Biological network growth in complex environments: A computational framework.

Spatial biological networks are abundant on all scales of life, from single cells to ecosystems, and perform various important functions including signal transmission and nutrient transport. These biological functions depend on the architecture of the network, which emerges as the result of a dynamic, feedback-driven developmental process. While cell behavior during growth can be genetically encoded, the resulting network structure depends on spatial constraints and tissue architecture. Since network growth is often difficult to observe experimentally, computer simulations can help to understand how local cell behavior determines the resulting network architecture. We present here a computational framework based on directional statistics to model network formation in space and time under arbitrary spatial constraints. Growth is described as a biased correlated random walk where direction and branching depend on the local environmental conditions and constraints, which are presented as 3D multilayer grid. To demonstrate the application of our tool, we perform growth simulations of a dense network between cells and compare the results to experimental data from osteocyte networks in bone. Our generic framework might help to better understand how network patterns depend on spatial constraints, or to identify the biological cause of deviations from healthy network function.

A functional variant in the neuropeptide S receptor 1 gene moderates the influence of urban upbringing on stress processing in the amygdala.

We have previously shown that urban upbringing and city living were associated with stress-induced activity in the amygdala and the perigenual anterior cingulate cortex (pACC). This finding might link the epidemiological risk factor "urbanicity" to neurobiological mechanisms of psychiatric disorders. However, given the heritability of stress-related phenotypes, it appears likely that genetic factors can modulate the effect of urbanicity on social stress processing. In the present exploratory study, we investigated if a functional sequence variation in the neuropeptide S receptor gene (NPSR1 rs324981) is associated with brain activation patterns under acute psychosocial stress and if it modulates the link between urbanicity and central stress processing. In animals, neuropeptide S has strong anxiolytic effects and it induces hypothalamus-pituitary-adrenal (HPA) axis activation. In humans, rs324981 was found to be associated with anxiety and stress-related phenotypes. Forty-two subjects were exposed to a psychosocial stress task for scanner environments (ScanSTRESS). While no main effect of rs324981 on amygdala and pACC activity was detected, we found a distinct interaction between rs324981 and urban upbringing modulating right amygdala responses. Moreover, right amygdala responses were significantly higher in subjects who also showed a salivary cortisol response to the stress exposure. The present finding of a gene × environment interaction further supports the view that the brain NPS system is involved in central stress regulation. This study provides first evidence for the assumption that a NPSR1 variant modulates brain activation under stress, interacting with the environmental risk factor urban upbringing.

Conversation-based AI for anxiety disorders might lower the threshold for traditional medical assistance: a case report.

Artificial intelligence (AI) offers a wealth of opportunities for medicine, if we also bear in mind the risks associated with this technology. In recent years the potential future integration of AI with medicine has been the subject of much debate, although practical clinical experience of relevant cases is still largely absent. This case study examines a particular patient's experience with different forms of care. Initially, the patient communicated with the conversation (chat) based AI (CAI) for self-treatment. However, over time she found herself increasingly drawn to a low-threshold internal company support system that is grounded in an existing, more traditional human-based care structure. This pattern of treatment May represent a useful addition to existing care structures, particularly for patients receptive to technology.

Fourier Ring Correlation and Anisotropic Kernel Density Estimation Improve Deep Learning Based SMLM Reconstruction of Microtubules.

Single-molecule super-resolution microscopy (SMLM) techniques like dSTORM can reveal biological structures down to the nanometer scale. The achievable resolution is not only defined by the localization precision of individual fluorescent molecules, but also by their density, which becomes a limiting factor e.g., in expansion microscopy. Artificial deep neural networks can learn to reconstruct dense super-resolved structures such as microtubules from a sparse, noisy set of data points. This approach requires a robust method to assess the quality of a predicted density image and to quantitatively compare it to a ground truth image. Such a quality measure needs to be differentiable to be applied as loss function in deep learning. We developed a new trainable quality measure based on Fourier Ring Correlation (FRC) and used it to train deep neural networks to map a small number of sampling points to an underlying density. Smooth ground truth images of microtubules were generated from localization coordinates using an anisotropic Gaussian kernel density estimator. We show that the FRC criterion ideally complements the existing state-of-the-art multiscale structural similarity index, since both are interpretable and there is no trade-off between them during optimization. The TensorFlow implementation of our FRC metric can easily be integrated into existing deep learning workflows.

Possible association between genetic variants at the GRIN1 gene and schizophrenia with lifetime history of depressive symptoms in a German sample.

Genetic variation in glutamatergic signalling pathways is believed to play a substantial role in the aetiology of schizophrenia. The N-methyl-D-aspartate receptor subunit gene GRIN1 has been proposed as a candidate gene for schizophrenia. We tested for a potential association between schizophrenia and four single nucleotide polymorphisms (rs4880213, rs11146020, rs6293, and rs10747050) and one microsatellite marker at GRIN1 in a German sample of 354 patients and 323 controls. We found significant associations in single-marker and haplotype-based analyses (P<0.05). Significance was more pronounced (P<0.01) in the subset of patients with a lifetime history of major depression, a subgroup of schizophrenia described previously as a promising phenotypic subtype in genetic studies of schizophrenia. Although significances did not withstand correction for multiple testing, the results of our exploratory analysis warrant further studies on GRIN1 and schizophrenia.

Disturbance of circadian rhythms in analgosedated intensive care unit patients with and without craniocerebral injury.

Melatonin, cortisol, heart rate, blood pressure, spontaneous motor activity, and body temperature follow stable circadian rhythms in healthy individuals. These circadian rhythms may be influenced or impaired by the loss of external zeitgebers during analgosedation, critical illness, continuous therapeutic intervention in the intensive care unit (ICU), and cerebral injury. This prospective, observational, clinical study examined 24 critically ill analgo-sedated patients, 13 patients following surgery, trauma, or acute respiratory distress (ICU), and 11 patients with acute severe brain injury following trauma or cerebral hemorrhage (CCI). Blood samples for the determination of melatonin and cortisol were obtained from each patient at 2 h intervals for 24 h beginning at 18:00 h on day 1 and ending 16:00 h on day 2. Blood pressure, heart rate, body temperature, and spontaneous motor activity were monitored continuously. Level of sedation was assessed using the Ramsey Sedation Scale. The severity of illness was assessed using the APACHE-II-score. The time series data were analyzed by rhythm analysis with the Chronos-Fit program, using partial Fourier series with up to six harmonics. The 24 h profiles of all parameters from both groups of patients were greatly disturbed/abolished compared to the well-known rhythmic 24 h patterns in healthy controls. These rhythm disturbances were more pronounced in patients with brain injury. The results of this study provide evidence for a pronounced disturbance of the physiological temporal organization in ICU patients. The relative contribution of analgosedation and/or brain injury, however, is a point of future investigation.

No association between genetic variants at the ASCT1 gene and schizophrenia or bipolar disorder in a German sample.

Altered glutamatergic neurotransmission is considered a potential etiological factor of schizophrenia (SCZ) and affective disorders. The gene ASCT1 (SLC1A4) coding for a Na+-dependent neutral aminoacid transporter is a member of the glutamate transporter superfamily and is located on 2p13-14, a region showing linkage to both SCZ and bipolar disorder (BD). ASCT1 can thus be considered a candidate gene for both disorders. In a German sample, we tested for association between ASCT1 and both SCZ and BD. Allele and haplotype frequencies, however, did not differ between cases and controls. Recent findings on the associations between brainderived neurotrophic factor (BDNF) and SCZ and between G72/G30 and BD suggest that SCZ patients with a history of major depressive episodes (MDE) outside psychotic episodes and BD cases with a history of persecutory delusions constitute genetically distinct subgroups of these disorders. Thus, we hypothesized that restricting case definition to those 95 SCZ individuals with MDE and to those 107 BD patients with a history of persecutory delusions might clarify the relationship between BD, SCZ and ASCT1. However, these stratification approaches did not yield any significant association either. Allele and haplotype frequencies did not differ between cases and controls. Our results do not support an association of the ASCT1 gene with BD or SCZ in the German population.

Prevalence of depression, suicidal ideation, alcohol intake and nicotine consumption in rural Central India. The Central India Eye and Medical Study.

BACKGROUND: To investigate the prevalence of depression, suicidal ideations, alcohol and nicotine consumption in adults in an agrarian society mostly unchanged by the effects of urbanization. METHODS: The Central India Eye and Medical Study is a population-based study in rural Central India close to the tribal belt and included 4711 subjects (aged 30+ years). Depression was assessed by the Center for Epidemiologic Studies Depression Scale (CESD), suicidal ideation by six standardized questions, nicotine use by the Fagerstroem Nicotine Tolerance Questionnaire (FTNQ), and alcohol consumption by the Alcohol Use Disorders Identification Test (AUDIT). RESULTS: Mild to moderate depression (CESD sum score: 15-21) was detected in 1862 (39.6%) individuals (33.5% of men, 44.8 of women), and major depression (CESD sum score >21) in 613 (13.0%) individuals (8.1 of men, 17.3% of women). Suicide attempt was reported by 199 (4.2%) participants and suicidal thoughts during the last 6 months by 238 (5.1%) individuals. There were 887 (18.9%) smokers and smokeless tobacco was consumed by 1968 (41.8%) subjects. Alcohol consumption was reported by 1081 (23.0%) participants; 283 (6.0%) subjects had an AUDIT score ≥ 8 (hazardous drinking), and 108 (4.63%) subjects a score ≥ 13 (women) or ≥ 15 (men) (alcohol dependence). CONCLUSIONS: In rural Central India, prevalence of major depression was comparable to figures reported from other developing countries. Prevalence of smoking and hazardous alcohol consumption was higher than as reported from urban regions. Measures should be taken to address the relatively high prevalence of suicide attempts and thoughts on suicide in rural Central India.

Dissection of phenotype reveals possible association between schizophrenia and Glutamate Receptor Delta 1 (GRID1) gene promoter.

Recent linkage and association data have implicated the Glutamate Receptor Delta 1 (GRID1) locus in the etiology of schizophrenia. In this study, we sought to test whether variants in the promoter region are associated with this disorder. The distribution of CpG islands, which are known to be relevant for transcriptional regulation, was computationally determined at the GRID1 locus, and the putative transcriptional regulatory region at the 5'-terminus was systematically tagged using HapMap data. Genotype analyses were performed with 22 haplotype-tagging single nucleotide polymorphisms (htSNPs) in a German sample of 919 schizophrenia patients and 773 controls. The study also included two SNPs in intron 2 and one in intron 3 which have been found to be significantly associated with schizophrenia in previous studies. For the transcriptional regulatory region, association was obtained with rs3814614 (p=0.0193), rs10749535 (p=0.0245), and rs11201985 (p=0.0222). For all further analyses, the patient samples were divided into more homogeneous subgroups according to sex, age at onset, positive family history of schizophrenia and lifetime history of major depression. The p-value of the schizophrenia association finding for the three markers decreased by approximately one order of magnitude, despite the reduction in the total sample size. Marker rs3814614 (unadjusted p=0.0005), located approximately 2.0 kb from the transcriptional start point, also withstood a two-step correction for multiple testing (p=0.030). No support was obtained for previously reported associations with the intronic markers. Our results suggest that genetic variants in the GRID1 transcriptional regulatory region may play a role in the etiology of schizophrenia, and that future association studies of schizophrenia may require stratification to ensure more homogeneous patient subgroups.

Predictors of mortality in ARDS patients referred to a tertiary care centre: a pilot study.

BACKGROUND AND OBJECTIVE: In order to identify parameters predicting intensive care unit mortality in patients transferred to a specialized tertiary centre because of progressive acute respiratory distress syndrome, an observational pilot study was carried out involving 94 patients. METHODS AND RESULTS: Forty-one patients (43.6%) died. Survival was defined as intensive care unit discharge. Survivors were younger (32.0 +/- 11.8 vs. 39.1 +/- 12.4 yr, P = 0.008), at admission they had a lower acute physiology and chronic health evaluation (APACHE) II score (21.7 +/- 5.4 vs. 25.4 +/- 5.2, P = 0.0009), higher PaO2/FiO2 (122 +/- 79 vs. 79 +/- 42 mmHg, P = 0.002), lower positive end-expiratory pressure (10.6 +/- 3.1 vs. 12.5 +/- 3.7 cmH2O, P = 0.02) and a lower Murray score (2.8 +/- 0.63 vs. 3.0 +/- 0.62, P = 0.04). No differences were observed for tidal volumes and peak inspiratory pressures. Days of hospitalization and mechanical ventilation prior to transferral were not related to survival. Multivariate analysis of variables assessed on admission detected only differences for age (P = 0.014) and APACHE II (P = 0.005). Odds ratio was 1.06 (95% confidence interval (CI): 1.013-1.119) for age and 1.21 (CI: 1.059-1.381) for APACHE II. Multivariate analysis of changes in respiratory parameters, APACHE II and Murray score during the first 3 days after transferral revealed a significant difference only for positive end-expiratory pressure (P < 0.008). Corresponding odds ratio was 2.40 (CI: 1.25-4.58) for an increase of 1 cmH2O/24 h. CONCLUSION: Age-related mortality in this small, but highly selected group of patients with established ARDS increased early in life even in a population with an overall mean age of 35.1 yr. APACHE II was the only clinical predictor for mortality on admission. The need for a substantial increase in positive end-expiratory pressure after transferral markedly reduced the chance to survive.