cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2611109
title: Discovery of tandem and interspersed segmental duplications using high throughput sequencing

description: We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing data sets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real data sets. In the  simulation experiments, using a 30x coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state of the art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (less than 5\% for the top 50 predictions).
description: Here we deposit current versions of TARDIS (1.0.2) and CNVSim, and all predictions, truth sets, and the CRAM files for the simulation data.
DOI: 10.17632/4jbzcftw53.1
title: Data for: Electrospun hierarchical frogspawn structured superhydrophobic membrane for gravity-driven high efficiency oil-water separation

description: This is the figure from Origin, hopefully this will increase the reliability of my work.
DOI: 10.25345/c5qs5v
title: MassIVE MSV000083651 - Bacterial inhibitory zone exp 20190118
title: Investigation of small molecules detected in bacterial inhibitory zone. Data were generated on a Thermo Q Exactive and C18 RP UHPLC. Positive polarity acquisition on LC-MS/MS.
DOI: 10.6073/pasta/124732e005aa1b226a462f3079a02e4d
title: Soil Particle Size Analysis at Permanent Quadrat locations, Jornada Experimental Range, 2001

description: This completed dataset, collected in 2001, contains soil particle size
  analysis (PSA) and sand fractionation data from soil cores collected
  at 116 quadrat locations that are part of the Jornada Experimental
  Range's long-term Permanent Quadrats study. The goal of this effort
  was to help characterize plant-scale factors related to vegetation
  dynamics observed in the Permanent Quadrats. At each quadrat location,
  4 cores were collected at 2 depths (0-5cm and 5-20cm) and assessed for
  percent sand, silt and clay. The sand fraction, if large enough, was
  then separated into 5 sand size classes (53-106 micrometers, 106-250
  micrometers, 250-500 micrometers, 500-1000 micrometers, 1000-2000
  micrometers) to measure the percent fraction of each.
DOI: 10.17632/p4t5w4zxy8.1
title: Data for: Electrospun hierarchical frogspawn structured superhydrophobic membrane for gravity-driven high efficiency oil-water separation
DOI: 10.17632/z9fs3p236r.1
title: Data for: Electrospun hierarchical frogspawn structured superhydrophobic membrane for gravity-driven high efficiency oil-water separation
DOI: 10.5066/p973obb0
title: Evaluating Adaptive Capacity of Desert Bighorn Sheep to Climate Change: Identifying Genetic Links to Climate Adaptations

description: Natural selection may result in local adaptation to different environmental conditions across the range of a species. Understanding local adaptation, in turn, informs management decisions such as translocation to restore locally-extinct populations. We used a landscape genomics approach to detect genetic signatures of selection related to climatic variation among desert bighorn sheep populations across their indigenous range in the western United States. This approach allowed us to investigate broad patterns of both neutral and adaptive genetic variation across very different environments. Analyses suggested that ancestry and isolation by distance were the most significant forces driving genetic variation in desert bighorn sheep, but that climate was associated with at least 1 locus (i.e., location on the genome) under directional selection. The alternate allele (i.e., variant) at this locus was associated with biologically significant increases in elevation and precipitation, decreases in temperature, and was nearly private to herds occupying the Great Basin ecosystem. Our results suggest climate conditions at higher latitudes may have resulted in a distinct ecotype of desert bighorn sheep whose adaptations are still apparent among the few remaining indigenous populations in the Great Basin. We also found 2 highly supported candidate genes in the genomic region linked to this outlier. How the molecular function of these candidate genes may affect physiological response of desert bighorn sheep to climate is unclear, although their identification provides new insight into the genetic mechanisms potentially underlying environmental adaptation. We identified several other loci under strong directional selection not related to climate and described a previously unknown pattern of strong genetic divergence of bighorn sheep within the White Mountains compared to other populations. Overall, these findings suggest selection from environmental factors may influence genomic variation at the ecosystem-scale in desert bighorn sheep and these results extend our understanding of how this subspecies may respond to different environmental conditions.
DOI: 10.5066/p9jvmlft
title: Rate of shoreline change statistics for New York State coastal wetlands

description: This data set contains shoreline rate of change statistics for New York State coastal wetlands. Analysis was performed using the Digital Shoreline Analysis System (DSAS), created by U.S. Geological Survey, version 5.0, an extension for ArcMap.  A reference baseline was used as the originating point for orthogonal transects cast by the DSAS software. The transects intersect each polyline vector shoreline establishing intersection measurement points, which were then used to calculate the rates of change. End-point rates, calculated by dividing the distance of shoreline movement by the time elapsed between the oldest and the most recent shoreline, were generated for wetlands where fewer than three historic shorelines were available. Linear regression rates, determined by fitting a least-squares regression line to all shoreline points for a particular transect, were used in areas where three or more shorelines were present.  Positive values indicate shoreline accretion while negative values indicate erosion.
DOI: 10.5258/soton/d0845
title: Dataset for "Towards dual frequency comb VECSELs with DMD laser-ablated spatial mode masks"

description: This dataset supports the publication: Jonathan Woods, Daniel Heath, Jake Daykin, Theo Chen Sverre, Ben Mills, Arnaud Garnache, Anne Tropper, and Vasilis Apostolopoulos 'Towards dual frequency comb VECSELs with DMD laser-ablated spatial mode masks' Proceedings Volume 10901, Vertical External Cavity Surface Emitting Lasers (VECSELs) IX; 109010I (2019) https://doi.org/10.1117/12.2508680
DOI: 10.5258/soton/d0825
title: Dataset for Modelling railway station choice: can probabilistic catchments improve demand forecasts for new stations?

description: Research Data supporting the PhD Thesis 'Modelling railway station choice: can probabilistic catchments improve demand forecasts for new stations?' by Marcus Young. See the readme file for further information.
DOI: 10.3886/e109167v1
title: Cora Dataset

description: The Cora data contains bibliographic records of machine learning papers that have been manually clustered into groups that refer to the same publication. Originally, Cora was prepared by Andrew McCallum, and his versions of this data set are available on his Data web page. The data is also hosted here. Note that various versions of the Cora data set have been used by many publications in record linkage and entity resolution over the years.
DOI: 10.5281/zenodo.2621777
title: Testing Zenodo Data Archive

description: Test
DOI: 10.5281/zenodo.2621778
title: Testing Zenodo Data Archive

description: Test
DOI: 10.17632/7mp25kyb4p.4
title: varRhoTurbVOF

description: The volume of fluid (VOF) method is a popular approach for multiphase flow modeling. The open-source computational fluid dynamics (CFD) software, OpenFOAM, has implemented a variety of VOF-based solvers and provides users a wide range of turbulence models. Since flows under the VOF framework belong to the variable-density incompressible flow category, the isothermal VOF-based solvers in OpenFOAM fail to use the correct turbulence models. varRhoTurbVOF is designed to solve this issue and with the hope to replace all the corresponding existing solvers in the future. With the object-oriented paradigm, varRhoTurbVOF guarantees the usability, reusability and maintainability of the codes. Aside from turbulence modeling, all other features in the original solvers are preserved in varRhoTurbVOF.
DOI: 10.5281/zenodo.2621969
title: Testing Zenodo Data Archive

description: Test
DOI: 10.25345/c5vh0f
title: MassIVE MSV000083650 - A targeted mass spectrometry strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancer
title: Protein biomarkers of early stages of disease are critical for managing the disease and improving outcomes. Unfortunately, discovery of protein biomarkers is hampered by the limited availability of assays for sensitive and reproducible quantification of proteins in complex biological matrices such as blood plasma. In the recent years, Selected Reaction Monitoring (SRM) has emerged as a robust mass spectrometric method, capable of overcoming this limitation. Here, we present a comprehensive SRM-based strategy for developing protein biomarkers for epithelial ovarian cancer, and illustrate the extent to which SRM platform, combined with sound experimental design and statistical analysis, results in robust detection of predictive analytes. First, the biomarker development was guided by a discovery-driven proteomic effort to detect potential N-glycoprotein biomarker candidates in tissue of a genetically stable ovarian cancer mouse model. Next, 65 candidate markers were reproducibly quantified with SRM assays across a large cohort of over 200 plasma samples from ovarian cancer patients and healthy controls. Finally, these measurements were used to derive 5-protein signatures for distinguishing individuals with epithelial ovarian cancer from healthy controls. The sensitivity of the candidate biomarker signature in combination with CA125 ELISA-based measurements currently used in clinic, exceeded that of CA125 ELISA-based measurements alone. The SRM-based strategy in this study is broadly applicable. It can be used in any study that requires accurate and reproducible quantification of selected proteins in a high-throughput and multiplexed fashion.
DOI: 10.25919/5ca3ce21e83f8
title: Proteomics Data: Hordein accumulation in developing barley grains

description: Proteomics data collected as part of the manuscript by Tanner et al (2019) Frontiers in Plant Science
Abstract: The temporal pattern of accumulation of hordein storage proteins in developing barley grains was studied by enzyme-linked immunosorbent assay (ELISA), western blot and liquid chromatography tandem mass spectrometry (LC-MS/MS). Hordein accumulation was compared to the pattern seen for two abundant control proteins, serpin Z4 (an early accumulator) and lipid transferase protein (LTP1, a late accumulator). Hordeins were detected from six days post-anthesis (DPA) and peaked at 30 DPA. Changes in fresh weight indicate that desiccation begins at 20 DPA and by 37 DPA fresh weight had decreased by 35%. ELISA analysis of hordein content, expressed on a protein basis, increased to a maximum at 30 DPA followed by a 17% decrease by 37 DPA. The accumulation of 39 tryptic and 29 chymotryptic hordein peptides representing all classes of hordein was studied by LC-MS/MS. Most peptides increased to a maximum at 30 DPA, and either remained at the maximum or did not decrease significantly. Only five tryptic peptides, members of the related B1- and γ1-hordeins decreased significantly by 21-51% at 37 DPA. Thus, the concentration of some specific peptides was reduced while remaining members of the same family were not affected. The N-terminal signal region was removed by proteolysis during co-translation. In addition to a suite of previously characterised hordeins, two novel barley B-hordein isoforms mapping to wheat low molecular weight glutenins (LMW-GS-like B-hordeins), and two avenin-like proteins (ALPs) sharing homology with wheat ALPs, were identified. These identified isoforms have not previously been mapped in the barley genome. Cereal storage proteins provide significant nutritional content for human consumption and seed germination. In barley, the bulk of the storage proteins comprise the hordein family and the final hordein concentration affects the quality of baked and brewed products. It is therefore important to study the accumulation of hordeins as this knowledge may assist plant breeding for improved health outcomes (by minimizing triggering of detrimental immune responses), nutrition and food processing properties.
DOI: 10.5281/zenodo.2621972
title: S7 | EAWAGSURF | Eawag Surfactants Suspect List

description: This is the collection associated with list S7 EAWAGSURF on the NORMAN Suspect List Exchange.

https://www.norman-network.com/?q=suspect-list-exchange

Note this collection does not contain explicit structures.

S7

EAWAGSURF

<strong>Eawag Surfactants Suspect List </strong>

Suspect formulas: CSV, XLSX

CompTox EAWAGSURF List

Schymanski <em>et al</em>. 2014. DOI: 10.1021/es4044374
DOI: 10.17632/75jcz72mvg.1
title: Data for: Changes in microbial composition on the crust by different air flow velocities and their effect on sensory properties of dry-aged beef

description: Research Data for "Changes in microbial composition on the crust by different air flow velocities and their effect on sensory properties of dry-aged beef" submitted to Meat Science by Lee et al.
DOI: 10.17632/vd3f6rr7sp.1
title: Data for: Count Citations by Section? Introduction, Background, Methods, Discussion, Results and Conclusions

description: Data behind Figures 1 to 8
DOI: 10.6073/pasta/acfbb45d8e698c26eeb4e4ea91b9e9a4
title: Co-dominant removal and N and C fertilization experiment for moist meadow tundra from 2002 to 2018

description: In 2002 seven experimental sites were set up in areas of moist meadow
  alpine tundra on Niwot Ridge. At each site, ten 1 m^2 plots were
  established where there was roughly even cover by two dominant plant
  species, Geum rossii (forb) and Deschampsia cespitosa (grass). In a
  factorial design, plots were assigned treatments of 1) removal of G.
  rossii, D. cespitosa, or control (no plant removal), and 2) nutrient
  addition of nitrogen (N), carbon (C), or control (no addition). A
  tenth plot was assigned a treatment of random biomass removal and no
  nutrient addition. Plots were visited annually to implement removal
  and fertilization treatments, and to measure plant species
  composition. Plant productivity was measured every other year. Carbon
  addition plots were dropped from the experiment in 2016.
DOI: 10.14457/tu.the.2014.558
title: Effect of potassium laurate on the stability of concentrated natural rubber latex preserved with an alternative to ammonia

description: 2-hydroxymethyl amino ethanol as a preservative was added into the concentrated natural rubber latex instead of ammonia. The whole system is called HMAE-NRL hereafter. The stability of this colloidal system was improved by addition of potassium laurate together with adjusting pH. The pH of HMAE-NRL was adjusted by adding potassium hydroxide to values of 8 and 10 before loading with various potassium laurate ranging from 0-1 wt% and 0-0.125 wt% for pH 8 and pH 10, respectively. Changes in colloidal stability of the latex were investigated by measuring mechanical stability time (MST), chemical stability time (CST), heat stability time (HST), chemical and heat stability time (CHST) along with the changes of some latex properties which are conductivity, VFA no., viscosity and surface tension at various storage times. Furthermore, critical coagulation concentration (CCC) of colloid system was also assessed. It was found that MST, CST, HST, CHST of all latices increased when storage time increased up to 80 days and then decreased afterward 120 days. The HMAE-NRL with pH 10 had longer stability time than that with pH 8 when adding the same potassium laurate loadings. The maximum increase in the stability time was observed for HMAE-NRL at pH 10 with adding 0.125 wt% of potassium laurate. The VFA number, conductivity and viscosity of all lattices increased when storage time increased. Relationship between log(MST) and conductivity of HMAE-NRL was observed consistent with linear equation. Comparing the stability of HMAE-NRL to that of HA-NRL, it was found that HA-NRL has higher degree of stability than HMAE-NR. However, it was observed that the stability of HMAE-NRL at pH 10 with 0.125 wt% potassium laurate was close to that of HA-NRL with 0.05 wt% ammonium laurate. This result indicates that natural rubber latex could be preserved with HMAE instead of ammonia to yieid acceptable MST. Regarding many disadvantages of ammonia, HMAE-NRL is a promising option but it needs to be used with potassium laurate as a surfactant and pH adjustment to 10.
DOI: 10.14457/tu.the.2014.559
title: Legal measures on sanitary food transportation

description: This thesis aims to focus on the subject of the control of sanitary food transportation by land, both road and rail, which transportation is one process of food chain, and needed to be governed in order to save the quality of food products for the consumers’ benefits, other than the benefits of the enterprises. Food transportation shall include catering or ready-to-eat food delivery by road vehicles.Thailand has not yet regulated specific law respecting the issue. Although we have ministerial regulations to control the standard of some food products, and preventive measures for food quality control, there is none of regulations specifies the general rules of sanitary food transportation, liabilities of persons engaged in food transportation, and also other rules that the food transport business should follow, e.g. the temperature control, the hygiene control, and the control of vehicles used in food  transportation.Due to the fact that food is one of the four significant factors of life, it is greatly important that the food is safe when we consume. Many fresh foods are deemed perishable foods or foods that easily spoiled when being kept in improper circumstance. Therefore, food safety control is necessary, and transportation is one step of the food chain that takes an important role since the food comes out from the slaughterhouse, to the manufacturers, then comes to the distributors, to the markets, or to the restaurants, and finally on our plates. The consumers will never know whether the food they eat is safe along the way, the regulations for controlling the transportation of food is necessary therefor. The applicable laws for the damage arising from food transportation are same as other consumer’s cases; in section 4 (3) of Consumer Protection Act B.E. 2522 which provides the consumers’ right protection, states that the consumer shall receive safety while using the products or services. In addition, section 5 of Liability for Damages arising from Unsafe Products Act B.E. 2551 state that the practitioners or operators must be jointly liable to the injured party for the damage caused by unsafe products, which has been sold to the consumer, whether the damage has been caused by willful act or negligence of the operator or not.  And, section 420 of Civil and Commercial Code specifies the rights of the injured persons that they shall be compensated for the damage they got.In this thesis, the author presents and compares the regulations of United States, United Kingdom, and Australia concerning sanitation control during food transport in order to apply with problems in Thailand. Most of them empower the state agency which is in charge of people’s health; the Ministry of Public Health. Moreover, The author suggests the Ministry of Public Health takes the responsibilities on the new regulations since it is the state agency which is accountable for people’s health. Consequently, it shall reduce the problems of food contamination and food spoilage during transport, and will benifit for the consumer’s protection.
DOI: 10.14457/tu.the.2014.560
title: ผลกระทบของการบริหารจัดการคุณภาพโดยรวมและเทคโนโลยีที่ส่งผลต่อประสิทธิภาพด้านคุณภาพในการดำเนินงานของสถานพยาบาลในประเทศไทย

description: งานวิจัยนี้ศึกษาถึงผลกระทบของกลยุทธ์ธุรกิจและการตัดสินใจในการบริหารจัดการคุณภาพโดยรวมและเทคโนโลยีที่ส่งผลต่อประสิทธิภาพด้านคุณภาพในการดำเนินงานของสถานพยาบาลในประเทศไทย โดยเก็บข้อมูลจากผู้ประกอบกิจการ ผู้บริหาร หรือผู้ที่มีส่วนเกี่ยวข้องกับการบริหารจัดการการดำเนินงานของสถานพยาบาลทั้งภาครัฐและภาคเอกชน จำนวน 256 ตัวอย่าง มีวัตถุประสงค์เพื่อศึกษาความสัมพันธ์ระหว่างกลยุทธ์ธุรกิจและการตัดสินใจในการบริหารจัดการคุณภาพโดยรวมและเทคโนโลยีกับประสิทธิภาพด้านคุณภาพในการดำเนินงานของสถานพยาบาลในประเทศไทย ซึ่งจะนำไปสู่การปรับปรุงและพัฒนาการบริหารจัดการระบบการให้บริการที่มีประสิทธิภาพมากยิ่งขึ้น และก่อให้เกิดความได้เปรียบทางการแข่งขันในอุตสาหกรรม กรอบแนวคิดการวิจัยมุ่งศึกษาความสัมพันธ์ระหว่างกลยุทธ์ธุรกิจและการตัดสินใจในการบริหารจัดการคุณภาพโดยรวมและเทคโนโลยีที่ส่งผลต่อประสิทธิภาพด้านคุณภาพในการดำเนินงานของสถานพยาบาล การศึกษาวิจัยนี้เป็นการวิจัยเชิงปริมาณ โดยใช้วิธีวิจัยเชิงสำรวจ และใช้เครื่องมือทางสถิติในการวิเคราะห์ข้อมูล ได้แก่ สถิติเชิงพตียงผู้ป่วยน้อยกว่า 151 เตียง รรณนา และสถิติเชิงอนุมานเพื่อวิเคราะห์ปัจจัยและการถดถอยจากการศึกษาพบว่า ผู้ตอบแบบสอบถามส่วนใหญ่ดำรงตำแหน่งผู้อำนวยการ สังกัดสถานพยาบาลภาครัฐ มีประสบการณ์ทำงานมากกว่า 10 ปี ทำงานในสถานพยาบาลที่มีพนักงานจำนวน 100 – 250 คน และมีจำนวนเตียงผู้ป่วยน้อยกว่า 151 เตียง ส่วนผลการวิเคราะห์ความสัมพันธ์พบว่า ที่ระดับนัยสำคัญทางสถิติ 0.05 กลยุทธ์ธุรกิจทั้งกลยุทธ์การสร้างความแตกต่างและกลยุทธ์ผู้นำด้านต้นทุนมีความสัมพันธ์เชิงบวกกับการตัดสินใจในการบริหารจัดการคุณภาพโดยรวมและเทคโนโลยีของสถานพยาบาล และการบริหารจัดการคุณภาพโดยรวมและเทคโนโลยีมีความสัมพันธ์เชิงบวกกับประสิทธิภาพด้านคุณภาพในการดำเนินงานของสถานพยาบาลนอกจากนี้ยังสามารถนำผลการวิจัยไปประยุกต์ใช้เพื่อปรับปรุงและพัฒนาการบริหารจัดการการดำเนินงานในสถานพยาบาล และนำไปสู่การเพิ่มคุณภาพในการให้บริการและตอบสนองความคาดหวังของผู้ใช้บริการได้ดียิ่งขึ้น
DOI: 10.21985/n2r193
title: US city crime
DOI: 10.25919/5ca42da5dcd92
title: Parkes observations for project P834 semester 2018OCTS_05

description: Finding the pulsar born in SN 1987A would be of major significance. It would be by far the youngest pulsar known and would enable unique investigations of the early evolution and birth properties of a pulsar, as well as acting as a probe of the circumstellar and interstellar medium. We propose to use the new Ultra-Wideband Low (UWL) receiver to attempt confirmation of dispersed pulse candidates from previous P834 observations, to search for more isolated (giant) pulses and to continue the search for periodic emission from a pulsar associated with SN 1987A. The UWL receiver, with its much wider bandwidth and much lower system noise compared to the 10cm/50cm system will allow searches with much higher sensitivity.