bluuebunny/crossref_metadata_2025 huggingface dataset:
Consensus core clinical data elements for meningiomas (v2021.1)
Authors: Nassiri Farshad , Wang Justin Z , Au Karolyn , Barnholtz-Sloan Jill , Jenkinson Michael D , Drummond Kate , Zhou Yueren , Snyder James M , Brastianos Priscilla , Santarius Thomas , Suppiah Suganth , Poisson Laila , Gaillard Francesco , Rosenthal Mark , Kaufmann Timothy , Tsang Derek S , Aldape Kenneth , Zadeh Gelareh
Published: November 2021

Background

With increasing molecular analyses of meningiomas, there is a need to harmonize language used to capture clinical data across centers to ensure that molecular alterations are appropriately linked to clinical variables of interest. Here the International Consortium on Meningiomas presents a set of core and supplemental meningioma-specific common data elements (CDEs) to facilitate comparative and pooled analyses.

Methods

The generation of CDEs followed the 4-phase process similar to other National Institute of Neurological Disorders and Stroke (NINDS) CDE projects: discovery, internal validation, external validation, and distribution.

Results

The CDEs were organized into patient- and tumor-level modules. In total, 17 core CDEs (10 patient level and 7 tumor level) as well as 14 supplemental CDEs (7 patient level and 7 tumor level) were defined and described. These CDEs are now made publicly available for dissemination and adoption.

Conclusions

CDEs provide a framework for discussion in the neuro-oncology community that will facilitate data-sharing for collaborative research projects and aid in developing a common language for comparative and pooled analyses. The meningioma-specific CDEs presented here are intended to be dynamic parameters that evolve with time and The Consortium welcomes international feedback for further refinement and implementation of these CDEs.
A metamaterial-free fluid-flow cloak
Authors: Tay Fuyang , Zhang Youming , Xu Hongyi , Goh Honghui , Luo Yu , Zhang Baile
Published: November 2021

The model of ideal fluid flow around a cylindrical obstacle exhibits a long-established physical picture, where originally straight streamlines are deflected over the whole space by the obstacle. Inspired by transformation optics and metamaterials, recent theories have proposed the concept of fluid cloaking, which is able to recover the straight streamlines, as if the obstacle did not exist. However, such a cloak, similar to all previous transformation-optics-based devices, relies on complex metamaterials with inhomogeneous parameters and is difficult to implement. Here we deploy the theory of scattering cancellation and report on the experimental realization of a fluid-flow cloak without metamaterials. This cloak is realized by engineering the geometry of the fluid channel, which effectively cancels the dipole-like scattering of the obstacle. The cloaking effect is demonstrated through the direct observation of recovered straight streamlines in the fluid flow. Our work sheds new light on conventional fluid control and may find application in microfluidic devices.
Prose Poetry
Authors: Desmarais Jane , Weir David
Published: November 2021

This chapter treats the prose poem as the decadent genre par excellence by focusing on Charles Baudelaire’s Le Spleen de Paris (Paris Spleen, 1869). The prose poem is well suited to the expression of decadent culture because of its formal subversion of conventional poetry, especially as adapted by Baudelaire to articulate “the bump and lurch” of urban experience. J. K. Huysmans certified the decadent credentials of the genre when he described it in À rebours (Against Nature, 1884) as “the osmazome of literature, the essential oil of art,” a literary distillation that makes it “an aesthetic treat to none but the most discerning.” The article analyzes “Any Where Out of the World” and other prose poems in relation to certain poems in Le Fleurs du mal (The Flowers of Evil, 1857), observing no loss of metaphorical power in the more “prosaic” medium despite Baudelaire’s secular and subversive treatment of many of the same poetic material given more elevated, spiritual treatment in the earlier collection.
Introduction to Gabriel García Márquez
Authors: Bell-Villada Gene H. , López-Calvo Ignacio
Published: November 2021

The publication in 1967 of his masterpiece Cien años de soledad, followed by the English-language translation in 1970, changed García Márquez’s personal and professional life forever and was arguably the main reason for his winning the 1982 Nobel Prize. Other masterworks would follow, notably The Autumn of the Patriarch, an experimental narrative about an aging Caribbean dictator that is also infused by magical realism while leaving behind the Macondo of One Hundred Years of Solitude. Also passed in review here are his short-story collections, his later novels of romantic love, and the highly praised novellas No One Writes to the Colonel and Chronicle of a Death Foretold. García Márquez’s literary success is placed within the context of the Cuban Revolution, the Latin American Boom, and the growing recognition received by previous Latin American authors (Cortázar, Fuentes, Vargas Llosa). In ensuing articles, García Márquez is examined via a broad array of perspectives, several of them unavoidable: biography, magical realism, and alchemy; local roots and world influence (especially in the Global South and Asia, as well as Spain); and issues of ethnicity, gender, myth, ecology, musical genres, left-wing politics, and anti-imperialism. Readings of individual works conclude our survey. Throughout these thirty-two essays, virtually all of García Márquez’s mature works—long and short, early and late, fictional, nonfictional, and even filmic—are expertly and subtly teased out for the benefit of his many devoted readers worldwide.
Sociological Perspectives on Disability
Authors: Mauldin Laura
Published: November 2021

This chapter outlines the roots of disability scholarship in sociology and how the sociology of disability subfield positions disability as an axis of inequality. The first part of the chapter argues that sociology is uniquely positioned to understand how disability as a social category is made through institutional structures, larger patterns of exclusion and inclusion, and emphasis on power and inequality. Yet it is often excluded in measurements and analyses in the discipline. The chapter then turns to the origins of disability scholarship in sociology, its influence on the interdisciplinary field of disability studies, and the emergent subfield of sociology of disability within the discipline. The remaining parts of the chapter survey how disability has been studied across subfields such as sociology of health and illness, sociology of body/embodiment, and feminist sociological scholarship. In discussing disability across these subfields, divergences between mainstream sociology and the sociology of disability are highlighted in an effort to map their departures and pinpoint why disability as a category or axis of inequality is persistently underresearched in sociology. The chapter concludes with thoughts about where new scholarship on disability might be going in sociology.
Irish song and the idea of tradition
Authors: Blankenhorn Virginia
Published: November 2021

Defining ‘tradition’ as something passed on within a community that provides a matrix for its understanding of past events and present choices, this essay discusses the evolution of Irish poetry and song since 1200. It explores the connections between vernacular poetry and various learned (literary) traditions, including bardic poetry (syllabic verse) and the later ‘poetic courts’ and ‘schools of poetry’, in terms of themes, verse structure, social context, and sung performance. It demonstrates that while some practices were bound to specific social contexts, the strand that most people today identify as ‘the Irish song tradition’ still employs centuries-old themes including panegyric and the Anglo-Norman ‘courtly love’ rhetoric, and displays prosodic features evidenced in Middle Irish bardic sources. Finally, we consider the emergence of ‘tradition’ as a concept, the impact since 1850 of song collecting and technology on repertoire and performance, and the implications of ‘authenticity’ for today’s definition of ‘tradition’.
The Public Music Theory of George Bernard Shaw
Authors: Biamonte Nicole
Published: November 2021

George Bernard Shaw is best known today for his plays, but he first exercised his incisive wit as a drama and music critic in London, intermittently from 1876, regularly from 1888 to 1894, and intermittently again to the end of his life. Shaw explicitly intended to make his reviews both educational and accessible to the general public, combining performance critiques with broader considerations, including aspects of music theory and music education, and avoiding technical terms to the extent possible. Thus, his music criticism serves as an example of public music theory. This chapter surveys Shaw’s music-theoretic comments through this lens, analyzing what they demonstrate about his own musical understanding and underlying ideologies, the educational purpose of his reviews, and the level of musical knowledge he assumed on the part of his late nineteenth-century London readership.
A CONCEPTUAL framework for combining brain mapping and brain stimulation
Authors: Karabanov Anke Ninija , Siebner Hartwig R.
Published: November 2021

Here, we introduce a conceptual framework for studies that combine non-invasive transcranial brain stimulation (NTBS) with neuroimaging. We outline the type of neuroscientific questions that can be addressed with a combined NTBS-neuroimaging approach and describe important experimental considerations. Neuroimaging methods differ with respect to their spatiotemporal resolution and reflect different neurobiological aspects of brain function, structure or metabolism. These characteristics need to be carefully considered in order to select the most appropriate neuroimaging modality. NTBS and neuroimaging can be combined concurrently (online) or sequentially (offline). The “online” approach applies neuroimaging while NTBS is delivered to the brain and thus, can reveal the immediate functional effects of NTBS on the targeted brain networks, but one has to deal with interfering effects of NTBS on brain mapping. The “offline” approach applies neuroimaging and NTBS in sequence: Offline neuroimaging can be performed BEFORE the stimulation session to inform NTBS parameter setting or AFTER the stimulation session to provide functional, metabolic or structural readouts of NTBS-effects. Since NTBS and neuroimaging can be separated in space and time, NTBS does not interfere with offline brain mapping. Finally, we discuss how NTBS and neuroimaging are gaining importance in clinical NTBS applications and how both techniques can be iteratively combined to create open-loop setups.
Computational neurostimulation
Authors: Johnstone Ainslie , Bonaiuto James J. , Bestmann Sven
Published: November 2021

Computational neurostimulation is the use of biologically grounded computational models to investigate the mechanism of action of brain stimulation and predict the impact of transcranial magnetic stimulation (TMS) on behavior in health and disease. Computational models are now widespread, and their success is incontrovertible, yet they have left a rather small footprint on the field of TMS. We highlight and discuss recent advances in models of primary motor cortex TMS, the brain region for which most models have been developed. These models provide insight into the putative, but unobservable, mechanisms through which TMS influences physiology, and help predicting the effects of different TMS applications. We discuss how these advances in computational neurostimulation provide opportunities for mechanistically understanding and predicting the impact of TMS on behavior.
How Does Artificial Intelligence Pose an Existential Risk?
Authors: Vold Karina , Harris Daniel R.
Published: November 2021

Alan Turing, one of the fathers of computing, warned that artificial intelligence (AI) could one day pose an existential risk to humanity. Today, recent advancements in the field of AI have been accompanied by a renewed set of existential warnings. But what exactly constitutes an existential risk? And how exactly does AI pose such a threat? In this chapter, we aim to answer these questions. In particular, we will critically explore three commonly cited reasons for thinking that AI poses an existential threat to humanity: the control problem, the possibility of global disruption from an AI race dynamic, and the weaponization of AI.
Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis
Authors: Huc Jonathan , Dziasek Katarzyna , Pachamuthu Kannan , Woh Tristan , Köhler Claudia , Borges Filipe
Published: November 2021

The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of “epimutagenized” plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.
AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes
Authors: Li Yang , Jiang Ning , Sun Yanni
Published: November 2021

Short interspersed nuclear elements (SINEs) are a widespread type of small transposable element (TE). With increasing evidence for their impact on gene function and genome evolution in plants, accurate genome-scale SINE annotation becomes a fundamental step for studying the regulatory roles of SINEs and their relationship with other components in the genomes. Despite the overall promising progress made in TE annotation, SINE annotation remains a major challenge. Unlike some other TEs, SINEs are short and heterogeneous, and they usually lack well-conserved sequence or structural features. Thus, current SINE annotation tools have either low sensitivity or high false discovery rates. Given the demand and challenges, we aimed to provide a more accurate and efficient SINE annotation tool for plant genomes. The pipeline starts with maximizing the pool of SINE candidates via profile hidden Markov model-based homology search and de novo SINE search using structural features. Then, it excludes the false positives by integrating all known features of SINEs and the features of other types of TEs that can often be misannotated as SINEs. As a result, the pipeline substantially improves the tradeoff between sensitivity and accuracy, with both values close to or over 90%. We tested our tool in Arabidopsis thaliana and rice (Oryza sativa), and the results show that our tool competes favorably against existing SINE annotation tools. The simplicity and effectiveness of this tool would potentially be useful for generating more accurate SINE annotations for other plant species. The pipeline is freely available at https://github.com/yangli557/AnnoSINE.
Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles
Authors: Apelt Federico , Mavrothalassiti Eleni , Gupta Saurabh , Machin Frank , Olas Justyna Jadwiga , Annunziata Maria Grazia , Schindelasch Dana , Kragler Friedrich
Published: November 2021

Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants’ transcriptome substantially changes throughout the day, shaped by the circadian clock, we performed scRNAseq on both Arabidopsis root and above-ground tissues at defined times of the day. For the root scRNAseq analysis, we used tissue-specific reporter lines grown on plates and harvested at the end of the day (ED). In addition, we submitted above-ground tissues from plants grown on soil at ED and end of the night to scRNAseq, which allowed us to identify common cell types/markers between root and shoot and uncover transcriptome changes to above-ground tissues depending on the time of the day. The dataset was also exploited beyond the traditional scRNAseq analysis to investigate non-annotated and di-cistronic transcripts. We experimentally confirmed the predicted presence of some of these transcripts and also addressed the potential function of a previously unidentified marker gene for dividing cells. In summary, this work provides insights into the spatial control of gene expression from nearly 70,000 cells of Arabidopsis for below- and whole above-ground tissue at single-cell resolution at defined time points.
Phosphorylation of transcription factor bZIP21 by MAP kinase MPK6-3 enhances banana fruit ripening
Authors: Wu Chao-Jie , Shan Wei , Liu Xun-Cheng , Zhu Li-Sha , Wei Wei , Yang Ying-Ying , Guo Yu-Fan , Bouzayen Mondher , Chen Jian-Ye , Lu Wang-Jin , Kuang Jian-Fei
Published: November 2021

Ripening of fleshy fruits involves both diverse post-translational modifications (PTMs) and dynamic transcriptional reprogramming, but the interconnection between PTMs, such as protein phosphorylation and transcriptional regulation, in fruit ripening remains to be deciphered. Here, we conducted a phosphoproteomic analysis during banana (Musa acuminata) ripening and identified 63 unique phosphopeptides corresponding to 49 proteins. Among them, a Musa acuminata basic leucine zipper transcription factor21 (MabZIP21) displayed elevated phosphorylation level in the ripening stage. MabZIP21 transcript and phosphorylation abundance increased during banana ripening. Genome-wide MabZIP21 DNA binding assays revealed MabZIP21-regulated functional genes contributing to banana ripening, and electrophoretic mobility shift assay, chromatin immunoprecipitation coupled with quantitative polymerase chain reaction, and dual-luciferase reporter analyses demonstrated that MabZIP21 stimulates the transcription of a subset of ripening-related genes via directly binding to their promoters. Moreover, MabZIP21 can be phosphorylated by MaMPK6-3, which plays a role in banana ripening, and T318 and S436 are important phosphorylation sites. Protein phosphorylation enhanced MabZIP21-mediated transcriptional activation ability, and transient overexpression of the phosphomimetic form of MabZIP21 accelerated banana fruit ripening. Additionally, MabZIP21 enlarges its role in transcriptional regulation by activating the transcription of both MaMPK6-3 and itself. Taken together, this study reveals an important machinery of protein phosphorylation in banana fruit ripening in which MabZIP21 is a component of the complex phosphorylation pathway linking the upstream signal mediated by MaMPK6-3 with transcriptional controlling of a subset of ripening-associated genes.
Torque Teno Virus quantification for monitoring of immunomodulation with biologic compounds in the treatment of rheumatoid arthritis
Authors: Studenic Paul , Bond Gregor , Kerschbaumer Andreas , Bécède Manuel , Pavelka Karel , Karateev Dmitry , Stieger Jutta , Puchner Rudolf , Mueller Ruediger B , Puchhammer-Stöckl Elisabeth  , Durechova Martina , Loiskandl Michaela , Perkmann Thomas  , Olejarova Martina , Luchikhina Elena , Steiner Carl-Walter , Bonelli Michael  , Smolen Josef S , Aletaha Daniel
Published: November 2021

Objectives

RA patients who fail to respond to MTX can receive biologic dMARDs (bDMARDs). The Torque Teno Virus (TTV) is a potential novel candidate for monitoring of immunosuppression. We explore TTV in these patients and its association with clinical response to bDMARDs.

Methods

The BioBio Study is a multicentre randomized open-label trial, including RA patients with insufficient response to MTX. Patients were randomized to either TNFi (infliximab, INF), anti-IL-6 (tocilizumab, TCZ), CTLA4-Ig (abatacept, ABA) or anti-CD20 (rituximab, RTX) in addition to MTX. PCR was used to quantify TTV in the peripheral blood.

Results

TTV was measured in 95 patients (INF, n = 23; TCZ, n = 22; ABA, n = 27; RTX; n = 23). TTV increased by a median of 4.5 × 104 copies/ml [c/ml; interquartile range (IQR) 0–7.5 × 105] after 3 months. TTV levels at month 3 were associated with the Simplified Disease Activity Index (SDAI) (P = 0.03) and the Clinical Disease Activity Index (CDAI) response (P = 0.026) at month 6. A TTV cut-off level of 1.2 × 106 c/ml at month 3 had a positive likelihood ratio of 2.7 for prediction of an 85% reduction in SDAI at month 6.

Conclusion

Our data suggest that TTV levels increase upon TNF, CD20 and costimulation blockade and are associated with the clinical response to bDMARDs in RA patients.

Trial registration

ClinicalTrials.gov; https://clinicaltrials.gov; NCT01638715
Work participation in patients with systematic lupus erythematosus: a systematic review
Authors: Blomjous Birgit S , Gajadin Gayle R S , Voskuyl Alexandre E , Falzon Louise , Hoving Jan L , Bultink Irene E M , ter Wee Marieke M
Published: November 2021

Objectives

This systematic review assessed which variables are associated with or are predictors for work participation outcomes in patients with systematic lupus erythematosus (SLE).

Methods

A literature search using MEDLINE, The Cochrane Library, Embase and CINAHL was conducted to identify all studies published from inception (1947) to June 2021 on factors related to and/or predicting employment status, absenteeism and/or presenteeism in SLE patients aged ≥18 years. The quality of included articles was assessed using the QUIPS tool. Narrative summaries were used to present the data.

Results

Fifteen studies (nine on associations, four on predictions, and two assessing both) were included, encompassing data of 3800 employed patients. Younger age, Caucasian ethnicity, higher educational level, lower disease activity score, shorter disease duration, absence of specific disease manifestations, higher levels of physical functioning and less physical job demands and higher levels of psychological/cognitive functioning were associated with or predicted favorable work outcomes. Older age, non-Caucasian ethnicity, female gender, never being married, poverty, lower educational level, higher disease activity score, longer disease duration, specific disease manifestations, lower levels of physical functioning, more physical job demands and low job control, less job tenure and lower levels of cognitive functioning were associated with or predicted an unfavorable work outcome. Limitations of the evidence were the quality of the studies and the use of heterogeneous outcome measures, applied statistical methods and instruments used to assess work participation.

Conclusion

We recommend applying the EULAR points to consider for designing, analysing and reporting on work participation in inflammatory arthritis also to SLE studies on work participation, to enhance the quality and comparability between studies and to better understand the impact of SLE on work participation.

Trial registration

registration in PROSPERO (CRD42020161275; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=161275).
The Mechanosensitive Ion Channel MSL10 Modulates Susceptibility to Pseudomonas syringae in Arabidopsis thaliana
Authors: Basu Debarati , Codjoe Jennette M. , Veley Kira M. , Haswell Elizabeth S.
Published: November 2021

Plants sense and respond to molecular signals associated with the presence of pathogens and their virulence factors. Mechanical signals generated during pathogenic invasion may also be important, but their contributions have rarely been studied. Here, we investigate the potential role of a mechanosensitive ion channel, MscS-like (MSL)10, in defense against the bacterial pathogen Pseudomonas syringae in Arabidopsis thaliana. We previously showed that overexpression of MSL10-GFP, phospho-mimetic versions of MSL10, and the gain-of-function allele msl10-3G all produce dwarfing, spontaneous cell death, and the hyperaccumulation of reactive oxygen species. These phenotypes are shared by many autoimmune mutants and are frequently suppressed by growth at high temperature in those lines. We found that the same was true for all three MSL10 hypermorphs. In addition, we show that the SGT1/RAR1/HSP90 cochaperone complex was required for dwarfing and ectopic cell death, PAD4 and SID2 were partially required, and the immune regulators EDS1 and NDR1 were dispensable. All MSL10 hypermorphs exhibited reduced susceptibility to infection by P. syringae strain Pto DC3000 and Pto DC3000 expressing the avirulence genes avrRpt2 or avrRpm1 but not Pto DC3000 hrpL and showed an accelerated induction of PR1 expression compared with wild-type plants. Null msl10-1 mutants were delayed in PR1 induction and displayed modest susceptibility to infection by coronatine-deficient P. syringae pv. tomato. Finally, stomatal closure was reduced in msl10-1 loss-of-function mutants in response to P. syringae pv. tomato COR−. These data show that MSL10 modulates pathogen responses and begin to address the possibility that mechanical signals are exploited by the plant for pathogen perception.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Pain and Opioid Consumption and Mobilization after Surgery: Post Hoc Analysis of Two Randomized Trials
Authors: Rivas Eva , Cohen Barak , Pu Xuan , Xiang Li , Saasouh Wael , Mao Guangmei , Minko Paul , Mosteller Lauretta , Volio Andrew , Maheshwari Kamal , Sessler Daniel I. , Turan Alparslan
Published: November 2021

Background

Early mobilization is incorporated into many enhanced recovery pathways. Inadequate analgesia or excessive opioids may restrict postoperative mobilization. The authors tested the hypotheses that in adults recovering from abdominal surgery, postoperative pain and opioid consumption are inversely related to postoperative mobilization, and that postoperative mobilization is associated with fewer potentially related complications.

Methods

The authors conducted a subanalysis of two trials that enrolled adults recovering from abdominal surgery. Posture and movement were continuously monitored for 48 postoperative hours using noninvasive untethered monitors. Mobilization was defined as the fraction of monitored time spent sitting or standing.

Results

A total of 673 patients spent a median [interquartile range] of 7% [3 to 13%] of monitored time sitting or standing. Mobilization time was 1.9 [1.0 to 3.6] h/day for patients with average pain scores 3 or lower, but only 1.2 [0.5 to 2.6] h/day in those with average scores 6 or greater. Each unit increase in average pain score was associated with a decrease in mobilization time of 0.12 (97.5% CI, 0.02 to 0.24; P = 0.009) h/day. In contrast, there was no association between postoperative opioid consumption and mobilization time. The incidence of the composite of postoperative complications was 6.0% (10 of 168) in the lower mobilization quartile, 4.2% (7 of 168) in the second quartile, and 0% among 337 patients in the highest two quartiles (P = 0.009).

Conclusions

Patients recovering from abdominal surgery spent only 7% of their time mobilized, which is considerably less than recommended. Lower pain scores are associated with increased mobility, independently of opioid consumption. Complications were more common in patients who mobilized poorly.

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Early Literacy Strategies for Parents of Young Dual Language Learners
Authors: Guiberson Mark
Published: November 2021

There is a large and growing population of dual language learners (DLLs) represented in early intervention programs in the United States, the majority of whom are from Spanish-speaking families. To adequately serve these families, educators and speech–language pathologists must work closely with parents and provide them with culturally responsive strategies and activities that align with their language background and interaction styles. The purpose of this convergent parallel mixed-methods study was to identify culturally consistent early literacy strategies specifically for parents of 2- to 3-year-old DLLs. Findings from a descriptive study that included 94 young DLLs and their parents engaged in a book-reading task plus findings from an integrative literature review were converged to identify potential parent-implemented strategies that may support early literacy in young DLLs. From this process, a total of 26 strategies were identified in the categories of enhanced interaction, engagement with texts or storybooks, questioning behaviors, and other language enhancement. Fifteen of the strategies had compelling strength based on available work. Use of these strategies in pilot programs and future treatment studies is recommended.
Spanish Language and Literacy Intervention for Bilingual Children at Risk for Developmental Language Disorder
Authors: Fiestas Christine E. , Lugo-Neris Mirza J. , Pratt Amy S. , Peña Elizabeth D. , Bedore Lisa M.
Published: November 2021

This pilot study evaluates the feasibility of an integrated intervention titled Language and Literacy Together developed to target semantic and narrative skills in bilingual children at risk for developmental language disorder (DLD). Thirteen first-grade bilingual children who scored in the risk range for DLD on the Bilingual English Spanish Oral Screener received intervention. Children completed pretest and posttest evaluations of semantics and narrative comprehension and production in Spanish and English. Intervention participants demonstrated significant gains in both semantics and narrative skills, in both the language of the intervention (Spanish) and in English. The largest gains were observed for Spanish narrative comprehension and English narrative production. The Spanish Language and Literacy Together intervention appears a feasible approach for improving bilingual children's semantic skills and supporting generalization to narrative comprehension and production skills, which underpin literacy. Gains in both languages suggest evidence of cross-language transfer.
In This Together
Authors: Ehren Barbara J. , Rosa-Lugo Linda I. , Hagan Audrey D. P.
Published: November 2021

English learners (ELs) struggle with vocabulary learning and often evidence serious vocabulary gaps. It is challenging, especially for professionals who do not speak the native language of the students, to teach EL students vocabulary that supports academic learning, is compatible with classroom instruction, and considers their changing language proficiency levels. A compounding factor may be the additional presence of a language disorder. The purpose of this article is to provide a context for professionals and nonprofessionals, monolinguals and bilinguals, to work together in developing strong lexicons in ELs to support academic growth. Toward that end, the authors discuss the nature of the school-age EL population, vocabulary needs of this heterogeneous population, the need for collaboration in the wise use of available resources, a technique called the Vocabulary Scenario Technique designed for collaborative implementation, and guiding principles about vocabulary instruction with ELs that can be of use to researchers and practitioners.
Vocal communication across cultures: theoretical and methodological issues
Authors: Bryant Gregory A.
Published: November 2021

The study of human vocal communication has been conducted primarily in Western, educated, industrialized, rich, democratic (WEIRD) societies. Recently, cross-cultural investigations in several domains of voice research have been expanding into more diverse populations. Theoretically, it is important to understand how universals and cultural variations interact in vocal production and perception, but cross-cultural voice research presents many methodological challenges. Experimental methods typically used in WEIRD societies are often not possible to implement in many populations such as rural, small-scale societies. Moreover, theoretical and methodological issues are often unnecessarily intertwined. Here, I focus on three areas of cross-cultural voice modulation research: (i) vocal signalling of formidability and dominance, (ii) vocal emotions, and (iii) production and perception of infant-directed speech. Research in these specific areas illustrates challenges that apply more generally across the human behavioural sciences but also reveals promise as we develop our understanding of the evolution of human communication.

This article is part of the theme issue ‘Voice modulation: from origin and mechanism to social impact (Part II)’.
Musicality in human vocal communication: an evolutionary perspective
Authors: Leongómez Juan David , Havlíček Jan , Roberts S. Craig
Published: November 2021

Studies show that specific vocal modulations, akin to those of infant-directed speech (IDS) and perhaps music, play a role in communicating intentions and mental states during human social interaction. Based on this, we propose a model for the evolution of musicality—the capacity to process musical information—in relation to human vocal communication. We suggest that a complex social environment, with strong social bonds, promoted the appearance of musicality-related abilities. These social bonds were not limited to those between offspring and mothers or other carers, although these may have been especially influential in view of altriciality of human infants. The model can be further tested in other species by comparing levels of sociality and complexity of vocal communication. By integrating several theories, our model presents a radically different view of musicality, not limited to specifically musical scenarios, but one in which this capacity originally evolved to aid parent–infant communication and bonding, and even today plays a role not only in music but also in IDS, as well as in some adult-directed speech contexts.

This article is part of the theme issue ‘Voice modulation: from origin and mechanism to social impact (Part II)’.
A cross-species framework to identify vocal learning abilities in mammals
Authors: Ravignani Andrea , Garcia Maxime
Published: November 2021

Vocal production learning (VPL) is the experience-driven ability to produce novel vocal signals through imitation or modification of existing vocalizations. A parallel strand of research investigates acoustic allometry, namely how information about body size is conveyed by acoustic signals. Recently, we proposed that deviation from acoustic allometry principles as a result of sexual selection may have been an intermediate step towards the evolution of vocal learning abilities in mammals. Adopting a more hypothesis-neutral stance, here we perform phylogenetic regressions and other analyses further testing a potential link between VPL and being an allometric outlier. We find that multiple species belonging to VPL clades deviate from allometric scaling but in the opposite direction to that expected from size exaggeration mechanisms. In other words, our correlational approach finds an association between VPL and being an allometric outlier. However, the direction of this association, contra our original hypothesis, may indicate that VPL did not necessarily emerge via sexual selection for size exaggeration: VPL clades show higher vocalization frequencies than expected. In addition, our approach allows us to identify species with potential for VPL abilities: we hypothesize that those outliers from acoustic allometry lying above the regression line may be VPL species. Our results may help better understand the cross-species diversity, variability and aetiology of VPL, which among other things is a key underpinning of speech in our species.

This article is part of the theme issue ‘Voice modulation: from origin and mechanism to social impact (Part II)’.
The neural control of volitional vocal production—from speech to identity, from social meaning to song
Authors: Scott Sophie K.
Published: November 2021

The networks of cortical and subcortical fields that contribute to speech production have benefitted from many years of detailed study, and have been used as a framework for human volitional vocal production more generally. In this article, I will argue that we need to consider speech production as an expression of the human voice in a more general sense. I will also argue that the neural control of the voice can and should be considered to be a flexible system, into which more right hemispheric networks are differentially recruited, based on the factors that are modulating vocal production. I will explore how this flexible network is recruited to express aspects of non-verbal information in the voice, such as identity and social traits. Finally, I will argue that we need to widen out the kinds of vocal behaviours that we explore, if we want to understand the neural underpinnings of the true range of sound-making capabilities of the human voice.

This article is part of the theme issue ‘Voice modulation: from origin and mechanism to social impact (Part II)’.
Vocal size exaggeration may have contributed to the origins of vocalic complexity
Authors: Pisanski Katarzyna , Anikin Andrey , Reby David
Published: November 2021

Vocal tract elongation, which uniformly lowers vocal tract resonances (formant frequencies) in animal vocalizations, has evolved independently in several vertebrate groups as a means for vocalizers to exaggerate their apparent body size. Here, we propose that smaller speech-like articulatory movements that alter only individual formants can serve a similar yet less energetically costly size-exaggerating function. To test this, we examine whether uneven formant spacing alters the perceived body size of vocalizers in synthesized human vowels and animal calls. Among six synthetic vowel patterns, those characterized by the lowest first and second formant (the vowel /u/ as in ‘boot’) are consistently perceived as produced by the largest vocalizer. Crucially, lowering only one or two formants in animal-like calls also conveys the impression of a larger body size, and lowering the second and third formants simultaneously exaggerates perceived size to a similar extent as rescaling all formants. As the articulatory movements required for individual formant shifts are minor compared to full vocal tract extension, they represent a rapid and energetically efficient mechanism for acoustic size exaggeration. We suggest that, by favouring the evolution of uneven formant patterns in vocal communication, this deceptive strategy may have contributed to the origins of the phonemic diversification required for articulated speech.

This article is part of the theme issue ‘Voice modulation: from origin and mechanism to social impact (Part II)’.
Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium
Authors: Tóth Ákos , Máté Rózsa , Kutasi József , Tóth Erika , Bóka Károly , Táncsics András , Nagy István , Kovács Gábor , Kosztik Judit , Bata-Vidács Ildikó , Kukolya József
Published: November 2021

A Gram-reaction-negative bacterial strain, designated Kb22T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to

Sphingobacterium nematocida

M-SX103T. The highest average nucleotide identity value (71.83 %) was found with

Sphingobacterium composti

T5-12T, and the highest amino acid identity value (66.65 %) was found with

Sphingobacterium olei

HAL-9T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C15:0 (28.4%), summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) (25.7 %) and iso-C17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22T is a member of the genus

Sphingobacterium

and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22T (=LMG 31574T=NCAIM B.02638T).
Bacterial genomic epidemiology with mixed samples
Authors: Mäklin Tommi , Kallonen Teemu , Alanko Jarno , Samuelsen Ørjan , Hegstad Kristin , Mäkinen Veli , Corander Jukka , Heinz Eva , Honkela Antti
Published: November 2021

Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
The primary transcriptome of hormogonia from a filamentous cyanobacterium defined by cappable-seq
Authors: Harwood Thomas V. , Risser Douglas D.
Published: November 2021

Hormogonia are motile filaments produced by many filamentous cyanobacteria that function in dispersal, phototaxis and the establishment of nitrogen-fixing symbioses. The gene regulatory network promoting hormogonium development is initiated by the hybrid histidine kinase HrmK, which in turn activates a sigma factor cascade consisting of SigJ, SigC and SigF. In this study, cappable-seq was employed to define the primary transcriptome of developing hormogonia in the model filamentous cyanobacterium

Nostoc punctiforme

ATCC 29133 in both the wild-type, and sigJ, sigC and sigF mutant strains 6 h post-hormogonium induction. A total of 1544 transcriptional start sites (TSSs) were identified that are associated with protein-coding genes and are expressed at levels likely to lead to biologically relevant transcripts in developing hormogonia. TSS expression among the sigma-factor deletion strains was highly consistent with previously reported gene expression levels from RNAseq experiments, and support the current working model for the role of these genes in hormogonium development. Analysis of SigJ-dependent TSSs corroborated the presence of the previously identified J-Box in the −10 region of SigJ-dependent promoters. Additionally, the data presented provides new insights on sequence conservation within the −10 regions of both SigC- and SigF-dependent promoters, and demonstrates that SigJ and SigC coordinate complex co-regulation not only of hormogonium-specific genes at different loci, but within an individual operon. As progress continues on defining the hormogonium gene regulatory network, this data set will serve as a valuable resource.
AI/ML Models to Aid in the Diagnosis of COVID-19 Illness from Forced Cough Vocalizations: Results and Challenges of a Systematic Review of the Relevant Literature
Authors: Kelley K. , Sakara A.A. , Kelley M. , Kelley S. C. , McLenaghan P. , Aldir R. , Cox M. , Donaldson N. , Stogsdill A. , Kotchou S. , Sula G. , Ramirez M.A.
Published: November 2021

From a comprehensive and systematic search of the relevant literature on signal data signature (SDS)-based artificial intelligence/machine learning (AI/ML) systems designed to aid in the diagnosis of COVID-19 illness, we aimed to reproduce the reported systems and to derive a performance goal for comparison to our own medical device with the same intended use. These objectives were in line with a pathway to regulatory approval of such devices, as well as to acceptance of this unfamiliar technology by disaster/pandemic decision makers and clinicians. To our surprise, none of the peer-reviewed articles or pre-print server records contained details sufficient to meet the planned objectives. Information amassed from the full review of more than 60 publications, however, did underscore discrete impediments to bringing AI/ML diagnostic solutions to the bedside during a pandemic. These challenges then were explored by the authors via a gap analysis and specific remedies were proposed for bringing AI/ML technologies in closer alignment with the needs of a Total Product Life Cycle (TPLC) regulatory approach.
Functional ultrasound imaging of recent and remote memory recall in the associative fear neural network in mice
Authors: Grohs-Metz Gillian , Smausz Rebecca , Gigg John , Boeckers Tobias , Hengerer Bastian
Published: November 2021

Scientific Abstract

Emotional learning and memory are affected in numerous psychiatric disorders. At a systems level, however, the underlying neural circuitry is not well defined. Rodent fear conditioning (FC) provides a translational model to study the networks underlying associative memory retrieval. In the current study, functional connectivity among regions related to the cue associative fear network were investigated using functional ultrasound (fUS), a novel imaging technique with great potential for detecting regional neural activity through cerebral blood flow. Behavioral fear expression and fUS imaging were performed one and thirty-one days after FC to assess recent and remote memory recall. Cue-evoked increases in functional connectivity were detected throughout the amygdala, with the lateral (LA) and central (CeA) amygdalar nuclei emerging as major hubs of connectivity, though CeA connectivity was reduced during remote recall. The hippocampus and sensory cortical regions displayed heightened connectivity with the LA during remote recall, whereas interconnectivity between the primary auditory cortex and temporal association areas was reduced. Subregions of the prefrontal cortex exhibited variable connectivity changes, where prelimbic connectivity with the amygdala was refined while specific connections between the infralimbic cortex and amygdalar subregions emerged during remote memory retrieval. Moreover, freezing behavior positively correlated with functional connectivity between hubs of the associative fear network, suggesting that emotional response intensity reflected the strength of the cue-evoked functional network. Overall, our data provide evidence of the functionality of fUS imaging to investigate the neural dynamics of memory encoding and retrieval, applicable in the development of innovative treatments for affective disorders.

Highlights

Functional ultrasound imaging can elucidate fear associated neural networks

Freezing behavior correlates with cue-evoked functional connectivity changes

The lateral and central amygdalar nuclei are major hubs in the fear network

The hippocampus is active during recent and remote cued fear memory retrieval

Connectivity profiles of the prelimbic and infralimbic areas vary in remote recall