bluuebunny/crossref_metadata_2025 huggingface dataset:
Readability assessment of patient educational materials for pediatric spinal deformity from top academic orthopedic institutions
Authors: Michel Christopher , Dijanic Christopher , Abdelmalek George , Sudah Suleiman , Kerrigan Daniel , Gorgy George , Yalamanchili Praveen
Published: July 2022

Study design

Cross-sectional analysis of patient educational materials from top pediatric orthopedic hospital websites.

Objective

To assess the readability of online educational materials of top pediatric orthopedic hospital websites for pediatric spinal deformity.

Summary of background data

The internet has become an increasingly popular source of health information for patients and their families. Healthcare experts recommend that the readability of online education materials be at or below a 6th-grade reading level. However, previous studies have demonstrated that the readability of online education materials on various orthopedic topics is too advanced for the average patient. To date, the readability of online education materials for pediatric spinal deformity has not been analyzed.

Methods

Online patient education materials from the top 25 pediatric orthopedic institutions, as ranked by the U.S. News and World Report hospitals for pediatric orthopedics, were accessed utilizing the following readability assessments: Flesch–Kincaid (FK), Flesch Reading Ease, Gunning Fog Index, Coleman–Liau Index, Simple Measure of the Gobbledygook Index (SMOG), Automated Readability Index, FORCAST, and the New Dale and Chall Readability. Correlations between academic institutional ranking, geographic location, and the use of concomitant multi-media modalities with FK scores were evaluated using a Spearman regression.

Results

Only 48% (12 of 25) of top pediatric orthopedic hospitals provided online information regarding pediatric spinal deformity at or below a 6th-grade reading level. The mean FK score was 9.0 ± 2.7, Flesch Reading Ease 50.8 ± 15.6, Gunning Fog Score 10.6 ± 3.1, Coleman–Liau Index 11.6 ± 2.6, SMOG index 11.7 ± 2.0, Automated Readability Index 8.6 ± 2.8, and Dale–Chall Readability Score 6.4 ± 1.4. There was no significant correlation between institutional ranking, geographic location, or use of multimedia with FK scores.

Conclusion

Online educational material for pediatric spinal deformity from top pediatric orthopedic institutional websites are associated with poor readability.
Environmental cleaning and disinfection: Sustaining changed practice and improving quality in the community hospital
Authors: Parry Michael F. , Sestovic Merima , Renz Christopher , Pangan Abegail , Grant Brenda , Shah Asha K.
Published: July 2022

Objective:

Short-term improvements in hospital room cleaning can readily be achieved but are difficult to maintain. This is particularly true for high-risk, “high-touch” surfaces. Therefore, we embarked on a process to sustain improvements in surface cleaning and disinfection to reduce hospital-acquired infection (HAI) rates.

Interventions:

Our environmental services (EVS) and infection prevention departments incorporated a formal education, monitoring, and feedback process for focused cleaning and disinfection of high-touch surfaces into their routine policies and procedures in 2011. Cleaning validation was performed by infection prevention liaison nurses using a fluorescent targeting method to evaluate the thoroughness of cleaning.

Results:

Surface cleaning performance on medical-surgical units in 2011 was 74.7%, but this rate incrementally increased in response to the interventions and has been sustained at >90% for the past 6 years. Similar patterns of improvement were observed in the operating room, labor and delivery, endoscopy suite and cardiac catheterization laboratory. Conversely, HAI rates, particularly C. difficile rates, decreased by 75% and surgical site infection rates decreased by 55%.

Conclusions:

EVS training, monitoring, and feedback interventions, instituted 10 years ago have enhanced our environmental cleaning and disinfection efforts in multiple areas of the hospital and have been sustained to the present. Although other concurrent initiatives to reduce infection rates also existed, the improvements in environmental cleaning were associated with dramatic reductions in HAI rates over the 10-year period.
Shallow mixing interfaces between parallel streams of unequal densities
Authors: Cheng Zhengyang , Constantinescu George
Published: July 2022

As opposed to the case of shallow mixing layers forming between parallel streams of unequal velocities and equal densities, the spatial development of the mixing interface (MI) between two parallel streams of unequal velocities and sufficiently large density contrast is controlled by the formation of a spatially developing, lock-exchange-like flow in transverse planes. Buoyancy effects are driven by the presence of a vertical density interface near the splitter plate. Eddy-resolving numerical simulations conducted in a wide and very long channel are used to investigate the mean flow structure and the effects of the lock-exchange-like flow and the associated coherent structures on mixing and the capacity of the flow to entrain sediment from the channel bed. When the two streams have unequal densities, quasi-two-dimensional Kelvin–Helmholtz (KH) vortices still form near the MI origin, but their coherence is lost over a much shorter distance compared with the case with no density contrast, and their cores are severely stretched in the transverse direction. A main cell of recirculating (cross-) flow forms in the mean flow, in between the fronts of the near-bed intrusion of heavier fluid and the free-surface intrusion of lighter fluid. The instantaneous flow fields contain streamwise-oriented vortical cells along the interface separating the regions containing heavier and lighter fluids. These vortical cells play an important role in enhancing mixing, similar to the KH billows forming in a classical lock-exchange flow. The regions of highest turbulence amplification are situated next to the boundaries of the main recirculating cell. Once the oscillating fronts of the intrusions get sufficiently close to the channel sidewalls, streamwise cells of secondary flow form near the channel boundaries. For cases with a strong density contrast, the free-surface mixing pattern is not a good indicator of mixing between the two streams. For the same flow velocities in the incoming channels, the two streams mix faster with increasing density difference between the two streams. This is because, as opposed to the KH vortices, coherent structures induced by the formation of the lock-exchange-like flow maintain their coherence and capacity to induce mixing at very large distances from the splitter plate. Meanwhile, the redistribution of the streamwise momentum leading to uniform, fully developed flow over the whole cross-section is delayed by buoyancy effects. Away from the splitter plate, the region with the highest sediment entrainment potential is situated next to the edge of the main recirculation cell on the high-speed side of the channel. For the same flow velocities in the incoming channels, the sediment entrainment capacity of the flow is much larger in the simulations conducted with density contrast between the incoming streams and peaks for the case when the faster stream contains the denser fluid.
Development and initial validation of a multivariable predictive Early Adversity Scale for Schizophrenia (EAS-Sz) using register data to quantify environmental risk for adult schizophrenia diagnosis after childhood exposure to adversity
Authors: Di Prinzio Patsy , Björk Jonas , Valuri Giulietta , Ambrosi Taryn , Croft Maxine , Morgan Vera A.
Published: July 2022

Background

Additional to a child's genetic inheritance, environmental exposures are associated with schizophrenia. Many are broadly described as childhood adversity; modelling the combined impact of these is complex. We aimed to develop and validate a scale on childhood adversity, independent of genetic and other environmental liabilities, for use in schizophrenia risk analysis models, using data from cross-linked electronic health and social services registers.

Method

A cohort of N = 428 970 Western Australian children born 1980–2001 was partitioned into three samples: scale development sample (N = 171 588), and two scale validation samples (each N = 128 691). Measures of adversity were defined before a child's 10th birthday from five domains: discontinuity in parenting, family functioning, family structure, area-level socioeconomic/demographic environment and family-level sociodemographic status. Using Cox proportional hazards modelling of follow-up time from 10th birthday to schizophrenia diagnosis or censorship, weighted combinations of measures were firstly developed into scales for each domain, then combined into a final global scale. Discrimination and calibration performance were validated using Harrell's C and graphical assessment respectively.

Results

A weighted combination of 42 measures of childhood adversity was derived from the development sample. Independent application to identical measures in validation samples produced Harrell's Concordance statistics of 0.656 and 0.624. Average predicted time to diagnosis curves corresponded with 95% CI limits of observed Kaplan–Meier curves in five prognostic categories.

Conclusions

Our Early Adversity Scale for Schizophrenia (EAS-Sz), the first using routinely collected register data, predicts schizophrenia diagnosis above chance, and has potential to help untangle contributions of genetic and environmental liability to schizophrenia risk.
Relational Care, Dementia, and Communication Challenges in Long-Term Care: A Meta-Ethnography
Authors: Novy Christine , Thomas Roanne , Grassau Pamela , Gifford Wendy , Hosseini Marjan
Published: July 2022

Few studies examine care as a relational process in long-term care, and still fewer describe the participation of residents with dementia. In this article, our objective was to understand the development of knowledge in this area by means of a meta-ethnography. Our search and selection process resulted in six eligible articles. Each documents a qualitative study of resident–staff interactions during care activities in a residential care setting, and includes participants with dementia. Tronto’s 4 Phases of Care were used to guide the identification of relational care practices within the articles selected. We identified five translatable concepts across the six studies: (1) doing with versus doing for, (2) staff responsiveness, (3) resident agency, (4) inclusive communication, and (5) time. In our new configuration of relational care, we combine these concepts to delineate an “interactive space” in which the agency of residents and initiative of staff are equally visible.
The Annual Global Incidence Rate of Extreme Weather Event Disasters Appears Positively Correlated with World GDP, 1961–2020
Authors: Keim Mark E. , Smith Thomas More , Burkle Frederick M.
Published: July 2022

Objective:

This study compared the per capita annual global incidence rate of disasters caused by natural hazards with the annual world real gross domestic product, GDP (per global capita), as reported during 1961 through 2020.

Methods:

Sixty (60) values for the world real GDP per global capita (in constant 2015 $USD) were compared to corresponding annual values for global incidence rates for five natural disaster subgroups and then for a total of twelve individual disaster types that comprise the subgroups; each expressed as an annual global incidence rate (in terms of annual incidence per 100,000 persons). Calculations of multiple linear regression, ANOVA, and Pearson’s correlation coefficient were performed for comparing population-adjusted values for GDP to corresponding values.

Results:

Four out of five hydrological and meteorological disasters were found to have a positive correlation with GDP. Results of the analysis revealed a relatively high degree of correlation between world GDP and the annual incidence of flood and storm disasters (P = 6.21 × 10−10 and P = 4.23 × 10−4, respectively). The annual incidence of heat waves and cold weather disasters also appeared to correlate with GDP (P = .002 and P = .019, respectively). In comparison, wet landslides indicated no such correlation (P = .862). No significant associations were found among the seven other individual biological, climatological, and geophysical disasters and GDP.

Conclusion:

The global incidence of four extreme weather (hydrometeorological) disasters appear to be positively associated with world real GDP during 1961-2020. These findings contradict previous postulates that the risk of disaster incidence is inversely associated with the capacity of the population.
The Neonatal Palliative Care Attitude Scale: Psychometric properties for Portuguese neonatal nurses
Authors: Sousa Fátima Pacheco , Roldão Maria Graça , Rebotim Ana Marisa , Figueira Ana Rita , Barbosa Joana , Fradique Emília , Santos Curado Maria Alice
Published: July 2022

Background

This study is aimed to perform the translation and cultural adaptation of the Neonatal Palliative Care Attitude Scale (NiPCAS) and evaluation of its psychometric properties with Portuguese neonatal nurses.

Methods

The research started with a scoping review that allowed the identification of the NiPCAS. It was a methodological study with a quantitative approach. The semantic equivalence of the items was adjusted with the participation of 20 neonatal nurse experts. They performed facial and quantitative content validation. Psychometric validation of the NiPCAS was performed on a nonprobability nurses sample (n = 283) in 13 level 3 neonatal units between July 2021 and February 2022. Confirmatory factor analysis using the polychoric correlation matrix was performed to estimate factor validity using the “lavaan” package for R statistical software. Internal consistency was estimated using Cronbach's alpha coefficient, and item sensitivity was assessed using the asymmetry and kurtosis coefficients. Empirical indices were considered: chi-square over degrees of freedom; comparative fit index; normed fit index; Tucker–Lewis index, and root mean square error of approximation; average extracted variance and composite reliability were used to assess convergent validity.

Results

Asymmetry and kurtosis were <|3| and <|7|, respectively, suggesting psychometric sensitivity. The convergent validity of the factors was: F1, FCF1 = 0.90 and for F2, FCF2 = 0.80, and a lower value for F3, FCF3 = 0.40. According to the squared correlation criterion average variance extracted (AVE) between the factors, there was no discriminant validity for F1 and F2, but there was discriminant validity for F1, F3, F2, and F3.

Significance of results

This instrument has implications for providing end-of-life care to newborns and their families. The use of this instrument reveals several barriers and facilitating elements inherent in the organization and culture of the facility and nursing education.
Donald T. Campbell on the institutions of scientific knowledge and the limits to interdisciplinarity
Authors: Hodgson Geoffrey M.
Published: July 2022

Extracts from an important article by the American psychologist, philosopher and social scientist Donald T. Campbell are reproduced here, with an introduction underlining the importance of his argument for today. Campbell identified disciplinary boundaries as enablers of specialization but often barriers to scientific innovation and shared knowledge. But instead of unbounded interdisciplinarity, Campbell argued for focused specialisms that cross disciplinary boundaries. This argument is particularly relevant for the development of institutional research in the future.
Quantifying Interdependencies in Geyser Eruptions at the Upper Geyser Basin, Yellowstone National Park
Authors: Fagan William F. , Swain Anshuman , Banerjee Amitava , Ranade Hamir , Thompson Peter , Staniczenko Phillip P. A. , Flynn Barrett , Hungerford Jefferson , Hurwitz Shaul
Published: July 2022

The Upper Geyser Basin at Yellowstone National Park (Wyoming, USA) harbors the greatest concentration of geysers worldwide. Research suggests that individual geysers are not isolated but rather are hydraulically connected in the subsurface with other geysers and thermal springs. To quantify such connections, we combined techniques from machine learning, causal inference, and dynamical systems to characterize the collective eruptive behavior of a set of 10 geysers over 18 months (April 2007 – September 2008) focusing on geyser‐geyser interactions. Model predictions were up to 15 times more accurate when we sought to predict a geyser's eruption time series based on outflow channel temperatures from the network than based on its own time series alone, suggesting the existence of a complex interconnected subsurface groundwater system. On average, cone‐type geysers had larger impacts on other geysers than did fountain‐type geysers. Similarly, cone‐type geysers were on average more insulated from other geysers. However, substantial unexplained variation remained after considering the cone versus fountain dichotomy. Distance between geysers also affected interactions: nearby geysers had stronger effects on focal geysers than did geysers located farther away. Collectively, results support the hypothesis of geyser interdependence at timescales of 5 min–10 days. Our analyses highlight the existence of quantifiable geyser‐to‐geyser interactions that can be resolved through pairwise and system‐level analyses. These findings emphasize the subsurface interconnectedness of thermal features, provide information relevant to visitor experiences in Yellowstone National Park, and suggest strategies for exploring patterns of interdependence that may exist among other episodic geological phenomena.
Flocculation of Riverine Sediment Draining to the Great Barrier Reef, Implications for Monitoring and Modeling of Sediment Dispersal Across Continental Shelves
Authors: Livsey D. N. , Crosswell J. R. , Turner R. D. R. , Steven A. D. L. , Grace P. R.
Published: July 2022

Sediment transport models, utilized to guide land management in the Great Barrier Reef (GBR), assume settling velocities for individual silt and clay particles on the order of 0.01 mm/s; however, silts and clays once flocculated exhibit settling velocities on the order of 1 mm/s. In this study, in‐situ (n = 144,912) and laboratory‐dispersed (n = 64) particle size measurements collected using laser diffractometry were compared from nine rivers discharging along 800 km of GBR coastline to determine the extent of in‐situ flocculation. Environmental controls on in‐situ particle size were investigated using decision tree algorithms trained on coeval measurements of salinity, shear rate, and turbidity. Comparison of in‐situ and dispersed particle size measurements demonstrate that suspended‐sediment across all catchments flocculated into larger aggregates with an order‐of‐magnitude difference in median particle size between in‐situ (D50v = 132 μm, σ = 60 μm for all data) and dispersed (D50v = 15 μm, σ = 11 μm for all data) particles. Machine learning algorithms showed excellent promise predicting various measures of in‐situ particle size. Model validation R2 ranged from 0.72 to 0.99, inclusion of catchment as a categorical variable only marginally (<1%) increased R2. These results demonstrate that flocculation is prevalent across all rivers surveyed and that hydrodynamics are more important than inter‐catchment differences (e.g., differences in climate, geology, or land‐use). Implications of widespread flocculation on the determination of end‐of‐catchment sediments loads and subsequent dispersal patterns across continental shelves are discussed to inform the refinement and monitoring of GBR sediment targets.
Observations of Atmospheric Tides in the Middle and Upper Atmosphere of Mars From MAVEN and MRO
Authors: Kumar Aishwarya , England Scott L. , Liu Guiping , Jain Sonal , Schneider Nicholas M.
Published: July 2022

Variability in the Martian upper atmosphere is strongly linked to the lower atmosphere and much of it can be attributed to vertical wave propagation. Atmospheric tides in particular are a well‐known phenomenon in the Martian atmosphere that play a key role in the transport of energy as they propagate to higher altitudes. Previous theoretical predictions and observations suggest that tides producing wavenumber‐2 and wavenumber‐3 patterns are strongest in a fixed local time at high altitudes, however, the energy they carry and the region of deposition are not well characterized. Given the availability of atmospheric observations from several spacecraft at the same time, in this paper, the nature and behavior of tides are studied concurrently at several altitudes. Here, six intervals are identified focused at fixed low latitudes utilizing simultaneous observations of the middle and upper atmosphere from in situ and remote sensing instruments on different spacecraft. In the middle atmosphere, strong wavenumber‐2 signatures are identified in the intervals north of the equator whereas, in the south, wavenumber‐3 signatures are strongest. Wave signatures observed in the upper atmosphere seem to be dominated by a mix of wavenumbers‐2 and ‐3. Seasonal variation is observed in the northern intervals, with very little interannual variability in all intervals considered. Estimates of energy based on dominant wavenumber amplitude suggest that most of the energy dissipates below ∼90 km. Furthermore, model sampled output captures the dominant wavenumbers observed in the middle atmosphere as well as the energy dissipation characteristics.
Disentangling the Relative Drivers of Seasonal Evapotranspiration Across a Continental‐Scale Aridity Gradient
Authors: Young Adam M. , Friedl Mark A. , Novick Kimberly , Scott Russell L. , Moon Minkyu , Frolking Steve , Li Xiaolu , Carrillo Carlos M. , Richardson Andrew D.
Published: July 2022

Evapotranspiration (ET) is a significant ecosystem flux, governing the partitioning of energy at the land surface. Understanding the seasonal pattern and magnitude of ET is critical for anticipating a range of ecosystem impacts, including drought, heat‐wave events, and plant mortality. In this study, we identified the relative controls of seasonal variability in ET, and how these controls vary among ecosystems. We used overlapping AmeriFlux and PhenoCam time series at a daily timestep from 20 sites to explore these linkages (# site‐years >100), and our study area covered a broad climatological aridity gradient in the U.S. and Canada. We focused on disentangling the most important controls of bulk surface conductance (Gs) and evaporative fraction (EF = LE/[H + LE]), where LE and H represent latent and sensible heat fluxes, respectively. Specifically, we investigated how vegetation phenology varied in importance relative to meteorological variables (vapor pressure deficit and antecedent precipitation) as a driver of Gs and EF using path analysis, a framework for quantifying and comparing the causal linkages among multiple response and explanatory variables. Our results revealed that the drivers of Gs and EF seasonality varied significantly between energy‐ and water‐limited ecosystems. Specifically, precipitation had a much higher effect in water‐limited ecosystems, while seasonal patterns in canopy greenness emerged as a stronger control in energy‐limited ecosystems. Given that phenology is expected to shift under future climate, our findings provide key information for understanding and predicting how phenology may impact 21st‐century hydroclimate regimes and the surface‐energy balance.
MicroRNA-21 is immunosuppressive and pro-metastatic via separate mechanisms
Authors: Chi Lap Hing , Cross Ryan S. N. , Redvers Richard P. , Davis Melissa , Hediyeh-zadeh Soroor , Mathivanan Suresh , Samuel Monisha , Lucas Erin C. , Mouchemore Kellie , Gregory Philip A. , Johnstone Cameron N. , Anderson Robin L.
Published: July 2022

MiR-21 was identified as a gene whose expression correlated with the extent of metastasis of murine mammary tumours. Since miR-21 is recognised as being associated with poor prognosis in cancer, we investigated its contribution to mammary tumour growth and metastasis in tumours with capacity for spontaneous metastasis. Unexpectedly, we found that suppression of miR-21 activity in highly metastatic tumours resulted in regression of primary tumour growth in immunocompetent mice but did not impede growth in immunocompromised mice. Analysis of the immune infiltrate of the primary tumours at the time when the tumours started to regress revealed an influx of both CD4+ and CD8+ activated T cells and a reduction in PD-L1+ infiltrating monocytes, providing an explanation for the observed tumour regression. Loss of anti-tumour immune suppression caused by decreased miR-21 activity was confirmed by transcriptomic analysis of primary tumours. This analysis also revealed reduced expression of genes associated with cell cycle progression upon loss of miR-21 activity. A second activity of miR-21 was the promotion of metastasis as shown by the loss of metastatic capacity of miR-21 knockdown tumours established in immunocompromised mice, despite no impact on primary tumour growth. A proteomic analysis of tumour cells with altered miR-21 activity revealed deregulation of proteins known to be associated with tumour progression. The development of therapies targeting miR-21, possibly via targeted delivery to tumour cells, could be an effective therapy to combat primary tumour growth and suppress the development of metastatic disease.
Time moderates the interplay between 5-HTTLPR and stress on depression risk: gene x environment interaction as a dynamic process
Authors: Delli Colli Claudia , Borgi Marta , Poggini Silvia , Chiarotti Flavia , Cirulli Francesca , Penninx Brenda W. J. H. , Benedetti Francesco , Vai Benedetta , Branchi Igor
Published: July 2022

The serotonin-transporter-linked promoter region (5-HTTLPR) has been widely investigated as contributing to depression vulnerability. Nevertheless, empirical research provides wide contrasting findings regarding its involvement in the etiopathogenesis of the disorder. Our hypothesis was that such discrepancy can be explained considering time as moderating factor. We explored this hypothesis, exploiting a meta analytic approach. We searched PubMed, PsychoINFO, Scopus and EMBASE databases and 1096 studies were identified and screened, resulting in 22 studies to be included in the meta-analyses. The effect of the 5-HTTLPR x stress interaction on depression risk was found to be moderated by the following temporal factors: the duration of stress (i.e. chronic vs. acute) and the time interval between end of stress and assessment of depression (i.e. within 1 year vs. more than 1 year). When stratifying for the duration of stress, the effect of the 5-HTTLPR x stress interaction emerged only in the case of chronic stress, with a significant subgroup difference (p = 0.004). The stratification according to time interval revealed a significant interaction only for intervals within 1 year, though no difference between subgroups was found. The critical role of time interval clearly emerged when considering only chronic stress: a significant effect of the 5-HTTLPR and stress interaction was confirmed exclusively within 1 year and a significant subgroup difference was found (p = 0.01). These results show that the 5-HTTLPR x stress interaction is a dynamic process, producing different effects at different time points, and indirectly confirm that s-allele carriers are both at higher risk and more capable to recover from depression. Overall, these findings expand the current view of the interplay between 5-HTTLPR and stress adding the temporal dimension, that results in a three-way interaction: gene x environment x time.
Hydroxylation of the NOTCH1 intracellular domain regulates Notch signaling dynamics
Authors: Ferrante Francesca , Giaimo Benedetto Daniele , Friedrich Tobias , Sugino Toshiya , Mertens Daniel , Kugler Sabrina , Gahr Bernd Martin , Just Steffen , Pan Leiling , Bartkuhn Marek , Potente Michael , Oswald Franz , Borggrefe Tilman
Published: July 2022

Notch signaling plays a pivotal role in the development and, when dysregulated, it contributes to tumorigenesis. The amplitude and duration of the Notch response depend on the posttranslational modifications (PTMs) of the activated NOTCH receptor – the NOTCH intracellular domain (NICD). In normoxic conditions, the hydroxylase FIH (factor inhibiting HIF) catalyzes the hydroxylation of two asparagine residues of the NICD. Here, we investigate how Notch-dependent gene transcription is regulated by hypoxia in progenitor T cells. We show that the majority of Notch target genes are downregulated upon hypoxia. Using a hydroxyl-specific NOTCH1 antibody we demonstrate that FIH-mediated NICD1 hydroxylation is reduced upon hypoxia or treatment with the hydroxylase inhibitor dimethyloxalylglycine (DMOG). We find that a hydroxylation-resistant NICD1 mutant is functionally impaired and more ubiquitinated. Interestingly, we also observe that the NICD1-deubiquitinating enzyme USP10 is downregulated upon hypoxia. Moreover, the interaction between the hydroxylation-defective NICD1 mutant and USP10 is significantly reduced compared to the NICD1 wild-type counterpart. Together, our data suggest that FIH hydroxylates NICD1 in normoxic conditions, leading to the recruitment of USP10 and subsequent NICD1 deubiquitination and stabilization. In hypoxia, this regulatory loop is disrupted, causing a dampened Notch response.
Cumulative cultural evolution and mechanisms for cultural selection in wild bird songs
Authors: Williams Heather , Scharf Andrew , Ryba Anna R. , Ryan Norris D. , Mennill Daniel J. , Newman Amy E. M. , Doucet Stéphanie M. , Blackwood Julie C.
Published: July 2022

Cumulative cultural evolution, the accumulation of sequential changes within a single socially learned behaviour that results in improved function, is prominent in humans and has been documented in experimental studies of captive animals and managed wild populations. Here, we provide evidence that cumulative cultural evolution has occurred in the learned songs of Savannah sparrows. In a first step, “click trains” replaced “high note clusters” over a period of three decades. We use mathematical modelling to show that this replacement is consistent with the action of selection, rather than drift or frequency-dependent bias. Generations later, young birds elaborated the “click train” song form by adding more clicks. We show that the new songs with more clicks elicit stronger behavioural responses from both males and females. Therefore, we suggest that a combination of social learning, innovation, and sexual selection favoring a specific discrete trait was followed by directional sexual selection that resulted in naturally occurring cumulative cultural evolution in the songs of this wild animal population.
Time diffraction-free transverse orbital angular momentum beams
Authors: Chen Wei , Zhang Wang , Liu Yuan , Meng Fan-Chao , Dudley John M. , Lu Yan-Qing
Published: July 2022

The discovery of optical transverse orbital angular momentum (OAM) has broadened our understanding of light and is expected to promote optics and other physics. However, some fundamental questions concerning the nature of such OAM remain, particularly whether they can survive from observed mode degradation and hold OAM values higher than 1. Here, we show that the strong degradation actually origins from inappropriate time-delayedkx–ωmodulation, instead, for transverse OAM having inherent space-time coupling, immediate modulation is necessary. Thus, using immediatex–ωmodulation, we demonstrate theoretically and experimentally degradation-free spatiotemporal Bessel (STB) vortices with transverse OAM even beyond 102. Remarkably, we observe a time-symmetrical evolution, verifying pure time diffraction on transverse OAM beams. More importantly, we quantify such nontrivial evolution as an intrinsic dispersion factor, opening the door towards time diffraction-free STB vortices via dispersion engineering. Our results may find analogues in other physical systems, such as surface plasmon-polaritons, superfluids, and Bose-Einstein condensates.
Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
Authors: Jelley Lauren , Douglas Jordan , Ren Xiaoyun , Winter David , McNeill Andrea , Huang Sue , French Nigel , Welch David , Hadfield James , de Ligt Joep , Geoghegan Jemma L.
Published: July 2022

New Zealand’s COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.
Body weight index indicates the responses of the fecal microbiota, metabolome and proteome to beef/chicken-based diet alterations in Chinese volunteers
Authors: Zhao Di , Shan Kai , Xie Yunting , Zhang Guanghong , An Qi , Yu Xiaobo , Zhou Guanghong , Li Chunbao
Published: July 2022

Relationships between meat consumption and gut diseases have been debated for decades, and the gut microbiota plays an important role in this interplay. It was speculated that the gut microbiota and relevant indicators of hosts with different body weight indexes (BMIs) might respond differentially to meat-based diet alterations, since lean and obese hosts have different gut microbiota composition. Forty-five young Chinese volunteers were recruited and assigned to high-, middle- and low-BMI groups. All of the volunteers were given a beef-based diet for 2 weeks and subsequently with a chicken-based diet for another 2 weeks. Body weight and blood indexes were measured, and fecal samples were obtained for 16S rRNA sequencing, metabolome and proteome analyses. The fecal metabolites of the low-BMI volunteers showed greater sensitivity to meat-based diet alterations. In contrast, the fecal proteome profiles and blood indexes of the high- and middle-BMI volunteers indicated greater sensitivity to meat-based diet alterations. Replacing the beef-based diet with the chicken-based diet largely changed operational taxonomic units of Bacteroides genus, and thus probably induced downregulation of immunoglobulins in feces. Compared with the beef-based diet, the chicken-based diet decreased inflammation-related blood indexes, especially in high- and middle-BMI volunteers. This work highlighted the role of BMI as an important factor predicting changes in gut homeostasis in response to meat consumption. Compared with the chicken-based diet, the beef-based diet may induce more allergic and inflammation-related responses in high- and middle- BMI Chinese at the current level.
Insulator-to-metal transition in ultrathin rutile VO2/TiO2(001)
Authors: Lahneman D. J. , Slusar Tetiana , Beringer D. B. , Jiang Haoyue , Kim Chang-Yong , Kim Hyun-Tak , Qazilbash M. M.
Published: July 2022

An insulator-to-metal transition (IMT) is an emergent characteristic of quantum materials. When the IMT occurs in materials with interacting electronic and lattice degrees of freedom, it is often difficult to determine if the energy gap in the insulating state is formed by Mott electron–electron correlation or by Peierls charge-density wave (CDW) ordering. To solve this problem, we investigate a representative material, vanadium dioxide (VO2), which exhibits both strong electron–electron interaction and CDW ordering. For this research, VO2 films of different thicknesses on rutile (001) TiO2 substrates have been fabricated. X-ray diffraction (XRD) data show that ultrathin VO2 films with thickness below 7.5 nm undergo the IMT between rutile insulator below Tc and rutile metal above Tc, while an ultrathin VO2 film with a thickness of 8 nm experiences the structural phase transition from the monoclinic structure below Tc to the rutile structure above Tc. Infrared and optical measurements on a film of 7.2 nm thickness, below Tc, reveal the energy gap of 0.6 eV in the rutile insulator phase and the absence of the 2.5 eV bonding-antibonding CDW structure. Above Tc, a Drude feature in the optical conductivity reveals the IMT to a metallic phase. These results suggest that for VO2 films below a critical thickness of about 7.5 nm, the IMT occurs in the rutile structure of VO2 without the Peierls lattice distortion.
Effects of feeding mode on the performance, life span and greenhouse gas emissions of a vertical flow macrophyte assisted vermifilter
Authors: Singh Rajneesh , Ray Chittaranjan , Miller Daniel N. , Durso Lisa M. , Meneses Yulie , Bartelt-Hunt Shannon , D’Alessio Matteo
Published: July 2022

This study was conducted to investigate the impact of intermittent feeding on performance, clogging, and gaseous emission on macrophyte assisted vermifiltration (MAVF) based treatment system. Synthetic slaughterhouse wastewater was applied to two different integrated vertical flow based MAVFs. Triplicates were used throughout the study. Eisenia fetida earthworms were added to MAVFs, and Carex muskingmenis plants were planted. Wastewater was applied to the reactors on 1) intermittent (8 h/day) (IMAVF) and 2) continuous (24 h/day) (CMAVF) basis. The average chemical oxygen demand, total nitrogen, and total phosphorous removals achieved by the IMAVF were 80.2 ± 1.6%, 53.9 ± 1.3% and 66.5 ± 1% respectively, and 68.3 ± 1.3%, 61.2 ± 1.4%, and 60.5 ± 1.4% by the CMAVF, respectively. The diffusion of air to the bedding of IMAVFs during no-flow conditions facilitated higher organics oxidation, adsorption of phosphorous, nitrification, and ammonification. At the end of the study, hydraulic conductivity of IMAVF and CMAVF were found to be 0.036 cm/s and 0.037 cm/s, respectively. CO2, CH4 and N2O emissions from IMAVF were 245.5 ± 38.0 mg C/m2, 5.0 ± 4.6 mg C/m2 and 2513.5 ± 2629.9 μg N/m2 respectively, while CO2, CH4 and N2O emissions from CMAVF were 123.3 ± 14.5 mg C/m2, 74.8±45.2 mg C/m2 and 328.4 ± 93.4 μg N/m2, respectively. Intermittent application of influent could be considered for improving the performance and lifespan of MAVFs, causing lower environmental footprints.
The heterogeneous pharmacological medical biochemical network PharMeBINet
Authors: Königs Cassandra , Friedrichs Marcel , Dietrich Theresa
Published: July 2022

Heterogeneous biomedical pharmacological databases are important for multiple fields in bioinformatics. Hetionet is a freely available database combining diverse entities and relationships from 29 public resources. Therefore, it is used as the basis for this project. 19 additional pharmacological medical and biological databases such as CTD, DrugBank, and ClinVar are parsed and integrated into Neo4j. Afterwards, the information is merged into the Hetionet structure. Different mapping methods are used such as external identification systems or name mapping. The resulting open-source Neo4j database PharMeBINet has 2,869,407 different nodes with 66 labels and 15,883,653 relationships with 208 edge types. It is a heterogeneous database containing interconnected information on ADRs, diseases, drugs, genes, gene variations, proteins, and more. Relationships between these entities represent drug-drug interactions or drug-causes-ADR relations, to name a few. It has much potential for developing further data analyses including machine learning applications. A web application for accessing the database is free to use for everyone and available at https://pharmebi.net. Additionally, the database is deposited on Zenodo at https://doi.org/10.5281/zenodo.6578218.
Intratracheal administration of mesenchymal stem cells modulates lung macrophage polarization and exerts anti-asthmatic effects
Authors: Mo Yosep , Kang Hanbit , Bang Ji-Young , Shin Jae Woo , Kim Hye Young , Cho Sang-Heon , Kang Hye-Ryun
Published: July 2022

Mesenchymal stem cells (MSCs) possess immunomodulatory properties that have therapeutic potential for the treatment of inflammatory diseases. This study investigates the effects of direct MSC administration on asthmatic airways. Umbilical cord MSCs (ucMSCs) were intratracheally administered to six-week-old female BALB/c mice sensitized and challenged with ovalbumin; airway hyperresponsiveness (AHR), analyses of airway inflammatory cells, lung histology, flow cytometry, and quantitative real-time PCR were performed. Furthermore, ex vivo and in vitro experiments were performed to assess the effects of ucMSC on M2 activation. Intratracheally administered ucMSCs decreased degree of airway resistance and the number of inflammatory cells such as T helper 2 (Th2) cells, type 2 innate lymphoid cells (ILC2), and macrophages in the murine asthma model. Particularly, MHCII and CD86 expression diminished in dendritic cells and alveolar macrophages (AMs) following ucMSC treatment. SiglecF+CD11c+CD11b- AMs show a negative correlation with type II inflammatory cells including Th2 cells, ILC2, and eosinophils in asthmatic mice and were restored following intratracheal ucMSCs treatment. In addition, ucMSCs decreased the macrophage polarization to M2, particularly M2a. The expression levels of markers associated with M2 polarization and Th2 inflammation were also decreased. ucMSC reduced Il-12 and Tnfa expression as well as that of M2 markers such as Cd206 and Retnla ex vivo. Furthermore, the in vitro study using IL-4 treated macrophages confirmed that both direct and indirect MSC treatment significantly reduced the expression of Il-5 and Il-13. In conclusion, ucMSCs appear to suppress type II inflammation by regulating lung macrophages via soluble mediators.
Clock-hour topography and extent of outer retinal damage in hydroxychloroquine retinopathy
Authors: Kim Ko Eun , Kim Ji Hong , Kim Young Hwan , Ahn Seong Joon
Published: July 2022

In this study, we investigated the clock-hour topographic characteristics and extent of photoreceptor and retinal pigment epithelium (RPE) damage and correlated the extent with functional defects in eyes with hydroxychloroquine retinopathy. A total of 146 eyes of 75 patients diagnosed with hydroxychloroquine retinopathy were included. The clock-hour topographic characteristics (relative to the fovea) and extent of the photoreceptor and RPE defects in the parafoveal and pericentral areas were evaluated by reviewing the radial-scan optical coherence tomography (OCT) and wide-field fundus autofluorescence (FAF) images. The extent of outer retinal damage in the parafoveal and pericentral areas were correlated with the perimetric parameters of the Humphrey 10–2 and 30–2 tests, respectively. Although the photoreceptor damage was most commonly noted at the temporal to inferior locations in both parafoveal and pericentral areas, the RPE damage in the pericentral eyes was most commonly noted in the nasal area and showed topographic discrepancies with photoreceptor damage. The extent of RPE damage was almost identical between OCT and FAF images, whereas photoreceptor defect extent was significantly greater on OCT images. The extent of parafoveal and pericentral photoreceptor damage on OCT images was significantly correlated with perimetric parameters of the 10–2 and 30–2 tests, respectively (all P < 0.05). Our findings on the detailed topographic characteristics using a clock-hour-based system and significant correlation between the structural extent and perimetric parameters suggest that this evaluation may facilitate more comprehensive descriptions of structural damage extent and predictions of visual function.
The CD226/TIGIT axis is involved in T cell hypo-responsiveness appearance in long-term kidney transplant recipients
Authors: Del Bello Arnaud , Gouin Anna , Chaubet Camille , Kamar Nassim , Treiner Emmanuel
Published: July 2022

T cell exhaustion refers to a dysfunctional state in which effector T cells present a decreased ability to proliferate and to produce cytokines, while the co-expression of inhibitory receptors increases. We investigated global and donor-specific T cell responses in a cohort of stable, living-donor kidney transplant patients that received similar immunosuppression. After transplantation, an increase in the ratio of TIGIT + /CD226 + in mCD4 + T cells (r = 0.47, p = 0.01), and a decrease of CD226 + TIGIT-mCD4 + T cells was observed (r = − 0.55, p = 0.001). This leads to an increase of dysfunctional T cells in patients far from transplantation. In mCD8 + T cells, a decrease of IL-2 production after mitogenic stimulation was observed far from transplantation. Phenotypic analyses revealed an increase of mCD8 + T cells co-expressing PD-1 and TIGIT over time (r = 0.51, p = 0.02). After donor-specific stimulation, the ability of CD4 + T cells to proliferate was decreased compared with third parties. CD4 + T cells expressing CD226 and TIGIT were correlated with allospecific CD4 + proliferation (r = 0.68, p = 0.04). Our study suggests that after kidney transplantation a T cell hyporesponsiveness appears over time, driven by a dysregulation of CD226/TIGIT axis in mCD4 + T cells, associated with an increase of PD1 + TIGIT + in mCD8 + T cells.
Lossy and noisy channel simulation in computational ghost imaging by using noise-induced pattern
Authors: Heo Jaesung , Kim Junghyun , Jeong Taek , Lee Sangkyung , Ihn Yong Sup , Kim Zaeill , Jo Yonggi
Published: July 2022

We provide a method to evaluate effects of a lossy and noisy optical channel in computational ghost imaging (CGI) technique. Instead of preparing an external noise source, we simulate the optical channel with a basic CGI experiment using programmatically generated noise-induced patterns. By using our method, we show that CGI can reject a noise of which intensity is similar with an imaging signal intensity at a target. The results with our method are well matched with experimental ones including external noise source. This method would provide useful knowledge to analyze environmental effects in CGI without realization of the environment.