bluuebunny/crossref_metadata_2025 huggingface dataset:
Bicentric evaluation of stabilizing sampling tubes for assessment of monocyte HLA-DR expression in clinical samples
Authors: Hamada Sarah , Jeannet Robin , Gossez Morgane , Cour Martin , Argaud Laurent , Francois Bruno , Daix Thomas , Venet Fabienne , Monneret Guillaume
Published: May 2021

Background

Diminished expression of human leukocyte antigen DR on circulating monocytes (mHLA-DR), measured by standardized flow cytometry procedure, is a reliable indicator of immunosuppression in severely injured intensive care unit patients. As such, it is used as stratification criteria in clinical trials evaluating novel immunostimulating therapies. Pre-analytical constraints relative to the short delay between blood sampling and flow cytometry staining have nevertheless limited its use in multicentric studies. The objective of the present work was to compare mHLA-DR expression between whole blood samples simultaneously drawn in EDTA or Cyto-Chex® BCT tubes.

Methods

In 2 university hospitals, mHLA-DR was assessed in fresh whole blood from septic patients (n = 12) and healthy donors (n = 6) simultaneously sampled on EDTA and Cyto-Chex® BCT tubes. Staining was performed immediately after sampling and after blood storage at room temperature.

Results

We observed the remarkable stability of mHLA-DR results when blood was collected in Cyto-Chex® BCT tubes (until 48-72 h). On baseline values, despite good correlation between tubes (r = 0.98, p< 0.001), mHLA-DR expression was systematically lower with Cyto-Chex® BCT.

Conclusion

The present reports confirms the great potential of Cyto-Chex® BCT tubes to delay mHLA-DR staining in centers without rapid access to flow cytometry facilities. However, a 30 % gap exists between results obtained with EDTA and Cyto-Chex® BCT tubes. As current thresholds for clinical decisions were obtained with EDTA samples, further studies are needed to confirm clinical thresholds with Cyto-Chex® BCT tubes.
Therapeutic Anticoagulation in Non-Critically Ill Patients with Covid-19
Authors:   The ATTACC, ACTIV-4a, and REMAP-CAP Investigators, Lawler Patrick R. , Goligher Ewan C. , Berger Jeffrey S. , Neal Matthew D. , McVerry Bryan J. , Nicolau Jose C. , Gong Michelle N. , Carrier Marc , Rosenson Robert S. , Reynolds Harmony R. , Turgeon Alexis F. , Escobedo Jorge , Huang David T. , Bradbury Charlotte Ann , Houston Brett L. , Kornblith Lucy Z. , Kumar Anand , Kahn Susan R. , Cushman Mary , McQuilten Zoe , Slutsky Arthur S. , Kim Keri S. , Gordon Anthony C. , Kirwan Bridget-Anne , Brooks Maria M. , Higgins Alisa M. , Lewis Roger J. , Lorenzi Elizabeth , Berry Scott M. , Berry Lindsay R. , Angus Derek C. , McArthur Colin J. , Webb Steven A. , Farkouh Michael E. , Hochman Judith S. , Zarychanski Ryan
Published: May 2021

Background

Thrombo-inflammation may contribute to morbidity and mortality in Covid-19. We hypothesized that therapeutic-dose anticoagulation may improve outcomes in non-critically ill patients hospitalized for Covid-19.

Methods

In an open-label adaptive multiplatform randomized controlled trial, non-critically ill patients hospitalized for Covid-19, defined by the absence of critical care-level organ support at enrollment, were randomized to a pragmatic strategy of therapeutic-dose anticoagulation with heparin or usual care pharmacological thromboprophylaxis. The primary outcome combined survival to hospital discharge and days free of organ support through 21 days, which was evaluated with Bayesian statistical models according to baseline D-dimer.

Results

The trial was stopped when prespecified criteria for superiority were met for therapeutic-dose anticoagulation in groups defined by high (≥2-fold elevated) and low (<2-fold elevated) D-dimer. Among 2219 participants in the final analysis, the probability that therapeutic anticoagulation increased organ support-free days compared to thromboprophylaxis was 99.0% (adjusted odds ratio 1.29, 95% credible interval 1.04 to 1.61). The adjusted absolute increase in survival to hospital discharge without organ support with therapeutic-dose anticoagulation was 4.6% (95% credible interval 0.7 to 8.1). In the primary adaptive stopping groups, the final probabilities of superiority for therapeutic anticoagulation were 97.3% in the high D-dimer group and 92.9% in the low D-dimer group. Major bleeding occurred in 1.9% and 0.9% of participants randomized to therapeutic anticoagulation and thromboprophylaxis, respectively.

Conclusions

In non-critically ill patients with Covid-19, an initial strategy of therapeutic-dose anticoagulation with heparin increases the probability of survival to hospital discharge with reduced use of organ support.

Trial registration numbers: NCT02735707, NCT04505774, NCT04359277, NCT04372589
Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness
Authors: Reyes Alhena , Carbo Ellen C. , thoe Slooten Joost van Harinxma , Kraakman Margriet E.M. , Sidorov Igor A. , Claas Eric C.J. , Kroes Aloys C.M. , Visser Leo G. , de Vries Jutte J.C.
Published: May 2021

Background

Diagnosis of infections in returning international travellers can be challenging because of the broad spectrum of potential infectious aetiologies potentially involved. Viral metagenomic next-generation sequencing (mNGS) has the potential to detect any virus present in a patient sample and is increasingly being used for difficult to diagnose cases. The aim of this study was to analyse the performance of mNGS for viral pathogen detection in the clinical setting of international travellers returning with febrile illness.

Methods

Thirty-eight serum samples from international travellers returning with febrile illness and presenting at the outpatient clinic of the Leiden University Medical Center in the Netherlands in the time period 2015-2016 were selected retrospectively. Samples were processed for viral metagenomic sequencing using a probe panel capturing all known vertebrate viruses. Bioinformatic analysis was performed using Genome Detective software for metagenomic virus detection. Metagenomic virus findings were compared with viral pathogen detection using conventional methods.

Results

In 8 out of the 38 patients (21%), a pathogenic virus was detected by mNGS. All viral pathogens detected by conventional assays were also detected by mNGS: dengue virus (n=4 patients), Epstein-Barr virus (n=2), hepatitis B virus (n=1). In addition, mNGS resulted in additional pathogenic findings in 2 patients (5%): dengue virus (n=1), and hepatitis C virus (n=1). Non-pathogenic viruses detected were: GB virus C (n=1) and torque teno viruses (n=3). High genome coverage and depth using capture probes enabled typing of the dengue viruses detected.

Conclusions

Viral metagenomics has the potential to assist the detection of viral pathogens and co-infections in one step in international travellers with a febrile syndrome. Furthermore, viral enrichment by probes resulted in high genome coverage and depth which enabled dengue virus typing.
Magnetic resonance spectroscopy of anoxic brain injury after cardiac arrest
Authors: Lee Jong Woo , Sreepada Lasya , Bevers Matthew , Li Karen , Scirica Benjamin , da Silva Danuzia Santana , Henderson Galen V. , Bay Camden , Lin Alexander P
Published: May 2021

Objective

We describe magnetic resonance spectroscopy (MRS) changes in comatose patients undergoing targeted temperature management (TTM) after cardiac arrest, and their relationships to relevant clinical, MRI, and EEG variables.

Methods

A prospective cohort of 50 patients was studied. The primary outcome was coma recovery to follow commands. Comparison of MRS measures in the posterior cingulate gyrus, parietal white matter, basal ganglia, and brainstem were also made to 25 normative control subjects.

Results

Fourteen of 50 achieved coma recovery. Compared to patients who recovered, there was a significant decrease in total N-acetyl-aspartate (NAA/Cr) and glutamate; and an increase in lactate (Lac/Cr) and glutamine in patients who did not recover, with changes most prominent in the posterior cingulate gyrus. Patients who recovered had a decrease in NAA/Cr as compared to control subjects. Coma recovery was seen in patients with a moderate decrease in NAA/Cr, but the appearance of lactate resulted in a poor outcome. NAA/Cr had a linear relationship with MRI cortical apparent diffusion coefficient (ADC); lactate level exponentially increased with decreasing ADC. EEG suppression/burst suppression was universally associated with lactate elevation.

Conclusions

NAA and lactate changes are associated with clinical/MRI/EEG changes consistent with anoxic brain injury and are most prominent in the posterior cingulate gyrus. NAA/Cr decrease observed in patients with good outcomes suggests mild anoxic injury in patients asymptomatic at hospital discharge. The appearance of cortical lactate represents a deterioration of aerobic energy metabolism and is associated with EEG background suppression, synaptic transmission failure, and severe, potentially irreversible anoxic injury.
Corpus callosal microstructure predicts bimanual motor performance in chronic stroke survivors: A preliminary cross-sectional study
Authors: Varghese Rini , Chang Brianna , Kim Bokkyu , Liew Sook-Lei , Schweighofer Nicolas , Winstein Carolee J.
Published: May 2021

Abstract

Microstructural changes in the corpus callosum are associated with more severe motor impairment in the paretic hand, poor recovery, and general disability. Considering its role in bimanual coordination, we suspected that these microstructural changes across the callosum may also be reflected in the performance of ecologically valid routine bimanual tasks. Thus, the purpose of this study was to determine if callosal microstructure predicts bimanual motor performance in chronic stroke survivors by examining the regions of the corpus callosum connecting both the sensorimotor and non-sensorimotor cortices. We examined the relationship between the fractional anisotropy across the CC and movement times for two self-initiated and self-paced bimanual tasks in 41 chronic stroke survivors. Using publicly available control datasets (n = 52), matched closely for acquisition parameters, we also explored the effect of stroke and age on callosal microstructure. There were two main findings: First, callosal microstructure was significantly associated with bimanual performance in chronic stroke survivors. Notably, a significant relationship was observed not only with the primary sensorimotor regions, but also regions of the premotor/supplementary motor and prefrontal regions. Second, chronic stroke survivors presented with significantly lower mean FA, compared to neurologically intact adults. We conclude that in mild-to-moderate chronic stroke survivors with relatively localized lesions to the motor areas, callosal microstructure can be expected to change in not only the primary sensorimotor region, but also more anteriorly in the secondary motor regions and the genu and is associated with performance on cooperative bimanual tasks.

Significance

A goal of rehabilitation after stroke is to promote the return to pre-stroke levels of upper limb function and use, predominantly characterized by coordinated bimanual activities. In this study, we find that in the chronic phase of stroke, microstructural disorganization within the corpus callosum predicts motor performance on real-world bimanual tasks and lends important insight into the indirect, remote effects of stroke.

Highlights

We provide initial evidence that corpus callosal microstructure predicts performance on two self-initiated and self-paced bimanual tasks.

Associations were strongest for fibers connecting the primary sensorimotor cortices followed by the pre- and supplementary motor, and prefrontal cortices.

Significant reductions in fractional anisotropy were observed in stroke survivors for all regions of the corpus callosum.
An updated suite of viral vectors for in vivo calcium imaging using local and retro-orbital injections
Authors: Grødem Sverre , Nymoen Ingeborg , Vatne Guro Helén , Björnsdottir Valgerdur , Lensjø Kristian Kinden , Fyhn Marianne
Published: May 2021

Calcium imaging using genetically encoded Ca2+ indicators (GECIs) is a widely adopted method to measure neural activity in modern neuroscience. Here, we explore the use of systemically administered viral vectors for brain-wide expression of GECIs, and adapt novel GECIs to optimize signal-to-noise. We show that systemic injections of PHP.eB AAVs to express GECIs is a highly promising technique for imaging neural activity and circumvent the need for transgenic GECI expressing mouse lines. We also establish the use of soma-targeted GECIs that outperform current Ca2+ indicators using both systemic and local virus injections.
RORγt serine 182 tightly regulates T cell heterogeneity to maintain mucosal homeostasis and restrict tissue inflammation
Authors: Ma Shengyun , Patel Shefali , Chen Nicholas , Patel Parth R. , Cho Benjamin S. , Abbasi Nazia , Chang John T. , Huang Wendy Jia Men
Published: May 2021

Intestine homeostasis is maintained by the delicate balance of Th17 effector cells and Treg cells. Dysregulation of these cell populations contributes to inflammation, tissue damage, and chronic conditions. RORγt is essential for the differentiation of Th17 and a subset of Treg (RORγt+ Treg) cells involved in intestinal inflammation. RORγt belongs to the nuclear receptor family of transcription factors with hinge regions that are highly flexible for co-activator/co-repressor interactions. Serine 182 at the hinge region of RORγt is phosphorylated. This study aims to uncover how S182 on RORγt contributes to mucosal homeostasis and diseases. We used CRISRP technology to generate a phosphor-null knock-in mutant mouse line (RORγtS182A) to assess its role in intestine physiology. scRNA-seq was performed on WT and RORγtS182A cohoused littermates to evaluate colonic T cell heterogeneity under steady state and colitis settings. Single-cell transcriptomics revealed that RORγtS182 maintains colonic T cell heterogeneity under steady state, without interfering T cell development and differentiation. In inflamed tissues, RORγtS182 simultaneously restricts IL-1β-mediated Th17 activities and promotes anti-inflammatory cytokine IL-10 production in LT-like Treg cells. Phospho-null RORγtS182A knock-in mice challenged with DSS induced colitis and EAE experienced delayed recovery and exacerbated pathology. The double switch role of RORγtS182 is critical in resolving T cell-mediated inflammation and provides a potential therapeutic target to combat autoimmune diseases.
Desert fish populations tolerate extreme salinity change to overcome hydrological constraints
Authors: Schunter Celia , Bonzi Lucrezia C. , Norstog Jessica , Sourisse Jade , Berumen Michael L. , Angel Yoseline , Parkes Stephen D. , McCabe Matthew F. , Ravasi Timothy
Published: May 2021

The unstable nature of freshwater ponds in arid landscapes represent a sizable challenge for strictly aquatic organisms, such as fishes. Yet the Arabian Desert, bordering the coastline of the Red Sea, plays host to a species very well adapted to such extreme environments: the Arabian pupfish, Aphanius dispar. In this study, we estimated patterns of hydrological connectivity; population structure and stable isotope for samples of A. dispar living in small, isolated ponds of nearly-freshwater in the Arabian desert and highly saline coastal lagoons along the Red Sea. The genomic and hydrological analyses indicate that populations are largely separated by drainage origin, as fish from desert ponds appear to be transported to coastal lagoons of the Red Sea along ephemeral river systems arising from flash flood events. Further, our study indicates there is an ecological change when being washed from pond environments to coastal waters, due to a significant shift in muscle stable isotopes ratios between both groups. Considering that the genetic breaks are mostly observed between drainage origin, this study suggests that A. dispar can survive large changes in salinity and ecological regimes over small time-scales.
Threonine phosphorylation regulates the molecular assembly and signaling of EGFR in cooperation with membrane lipids
Authors: Maeda Ryo , Tamagaki-Asahina Hiroko , Sato Takeshi , Yanagawa Masataka , Sako Yasushi
Published: May 2021

The cytoplasmic domain of the receptor tyrosine kinases (RTKs) plays roles as a phosphorylation enzyme and a protein scaffold but the allocation of these two functions is not fully understood. We here analyzed assembly of the transmembrane (TM)-juxtamembrane (JM) region of EGFR, one of the best studied species of RTKs, by combining single-pair FRET imaging and a nanodisc technique. The JM domain of EGFR contains a threonine residue (Thr654) that is phosphorylated after ligand association. We observed that the TM-JM peptides of EGFR form anionic lipid-induced dimers and cholesterol-induced oligomers. The two forms involve distinct molecular interactions, with a bias towards oligomer formation upon threonine phosphorylation. We further analyzed the functions and oligomerization of whole EGFR molecules, with or without a substitution of Thr654 to alanine, in living cells. The results suggested an autoregulatory mechanism in which Thr654 phosphorylation causes a switch of the major function of EGFR from kinase activation dimers to scaffolding oligomers.
Agrobacterium-Mediated Transient Transformation of Marchantia Liverworts
Authors: Iwakawa Hidekazu , Melkonian Katharina , Schlüter Titus , Nishihama Ryuichi , Motose Hiroyasu , Nakagami Hirofumi
Published: May 2021

Agrobacterium-mediated transient gene expression is a rapid and useful approach for characterizing functions of gene products in planta. However, the practicability of the method in the model liverwort Marchantia polymorpha has not yet been thoroughly described. Here we report a simple and robust method for Agrobacterium-mediated transient transformation of Marchantia thalli and its applicability. When thalli of M. polymorpha were co-cultured with Agrobacterium tumefaciens carrying GUS genes, GUS staining was observed primarily in assimilatory filaments and rhizoids. GUS activity was detected 2 days after infection and saturated 3 days after infection. We were able to transiently co-express fluorescently tagged proteins with proper localizations. Furthermore, we demonstrate that our method can be used as a novel pathosystem to study liverwort-bacteria interactions. We also provide evidence that air chambers support bacterial colonization.
Linear and partially linear models of behavioral trait variation using admixture regression
Authors: Connor Gregory , Fuerst Gerard R.
Published: May 2021

Admixture regression methodology exploits the natural experiment of random mating between individuals with different ancestral backgrounds to infer the environmental and genetic components to trait variation across racial and ethnic groups. This paper provides a statistical framework for admixture regression based on the linear polygenic index model and applies it to neuropsychological performance data from the Adolescent Brain Cognitive Development (ABCD) database. We develop and apply a new test of the differential impact of multi-racial identities on trait variation, an orthogonalization procedure for added explanatory variables, and a partially linear semiparametric functional form. We find a statistically significant genetic component to neuropsychological performance differences across racial identities, and find some possible evidence of nonlinearity in the link between admixture and neuropsychological performance scores in the ABCD data.
Fluctuations in functional connectivity associated with interictal epileptiform discharges (IEDs) in intracranial EEG
Authors: Stiso Jennifer , Caciagli Lorenzo , Hadar Peter , Davis Kathryn A. , Lucas Timothy H. , Bassett Dani S.
Published: May 2021

All epilepsies are defined by a propensity for recurrent seizures, characterized by hypersynchronous electrographic activity. Understanding this overarching property would be advanced by a thorough quantification of how the global synchrony of the epileptic brain responds to small perturbations that do not trigger seizures. Here, we leverage analysis of transient focal bursts of epileptiform activity, termed interictal epileptiform discharges (IEDs), to characterize this response. Specifically, we use a group of 145 participants implanted with intracranial EEG (iEEG) electrodes to quantify changes in five functional connectivity measures associated with three properties of IEDs: their presence, spread, and number. We perform this analysis in five frequency bands in order to contextualize our findings in relation to ongoing neural processes at different spatial and temporal scales. We find that, across frequency bands, both the presence and spread of IEDs tend to lead to independent increases of functional connectivity, but only in functional connectivity measures influenced by the amplitude, rather than the phase, of a signal. We find that these increases are not explained by simple subgroups of connections, such as the weakest connections in the brain, or only connections within the seizure onset zone. Evaluating patterns of similarity across different bands and measure combinations, we find that the presence of IEDs impacts high frequencies (gamma and high gamma) and low frequencies (theta, alpha, and beta) differently, although responses within each group are similar. Using grouped LASSO regression, we identify which individual-level features explain differences in functional connectivity changes associated with IEDs. While no single feature robustly explains observed differences, the most consistently included predictors across bands and measures are the rate of IEDs and the anatomical locus of IEDs. Overall, this work provides compelling evidence for increases in global synchrony associated with IEDs, and delivers a thorough exploration of different functional connectivity measures, frequency bands, and IED properties. These observations show a disruption of several types of ongoing neural dynamics associated with IEDs. Additionally, we provide a starting point for future models of how small perturbations affect neural systems and how those systems support the hypersynchrony seen in epilepsy.
EvolvedBmp6enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks
Authors: Stepaniak Mark D. , Square Tyler A. , Miller Craig T.
Published: May 2021

Mutations in enhancers have been shown to often underlie natural variation but the evolved differences between enhancer activity can be difficult to identifyin vivo. Threespine sticklebacks (Gasterosteus aculeatus) are a robust system for studying enhancer evolution due to abundant natural genetic variation, a diversity of evolved phenotypes between ancestral marine and derived freshwater forms, and the tractability of transgenic techniques. Previous work identified a series of polymorphisms within an intronic enhancer of theBone morphogenetic protein 6(Bmp6) gene that are associated with evolved tooth gain, a derived increase in freshwater tooth number that arises late in development. Here we use a bicistronic reporter construct containing a genetic insulator and a pair of reciprocal two-color transgenic reporter lines to compare enhancer activity of marine and freshwater alleles of this enhancer. In older fish the two alleles drive partially overlapping expression in both mesenchyme and epithelium of developing teeth, but the freshwater enhancer drives a reduced mesenchymal domain and a larger epithelial domain relative to the marine enhancer. In younger fish these spatial shifts in enhancer activity are less pronounced. ComparingBmp6expression byin situhybridization in developing teeth of marine and freshwater fish reveals similar evolved spatial shifts in gene expression. Together, these data support a model in which the polymorphisms within this enhancer underlie evolved tooth gain by shifting the spatial expression ofBmp6during tooth development, and provide a general strategy to identify spatial differences in enhancer activityin vivo.
The structure of hippocampal circuitry relates to rapid category learning in humans
Authors: Schlichting Margaret L. , Gumus Melisa , Zhu Teresa , Mack Michael L.
Published: May 2021

Prior work suggests that complementary white matter pathways within the hippocampus differentially support learning of specific versus general information. In particular, while the trisynaptic pathway (TSP) rapidly forms memories for specific experiences, the monosynaptic pathway (MSP) slowly learns generalities. However, despite the theorized significance of such circuitry, characterizing how information flows within hippocampus (HPC) to support learning in humans remains a challenge. We leveraged diffusion-weighted imaging as a proxy for individual differences in white matter structure linking key regions along TSP (HPC subfields CA3 and CA1) and MSP (entorhinal cortex and CA1) and related these differences in hippocampal structure to category learning ability. We hypothesized that learning to categorize the “exception” items that deviated from category rules would benefit from TSP-supported mnemonic specificity. Participant-level estimates of TSP- and MSP-related integrity were constructed from HPC subfield connectomes of white matter streamline density. Consistent with theories of TSP-supported learning mechanisms, we found a specific association between the integrity of CA3-CA1 white matter connections and exception learning. These results highlight the significant role of HPC circuitry in complex human learning.
More sustainable vegetable oil: balancing productivity with carbon storage opportunities
Authors: Alcock Thomas D , Salt David E , Wilson Paul , Ramsden Stephen J
Published: May 2021

Intensive cultivation and post-harvest vegetable oil production stages are major sources of greenhouse gas (GHG) emissions. Variation between production systems and reporting disparity have resulted in discordance in previous emissions estimates. To assess systems-wide GHG implications of meeting increasing edible oil demand, we performed a unified re-analysis of life cycle input data from diverse oil palm, soybean, rapeseed, and sunflower production systems, from a saturating search of published literature. The resulting dataset reflects almost 6,000 producers in 38 countries, and is representative of over 74% of global vegetable oil production. Determination of the carbon cost of agricultural land occupation revealed that carbon storage potential drives variation in production GHG emissions, and indicates that expansion of production in low carbon storage potential land, whilst reforesting areas of high carbon storage potential, could reduce net GHG emissions whilst boosting productivity. Nevertheless, there remains considerable scope to improve sustainability within current production systems.
Portable low-cost optical density meter
Authors: Puccinelli Robert R. , Cabrera Joana P. , Huynh Emily , Lebel Paul M. , Gómez-Sjöberg Rafael
Published: May 2021

Measuring optical density (OD) is a very common technique in biological laboratories to determine the concentration of a substance in solution or of bacteria (or microscopic particles) in suspension. For example, bacterial cultures engineered to produce (express) a protein or compound of interest are a workhorse of modern molecular biology laboratories. Commonly, the expression of the product is triggered (induced) by a chemical signal added to the culture at the proper time in the growth curve of the culture (typically in the middle of the exponential growth phase, at an OD value of ∼0.6). The most common tool for measuring OD is a spectrophotometer. However, most spectrophotometers are sophisticated, non-portable and expensive laboratory instruments, costing tens of thousands of dollars. Even a very low cost spectrophotometer for educational use costs at least US$1,000. Because of the cost, even well resourced labs have only one instrument, which becomes a bottleneck when multiple bacterial cultures need to be monitored simultaneously. The problem is more acute in developing countries, where multiple labs have to share a single spectrophotometer, or there’s no such instrument at all. Having a cheap and simple device to measure OD would enable multiple people in a laboratory to monitor their bacterial cultures independently, even in resource-limited settings. At the same time, a portable OD meter could be useful for field work. Here we present the detailed build instructions and characterization of a very simple OD meter that costs only US$60, and can measure OD values from ∼0.05 to 2.0.

Specifications table
zmiz1a zebrafish mutants have defective erythropoiesis, altered expression of autophagy genes, and a deficient response to vitamin D
Authors: Castillo-Castellanos Francisco , Ramírez Laura , Lomelí Hilda
Published: May 2021

ZMIZ1 is a transcriptional coactivator that is related to members of the protein inhibitor of activated STAT (PIAS) family. ZMIZ1 regulates the activity of various transcription factors including the androgen receptor, p53, and Smad3. ZMIZ1 also interacts with Notch1 and selectively regulates Notch1 target genes relevant for T cell development and leukemogenesis in mammals. Human ZMIZ1 is additionally characterized as a latitude-dependent autoimmune disease (LDAD) risk gene, as it is responsive to vitamin D and has been associated with at least eleven blood cell traits.

To address the function of ZMIZ1 in fish, we introduced CRISPR/Cas9 mutations in the zmiz1a gene in zebrafish. We observed that inactivation of zmiz1a in developing zebrafish larvae results in lethality at 15 dpf and delayed erythroid maturation. Differential gene expression analysis indicated that 15 dpf zmiz1a-null larvae had altered expression of autophagy genes, and erythrocytes that lacked Zmiz1a function exhibited an accumulation of mitochondrial DNA. Furthermore, we observed that autophagy gene expression was dysregulated at earlier stages of development, which suggests the involvement of Zmiz1a in the regulation of autophagy genes beyond the process of red blood cell differentiation. Finally, we showed that the loss of Zmiz1a decreased the capacity of the embryos to respond to vitamin D, indicating additional participation of Zmiz1a as a mediator of vitamin D activity.
Development of antibiotic resistance reveals diverse evolutionary pathways to face the complex and dynamic environment of a long-term treated patient
Authors: Colque Claudia A. , Tomatis Pablo E. , Albarracín Orio Andrea G. , Dotta Gina , Moreno Diego M. , Hedemann Laura G. , Hickman Rachel A. , Sommer Lea M. , Feliziani Sofía , Moyano Alejandro J. , Bonomo Robert A. , Johansen Helle K. , Molin Søren , Vila Alejandro J. , Smania Andrea M.
Published: May 2021

Antibiotic resistance development has been studied using approaches that range from laboratory experimental evolution, surveillance and epidemiology, to clinical isolate sequencing. However, evolutionary trajectories depend on the environment in which selection takes place, compelling to address evolutionary analyses in antibiotic-treated patients, to embrace the whole inherent environmental complexities as well as their dynamics over time. Herein, we address the complexity of the bacterial adaptive response to changing antibiotic selective pressures by studying the long-term in-patient evolution of a broad diversity of β-lactam resistant Pseudomonas aeruginosa clones. By using mutational and ultra-deep amplicon sequencing, we analyzed multiple generations of a P. aeruginosa hypermutator strain persisting for more than 26 years of chronic infection in the airways of a cystic fibrosis (CF) patient. We identified the accumulation of multiple alterations targeting the chromosomally encoded class C β-lactamase (blaPDC), providing structural and functional protein changes that resulted in a continuous enhancement of its catalytic efficiency and high level of cephalosporin resistance. This evolution was linked to the persistent treatment with ceftazidime, which we demonstrate selected for variants with robust catalytic activity against this expanded-spectrum cephalosporin. Surprisingly, “a gain of function” of collateral resistance towards ceftolozane, a more recently introduced cephalosporin that was not prescribed to this patient, was also observed and the biochemical basis of this cross-resistance phenomenon was elucidated. This work unveils the diversity of evolutionary trajectories driven by bacteria in the natural CF environmental setting, towards a multidrug resistant phenotype after years of antibiotic treatment against a formidable pathogen.
Excess mortality during the COVID-19 pandemic: a geospatial and statistical analysis in Mogadishu, Somalia
Authors: Warsame Abdihamid , Bashiir Farah , Freemantle Terri , Williams Chris , Vazquez Yolanda , Reeve Chris , Aweis Ahmed , Ahmed Mohamed , Checchi Francesco , Dalmar Abdirisak
Published: May 2021

Background

While the impact of the COVID-19 pandemic has been well documented in high-income countries, much less is known about its impact in Somalia where health systems are weak and vital registration is under developed.

Methods

We used remote sensing and geospatial analysis to quantify the number of burials from January 2017 to September 2020 in Mogadishu. We imputed missing grave counts using surface area data. Simple interpolation and a generalised additive mixed growth model were used to predict both actual and counterfactual burial rates by cemetery and across Mogadishu during the most likely period of COVID-19 excess mortality and to compute excess burials. We also undertook a qualitative survey of key informants to determine the drivers of COVID-19 excess mortality.

Results

Burial rates increased during the pandemic period with a ratio to pre-pandemic levels averaging 1.5-fold and peaking at 2.2-fold. When scaled to plausible range of baseline Crude Death Rates (CDR), excess death toll between January and September 2020 ranged between 3,200 and 11,800. When compared to burial records of the Barakaat Cemetery Committee our estimates were found to be lower.

Conclusions

Our study points to considerable under estimation of COVID-19 impact in Banadir and an overburdened public health system struggling to deal with the increasing severity of the epidemic in 2020.
Reagent- and actuator-free analysis of individual erythrocytes using three-dimensional quantitative phase imaging and capillary microfluidics
Authors: Ryu DongHun , Nam Hyeono , Jeon Jessie S. , Park YongKeun
Published: May 2021

Histopathological examination of blood cells plays a crucial role in the diagnosis of various diseases. However, it involves time-consuming and laborious staining procedures required for microscopic review by medical experts and is not directly applicable for point-of-care diagnosis in resource-limited locations. This study reports a dilution-, actuation- and label-free method for the analysis of individual red blood cells (RBCs) using a capillary microfluidic device and quantitative phase imaging. Blood, without any sample treatment, is directly loaded into a micrometer-thick channel such that it forms a quasi-monolayer inside the channel. The morphological and biochemical properties of RBCs, including hemoglobin concentration, hemoglobin content, and corpuscular volume, were retrieved using the refractive index tomograms of individual RBCs measured using 3D quantitative phase imaging. The deformability of individual RBCs was also obtained by measuring the dynamic membrane fluctuations. The proposed framework applies to other imaging modalities and biomedical applications, facilitating rapid and cost-effective diagnosis and prognosis of diseases.
A novel MRI-based data fusion methodology for efficient, personalised, compliant simulations of aortic haemodynamics
Authors: Stokes Catriona , Bonfanti Mirko , Li Zeyan , Xiong Jiang , Chen Duanduan , Balabani Stavroula , Díaz-Zuccarini Vanessa
Published: May 2021

We present a novel, cost-efficient methodology to simulate aortic haemo-dynamics in a patient-specific, compliant aorta using an MRI data fusion process. Based on a previously-developed Moving Boundary Method, this technique circumvents the high computational cost and numerous structural modelling assumptions required by traditional Fluid-Structure Interaction techniques. Without the need for Computed Tomography (CT) data, the MRI images required to construct the simulation can be obtained during a single imaging session. Black Blood MR Angiography and 2D Cine-MRI data were used to reconstruct the luminal geometry and calibrate wall movement specifically to each region of the aorta. 4D-Flow MRI and non-invasive pressure measurements informed patient-specific inlet and outlet boundary conditions. Luminal area closely matched 2D Cine-MRI measurements with a mean error of less than 4.6% across the cardiac cycle, while physiological pressure and flow distributions were simulated to within 3.3% of patient-specific targets. Moderate agreement with 4D-Flow MRI velocity data was observed. Despite lower peak velocity, an equivalent rigid-wall simulation predicted a mean Time-Averaged Wall Shear Stress (TAWSS) 13% higher than the compliant simulation. The agreement observed between compliant simulation results and MRI data is testament to the accuracy and efficiency of this MRI-based simulation technique.
Differential sphingosine-1-phosphate receptor-1 protein expression in the dorsolateral prefrontal cortex between schizophrenia Type 1 and Type 2
Authors: Chand Ganesh B. , Jiang Hao , Miller J. Philip , Rhodes C. Harker , Tu Zhude , Wong Dean F.
Published: May 2021

Understanding the etiology and treatment approaches in schizophrenia is challenged in part by the heterogeneity of this disorder. One encouraging progress is the growing evidence that there are subtypes of schizophrenia that may relate to disease duration and premorbid severity. Recent in vitro findings of messenger ribonucleic acid (mRNA) gene expression on postmortem dorsolateral prefrontal cortex (DLPFC) showed that schizophrenia has two subtypes, those with a relatively normal DLPFC transcriptome (Type 1) and those with differentially expressed genes (Type 2). Sphingosine-1-phosphate receptor-1 (S1PR1) is one of the genes that was highly upregulated in Type 2 compared to Type 1 and controls. The impact of that finding is limited because it only can be confirmed through analysis of autopsy tissue, and the clinical characteristics such as symptoms severity or illness duration was not available from that Medical Examiner based autopsy study. However, S1PR1 has great potential because it is a target gene that can be accessed via positron emission tomography (PET) in vivo using specific radioligands (starting with [11C]CS1P1) successfully developed at our center in human brain imaging. As a preliminary study to validate this PET target in schizophrenia, S1PR1 protein expression was assessed by receptor autoradiography (ARG) using [3H]CS1P1 and immunohistochemistry (IHC) in the DLPFC from patients with schizophrenia classified as Type 1 or Type 2 based on their DLPFC transcriptomes and from controls. Our analyses demonstrate that ARG S1PR1 protein expression is significantly higher in Type 2 compared to Type 1 (p < 0.05) and controls (p < 0.05), which was consistent with previous mRNA S1PR1. These findings support the possibility that PET S1PR1 can be used as a future imaging biomarker to distinguish these subgroups of schizophrenic patients during life with obvious implications for both patient management and the design of clinical trials to validate novel pharmacologic therapies.
DeepImageTranslator: a free, user-friendly graphical interface for image translation using deep-learning and its applications in 3D CT image analysis
Authors: Ye Run Zhou , Noll Christophe , Richard Gabriel , Lepage Martin , Turcotte Éric E. , Carpentier André C.
Published: May 2021

Objectives

The advent of deep-learning has set new standards in an array of image translation applications. At present, the use of these methods often requires computer programming experience. Non-commercial programs with graphical interface usually do not allow users to fully customize their deep-learning pipeline. Therefore, our primary objective is to provide a simple graphical interface that allows students and researchers with no programming experience to easily create, train, and evaluate custom deep-learning models for image translation. We also aimed to test the applicability of our tool (the DeepImageTranslator) in two different tasks: semantic segmentation and noise reduction of CT images.

Methods

The DeepImageTranslator was implemented using the Tkinter library; backend computations were implemented using Pillow, Numpy, OpenCV, Augmentor, Tensorflow, and Keras libraries. Convolutional neural networks (CNNs) were trained using DeepImageTranslator and assessed with three-way cross-validation. The effects of data augmentation, deep-supervision, and sample size on model accuracy were also systematically assessed.

Results

The DeepImageTranslator a simple tool that allows users to customize all aspects of their deep-learning pipeline, including the CNN, the training optimizer, the loss function, and the types of training image augmentation scheme. We showed that DeepImageTranslator can be used to achieve state-of-the-art accuracy and generalizability in semantic segmentation and noise reduction. Highly accurate 3D segmentation models for body composition can be obtained using training sample sizes as small as 17 images. Therefore, for studies with small datasets, researchers can randomly select a very small subset of images for manual labeling, which can then be used to train a specialized CNN model with DeepImageTranslator to fully automate segmentation of the entire dataset, thereby saving tremendous time and effort.

Conclusions

An open-source deep-learning tool for accurate image translation with a user-friendly graphical interface was presented and evaluated. This standalone software can be downloaded for Windows 10 at: https://sourceforge.net/projects/deepimagetranslator/
Modulation of P2X4 pore closure by magnesium, potassium, and ATP
Authors: Immadisetty Kalyan , Alenciks Josh , Kekenes-Huskey Peter
Published: May 2021

The P2X4 receptor plays a prominent role in cellular responses to extracellular ATP. Through classical all-atom molecular dynamics (MD) simulations totaling 24 µs we have investigated how metal-complexed ATP stabilizes the channel’s open state and prevents its closing. We have identified two metal-binding sites, magnesium (Mg2+) and potassium (K+), one at the intersection of the three subunits in the ectodomain (MBS1) and the second one near the ATP binding site (MBS2), similar to those characterized in Gulf coast P2X. Our data indicate that when Mg2+ and K+ ions are complexed with ATP, the channel is locked into an open state. Interestingly, irrespective of the number of bound ATP molecules, Mg2+ ions bound to the MBS2 resisted collapsing of the open state protein to a closed state by stabilizing the ATP-protein interactions. However, when Mg2+ in the MBS2 was replaced with K+ ions, as might be expected when in equilibrium with an extracellular solution, the interactions between the subunits were weakened and we found evidence of pore collapse. This collapse was apparent when fewer than two ATP were bound to MBS2 in the presence of K+. Therefore, the different capacities of common cations to stabilize the channel may underlie a mechanism governing P2X4 channel gating in physiological systems. This study provides structural insights into the differential modulation of ATP activation of P2X4 by Mg2+ and K+.
Spatial modeling of tidal and land use impacts on Escherichia coli contamination and fluctuation in Asia’s urban river environmental gradient
Authors: Wibowo Andri
Published: May 2021

In the river, pathogens are the leading cause for rivers to exceed water and health quality standards. The GIS based spatial modeling and analysis were conducted to estimate Escherichia coli (E. coli) contaminated river bodies based on environmental and spatial gradients such as dissolved oxygen, pH, tidal, temperature and current in Asia’s urban river located in Kapuas river of Kalimantan. The E. coli was sampled from the river mouth up to the upstream land uses dominated by residential. The E. coli contamination was higher in the river mouth and in residential area as well. Likewise, E. coli contamination was higher during the low tide than high tide. During the high tide, the E. coli contamination were significantly affected by temperature and current (r2>0.5). Meanwhile, during the low tide, there were no dominant environmental factors that affect E. coli contamination. Hence, by knowing the spatial model of E. coli contamination driven by tidal, land use and environmental gradients, this paper has contributed to the advance management of water and river system.
OmpF Downregulation Mediated by Sigma E or OmpR Activation Confers Cefalexin Resistance in Escherichia coli in the Absence of Acquired β-Lactamases
Authors: Alzayn Maryam , Dulyayangkul Punyawee , Satapoomin Naphat , Heesom Kate J. , Avison Matthew B.
Published: May 2021

Cefalexin is a widely used 1st generation cephalosporin, and resistance in Escherichia coli is caused by Extended-Spectrum (e.g. CTX-M) and AmpC β-lactamase production and therefore frequently coincides with 3rd generation cephalosporin resistance. However, we have recently identified large numbers of E. coli isolates from human infections, and from cattle, where cefalexin resistance is not β-lactamase mediated. Here we show, by studying laboratory selected mutants, clinical isolates, and isolates from cattle, that OmpF porin disruption or downregulation is a major cause of cefalexin resistance in E. coli. Importantly, we identify multiple regulatory mutations that cause OmpF downregulation. In addition to mutation of ompR, already known to downregulate OmpF and OmpC porin production, we find that rseA mutation, which strongly activates the Sigma E regulon, greatly increasing DegP production, which degrades OmpF, OmpC and OmpA porins. Furthermore, we reveal that mutations affecting lipopolysaccharide structure, exemplified by the loss of GmhB, essential for lipopolysaccharide heptosylation, also modestly activate DegP production, resulting in OmpF degradation. Remarkably, given the critical importance attached to such systems for normal E. coli physiology, we find evidence for DegP-mediated OmpF downregulation, gmhB and rseA loss of function mutation in E. coli isolates derived from human infections. Finally, we show that these regulatory mutations enhance the ability of group 1 CTX-M β-lactamase to confer reduced carbapenem susceptibility, particularly those mutations that cause OmpC in addition to OmpF downregulation.
Identification of SSX2IP/Msd1 as a Wtip-binding partner by targeted proximity biotinylation
Authors: Xiang Bo , Reis Alice H. , Itoh Keiji , Sokol Sergei Y.
Published: May 2021

Wilms tumor-1-interacting protein (Wtip) is a LIM-domain-containing adaptor that links cell junctions with actomyosin complexes and modulates actomyosin contractility and ciliogenesis in Xenopus embryos. The Wtip C-terminus with three LIM domains binds binds Shroom3 and modulates Shroom3-induced apical constriction in ectoderm cells. We found that the N-terminal domain localizes to the basal bodies in skin multiciliated cells, but its interacting partners remain largely unknown. Using a novel targeted proximity biotinylation approach with anti-GFP antibody attached to the biotin ligase BirA in the presence of GFP-Wtip-N, we identified SSX2IP as the candidate binding protein. SSX2IP, also known as Msd1 or ADIP, is a centriolar satellite protein that functions as a targeting factor for ciliary membrane proteins. Wtip physically associated with SSX2IP and the two proteins formed mixed spherical aggregates in overexpressing cells in a dose-dependent manner, in a process that resembles phase separation. These results suggest that the interaction between SSX2IP and Wtip is relevant to their functions at the centrosome and basal bodies. The described antibody targeting of biotin ligase should be applicable to other GFP-tagged proteins.