Defining and benchmarking open problems in single-cell analysis.

With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. However, a lack of standardisation and extensibility in current benchmarks limits their usability, longevity, and relevance to the community. We present Open Problems, a living, extensible, community-guided benchmarking platform including 10 current single-cell tasks that we envision will raise standards for the selection, evaluation, and development of methods in single-cell analysis.

Squidpy: a scalable framework for spatial omics analysis.

Spatial omics data are advancing the study of tissue organization and cellular communication at an unprecedented scale. Flexible tools are required to store, integrate and visualize the large diversity of spatial omics data. Here, we present Squidpy, a Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins. Squidpy provides efficient infrastructure and numerous analysis methods that allow to efficiently store, manipulate and interactively visualize spatial omics data. Squidpy is extensible and can be interfaced with a variety of already existing libraries for the scalable analysis of spatial omics data.

CellRank for directed single-cell fate mapping.

Computational trajectory inference enables the reconstruction of cell state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its application to differentiating systems in normal development. Here, we present CellRank ( https://cellrank.org ) for single-cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease, for which direction is unknown. Our approach combines the robustness of trajectory inference with directional information from RNA velocity, taking into account the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in velocity vectors. On pancreas development data, CellRank automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage-traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes. CellRank also predicts a new dedifferentiation trajectory during postinjury lung regeneration, including previously unknown intermediate cell states, which we confirm experimentally.

Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.

Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources covering interactions and roles of proteins in inter- and intracellular signaling, as well as transcriptional and post-transcriptional regulation. We added protein complex information and annotations on function, localization, and role in diseases for each protein. The resource is available for human, and via homology translation for mouse and rat. The data are accessible via OmniPath's web service (https://omnipathdb.org/), a Cytoscape plug-in, and packages in R/Bioconductor and Python, providing access options for computational and experimental scientists. We created workflows with tutorials to facilitate the analysis of cell-cell interactions and affected downstream intracellular signaling processes. OmniPath provides a single access point to knowledge spanning intra- and intercellular processes for data analysis, as we demonstrate in applications studying SARS-CoV-2 infection and ulcerative colitis.

Child restraint safety practices among Arab children in Israel.

OBJECTIVE: Because the rate of injury and mortality from car crashes among Arab children is higher than among Jewish children in Israel, this study assesses the patterns of age-appropriate child restraint system (CRS) use in Arab towns in Israel. METHODS: From October 2010 to September 2011, 4396 children ages 0 to 14 were observed while seated in vehicles in 9 Arab towns and villages in Israel. RESULTS: Among infants aged 0 to 1 year old, 31.2 percent were observed in an age-appropriate restraint, whereas among children aged 1 to 4 years, only 12.4 percent were age-appropriately restrained. Children aged 5 to 9 were observed to have the lowest levels of age-appropriate restraint use (1.3%). The variation between the various villages was large and dependent on the age of the child. CONCLUSIONS: The low rates of CRS use may explain to some degree the high rates of injury and mortality of Arab children in car crashes. These low rates indicate that previous interventions have not been successful in increasing restraint use in the Arab community in Israel and there is a need to plan targeted interventions specifically for this population. Supplemental materials are available for this article. Go to the publisher's online edition of Traffic Injury Prevention to view the supplemental file.

[Childhood injuries in Israel--current status and the role of the community pediatrician].

In Israel, as in other developed countries, injury is a major problem in children's health. Injuries are a main cause of morbidity and mortality of children in all age groups, both genders, Jews and Arabs and is also a Leading cause of disability and loss of potential life years. In Israel, every year injuries account for 144 child deaths, approximately 24,000 hospitalizations and about 182,000 ED visits, and it is estimated that about half of all Israeli children sustain an injury requiring primary medical care in the community. The vast majority of those injuries are unintentional. The leading cause of child death from injury is traffic accidents, while home and Leisure accidents are common causes for children's hospitalization due to injury. The death rate is higher among children from low socioeconomic clusters compared to high socioeconomic clusters. Between 2000 and 2008, there was a decrease in child death rates from injury and unintentional injury. Intervention programs involving the safety education of parents by community pediatricians showed effectiveness in increasing safe behaviors and prevention of child injuries. In Israel several programs for injury prevention are implemented in the health system, including parents' education in well-baby clinics for child safety by nurses. Since the community pediatrician is a significant factor in parents' decisions regarding their child's health, it is recommended that he will also educate them concerning child injury prevention.

[The rationale for promotion of bicycle helmet legislation for children up to 18 years].

BACKGROUND: Each year, many children suffer from injuries caused by bicycles, scooters, skateboards, and roller skates accidents. Head injury is the most common cause of death and serious disability in bicycle-related crashes. In various studies the use of bicycle helmets has been proven to be the most effective measure in preventing head injury: the use of bicycle helmets reduced the risk of head and brain injury by 85-88%. Legislation that mandates the use of helmets has been shown to effectively increase helmet use and, therefore, significantly decrease head injuries among riders. COST-BENEFIT: Legislation requiring helmets will save $44.2 million (direct benefit) to society over a 5-year period, and save approximately 57 lives, 2,544 hospitalizations, and 13,355 emergency room visits. BICYCLE-RELATED DEATHS AND INJURIES IN ISRAEL: Data from trauma registry of 10 hospitals of the Israeli Center for Trauma and Emergency Medicine research indicate that 649 children ages 17 years and under were injured in a bicycle-related accidents (58-serious, 77-medium injury). Bicycle-related injuries accounted for approximately 33% of motor vehicle accidents among children ages 17 years and under. LEGISLATION: Many countries have legislation requiring helmets for riders. In Israel, there is no law requiring helmets. On a telephone survey, conducted by 'Beterem', a high support rate for a law requiring bicycle helmets (89%) was found among parents to children up to 15 years of age. Based on the evidence of the effectiveness of helmets as a means for reducing head injuries in cyclists, and the importance of a law to this effect, the medical community in Israel should act to promote the legislation requiring helmets for children on bicycles, scooters, skateboards, roller skates, and rollerblades.

[Parents' risk perception and analysis of children's injuries scenarios from cold fat removers].

BACKGROUND: Cold fat removers cause serious injuries to children. OBJECTIVES: (1) To examine the knowledge, awareness and reported behaviors of parents concerning cold fat removers and to follow trends over time, before and after an intervention program. (2) To learn the common scenarios of injuries from cold fat removers in order to deepen the understanding of their occurrence and to promote prevention activities. METHODOLOGY: (1) Three telephone surveys of a representative sample of parents of children under the age of 15 years in the Jewish population were conducted during the period January 2004-June 2006. The sampling was performed in two stages: a stratified sample and a random sample in each layer. Results were analyzed in accordance with the children's age and the socio-demographic characteristics of the families. (2) Analysis of the children's injuries scenarios from cold fat removers of hospitalized children was conducted. The scenarios were collected from seven hospitals in Israel during January 2004-June 2006. RESULTS: The percentage of parents that were aware of the danger of ingestion of cold fat removers was significantly higher in June 2005 (40%) in comparison to January 2004 (22%). Only half of the sampled parents in January 2005 (53%) were aware of the fact that body contact with cold fat removers is more dangerous than bleach. About two thirds of sampled parents in June 2005 stated that they store their detergents in a safe place: 46.5% of parents store their detergents on a high shelf and 18% store them in a locked place. Thirteen scenarios of children's injuries due to cold fat removers were analyzed. The results showed that most injuries were at home, and that the main failures were due to human factors, underestimation of danger and a combination of these factors. Most of the injuries occurred both to infants and toddlers under 4 years of age and also in young children (6-8 years old); half of the scenarios occurred in the Arab population. CONCLUSIONS: A positive trend in parents' awareness of the danger of cold fat removers was observed. This trend was noted over the same period of time that the intervention program conducted by Beterem and the Israeli Ministry of Health took place. Yet, we cannot determine in certainty that this positive trend was due to the intervention program. Intervention programs implemented through health professionals, changes in the product and research and evaluation should be continued and promoted.

Child injury in Israel: emergency room visits to a children's medical center.

The object of this study was to provide data for policy making and prevention program planning in Israel. The study examined all visits to the Department of Emergency Medicine at the Schneider Children's Medical Center in 1996 (41,279 visits in total). Approximately 22.6% of the emergency room patients were admitted following injury. Most (97%) were unintentional injury. Approximately 42% of the patients were less than 4 years old and about 20% were 2 years old. In all age groups, the rate of boys was double. Approximately 92% were Jews. Despite this low rate of non-Jewish patients, however, they constituted 20% of later hospitalizations. The main injuries recorded were bruises and wounds from blunt objects, falls, motor vehicle-related accidents, and sport injuries. The most commonly injured body parts were the head and upper and lower limbs. In 82%, medical treatment was reported and 7% were hospitalized. In examining injuries over the year, there were no significant differences between the different months, but there were clusters of injuries around various holidays--bicycle and skateboard accidents at Rosh Hashanah, Yom Kippur, and Succoth; pedestrian accidents around Lag BaOmer; burns on Purim, Hannukkah, and Passover; and accidental poisoning around Passover. The findings gave an indication of the nature of the injured population groups. These data could be useful for prevention strategy, both on the level of physical injury as well as on the level of the times of the year, when the risk was higher. The data collected very strongly raise the urgent need for establishing a national surveillance system, which would allow tracking injury-related data with respect to young people throughout the country.