bluuebunny/crossref_metadata_2025 huggingface dataset:
Posterior ischemic optic neuropathy following a major burn injury and review of the literature
Authors: Hughes Benedict , Natalwala Ibrahim , Kiely John , Ahmad Mohammad , Rathi Bharti , Phipps Alan , Anwar Mohammad Umair , Muthayya Preetha
Published: November 2020

Posterior ischemic optic neuropathy following burns is a rare but devastating condition that can result in total bilateral visual loss. Numerous treatment modalities have been trialed, yet there is no effective therapy to delay or reverse the disease. Hence, it is imperative for burns surgeons to be aware of the potential risk factors and have a high index of suspicion right from the outset to prevent this outcome. Here, we discuss the case of a patient that developed posterior ischemic optic neuropathy subsequent to a major burn injury. We also present a literature review on optic neuropathies following burns to describe the etiology, clinical signs, and potential management.
Thresholds in Flux—the Standard for Ascertaining the Requirement of Organization for Armed Groups under International Humanitarian Law
Authors: Arai-Takahashi Yutaka
Published: November 2020

The requirement of organization is supposed to be of special importance in international humanitarian law (IHL). In the situation of international armed conflict (IAC), this requirement is implicit as part of the collective conditions to be fulfilled by irregular/independent armed groups to enable their members to claim the prisoners of war status under Article 4 A(2) of the Third Geneva Convention. In a non-international armed conflict (NIAC), the eponymous requirement serves, alongside the requirement of intensity of violence, as the threshold condition for ascertaining the onset of a NIAC. While the requirement of organization has not caused much of disputes in IACs, the international criminal tribunals have shown a willingness to examine scrupulously if armed groups in NIACs are sufficiently organized. Still, this article argues that there is need for a nuanced assessment of the organizational level of an armed group in some specific phases of the ongoing armed conflict whose legal character switches (from an NIAC to an IAC, vice-versa, and from a NIAC to a law-enforcement model). It explores what rationales and argumentative model may be adduced to explain such varying standards for organization in different contexts.
Cutaneous manifestation of leukaemia on the penis—the possible implications
Authors: Ng Angela , Gurun Murat
Published: November 2020

Skin lesions are common in the patients with chronic lymphoid leukaemia (CLL); however, leukaemia cutis is a cutaneous manifestation secondary to any form of leukaemia and generally an uncommon phenomenon. They typically present on the face and neck as well as exposed areas. Our case looks at a 78-year-old gentleman with known CLL who presented with an asymptomatic raised lesion in his inner prepuce. The lesion was excised and his immunohistology staining confirms expression of CD5, CD20 and CD23 that is consistent with cutaneous manifestation of CLL. This case highlights the importance of taking leukaemia cutis into consideration in patients with known CLL with unusual features.
Effects of different cosmic ray transport models on galaxy formation
Authors: Hopkins Philip F , Chan T K , Squire Jonathan , Quataert Eliot , Ji Suoqing , Kereš Dušan , Faucher-Giguère Claude-André
Published: November 2020

Cosmic rays (CRs) with ∼GeV energies can contribute significantly to the energy and pressure budget in the interstellar, circumgalactic, and intergalactic medium (ISM, CGM, IGM). Recent cosmological simulations have begun to explore these effects, but almost all studies have been restricted to simplified models with constant CR diffusivity and/or streaming speeds. Physical models of CR propagation/scattering via extrinsic turbulence and self-excited waves predict transport coefficients which are complicated functions of local plasma properties. In a companion paper, we consider a wide range of observational constraints to identify proposed physically motivated cosmic ray propagation scalings which satisfy both detailed Milky Way (MW) and extragalactic γ-ray constraints. Here, we compare the effects of these models relative to simpler ‘diffusion+streaming’ models on galaxy and CGM properties at dwarf through MW mass scales. The physical models predict large local variations in CR diffusivity, with median diffusivity increasing with galactocentric radii and decreasing with galaxy mass and redshift. These effects lead to a more rapid dropoff of CR energy density in the CGM (compared to simpler models), in turn producing weaker effects of CRs on galaxy star formation rates (SFRs), CGM absorption profiles, and galactic outflows. The predictions of the more physical CR models tend to lie ‘in between’ models which ignore CRs entirely and models which treat CRs with constant diffusivity.
Rapid orbital expansion in millisecond pulsar PSR J0636+5128: evaporation winds?
Authors: Chen Wen-Cong
Published: November 2020

PSR J0636+5128 is a 2.87 ms binary millisecond pulsar (MSP) discovered by the Green Bank Northern Celestial Cap Pulsar Survey, and possesses the third shortest orbital period ( P = 1.6 h) among confirmed binary pulsars. Recent observations reported that this source is experiencing a rapid orbital expansion at a rate of $\dot{P}=(1.89\pm 0.05)\times 10^{-12}\,\rm s\, s^{-1}$. The evaporation winds of the companion induced by the spin-down luminosity of the MSP may be responsible for such a positive orbital period derivative. However, our calculations show that the winds ejecting from the vicinity of the companion or the inner Lagrangian point cannot account for the observation due to an implausible evaporation efficiency. Assuming that the evaporation winds eject from the vicinity of the MSP in the form of asymmetric disc winds or outflows, the evaporation efficiency can be constrained to be ∼0.1. Therefore, the rapid orbital expansion detected in PSR J0636+5128 provides evidence of outflows and accretion disc around the MSP.
First Light And Reionisation Epoch Simulations (FLARES) II: The Photometric Properties of High-Redshift Galaxies
Authors: Vijayan Aswin P , Lovell Christopher C , Wilkins Stephen M , Thomas Peter A , Barnes David J , Irodotou Dimitrios , Kuusisto Jussi , Roper William J
Published: November 2020

We present the photometric properties of galaxies in the First Light and Reionisation Epoch Simulations (Flares). The simulations trace the evolution of galaxies in a range of overdensities through the Epoch of Reionistion (EoR). With a novel weighting scheme we combine these overdensities, extending significantly the dynamic range of observed composite distribution functions compared to periodic simulation boxes. Flares predicts a significantly larger number of intrinsically bright galaxies, which can be explained through a simple model linking dust-attenuation to the metal content of the interstellar medium, using a line-of-sight (LOS) extinction model. With this model we present the photometric properties of the Flares galaxies for z ∈ [5, 10]. We show that the ultraviolet (UV) luminosity function (LF) matches the observations at all redshifts. The function is fit by Schechter and double power-law forms, with the latter being favoured at these redshifts by the Flares composite UV LF. We also present predictions for the UV continuum slope as well as the attenuation in the UV. The impact of environment on the UV LF is also explored, with the brightest galaxies forming in the densest environments. We then present the line luminosity and equivalent widths of some prominent nebular emission lines arising from the galaxies, finding rough agreement with available observations. We also look at the relative contribution of obscured and unobscured star formation, finding comparable contributions at these redshifts.
The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states
Authors: Santosh Vishaka , Musayev Faik N , Jaiswal Rahul , Zárate-Pérez Francisco , Vandewinkel Bram , Dierckx Caroline , Endicott Molly , Sharifi Kamyar , Dryden Kelly , Henckaerts Els , Escalante Carlos R
Published: November 2020

The adeno-associated virus (AAV) non-structural Rep proteins catalyze all the DNA transactions required for virus viability including, DNA replication, transcription regulation, genome packaging, and during the latent phase, site-specific integration. Rep proteins contain two multifunctional domains: an Origin Binding Domain (OBD) and a SF3 helicase domain (HD). Studies have shown that Rep proteins have a dynamic oligomeric behavior where the nature of the DNA substrate molecule modulates its oligomeric state. In the presence of ssDNA, Rep68 forms a large double-octameric ring complex. To understand the mechanisms underlying AAV Rep function, we investigated the cryo-EM and X-ray structures of Rep68–ssDNA complexes. Surprisingly, Rep68 generates hybrid ring structures where the OBD forms octameric rings while the HD forms heptamers. Moreover, the binding to ATPγS promotes a large conformational change in the entire AAA+ domain that leads the HD to form both heptamer and hexamers. The HD oligomerization is driven by an interdomain linker region that acts as a latch to ‘catch’ the neighboring HD subunit and is flexible enough to permit the formation of different stoichiometric ring structures. Overall, our studies show the structural basis of AAV Rep's structural flexibility required to fulfill its multifunctional role during the AAV life cycle.
TOUCAN: a framework for fungal biosynthetic gene cluster discovery
Authors: Almeida Hayda , Palys Sylvester , Tsang Adrian , Diallo Abdoulaye Baniré
Published: November 2020

Fungal secondary metabolites (SMs) are an important source of numerous bioactive compounds largely applied in the pharmaceutical industry, as in the production of antibiotics and anticancer medications. The discovery of novel fungal SMs can potentially benefit human health. Identifying biosynthetic gene clusters (BGCs) involved in the biosynthesis of SMs can be a costly and complex task, especially due to the genomic diversity of fungal BGCs. Previous studies on fungal BGC discovery present limited scope and can restrict the discovery of new BGCs. In this work, we introduce TOUCAN, a supervised learning framework for fungal BGC discovery. Unlike previous methods, TOUCAN is capable of predicting BGCs on amino acid sequences, facilitating its use on newly sequenced and not yet curated data. It relies on three main pillars: rigorous selection of datasets by BGC experts; combination of functional, evolutionary and compositional features coupled with outperforming classifiers; and robust post-processing methods. TOUCAN best-performing model yields 0.982 F-measure on BGC regions in the Aspergillus niger genome. Overall results show that TOUCAN outperforms previous approaches. TOUCAN focuses on fungal BGCs but can be easily adapted to expand its scope to process other species or include new features.
The Nightmare Disorder Index: development and initial validation in a sample of nurses
Authors: Dietch Jessica R , Taylor Daniel J , Pruiksma Kristi , Wardle-Pinkston Sophie , Slavish Danica C , Messman Brett , Estevez Rosemary , Ruggero Camilo J , Kelly Kimberly
Published: November 2020

Study Objectives

Nurses are a group at high risk for nightmares, yet little is known about the rate of nightmare disorder and associated psychosocial factors in this group in part attributable to the lack of a self-report questionnaire to assess DSM-5 criteria for nightmare disorder. Aims of the current study were to (1) report on development and initial validity of a self-report measure of DSM-5 nightmare disorder, and (2) examine the rate and associated factors of nightmare disorder among nurses.

Methods

Nurses (N = 460) completed baseline measures online including Nightmare Disorder Index (NDI), psychosocial and demographic questionnaires. A subset (n = 400) completed 14 days of sleep diaries and actigraphy.

Results

NDI demonstrated satisfactory psychometric characteristics as indicated by good internal consistency (α = 0.80), medium inter-item correlations (r = 0.50), medium to large item-total (r = 0.55–0.85) and convergent correlations (0.32–0.45), and small to medium discriminant correlations (–0.12–0.33). Per NDI, 48.7% of nurses reported no nightmares in the past month, 43.9% met partial/subthreshold criteria and 7.4% met full criteria for probable nightmare disorder. Nurses with nightmare disorder demonstrated significantly poorer psychosocial functioning (i.e. posttraumatic stress, depression, anxiety, stress) than those with subthreshold nightmare symptoms, who had poorer functioning than those with no nightmares.

Conclusions

NDI is an efficient and valid self-report assessment of nightmare disorder. Nurses have high rates of nightmares and nightmare disorder which are associated with poorer psychosocial functioning. We recommend increased nightmare screening particularly for high-risk populations such as healthcare workers.
A Thankfully Wide Sea between England and Apprendi-Land
Authors: Curr Thomas
Published: November 2020

This article uses the US Supreme Court’s line of cases beginning with Apprendi v. New Jersey to illuminate territory in which English law, in comparison to American law, is comparatively underdeveloped—currently affording a Newton-style hearing only where a guilty plea obliterates any previous evidence. This need not be so. Both before and after Apprendi, US federal and state courts have implemented post-trial fact-finding procedures for sentencing purposes, and we could do the same. The Davies case, where the requirement of proof beyond a reasonable doubt was imported from the trial phase, into consideration of the statutory starting points for murder sentencing, will, for reasons to be given, be doubted.
Effect of tea consumption on oxidative stress and expression of DNA repair genes among metal press workers exposed to occupational noise
Authors: Panjali Zahra , Jafari-Tehrani Behjat , Münzel Thomas , Hahad Omar , Tansaz Mozhgan , Hamidi Mansoureh , Hajipour-Verdom Behnam , Zendehdel Rezvan
Published: November 2020

Several studies have shown that tea consumption is associated with beneficial effects on human health, which is mainly explained by the antioxidant properties of tea. However, evidence on the effect of nutrition interventions on oxidative stress in an occupational setting is limited. Therefore, the present study aimed to investigate the effect of tea consumption on oxidative stress in noise-exposed metal press workers. The study sample comprised 24 metal press workers and 24 age-matched control subjects. Metal press workers were assigned to the intervention group consisting of a glass of jujube tea and a portion of raisins per day for 4 weeks. Full-shift noise dosimetry was performed to measure noise exposure with average noise levels of 89.91 ± 2.92 dB for metal press workers and 61.54 ± 1.03 dB for control subjects. Elevated levels of baseline oxidative stress were observed in metal press workers compared with control subjects as indicated by significantly decreased levels of total antioxidant capacity (TAC) (P = 0.026) and total thiol groups (TTG) (P = 0.0001), whereas no significant difference was observed in case of malondialdehyde (MDA). Intervention with jujube tea and raisins in metal press workers led to a decrease of oxidative stress as displayed by increased levels of TAC and TTG (P = 0.0001) as well as decreased levels of MDA (P = 0.012). Moreover, the intervention significantly altered expression of repair genes in metal press workers as demonstrated by decreased levels of OGG1 (P = 0.0002) and ITPA (P = 0.009), whereas no significant difference was observed in case of MTH1. These data suggest that regular tea consumption may protect occupational noise-exposed subjects from oxidative damages.
SnRK1 phosphorylation of SDH positively regulates sorbitol metabolism and promotes sugar accumulation in peach fruit
Authors: Yu Wen , Peng Futian , Wang Wenru , Liang Jiahui , Xiao Yuansong , Yuan Xuefeng
Published: November 2020

Fruit quality depends largely on the type and amount of sugar accumulated in the fruit. In peach [Prunus persica (L.) Batsch], sorbitol is the main photosynthetic product and plays a crucial role in sugar metabolism. As a conserved energy sensor, SNF1-related kinase 1 (SnRK1) is involved in the regulation of carbon metabolism. In this study, SnRK1 was able to respond to induction by treatment with exogenous trehalose and sorbitol on ‘Ruipan 17’ peach fruit. After treatment with 100-mM trehalose for 3 h, the SnRK1 activity decreased by 18% and the activities of sorbitol dehydrogenase (SDH) and sucrose synthase (SS) also decreased significantly, but sucrose phosphate synthase (SPS) activity increased significantly; whereas sorbitol treatment under the same conditions resulted in a 12.6% increase in SnRK1 activity and the activities of SDH and SS synthase also increased significantly, compared with the control. The contents of glucose, fructose and sucrose in peach fruit increased significantly after 3 h of sorbitol treatment. In addition, the interactions between PpSnRK1α and enzymes PpSDH and PpSPS were confirmed by yeast two-hybrid method and the phosphorylation of PpSnRK1α and PpSDH was detected in vitro. Taken together, these results suggest that SnRK1 promotes sorbitol metabolism by activating SDH and it also regulates the activities of SS and SPS that enhance sucrose accumulation in peach fruit. SnRK1 protein kinase is involved in sugar metabolism and has the potential to be used for improving fruit quality.
Comparative Genomic Analyses Reveal Functional Insights Into Key Determinants of the Pathogenesis ofPectobacterium actinidiaein Kiwifruit
Authors: Lu Qi , Yan Fuhua , Liu Yuanyuan , Li Qiaohong , Yang Meng , Liu Pu
Published: November 2020

The Gram-negative bacterial species Pectobacterium actinidiae causes summer canker in kiwifruit plants. However, little is known about its virulence factors and mechanisms of genetic adaptation. We aimed to identify the key determinants that control the virulence of P. actinidiae in kiwifruit by genomic and functional analyses. Analysis of four P. actinidiae isolates indicated low genetic variability with an average of 98.7% genome-level sequence similarity and 82% shared protein-coding gene content. Phylogenetic analysis, based on both bulk single nucleotide polymorphisms (SNPs) and single-copy genes, revealed that P. actinidiae strains cluster into a single clade, which is closely related to the clades of P. odoriferum (species with a completely different host range). Through comparison between these two clades of strains, 746 unique core orthologs/genes were clustered in the clades of P. actinidiae, especially key virulence determinants involved in the biosynthesis of secretion systems (type III, IV, and VI), iron, flagellar structure, and the quorum-sensing system. Our results provide insights into the pathogenomics underlying the genetic diversification and evolution of pathogenicity in P. actinidiae species.
SARS-CoV-2 Seroprevalence among First Responders in the District of Columbia, May – July 2020
Authors: Reuben Jacqueline , Sherman Adrienne , Ellison James A. , Gunn Jayleen K. L. , Tran Anthony , McCarroll Matthew , Raj Pushker , Lloyd Patricia , Iyengar Preetha , Johnson-Clarke Fern , Davies-Cole John , Nesbitt LaQuandra
Published: November 2020

First responders are at increased risk of occupational exposure to SARS-CoV-2 while providing frontline support to communities during the COVID-19 pandemic. In the District of Columbia (DC), first responders were among the first people exposed to and infected with SARS-CoV-2, with over 200 first responders diagnosed with COVID-19 by May 15, 2020. From June – July 2020, DC Health conducted a serologic survey to estimate SARS-CoV-2 seroprevalence and assess risk factors and occupational exposures among a convenience sample of first responders in DC. Of the 310 first responders tested, 3.5% (n = 11) had anti-SARS-CoV-2 antibodies. Seropositivity varied by occupation, with 4.8% (3/62) of firefighters; 3.6% (8/220) of police officers; and no paramedics (0/10) or administration and support staff (0/18) testing positive. Type and consistency of personal protective equipment (PPE) use also varied: all paramedics (n=10) reported wearing a N95 respirator all or most of the time, compared to 83.3% of firefighters, 38.8% of police officers, and 23.5% of administration and support staff (p<0.001). All paramedics reported wearing gloves all or most of the time, compared to 80.0% of firefighters, 27.8% of administration and support staff, and 24.3% of police (p<0.001). The relatively low seroprevalence among first responders highlights the benefits of continuous training on and reinforcement of the proper use of PPE while performing job duties to mitigate potential transmission within and between first responders and the community.

Understanding occupational exposure to and infection with SARS-CoV-2 among first responders is important for workforce planning and emergency preparedness and response. Seroprevalence among first responders (3.5%; 11/310) who participated in a survey conducted by the District of Columbia Department of Health (DC Health) from May 28 – July 15 was 48% lower than reported in the DC community (6.7%; 876/12990). The lower prevalence of SARS-CoV-2 among first responders highlights the importance of continuous training on and reinforcement of the proper use of personal protective equipment (PPE). Proper use of PPE is a critical mitigation strategy to reduce transmission among and between first responders and the community.
Psychological trauma and the genetic overlap between posttraumatic stress disorder and major depressive disorder
Authors: Mundy Jessica , Hübel Christopher , Gelernter Joel , Levey Daniel , Murray Robin M. , Skelton Megan , Stein Murray B. ,   The Million Veteran Program,   Post Traumatic Stress Disorder Working Group of the Psychiatric Genomics Consortium, Vassos Evangelos , Breen Gerome , Coleman Jonathan R. I.
Published: November 2020

Background

Posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) are commonly reported co-occurring mental health consequences following psychological trauma exposure. The disorders have high genetic overlap. We investigated whether the genetics of PTSD were associated with reported trauma in individuals with MDD. Since trauma is associated with recurrent MDD, we also investigated whether the genetics of PTSD were associated with episode recurrence.

Methods

Genetic correlations were estimated between PTSD and MDD in the presence and MDD in the absence of reported exposure to psychological trauma, and recurrent and single-episode MDD, based on genetic data from UK Biobank Mental Health Questionnaire respondents (N=157,358). Genetic correlations were replicated using PTSD data from the Psychiatric Genomics Consortium and Million Veteran Program. Polygenic risk scores were generated to investigate whether individuals with MDD who have higher genetic risk for PTSD were more likely to report psychological trauma than those with lower genetic risk.

Results

Individuals with MDD with a higher genetic risk for PTSD were significantly more likely to report exposure to psychological trauma than those with lower risk [OR=1.06 (1.03-1.09) Empricial p<0.001]. PTSD was significantly more genetically correlated with recurrent MDD than with MDD in the absence of reported psychological trauma [rg differences = ∼0.2, p<0.008]. Participants who had experienced recurrent depressive episodes reported significantly higher trauma rates than participants who had experienced a single episode [chisquare>167, p<0.001].

Conclusions

Genetic risk for PTSD in individuals with MDD may influence the way in which traumatic life events are perceived, responded to and reported.
Regional Anesthesia use in Pediatric Burn Surgery: A Retrospective Observational Cohort Study
Authors: Richman M , Berman J , Ross EM
Published: November 2020

Approximately 77,000 children 16 years or less suffered burn injuries in the United States in 2018. Treatment, reconstruction, and rehabilitation are painful experiences. For some, the experience triggers post-traumatic stress disorder (PTSD) and/or a chronic pain syndrome. Given the role pain plays as a major secondary disease, it must be addressed to achieve optimal healing. Regional anesthesia has been used extensively to manage postoperative pain and reduce the need for opioids following other surgical procedures in children. Nevertheless, regional anesthesia has not yet been widely used in pediatric burn care. We present a demonstration project utilizing regional anesthesia in 15 pediatric burn patients over an eight-month period. Our results indicate that the use of regional anesthesia reliably reduces perioperative pain and opioid requirements in the immediate peri-operative period. In this cohort, 93% of patients scored a 0/10 on a FLACC scale for pain by post-anesthesia care unit (PACU) discharge, with an average PACU stay of 70 minutes. Thirty-three percent of patients received no opioids, and the average opioid dose was only 0.06mg/kg morphine equivalents. We conclude that regional anesthesia can be used to improve patient comfort and decrease opioid requirement.
Base-substitution mutation rate across the nuclear genome ofAlpheussnapping shrimp and the timing of isolation by the Isthmus of Panama
Authors: Silliman Katherine , Indorf Jane L. , Knowlton Nancy , Browne William E. , Hurt Carla
Published: November 2020

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate this genomewide neutral mutation rate (μ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs inAlpheussnapping shrimp. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated μ to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. This estimate is remarkably similar to experimentally derived mutation rates in model arthropod systems, strengthening the argument for a recent closure of the CAS. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.
Vessel compression biases red blood cell partitioning at bifurcations in a haematocrit-dependent manner: implications for tumour blood flow
Authors: Enjalbert Romain , Hardman David , Krüger Timm , Bernabeu Miguel O.
Published: November 2020

The tumour microenvironment is abnormal and associated with tumour tissue hypoxia, immunosuppression, and poor response to treatment. One important abnormality present in tumours is vessel compression. Vessel decompression has been shown to increase survival rates in animal models via enhanced and more homogeneous oxygenation. However, our knowledge of the biophysical mechanisms linking tumour decompression to improved tumour oxygenation is limited. In this study, we propose a computational model to investigate the impact of vessel compression on red blood cell (RBC) dynamics in tumour vascular networks. Our results demonstrate that vessel compression can alter RBC partitioning at bifurcations in a haematocrit-dependent and flowrate-independent manner. We identify RBC focussing due to cross-streamline migration as the mechanism responsible and characterise the spatiotemporal recovery dynamics controlling downstream partitioning. Based on this knowledge, we formulate a reduced-order model that will help future research to elucidate how these effects propagate at a whole vascular network level. These findings contribute to the mechanistic understanding of haemodilution in tumour vascular networks and oxygen homogenisation following pharmacological solid tumour decompression.
3D Adaptive Optical Nanoscopy for Thick Specimen Imaging at sub-50 nm Resolution
Authors: Hao Xiang , Allgeyer Edward S. , Antonello Jacopo , Watters Katherine , Gerdes Julianne A. , Schroeder Lena K. , Bottanelli Francesca , Zhao Jiaxi , Kidd Phylicia , Lessard Mark D. , Rothman James E. , Cooley Lynn , Biederer Thomas , Booth Martin J. , Bewersdorf Joerg
Published: November 2020

Understanding cellular organization demands the best possible spatial resolution in all three dimensions (3D). In fluorescence microscopy, this is achieved by 4Pi nanoscopy methods that combine the concepts of using two opposing objectives for optimal diffraction-limited 3D resolution with switching fluorescent molecules between bright and dark states to break the diffraction limit. However, optical aberrations have limited these nanoscopes to thin samples and prevented their application in thick specimens. Here, we have developed a nanoscope that, by utilizing an advanced adaptive optics strategy, achieves sub-50 nm isotropic resolution of structures such as neuronal synapses and ring canals previously inaccessible in tissue.
IP3/Ca2+signals regulate larval to pupal transition under nutrient stress through the H3K36 methyltransferase dSET2
Authors: Mitra Rishav , Richhariya Shlesha , Jayakumar Siddharth , Notani Dimple , Hasan Gaiti
Published: November 2020

Persistent loss of dietary protein usually signals a shutdown of key metabolic pathways. InDrosophilalarvae, that have crossed “critical weight” and can pupariate to form viable adults, such a metabolic shut-down would needlessly lead to death. IP3/Ca2+signals in certain interneurons (vGlutVGN6341) allowDrosophilalarvae to pupariate on a protein-deficient diet by partially circumventing this shutdown through upregulation of neuropeptide signaling and the expression of ecdysone synthesis genes. Here we show that IP3/Ca2+signals invGlutVGN6341neurons drive expression ofdSET2, aDrosophilaHistone 3 Lysine 36 methyltransferase. Further,dSET2expression is required for larvae to pupariate in the absence of dietary protein. IP3/Ca2+signal-drivendSET2expression upregulates key Ca2+signaling genes through a novel positive feedback loop. Transcriptomic studies coupled with analysis of existing ChIP-seq datasets identified genes from larval and pupal stages, that normally exhibit robust H3K36 trimethyl marks on their gene bodies and concomitantly undergo stronger downregulation by knockdown of either an intracellular Ca2+release channel the IP3R or dSET2. IP3/Ca2+signals thus regulate gene expression through dSET2 mediated H3K36 marks on select neuronal genes for the larval to pupal transition.
Drug and siRNA screens identify ROCK2 as a therapeutic target for ciliopathies
Authors: Lake Alice V. R. , Smith Claire E. L. , Natarajan Subaashini , Basu Basudha , Best Sunayna K. , Stevenson Thomas , Trowbridge Rachel , Grellscheid Sushma N. , Bond Jacquelyn , Foster Richard , Johnson Colin A.
Published: November 2020

Primary cilia are microtubule-based organelles that act as cellular antennae to mediate vertebrate development and growth factor signalling. Defects in primary cilia result in a group of inherited developmental conditions known as ciliopathies. Ciliopathies often present with cystic kidney disease, a major cause of early renal failure that requires renal replacement therapies. Currently, only one drug, Tolvaptan, is licensed to slow the decline of renal function for the ciliopathy polycystic kidney disease. Novel therapeutic interventions for these conditions remain a pressing clinical need.

We screened clinical development compounds for positive effects on cilia formation and function and identified fasudil hydrochloride as the top hit. Fasudil is a generic, off-patent drug that is a potent but broadly selective Rho-associated coiled-coil-containing protein kinase (ROCK) inhibitor. In a parallel whole genome siRNA-based reverse genetics phenotypic screen of positive modulators of cilia formation, we identified ROCK2 as the target molecule. We demonstrate that ROCK2 is a key mediator of cilium formation and function through effects on actin cytoskeleton remodelling. Our results indicate that specific ROCK2 inhibitors such as belumosudil (KD-025) could be repurposed for pharmacological intervention in cystic kidney disease. We propose that ROCK2 inhibition represents a novel, disease-modifying therapeutic approach for heterogeneous ciliopathies.
The selfing syndrome overshadows other differences when comparing fitness acrossCapsellaspecies
Authors: Orsucci Marion , Vanikiotis Theofilos , Guerrina Maria , Duan Tianlin , Glémin Sylvain , Lascoux Martin
Published: November 2020

Self-fertilization has recurrently evolved from outcrossing. Self-fertilization provides an advantage in the short-term as individuals do not require a mate to reproduce, but self-fertilization is also associated with both decreased genetic diversity and accumulation of weakly deleterious mutations, which could, however, be alleviated in polyploid selfers. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers. We measured several life history traits in fourCapsellaspecies under two different treatments (disturbed and undisturbed) to assess the effects of mating system and ploidy level on reproductive, vegetative and phenological traits. The experiment was carried out outdoor in Northwest Greece, within the range of the obligate outcrossing species,C. grandiflora, so it could be naturally pollinated and its fitness directly compared to that of its self-fertilizing relatives. Disturbance of the environment did not affect the phenotype in any of the four species. However, for most traits the obligate outcrossing species performed better than all selfing ones. In contrast, polyploidy did not seem to confer an advantage in terms of survival or reproduction compared to diploidy. Finally, plants from Asia and northern Europe had lower performances than accessions from southern Europe and the Middle-East.
An unexpected donor in the adaptive introgression candidate Helianthus annuus subsp. texanus
Authors: Owens Gregory. L , Todesco Marco , Bercovich Natalia , Légaré Jean-Sébastien , Mitchell Nora , Whitney Kenneth D. , Rieseberg Loren H.
Published: November 2020

Hybridization is widely acknowledged as an important mechanism of acquiring adaptive variation. In Texas, the sunflower Helianthus annuus subsp. texanus is thought to have acquired herbivore resistance and morphological traits via introgression from a local congener, H. debilis. Here we test this hypothesis using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We find that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Patterson’s D and TreeMix) only find evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but non-zero introgression from H. debilis and significant introgression from H. argophyllus. Putative introgressions mainly occur in high recombination regions as predicted by theory if introgressed ancestry contains maladaptive alleles. To reconcile the disparate findings of our analyses, we discuss potential test-specific confounding features, including introgression from other taxa. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is likely independent of introgression.
Effect size, sample size and power of forced swim test assays in mice: Guidelines for investigators to optimize reproducibility
Authors: Smalheiser Neil R. , Graetz Elena E. , Yu Zhou , Wang Jing
Published: November 2020

A recent flood of publications has documented serious problems in scientific reproducibility, power, and reporting of biomedical articles, yet scientists persist in their usual practices. Why? We examined a popular and important preclinical assay, the Forced Swim Test (FST) in mice used to test putative antidepressants. Whether the mice were assayed in a naïve state vs. in a model of depression or stress, and whether the mice were given test agents vs. known antidepressants regarded as positive controls, the mean effect sizes seen in the experiments were indeed extremely large (1.5 – 2.5 in Cohen’s d units); most of the experiments utilized 7-10 animals per group which did have adequate power to reliably detect effects of this magnitude. We propose that this may at least partially explain why investigators using the FST do not perceive intuitively that their experimental designs fall short -- even though proper prospective design would require ~21-26 animals per group to detect, at a minimum, large effects (0.8 in Cohen’s d units) when the true effect of a test agent is unknown. Our data provide explicit parameters and guidance for investigators seeking to carry out prospective power estimation for the FST. More generally, altering the real-life behavior of scientists in planning their experiments may require developing educational tools that allow them to actively visualize the inter-relationships among effect size, sample size, statistical power, and replicability in a direct and intuitive manner.
Dependence of perceptual saccadic suppression on peri-saccadic image flow properties and luminance contrast polarity
Authors: Baumann Matthias P. , Idrees Saad , Münch Thomas A , Hafed Ziad M.
Published: November 2020

Across saccades, perceptual detectability of brief visual stimuli is strongly diminished. We recently observed that this perceptual suppression phenomenon is jumpstarted in the retina, suggesting that the phenomenon might be significantly more visual in nature than normally acknowledged. Here, we explicitly compared saccadic suppression strength when saccades were made across a uniform image of constant luminance versus when saccades were made across image patches of different luminance, width, and trans-saccadic luminance polarity. We measured perceptual contrast thresholds of human subjects for brief peri-saccadic flashes of positive (luminance increments) or negative (luminance decrements) polarity. Perceptual thresholds were >6-7 times higher when saccades translated a luminance stripe or edge across the retina than when saccades were made over a completely uniform image patch. Critically, both background luminance and flash luminance polarity relative to the background strongly modulated peri-saccadic contrast thresholds. In addition, all of these very same visual dependencies also occurred in the absence of any saccades, but with qualitatively similar rapid translations of image patches across the retina. Our results support the notion that perceptual saccadic suppression may be fundamentally a visual phenomenon, and they motivate neurophysiological and theoretical investigations on the role of saccadic eye movement commands in modulating its properties.
Digestion, fermentation, and pathogen anti-adhesive properties of the hMO-mimic di-fucosyl-β-cyclodextrin
Authors: Verkhnyatskaya Stella A. , Kong Chunli , Klostermann Cynthia , Schols Henk A. , de Vos Paul , Walvoort Marthe T.C.
Published: November 2020

Scope

Human milk is widely acknowledged as the best food for infants, and that is not just because of nutritional features. Human milk also contains a plethora of bioactive molecules, including a large set of human milk oligosaccharides (hMOs). Especially fucosylated hMOs have received attention for their anti-adhesive effects on pathogens by preventing attachment to the intestinal wall. Because hMOs are generally challenging to produce in sufficient quantities to study and ultimately apply in (medical) infant formula, hMO mimics are interesting compounds to produce and evaluate for their biological effects.

Methods and results

We investigated the digestion, fermentation, and pathogen anti-adhesive capacity of the novel hMO mimic di-fucosyl-β-cyclodextrin (DFβCD). We establish that DFβCD is not digested by α-amylase and also resists fermentation by the microbiota from a 9 month-old infant. In addition, we reveal that DFβCD blocks adhesion of enterotoxigenic E. coli (ETEC) to Caco-2 cells, especially when DFβCD is pre-incubated with ETEC prior to addition to the Caco-2 cells.

Conclusion

Our results suggests that DFβCD functions through a decoy effect. We expect that our results inspire the generation and biological evaluation of other fucosylated hMOs and mimics, to obtain a comprehensive overview of the anti-adhesive power of fucosylated glycans.
Transcription factor residence time dominates over concentration in transcription activation
Authors: Popp Achim P. , Hettich Johannes , Gebhardt J. Christof M.
Published: November 2020

Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases a burst of transcripts before turning inactive again. While the basic course of transcription is well understood, it is unclear how binding of a TF affects the frequency, duration and size of a transcriptional burst. We systematically varied the residence time and concentration of a synthetic TF and characterized the transcription of a reporter gene by combining single molecule imaging, single molecule RNA-FISH, live transcript visualisation and analysis with a novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that TF binding solely affected burst frequency and variations in TF residence time had a stronger influence than variations in concentration. This enabled us to device a model of gene transcription, in which TF binding triggers multiple successive steps before the gene transits to the active state and actual mRNA synthesis is decoupled from TF presence. We quantified all transition times of the TF and the gene, including the TF search time and the delay between TF binding and the onset of transcription. Our quantitative measurements and analysis revealed detailed kinetic insight, which may serve as basis for a bottom-up understanding of gene regulation.
Type VI secretion system killing by commensal Neisseria is influenced by the spatial dynamics of bacteria
Authors: Custodio Rafael , Ford Rhian M. , Ellison Cara J. , Liu Guangyu , Mickute Gerda , Tang Christoph M. , Exley Rachel M.
Published: November 2020

Type VI Secretion Systems (T6SS) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can limit growth of related pathogens. We explored the impact of Tfp expression on N. cinerea T6SS-dependent killing and show that expression of Tfp by prey strains enhances their susceptibility to T6SS, by keeping them in close proximity of T6SS-wielding attacker strains. Our findings have important implications for understanding how spatial constraints during contact-dependent antagonism can shape the evolution of microbial communities.
Microstructural underpinnings and macroscale functional implications of temporal lobe connectivity gradients
Authors: Vos de Wael Reinder , Royer Jessica , Tavakol Shahin , Wang Yezhou , Paquola Casey , Benkarim Oualid , Eichert Nicole , Larivière Sara , Misic Bratislav , Smallwood Jonathan , Valk Sofie L. , Bernhardt Boris C.
Published: November 2020

Abstract

The temporal lobe is implicated in higher cognitive processes and is one of the regions that underwent substantial reorganization during primate evolution. Its functions are instantiated, in part, by its complex layout of structural connections. This study identified low-dimensional representations of structural connectivity variations in human temporal cortex and explored their microstructural underpinnings and associations to macroscale function. We identified three eigenmodes which described gradients in structural connectivity. These gradients reflected interregional variations in cortical microstructure derived from quantitative MRI and post-mortem histology. Gradient-informed models accurately predicted macroscale measures of temporal lobe function. Gradients aligned closely with established measures of functional reconfiguration and areal expansion between macaques and humans, highlighting the important role evolution has played in shaping temporal lobe function. Our results provide robust evidence for three axes of structural connectivity in human temporal cortex with consistent microstructural underpinnings and contributions to large-scale brain network function.
Effects of parasocial interaction, brand credibility and product involvement on celebrity endorsement on microblog
Authors: Gong Wanqi
Published: November 2020

Purpose

This study explores the influence of parasocial interaction (PSI), brand credibility and product involvement on celebrity endorsement, and how PSI interacts with brand and product factors and affects celebrity endorsement synthetically.

Design/methodology/approach

This study employs a 2 (high/low product involvement) by 2 (high/low brand credibility) between-subjects factorial design experiment to test the hypotheses.

Findings

Brand credibility has a positive effect on followers' attitudes toward advertising and products, and product involvement influences its moderation. PSI has salient positive effects on followers' attitudes and behavioral intention, regardless of high/low product involvement. Brand credibility mediates PSI's influence on celebrity endorsement.

Research limitations/implications

The results reinforce the significant effect of PSI on endorsement effectiveness and brand credibility, show the influence of brand credibility and product involvement and show how their influence conditionally interacts with others.

Practical implications

The corporate advertiser should prefer a high PSI celebrity as their endorser. The advertising message design on the microblog also deserves the attention of advertisers.

Originality/value

This study is the primary attempt to construct an integral model to demonstrate the synthetic effect and interaction process of consumers' perception of the endorser, brand and product category factors on celebrity endorsement within the social media context.