bluuebunny/crossref_metadata_2025_split huggingface dataset:
plantTracker: An R package to translate maps of plant occurrence into demographic data
Authors: Stears Alice E. , Adler Peter B. , Albeke Shannon E. , Atkins David H. , Studyvin Jared , Laughlin Daniel C. 
Published: August 2022

Abstract

Long‐term demographic data are rare yet invaluable for conservation, management, and basic research on the underlying mechanisms of population and community dynamics. Historical and contemporary mapped datasets of plant location and basal area present a relatively untapped source of demographic records that, in some cases, span over 20 years of sequential data collection. However, these maps do not uniquely mark individual plants, making the process of collecting growth, survival, and recruitment data difficult.

Recent efforts to translate historical maps of plant occurrence into shapefiles make it possible to use computer algorithms to track individuals through time and determine individual growth and survival. We summarize the plantTracker R package, which contains user‐friendly functions to extract neighbourhood density, growth, and survival data from repeatedly‐sampled maps of plant location and basal area. These functions can be used with data derived from quadrat maps, aerial photography, and remote sensing, and while designed for use with perennial plants, can be applied to any repeatedly mapped sessile organism.

This package contains two primary functions: trackSpp(), which tracks individuals through time and assigns demographic data, as well as getNeighbors(), which calculates both within and between‐species neighbourhood occupancy around each mapped individual. plantTracker also contains functions to estimate plot‐level recruitment, calculate plot‐level population growth rate, and create quadrat maps.

We tested the accuracy of the trackSpp() function on two spatial demographic datasets. The function was nearly perfect at assigning individual identities and survival status when tested on maps of tree basal area and perennial forb point locations. In both cases, the function correctly assigned survival and recruitment with 99% accuracy. These accurate and precise functions will expand the amount of data available to investigate demographic processes, which are fundamental drivers of population, community, and ecosystem processes.
Comparison of patient characteristics and long‐term mortality between transferred and non‐transferred COVID‐19 patients in Dutch intensive care units: A national cohort study
Authors: Wortel Safira A. , Bakhshi‐Raiez Ferishta , Termorshuizen Fabian , de Lange Dylan W. , Dongelmans Dave A. , de Keizer Nicolette F. ,   the Dutch COVID‐19 Research Consortium
Published: August 2022

AbstractBackgroundCOVID‐19 patients were often transferred to other intensive care units (ICUs) to prevent that ICUs would reach their maximum capacity. However, transferring ICU patients is not free of risk. We aim to compare the characteristics and outcomes of transferred versus non‐transferred COVID‐19 ICU patients in the Netherlands.MethodsWe included adult COVID‐19 patients admitted to Dutch ICUs between March 1, 2020 and July 1, 2021. We compared the patient characteristics and outcomes of non‐transferred and transferred patients and used a Directed Acyclic Graph to identify potential confounders in the relationship between transfer and mortality. We used these confounders in a Cox regression model with left truncation at the day of transfer to analyze the effect of transfers on mortality during the 180 days after ICU admission.ResultsWe included 10,209 patients: 7395 non‐transferred and 2814 (27.6%) transferred patients. In both groups, the median age was 64 years. Transferred patients were mostly ventilated at ICU admission (83.7% vs. 56.2%) and included a larger proportion of low‐risk patients (70.3% vs. 66.5% with mortality risk <30%). After adjusting for age, APACHE IV mortality probability, BMI, mechanical ventilation, and vasoactive medication use, the hazard of mortality during the first 180 days was similar for transferred patients compared to non‐transferred patients (HR [95% CI] = 0.99 [0.91–1.08]).ConclusionsTransferred COVID‐19 patients are more often mechanically ventilated and are less severely ill compared to non‐transferred patients. Furthermore, transferring critically ill COVID‐19 patients in the Netherlands is not associated with mortality during the first 180 days after ICU admission.
Nitric oxide‐soluble guanylyl cyclase pathway as a contributor to age‐related memory impairment in Drosophila
Authors: Tonoki Ayako , Nagai Saki , Yu Zhihua , Yue Tong , Lyu Sizhe , Hou Xue , Onuki Kotomi , Yabana Kaho , Takahashi Hiroki , Itoh Motoyuki 
Published: August 2022

AbstractAge‐related changes in the transcriptome lead to memory impairment. Several genes have been identified to cause age‐dependent memory impairment (AMI) by changes in their expression, but genetic screens to identify genes critical for AMI have not been performed. The fruit fly is a useful model for studying AMI due to its short lifespan and the availability of consistent techniques and environments to assess its memory ability. We generated a list of candidate genes that act as AMI regulators by performing a comprehensive analysis of RNAsequencing data from young and aged fly heads and genome‐wide RNAi screening data to identify memory‐regulating genes. A candidate screen using temporal and panneuronal RNAi expression was performed to identify genes critical for AMI. We identified the guanylyl cyclase β‐subunit at 100B (gycβ) gene, which encodes a subunit of soluble guanylyl cyclase (sGC), the only intracellular nitric oxide (NO) receptor in fruit flies, as a negative regulator of AMI. RNAi knockdown of gycβ in neurons and NO synthase (NOS) in glia or neurons enhanced the performance of intermediate‐term memory (ITM) without apparent effects on memory acquisition. We also showed that pharmacological inhibition of sGC and NOS enhanced ITM in aged individuals, suggesting the possibility that age‐related enhancement of the NO‐sGC pathway causes memory impairment.
Tobacco/nicotine use among individuals using cannabis for therapeutic purposes
Authors: Steinberg Marc L. , Rosen Rachel L. , Billingsley Benjamin , Shah Drashya , Bender Michele , Shargo Kyra , Aamir Affan , Bridgeman Mary Barna 
Published: August 2022

AbstractBackground and ObjectivesWhile the relationship between recreational cannabis and nicotine use is well established, little is known about nicotine use among users of cannabis for therapeutic purposes (CTP).MethodsPatients attending a medical marijuana dispensary (N = 697; 75.3% White; 60.0% male) completed a survey examining nicotine use, motivation to quit cigarette smoking, routes of administration of nicotine and cannabis, and CTP qualifying conditions.ResultsMore than one‐third (39.3%) of participants reported current nicotine use. Compared to exclusive cigarette smokers, e‐cigarette users and non‐users of nicotine were approximately four times more likely to vape, rather than to smoke, cannabis. Furthermore, 46.8% of cigarette smokers reported plans to quit smoking in the next 6 months (but not in the next month) and an additional 31.6% planned to quit in the next month. Having a psychiatric condition was associated with nicotine use and higher motivation to quit smoking.Discussion and ConclusionsUsers of CTP are more likely to use nicotine products than the general population and the route of administration of nicotine products is related to the route of administration of CTP. If aerosolized CTP is a less harmful route of administration than smoked CTP, dispensary staff should be aware of this relationship and take this into account when recommending a noncombustible route.Scientific SignificanceThis study further characterizes nicotine use behaviors and motivation to quit smoking among users of CTP and may be among the first to examine nicotine use among patients of a medical marijuana dispensary.
Impact of volute design features on hemodynamic performance and hemocompatibility of centrifugal blood pumps used in ECMO
Authors: Li Yuan , Wang Hongyu , Xi Yifeng , Sun Anqiang , Deng Xiaoyan , Chen Zengsheng , Fan Yubo 
Published: August 2022

AbstractBackgroundThe centrifugal blood pump volute has a significant impact on its hemodynamic performance hemocompatibility. Previous studies about the effect of volute design features on the performance of blood pumps are relatively few.MethodsIn the present study, the computational fluid dynamics (CFD) method was utilized to evaluate the impact of volute design factors, including spiral start position, volute tongue radius, inlet height, size, shape and diffuser pipe angle on the hemolysis index and thrombogenic potential of the centrifugal blood pump.ResultsCorrelation analysis shows that flow losses affect the hemocompatibility of the blood pump by influencing shear stress and residence time. The closer the spiral start position of the volute, the better the hydraulic performance and hemocompatibility of the blood pump. Too large or too small volute inlet heights can worsen hydraulic performance and hemolysis, and higher volute inlet height can increase the thrombogenic potential. Small volute sizes exacerbate hemolysis and large volute sizes increase the thrombogenic risk, but volute size does not affect hydraulic performance. When the diffuser pipe is tangent to the base circle of the volute, the best hydraulic performance and hemolysis performance of the blood pump is achieved, but the thrombogenic potential is increased. The trapezoid volute has poor hydraulic performance and hemocompatibility. The round volute has the best hydraulic and hemolysis performance, but the thrombogenic potential is higher than that of the rectangle volute.ConclusionThis study found that the hemolysis index shows a significant correlation with spiral start position, volute size, and diffuser pipe angle. Thrombogenic potential exhibits a good correlation with all the studied volute design features. The flow losses affect the hemocompatibility of the blood pump by influencing shear stress and residence time. The finding of this study can be used to guide the optimization of blood pump for improving the hemodynamic performance and hemocompatibility.
Coronary microembolization sheep model by adjusting the number of microspheres based on coronary blood flow
Authors: Tanaka Shun , Nishinaka Tomohiro , Umeki Akihide , Fujii Masahiko , Imaoka Shusuke , Kobayashi Futoshi , Inatomi Ayako , Katagiri Nobumasa , Tsukiya Tomonori , Mizuno Toshihide , Ono Minoru 
Published: August 2022

AbstractBackgroundA heart failure (HF) model using coronary microembolization in large animals is indispensable for medical research. However, the heterogeneity of myocardial response to microembolization is a limitation. We hypothesized that adjusting the number of injected microspheres according to coronary blood flow could stabilize the severity of HF. This study aimed to evaluate the effect of microsphere injection based on the left coronary artery blood flow in an animal model.MethodsMicroembolization was induced by injecting different numbers of microspheres (polystyrene, diameter: 90 μm) into the left descending coronary artery of the two groups of sheep (400 and 600 times coronary blood flow [ml/min]). Hemodynamic parameters, the pressure–volume loop of the left ventricle, and echocardiography findings were examined at 0.5, 1.5, 3.5, and 6.5 h after microembolization.ResultsEnd‐diastolic pressure and normalized heart rate increased over time, and were significantly higher in 600 × coronary blood flow group than those in 400 × coronary blood flow group (p = 0.04 and p < 0.01, respectively). The maximum rate of left‐ventricular pressure rise and normalized stroke volume decreased over time, and were significantly lower in 600 × coronary blood flow group than those in 400 × coronary blood flow group (p < 0.01 and p < 0.01, respectively). The number of microspheres per coronary blood flow was significantly correlated with the decrease in stroke volume and the maximum rate of left ventricular pressure rise in 6.5 h (r = 0.74, p = 0.01 and r = 0.71, p = 0.02, respectively).ConclusionsAdjusting the number of injected microspheres based on the coronary blood flow enabled the creation of HF models with different degrees of severity.
A High-Dimensional Mediation Model for a Neuroimaging Mediator: Integrating Clinical, Neuroimaging, and Neurocognitive Data to Mitigate Late Effects in Pediatric Cancer
Authors: Wang Jade Xiaoqing , Li Yimei , Reddick Wilburn E. , Conklin Heather M. , Glass John O. , Onar-Thomas Arzu , Gajjar Amar , Cheng Cheng , Lu Zhao-Hua 
Published: August 2022

Abstract
Pediatric cancer treatment, especially for brain tumors, can have profound and complicated late effects. With the survival rates increasing because of improved detection and treatment, a more comprehensive understanding of the impact of current treatments on neurocognitive function and brain structure is critically needed. A frontline medulloblastoma clinical trial (SJMB03) has collected data, including treatment, clinical, neuroimaging, and cognitive variables. Advanced methods for modeling and integrating these data are critically needed to understand the mediation pathway from the treatment through brain structure to neurocognitive outcomes. We propose an integrative Bayesian mediation analysis approach to model jointly a treatment exposure, a high-dimensional structural neuroimaging mediator, and a neurocognitive outcome and to uncover the mediation pathway. The high-dimensional imaging-related coefficients are modeled via a binary Ising–Gaussian Markov random field prior (BI-GMRF), addressing the sparsity, spatial dependency, and smoothness and increasing the power to detect brain regions with mediation effects. Numerical simulations demonstrate the estimation accuracy, power, and robustness. For the SJMB03 study, the BI-GMRF method has identified white matter microstructure that is damaged by cancer-directed treatment and impacts late neurocognitive outcomes. The results provide guidance on improving treatment planning to minimize long-term cognitive sequela for pediatric brain tumor patients.
Pain measurement in painful skin conditions and rheumatoid arthritis randomized controlled trials: a scoping review to inform pain measurement in hidradenitis suppurativa
Authors: Hasan Samar B. , Gendra Riham , James JaBreia , Morris Delyth , Orenstein Lauren A.V. , Ingram John R. 
Published: August 2022

Abstract

Background
Pain is the most common and bothersome symptom experienced by people with hidradenitis suppurativa (HS) and has been prioritized as an outcome domain by the HIdradenitis SuppuraTiva cORe outcomes set International Collaboration (HISTORIC).

Objectives
To perform a scoping review of pain measurement in randomized control trials (RCTs) of painful skin conditions (PSCs) and use of the pain numerical rating scale (NRS) and visual analogue scale (VAS) in rheumatoid arthritis RCTs, to inform the efforts of HISTORIC to reach consensus on how to measure pain intensity in HS trials.

Methods
A search was conducted on several publication databases. Inclusion criteria were RCTs with a minimum of 10 participants that measured pain intensity.

Results
Pain NRS and VAS were used in 68% of PSC trials. Respectively, 77% and 87% of PSC and rheumatoid arthritis RCTs did not specify the recall window. The commonest recall window in PSCs when specified was 24 h. In total, 33% of PSC trials assessed maximum pain intensity and 3% average pain intensity, while 87% of rheumatoid arthritis trials did not provide details. Pain data were reported as mean difference by 76% of PSC trials and 75% of rheumatoid arthritis trials. Respectively, 10% and 11% of PSC and rheumatoid arthritis studies reported pain as the percentage of patients reaching a desirable state and only 1% and 2% reported number needed to treat.

Conclusions
While pain NRS and VAS are standard methods to measure pain intensity in PSCs, key details such as the recall window are often omitted and there is no consensus on how to report pain NRS data.
What is already known about this topic? Pain is the most burdensome symptom experienced by patients with hidradenitis suppurativa and has been prioritized as an outcome domain by the HIdradenitis SuppuraTiva cORe outcomes set International Collaboration (HISTORIC).
What does this study add? Our review shows substantial variation in how pain numerical rating scale (NRS) and visual analogue scale are utilized in clinical trials. This variation restricts meta-analysis of pain intensity results.There is a need for consensus regarding the recall window for pain NRS and maximum vs. average pain, and whether current pain should be measured.
Clinicopathological characteristics and long‐term outcomes of plasmablastic lymphoma in British Columbia
Authors: Jessa Rehan , Chien Nicole , Villa Diego , Freeman Ciara L. , Slack Graham W. , Savage Kerry J. , Scott David W. , Sehn Laurie H. , Song Kevin W. , Gerrie Alina S. 
Published: August 2022

SummaryPlasmablastic lymphoma (PBL) is an aggressive and rare subtype of non‐Hodgkin lymphoma with no standard‐of‐care therapy. We reviewed all patients diagnosed with histologically confirmed PBL in British Columbia, Canada between 1997 and 2019. Overall, 42 patients were identified, including 15 (36%) positive for HIV and nine (21%) on chronic immunosuppression. Curative‐intent treatment consisting primarily of cyclophosphamide, doxorubicin, vincristine and prednisone was administered to 31 patients, of which 74% achieved response, however 61% relapsed after a median of 7.5 months. At a median follow‐up of eight years for the whole cohort, five‐year progression‐free survival (PFS) and overall survival (OS) were 18% [95% confidence interval (CI): 6%, 30%] and 22% (95% CI: 8%, 36%) with median eight and 15 months respectively. There were no differences in relapse rate (p = 0.962), PFS (p = 0.228) or OS (p = 0.340) according to immune status. For those treated with curative intent, five‐year PFS and OS were 24% (95% CI: 8%, 40%) and 31% (95% CI: 13%, 49%) with median 18 and 27 months respectively. In this population‐based cohort of PBL patients spanning 20 years, survival outcomes were poor. Ultimately, further research is needed to develop more effective treatment strategies and to improve survival for patients.
Trophic allometry in a predator that carries corpses of its prey
Authors: Victor Nicole Riatto , Costa‐Pereira Raul 
Published: August 2022

AbstractAnt‐snatching assassin bugs carry a 'backpack’ of ant corpses as an antipredator strategy. From photographs, we quantified the relative size and number of ants in these backpacks. We found a trade‐off between size and number of carried ants, suggesting that trophic allometry has implications beyond energy acquisition, potentially affecting camouflage.Abstract in Portuguese is available with online material
Benzimidazole‐based protein kinase inhibitors: Current perspectives in targeted cancer therapy
Authors: Ali Alaa M. , Tawfik Samar S. , Mostafa Amany S. , Massoud Mohammed A. M. 
Published: August 2022

AbstractTargeted therapy has emerged to be the cornerstone of advanced cancer treatment, allowing for more selectivity and avoiding the common drug toxicity and resistance. Identification of potential targets having vital role in growth and survival of cancer cells got much easier with the aid of the recent advances in high throughput screening approaches. Various protein kinases came into focus as valuable targets in cancer therapy. Meanwhile, benzimidazole‐based scaffolds have gained significant attention as promising protein kinase inhibitors with high potency and varied selectivity. Great diversity of these scaffolds has inspired the medicinal chemists to inspect the effect of structural changes upon inhibitory activity on the molecular level through modeling studies. The present review gathers all the considerable attempts to develop benzimidazole‐based compounds; designed as protein kinase inhibitors with anticancer activity since 2015; that target aurora kinase, CDK, CK2, EGFR, FGFR, and VEGFR‐2; to allow further development and progression regarding benzimidazoles.
NRAS p.Q61R/K allele load is correlated to different phenotypes of congenital melanocytic naevi
Authors: Zhao Xiong , Dai Yefeng , Zhang Lulu , Liu Yuxin , Chen Hongyu , Yue Xiaojie , Yu Lan 
Published: August 2022

Abstract

Background
Congenital melanocytic naevi (CMN) are known to be associated with mosaic NRAS or BRAF variants. However, the exact correlations of the allele load of mosaic variants in CMN with phenotypic characteristics have not been determined.

Aim
To determine the correlation of variants allele load and different phenotypes of CMN.

Methods
A panel of genes in the Ras/Raf/MAPK signalling pathway was selected for sequencing in 110 patients with CMN. Correlations between variant allele load and clinical phenotypes, including anatomical localization, projected adult size of the lesion, satellites, subcutaneous nodules, surface rugosity, colour variation and hypertrichosis, were analysed.

Results
In addition to the predominant NRAS p.Q61R/K (61.8%) and BRAF p.V600E variants (10%) in patients, we also detected additional variants of NRAS (p.G13R and p.M72fs), BRAF (p.D22N) and MAP2K1 (p.I107fs, p.F209fs, p.Q354H and p.G91_L92insHDQARRLVGDLEHHKPSG). Furthermore, a higher allele load of NRAS p.Q61R/K was found in the trunk and limbs of CMN. It was also found in CMN with larger size, higher colour variation and more significant hypertrichosis, surface rugosity and asymmetry.

Conclusion
We discovered more genetic variants of NRAS, BRAF and MAP2K1 and established a correlation between the allele load of NRAS p.Q61R/K and various phenotypes in CMN. The findings of this study potentially facilitate a more accurate and comprehensive classification of CMN in addition to the phenotypic or pathological characteristics used in clinical practice.
Secukinumab significantly reduces inflammation but only mildly improves scaling in four cases of autosomal recessive congenital ichthyosis
Authors: Subramani Dharshini , Sardana Gitika , Kothari Rohit , Gupta Aayush 
Published: August 2022

Abstract
Using the psoriasis regimen, administration of secukinumab 150 mg led to a significant reduction in inflammation and some reduction in scaling in four paediatric cases of autosomal recessive congenital ichthyosis.