bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of viscosity on the linear stability of damped Stokes waves, downshifting, and rogue wave generation
Authors: Calini A. , Ellisor C. L. , Schober C. M. , Smith E. 
Published: November 2023

AbstractWe investigate a higher order nonlinear Schrödinger equation with linear damping and weak viscosity, recently proposed as a model for deep water waves exhibiting frequency downshifting. Through analysis and numerical simulations, we discuss how the viscosity affects the linear stability of the Stokes wave solution, enhances rogue wave formation, and leads to permanent downshift in the spectral peak. The novel results in this work include the analysis of the transition from the initial Benjamin–Feir instability to a predominantly oscillatory behavior, which takes place in a time interval when most rogue wave activity occurs. In addition, we propose new criteria for downshifting in the spectral peak and determine the relation between the time of permanent downshift and the location of the global minimum of the momentum and the magnitude of its second derivative.
Frequency and predictors of virtual hope box use in individuals experiencing suicidal ideation: An ecological momentary assessment investigation
Authors: Moscardini Emma H. , Le Thanh P. , Cowan Tovah , Gerner Jessica , Robinson Anthony , Cohen Alex S. , Tucker Raymond P. 
Published: November 2023

AbstractIntroductionThe Virtual Hope Box (VHB) is a smartphone application designed to support emotion regulation when one is distressed, in a crisis, or experiencing suicidal ideation (SI). Initial proof of concept studies indicate that individuals are more likely to use the VHB than traditional hope boxes, and find it both easy to setup and helpful. To our knowledge, no studies have harnessed ambulatory assessment methodology to assess VHB use as it relates to incidence of suicidal thinking.MethodsAs such, we recruited N = 50 undergraduates who endorsed SI either the past year or past 2 weeks to complete a 10‐day investigation. At baseline, participants were oriented to the VHB and instructed on how to use the application. Over the next 10 days, participants responded to prompts five times per day on their personal smartphones regarding their current experiences of SI and stress as well as VHB usage.ResultsResults found that most participants used the VHB at least once, rated its usefulness as high, and rated their perceived likelihood of future use as high. In addition, increases in state SI severity were related to subsequent VHB use.ConclusionThe VHB may be a useful tool for managing crises in undergraduates experiencing suicidal thoughts.
Storytelling as Inverse Inverse Planning
Authors: Chandra Kartik , Li Tzu‐Mao , Tenenbaum Joshua B. , Ragan‐Kelley Jonathan 
Published: November 2023

AbstractGreat storytelling takes us on a journey the way ordinary reality rarely does. But what exactly do we mean by this “journey?” Recently, literary theorist Karin Kukkonen proposed that storytelling is “probability design:” the art of giving an audience pieces of information bit by bit, to craft the journey of their changing beliefs about the fictional world. A good “probability design” choreographs a delicate dance of certainty and surprise in the reader's mind as the story unfolds from beginning to end. In this paper, we computationally model this conception of storytelling. Building on the classic Bayesian inverse planning model of human social cognition, we treat storytelling as inverse inverse planning: the task of choosing actions to manipulate an inverse planner's inferences, and therefore a human audience's beliefs. First, we use an inverse inverse planner to depict social and physical situations, and present behavioral studies indicating that inverse inverse planning produces more expressive behavior than ordinary “naïve planning.” Then, through a series of examples, we demonstrate how inverse inverse planning captures many storytelling elements from first principles: character, narrative arcs, plot twists, irony, flashbacks, and deus ex machina are all naturally encoded in the flexible language of probability design.
The Move2Smile Online Hub for Parents to Support Aspects of Preschoolers’ Physical Literacy at Home: A Feasibility Study
Authors: James Maeghan E. , Cairney John , Odorico Nikoleta , Finlay-Watson Tracia , Arbour-Nicitopoulos Kelly P. 
Published: November 2023

This study aimed to develop and evaluate the acceptability and feasibility of a web-based platform for parents to support preschoolers’ development of physical literacy. Specifically, this intervention focused on children’s motor and social-emotional skill development. Twenty parents (Mage = 35.7, SD = 4.2) of preschool-aged children (Mage = 4.1, SD = 0.6) were assigned three intervention modules and completed weekly usage and feedback questionnaires (1 = strongly disagree, 5 = strongly agree). Parents (n = 15) also completed a follow-up interview. Parents indicated the modules were useable (4.5/5), useful (4.5/5), feasible (4.4/5), enjoyable (4.5/5), and acceptable (4.5/5). Five themes underlying parental engagement were generated: (a) activity organization and planning, (b) (de)motivators, (c) parent knowledge and skills, (d) experience with the platform, and (e) application to everyday routines. The online modules under investigation were deemed both acceptable and feasible by parents. However, factors such as time and knowledge may impact parental engagement at home. Future research is needed to better understand the antecedents to parent physical literacy support behaviors in the early years.
The Effects of Spectators on National Basketball Association Free Throw Performance
Authors: Markwell Logan T. , Singh Harjiv , Strick Andrew J. , Porter Jared M. 
Published: November 2023

Free throw shooting percentage has averaged around 75% for nearly five decades. However, free throw percentages significantly increased to 79% during the 2020 spectator-less National Basketball Association season. The current study investigated if the elevated free throw shooting percentage observed during the spectator-less season has returned to the 50-year average now that spectators have returned to National Basketball Association arenas. Moreover, home and away free throw percentages were examined to determine if a potential home-field advantage contributed to this phenomenon. Analyses revealed that the free throw shooting percentage from the spectator-less season was significantly higher than the two spectator-filled seasons preceding and following the spectator-less season. Furthermore, the analyses found no differences in free throw percentages between home and away games. While the free throw shooting percentage increased to 79% during the spectator-less season, the free throw shooting percentage returned to the 50-year average (i.e., ∼75%), following the spectator-less season. Additionally, it does not appear that a perceived home-field advantage influenced the increased free throw performance observed in the spectator-less season. Multiple factors likely contributed to this free throw phenomenon, including the environmental characteristics shaped by the lack of spectators.
Adenovirus E1A binding to DCAF10 targets proteasomal degradation of RUVBL1/2 AAA+ ATPases required for quaternary assembly of multiprotein machines, innate immunity, and responses to metabolic stress
Authors: Zemke Nathan R. , Hsu Emily , Barshop William D. , Sha Jihui , Wohlschlegel James A. , Berk Arnold J. 
Published: November 2023

ABSTRACT
Adenovirus small e1a protein modifies host cell physiology to optimize virus replication. The N-terminal ~140 aa of e1a interacts with RB-family proteins to derepress dNTP and DNA synthesis and with EP300/CREBBP lysine acetyltransferases and EP400-TIP60 chromatin-modifying complexes to inhibit host anti-viral innate immune responses. However, the e1a N-terminal region activates a late host anti-viral response due to stabilization and activation of IRF3. The E1A C-terminal region counteracts IRF3 stabilization through interactions with three host nuclear proteins with seemingly unrelated functions. All three C-terminal interactions are required for e1a-association into a multi-protein complex with scaffold subunits of a CRL4 E3 ubiquitin ligase and DCAF10, a presumed specificity subunit. This e1a-DCAF10-CRL4 prevents IRF3 stabilization indirectly by targeting the essential AAA+ ATPases RUVBL1/2, subunits of several HSP90 co-chaperones required for quaternary assembly of cellular protein machines required for anti-viral defenses and responses to genotoxic and metabolic stress.

IMPORTANCE
Inactivation of EP300/CREBB paralogous cellular lysine acetyltransferases (KATs) during the early phase of infection is a consistent feature of DNA viruses. The cell responds by stabilizing transcription factor IRF3 which activates transcription of scores of interferon-stimulated genes (ISGs), inhibiting viral replication. Human respiratory adenoviruses counter this by assembling a CUL4-based ubiquitin ligase complex that polyubiquitinylates RUVBL1 and 2 inducing their proteasomal degradation. This inhibits accumulation of active IRF3 and the expression of anti-viral ISGs, allowing replication of the respiratory HAdVs in the face of inhibition of EP300/CBEBBP KAT activity by the N-terminal region of E1A.
Complete genome sequence of
Actinoplanes sichuanensis
strain 03-723
T
Authors: Kawashima Taketsugu , Watanabe Yasuha , Arakawa Kazuharu 
Published: November 2023

ABSTRACT

A mesophilic bacterium
Actinoplanes sichuanensis
strain 03-723

T

was previously isolated from soil by Sun et al. Here, we present a complete and annotated genome sequence of this strain, which has a total size of 12.1 Mbp with a G + C content of 70.1%.
A novel botybirnavirus with a unique satellite dsRNA causes latent infection in
Didymella theifolia
isolated from tea plants
Authors: Ye Liangchao , Shi Xinyu , He Yunqiang , Chen Jiao , Xu Qingeng , Shafik Karim , Fu Lanning , Yin Yumeng , Kotta-Loizou Ioly , Xu Wenxing 
Published: November 2023

ABSTRACT

The unique, recently discovered fungus
Didymella theifolia
specifically infects local varieties of tea plant
Camellia sinensis
in China, and therefore, the characterization of its mycoviruses is important. Three double-stranded (ds) RNAs (1, 2, and 3, with 6,338, 5,910, and 727 bp in size, respectively) were identified in the avirulent
D. theifolia
strain CJP4-1, which exhibits normal growth and morphology. Characterization of these double-stranded RNAs (dsRNAs) revealed that the two largest elements are the genomic components of a novel botybirnavirus, tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1). Conversely, dsRNA3 shares no detectable similarity with sequences deposited in public databases but has high similarity with the 5′-terminal regions of dsRNAs 1 and 2 and contains a duplicated region encoding a putative small peptide. All three dsRNAs are encapsidated in isometric virions
ca
. 40 nm in diameter, supporting the notion that dsRNA3 is a DtBRV1 satellite. SDS-polyacrylamide gel electrophoresis in combination with peptide mass fingerprint analysis revealed that the DtBRV1 capsid protein consists of polypeptides encoded by the 5′-terminal regions of both genomic components dsRNA1 and dsRNA2. Vertical transmission of DtBRV1 through conidia is efficient, while its horizontal transmission from CJP4-1 to other strains was not detected. DtBRV1, with or without dsRNA3, has no obvious effects on fungal growth and virulence, as illustrated following transfection of the virulent
D. theifolia
strain JYC1-6. In summary, DtBRV1 exhibits unique molecular traits and contributes to our understanding of mycovirus diversity.

IMPORTANCE

A novel botybirnavirus, infecting the tea plant pathogen
Didymella theifolia
and tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1), together with an additional double-stranded RNA (dsRNA), was characterized. DtBRV1 comprises two dsRNAs (1 and 2) encapsidated in isometric virions, while dsRNA3 is a satellite. The satellite represents a unique specimen since it contains a duplicated region and has high similarity to the two botybirnavirus dsRNAs, supporting the notion that it most likely originated from a deficient genomic component. The biological characteristics of DtBRV1 were further determined. With their unique molecular traits, DtBRV1 and its related dsRNA expand our understanding of virus diversity, taxonomy, and evolution.
Identification of common fungal extracellular membrane (CFEM) proteins inFusarium saccharithat inhibit plant immunity and contribute to virulence
Authors: Huang Zhen , Zhou Yuming , Li Huixue , Bao Yixue , Duan Zhenzhen , Wang Caixia , Powell Charles A. , Wang Kai , Hu Qin , Chen Baoshan , Zhang Jisen , Zhang Muqing , Yao Wei 
Published: November 2023

ABSTRACTFusarium sacchariis one of the primary pathogens causing pokkah boeng disease in sugarcane in China. Common fungal extracellular membrane (CFEM) domain-containing proteins only exist in fungi and play a significant role in the interaction of pathogens and plants. However, the CFEM proteins inF. sacchariwere not identified and functionally resolved. Of the 20 FsCFEM proteins identified from the genome ofF. sacchari, 16 FsCFEM genes were cloned, while 4 FsCFEM proteins (Fs06761, Fs08184, Fs10706, and Fs13617) were identified as effector proteins that could suppress the programmed cell death triggered by BCL2-associated X protein inNicotiana benthamiana. Subcellular localization analysis revealed that these four effectors could enter plant cells and are mainly located in the cell membrane and nucleus. By the yeast YTK12 secretion system, the signal peptides of four CFEM proteins were functionally verified. The expression levels of these four effector proteins were significantly increased in theF. sacchari-infected sugarcane plants. Through fungal gene knockout, three genes (Fs06761, Fs08184, and Fs13617) were found to be important pathogenic factors for pathogens. Our results support that the FsCFEM effector proteins were virulence effectors and might be involved in regulating plant immunity.IMPORTANCECommon fungal extracellular membrane (CFEM) domain-containing protein has long been considered an essential effector, playing a crucial role in the interaction of pathogens and plant. Strategies aimed at understanding the pathogenicity mechanism ofF. sacchariare eagerly anticipated to ultimately end the spread of pokkah boeng disease. Twenty FsCFEM proteins in the genome ofF. saccharihave been identified, and four FsCFEM effector proteins have been found to suppress BCL2-associated X protein-triggered programmed cell death inN. benthamiana. These four effector proteins have the ability to enter plant cells and inhibit plant immunity. Furthermore, the expression of these four FsCFEM effector proteins significantly increases during the infection stage, with the three of them playing an essential role in achieving full virulence. These study findings provide a direction toward further exploration of the immune response in sugarcane. By applying these discoveries, we can potentially control the spread of disease through techniques such as host-induced gene silencing.
Honduras HIV cohort: HLA class I and CCR5-Δ32 profiles and their associations with HIV disease outcome
Authors: Valenzuela-Ponce Humberto , Carbajal Candy , Soto-Nava Maribel , Tapia-Trejo Daniela , García-Morales Claudia , Murillo Wendy , Lorenzana Ivette , Reyes-Terán Gustavo , Ávila-Ríos Santiago 
Published: November 2023

ABSTRACT

Human leukocyte antigen (HLA) polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distributions can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency, and the impact of these variants on HIV disease outcome. HLA class I loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, antiretroviral treatment-naïve individuals from Honduras. HLA LD was assessed using Fisher’s exact test. Using univariable and multivariable analyses, we evaluated HLA associations with HIV plasma viral load (pVL) and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. The previously defined HLA associations were found to be
B*57:01/03
,
B*42:01
,
A*25:01
, and
C*12:03
(protective) and
B*53:01
and
A*68:01
(risk). Consistent with our previous research in a Mesoamerican HIV cohort, Amerindian
B*35:12
was associated with poor HIV control. Other HLA-HIV associations not previously described were
C*03:04
and
B*08:01
, which were associated with higher pVL. Overall, this first report highlights the immunogenetic uniqueness of the Honduras population that expresses Amerindian, Caucasian, and African HLA subtypes. These findings not only support this cohort as ideal for identifying HLA correlates of HIV control but also may improve future research regarding allotransplantation and disease association.

IMPORTANCE
We identify both canonical and novel human leukocyte antigen (HLA)-HIV associations, providing a first step toward improved understanding of HIV immune control among the understudied Honduras Mestizo population. Our results are relevant to understanding the protective or detrimental effects of HLA subtypes in Latin America because their unique HLA diversity poses challenges for designing vaccines against HIV and interpreting results from such vaccine trials. Likewise, the description of the HLA profile in an understudied population that shows a unique HLA immunogenetic background is not only relevant for HIV immunology but also relevant in population genetics, molecular anthropology, susceptibility to other infections, autoimmune diseases, and allograft transplantation.
Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China
Authors: Zhang Zhaojuan , Yang Yingkun , Zhao Jing , Li Yu , Stephenson Steven L. , Qiu Junzhi , Liu Pu 
Published: November 2023

ABSTRACT

Dictyostelid cellular slime molds (dictyostelids) are one of the major groups of eukaryotic amoeboid protists occurring in the soil microhabitat. The past few decades have witnessed an unprecedented interest in the ecology of dictyostelids, stimulated in part by the hidden soil protist diversity that has long been overlooked. However, a better understanding of the impact of various environmental factors on the biodiversity of dictyostelids is needed to understand the critical functional role of these organisms in the soil ecosystem. Species diversity of dictyostelids has been surveyed in some provinces of China, but little data exist for Gansu and Guizhou Provinces in western China. In this paper, we report data on the distribution and occurrence of dictyostelids in the soils of these two provinces. Samples were collected from 13 localities in central Gansu and the southeastern and southcentral portions of Guizhou Province. Eleven species of dictyostelids were recovered from 99 samples of soil. Six new records of dictyostelids are reported from Gansu Province and six species from Guizhou Province, respectively.
Polysphondylium violaceum
is a common species in both regions, while
Dictyostelium sphaerocephalum
and
Dictyostelium mucoroides
are widely distributed in Lanzhou, Gansu Province. The total number of species (seven) and the number of endemic species (three) of dictyostelids in mixed forests were higher than those in other forest types. Redundancy analysis indicated that soil pH, temperature, and elevation were the primary factors that affected dictyostelid occurrence. Nonmetric multidimensional scaling and principal component analysis indicated that the dictyostelid communities were significantly different between Gansu and Guizhou Provinces.

IMPORTANCE
Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.
Development of a touchdown droplet digital PCR assay for the detection and quantitation of human papillomavirus 16 and 18 from self-collected anal samples
Authors: Haqshenas Gholamreza , Garland Suzanne M. , Balgovind Prisha , Cornall Alyssa , Danielewski Jennifer , Molano Monica , Machalek Dorothy A. , Murray Gerald 
Published: November 2023

ABSTRACT

Broad-spectrum droplet digital polymerase chain reaction (ddPCR) assays can be used to quantitate multiple human papillomavirus (HPV) types. However, the presence of nucleotide mismatches at the primer binding sites may result in different optimal annealing temperatures and, consequently, under detection of some HPV types. Touchdown PCR uses decreasing annealing temperature over the first PCR cycles allowing for specific and efficient amplification of the target sequence. Here, as a proof-of-concept, we assessed if touchdown ddPCR (TD-ddPCR) using broad-spectrum oligonucleotides and genotype-specific probes targeting HPV L1 can be used to quantitate HPV. We tested our hypothesis using HPV positive cell lines and anal samples which potentially contain PCR inhibitors. Using serial dilutions of HPV16 and HPV18 DNA, the TD-ddPCR assays were performed with linearity across the dilution series (Pearson’s correlation
r
= 0.9999) and detected one copy of both HPV types, with no cross-reactivity to 27 other low-risk and high-risk HPV types. The PCRs were highly reproducible, with inter- and intra-assay coefficient of variations ranging 2.0–6.3% for HPV16 and 4.9–11.6% for HPV18. Testing self-collected anal samples positive for HPV16 (
n
= 29) or HPV18 (
n
= 33) and those negative for both HPV types (
n
= 22) with the ddPCR assay and Seegene Anyplex II HPV28 (Seegene, TD-ddPCR) showed high agreements between the two assays. In conclusion, HPV broad-spectrum primers containing mismatches at their target binding sites and a touchdown thermal cycling approach resulted in sensitive and specific amplification of HPV genome using ddPCR. The assay has potential clinical diagnostic applications for detection, quantitation, and monitoring of anal HPV infections.

IMPORTANCE
The quantity of the human papillomavirus (HPV) is associated with disease outcome. We designed an accurate and precise digital PCR assay for quantitating HPV in anal samples, a sample type that is typically problematic due to the presence of PCR inhibitors.