cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
How genomic selection has increased rates of genetic gain and inbreeding in the Australian national herd, genomic information nucleus, and bulls
Creators: name: Scott, Beth
name: Haile-Mariam, Mekonnen
name: Cocks, Benjamin
name: Pryce, Jennie
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 30
subject: Agricultural, veterinary and food sciences
classificationCode: 3003
subject: Animal production
classificationCode: 3006
subject: Food sciences
classificationCode: 3009
subject: Veterinary sciences
subject: FOS: Veterinary sciences

description: Genomic selection has been commonly used for selection for over a decade. In this time, the rate of genetic gain has more than doubled in some countries, while inbreeding per year has also increased. Inbreeding can result in a loss of genetic diversity, decreased long-term response to selection, reduced animal performance and ultimately, decreased farm profitability. We quantified and compared changes in genetic gain and diversity resulting from genomic selection in Australian Holstein and Jersey cattle populations. To increase the accuracy of genomic selection, Australia has had a female genomic reference population since 2013, specifically designed to be representative of commercial populations and thus including both Holstein and Jersey cows. Herds that kept excellent health and fertility data were invited to join this population and most their animals were genotyped. In both breeds, the rate of genetic gain and inbreeding was greatest in bulls, and then the female genomic reference population, and finally the wider national herd. When comparing pre- and postgenomic selection, the rates of genetic gain for the national economic index has increased by ~160% in Holstein females and ~100% in Jersey females. This has been accompanied by doubling of the rates of inbreeding in female populations, and the rate of inbreeding has increased several fold in Holstein bulls since the widespread use of genomic selection. Where cow genotype data were available to perform a more accurate genomic analysis, greater rates of pedigree and genomic inbreeding were observed, indicating actual inbreeding levels could be underestimated in the national population due to gaps in pedigrees. Based on current rates of genetic gain, the female reference population is progressing ahead of the national herd and could be used to infer and track the future inbreeding and genetic trends of the national herds.
Scorpiops (Neoscorpiops) nagphani Sulakhe, Deshpande, Dandekar, Padhye & Bastawade 2021
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops nagphani

description: - S. (Neoscorpiops) nagphani Sulakhe, Deshpande, Dandekar, Padhye & Bastawade, 2021
India
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 4, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
How genomic selection has increased rates of genetic gain and inbreeding in the Australian national herd, genomic information nucleus, and bulls
Creators: name: Scott, Beth
name: Haile-Mariam, M
name: Cocks, Benjamin
name: Pryce, Jennie
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Genomic selection has been commonly used for selection for over a decade. In this time, the rate of genetic gain has more than doubled in some countries, while inbreeding per year has also increased. Inbreeding can result in a loss of genetic diversity, decreased long-term response to selection, reduced animal performance and ultimately, decreased farm profitability. We quantified and compared changes in genetic gain and diversity resulting from genomic selection in Australian Holstein and Jersey cattle populations. To increase the accuracy of genomic selection, Australia has had a female genomic reference population since 2013, specifically designed to be representative of commercial populations and thus including both Holstein and Jersey cows. Herds that kept excellent health and fertility data were invited to join this population and most their animals were genotyped. In both breeds, the rate of genetic gain and inbreeding was greatest in bulls, and then the female genomic reference population, and finally the wider national herd. When comparing pre- and postgenomic selection, the rates of genetic gain for the national economic index has increased by ~160% in Holstein females and ~100% in Jersey females. This has been accompanied by doubling of the rates of inbreeding in female populations, and the rate of inbreeding has increased several fold in Holstein bulls since the widespread use of genomic selection. Where cow genotype data were available to perform a more accurate genomic analysis, greater rates of pedigree and genomic inbreeding were observed, indicating actual inbreeding levels could be underestimated in the national population due to gaps in pedigrees. Based on current rates of genetic gain, the female reference population is progressing ahead of the national herd and could be used to infer and track the future inbreeding and genetic trends of the national herds.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Pon Soon, Dang Tong, Mr. Jung [Pang], Lum Lee, Chow [Fook] Hong, Jung Hong, Leong [?] Wah, Cho [?] Chu, and Jew Bing Jen. Two names in booklet are illegible.
Draft genome sequence of enterobacter asburiae ncr1, a plant growth-promoting rhizobacterium isolated from a cadmium-contaminated environment
Creators: name: Francois, Charlotte
name: Batinovic, Steven
name: Petrovski, Steve
name: Gendall, Anthony
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Enterobacter asburiae NCR1 is a plant growth-promoting rhizobacterium isolated from the rhizosphere of Carpobrotus rossii. We report the draft genome sequence of E. asburiae strain NCR1, which revealed many genes facilitating beneficial interactions with plant hosts.
Quantification of the demands of cricket bowling and the relationship to injury risk: a systematic review
Creators: name: Constable, Matthew
name: Wundersitz, Daniel
name: Rico-Bini, Rodrigo
name: Kingsley, Michael
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Abstract Background Bowling in cricket is a complex sporting movement which, despite being well characterised, still produces a significant number of injuries each year. Fast bowlers are more likely to be injured than any other playing role. Frequency, duration, intensity and volume of bowling, which have been generalised as measurements of workload, are thought to be risk factors for injuries. Injury rates of fast bowlers have not reduced in recent years despite the implementation of various workload monitoring practices. Objective To identify the variables used to quantify frequency, intensity, time and volume of bowling; and evaluate relationships between these variables and injury risk. Methods Six online databases were systematically searched for studies on fast bowling that included terms related to workload. Population characteristics, variables relating to demand and their relationship to standardised definitions of physical activity were extracted from all included studies. Results Bowling workload is typically quantified through measures of frequency, duration, or indirect intensity, with few studies reporting on bowling volume. Conclusions When reported on, volume was often described using imprecise or insufficient measures of intensity. There is a need to develop more appropriate measures of intensity during bowling and improve the quality of evidence to inform on bowling programme management practices.
Additional file 1 of Factors used by general practitioners for referring patients with chronic musculoskeletal pain: a qualitative study
Creators: name: Slatman, Syl
name: Mossink, Annemiek
name: Jansen, Duncan
name: Broeks, José
name: van der Lugt, Peter
name: Prosman, Gert-Jan
name: d’Hollosy, Wendy Oude Nijeweme -
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 1.
Additional file 2 of Factors used by general practitioners for referring patients with chronic musculoskeletal pain: a qualitative study
Creators: name: Slatman, Syl
name: Mossink, Annemiek
name: Jansen, Duncan
name: Broeks, José
name: van der Lugt, Peter
name: Prosman, Gert-Jan
name: d’Hollosy, Wendy Oude Nijeweme -
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 2.
Duration of intervals in the care seeking pathway for lung cancer in Bangladesh: A journey from symptoms triggering consultation to receipt of treatment
Creators: name: Ansar, Adnan
name: Lewis, Virginia
name: McDonald, Christine Faye
name: Liu, Chaojie
name: Rahman, Muhammad
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 32
subject: Biomedical and clinical sciences
classificationCode: 3202
subject: Clinical sciences
classificationCode: 42
subject: Health sciences
subject: FOS: Health sciences
classificationCode: 4203
subject: Health services and systems
classificationCode: 4205
subject: Nursing

description: Timeliness in seeking care is critical for lung cancer patients’ survival and better prognosis. The care seeking trajectory of patients with lung cancer in Bangladesh has not been explored, despite the differences in health systems and structures compared to high income countries. This study investigated the symptoms triggering healthcare seeking, preferred healthcare providers (including informal healthcare providers such as pharmacy retailers, village doctors, and “traditional healers”), and the duration of intervals in the lung cancer care pathway of patients in Bangladesh. A cross-sectional study was conducted in three tertiary care hospitals in Bangladesh among diagnosed lung cancer patients through face-to-face interview and medical record review. Time intervals from onset of symptom and care seeking events were calculated and compared between those who sought initial care from different providers using Wilcoxon rank sum tests. Among 418 study participants, the majority (90%) of whom were males, with a mean age of 57 ±9.86 years, cough and chest pain were the most common (23%) combination of symptoms triggering healthcare seeking. About two-thirds of the total respondents (60%) went to informal healthcare providers as their first point of contact. Living in rural areas, lower levels of education and lower income were associated with seeking care from such providers. The median duration between onset of symptom to confirmation of diagnosis was 121 days, between confirmation of diagnosis and initiation of treatment was 22 days, and between onset of symptom and initiation of treatment was 151 days. Pre-diagnosis durations were longer for those who had sought initial care from an informal provider (p<0.05). Time to first contact with a health provider was shorter in this study compared to other developed and developing countries but utilizing informal healthcare providers caused delays in diagnosis and initiation of treatment. Encouraging people to seek care from a formal healthcare provider may reduce the overall duration of the care seeking pathway.
Duration of intervals in the care seeking pathway for lung cancer in Bangladesh: A journey from symptoms triggering consultation to receipt of treatment
Creators: name: Ansar, Adnan
name: Lewis, Virginia
name: McDonald, Christine Faye
name: Liu, Chaojie
name: Rahman, Muhammad Aziz
Publisher: name: La Trobe
Year: 2021

description: Timeliness in seeking care is critical for lung cancer patients’ survival and better prognosis. The care seeking trajectory of patients with lung cancer in Bangladesh has not been explored, despite the differences in health systems and structures compared to high income countries. This study investigated the symptoms triggering healthcare seeking, preferred healthcare providers (including informal healthcare providers such as pharmacy retailers, village doctors, and “traditional healers”), and the duration of intervals in the lung cancer care pathway of patients in Bangladesh. A cross-sectional study was conducted in three tertiary care hospitals in Bangladesh among diagnosed lung cancer patients through face-to-face interview and medical record review. Time intervals from onset of symptom and care seeking events were calculated and compared between those who sought initial care from different providers using Wilcoxon rank sum tests. Among 418 study participants, the majority (90%) of whom were males, with a mean age of 57 ±9.86 years, cough and chest pain were the most common (23%) combination of symptoms triggering healthcare seeking. About two-thirds of the total respondents (60%) went to informal healthcare providers as their first point of contact. Living in rural areas, lower levels of education and lower income were associated with seeking care from such providers. The median duration between onset of symptom to confirmation of diagnosis was 121 days, between confirmation of diagnosis and initiation of treatment was 22 days, and between onset of symptom and initiation of treatment was 151 days. Pre-diagnosis durations were longer for those who had sought initial care from an informal provider (p<0.05). Time to first contact with a health provider was shorter in this study compared to other developed and developing countries but utilizing informal healthcare providers caused delays in diagnosis and initiation of treatment. Encouraging people to seek care from a formal healthcare provider may reduce the overall duration of the care seeking pathway.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Mah Ting [Choy], Lim Kong Yow, Chu Chuck Kay, Jung Yuey, Huey Foon, Chin [Guey], Chin [Suia?] Kwong, Yip Guey Hong, Chan Tong, and Lee [Thick] Fon.
Additional file 3 of Factors used by general practitioners for referring patients with chronic musculoskeletal pain: a qualitative study
Creators: name: Slatman, Syl
name: Mossink, Annemiek
name: Jansen, Duncan
name: Broeks, José
name: van der Lugt, Peter
name: Prosman, Gert-Jan
name: d’Hollosy, Wendy Oude Nijeweme -
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 3.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Joe Yong, [Dan Hin Kee], [Wong Toan Gin], Dong Young, Ho Yow, Wong Bing Kee, Lee Yow Big, Leong Ying Song, Leong Ho Ging, Jong Bank Yuey.
Scorpiops (Neoscorpiops) neera Sulakhe, Deshpande, Dandekar, Padhye & Bastawade 2021
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops neera

description: - S. (Neoscorpiops) neera Sulakhe, Deshpande, Dandekar, Padhye & Bastawade, 2021
India
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 4, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
Additional file 1 of EORTC QLQ-C30 general population normative data for Italy by sex, age and health condition: an analysis of 1,036 individuals
Creators: name: Pilz, Micha J.
name: Gamper, Eva-Maria
name: Efficace, Fabio
name: Arraras, Juan I.
name: Nolte, Sandra
name: Liegl, Gregor
name: Rose, Matthias
name: Giesinger, Johannes M.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Supplementary Table S1: Regression models for the EORTC QLQ-C30 values in the General Population of Italy.
Supplementary document for Deflecting and routing nematicons via orientation programmable liquid crystal array - 6414405.pdf
Creators: name: zhang, zhangsongyu
name: Wang, Yifei
name: Shen, D
name: Luo, Duanbin
name: Zheng, Zhi-gang
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: Supplemental Materials for supporting the presentations in the manuscript.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Mah Look Wai, Jong Fat Chung, Low Kee, Joe Hing, Young Bow, Lew Lai, Lew Kim, Fong Hop, Lim Chin, and Ng King.
Enhancing Indoor Localization through Precise Radio Map Construction and Fingerprint Interpolation in Complex and Dynamic Environments
Creators: name: YONG, YUN FEN
Publisher: name: Monash University
Year: 2024
Subjects: classificationCode: 460609
subject: Networking and communications
classificationCode: 400608
subject: Wireless communication systems and technologies (incl. microwave and millimetrewave)

description: This research develops novel methods to enhance indoor positioning systems (IPS), which are crucial for navigating inside buildings. Traditional positioning techniques often face challenges due to the unpredictable nature of indoor signals and layout changes. This research introduces new methods to improve accuracy by stabilizing signal variations, balancing data distribution in underrepresented areas such as near walls or obstructive objects, and adapting to dynamic indoor changes. Additionally, it utilizes human movement data to optimize the placement of navigation points, thus enhancing localization performance. These innovative techniques demonstrate superior performance against existing methods, marking a significant advancement in IPS technology.
title: Brine management options for carbon capture and storage in Australia
Creators: name: C., Patterson
name: C., Patterson
name: A., Kalinowski
name: E., Tenthorey
Publisher: name: Commonwealth of Australia (Geoscience Australia)
Year: 2024
Subjects: subject: EFTF – Exploring for the Future
subject: Australia’s Future Energy Resources
subject: CCS
subject: Carbon Capture and Storage
subject: EFTF – Exploring For The Future
subject: low carbon
subject: Australia's Future Energy Resources
subject: Brine Management
subject: groundwater
subject: EARTH SCIENCES
subject: Published_External

description: Carbon capture and storage (CCS) is gaining momentum globally. The Global CCS Institute notes in their Status of CCS 2023 report that there are 26 capture capacity of projects under construction and a further 325 projects in development, with a total capture capacity of 361 million tonnes per year (Mt/y) of carbon dioxide (CO2). Some CCS projects require the extraction of brackish or saline water (referred to here on in as brine) from the storage formation to manage increased pressure resulting from CO2 injection and/or to optimise subsurface storage space. It is important to consider the management of extracted brine as the CCS industry scales up due to implications for project design, cost and location as well as for the responsible management of the ‘waste’ or by-product brine. The use and disposal of reservoir brine has been investigated for CCS projects around the world, but not for Australian conditions. We have undertaken this review to explore how extracted brine could potentially be managed by CCS projects across Australia.
Additional file 1 of Development and internal validation of a machine-learning-developed model for predicting 1-year mortality after fragility hip fracture
Creators: name: Kitcharanant, Nitchanant
name: Chotiyarnwong, Pojchong
name: Tanphiriyakun, Thiraphat
name: Vanitcharoenkul, Ekasame
name: Mahaisavariya, Chantas
name: Boonyaprapa, Wichian
name: Unnanuntana, Aasis
Publisher: name: figshare
Year: 2022
Subjects: subject: Artificial Intelligence and Image Processing
subject: FOS: Computer and information sciences

description: Additional file 1.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Meh Man, Chow Tai Tam, Loc Chum, Lew Chong, Lee Sun, Lee Kee Sun, Chan Jong, Ng Yat Sun, Jung You Hong, Wong Kew Why.
Young people in residential aged care: Is Australia on track to meet its targets?
Creators: name: Brown, Mark
name: Condi, A
name: Davis, Elise
name: Goodwin, I
name: Winkler, Dianne
name: Douglas, Jacinta
Publisher: name: La Trobe
Year: 2022
Subjects: classificationCode: 44
subject: Human society
classificationCode: 4409
subject: Social work

description: Over 4500 people under 65 years of age live in residential aged care (RAC) in Australia, and they experience poorer quality of life than people with similar disabilities in other settings. Governments have long aimed to reduce admissions of young people to RAC, but in 2019, for the first time, the Australian Government adopted target dates for resolving the issue. The targets include reducing admissions of young people to near zero by 2022 and ensuring almost no one remains in RAC beyond 2025. The national strategy focuses mostly on housing and support needs being met via the National Disability Insurance Scheme. The present study drew on quarterly data from the National Aged Care Data Clearinghouse to examine progress toward these targets. Significant progress was evident in terms of young people entering RAC: admissions reduced each quarter between September 2018 and July 2020, halving over two years. No progress was evident in terms of young people leaving RAC for better arrangements; the trend neither increased nor decreased. Prospects for achieving the targets are discussed.
Additional file 2 of Antimicrobial resistance in urinary pathogens and culture-independent detection of trimethoprim resistance in urine from patients with urinary tract infection
Creators: name: Somorin, Yinka M.
name: Weir, Nichola-Jane M.
name: Pattison, Sally H.
name: Crockard, Martin A.
name: Hughes, Carmel M.
name: Tunney, Michael M.
name: Gilpin, Deirdre F.
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 2: Table S2. Antimicrobial susceptibility of urinary E. coli and Klebsiella spp. isolates. Abbreviations: S: Susceptible; I: Intermediate; R: Resistant. Breakpoints: Amoxicillin (S ≤ 8; R > 8); Ceftazidime (S ≤ 1; I = 1.5 – 4; R > 4); Ciprofloxacin (S ≤ 0.5; I = 0.75 – 1; R > 1); Co-amoxiclav (S ≤ 32; R > 32); Nitrofurantoin (S ≤ 64; R > 64); Trimethoprim (S ≤ 2; I = 3 - 4; R > 4). NA: Not Applicable. Intermediate category not approved for amoxicillin, co-amoxiclav and nitrofurantoin by EUCAST. MIC: minimum inhibitory concentration; MIC50 and MIC90, MICs that inhibit 50% and 90% of the isolates, respectively.
Additional file 1 of Antimicrobial resistance in urinary pathogens and culture-independent detection of trimethoprim resistance in urine from patients with urinary tract infection
Creators: name: Somorin, Yinka M.
name: Weir, Nichola-Jane M.
name: Pattison, Sally H.
name: Crockard, Martin A.
name: Hughes, Carmel M.
name: Tunney, Michael M.
name: Gilpin, Deirdre F.
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1: Table S1. Primers used for the detection of dfrA genes.
Scorpiops (Neoscorpiops) vrushchik Sulakhe, Deshpande, Dandekar, Padhye & Bastawade 2021
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Scorpiops
Scorpiops vrushchik

description: - S. (Neoscorpiops) vrushchik Sulakhe, Deshpande, Dandekar, Padhye & Bastawade, 2021
India
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 4, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
Additional file 3 of Antimicrobial resistance in urinary pathogens and culture-independent detection of trimethoprim resistance in urine from patients with urinary tract infection
Creators: name: Somorin, Yinka M.
name: Weir, Nichola-Jane M.
name: Pattison, Sally H.
name: Crockard, Martin A.
name: Hughes, Carmel M.
name: Tunney, Michael M.
name: Gilpin, Deirdre F.
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 3: Table S3. Microorganisms isolated from clinical urine samples.
The Age-Related Changes in Speed of Visual Perception, Visual Verbal and Visuomotor Performance, and Nonverbal Intelligence During Early School Years
Creators: name: Alghamdi, Rana
name: Murphy, Melanie
name: Goharpey, Nahal
name: Crewther, Sheila
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Speed of sensory information processing has long been recognized as an important characteristic of global intelligence, though few studies have concurrently investigated the contribution of different types of information processing to nonverbal IQ in children, nor looked at whether chronological age vs. months of early schooling plays a larger role. Thus, this study investigated the speed of visual information processing in three tasks including a simple visual inspection time (IT) task, a visual-verbal processing task using Rapid Automatic Naming (RAN) of objects as an accepted preschool predictor of reading, and a visuomotor processing task using a game-like iPad application, (the “SLURP” task) that requires writing like skills, in association with nonverbal IQ (Raven’s Coloured Progressive Matrices) in children (n = 100) aged 5–7 years old. Our results indicate that the rate and accuracy of information processing for all three tasks develop with age, but that only RAN and SLURP rates show significant improvement with years of schooling. RAN and SLURP also correlated significantly with nonverbal IQ scores, but not with IT. Regression analyses demonstrate that months of formal schooling provide additional contributions to the speed of dual-task visual-verbal (RAN) and visuomotor performance and Raven’s scores supporting the domain-specific hypothesis of processing speed development for specific skills as they contribute to global measures such as nonverbal IQ. Finally, RAN and SLURP are likely to be useful measures for the early identification of young children with lower intelligence and potentially poor reading.
Data reduction for serial crystallography using a robust peak finder
Creators: name: Hadian Jazi, Marjan
name: Sadri, Alireza
name: Barty, Anton
name: Yefanov, Oleksandr
name: Galchenkova, Marina
name: Oberthuer, Dominik
name: Komadina, Dana
name: Brehm, Wolfgang
name: Kirkwood, Henry
name: Mills, Grant
name: de Wijn, Raphael
name: Letrun, Romain
name: Kloos, Marco
name: Vakili, Mohammad
name: Gelisio, Luca
name: Darmanin, Connie
name: Mancuso, Adrian
name: Chapman, Henry N
name: Abbey, Brian
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 34
subject: Chemical sciences
subject: FOS: Chemical sciences
classificationCode: 3402
subject: Inorganic chemistry
classificationCode: 3406
subject: Physical chemistry
classificationCode: 5104
subject: Condensed matter physics

description: A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.
Data reduction for serial crystallography using a robust peak finder
Creators: name: Hadian Jazi, Marjan
name: Sadri, Alireza
name: Barty, Anton
name: Yefanov, Oleksandr
name: Galchenkova, Marina
name: Oberthuer, Dominik
name: Komadina, Dana
name: Brehm, Wolfgang
name: Kirkwood, Henry
name: Mills, Grant
name: de Wijn, Raphael
name: Letrun, Romain
name: Kloos, Marco
name: Vakili, Mohammad
name: Gelisio, Luca
name: Darmanin, Connie
name: Mancuso, Adrian P
name: Chapman, Henry N
name: Abbey, Brian
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Jung Him Jong, [Moy Ching Jang], Won Fook Shong, Wong Fong, Mah Hong Him, Mah Git, Pon Sum, Wong Wei Choy, Wong Yat Norm, Chow Sai Song.
Additional file 4 of Antimicrobial resistance in urinary pathogens and culture-independent detection of trimethoprim resistance in urine from patients with urinary tract infection
Creators: name: Somorin, Yinka M.
name: Weir, Nichola-Jane M.
name: Pattison, Sally H.
name: Crockard, Martin A.
name: Hughes, Carmel M.
name: Tunney, Michael M.
name: Gilpin, Deirdre F.
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 4: Figure S1. Gels showing detection of dfrA1 (a), dfrA5 (b), dfrA12 (c) and dfrA7&17 (d) genes.
Plethoscorpiops (Plethoscorpiops) Lourenco 2017
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Plethoscorpiops

description: Subgenus Plethoscorpiops Lourenço, 2017
1 species
type species: S. (Plethoscorpiops) profusus (Lourenço, 2017)
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 4, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
Ciprofloxacin reduces tenocyte viability and proteoglycan synthesis in short-term explant cultures of equine tendon
Creators: name: James, Stuart
name: Schuijers, Johannes
name: Daffy, J
name: Cook, Jillianne
name: Samiric, Tomislav
Publisher: name: La Trobe
Year: 2021
Subjects: Uncategorized

description: Fluoroquinolones are an effective, broad-spectrum antibiotic used to treat an array of bacterial infections. However, they are associated with an increased risk of tendinopathy and tendon rupture even after discontinuation of treatment. This condition is known as fluoroquinolone-associated tendinopathy, the underlying mechanisms of which are poorly understood. While many factors may be involved in the pathophysiology of tendinopathies in general, changes in tenocyte metabolism and viability, as well as alteration of proteoglycan metabolism are prominent findings in the scientific literature. This study investigated the effects of ciprofloxacin, a common fluoroquinolone, on cell viability, proteoglycan synthesis, and proteoglycan mRNA expression in equine superficial digital flexor tendon explants after 96 h treatment with between 1-300 μg/mL ciprofloxacin, and again after 8 days discontinuation of treatment. Ciprofloxacin caused significant reductions in cell viability by between 25-33% at all dosages except 10 μg/mL, and viability decreased further after 8 days discontinuation of treatment. Proteoglycan synthesis significantly decreased by approximately 50% in explants treated with 100 μg/mL and 300 μg/mL, however this effect reversed after 8 days in the absence of treatment. No significant mRNA expression changes were observed after the treatment period with the exception of versican which was down-regulated at the highest concentration of ciprofloxacin. After the recovery period, aggrecan, biglycan and versican genes were all significantly downregulated in explants initially treated with 1-100 μg/mL. Results from this study corroborate previously reported findings of reduced cell viability and proteoglycan synthesis in a whole tissue explant model and provide further insight into the mechanisms underlying fluoroquinolone-associated tendinopathy and rupture. This study further demonstrates that certain ciprofloxacin induced cellular changes are not rapidly reversed upon cessation of treatment which is a novel finding in the literature.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Wong Mon Bing, Wong Wah Tin, Sam Yow, Ah Him, Yip Shee, Jung Shue, Chin Dane, Leong Jong Chun, Lee Shong, and Luey Jang.
How a crisis at one maternity service became a catalyst for change across the Victorian public hospital system: A discussion paper
Creators: name: Zugna, Stefanie
name: Cullinane, Meabh
name: McLachlan, Helen
name: Forster, Della
Publisher: name: La Trobe
Year: 2022
Subjects: classificationCode: 3901
subject: Curriculum and pedagogy
classificationCode: 42
subject: Health sciences
subject: FOS: Health sciences
classificationCode: 4203
subject: Health services and systems
classificationCode: 4204
subject: Midwifery
classificationCode: 4205
subject: Nursing

description: No description supplied
Plethoscorpiops (Plethoscorpiops) profusus
Creators: name: Lourenço, Wilson R.
name: Ythier, Eric
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Scorpiones
Scorpiopidae
Plethoscorpiops

description: - S. (Plethoscorpiops) pr o fusus (Lourenço, 2017)
Myanmar
description: Published as part of Lourenço, Wilson R. & Ythier, Eric, 2022, A new species of the genus Scorpiops Peters, 1861, subgenus Euscorpiops Vachon, 1980 from Laos (Scorpiones: Scorpiopidae), pp. 1-9 in Faunitaxys 10 (27) on page 4, DOI: 10.57800/faunitaxys-10(27), http://zenodo.org/record/15352467
Constructing and analyzing disease-specific or developmental stage-specific transcription factor and miRNA co-regulatory networks
Creators: name: Nazarieh, Maryam
name: Will, Thorsten
name: Hamed, Mohamed
name: Spaniol, Christian
name: Helms, Volkhard
Publisher: name: F1000Research
Year: 2016

description: TFmiR is a freely available web server for integrative analysis of combinatorial regulatory interactions between transcription factors, miRNAs and target genes that are involved in disease processes in human. To better characterize the cellular processes at the molecular level from a network perspective in human and mouse, we have extended the published version of TFmiR by various new features such as the construction of process-specific and tissue-specific networks. Besides disease processes, the successor of TFmiR can now also be applied to identify regulatory motifs associated with the transitions between different developmental stages from the sets of genes and miRNAs provided by the user. One particular challenge in studying gene regulatory networks is to identify the main drivers and master regulatory genes that control such cell fate transitions. In addition to common topological measures and by considering tissue-exclusive genes, we reformulate this problem as an optimization problem of computing a Minimum Connected Dominating Set (MCDS) for directed graphs. MCDS is applied to the well-studied gene regulatory networks of E. coli and S. cerevisiae and to a pluripotency network for mouse embryonic stem cells. The results show that the MCDS captures most of the known key player genes identified so far in the model organisms. Moreover, this method suggests an additional small set of transcription factors as novel key players for governing cell-specific gene regulatory networks. This set can also be investigated with regard to diseases.
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Mah Wing Bong, Hong Hong Choe, Gin Kan Ming, Gin Fay Ming, Gin Lam Ming, Chow How Kee, Pon Chew, Lum Ming, [Lum Him], Lum Soon.
Fully reproducible data analysis with Snakemake and Bioconda
Creators: name: Köster, Johannes
Publisher: name: F1000Research
Year: 2016

description: Reproducible and scalable data analyses are crucial to obtain reliable insights from today's high throughput technologies. With the popular workflow management system Snakemake we have previously provided a powerful framework to formalize and execute data analyses on workstations, compute servers and clusters without the need to modify the workflow definition.

In bioinformatics, analyses typically rely on the application of diverse tools and libraries coming from various, sometimes conflicting software ecosystems, and requiring diverse ways of installation. We extend the notion of reproducibility to the definition and automated deployment of software dependencies, and present Bioconda, a distribution of bioinformatics software for the Conda package manager. Bioconda normalizes and unifies the diverse ways of installing bioinformatics software and allows the easy deployment and automatic dependency resolution without admin rights. It is growing rapidly and provides over 1400 packages today, from standalone compiled programs like BWA or Cufflinks to R, Python and Perl packages.

In addition, we present the integration of the Conda package manager into the Snakemake workflow management system. This turns Snakemake into the first text-based workflow management system that allows to define a workflow together with its software dependencies. In consequence, the installation of the required software in strictly defined versions becomes a part of the automated workflow execution itself.

In combination with Bioconda, Snakemake provides self-contained documentation, fully automated deployment and scalable as well as reproducible execution of bioinformatics analyses.
Licmophoraceae Kutzing
Creators: name: Al-Handal, Adil Y.
name: Compère, Pierre
name: Criobe-Usr, Catherine Riaux-Gobin
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Chromista
Ochrophyta
Bacillariophyceae
Licmophorales
Licmophoraceae

description: Family Licmophoraceae Kützing   Licmophora abbreviata C. Agardh (Pl. 4, Figs 2, 3) References: Hustedt 1931 -59, p. 66, fig. 590; Desikachary 1988, pl. 611, figs 4, 5; Witkowski et al. 2000, p. 63, pl. 20, figs 3-5.
 Features: Apical axis: 65-75µm, transapical axis (at widest part): 6-17µm, striae 15-18 in 10 µm. Frustules broadly cuneate in girdle view. Valves clavate with slightly rounded apices. Sternum linear, very narrow. When seen in girdle view, several longitudinal septa appear as lines.
 Remarks: Widely distributed epiphytic species in the marine littoral.
 Occurrence: Frequent in Reunion and Rodrigues Islands. Previously reported from Seychelles (G).
description: Published as part of Al-Handal, Adil Y., Compère, Pierre & Criobe-Usr, Catherine Riaux-Gobin, 2016, Marine benthic diatoms in the coral reefs of Reunion and Rodrigues Islands, West Indian Ocean, pp. 1-78 in Micronesica 2016 (3) on page 10, DOI: 10.5281/zenodo.13282811
Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions
Creators: name: Yi, Changyu
name: Wang, Xinchao
name: Chen, Qian
name: Callahan, Damien L
name: Fournier-Level, Alexandre
name: Whelan, James
name: Jost, Ricarda
Publisher: name: La Trobe
Year: 2023
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3105
subject: Genetics
classificationCode: 3108
subject: Plant biology

description: No description supplied.
Time-dependent interactome-transcriptome analysis of PDAC tumorigenesis
Creators: name: Costa, Quentin Da
name: Guillaumond, Fabienne
name: Rioualen, Claire
name: Beloribi-Djefaflia, Sadia
name: Gouirand, Victoire
name: Roques, Julie
name: Crenon, Isabelle
name: Mas, Eric
name: Vasseur, Sophie
name: Bidaut, Ghislain
Publisher: name: F1000Research
Year: 2016

description: Time-ITI is a network-based analysis program, allowing the identification of differentially expressed gene modules by integrating biological interaction data, on top of gene expression profiles of different timepoints.

Based on transcriptomic profiles of mouse model pancreata, we propose to identify clusters of interlinked genes contributing to the tumoral metabolic processes over the different stages of tumorigenesis, in Pancreatic Ductal Adenocarcinoma (PDAC).
Canadian Pacific Steamships agent's stubs
Creators: name: Yip Sang Company
name: Canadian Pacific Steamships
Publisher: name: The University of British Columbia
Year: 2016

description: Ticket stubs for the following passengers: Chow Hing Wei, Dar Wing Jum, Dar Song Chew, Chan Ting, Ow Shew Jar, Lai Bing Quon, Fong Fon, Chow Hing, Jung Goon Jong, and Jung Nay Hank.