bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome
Authors: Florkowski Melanie R , Hamer Sarah A , Yorzinski Jessica L 
Published: August 2023

AbstractThe gut microbiome is important for host fitness and is influenced by many factors including the host’s environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture (“wild sample”) and again 5–10 days after capture (“captive sample”). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds’ microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds’ diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.
Bacteria and microalgae associations in periphyton—mechanisms and biotechnological opportunities
Authors: Vale Francisca , Sousa Cátia A , Sousa Henrique , Simões Lúcia C , McBain Andrew J , Simões Manuel 
Published: August 2023

AbstractPhototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae–bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture, biorefinery, and wastewater bioremediation). In this review, we analyze the species dynamics (i.e. periphyton formation and factors determining the prevalence of one species over another), coexisting communities, exchange of resources, and communication mechanisms of periphytic microalgae and bacteria. We extend periphyton mathematical modelling as a tool to comprehend complex interactions. This review is expected to boost the applicability of microalgae–bacteria consortia, by drawing out knowledge from natural periphyton.
ARA: a flexible pipeline for automated exploration of NCBI SRA datasets
Authors: Maurya Anand , Szymanski Maciej , Karlowski Wojciech M 
Published: August 2023

Abstract

Background
One of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data generated by the next-generation sequencing (NGS) technologies, this approach is often not available. The hierarchical organization of the NGS records is primarily designed for browsing or text-based searches of the information provided in metadata-related keywords, limiting the efficiency of database exploration.

Findings
We developed an automated pipeline that incorporates the well-established NGS data-processing tools and procedures to allow easy and effective sampling of the NCBI SRA database records. Given a file with query nucleotide sequences, our tool estimates the matching content of SRA accessions by probing only a user-defined fraction of a record's sequences. Based on the selected parameters, it allows performing a full mapping experiment with records that meet the required criteria. The pipeline is designed to be easy to operate—it offers a fully automatic setup procedure and is fixed on tested supporting tools. The modular design and implemented usage modes allow a user to scale up the analyses into complex computational infrastructure.

Conclusions
We present an easy-to-operate and automated tool that expands the way a user can access and explore the information contained within the records deposited in the NCBI SRA database.
Bronchial branching patterns and volumetry in the right upper lobe: impact on segmentectomy planning
Authors: Miura Kentaro , Eguchi Takashi , Ide Shogo , Mishima Shuji , Matsuoka Shunichiro , Takeda Tetsu , Hamanaka Kazutoshi , Shimizu Kimihiro 
Published: August 2023

Abstract

OBJECTIVES
The use of segmentectomy is expected to increase. However, understanding of the segmental bronchial branching is limited. Herein, we aimed to investigate bronchial branching pattern complexity and segmental volumetry of the right upper lung lobe to develop an accurate understanding of segmental anatomy and contribute to the advancement of safe and efficient lung segmentectomy.

METHODS
We evaluated chest computed tomography scans of 303 patients and categorized the branching of segmental bronchi (segment 1, apical; segment 2, posterior; and segment 3, anterior) into 4 major types (typical trifurcated, bifurcated non-defective, bifurcated defective and atypical trifurcated) and 11 subtypes. Segmental volumetry was performed to determine the predominant segment in each case (volume difference &lt;5% was considered equal). Branching complexity was evaluated separately for volumetry-predominant and volumetry-non-predominant segments.

RESULTS
Trifurcated non-defective was the most frequent branching type (64.4%), followed by bifurcated non-defective (22.1%), bifurcated defective (8.6%) and trifurcated half-defective (4.0%). In terms of segmental volumetry, most cases had a one-segment-predominant distribution (71%) and only 5% of cases had equal distribution (segment 1 = segment 2 = segment 3). More than half of the cases had a segment 3-predominant distribution (52%). Branching complexity analysis revealed that the volumetry-non-predominant segment was associated with a higher risk of complex branching patterns compared with the volumetry-predominant segment (37% vs 19%, respectively; P &lt; 0.005).

CONCLUSIONS
Volumetric assessment of the right upper lobe showed a heterogeneous segmental volume distribution. Care should be taken during lung segmentectomy of the volumetry-non-predominant segments because of the high risk associated with complex bronchial branching patterns.

Clinical trial registration
No. 4840.
Clonal dissemination of Klebsiella pneumoniae resistant to cefiderocol, ceftazidime/avibactam, meropenem/vaborbactam and imipenem/relebactam co-producing KPC and OXA-181 carbapenemase
Authors: Bovo Federica , Amadesi Stefano , Palombo Marta , Lazzarotto Tiziana , Ambretti Simone , Gaibani Paolo 
Published: August 2023

Abstract

Objectives
Herein, we describe the epidemiology of carbapenemase-producing Enterobacterales (CPE) before and during the COVID-19 pandemic. Also, we report the emergence of an outbreak of Klebsiella pneumoniae strains co-producing KPC and OXA-181 carbapenemase, resistant to novel β-lactam/β-lactamase inhibitors (βL-βLICs) and cefiderocol.

Methods
CPE were collected during a period of 3 years from 2019 to 2021. Antimicrobial susceptibility testing for novel βL-βLICs and cefiderocol was performed by MIC test strips and microdilution with iron-depleted broth. WGS was performed on 10 selected isolates using the Illumina platform, and resistome analysis was carried out by a web-based pipeline.

Results
Between January 2019 and December 2021, we collected 1430 carbapenemase producers from 957 patients with infections due to CPE. KPC was the most common carbapenemase, followed by VIM, OXA-48 and NDM. During 2021, we identified 78 K. pneumoniae co-producing KPC and OXA-181 carbapenemases in 60 patients, resistant to meropenem/vaborbactam and imipenem/relebactam. Resistance to ceftazidime/avibactam and cefiderocol was observed respectively in 7 and 8 out of the 10 sequenced K. pneumoniae. Genome analysis showed that all isolates were clonally related, shared a common porin and plasmid content, and carried blaOXA-181 and blaKPC carbapenemases. Specifically, 4 out of 10 isolates carried blaKPC-3, while 6 harboured mutated blaKPC. Of note, KPC producers resistant to ceftazidime/avibactam and harbouring mutated blaKPC exhibited higher MICs of cefiderocol (median MIC 16 mg/L, IQR 16–16) than strains harbouring WT blaKPC-3 (cefiderocol 9 mg/L, IQR 1.5–16).

Conclusions
Our results highlight the need for continuous monitoring of CPE to limit widespread MDR pathogens carrying multiple mechanisms conferring resistance to novel antimicrobial molecules.
Generalization of finetuned transformer language models to new clinical contexts
Authors: Xie Kevin , Terman Samuel W , Gallagher Ryan S , Hill Chloe E , Davis Kathryn A , Litt Brian , Roth Dan , Ellis Colin A 
Published: August 2023

Abstract

Objective
We have previously developed a natural language processing pipeline using clinical notes written by epilepsy specialists to extract seizure freedom, seizure frequency text, and date of last seizure text for patients with epilepsy. It is important to understand how our methods generalize to new care contexts.

Materials and methods
We evaluated our pipeline on unseen notes from nonepilepsy-specialist neurologists and non-neurologists without any additional algorithm training. We tested the pipeline out-of-institution using epilepsy specialist notes from an outside medical center with only minor preprocessing adaptations. We examined reasons for discrepancies in performance in new contexts by measuring physical and semantic similarities between documents.

Results
Our ability to classify patient seizure freedom decreased by at least 0.12 agreement when moving from epilepsy specialists to nonspecialists or other institutions. On notes from our institution, textual overlap between the extracted outcomes and the gold standard annotations attained from manual chart review decreased by at least 0.11 F1 when an answer existed but did not change when no answer existed; here our models generalized on notes from the outside institution, losing at most 0.02 agreement. We analyzed textual differences and found that syntactic and semantic differences in both clinically relevant sentences and surrounding contexts significantly influenced model performance.

Discussion and conclusion
Model generalization performance decreased on notes from nonspecialists; out-of-institution generalization on epilepsy specialist notes required small changes to preprocessing but was especially good for seizure frequency text and date of last seizure text, opening opportunities for multicenter collaborations using these outcomes.
Introduction
Authors: Tolin David F. 
Published: August 2023

Abstract
The second edition of The Oxford Handbook of Obsessive-Compulsive and Related Disorders focuses on the obsessive-compulsive and related disorders (OCRDs), newly described in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM). The OCRDs include obsessive-compulsive disorder (OCD), body dysmorphic disorder, hoarding disorder, trichotillomania (hair-pulling disorder), and excoriation (skin-picking) disorder. In the handbook, leading experts review current evidence on the phenomenology, epidemiology, assessment, and treatment of the OCRDs, as well as the presentation of the conditions in special populations. The introductory chapter provides a brief history of OCD, an account of its role in the DSM, and an overview of the chapters to follow.
Behavioral Conceptualizations of Obsessive-Compulsive and Related Disorders
Authors: Cassin Stephanie E. , Regev Rotem , Fournier Sandra , Rector Neil A. 
Published: August 2023

Abstract
The current chapter provides a selective overview of behavioral theories of obsessive-compulsive and related disorders (OCRDs) and reviews the empirical support for these theories. Behavioral theories revolutionized the psychological conceptualization and treatment of the OCRDs, and there is strong evidence accumulated over the past 50 years demonstrating the seminal role of learning processes in the maintenance of the conditions. The evidence supporting the role of learning factors in the development of the OCRDs is somewhat less clear. In the past decade, there has been renewed interest in modeling the full range of learning factors related to fear extinction in the context of exposure-based therapy, and the principles and empirical evidence for the role of inhibitory learning are addressed in the chapter.
Assessing Comorbidity, Insight, Family, and Functioning
Authors: Merritt Olivia A. , Purdon Christine 
Published: August 2023

Abstract
Obsessive-compulsive disorder (OCD) is a complex and debilitating disorder that has a high degree of comorbidity with mood and anxiety disorders. Strategies for differential diagnosis of OCD and these disorders, as well as the interactions of the diagnoses in treatment settings, are discussed. The chapter also explores the relationships between OCD and personality disorders, as well as between OCD and the OCD-related disorders. OCD is also characterized by impaired quality of life, family involvement, and varying insight. The presence of OCD is associated with high levels of functional impairment, especially in the social and emotional domains. Relationships with important others can be affected by the disorder. Family members are often involved in OCD symptoms, and family variables like symptom accommodation and hostility are related to poorer treatment outcomes. Treatment outcomes can also be influenced by level of insight held by the individual with OCD; those with poor insight into the irrationality of their symptoms often face challenges with treatment engagement. The chapter aims to provide a brief overview of comorbidity, family, insight, and quality-of-life issues and to review assessment and treatment implications of those issues. Measures for assessing relevant constructs are described.
Exposure-Based Treatment for Obsessive-Compulsive Disorder
Authors: Abramowitz Jonathan S. , Taylor Steven , McKay Dean 
Published: August 2023

Abstract
Exposure and response prevention (E/RP) is one of the oldest and most effective treatments for obsessive-compulsive disorder. The present chapter describes the empirical foundations, development, delivery, and latest research on E/RP. Commonly used methods and procedural variants of E/RP are described, along with the underlying mechanisms of action. The efficacy of E/RP in relation to other treatments is discussed, in addition to research on the long-term effects of E/RP and its effects in non-research settings. Pretreatment predictors of the outcome of using E/RP are also considered. Efforts to improve treatment outcome are discussed, such as research into the benefits of including a spouse or partner in E/RP. The chapter concludes by considering important future research directions for improving the outcome of treatment packages that include E/RP.
Treatment of Body Dysmorphic Disorder
Authors: Summers Berta J. , Laky Zoë E. , Greenberg Jennifer L. , Chosak Anne , Fang Angela , Wilhelm Sabine 
Published: August 2023

Abstract
Body dysmorphic disorder (BDD) is characterized by an excessive preoccupation with an imagined or slight defect in one’s appearance. BDD is a severe and common disorder associated with high levels of functional impairment and high rates of suicidality. Interventions, including cognitive-behavioral therapy and pharmacotherapy, are effective for BDD. This chapter outlines the cognitive-behavioral model and therapy of BDD. The chapter reviews pharmacotherapy of BDD and discusses the role of combination therapy. The chapter also addresses ineffective approaches for the treatment of BDD, including the role of cosmetic procedures. Early recognition and intervention are critical, as they limit the disorder’s chronicity and subsequent morbidity.
The Rise and Decline of the European Struggle against Social Exclusion
Authors: Atkinson Rob 
Published: August 2023

Abstract
Throughout the 1990s and early 2000s, addressing social exclusion and achieving greater social inclusion figured prominently in the “social policy” discourse of the European Union and of many national governments within it. This chapter discusses social exclusion and why it came to largely replace, or subsume, poverty and associated notions such as the “slum” in the EU and wider European debates. However, despite its apparent recent prominence, social exclusion has always been subordinate, to a greater or lesser degree, to the enhancement of economic competitiveness through the pursuit of a neoliberal policy agenda. Since the crash of 2007–2008 and the prolonged subsequent period of austerity and welfare state restructuring/retrenchment, social exclusion has been further downgraded in pursuit of the “holy grail” of economic competitiveness.
NGO Representation of Informal Settlements
Authors: Huchzermeyer Marie 
Published: August 2023

Abstract
Slum/Shack Dwellers International or SDI is an international NGO with grassroots and NGO affiliates in twenty-three countries in 2018, the vast majority of these on the African continent. Its governance incorporates selected and remunerated grassroots representatives, and until 2019 was intertwined with that of global agencies. While framing itself as being made up of grassroots savings collectives engaging in a set of non-confrontational approaches based on self-reliance and exchanges, SDI increasingly purported to represent and chart solutions for the urban poor globally. The organization’s savings-based structure of grassroots representation also sits at odds with an expansion drive, which had led to an uneven loosening of the methodological orthodoxy and therefore a diversification across the network. At the time of research in 2018, tensions existed between SDI’s representational procedures, the de facto nature of the network and its global narrative. This chapter combines a review of the extensive published and grey literature on SDI with selected interviews at the height of the organization’s global legitimacy.
Popular Housing Processes in Caribbean Colombia
Authors: Kellett Peter 
Published: August 2023

Abstract
Informal settlements are characterized by incremental change, often over long periods. This chapter draws on an ongoing longitudinal ethnographic study over a thirty-year period in informal settlements in the city of Santa Marta, Colombia. It explores the diverging trajectories of households as they attempt to build new lives through the generations. Contrasting cases demonstrate different strategies and levels of achievement and explain how the construction of owner-built dwellings is a powerfully symbolic process in which the physical construction of the dwelling parallels more fundamental transformations of social relationships and personal identity. The chapter draws on Bourdieu’s concepts of social and cultural capital, and theories of asset accumulation and exchange, to help explain the observed phenomena. Analysis of building and dwelling practices reconfirms the central role of the house in multiple aspects of life and in the realization of ambitious social aspirations.
Living at the Center, Pushed to the Edge
Authors: Sharma Kalpana 
Published: August 2023

Abstract
Informal urban settlements, often referred to pejoratively as “slums,” cover just 10 percent of Mumbai, India’s financial capital, and yet make up almost 50 percent of its population. Strategies to move these settlements or redevelop them have usually failed to appreciate the survival strategies that people inhabiting such spaces have developed over time. This chapter looks closely at Dharavi, a large disadvantaged settlement in Mumbai that the state has attempted to redevelop, to illustrate how the urban poor negotiate such urban development plans. It describes the history and inhabitants of the area before analyzing several failed redevelopment efforts: the Prime Minister’s Grant Project (PMGP) of the 1980s, the Slum Rehabilitation Scheme (SRS) of the 1990s, and the Dharavi Redevelopment Project (DRP) that began in 2005.
Introduction
Authors: Mayne Alan 
Published: August 2023

Abstract
This historiographical overview of slums in the modern world discusses the key texts that have shaped this research field since the social history revolution of the 1960s. It provides context, drawing attention to the urban transformation of human society in the modern era, and the entrenching of social disadvantage and poverty as cities grew ever larger. And it introduces a puzzle: is “slum” an unproblematic term to describe poor places and social life within them, or is it a loaded word that distorts the essential characteristics of poor communities and skews efforts to address urban social problems? It asks the question: can an historical perspective help us to resolve that puzzle?
Slums
Authors: Mitullah Winnie V. 
Published: August 2023

Abstract
Slum development interventions are often off-target, taking a “basic needs” welfare approach that has neither benefited the poor nor solved the problem of proliferating slums. This chapter uses political economy analysis to examine institutional and governance issues that play a central role in the development and persistence of slums. The chapter contextualizes slums using dignity and “right to the city” perspectives in order to explore slums as an element in urban development, and governance deficits in addressing slum problems. The chapter argues that slum development is a political economy issue that must be addressed by considering deep-rooted institutional and governance issues which create deficits in both economic development and slum interventions.
The Spatial Politics of US Homelessness
Authors: Howard Ella 
Published: August 2023

Abstract
The term “slum” has fallen out of fashion in discussions of contemporary American cities. Yet, over the course of the twentieth century, federal, state, and local forces have increasingly divided American cities along lines of race and socioeconomic class. Throughout the century, homeless people, the most vulnerable of all in this polarizing process, congregated on “skid rows.” Many of these were subsequently flattened by “urban renewal” projects, and their inhabitants were dispersed to new poverty districts. This chapter uses nineteenth- through twenty-first-century Boston as a case study to explore these themes, focusing on the spaces occupied by the city’s most destitute residents.
Painting
Authors: Schellekens Elisabeth 
Published: August 2023

Abstract
Painting has largely been absent from the forefront of morally provocative and politicized art of late. Nonetheless, painting has a long and rich history of representing moral content by depicting moral dilemmas, deliberations, actions, attitudes, and more. Distinguishing between internal/external and general/specific ethical issues in painting, the main aim of this chapter is to shed light on what it means for a painting to have moral content and how such content influences the value we accord the work as a painting. Painting can have several kinds of moral content which one can relate to in rich and varied ways. Where there are ethical dimensions to painting, engaging with the moral content of a painting is inseparable from engaging with the artwork as such, as is the possibility of learning from it.