julilili42/papers huggingface dataset:
IMPULS: Impulsivity-Focused Group Intervention to Reduce Binge Eating Episodes in Patients with Binge Eating Disorder – A Randomised Controlled Trial
2019-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Impulsivity is a risk factor for binge eating disorder, and binge eating (BE) equates to impulsive eating behaviour. Hence, we developed IMPULS, a cognitive behavioural group intervention focusing on impulsive eating. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; We randomised 41 patients to the IMPULS group and 39 to the control group. The IMPULS group participated in the IMPULS treatment, while both groups completed weekly self-observations. We compared both groups concerning BE episodes in the past 4 weeks at the end of treatment (primary outcome). As secondary outcomes, we investigated eating pathology, depression, general impulsivity and body mass index (BMI) at the end of treatment and in a 3-month follow-up. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; The primary outcome failed, because BE episodes in the past 4 weeks were reduced in both groups at the end of treatment. At follow-up, the IMPULS group showed further improvement, contrary to the control group. The BE days/episodes in the 2 months before were overall reduced in both groups. Eating pathology was reduced in the IMPULS group at the end of treatment and partly in both groups at the follow-up. Depression was only reduced in the IMPULS group. General impulsivity and BMI did not change. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; The IMPULS study has a negative primary outcome. However, secondary outcomes indicate that the IMPULS treatment might be promising, as BE, eating pathology and depression were reduced in the IMPULS group. The initially reduced BE in the control group might represent a short-term effect from the self-observations. General impulsivity and BMI might need a longer time or more intensive treatment to change.
Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
2019-01-01

Metagenomics has become a part of the standard toolkit for scientists interested in studying microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse taxonomic profiling of samples, shotgun metagenomic sequencing provides a more detailed analysis of the taxonomic and functional content of samples. Long read technologies, such as developed by Pacific Biosciences or Oxford Nanopore, produce much longer stretches of informative sequence, greatly simplifying the difficult and time-consuming process of metagenomic assembly. MEGAN6 provides a wide range of analysis and visualization methods for the analysis of short and long read metagenomic data. A simple and efficient analysis pipeline for metagenomic analysis consists of the DIAMOND alignment tool on short reads, or the LAST alignment tool on long reads, followed by MEGAN. This approach performs taxonomic and functional abundance analysis, supports comparative analysis of large-scale experiments, and allows one to involve experimental metadata in the analysis.
Prevalence, 12-Month Prognosis, and Clinical Management Need of Depression in Coronary Heart Disease Patients: A Prospective Cohort Study
2019-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Screening for depression in patients with coronary heart disease (CHD) remains controversial. There is limited data on the actual depression management need in routine care. The aim of this study was to examine the prevalence, treatment rates, prognosis, and management need of clinical and subclinical depression in CHD patients according to the American Heart Association recommendations and the National Institute for Health and Care Excellence (NICE) guideline “Depression in Adults with a Chronic Physical Health Problem”. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Patients were recruited at 2 German university clinics between 2012 and 2014. Depressive disorders were assessed according to the DSM-IV and depressive symptom severity at baseline and during follow-up was evaluated with the Patient Health Questionnaire (PHQ-9). Depression management need was determined by the severity and longitudinal course of depression symptoms. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Of 1,024 patients (19% women), 12% had clinical depression (depressive disorder) and 45% had subclinical depression (PHQ-9 score ≥5) at baseline. Among those with clinical depression, 46% were in treatment at least once during 12 months; 26% were continuously in treatment during follow-up. Depressive disorder and depressive symptoms were significant risk factor-adjusted predictors of the 12-months mortality (adjusted HR = 3.19; 95% CI 1.32–7.69, and adjusted HR = 1.09; 95% CI 1.02–1.16, respectively). Depressive symptoms persisted in 85% of the clinically depressed and in 47% of the subclinically depressed patients. According to current recommendations, 29% of all CHD patients would require depression management within 1 year. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; There is a need for enhanced recognition, referral, and continuous and improved clinical management of depression in CHD patients.
The Endoplasmic Reticulum-Mitochondria Encounter Structure Complex Coordinates Coenzyme Q Biosynthesis
2019-01-01

Loss of the endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) complex that resides in contact sites between the yeast ER and mitochondria leads to impaired respiration; however, the reason for that is not clear. We find that in ERMES null mutants, there is an increase in the level of mRNAs encoding for biosynthetic enzymes of coenzyme Q 6 (CoQ 6 ), an essential electron carrier of the mitochondrial respiratory chain. We show that the mega complexes involved in CoQ 6 biosynthesis (CoQ synthomes) are destabilized in ERMES mutants. This, in turn, affects the level and distribution of CoQ 6 within the cell, resulting in reduced mitochondrial CoQ 6 . We suggest that these outcomes contribute to the reduced respiration observed in ERMES mutants. Fluorescence microscopy experiments demonstrate close proximity between the CoQ synthome and ERMES, suggesting a spatial coordination. The involvement of the ER-mitochondria contact site in regulation of CoQ 6 biogenesis highlights an additional level of communication between these two organelles.
Drawing Careers: The Value of a Biographical Mapping Method in Qualitative Health Research
2019-01-01

Narrative interviews are the methodological gold standard for biographical research. To facilitate memory work in interviewees, qualitative researchers increasingly fuse interviewing with visual elicitation strategies. In this article, we advance the integration of methods by introducing a graphic elicitation strategy that allows interviewees to map biographical developments and critical health experiences, in addition to verbalizing them. The biographical mapping approach was originally developed for a research project on adolescents’ health and illness experiences in elite sport but lends itself to qualitative biographical research in general. Using case material, we first demonstrate how the mapping process helps interviewees to recall past episodes and to produce more detailed biographical data. Second, we describe how the depth of focus in the biographical drawing and interview data allows researchers to identify biographical turning points and to analyze interactions between context, life events, and health in a unique way. By visualizing different strands of development, the elicited drawings also hold heuristic value, as they show the nonlinearity and multidimensionality of biographical developments.
The role of attractive and repellent scene memories in ant homing (Myrmecia croslandi)
2019-01-01

Solitary foraging ants rely on vision when travelling along routes and when pinpointing their nest. We tethered foragers of Myrmecia croslandi on a trackball and recorded their intended movements when the trackball was located on their normal foraging corridor (on-route), above their nest and at a location several meters away where they have never been before (off-route). We find that at on- and off-route locations, most ants walk in the nest or foraging direction and continue to do so for tens of metres in a straight line. In contrast, above the nest, ants walk in random directions and change walking direction frequently. In addition, the walking direction of ants above the nest oscillates at a fine scale, reflecting search movements that are absent from the paths of ants at the other locations. An agent-based simulation shows that the behaviour of ants at all three locations can be explained by the integration of attractive and repellent views directed towards or away from the nest, respectively. Ants are likely to acquire such views via systematic scanning movements during their learning walks. The model predicts that ants placed in a completely unfamiliar environment should behave as if at the nest, which our subsequent experiments confirmed. We conclude first, that the ants’ behaviour at release sites is exclusively driven by what they currently see and not by information on expected outcomes of their behaviour. Second, that navigating ants might continuously integrate attractive and repellent visual memories. We discuss the benefits of such a procedure.
The Space–Time Congruency Effect: A Meta‐Analysis
2019-01-01

Abstract Several reaction time (RT) studies report faster responses when responses to temporal information are arranged in a spatially congruent manner than when this arrangement is incongruent. The resulting space–time congruency effect is commonly attributed to a culturally salient localization of temporal information along a mental timeline (e.g., a mental timeline that runs from left to right). The present study aims to provide a compilation of the published RT studies on this time–space association in order to estimate the size of its effect and the extent of potential publication bias in this field of research. In this meta‐analysis, three types of task are distinguished due to hitherto existing empirical findings. These findings suggest that the extent to which time is made relevant to the experimental task has a systematic impact on whether or not the mental timeline is activated. The results of this meta‐analysis corroborate these considerations: First, experiments that make time a task‐relevant dimension have a mean effect size of d = 0.46. Second, in experiments in which time is task irrelevant, the effect size does not significantly deviate from zero. Third, temporal priming studies have a surprisingly high mean effect size of d = 0.47, which, however, should be adjusted to d = 0.36 due to publication bias.
Hypercapnic BOLD MRI compared to H215O PET/CT for the hemodynamic evaluation of patients with Moyamoya Disease
2019-01-01

The present analysis indicates that CO<sub>2</sub>-triggered BOLD MRI is a very promising tool for the hemodynamic evaluation of MMD patients with results comparable to those seen in H<sub>2</sub><sup>15</sup>O PET/CT with ACZ challenge. It therefore holds future potential in becoming a routine examination in the pre- and postoperative evaluation of MMD patients after further prospective evaluation.
Experimental evidence that physical activity affects the multivariate associations among muscle attachments (entheses)
2019-01-01

The morphology of entheses (muscle/tendon attachment sites) on bones is routinely used in paleontological and bioarcheological studies to infer the physical activity patterns of ancient vertebrate species including hominins. However, such inferences have often been disputed due to limitations of the quantitative methods commonly employed and a lack of experimental evidence demonstrating direct effects of physical activity on entheseal morphology. Recently, we introduced a new and improved method of quantifying and analyzing entheseal morphology that involves repeatable three-dimensional measurements combined with multivariate statistics focused on associations among multiple entheses. Here, to assess the validity of our method for investigating variation in entheseal morphology related to physical activity patterns, we analyzed femora of growing turkeys that were experimentally exercised for 10 weeks on either an inclined or declined treadmill or served as controls (n= 15 specimens, 5/group). Our multivariate approach identified certain patterns involving three different entheses (associated with muscles gluteus primus, medial gastrocnemius, vastus medialis and adductor magnus) that clearly differentiated controls from runners. Importantly, these differences were not observable when comparing groups within each of the three entheseal structures separately. Body mass was not correlated with the resulting multivariate patterns. These results provide the first experimental evidence that variation in physical activity patterns has a direct influence on entheseal morphology. Moreover, our findings highlight the promise of our newly-developed quantitative methods for analyzing the morphology of entheses to reconstruct the behavior of extinct vertebrate species based on their skeletal remains.
Longitudinal cortical network reorganization in early relapsing–remitting multiple sclerosis
2019-01-01

Background: Network science provides powerful access to essential organizational principles of the brain. The aim of this study was to investigate longitudinal evolution of gray matter networks in early relapsing–remitting MS (RRMS) compared with healthy controls (HCs) and contrast network dynamics with conventional atrophy measurements. Methods: For our longitudinal study, we investigated structural cortical networks over 1 year derived from 3T MRI in 203 individuals (92 early RRMS patients with mean disease duration of 12.1 ± 14.5 months and 101 HCs). Brain networks were computed based on cortical thickness inter-regional correlations and fed into graph theoretical analysis. Network connectivity measures (modularity, clustering coefficient, local efficiency, and transitivity) were compared between patients and HCs, and between patients with and without disease activity. Moreover, we calculated longitudinal brain volume changes and cortical atrophy patterns. Results: Our analyses revealed strengthening of local network properties shown by increased modularity, clustering coefficient, local efficiency, and transitivity over time. These network dynamics were not detectable in the cortex of HCs over the same period and occurred independently of patients’ disease activity. Most notably, the described network reorganization was evident beyond detectable atrophy as characterized by conventional morphometric methods. Conclusion: In conclusion, our findings provide evidence for gray matter network reorganization subsequent to clinical disease manifestation in patients with early RRMS. An adaptive cortical response with increased local network characteristics favoring network segregation could play a primordial role for maintaining brain function in response to neuroinflammation.
Two-Year Follow-Up after Treatment with the Cognitive Behavioral Analysis System of Psychotherapy versus Supportive Psychotherapy for Early-Onset Chronic Depression
2019-01-01

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Evidence on the long-term efficacy of psychotherapeutic approaches for chronic depression is scarce. &lt;b&gt;&lt;i&gt;Objective:&lt;/i&gt;&lt;/b&gt; To evaluate the effects of the Cognitive Behavioral Analysis System of Psychotherapy (CBASP) compared to Supportive Psychotherapy (SP) 1 year and 2 years after treatment termination. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; In this study, we present 1- and 2-year follow-up assessments of a prospective, multicenter, evaluator-blinded, randomized clinical trial of outpatients with early-onset chronic major depression (&lt;i&gt;n&lt;/i&gt; = 268). The initial treatment included 32 sessions of CBASP or SP over 48 weeks. The primary outcome was the rate of “well weeks” (Longitudinal Interval Follow-Up Evaluation; no/minimal symptoms) after 1 year and 2 years. The secondary outcomes were, among others, clinician- and self-rated depressive symptoms, response/remission rates, and quality of life. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Of the 268 randomized patients, 207 (77%) participated in the follow-up. In the intention-to-treat analysis, there was no statistically significant difference between CBASP and SP patients in experiencing well weeks (CBASP: mean [SD] of 48.6 [36.9] weeks; SP: 39.0 [34.8]; rate ratio 1.26, 95% CI 0.99–1.59, &lt;i&gt;p&lt;/i&gt; = 0.057, &lt;i&gt;d&lt;/i&gt; = 0.18) and in remission rates (CBASP: 1 year 40%, 2 years 40.2%; SP: 1 year 28.9%, 2 years 33%) in the 2 years after treatment. Statistically significant effects were found in favor of CBASP 1 year after treatment termination regarding the rate of well weeks, self-rated depressive symptoms, and depression-related quality of life. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; CBASP lost its superiority over SP at some point between the first and the second year. This suggests the necessity of maintenance treatment for early-onset chronically depressed patients remitted with CBASP during the acute therapy phase, as well as the sequential integration of other treatment strategies, including medication for those who did not reach remission.
A new species of the metriorhynchid crocodylomorph Cricosaurus from the Upper Jurassic of southern Germany
2019-01-01

Sachs, Sven, Young, Mark T., Abel, Pascal, Mallison, Heinrich (2019): A new species of the metriorhynchid crocodylomorph Cricosaurus from the Upper Jurassic of southern Germany. Acta Palaeontologica Polonica 64 (2): 343-356, DOI: 10.4202/app.00541.2018, URL: http://dx.doi.org/10.4202/app.00541.2018
Aggressive B-cell lymphomas—from morphology to molecular pathogenesis
2019-01-01

Abstract: The 2016 revised World Health Organization (WHO) classification of lymphoid malignancies recognizes several distinct entities within the group of diffuse large B-cell lymphoma (DLBCL) characterized by unique clinical and pathological features. Nevertheless, diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common aggressive B-cell lymphoma. In the last 20 years our understanding of the genetic changes and biology of DLBCL has increased tremendously. According to the 2016 WHO classification, the diagnosis of DLBCL, NOS, should include cell of origin (COO); germinal centre B-cell (GCB) or activated B-cell (ABC)/non-GCB subtypes, because of their different molecular features, biologic behavior, prognosis and treatment. High-grade B-cell lymphoma (HGBL) with MYC and BCL2 and/or BCL6 rearrangements (i.e., double-hit or triple-hit lymphoma, DHL or THL) as well as HGBL, NOS, are two new categories in the 2016 revised WHO classification that substituted the provisional category of B-cell lymphoma, unclassifiable (BCLU) with features intermediate between DLBCL and Burkitt lymphoma (BL), which was introduced in the 2008 WHO classification. The pathogenesis and molecular changes of BL are better understood and led to the recognition of a new provisional entity called Burkitt-like lymphoma with 11q aberration. In this article, we will review the progress made in the last years within the most commonly encountered aggressive B-cell lymphomas, highlighting the better understanding of the underlying disease mechanisms that eventually might be translated into more rational and effective therapeutic strategies. Controversial issues about fluorescent in situ hybridization (FISH) for the detection of MYC, BCL2 and BCL6 translocations will be addressed, as well as new molecular techniques used to improve diagnosis and prognostication in aggressive B-cell lymphomas.
Frontal brain activity and cognitive processing speed in multiple sclerosis: An exploration of EEG neurofeedback training
2019-01-01

These findings provide support for utilizing frontal EEG theta activity as an inverse marker of processing speed in MS. Across sessions, there was no support for successful operant conditioning of the theta/beta ratio during the two-week training period. The observed state-specific shift within sessions, involving a transient reduction in theta activity, nevertheless may provide a rationale for a further investigation of neurofeedback as a treatment approach in MS.
Variable vision in variable environments: the visual system of an invasive cichlid (Cichla monoculus, Agassiz, 1831) in Lake Gatun, Panama
2019-01-01

An adaptive visual system is essential for organisms inhabiting new or changing light environments. The Panama Canal exhibits such variable environments due to its anthropogenic origin and current human activities. Within the Panama Canal, Lake Gatun harbours several exotic fish species including the invasive peacock bass (Cichla monoculus, Agassiz, 1831), a predatory Amazonian cichlid. In this research, through spectral measurements and molecular and physiological experiments, we studied the visual system of C. monoculus and its adapative capabilities. Our results suggest that (1) Lake Gatun is a highly variable environment where light transmission changes throughout the canal-waterway, and that (2) C. monoculus has several visual adaptations suited for this red-shifted light enviroment. C. monoculus filters short-wavelengths (∼400 nm) from the environment through their ocular media and they tune their visual sensitivities to the available light through opsin gene expression. More importantly, based on shifts in spectral sensitivities of photoreceptors alone, and on transcriptome analysis, C. monoculus exhibits extreme intraspecific variation in the use of vitamin A1/A2 chromophore in their photoreceptors. Fish living in turbid water had higher proportions of vitamin A2, shifting sensitivities to longer-wavelengths, than fish living in clear waters. Furthermore, we also found variation in retinal transcriptomes where fish from turbid and clear-waters exhibited differentially expressed genes that vary greatly in their function. We suggest this phenotypic plasticity has been key in C. monoculus’ invasion.
Mapping the creep compliance of living cells with scanning ion conductance microscopy reveals a subcellular correlation between stiffness and fluidity
2019-01-01

Extending the scanning ion conductance microscope (SICM) towards mapping of the viscoelastic creep compliance reveals a subcellular correlation between stiffness and fluidity across individual living cells.