Miracle-dz/UniFAR-FTUs huggingface dataset:
Extreme growth plasticity in the early branching sauropodomorph Massospondylus carinatus

There is growing evidence of developmental plasticity in early branching dinosaurs and their outgroups. This is reflected in disparate patterns of morphological and histological change during ontogeny. In fossils, only the osteohistological assessment of annual lines of arrested growth (LAGs) can reveal the pace of skeletal growth. Some later branching non-bird dinosaur species appear to have followed an asymptotic growth pattern, with declining growth rates at increasing ontogenetic ages. By contrast, the early branching sauropodomorph Plateosaurus trossingensis appears to have had plastic growth, suggesting that this was the plesiomorphic condition for dinosaurs. The South African sauropodomorph Massospondylus carinatus is an ideal taxon in which to test this because it is known from a comprehensive ontogenetic series, it has recently been stratigraphically and taxonomically revised, and it lived at a time of ecosystem upheaval following the end-Triassic extinction. Here, we report on the results of a femoral osteohistological study of M. carinatus comprising 20 individuals ranging from embryo to skeletally mature. We find major variability in the spacing of the LAGs and infer disparate body masses for M. carinatus individuals at given ontogenetic ages, contradicting previous studies. These findings are consistent with a high degree of growth plasticity in M. carinatus.
Ruga mechanics of soft-orifice closure under external pressure

Here, we report the closure resistance of a soft-material bilayer orifice increases against external pressure, along with ruga-phase evolution, in contrast to the conventional predictions of the matrix-free cylindrical-shell buckling pressure. Experiments demonstrate that the generic soft-material orifice creases in a threefold symmetry at a limit-load pressure of p/μ ≈ 1.20, where μ is the shear modulus. Once the creasing initiates, the triple crease wings gradually grow as the pressure increases until the orifice completely closes at p/μ ≈ 3.0. By contrast, a stiff-surface bilayer orifice initially wrinkles with a multifold symmetry mode and subsequently develops ruga-phase evolution, progressively reducing the orifice cross-sectional area as pressure increases. The buckling-initiation mode is determined by the layer's thickness and stiffness, and the pressure by two types of the layer's instability modes—the surface-layer-wrinkling mode for a compliant and the ring-buckling mode for a stiff layer. The ring-buckling mode tends to set the twofold symmetry for the entire post-buckling closure process, while the high-frequency surface-layer-wrinkling mode evolves with successive symmetry breaking to a final closure configuration of two- or threefold symmetry. Finally, we found that the threefold symmetry mode for the entire closure process provides the orifice's strongest closure resistance, and human saphenous veins remarkably follow this threefold symmetry ruga evolution pathway.
Behavioral manipulation of a “Trashline Orb-weaving spider” Cyclosa fililineata (Araneidae) by the parasitoid wasp Zatypota riverai (Ichneumonidae: Pimplinae)

Abstract. In this study, we report a new interaction of the wasp Zatypota riverai Gauld, 1991 (Ichneumonidae) parasitizing the spider Cyclosa fililineata Hingston, 1932 (Araneidae) and we describe the modified spider web. Our results show that parasitized spiders build modified webs that are clearly different from normal capture webs. This modified web presents several additional lines at the center of the web, forming a disk-like structure that was also observed in modified webs of other host orb-weaving spiders. To our knowledge, Z. riverai (this study) and Z. kauros Gauld, 1984 are the only two species of the genus Zatypota that use spiders from different families as host. However, the unexpected host C. fililineata could be an accidental host, since in the same region there are two of the typical hosts, the theridiid spiders Anelosimus baeza Agnarsson, 2006 and Theridion sp.
Lichen Diversity on an Arborescent Runner Oak (Quercus pumila) in South Florida, USA

Abstract. Lichens from an unusually large, arborescent runner oak (Quercus pumila) from Miami-Dade County, Florida, were collected and inventoried. A total of 56 lichen species and one lichenicolous lichen species were found, representing 17 families with Graphidaceae bearing the most (14) species. Several species recorded were also recently reported or newly described from South Florida, which has a tropical climate and ecoregion that are distinct in the continental United States. Some lichen species (especially crustose Arthoniaceae and Graphidaceae) are twig specialists not normally found on trunks and branches; therefore, future studies of lichen diversity on single trees should include as much twig material as possible.
Structural basis for backtracking by the SARS-CoV-2 replication–transcription complex

Significance The COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome is replicated and transcribed by its RNA-dependent RNA polymerase (RdRp), which is the target for antivirals such as remdesivir. We use a combination of approaches to show that backtracking (backward motion of the RdRp on the template RNA) is a feature of SARS-CoV-2 replication/transcription. Backtracking may play a critical role in proofreading, a crucial process for SARS-CoV-2 resistance against many antivirals. Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA–protein cross-linking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3′ segment of the product RNA generated by backtracking extrudes through the RdRp nucleoside triphosphate (NTP) entry tunnel, that a mismatched nucleotide at the product RNA 3′ end frays and enters the NTP entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.
Transmission Dynamics of Shiga Toxin-Producing Escherichia coli in New Zealand Cattle from Farm to Slaughter

Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) strains, which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. ABSTRACT Cattle are asymptomatic carriers of Shiga toxin-producing Escherichia coli (STEC) strains that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STEC strains also leads to the potential for rejection of consignments by importing countries. We used a combination of PCR/matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) and whole-genome sequencing (WGS) to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples (n = 2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed that 6.2% were positive for “Top 7” STEC. Top 7 STEC strains were identified in all sample sources (n = 17) tested. A marked increase in Top 7 STEC prevalence was observed between calf hides on farm (6.3% prevalence) and calf hides at processing plants (25.1% prevalence). Whole-genome sequencing was performed on Top 7 STEC bacterial isolates (n = 40). Analysis of STEC O26 (n = 25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport, and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage, and slaughter. IMPORTANCE Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) strains, which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over 2 years. An advanced molecular detection method and whole-genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.
Explicitly Modeling Syntax in Language Models with Incremental Parsing and a Dynamic Oracle

Syntax is fundamental to our thinking about language. Failing to capture the structure of input language could lead to generalization problems and over-parametrization. In the present work, we propose a new syntax-aware language model: Syntactic Ordered Memory (SOM). The model explicitly models the structure with an incremental parser and maintains the conditional probability setting of a standard language model (left-to-right). To train the incremental parser and avoid exposure bias, we also propose a novel dynamic oracle, so that SOM is more robust to wrong parsing decisions. Experiments show that SOM can achieve strong results in language modeling, incremental parsing, and syntactic generalization tests while using fewer parameters than other models.
Direct numerical simulation of bubble-induced turbulence

Abstract We report on an investigation of bubble-induced turbulence. Bubbles of a size larger than the dissipative scale cannot be treated as pointwise inclusions, and generate important hydrodynamic fields in the carrier fluid when in motion. Furthermore, bubble motions may induce a collective agitation due to hydrodynamic interactions which display some turbulent-like features. We tackle this complex phenomenon numerically, performing direct numerical simulations with a volume-of-fluid method. In the first part of the work, we perform both two-dimensional and three-dimensional tests in order to determine appropriate numerical and physical parameters. We then carry out a highly resolved simulation of a three-dimensional bubble column, with a set-up and physical parameters similar to those used in laboratory experiments. This is the largest simulation attempted for such a configuration and is only possible thanks to adaptive grid refinement. Results are compared both with experiments and previous coarse-mesh numerical simulations. In particular, the one-point probability density function of the velocity fluctuations is in good agreement with experiments. The spectra of the kinetic energy show a clear $k^{-3}$ scaling. The mechanisms underlying the energy transfer and notably the possible presence of a cascade are unveiled by a local scale-by-scale analysis in physical space. The comparison with previous simulations indicates to what extent simulations not fully resolved may yet give correct results, from a statistical point of view.
Evanescent inertial waves

Abstract We investigate evanescent inertial waves, both theoretically and experimentally, in a fluid subject to a background rotation of $\varOmega$. We predict that there is a smooth transition from conventional inertial waves to evanescent disturbances at a frequency of $\varpi = 2\varOmega$, and that at this cross-over frequency the evanescent disturbances are spatially extensive, having a horizontal extent which is limited only by viscosity, or by the size of the domain. These findings are confirmed by our experiments, which, to the best of our knowledge, represent the first quantitative experimental investigation of evanescent inertial waves.
Production and management of cattle manure in the UK and implications for land application practice

A review of livestock and manure management across the UK was undertaken as part of a wider study of important factors impacting on greenhouse and other gaseous emissions from agriculture. All major livestock sectors were covered by the review, but only data on cattle manure are reported in this study. Cattle manure comprises 67 Mt (80%) of the total 83 Mt of UK annual livestock manure production during the housing period. Overall, about 47% of total UK cattle manure production was estimated to be as undiluted slurry and 53% as solid, mainly straw‐based farmyard manure (FYM). Survey data suggested important regional differences in cattle manure management across the UK; examples include the predominance of slurry in SW Scotland, N Ireland and to a lesser extent, in Wales, compared to the continued importance of straw‐based FYM systems in England. Survey data on land application of manures from the British Survey of Fertiliser Practice (BSFP) generally showed the expected distribution of cattle manure application timings, dominated by crop sowing/establishment or growth patterns. However, in recent years, an apparent increase in land spreading in February–April, with less application in November–January is encouraging, the trend towards spring/early summer spreading of cattle slurry suggesting greater appreciation of its value as a nutrient source. BSFP returns on manure application techniques have also shown increasing uptake of shallow injection of cattle slurry, from <1% (2004) to 10% (2013) and for increasing rapid (<6 h) incorporation of FYM, from 3% (2007) to 14% (2013).
Immuno-fibrotic drivers of impaired lung function in post-acute sequelae of SARS-CoV-2 infection (PASC)

Introduction: Subjects recovering from COVID-19 frequently experience persistent respiratory ailments; however, little is known about the underlying biological factors that may direct lung recovery and the extent to which these are affected by COVID-19 severity. Methods: We performed a prospective cohort study of subjects with persistent symptoms after acute COVID-19, collecting clinical data, pulmonary function tests, and plasma samples used for multiplex profiling of inflammatory, metabolic, angiogenic, and fibrotic factors. Results: Sixty-one subjects were enrolled across two academic medical centers at a median of 9 weeks (interquartile range 6–10) after COVID-19 illness: n=13 subjects (21%) mild/non-hospitalized, n=30 (49%) hospitalized/non-critical, and n=18 subjects (30%) hospitalized/intensive care (“ICU”). Fifty-three subjects (85%) had lingering symptoms, most commonly dyspnea (69%) and cough (58%). Forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and diffusing capacity for carbon monoxide (DLCO) declined as COVID-19 severity increased (P<0.05), but did not correlate with respiratory symptoms. Partial least-squares discriminant analysis of plasma biomarker profiles clustered subjects by past COVID-19 severity. Lipocalin 2 (LCN2), matrix metalloproteinase-7 (MMP-7), and hepatocyte growth factor (HGF) identified by the model were significantly higher in the ICU group (P<0.05) and inversely correlated with FVC and DLCO (P<0.05), and were confirmed in a separate validation cohort (n=53). Conclusions: Subjective respiratory symptoms are common after acute COVID-19 illness but do not correlate with COVID-19 severity or pulmonary function. Host response profiles reflecting neutrophil activation (LCN2), fibrosis signaling (MMP-7), and alveolar repair (HGF) track with lung impairment and may be novel therapeutic or prognostic targets. Funding: The study was funded in part by the NHLBI (K08HL130557 to BDK and R01HL142818 to HJC), the DeLuca Foundation Award (AP), a donation from Jack Levin to the Benign Hematology Program at Yale, and Divisional/Departmental funds from Duke University.
A framework for culturally diverse teams and the importance of agility: findings from a qualitative study

Abstract In this study, we investigated the conditions for successful collaboration in culturally diverse teams from a Positive Organizational Scholarship perspective. As a result of globalization, organizations increasingly rely on culturally diverse teams. Based on 19 semi-structured interviews with international managers of a large German car manufacturer, we analyzed how these teams work together and which factors promote collaboration. Our findings result in a new framework for understanding culturally diverse teams, which indicates that agile team behavior is an important factor for performance in culturally diverse teams. Agile forms of collaboration enable better adaption to change through iterative learning processes. Agile methods have strong structural elements, but in between, allow the greatest possible scope for continuous adjustment. These structuring and flexible elements seem to meet the requirements of culturally diverse teams in particular. The minimal structure provides the opportunity to bring in all perspectives and views of a culturally diverse team. In addition, we confirm the influence of well-studied factors such as openness, perspective taking and leadership behavior. Our findings help to further sharpen the understanding of culturally diverse teams and point to a fruitful future research direction on agile behavior and cultural diversity in teams.
Religious bonds, low self-control, and deviant behavior: a fixed-effects approach

ABSTRACT Prior scholarship has raised concerns over potential selection effects with religion-deviant behavior relationships. Yet, few studies have attempted to account for selection beyond incorporating control measures in statistical models, and fewer still have done so using adult samples. Using data from the National Study of Adolescent to Adult Health (N = 9,799), this study employs fixed-effects techniques to examine if religious bonds are related to deviant behaviors, and if these relationships are mediated by low self-control. Results from the fixed-effects logistic regressions show that increases in religious bonds are related to decreased odds of both substance use outcomes (binge drinking and marijuana use), but do not relate to non-violent deviance and are related to increased odds of violent deviance. Results further show that low self-control, while a significant predictor of each type of deviant behavior, fails to substantially mediate any of the relationships.
Using Situated Interviews to Engage Frail Older People in the Co-production of Improved Emergency Healthcare

ABSTRACT Including frail older people in the development and improvement of healthcare is a topical issue and co-production represents a common approach. How to practice co-production effectively, however, remains challenging, particularly when including vulnerable populations. This paper provides methodological highlights from a project designed to improve care pathways for frail older people. The project applied a co-constructive approach to co-production using situated interviews. We make four recommendations for practice and two linked conclusions – that situated interviews represent a flexible and accessible method for engaging vulnerable populations and that conceptual clarity is essential to the delivery of effective co-production.
Synthesis of Structure-Controlled Polyborosiloxanes and Investigation on Their Viscoelastic Response to Molecular Mass of Polydimethylsiloxane Triggered by Both Chemical and Physical Interactions

A series of polyborosiloxanes (PBSs) was synthesized by mixing hydroxy-terminated polydimethylsiloxanes (PDMS) and boric acid (BA) in toluene at 120 °C. The molecular masses of selected PDMS precursors were in a wide range, covering from below up to far above the critical entanglement molecular mass of PDMS. The reaction kinetics was followed by using Fourier transform infrared (FTIR) spectroscopy. Unreacted BA was removed from raw PBSs after the reactions. The influence of molecular mass of PDMS precursors on the rheological property of PBSs was explored by dynamic oscillatory frequency sweeps. The results showed that the plateau elastic moduli of PBSs were highly dependent on the molecular mass of PDMS precursors. The plateau elastic moduli of PBSs decreased at first and then increased with increasing molecular mass of PDMS precursors. PBS1 and PBS2 prepared from unentangled PDMS precursors showed sufficient fits by using the two-mode Maxwell model, whereas PBS3 to PBS6 prepared from highly entangled PD.
Psychometric Properties of the Nine-Item Problematic Internet Use Questionnaire in a Brazilian General Population Sample

Objective: The goal of the study is to adapt and examine the psychometric properties of the Brazilian version of the nine-item Problematic Internet Use Questionnaire (PIUQ-SF-9). Methods: A convenience sample of Brazilian internet users aged between 18 and 89 years (72.7% female, mean age 38.7 years ± 13.5) was recruited online from September 2018 to July 2019 (test sample = 1,525; retest sample = 237). Participants responded to the adapted version of the PIUQ-SF-9, as well as the Center for Epidemiologic Studies-Depression Scale (CES-D-10) and sociodemographic questions. Results: A bifactor model with one general factor and three specific dimensions (obsession, neglect and control disorder) yielded the best fit indices [χ2 = 67.66, df = 15, CFI = 0.99, TLI = 0.99, RMSEA = 0.048 (0.037–0.060), RMSEA p close = 0.587 and SRMR = 0.01]. McDonald's hierarchical omega coefficient was 0.76 for the general factor and varied between 0.16 and 0.33 for the specific dimensions. The intraclass correlation coefficient was 0.73 for the general factor and varied between 0.64 and 0.72 for the specific dimensions. The MIMIC model supported the scale's construct validity as the relationship of the predictors (age, time spent online, self-perception of problematic internet use, and depression symptoms) with the PIUQ-SF-9 factors was in line with the assumptions based on the literature. Conclusion: PIUQ-SF-9 seems to be a brief and culturally validated instrument with sound psychometric properties to be used in future studies on problematic internet use in the Brazilian population.