bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Chlamydomonas reinhardtii chloroplast envelope protein LCIA transports bicarbonate in planta
Authors: Förster Britta , Rourke Loraine M , Weerasooriya Hiruni N , Pabuayon Isaiah C M , Rolland Vivien , Au Eng Kee , Bala Soumi , Bajsa-Hirschel Joanna , Kaines Sarah , Kasili Remmy W , LaPlace Lillian M , Machingura Marylou C , Massey Baxter , Rosati Viviana C , Stuart-Williams Hilary , Badger Murray R , Price G Dean , Moroney James V 
Published: March 2023

Abstract
LCIA (low CO2-inducible protein A) is a chloroplast envelope protein associated with the CO2-concentrating mechanism of the green alga Chlamydomonas reinhardtii. LCIA is postulated to be a HCO3– channel, but previous studies were unable to show that LCIA was actively transporting bicarbonate in planta. Therefore, LCIA activity was investigated more directly in two heterologous systems: an Escherichia coli mutant (DCAKO) lacking both native carbonic anhydrases and an Arabidopsis mutant (βca5) missing the plastid carbonic anhydrase βCA5. Neither DCAKO nor βca5 can grow in ambient CO2 conditions, as they lack carbonic anhydrase-catalyzed production of the necessary HCO3– concentration for lipid and nucleic acid biosynthesis. Expression of LCIA restored growth in both systems in ambient CO2 conditions, which strongly suggests that LCIA is facilitating HCO3– uptake in each system. To our knowledge, this is the first direct evidence that LCIA moves HCO3– across membranes in bacteria and plants. Furthermore, the βca5 plant bioassay used in this study is the first system for testing HCO3– transport activity in planta, an experimental breakthrough that will be valuable for future studies aimed at improving the photosynthetic efficiency of crop plants using components from algal CO2-concentrating mechanisms.
Rescheduling rehabilitation sessions with answer set programming
Authors: Cardellini Matteo , Dodaro Carmine , Galatà Giuseppe , Giardini Anna , Maratea Marco , Nisopoli Nicholas , Porro Ivan 
Published: March 2023

Abstract
The rehabilitation scheduling process consists of planning rehabilitation physiotherapy sessions for patients, by assigning proper operators to them in a certain time slot of a given day, taking into account several requirements and optimizations, e.g. patient’s preferences and operator’s work balancing. Being able to efficiently solve such problem is of upmost importance, in particular as a consequence of the COVID-19 pandemic that significantly increased rehabilitation’s needs. The problem has been recently successfully solved via a two-phase solution based on answer set programming (ASP). In this paper, we focus on the problem of rescheduling the rehabilitation sessions, which comes into play when the original schedule cannot be implemented, for reasons that involve the unavailability of operators and/or the absence of patients. We provide rescheduling solutions based on ASP for both phases, considering different scenarios. Results of experiments performed on real benchmarks, provided by ICS Maugeri, show that also the rescheduling problem can be solved in a satisfactory way. Finally, we present a web application that supports the usage of our solution.
Historical and Philosophical Considerations in Studying Psychopathology
Authors: Zachar Peter , Banicki Konrad , Aftab Awais 
Published: March 2023

Abstract
In this chapter, the authors trace a tug of war between adopting more descriptive versus more conjectural approaches to the study of psychopathology from the seventeenth century onward. The contrast between descriptive versus conjectural is somewhat relative. Statements which rely on shared background assumptions tend to be viewed as descriptions, while those that do not are viewed as conjectural. Throughout the history of psychopathology attempts to offer causal explanations have relied on conjecture hoping to extend our knowledge, but when conjecture was seen as going too far, there were calls to return to descriptions, on which there is more consensus. Recently, the descriptive psychopathology paradigm that was introduced in the DSM-III has been challenged by renewed calls for explaining disorders with respect to etiology and pathogenesis. Turning to causal explanations, the authors contrast production versus regularity accounts of causality. Production accounts tend to favor reducing mind to brain, whereas regularity accounts do not place a priori restrictions on which levels of analysis have genuine casual power. The authors also look at a recently proposed nonreductive perspective in the philosophy of mind, the 4E framework, in which the mind is seen as embodied, embedded, enactive, and extended. The chapter closes by examining the contrast between scientific realism and scientific anti-realism in the study of psychopathology, emphasizing the common ground between scientific realism and factor analytic models and describing some alternative anti-realist views.
The Research Domain Criteria Project: Integrative Translation for Psychopathology
Authors: Cuthbert Bruce N. , Miller Gregory A. , Sanislow Charles , Vaidyanathan Uma 
Published: March 2023

Abstract
This chapter provides an introduction to the Research Domain Criteria (RDoC) project. RDoC is a framework for psychopathology research created in 2009 by the US National Institute of Mental Health in order to foster innovative research that transcends the reliance on current disorder categories in studying mental illness. RDoC takes a translational approach that considers psychopathology in terms of deviations in normal dimensions of functioning (such as cognitive processes or motivational systems) that often reflect transdiagnostic effects across multiple disorder classes. The framework calls for studies that integrate multiple data types (e.g., behavioral, physiological, and self-report measures) and emphasizes developmental trajectories and the impact of various environmental influences. Fundamental issues regarding relevant philosophy of science issues are discussed, and selected recent studies are reviewed that illustrate exemplars of research designs. The conclusion briefly summarizes RDoC’s current status and potential future directions.
Developmental Psychopathology
Authors: Cicchetti Dante 
Published: March 2023

Abstract
Developmental psychopathology is an integrative scientific discipline focused on individual biological and psychological adaptation and maladaptation in the context of developmental change. Developmental psychopathology owes the emergence and coalescence of its framework to many historically based disciplines including, but not limited to neuroscience, ethology, sociology, psychiatry, pediatrics, and clinical, developmental, experimental and physiological psychology. A developmental analysis presupposes change and novelty, highlights the important role of timing in the organization of behavior, underscores multiple determinants, and cautions against expecting invariant relations between causes and outcomes. From a developmental psychopathology framework, mental disorders are conceived as being dynamic and should be studied from an interdisciplinary perspective and a multiple levels of analysis approach. The continuation and elaboration of multiple levels of analysis longitudinal studies within and across disciplines interested in typical and atypical development not only will enhance the science of developmental psychopathology, but also will increase the benefits derived for individuals with high-risk conditions or mental disorders, families, and society as a whole.
Diagnosis, Comorbidity, and Psychopathology of Substance-Related Disorders
Authors: Brumback Ty , Brown Sandra A. 
Published: March 2023

Abstract
This chapter describes substance use disorders (SUDs) beginning with the categorical diagnostic categories and the identified etiological risk factors for developing SUDs before moving to the various outcomes among those with SUDs, including comorbid psychopathology. Alcohol use disorder is the most common SUD and, as such, is a focal point of this chapter, although the authors also describe the growing literature related to other SUDs and comorbidities. The chapter represents a biopsychosocial understanding of SUDs, which recognizes that the factors contributing to the onset of SUDs must reflect the complexity of the disorders and include biological underpinnings (e.g., genetic predispositions and physiological factors), psychological contributions (e.g., psychopathology that may contribute to and exacerbate SUDs), and social factors (e.g., peer influences and early life stressors) that influence the heterogenous etiological pathways and symptom profiles of patients with SUDs.
Social Functioning and Schizophrenia
Authors: Hooley Jill M. , DeCross Stephanie N. 
Published: March 2023

Abstract
Schizophrenia is associated with significant problems in social functioning. This chapter provides an overview of the literature concerning social functioning in schizophrenia, tracing progress over time. It begins by considering the nature of social exchanges and describing the social problems experienced by patients with schizophrenia, then discusses factors associated with better or worse social functioning, focusing particularly on the role of gender, and positive and negative symptoms. The authors review the literature concerning social impairments in the premorbid phases of the illness as well as in those at risk for developing the disorder. Following a review of early and foundational literature, the authors turn attention toward newer areas of research and evolving conceptualization of schizophrenia, highlighting current understanding of the complex interplay of social cognition, social motivation, and social anhedonia and discussing evidence on the altered neurobiological bases for these processes. Finally, they consider the role of the patient’s social environment for the course of schizophrenia, ending with a discussion of treatment options available to help patients and their families function more effectively in the face of this illness.
Sleep and Circadian Rhythm Disorders
Authors: Bisdounis Lampros , Kyle Simon D. , Saunders Kate E. A. , Hill Elizabeth A. , Espie Colin A. 
Published: March 2023

Abstract
Sleep and circadian rhythm disorders are highly prevalent and impairing, yet they are often misdiagnosed and undertreated. This chapter covers such disorders presenting either as independent conditions or as comorbid diagnoses with other psychiatric disorders. First, an overview is provided of the fundamental principles, assessment tools, and nosology systems in sleep medicine. Subsequent sections focus specifically on the etiology, assessment, and evidence-based treatment of the following conditions: insomnia disorder, delayed and advanced circadian phase disorders, irregular sleep–wake rhythm disorder, non–24-hour sleep–wake rhythm disorder, narcolepsy, hypersomnolence disorder, and parasomnias. These represent the sleep and circadian rhythm disorders that are most commonly encountered by mental health practitioners. The final section highlights sleep and circadian disturbances in the context of four other psychiatric disorders: depression, anxiety, bipolar disorder, and schizophrenia.
Psychopathy and Antisocial Personality Disorder
Authors: Patrick Christopher J. , Drislane Laura E. , Bertoldi Bridget M. , Lowman Kelsey L. 
Published: March 2023

Abstract
Psychopathy and antisocial personality disorder (ASPD) have been of long-standing interest to clinicians and researchers due to their serious detrimental effects on both individuals and society as a whole. This chapter begins with an overview of historical writings that served as the foundation for modern conceptualizations of psychopathy and ASPD. Next, the chapter describes the main inventories for assessing psychopathy in use today and discusses how these various inventories differ from one another and how they relate to ASPD and other conditions in the official psychiatric nosology (the DSM-5). The chapter also summarizes findings regarding their neurobiological correlates. Following this, the authors describe an integrative conceptual-empirical framework—the triarchic model—for characterizing relations among different psychopathy measures and organizing what is known about their clinical and neurobiological correlates. The chapter then considers how the three constructs of the triarchic model—boldness, meanness, and disinhibition—are represented in the dimensional system for personality pathology within the DSM-5 and how they interface with the Hierarchical Taxonomy of Psychopathology (HiTOP), a new dimensional framework for psychopathology as a whole. Finally, the authors discuss how the triarchic model can be used to guide developmental research on psychopathy and coordinate further research on the role of neurobiological systems and processes in psychopathy.
Specific targeting of plasmids with Argonaute enables genome editing
Authors: Esyunina Daria , Okhtienko Anastasiia , Olina Anna , Panteleev Vladimir , Prostova Maria , Aravin Alexei A , Kulbachinskiy Andrey 
Published: March 2023

Abstract
Prokaryotic Argonautes (pAgos) are programmable nucleases involved in cell defense against invading DNA. In vitro, pAgos can bind small single-stranded guide DNAs to recognize and cleave complementary DNA. In vivo, pAgos preferentially target plasmids, phages and multicopy genetic elements. Here, we show that CbAgo nuclease from Clostridium butyricum can be used for genomic DNA engineering in bacteria. We demonstrate that CbAgo loaded with plasmid-derived guide DNAs can recognize and cleave homologous chromosomal loci, and define the minimal length of homology required for this targeting. Cleavage of plasmid DNA at an engineered site of the I-SceI meganuclease increases guide DNA loading into CbAgo and enhances processing of homologous chromosomal loci. Analysis of guide DNA loading into CbAgo also reveals off-target sites of I-SceI in the Escherichia coli genome, demonstrating that pAgos can be used for highly sensitive detection of double-stranded breaks in genomic DNA. Finally, we show that CbAgo-dependent targeting of genomic loci with plasmid-derived guide DNAs promotes homologous recombination between plasmid and chromosomal DNA, depending on the catalytic activity of CbAgo. Specific targeting of plasmids with Argonautes can be used to integrate plasmid-encoded sequences into the chromosome thus enabling genome editing.
RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins
Authors: Stenum Thomas Søndergaard , Kumar Ankith D , Sandbaumhüter Friederike A , Kjellin Jonas , Jerlström-Hultqvist Jon , Andrén Per E , Koskiniemi Sanna , Jansson Erik T , Holmqvist Erik 
Published: March 2023

Abstract
RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to direct and global identification of bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down RNA–protein complexes. Overexpressing poly(A) polymerase I in Escherichia coli drastically increased transcriptome-wide RNA polyadenylation, enabling pull-down of crosslinked RNA–protein complexes using immobilized oligo(dT) as bait. With this approach, we identified 169 putative RBPs, roughly half of which are already annotated as RNA-binding. We experimentally verified the RNA-binding ability of a number of uncharacterized RBPs, including YhgF, which is exceptionally well conserved not only in bacteria, but also in archaea and eukaryotes. We identified YhgF RNA targets in vivo using CLIP-seq, verified specific binding in vitro, and reveal a putative role for YhgF in regulation of gene expression. Our findings present a simple and robust strategy for RBP identification in bacteria, provide a resource of new bacterial RBPs, and lay the foundation for further studies of the highly conserved RBP YhgF.
Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI
Authors: Kennedy Madison A , Hosford Christopher J , Azumaya Caleigh M , Luyten Yvette A , Chen Minyong , Morgan Richard D , Stoddard Barry L 
Published: March 2023

Abstract
Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0
Authors: Jiang Andrew , You Linya , Snell Russell G , Lehnert Klaus 
Published: March 2023

AbstractComplex biological traits and disease often involve patterns of gene expression that can be characterised and examined. Here we present ICARUS v2.0, an update to our single cell RNA-seq analysis web server with additional tools to investigate gene networks and understand core patterns of gene regulation in relation to biological traits. ICARUS v2.0 enables gene co-expression analysis with MEGENA, transcription factor regulated network identification with SCENIC, trajectory analysis with Monocle3, and characterisation of cell-cell communication with CellChat. Cell cluster gene expression profiles may be examined against Genome Wide Association Studies with MAGMA to find significant associations with GWAS traits. Additionally, differentially expressed genes may be compared against the Drug-Gene Interaction database (DGIdb 4.0) to facilitate drug discovery. ICARUS v2.0 offers a comprehensive toolbox of the latest single cell RNA-seq analysis methodologies packed into an efficient, user friendly, tutorial style web server application (accessible at https://launch.icarus-scrnaseq.cloud.edu.au/) that enables single cell RNA-seq analysis tailored to the user's dataset.
Marine natural products and derivatives
Authors: Avhad Ashwini B , Bhangale Charushila J 
Published: March 2023

Abstract

Objectives
There are many reasons why marine resources are currently being examined extensively. One of the causes is that 70% of the earth’s surface is covered by oceans. From marine resources, some natural products and their derivatives are derived. These marine natural products are produced by the following organisms: marine invertebrates, marine algae and marine microbes are the three main biological classes. An overview of the marine natural products (MNPs) industry is presented, along with a current list of medications that the FDA has approved as well as those that are undergoing clinical trials and could be regarded as MNP derivatives.

Methods
Secondary metabolites from marine organisms such as snails, tunicates, sponges, soft corals and mollusks have been extracted to produce bio active compounds, which have sparked the creation of new classes of therapeutic agents. Marine life is a significant source of structurally diverse and biologically active secondary metabolites.

Key findings
It is observed that marine source is one of the powerful way of producing products that are natural and effective.

Conclusion
Some commercially available preparations treat diseases like HIV, cancer and various skin conditions using their collected resources.
A review on the colours, flavours and shapes used in paediatric 3D printed oral solid dosage forms
Authors: Vlachou Marilena , Siamidi Angeliki , Protopapa Chrystalla , Sotiropoulou Ioanna 
Published: March 2023

Abstract

Objectives
This review aims at gleaning the currently available research reports that relate to 3D printlets for paediatric patients and especially the excipients used to produce various colours, flavours, shapes and sizes.

Methods
A thorough literature review on paediatric 3D printed oral solid dosage forms, focusing on the use of colours, flavours and various shapes/dimensions, was conducted with an adjusted time frame between 2017 and 2022.

Key findings
3D printlets for the paediatric population include the chewable dosage forms (including solid forms and soft forms or gummies), the swallowing dosage forms and the orodispersable dosage forms (printlets or films). Researchers have tested many colours, flavours, shapes and dimensions for chewable formulation production using pectin and gelatin to create gummies or chocolate and cereals. Scientists have also used many methods and excipients to produce printlets with various colours, flavours, shapes and small sizes (minitablets or minicaplets) for the swallowing dosage forms. Concerning the orodispersable’s, the research was rather limited.

Conclusions
Compared with conventional oral dosage form manufacturing processes, 3D printing techniques use a different approach. More specifically, these techniques can provide personalisation of dose, shape, size, taste, colour and appropriate drug release rates, which is of paramount importance, especially for paediatric patients. With the correct excipients, the printlets can serve as ideal dosage forms candidates for the treatment of the paediatric population.
Providing Digital Technology Training as a Way to Retain Older Workers: The Importance of Perceived Usefulness and Growth Need
Authors: Xie Hanji , Fang Yanran , Wang Mo , Liu Junming , Lv Aiqin 
Published: March 2023

Abstract
The increasing prevalence of aging workforce around the globe renders older worker retention an integral approach for organizations to maintain human capital. In the meantime, the increasing application of digital technologies at work poses new challenges for older workers. Providing digital technology training is therefore considered as a potential approach to retaining older workers. Yet, we have limited knowledge about the role played by digital technology training availability in facilitating older worker retention. Addressing this important research void, we examine the motivation-based (i.e., autonomy need satisfaction at work) and the ability-based (i.e., competence need satisfaction at work) mechanisms that transmit the positive indirect effects of digital technology training availability on older workers’ intention to remain. We also examine the critical roles of the relevance of the training (both the relevance to the situation and to the participant) in shaping the impacts of digital technology training availability. Analyzing data collected from 285 workers aged 40 years or older, we found that when digital technology was perceived to be more (vs. less) useful at work, digital technology training availability indirectly facilitated older workers’ intention to remain via both autonomy and competence needs satisfaction at work. Moreover, the amplifying effects of perceived usefulness of digital technology at work were more (vs. less) pronounced for participants who had higher (vs. lower) growth need. Theoretical and practical implications were also discussed based on our findings.