bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell multi-omics sequencing and its application in tumor heterogeneity
Authors: Sun Yuqing , Liu Zhiyu , Fu Yue , Yang Yuwei , Lu Junru , Pan Min , Wen Tian , Xie Xueying , Bai Yunfei , Ge Qinyu 
Published: April 2023

Abstract
In recent years, the emergence and development of single-cell sequencing technologies have provided unprecedented opportunities to analyze deoxyribonucleic acid, ribonucleic acid and proteins at single-cell resolution. The advancements and reduced costs of high-throughput technologies allow for parallel sequencing of multiple molecular layers from a single cell, providing a comprehensive insight into the biological state and behavioral mechanisms of cells through the integration of genomics, transcriptomics, epigenomics and proteomics information. Researchers are actively working to further improve the cost-effectiveness, stability and high-throughput capabilities of single-cell multi-omics sequencing technologies and exploring their potential in precision medicine through clinical diagnostics. This review aims to survey the cutting-edge advancements in single-cell multi-omics sequencing, summarizing the representative technologies and their applications in profiling complex diseases, with a particular focus on tumors.
Molecular language models: RNNs or transformer?
Authors: Chen Yangyang , Wang Zixu , Zeng Xiangxiang , Li Yayang , Li Pengyong , Ye Xiucai , Sakurai Tetsuya 
Published: April 2023

Abstract
Language models have shown the capacity to learn complex molecular distributions. In the field of molecular generation, they are designed to explore the distribution of molecules, and previous studies have demonstrated their ability to learn molecule sequences. In the early times, recurrent neural networks (RNNs) were widely used for feature extraction from sequence data and have been used for various molecule generation tasks. In recent years, the attention mechanism for sequence data has become popular. It captures the underlying relationships between words and is widely applied to language models. The Transformer-Layer, a model based on a self-attentive mechanism, also shines the same as the RNN-based model. In this research, we investigated the difference between RNNs and the Transformer-Layer to learn a more complex distribution of molecules. For this purpose, we experimented with three different generative tasks: the distributions of molecules with elevated scores of penalized LogP, multimodal distributions of molecules and the largest molecules in PubChem. We evaluated the models on molecular properties, basic metrics, Tanimoto similarity, etc. In addition, we applied two different representations of the molecule, SMILES and SELFIES. The results show that the two language models can learn complex molecular distributions and SMILES-based representation has better performance than SELFIES. The choice between RNNs and the Transformer-Layer needs to be based on the characteristics of dataset. RNNs work better on data focus on local features and decreases with multidistribution data, while the Transformer-Layer is more suitable when meeting molecular with larger weights and focusing on global features.
How a Rising Power Treats Small States amid Power Transition: Evidence from the Sui and Tang Dynasties
Authors: Wan Xiao , Wu Yu-Shan 
Published: April 2023

Abstract
In a world buffeted by chaos emanating from the power transition between the USA and China, the behaviour patterns of a rising power carry considerable significance. This article explains a rising power’s choice of policies towards small states and why it adopts them. We then test the competing “power” and “culture” hypotheses by analysing asymmetric interactions during the “power transition” between the Turkic/Eastern Turkic Khanate and Sui-Tang China. The policies of Sui-Tang China towards Tuyuhun, Koguryo, and the Serindian oasis city-states confirm the materialist logic whereby it is the power balance between the major powers that determines a rising power’s strategic tendency when confronting the hegemon and which, in turn, generates the overall approaches of its policies towards small countries. However, the most-similar sub-cases invalidate the cultural affinity hypothesis. The study undermines the Chinese exceptionalism argument through its provision of a causal chain connecting great-power relations and asymmetric relations. Our findings suggest that, prior to overtaking the USA, China will maintain a defensive posture towards the USA and adopt moderate policies towards lesser nations.
Arterial wall inflammation assessed by 18F-FDG-PET/CT is higher in individuals with Type 1 diabetes and associated with circulating inflammatory proteins
Authors: Janssen Anna W M , van Heck Julia I P , Stienstra Rinke , Aarntzen Erik H J G , van Diepen Janna A , Riksen Niels P , Tack Cees J 
Published: April 2023

Abstract

Aims
The article investigates whether chronic hyperglycaemia in Type 1 diabetes (T1D) is associated with a proinflammatory immune signature and with arterial wall inflammation, driving the development of atherosclerosis.

Methods and results
Patients with T1D (n = 41), and healthy age-, sex-, and body mass index–matched controls (n = 20) were recruited. Arterial wall inflammation and haematopoietic activity were measured with 2′-deoxy-2′-(18F)-fluoro-D-glucose (18F-FDG) positron emission tomography/computed tomography. In addition, flow cytometry of circulating leucocytes was performed as well as targeted proteomics to measure circulating inflammatory markers. 18F-FDG uptake in the wall of the abdominal aorta, carotid arteries, and iliac arteries was higher in T1D compared with that in the healthy controls. Also, 18F-FDG uptake in the bone marrow and spleen was higher in patients with T1D. CCR2 and CD36 expressions on circulating monocytes were higher in patients with T1D, as well as several circulating inflammatory proteins. In addition, several circulating inflammatory markers (osteoprotegerin, transforming growth factor-alpha, CX3CL1, and colony-stimulating factor-1) displayed a positive correlation with FDG uptake. Within T1D, no differences were found between people with a high and low HbA1c.

Conclusion
These findings strengthen the concept that chronic hyperglycaemia in T1D induces inflammatory changes that fuel arterial wall inflammation leading to atherosclerosis. The degree of hyperglycaemia appears to play a minor role in driving this inflammatory response in patients with T1D.
Meat fermentation at a crossroads: where the age-old interplay of human, animal, and microbial diversity and contemporary markets meet
Authors: Leroy Frédéric , Charmpi Christina , De Vuyst Luc 
Published: April 2023

Abstract
Despite being part of the now often unfavourably perceived category of processed meats, fermented meats remain of substantial nutritional, economic, and cultural importance in today’s foodscapes. This translates into a vast assortment of different products. Fermentation is driven by microorganisms (e.g. in fermented sausages), although the terminology is sometimes used to also designate products in which microbial contributions are less dominant and that depend primarily on the activity of endogenous meat enzymes (e.g. in raw hams). A summary is given of the main microbial groups that characterize various types of meat and, in particular, their fermented derivatives. Moreover, it is argued that producers of fermented meat products struggle to adapt to a contemporary dietary context of change. On the one hand, they wish to reassure consumers by reaffirming the position of fermented meat products as traditional strongholds. On the other hand, producers are trying to alleviate some of the perceived concerns through technological innovation, for instance related to the impact of processing on food safety and health. This review raises the point that these sometimes contradictory trends can affect the choice of meat type, ingredients, and processing parameters, and how these choices, in turn, can affect microbial diversity.
The Hunger Games as the Key to Happily Ever After?
Authors: Deere Jacques A , Xu Clarice , Adelmant Celestine , Aboobaker Aziz , Salguero-Gómez Roberto 
Published: April 2023

AbstractThe world’s human population is reaching record longevities. Consequently, our societies are experiencing the impacts of prolonged longevity, such as increased retirement age. A major hypothesized influence on aging patterns is resource limitation, formalized under calorie restriction (CR) theory. This theory predicts extended organismal longevity due to reduced calorie intake without malnutrition. However, several challenges face current CR research and, although several attempts have been made to overcome these challenges, there is still a lack of holistic understanding of how CR shapes organismal vitality. Here, we conduct a literature review of 224 CR peer-reviewed publications to summarize the state-of-the-art in the field. Using this summary, we highlight the challenges of CR research in our understanding of its impacts on longevity. We demonstrate that experimental research is biased toward short-lived species (98.2% of studies examine species with &lt;5 years of mean life expectancy) and lacks realism in key areas, such as stochastic environments or interactions with other environmental drivers (eg, temperature). We argue that only by considering a range of short- and long-lived species and taking more realistic approaches, can CR impacts on longevity be examined and validated in natural settings. We conclude by proposing experimental designs and study species that will allow the discipline to gain much-needed understanding of how restricting caloric intake affects long-lived species in realistic settings. Through incorporating more experimental realism, we anticipate crucial insights that will ultimately shape the myriad of sociobioeconomic impacts of senescence in humans and other species across the Tree of Life.
What is Phenomenological Bioethics? A Critical Appraisal of Its Ends and Means
Authors: Coyne Lewis 
Published: April 2023

Abstract
In recent years the phenomenological approach to bioethics has been rejuvenated and reformulated by, among others, the Swedish philosopher Fredrik Svenaeus. Building on the now-relatively mainstream phenomenological approach to health and illness, Svenaeus has sought to bring phenomenological insights to bear on the bioethical enterprise, with a view to critiquing and refining the “philosophical anthropology” presupposed by the latter. This article offers a critical but sympathetic analysis of Svenaeus’ efforts, focusing on both his conception of the ends of phenomenological bioethics and the predominantly Heideggerian means he employs. Doing so reveals certain problems with both. I argue that the main aim of phenomenological bioethics as set out by Svenaeus needs to be reformulated, and that there are important oversights in his approach to reaching this end. I conclude by arguing that to overcome the latter problem we should draw instead on the works of Max Scheler and Hans Jonas.
Phenomenological Bioethics
Authors: Ferrarello Susi 
Published: April 2023

AbstractEudaimonia, that is, the experience of flourishing and welfare at the center of Greek philosophical investigations, describes the qualitative experience of being able to feel well in our bodies. Reductionism in medicine as well as in philosophy would instead reduce well-being to a set of standards that the human body or its mind must meet in order to be recognized as functioning. This journal issue, dedicated to a phenomenological approach in bioethics, represents a way to overcome this dangerous constraint thanks to the methodological support of the phenomenological investigations. The authors invited to write in this journal issue will tackle the problem of reductionism in bioethics through a phenomenological approach.
The Logic of Pregnancy
Authors: Bornemark Jonna 
Published: April 2023

AbstractThis article takes its point of departure in Bracha Ettinger’s discussion on the “matrixial borderspace”: the structure of the experience of “the womb,” both from a “mother-pole” and a “fetus-pole”. Ettinger describes this borderspace as a place of differentiation-in-co-emergence, separation-in-jointness, and distance-in-proximity. The question this article poses is what kind of logic this experience is an expression of, as there seems to be a discrepancy in relation to the classical Aristotelian logic of identity. As an alternative to classical Aristotelian logic, Nicholas of Cusa’s logic of the non-aliud is explored as a paradigm more in line with Ettinger’s description of pregnancy specifically and more generally, to an understanding of life as a co-poietic emergence of structures of pactivity and permeability.
The Phenomenology of Objectification in and Through Medical Practice and Technology Development
Authors: Svenaeus Fredrik 
Published: April 2023

AbstractObjectification is a real problem in medicine that can lead to bad medical practice or, in the worst case, dehumanization of the patient. Nevertheless, objectification also plays a major and necessary role in medicine: the patient’s body should be viewed as a biological organism in order to find diseases and be able to cure them. Listening to the patient’s illness story should not be replaced, but, indeed, developed by the physical examination of his body searching for the causes of his complaints. Whereas phenomenologists have so far mainly been identifying the back sides of objectification in medicine, in this paper the aim is to analyze differences between detrimental objectifications and objectifications that do not deprive the patient of his subjectivity but, rather, at least in some cases, may lead the patient to feel more at home with his body.
The Performance and Development of Deliberative Routines: A Practice-Based Ethnographic Study
Authors: Visser E Lianne , van Hulst Merlijn 
Published: April 2023

Abstract
Deliberation is ubiquitous in street-level work. Scholars and practitioners increasingly promote it, as it has the potential to improve existing practices and procedures and provide customized, yet consistent, services. Little is known, however, about the situated performance of deliberation in street-level work. Drawing on Routine Dynamics Theory and based on an ethnographic study of street-level decision-making in child and family services in the Netherlands (including document analysis, ~300 hours of observations, and interviews in two teams in one organization), we uncover the performance of deliberative routines and their development over time. Demonstrating how contextual factors and the prioritization of particular ends play a role in these routines, we contribute to a better understanding of the dynamic and reflective performance of street-level deliberation. In addition, providing a more nuanced view of routines and elaborating on some possibilities for enabling management thereof, we contribute to a better understanding of the complex and iterative organization of street-level work.
Subcoronal inflatable penile prosthesis implantation: indications and outcomes
Authors: Feng Carol L , Langbo William A , Anderson Lauren K , Cao David , Bajic Petar , Amarasekera Channa , Wang Vinson , Levine Laurence A 
Published: April 2023

Abstract

Background
While implantation of an inflatable penile prosthesis (IPP) is commonly performed via infrapubic or penoscrotal approaches, the subcoronal (SC) approach for IPP implantation may safely and reliably allow for additional reconstructive procedures through a single incision.

Aim
The aim of this study is to report outcomes, including complications, of the SC approach and to determine common characteristics of patients undergoing the SC approach.

Methods
A retrospective chart review from May 11, 2012, to January 31, 2022, was performed at a single, tertiary care institution to identify patients with IPP implantation via the SC approach.

Outcomes
Postoperative information was reviewed and extracted from all clinic notes available following the date of IPP implantation in the electronic medical record, detailing any complications including wound complications, need for revision or removal, device malfunction, and infections.

Results
Sixty-six patients had IPP implantation via the SC approach. Median follow-up duration was 29.4 (interquartile range 14.9-50.1) months. One (1.8%) patient had a simple wound complication. Two (3.6%) experienced postoperative infection of the prosthesis, which resulted in explantation of the device. One of these infected prostheses later experienced partial glans necrosis. Revision for mechanical failure or unsatisfactory cosmetic result was performed in 3 (7.3%) IPPs placed via a SC incision.

Clinical implications
The SC approach for implantation of IPP is safe and feasible with low complication and revision rates. It offers urologists an alternative to the classic infrapubic and penoscrotal approaches, both of which would require a second incision for additional reconstructive procedures required to adequately address deformities associated with severe Peyronie’s disease. Therefore, urologists who treat these specialized populations of men may benefit from having the SC approach in their array of techniques for IPP implantation.

Strengths and limitations
The limitations of this study include its retrospective nature, risk of selection bias, lack of comparison groups, and sample size. This study reports on early experience with the SC approach performed by a single high-volume reconstructive surgeon, who treats a specialized population of patients requiring complex repair during implantation of an IPP, particularly those with Peyronie’s disease.

Conclusion
The SC incision for IPP implantation has low rates of complications and remains our approach of choice for IPP implantation in patients with severe Peyronie’s disease, including curvatures &gt;60°, severe indentation with hinge, and grade 3 calcification, which are unlikely to respond adequately to manual modeling alone.
Fractured Fifties
Authors: Sprengler Christine 
Published: April 2023

Abstract
Fractured Fifties: The Cinematic Periodization and Evolution of a Decade presents a two-pronged argument that (1) cinema has helped define the 1950s by contributing in considerable and meaningful ways to the process of periodization and thus a general conception of the decade, and (2) cinema has fractured our sense of the 1950s. It challenges a reductive and fairly cohesive set of tropes with a complex amalgam of representations that also intervene in debates about historiography, historicity, cultural memory, mediation, nostalgia, and periodization. In other words, cinema has fractured our sense of the 1950s, yielding in the process a series of 1950s types or kinds (e.g., The Leave It to Beaver Fifties, The Jukebox Fifties, The Cold War Fifties, The Retromediated Fifties) as well as a wealth of critical insights into myriad pasts, presents, and the evolving relationships between them.
Periodization, Cinema, and the Decade
Authors: Sprengler Christine 
Published: April 2023

Abstract
Chapter 1, “Periodization, Cinema, and the Decade,” excavates a series of theoretical concerns, dealing specifically with periodization as a process, the significance of the decade as a historically specific measure of time, and the cinema as a phenomenological vector embroiled in the machinations of the first two. It also reflects on the contributions made by discussions around “period films” and considers the relationship between the 1950s and the Fifties, surveying the various ways in which this distinction has been articulated and used. This chapter examines a number of theoretical and historical projects that have had a hand in determining the questions posed in relation to the case studies pursued in this book. In particular, it looks to Michel Serres and Penelope Corfield’s work on periodization and time, Fred Davis’s and Jason Scott Smith’s isolated studies on the decade, and Susan Buck-Morss’s analysis of the phenomenology of cinema in relation to mass events.
The Leave It to Beaver Fifties
Authors: Sprengler Christine 
Published: April 2023

Abstract
Chapter 3, “The Leave It to Beaver Fifties,” is concerned with cinematic representations of suburban life and domesticity, particularly in relation to gender and race. The title of this chapter is pirated from the postwar sitcom of the same name because of its continued currency as a shorthand in political and cultural realms, an expression that invokes a certain vision of family life in the 1950s, both for those who idealized its power structures and relations and for those who sought to critique its internal oppressions and external exclusions. This chapter starts with a few examples from the 1990s and 2000s that deserve mention, but then concentrates its analysis on Revolutionary Road (2008) and Suburbicon (2017), concluding with a consideration of the television anthology series, Them (2021).
The Cold War Fifties
Authors: Sprengler Christine 
Published: April 2023

Abstract
Chapter 5, “The Cold War Fifties,” is expansive in scope and includes three definitive subcategories that concern the first phase of the Cold War (1947–62): The Korean War Fifties, The McCarthyite Fifties, and The Atomic Fifties. The Korean War Fifties offers the first instances of retrospective representations of the 1950s in several films released during the early 1960s. A recent resurgence in cinematic interest in the conflict has resulted in several titles, including Steve Wallace’s independent R&B opera film, Hal King, the primary case study here, as well as the television series Lovecraft Country (2020). The McCarthyite Fifties focuses on the trials and consequences of the House Un-American Activities Committee, often in an effort to shed light on contemporary ideological conflicts. Good Night, and Good Luck (2005) and Trumbo (2015) occupy the center of this analysis. The Atomic Fifties includes a body of films concerned primarily with the space race during the 1950s and early 1960s. The focus in this section is on Hidden Figures (2016), a film that not only invokes questions about historicity but also provides a point of contact with Hal King through the situation of the civil rights movement in relation to the Cold War. The ways in which Hidden Figures negotiates this relationship—and also the ways in which it fails to—are particularly instructive for thinking through the connections between the new civil rights movement (Black Lives Matter) and the New Cold War, both of which are implicitly acknowledged by the film.
The Retromediated Fifties
Authors: Sprengler Christine 
Published: April 2023

Abstract
Chapter 6, “The Retromediated Fifties,” examines films that are ostensibly about other media practices in the 1950s and often tell their stories through the aesthetic lenses of these media. As such, they are engaged with the mediation of historical periods and the role of film and photography in shaping conceptions of earlier moments. It begins with a brief analysis of Hail, Caeser! (2016) and La La Land (2016) as instances of what might be called a “Hollywood Fifties” subtype for their investments in both the aesthetics and practices of postwar cinema, that is, an engagement with a kind of deliberate archaism. In a marked departure, Sylvie’s Love (2020) fully and unabashedly inhabits its genre of choice, melodrama. This chapter briefly considers this approach before turning to an example of retromediation that leaves film behind: Carol (2015). Directed by Todd Haynes, the film documents the developing love affair between a socialite and shop girl, but does so through an aesthetic template borrowed from 1950s street photography.