bluuebunny/crossref_metadata_2025_split huggingface dataset:
UFold: fast and accurate RNA secondary structure prediction with deep learning
Authors: Fu Laiyi , Cao Yingxin , Wu Jie , Peng Qinke , Nie Qing , Xie Xiaohui 
Published: October 2021

Abstract
For many RNA molecules, the secondary structure is essential for the correct function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau over time. Traditional RNA secondary structure prediction algorithms are primarily based on thermodynamic models through free energy minimization, which imposes strong prior assumptions and is slow to run. Here, we propose a deep learning-based method, called UFold, for RNA secondary structure prediction, trained directly on annotated data and base-pairing rules. UFold proposes a novel image-like representation of RNA sequences, which can be efficiently processed by Fully Convolutional Networks (FCNs). We benchmark the performance of UFold on both within- and cross-family RNA datasets. It significantly outperforms previous methods on within-family datasets, while achieving a similar performance as the traditional methods when trained and tested on distinct RNA families. UFold is also able to predict pseudoknots accurately. Its prediction is fast with an inference time of about 160 ms per sequence up to 1500 bp in length. An online web server running UFold is available at https://ufold.ics.uci.edu. Code is available at https://github.com/uci-cbcl/UFold.
The role of diffusion tensor imaging metrics in machine learning-based characterisation of paediatric brain tumors and their practicality for multicentre clinical assessment
Authors: Rose Heather , Li Huijun , Bennett Christopher D , Novak Jan , Sun Yu , MacPherson Lesley , Avula Shivaram , Arvanitis Theodoros , Clark Christopher , Bailey Simon , Mitra Dipayan , Auer Dorothee , Grundy Richard , Peet Andrew 
Published: October 2021

Abstract

Aims
Magnetic resonance imaging (MRI) is a valuable tool for non-invasive diagnosis of paediatric brain tumours. The rarity of the disease dictates multi-centre studies and imaging biomarkers that are robust to protocol variability. We investigated diffusion tensor MRI (DT-MRI), combined with machine learning, as an aid to diagnosis and evaluated the robustness of the imaging metrics.

Method
A multi-centre cohort of 52 clinical DT-MRI scans (20 medulloblastomas (MB), 21 pilocytic astrocytomas (PA), 11 ependymomas (EP)) were analysed retrospectively. Histograms for regions of solid tumour for fractional anisotropy (FA), mean diffusivity (MD), pure anisotropic diffusion (q) and pure isotropic diffusion (p) were compared to assess diagnostic capability. Linear discriminate analysis (LDA) was used for classification and validated using leave-one-out-cross-validation (LOOCV).

Results
Histogram medians for FA, MD, q and p were all different between tumor groups (P&lt;.0001, Kruskal Wallis test). Median MD, p and q values were highest in PA, then EP and lowest in MB (P&lt;.0001, Pairwise Wilcox test). FA median was higher for EP than PA (P=.004) with no significant difference between EP and MB (P=.591). ROC analysis showed that median MD, q and p perform best as a diagnostic marker (AUC= 0.92 to 0.99). LOOCV showed an overall accuracy of the LDA classification, ranging between 67% - 87%. FA values were highly dependent on protocol parameters, whereas pure anisotropic diffusion, q, was not.

Conclusion
DT-MRI metrics from multi-centre acquisitions can classify paediatric brain tumours. FA is the least robust metric to protocol variability and q provides the most robust quantification of anisotropic behaviour.
Smoking Status and Factors associated with COVID-19 In-Hospital Mortality among US Veterans
Authors: Razjouyan Javad , Helmer Drew A , Lynch Kristine E , Hanania Nicola A , Klotman Paul E , Sharafkhaneh Amir , Amos Christopher I 
Published: October 2021

Abstract

Introduction
The role of smoking in risk of death among patients with COVID-19 remains unclear. We examined the association between in-hospital mortality from COVID-19 and smoking status and other factors in the United States Veterans Health Administration (VHA).

Methods
This is an observational, retrospective cohort study using the VHA COVID-19 shared data resources for February 1 to September 11, 2020. Veterans admitted to the hospital who tested positive for SARS-CoV-2 and hospitalized by VHA were grouped into Never (as reference, NS), Former (FS), and Current smokers (CS). The main outcome was in-hospital mortality. Control factors were the most important variables (among all available) determined through a cascade of machine learning. We reported adjusted odds ratios (aOR) and 95% confidence intervals (95%CI) from logistic regression models, imputing missing smoking status in our primary analysis.

Results
Out of 8 667 996 VHA enrollees, 505 143 were tested for SARS-CoV-2 (NS = 191 143; FS = 240 336; CS = 117 706; Unknown = 45 533). The aOR of in-hospital mortality was 1.16 (95%CI 1.01, 1.32) for FS vs. NS and 0.97 (95%CI 0.78, 1.22; p &gt; .05) for CS vs. NS with imputed smoking status. Among other factors, famotidine and nonsteroidal anti-inflammatory drugs (NSAID) use before hospitalization were associated with lower risk while diabetes with complications, kidney disease, obesity, and advanced age were associated with higher risk of in-hospital mortality.

Conclusions
In patients admitted to the hospital with SARS-CoV-2 infection, our data demonstrate that FS are at higher risk of in-hospital mortality than NS. However, this pattern was not seen among CS highlighting the need for more granular analysis with high-quality smoking status data to further clarify our understanding of smoking risk and COVID-19-related mortality. Presence of comorbidities and advanced age were also associated with increased risk of in-hospital mortality.

Implications
Veterans who were former smokers were at higher risk of in-hospital mortality compared to never smokers. Current smokers and never smokers were at similar risk of in-hospital mortality. The use of famotidine and nonsteroidal anti-inflammatory drugs (NSAIDs) before hospitalization were associated with lower risk while uncontrolled diabetes mellitus, advanced age, kidney disease, and obesity were associated with higher risk of in-hospital mortality.
Robotic Sacroiliac Fixation Technique for Triangular Titanium Implant in Adult Degenerative Scoliosis Surgery: 2-Dimensional Operative Video
Authors: Berlin Connor , Patel Parantap , Lieberman Isador , Shaffrey Mark , Buchholz Avery 
Published: October 2021

Abstract
Corrective surgery remains a definitive treatment for adult spinal deformity, improving pain and disability. With these cases, instrumentation to the pelvis with iliac fixation is recommended. Whether iliac or S2-Alar-Iliac (S2AI) trajectories are used, sacroiliac joint pain and long-term sacroilitis can be common after long-fusion constructs.
1-3
Sacroiliac fusion with triangular titanium implants during fusion can reduce back pain associated with sacroiliac joint degeneration,
3
provides reduction in sacroiliac joint motion and stress when added to S2AI screws, and potentially enhances mechanical stability of fusion constructs.
4

Here, we present a technique for placing triangular titanium sacroiliac implants (iFuse BedrockTM; SI-BONE Inc, Santa Clara, California) alongside S2AI screws using a robotic platform (Mazor X; Medtronic Sofamor Danek, Medtronic Inc, Dublin, Ireland). Navigated robotics allows reduction in human error with implant placement, and potentially decreased operative time/fluoroscopy.
5-7
Key surgical steps include placement of K wires for S2AI and bilateral SI-implants, tapping, replacing SI-implant K wires with guide pins, placing S2AI screws, and finally placing the SI-implant. Final placement is verified with intraoperative fluoroscopy.
The patient described is a 61-yr-old woman with worsening adult degenerative scoliosis, lower back pain, left leg radicular pain, and mild right leg pain who failed conservative treatment. Examination revealed diminished strength in both legs. Imaging was significant for moderate sigmoid scoliosis, discogenic disease, and osteoarthritis at all levels. She consented to undergo corrective surgery. Postoperatively, the patient experienced resolution of her leg weakness and pain. Imaging demonstrated appropriate positioning of hardware. Prospective studies on the efficacy of the SI-implant are underway.
Simultaneous Endoscopic and Microscopic Visualization in Microvascular Decompression for Hemifacial Spasm
Authors: McGahan Ben G , Albonette-Felicio Thiago , Kreatsoulas Daniel C , Magill Stephen T , Hardesty Douglas A , Prevedello Daniel M 
Published: October 2021

Abstract

BACKGROUND
Hemifacial spasm (HFS) is a socially limiting condition leading to decreased quality of life that can be treated with microvascular decompression (MVD). Endoscopy has been described as an adjunct to traditional microscopy for MVD, although the best visualization technique is debated.

OBJECTIVE
To review the current literature on use of endoscopy in MVD for HFS and to describe the simultaneous microscopic and endoscopic visualization technique along with a video illustration.

METHODS
Patients who underwent MVD for HFS were retrospectively reviewed from January 2011 to December 2019. The first set of patients in the series were done using traditional endoscopic assisted visualization, followed by a change in technique in the subsequent patients using the simultaneous endoscopic technique. The surgical technique is described as well as illustrated with a video.

RESULTS
In total, 21 patients underwent 24 MVDs to treat HFS. The simultaneous endoscopic/microscopic technique was used in 48% of cases for visualization. All but one patient had resolution of their symptoms immediately after the procedure. In total, 7 patients had recurrence of HFS, with 4 (17%) resolving spontaneously and 3 (13%) ultimately undergoing redo MVD. Postoperatively 7 patients (29%) had transient complications that all resolved completely. There was no significant difference between the traditional alternating microscopic and endoscopic technique with the simultaneous endoscopic microscopic technique.

CONCLUSION
Endoscopic assistance during MVD for HFS is beneficial and may be streamlined by using the simultaneous microscope and endoscope visualization technique.
Beyond Peak Oil and Gas
Authors: Gordon Deborah 
Published: October 2021

Abstract
Chapter 1 challenges conventional wisdom that oil and gas were once thought to be running out. But peak oil supply is a myth, and there is a huge trove of hydrocarbons on Earth and even in space and on other planets. This chapter argues that not only are oil and gas resources plentiful but also there are few substitutes available to readily replace them. Moreover, these resources are entrenched in the global economy through well-established consumer bases, infrastructure, financial investments, social contracts, special interests, and regulations. The techniques used to convert hydrocarbons to petroleum products are discussed. Even as clean energy technologies get dramatically better and cheaper, they won’t easily displace oil and gas. The market forces that govern oil and gas are explained, as are the market failures that mean the best barrels are not necessarily prioritized.
The Overlooked Perils of Heterogeneous Oil and Gas
Authors: Gordon Deborah 
Published: October 2021

Abstract
Chapter 2 details the differences and similarities among twenty-first-century petroleum resources and distinguishes conventional from unconventional resources. The chapter argues that, while these definitions are muddled, there is value to understanding and parsing unconventional oil and gas. Numerous different oil and gas resources are then surveyed, including shale gas, ultradeep gas, Arctic gas, tight gas, coalbed methane, biogas, acid gas, geopressurized gas, methane hydrates, condensates, light tight oil, extra-heavy oil, ultradeep oil, Arctic oil, depleted oil, kerogen, biofuels, gas-to-liquids, and coal-to-liquids. Estimates are provided of cumulative industry greenhouse gas emissions for conventional versus unconventional oil and gas resources. The chapter concludes with a discussion of hydrogen—the ultimate unconventional resource—and its production pathways.
Civil Society: Driving Change
Authors: Gordon Deborah 
Published: October 2021

Abstract
Chapter 7 explores the role that civil society actors can play in driving change to reduce oil sector climate impacts. It argues that consumers need to be put under a microscope to examine the wide-held misconception that they are sovereign and can control markets by shifting demand. This chapter refocuses nongovernmental organizations, campaigners, academics, and the public on the supply chain and lays out different approaches they can take, including (1) disseminating information, (2) conducting advocacy, (3) providing accountability, and (4) participating in social movements. Success rests on coordinating civil society so that each actor plays its most important role.
Communication Through Law?
Authors: Stilz Anna 
Published: October 2021

Abstract
This commentary raises four critical questions for Shiffrin’s account of democratic law. First, why does our duty to communicate recognition for others as moral equals ground a special duty to our fellow citizens to cooperate together in a democracy? Second, whose messages exactly does democratic law communicate—is it the messages of individual citizens or the messages of the state as a corporate agent? Third, why does discharging our communicative duties require us to play an equal role in our political system, especially given Shiffrin’s endorsement of the idea that common law counts as a form of democratic co-authorship? And finally, how does the state’s pursuit of discretionary interests, for example in the promotion of a national culture or the preservation of fetal life, help us to send morally valuable messages to one another?
Keep the Conversation Going: Theory and Method in Strategic Management
Authors: Hoskisson Robert E. , Harrison Jeffrey S. 
Published: October 2021

Abstract
As a relatively young discipline, the field of strategic management has not been as stifled as some other fields by what might be called a “normal science straitjacket” of established theories and methods. Instead, interesting conversations have emerged, based on homegrown ideas and drawing from numerous other disciplines. In the first few decades, these conversations shifted like a pendulum from an internal organizational emphasis to a focus on the competitive environment, and back with an emphasis on the resource-based view. This chapter demonstrates how many of the recent interesting findings are based on moving the pendulum toward the center, applying external perspectives to internal questions, and vice versa. The chapter provides examples of this phenomenon for a number of external and internal topics that are important to solving important strategic challenges. It also highlights promising research questions in these areas that have yet to be adequately addressed.
The Organizational View of Strategic Management
Authors: Greve Henrich R. 
Published: October 2021

Abstract
The organizational view of strategic management views strategic decisions as outcomes of organizational goals and environmental influences. Central research streams are institutional theory and network theory on environmental influences, and learning theory and resource dependence theory on organizational interaction with the environment. Currently active research topics are centered on how societal groups influence organizations, intraorganizational individuals and groups pursue their own goals, and organizations pursue their goals by choosing strategic actions that maneuver societal constraints. Research is beginning to crystallize a view of environments and organizational structures interacting closely with strategy, with organizations learning to shape their interorganizational networks and surrounding institutions to their benefit. Comparison of performance and aspiration levels on multiple goals helps organizations time and direct strategic changes. The organizational view is a prominent part of strategic management and has enough unanswered questions to spur significant future research.
Evolution of Qualitative Research Methods in Strategic Management
Authors: Graebner Melissa E. 
Published: October 2021

Abstract
Qualitative research has played an influential role in strategic management since the inception of the field. Qualitative data are open-ended, vivid, rich, and nuanced, fostering a more sophisticated and ecologically valid understanding of organizational strategies and strategy making. Qualitative methodologies are diverse and include multicase theory building; process analysis; strategy-as-practice; narrative, discursive, and rhetorical approaches; and deductive and illustrative case studies. Despite contributing to scholarship on critical topics such as alliances, mergers and acquisitions, responses to technological change, corporate governance, managerial cognition, and strategy in entrepreneurial ventures, qualitative research faces hurdles in the publication process. Nonetheless, qualitative approaches will be essential for the future of strategy scholarship and offer opportunities to better understand the intersection of strategic management and broader societal concerns such as coping with crises and achieving greater equity and inclusion in organizations.
Alliances and Networks
Authors: Lavie Dovev 
Published: October 2021

Abstract
Strategy research underscores the role of alliances and networks in driving cooperation and value creation across firm boundaries. This chapter discusses the relational and structural characteristics of alliance ties, centering on questions related to the formation and performance implications of alliances and networks, including multiparty alliances, alliance portfolios, and ecosystems. The chapter discusses the various theoretical perspectives used in studying the formation and development of alliances, the choice of partners, value creation and capture, the governance of alliances, their portfolio configuration, and network dynamics. Besides discussing the foundations and recent work on alliances and networks, future research directions are identified. Some opportunities include examining the microfoundations of alliance relationships, analyzing the failure of relational mechanisms, disentangling value creation from value capture dynamics, studying cognitive and behavioral antecedents of network evolution, the tradeoff between routinization and flexibility in alliance management, and the unique nature of cooperation in ecosystems versus dyadic alliances.
Emerging Economies: The Impact of Context on Global Strategic Management
Authors: Williamson Peter J. , Santos José F. P. 
Published: October 2021

Abstract
This chapter begins by exploring what defines emerging economies based on how they are different from the viewpoint of strategy making. Then the chapter turns to examine the strategies adopted by leading domestic firms in emerging economies and emerging market multinationals, highlighting their potential for market disruption and the implications for the study and practice of global strategic management. Acknowledging the growing importance of emerging economies in the global economy, the chapter explores the implications of the emerging economies context for the strategies of multinationals from developed economies. The chapter concludes by proposing avenues for future research on how emerging economies impact global strategic management, including the need to recognize that they are complex dynamic systems with rising economic complexity that demand new types of dynamic capabilities and innovative sources of competitive advantage to enable success.
Corporate Governance
Authors: Aguilera Ruth V. 
Published: October 2021

Abstract
Corporate governance entails the design of a bundle of practices and processes to distribute the allocation of decision-making power among the different actors in the firm to promote value creation in the long term. It is at the heart of strategic thinking and implementation, because governance practices are designed to incentivize certain behavioral strategies, such as promoting sustainability, and to monitor that other courses of action are not taken, such as ethical lapses. This chapter first discusses what corporate governance is and why it is important for strategic management. Then the chapter reviews key areas that have received the most attention in the strategy literature, such as shareholder engagement and international corporate governance. The last and largest section of this chapter discusses three emerging corporate governance themes relevant to firm strategy in these changing global, digital, and pandemic times.
Boards of Directors and Strategic Management in Public Firms and New Ventures
Authors: Westphal James D. , Garg Sam 
Published: October 2021

Abstract
This chapter examines contemporary theory and research on boards of directors in strategic management. After briefly reviewing the evolution of research on corporate boards and strategic management, we describe contemporary theoretical perspectives and emerging topics in the literature, and identify a variety of future research opportunities. We then turn to recent research in the rapidly growing literature on venture boards and strategy. Our review of recent work on boards of public companies and new ventures reveals a common emphasis on behavioral processes in the boardroom, in dyadic CEO-board interactions outside the boardroom, and in relations between directors and external constituents. We describe numerous opportunities to extend these complementary literatures by linking behavioral processes in boards to issues of diversity, technology and innovation, culture and institutions, and competitive strategy.
Knowledge and Innovation: From Path Dependency Toward Managerial Agency
Authors: Volberda Henk W. , Schneidmuller Tatjana , Zadeh Taghi 
Published: October 2021

Abstract
In this chapter we argue that in foundational theories of knowledge and innovation, innovation is either path-dependent, and thus incremental and largely passive, or active and radical, with strategists playing a decisive role in shaping innovation outcomes. Moving on from foundational theories of knowledge and innovation, we show in this chapter that the field has diversified into five interrelated clusters: (1) international knowledge transfer, (2) organizational capabilities and learning, (3) networks and ties, (4) regional clusters, and (5) open innovation. While some clusters have shown the importance of managerial agency, the chapter concludes with describing four research avenues considered most important for future-proofing this field of study: (1) diverse audiences, (2) regulation and regulators, (3) misalignment capabilities, and (4) internal agents as active movers of innovation. These research avenues may further contribute toward a managerial agency of innovation view in which managers are regarded as playing an active role as strategists in knowledge development and innovation.