bluuebunny/crossref_metadata_2025 huggingface dataset:
Superdeterministic hidden-variables models II: conspiracy
Authors: Sen Indrajit , Valentini Antony
Published: November 2020

We prove that superdeterministic models of quantum mechanics are conspiratorial in a mathematically well-defined sense, by further development of the ideas presented in a previous article

A

. We consider a Bell scenario where, in each run and at each wing, the experimenter chooses one of
N
devices to determine the local measurement setting. We prove, without assuming any features of quantum statistics, that superdeterministic models of this scenario must have a finely tuned distribution of hidden variables. Specifically, fine-tuning is required so that the measurement statistics depend on the measurement settings but not on the details of how the settings are chosen. We quantify this as the overhead fine-tuning
F
of the model, and show that
F
 > 0 (corresponding to ‘fine-tuned’) for any
N
 > 1. The notion of fine-tuning assumes that arbitrary (‘non-equilibrium’) hidden-variables distributions are possible in principle. We also show how to quantify superdeterministic conspiracy without using non-equilibrium. This second approach is based on the fact that superdeterministic correlations can mimic actual signalling. We argue that an analogous situation occurs in equilibrium where, for every run, the devices that the hidden variables are correlated with are coincidentally the same as the devices in fact used. This results in extremely large superdeterministic correlations, which we quantify as a drop of an appropriately defined formal entropy. Non-local and retrocausal models turn out to be non-conspiratorial according to both approaches.
A fundamental class of stress elements in lower bound limit analysis
Authors: Makrodimopoulos Athanasios
Published: November 2020

There is a major restriction in the formulation of rigorous lower bound limit analysis by means of the finite-element method. Once the stress field has been discretized, the yield criterion and the equilibrium conditions must be applied at a finite number of points so that they are satisfied everywhere throughout the discretized structure. Until now, only the linear stress elements fulfil this requirement for several types of loads and structural conditions. However, there are also standard types of problems, like the one of plates under uniformly distributed loads, where the implementation of the lower bound theorem is still not possible. In this paper, it is proven for the first time that there is a class of stress interpolation elements which fulfils all the requirements of the lower bound theorem. Moreover, there is no upper restriction of the polynomial interpolation order. The efficiency is examined through plane strain, plane stress and Kirchhoff plate examples. The generalization to three-dimensional and other structural conditions is also straightforward. Thus, this interpolation scheme which is based on the Bernstein polynomials is expected to play a fundamental role in future developments and applications.
Electrocharged facepiece respirator fabrics using common materials
Authors: Bandi M. M.
Published: November 2020

Face masks in general, and N95 filtering facepiece respirators (FRs) that protect against SARS-Cov-2 virion in particular, have become scarce during the ongoing COVID-19 global pandemic. This work presents practical design principles for the fabrication of electrocharged filtration layers employed in N95 FRs using commonly available materials and easily replicable methods. The input polymer is polypropylene or polystyrene, and can include discarded plastic containers of these materials, and the fabrication set-up is based on the cotton candy (CC) principle. The primary parameters underlying the CC principle are translated to simple design rules that allow anyone to construct their own fabrication system from common parts, or employ a commercial CC machine with minimal modifications. Finally, basic characterization results for structural and filtration properties of electrocharged fabrics made using the CC principle are detailed.
Diffraction by a rigid strip in a plate modelled by Mindlin theory
Authors: Thompson Ian
Published: November 2020

We consider a plane flexural wave incident on a semi-infinite rigid strip in a Mindlin plate. The boundary conditions on the strip lead to three Wiener–Hopf equations, one of which decouples, leaving a scalar problem and a 2 × 2 matrix problem. The latter is solved using a simple method based on quadrature. The far-field diffraction coefficient is calculated and some numerical results are presented. We also show how the results reduce to the simpler Kirchhoff model in the low-frequency limit.
Species functional traits and abundance as drivers of multiplex ecological networks: first empirical quantification of inter-layer edge weights
Authors: Hervías-Parejo S. , Tur C. , Heleno R. , Nogales M. , Timóteo S. , Traveset A.
Published: November 2020

Many vertebrate species act as both plant pollinators and seed-dispersers, thus interconnecting these processes, particularly on islands. Ecological multilayer networks are a powerful tool to explore interdependencies between processes; however, quantifying the links between species engaging in different types of interactions (i.e. inter-layer edges) remains a great challenge. Here, we empirically measured inter-layer edge weights by quantifying the role of individually marked birds as both pollinators and seed-dispersers of Galápagos plant species over an entire year. Although most species (80%) engaged in both functions, we show that only a small proportion of individuals actually linked the two processes, highlighting the need to further consider intra-specific variability in individuals' functional roles. Furthermore, we found a high variation among species in linking both processes, i.e. some species contribute more than others to the modular organization of the multilayer network. Small and abundant species are particularly important for the cohesion of pollinator seed-dispersal networks, demonstrating the interplay between species traits and neutral processes structuring natural communities.
Osteohistological analyses reveal diverse strategies of theropod dinosaur body-size evolution
Authors: Cullen Thomas M. , Canale Juan I. , Apesteguía Sebastián , Smith Nathan D. , Hu Dongyu , Makovicky Peter J.
Published: November 2020

The independent evolution of gigantism among dinosaurs has been a topic of long-standing interest, but it remains unclear if gigantic theropods, the largest bipeds in the fossil record, all achieved massive sizes in the same manner, or through different strategies. We perform multi-element histological analyses on a phylogenetically broad dataset sampled from eight theropod families, with a focus on gigantic tyrannosaurids and carcharodontosaurids, to reconstruct the growth strategies of these lineages and test if particular bones consistently preserve the most complete growth record. We find that in skeletally mature gigantic theropods, weight-bearing bones consistently preserve extensive growth records, whereas non-weight-bearing bones are remodelled and less useful for growth reconstruction, contrary to the pattern observed in smaller theropods and some other dinosaur clades. We find a heterochronic pattern of growth fitting an acceleration model in tyrannosaurids, with allosauroid carcharodontosaurids better fitting a model of hypermorphosis. These divergent growth patterns appear phylogenetically constrained, representing extreme versions of the growth patterns present in smaller coelurosaurs and allosauroids, respectively. This provides the first evidence of a lack of strong mechanistic or physiological constraints on size evolution in the largest bipeds in the fossil record and evidence of one of the longest-living individual dinosaurs ever documented.
The smell of cooperation: rats increase helpful behaviour when receiving odour cues of a conspecific performing a cooperative task
Authors: Gerber Nina , Schweinfurth Manon K. , Taborsky Michael
Published: November 2020

Reciprocity can explain cooperative behaviour among non-kin, where individuals help others depending on their experience in previous interactions. Norway rats (Rattus norvegicus) cooperate reciprocally according to direct and generalized reciprocity. In a sequence of four consecutive experiments, we show that odour cues from a cooperating conspecific are sufficient to induce the altruistic help of rats in a food-exchange task. When rats were enabled to help a non-cooperative partner while receiving olfactory information from a rat helping a conspecific in a different room, they helped their non-cooperative partner as if it was a cooperative one. We further show that the cues inducing altruistic behaviour are released during the act of cooperation and do not depend on the identity of the cue provider. Remarkably, olfactory cues seem to be more important for cooperation decisions than experiencing a cooperative actper se. This suggests that rats may signal their cooperation propensity to social partners, which increases their chances to receive help in return.
Multidrug-resistant bacteria as intestinal colonizers and evolution of intestinal colonization in healthy university students in Portugal
Authors: Mota Raquel , Pinto Marisa , Palmeira Josman , Gonçalves Daniela , Ferreira Helena
Published: November 2020

Multidrug-resistant bacteria have been increasingly described in healthcare institutions, however community resistance also seems to be emerging.

Escherichia coli

an intestinal commensal bacteria, is also a pathogen and represents an important intestinal reservoir of resistance. Our aim was the study of the intestinal colonization and of the persistence of antibiotic resistant intestinal bacteria in healthy university students of Porto, in the north of Portugal. Samples from 30 university students were collected and analysed. Two

E. coli

isolates were randomly obtained from each student and Gram-negative bacilli resistant to antibiotics were studied. In addition, we evaluated changes in the Gram-negative intestinal colonization of ten university students in a short period of time. Molecular characterization showed a high presence of bla
TEM in commensal

E. coli

. Gram-negative bacteria with intrinsic and extrinsic resistance were isolated, namely

Pseudomonas

spp.,

Enterobacter

spp. and

Pantoea

spp. We isolated three ESBL-producing

E. coli

from two students. These isolates showed bla
CTX-M group 1 (n=1), bla
CTX-M group 9 (n=2), bla
TEM (n=2), bla
SHV (n=1) and tetA (n=2) genes. Additionally, they showed specific virulence factors and conjugational transfer of antibiotic resistance and virulence genes. One

Pseudomonas

spp. isolate resistant to carbapenems was detected colonizing one student. Our results confirm that healthy young adults may be colonized with commensals showing clinically relevant antibiotic resistance mechanisms, creating a risk of silent spread of these bacteria in the community.
Phycobilins as potent food bioactive broad-spectrum inhibitor compounds against Mproand PLproof SARS-CoV-2 and other coronaviruses: A preliminary Study
Authors: Pendyala Brahmaiah , Patras Ankit , Dash Chandravanu
Published: November 2020

In the twenty first century, we have witnessed three corona virus outbreaks; SARS in 2003, MERS in 2012 and ongoing pandemic COVID-19. To prevent outbreaks by novel mutant strains, we need broad-spectrum antiviral agents that are effective against wide array of coronaviruses. In this study, we scientifically investigated potent food bioactive broad-spectrum antiviral compounds by targeting Mproand PLproproteases of CoVs usingin silicoandin vitroapproaches. The results revealed that phycocyanobilin (PCB) showed potential inhibitor activity against both proteases. PCB had best binding affinity to Mproand PLprowith IC50values of 71 μm and 62 μm, respectively. In addition,in silicostudies of Mproand PLproenzymes of other human and animal CoVs indicated broad spectrum inhibitor activity of the PCB. Like PCB, other phycobilins such as phycourobilin (PUB), Phycoerythrobilin (PEB) and Phycoviolobilin (PVB) showed similar binding affinity to SARS-CoV-2 Mproand PLpro
Development and validation of risk scores for all-cause mortality for the purposes of a smartphone-based ‘general health score’ application: a prospective cohort study using the UK Biobank
Authors: Clift Ashley K. , Lannou Erwann Le , Tighe Christian P. , Shah Sachin S. , Beatty Matthew , Hyvärinen Arsi , Lane Stephen J. , Strauss Tamir , Dunn Devin D. , Lu Jiahe , Aral Mert , Vahdat Dan , Ponzo Sonia , Plans David
Published: November 2020

Background

Even though established links exist between individuals behaviours and potentially adverse health outcomes, to date either univariate, simpler models or multivariate, yet difficult to employ ones, have been developed. Such models are unlikely to be successful at capturing the wider determinants of health in the broader population. Hence, there is a need for a multidimensional, yet widely employable and accessible, way to obtain a comprehensive health metric.

Objective

To develop and validate a novel, easily interpretable points-based health score (“C-Score”) derived from metrics measurable using smartphone components, and iterations thereof that utilise statistical modelling and machine learning approaches.

Methods

Comprehensive literature review to identify suitable predictor variables for inclusion in a first iteration points-based model. This was followed by a prospective cohort study in a UK Biobank population for the purposes of validating the C-Score, and developing and comparatively validating variations of the score using statistical/machine learning models to assess the balance between expediency and ease of interpretability versus model complexity. Primary and secondary outcome measures: Discrimination of a points-based score for all-cause mortality within 10 years (Harrell’s c-statistic). Discrimination and calibration of Cox proportional hazards models and machine learning models that incorporate C-Score values (or raw data inputs) and other predictors to predict risk of all-cause mortality within 10 years.

Results

The cohort comprised 420,560 individuals. During a cohort follow-up of 4,526,452 person-years, there were 16,188 deaths from any cause (3.85%). The points-based model had good discrimination (c-statistic = 0.66). There was a 31% relative reduction in risk of all-cause mortality per decile of increasing C-Score (hazard ratio: 0.69, 95% CI: 0.663 to 0.675). A Cox model integrating age and C-Score had improved discrimination (8% percentage points, c-statistic = 0.74) and good calibration. Machine learning approaches did not offer improved discrimination over statistical modelling.

Conclusions

The novel health metric (‘C-Score’) has good predictive capabilities for all-cause mortality within 10 years. Embedding C-Score within a smartphone application may represent a useful tool for democratised, individualised health risk prediction. A simple Cox model using C-Score and age optimally balances parsimony and accuracy of risk predictions and could be used to produce absolute risk estimations for application users.
Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress
Authors: Bloemendaal Mirjam , Szopinska-Tokov Joanna , Belzer Clara , Boverhoff David , Papalini Silvia , Michels Franziska , van Hemert Saskia , Vasquez Alejandro Arias , Aarts Esther
Published: November 2020

Stress negatively affects cognitive performance. Probiotics remediate somatic and behavioral stress responses, hypothetically by acting on the gut microbiota. Here, we assessed gut microbial alterations after 28-days supplementation of multi-strain probiotics (EcologicBarrier consisting of Lactobacilli, Lactococci and Bifidobacteria in healthy, female subjects (probiotics group n=27, placebo group n=29). In an identical pre- and post-session, subjects performed a working memory task before and after an acute stress intervention. One-month supplementation of probiotics changed the gut microbial community (within probiotics group Pweighted unifrac=0.008). This change was driven by a nominal increase in eight genera in the probiotics group relative to the placebo group: Butyricimonas, Parabacteroides, Alistipes, Christensenellaceae_R-7_group, Family_XIII_AD3011_group, Ruminococcaceae_UCG-003, Ruminococcaceae_UCG-005 and Ruminococcaceae_UCG-010. Of these, the probiotics-induced change in genus Ruminococcaceae_UCG-003 was significantly associated with probiotics’ effect on stress-induced working memory changes (rspearman(27) = 0.565; pFDR = 0.014) in the probiotics group only and independent of potential confounders (i.e., age, BMI, and baseline dietary fibre intake). That is, subjects with a higher increase in Ruminococcaceae_UCG-003 abundance after probiotics were also more protected from negative effects of stress on working memory after probiotic supplementation. The bacterial taxa showing an increase in relative abundance in the probiotics group are plant fibre degrading bacteria and produce short-chain fatty acids that are known for their beneficial effect on gut and brain health, e.g. maintaining intestinal- and blood-brain-barrier integrity. This study shows that gut microbial alterations, modulated through probiotics use, are related to improved cognitive performance in acute stress circumstances.
Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: a prospective comparative clinical trial
Authors: Schwob Jean Marc , Miauton Alix , Petrovic Dusan , Perdrix Jean , Senn Nicolas , Jaton Katia , Onya Opota , Maillard Alain , Minghelli Gianni , Cornuz Jacques , Greub Gilbert , Genton Blaise , D’Acremont Valérie
Published: November 2020

Background

Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs) and saliva RT-PCR have shown variable performance to detect SARS-CoV-2.

Methods

In October 2020, we conducted a prospective trial involving patients presenting at testing centers with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR.

Results

Out of 949 patients enrolled, 928 patients had all three tests. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) ≥106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively.

Sensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients and 96.5% (93.6-98.3%) for those with VL≥106. Sensitivity of STANDARD-Q®, Panbio™ and COVID-VIRO® Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL≥106, sensitivities were 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%) and ≥4 days (85.7%) after symptoms onset (p=0.6). Sensitivities of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR.

Conclusions

The high performance of RDTs allows rapid identification of COVID cases with immediate isolation of the vast majority of contagious individuals. RDT could be a game changer in primary care practices, and even more so in resource-constrained settings. PCR on saliva can replace NP PCR.

ClinicalTrial.gov Identifier: NCT04613310
Effects of High-dose Intravenous Vitamin C on Point-of-Care Blood Glucose Level in Septic Patients: A Retrospective, Single-Center, Observational Case Series
Authors: He Juan , Zheng Guanhao , Qian Xian , Sheng Huiqiu , Chen Bing , Zhao Bing , Chen Erzhen , Mao Enqiang , Bian Xiaolan
Published: November 2020

Introduction

High-dose vitamin C (hdVC) is regarded as one of the essential adjunctive drugs for sepsis treatment. The present study aimed to deduce if hdVC could lead to erroneous testing results from the point-of-care glucose (POCG) measurement.

Methods and materials

This retrospective, single-center, observational case series involved septic patients treated by hdVC and monitored their paired POCG and laboratory glucose (LG) level for statistical analysis. The Parkes Consensus Error Grid Analysis was used as clinical influence assessment for paired blood glucose values. Subgroup analyses were conducted to explore the affecting extent of POCG readings by different VC dosage and various renal function level respectively.

Results

During the 3-year research period, 82 eligible septic patients who accepted at least three-day hdVC treatment were included in the current study. Compliance with ISO15197:2013 criteria was met in 30 (36.59%) paired values, which was far from the minimum criteria for accuracy. Subgroup analysis showed that worse renal function or higher VC dosage could lead to greater bias of POCG reading, but clinical risk would come forth scarcely while dealing with inaccurate POCG value.

Conclusions

High-dose intravenous ascorbate acid infusion could interfere POCG measurement values and LG method is more recommended, although significant medical risk hardly appears when physicians alter clinical action based on unreliable POCG reading.
Genomic diversity and antimicrobial resistance ofHaemophiluscolonising the airways of young children with cystic fibrosis
Authors: Watts Stephen C. , Judd Louise M. , Carzino Rosemary , Ranganathan Sarath , Holt Kathryn E.
Published: November 2020

Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression.Haemophilus influenzae(Hi) andHaemophilus parainfluenzae(Hpi) are routinely isolated from the lungs of children with CF, however little is known about the frequency and characteristics ofHaemophiluscolonisation in this context. Here, we describe detection, antimicrobial resistance (AMR) and genome sequencing ofHi/Hpiisolated from sputum, cough swab, and bronchoalveolar lavage samples regularly collected from 147 participants aged ≤12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program. The frequency of colonisation per visit was 4.6% forHiand 32.1% forHpi, 80.3% of participants hadHiand/orHpidetected on at least one visit, and using genomic data we estimate 15.6% of participants had persistent colonisation with the same strain for at least two consecutive visits. Colonising strains were genetically highly diverse and AMR was common, with 52% ofHiand 82% ofHpidisplaying resistance to at least one drug. The genetic basis for AMR could be identified in most cases; novel determinants include a new plasmid encodingblaTEM-1(ampicillin resistance), a new inhibitor-resistantblaTEMallele (augmentin resistance), and previously unreported mutations in chromosomally-encoded genes (pbp3, ampicillin resistance;folAandfolP, co-trimoxazole resistance;rpoB, rifampicin resistance). Acquired AMR genes were significantly more common inHpithanHi(51% vs 21%, p=0.0107) and were mostly associated with the ICEHinmobile element carryingblaTEM-1, resulting in higher rates of ampicillin resistance inHpi(73% vs 30%, p=0.0004). The genome data identified six potential instances ofHaemophilustransmission between participants, three of which involved participant pairs who attended the clinic on the same day. The high prevalence ofHaemophiluscolonisation and high burden of antimicrobial use in children with CF likely provides a reservoir for emergence and spread of AMR as well as a source of infections.
Co-surveillance of ribosomal RNA by the exosome complex and nucleolar RNAi inC. elegans
Authors: Liao Shimiao , Chen Xiangyang , Xu Ting , Jin Qile , Xu Zongxiu , Xu Demin , Zhou Xufei , Zhu Chengming , Guang Shouhong , Feng Xuezhu
Published: November 2020

Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation inCaenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed a NRDE-dependent silencing of pre-rRNAs in the nucleolus. In the presence of risiRNA, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNA inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the site of RNAi. Meanwhile, exosome mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA(susi)mutants, in which erroneous rRNAs accumulated. These results establish a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.
The Effect of Radiotherapy on Head and Neck Cancer Cell Lines Following Exposure to Heat
Authors: Atkinson Ben , Wilson Jamie
Published: November 2020

Fanconi anaemia (FA) is a rare, recessive, genetic disorder characterised by a predisposition to cancer. Patients with FA are 700 times more likely to develop head and neck squamouscell carcinomas including oral epithelial dysplasia (OED), a potentially malignant disorder of the oral mucosa. This increased likelihood suggests that the molecular mechanism responsible for dysplastic transformation may involve defects in the FA pathway. In this study, the significance of ataxia telangiectasia and Rad3-related protein (ATR), which is responsible for homologous recombination repair (HRR), was investigated. ATR protects against mutations in both normal squamous cells and cancer cells by inducing HRR, and thus is associated with radiotherapy resistance. This investigation was designed to study the effects of heat on DNA repair specific to the FA pathway. Western blotting was carried out to determine whether heat affects the ATR pathway, followed by survival assays to determine the viability of cells after heat treatment and then compared to cells treated with a specific ATR inhibitor. This project aims to discover whether heat could be used as a non-invasive treatment to increase the sensitivity of tumour cells towards radiotherapy leading to an improved treatment plan for patients suffering from head and neck cancers.
Transcriptome analysis of an albino mutant inHaworthia cooperivar.pilifera
Authors: Ren Maofei , Zhang Yan , Xu Hanbing , Zhu Qingsong , Wang Zhiyong , Liu Songhu , Li Peiling , Liang Benguo
Published: November 2020

Photosynthetic organisms appear green due to the accumulation of chlorophyll (Chl) pigments in their chloroplasts. Although the genes encoding key enzymes related to Chl biosynthesis have been well characterized in herbaceous plants, such as rice, Arabidopsis and maize, white leaf mutants have not yet been fully studied in succulent plants. In this work, we explored the molecular mechanism of leaf color formation in an albino mutant (HUA) ofHaworthia cooperivar.pilifera. We investigated the differentially expressed genes (DEGs) between HUA and control plants (wild type, LV) by transcriptome sequencing. Approximately 2,586 genes (1,996 downregulated and 590 upregulated) were found to be differentially expressed in HUA compared with LV using a threshold of ratio change ≥ 2 and false discovery rate (FDR) ≤0.05. GO analysis predicted that these DEGs participate in 12 cellular component, 20 biological process and 13 molecular function terms. Among the DEGs were well-recognized genes associated with chloroplast division and the biosynthesis of plant pigments, including chlorophyll, carotenoids and anthocyanin, as well as various transcription factor families. Overall, these results can help confirm the molecular regulatory mechanisms controlling leaf pigmentation and provide a comprehensive resource for breeding colorful leaf phenotypes in succulent plants.
Albofungin and chloroalbofungin: antibiotic crystals with 2D but not 3D isostructurality
Authors: Ye Wenkang , She Weiyi , Sung Herman H.-Y. , Qian Peiyuan , Williams Ian D.
Published: November 2020

The potent antibiotics albofungin [systematic name: (1S,4R,8aR)-13-amino-1,15,16-trihydroxy-4-methoxy-12-methyl-3,4,8a,13-tetrahydro-1H-xantheno[4′,3′,2′:4,5][1,3]benzodioxino[7,6-g]isoquinoline-14,17(2H,9H)-dione, C27H24N2O9, 1] and its chlorinated analogue chloroalbofungin (the 11-chloro analogue, C27H23ClN2O9, 2) have been crystallized following their isolation from the bacterial strain Streptomyces chrestomyceticus and their structures determined by single-crystal X-ray diffraction. The novel N-aminoquinolone molecular arrangement shows N—N bond lengths of 1.4202 (16) and 1.424 (2) Å in 1 and 2, respectively. The regiochemistry of chloro substitution in the A-ring is para to the quinolone O atom, with a C—Cl bond length of 1.741 (2) Å. The absolute stereochemistry at three chiral centres of the xanthone rings (i.e. 10S, 13R and 19R) is confirmed. Both compounds crystallize in chiral Sohncke space groups consistent with enantiopurity, but are not fully isostructural. A preserved supramolecular construct (SC) confers two-dimensional (2D) isostructurality, but the SC self-associates via either a twofold screw operation in 1, giving a monoclinic P21 structure, or a twofold rotation in 2, affording a monoclinic C2 structure with a doubled unit-cell axis.
The A component (SmhA) of a tripartite pore-forming toxin from Serratia marcescens: expression, purification and crystallographic analysis
Authors: Churchill-Angus Alicia M. , Sedelnikova Svetlana E. , Schofield Thomas H. B. , Baker Patrick J.
Published: November 2020

Tripartite α-pore-forming toxins are constructed of three proteins (A, B and C) and are found in many bacterial pathogens. While structures of the B and C components from Gram-negative bacteria have been described, the structure of the A component of a Gram-negative α-pore-forming toxin has so far proved elusive. SmhA, the A component from the opportunistic human pathogen Serratia marcescens, has been cloned, overexpressed and purified. Crystals were grown of selenomethionine-derivatized protein and anomalous data were collected. Phases were calculated and an initial electron-density map was produced.
Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals
Authors: Nakamura Yuki , Baba Seiki , Mizuno Nobuhiro , Irie Takaki , Ueno Go , Hirata Kunio , Ito Sho , Hasegawa Kazuya , Yamamoto Masaki , Kumasaka Takashi
Published: November 2020

Cryocrystallography is a technique that is used more often than room-temperature data collection in macromolecular crystallography. One of its advantages is the significant reduction in radiation damage, which is especially useful in synchrotron experiments. Another advantage is that cryopreservation provides simple storage of crystals and easy transportation to a synchrotron. However, this technique sometimes results in the undesirable adhesion of frost to mounted crystals. The frost produces noisy diffraction images and reduces the optical visibility of crystals, which is crucial for aligning the crystal position with the incident X-ray position. To resolve these issues, a computer-controlled device has been developed that drizzles liquid nitrogen over a crystal to remove frost. It was confirmed that the device works properly, reduces noise from ice rings in diffraction images and enables the centering of crystals with low visibility owing to frost adhesion.
The crystal structure of benzophenone synthase fromGarcinia mangostanaL. pericarps reveals the basis for substrate specificity and catalysis
Authors: Songsiriritthigul Chomphunuch , Nualkaew Natsajee , Ketudat-Cairns James , Chen Chun-Jung
Published: November 2020

Benzophenone synthase (BPS) catalyzes the production of 2,4,6-trihydroxybenzophenone via the condensation of benzoyl-CoA and three units of malonyl-CoA. The biosynthetic pathway proceeds with the formation of the prenylated xanthone α-mangostin from 2,4,6-trihydroxybenzophenone. Structural elucidation was performed to gain a better understanding of the structural basis of the function ofGarcinia mangostanaL. (mangosteen) BPS (GmBPS). The structure reveals the common core consisting of a five-layer αβαβα fold as found in other type III polyketide synthase enzymes. The three residues Met264, Tyr266 and Gly339 are proposed to have a significant impact on the substrate-binding specificity of the active site. Crystallographic and docking studies indicate why benzoyl-CoA is preferred over 4-coumaroyl-CoA as the substrate for GmBPS. Met264 and Tyr266 in GmBPS are properly oriented for accommodation of the 2,4,6-trihydroxybenzophenone product but not of naringenin. Gly339 offers a minimal steric hindrance to accommodate the extended substrate. Moreover, the structural arrangement of Thr133 provides the elongation activity and consequently facilitates extension of the polyketide chain. In addition to its impact on the substrate selectivity, Ala257 expands the horizontal cavity and might serve to facilitate the initiation/cyclization reaction. The detailed structure of GmBPS explains its catalytic function, facilitating further structure-based engineering to alter its substrate specificity and obtain the desired products.
The X-ray crystal structure of the N-terminal domain of Ssr4, a Schizosaccharomyces pombe chromatin-remodelling protein
Authors: Newman Janet , Nebl Tom , Van Huy , Peat Thomas S.
Published: November 2020

Ssr4 is a yeast protein from Schizosaccharomyces pombe and is an essential part of the chromatin-remodelling [SWI/SNF and RSC (remodelling the structure of chromatin)] complexes found in S. pombe. These complexes (or their homologues) regulate gene expression in eukaryotic organisms, affecting a large number of genes both positively and negatively. The downstream effects are seen in development, and in humans have implications for disease such as cancer. The chromatin structure is altered by modifying the DNA–histone contacts, thus opening up or closing down sections of DNA to specific transcription factors that regulate the transcription of genes. The Ssr4 sequence has little homology to other sequences in the Protein Data Bank, so the structure was solved using an iodine derivative with SAD phasing. The structure of the N-terminal domain is an antiparallel β-sheet of seven strands with α-helices on one side and random coil on the other. The structure is significantly different to deposited structures and was used as a target in the most recent Critical Assessment of Techniques for Protein Structure Prediction (CASP; https://predictioncenter.org/) competition.
Evidence on going concern reporting before and after ASU 2014–15
Authors: Bakarich Kathleen , Baranek Devon
Published: November 2020

Purpose

This study aims to examine the impact of Financial Accounting Standard Board’s Accounting Standard Update (ASU) 2014–15 on auditors’ going concern reporting. ASU 2014–15 provides accounting guidance for managers related to going concern issues, but there is evidence that regulatory changes affect auditor behavior. The authors examine if auditors’ propensity to issue going concern opinions (GCOs) for non-bankrupt, financially distressed firms changes after ASU 2014–15 became effective, and if the proportion of client bankruptcies with prior GCOs changes after ASU 2014–15 became effective.

Design/methodology/approach

The authors examine audit reports for non-bankrupt, financially stressed firms three years before and after the effective date of ASU 2014–15 to see if the propensity to issue a GCO differs in the pre- vs post-period. The authors then examine bankrupt, financially stressed firms to determine if the proportion of bankruptcies preceded by a GCO differs in the pre- vs post-period.

Findings

The authors find a significant increase in GCO reporting for non-bankrupt, financially stressed firms in the post-ASU 2014–15 period, suggesting auditor conservatism increased. The propensity for auditors to issue a GCO to bankrupt firms also increased significantly in the post-ASU period, providing evidence that auditors became more accurate, as more bankruptcies were preceded by a GCO than in the pre-ASU period.

Originality/value

This study uses new legislation which creates an exogenous shock to going concern reporting. Models and techniques are combined from prior literature and extended to investigate auditors’ reporting behaviors using two important and distinct samples.
LES/FMDF of turbulent reacting jet in cross-flow
Authors: Esmaeili Mostafa , Afshari Asghar
Published: November 2020

Purpose

This study aims to numerically investigate the flow features and mixing/combustion efficiencies in a turbulent reacting jet in cross-flow by a hybrid Eulerian-Lagrangian methodology.

Design/methodology/approach

A high-order hybrid solver is employed where, the velocity field is obtained by solving the Eulerian filtered compressible transport equations while the species are simulated by using the filtered mass density function (FMDF) method.

Findings

The main features of a reacting JICF flame are reproduced by the large-eddy simulation (LES)/FMDF method. The computed mean and root-mean-square values of velocity and mean temperature field are in good agreement with experimental data. Reacting JICF’s with different momentum ratios are considered. The jet penetrates deeper for higher momentum ratios. Mixing and combustion efficiency are improved by increasing the momentum ratio.

Originality/value

The authors investigate the flow and combustion characteristics in subsonic reacting JICFs for which very limited studies are reported in the literature.
The impact of the 2012 NZX listing rule change on board composition and company performance
Authors: Boyle Glenn , Hong Sanghyun , Foley Michael
Published: November 2020

Purpose

This study aims to examine the impact of December 2012, New Zealand (NZ) stock exchange operator listing rule change that introduced compulsory disclosure about gender diversity on NZ boards.

Design/methodology/approach

A quasi-natural experiment setting with a clearly identifiable exogenous event.

Findings

The rate of growth in female-held directorships increased significantly after the introduction of the new rule, resulting in, by 2016, the average female board representation being more than double what it had been in 2012. However, this paper finds no relationship between this response and company performance.

Research limitations/implications

This study cannot attribute causality to the observed jump in female directorships following the 2012 listing rule change due to the absence of a control group of firms not subject to this change.

Practical implications

The results are consistent with an efficient director appointment process in NZ.

Originality/value

Low-key regulatory changes can have a significant impact on company behaviour.
Do institutional investors stabilize stock returns? Evidence from emerging IPO markets
Authors: Dumrongwong Konpanas
Published: November 2020

Purpose

The purpose of this paper is to investigate how institutional ownership is related to the stock return volatility of initial public offerings (IPOs) in an emerging market and to examine the relationship between institutional ownership and underpricing.

Design/methodology/approach

This paper investigates these relationships using White’s (1980) regression and 2 × 3 portfolios sorted by firm size and institutional holdings. The regression method examines the relationships across firms with different characteristics such as size, stock price, growth potential, firm age and type of investors. The data were chosen for this sample to cover the new equity issuances listed on the Thailand Stock Exchange for the period 2001–2019.

Findings

The empirical results suggest that institutional ownership is negatively associated with initial stock return volatility. This highlights the importance of institutional investors in maintaining stability in emerging stock markets. Additionally, it was found that institutional holding and underpricing are negatively correlated. The results are robust after controlling for potential heteroskedasticity and differences in firm characteristics.

Originality/value

To the best knowledge of the author, this paper is the first to study the relationship between institutional investors and volatility in Thai IPOs, and hence provides a deeper understanding of how investors influence the price formation and volatility of stock prices in emerging markets. Furthermore, besides academics, the results presented in this paper could be useful for market regulators and policymakers in designing future market regulations to efficiently stabilize equity markets.
The reception of the “New Qing History” in China: confrontation between global and nationalist historical narratives
Authors: Déry Carl
Published: November 2020

Purpose

This paper aims to explore various tensions related to the diffusion and reception of the New Qing History (NQH) in China, and more specifically, it aims at underlying a recurrent tension within the core of this debate, between a Global and a Nationalist historical narrative.

Design/methodology/approach

The author’s focus is to analyze various texts published in China between 2006 and 2018.

Findings

The author argues that the intensity of the current debate is partly related on the one hand, to the fact that NQH undermines various aspects of China’s Nationalist teleology and territorial claims and, on the other hand, to the basic difficulty of accepting the coexistence of various historical representations that are risking to weaken contemporary’s justifications of its rising schemes.

Originality/value

The text presents an original reading of some important issues raised by the NQH debate.
In situ resistance, not immigration, supports invertebrate community resilience to drought intensification in a Neotropical ecosystem
Authors: Bonhomme Camille , Céréghino Régis , Carrias Jean‐François , Compin Arthur , Corbara Bruno , Jassey Vincent E. J. , Leflaive Joséphine , Farjalla Vinicius F. , Marino Nicholas A. C. , Rota Thibaut , Srivastava Diane S. , Leroy Céline
Published: November 2020

While future climate scenarios predict declines in precipitations in many regions of the world, little is known of the mechanisms underlying community resilience to prolonged dry seasons, especially in ‘naïve’ Neotropical rainforests. Predictions of community resilience to intensifying drought are complicated by the fact that the underlying mechanisms are mediated by species' tolerance and resistance traits, as well as rescue through dispersal from source patches.

We examined the contribution of in situ tolerance‐resistance and immigration to community resilience, following drought events that ranged from the ambient norm to IPCC scenarios and extreme events.

We used rainshelters above rainwater‐filled bromeliads of French Guiana to emulate a gradient of drought intensity (from 1 to 3.6 times the current number of consecutive days without rainfall), and we analysed the post‐drought dynamics of the taxonomic and functional community structure of aquatic invertebrates to these treatments when immigration is excluded (by netting bromeliads) or permitted (no nets).

Drought intensity negatively affected invertebrate community resistance, but had a positive influence on community recovery during the post‐drought phase. After droughts of 1 to 1.4 times the current intensities, the overall invertebrate abundance recovered within invertebrate life cycle durations (up to 2 months). Shifts in taxonomic composition were more important after longer droughts, but overall, community composition showed recovery towards baseline states. The non‐random patterns of changes in functional community structure indicated that deterministic processes like environmental filtering of traits drive community re‐assembly patterns after a drought event. Community resilience mostly relied on in situ tolerance‐resistance traits. A rescue effect of immigration after a drought event was weak and mostly apparent under extreme droughts.

Under climate change scenarios of drought intensification in Neotropical regions, community and ecosystem resilience could primarily depend on the persistence of suitable habitats and on the resistance traits of species, while metacommunity dynamics could make a minor contribution to ecosystem recovery. Climate change adaptation should thus aim at identifying and preserving local conditions that foster in situ resistance and the buffering effects of habitat features.
Biotic and abiotic drivers of plant–pollinator community assembly across wildfire gradients
Authors: LaManna Joseph A. , Burkle Laura A. , Belote R. Travis , Myers Jonathan A.
Published: November 2020

Understanding how abiotic disturbance and biotic interactions determine pollinator and flowering‐plant diversity is critically important given global climate change and widespread pollinator declines. To predict responses of pollinators and flowering‐plant communities to changes in wildfire disturbance, a mechanistic understanding of how these two trophic levels respond to wildfire severity is needed.

We compared site‐to‐site variation in community composition (β‐diversity), species richness and abundances of pollinators and flowering plants among landscapes with no recent wildfire (unburned), mixed‐severity wildfire and high‐severity wildfire in three sites across the Northern Rockies Ecoregion, USA. We used variation partitioning to assess the relative contributions of wildfire, other abiotic variables (climate, soils and topography) and biotic associations among plant and pollinator composition to community assembly of both trophic levels.

Wildfire disturbance generally increased species richness and total abundance, but decreased β‐diversity, of both pollinators and flowering plants. However, reductions in β‐diversity from wildfire appeared to result from increased abundances following fires, resulting in higher local species richness of pollinators and flowers in burned than unburned landscapes. After accounting for differences in abundance, standardized effect sizes of β‐diversity were higher in burned than unburned landscapes, suggesting that wildfire enhances non‐random assortment of pollinator and flowering‐plant species among local communities.

Wildfire disturbance mediated the relative importance of mutualistic associations to β‐diversity of pollinators and flowering plants. The influence of pollinator β‐diversity on flowering‐plant β‐diversity increased with wildfire severity, whereas the influence of flowering‐plant β‐diversity on pollinator β‐diversity was greater in mixed‐severity than high‐severity wildfire or unburned landscapes. Moreover, biotic associations among pollinator and plant species explained substantial variation in β‐diversity of both trophic levels beyond what could be explained by wildfire and all other abiotic and spatial factors combined.

Synthesis. Wildfire disturbance and plant–pollinator interactions both strongly influenced the assembly of pollinator and flowering‐plant communities at local and regional scales. However, biotic interactions were generally more important drivers of community assembly in disturbed than undisturbed landscapes. As wildfire regimes continue to change globally, predicting its effects on biodiversity will require a deeper understanding of the ecological processes that mediate biotic interactions among linked trophic levels.