bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial
Authors: O'Grady Nicholas , Gibbs David L , Abdilleh Kawther , Asare Adam , Asare Smita , Venters Sara , Brown-Swigart Lamorna , Hirst Gillian L , Wolf Denise , Yau Christina , van 't Veer Laura J , Esserman Laura , Basu Amrita 
Published: June 2021

AbstractObjectivesIn this paper, we discuss leveraging cloud-based platforms to collect, visualize, analyze, and share data in the context of a clinical trial. Our cloud-based infrastructure, Patient Repository of Biomolecular Entities (PRoBE), has given us the opportunity for uniform data structure, more efficient analysis of valuable data, and increased collaboration between researchers.Materials and MethodsWe utilize a multi-cloud platform to manage and analyze data generated from the clinical Investigation of Serial Studies to Predict Your Therapeutic Response with Imaging And moLecular Analysis 2 (I-SPY 2 TRIAL). A collaboration with the Institute for Systems Biology Cancer Gateway in the Cloud has additionally given us access to public genomic databases. Applications to I-SPY 2 data have been built using R Shiny, while leveraging Google's BigQuery tables and SQL commands for data mining.ResultsWe highlight the implementation of PRoBE in several unique case studies including prediction of biomarkers associated with clinical response, access to the Pan-Cancer Atlas, and integrating pathology images within the cloud. Our data integration pipelines, documentation, and all codebase will be placed in a Github repository.Discussion and conclusionWe are hoping to develop risk stratification diagnostics by integrating additional molecular, magnetic resonance imaging, and pathology markers into PRoBE to better predict drug response. A robust cloud infrastructure and tool set can help integrate these large datasets to make valuable predictions of response to multiple agents. For that reason, we are continuously improving PRoBE to advance the way data is stored, accessed, and analyzed in the I-SPY 2 clinical trial.
Quantification of Usaramine and its N-Oxide Metabolite in Rat Plasma Using Liquid Chromatography-Tandem Mass Spectrometry
Authors: Lin Feifei , Ma Yan , Pan Anni , Ye Yang , Liu Jia 
Published: June 2021

Abstract
A sensitive, fast and robust liquid chromatography--tandem mass spectrometry (LC–MS-MS) method was developed and validated for the determination of usaramine (URM) and usaramine N-oxide (UNO) in rat plasma. The separation was conducted on an ACQUITY UPLC BEH C18 Column (50 × 2.1 mm, 1.7 μm) and gradient eluted with mobile phase A (0.1% formic acid with 5 mM ammonium acetate in water) and B (0.1% formic acid in acetonitrile/methanol, 9/1, v/v). The method was linear over the range of 1–2,000 ng/mL for both analytes. The validated method was applied to investigate the pharmacokinetic behaviors and sex differences of URM and its N-oxide metabolite in rats. After intravenous administration of URM at 1 mg/kg, the AUC0-t values for URM and UNO were 363 ± 65 and 172 ± 32 ng/mL*h in male rats, while 744 ± 122 and 30.7 ± 7.4 ng/mL*h in females, respectively. The clearance of URM was significantly higher in male rats than in females (2.77 ± 0.50 vs 1.35 ± 0.19 L/h/kg, P &lt; 0.05). After oral administration of URM at 10 mg/kg, the AUC0-t values of URM and UNO were 1,960 ± 208 and 1,637 ± 246 ng/mL*h in male rats, while 6,073 ± 488 and 300 ± 62 ng/mL*h in females, respectively. The oral bioavailability of URM in female rats (81.7%) was much higher than in males (54.0%). In conclusion, sex-based differences were observed in the pharmacokinetics, N-oxide metabolism and oral bioavailability of URM.
Can the Intake of a Synthetic Tryptamine be Detected Only by Blood Plasma Analysis? A Clinical Toxicology Case Involving 4-HO-MET
Authors: Wagmann Lea , Manier Sascha K , Meyer Markus R 
Published: June 2021

Abstract
Tryptamines represent a group of hallucinogenic new psychoactive substances with increasing prevalence. Unfortunately, only limited data concerning their toxicology and bioanalysis are available as tryptamines are not included in routine screening procedures in many laboratories. In order to expand the current knowledge, we report a non-fatal clinical toxicology case involving the synthetic tryptamine 4-HO-MET (4-hydroxy-N-methyl-N-ethyl-tryptamine, 3-{2-[ethyl(methyl)amino]ethyl}-1H-indol-4-ol, metocin or methylcybin). As only blood of the intoxicated patient was available, our systematic blood plasma screening approaches based on gas chromatography–mass spectrometry (GC–MS) and liquid chromatography (LC) coupled to low-resolution linear ion trap mass spectrometry (ITMSn) or high-resolution tandem mass spectrometry (HRMS-MS) were conducted. The ingestion of the synthetic tryptamine 4-HO-MET could be revealed by blood plasma analysis using both LC-based systematic screening approaches. However, 4-HO-MET was not detected by GC–MS. Furthermore, the detection of metabolites, which may be used to confirm an intake of the parent compound 4-HO-MET, was only successful using LC–HRMS-MS most probably due to its increased sensitivity compared to LC–ITMSn. A total of four metabolites were detected in blood, including N-demethyl-, oxo- and hydroxy-4-HO-MET, as well as the N-oxide. Finally, LC–HRMS-MS analysis revealed a plasma concentration of 193 ng/mL for 4-HO-MET using the standard addition method. The presented data may help clinical and forensic toxicologists with the interpretation of future cases involving synthetic tryptamines, especially if only blood samples are available.
Short- and Long-Term Stability of Methylphenidate and Its Metabolites in Blood
Authors: Smith Christina R , Swortwood Madeleine J 
Published: June 2021

Abstract
Methylphenidate (MPH) is a medication used to combat attention-deficit/hyperactivity disorder by speeding up brain activity. MPH has two chiral centers; however, d-threo-MPH is responsible for its effects. Few studies have analyzed MPH and its metabolites, ritalinic acid (RA) and ethylphenidate (EPH), in blood. Stability studies are crucial in a forensic setting to provide insight on ideal storage conditions and analysis time. In this study, d,l-MPH, d,l-EPH and RA were analyzed at two concentrations (15 and 150 ng/mL) over 5 months at room temperature (∼25°C), refrigerated (4°C), frozen (–20°C) and elevated (35°C) temperatures. Analytes were analyzed using a validated liquid chromatography--mass spectrometry method. RA concentrations increased 53% at 25°C after 24 h, while d- and l-MPH concentrations dropped 18.1 and 20.6%, respectively. Additionally, d- and l-EPH concentrations decreased 22.3 and 28.8%, respectively. All analytes were stable at 4°C for 1 week (±17% change). At −20°C, all analytes were stable for 5 months. At 35°C, l-EPH remained stable for 24 h (14.4% loss) at the high concentration, while RA increased 244%. Losses of 64.1, 68.7 and 27.2% were observed for d- MPH, l-MPH and d-EPH, respectively. Due to this, a follow-up study was designed to assess the breakdown of MPH. The short-term experiment assessed d,l-MPH at two concentrations for 1 month in the same conditions. As MPH decreased, RA concentrations rose. At 25°C, it took 2 weeks for MPH to metabolize completely into RA. In refrigerated and frozen temperatures, MPH did not completely metabolize to RA. In elevated temperatures, MPH broke down to RA within 2 weeks. Due to this, it was concluded that d,l-MPH breaks down in the blood to its metabolite RA and may make data interpretation difficult if samples are not properly stored. The optimal storage for these analytes is recommended at −20°C.
Horn Fly (Diptera: Muscidae)—Biology, Management, and Future Research Directions
Authors: Brewer Gary J , Boxler Dave J , Domingues Luísa N , Trout Fryxell Rebecca T , Holderman Chris , Loftin Kelly M , Machtinger Erika , Smythe Brandon , Talley Justin L , Watson Wes 
Published: June 2021

AbstractThe horn fly, Haematobia irritans irritans (L.), is one of the most important external parasites of cattle in North America and elsewhere. Horn fly adults have an intimate association with cattle, their primary host. With their often-high numbers and by feeding up to 38 times per day per fly, horn flies stress cattle. The resulting productivity loss is valued at more than 2.3 billion USD in the United States. Insecticides are commonly used to mitigate direct injury from feeding and indirect injury from disease transmission. This paper discusses horn fly biology, distribution, and management. Emphasis is on promising new approaches in novel insecticides, repellents, biological control, vaccines, animal genetics, and sterile insect technology that will lead to effective preventative tactics and the integration of smart technologies with horn fly management. We conclude with a discussion of research needs necessary to shift horn fly integrated pest management to an emphasis on preventative tactics and the precision use of reactive techniques.
An investigation into the nonstationary characteristics of separation-bubble formation on a smooth circular cylinder in the critical transition range
Authors: Lai Yi-Huei , Miau Jiun-Jih 
Published: June 2021

Abstract
To investigate the characteristics of the separation-bubble formation of flow over a smooth circular cylinder in the critical transition range, a sliding-window (SW) method and a peak-valley (PV) method were proposed to identify the intermittent jumps, named the characteristic events, in the real-time pressure signal obtained on both sides of the cylinder model. By evaluating the counts of the qualified events of the SW and PV methods, the PV method was found less sensitive to the small-scale disturbances in the pressure signal, therefore was adopted for later analysis. With the PV method, the characteristic events were identified from the pressure signal and categorized into two types: Type-1 is referred to the events of pressure descending and Type-2 is referred to the events of pressure ascending. Subsequently, the count per minute of the characteristic events was determined for describing the intermittency of the separation-bubble formation, and the time scale of each of the characteristic event was regarded as the time length of the separation-bubble formation. The count per minute of the characteristic events appeared to be the highest in the transitional regime. While the time scales of the characteristic events were varying with Reynolds number, the weighting-averaged normalized time scales in the transitional regime of the three cases studied were found comparable to the normalized time scale of the lift jump noted in the literature. Physically, the characteristic events found in the pressure signals in this study can be attributed to the three-dimensional aspect of separation-bubble formation.
Influence of anthropic and eco-hydrological factors on the floristic diversity of the herbaceous vegetation around the temporary ponds in Ferlo, northern Senegal
Authors: Faye Ndiabou , Diallo Aly , Sagna Moustapha Bassimbé , Peiry Jean Luc , Sarr Papa Saliou , Guisse Aliou 
Published: June 2021

AbstractTemporary ponds play substantial roles in preserving biodiversity in the Sahel. This study investigated the influence of anthropic and eco-hydrological factors on the plant diversity around two grazed ponds and one ungrazed pond in Ferlo, northern Senegal. Two phytoecological transects were established per pond. On each transect, homogenous herbaceous vegetation units were identified and characterized (herbaceous cover, exposure, soil texture, soil moisture and pH, average height and slope). The herbaceous flora comprised 55 species, 41 genera and 22 families across the three ponds. Species of the Poaceae, particularly Eragrostis tremula and Enteropogon prieurii, mostly colonized the grazed ponds, while the ungrazed pond favored other families’ species such as Achyranthes sp., Commelina forsskaolii, Corchorus sp. The Shannon’s diversity index (H′) of Wendu Marodi (ungrazed pond) was slightly higher (4.9 bits) than that of Belel Lougal and Belel Sow (grazed ponds) with 4.8 and 4.5 bits, respectively. The equitability indices were relatively high in the three ponds (0.85, 0.83 and 0.78). Eco-ecological factors distinguished four species’ groupings: a Tribulus terrestris grouping colonizing the constraining and over-grazed zones, a Digitaria horizontalis grouping, and Chloris barbata grouping found in the transition zones, and an Achyranthes aspera grouping in the wetlands, where woody plants were strongly present and the anthropic action low. This study highlighted the importance of maintaining a landscape mosaic of ungrazed or semi-protected ponds and grazed ponds to preserve the herbaceous floristic diversity in the center of Ferlo (Senegal) and the Sahel in general.
Endovascular aortic aneurysm repair with reversed chimney graft technique in a patient with crossed fused renal ectopia: a technical note
Authors: Kawatani Yohei , Yamasaki Motoshige , Oguri Atsushi 
Published: June 2021

Abstract
Crossed fused renal ectopia is a very rare congenital ectopia and poses great challenges when performing abdominal aortic surgery because of the accompanying abnormal vessels and urinary tracts. A 79-year-old woman with an abdominal aortic aneurysm and L-shaped crossed fused renal ectopia was referred to our facility. One of the large ectopic renal arteries arose from the right common iliac artery. The aneurysm was treated with an endovascular aortic repair. The reversed chimney graft technique was applied to preserve the ectopic renal artery while elongating the distal landing zone on the right side. The patient experienced no complications such as renal dysfunction or recurrence of the abdominal aortic aneurysm during the 6-month follow-up period.
Liposarcoma of gallbladder: a case report and literature review
Authors: Ushida Yuta , Ito Hiromichi , Inoue Yosuke , Sato Takafumi , Ono Yoshihiro , Oba Atsushi , Takahashi Yu 
Published: June 2021

Abstract
A 53-year-old man with prior history of resection of liposarcoma in his leg presented with gallbladder mass. Computed tomography showed 4-cm tumor at gallbladder fundus with weak enhancement with IV contrast. Differential diagnoses included hemangioma and liposarcoma, and laparoscopic cholecystectomy was recommended. In the operating room, the tumor appeared without serosal and liver invasions and uncomplicated laparoscopic cholecystectomy was completed. Histopathological examination revealed the tumor as myxoid liposarcoma with round cells. Adjuvant chemotherapy was not given, and he was placed on imaging surveillance. At 16 months after the operation, he developed recurrence of liposarcoma in the left popliteal fossa.
Determining quarantine length and testing frequency for international border opening during the COVID-19 pandemic
Authors: Dickens Borame L , Koo Joel R , Lim Jue Tao , Park Minah , Sun Haoyang , Sun Yinxiaohe , Zeng Zitong , Quaye Sharon Esi Duoduwa , Clapham Hannah E , Wee Hwee Lin , Cook Alex R 
Published: June 2021

Abstract

Background
The COVID-19 pandemic has resulted in the closure or partial closure of international borders in almost all countries. Here, we investigate the efficacy of imported case detection considering quarantine length and different testing measures for travellers on arrival.

Methods
We examine eight broad border control strategies from utilizing quarantine alone, pre-testing, entry and exit testing, and testing during quarantine. In comparing the efficacy of these strategies, we calculate the probability of detecting travellers who have been infected up to 2 weeks pre-departure according to their estimated incubation and infectious period. We estimate the number of undetected infected travellers permitted entry for these strategies across a prevalence range of 0.1–2% per million travellers.

Results
At 14-day quarantine, on average 2.2% (range: 0.5–8.2%) of imported infections are missed across the strategies, leading to 22 (5–82) imported cases at 0.1% prevalence per million travellers, increasing up to 430 (106–1641) at 2%. The strategy utilizing exit testing results in 3.9% (3.1–4.9%) of imported cases being missed at 7-day quarantine, down to 0.4% (0.3–0.7%) at 21-day quarantine, and the introduction of daily testing, as the most risk averse strategy, reduces the proportion further to 2.5–4.2% at day 7 and 0.1–0.2% at day 21 dependent on the tests used. Rapid antigen testing every 3 days in quarantine leads to 3% being missed at 7 days and 0.7% at 14 days, which is comparable to PCR testing with a 24-hour turnaround.

Conclusions
Mandatory testing, at a minimal of pre-testing and on arrival, is strongly recommended where the length of quarantining should then be determined by the destination country’s level of risk averseness, pandemic preparedness and origin of travellers. Repeated testing during quarantining should also be utilized to mitigate case importation risk and reduce the quarantining duration required.
Thermophysical evolution of planetesimals in the primordial disc
Authors: Davidsson Björn J R 
Published: June 2021

ABSTRACT
The primordial disc of small icy planetesimals, once located at 15–$30\, \mathrm{au}$ from the Sun, was disrupted by giant planet migration in the early Solar system. The primordial disc thereby became the source region of objects in the present-day Kuiper belt, scattered disc, and Oort Cloud. I present the thermophysical code ‘Numerical Icy Minor Body evolUtion Simulator’, or nimbus, and use it to study the thermophysical evolution of planetesimals in the primordial disc prior to its disruption. Such modelling is mandatory in order to understand the behaviour of dynamically new comets from the Oort Cloud, as well as the activity of Centaurs and short-period comets from the scattered disc, that return pre-processed to the vicinity of the Sun. I find that bodies in the midst of the primordial disc with diameters ranging 4–$200\, \mathrm{km}$ lost all their CO ice on time-scales of order 0.1–$10\, \mathrm{Myr}$ depending on size, through a combination of protosolar and long-lived radionuclide heating. CO and other hypervolatiles therefore require a less volatile host for their storage. I consider two possible hosts: amorphous water ice and CO2 ice. Because of the high luminosity of the protosun, some primordial disc bodies may have sustained significant crystallization, CO:CO2 segregation, and CO2 sublimation in the uppermost few tens of metres. I discuss how this may affect coma abundance ratios and distant activity in dynamically new comets.
Deep Extragalactic VIsible Legacy Survey (DEVILS): consistent multiwavelength photometry for the DEVILS regions (COSMOS, XMMLSS, and ECDFS)
Authors: Davies L J M , Thorne J E , Robotham A S G , Bellstedt S , Driver S P , Adams N J , Bilicki M , Bowler R A A , Bravo M , Cortese L , Foster C , Grootes M W , Häußler B , Hashemizadeh A , Holwerda B W , Hurley P , Jarvis M J , Lidman C , Maddox N , Meyer M , Paolillo M , Phillipps S , Radovich M , Siudek M , Vaccari M , Windhorst R A 
Published: June 2021

ABSTRACT
The Deep Extragalactic VIsible Legacy Survey (DEVILS) is an ongoing high-completeness, deep spectroscopic survey of ∼60 000 galaxies to Y &lt; 21.2 mag, over ∼6 deg2 in three well-studied deep extragalactic fields: D10 (COSMOS), D02 (XMMLSS), and D03 (ECDFS). Numerous DEVILS projects all require consistent, uniformly derived and state-of-the-art photometric data with which to measure galaxy properties. Existing photometric catalogues in these regions either use varied photometric measurement techniques for different facilities/wavelengths leading to inconsistencies, older imaging data and/or rely on source detection and photometry techniques with known problems. Here, we use the ProFound image analysis package and state-of-the-art imaging data sets (including Subaru-HSC, VST-VOICE, VISTA-VIDEO, and UltraVISTA-DR4) to derive matched-source photometry in 22 bands from the FUV to 500 $\mu$m. This photometry is found to be consistent, or better, in colour analysis to previous approaches using fixed-size apertures (which are specifically tuned to derive colours), but produces superior total source photometry, essential for the derivation of stellar masses, star formation rates, star formation histories, etc. Our photometric catalogue is described in detail and, after internal DEVILS team projects, will be publicly released for use by the broader scientific community.
Analysis of modern astrometric catalogues in the Gaia era
Authors: Akhmetov V S , Fedorov P N , Tsvetkova V S , Bannikova E Yu 
Published: June 2021

ABSTRACT
We investigate the systems of proper motions of stars in the ground-based catalogues HSOY, UCAC5, GPS1, and PMA derived by combining with the Gaia DR1 space data. Assuming the systematic differences of stellar proper motions of two catalogues to be caused by the mutual solid-body rotation and glide of the coordinate systems produced by the data of the catalogues under comparison, we analyse the components of the mutual rotation vector and displacement of the origins of these systems. The equatorial components of the vector of mutual rotation velocity of the compared coordinate systems, as well as velocities of the mutual displacement of their origins, vary within the range from 0.2 to 2.9 mas yr−1, were derived from a comparison of proper motions of the sources that are common for Gaia EDR3 and the TGAS, UCAC5, HSOY, GPS1, and PMA catalogues, respectively. The systematic errors of proper motions of stars in the HSOY, GPS1, PMA, and Gaia EDR3 catalogues in the range of faint stellar magnitudes were estimated by analysing the formal proper motions of extragalactic objects contained in these catalogues. The coordinate system realized by the Gaia EDR3 data at the level of &lt;0.1 mas yr−1 is shown to have no rotation and glide relative to the LQAC-5, ALLWISEAGN, Milliquas extragalactis sources within the range from 15 to 21 stellar G mag. Among the ground-based catalogues, the system of proper motions of the PMA stars, which is independent of the Gaia EDR3 data, is the closest to the Gaia EDR3 system of proper motions in G magnitude range from 15 to 21 and UCAC5 is closer to Gaia EDR3 system than PMA in the 10–15 mag range.
High-ionization emission-line ratios from quasar broad-line regions: metallicity or density?
Authors: Temple Matthew J , Ferland Gary J , Rankine Amy L , Chatzikos Marios , Hewett Paul C 
Published: June 2021

ABSTRACT
The flux ratios of high-ionization lines are commonly assumed to indicate the metallicity of the broad emission-line region in luminous quasars. When accounting for the variation in their kinematic profiles, we show that the N v/C iv, (Si iv + O iv])/C iv, and N v/Ly α line ratios do not vary as a function of the quasar continuum luminosity, black hole mass, or accretion rate. Using photoionization models from cloudy, we further show that the observed changes in these line ratios can be explained by emission from gas with solar abundances, if the physical conditions of the emitting gas are allowed to vary over a broad range of densities and ionizing fluxes. The diversity of broad-line emission in quasar spectra can be explained by a model with emission from two kinematically distinct regions, where the line ratios suggest that these regions have either very different metallicity or density. Both simplicity and current galaxy evolution models suggest that near-solar abundances, with parts of the spectrum forming in high-density clouds, are more likely. Within this paradigm, objects with stronger outflow signatures show stronger emission from gas that is denser and located closer to the ionizing source, at radii consistent with simulations of line-driven disc-winds. Studies using broad-line ratios to infer chemical enrichment histories should consider changes in density and ionizing flux before estimating metallicities.