julilili42/papers huggingface dataset:
How to measure sustained psychic transformations in long-term treatments of chronically depressed patients: Symptomatic and structural changes in the LAC Depression Study of the outcome of cognitive-behavioural and psychoanalytic long-term treatments
2019-01-02

Worldwide, the pressure on psychoanalysis to prove the results of its treatments according to the criteria of so-called evidence-based medicine has increased. While a large number of studies on the results of psychoanalytic short-term therapies are now available, such studies are still largely lacking on psychoanalysis and psychoanalytic long-term therapies. In a large multicentre study, the results of psychoanalytical and cognitive-behavioural longterm therapies in chronically depressed patients were compared, Both psychotherapies led to statistically highly significant changes in depressive symptoms three years after the start of the treatments However, the focus of psychoanalytic treatments is not exclusively on reducing psychopathological symptoms, but on changes in the inner world of the patients that are reminiscent of the goal of psychoanalyses that Freud has characterized as developing "the ability to love, work and enjoy life." In the German-speaking community, such transformations are called "structural changes." This article reports results on such structural changes achieved with the help of a sophisticated measuring instrument, the Operationalized Psychodynamic Diagnostics (OPD). These so-called structural changes are compared with symptomatic changes. Three years after the start of the treatments, significantly more patients in psychoanalytical treatments show such structural changes than patients in cognitive-behavioural treatments.
The quest for an optimal alpha
2019-01-02

Researchers who analyze data within the framework of null hypothesis significance testing must choose a critical "alpha" level, α, to use as a cutoff for deciding whether a given set of data demonstrates the presence of a particular effect. In most fields, α = 0.05 has traditionally been used as the standard cutoff. Many researchers have recently argued for a change to a more stringent evidence cutoff such as α = 0.01, 0.005, or 0.001, noting that this change would tend to reduce the rate of false positives, which are of growing concern in many research areas. Other researchers oppose this proposed change, however, because it would correspondingly tend to increase the rate of false negatives. We show how a simple statistical model can be used to explore the quantitative tradeoff between reducing false positives and increasing false negatives. In particular, the model shows how the optimal α level depends on numerous characteristics of the research area, and it reveals that although α = 0.05 would indeed be approximately the optimal value in some realistic situations, the optimal α could actually be substantially larger or smaller in other situations. The importance of the model lies in making it clear what characteristics of the research area have to be specified to make a principled argument for using one α level rather than another, and the model thereby provides a blueprint for researchers seeking to justify a particular α level.
Metacognitive myopia and the overutilization of misleading advice
2019-01-02

Abstract Previous research on advice taking has explained the failure to exploit collective wisdom in terms of the egocentric underweighting of advice provided by independent others. The present research is concerned with an opposite and more radical source of irrational advice taking, namely, the failure to critically assess the validity of advice due to metacognitive myopia. Participants could use the advice of one or two experts when estimating health risks. They read sketches of the study samples that experts had drawn to estimate conditional probabilities (e.g., of HIV‐given drug addiction). Whether samples were valid or seriously biased, subsequent judgments were strongly affected by any advice (Experiment 1). Uncritical reliance on any advice persisted when participants were sensitized to the contrast of valid and invalid advice in a repeated measures design (Experiment 2), when participants themselves believed advice not to be valid (Experiment 3), and even after full debriefing about invalid advice (Experiment 4). Lay advice exerted a similar influence as expert advice (Experiment 5). Although these provocative results are independent of numeracy and consensus (Experiment 6), they highlight the impact of metacognitive myopia as an impediment of social rationality.
Marker-Independent In Situ Quantitative Assessment of Residual Cryoprotectants in Cardiac Tissues
2019-01-02

Cryomedium toxicity is a major safety concern when transplanting cryopreserved organs. Therefore, thorough removal of potentially toxic cryoprotective agents (CPAs) is required before transplantation. CPAs such as dimethyl-sulfoxide (DMSO), propylene glycol (PG), and formamide (FMD), routinely employed in ice-free cryopreservation (IFC), have advantages in long-term preservation of tissue structures compared with conventional cryopreservation employing lower CPA concentrations. This study evaluated the impact of potential residual CPAs on human cardiac valves. Raman microspectroscopy and Raman imaging were established as nondestructive marker-independent techniques for in situ quantitative assessment of CPA residues in IFC valve tissues. In detail, IFC valve leaflets and supernatants of the washing solutions were analyzed to determine the washing efficiency. A calibration model was developed according to the CPA's characteristic Raman signals to quantify DMSO, PG and FMD concentrations in the supernatants. Single point Raman measurements were performed on the intact tissues to analyze penetration properties. In addition, Raman imaging was utilized to visualize potential CPA residues. Our data showed that washing decreased the CPA concentration in the final washing solution by 99%, and no residues could be detected in the washed tissues, validating the multistep CPA removal protocol routinely used for IFC valves. Raman analysis of unwashed tissues showed different permeation characteristics depending on each CPA and their concentration. Our results demonstrate a great potential of Raman microspectroscopy and Raman imaging as marker-independent in situ tissue quality control tools with the ability to assess the presence and concentration of different chemical agents or drugs in preimplantation tissues.
Characterization of traumatic spinal cord injury model in relation to neuropathic pain in the rat
2019-01-02

Our study suggests that moderate SCI causes a progressive and long-lasting painful condition (at least 8 weeks), in addition to motor impairment, and thus represents a reliable animal model for the study of chronic neuropathic pain after SCI.
Qualitative interviews in sport and physical activity research – do not forget the body
2019-01-02

Narrative Interviews are considered as the methodological gold standard when it comes to researching complex phenomena associated with embodiment (Dowling & Garrett, 2016), critical life events or ...
Draft Genome Sequence of the Novonestmycin-Producing Strain Streptomyces sp. Z26, Isolated from Potato Rhizosphere in Morocco
2019-01-02

Streptomyces sp. strain Z26 exhibited antifungal activity and turned out to be a producer of the secondary metabolites novonestmycin A and B. The 6.5-Mb draft genome gives insight into the complete secondary metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster encoding the novonestmycins.
Changing Lives in Laos – Society, Politics and Culture in a Post-Socialist State
2019-01-02

For many people working about and being interested in Laos the two editors (Boute and Pholsena) are well known icons of scientific research about their area of expertise. Vatthana Pholsena, in part...
A novel scaffold for EGFR inhibition: Introducing N-(3-(3-phenylureido)quinoxalin-6-yl) acrylamide derivatives
2019-01-03

Abstract Clinical data acquired over the last decade on non-small cell lung cancer (NSCLC) treatment with small molecular weight Epidermal Growth Factor Receptor (EGFR) inhibitors have shown significant influence of EGFR point mutations and in-frame deletions on clinical efficacy. Identification of small molecules capable of inhibiting the clinically relevant EGFR mutant forms is desirable, and novel chemical scaffolds might provide knowledge regarding selectivity among EGFR forms and shed light on new strategies to overcome current clinical limitations. Design, synthesis, docking studies and in vitro evaluation of N -(3-(3-phenylureido)quinoxalin-6-yl) acrylamide derivatives (7a-m) against EGFR mutant forms are described. Compounds 7h and 7l were biochemically active in the nanomolar range against EGFR wt and EGFR L858R . Molecular docking and reaction enthalpy calculations have shown the influence of the combination of reversible and covalent binding modes with EGFR on the inhibitory activity. The inhibitory profile of 7h against a panel of patient-derived tumor cell lines was established, demonstrating selective growth inhibition of EGFR related cells at 10 μM among a panel of 30 cell lines derived from colon, melanoma, breast, bladder, kidney, prostate, pancreas and ovary tumors.
8‐Aminoquinolines with an Aminoxyalkyl Side Chain Exert in vitro Dual‐Stage Antiplasmodial Activity
2019-01-03

Abstract A series of novel 8‐aminoquinolines (8‐AQs) with an aminoxyalkyl side chain were synthesized and evaluated for in vitro antiplasmodial properties against asexual blood stages, liver stages, and sexual stages of Plasmodium falciparum . 8‐AQs bearing 2‐alkoxy and 5‐phenoxy substituents on the quinoline ring system were found to be the most promising compounds under study, exhibiting potent blood schizontocidal and moderate tissue schizontocidal in vitro activity.
The Digital and the Real Universe. Foundations of Natural Philosophy and Computational Physics
2019-01-03

In the age of digitization, the world seems to be reducible to a digital computer. However, mathematically, modern quantum field theories do not only depend on discrete, but also continuous concepts. Ancient debates in natural philosophy on atomism versus the continuum are deeply involved in modern research on digital and computational physics. This example underlines that modern physics, in the tradition of Newton’s Principia Mathematica Philosophiae Naturalis, is a further development of natural philosophy with the rigorous methods of mathematics, measuring, and computing. We consider fundamental concepts of natural philosophy with mathematical and computational methods and ask for their ontological and epistemic status. The following article refers to the author’s book, “The Digital and the Real World. Computational Foundations of Mathematics, Science, Technology, and Philosophy.”
Targeting DNA Double-Strand Break Repair Pathways to Improve Radiotherapy Response
2019-01-04

More than half of cancer patients receive radiotherapy as a part of their cancer treatment. DNA double-strand breaks (DSBs) are considered as the most lethal form of DNA damage and a primary cause of cell death and are induced by ionizing radiation (IR) during radiotherapy. Many malignant cells carry multiple genetic and epigenetic aberrations that may interfere with essential DSB repair pathways. Additionally, exposure to IR induces the activation of a multicomponent signal transduction network known as DNA damage response (DDR). DDR initiates cell cycle checkpoints and induces DSB repair in the nucleus by non-homologous end joining (NHEJ) or homologous recombination (HR). The canonical DSB repair pathways function in both normal and tumor cells. Thus, normal-tissue toxicity may limit the targeting of the components of these two pathways as a therapeutic approach in combination with radiotherapy. The DSB repair pathways are also stimulated through cytoplasmic signaling pathways. These signaling cascades are often upregulated in tumor cells harboring mutations or the overexpression of certain cellular oncogenes, e.g., receptor tyrosine kinases, PIK3CA and RAS. Targeting such cytoplasmic signaling pathways seems to be a more specific approach to blocking DSB repair in tumor cells. In this review, a brief overview of cytoplasmic signaling pathways that have been reported to stimulate DSB repair is provided. The state of the art of targeting these pathways will be discussed. A greater understanding of the underlying signaling pathways involved in DSB repair may provide valuable insights that will help to design new strategies to improve treatment outcomes in combination with radiotherapy.
Do perceived working conditions and patient safety culture correlate with objective workload and patient outcomes: A cross-sectional explorative study from a German university hospital
2019-01-04

Perceptions of hospital personnel regarding sub-optimal workplace safety and teamwork issues correlated with worse patient outcome measures. Furthermore, objective measures of overtime work as well as objective measures of workload correlated clearly with subjective work-related stress and strain. This suggests that objective workload measures (such as overtime worked) could be used to indirectly monitor job-related psychosocial strain on employees and, thus, improve not only staff wellbeing but also patient outcomes. On the other hand, listening to their personnel could help hospitals to improve patient (and employee) safety.
Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis
2019-01-04

Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked to establishment of the protein import pathways. The initial import of most proteins is mediated by the translocase of the outer membrane (TOM). Although TOM is common to all forms of mitochondria, an unexpected diversity of subunits between eukaryotic lineages has been predicted. However, experimental knowledge is limited to a few organisms, and so far, it remains unsettled whether the triplet-pore or the twin-pore structure is the generic form of TOM complex. Here, we analysed the TOM complex in hydrogenosomes, a metabolically specialised anaerobic form of mitochondria found in the excavate Trichomonas vaginalis. We demonstrate that the highly divergent β-barrel T. vaginalis TOM (TvTom)40-2 forms a translocation channel to conduct hydrogenosomal protein import. TvTom40-2 is present in high molecular weight complexes, and their analysis revealed the presence of four tail-anchored (TA) proteins. Two of them, Tom36 and Tom46, with heat shock protein (Hsp)20 and tetratricopeptide repeat (TPR) domains, can bind hydrogenosomal preproteins and most likely function as receptors. A third subunit, Tom22-like protein, has a short cis domain and a conserved Tom22 transmembrane segment but lacks a trans domain. The fourth protein, hydrogenosomal outer membrane protein 19 (Homp19) has no known homology. Furthermore, our data indicate that TvTOM is associated with sorting and assembly machinery (Sam)50 that is involved in β-barrel assembly. Visualisation of TvTOM by electron microscopy revealed that it forms three pores and has an unconventional skull-like shape. Although TvTOM seems to lack Tom7, our phylogenetic profiling predicted Tom7 in free-living excavates. Collectively, our results suggest that the triplet-pore TOM complex, composed of three conserved subunits, was present in the last common eukaryotic ancestor (LECA), while receptors responsible for substrate binding evolved independently in different eukaryotic lineages.
Ion mobility spectrometry as a fast screening tool for synthetic cannabinoids to uncover drug trafficking in jail via herbal mixtures, paper, food, and cosmetics
2019-01-04

Abstract The greatest challenge for European drug policies is how to effectively respond to the dynamic and constantly changing market for new psychoactive substances (NPS). Even small modifications in the chemical structure of substances often allow circumventing existing laws. Also in prison, the consumption of NPS is rising and there is growing evidence that NPS are responsible for a large share of drug‐related problems. Ion mobility spectrometry (IMS) is the technique of choice for trace analysis of illicit drugs or explosives at security points, for example airports. Currently, databases of the reduced mobility (K 0 ) values are limited to classical drugs and should be completed with data of emerging NPS. In this article, K 0 values, LODs (0.7–3.6 ng) and drift times of 25 synthetic cannabinoids were evaluated. The data were added to existing databases of IMS which were then applied for fast screening in prison. The detection capability of the portable IMS technique was evaluated by the determination of intra‐day (0.089%) and inter‐day precision (0.004% to 0.14%), systematic error (0.19%), and separation capability for structurally related NPS. The applicability of the methodology was demonstrated by the successful analysis of 12 different pieces of paper impregnated with synthetic cannabinoids, 7 different cosmetics, and 5 food samples (liquids), spiked with a mixture of narcotic drugs and a synthetic cannabinoid. In addition, 14 herbal mixtures and 36 different casework samples from prisons were analyzed provided by the State Office of Criminal Investigation Rhineland‐Palatinate (Germany).
Rhinella marina oocytes: a suitable alternative expression system for functional characterization of aquaglyceroporins
2019-01-04

Abstract Amphibian oocytes have been extensively used for heterologous expression of membrane proteins for studying their biochemical and biophysical properties. So far, Xenopus laevis is the main amphibian used as oocytes source to express aquaglyceroporins in order to assess water and solutes permeability. However, this well-established amphibian model represents a threat to the biodiversity in many countries, especially in those from tropical regions. For that reason, the import of Xenopus laevis is subjected to strict control, which essentially has restricted its use in these regions. Therefore, a wider variety of expression systems for aquaglyceroporins is needed. Rhinella marina is extensively distributed in the Americas and its native range spreads from South America to Texas, US. Here we report the use of Rhinella marina oocytes as an alternative expression system for aquaglyceroporins and demonstrated its suitability to determine the permeability to water and non-ionic solutes. Rhinella marina oocytes were able to functionally express channels from human and the protozoan pathogen Trypanosoma brucei , two very distant organisms on the evolutionary scale. Permeability values obtained from Rhinella marina oocytes expressing members of aquaporin family were similar and comparable to those values reported in the literature for the same channels expressed in Xenopus laevis oocytes.
A comparison of tarsal morphology and traction force in the two burying beetles Nicrophorus nepalensis and Nicrophorus vespilloides (Coleoptera, Silphidae)
2019-01-04

Our aim was to compare friction and traction forces between two burying beetle species of the genus Nicrophorus exhibiting different attachment abilities during climbing. Specifically, the interaction of adhesive hairs and claws during attachment with respect to various surface properties was investigated by using a 2 × 3 experimental design. Traction force was measured for two different surface energies (hydrophilic vs hydrophobic) varying in roughness from smooth to micro-rough to rough. Nanotribometric tests on single legs were also performed. The external morphology of the attachment devices investigated by scanning electron microscopy suggested higher intra-specific (intersexual) than inter-specific differences. Whereas differences between the two species in traction force were high on smooth surfaces, no differences could be detected between males and females within each species. With claws intact, both species showed the highest forces on rough surfaces, although N. nepalensis with clipped claws performed best on a smooth surface. However, N. nepalensis beetles outperformed N. vespilloides , which showed no differences between smooth and rough surfaces with clipped claws. Both species demonstrated poor traction forces on micro-rough surfaces. Results concerning the impact of surface polarity were inconclusive, whereas roughness more strongly affected the attachment performance in both species. Nanotribometric analyses of the fore tarsi performed on micro-rough and rough surfaces revealed higher friction in the proximal (pull) direction compared with the distal (push) direction. In these experiments, we detected neither differences in friction performance between the two species, nor clear trends concerning the influence of surface polarity. We conclude that the investigated morphological traits are not critical for the observed interspecific difference in attachment ability on smooth surfaces. Furthermore, interspecific differences in performance are only clear on smooth surfaces and vanish on micro-rough and rough surfaces. Our results suggest that even subtle differences in the adhesion-mediating secretion in closely related species might result in qualitative performance shifts.
Annotated bacterial chromosomes from frame-shift-corrected long read metagenomic data
2019-01-04

Abstract Background Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results We demonstrate that whole bacterial chromosomes can be obtained from a complex community, by application of MinION sequencing to a sample from an EBPR bio-reactor, producing 6Gb of sequence that assembles in to multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. Conclusions Advances in long read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.
Design and Analysis of Infectious Disease Studies
2019-01-04

This was the fifth workshop on mathematical and statistical methods on the transmission of infectious diseases. Building on epidemiologic models which were the subject of earlier workshops, this workshop concentrated on disentangling who infected whom by analysing high-resolution genomic data of pathogens which were routinely collected during disease outbreaks. Following the trail of the small mutations which continuously occur in different places of the pathogens’ genomes, mathematical tools and computational algorithms were used to reconstruct transmission trees and contact networks.