bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serverless computing in omics data analysis and integration
Authors: Grzesik Piotr , Augustyn Dariusz R , Wyciślik Łukasz , Mrozek Dariusz 
Published: August 2021

AbstractA comprehensive analysis of omics data can require vast computational resources and access to varied data sources that must be integrated into complex, multi-step analysis pipelines. Execution of many such analyses can be accelerated by applying the cloud computing paradigm, which provides scalable resources for storing data of different types and parallelizing data analysis computations. Moreover, these resources can be reused for different multi-omics analysis scenarios. Traditionally, developers are required to manage a cloud platform’s underlying infrastructure, configuration, maintenance and capacity planning. The serverless computing paradigm simplifies these operations by automatically allocating and maintaining both servers and virtual machines, as required for analysis tasks. This paradigm offers highly parallel execution and high scalability without manual management of the underlying infrastructure, freeing developers to focus on operational logic. This paper reviews serverless solutions in bioinformatics and evaluates their usage in omics data analysis and integration. We start by reviewing the application of the cloud computing model to a multi-omics data analysis and exposing some shortcomings of the early approaches. We then introduce the serverless computing paradigm and show its applicability for performing an integrative analysis of multiple omics data sources in the context of the COVID-19 pandemic.
Comparison of left atrial strain measured by feature tracking computed tomography and speckle tracking echocardiography in patients with aortic stenosis
Authors: Hirasawa Kensuke , Kuneman Jurrien H , Singh Gurpreet K , Gegenava Tea , Hautemann David , Reiber Johan H C , Ajmone Marsan Nina , Bax Jeroen J , Delgado Victoria 
Published: August 2021

Abstract

Aims
Peak left atrial longitudinal strain (PALS) is a marker of the left atrial (LA) reservoir function. Novel feature tracking (FT) software allows assessment of LA strain from multidetector computed tomography (MDCT) data. This study aimed at evaluating the agreement between speckle tracking echocardiography (STE) and FT MDCT for the measurement of PALS in patients with sinus rhythm (SR) and with atrial fibrillation (AF).

Methods and results
The current study included 318 patients (80 ± 7 years, 54% male) with dynamic MDCT data acquired prior to transcatheter aortic valve implantation. PALS was measured by transthoracic echocardiography using STE (PALSecho) and MDCT using dedicated FT software (PALSCT). In the overall population, the median values of PALSecho and PALSCT were 19.0 [interquartile range (IQR) 12.0–25.0] % and 15.3 (IQR 9.2–19.7) %, respectively. High correlation between PALSecho and PALSCT was observed (r = 0.789, P &lt; 0.001) with a mean bias of −3.7%. The correlation between PALSecho and PALSCT was better among patients with SR (N = 258; r = 0.704, P &lt; 0.001) as compared to patients with AF (N = 60; r = 0.622, P &lt; 0.001).

Conclusion
PALSecho and PALSCT showed a good agreement in patients with severe aortic stenosis (AS) regardless of the cardiac rhythm. FT MDCT may be an important adjuvant modality for assessing LA reservoir function in patients with severe AS.
Prosthetic valve endocarditis presenting as meningoencephalitis complicated by pseudo-aneurysms in a remote Aboriginal healthcare setting in Australia: a case report
Authors: Watson Anna Louise , Rice Gregory , Hieu Vo Tony , Kangaharan Nadarajah 
Published: August 2021

Abstract

Background
The Australian Aboriginal population has a high burden of cardiac conditions predisposing patients to infective endocarditis. Pseudo-aneurysms are a rare and potentially fatal complication of both prior valvular surgery and endocarditis.

Case summary
A 31-year-old female with a history of bicuspid aortic valve requiring valve replacement presented with meningoencephalitis. Transoesophageal echo and positive blood cultures for Staphylococcus aureus confirmed prosthetic valve endocarditis (PVE). Aortic root mycotic pseudo-aneurysms developed during antimicrobial therapy and two large pseudo-aneurysms remain post-redo valve, root and arch replacement.

Discussion
Complications associated with PVE are common, especially due to S. aureus. Redo cardiac surgery is high risk, percutaneous treatments may be technically difficult due to altered post-operative anatomy, and medication adherence issues and lack of healthcare engagement further compromise optimal care in this patient population.
Does face mask use elicit risk-compensation? Quasi-experimental evidence from Denmark during the SARS-CoV-2 pandemic
Authors: Jørgensen Frederik , Lindholt Marie Fly , Bor , Alexander , Petersen Michael Bang 
Published: August 2021

Abstract

Background
Public use of face masks has been widely adopted to halter the SARS-CoV-2 pandemic, but a key concern has been whether the effectiveness of face mask use is limited due to the elicitation of false feelings of security that decrease the observance of other protective behaviors, the so-called risk-compensation.

Methods
We exploit quasi-experimental variation, prompted by three major changes in policy, to assess whether public use of face masks elicit risk-compensation by increasing the number of close contacts or decreasing attention to distancing and hygiene measured in daily nationally representative surveys (N = 106 880).

Results
Number of close contacts: face mask use prompted by the policy changes decrease the number of contacts in two of the three interventions. In the remaining intervention, it has no effect. Attention to hygiene: across the changes, face masks use does not affect people’s attention to hygiene. Attention to distancing: in two of three interventions, face mask use increase attention to distancing. In the remaining intervention, we see a decrease in attention.

Conclusions
Overall, public use of face masks may occasionally elicit a narrow form of risk-compensation; specifically, reducing engagement in physical distancing. However, such narrow forms of risk-compensation are limited: the results do not reveal any effects on the actual number of physical contacts, only on the psychological attention to distancing advice. Moreover, the negative effect only appears for one of three interventions. The other two interventions suggest that face mask use increases attention to physical distancing.
Six Decades of Growth and Yield and Financial Return in a Silviculture Experiment in Northern Hardwoods
Authors: Draper Maeve C , Froese Robert E 
Published: August 2021

AbstractThe Cutting Methods Study at the Ford Forest in the Upper Peninsula of Michigan, USA, was established in 1956 and has been maintained continuously on a 10-year cycle. Methods consist of three diameter limits (DL; 13, 30, and 41 cm), single-tree selection to three residual basal area limits (STS; 11, 16, and 21 m2ha−1), and light improvement (LI) focused on improving tree grade. Long-term results show that the 41 cm DL produced the greatest managed forest value and cumulative sawlog production, followed by the STS to 11 m2ha−1 residual basal area. STS treatments and LI were uniformly superior at improving standing tree grade. In contrast, treatments that emphasize removal of large diameter trees while retaining moderate residual basal area (the 41 cm DL and 11 m2ha−1 STS) produced the largest harvest volumes of high-grade sawlogs, driving financial performance. Stand density has declined in all treatments except the 30 and 41 cm DL, where it has increased, and these two treatments have larger abundance of saplings and poles. Alternative partial cutting methods such as selection to lower residual basal areas and medium-intensity diameter-limit cuts thus may provide greater financial returns and higher average quality, and could have implications on regeneration and long-term sustainability.
Effective moduli of rocks predicted by the Kuster–Toksöz and Mori–Tanaka models
Authors: Wang Zidong , Zhang Qian , Liu Jianlin , Fu Li-Yun 
Published: August 2021

Abstract
Natural rocks are polymineral composites with complex microstructures. Such strong heterogeneities significantly affect the estimation of effective moduli by some theoretical models. First, we have compared the effective moduli of isotropic rocks predicted by the Kuster–Toksöz (KT) model and the Mori–Tanaka (MT) model. The widely used KT model only has finite precision in many cases because of its assumption that is restricted to the first-order scattering approximation. However, the MT model based on the Eshelby tensor in mesomechanics has the advantage of predicting effective moduli of rocks, especially when the volume fraction of embedded inclusions is sufficiently large. In addition, the MT model can be used to predict the effective modulus of anisotropic rocks, but the KT model cannot. For a certain kind of shale or tight sandstones, which are viewed as isotropic composites, both the models work well. For the medium containing spherical pores, both the models produce the same results, whereas for ellipsoidal pores the MT model is more accurate than the KT model, validated by the finite element simulations. In what follows, the applicable ranges of simplified formulas for pores with needle, coin and disk shapes, widely used in engineering, are quantitatively given based on the comparison with the results according to the reduced ellipsoidal formulas of the MT and KT models. These findings provide a comprehensive understanding of the two models in calculating the effective modulus of rocks, which are beneficial to such areas as petroleum exploration and exploitation, civil engineering, and geophysics.
Segmental arterial mediolysis: a rare cause of an acute abdomen
Authors: Kennedy Czara A , Toomey Desmond P 
Published: August 2021

Abstract
Segmental arterial mediolysis (SAM) is a nonatherosclerotic, noninflammatory and nonimmune arteriopathy of unknown aetiology. We present the case of a 43-year-old male who presented to the emergency department with abdominal pain. A computed tomography of abdomen and pelvis showed a narrow, hypodense superior mesenteric artery after the origin, raising the possibility of thrombus or vasculitis. He was commenced on rivaroxaban and steroids. He subsequently presented with an acute abdomen in a collapsed state. Repeat imaging of his abdomen and pelvis revealed an ischaemic ileal segment and caecum. He required an emergency laparotomy with resection of the ischaemic segment and formation of a double-barrelled stoma. SAM is an important diagnosis for clinicians and radiologists to be aware of, given the risks of life-threatening haemorrhage and acute organ ischaemia. This is a commonly overlooked cause of abdominal pain, where an early diagnosis with lifestyle modifications may prevent disease progression and subsequent development of life-threatening complications.
Psychophysiological Predictors of Soldier Performance in Tunnel Warfare: A Field Study on the Correlates of Optimal Performance in a Simulation of Subterranean Combat
Authors: Berger Corinne , Ben-Shalom Uzi , Gold Niv , Antonovsky Avishai 
Published: August 2021

ABSTRACTTunnel operations produce unique psychophysiological activation that is correlated with cognitive impairment and lower performance. This study introduces a new concept: subterranean operational potential (SOP) and assesses its psychophysiological correlates for performance prediction in underground spaces. 138 soldiers of elite infantry battalions, with/without previous experience, who participated in a simulation of tunnel warfare. Physical, psychological, cognitive style, and performance measures were collected. SOP has three sub-components: performance, leadership, and orientation. Leadership and performance both were negatively correlated with perceived stress. Claustrophobia was negatively correlated with leadership. The cognitive style was positively correlated with performance. Saliva cortisol levels were significantly higher before the simulation. Inexperienced and experienced differed in the change in before-after saliva cortisol levels.
TRLS-01. Trial in Progress: A Prospective, Multicenter Phase 2b Study to Establish Image Interpretation Criteria for 18F-Fluciclovine PET in Detecting Recurrent Brain Metastases after Radiation Therapy (PURSUE)
Authors: Kotecha Rupesh , Chaglassian Alain , Tainer Nancy , Teoh Eugene 
Published: August 2021

Abstract

Background
Brain metastases are the most common intracranial tumor in adults, occurring in 10–40% of patients with cancer. Despite multimodal treatment approaches, the prognosis remains poor and post-treatment follow-up with conventional MRI (CE-T1-weighted and FLAIR/T2-weighted) of the brain is recommended to monitor for disease recurrence. However, owing to the similar appearance of treatment-related changes like radiation necrosis with that of true recurrence, conventional MRI has low specificity.
Given the high mortality of patients with brain metastases and the considerable treatment-associated morbidity, a need remains for an imaging modality that accurately differentiates recurrence from treatment-related changes. Accurate imaging could help physicians identify patients for whom non-effective or unneeded treatments can be ceased in order to minimize treatment-associated morbidity, and to avoid erroneous premature cessation of potentially effective therapy.
18F-Fluciclovine is a synthetic amino acid-based PET imaging agent that has potential to evaluate primary and metastatic brain cancers owing to its low normal background uptake in the brain and increased uptake in brain tumors.

Methods
NCT04410367 is a prospective, open-label, single-arm, single-dose (185 MBq ± 20%) study with a primary objective to establish visual image interpretation criteria for 18F-fluciclovine PET studies of recurrent brain metastases. Forty subjects with solid tumor brain metastases who have undergone radiation therapy will be enrolled across 8 US sites if they have a reference lesion considered equivocal on MRI for recurrent brain metastasis and are planned for craniotomy. Subjects will undergo 18F-fluciclovine PET &lt;28 days after the equivocal MRI and 2–21 days before planned craniotomy. Outcome measures comprise diagnostic performance of 18F-fluciclovine PET at different thresholds of 18F-fluciclovine uptake compared with histopathology, subject- and lesion-level diagnostic performance based on application of the established image interpretation criteria, and safety evaluations. Enrolment began in August 2020 and the trial is open at the time of submission.
TRLS-07. Intracavitary carrier-embedded Cs131 brachytherapy for recurrent brain metastases: A randomized phase II study
Authors: Moss Nelson S , Imber Brandon S , Cohen Gilad , Prasad Kavya , Nunez David Aramburu , Brennan Cameron W , Tabar Viviane , Beal Kathryn P 
Published: August 2021

Abstract

Background
The salvage treatment of recurrent brain metastases after failed irradiation is a clinical challenge. Adjuvant SRS is standard of care for resected brain metastases in the upfront post-resection setting given a significant local control advantage over surgery alone. However, the role of reirradiation following salvage resection of recurrent post-irradiation metastases is unclear owing to both reduced efficacy of subsequent courses of external beam radiation, and likely increased risk of radiation injury. Intracavitary cesium 131 (Cs131) brachytherapy offers a highly conformal adjunct radiation option that we hypothesize may allow for improved local control while also theoretically conveying a low risk of radiation necrosis. In this randomized controlled study, we aim to define the potential benefits and risks of resection plus permanently implanted, carrier-embedded intracavitary Cs131 brachytherapy versus conventional care (surgery alone).

Methods
This is a single-center randomized controlled study of patients undergoing resection of recurrent, previously-irradiated brain metastases. Exclusion criteria include prior in-field infection, prior radiation &gt;100Gy (in 2Gy fraction equivalents), &gt;5 additional active or untreated CNS lesions, or leptomeningeal carcinomatosis. Subjects are randomized 1:1 to undergo either surgery with placement of Cs131 brachytherapy or surgery alone. The primary endpoint is freedom from treated-site progression at 9 months. Secondary endpoints include wound complications at 3 months and time to local retreatment at the index site, and exploratory objectives include neurocognitive function prior to surgery and at 3 and 12 months postoperatively, with correlative analyses of the previously irradiated brain metastasis tissue. Accrual began on December 24, 2020 and 5 of a planned 76 patients have enrolled. This is the first randomized controlled trial of surgery plus permanently implanted intracavitary Cs131 brachytherapy versus surgery alone for recurrent brain metastases.
ClinicalTrials.gov Identifier: NCT04690348
LMD-09. Outcomes and symptom benefit from palliative radiotherapy for leptomeningeal disease in breast cancer patients
Authors: Takayesu Jamie , Sapir Eli , Xie Jiaheng , Sun Yilun , Morikawa Aki , Junck Larry , Leung Denise , Umemura Yoshie , Heth Jason , Al-Holou Wajd , Wahl Daniel , Lawrence Theodore , Mayo Charles , Hayman James , Kim Michelle 
Published: August 2021

Abstract

Objective
The benefit of radiotherapy (RT) in patients with leptomeningeal disease (LMD) is poorly characterized. This study assessed the overall survival (OS) and clinical improvement of a largely symptomatic cohort of breast cancer patients with LMD, to identify patient subsets most likely to benefit from palliative RT.

Methods
Patients with breast cancer-related classic radiographic LMD (36% cytology-confirmed) were treated with palliative whole brain and/or partial spine RT between 2000–2020 at a single academic institution in this retrospective analysis. OS was calculated from date of LMD diagnosis using the Kaplan-Meier method. A multivariate logistic regression model incorporating ER/PR status, HER2 status, ECOG and steroid use was developed to identify factors associated with symptom benefit, which was ascertained retrospectively by chart review.

Results
Among 64 patients, the radiographic distribution of LMD was in the brain (58%), spine (22%), or both (20%). A total of 63% had brain metastases, and 57% of patients had ER+ and/or PR+, 22% HER2+, and 38% triple-negative disease. Of the symptomatic patients (94%), primary symptom domains included cranial nerve deficits (34%), sensory/motor deficits from intracranial disease (25%) or spinal disease (27%), and headaches/nausea (14%), with 42% of patients reporting &gt;1 symptom domain. Two-thirds of patients were on steroids prior to RT, and 13% of patients received intrathecal therapy. OS was 3.75 months. Following a median dose of 30Gy in 10 fractions, 59% of symptomatic patients experienced symptom improvement, with similar improvement rate across domains (12%, 15%, 19%, 14%, respectively); 21% of patients had improvement in &gt;1 symptom domain. Hormone receptor positivity was independently associated with symptom improvement following RT (OR 3.5, 95% CI 1.2–11, p=0.029).

Conclusions
In this poor-prognosis cohort of breast cancer patients with LMD, palliative RT yielded symptomatic improvement, and may be particularly beneficial among better-prognosis patients with hormone receptor-positive disease.
LMD-12. Ubiquitin Conjugating Enzymes promote leptomeningeal dissemination and decrease survival in patients with brain metastatic disease
Authors: Paisana Eunice , Cascão Rita , Custódia Carlos , Qin Nan , Picard Daniel , Pauck David , Carvalho Tânia , Ruivo Pedro , Pereira Pedro , Roque Rafael , Pimentel José , Miguéns José , Remke Marc , Barata João T , Faria Claudia C 
Published: August 2021

Abstract
The dissemination of cancer cells to the brain parenchyma (brain metastases - BMs) and to the leptomeninges (leptomeningeal dissemination – LD) are a late-stage complication of systemic cancers, with a poor survival. Despite advances in radiation and chemotherapy, including intrathecal administration of anticancer agents, these forms of advanced cancer are incurable. Therefore, there is an unmet clinical need for novel effective therapies that target both parenchymal and leptomeningeal disease.
We analysed the transcriptomic profile of BMs from patients with diverse primary tumors, treated at CHULN, to identify genetic drivers of cancer cell dissemination to the brain and potential novel targets for therapy. The most differentially expressed gene codifies a ubiquitin conjugating enzyme (UCE). UCE levels were evaluated in tissue microarrays of BMs from an independent cohort of patients and correlated with clinical data. UCE functional role was assessed in vitro and in vivo using modulated lung and breast cancer cell lines. A high-throughput drug screening was performed to find UCE-targeting compounds.
High protein levels of the UCE were associated with decreased survival in patients with BMs, independently of the primary tumor origin. High levels of UCE led to increased migration and invasion abilities in cancer cell lines in vitro, with no effect in proliferation. In vivo, high levels of UCE increased leptomeningeal dissemination and decreased survival in orthotopic models of breast cancer BMs. Leptomeningeal disease promoted by UCE was prevented by oral administration of inhibitor A, identified in our high-throughput drug screening.
In conclusion, we have identified UCE as a prognostic marker in patients with BMs from different primary tumors. In orthotopic mouse models of the disease, UCE led to a worse survival and promoted leptomeningeal dissemination. Strikingly, this aggressive disease phenotype was prevented by oral therapy with inhibitor A.
LMD-14. Preclinical safety and activity of intraventricular Rhenium-186 Nanoliposome (186RNL) for leptomeningeal metastases
Authors: Guerra-Garcia Maria , Balinda Henriette , Bao Ande , Garcia Michael , Gilbert Andrea , Phillips William , Floyd John , Brenner Andrew 
Published: August 2021

Abstract

Introduction
Leptomeningeal metastases (LM) is a clinical complication that occurs when cancer cells invade the leptomeninges and cerebrospinal fluid of patients with malignant tumors. Once diagnosed, limited treatment options exist, and survival is poor. Rhenium-186 Nanoliposome (186RNL) is a liposomal encapsulated beta emitter with a short path length of 1.8 mm, thereby allowing high specific activity brachytherapy with limited exposure to surrounding tissues.

Methods
To establish the maximum tolerated dose (MTD) of 186RNL by intraventricular (IT) injection, eight cohorts of Wistar rats (n=3 each) were injected IT with increasing activity of 186RNL at doses of 0 (control), 0.480, 0.800, 1.000, 1.150, and 1.340 mCi. Toxicity was assessed by daily food and water intake, daily weights, and observing for neurological deficits. To assess efficacy, C6-Luc glioma cells were injected IT and 15 days post inoculation the animals were treated with 0.69 mCi of 186RNL. Absorbed doses were assessed with gamma camera imaging at 0h, 24h, and 48h post-treatment. Tumor growth was assessed by luciferase bioluminescence.

Results
No evidence of adverse 186RNL-related effects was observed in rats through 3 months following administration of up to 1.34 mCi with an absorbed dose of up to 1075 Gy. Hence, the MTD exceeded the doses evaluated in this study. A significant difference in survival between the control and treatment groups (n=8 each) was observed at 2 weeks post treatment, with 50% survival in the control group and 100% survival in the treatment group (p=0.0087). The only significant treatment-related histologic finding among treated rats was slight focal thickening of the leptomeninges, suggesting a mild reactive hypertrophy.

Conclusion
Intraventricular delivery of 186RNL is well tolerated and improves animal survival at 2 weeks in a rat model of LM.