bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination
Authors: Hirokawa Soichi , Chure Griffin , Belliveau Nathan M , Lovely Geoffrey A , Anaya Michael , Schatz David G , Baltimore David , Phillips Rob 
Published: May 2020

AbstractDeveloping lymphocytes of jawed vertebrates cleave and combine distinct gene segments to assemble antigen–receptor genes. This process called V(D)J recombination that involves the RAG recombinase binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG–RSS interaction. We employ a single-molecule method known as tethered particle motion to track the formation, lifetime and cleavage of individual RAG–12RSS–23RSS paired complexes (PCs) for numerous synthetic and endogenous 12RSSs. We reveal that single-bp changes, including in the 12RSS spacer, can significantly and selectively alter PC formation or the probability of RAG-mediated cleavage in the PC. We find that some rarely used endogenous gene segments can be mapped directly to poor RAG binding on their adjacent 12RSSs. Finally, we find that while abrogating RSS nicking with Ca2+ leads to substantially shorter PC lifetimes, analysis of the complete lifetime distributions of any 12RSS even on this reduced system reveals that the process of exiting the PC involves unidentified molecular details whose involvement in RAG–RSS dynamics are crucial to quantitatively capture kinetics in V(D)J recombination.
DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL
Authors: Lu Xiang-Jun 
Published: May 2020

Abstract
Sophisticated analysis and simplified visualization are crucial for understanding complicated structures of biomacromolecules. DSSR (Dissecting the Spatial Structure of RNA) is an integrated computational tool that has streamlined the analysis and annotation of 3D nucleic acid structures. The program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options. In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR-enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious. These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the web application, and the web application programming interface. The supplemental PDF serves as a practical guide, with complete and reproducible examples. Thus, even beginners or occasional users can get started quickly, especially via the web application at http://skmatic.x3dna.org.
The impact of having inadequate safety equipment on mental health
Authors: Simms A , Fear N T , Greenberg N 
Published: May 2020

AbstractBackgroundConcerns are being raised about the impact of inadequate safety equipment on the mental health of healthcare workers during the COVID-19 medical response.AimsTo assess the impact of inadequate safety equipment on the mental health of service personnel deployed on operations in order to better understand the impact on those working under the similarly demanding conditions of the COVID-19 medical response.MethodsSelf-report surveys were conducted in four operational environments with 3435 personnel providing data. Surveys recorded data on socio-demographic, military and operational characteristics, mental health measures and specific occupational stressors. Analysis through logistic regression explored the association between inadequate equipment and all other factors.ResultsA total of 3401 personnel provided data on their perceptions of the adequacy of their equipment, of which 532 (15%) stated that they had a lot of concerns that they did not have the right equipment in working order. Analysis found significantly greater odds of reporting symptoms of common mental health disorders (CMD), 2.49 (2.03–3.06), post-traumatic stress disorder (PTSD), 2.99 (2.11–4.24), poorer global health 2.09 (1.62–2.70) and emotional problems 1.69 (1.38–2.06) when individuals reported working with inadequate equipment. Analyses remained significant when adjusted for confounding factors such as rank, sex and operational environment.ConclusionsAn individual’s perception of having inadequate equipment is significantly associated with symptoms of CMD, probable PTSD, poorer global health and increased reporting of emotional problems. This in turn may impact on their ability to safely carry out their duties and may have longer-term mental health consequences.
Training and Improving Accuracy of Personality Trait Judgments
Authors: Blanch-Hartigan Danielle , Cummings Krista Hill 
Published: May 2020

Abstract
Given that accurate trait judgments are related to myriad positive characteristics and outcomes, this chapter focuses on approaches for improving trait judgment accuracy. The chapter outlines potential trait judgment training approaches aligned with the realistic accuracy model (RAM) and presents available evidence from previous training research in other domains of person perception and basic personality research. In addition, the chapter examines how characteristics of the trait, target, and judge can potentially impact training effectiveness. More research is needed to develop effective, generalizable, and impactful training interventions for personality and trait judgment accuracy.
Affixal Negation
Authors: Joshi Shrikant 
Published: May 2020

AbstractThis chapter studies the phenomenon of affixal negation, which is a relatively understudied subdomain in linguistic negation. The focus here is on the phenomenon itself, rather than on the individual affixes participating in it. The chapter starts by determining the place of affixal negation in the broad spectrum of negation and linguistic negation. It then goes on to examine the structural and semantic mechanism of affixal negation, including the morpho-syntactic and semantic characteristics of the elements involved in it. Later this chapter will throw light on some proposed categorization schemes of affixal negation based on morphological, syntactic, and semantic criteria. The chapter also proposes some possible exploration in the applied aspects of affixal negation.
Minimizers and Maximizers as Different Types of Polarity Items
Authors: Tubau Susagna 
Published: May 2020

AbstractThis chapter examines the properties of minimizers and maximizers (i.e. minimal and maximal extent- or quantity-denoting expressions) in English, Catalan, and Spanish. Special emphasis is put on (i) establishing which type of polarity item these expressions align with, and (ii) identifying connections between them and other elements of the polarity landscape such as negative quantifiers and Negative Concord Items. It is shown that different minimizers and maximizers pattern with Affective Polarity Items, Negative Polarity Items, or Positive Polarity Items in the three studied languages, and that English minimizers behave similarly to negative quantifiers when negation is adjacent to them, while in Catalan and Spanish they behave like Negative Concord Items when headed by the particle ni ‘not even’. Vulgar (taboo word) minimizers, which have been argued to carry an incorporated zero numeral in the literature, are claimed to be lexically ambiguous between zero-incorporated structures and Affective Polarity Items.
Negative Concord and the Nature of Negative Concord Items
Authors: Giannakidou Anastasia 
Published: May 2020

AbstractThis chapter discusses the expressions often referred to as n-words. While this term has been used extensively in the literature, we use here the more neutral term ‘negative concord items’ (NCI) since these expressions do not always contain negation. NCIs behave largely as negative polarity items (NPIs) in requiring negation for grammaticality; and questions arise about whether or not they are semantically negative, and whether they are uniform across languages. The chapter shows that NCIs exhibit variation in their distribution and interpretation. Main aspects of variation are whether NCIs always require negation (strict negative concord), or not (non-strict), and whether they can appear with non-negative meanings. The chapter assesses research of the past twenty years, and proposes a new, more synthesized, understanding of the attested variation.
Double Negation Readings
Authors: de Swart Henriëtte 
Published: May 2020

AbstractThis chapter is concerned with the linguistic environments in which double negation readings do and do not arise in double negation and negative concord languages. The theoretical background comes from other chapters in the Oxford Handbook of Negation. The chapter briefly surveys the experimental literature on the role of prosody in the comprehension of negative concord and double negation, and continues with a multilingual corpus investigation that focuses on language use. Under the assumption that all languages convey the same message in a specific context, production data in parallel corpora enable us to detect grammatical variation through translation. The examples are extracted from the parallel corpus EuroParl and the languages discussed are English, Dutch, German, Italian, French, and Spanish. Even though the set of languages is relatively small, the spread of grammars should be wide enough to shed light on the phenomenon of double negation in natural language.
Understanding Negation
Authors: Kaup Barbara , Dudschig Carolin 
Published: May 2020

AbstractThis chapter gives an overview of experimental studies concerned with the processing of explicit and implicit negation during language comprehension. The studies reported employ a large variety of experimental methods and paradigms, ranging from reaction or reading time experiments, to experiments measuring eye-tracking, EEG, or fMRI during reading. The chapter begins with an overview of early studies on negation processing and is structured according to the five main issues in the literature on negation processing: Is suppression routinely involved in negation processing? Does negation processing per default involve one or two meaning representations? Is negation integration delayed during the processing of negative sentences, and what role do pragmatic aspects play in this respect? How do embodied accounts of meaning representation deal with negation? Does negation processing involve general cognitive mechanisms that are also utilized during non-linguistic conflict processing?
Negation in L2 Acquisition and Beyond
Authors: Sánchez Liliana , Austin Jennifer 
Published: May 2020

AbstractThis chapter provides an overview of generative research on the acquisition of negation by multilingual learners. While early research compared the development of negation in adult L2 learners with L1 children to assess L2 learners’ access to Universal Grammar), subsequent studies focused instead on how verbal feature specification influences L2 acquisition of the relative position of negation and verbs. More recently, research on L2 negation has examined what the earliest stages of the acquisition of negation reveal about the relationship between the lexicon and syntax and has compared adult and child L2 acquisition. Other recent studies have examined the acquisition of relative scope and the source of difficulties in the L2 acquisition of negation at the interface between syntax, semantics, and pragmatics.
The Neurology of Negation
Authors: Christensen Ken Ramshøj 
Published: May 2020

AbstractThis chapter provides an overview of psycho- and neurolinguistic studies on negation with healthy adult speakers, as well as studies on patients with focal brain damage. Semantically, negation inverts the truth value and the direction of entailment, and it is associated with a more complex syntactic structure. Behavioral evidence shows that negative sentences are associated with increased complexity and processing load. In the ERP data, an unlicensed negative polarity item (NPI) elicits an N400, due to semantic integration cost, whereas a positive one (PPI) elicits a P600, due to structural reanalysis or pragmatic discourse processing. Neuroimaging studies with fMRI have shown that while positive polarity engages the temporo-parietal region, the syntactic complexity of negation increases activation in promoter cortex (BA 6), not in Broca’s area—which converges with the evidence showing that negation is relatively spared in Broca’s aphasia.
Central Sudanic
Authors: Boyeldieu Pascal 
Published: May 2020

Abstract
The Central Sudanic family consists of some sixty languages that are spoken in the center of Africa. According to Greenberg, who coined the label, it is part of the Nilo-Saharan phylum (this point is, however, debatable and not addressed here). The chapter discusses the genetic unity of Central Sudanic, a hypothesis that still needs to be confirmed by application of a strict comparative-historical method. After reviewing previous internal classifications, it establishes five consistent subgroups, plus several ‘indeterminate’ languages. The subgroups are then submitted to a series of criteria—lexicostatistics, distribution of likely cognates, regular consonantal correspondences, derivational affixes, and syntactic typology—which lead to the provisional conclusion that these subgroups represent more or less equidistant parts of a genetic Central Sudanic unit. It considers whether the linguistic distance between languages spoken in such a limited area can simply be explained by diversification.
Phineas Gage
Authors: Lewandowski Alan G. , Weirick Joshua D. , Lewandowski Caroline A. , Spector Jack 
Published: May 2020

Abstract
The case of Phineas Gage is one of the most frequently cited cases from 19th century medical literature and represents the first of a series of famous cases involving the brain and behavior. While many reiterations of Gage’s case have been published, it remains important to modern neuroscience due to its unique historical significance, ongoing clinical relevance, and the insights it offers neuropsychology into the functional effects of brain injury on thinking, emotions, and behavior. This chapter revisits the critical aspects of this landmark case from a contemporary clinical perspective and discusses the implications of injury to the prefrontal cortex and pathways.
Origins of Neuropsychology Research and Teaching at the University of Melbourne, Australia
Authors: Bowden Stephen C. , Scalzo Simon J. , Stanley Gordon V. 
Published: May 2020

Abstract
The University of Melbourne hosts a well-known graduate training program in clinical neuropsychology, which was the first formal training program in neuropsychology established in Australia. What is less well known is that neuropsychology research has a much longer history at the University of Melbourne, beginning in the second decade of the 20th century. This chapter briefly traces the early history, which centered on collaborations between staff at the then Melbourne Teachers College and the university department of anatomy. The historical account then leaps forward half a century to describe some of the University staff and key decisions involved in establishing the graduate neuropsychology training program that continues to the current time. Again, many aspects of this more recent history, including the diversity of staff involved, are not well known. Relying on personal recollections, correspondence between staff, and minutes of faculty meetings, this account aims to pay tribute to the many staff involved in the origins of clinical neuropsychology teaching at the University of Melbourne.
A Quantitative Review of the History of Clinical Neuropsychology in North America
Authors: Rohling Martin L. , Larrabee Glenn J. 
Published: May 2020

Abstract
Objective: To quantitatively measure influence of both individuals and organizations in the field of neuropsychology, analyzing data from four organizations: The International Neuropsychological Society (INS), the National Academy of Neuropsychology (NAN), Society for Neuropsychology (SCN; APA Division 40), and the American Academy of Clinical Neuropsychology (AACN).
Methods: Individuals were ranked in four domains of influence: (1) organizational leadership (e.g., number, significance of offices); (2) speaking at annual meetings (number, significance of presentations); (3) editorial board membership (number, significance of board membership) for the official journals of INS, NAN, SCN and AACN; (4) impact of publications (citation impact). The top 100 individuals were ranked for each of the four domains, extending back in time to the founding year of each organization up through and including 2017. Rankings were transformed to a common metric. For the analysis of organizational influence (membership size, size of meeting, impact factor of each official organization journal), we analyzed data from the past 20 years through and including 2017.
Results: The top 100 neuropsychologists in each of the four domains represent about 3% of persons surveyed, and often appeared in other domains. Nonetheless, factor analysis yielded two factors: (1) a factor characterizing organizational leadership, editorial board membership, and speaking at annual meetings; and (2) a factor defined solely by citation impact. Organizationally, AACN is growing most rapidly, with membership stable in INS and declining slightly in NAN and SCN. Many leading neuropsychologists belong to all four organizations.
Is There a Relationship Between Kinesiophobia and Physical Activity Level in Patients with Knee Osteoarthritis?
Authors: Aykut Selçuk Melek , Karakoyun Ahmet 
Published: May 2020

Abstract

Objective
To investigate the levels of kinesiophobia, physical activity, depression, disability, and quality of life in patients with knee osteoarthritis.

Design
A cross-sectional study.

Setting
A tertiary health care center.

Subjects
Ninety-six patients with knee osteoarthritis.

Methods
Pain intensity was evaluated by the Visual Analog Scale, kinesiophobia by the Tampa Scale of Kinesiophobia and Brief Fear of Movement Scale, depression by the Beck Depression Inventory, disability by the Western Ontario and McMaster Universities Arthritis Index, physical activity level by the International Physical Activity Questionnaire short form, and quality of life by the Short Form 12 Health Survey Questionnaire.

Results
Of the patients, 85.7% had high-level kinesiophobia, 70.6% had depression, and 64.4% had low, 27.8% moderate, and 7.8% high physical activity levels. Age, activity-related pain score of the Visual Analog Scale, Tampa Scale of Kinesiophobia and Brief Fear of Movement Scale scores, and Western Ontario and McMaster Universities Arthritis Index and Beck Depression Inventory scores were higher in the group with high-level kinesiophobia, whereas the mental, physical, and total scores obtained from the Short Form 12 Health Survey Questionnaire were higher in the group with low-level kinesiophobia (P &lt; 0.05).

Conclusions
As the treatment of pain alone in patients with knee osteoarthritis is not sufficient to reduce fear of movement, we suggest that approaches to increase awareness of fear of movement and physical activity and cognitive behavioral therapy related to fear of movement should be included in the treatment program.
Sleep slow-wave homeostasis and cognitive functioning in children with electrical status epilepticus in sleep
Authors: van den Munckhof Bart , Gefferie Silvano R , van Noort Suus A M , van Teeseling Heleen C , Schijvens Mischa P , Smit William , Teunissen Nico W , Plate Joost D J , Huiskamp Geert Jan M , Leijten Frans S S , Braun Kees P J , Jansen Floor E , Bölsterli Bigna K 
Published: May 2020

Abstract

Study Objectives
Encephalopathy with electrical status epilepticus in sleep (ESES) is characterized by non-rapid eye movement (non-REM)-sleep-induced epileptiform activity and acquired cognitive deficits. The synaptic homeostasis hypothesis describes the process of daytime synaptic potentiation balanced by synaptic downscaling in non-REM-sleep and is considered crucial to retain an efficient cortical network. We aimed to study the overnight decline of slow waves, an indirect marker of synaptic downscaling, in patients with ESES and explore whether altered downscaling relates to neurodevelopmental and behavioral problems.

Methods
Retrospective study of patients with ESES with at least one whole-night electroencephalogram (EEG) and neuropsychological assessment (NPA) within 4 months. Slow waves in the first and last hour of non-REM-sleep were analyzed. Differences in slow-wave slope (SWS) and overnight slope course between the epileptic focus and non-focus electrodes and relations to neurodevelopment and behavior were analyzed.

Results
A total of 29 patients with 44 EEG ~ NPA combinations were included. Mean SWS decreased from 357 to 327 µV/s (−8%, p &lt; 0.001) across the night and the overnight decrease was less pronounced in epileptic focus than in non-focus electrodes (−5.6% vs. −8.7%, p = 0.003). We found no relation between SWS and neurodevelopmental test results in cross-sectional and longitudinal analyses. Patients with behavioral problems showed less SWS decline than patients without and the difference was most striking in the epileptic focus (−0.9% vs. −8.8%, p = 0.006).

Conclusions
Slow-wave homeostasis—a marker of synaptic homeostasis—is disturbed by epileptiform activity in ESES. Behavioral problems, but not neurodevelopmental test results, were related to severity of this disturbance.
Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome
Authors: Bouadma Lila , Wiedemann Aurélie , Patrier Juliette , Surénaud Mathieu , Wicky Paul-Henri , Foucat Emile , Diehl Jean-Luc , Hejblum Boris P. , Sinnah Fabrice , Montmollin Etienne de , Lacabaratz Christine , Thiébaut Rodolphe , Timsit JF , Lévy Yves 
Published: May 2020

AbstractWe report a longitudinal analysis of the immune response associated with a fatal case of COVID-19. This patient exhibited a rapid evolution towards multiorgan failure. SARS-CoV-2 was detected in multiple nasopharyngeal, blood, and pleural samples, despite antiviral and immunomodulator treatment. Clinical evolution in the blood was marked by an increase (2-3 fold) in differentiated effector T cells expressing exhaustion (PD-1) and senescence (CD57) markers, an expansion of antibody-secreting cells, a 15-fold increase in γδ T-cell and proliferating NK-cell populations, and the total disappearance of monocytes, suggesting lung trafficking. In the serum, waves of a proinflammatory cytokine storm, Th1 and Th2 activation, and markers of T-cell exhaustion, apoptosis, cell cytotoxicity, and endothelial activation were observed until the fatal outcome. This case underscores the need for well-designed studies to investigate complementary approaches to control viral replication, the source of the hyperinflammatory status, and immunomodulation to target the pathophysiological response.