bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020
Authors: Giunta Simona 
Published: June 2021

AbstractCancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as well as the corresponding healthy tissue, with the aim of identifying genome-wide mutations exclusively found in cancer and uncovering new genetic changes that drive tumor formation. What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer’s non-coding genome. WGS of the entire cohort allowed to tease apart driving mutations that initiate and support carcinogenesis from passenger mutations that do not play an overt role in the disease. At least one causative mutation was found in 95% of all cancers, with many tumors showing an average of 5 driver mutations. The PCAWG Project also assessed the transcriptional output altered in cancer and rebuilt the evolutionary history of each tumor showing that initial driver mutations can occur years if not decades prior to a diagnosis. Here, I provide a concise review of the Pan-Cancer Project papers published on February 2020, along with key computational tools and the digital framework generated as part of the project. This represents an historic effort by hundreds of international collaborators, which provides a comprehensive understanding of cancer genetics, with publicly available data and resources representing a treasure trove of information to advance cancer research for years to come.
Phylogeography of Aphanius fasciatus (Osteichthyes: Aphaniidae) in the Mediterranean Sea, with a focus on its conservation in Cyprus
Authors: Langeneck Joachim , Englezou Chris , Di Maggio Matteo , Castelli Alberto , Maltagliati Ferruccio 
Published: June 2021

AbstractAphanius fasciatus is a small fish occurring in Mediterranean brackish environments. In Cyprus it is known from three localities separated by long stretches of coast. The genetic diversity of these populations was evaluated using fragments of two mitochondrial genes. A comparison with the other available data showed that Cyprus populations represent a distinct lineage. The other lineages are concentrated in a relatively small area between the Strait of Sicily and the Western Ionian Sea, while all other areas include a subset of these lineages, suggesting that the aforementioned area might have acted as a glacial refugium. Landlocked North-African populations diverge from all other populations, suggesting that they might have originated in the Late Pleistocene, during transgression events of the Mediterranean Sea in North-African inland water bodies. The genetic diversity of A. fasciatus varied across different Cyprus populations, with a pattern mirroring the degree of environmental degradation, which likely affected population genetic variability through demographic reductions. The three Cyprus populations showed genetic uniqueness, suggesting the need of population-based management practices; the low genetic diversity of two populations, and the number of threats affecting them, suggest that the species should be considered endangered at national level and deserves protection measures.
The Impact of Age Stereotypes on Well-being: Strategies of Selection, Optimization, and Compensation as Mediator and Regulatory Focus as Moderator: Findings from a Cross-Sectional and a Longitudinal Study
Authors: Söllner Martin , Dürnberger Mirjam , Keller Johannes , Florack Arnd 
Published: June 2021

AbstractIn a cross-sectional (Study 1) and a longitudinal study (Study 2), the authors examined whether the association between age stereotypes and well-being is mediated by self-regulatory engagement in goal pursuit. In Study 1 (N = 666), engagement in self-regulatory strategies of selection (e.g., selecting appropriate goals), optimization (e.g., acquiring resources for goal achievement), and compensation (e.g., searching for help) were assessed as potential mediators and, concurrently, regulatory focus was explored as a moderator of the association of age stereotypes and well-being. The results demonstrated consistent positive associations of positive age stereotypes and different kinds of well-being. These associations were partially mediated by optimization, but not by selection or compensation. Furthermore, the relationships between positive age stereotypes and well-being were attenuated for promotion-focused individuals. In Study 2 (N = 2325), we measured age stereotypes at baseline and several well-being measures at baseline as well as 6 and 9 years later. Age stereotypes at baseline predicted well-being at the later measurement times. Also, the associations between age stereotypes and different aspects of well-being were mediated by self-regulatory engagement in selection, optimization, and compensation.
Simulation of chemo-thermo-mechanical problems in cement-based materials with Peridynamics
Authors: Bazazzadeh Soheil , Morandini Marco , Zaccariotto Mirco , Galvanetto Ugo 
Published: June 2021

AbstractA chemo-thermo-mechanical problem is solved using a peridynamic approach to investigate crack propagation in non-reinforced concrete at early-age. In the present study, the temperature evolution and the variation of the hydration degree in conjunction with the mechanical behaviour of cement-based materials are examined. Firstly, a new peridynamic model is introduced to solve fully coupled chemo-thermal problems by satisfying thermal equilibrium condition and hydration law simultaneously and then the effects of the chemo-thermal analysis are imposed in the mechanical framework to investigate all the interactions. The proposed approach is used to solve 2D chemo-thermo-elastic problems and then it is applied to investigate the fracture of concrete structures. Additionally, we examine the accuracy of the method by comparing the crack paths, temperature and hydration degree with those achieved by applying other numerical methods and the experimental data available in the literature. A good agreement is obtained between all sets of results.
Understanding bikeability: a methodology to assess urban networks
Authors: Reggiani Giulia , van Oijen Tim , Hamedmoghadam Homayoun , Daamen Winnie , Vu Hai L. , Hoogendoorn Serge 
Published: June 2021

AbstractA fully separated bicycle network from vehicular traffic is not realistic even for the most bicycle-friendly cities. Thus, all around the world urban cycling entails switching between streets of different safety, convenience, and comfort levels. As a consequence, the quality of bicycle networks should be evaluated not based on one but multiple factors and by considering the different user preferences regarding these factors. More comprehensive methodologies to assess urban bicycle networks are essential to the operation and planning of modern city transportation. This work proposes a multi-objective methodology to assess—what we refer to as—bikeability between origin–destination locations and over the entire network, useful for evaluation and planning of bicycle networks. We do so by introducing the concept of bikeability curves which allows us to assess the quality of cycling in a city network with respect to the heterogeneity of user preferences. The application of the proposed methodology is demonstrated on two cities with different bike cultures: Amsterdam and Melbourne. Our results suggest the effectiveness of bikeability curves in describing the characteristic features and differences in the two networks.
Maturation in Atlantic salmon (Salmo salar, Salmonidae): a synthesis of ecological, genetic, and molecular processes
Authors: Mobley Kenyon B. , Aykanat Tutku , Czorlich Yann , House Andrew , Kurko Johanna , Miettinen Antti , Moustakas-Verho Jacqueline , Salgado Andrés , Sinclair-Waters Marion , Verta Jukka-Pekka , Primmer Craig R. 
Published: June 2021

AbstractOver the past decades, Atlantic salmon (Salmo salar, Salmonidae) has emerged as a model system for sexual maturation research, owing to the high diversity of life history strategies, knowledge of trait genetic architecture, and their high economic value. The aim of this synthesis is to summarize the current state of knowledge concerning maturation in Atlantic salmon, outline knowledge gaps, and provide a roadmap for future work. We summarize the current state of knowledge: 1) maturation in Atlantic salmon takes place over the entire life cycle, starting as early as embryo development, 2) variation in the timing of maturation promotes diversity in life history strategies, 3) ecological and genetic factors influence maturation, 4) maturation processes are sex-specific and may have fitness consequences for each sex, 5) genomic studies have identified large-effect loci that influence maturation, 6) the brain-pituitary–gonadal axis regulates molecular and physiological processes of maturation, 7) maturation is a key component of fisheries, aquaculture, conservation, and management, and 8) climate change, fishing pressure, and other anthropogenic stressors likely have major effects on salmon maturation. In the future, maturation research should focus on a broader diversity of life history stages, including early embryonic development, the marine phase and return migration. We recommend studies combining ecological and genetic approaches will help disentangle the relative contributions of effects in different life history stages to maturation. Functional validation of large-effect loci should reveal how these genes influence maturation. Finally, continued research in maturation will improve our predictions concerning how salmon may adapt to fisheries, climate change, and other future challenges.
Integrating immediate gains with sustainable performance: systematic review of paradox at the intersection of strategic management and innovation
Authors: Schulte Leonie 
Published: June 2021

AbstractDigital technologies introduce change as a permanent feature of organizational life, creating an imbalance between market requirements and organizational capabilities. This article seeks to explore the tensions that organizations are confronted with when they engage in the strategic management of innovation (SMI) to achieve immediate and simultaneously lasting success. The divergent nature of strategic management and innovation promotes opposing organizational demands routed in a diversity of stakeholder agendas that foster an unhealthy tug-of-war over scarce resources. The resulting paradoxes are mirrored in the SMI literature. Hence to promote a more accurate understanding of complex organisational dynamics, this study organizes and integrates the diverse body of knowledge on SMI within the scope of a systematic literature review. By adopting a paradox perspective, a conceptual scheme is developed onto which competing demands are mapped. The application of framework synthesis reveals a wide array of paradoxes at the intersection of innovation and strategic management, including the inter-organisational, firm, project and individual level of analysis, while accounting for certain contextual factors that expose paradoxical tensions. The study thus contributes to the advancement of SMI literature by applying a new conceptual perspective, by employing a fairly new method to framework synthesis, and by recognizing the potential of environmental complexity in reference to subliminal tensions. The article proposes a research agenda with a more nuanced perspective on competing demands inherent in SMI, while also offering managerial implications that account for contemporary imperatives.
C﻿hief digital officers: the state of the art and the road ahead
Authors: Kessel Lena , Graf-Vlachy Lorenz 
Published: June 2021

AbstractThere is a lively debate on chief digital officers (CDOs). Some practitioners stress CDOs’ critical role in recrafting digital strategies and accelerating digital transformation, while others predict their disappearance. Academics have also recently begun to study this new executive position and conducted research on CDOs which is, however, scattered across different disciplines and publication outlets. We conduct a systematic literature review that consolidates these initial gains in knowledge. Specifically, we integrate findings on theoretical lenses, research designs, and key themes in studies on CDOs and we propose a framework that organizes CDO research in three broad themes: antecedents of CDO presence, the CDO role, and consequences of CDO presence. We then build on identified gaps to develop an extensive agenda for future research on CDOs. For academic researchers, we not only offer a discipline-spanning overview of knowledge on the topic at hand but also provide useful direction towards fruitful avenues for future research on CDOs. For practitioners, we offer a summary of the current scientific literature on CDOs, including relevant insights on CDO appointments, governance, and performance consequences.
Effects of urban street trees on human thermal comfort and physiological indices: a case study in Changchun city, China
Authors: Ren Zhibin , Zhao Hongbo , Fu Yao , Xiao Lu , Dong Yulin 
Published: June 2021

AbstractPlanting trees along urban streets is one of the most important strategies to improve the urban thermal environment. However, the net impacts of urban street trees on human thermal comfort and physiological parameters are still less clear. On three similar east–west orientated streets with different degrees of tree cover—low (13%), medium (35%), and high (75%), urban microclimatic parameters and human physiological indices for six male students were simultaneously measured on three cloudless days in summer 2018. The results show that the differences in tree cover were predominant in influencing urban thermal environment and comfort. The street with the highest tree cover had significantly lower physiological equivalent temperature (PET) and more comfortable than the other two streets. The frequency of strong heat stress (PET > 35 °C) was 64%, 11%, and 0%, respectively, for streets with low, medium, and high tree cover. For the six male university students, human physiological indices varied greatly across the three streets with different tree cover. Systolic blood pressure, diastolic blood pressure, and pulse rate increased with decreasing tree cover. The results also suggest that urban thermal environment and comfort had considerable impact on human physiological parameters. Our study provides reasons for urban planners to plant trees along streets to improve the thermal environment and promote urban sustainability.
Spinal Cord Perfusion Pressure Correlates with Anal Sphincter Function in a Cohort of Patients with Acute, Severe Traumatic Spinal Cord Injuries
Authors: Hogg Florence R. A. , Kearney Siobhan , Gallagher Mathew J. , Zoumprouli Argyro , Papadopoulos Marios C. , Saadoun Samira 
Published: June 2021

Abstract
Background
Acute, severe traumatic spinal cord injury often causes fecal incontinence. Currently, there are no treatments to improve anal function after traumatic spinal cord injury. Our study aims to determine whether, after traumatic spinal cord injury, anal function can be improved by interventions in the neuro-intensive care unit to alter the spinal cord perfusion pressure at the injury site.

Methods
We recruited a cohort of patients with acute, severe traumatic spinal cord injuries (American Spinal Injury Association Impairment Scale grades A–C). They underwent surgical fixation within 72 h of the injury and insertion of an intrathecal pressure probe at the injury site to monitor intraspinal pressure and compute spinal cord perfusion pressure as mean arterial pressure minus intraspinal pressure. Injury-site monitoring was performed at the neuro-intensive care unit for up to a week after injury. During monitoring, anorectal manometry was also conducted over a range of spinal cord perfusion pressures.

Results
Data were collected from 14 patients with consecutive traumatic spinal cord injury aged 22–67 years. The mean resting anal pressure was 44 cmH2O, which is considerably lower than the average for healthy patients, previously reported at 99 cmH2O. Mean resting anal pressure versus spinal cord perfusion pressure had an inverted U-shaped relation (Ȓ2 = 0.82), with the highest resting anal pressures being at a spinal cord perfusion pressure of approximately 100 mmHg. The recto-anal inhibitory reflex (transient relaxation of the internal anal sphincter during rectal distension), which is important for maintaining fecal continence, was present in 90% of attempts at high (90 mmHg) spinal cord perfusion pressure versus 70% of attempts at low (60 mmHg) spinal cord perfusion pressure (P < 0.05). During cough, the rise in anal pressure from baseline was 51 cmH2O at high (86 mmHg) spinal cord perfusion pressure versus 37 cmH2O at low (62 mmHg) spinal cord perfusion pressure (P < 0.0001). During anal squeeze, higher spinal cord perfusion pressure was associated with longer endurance time and spinal cord perfusion pressure of 70–90 mmHg was associated with stronger squeeze. There were no complications associated with anorectal manometry.

Conclusions
Our data indicate that spinal cord injury causes severe disruption of anal sphincter function. Several key components of anal continence (resting anal pressure, recto-anal inhibitory reflex, and anal pressure during cough and squeeze) markedly improve at higher spinal cord perfusion pressure. Maintaining too high of spinal cord perfusion pressure may worsen anal continence.
Thyroid nodules with indeterminate cytology: association between nodule size, histopathological characteristics and clinical outcome in differentiated thyroid carcinomas — a multicenter retrospective cohort study on 761 patients
Authors: Cozzani Federico , Bettini Dario , Rossini Matteo , Bonati Elena , Nuzzo Simona , Loderer Tommaso , Pedrazzi Giuseppe , Zaccaroni Alberto , Del Rio Paolo 
Published: June 2021

AbstractA great number of surgical diagnostic procedures are performed every year for thyroid nodules that are included in undetermined cytological classes that reveal to be malignant thyroid carcinomas in one-third of cases. In the most recent guidelines, lobectomy is the most recommended surgical approach for this classes of nodules, but total thyroidectomy is the recommended treatment for undetermined nodules larger than 4 cm. The main study aim is to support or question the dimensional criteria as an independent clinical decision element for undetermined thyroid nodules management. We examined data regarding 761 patients undergoing thyroid surgery for undetermined thyroid nodules at two high-volume endocrine surgery units in Italy. Patients were divided into three groups based on the preoperative size of the nodules (N < 1, 1 < N < 4, N > 4 cm). Among the patients belonging to the different groups, we analyzed: differences in malignancy rate, histological characteristics of invasiveness and neoplastic aggressiveness, rates of recurrence and response to therapy. Nodule size (evaluated as a categorical variable and as a continuous variable) did not show any statistically significant correlation with the rate of malignancy, histopathological characteristics of tumor aggressiveness and the patient’s clinical outcome. Most of the tumors found were included in the low risk class (79.2%) and only one was classified as high risk. Follow up of cancer cases showed excellent results in terms of survival, response to therapy and disease recurrence. Malignant thyroid tumors of any size resulting from a nodule identified as cytologically indeterminate are usually characterized by a low risk follicular pattern, well-differentiated and with an excellent outcome. As a result, preferring an extended surgical attitude for undetermined nodules based on tumor size, in absence of other risk factors, can lead to overtreatment in a significant percentage of cases.
Amine-modified silica for removing aspirin from water
Authors: Danil de Namor A. F. , Al Nuaim M. , Fairclough G. , Khalife R. , Al Hakawati N. 
Published: June 2021

AbstractThe synthesis and structural characterisation (Fourier transform infrared, FTIR spectrometry, scanning electron microscopy, SEM and energy-dispersive X-ray, EDX) of amino-modified silicates (unloaded L1, and aspirin-loaded, L2) are reported. The optimal conditions for the extraction of aspirin from water by the modified silicate material were determined as a function of the mass of the extracting agent and the pH of the aqueous solution. The optimum mass was found to be 0.08–0.10 g with 99.9% removal of aspirin. Maximum extraction of aspirin by the material was observed at pH 4. The kinetics, the removal capacity of the material, as well as its recycling, were investigated. The results indicate that (i) the process is fast and (ii) the removal capacity for the drug is greater than that of previously reported materials and (iii)the modified silicate can be easily recycled. These data along with the low cost involved in the production of the material led to the conclusion that the modified silicate has the required potential for industrial use. Molecular simulation calculations suggest that one unit of aspirin interacts with one unit of the modified silicate L1 through hydrogen bond formation between the amine functional group of the silicate and the oxygen donor atoms of aspirin. Final conclusions are given.
Quantitative normal approximations for the stochastic fractional heat equation
Authors: Assaad Obayda , Nualart David , Tudor Ciprian A. , Viitasaari Lauri 
Published: June 2021

AbstractIn this article we present aquantitativecentral limit theorem for the stochastic fractional heat equation driven by a a general Gaussian multiplicative noise, including the cases of space–time white noise and the white-colored noise with spatial covariance given by the Riesz kernel or a bounded integrable function. We show that the spatial average over a ball of radiusRconverges, asRtends to infinity, after suitable renormalization, towards a Gaussian limit in the total variation distance. We also provide a functional central limit theorem. As such, we extend recently proved similar results for stochastic heat equation to the case of the fractional Laplacian and to the case of general noise.