bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic and Theragnostic Applications of Circulating Tumor DNA (CtDNA) in Metastatic Castrate- resistant Prostatic Carcinoma in Veterans: A Novel Promise in Precision Oncology
Authors: Dalal S , Jhala D 
Published: October 2020

Abstract

Introduction/Objective
Utility of CtDNA in peripheral blood through liquid biopsies serves as a robust biomarker for precision oncology. Prostate cancer is most common cancer diagnosed in veterans, more commonly presenting at advanced stage with increased incidence of metastatic castrate-resistant prostatic carcinoma (MCRPC). Minimally invasive liquid biopsy is not limited by tumor site, type, tumor heterogeneity, and most importantly enables real time disease monitoring for best therapy decisions in MCRPC. The literature is sparse depicting the role of CtDNA in MCRPC in veteran patient population with distinct demographics/frequency of Tp53 mutations. We herein aim to study role of CtDNA in liquid biopsies for prognosis, treatment decisions and outcome in veterans with MCRPC.

Methods
QA documents from Foundation One (Cambridge MA, NGS) on liquid biopsies performed for the Corporal Michael J. Crescenz Veteran Affairs Medical Center (CMCVAMC) from May 2019 to April 15, 2020 were reviewed. All liquid biopsies were performed on MCRPC with evidence of tumor progression. Statistical data for adequacy, type of mutations either altering therapy, disease course or outcome was noted.

Results
A total of 23 liquid biopsies were performed. 21/23 (91.3%) biopsies were adequate, 19/21 (90.4%) showed signature mutations for resistance to therapy, predicting prognosis, or suggesting poor outcome with decreased overall survival. 4/21 (19%) showed androgen receptor amplification (ARV7 mutation) that helped in making treatment decisions. Increased frequency of Tp53 mutations were noted (12/21 (57.1%) compared to general population (30- 40%)) indicating worse prognosis/aggressive disease course with decreased survival.

Conclusion
Combined exposure of herbicide agent orange and smoking may be a fertile soil for observed differences in type and frequency of genomic alterations in veteran patient population with MCRPC. Comprehensive genomic profiling on CtDNA through minimally invasive liquid biopsy is feasible and can be successfully implemented in veterans with multiple co-morbidities. Although ARV7 mutation is much more common in general population, veterans with advanced hormone resistant prostatic carcinoma may benefit from aggressive approach in developing targeted therapy focused on DNA repair genes, especially Tp53.
Loss-Of-Function Mutation Of ARID1A Tumor Suppressor Gene In A Glycogen-Rich Clear Cell Mammary Carcinoma
Authors: De la Sancha Verduzco C A , Popnikolov N , Ruiz-Cordero R 
Published: October 2020

Abstract

Introduction/Objective
Glycogen-rich clear cell carcinoma (GRCC-CA) is a rare subtype of breast carcinoma accounting for 0.9 - 3% of all breast malignancies. It is characterized by more than 90% of the neoplastic cells containing glycogen-abundant clear cytoplasm. Due to the rarity of this tumor, the information about the specific genetic alterations, their prognostic significance and potential therapeutic implications are quite limited. Here we report the molecular alterations of a GRCC-CA diagnosed in a 69-year-old woman.

Methods
Tumor-only sequencing using a hybrid-capture next-generation sequencing (HC-NGS) assay was performed using formalin-fixed paraffin-embedded tissue. The HC-NGS panel included the coding regions of 479 cancer-related genes, select introns of 47 genes and the TERT promoter.

Results
The HC-NGS showed the following alterations: 1) large inversion in chromosome 1 between exon 20 of gene ARID1A (1p36.12) and intron 2 of KDM5B (1q32.1) leading to loss-of-function of ARID1A tumor suppressor gene, 2) MAP2K4 p.E376 truncating mutation with a variant allelic frequency of 87% suggestive of loss-of-heterozygosity, 3) c- MYC gene amplification (5x), 4) variant of uncertain significance in gene PTPRB (p.D1848N) and 5) deep deletions of NCKAP5, CCNT2, MAP3K19, LRP1B, and KMT2A genes.

Conclusion
We report for the first time a loss-of-function mutation of ARID1A gene in mammary GRCC-CA. Loss of function of ARID1A gene, as shown by molecular studies or loss of protein expression, is often seen in clear cell carcinomas with high glycogen contents from other sites (ovary and kidney), indicating similarities in the molecular mechanisms of development. In our patient, the loss of ARID1A probably enhanced the effect of the c-MYC amplification, since ARID1A is involved in the repression of c-MYC and other proliferation associated genes during differentiation. Larger molecular studies are needed to elucidate further the genetic mechanisms of mammary GRCC- CA.
Effects of Blackboard Resources Utilization on Students’ Performance in Molecular Biology Course
Authors: Kandel B P , Hackfeld M , Zhang J , Guo F 
Published: October 2020

Abstract

Introduction/Objective
Molecular diagnostics utilizes structural and functional fundamentals of molecular biology and finds its scope in clinical education for disease diagnosis and monitoring, and evaluation of non-disease status. Time and financial constraints make molecular biology education challenging for both teachers and students. Advances in information technologies have helped teachers to provide a rich resource to students which if properly utilized is expected to generate better teaching-learning outcomes. However, the pattern of utilization of digital resources by students and its impact on their performance is still unknown. The aim of this study was to assess students’ behavior to Blackboard resource utilization and its impact on their performance in molecular biology course.

Methods
We conducted a retrospective cross-sectional study including all the 46 students (9 graduate and 37 undergraduate students; 14 distant and 32 regular students) enrolled for molecular biology course in the year 2017 and assessed the associations between blackboard resource visits and students’ final weighted total grades.
Blackboard resource visit variables included “Tegrity” viewing duration, viewing times, and contents viewed (“My Grades”, “Announcement”, “Discussion”, “Contacts”, “Content Item”).

Results
Among all students, the most and least visited contents were “Content Item” (261 average hits) and “Contacts” (1.28 average hits), respectively with similar patterns of the visit among all student sub-categories. The longest average Tegrity viewing duration (25 hours) and the highest average Tegrity viewing times (56 hits) were noted among undergraduate distance students. The average grade was higher among graduate students than undergraduate students. The overall blackboard resource visit and the individual category visit among graduate and undergraduate students had no association with students’ final weighted scores.

Conclusion
Our findings have important implications for the utility of blackboard resources among graduate and undergraduate clinical laboratory science students. Similar assessments including students from many different years are recommended to generate more accurate evidence.
Mucinous Adenocarcinoma With Intrapulmonary Metastasis HarboringKRASandGNASMutations Arising in Congenital Pulmonary Airway Malformation
Authors: de Cordova Ximena Fernandez , Wang Huiying , Mehrad Mitra , Eisenberg Rosana , Johnson Joyce , Wei Qiang , Borinstein Scott , Danko Melissa E , Liang Jiancong 
Published: October 2020

AbstractObjectivesMucinous adenocarcinoma arising in unresected congenital pulmonary airway malformation (CPAM) is rare. Underlying driver mutations in addition to KRAS gain-of-function mutations in this setting and the long-term outcomes of these patients are unknown.MethodsWe report a case of metastatic mucinous adenocarcinoma harboring both KRAS and GNAS mutations arising in a type 1 CPAM of a 14-year-old male. A literature review was performed.ResultsNext-generation sequencing revealed identical KRAS (G12V) mutations in both the CPAM and metastatic adenocarcinoma and a missense mutation in the GNAS (R201C) gene in the metastatic adenocarcinoma only. Median survival was 23 and 4 years for patients with localized (no or limited spread within the same lobe of CPAM) and distant involvement (spread to any different lobe of CPAM) of mucinous cells, respectively (95% confidence interval, 23-23 and 1.5-22 years, respectively; P = .017).ConclusionsMucinous cell proliferation associated with type 1 CPAM has exceptionally good long-term outcomes if confined within the same lobe of CPAM. A second oncogenic mutation in the GNAS gene may be necessary for progression to malignancy and distant spread.
Dealing With Treatment-Confounder Feedback and Sparse Follow-up in Longitudinal Studies: Application of a Marginal Structural Model in a Multiple Sclerosis Cohort
Authors: Karim Mohammad Ehsanul , Tremlett Helen , Zhu Feng , Petkau John , Kingwell Elaine 
Published: October 2020

Abstract
The beta-interferons are widely prescribed platform therapies for patients with multiple sclerosis (MS). We accessed a cohort of patients with relapsing-onset MS from British Columbia, Canada (1995–2013), to examine the potential survival advantage associated with beta-interferon exposure using a marginal structural model. Accounting for potential treatment-confounder feedback between comorbidity, MS disease progression, and beta-interferon exposure, we found an association between beta-interferon exposure of at least 6 contiguous months and improved survival (hazard ratio (HR) = 0.63, 95% confidence interval 0.47, 0.86). We also assessed potential effect modifications by sex, baseline age, or baseline disease duration, and found these factors to be important effect modifiers. Sparse follow-up due to variability in patient contact with the health system is one of the biggest challenges in longitudinal analyses. We considered several single-level and multilevel multiple imputation approaches to deal with sparse follow-up and disease progression information; both types of approach produced similar estimates. Compared to ad hoc imputation approaches, such as linear interpolation (HR = 0.63), and last observation carried forward (HR = 0.65), all multiple imputation approaches produced a smaller hazard ratio (HR = 0.53), although the direction of effect and conclusions drawn concerning the survival advantage remained the same.
Chapter FiveDidymus and the Greek historians
Authors: Montana Fausto 
Published: October 2020

Abstract
We lack positive evidence that Didymus composed scholarly works specifically devoted to Greek historians. Even more, the very origins and characteristics of the Alexandrian interest in the historiographic genre, not to say in literary prose, represent open issues for the historian of Hellenistic scholarship. In this chapter, the rare and sparse pieces of information are gathered, in order to obtain a possibly systematic and organic overview on the very defective puzzle of the Didymean approach in this field. In the first part, clues from testimonies and fragments directly concerning historians (Herodotus, Thucydides) and antiquarian subjects (Solon’s axones) are taken into special consideration. The second part deals with the use and abuse of history and historical sources detectable in fragments from Didymean works which were devoted to fields and genres other than historiography. As a result, the testimony of the Pindar scholia and of the writing On Demosthenes attested to by P.Berol. inv. 9780 recto (second century ad) proves to be especially decisive for a reassessment of Didymus’ approach to historiography and history.
Parenting in fear: Child welfare micro strategies of Nigerian parents in Britain
Authors: Okpokiri Cynthia 
Published: October 2020

Abstract
Parental engagement with British child-rearing normative practices and policies has been a source of conflict between Black African parents and professionals involved in child-safeguarding in Britain. These professionals include teachers, police, healthcare practitioners such as health visitors, nurses and doctors, and most importantly, social workers, because Children Act 1989, section 47 legally tasks social workers to investigate child-safeguarding concerns. Child-rearing norms and practices across all four UK countries are largely similar, although substantive legislative differences necessitate the application of only child welfare laws/policies of England and Wales in this study. This article focuses on Nigerian parents’ experiences of British child welfare system, tensions ensuing from those interactions and how parents mitigate them. Insights are drawn from 25 in-depth semi-structured interviews and two focus group discussions with Nigerian parents living in Greater London. Honneth’s recognition theory and Fraser’s participatory parity undergird the conceptual framework. The findings reveal an interplay of the structural forces of race, power and cultural differentials on participants’ thinking processes and actions. Thus, suggesting that social workers perpetuate the British public’s misrecognition of Nigerian parents through uncritical social work practices, which are implicated in further disempowerment of Black African parents, to the detriment of the families’ well-being.
Context Matters: Situational Stress Impedes Functional Reorganization of Intrinsic Brain Connectivity during Problem-Solving
Authors: Liu Mengting , Backer Robert A , Amey Rachel C , Splan Eric E , Magerman Adam , Forbes Chad E 
Published: October 2020

Abstract
Extensive research has established a relationship between individual differences in brain activity in a resting state and individual differences in behavior. Conversely, when individuals are engaged in various tasks, certain task-evoked reorganization occurs in brain functional connectivity, which can consequently influence individuals’ performance as well. Here, we show that resting state and task-dependent state brain patterns interact as a function of contexts engendering stress. Findings revealed that when the resting state connectome was examined during performance, the relationship between connectome strength and performance only remained for participants under stress (who also performed worse than all other groups on the math task), suggesting that stress preserved brain patterns indicative of underperformance whereas non-stressed individuals spontaneously transitioned out of these patterns. Results imply that stress may impede the reorganization of a functional network in task-evoked brain states. This hypothesis was subsequently verified using graph theory measurements on a functional network, independent of behavior. For participants under stress, the functional network showed less topological alterations compared to non-stressed individuals during the transition from resting state to task-evoked state. Implications are discussed for network dynamics as a function of context.
Model-Driven Simulation of Elastic OCCI Cloud Resources
Authors: Ahmed-Nacer Mehdi , Kallel Slim , Zalila Faiez , Merle Philippe , Gaaloul Walid 
Published: October 2020

Abstract
Deploying a cloud configuration in a real cloud platform is mostly cost- and time- consuming, as large number of cloud resources have to be rented for the time needed to run the configuration. Thereafter, cloud simulation tools are used as a cheap alternative to test cloud configuration. However, most of the existing cloud simulation tools require extensive technical skills and do not support simulation of any kind of cloud resources. In this context, using a model-driven approach can be helpful as it allows developers to efficiently describe their needs at a high level of abstraction. To do, we propose, in this article, a model-driven engineering approach based on the Open Cloud Computing Interface(OCCI) standard metamodel and CloudSim toolkit. We firstly extend OCCI metamodel for the supporting simulation of any kind of cloud resources. Afterward, to illustrate the extensibility of our approach, we enrich the proposed metamodel by new simulation capabilities. As proof of concept, we study the elasticity and pricing strategies of Amazon Web Services (AWS). This article benefits from OCCIware Studio to design an OCCI simulation extension and to provide a simulation designer for designing cloud configurations to be simulated. We detail the approach process from defining an OCCI simulation extension until the generation and the simulation of the OCCI cloud configurations. Finally, we validate the proposed approach by providing a realistic experimentation to study its usability, the resources coverage rate and the cost. The results are compared with the ones computed from AWS.
Proposed Artificial Bee Colony Algorithm as Feature Selector to Predict the Leadership Perception of Site Managers
Authors: Kaya Keles Mumine , Kilic Umit , Keles Abdullah Emre 
Published: October 2020

AbstractDatasets have relevant and irrelevant features whose evaluations are fundamental for classification or clustering processes. The effects of these relevant features make classification accuracy more accurate and stable. At this point, optimization methods are used for feature selection process. This process is a feature reduction process finding the most relevant feature subset without decrement of the accuracy rate obtained by original feature sets. Varied nature inspiration-based optimization algorithms have been proposed as feature selector. The density of data in construction projects and the inability of extracting these data cause various losses in field studies. In this respect, the behaviors of leaders are important in the selection and efficient use of these data. The objective of this study is implementing Artificial Bee Colony (ABC) algorithm as a feature selection method to predict the leadership perception of the construction employees. When Random Forest, Sequential Minimal Optimization and K-Nearest Neighborhood (KNN) are used as classifier, 84.1584% as highest accuracy result and 0.805 as highest F-Measure result were obtained by using KNN and Random Forest classifier with proposed ABC Algorithm as feature selector. The results show that a nature inspiration-based optimization algorithm like ABC algorithm as feature selector is satisfactory in prediction of the Construction Employee’s Leadership Perception.
The effect of intrinsic physiological traits on diapause survival and their underlying mechanisms in an annual bee speciesBombus impatiens
Authors: Treanore Erin , Amsalem Etya 
Published: October 2020

AbstractIn the face of insect declines, identifying phases of the life cycle when insects are particularly vulnerable to mortality is critical to conservation efforts. For numerous annual insect groups, diapause is both a key adaptation that allows survival of inhospitable conditions and a physiologically demanding life stage that can result in high rates of mortality. As bees continue to garner attention as a group experiencing high rates of decline, improving our understanding of how annual bees prepare for diapause and identifying factors that reduce survival is imperative. Here, we studied factors affecting diapause survival length and their underlying mechanisms using an economically and ecologically important annual bee species, Bombus impatiens. We examined how age and mass upon diapause onset correlate with diapause survival length, and the mechanistic role of nutrient acquisition and oxidative stress post pupal eclosion in mediating these effects. Our findings show that both age and mass were strong predictors of diapause survival length. Heavier queens or queens in the age range of ~6–17 days survived longer in diapause. Mass gain was attributed to increases in lipid, protein and glycerol amounts following pupal eclosion, and the ability to deal with oxidative stress was significantly compromised in older pre-diapause queens. Our results demonstrate that age-related shifts in bee physiology and timing of nutrient acquisition may both be critical factors driving diapause survival.
In patients undergoing coronary artery bypass grafting, is endoscopic harvesting superior to open radial artery harvesting?
Authors: Lei Jonathan Jin Hei , Ravendren Andrew , Snosi Mostafa , Harky Amer 
Published: October 2020

Summary
A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was ‘In patients undergoing coronary artery bypass grafting, is endoscopic radial artery harvesting (ERAH) superior to open radial artery harvesting in terms of postoperative complications, mortality, graft quality and patency rates?’. Altogether 130 papers were found using the reported search, of which 5 represented the best evidence to answer the clinical question. Two studies were meta-analyses and 3 were randomized trials. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. In terms of graft quality, 2 randomized studies showed preserved endothelial integrity and vasoreactivity with ERAH, whereas 1 randomized study found superior endothelial function with open radial artery harvesting. Importantly, 3 studies showed graft patency was not compromised with ERAH. One meta-analysis reported no differences in graft patency between groups at 1 year [odds ratio (OR) 1.24] and up to 3–5-years follow-up (OR 1.81), as well as similar perioperative myocardial infarction rates (OR 0.80). Two meta-analyses found similar mortality in the perioperative period (OR 0.62–0.78) and up to 5 years (OR 0.64–0.67); ERAH reduced the incidence of perioperative wound complications (P-values 0.001–0.03); however, harvest times were increased with ERAH (P &lt; 0.0005). We conclude that ERAH is non-inferior to open radial artery harvesting in terms of mortality, graft quality and patency rates, but superior in terms of reducing perioperative wound complications, with good cosmetic effect. However, these benefits come at the cost of increased harvesting time.
Double Grothendieck Polynomials and Colored Lattice Models
Authors: Buciumas Valentin , Scrimshaw Travis 
Published: October 2020

Abstract
We construct an integrable colored six-vertex model whose partition function is a double Grothendieck polynomial. This gives an integrable systems interpretation of bumpless pipe dreams and recent results of Weigandt relating double Grothendieck polynomias with bumpless pipe dreams. For vexillary permutations, we then construct a new model that we call the semidual version model. We use our semidual model and the five-vertex model of Motegi and Sakai to give a new proof that double Grothendieck polynomials for vexillary permutations are equal to flagged factorial Grothendieck polynomials. Taking the stable limit of double Grothendieck polynomials, we obtain a new proof that the stable limit is a factorial Grothendieck polynomial as defined by McNamara. The states of our semidual model naturally correspond to families of nonintersecting lattice paths, where we can then use the Lindström–Gessel–Viennot lemma to give a determinant formula for double Schubert polynomials corresponding to vexillary permutations.