CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics

Evaluating assumptions of scales for subjective assessment of thermal environments – Do laypersons perceive them the way, we researchers believe?

International audienc

Ebola: translational science considerations

We are currently in the midst of the most aggressive and fulminating outbreak of Ebola-related disease, commonly referred to as “Ebola”, ever recorded. In less than a year, the Ebola virus (EBOV, Zaire ebolavirus species) has infected over 10,000 people, indiscriminately of gender or age, with a fatality rate of about 50%. Whereas at its onset this Ebola outbreak was limited to three countries in West Africa (Guinea, where it was first reported in late March 2014, Liberia, where it has been most rampant in its capital city, Monrovia and other metropolitan cities, and Sierra Leone), cases were later reported in Nigeria, Mali and Senegal, as well as in Western Europe (i.e., Madrid, Spain) and the US (i.e., Dallas, Texas; New York City) by late October 2014. World and US health agencies declared that the current Ebola virus disease (EVD) outbreak has a strong likelihood of growing exponentially across the world before an effective vaccine, treatment or cure can be developed, tested, validated and distributed widely. In the meantime, the spread of the disease may rapidly evolve from an epidemics to a full-blown pandemic. The scientific and healthcare communities actively research and define an emerging kaleidoscope of knowledge about critical translational research parameters, including the virology of EBOV, the molecular biomarkers of the pathological manifestations of EVD, putative central nervous system involvement in EVD, and the cellular immune surveillance to EBOV, patient-centered anthropological and societal parameters of EVD, as well as translational effectiveness about novel putative patient-targeted vaccine and pharmaceutical interventions, which hold strong promise, if not hope, to curb this and future Ebola outbreaks. This work reviews and discusses the principal known facts about EBOV and EVD, and certain among the most interesting ongoing or future avenues of research in the field, including vaccination programs for the wild animal vectors of the virus and the disease from global translational science perspective

Cortisol levels are related to neonatal pain exposure in children born very preterm at age 18 months in two independent cohorts

Abstract Exposure to pain‐related stress from frequent invasive procedures in the neonatal intensive care unit (NICU) has been associated with altered physiological stress regulation, neurodevelopment, and behavior in children born very preterm (≤32 weeks gestation). Previously, in a cohort born 2003–2006 (Cohort 1), we found that, at 18 months corrected age (CA), children born extremely low gestational age (ELGA; 24–28 weeks) and very low gestational age (VLGA; 29–32 weeks), had higher pre‐test cortisol levels and a different pattern of cortisol output across a developmental assessment involving cognitive challenge compared to children born full‐term (FT; 39–41 weeks). Also, greater neonatal pain‐related stress exposure among the preterm children was related to higher pre‐test cortisol levels. Given the adverse long‐term effects of neonatal pain in preterm infants and the ensuing rise in clinical concerns to appropriately manage pain in the NICU in recent years, we aimed to examine whether our findings from Cohort 1 would still be evident in an independent cohort (Cohort 2) born 2006–2011 and recruited from the same tertiary NICU in Vancouver, Canada. We also compared the cortisol patterns, clinical and socio‐demographic factors, and their interrelationships between the two cohorts. In Cohort 2, our findings using multi‐level modeling support and extend our earlier findings in Cohort 1, demonstrating that children born ELGA display higher pre‐test cortisol levels than FT. As well, greater cortisol output across assessment was related to more anxiety/depressive behaviors in children born VLGA. Importantly, children born ELGA were exposed to less neonatal pain/stress, mechanical ventilation, and morphine in Cohort 2 than Cohort 1. In both cohorts, however, cortisol levels and patterns were related to neonatal pain/stress and clinical factors (days on mechanical ventilation, overall morphine exposure). Despite less exposure to pain/stress and adverse clinical factors in Cohort 2 compared to Cohort 1, cortisol levels and patterns across cognitive challenge in preterm children at 18‐month CA were consistent across the two independent cohorts. These findings highlight that, despite improvements to neonatal care, children born extremely preterm continue to display altered HPA axis activity, which is associated with their poorer neurodevelopmental and behavioral outcomes

Cooling energy savings and occupant feedback in a two year retrofit evaluation of 99 automated ceiling fans staged with air conditioning

Funding Information: This research was supported by the California Energy Commission (CEC) Electric Program Investment Charge grant EPC-16-013, with cost share provided by Big Ass Fans, and cost share and additional support from Center for the Built Environment. We are thankful to many additional people who were involved in and contributed to this research project. At the CBE: Edward Arens, Fred Bauman, Wenhua Chen, Carlos Duarte, Yingdong He, Maohui Luo, Yang Li, Amy Mostacho, Jovan Pantelic, Tom Parkinson, Elaina Present, Stefano Schiavon, and Wang Zi. At TRC: Kristen Bellows and Abhijeet Pande. At the UC Berkeley Buildings, Energy, and Transportation Systems lab in the School of Electrical Engineering and Computer Science: Gabe Fierro and Michael Andersen for the Hamilton dataloggers and associated server. At Big Ass Fans: Jay Fizer, Michael Harp, Pete Maley, Justin Risner, Michael Smith, Christian Taber, Jayme Webb, Oleg Dantchenko, Funding Information: This research was supported by the California Energy Commission (CEC) Electric Program Investment Charge grant EPC-16-013, with cost share provided by Big Ass Fans, and cost share and additional support from Center for the Built Environment. We are thankful to many additional people who were involved in and contributed to this research project. At the CBE: Edward Arens, Fred Bauman, Wenhua Chen, Carlos Duarte, Yingdong He, Maohui Luo, Yang Li, Amy Mostacho, Jovan Pantelic, Tom Parkinson, Elaina Present, Stefano Schiavon, and Wang Zi. At TRC: Kristen Bellows and Abhijeet Pande. At the UC Berkeley Buildings, Energy, and Transportation Systems lab in the School of Electrical Engineering and Computer Science: Gabe Fierro and Michael Andersen for the Hamilton dataloggers and associated server. At Big Ass Fans: Jay Fizer, Michael Harp, Pete Maley, Justin Risner, Michael Smith, Christian Taber, Jayme Webb, Oleg Dantchenko, David Walton, and installers and electricians. This research would not have been possible without the support of staff and facility managersat all of the field sites, and we are grateful for their collaboration. This work used computational resources from the Extreme Science and Engineering Discovery Environment (XSEDE) which is supported by National Science Foundation grant number ACI-1548562, specifically the Jetstream cloud compute resources at Indiana University through allocation ECS180009. Funding Information: David Walton, and installers and electricians. This research would not have been possible without the support of staff and facility managers at all of the field sites, and we are grateful for their collaboration. This work used computational resources from the Extreme Science and Engineering Discovery Environment (XSEDE) which is supported by National Science Foundation grant number ACI-1548562, specifically the Jetstream cloud compute resources at Indiana University through allocation ECS180009. Publisher Copyright: © 2021 The Author(s)Controlled air movement is an effective strategy for maintaining occupant comfort while reducing energy consumption, since comfort at moderately warmer temperatures requires less space cooling. Modern ceiling fans provide a 2–4 °C cooling effect at power consumption comparable to LED lightbulbs (2–30 W) with gentle air speeds (0.5–1 m/s). However, very limited design guidance and performance data are available for using ceiling fans and air conditioning together, especially in commercial buildings. We present results from a 29-month field study of 99 automated ceiling fans and 12 thermostats installed in ten air-conditioned buildings in a hot/dry climate in California. Staging ceiling fans to automatically cool before, and then operate together with air conditioning enabled raising air conditioning cooling temperature setpoints in most zones, with overall positive occupant interview and survey responses. Overall measured cooling season (April– October) compressor energy savings were 36%, normalized by floor area served (41% during summer peak billing hours). Weather-normalized changes in zone energy use varied from 24% increase to 73% decrease across 13 compressors, reflecting variation in occupant schedules and other uncontrolled factors in occupied buildings. Median weather-normalized energy savings per compressor were 21%. Staging ceiling fans and air conditioning provided comfort across a wider temperature range, using less energy, than air conditioning alone.Peer reviewe