Project description:Single-cell RNA-seq suffers from unwanted technical variation between cells, caused by its complex experiments and shallow sequencing depths. We present GTestimate a new normalization method based on the Good-Turing estimator, which improves upon conventional methods by accounting for unobserved genes. We validate GTestimate using new ultra-deep sequencing data, generated via a novel cell targeted PCR-amplification approach, and show substantial improvements in cell-cell distance estimation and downstream results.
Project description:Despite many recent advances on cancer novel therapies, researchers have yet a long way to cure cancer. They have to deal with tough challenges before they can reach success. Nonetheless, it seems that recently developed immunotherapy-based therapy approaches such as adoptive cell transfer (ACT) have emerged as a promising therapeutic strategy against various kinds of tumors even the cancers in the blood (liquid cancers). The hematological (liquid) cancers are hard to be targeted by usual cancer therapies, for they do not form localized solid tumors. Until recently, two types of ACTs have been developed and introduced; tumor-infiltrating lymphocytes (TILs) and chimeric antigen receptor (CAR)-T cells which the latter is the subject of our discussion. It is interesting about engineered CAR-T cells that they are genetically endowed with unique cancer-specific characteristics, so they can use the potency of the host immune system to fight against either solid or liquid cancers. Multiple myeloma (MM) or simply referred to as myeloma is a type of hematological malignancy that affects the plasma cells. The cancerous plasma cells produce immunoglobulins (antibodies) uncontrollably which consequently damage the tissues and organs and break the immune system function. Although the last few years have seen significant progressions in the treatment of MM, still a complete remission remains unconvincing. MM is a medically challenging and stubborn disease with a disappointingly low rate of survival rate. When comparing the three most occurring blood cancers (i.e., lymphoma, leukemia, and myeloma), myeloma has the lowest 5-year survival rate (around 40%). A low survival rate indicates a high mortality rate with difficulty in treatment. Therefore, novel CAR-T cell-based therapies or combination therapies along with CAT-T cells may bring new hope for multiple myeloma patients. CAR-T cell therapy has a high potential to improve the remission success rate in patients with MM. To date, many preclinical and clinical trial studies have been conducted to investigate the ability and capacity of CAR T cells in targeting the antigens on myeloma cells. Despite the problems and obstacles, CAR-T cell experiments in MM patients revealed a robust therapeutic potential. However, several factors might be considered during CAR-T cell therapy for better response and reduced side effects. Also, incorporating the CAT-T cell method into a combinational treatment schedule may be a promising approach. In this paper, with a greater emphasis on CAR-T cell application in the treatment of MM, we will discuss and introduce CAR-T cell's history and functions, their limitations, and the solutions to defeat the limitations and different types of modifications on CAR-T cells.
Project description:Direct targeting of oncogenic MYC proteins has been an elusive goal of many cancer drug development efforts. In this issue of Cancer Discovery, Stegmaier and colleagues demonstrate that pharmacologically interfering with the bromodomain and extraterminal (BET) class of proteins potently depletes MYCN in neuroblastoma cells, resulting in cellular cytotoxicity and thus providing a novel approach with a potential impact on a previously undruggable major oncogene.
Project description:Throughout the COVID-19 pandemic, governments and individuals have attempted a wide variety of strategies to limit the damage of the pandemic on human lives, population health, and economies. Contact tracing has been a commonly used strategy, and various approaches have been proposed and attempted. We summarise some methods of contact tracing and testing, considering the resources demanded by each and how features of SARS-CoV-2 transmission affect their effectiveness. We also propose an approach focusing on tracing transmission events, which can be particularly effective when superspreading events play a large role in transmission. Accounting for the best available evidence on a pathogen and for the availability of resources can make control strategies more effective, even if they are not perfect.
Project description:In 2002, Shlaes and Moellering warned that pharmaceutical companies were abandoning antibiotic research and development due to changing regulatory standards regarding noninferiority (NI) clinical trials. NI trials are subject to unique biases that may yield false-positive conclusions. The US Food and Drug Administration (FDA) developed guidance to ensure that NI results truly reflect drug efficacy. These changes, intended to reduce uncertainty in trial results, have shaped trial enrollment and conduct in ways that now require reflection.
Project description:More than 50 million cattle are likely exposed to bovine tuberculosis (bTB) worldwide, highlighting an urgent need for bTB control strategies in low- and middle-income countries (LMICs) and other regions where the disease remains endemic and test-and-slaughter approaches are unfeasible. While Bacillus Calmette-Guérin (BCG) was first developed as a vaccine for use in cattle even before its widespread use in humans, its efficacy against bTB remains poorly understood. To address this important knowledge gap, we conducted a systematic review and meta-analysis to determine the direct efficacy of BCG against bTB challenge in cattle, and performed scenario analyses with transmission dynamic models incorporating direct and indirect vaccinal effects ("herd-immunity") to assess potential impact on herd level disease control. The analysis shows a relative risk of infection of 0.75 (95% CI: 0.68, 0.82) in 1,902 vaccinates as compared with 1,667 controls, corresponding to a direct vaccine efficacy of 25% (95% CI: 18, 32). Importantly, scenario analyses considering both direct and indirect effects suggest that disease prevalence could be driven down close to Officially TB-Free (OTF) status (<0.1%), if BCG were introduced in the next 10-year time period in low to moderate (<15%) prevalence settings, and that 50-95% of cumulative cases may be averted over the next 50 years even in high (20-40%) disease burden settings with immediate implementation of BCG vaccination. Taken together, the analyses suggest that BCG vaccination may help accelerate control of bTB in endemic settings, particularly with early implementation in the face of dairy intensification in regions that currently lack effective bTB control programs.
Project description:This state-of-the art manuscript highlights our current understanding of maternal immunization-the practice of vaccinating pregnant women to confer protection on them as well as on their young infants, and thereby reduce vaccine-preventable morbidity and mortality. Advances in our understanding of the immunologic processes that undergird a normal pregnancy, studies from vaccines currently available and recommended for pregnant women, and vaccines for administration in special situations are beginning to build the case for safe scale-up of maternal immunization. In addition to well-known diseases, new diseases are emerging which pose threats. Several new vaccines are currently under development and increasingly include pregnant women. In this manuscript, targeted at clinicians, vaccinologists, scientists, public health practitioners, and policymakers, we also outline key considerations around maternal immunization introduction and delivery, discuss noninfectious horizons for maternal immunization, and provide a framework for the clinician faced with immunizing a pregnant woman.
Project description:Introduction:Administrative data arising via the operation of public service delivery systems hold great benefits for citizens and society by enabling new research questions to be addressed, providing they can be made available in a safe, socially acceptable way. In recognition of this potential, the UK Administrative Data Research Network was established in 2013 to enable new research for public benefit. However, there are considerable challenges to be overcome for effective data use, and many of these are common to administrative data enterprises in general. Using this network as a practical case study, we set out to explore the issues and propose how to share the 'good', suggest solutions to the 'bad', and improve the 'clunky' issues, to lead to improvements in administrative data use. Methods:A qualitative survey representing the data use pathway was carried out across the network, followed by a workshop to discuss the summarised findings and make further suggestions. This led to a set of recommendations to inform the development of an action plan for implementation. Results:The survey respondents (N=27) and workshop participants (N=95) comprised multi disciplinary staff from across the network. The responses were summarised by consensus of three researchers and grouped into six areas: A) Data acquisition pathway; B) Approval processes; C) Controls on access & disclosure; D) Data and metadata; E) Researcher support; and F) Data reuse & retention, leading to an embedded set of 18 recommendations. Key developments promoted by this study were the development of themed research partnerships to progress data acquisition, and a policy of data retention and reuse for research. Conclusions:The network has broken new ground in using administrative data for research. This study informed the development of an evidence-based action plan to address many challenges in the effective use of administrative data. It represents a practical worked example, and the learning is widely relevant to enterprises working with administrative data across the world.
Project description:Auditory spatial localization in humans is performed using a combination of interaural time differences, interaural level differences, as well as spectral cues provided by the geometry of the ear. To render spatialized sounds within a virtual reality (VR) headset, either individualized or generic Head Related Transfer Functions (HRTFs) are usually employed. The former require arduous calibrations, but enable accurate auditory source localization, which may lead to a heightened sense of presence within VR. The latter obviate the need for individualized calibrations, but result in less accurate auditory source localization. Previous research on auditory source localization in the real world suggests that our representation of acoustic space is highly plastic. In light of these findings, we investigated whether auditory source localization could be improved for users of generic HRTFs via cross-modal learning. The results show that pairing a dynamic auditory stimulus, with a spatio-temporally aligned visual counterpart, enabled users of generic HRTFs to improve subsequent auditory source localization. Exposure to the auditory stimulus alone or to asynchronous audiovisual stimuli did not improve auditory source localization. These findings have important implications for human perception as well as the development of VR systems as they indicate that generic HRTFs may be enough to enable good auditory source localization in VR.