The risk of acute infections in new users of antidepressants: An observational cohort study

BACKGROUND

Preclinical studies suggested that drugs that functionally inhibit acid sphingomyelinase (FIASMA)may enhance immune cell longevity and potentially offer protection against infections. Many antidepressants have shown FIASMA activity.

METHODS

We conducted a cohort study using primary-care data from the UK-based Clinical Practice Research Datalink (2000-2021). We assessed the association of composite diagnosed acute infections in new users of fluoxetine, sertraline, paroxetine, or venlafaxine aged 18-80 years compared to citalopram. We compared SARS-CoV-2 infections between groups in a secondary analysis. We estimated incidence rates (IR) and IR ratios (IRR) of acute infections in four pairwise comparisons using negative binomial regression. We applied propensity score (PS) fine stratification to control for confounding.

RESULTS

In the PS-weighted cohorts, we included 353,138 fluoxetine, 222,463 sertraline, 69,963 paroxetine, 32,608 venlafaxine, and between 515,996 and 516,583 new citalopram users. PS-weighted IRs ranged between 76.8 acute infections /1000 person-years (py) (sertraline) and 98.9 infections/1000 py (citalopram). We observed PS-weighted IRRs around unity for paroxetine (0.97, 95 % CI, 0.95-1.00), fluoxetine (0.94, 95 % CI, 0.92-0.95), and venlafaxine (0.90, 95 % CI, 0.87-0.94) vs citalopram. Reduced IRR for sertraline vs citalopram (0.84, 95 % CI, 0.82-0.85), became null within subgroups by cohort entry date. In the analysis of SARS-CoV-2 infection, no statistically relevant risk reduction was seen.

LIMITATIONS

Analysis not limited to patients with diagnosed depression, possible underestimation of infection incidence, and unclear FIASMA activity of citalopram.

CONCLUSIONS

Fluoxetine, sertraline, paroxetine, and venlafaxine were not associated with a reduced risk of acute infection when compared with the presumably weak FIASMA citalopram.

A multiserological line assay to potentially discriminate current from past Helicobacter pylori infection

OBJECTIVES

Early diagnosis is important in controlling Helicobacter pylori-induced gastritis and progression to gastric malignancy. Serological testing is an efficient non-invasive diagnostic method, but currently does not allow differentiation between active and past infections. To fill this diagnostic gap we investigated the diagnostic value of a panel of ten H. pylori-specific antibodies in individuals with different H. pylori infection status within a German population.

METHODS

We used the recomLine Helicobacter IgG 2.0 immunoblotting assay to analyse ten H. pylori-specific antibodies in serum samples collected from 1108 volunteers. From these, 788 samples were used to build exposure and infection status models and 320 samples for model validation. H. pylori infection status was verified by histological examination. We applied logistic regression to select antibodies correlated to infection status and developed, with independent validation, discriminating models and risk scores. Receiving operating characteristic analysis was performed to assess the accuracy of the discriminating models.

RESULTS

Antibody reactivity against cytotoxin-associated gene A (CagA), H. pylori chaperone (GroEL), and hook-associated protein 2 homologue (FliD) was independently associated with the risk of H. pylori exposure with ORs and 95% CIs of 99.24 (46.50-211.80), 46.17 (17.45-122.17), and 22.16 (8.46-55.04), respectively. A risk score comprising these three selected antibodies differentiated currently H. pylori infected or eradicated participants from negatives with an area under the curve of 0.976 (95% CI: 0.965-0.987) (Model 1). Seropositivity for vacuolating cytotoxin A (VacA), GroEL, FliD, H. pylori adhesin A (HpaA), and γ-glutamyl transpeptidase (gGT) was associated with a current infection with an area under the curve of 0.870 (95% CI: 0.837-0.903), which may help discriminate currently infected patients from eradicated ones (Model 2).

DISCUSSION

The recomLine assay is sensitive and specific in determining H. pylori infection and eradication status and thus represents a valuable tool in the management of H. pylori infection.

Binned k-d Tree Construction for Sparse Volume Data on Multi-Core and GPU Systems

While k-d trees are known to be effective for spatial indexing of sparse 3-d volume data, full reconstruction, e.g. due to changes to the alpha transfer function during rendering, is usually a costly operation with this hierarchical data structure. In a recent publication we showed how to port a clever state of the art k-d tree construction algorithm to a multi-core CPU architecture and by means of thorough optimization we were able to obtain interactive reconstruction rates for moderately sized to large data sets. The construction scheme is based on maintaining partial summed-volume tables that fit in the L1 cache of the multi-core CPU and that allow for fast occupancy queries. In this work we propose a GPU implementation of the parallel k-d tree construction algorithm and compare it with the original multi-core CPU implementation. We conduct a thorough comparative study that outlines performance and scalability of our implementation.

Ray Tracing Structured AMR Data Using ExaBricks

Structured Adaptive Mesh Refinement (Structured AMR) enables simulations to adapt the domain resolution to save computation and storage, and has become one of the dominant data representations used by scientific simulations; however, efficiently rendering such data remains a challenge. We present an efficient approach for volume- and iso-surface ray tracing of Structured AMR data on GPU-equipped workstations, using a combination of two different data structures. Together, these data structures allow a ray tracing based renderer to quickly determine which segments along the ray need to be integrated and at what frequency, while also providing quick access to all data values required for a smooth sample reconstruction kernel. Our method makes use of the RTX ray tracing hardware for surface rendering, ray marching, space skipping, and adaptive sampling; and allows for interactive changes to the transfer function and implicit iso-surfacing thresholds. We demonstrate that our method achieves high performance with little memory overhead, enabling interactive high quality rendering of complex AMR data sets on individual GPU workstations.

A mechanistic classification of clinical phenotypes in neuroblastoma

Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Its clinical course ranges from spontaneous tumor regression to fatal progression. To investigate the molecular features of the divergent tumor subtypes, we performed genome sequencing on 416 pretreatment neuroblastomas and assessed telomere maintenance mechanisms in 208 of these tumors. We found that patients whose tumors lacked telomere maintenance mechanisms had an excellent prognosis, whereas the prognosis of patients whose tumors harbored telomere maintenance mechanisms was substantially worse. Survival rates were lowest for neuroblastoma patients whose tumors harbored telomere maintenance mechanisms in combination with RAS and/or p53 pathway mutations. Spontaneous tumor regression occurred both in the presence and absence of these mutations in patients with telomere maintenance-negative tumors. On the basis of these data, we propose a mechanistic classification of neuroblastoma that may benefit the clinical management of patients.

iRODS metadata management for a cancer genome analysis workflow

BACKGROUND

The massive amounts of data from next generation sequencing (NGS) methods pose various challenges with respect to data security, storage and metadata management. While there is a broad range of data analysis pipelines, these challenges remain largely unaddressed to date.

RESULTS

We describe the integration of the open-source metadata management system iRODS (Integrated Rule-Oriented Data System) with a cancer genome analysis pipeline in a high performance computing environment. The system allows for customized metadata attributes as well as fine-grained protection rules and is augmented by a user-friendly front-end for metadata input. This results in a robust, efficient end-to-end workflow under consideration of data security, central storage and unified metadata information.

CONCLUSIONS

Integrating iRODS with an NGS data analysis pipeline is a suitable method for addressing the challenges of data security, storage and metadata management in NGS environments.

Temporal changes of the endothelin system in human cytotrophoblasts during the first trimester of pregnancy

The first trimester of pregnancy is characterized by continuous proliferation, invasion and differentiation of cytotrophoblasts. These processes are precisely controlled both, in space and time by molecules such as endothelin-1 (ET-1). ET-1 is expressed in human first trimester trophoblast and is known to stimulate cytotrophoblast proliferation through endothelin A and B receptor subtypes (ET(A) and ET(B)), and cytotrophoblast invasion through ET(B). However, temporal changes of the ET system during the first trimester of pregnancy have not been previously studied. This study tested the hypothesis that ET-1 release, ET(A) and ET(B) expression are increased towards the end of the first trimester of pregnancy (weeks 10-12 vs. weeks 6-9), resulting in increased cytotrophoblast proliferation and invasion. Tissue samples were obtained from 17 surgical pregnancy interruptions (week 6-9: n=9; week 10-12: n=8). After cytotrophoblast isolation, the invasive and proliferative phenotypes were immune-separated by an alpha(6)-integrin antibody. Both proliferative and invasive cytotrophoblasts were cultured separately on plastic or Matrigel for 24 h. ET-1 release into the culture medium of both cytotrophoblast subtypes was measured by radioimmunoassay. ET(A) and ET(B) mRNA expression was measured by RT-PCR, and the ET-1 effect on cytotrophoblast proliferation and invasion was determined using proliferation and invasion assays, respectively. ET-1 release increased from early to late first trimester of pregnancy in both proliferative (1.8-4.5 fold) and invasive cytotrophoblasts (9.3-28 fold), especially when cultured on Matrigel. This was paralleled by less ET(B) mRNA on invasive cytotrophoblasts independent of the time period in first trimester, whereas ET(A) expression was similar on proliferative an invasive cytotrophoblasts. Proliferation and invasion of cytotrophoblasts under control conditions decreased from early to late first trimester. ET-1 stimulated both processes at both periods with the most pronounced effect (7-fold) on invasion in late first trimester. The ET-1/ET-receptor system changes between weeks 6-9 and 10-12 in pregnancy. Our data suggest an autocrine and endocrine ET-1 effect, which is stronger in late than in early first trimester of pregnancy paralleled by different stimulatory effects on trophoblast invasion and proliferation. In general, this suggests time as an additional effector of the critical processes governing placental development in the first trimester of human pregnancy.

Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB)

Background

Recent cancer genome studies on many human cancer types have relied on multiple molecular high-throughput technologies. Given the vast amount of data that has been generated, there are surprisingly few databases which facilitate access to these data and make them available for flexible analysis queries in the broad research community. If used in their entirety and provided at a high structural level, these data can be directed into constantly increasing databases which bear an enormous potential to serve as a basis for machine learning technologies with the goal to support research and healthcare with predictions of clinically relevant traits.

Results

We have developed the Cancer Systems Biology Database (CancerSysDB), a resource for highly flexible queries and analysis of cancer-related data across multiple data types and multiple studies. The CancerSysDB can be adopted by any center for the organization of their locally acquired data and its integration with publicly available data from multiple studies. A publicly available main instance of the CancerSysDB can be used to obtain highly flexible queries across multiple data types as shown by highly relevant use cases. In addition, we demonstrate how the CancerSysDB can be used for predictive cancer classification based on whole-exome data from 9091 patients in The Cancer Genome Atlas (TCGA) research network.

Conclusions

Our database bears the potential to be used for large-scale integrative queries and predictive analytics of clinically relevant traits.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2157-7) contains supplementary material, which is available to authorized users.

Clonal dynamics towards the development of venetoclax resistance in chronic lymphocytic leukemia

Deciphering the evolution of cancer cells under therapeutic pressure is a crucial step to understand the mechanisms that lead to treatment resistance. To this end, we analyzed whole-exome sequencing data of eight chronic lymphocytic leukemia (CLL) patients that developed resistance upon BCL2-inhibition by venetoclax. Here, we report recurrent mutations in BTG1 (2 patients) and homozygous deletions affecting CDKN2A/B (3 patients) that developed during treatment, as well as a mutation in BRAF and a high-level focal amplification of CD274 (PD-L1) that might pinpoint molecular aberrations offering structures for further therapeutic interventions.

BCL2-inhibitor venetoclax is used to treat relapsed/refractory chronic lymphocytic leukemia (CLL). Here, the authors show the clonal dynamics towards venetoclax resistance by performing whole-exome sequencing of 8 CLL patients undergoing venetoclax treatment.

Increased thalamic resting-state connectivity as a core driver of LSD-induced hallucinations

OBJECTIVE

It has been proposed that the thalamocortical system is an important site of action of hallucinogenic drugs and an essential component of the neural correlates of consciousness. Hallucinogenic drugs such as LSD can be used to induce profoundly altered states of consciousness, and it is thus of interest to test the effects of these drugs on this system.

METHOD

100 μg LSD was administrated orally to 20 healthy participants prior to fMRI assessment. Whole brain thalamic functional connectivity was measured using ROI-to-ROI and ROI-to-voxel approaches. Correlation analyses were used to explore relationships between thalamic connectivity to regions involved in auditory and visual hallucinations and subjective ratings on auditory and visual drug effects.

RESULTS

LSD caused significant alterations in all dimensions of the 5D-ASC scale and significantly increased thalamic functional connectivity to various cortical regions. Furthermore, LSD-induced functional connectivity measures between the thalamus and the right fusiform gyrus and insula correlated significantly with subjective auditory and visual drug effects.

CONCLUSION

Hallucinogenic drug effects might be provoked by facilitations of cortical excitability via thalamocortical interactions. Our findings have implications for the understanding of the mechanism of action of hallucinogenic drugs and provide further insight into the role of the 5-HT_2A -receptor in altered states of consciousness.

Labour and Childbirth After Previous Caesarean Section: Recommendations of the Austrian Society of Obstetrics and Gynaecology (OEGGG)

The new expert recommendation from the Austrian Society of Obstetrics and Gynaecology (OEGGG) comprises an interpretation and summary of guidelines from the leading specialist organisations worldwide (RCOG, ACOG, SOGC, CNGOF, WHO, NIH, NICE, UpToDate). In essence it outlines alternatives to the direct pathway to elective repeat caesarean section (ERCS). In so doing it aligns with international trends, according to which a differentiated, individualised clinical approach is recommended that considers benefits and risks to both mother and child, provides detailed counselling and takes the patient's wishes into account. In view of good success rates (60-85 %) for vaginal birth after caesarean section (VBAC) the consideration of predictive factors during antenatal birth planning has become increasingly important. This publication provides a compact management recommendation for the majority of standard clinical situations. However it cannot and does not claim to cover all possible scenarios. The consideration of all relevant factors in each individual case, and thus the ultimate decision on mode of delivery, remains the discretion and responsibility of the treating obstetrician.

Endothelin-1 Attenuates Apoptosis in Cultured Trophoblasts From Term Human Placentas

The authors test the hypothesis that endothelin-1 (ET-1) modulates apoptosis in human term trophoblasts. Primary cultures of cytotrophoblasts from term human placentas (n = 5) were cultured for 16 hours total or 24 hours prior to harvest at 72 hours in atmospheres of <1%, 8%, and 20% oxygen, in the presence of 10% serum, ET-1 (1-100 pmol/mL), both, or neither. The apoptotic cleavage products of poly-ADP-ribose polymerase and cytokeratin 18 filaments were quantified by Western analysis and immunocytochemistry. The expression of BAD, pBAD-serine 112, p53, and 2 isoforms of MDM2 were quantified by immunoblotting, and endothelin A and B receptors were analyzed by immunocytochemistry. Compared to vehicle control, increasing concentrations of ET-1 reduce by 3- to 6-fold the level of apoptosis in cytotrophoblasts exposed to serum-free conditions at 20% oxygen. Similarly, syncytiotrophoblast cultures grown for 24 hours without serum in 100 pmol/mL ET-1 show a 3-fold lower level of apoptosis compared with vehicle control. ET-1 significantly reduces apoptosis in cultures exposed to 20% oxygen but not in cultures exposed to 8% or 1% oxygen. The effect of ET-1 on apoptosis in 20% oxygen is accompanied by reduced p53 expression and is correlated with enhanced expression of endothelin B receptor, compared to cultures in 8% or 1% oxygen. ET-1 reduces apoptosis in cultured human trophoblasts, and this finding suggests a role for ET-1 in protecting trophoblasts against injury.

A groundwater management plan for Stuttgart

In general, groundwater in urban areas is exposed to anthropogenic influence and suffers from concentrations of contaminants. Stuttgart, as a highly industrialized city, has more than 5000 contaminated sites which might influence the Stuttgart's mineral water quality. Despite tremendous efforts and intensive single site orientated remediation since 1984 in downtown, the mineral springs were still affected with chlorinated hydrocarbons at low concentrations. Therefore, the applied practices of environmental management and measures for mitigation of pollution sources were not sufficient and had to be adjusted. The main goal of this study is to define an integral remediation plan (a groundwater management plan), focusing on the key sources of chlorinated solvents which are relevant for the mineral springs. For the large-scale investigated area of 26.6km(2) and eight aquifers, an extensive investigation and characterization methods were used in order to delineate the contamination plumes. By means of a 3D numerical model, the prioritization of the contaminated sites could be performed. Five contaminated sites with high remediation priority and need for optimized or additional remediation efforts were determined. For those five contaminated sites feasibility studies were performed which resulted in recommendation of remediation measures with total costs of more than 12.5 million euros. The proposed strategy and approach are suitable for multiple sources of contamination. Only in this way, the contributions of single contaminated sites to the total groundwater contamination can be identified and local remediation measures with their spatial impact simulated. Due to very complex geological conditions, technically there is no alternative to this strategy in order to achieve the contamination reduction in groundwater.

Shall we really say goodbye to first rank symptoms?

BACKGROUND

First rank symptoms (FRS) of schizophrenia have been used for decades for diagnostic purposes. In the new version of the DSM-5, the American Psychiatric Association (APA) has abolished any further reference to FRS of schizophrenia and treats them like any other "criterion A" symptom (e.g. any kind of hallucination or delusion) with regard to their diagnostic implication. The ICD-10 is currently under revision and may follow suit. In this review, we discuss central points of criticism that are directed against the continuous use of first rank symptoms (FRS) to diagnose schizophrenia.

METHODS

We describe the specific circumstances in which Schneider articulated his approach to schizophrenia diagnosis and discuss the relevance of his approach today. Further, we discuss anthropological and phenomenological aspects of FRS and highlight the importance of self-disorder (as part of FRS) for the diagnosis of schizophrenia. Finally, we will conclude by suggesting that the theory and rationale behind the definition of FRS is still important for psychopathological as well as neurobiological approaches today.

RESULTS

Results of a pivotal meta-analysis and other studies show relatively poor sensitivity, yet relatively high specificity for FRS as diagnostic marker for schizophrenia. Several methodological issues impede a systematic assessment of the usefulness of FRS in the diagnosis of schizophrenia. However, there is good evidence that FRS may still be useful to differentiate schizophrenia from somatic causes of psychotic states. This may be particularly important in countries or situations with little access to other diagnostic tests. FRS may thus still represent a useful aid for clinicians in the diagnostic process.

CONCLUSION

In conclusion, we suggest to continue a tradition of careful clinical observation and fine-grained psychopathological assessment, including a focus on symptoms regarding self-disorders, which reflects a key aspect of psychosis. We suggest that the importance of FRS may indeed be scaled down to a degree that the occurrence of a single FRS alone should not suffice to diagnose schizophrenia, but, on the other hand, absence of FRS should be regarded as a warning sign that the diagnosis of schizophrenia or schizoaffective disorder is not warranted and requires specific care to rule out other causes, particularly neurological and other somatic disorders. With respect to the current stage of the development of ICD-11, we appreciate the fact that self-disorders are explicitly mentioned (and distinguished from delusions) in the list of mandatory symptoms but still feel that delusional perceptions and complex hallucinations as defined by Schneider should be distinguished from delusions or hallucinations of "any kind". Finally, we encourage future research to explore the psychopathological context and the neurobiological correlates of self-disorders as a potential phenotypic trait marker of schizophrenia.