bluuebunny/crossref_metadata_2025 huggingface dataset:
Brief Report: Time to Repeat Viral Load Testing Among Unsuppressed Adolescents and Young Adults Living With HIV in Kenya
Authors: Mugo Cyrus , Wilson Katherine S. , Onyango Alvin , Njuguna Irene N. , Mburu Caren W. , Richardson Barbra A. , Oyiengo Laura , Inwani Irene , John-Stewart Grace , Wamalwa Dalton C. , Kohler Pamela K.
Published: September 2020

Background:

Repeat HIV viral load (VL) testing is required after unsuppressed VL to confirm treatment failure. We assessed proportion of adolescents and young adults living with HIV (AYALHIV) in Kenya with a confirmatory VL test and time to repeat testing.

Design:

A retrospective analysis of longitudinal data abstracted from Kenya's national VL database.

Methods:

VL data for AYALHIV who were 10–24 year old between April 2017 and May 2019 were abstracted from 117 HIV care clinics. Records were eligible if at least one VL test was performed ≥6 months after antiretroviral therapy (ART) initiation. The proportion of unsuppressed AYALHIV (≥1000 copies/mL) and time in months between first unsuppressed VL and repeat VL was determined.

Results:

We abstracted 40,928 VL records for 23,969 AYALHIV; of whom, 17,092 (71%) were eligible for this analysis. Of these, 12,122 (71%) were women, median age of 19 years [interquartile range (IQR): 13–23], and median ART duration of 38 months (IQR: 16–76). Among eligible AYALHIV, 4010 (23%) had an unsuppressed VL at first eligible measurement. Only 316 (8%) of the unsuppressed AYALHIV had a repeat VL within 3 months and 1176 (29%) within 6 months. Among 2311 virally unsuppressed AYALHIV with a repeat VL, the median time between the first and the repeat VL was 6 months (IQR: 4–8), with 1330 (58%) having confirmed treatment failure.

Conclusions:

One-quarter of AYALHIV on ART had unsuppressed VL, with less than a third receiving a repeat VL within 6 months. Strategies to improve VL testing practices are needed to improve AYALHIV's outcomes.
Reduction of aggressive and violent behavior toward behavioral health unit staff and other patients: a best practice implementation project
Authors: Badeaux Jennifer E. , Triche Tyrus , Bennett Marsha J.
Published: September 2020

Objectives:

The current project aimed to implement evidence-based recommendations for the management of inpatient aggressive and violent behaviors in four behavioral health units (BHUs) in a mental healthcare area within an academic medical center.

Introduction:

Patient violence against healthcare workers is a global concern, particularly in mental health care. All employees who work in inpatient psychiatric environments are at higher risk for targeted violence than are other healthcare workers. For healthcare organizations and staff, violent episodes involving patients can bring about medical expenses, potential legal expenditure, sick leave and a high turnover rate. The hospital at which this project was implemented had been experiencing a steady increase in violence and aggressive behavior.

Methods:

The project used the Joanna Briggs Institute Practical Application of Clinical Evidence System and Getting Research into Practice audit tool for promoting practice change in four BHUs. A baseline retrospective audit of 10 electronic health records from four BHUs assessed compliance with best practice regarding violent episodes. The Getting Research into Practice tool was used to identify barriers and develop an evidence-based educational strategy for 70 BHU staff aimed to improve compliance with best practice for managing aggression and violence. Staff education compliance was assessed via hospital education department records. A pre and postimplementation staff satisfaction survey assessed perceptions about education, confidence and unit safety.

Results:

The baseline audit indicated that one of the three criteria had 0% compliance. Following implementation of an educational strategy using mock codes for BHU staff, there was 96% improvement in compliance for the BHU staff education audit criterion. Staff de-escalated patients in 83% of the episodes postimplementation. There was a slight decrease (9.1%) in the rate of violence across all four inpatient BHUs. Staff satisfaction survey findings did not show a statistically significant difference.

Conclusion:

Enhanced evidence-based education and mock codes resulted in BHU staff competence and confidence in managing aggressive and/or violent patients. Early signs of a decrease in the violence rate and improvement in the efficient use of de-escalation will be sustained with on-going yearly education, quarterly mock codes and future audits. This project was limited by its small size and short timeframe (21 weeks), making results not generalizable.
The first French translation of Book II of Newton's
Opticks
: omissions, abridgements and the quest for authorship
Authors: Moura Breno Arsioli
Published: September 2020

In this paper, I analyse extracts of what is possibly the first French translation of Newton's
Opticks
, a manuscript discovered by I. Bernard Cohen in the 1960s that is kept today at the Bibliothèque de l'Arsenal in Paris. This manuscript is presumed to have been written by Étienne-François Geoffroy, a French savant who obtained a copy of the first edition of
Opticks
from his close friend Hans Sloane, the then Secretary of the Royal Society. Geoffroy read his translation to the members of the Académie des Sciences at a series of meetings between 1706 and 1707, but the précis was never published. The extracts correspond to Book II in
Opticks
, in which Newton discussed the colours of bodies and the coloured rings in thin and in thick films. This analysis will show that the anonymous author of the translation made several omissions from and abridgments to the content of Book II. In accordance with current historiography on the reception of Newtonian ideas in France, I will also discuss how these omissions and abridgements offer further and relevant evidence to support the presumption that Geoffroy was the real author of the manuscript.
Convalescent plasma therapy: a promising coronavirus disease 2019 treatment strategy
Authors: Piyush Ravikant , Rajarshi Keshav , Khan Rajni , Ray Shashikant
Published: September 2020

The world is passing through a very difficult phase due to the coronavirus disease 2019 (COVID-19) pandemic, which has disrupted almost all spheres of life. Globally, according to the latest World Health Organization report (10 August 2020), COVID-19 has affected nearly 20 million lives, causing 728 013 deaths. Due to the lack of specific therapeutic drugs and vaccines, the outbreak of disease has spawned a corpus of contagious infection all over the world, day by day, without control. As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a very rapid infection rate, it is essential to develop a novel ameliorative and curative strategy as quickly as possible. Convalescent plasma (CP) therapy is a type of adaptive immunity that has already been found to be effective in confronting several infectious diseases from the last two decades. For example, CP therapy was used in the treatment of viral-induced diseases like SARS-CoV epidemics, Middle East respiratory syndrome coronavirus (MERS-CoV) pandemics, Ebola epidemics and H1N1 pandemic. In this review, we have mainly focused on the therapeutic role of CP therapy and its neutralizing effect to fight against the COVID-19 outbreak.
Methanofollis fontis sp. nov., a methanogen isolated from marine sediment near a cold seep at Four-Way Closure Ridge offshore southwestern Taiwan
Authors: Chen Sheng-Chung , Teng Nai-Hsuan , Lin Yu-Shih , Lai Mei-Chin , Chen Hsin-Hung , Wang Chau-Chang
Published: September 2020

A mesophilic, hydrogenotrophic methanogen, strain FWC-SCC2T, was isolated from deep-sea sediments collected by a real-time video multiple-corer at the C5-6 station near a cold seep at Four-Way Closure Ridge region during R/V Ocean Researcher III ORIII-1900 cruise in 2015. The cells were irregular cocci, non-motile and 0.8–1.2 µm in diameter. The methanogenic substrates utilized by strain FWC-SCC2Twere formate or H2+CO2, but not acetate, methanol, ethanol or methylamines. Strain FWC-SCC2Twas lysed in SDS (0.01 %, w/v). TheMrof surface-layer protein was 116 400. The optimum growth conditions of strain FWC-SCC2Twere 37 °C, 0.17 M NaCl and pH 6.7–7.0. The genomic DNA G+C content calculated from the genome sequence of strain FWC-SCC2Twas 59.5 mol %. Phylogenetic analysis revealed that strain FWC-SCC2Twas a member of the genusMethanofollis, and was most closely related toMethanofollis tationisChile 9T(97.6 % similarity of 16S rRNA gene sequence) and shared 97.4, 95.9, 95.9 and 95.4 % withMethanofollis liminatansGKZPZT,Methanofollis formosanusML15T,Methanofollis aquaemarisN2F9704TandMethanofollis ethanolicusHASUT, respectively. The genome relatedness values between strain FWC-SCC2TandM. tationisDSM 2702Twere estimated by average nucleotide identity and digital DNA–DNA hybridization analyses and the results were 79.4 and 21.2 %, respectively. Based on the differences in physiological and biochemical properties, 16S rRNA gene phylogeny and genome relatedness presented here, it is suggested that strain FWC-SCC2Trepresents a novel species of the genusMethanofollis, and the nameMethanofollis fontissp. nov. is proposed. The type strain is FWC-SCC2T(=BCRC AR10052T=DSM 107935T= NBRC 113164T).
Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts
Authors: Suryawanshi Hemant , Yang Hua , Lubetzky Michelle , Morozov Pavel , Lagman Mila , Thareja Gaurav , Alonso Alicia , Li Carol , Snopkowski Catherine , Belkadi Aziz , Mueller Franco B. , Lee John R. , Dadhania Darshana M. , Salvatore Steven P. , Seshan Surya V. , Sharma Vijay K. , Suhre Karsten , Suthanthiran Manikkam , Tuschl Thomas , Muthukumar Thangamani
Published: September 2020

We tested the hypothesis that single-cell RNA-sequencing (scRNA-seq) analysis of human kidney allograft biopsies will reveal distinct cell types and states and yield insights to decipher the complex heterogeneity of alloimmune injury. We selected 3 biopsies of kidney cortex from 3 individuals for scRNA-seq and processed them fresh using an identical protocol on the 10x Chromium platform; (i) HK: native kidney biopsy from a living donor, (ii) AK1: allograft kidney with transplant glomerulopathy, tubulointerstitial fibrosis, and worsening graft function, and (iii) AK2: allograft kidney after successful treatment of active antibody-mediated rejection. We did not study T-cell-mediated rejections. We generated 7217 high-quality single cell transcriptomes. Taking advantage of the recipient-donor sex mismatches revealed by X and Y chromosome autosomal gene expression, we determined that in AK1 with fibrosis, 42 months after transplantation, more than half of the kidney allograft fibroblasts were recipient-derived and therefore likely migratory and graft infiltrative, whereas in AK2 without fibrosis, 84 months after transplantation, most fibroblasts were donor-organ-derived. Furthermore, AK1 was enriched for tubular progenitor cells overexpressing profibrotic extracellular matrix genes. AK2, eight months after successful treatment of rejection, contained endothelial cells that expressed T-cell chemoattractant cytokines. In addition to these key findings, our analysis revealed unique cell types and states in the kidney. Altogether, single-cell transcriptomics yielded novel mechanistic insights, which could pave the way for individualizing the care of transplant recipients.
Genome assembly and transcriptome analysis provide insights into the anti-schistosome mechanism ofMicrotus fortis
Authors: Li Hong , Wang Zhen , Chai Shumei , Bai Xiong , Ding Guohui , Li Junyi , Xiao Qingyu , Miao Benpeng , Lin Weili , Feng Jie , Gao Cheng , Li Yuanyuan , Li Bin , Hu Wei , Lin Jiaojiao , Fu Zhiqiang , Xie Jianyuan , Li Yixue
Published: September 2020

Microtus fortis(M. fortis) so far is the only mammal host that exhibits intrinsic resistance againstSchistosoma japonicuminfection. However, the underlying molecular mechanisms of this intrinsic resistance are not yet known. Here we performed the firstde novogenome assembly ofM. fortis, comprehensive gene annotation and evolution analysis. Furthermore, we compared the recovery rate of schistosome, pathological change and liver transcriptome between non-permissive hostM. fortisand susceptible host mouse at different time points after Schistosome infection. We reveal that Immune response ofM. fortisand mouse is different in time and type.M. fortisactivates immune and inflammatory responses on the 10thdays post infection, involving in multiple pathways, such as leukocyte extravasation, antibody activation (especially IgG3), Fc-gamma receptor mediated phagocytosis, and interferon signaling cascade. The strong immune responses ofM. fortisin early stages of infection play important roles in preventing the development of schistosome. On the contrary, intense immune response occurred in mouse in late stages of infection (28~42 days post infection), and cannot eliminate schistosome. Infected mouse suffers severe pathological injury and continuous decrease of important functions such as cell cycle and lipid metabolism. Our findings offer new insights to the intrinsic resistance mechanism ofM. fortisagainst schistosome infection. The genome sequence also provides bases for future studies of other important traits inM. fortis.
Cell-to-cell spread inhibiting antibodies constitute a correlate of protection against Herpes Simplex Virus Type 1 reactivations
Authors: Wolf Susanne , Alt Mira , Dittrich Robin , Dirks Miriam , Schipper Leonie , Aufderhorst Ulrich Wilhelm , Rainer Kordula , Dittmer Ulf , Witzke Oliver , Giebel Bernd , Trilling Mirko , Heilingloh Christiane Silke , Lotfi Ramin , Roggendorf Michael , Krawczyk Adalbert
Published: September 2020

Herpes simplex viruses (HSV) cause ubiquitous human infections. For vaccine development, knowledge concerning correlates of protection against HSV is essential. Therefore, we investigated if humans principally can produce highly protective cell-to-cell spread inhibiting antibodies upon natural infection and whether such antibody responses correlate with protection from HSV reactivation. We established a high-throughput HSV-1 GFP reporter virus-based assay and screened 2496 human plasma samples for HSV-1 cell-to-cell spread inhibiting antibodies. We conducted a survey among the blood donors to analyze the correlation between the presence of cell-to-cell spread inhibiting antibodies in plasma and the frequency of HSV reactivations. In total, 128 of 2496 blood donors (5.1 %) exhibited high levels of HSV-1 cell-to-cell spread inhibiting antibodies in the plasma. Such individuals showed a significantly lower frequency of HSV reactivations compared to subjects without sufficient levels of HSV-1 cell-to-cell spread inhibiting antibodies. This study provides two important findings: (I) a fraction of humans produce HSV cell-to-cell spread inhibiting antibodies upon natural infection and (II) such antibodies correlate with protection against recurrent HSV. Moreover, these elite neutralizers can provide promising material for hyperimmunoglobulin, the isolation of superior antiviral antibodies and information for the design of a vaccine against HSV.

Importance

Herpes simplex virus 1 infections can cause painful mucosal lesions at the oral or genital tract and severe, life threatening disease in immunosuppressed patients or neonates. There is no approved vaccine available, and the emergence of drug resistances especially in long time treated patients makes the treatment increasingly difficult. We tested 2496 people for HSV-1 cell-to-cell spread inhibiting antibodies. Five percent exhibited functional titers such antibodies and showed significantly lower risk of reactivations, uncovering cell-to-cell spread inhibiting antibodies as a correlate of protection against Herpes simplex virus reactivations. Isolation of the cell-to-cell spread inhibiting antibodies from B-cells of these donors may contribute to develop novel antibody-based interventions for prophylactic and therapeutic use and provide starting material for vaccine development.
Effects of kin recognition on root traits of wheat germplasm over 100 years of breeding
Authors: Kiær Lars Pødenphant , Weiner Jacob , Rasmussen Camilla Ruø
Published: September 2020

Plant root and shoot growth has been shown to depend on the relatedness of co-cultivated genotypes, implying the existence of ‘kin recognition’ mechanisms mediated by root exudates. If confirmed, this has important implications for crop breeding.

We present the first large-sale investigation of kin recognition in a crop germplasm collection comprising 30 North-European cultivars and landraces of spring wheat, spanning 100 years of breeding history. In a full diallelin vitrobioassay, we compared root growth of seedlings when growing in pure substrate, or in substrate previously occupied by a donor seedling from the same (KIN) or another (NONKIN) genotype.

Seedlings growing in KIN or NONKIN substrate generally had longer but not more roots than seedlings growing in pure substrate. Responses were generally larger in longer roots, suggesting that root elongation was promoted throughout the growth period. Responses to KIN and NONKIN substrates were found to range from positive to negative, with root length responses to kin being increasingly positive with year of release. Seedlings growing in KIN substrate generally had shorter but not fewer roots than seedlings growing in NONKIN substrate. This kin recognition ranged from positive to negative across the specific donor-receiver combinations and did not change systematically with year of release of either genotype. Root traits in both KIN and NONKIN substrate were affected by both donor and receiver genotype, and these effects were generally larger than the effect of specific combinations. Genotypes showing higher levels of kin recognition also tended to invoke larger responses in other genotypes. Kin recognition was reduced in most cases by the addition of sodiumorthovanadate, a chemical inhibitor, supporting the hypothesis that kin responses were mediated by changes in the chemical constitution of the substrate.

The identified patterns of kin recognition across the germplasm collection were complex, suggesting a multigenic background and shared breeding history of the genotypes. We conclude that kin response represents a potential target for crop breeding which can improve root foraging and competitive interactions.
Sex, males, and hermaphrodites in the scale insectIcerya purchasi
Authors: Mongue Andrew J. , Michaelides Sozos , Coombe Oliver , Tena Alejandro , Kim Dong-Soon , Normark Benjamin B. , Gardner Andy , Hoddle Mark S. , Ross Laura
Published: September 2020

Androdioecy (the coexistence of males and hermaphrodites) is a rare mating system for which the evolutionary dynamics are poorly understood. Here we study the only presumed case of androdioecy in insects, found in the cottony cushion scale,Icerya purchasi. In this species, female-like hermaphrodites have been shown to produce sperm and self-fertilize. However, rare males are sometimes observed too. In a large population-genetic analysis, we show for the first time that although self-fertilization appears to be the primary mode of reproduction, rare outbreeding events between males and hermaphrodites do occur, and we thereby confirm androdioecy as the mating system ofI. purchasi. Thus, this insect appears to have the colonization advantages of a selfing organism while also benefitting from periodic reintroduction of genetic variation through outbreeding with males.
QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI
Authors: Cieslak Matthew , Cook Philip A. , He Xiaosong , Yeh Fang-Cheng , Dhollander Thijs , Adebimpe Azeez , Aguirre Geoffrey K. , Bassett Danielle S. , Betzel Richard F. , Bourque Josiane , Cabral Laura M. , Davatzikos Christos , Detre John , Earl Eric , Elliott Mark A. , Fadnavis Shreyas , Fair Damien A. , Foran Will , Fotiadis Panagiotis , Garyfallidis Eleftherios , Giesbrecht Barry , Gur Ruben C. , Gur Raquel E. , Kelz Max , Keshavan Anisha , Larsen Bart S. , Luna Beatriz , Mackey Allyson P. , Milham Michael , Oathes Desmond J. , Perrone Anders , Pines Adam R. , Roalf David R. , Richie-Halford Adam , Rokem Ariel , Sydnor Valerie J. , Tapera Tinashe M. , Tooley Ursula A. , Vettel Jean M. , Yeatman Jason D. , Grafton Scott T. , Satterthwaite Theodore D.
Published: September 2020

Diffusion-weighted magnetic resonance imaging (dMRI) has become the primary method for non-invasively studying the organization of white matter in the human brain. While many dMRI acquisition sequences have been developed, they all sample q-space in order to characterize water diffusion. Numerous software platforms have been developed for processing dMRI data, but most work on only a subset of sampling schemes or implement only parts of the processing workflow. Reproducible research and comparisons across dMRI methods are hindered by incompatible software, diverse file formats, and inconsistent naming conventions. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing upon a diverse set of software suites to capitalize upon their complementary strengths, QSIPrep automatically applies best practices for dMRI preprocessing, including denoising, distortion correction, head motion correction, coregistration, and spatial normalization. Throughout, QSIPrep provides both visual and quantitative measures of data quality as well as “glass-box” methods reporting. Taken together, these features facilitate easy implementation of best practices for processing of diffusion images while simultaneously ensuring reproducibility.
Melanopsin retinal ganglion cell-driven contribution to visual and cognitive brain responses in LHON
Authors: Evangelisti Stefania , Morgia Chiara La , Testa Claudia , Manners David N , Brizi Leonardo , Bianchini Claudio , Carbonelli Michele , Barboni Piero , Sadun Alfredo A. , Tonon Caterina , Carelli Valerio , Vandewalle Gilles , Lodi Raffaele
Published: September 2020

Melanopsin retinal ganglion cells (mRGCs) are intrinsically photosensitive photoreceptors contributing to visual and non-image-forming functions of the eye. Isolating mRGC roles in humans is challenging, therefore mRGCs functions remains to be fully characterized.

We explored mRGCs contribution to light-driven visual and cognitive brain responses in Leber’s Hereditary Optic Neuropathy (LHON), given mRGC relative sparing in LHON. Twelve patients and twelve matched healthy controls (HC) participated in an fMRI protocol including visual and visual-cognitive paradigms under blue (480nm) and red light (620nm).

Higher occipital activation was found in response to sustained bluevs.red stimulation in LHONvs.HC. Similarly, brain responses to the executive task were larger under bluevs.red light in LHON over lateral prefrontal cortex.

These findings are in line with LHON mRGCs relative sparing and support mRGCs contribution to non-visual and visual functions in humans, with potential implication for visual rehabilitation in optic neuropathy patients.
Pharmacological and genetic manipulations of Ca2+signaling have contrasting effects on auxin-regulated trafficking
Authors: Wang Ren , Himschoot Ellie , Grenzi Matteo , Chen Jian , Krebs Melanie , Schumacher Karin , Nowack Moritz K. , Van Damme Daniël , De Smet Ive , Beeckman Tom , Costa Alex , Friml Jiří , Vanneste Steffen
Published: September 2020

A large part of a plants’ developmental plasticity relies on the activities of the phytohormone auxin and the regulation of its own distribution. This process involves a cohort of transcriptional and non-transcriptional effects of auxin on polar auxin transport, regulating the abundancy, biochemical activity and polar localization of the molecular components, predominantly PIN auxin exporters. While the transcriptional auxin signaling cascade has been well characterized, the mechanism and role of non-transcriptional auxin signaling remains largely elusive. Here, we addressed the potential involvement of auxin-induced Ca2+signaling in auxin’s inhibitory effect on PIN endocytic trafficking. On the one hand, exogenous manipulations of Ca2+availability and signaling effectively antagonized auxin effects suggesting that auxin-induced Ca2+signaling is required for inhibition of internalization. On the other hand, we addressed the auxin-mediated inhibition of PIN internalization in the auxin signaling (tir1afb2,3) or Ca2+channel (cngc14) mutants. These mutants were strongly defective in auxin-triggered Ca2+signaling, but not in auxin-inhibited internalization. These data imply that, while Ca2+signaling may be required for normal PIN trafficking, auxin-mediated increase in Ca2+signaling is not a direct part of a downstream mechanism that mediates auxin effects on Brefeldin A-visualized PIN intercellular aggregation. These contrasting results obtained by comparing the mutant analysis versus the exogenous manipulations of Ca2+availability and signaling illustrate the critical importance of genetics to unravel the role of Ca2+in a process of interest.
A trans-omics comparison reveals common gene expression strategies in four model organisms and exposes similarities and differences between them
Authors: Forés-Martos Jaume , Forte Anabel , García-Martínez José , Pérez-Ortín José E.
Published: September 2020

The ultimate goal of gene regulation should focus on the protein level. However, as mRNA is an obligate intermediary, and because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained following different strategies. By studying omics datasets for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CES) for functionally-related genes in the yeastSaccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the distantly related yeastSchizosaccharomyces pombeand cultured human HeLa cells. We also use genomic datasets from the model prokaryoteEscherichia colias an external reference. We show that CES are also present in all the studied organisms and the differences in them between organisms can be used to establish their phylogenetic relationships. The phenogram based on 6VP has the expected topology for the phylogeny of these four organisms, but shows interesting branch length differences to DNA sequence-based trees.

The analysis of the correlations among the six variables supports that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role in it. We propose that all living cells use CES for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CES have been modeled by evolution to adapt to the specific life circumstances of each organism. The obtained phenograms may reflect both evolutionary constraints in expression strategies, and lifestyle convergences.
Determination of the molecular reach of the protein tyrosine phosphatase SHP-1
Authors: Clemens Lara , Kutuzov Mikhail , Bayer Kristina Viktoria , Goyette Jesse , Allard Jun , Dushek Omer
Published: September 2020

Immune receptor signalling proceeds by the binding (or tethering) of enzymes to their cytoplasmic tails before they catalyse reactions on substrates within reach. This is the case for the enzyme SHP-1 that, upon tethering to the inhibitory receptor PD-1, dephosphorylates membrane substrates to suppress T cell activation. Precisely how tethering regulates SHP-1 activity is incompletely understood. Here, we use surface plasmon resonance to measure binding, catalysis, and molecular reach for PD-1 tethered SHP-1 reactions. We find that the reach of PD-1—SHP-1 complexes is dominated by the 13.0 nm reach of SHP-1 itself. This is longer than an estimate from the structure of the allosterically active conformation (5.3 nm), suggesting that SHP-1 explores multiple active conformations. Using modelling, we show that when uniformly distributed, PD-1—SHP-1 complexes can only reach 15% of substrates but this increases to 90% when they are co-clustered. When within reach, we show that membrane recruitment increases the activity of SHP-1 by a 1000-fold increase in local concentration. The work highlights how molecular reach regulates the activity of membrane-recruited SHP-1 with insights applicable to other membrane-tethered reactions.

Significance statement

Immune receptors transduce signals by recruiting (or tethering) cytoplasmic enzymes to their tails at the membrane. When tethered, these enzymes catalyse reactions on other substrates to propagate signalling. Precisely how membrane tethering regulates enzyme activity is incompletely understood. Unlike other tethered reactions, where the enzyme tethers to the substrate, the substrate in this case is a different receptor tail. Therefore, the ability of the receptor-tethered enzyme to reach a substrate can be critical in controlling reaction rates. In this work, we determine the molecular reach for the enzyme SHP-1 and the receptor PD-1 to which it can tether, and show how molecular reach controls receptor signalling.
BayesSpace enables the robust characterization of spatial gene expression architecture in tissue sections at increased resolution
Authors: Zhao Edward , Stone Matthew R. , Ren Xing , Pulliam Thomas , Nghiem Paul , Bielas Jason H. , Gottardo Raphael
Published: September 2020

Recently developed spatial gene expression technologies such as the Spatial Transcriptomics and Visium platforms allow for comprehensive measurement of transcriptomic profiles while retaining spatial context. However, existing methods for analyzing spatial gene expression data often do not efficiently leverage the spatial information and fail to address the limited resolution of the technology. Here, we introduce BayesSpace, a fully Bayesian statistical method for clustering analysis and resolution enhancement of spatial transcriptomics data that seamlessly integrates into current transcriptomics analysis workflows. We show that BayesSpace improves the identification of transcriptionally distinct tissues from spatial transcriptomics samples of the brain, of melanoma, and of squamous cell carcinoma. In particular, BayesSpace’s improved resolution allows the identification of tissue structure that is not detectable at the original resolution and thus not recovered by other methods. Using anin silicodataset constructed from scRNA-seq, we demonstrate that BayesSpace can spatially resolve expression patterns to near single-cell resolution without the need for external single-cell sequencing data. In all, our results illustrate the utility BayesSpace has in facilitating the discovery of biological insights from a variety of spatial transcriptomics datasets.
Laser nanobubbles induce immunogenic cell death in breast cancer
Authors: Nguyen Hieu T.M. , Katta Nitesh , Widman Jessica A. , Takematsu Eri , Feng Xu , Torres Susana H. , Betancourt Tania , Baker Aaron B. , Suggs Laura J. , Milner Thomas E. , Tunnell James W.
Published: September 2020

Recent advances in immunotherapy have highlighted a need for therapeutics that initiate immunogenic cell death in tumors to stimulate the body’s immune response to cancer. This study examines whether laser-generated bubbles surrounding nanoparticles (“nanobubbles”) induce an immunogenic response for cancer treatment. A single nanosecond laser pulse at 1064 nm generates micron-sized bubbles surrounding gold nanorods in the cytoplasm of breast cancer cells. Cell death occurred in cells treated with nanorods and irradiated but not in cells with irradiation treatment alone. Cells treated with nanorods and irradiation had increased damage-associated molecular patterns (DAMPs), including increased expression of chaperone proteins human high mobility group box 1 (HMGB1), adenosine triphosphate (ATP), and heat shock protein 70 (HSP70). This enhanced expression of DAMPs led to the activation of dendritic cells. Overall, this treatment approach is a rapid and highly specific method to eradicate tumor cells with simultaneous immunogenic cell death signaling, showing potential as a combination strategy for immunotherapy.
Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate
Authors: Himeoka Yusuke , Gummesson Bertil , Sørensen Michael A. , Svenningsen Sine Lo , Mitarai Namiko
Published: September 2020

Stationary phase is the general term for the state a bacterial culture reaches when no further increase in cell number occurs due to the exhaustion of nutrients in the growth medium. Depending on the type of nutrient that is first depleted, the metabolic state of the stationary phase cells may vary greatly, and the subsistence strategies that best support cell survival may differ. As ribosomes play a central role in bacterial growth and energy expenditure, ribosome preservation is a key element of such strategies. To investigate the degree of ribosome preservation during long-term starvation, we compared the dynamics of ribosomal RNA (rRNA) levels of carbon-starved and phosphorus-starvedEscherichia colicultures for up to 28 days. The starved cultures’ contents of full-length 16S and 23S rRNA decreased exponentially and phosphorus starvation resulted in much more rapid rRNA degradation than carbon starvation. Bacterial survival kinetics were also quantified over the starvation period. Upon replenishment of the nutrient in question, carbon-starved cells resumed growth faster than cells starved for phosphate for the equivalent amount of time, and for both conditions, the lag time increased with the starvation time. While these results are in accordance with the hypothesis that cells with a larger ribosome pool recover more readily upon replenishment of nutrients, we also observed that the lag time kept increasing with increasing starvation time, also when the amount of rRNA per viable cell remained constant.

Importance

Bacteria grow exponentially consuming nutrients, and then starve until the next nutrient is added. To elucidate the survival kinetics of the cells under starvation, we performed month-long, carbon and phosphorus starvation experiments ofEscherichia colimonitoring ribosomal RNA levels and survival of the cells. The starved cultures’ concentration of ribosomal RNA dropped exponentially with time, and the speed of degradation was much quicker under the phosphorus starvation than the carbon starvation. We have also quantified the lag time, i.e., the time needed to resume growth when the starved cells are transferred into fresh media. The observation revealed that the lag time increases with starvation time and the phosphorus starvation has a greater impact on the increase of the lag time.
VisualizingBorrelia burgdorferiinfection using a small molecule imaging probe
Authors: Sell Madeline G , Alcorta David A. , Padilla Andrew E. , Nollner Dakota W. , Hasenkampf Nicole R. , Lambert Havard S. , Embers Monica E. , Spector Neil L.
Published: September 2020

In vivodiagnostic imaging of bacterial infections is currently reliant on targeting their metabolic pathways, an ineffective method to identify microbial species with low metabolic activity. Here we establish HS-198 as a small molecule-fluorescent conjugate that selectively targets the highly conserved bacterial protein, HtpG (High temperature protein G), withinB. burgdorferi, the bacteria responsible for Lyme Disease. We describe the use of HS-198 to target morphologic forms ofB. burgdorferiin both the logarithmic growth phase and the metabolically dormant stationary phase. Furthermore, in a murine infection model, systemically injected HS-198 identifiedB. burgdorferias revealed by imaging in post necropsy tissue sections. These findings demonstrate how small molecule probes directed at conserved bacterial protein targets can function to identify the microbe using non-invasive imaging and potentially as scaffolds to deliver antimicrobial agents to the pathogen.
Diagnosing Chronic Obstructive Airway Disease: a diagnostic accuracy study of a smartphone delivered algorithm combining patient-reported symptoms and cough analysis for use in acute care consultations
Authors: Porter Paul , Brisbane Joanna , Abeyratne Udantha , Bear Natasha , Wood Javan , Peltonen Vesa , Della Phill , Purdie Fiona , Smith Claire , Claxton Scott
Published: September 2020

Background

Rapid and accurate diagnosis of Chronic Obstructive Pulmonary Disease (COPD) is problematic in acute-care settings, particularly in the presence of infective comorbidities.

Objective

The aim of this study was to develop a rapid, smartphone-based algorithm for the detection of COPD, in the presence or absence of acute respiratory infection, and then evaluate diagnostic accuracy on an independent validation set.

Methods

Subjects aged 40-75 years with or without symptoms of respiratory disease who had no chronic respiratory condition apart from COPD, chronic bronchitis or emphysema, were recruited into the study. The algorithm analysed 5 cough sounds and 4 patient-reported clinical symptoms, providing a diagnosis in less than 1 minute. Clinical diagnoses were determined by a specialist physician using all available case notes, including spirometry where available.

Results

The algorithm demonstrated high percent agreement (PA) with clinical diagnosis for COPD in the total cohort (n=252, Positive PA=93.8%, Negative PA=77.0%, AUC=0.95); in subjects with pneumonia or infective exacerbations of COPD (n=117, PPA=86.7%, NPA=80.5%, AUC=0.93) and in subjects without an infective comorbidity (n=135, PPA=100.0%, NPA=74.0%, AUC=0.97.) In those who had their COPD confirmed by spirometry (n=229), PPA = 100.0% and NPA = 77.0%, AUC=0.97.

Conclusions

The algorithm demonstrates high agreement with clinical diagnosis and rapidly detects COPD in subjects presenting with or without other infective lung illnesses. The algorithm can be installed on a smartphone to provide bedside diagnosis of COPD in acute care settings, inform treatment regimens and identify those at increased risk of mortality due to seasonal or other respiratory ailments.
Detecting sleep in free-living conditions without sleep-diaries: a device-agnostic, wearable heart rate sensing approach
Authors: Perez-Pozuelo Ignacio , Posa Marius , Spathis Dimitris , Westgate Kate , Wareham Nicholas , Mascolo Cecilia , Brage Søren , Palotti Joao
Published: September 2020

The rise of multisensor wearable devices offers a unique opportunity for the objective inference of sleep outside laboratories, enabling longitudinal monitoring in large populations. To enhance objectivity and facilitate cross-cohort comparisons, sleep detection algorithms in free-living conditions should rely on personalized but device-agnostic features, which can be applied without laborious human annotations or sleep diaries. We developed and tested a heart rate-based algorithm that captures inter- and intra-individual sleep differences, does not require human input and can be applied in free-living conditions. The algorithm was evaluated across four study cohorts using different research- and consumer-grade devices for over 2,000 nights. Recording periods included both 24-hour free-living and conventional lab-based night-only data. Our method was systematically optimized and evaluated against polysomnography (PSG) and sleep diaries and compared to sleep periods produced by accelerometry-based angular change algorithms. Against sleep diaries, the algorithm yielded a mean squared error (MSE) of 0.04 to 0.06 and a total sleep time deviation of -2.70 (±5.74) and 12.80 (±3.89) minutes, respectively. When evaluated with PSG lab studies, the MSE ranged between 0.06 and 0.11 yielding a time deviation between -29.07 and -55.04 minutes. Our findings suggest that the heart rate-based algorithm can reliably and objectively infer sleep under longitudinal, free-living conditions, independent of the wearable device used. This represents the first open-source algorithm that can infer sleep using heart rate signals without actigraphy or diary annotations.
Quantifying Inaccuracies in Modeling COVID-19 Pandemic within a Continuous Time Picture
Authors: Bâldea Ioan
Published: September 2020

Typically, mathematical simulation studies on COVID-19 pandemic forecasting are based on deterministic differential equations which assume that both the number (n) of individuals in various epidemiological classes and the time (t) on which they depend are quantities that vary continuous. This picture contrasts with the discrete representation ofnandtunderlying the real epidemiological data reported in terms daily numbers of infection cases, for which a description based on finite difference equations would be more adequate. Adopting a logistic growth framework, in this paper we present a quantitative analysis of the errors introduced by the continuous time description. This analysis reveals that, although the height of the epidemiological curve maximum is essentially unaffected, the positionobtained within the continuous time representation is systematically shifted backwards in time with respect to the positionpredicted within the discrete time representation. Rather counterintuitively, the magnitude of this temporal shiftis basically insensitive to changes in infection rateκ. For a broad range ofκvalues deduced from COVID-19 data at extreme situations (exponential growth in time and complete lockdown), we found a rather robust estimateτ≃ −2.65 day−1. Being obtained without any particular assumption, the present mathematical results apply to logistic growth in general without any limitation to a specific real system.
Beneficial and harmful outcomes of tocilizumab in severe COVID-19: a systematic review and meta-analysis
Authors: Rubio-Rivas Manuel , Mora-Luján Jose María , Montero Abelardo , Homs Narcís A. , Rello Jordi , Corbella Xavier
Published: September 2020

Objectives

Pending for randomized control trials, the use of tocilizumab (TCZ) in COVID-19 remains controversial. We performed a systematic review and meta-analysis to investigate the effect on clinical outcomes of TCZ to treat severe COVID-19.

Methods

From 1 January to 21 August 2020, we searched PubMed (via MEDLINE), Scopus, and medRxiv repository databases for observational studies in any language reporting efficacy and safety of TCZ use in hospitalized adults with COVID-19. Independent and dually data extraction and quality assessment were performed.

Results

Of 57 eligible studies, 27 controlled and 30 not. The overall included patients were 8,128: 4,021 treated with TCZ, in addition to standard of care (SOC), and 4,107 only receiving SOC. The pooled mortality was lower in the TCZ-group, with a relative risk (RR) of 0.73 (95%CI 0.57-0.93; p=0.010). TCZ-treated patients were transferred to the intensive care unit (ICU) in a higher proportion, but ICU mortality was lower than in the control group. Conversely, a higher proportion of TCZ-treated patients developed secondary infections after TCZ use.

Conclusions

TCZ seems beneficial in preventing in-hospital mortality in severe, non-critically ill COVID-19 patients. However, patients receiving TCZ appear to be at higher risk for secondary infections, especially those admitted to ICU.
Optimized iLID membrane anchors for local optogenetic protein recruitment
Authors: Natwick Dean E. , Collins Sean R.
Published: September 2020

Optogenetic protein dimerization systems are powerful tools to investigate the biochemical networks that cells use to make decisions and coordinate their activities. These tools, including the improved Light-Inducible Dimer (iLID) system, offer the ability to selectively recruit components to subcellular locations, such as micron-scale regions of the plasma membrane. In this way, the role of individual proteins within signaling networks can be examined with high spatiotemporal resolution. Currently, consistent recruitment is limited by heterogeneous optogenetic component expression, and spatial precision is diminished by protein diffusion, especially over long timescales. Here, we address these challenges within the iLID system with alternative membrane anchoring domains and fusion configurations. Using live cell imaging and mathematical modeling, we demonstrate that the anchoring strategy affects both component expression and diffusion, which in turn impact recruitment strength, kinetics, and spatial dynamics. Compared to the commonly used C-terminal iLID fusion, fusion proteins with large N-terminal anchors show stronger local recruitment, slower diffusion of recruited components, and efficient recruitment over wider gene expression ranges. We also define guidelines for component expression regimes for optimal recruitment for both cell-wide and subcellular recruitment strategies. Our findings highlight key sources of imprecision within light-inducible dimer systems and provide tools that allow greater control of subcellular protein localization across diverse cell biological applications.

Significance

Optogenetic light-inducible dimer systems, such as iLID, offer the ability to examine cellular signaling networks on second timescales and micrometer spatial scales. Confined light stimulation can recruit proteins to subcellular regions of the plasma membrane, and local signaling effects can be observed. Here, we report alternative iLID fusion proteins that display stronger and more spatially confined membrane recruitment. We also define optogenetic component expression regimes for optimal recruitment and show that slow-diffusing iLID proteins allow more robust recruitment in cell populations with heterogenous expression. These tools should improve the spatiotemporal control and reproducibility of optogenetic protein recruitment to the plasma membrane.
Spatial heterogeneity in resources alters selective dynamics inDrosophila melanogaster
Authors: Wilson Audrey E , Siddiqui Ali , Dworkin Dr. Ian
Published: September 2020

Environmental features can alter the behaviours and phenotypes of organisms and populations evolving within them including the dynamics between natural and sexual selection. Experimental environmental manipulation, particularly when conducted in experiments where the dynamics of the purging of deleterious alleles are compared, has demonstrated both direct and indirect effects on the strength and direction of selection. However, many of these experiments are conducted with fairly simplistic environments when it is not always clear how or why particular forms of spatial heterogeneity may influence behaviour or selection. UsingDrosophila melanogaster, we tested three different spatial environments designed to determine if spatial constraint of critical resources influences the efficiency of natural and sexual selection. We conducted two allele purging experiments to 1) assess the effects of these spatial treatments on the selective dynamics of six recessive mutations, and 2) determine how these dynamics changed when sexual selection was relaxed and the spatial area was reduced. We found that allele purging dynamics depended on spatial environment, however the patterns of purging rates between the environments differed across distinct deleterious mutations. We also found that for two of the mutations, the addition of sexual selection increased the purging rate.