Miracle-dz/UniFAR-FTUs huggingface dataset:
On inference of causality for discrete state models in a multiscale context

Significance The presented framework is capable of parameter identification and optimal causality inference for discrete/Boolean-valued processes in a multiscale context, allowing us to understand such processes beyond the usual statistical assumptions of standard approaches. By applying this framework to appropriately coarse-grained molecular dynamics data it is demonstrated that the optimal causality of the considered process is localized in time and space. This offers new opportunities for applying localized parameterization tools from other areas in a molecular dynamics context, thus opening up new possibilities to bridge the gap toward long timescales in molecular dynamics simulations. The new methodology is expected to become very useful in various scientific fields (bioinformatics, geoscience) where large amounts of multiscale discrete/Boolean data have been accumulated. Discrete state models are a common tool of modeling in many areas. E.g., Markov state models as a particular representative of this model family became one of the major instruments for analysis and understanding of processes in molecular dynamics (MD). Here we extend the scope of discrete state models to the case of systematically missing scales, resulting in a nonstationary and nonhomogeneous formulation of the inference problem. We demonstrate how the recently developed tools of nonstationary data analysis and information theory can be used to identify the simultaneously most optimal (in terms of describing the given data) and most simple (in terms of complexity and causality) discrete state models. We apply the resulting formalism to a problem from molecular dynamics and show how the results can be used to understand the spatial and temporal causality information beyond the usual assumptions. We demonstrate that the most optimal explanation for the appropriately discretized/coarse-grained MD torsion angles data in a polypeptide is given by the causality that is localized both in time and in space, opening new possibilities for deploying percolation theory and stochastic subgridscale modeling approaches in the area of MD.
An open trial targeting emotional eating among adolescents with overweight or obesity

ABSTRACT Emotional eating is associated with obesity and disordered eating in adolescents, and thus, is an important target for treatment. We developed a program called PEER (Preventing Emotional Eating Routines), which incorporates emotion regulation skills with behavioral weight loss and parenting techniques for adolescents who are overweight or obese (OW/OB) and their parent. This open label trial evaluated the feasibility, acceptability, and initial efficacy of the PEER program. Thirty adolescents who were OW/OB (86.7% female; mean age = 14.6 years (SD = 1.2); Body Mass Index (BMI) = 34.0 kg/m2 (SD = 5.6); 33.3% White non-Hispanic) and their parent (66.7% biological mother) participated in a 4-month treatment and 3-month follow-up. The PEER program was well accepted. Initial efficacy showed significant decreases in emotional eating, and there were trends towards weight loss and a decrease in emotion dysregulation. This trial provides preliminary evidence for the feasibility, acceptability, and initial efficacy of the PEER program among adolescents who are OW/OB and their parent. Further treatment development and randomized controlled studies are needed.
Measurement of energy and timing resolution of very highly pixellated LYSO crystal blocks with multiplexed SiPM readout for use in a small animal PET/MR insert

Arrays of silicon photo-multipliers (SiPMs) are good candidates for the readout of detectors in PET MR inserts due to their high packing density, efficiency, low bias voltage and insensitivity to magnetic fields. In this study we report the readout performance of SensL SiPM arrays in terms of their ability to resolve all elements of pixellated lutetium oxy-orthosilicate (LYSO) crystals, and their energy and timing resolution. A SensL SB4-300-35-CER SiPM array consisting of sixteen 3 × 3 mm elements were used as light sensor. An LYSO crystal block consisting of 10×10 1.2 mm × 1.2 mm × 6.0 mm crystals on the bottom layer and 9×9 1.2 mm × 1.2 mm × 4.0 mm crystals on the top layer (which is offset by ½ the crystal width) was mounted on the SensL array, and covers over 95% of its area. A DPC encoding multiplexor with HDMI cable readout made by the Triumf Instrumentation group with a footprint suitable for allowing 16 modules to form a ring inside a Brooker 7T MR rodent imager was used as a readout. The HDMI cable supplies power, and provides readout of four channels and the device temperature. The average energy resolution for all 100 crystals in the lower layer was 11.3±1.8% and 10.8±1.2% for the 81 crystals in the upper layer. The average timing resolution for all 100 crystals in the lower layer was 2.52±0.23 nsec. and 2.55±0.23 nsec. for the 81 crystals in the upper layer.
Nursing lives in the blogosphere: A thematic analysis of anonymous online nursing narratives

AIM The aim of this study was to explore the work-life narratives of nurses through a thematic analysis of the nursing accounts they post in their publicly accessible, anonymous blogs. BACKGROUND Many nurses participate on social media. Blogs have been advocated as a self-reflective tool in nursing practice, yet as far as the authors are aware, no previous studies have explored nurses' individual blogs for their potential to reveal nurses' perceptions of nursing work. DESIGN The research design was qualitative description. METHODS Between May-August 2015, Internet search engines were used to discover lists of nursing blogs recommended by organizations representing nurses' interests. Recommended blogs were purposively sampled. Four anonymous blogs written by nurses from different nursing specialties met the sampling criteria. All 520 of their entries from 2014 were read and copied into NVivo 10, where an inductive coding process was followed. FINDINGS Three major themes arose in these nurses' online discussions of their work lives: they truly care about and value their nursing work, but they are feeling stressed and burnt out and they are using their anonymous blogs to share factors that frustrate them in their nursing work. Three main areas of frustration were revealed: teamwork problems, challenging patients and families, and management issues. CONCLUSION Anonymous nursing blogs offer valuable, longitudinal insights into nurses' perceptions of their work lives. Nursing blogs should be further explored for ongoing insights into nurses' experiences of nursing work, as well as nurses' recommendations for addressing issues causing them to feel frustrated in their work environments.
Inhibition of Murine Leukemia Virus Envelope Protein (Env) Processing by Intracellular Expression of the Env N-Terminal Heptad Repeat Region

ABSTRACT A conserved structural motif in the envelope proteins of several viruses consists of an N-terminal, alpha-helical, trimerization domain and a C-terminal region that refolds during fusion to bind the N-helix trimer. Interaction between the N and C regions is believed to pull viral and target membranes together in a crucial step during membrane fusion. For several viruses with type I fusion proteins, C regions pack as alpha-helices in the grooves between N-helix monomers, and exogenously added N- and C-region peptides block fusion by inhibiting the formation of the six-helix bundle. For other viruses, including influenza virus and murine leukemia virus (MLV), there is no evidence for comparably extended C-region alpha-helices, although a short, non-alpha-helical interaction structure has been reported for influenza virus. We tested candidate N-helix and C-region peptides from MLV for their ability to inhibit cell fusion but found no inhibitory activity. In contrast, intracellular expression of the MLV N-helix inhibited fusion by efficiently blocking proteolytic processing and intracellular transport of the envelope protein. The results highlight another mechanism by which the N-helix peptides can inhibit fusion.
Cooperación, conocimiento e innovación: políticas y agentes regionales de I+D

El punto de partida de este articulo es la importancia del capital social y las redes formales e informales de confianza y cooperacion entre los actores que participan en los procesos de generacion y aplicacion de conocimiento. Se dedica una especial atencion al papel de las politicas publicas en la creacion, dinamizacion y coordinacion de los agentes de I+D. Desde esta perspectiva se analiza el caso vasco considerando, en primer lugar, la creacion de una estructura de I+D (los centros tecnologicos) y, en segundo lugar, la relacion entre estos y el resto de agentes del sistema (universidad y empresa). Se analizan, por un lado, los problemas de consolidacion y ajuste de los agentes, y por otro, la coordinacion entre los mismos.
Brunswikian Resources for Event-Perception Research

Recent psychological research aimed at determining whether dynamic event perception is direct or mediated by cue-based inference convincingly demonstrates evidence of both modes of perception or apprehension. This work also shows that noise is involved in attaining any perceptual variable, whether it perfectly (invariantly) specifies or imperfectly (fallibly) indicates the value of a target or criterion variable. As such, event-perception researchers encounter both internal (sensory or inferential) and external ecological sources of noise or uncertainty, owing to the organism's possible use of imperfect or ‘nonspecifying’ variables (or cues) and cue-based inference. Because both sources play central roles in Egon Brunswik's theory of probabilistic functionalism and methodology of representative design, event-perception research will benefit by explicitly leveraging original Brunswikian and, more recent, neo-Brunswikian scientific resources. Doing so will result in a more coherent and powerful approach to perceptual and cognitive psychology than is currently displayed in the scientific literature.
Effects of pyruvate and glucose on the development of human preimplantation embryos in vitro.

Although human embryos will develop in vitro for six days or more, little is known about the effects of the primary nutrients, pyruvate and glucose, on development. Because the nutrient requirements of embryos change throughout preimplantation development, the effects of altering substrate concentrations in the culture medium were examined, using 'surplus' human preimplantation embryos cultured from the two-four-cell stage to the blastocyst stage in medium containing various concentrations of pyruvate and glucose. Between the one-cell stage and the two-four-cell stage all of the embryos were exposed to 0.47 mmol pyruvate l-1 and 5.5 mmol glucose l-1. Pyruvate as sole substrate in the medium could support blastocyst development to an extent of 59% (10 of 17). Conversely, culture of embryos in pyruvate-free medium resulted in the developmental arrest of 84% (21 of 25) of embryos, and for the 16% (4 of 25) that did reach the blastocyst stage there was a significant decrease in metabolic activity on day 4-5, during the morula to blastocyst stage transition. Embryos could not use glucose to compensate for the lack of pyruvate in the medium. Pyruvate uptake was related to exogenous concentration and optimal development occurred at the highest concentration tested, 0.47 mmol l-1. Embryo development to the eight-cell stage was slightly enhanced 82% (14 of 17) versus 60% (24 of 40) when no glucose was added to the medium, and the resulting blastocysts had significantly more cells (99.1 +/- 13.5 versus 58.4 +/- 8.2; P < 0.02) than did embryos grown in the presence of 1 mmol glucose l-1. (ABSTRACT TRUNCATED AT 250 WORDS)
Detection of a polymorphic site of the porcine C8G gene and evaluation of association with haemolytic complement activity

C8 is a component of the membrane attack complex (MAC) of the complement system, which causes lysis of the target cells. C8 consists of three subunits C8A, C8B, and C8G. This study focus on the porcine C8G gene aiming to identify its cDNA sequence, to detect single nucleotide polymorphism (SNP), and to analyse its association with haemolytic complement activity in the classical (CH50) and the alternative (AH50) pathway. The C8G is 840 bp in length encoding 202 amino acids. The C8G is similar (≥65 %) among mammalian species (pig, human, cattle, dog, and mouse) at both the cDNA and the protein level. One SNP was detected at nucleotide 423C→T (SNP c.423C>T; codon 124GAC→GAT). The SNP does not segregate among the European commercial breeds German Landrace and Pietrain but in the Vietnamese autochthonous breed Muong Khuong (Vietnamese potbelly pig) and an experimental F 2 crossbreed population based on Duroc and Berlin Miniature Pig (DUMI). Haemolytic complement activity of animals of the DUMI populations obtained at about 6, 14 and 16 weeks of age before and after vaccinations showed short-termed increments due to the immune stimulation and long-term increase due to aging. Family based association tests indicate effects of C8G on AH50 and CH50 at 16 weeks of age immediately before PRRS vaccination (AH50_PRRS0, P=0.087; CH50_PRRS0, P=0.027). However, the results did not indicate a consistent effect of the respective alleles on haemolytic complement activity in the alternative and the classical pathway. The study provides weak evidence for the candidacy of the porcine C8G for innate immune response and disease resistance in pigs.
UvA-DARE ( Digital Academic Repository ) Epiretinal membranes and neural plasticity of the retina

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RNA- and Virus-Independent Inhibition of Antiviral Signaling by RNA Helicase LGP2

ABSTRACT Antiviral innate immune responses can be triggered by accumulation of intracellular nucleic acids resulting from virus infections. Double-stranded RNA (dsRNA) can be detected by the cytoplasmic RNA helicase proteins RIG-I and MDA5, two proteins that share sequence similarities within a caspase recruitment domain (CARD) and a DExD/H box RNA helicase domain. These proteins are considered dsRNA sensors and are thought to transmit the signal to the mitochondrial adapter, IPS-1 (also known as MAVS, VISA, or CARDIF) via CARD interactions. IPS-1 coordinates the activity of protein kinases that activate transcription factors needed to induce beta interferon (IFN-β) gene transcription. Another helicase protein, LGP2, lacks the CARD region and does not activate IFN-β gene expression. LGP2 mRNA is induced by interferon, dsRNA treatments, or Sendai virus infection and acts as a feedback inhibitor for antiviral signaling. Results indicate that LGP2 can inhibit antiviral signaling independently of dsRNA or virus infection intermediates by engaging in a protein complex with IPS-1. Experiments suggest that LGP2 can compete with the kinase IKKi (also known as IKKε) for a common interaction site on IPS-1. These results provide the first demonstration of protein interaction as an element of negative-feedback regulation of intracellular antiviral signaling by LGP2.
Contraceptive use among the poor in Indonesia.

CONTEXT Indonesia has experienced a dramatic increase in contraceptive use and an equally dramatic fertility decline over the last 30 years. Yet recent reductions in family planning funding, program decentralization and the diminishing role of the public sector as a service provider may lead to lower use among poor women. METHODS The data for analysis were drawn from the 2002-2003 Indonesia Demographic and Health Survey. Bivariate techniques were used to compare overall contraceptive use, reliance on specific methods, source of supplies and reasons for nonuse of contraceptives between poor and better-off women. Multivariate regression assessed the association between use of a modern method and selected social, demographic and attitudinal characteristics. RESULTS Better-off women wanted significantly fewer children than did moderately or extremely poor women (2.8 vs. 3.0-3.4), were more likely to approve of family planning (93% vs. 87-91%) and were more likely to believe their spouses approved (91% vs. 80-87%). Better-off women and moderately poor women had higher odds of using modern contraceptives than did extremely poor women (odds ratios, 1.6 and 1.4, respectively). Compared with women who gave a non-numeric response, those who wanted two or fewer children had higher odds of using a modern method (2.0). The odds were also higher among women who lived in a district in which the mean ideal number of children was below the national median (1.5). CONCLUSION Governmental efforts to increase contraceptive use among poor women need to focus on changing attitudes toward smaller family sizes and family planning.
ISI-Avoiding Modulation for Diffusion-Based Molecular Communication

A molecular diffusion channel is a channel with memory, as molecules released into the medium hit the receptors after a random delay. Modulating over the diffusion channel is performed by choosing the type, intensity, or the released time of molecules diffused in the environment over time. Motivated by the desire to keep the encoder and decoder simple and the fact that channel state information is difficult to obtain in diffusion channels, we consider modulation schemes that avoid intersymbol interference (ISI), wherein molecules of the same type are released at time instances that are sufficiently far apart. This ensures that molecules of a previous transmission are faded in the environment, before molecules of the same type are reused for signaling. Avoiding ISI puts a constraint on the input sequence to the channel. In this paper, we study the fundamental limits on reliable communication rate, due to this constraint on input sequences. The maximum reliable transmission rate of ISI-avoiding modulations is given by the constrained coding capacity of the graph that represents the permissible transmission sequences. However, achieving the constrained coding capacity requires long blocklengths and delays at the decoder, making it impractical for simple nano-machines. The main contribution of this paper is to consider modulations with small delay (short blocklength) and show that they get very close to constrained coding capacity.
Identification of a New Family of Genes Involved in β-1,2-Mannosylation of Glycans in Pichia pastoris and Candida albicans*

Structural studies of cell wall components of the pathogenic yeast Candida albicans have demonstrated the presence of β-1,2-linked oligomannosides in phosphopeptidomannan and phospholipomannan. During C. albicans infection, β-1,2-oligomannosides play an important role in host/pathogen interactions by acting as adhesins and by interfering with the host immune response. Despite the importance of β-1,2-oligomannosides, the genes responsible for their synthesis have not been identified. The main reason is that the reference species Saccharomyces cerevisiae does not synthesize β-linked mannoses. On the other hand, the presence of β-1,2-oligomannosides has been reported in the cell wall of the more genetically tractable C. albicans relative, P. pastoris. Here we present the identification, cloning, and characterization of a novel family of fungal genes involved in β-mannose transfer. Employing in silico analysis, we identified a family of four related new genes in P. pastoris and subsequently nine homologs in C. albicans. Biochemical, immunological, and structural analyses following deletion of four genes in P. pastoris and deletion of four genes acting specifically on C. albicans mannan demonstrated the involvement of these new genes in β-1,2-oligomannoside synthesis. Phenotypic characterization of the strains deleted in β-mannosyltransferase genes (BMTs) allowed us to describe the stepwise activity of Bmtps and acceptor specificity. For C. albicans, despite structural similarities between mannan and phospholipomannan, phospholipomannan β-mannosylation was not affected by any of the CaBMT1–4 deletions. Surprisingly, depletion in mannan major β-1,2-oligomannoside epitopes had little impact on cell wall surface β-1,2-oligomannoside antigenic expression.
The Imperial War Relief Fund and the All British Appeal: Commonwealth, Conflict and Conservatism within the British Humanitarian Movement, 1920–25

This article explores the intersection of internationalist and imperial humanitarian ideals in the aftermath of the First World War via a case study of a hitherto overlooked humanitarian organisation—the Imperial War Relief Fund. In an era of increased international collaboration between humanitarian organisations, the Imperial War Relief Fund instead promoted an imperial approach, seeking to unite the ‘efforts of the dominions and mother country’ for the relief of Europeans suffering the effects of the First World War. The Fund was enthusiastically supported in Britain by a number of leading conservative public figures, who hoped that an empire-wide humanitarian campaign might guard against imperial disintegration and reverse Britain's perceived loss of prestige in the postwar order. Despite its initial successes, the Imperial Fund was subsequently usurped by British humanitarian organisations which were more internationalist in their outlook and rhetoric, most significantly the Save the Children Fund. This did not represent, however, a straightforward displacement of imperial co-ordination in favour of more internationally focused humanitarian action. Rather, the Save the Children Fund was able to draw support away from the Imperial Fund only by echoing its imperial rhetoric. This article argues, therefore, that, while the Imperial Fund was a relatively short-lived venture, its lasting legacy was to ensure that the British humanitarian movement was a space in which notions of Britain's imperial status, and its concomitant duties, would survive within an humanitarian landscape in which internationalist ideals were increasingly prevalent.