cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568094.v1
title: Embryonic development and maternal regulation of murine circadian clock function

description: The importance of circadian clocks in the regulation of adult physiology in mammals is well established. In contrast, the ontogenesis of the circadian system and its role in embryonic development are still poorly understood. Although there is experimental evidence that the clock machinery is present prior to birth, data on gestational clock functionality are inconsistent. Moreover, little is known about the dependence of embryonic rhythms on maternal and environmental time cues and the role of circadian oscillations for embryonic development. The aim of this study was to test if fetal mouse tissues from early embryonic stages are capable of expressing endogenous, self-sustained circadian rhythms and their contribution to embryogenesis. Starting on embryonic day 13, we collected precursor tissues for suprachiasmatic nucleus (SCN), liver and kidney from embryos carrying the circadian reporter gene <i>Per2::Luc</i> and investigated rhythmicity and circadian traits of these tissues <i>ex vivo</i>. We found that even before the respective organs were fully developed, embryonic tissues were capable of expressing circadian rhythms. Period and amplitude of which were determined very early during development and phases of liver and kidney explants are not influenced by tissue preparation, whereas SCN explants phasing is strongly dependent on preparation time. Embryonic circadian rhythms also developed in the absence of maternal and environmental time signals. Morphological and histological comparison of offspring from matings of <i>Clock-Δ19</i> mutant and wild-type mice revealed that both fetal and maternal clocks have distinct roles in embryogenesis. While genetic disruptions of maternal and embryonic clock function leads to increased fetal fat depots, abnormal ossification and organ development, <i>Clock</i> gene mutant newborns from mothers with a functional clock showed a larger body size compared to wild-type littermates. These data may contribute to the understanding of the ontogenesis of circadian clocks and the risk of disturbed maternal or embryonic circadian rhythms for embryonic development.
DOI: 10.6084/m9.figshare.1568087
title: A constructive algorithm and a simulated annealing approach for solving flowshop problems with missing operations

description: In many practical cases of flowshop environments and especially in flowline manufacturing cells, some or all jobs may not require processing on all machines. Hence, this paper focuses on the flowshop scheduling problem with missing operations. A modification of the constructive NPS-set heuristic is proposed, which generates non-permutation schedules effectively. Furthermore, a two-phase simulated annealing (SA) method is presented that specifically considers missing operations in its procedure. The modified NPS-set heuristic and the two-phase SA are tested and statistically evaluated by an extensive computational study for total flow time criteria. The results show that the modified NPS-set heuristic as well as the specific consideration of missing operations can enhance the algorithms’ performance significantly.
DOI: 10.6084/m9.figshare.1568087.v1
title: A constructive algorithm and a simulated annealing approach for solving flowshop problems with missing operations

description: In many practical cases of flowshop environments and especially in flowline manufacturing cells, some or all jobs may not require processing on all machines. Hence, this paper focuses on the flowshop scheduling problem with missing operations. A modification of the constructive NPS-set heuristic is proposed, which generates non-permutation schedules effectively. Furthermore, a two-phase simulated annealing (SA) method is presented that specifically considers missing operations in its procedure. The modified NPS-set heuristic and the two-phase SA are tested and statistically evaluated by an extensive computational study for total flow time criteria. The results show that the modified NPS-set heuristic as well as the specific consideration of missing operations can enhance the algorithms’ performance significantly.
DOI: 10.6084/m9.figshare.1568082
title: A Subsampled Double Bootstrap for Massive Data

description: The bootstrap is a popular and powerful method for assessing precision of estimators and inferential methods. However, for massive datasets that are increasingly prevalent, the bootstrap becomes prohibitively costly in computation and its feasibility is questionable even with modern parallel computing platforms. Recently, Kleiner and co-authors proposed a method called BLB (bag of little bootstraps) for massive data, which is more computationally scalable with little sacrifice of statistical accuracy. Building on BLB and the idea of fast double bootstrap, we propose a new resampling method, the subsampled double bootstrap, for both independent data and time series data. We establish consistency of the subsampled double bootstrap under mild conditions for both independent and dependent cases. Methodologically, the subsampled double bootstrap is superior to BLB in terms of running time, more sample coverage, and automatic implementation with less tuning parameters for a given time budget. Its advantage relative to BLB and bootstrap is also demonstrated in numerical simulations and a data illustration. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568082.v1
title: A subsampled double bootstrap for massive data

description: The bootstrap is a popular and powerful method for assessing precision of estimators and inferential methods. However, for massive datasets which are increasingly prevalent, the bootstrap becomes prohibitively costly in computation and its feasibility is questionable even with modern parallel computing platforms. Recently Kleiner, Talwalkar, Sarkar, and Jordan (2014) proposed a method called BLB (Bag of Little Bootstraps) for massive data which is more computationally scalable with little sacrifice of statistical accuracy. Building on BLB and the idea of fast double bootstrap, we propose a new resampling method, the subsampled double bootstrap, for both independent data and time series data. We establish consistency of the subsampled double bootstrap under mild conditions for both independent and dependent cases. Methodologically, the subsampled double bootstrap is superior to BLB in terms of running time, more sample coverage and automatic implementation with less tuning parameters for a given time budget. Its advantage relative to BLB and bootstrap is also demonstrated in numerical simulations and a data illustration.
DOI: 10.6084/m9.figshare.1568073
title: Diel diving behavior of breeding gentoo penguins on King George Island in Antarctica

description: Many marine birds dive to catch prey in water. The gentoo penguin (<i>Pygoscelis papua</i>), a specialized diving seabird that preys on krill and fish, is distributed from the sub-Antarctic islands to Antarctic regions. Here, we observed the diving behavior of breeding gentoo penguins on King George Island, South Shetland Islands, Antarctica. Using a time–depth recorder, we collected diving depths every second from seven gentoo breeders for 5–21 days during the chick-rearing period and analyzed their diving characteristics. Most dives occurred in shallow water, although the dive efficiency (=bottom duration time/[dive duration + post-dive surface time]) was highest at depths of 30–35 m and decreased as the penguins dove deeper. Gentoo penguins did not dive more frequently during the day than at night, but during nighttime, most dives occurred in shallow water (&lt;20 m) and the dive efficiency was also higher at this time. As penguins repeated their foraging trips, the number of dives, depth of dives, and trip duration did not change significantly. Our results suggest that the diel dive patterns of gentoo penguins might be related to the vertical migration of krill (upward to the surface at night). In addition, we observed that gentoo penguins could perform active diving behavior even at night, possibly aided by civil twilight during the chick-rearing period in Antarctic regions.
DOI: 10.6084/m9.figshare.1568073.v1
title: Diel diving behavior of breeding gentoo penguins on King George Island in Antarctica

description: Many marine birds dive to catch prey in water. The gentoo penguin (<i>Pygoscelis papua</i>), a specialized diving seabird that preys on krill and fish, is distributed from the sub-Antarctic islands to Antarctic regions. Here, we observed the diving behavior of breeding gentoo penguins on King George Island, South Shetland Islands, Antarctica. Using a time–depth recorder, we collected diving depths every second from seven gentoo breeders for 5–21 days during the chick-rearing period and analyzed their diving characteristics. Most dives occurred in shallow water, although the dive efficiency (=bottom duration time/[dive duration + post-dive surface time]) was highest at depths of 30–35 m and decreased as the penguins dove deeper. Gentoo penguins did not dive more frequently during the day than at night, but during nighttime, most dives occurred in shallow water (&lt;20 m) and the dive efficiency was also higher at this time. As penguins repeated their foraging trips, the number of dives, depth of dives, and trip duration did not change significantly. Our results suggest that the diel dive patterns of gentoo penguins might be related to the vertical migration of krill (upward to the surface at night). In addition, we observed that gentoo penguins could perform active diving behavior even at night, possibly aided by civil twilight during the chick-rearing period in Antarctic regions.
DOI: 10.6084/m9.figshare.1568072
title: Protein DHX38 is a novel inhibitor of protein phosphatase 4

description: DHX38 is a DEAH-box RNA helicase involved in RNA splicing. Recently, there was a report that DHX38 interacts with protein phosphatase 4 (PP4) as a subunit of PP4 complex. However, the role of DHX38 in connection with the function of PP4 has not been elucidated. Here, we demonstrated a functional role of DHX38 as an inhibitor of PP4 complex. We observed that DHX38 interacts with PP4 subunits (PP4R2, PP4R3α, PP4R3β, and PP4C), except PP4R1, and there is no significant change in the interaction between DHX38 and PP4 after DNA damage, suggesting that interaction is damage-independent. Furthermore, DHX38 has no detectable association with other Seine/Threonine phosphatases, implying that DHX38 interacts with PP4 in a phosphatase-specific manner. Interestingly, we observed that the amount of PP4R2 is substantially elevated when DHX38 is absent, but there is no effect on other subunits. Consequently, the stabilization of PP4R2 enhances PP4C/PP4R2-mediated dephosphorylation of target proteins, RPA2, and KAP1. In contrast, overexpressing DHX38 inhibits dephosphorylational activity of PP4, which is compatible with PP4C or PP4R2 depletion. Consistent with previous observations that PP4R2 is essential for DNA replication and double-strand DNA breaks (DSBs) repairs, the inhibition of PP4R2 by DHX38 expression significantly impairs these processes and the depletion of DHX38 expectedly promotes them. Defects in the efficiency of DNA replication and DSB repairs would be expected to be biologically relevant and indeed, cells expressing DHX38 have lower viability than control cells. Together, our results suggest that DHX38 functions as an endogenous inhibitor of PP4 by disrupting PP4C/PP4R2-mediated functions.
DOI: 10.6084/m9.figshare.1568072.v1
title: Protein DHX38 is a novel inhibitor of protein phosphatase 4

description: DHX38 is a DEAH-box RNA helicase involved in RNA splicing. Recently, there was a report that DHX38 interacts with protein phosphatase 4 (PP4) as a subunit of PP4 complex. However, the role of DHX38 in connection with the function of PP4 has not been elucidated. Here, we demonstrated a functional role of DHX38 as an inhibitor of PP4 complex. We observed that DHX38 interacts with PP4 subunits (PP4R2, PP4R3α, PP4R3β, and PP4C), except PP4R1, and there is no significant change in the interaction between DHX38 and PP4 after DNA damage, suggesting that interaction is damage-independent. Furthermore, DHX38 has no detectable association with other Seine/Threonine phosphatases, implying that DHX38 interacts with PP4 in a phosphatase-specific manner. Interestingly, we observed that the amount of PP4R2 is substantially elevated when DHX38 is absent, but there is no effect on other subunits. Consequently, the stabilization of PP4R2 enhances PP4C/PP4R2-mediated dephosphorylation of target proteins, RPA2, and KAP1. In contrast, overexpressing DHX38 inhibits dephosphorylational activity of PP4, which is compatible with PP4C or PP4R2 depletion. Consistent with previous observations that PP4R2 is essential for DNA replication and double-strand DNA breaks (DSBs) repairs, the inhibition of PP4R2 by DHX38 expression significantly impairs these processes and the depletion of DHX38 expectedly promotes them. Defects in the efficiency of DNA replication and DSB repairs would be expected to be biologically relevant and indeed, cells expressing DHX38 have lower viability than control cells. Together, our results suggest that DHX38 functions as an endogenous inhibitor of PP4 by disrupting PP4C/PP4R2-mediated functions.
DOI: 10.6084/m9.figshare.1568060
title: Lab 3: Biol2050 Abundance and Diversity in Insects Data Set 1

description: The experiment was conducted for the third biol2050 lab for dataset 1. The experiment was performed in the woodlot, and grassland at York University on Thursday Oct 1st, 2015 at approximately 330-415pm. The weather during this time was 15 degrees Celsius, with 0% chance of rain, and wind with the speed of 24 km/h. When the wind speed was found in the Beaufort scale, it was given a Beaufort number of 5, which corresponded to Fresh Breeze in Seaman's term. Group Members: Simranjit Kang, Ava Kamali, Katrin Chapkis, Jennifer Mariathas The purpose of the lab was to understand, and gain knowledge about the process of calculating the abundance of insects as well as the number of recognizable taxonomic units (RTU's) using a quadrat in both grasslands, and woodlots. The sample size in this experiment was 10 replicates in the grassland, and 10 replicates in the woodlot for a total of 20. The quadrats were placed randomly within each habitat of interest, 1 meter apart from one another. The quadrat was placed 10 times in the grassland, and 10 times in the woodlot, and a total of 30 seconds were measured each time using a timer on one of the group member's phone. During that time the number of insects that were inside or had flown over the quadrat were calculated as well as the # of RTU's, and both were recorded using a paper and pen. 2 of the 4 group members participated in observing the quadrat carefully to decrease the chances of possible error. As previously stated the weather during this lab was windy, and relatively cold, and this may have affected the number of insects identified. The ground in the grassland was almost completely covered by grass which made it very difficult to identify the insects as well. All the data calculated was presented in a table.
DOI: 10.6084/m9.figshare.1567650
title: Lab 3 Dataset 3- Sweep test along transects

description: The data was collected at Danby Grassland at York University Keele Campus on Thursday October 1 2015 at approximately 4:20pm. The duration of the experiment took approximately 25 mins and was completed at around 4:45pm. The temperature was 15°C and it was sunny with clear skies. The area site where the sweep nets took place was large, dry and open area. The vegetation increased as you went further into the site. The experiment was done in groups of four and each dataset was divided amongst the group members; Azeb, Eman, Bava and Saraswatie. This particular dataset was conducted by Azeb with the help of Eman. The organisms caught were primarily misquotes and bees. The purpose of this lab was to determine the distribution and abundance of mobile organisms in a short amount of time. This lab was also meant for students to become familiar with the tools used in the experiment, such and transect and sweep nets, and publishing data found in the field .The sample size for this dataset is 10. The data was collected by randomly laying out 10 meters transects across Danby Grassland and vigorously sweeping the net left to right in a diagonal pattern to prevent captured organisms from escaping. Once reaching the end of each transect, the sweeper would enclose the net with their hand and lift the net to observe the finding. This was repeated 10 times which took approximately 45 seconds each and was recorded using pen and paper in an organized chart. This was done to obtain an accurate representation of the site. Total abundance was obtained by counting the number or living organisms caught in the net by the end of each transect. The number of recognizable taxonomic units (#RTU’s) was determined by visually identifying each organism and mentally categorizing them into groups based on physical features such and colour, size, number of legs and wings etc. Once determining the general species the number of different species caught is that recorded.
DOI: 10.6084/m9.figshare.1567797
title: BIOL 2050 - Dataset #1: Abundance and Diversity

description: This dataset was collected by Eman, Azeb, Bava and Saraswatie. Different insect organisms were measured within the confinements of a 1 meter by 1 meter quadrat. Twenty different replicates were observed and recorded. Recordings 1-10 occurred in the grasslands, 11-20 occurred in the woodlots. Any insects that were in the confinements of the quadrat were recorded. Recordings took place within 1 minute intervals. The number of individual species and the number of the species family (Recognizable Taxonomic Unit) were recorded. Abundance represents the total number of individual species within the confinements of the quadrat. RTU represents the actual number of a species group within the quadrat. A timer was used to make sure we did not stray from the 1 minute intervals. Any insects (excluding dead) regardless of their size and colour, were recorded. Any insects such as bees that flew within our quadrat confinements were also recorded. Data collection occurred in the Danby grasslands and woodlots at York University – Keele Campus on October 1, 2015 at approximately 3:00 pm to 3:30 pm. The weather was approximately 15 degrees with the sun clearly visible and small amounts of cloud activity. The grassland and woodlots were completely dry as no rain had fell earlier. The vegetation of the grasslands would increase in size the further you walked in. Primarily, ants and bees would frequent our areas of observation. The dataset was collected in a group of 4, 2 members would record observations in the grassland while the other 2 recorded observations in the woodlot. This was done to save time and to be more efficient. The purpose of this lab was to further attain knowledgeable skills in field work experience by collecting, recording and publishing data.
DOI: 10.6084/m9.figshare.1567797.v1
title: BIOL 2050 - Dataset #1: Abundance and Diversity

description: This dataset was collected by Eman, Azeb, Bava and Saraswatie. Different insect organisms were measured within the confinements of a 1 meter by 1 meter quadrat. Twenty different replicates were observed and recorded. Recordings 1-10 occurred in the grasslands, 11-20 occurred in the woodlots. Any insects that were in the confinements of the quadrat were recorded. Recordings took place within 1 minute intervals. The number of individual species and the number of the species family (Recognizable Taxonomic Unit) were recorded. Abundance represents the total number of individual species within the confinements of the quadrat. RTU represents the actual number of a species group within the quadrat. A timer was used to make sure we did not stray from the 1 minute intervals. Any insects (excluding dead) regardless of their size and colour, were recorded. Any insects such as bees that flew within our quadrat confinements were also recorded. Data collection occurred in the Danby grasslands and woodlots at York University – Keele Campus on October 1, 2015 at approximately 3:00 pm to 3:30 pm. The weather was approximately 15 degrees with the sun clearly visible and small amounts of cloud activity. The grassland and woodlots were completely dry as no rain had fell earlier. The vegetation of the grasslands would increase in size the further you walked in. Primarily, ants and bees would frequent our areas of observation. The dataset was collected in a group of 4, 2 members would record observations in the grassland while the other 2 recorded observations in the woodlot. This was done to save time and to be more efficient. The purpose of this lab was to further attain knowledgeable skills in field work experience by collecting, recording and publishing data.
DOI: 10.6084/m9.figshare.1567474
title: Lab 03 - The abundance of different bird species.

description: The experiment was conducted on October 1,2015 at Danby woodlot and grassland, York university around 2:30-5:00pm. The temperature was around 15° C with slight clear sky. The experiment was done along with Harshvir Hehar, Olivia Kazmierczak and Adilah Ismail. The purpose of this experiment was to identify different bird species and their abundance at grassland and woodlot of York university. 10 belt transect lines were used in this experiment with 5 being placed randomly at Danby woodlot and 5 at grassland. A transect measuring tape was laid along the ground at a distance of 20 m. An observer walked along the transect looking for birds above or around the surrounding area. Once the bird was spotted, the name of the bird specie was recorded with the help of a bird field guide. The abundance was measured by simply counting the total number of different species that was seen while walking along the transect for a duration of 1 minute. The wind speed was also determined by observing the movement of trees with our eyes on a scale of 1-3 with 3 being lots of wrestling of trees, 2 being somewhat movement of tress and 1 being little or no movement of trees. The distance the bird was away from the transect line was measured in meters. The sample size of this experiment was 26.