NetworKIN: a resource for exploring cellular phosphorylation networks

Protein kinases control cellular responses by phosphorylating specific substrates. Recent proteome-wide mapping of protein phosphorylation sites by mass spectrometry has discovered thousands of in vivo sites. Systematically assigning all 518 human kinases to all these sites is a challenging problem. The NetworKIN database (http://networkin.info) integrates consensus substrate motifs with context modelling for improved prediction of cellular kinase–substrate relations. Based on the latest human phosphoproteome from the Phospho.ELM and PhosphoSite databases, the resource offers insight into phosphorylation-modulated interaction networks. Here, we describe how NetworKIN can be used for both global and targeted molecular studies. Via the web interface users can query the database of precomputed kinase–substrate relations or obtain predictions on novel phosphoproteins. The database currently contains a predicted phosphorylation network with 20 224 site-specific interactions involving 3978 phosphoproteins and 73 human kinases from 20 families.Genome Canada (through Ontario Genomics Institute)National Institutes of Health (U.S.) (U54-CA112967)National Institutes of Health (U.S.) (GM60594)European Community’s Human Potential Programme (BioSapiens Network of Excellence (contract number LSHG-CT-2003-503265))European Community’s Human Potential Programme (ADIT Integrated Project (contract number LSHB-CT-2005511065)

Role of the mesoamygdaloid dopamine projection in emotional learning

Amygdala dopamine is crucially involved in the acquisition of Pavlovian associations, as measured via conditioned approach to the location of the unconditioned stimulus (US). However, learning begins before skeletomotor output, so this study assessed whether amygdala dopamine is also involved in earlier 'emotional' learning. A variant of the conditioned reinforcement (CR) procedure was validated where training was restricted to curtail the development of selective conditioned approach to the US location, and effects of amygdala dopamine manipulations before training or later CR testing assessed. Experiment 1a presented a light paired (CS+ group) or unpaired (CS- group) with a US. There were 1, 2 or 10 sessions, 4 trials per session. Then, the US was removed, and two novel levers presented. One lever (CR+) presented the light, and lever pressing was recorded. Experiment 1b also included a tone stimulus. Experiment 2 applied intra-amygdala R(+) 7-OH-DPAT (10 nmol/1.0 A mu l/side) before two training sessions (Experiment 2a) or a CR session (Experiment 2b). For Experiments 1a and 1b, the CS+ group preferred the CR+ lever across all sessions. Conditioned alcove approach during 1 or 2 training sessions or associated CR tests was low and nonspecific. In Experiment 2a, R(+) 7-OH-DPAT before training greatly diminished lever pressing during a subsequent CR test, preferentially on the CR+ lever. For Experiment 2b, R(+) 7-OH-DPAT infusions before the CR test also reduced lever pressing. Manipulations of amygdala dopamine impact the earliest stage of learning in which emotional reactions may be most prevalent

Academic self-concept, gender and single-sex schooling

This paper assesses gender differences in academic self-concept for a cohort of children born in 1958 (the National Child Development Study). We address the question of whether attending single-sex or co-educational schools affected students’ perceptions of their own academic abilities (academic self-concept). Academic selfconcept was found to be highly gendered, even controlling for prior test scores. Boys had higher self-concepts in maths and science, and girls in English. Single-sex schooling reduced the gender gap in self-concept, while selective schooling was linked to lower academic self-concept overall

Research surveys and their evolution: Past, current and future uses in healthcare.

Research surveys are believed to have originated in antiquity with evidence of them being performed in ancient Egypt and Greece. In the past century, their use has grown significantly and they are now one of the most frequently employed research methods including in the field of healthcare. Modern validation techniques and processes have allowed researchers to broaden the scope of qualitative data they can gather through these surveys such as an individual's views on service quality to nationwide surveys that are undertaken regularly to follow healthcare trends. This article focuses on the evolution and current utility of research surveys, different methodologies employed in their creation, the advantages and disadvantages of different forms and their future use in healthcare research. We also review the role artificial intelligence and the importance of increased patient participation in the development of these surveys in order to obtain more accurate and clinically relevant data

Gastrointestinal tuberculosis: Diagnostic approaches for this uncommon pathology.

A case report entitled "Primary gastroduodenal tuberculosis presenting as gastric outlet obstruction" recently published in the World Journal of Clinical Cases presented a rare cause of gastric outlet obstruction and highlighted the atypical manner in which gastrointestinal tuberculosis (TB) can present. The literature with regards to this rare pathology is limited to case reports and case series with the largest being published using data from between 2003 and 2013. However, since then the diagnostic tools available have significantly changed with more modern and increasingly accurate tests now available. This editorial reviews the current state of the art with regards to diagnosis in gastrointestinal TB

Biobanks and biomarkers: Their current and future role in biomedical research.

The importance and utility of biobanks has increased exponentially since their inception and creation. Initially used as part of translational research, they now contribute over 40% of data for all cancer research papers in the United States of America and play a crucial role in all aspects of healthcare. Multiple classification systems exist but a simplified approach is to either classify as population-based or disease-oriented entities. Whilst historically publicly funded institutions, there has been a significant increase in industry funded entities across the world which has changed the dynamic of biobanks offering new possibilities but also new challenges. Biobanks face legal questions over data sharing and intellectual property as well as ethical and sustainability questions particularly as the world attempts to move to a low-carbon economy. International collaboration is required to address some of these challenges but this in itself is fraught with complexity and difficulty. This review will examine the current utility of biobanks in the modern healthcare setting as well as the current and future challenges these vital institutions face

Impact of gender identity in the inflammatory bowel disease population: an evidence review and practical steps for gastroenterologists

There has been greater societal awareness of differences in gender identity and sexual orientation in recent years. The rates of identifying as transgender or gender non-conforming (TGNC) are increasing and are known to be higher in the younger population and will therefore be over-represented in the inflammatory bowel disease (IBD) subpopulation. However, despite this there is very little in the literature with regards to those who identify as TGNC and are diagnosed with IBD (TGNC-IBD). Many TGNC individuals have poor experiences when seeking healthcare and many physicians find it a challenging and daunting clinical situation to be faced with. We reviewed the available literature with regards to TGNC-IBD population demographics, physical, mental and sexual health considerations, medication interactions and implications for surgery in this heterogenous group. We have identified areas that need further research and suggested simple and practical steps that can be adopted in order to help healthcare providers improve the experience for TGNC individuals diagnosed with IBD and the quality of care they provide

Using clinical cases to guide healthcare.

Evidence-based practice (EBP) has been the gold standard in healthcare for nearly three centuries and aims to assist physicians in providing the safest and most effective healthcare for their patients. The well-established hierarchy of evidence lists systematic reviews and meta-analyses at the top however these methodologies are not always appropriate or possible and in these instances case-control studies, case series and case reports are utilised to support EBP. Case-control studies allow simultaneous study of multiple risk factors and can be performed rapidly and relatively cheaply. A recent example was during the Coronavirus pandemic where case-control studies were used to assess the efficacy of personal protective equipment for healthcare workers. Case series and case reports also play a role in EBP and are particularly useful to study rare diseases such as inflammatory bowel disease in transgender and gender non-conforming individuals. They are also vital in generating and disseminating early signals and encouraging further research. Whilst these methodologies have weaknesses, particularly with regards to bias and loss of patient confidentiality for rare pathologies, they have an important part to play in EBP and when appropriately utilised can significantly impact upon clinical practice

Patient experiences of gender identity and inflammatory bowel disease: a focus group study

Objective Individuals who identify as transgender or gender non-conforming (TGNC) number approximately 262 000 in England and Wales. However, they are under-represented in healthcare research and little is known about their experiences managing a chronic health condition and their unique needs. Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract which can lead to long-term complications such as surgery and colorectal cancer. Ensuring a positive patient experience is crucial to maintaining good adherence with medical therapy and compliance with regular invasive surveillance procedures to reduce the risks of these occurring. However, there is no data on the experiences of people who identify as TGNC and who suffer from IBD (TGNC-IBD) when engaging with IBD healthcare services. Our focus group aimed to provide qualitative data on the experiences of this population. Methods Following established qualitative research processes, and through work with Crohn’s and Colitis UK, we held a focus group with TGNC-IBD to gain, for the first time in the UK, patient-centred insight into their experiences engaging with IBD services and highlight areas that need improving. Results Common themes identified were healthcare professionals making assumptions regarding gender identity, poor mental health support, a lack of research into TGNC-IBD and poor facilities. Conclusion The findings underscore the need for improved training for healthcare providers and modification to IBD services as well as further research to address the unique needs of TGNC-IBD

Towards NHS Zero: greener gastroenterology and the impact of virtual clinics on carbon emissions and patient outcomes. A multisite, observational, cross-sectional study

OBJECTIVE: The National Health Service (NHS) produces more carbon emissions than any public sector organisation in England. In 2020, it became the first health service worldwide to commit to becoming carbon net zero, the same year as the COVID-19 pandemic forced healthcare systems globally to rapidly adapt service delivery. As part of this, outpatient appointments became largely remote. Although the environmental benefit of this change may seem intuitive the impact on patient outcomes must remain a priority. Previous studies have evaluated the impact of telemedicine on emission reduction and patient outcomes but never before in the gastroenterology outpatient setting. METHOD: 2140 appointments from general gastroenterology clinics across 11 Trusts were retrospectively analysed prior to and during the pandemic. 100 consecutive appointments during two periods of time, from 1 June 2019 (prepandemic) to 1 June 2020 (during the pandemic), were used. Patients were telephoned to confirm the mode of transport used to attend their appointment and electronic patient records reviewed to assess did-not-attend (DNA) rates, 90-day admission rates and 90-day mortality rates. RESULTS: Remote consultations greatly reduced the carbon emissions associated with each appointment. Although more patients DNA their remote consultations and doctors more frequently requested follow-up blood tests when reviewing patients face-to-face, there was no significant difference in patient 90-day admissions or mortality when consultations were remote. CONCLUSION: Remote consultations greatly reduced the carbon emissions associated with each appointment. Although more patients DNA their remote consultations and doctors more frequently requested follow-up blood tests when reviewing patients face-to-face, there was no significant difference in patient 90-day admissions or mortality when consultations were remote