Designing Eukaryotic Gene Expression Regulation Using Machine Learning.

Controlling the expression of genes is one of the key challenges of synthetic biology. Until recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their complexity of gene regulation. With advances in machine learning (ML) and in particular with increasing dataset sizes, models predicting gene expression levels from regulatory sequences can now be successfully constructed.

Cueing healthier alternatives for take-away: a field experiment on the effects of (disclosing) three nudges on food choices.

Background: The current field experiment demonstrates the effectiveness of nudging to promote healthy food choices.

Methods: Three types of nudges were implemented at a take-away food vendor: 1) an accessibility nudge that placed fruits at the front counter; 2) a salience nudge that presented healthy bread rolls to be more visually attractive; and 3) a social proof nudge that conveyed yoghurt as a popular choice. We additionally assessed whether nudging effects would remain robust when a disclosure message was included.

Assessing quality of life in obstetric fistula patients: Validation of the urogenital distress inventory (UDI-6) and Incontinence Impact Questionnaire (IIQ-7) in Lingala and Kikongo in DR Congo.

Aims: The Urogenital Distress Inventory (UDI-6) and the Incontinence Impact Questionnaire (IIQ-7) are both well-known. In obstetric fistula (OF) repair outcome is usually assessed by the surgical team. The patient perspective is often neglected.

Long-Term Assessment of a Prospective Cohort of Patients Undergoing Laparoscopic Sacrocolpopexy.

Objective: To report long-term outcomes after laparoscopic sacrocolpopexy.

Methods: We conducted a prospective descriptive cohort study on 331 consecutive patients who underwent laparoscopic sacrocolpopexy for symptomatic prolapse (Pelvic Organ Prolapse Quantification [POP-Q] system stage 2 or greater) at one center, with minimum 1.5 years of follow-up by April 30, 2014.

Metabolic Model of the -Tomato Interaction Reveals Metabolic Switches during Host Colonization.

The oomycete pathogen causes potato and tomato late blight, a disease that is a serious threat to agriculture. is a hemibiotrophic pathogen, and during infection, it scavenges nutrients from living host cells for its own proliferation. To date, the nutrient flux from host to pathogen during infection has hardly been studied, and the interlinked metabolisms of the pathogen and host remain poorly understood.

GeneNoteBook, a collaborative notebook for comparative genomics.

Summary: Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics.

Tinnitus distress: a paradoxical attention to the sound?

Tinnitus, the perception of sound in the absence of external stimuli, is often a disturbing symptom for which the underlying functional neuroanatomy still remains poorly understood. Most studies have focused solely on functional connectivity changes in the auditory cortex of tinnitus patients. The aim of this study was to investigate whether a correlation exists between tinnitus behavioural scores and functional brain connectivity of five resting-state networks comprising the auditory, the default mode, the external control left and right, and the salience network.

Paradoxical effects of JZL184, an inhibitor of monoacylglycerol lipase, on bone remodelling in healthy and cancer-bearing mice.

Background: Cancer-associated bone disease is a serious complication in bone sarcomas and metastatic carcinomas of breast and prostate origin. Monoacylglycerol lipase (MAGL) is an enzyme of the endocannabinoid system, and is responsible for the degradation of the most abundant endocannabinoid in bone, 2-arachidonoyl glycerol (2AG).

Methods: The effects of the verified MAGL inhibitor on bone remodelling were assessed in healthy mice and in mouse models of bone disease caused by prostate and breast cancers and osteosarcoma.

Is Tracheostomy Insertion an Indication for Gastrostomy Insertion?

The aim of the study was to determine the frequency of surgical patients who undergo tracheostomy and gastrostomy insertion during the same hospitalization. Secondary outcomes included ICU and hospital length of stay (LOS) for patients who underwent concomitant tracheostomy and gastrostomy those who did not. This study is a retrospective review of trauma and acute care surgery (ACS) patients between 2006 and 2015 who underwent tracheostomy.

Real-Life Data on Mirabegron in Neurogenic Bladder Dysfunction.

Aims: To determine factors for treatment persistence in a real-life cohort of adult neurogenic lower urinary tract dysfunction.

Methods: We reviewed records of patients with neurogenic lower urinary tract dysfunction and mirabegron prescriptions. Exclusion criteria were indwelling urethral or suprapubic catheters and implanted neurostimulators.

Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads.

DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage).

Comparison of Neural Activity in Chronic Pain Patients During Tonic and Burst Spinal Cord Stimulation Using Fluorodeoxyglucose Positron Emission Tomography.

Objective: Burst spinal cord stimulation (SCS) is a novel stimulation paradigm that seems to provide better pain relief compared to the classic tonic SCS with minimal paresthesia sensation. Based on source localized electroencephalography and clinical data, it has been proposed that burst stimulation as defined by Dirk De Ridder exerts this greater effect by not only modulating the lateral and the descending pain-inhibitory pathways (similar to tonic SCS) but also modulating the medial pain pathway, which encodes the affective, motivational aspects of pain.

Material And Methods: The current study evaluates the supraspinal differences between burst and tonic stimulation with another functional imaging technique, namely fluorodeoxyglucose positron emission tomography (FGD-PET) scanning, in seven patients, who underwent both burst and tonic SCS, to confirm this notion of medial pain pathway modulation.

Unraveling the Relationship Between Trait Self-Control and Subjective Well-Being: The Mediating Role of Four Self-Control Strategies.

Although several studies provide evidence that trait self-control contributes to subjective well-being, the self-control strategies that promotes happiness and life satisfaction remains unknown. The present study aims to shed light on this relation by investigating the mediating role of four self-control strategies: situation selection, attentional deployment, reappraisal, and inhibition. To test the hypothesis that self-control strategies mediate trait self-control's effect on well-being, an online questionnaire on trait self-control, self-control strategies, and cognitive and affective well-being was administered to 4,036 participants from four countries (ages 18-65 and 56.

Distinguishing between self-control and perceived control over the environment to understand disadvantaged neighbourhood health and lifestyle outcomes.

: The current study aimed to test whether and how self-control and perceived control play a role in health outcomes and lifestyle differences between disadvantaged and non-disadvantaged neighbourhoods. : Cross-sectional survey data including demographics was collected from 3758 participants. Main outcome measures: With the survey, self-control, perceived control, health status and lifestyle variables were assessed.

Drug utilization patterns and healthcare resource use and costs in patients with neurogenic bladder in the United Kingdom: A retrospective primary care database study.

Aim: To characterize patients with neurogenic bladder (NGB), their treatment patterns, healthcare resource utilization, and associated costs based on records from a primary care database in the United Kingdom.

Methods: This was a retrospective, descriptive, observational study of anonymized data from the Clinical Practice Research Datalink and Hospital Episode Statistics databases (selection period, 1 January 2004 to 31 December 2016). Adults with a definitive or probable diagnosis of NGB and ≥1 referral to a urologist were included.

Pharmacological inhibition of the IKKε/TBK-1 axis potentiates the anti-tumour and anti-metastatic effects of Docetaxel in mouse models of breast cancer.

IκB kinase subunit epsilon (IKKε), a key component of NFκB and interferon signalling, has been identified as a breast cancer oncogene. Here we report that the IKKε/TBK1 axis plays a role in the initiation and progression of breast cancer osteolytic metastasis. Cancer-specific knockdown of IKKε in the human MDA-MB-231-BT cells and treatment with the verified IKKε/TBK1 inhibitor Amlexanox reduced skeletal tumour growth and osteolysis in mice.

2D and 3D In Vitro Co-Culture for Cancer and Bone Cell Interaction Studies.

Co-culture assays are used to study the mutual interaction between cells in vitro. This chapter describes 2D and 3D co-culture systems used to study cell-cell signaling crosstalk between cancer cells and bone marrow adipocytes, osteoblasts, osteoclasts, and osteocytes. The chapter provides a step-by-step guide to the most commonly used cell culture techniques, functional assays, and gene expression.

Achieving quadruple aim goals through clinical networks: A systematic review.

Introduction: Clinical Networks are complex interventions that enable healthcare professionals from various disciplines to work in a coordinated manner in the context of multiple care settings, to provide a high quality response to a specific disease. The aim of this study was to evaluate if clinical networks are able to improve effectiveness, efficiency, patients' satisfaction and professionals' behavior in the health care settings, namely the "quadruple aim" quality goals.

Materials And Methods: A systematic review of documents published until February 28, 2018, in Medline, Embase and CINAHL was performed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses approach.

Frontostriatal network dysfunction as a domain-general mechanism underlying phantom perception.

In the present study, we use resting state fMRI to investigate whether nucleus accumbens (NAc) and extended frontostriatal networks are involved in the pathology of auditory phantom perception, i.e., tinnitus, through a study of functional connectivity.

[Hepatocellular carcinoma in an inflammatory adenoma with β-catenin mutation in a patient with hepatocellular adenomatosis due to germline mutation in HNF1α].

Hepatocyte nuclear factor 1 α (HNF1α) mutations cause maturity-onset diabetes of the young (MODY) type 3 and are associated with hepatocellular adenomatosis. Malignant transformation of HNF1α-mutated hepatocellular adenomas is rare. We report a case of a 28-year-old man with HNF1α-inactivated adenomatosis who developed an inflammatory adenoma with β catenin mutation with malignant transformation into a well-differentiated hepatocellular carcinoma (HCC).

poreTally: run and publish de novo nanopore assembler benchmarks.

Summary: Nanopore sequencing is a novel development in nucleic acid analysis. As such, nanopore-sequencing hardware and software are updated frequently and extensively, which quickly renders peer-reviewed publications on analysis pipeline benchmarking efforts outdated. To provide the user community with a faster, more flexible alternative to peer-reviewed benchmark papers for de novo assembly tool performance we constructed poreTally, a comprehensive benchmarking tool.

Functional and molecular characterisation of the bilateral pelvic nerve crush injury rat model for neurogenic detrusor underactivity.

Objectives: To create a rat model for neurogenic detrusor underactivity (DU) by bilateral pelvic nerve crush injury (BPNI) and to study temporal changes in detrusor contractility and morphology.

Materials And Methods: Male Sprague-Dawley rats were subjected to BPNI or sham surgery and evaluated at 1, 3 and 9 weeks after surgery. Bladder function was determined in vivo by awake cystometry, micturition pattern analysis, and 24-h urine collection.

Simvastatin and the Rho-kinase inhibitor Y-27632 prevent myofibroblast transformation in Peyronie's disease-derived fibroblasts via inhibition of YAP/TAZ nuclear translocation.

Objectives: To uncover the anti-myofibroblast (MFB) properties of Rho-kinase inhibitor (compound Y-27632) and simvastatin in an in vitro model of Peyronie's disease (PD), a sexually debilitating disease caused by an irreversible fibrotic plaque in the penile tunica albuginea (TA).

Materials And Methods: Primary human fibroblasts (FBs) were isolated from surgically obtained TA tissue from patients with PD. To induce MFB status, cells were stimulated with 3 ng/mL transforming growth factor-β1 (TGF-β1).