OnTarget: in silico design of MiniPromoters for targeted delivery of expression.

MiniPromoters, or compact promoters, are short DNA sequences that can drive expression in specific cells and tissues. While broadly useful, they are of high relevance to gene therapy due to their role in enabling precise control of where a therapeutic gene will be expressed. Here, we present OnTarget (http://ontarget.cmmt.ubc.ca), a webserver that streamlines the MiniPromoter design process. Users only need to specify a gene of interest or custom genomic coordinates on which to focus the identification of promoters and enhancers, and can also provide relevant cell-type-specific genomic evidence (e.g. accessible chromatin regions, histone modifications, etc.). OnTarget combines the provided data with internal data to identify candidate promoters and enhancers and design MiniPromoters. To illustrate the utility of OnTarget, we designed and characterized two MiniPromoters targeting different cell populations relevant to Parkinson Disease.

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper.

Across the life sciences, processing next generation sequencing data commonly relies upon a computationally expensive process where reads are mapped onto a reference sequence. Prior to such processing, however, there is a vast amount of information that can be ascertained from the reads, potentially obviating the need for processing, or allowing optimized mapping approaches to be deployed. Here, we present a method termed FlexTyper which facilitates a "reverse mapping" approach in which high throughput sequence queries, in the form of k-mer searches, are run against indexed short-read datasets in order to extract useful information. This reverse mapping approach enables the rapid counting of target sequences of interest. We demonstrate FlexTyper's utility for recovering depth of coverage, and accurate genotyping of SNP sites across the human genome. We show that genotyping unmapped reads can correctly inform a sample's population, sex, and relatedness in a family setting. Detection of pathogen sequences within RNA-seq data was sensitive and accurate, performing comparably to existing methods, but with increased flexibility. We present two examples of ways in which this flexibility allows the analysis of genome features not well-represented in a linear reference. First, we analyze contigs from African genome sequencing studies, showing how they distribute across families from three distinct populations. Second, we show how gene-marking k-mers for the killer immune receptor locus allow allele detection in a region that is challenging for standard read mapping pipelines. The future adoption of the reverse mapping approach represented by FlexTyper will be enabled by more efficient methods for FM-index generation and biology-informed collections of reference queries. In the long-term, selection of population-specific references or weighting of edges in pan-population reference genome graphs will be possible using the FlexTyper approach. FlexTyper is available at https://github.com/wassermanlab/OpenFlexTyper.

BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data.

CONCLUSION: BEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of microbiome data.

GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases.

Mendelian rare genetic diseases affect 5%-10% of the population, and with over 5300 genes responsible for ∼7000 different diseases, they are challenging to diagnose. The use of whole-genome sequencing (WGS) has bolstered the diagnosis rate significantly. The effective use of WGS relies on the ability to identify the disrupted gene responsible for disease phenotypes. This process involves genomic variant calling and prioritization, and is the beneficiary of improvements to sequencing technology, variant calling approaches, and increased capacity to prioritize genomic variants with potential pathogenicity. As analysis pipelines continue to improve, careful testing of their efficacy is paramount. However, real-life cases typically emerge anecdotally, and utilization of clinically sensitive and identifiable data for testing pipeline improvements is regulated and limiting. We identified the need for a gene-based variant simulation framework that can create mock rare disease scenarios, utilizing known pathogenic variants or through the creation of novel gene-disrupting variants. To fill this need, we present GeneBreaker, a tool that creates synthetic rare disease cases with utility for benchmarking variant calling approaches, testing the efficacy of variant prioritization, and as an educational mechanism for training diagnostic practitioners in the expanding field of genomic medicine. GeneBreaker is freely available at http://GeneBreaker.cmmt.ubc.ca.

Force-Feeding and Resuscitation of Patients with Advanced Dementia: A Public Opinion Study.

BACKGROUND: The treatment of advanced dementia patients is very complex and presents a difficult dilemma for physicians, and especially for the patient's family. In many cases, when the advanced dementia patient has no decisional capacity, the family needs to decide about force-feeding and resuscitation for their relative. OBJECTIVES: To examine public opinion regarding force-feeding and resuscitation of patients with advanced dementia. METHODS: Data from 1002 people who accompanied a patient to a hospital emergency department in Israel were collected and analyzed. RESULTS: We noted the following results: the more religious the orientation of the respondents, the more likely they were to agree to forcefully feed and resuscitate advanced dementia patients and advanced dementia patients older than 80 years; those accompanying younger patients were more likely to think that the medical staff should resuscitate advanced dementia patients and advanced dementia patients older than 80 years compared to those accompanying elderly patients; younger people were more likely than older people to agree to force-feed and resuscitate patients. CONCLUSIONS: This paper attempts to provide decision-makers and medical staff with some knowledge about public opinion regarding a sensitive and complex issue. This awareness may guide physicians in making critical medical decisions about those with dementia.

[Use of a structured integrative oncology evaluation as a tool to improve patient adherence to a complementary medicine treatment program].

BACKGROUND: The introduction of a quality of life (QOL)-centered complementary medicine (CM) consultation over the past decade has been integrated within various oncology departments in Israel and around the globe. The consultation is provided by an integrative physician (IP) trained in CM who recommends treatment options attuned with patients' expectations, concerns and QOL, while taking safety and efficacy into consideration. OBJECTIVE: To identify, based on the initial IP consultation, factors predicting patients' compliance to a QOL-oriented integrative treatment. METHODS: Analysis of demographic data was conducted, together with an assessment of patients' concerns and well-being as documented in a registry protocol. Dependent and non-dependent factors were compared in two groups of patients: those with a low and a high degree of adherence to the integrative consultation. RESULTS: Patients in the low- and high-adherence groups (83 and 160, respectively) shared similar demographic, disease- and treatment-related, as well as QOL-dependent data. Adherence to the CM treatments was higher in patients reporting prior CM use, and in patients with less severe gastro-intestinal complaints. IP assessment regarding patients' difficulties in undergoing the CM treatment process predicted low patient adherence. CONCLUSIONS: We recommend including an initial IP assessment of patients undergoing chemotherapy, using a structured assessment in order to identify the following factors predicting low adherence to a CM treatment program: absence of prior CM use, severe gastro-intestinal symptoms, and IP assessment of expected difficulties in implementing the treatment plan.

Assessing patient adherence to a complementary medicine treatment regimen in an integrative supportive care setting.

INTRODUCTION: Patients with cancer are frequently turning to complementary medicine (CM), often with the goal of improving quality of life outcomes. The purpose of the present study was to assess the adherence of patients referred by oncology practitioners to a CM consultation and treatment program. PATIENTS AND METHODS: A prospective registry protocol-based, preference study was conducted at a conventional oncology department. Patients undergoing chemotherapy were referred by participating oncology practitioners to a CM-trained integrative physician (IP) for consultation. Adherence to the integrative care (AIC) program was defined as attendance by patients at ≥4 CM treatment sessions, with an interval of no more than 30 days between each session. RESULTS: A total of 282 patients were referred by the study health-care professionals (HCPs), of whom 243 (85.8%) were eventually seen by the study IP. Of these, 160 were found to be adherent to the treatment plan (AIC group), and 83 were nonadherent (non-AIC group). No significant differences were found between the two groups with respect to demographic characteristics, medical history, site of malignancy and/or recurrence, chemotherapy regimen, or severity of symptoms at baseline. The AIC group reported significantly greater rates of CM use for noncancer-related indications than the non-AIC group (EXP(B)=2.174, 95% confidence interval (C.I.)=1.1­4.295, p =0.025). Patients in the non-AIC group were referred more frequently by their HCP for gastrointestinal concerns than those in the AIC group (p =0.022). CONCLUSIONS: Previous use of CM for noncancer-related outcomes was found to be predictive of patient adherence to a CM treatment regimen provided within conventional oncology service.

Evaluation of Telephone Visits in Primary Care: Satisfaction of Pediatricians and Family Physicians and Their Perceptions of Quality of Care and Safety.

Telehealth has accelerated since the outbreak of the COVID-19 virus. As telephone visits become more common, it is important to examine the challenges involved in using this modality of care. In this study, we examined family physicians' and pediatricians' perceptions regarding three aspects of the use of telephone visits: quality of care, safety of care, and physicians' satisfaction. A total of 342 family physicians and pediatricians responded to an online survey. Respondents were asked to rate their degree of agreement with 17 statements inquiring about quality, safety, and satisfaction with telephone visits on a Likert scale ranging from 1 (strongly disagree) to 5 (strongly agree). This was followed by in-depth interviews between January and April 2023 with 26 physicians. Participants expressed satisfaction (3.66 ± 0.80) with the use of telephone visits and lower assessments of safety (3.03 ± 0.76) and quality (2.27 ± 0.76) of care using the telephone modality. Eighty percent of the respondents think combining a face-to-face visit with a telephone visit is recommended, and 51% noted that the inability to examine patients closely affects and impedes a physician's decision making. Most interviewees indicated that telephone visits are safe only with former patients they had already seen in the clinic. The findings shed light on the perceptions of family physicians and pediatricians regarding telephone visits. The lower assessments of quality and safety compared to the assessment of satisfaction underscore the need for careful use of telephone visits in healthcare. A proper and balanced selection of patients, implementing technological upgrades to the modality, and performing patient education practices are recommended.

Towards integrative plant pathology.

The field of plant pathology has revealed many of the mechanisms underlying the arms race, providing crucial knowledge and genetic resources for improving plant health. Although the host-microbe interaction seemingly favors rapidly evolving pathogens, it has also generated a vast evolutionary history of largely unexplored plant immunodiversity. We review studies that characterize the scope and distribution of genetic and ecological diversity in model and non-model systems with specific reference to pathogen effector diversity, plant immunodiversity in both cultivated species and their wild relatives, and diversity in the plant-associated microbiota. We show how the study of evolutionary and ecological processes can reveal patterns of genetic convergence, conservation, and diversification, and that this diversity is increasingly tractable in both experimental and translational systems. Perhaps most importantly, these patterns of diversity provide largely untapped resources that can be deployed for the rational engineering of durable resistance for sustainable agriculture.

Barriers to integration of traditional and complementary medicine in supportive cancer care of arab patients in northern Israel.

In 2008, an Integrative Oncology Program (IOP), aiming to improve patients' quality of life during chemotherapy and advanced cancer, was launched within the Clalit Health Organization's oncology service at the Lin Medical Center, Haifa, Israel. The IOP clinical activity is documented using a research-based registry protocol. In this study, we present an analysis of the registry protocol of 15 Arab patients with cancer who were referred to the IOP. Analysis of patients' reported outcomes using the Edmonton Symptom Assessment Scale suggests that integrative medicine care improves fatigue (P = 0.024), nausea (P = 0.043), depression (P = 0.012), anxiety (P = 0.044), appetite (P = 0.012), and general well-being (P = 0.031). Barriers to integration of traditional and complementary medicine in supportive care of Arab patients are discussed followed by six practical recommendations aimed at improving accessibility of patients to integrative supportive care, as well as compliance with treatments.

Informed consent in complementary and alternative medicine.

The objective of this study was to examine complementary and alternative medicine (CAM) practitioners' (i) attitudes toward informed consent and (ii) to assess whether standards of practice exist with respect to informed consent, and what these standards look like. The design and setting of the study constituted face-to-face qualitative interviews with 28 non-MD, community-based providers representing 11 different CAM therapeutic modalities. It was found that there is great deal of variability with respect to the informed consent process in CAM across providers and modalities. No unique profession-based patterns were identified. The content analysis yielded five major categories related to (i) general attitude towards the informed consent process, (ii) type and amount of information exchange during that process, (iii) disclosure of risks, (iv) discussions of alternatives, and (v) potential benefits. There is a widespread lack of standards with respect to the practice of informed consent across a broad range of CAM modalities. Addressing this problem requires concerted and systematic educational, ethical and judicial remedial actions. Informed consent, which is often viewed as a pervasive obligation is medicine, must be reshaped to have therapeutic value. Acknowledging current conceptions and misconception surrounding the practice of informed consent may help to bring about this change. More translational research is needed to guide this process.

[Integrating complementary medicine in oncology supportive care: assessment of patients' needs and expectations during chemotherapy].

BACKGROUND: During the Last decade complementary medicine is gradually being integrated within conventional oncology care in Western countries. In 2008, an integrative oncology program was implemented within the Clalit Oncology Service (COS) of the Haifa and Western-Galilee district of Clalit Health Organization aiming to promote patients' well-being during chemotherapy and in advanced disease. OBJECTIVE: To identify needs and distress of patients with regard to combining complementary medicine with the supporting treatment for improvement of quality of life. METHODS: A study using semi-constructed interviews with 31 patients during chemotherapy was performed at two outpatient oncology centers of the Clalit HMO in northern Israel. RESULTS: Most participants reported significant deterioration in their quality of life during chemotherapy, mainly related to fatigue, work cessation and mood disorder. Interest in complementary medicine significantly correlated with the participants' awareness of the mind-body connection. Most participants reported on their interest to consult with physicians specializing in complementary medicine as an integral part of the oncology service care. The most favorable complementary therapies reported by patients were nutritional counseling, herbal medicine and traditional healing. CONCLUSIONS: Asking patients during chemotherapy on their beliefs regarding mind and body connections may be used as a screening question to identify patients interested in experiencing complementary therapies. Integrating physician counseling regarding complementary medicine within the oncology service may address patients' needs and concerns by matching therapies to specific symptoms and chemotherapy side-effects.

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data.

BACKGROUND: The dynamics of microbial communities is driven by a range of interactions from symbiosis to predator-prey relationships, the majority of which are poorly understood. With the increasing availability of high-throughput microbiome taxonomic profiling data, it is now conceivable to directly learn the ecological models that explicitly define microbial interactions and explain community dynamics. The applicability of these approaches is severely limited by the lack of accurate absolute cell density measurements (biomass). METHODS: We present a new computational approach that resolves this key limitation in the inference of generalized Lotka-Volterra models (gLVMs) by coupling biomass estimation and model inference with an expectation-maximization algorithm (BEEM). RESULTS: BEEM outperforms the state-of-the-art methods for inferring gLVMs, while simultaneously eliminating the need for additional experimental biomass data as input. BEEM's application to previously inaccessible public datasets (due to the lack of biomass data) allowed us to construct ecological models of microbial communities in the human gut on a per-individual basis, revealing personalized dynamics and keystone species. CONCLUSIONS: BEEM addresses a key bottleneck in "systems analysis" of microbiomes by enabling accurate inference of ecological models from high throughput sequencing data without the need for experimental biomass measurements.

My brain knows numbers! - an ERP study of preschoolers' numerical knowledge.

This study investigated brain activity in numerical processing at early stages of development. Brain activity of preschoolers was measured while they performed a numerical Stroop task. Participants were asked to decide which of two digits was numerically or physically larger. Behavioral distance and size congruity effects (SiCEs) were found. However, a reverse facilitation was observed, where responses to neutral trials were faster than to congruent ones. The event-related potentials data showed the expected distance effect at occipitoparietal scalp areas. Moreover, conflict was related to effects both at frontal and parietal scalp areas. In addition, there was a difference between the timing of the interference compared to the facilitation components in the SiCE. In parietal scalp areas, facilitation was significant in an early time window and interference was significant at a later time window. This is consistent with the idea that facilitation and interference are separate processes. Our findings indicate that children as young as 5-6 years old can automatically process the numerical meaning of numerals. In addition, our findings are consistent with the idea that, children might use both frontal and parietal areas in order to process irrelevant numerical information.

Modeling an integrative oncology program within a community-centered oncology service in Israel.

OBJECTIVE: Describing the processes that preceded the opening of an integrative oncology program (IOP) within the oncology service (OS) of the largest health maintenance organization in northern Israel. METHODS: The groundwork towards initiation of the IOP was based on three key elements (1) Interviews with patients, practitioners and directors were performed in order to explore perspectives regarding complementary medicine integration (CM) within the OS; (2) review of research data on CM efficacy and safety in cancer care; (3) critical comparative analysis of seven models of IOPs in Israel, Europe, and the U.S. RESULTS: Ninety-three interviews included 24 patients, 34 conventional practitioners, 9 medical directors, and 26 CM-trained practitioners. The interviews revealed that there is a need for CM in the OS, aimed towards improving patients' well-being during chemotherapy and advanced disease. An integrative oncology score (IOS) was formulated based on 6 themes considered promoters of successful integration. CONCLUSIONS: Integration of CM within an oncology service should address patients' needs and research knowledge and be built upon mandatory practitioners' communication. PRACTICE IMPLICATIONS: IOP modeling necessitates in-depth study aimed at revealing the OS needs and expectations, adjusting research data to the OS clinical challenges, and tailoring an appropriate model of integrative care.