays such as flow cytometry and viral neutralization into an iterative phage display workflow. Significance: This approach expands the power of a critical biotechnology. Phage display is a key technology for the identification and maturation of high affinity peptides, antibodies, and other proteins. However, limitations of bacterial expression restrict the range and sensitivity of assays that can be used to evaluate phage-selected variants. To address this problem, selected genes are typically transferred to mammalian expression vectors, a major rate-limiting step in the iterative improvement of peptides and proteins. Here we describe a system that combines phage display and efficient mammalian expression in a single vector, pDQ1. This system permits immediate expression of phage-selected genes as IgG1-Fc fusions in mammalian cells, facilitating the rapid, sensitive characterization of a large number of library outputs for their biochemical and functional properties. We demonstrate the utility of this system by improving the ability of a CD4-mimetic peptide to bind the HIV-1 envelope glycoprotein and neutralize HIV-1 entry. We further improved the potency of the resulting peptide, CD4mim6, by limiting its ability to induce the CD4-bound conformation of the envelope glycoprotein. Thus, CD4mim6 and its variants can be used to investigate the properties of the HIV-1 envelope glycoprotein, and pDQ1 can accelerate the discovery of new peptides and proteins through phage display.
E-cadherin Polarity Is Determined by a Multifunction Motif Mediating Lateral Membrane Retention through Ankyrin-G and Apical-lateral Transcytosis through Clathrin

Background: E-cadherin targets to the epithelial lateral membrane. Results: Ankyrin-G and clathrin cooperate to control E-cadherin localization. Conclusion: A multifunction motif on E-cadherin interacts with multiple pathways. Significance: This finding provides novel insights into how basolateral targeting motifs function. We report a highly conserved motif in the E-cadherin juxtamembrane domain that determines apical-lateral polarity by conferring both restricted mobility at the lateral membrane and transcytosis of apically mis-sorted protein to the lateral membrane. Mutations causing either increased lateral membrane mobility or loss of apical-lateral transcytosis result in partial mis-sorting of E-cadherin in Madin-Darby canine kidney cells. However, loss of both activities results in complete loss of polarity. We present evidence that residues required for restricted mobility mediate retention at the lateral membrane through interaction with ankyrin-G, whereas dileucine residues conferring apical-lateral transcytosis act through a clathrin-dependent process and function in an editing pathway. Ankyrin-G interaction with E-cadherin is abolished by the same mutations resulting in increased E-cadherin mobility. Clathrin heavy chain knockdown and dileucine mutation of E-cadherin both cause the same partial loss of polarity of E-cadherin. Moreover, clathrin knockdown causes no further change in polarity of E-cadherin with dileucine mutation but does completely randomize E-cadherin mutants lacking ankyrin-binding. Dileucine mutation, but not loss of ankyrin binding, prevented transcytosis of apically mis-sorted E-cadherin to the lateral membrane. Finally, neurofascin, which binds ankyrin but lacks dileucine residues, exhibited partial apical-lateral polarity that was abolished by mutation of its ankyrin-binding site but was not affected by clathrin knockdown. The polarity motif thus integrates complementary activities of lateral membrane retention through ankyrin-G and apical-lateral transcytosis of mis-localized protein through clathrin. Together, the combination of retention and editing function to ensure a high fidelity steady state localization of E-cadherin at the lateral membrane.
Impact of prescriber's handwriting style and nurse's duty duration on the prevalence of transcription errors in public hospitals.

AIMS AND OBJECTIVES To investigate the prevalence of transcription errors in a main public hospital in Pakistan and to test the impact of medication name and dose writing styles and the nurse duty duration on the occurrence of transcription errors. BACKGROUND Medication errors occur frequently in public hospitals. Errors occurring at the transcription stage have not been sufficiently investigated. DESIGN Medications transcripts and dispensed item labels were prospectively reviewed. In the second stage, nurses (n=25) transcribed medication charts in a double-blind randomised cross-over design administered at one, six and 10 hours after the commencement of their duty. METHODS. Inpatient (n=1000), discharge patient (n=1000) medication transcripts and labels of dispensed items for (n=1000) transcripts were reviewed. On medication charts, orthographically similar medications (n=20) were written in lowercase and Tall Man, decimal doses were written covered and uncovered, and metric doses were written with and without trailing zeros. RESULTS Of the 6583 and 5329 medications transcribed from inpatient and discharge patient charts, error rates were 16·9 and 13·8%, respectively. Labels for 6734 dispensed items were reviewed, and error rate was 6·1%. Tall Man, covered decimal points and avoiding trailing zeros with decimal units significantly reduced transcription errors. CONCLUSION Errors increased with increasing nurse duty duration. Highlighting orthographically similar medications and the use of proper decimal and metric units reduce errors. RELEVANCE TO CLINICAL PRACTICE Transcription errors are highly prevalent in Pakistan public hospitals; therefore, elimination of transcription stage is encouraged.
Signaling to Extracellular Signal-regulated Kinase from ErbB1 Kinase and Protein Kinase C

Background: The mechanisms underlying acute ERK signaling are poorly understood. Results: Feedback influences basal and acutely stimulated ERK responses but does not render signaling kinetics robust to ERK concentration. Conclusion: Acute ERK response kinetics depend on ERK concentration and activation mechanism as well as feedback. Significance: ERK responses to transient stimulation can be gated by ERK concentration, and short-term activation appears distributive rather than processive. Many extracellular signals act via the Raf/MEK/ERK cascade in which kinetics, cell-cell variability, and sensitivity of the ERK response can all influence cell fate. Here we used automated microscopy to explore the effects of ERK-mediated negative feedback on these attributes in cells expressing endogenous ERK or ERK2-GFP reporters. We studied acute rather than chronic stimulation with either epidermal growth factor (ErbB1 activation) or phorbol 12,13-dibutyrate (PKC activation). In unstimulated cells, ERK-mediated negative feedback reduced the population-average and cell-cell variability of the level of activated ppERK and increased its robustness to changes in ERK expression. In stimulated cells, negative feedback (evident between 5 min and 4 h) also reduced average levels and variability of phosphorylated ERK (ppERK) without altering the “gradedness” or sensitivity of the response. Binning cells according to total ERK expression revealed, strikingly, that maximal ppERK responses initially occur at submaximal ERK levels and that this non-monotonic relationship changes to an increasing, monotonic one within 15 min. These phenomena occur in HeLa cells and MCF7 breast cancer cells and in the presence and absence of ERK-mediated negative feedback. They were best modeled assuming distributive (rather than processive) activation. Thus, we have uncovered a novel, time-dependent change in the relationship between total ERK and ppERK levels that persists without negative feedback. This change makes acute response kinetics dependent on ERK level and provides a “gating” or control mechanism in which the interplay between stimulus duration and the distribution of ERK expression across cells could modulate the proportion of cells that respond to stimulation.
The behavioral context of visual displays in common marmosets (Callithrix jacchus)

Communication is important in social species, and may occur with the use of visual, olfactory or auditory signals. However, visual communication may be hampered in species that are arboreal have elaborate facial coloring and live in small groups. The common marmoset fits these criteria and may have limited visual communication. Nonetheless, some (contradictive) propositions concerning visual displays in the common marmoset have been made, yet quantitative data are lacking. The aim of this study was to assign a behavioral context to different visual displays using pre–post‐event‐analyses. Focal observations were conducted on 16 captive adult and sub‐adult marmosets in three different family groups. Based on behavioral elements with an unambiguous meaning, four different behavioral contexts were distinguished: aggression, fear, affiliation, and play behavior. Visual displays concerned behavior that included facial expressions, body postures, and pilo‐erection of the fur. Visual displays related to aggression, fear, and play/affiliation were consistent with the literature. We propose that the visual display “pilo‐erection tip of tail” is related to fear. Individuals receiving these fear signals showed a higher rate of affiliative behavior. This study indicates that several visual displays may provide cues or signals of particular social contexts. Since the three displays of fear elicited an affiliative response, they may communicate a request of anxiety reduction or signal an external referent. Concluding, common marmosets, despite being arboreal and living in small groups, use several visual displays to communicate with conspecifics and their facial coloration may not hamper, but actually promote the visibility of visual displays. Am. J. Primatol. 75:1084–1095, 2013. © 2013 The Authors. American Journal of Primatology Published by Wiley Periodicals, Inc.
Diacylglycerol Kinases Terminate Diacylglycerol Signaling during the Respiratory Burst Leading to Heterogeneous Phagosomal NADPH Oxidase Activation*

Background: Cell population-based studies obscure potential phagosomal heterogeneity. Results: We used a dynamic assay to monitor superoxide production in single phagosomes and uncovered variability in NADPH oxidase activity. Conclusion: The heterogeneity is attributable to variations in local DAG accumulation, which is controlled by DAG kinases. Significance: Heterogeneity in phagosome responsiveness could enable the survival of a fraction of invading microorganisms. It is commonly assumed that all phagosomes have identical molecular composition. This assumption has remained largely unchallenged due to a paucity of methods to distinguish individual phagosomes. We devised an assay that extends the utility of nitro blue tetrazolium for detection and quantification of NAPDH oxidase (NOX) activity in individual phagosomes. Implementation of this assay revealed that in murine macrophages there is heterogeneity in the ability of individual phagosomes to generate superoxide, both between and within cells. To elucidate the molecular basis of the variability in NOX activation, we employed genetically encoded fluorescent biosensors to evaluate the uniformity in the distribution of phospholipid mediators of the oxidative response. Despite variability in superoxide generation, the distribution of phosphatidylinositol 3,4,5-trisphosphate, phosphatidylinositol 3-phosphate, and phosphatidic acid was nearly identical in all phagosomes. In contrast, diacylglycerol (DAG) was not generated uniformly across the phagosomal population, varying in a manner that directly mirrored superoxide production. Modulation of DAG levels suggested that NOX activation is precluded when phagosomes fail to reach a critical DAG concentration. In particular, forced expression of diacylglycerol kinase β abrogated DAG accumulation at the phagosome, leading to impaired respiratory burst. Conversely, pharmacological inhibition of DAG kinases or expression of an inactive diacylglycerol kinase β mutant increased the proportion of DAG-positive phagosomes, concomitantly potentiating phagosomal NOX activity. Our data suggest that diacylglycerol kinases limit the extent of NADPH oxidase activation, curtailing the production of potentially harmful reactive oxygen species. The resulting heterogeneity in phagosome responsiveness could enable the survival of a fraction of invading microorganisms.