bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospective Observational Evaluation of the ER-REBOA Catheter at 6 U.S. Trauma Centers
Authors: Moore Laura J. , Fox Erin E. , Meyer David E. , Wade Charles E. , Podbielski Jeanette M. , Xu Xun , Morrison Jonathon J. , Scalea Thomas , Fox Charles J. , Moore Ernest E. , Morse Brian C. , Inaba Kenji , Bulger Eileen M. , Holcomb John B.
Published: June 2020

Objective:

To describe the current use of the ER-REBOA catheter and associated outcomes and complications.

Introduction:

Noncompressible truncal hemorrhage is the leading cause of potentially preventable death in trauma patients. Resuscitative endovascular balloon occlusion of the aorta (REBOA) is a novel strategy to obtain earlier temporary hemorrhage control, supporting cardiac, and cerebral perfusion before definitive hemostasis.

Methods:

Prospective, observational study conducted at 6 Level 1 Trauma Centers over 12-months. Inclusion criteria were age >15 years of age with evidence of truncal hemorrhage below the diaphragm and decision for emergent hemorrhage control intervention within 60 minutes of arrival. REBOA details, demographics, mechanism of injury, complications, and outcomes were collected.

Results:

A total of 8166 patients were screened for enrollment. In 75, REBOA was utilized for temporary hemorrhage control. Blunt injury occurred in 80% with a median injury severity score (ISS) 34 (21, 43). Forty-seven REBOAs were placed in Zone 1 and 28 in Zone 3. REBOA inflation increased systolic blood pressure from 67 (40, 83) mm Hg to 108 (90, 128) mm Hg 5 minutes after inflation (P = 0.02). Cardiopulmonary resuscitation was ongoing during REBOA insertion in 17 patients (26.6%) and 10 patients (58.8%) had return of spontaneous circulation after REBOA inflation. The procedural complication rate was 6.6%. Overall mortality was 52%.

Conclusion:

REBOA can be used in blunt and penetrating trauma patients, including those in arrest. Balloon inflation uniformly improved hemodynamics and was associated with a 59% rate of return of spontaneous circulation for patients in arrest. Use of the ER-REBOA catheter is technically safe with a low procedural complication rate.
Bleeding to death in a big city: An analysis of all trauma deaths from hemorrhage in a metropolitan area during 1 year
Authors: Kalkwarf Kyle J. , Drake Stacy A. , Yang Yijiong , Thetford Caitlin , Myers Lauren , Brock Morgan , Wolf Dwayne A. , Persse David , Wade Charles E. , Holcomb John B.
Published: June 2020

BACKGROUND

Hemorrhage is the most common cause of potentially preventable trauma deaths, but no studies have focused on all civilian traumatic deaths from hemorrhage, so we describe a year of these deaths from a large county to identify opportunities for preventing hemorrhagic deaths.

METHODS

All trauma-related deaths in Harris County, Texas, in 2014 underwent examination by the medical examiner; patients were excluded if hemorrhage was not their primary reason for death. Deaths were then categorized as preventable/potentially preventable hemorrhage (PPH) or nonpreventable hemorrhage. These categories were compared across mechanism of injury, death location, and anatomic locations of hemorrhage to determine significant differences.

RESULTS

A total of 1,848 deaths were reviewed, and 305 were from uncontrolled hemorrhage. One hundred thirty-seven (44.9%) of these deaths were PPH. Of these PPH, 49 (35.8%) occurred prehospital and an additional 28 (20.4%) died within 1 hour of arriving at an acute care setting. Of the 83 PPH who arrived at a hospital, 21 (25.3%) died at a center not designated as level 1. Isolated truncal bleeding was the source of hemorrhage in 102 (74.5%) of the PPH. Of those who died with truncal PPH, the distribution was 22 chest (21.6%), 39 chest and abdomen (38.2%), 16 abdomen (15.7%), and 25 all other combinations (24.5%). When patients who died within 1 hour of arrival to a hospital were combined with the 168 deaths that occurred prehospital, 223 (74.3%) of 300 deaths occurred before spending 1 hour in a hospital and 77 (34.5%) of 223 of these deaths were PPH.

CONCLUSION

In a well-developed, urban trauma system, 34.5% of patients died from PPH in the prehospital setting or within an hour of hospitalization. Earlier, more effective prehospital resuscitation and truncal hemorrhage control strategies are needed to decrease deaths from PPH.

LEVEL OF EVIDENCE

Therapeutic/Care management, level IV.
Treatment of Isolated Cataplexy With Low-dose Aripiprazole in an Adolescent Patient
Authors: Uzun Necati , Akıncı Mehmet Akif
Published: June 2020

Background

Cataplexy is a clinical entity that is characterized by transient muscle tone loss that mostly occurring as a part of narcolepsy. On the other hand, isolated cataplexy (IC) (hereditary cataplexy) is defined as loss of muscle tone that is not accompanied by narcolepsy. Emotional reactions may trigger IC episodes. Additionally, human leukocyte antigen (HLA) DQB1 alleles were shown to be related to IC. Various antidepressants are useful in the treatment of IC; however, there is limited knowledge on the use of antipsychotics in the treatment of IC.

Case Report

A 16-year-old adolescent girl was consulted child and adolescent psychiatry outpatient clinic with complaint of sudden episodes of loss of muscle tone. Her HLA typing showed HLA DQB1*03 haplotype. She was diagnosed with IC and was prescribed aripiprazole 2.5 mg/d and her IC symptoms disappeared and never recurred over 6 months of follow-up.

Conclusions

In this case report, we present an adolescent girl with IC that is successfully treated with aripiprazole, an antipsychotic. This case report suggests that aripiprazole may be safely used in some adolescents who diagnosed with IC.
Validity of International Classification of Diseases Codes for Identifying Neuro-Ophthalmic Disease in Large Data Sets: A Systematic Review
Authors: Hamedani Ali G. , De Lott Lindsey B. , Deveney Tatiana , Moss Heather E.
Published: June 2020

Background:

Administrative health claims data have been used for research in neuro-ophthalmology, but the validity of International Classification of Diseases (ICD) codes for identifying neuro-ophthalmic conditions is unclear.

Evidence Acquisition:

We performed a systematic literature review to assess the validity of administrative claims data for identifying patients with neuro-ophthalmic disorders. Two reviewers independently reviewed all eligible full-length articles and used a standardized abstraction form to identify ICD code–based definitions for 9 neuro-ophthalmic conditions and their sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). A quality assessment of eligible studies was also performed.

Results:

Eleven articles that met criteria for inclusion are as follows: 3 studies of idiopathic intracranial hypertension (PPV 54%–91% and NPV 74%–85%), 2 studies of giant cell arteritis (sensitivity 30%–96% and PPV 94%), 3 studies of optic neuritis (sensitivity 76%–99%, specificity 83%–100%, PPV 25%–100%, and NPV 98%–100%), 1 study of neuromyelitis optica (sensitivity 60%, specificity 100%, PPV 43%–100%, and NPV 98%–100%), 1 study of ocular motor cranial neuropathies (PPV 98%–99%), and 2 studies of myasthenia gravis (sensitivity 53%–97%, specificity 99%–100%, PPV 5%–90%, and NPV 100%). No studies met eligibility criteria for nonarteritic ischemic optic neuropathy, thyroid eye disease, and blepharospasm. Approximately 45.5% provided only one measure of diagnostic accuracy. Complete information about the validation cohorts, inclusion/exclusion criteria, data collection methods, and expertise of those reviewing charts for diagnostic accuracy was missing in 90.9%, 72.7%, 81.8%, and 36.4% of studies, respectively.

Conclusions:

Few studies have reported the validity of ICD codes for neuro-ophthalmic conditions. The range of diagnostic accuracy for some disorders and study quality varied widely. This should be taken into consideration when interpreting studies of neuro-ophthalmic conditions using administrative claims data.
Predictive Value of International Classification of Diseases Codes for Idiopathic Intracranial Hypertension in a University Health System
Authors: Khushzad Fareshta , Kumar Riya , Muminovic Irma , Moss Heather E.
Published: June 2020

Background:

Misclassification bias is introduced into medical claims–based research because of reliance on diagnostic coding rather than full medical record review. We sought to characterize this bias for idiopathic intracranial hypertension (IIH) and evaluate strategies to reduce it.

Methods:

A retrospective review of medical records was conducted using a clinical data warehouse containing medical records and administrative data from an academic medical center. Patients with 1 or more instances of International Classification of Diseases (ICD)-9 or -10 codes for IIH (348.2 or G93.2) between 1989 and 2017 and original results of neuroimaging (head CT or MRI), lumbar puncture, and optic nerve examination were included in the study. Diagnosis of IIH was classified as definite, probable, possible, or inaccurate based on review of medical records. The positive predictive value (PPV) for IIH ICD codes was calculated for all subjects, subjects with an IIH code after all testing was completed, subjects with high numbers of IIH ICD codes and codes spanning longer periods, subjects with IIH ICD codes associated with expert encounters (ophthalmology, neurology, or neurosurgery), and subjects with acetazolamide treatment.

Results:

Of 1,005 patients with ICD codes for IIH, 103 patients had complete testing results and were included in the study. PPV of ICD-9/-10 codes for IIH was 0.63. PPV in restricted samples was 0.82 (code by an ophthalmologist n = 57), 0.70 (acetazolamide treatment n = 87), and 0.72 (code after all testing, n = 78). High numbers of code instances and longer duration between the first and last code instance also increased the PPV.

Conclusions:

An ICD-9 or -10 code for IIH had a PPV of 63% for probable or definite IIH in patients with necessary diagnostic testing performed at a single institution. Coding accuracy was improved in patients with an IIH ICD code assigned by an ophthalmologist. Use of coding algorithms considering treatment providers, number of codes, and treatment is a potential strategy to reduce misclassification bias in medical claims–based research on IIH. However, these are associated with a reduced sample size.
Recurrent Third Nerve Palsy Secondary to Instrinsic Schwannoma of the Third Cranial Nerve
Authors: Margolin Edward , Jeeva-Patel Trishal , Al Shafai Laila
Published: June 2020

A 78 year-old woman has experienced multiple episodes of transient right third nerve palsy over the course of 15 years and has undergone multiple imaging studies as well as investigations for myasthenia gravis and giant cell arteritis in search for the diagnosis. When seen after the most recent episode, MRI with contrast and Fast-Imaging Employing Steady-State Acquisition protocol revealed a subtle enlargement and enhancement of the cisternal and proximal cavernous portions of the right third cranial nerve. An empiric diagnosis of schwannoma intrinsic to third cranial nerve was made. All patients with cyclical third nerve palsies should have appropriate neuroimaging to rule out subtle structural lesions before other investigations are undertaken.
Unilateral Blindness With Bilateral Brain Infarction After Cosmetic Facial Filler Injection
Authors: Lee Jong Suk , Kim Jun Yup , Woo Se Joon
Published: June 2020

Background:

To describe a case of bilateral brain infarction associated with iatrogenic ophthalmic artery occlusion after cosmetic facial filler injection and to elucidate the pathogenic mechanism of bilateral brain infarction.

Methods:

Case report and review of the literature.

Results:

A case of unilateral blindness due to iatrogenic ophthalmic artery occlusion accompanied by bilateral brain infarction after cosmetic facial filler injection is described. Fluorescein angiographic images demonstrate ischemia of the retina and choroid. Associated bilateral brain infarction was observed on MRI.

Conclusions:

Bilateral embolic events after facial filler injection are very rare. However, several cases of unilateral iatrogenic ophthalmic or retinal artery occlusion accompanied by bilateral brain infarction have been reported. The possible route of filler material to the contralateral cerebral artery is through the anterior communicating artery. Brain infarction, especially contralateral embolic events, should be considered in severe cases of iatrogenic ophthalmic artery occlusion after facial filler injection.
Obeying orders reduces vicarious brain activation towards victims’ pain
Authors: Caspar Emilie A. , Ioumpa Kalliopi , Keysers Christian , Gazzola Valeria
Published: June 2020

Past historical events and experimental research have shown complying with the orders from an authority has a strong impact on people’s behaviour. However, the mechanisms underlying how obeying orders influences moral behaviours remain largely unknown. Here, we test the hypothesis that when male and female humans inflict a painful stimulation to another individual, their empathic response is reduced when this action complied with the order of an experimenter (coerced condition) in comparison with being free to decide to inflict that pain (free condition). We observed that even if participants knew that the shock intensity delivered to the ‘victim’ was exactly the same during coerced and free conditions, they rated the shocks as less painful in the coerced condition. MRI results further indicated that obeying orders reduced activity associated with witnessing the shocks to the victim in the ACC, insula/IFG, TPJ, the MTG and dorsal striatum (including the caudate and the putamen) as well as neural signatures of vicarious pain in comparison with being free to decide. We also observed that participants felt less responsible and showed reduced activity in a multivariate neural guilt signature in the coerced than in the free condition, suggesting that this reduction of neural response associated with empathy could be linked to a reduction of felt responsibility and guilt. These results highlight that obeying orders has a measurable influence on how people perceive and process others’ pain. This may help explain how people’s willingness to perform moral transgressions is altered in coerced situations.
Influence of Various Temporal Recoding on Pavlovian Eyeblink Conditioning in The Cerebellum
Authors: Kim Sang-Yoon , Lim Woochang
Published: June 2020

We consider the Pavlovian eyeblink conditioning (EBC) via repeated presentation of paired conditioned stimulus (tone) and unconditioned stimulus (airpuff). The influence of various temporal recoding of granule cells on the EBC is investigated in a cerebellar network where the connection probabilitypcfrom Golgi to granule cells is changed. In an optimal case of, individual granule cells show various well- and ill-matched firing patterns relative to the unconditioned stimulus. Then, these variously-recoded signals are fed into the Purkinje cells (PCs) through parallel-fibers (PFs), and the instructor climbing-fiber (CF) signals from the inferior olive depress them effectively. In the case of well-matched PF-PC synapses, their synaptic weights are strongly depressed through strong long-term depression (LTD). On the other hand, practically no LTD occurs for the ill-matched PF-PC synapses. This type of “effective” depression at the PF-PC synapses coordinates firings of PCs effectively, which then make effective inhibitory coordination on cerebellar nucleus neuron [which elicits conditioned response (CR; eyeblink)]. When the learning trial passes a threshold, acquisition of CR begins. In this case, the timing degree 𝒯dof CR becomes good due to presence of the ill-matched firing group which plays a role of protection barrier for the timing. With further increase in the trial, strength 𝒮 of CR (corresponding to the amplitude of eyelid closure) increases due to strong LTD in the well-matched firing group, while its timing degree 𝒯ddecreases. In this way, the well- and the ill-matched firing groups play their own roles for the strength and the timing of CR, respectively. Thus, with increasing the learning trial, the (overall) learning efficiency degree ℒe(taking into consideration both timing and strength of CR) for the CR is increased, and eventually it becomes saturated. By changingpcfrom, we also investigate the influence of various temporal recoding on the EBC. It is thus found that, the more various in temporal recoding, the more effective in learning for the Pavlovian EBC.
Olfactory-Trigeminal Integration in the Primary Olfactory Cortex
Authors: Karunanayaka Prasanna R. , Lu Jiaming , Elyan Rommy , Yang Qing X. , Sathian K.
Published: June 2020

Humans naturally integrate signals from the olfactory and intranasal trigeminal systems. A tight interplay has been demonstrated between these two systems, and yet the underlying neural circuitry that mediates olfactory-trigeminal integration remains poorly understood. Using functional magnetic resonance imaging (fMRI), combined with psychophysics, this study investigated the neural mechanisms underlying olfactory-trigeminal integration. Fifteen participants with normal olfactory function performed a localization task with air-puff stimuli, phenylethyl alcohol (PEA; rose odor), or a combination thereof while being scanned. The ability to localize PEA to either nostril was at chance. Yet, its presence significantly improved the localization accuracy of weak, but not strong, air-puffs, relative to air-puff localization without concomitant PEA when both stimuli were delivered concurrently to the same nostril, but not when different nostrils received the two stimuli. This enhancement in localization accuracy, exemplifying the principles of spatial coincidence and inverse effectiveness in multisensory integration, was associated with multisensory integrative activity in the primary olfactory (POC), orbitofrontal (OFC), superior temporal (STC), inferior parietal (IPC) and cingulate cortices, and in the cerebellum. Multisensory enhancement in most of these regions, except the OFC, correlated with behavioral multisensory enhancement, as did increases in connectivity between some of these regions. We interpret these findings as indicating that the POC is part of a distributed brain network mediating integration between the olfactory and trigeminal systems.

HIGHLIGHTS

Psychophysical and neuroimaging study of olfactory-mechanosensory (OM) integration

Behavior, cortical activity and network connectivity show OM integration

OM integration obeys principles of inverse effectiveness and spatial coincidence

Behavioral and neural measures of OM integration are correlated
Elucidation of the antiviral mechanism of cystine and theanine through transcriptome analysis of mice and comparison with COVID-19 gene set data
Authors: Mitsui Akira , Sakai Ryosei , Miwa Kiyoshi , Shibahara Susumu , Kurihara Shigekazu , Nagao Kenji
Published: June 2020

We previously showed that oral administration of cystine and theanine (CT) to mice confers resistance to influenza virus infection. In human studies, CT prevented colds in healthy subjects and enhanced antibody production after influenza vaccination in elderly individuals with a poor nutritional status. The mechanism of action of CT is thought to be glutathione (GSH)-mediated regulation of intracellular redox, which might affect innate immune systems such as macrophages to exert physiological effects. The effect of CT on influenza is independent of viral type, and this treatment has a broad range of antiviral activities. To explore the mechanisms of CT in viral infection, we performed transcriptome profiling of spleen tissues isolated from influenza A virus (IAV)-infected mice. We identified unique gene signatures in response to CT in the IAV-infected mice. Genes upregulated by CT included redox-regulated genes such as GCLC/GCLM (subunits of glutamate cysteine ligase, a rate-limiting enzyme of GSH biosynthesis), TXN1, TXN2, TXNRD2, and SOD1, suggesting that the intracellular redox environment is substantially altered by CT. However, genes downregulated in response to CT included chemokine/chemokine receptor genes (CCL5, CCL19, CXCL9, CXCL12, CXCR3, CXCR4, and ACKR3), some of which are related to cytokine storm. A comparison with public COVID-19-related gene set data showed that the upregulated gene signature was highly similar to the downregulated gene sets of SARS-CoV/SARS-CoV-2-infected cells and the upregulated gene set of attenuated SARS-CoV-infected cells. In conclusion, the unique gene signatures observed in response to orally administered CT in IAV-infected mouse spleen tissues suggested that CT may attenuate viral infection, replication and associated symptoms such as cytokine storm.
Evolution of the potassium channel geneKcnj13underlies colour pattern diversification inDaniofish
Authors: Podobnik Marco , Frohnhöfer Hans Georg , Dooley Christopher M. , Eskova Anastasia , Nüsslein-Volhard Christiane , Irion Uwe
Published: June 2020

The genetic basis of morphological variation provides a major topic in evolutionary biology1-6. Colour patterns in fish are among the most diverse of all vertebrates. Species of the genusDaniodisplay strikingly different colour patterns ranging from horizontal stripes, to vertical bars or spots7-10. Stripe formation in zebrafish,Danio rerio, oriented by the horizontal myoseptum, is a self-organizing process based on cell-contact-mediated interactions between three types of chromatophores with a leading role of iridophores11-14. We investigated genes known to regulate chromatophore interactions in zebrafish as candidates that might have evolved to produce a pattern of vertical bars in its sibling species,Danio aesculapii8,10. Using gene editing15-17we generated several mutants inD. aesculapiithat demonstrate a lower complexity in the interactions between chromatophores in this species, as well as a minor role of iridophores in patterning. Complementation tests in interspecific hybrids18,19identifiedobelix/Kcnj13, which encodes an inwardly rectifying potassium channel (Kir7.1)20, as a gene evolved betweenD. rerioandD. aesculapiias well as in two of seven moreDaniospecies tested. Our results demonstrate that the CRISPR/Cas9-system allows straightforward genetic tests also in non-model vertebrates to identify genes that underlie morphological evolution.
Tempo and mode of morphological evolution are decoupled from latitude in birds
Authors: Drury J. , Clavel J. , Tobias J.A. , Rolland J. , Sheard C. , Morlon H.
Published: June 2020

The latitudinal diversity gradient is one of the most striking patterns in nature yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions—namely, competition—can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait-dependent. Our results indicate that competition does not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.
Label-free amino acid identification forde novoprotein sequencing via tRNA charging and current blockade in a nanopore
Authors: Sampath G.
Published: June 2020

A label-free procedure to identify single amino acids (AAs) for protein sequencing is developed in theory and simulated in part. A terminal AA cleaved from a protein/peptide, a tRNA, its cognate amino-acyl tRNA synthetase (AARS), and adenosine triphosphate (ATP) are brought together in a container where tRNA, if cognate, gets charged with AA and adenosine monophosphate (AMP) is released. The released AMP (and any free AA and ATP molecules) filters into thecischamber of an adjoining electrolytic cell (e-cell) from where they pass through a nanopore into thetranschamber. Addition of NaOH to the container deacylates the tRNA if it is charged. The resulting free AA passes into thecischamber of the e-cell, translocates intotrans, and causes a current blockade; AA is immediately known from the identity of the tRNA (the two are cognate). If the tRNA is not charged there is no AA bound to it so AA remains unidentified. In this approach there is no need to distinguish among the 20 AAs by blockade size; it suffices to distinguish blockades from noise: thus a high-precision analog measurement has been transformed into a low-precision binary one. Identification is accurate because of tRNA superspecificity (the tRNA charging error rate is < 1/350); parallel execution with 20 different tRNAs can identify AA in one cycle. This is ade novomethod in which no prior information about the protein is used or needed.
Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome
Authors: Wang Xi , Ingvarsson Pär K
Published: June 2020

Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequence whole genomes of 34Picea abiesindividuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that negative selection is very limited in coding regions, while positive selection is rare in coding regions but very strong in non-coding regions, suggesting the great importance of regulatory changes in evolution of Norway spruce. Additionally, we found a positive correlation between adaptive rate with recombination rate and a negative correlation between adaptive rate and gene density, suggesting a widespread influence from Hill-Robertson interference to efficiency of protein adaptation inP. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated impact from selection to genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted specific molecular functions and biological processes in that appear to be targets of selection in Norway spruce.
The Set Increment with Limited Views Encoding Ratio (SILVER) Method for Optimizing Radial Sampling of Dynamic MRI
Authors: Schauman S. Sophie , Okell Thomas W. , Chiew Mark
Published: June 2020

Purpose

To present and assess a method for choosing a fixed increment between spokes in radially sampled MRI that results in higher SNR than other radial sampling increments.

Theory and Methods

Sampling uniformity contributes to image SNR when reconstructed using linear methods. Thus, for a radial trajectory, uniformly spaced sampling is ideal. However, uniform sampling lacks post-acquisition reconstruction flexibility, which is often needed in dynamic imaging. Golden ratio-based increments are often used for this purpose. The method presented here, Set Increment with Limited Views Encoding Ratio (SILVER), optimizes sampling uniformity when a limited number of temporal resolutions are required. With SILVER, an optimization algorithm finds the angular increment that provides the highest uniformity for a pre-defined set of reconstruction window sizes. SILVER was tested over multiple sets and assessed in terms of uniformity, noise amplification, and SNR both in simulations and in acquisitions of a phantom and healthy volunteers.

Results

The proposed algorithm produced trajectories that, for the optimized window sizes, had higher uniformity and lower image noise than golden ratio sampling both in a simulated single-coil system and in a multi-coil system, assessed using simulation, phantom, and in vivo experiments. The noise in SILVER optimized trajectories was comparable to uniformly distributed spokes whilst retaining flexibility in reconstruction at multiple temporal resolutions. In a resting state fMRI experiment, tSNR increases at different spatial and temporal resolutions ranged from 21-72%.

Conclusion

SILVER is a simple addition to any sequence currently using golden ratio sampling and significantly increases sampling efficiency and SNR.
Direct Supercritical Angle Localization Microscopy for Nanometer 3D Superresolution
Authors: Dasgupta Anindita , Deschamps Joran , Matti Ulf , Hübner Uwe , Becker Jan , Strauss Sebastian , Jungmann Ralf , Heintzmann Rainer , Ries Jonas
Published: June 2020

3D single molecule localization microscopy (SMLM) is an emerging superresolution method for structural cell biology, as it allows probing precise positions of proteins in cellular structures. Supercritical angle fluorescence strongly depends on the z-position of the fluorophore and can be used for z localization in a method called supercritical angle localization microscopy (SALM). Here, we realize the full potential of SALM by directly splitting supercritical and undercritical emission, using an ultra-high NA objective, and applying new fitting routines to extract precise intensities of single emitters, resulting in a four-fold improved z-resolution compared to the state of the art. We demonstrate nanometer isotropic localization precision on DNA origami structures, and on clathrin coated vesicles and microtubules in cells, illustrating the potential of SALM for cell biology.
Facilitating candidate gene discovery in an emerging model plant lineage: Transcriptomic and genomic resources forThalictrum(Ranunculaceae)
Authors: Arias Tatiana , Riaño-Pachón Diego Mauricio , Di Stilio Verónica S.
Published: June 2020

The plant genusThalictrumis a representative of the order Ranunculales (a sister lineage to all other Eudicots) with diverse floral morphologies, encompassing four sexual systems and two pollination modes. Previous studies suggest multiple transitions from insect to wind pollination within this genus, in association with polyploidy and unisexual flowers, but the underlying genes remain unknown. We generated a draft reference genome forThalictrum thalictroides, a representative of a clade with ancestral floral traits (diploidy, hermaphroditism, and insect pollination) and a model for functional studies. To facilitate candidate gene discovery in flowers with different sexual and pollination systems we also generated floral transcriptomes ofT. thalictroidesand of wind-pollinated, andromonoecious (staminate and hermaphroditic flowers on the same plant)T. hernandezii.

TheT. thalictroidesdraft genome assembly consisted of 44,860 contigs (N50=12,761 bp. and 243 Mbp. total length) and contained 84.5% conserved embryophyte single-copy genes. Floral transcriptomes from Illumina sequencing andde novoassembly contained representatives of most eukaryotic core genes (approximately 80%), with most of their genes falling into common orthologous groups (orthogroups). Simple Sequence Repeat (SSR) motifs were also identified, which together with the single-copy genes constitute a resource for population-level or phylogenetic studies. Finally, to validate the utility of these resources, putative candidate genes were identified for the different floral morphologies using stepwise dataset comparisons. In conclusion, we present genomic and transcriptomic resources forThalictrum, including the first genome ofT. thalictroidesand potential candidate genes for flowers with distinct sexual and pollination systems.
Crossing the Blood-Brain-Barrier: A bifunctional liposome for BDNF gene delivery – A Pilot Study
Authors: Diniz Danielle M. , Franze Silvia , Homberg Judith R.
Published: June 2020

To achieve their therapeutic effect on the brain, molecules need to pass the blood-brain-barrier (BBB). Many pharmacological treatments of neuropathologies encounter the BBB as a barrier, hindering their effective use. Pharmaceutical nanotechnology based on optimal physicochemical features and taking advantage of naturally occurring permeability mechanisms, nanocarriers such as liposomes offer an attractive alternative to allow drug delivery across the BBB. Liposomes are spherical bilayer lipid-based nanocapsules that can load hydrophilic molecules in their inner compartment and on their outer surface can be functionally modified by peptides, antibodies and polyethyleneglycol (PEG). When composed of cationic lipids, liposomes can serve as gene delivery devices, encapsulating and protecting genetic material from degradation and promoting nonviral cell transfection. In this study, we aimed to develop a liposomal formulation to encapsulate a plasmid harbouring brain-derived neurotrophic factor (BDNF) and infuse these liposomes via the peripheral bloodstream into the brain. To this end, liposomes were tagged with PEG, transferrin, and arginine and characterized regarding their physical properties, such as particle size, zeta-potential and polydispersity index (PDI). Moreover, we selected liposomes preparations for plasmid DNA (pDNA) encapsulation and checked for loading efficiency, in vitro cell uptake, and transfection. The preliminary results from this pilot study revealed that we were able to replicate the liposomes synthesis described in literature, achieving compatible size, charge, PDI, and loading efficiency. However, we could not properly determine whether the conjugation of the surface ligands transferrin and arginine to PEG worked and whether they were attached to the surface of the liposomes. Additionally, we were not able to see transfection in SH-SY5Y cells after 24 or 48 hours of incubation with the pDNA loaded liposomes. In conclusion, we synthesized liposomes encapsulation pBDNF, however, further research will be necessary to address the complete physicochemical characterization of the liposomes. Furthermore, preclinical studies will be helpful to verify transfection efficiency, cytotoxicity, and in the future, safe delivery of BDNF through the BBB.
Interferon-Induced Transmembrane Protein 3 Blocks Fusion of Diverse Enveloped Viruses by Locally Altering Mechanical Properties of Cell Membranes
Authors: Guo Xiangyang , Steinkühler Jan , Marin Mariana , Li Xiang , Lu Wuyuan , Dimova Rumiana , Melikyan Gregory B.
Published: June 2020

Interferon-induced transmembrane protein 3 (IFITM3) potently inhibits entry of diverse enveloped viruses by trapping the viral fusion at a hemifusion stage, but the underlying mechanism remains unclear. Here, we show that recombinant IFITM3 reconstituted into lipid vesicles induces negative membrane curvature and that this effect maps to its small amphipathic helix (AH). We demonstrate that AH: (i) partitions into lipid-disordered domains where IAV fusion occurs, (ii) induces negative membrane curvature, and (iii) increases lipid order and membrane stiffness. Additionally, replacing the IFITM3 AH with AH from an unrelated protein did not compromise its antiviral activity. These effects on membrane properties correlate with the fusion-inhibitory activity, as exogenous addition of AH to insulin-producing cells reduces glucose-stimulated insulin secretion. Our results thus imply that IFITM3 inhibits the transition from hemifusion to full fusion by imposing an unfavorable membrane curvature and increasing the order and stiffness of the cytoplasmic leaflet of endosomal membranes.
DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies
Authors: Faure Andre J. , Schmiedel Jörn M. , Baeza-Centurion Pablo , Lehner Ben
Published: June 2020

Deep mutational scanning (DMS) enables multiplexed measurement of the effects of thousands of variants of proteins, RNAs and regulatory elements. Here, we present a customizable pipeline – DiMSum – that represents an end-to-end solution for obtaining variant fitness and error estimates from raw sequencing data. A key innovation of DiMSum is the use of an interpretable error model that captures the main sources of variability arising in DMS workflows, outperforming previous methods. DiMSum is available as an R/Bioconda package and provides summary reports to help researchers diagnose common DMS pathologies and take remedial steps in their analyses.
Bi-compartmentalized stem cell organization of the corneal limbal niche
Authors: Farrelly Olivia , Suzuki-Horiuchi Yoko , Brewster Megan , Kuri Paola , Huang Sixia , Rice Gabriella , Xu Jianming , Dentchev Tzvete , Lee Vivian , Rompolas Panteleimon
Published: June 2020

Stem cells exist in precise locations within tissues, yet how their organization supports tissue architecture and function is poorly understood. The limbus is the presumptive stem cell niche of the corneal epithelium. Here, we visualize the live limbus and track the activity of single stem cells in their native environment by 2-photon microscopy. We identify previously unknown niche compartments and show that long implicated slow-cycling cells form separate lineages in the outer limbus, with only local clonal dynamics. Instead, we find distinct stem cells in the pericorneal limbus to be required for corneal regeneration. Unbiased photolabeling captures their progeny exiting the niche, then moving centripetally in unison before undergoing terminal differentiation. This study demonstrates how a compartmentalized stem cell organization coordinates tissue regeneration.

One Sentence Summary

In vivo live imaging of the regenerating cornea reveals distinct stem cell activities in the limbal niche
Follicle Stem Cells (FSCs) in the Drosophila ovary; a critique of published studies defining the number, location and behavior of FSCs
Authors: Kalderon Daniel , Melamed David , Reilein Amy
Published: June 2020

A paper by Reilein et al., (2017) presented several key new insights into the behavior of adult Follicle Stem Cells (FSCs) in the Drosophila ovary, including overwhelming evidence that each ovariole hosts a large number of FSCs (about 14-16) maintained by population asymmetry (Reilein et al., 2017), rather than just two FSCs, dividing with largely individually asymmetric outcomes, as originally proposed (Margolis and Spradling, 1995; Nystul and Spradling, 2007). Here we provide further discussion asserting the merits of the conclusions of Reilein et al., (2017) and the deficiencies in the contrary assertions recently presented by Fadiga and Nystul (Fadiga and Nystul, 2019). The principles that we discuss here, particularly with regard to lineage tracing and population asymmetry, are common to the investigation of most types of adult stem cell and should therefore be instructive and of interest to investigators studying any type of adult stem cell. The improved understanding of FSC numbers, location and behavior afforded by Reilein et al., (2017) and Reilein et al., (2018) can only provide a firm foundation for future progress once they are widely appreciated and seen to be resistant to challenge, as described in detail here.
A targeted next generation sequencing approach to develop robust, genotype-specific mutation profiles and uncover novel variants inSaccharomyces cerevisiae
Authors: Lamb Natalie A. , Bard Jonathan , Buck Michael J. , Surtees Jennifer A.
Published: June 2020

Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature in a cell or a tumor can therefore predict the underlying mechanism of mutagenesis, which, in practice, may be clinically important. These insults to the genome often alter dNTP pools, which itself impacts replication fidelity. Therefore, the impact of altered dNTP pools should be considered when making mechanistic predictions based on mutation signatures. We developed a targeted deep-sequencing approach on theCAN1gene inSaccharomyces cerevisiaeto define information-rich mutational profiles associated with distinctrnr1backgrounds that alter replication fidelity by elevating dNTP levels.. The mutation spectra ofrnr1Y285Fandrnr1Y285Aalleles were characterized previously; our analysis was consistent with this prior work but the sequencing depth achieved in our study allowed a significantly more robust and nuanced computational analysis of the variants observed, generating profiles that integrated information about mutation spectra, position effects, and sequence context. This approach revealed novel, genotype-specific mutation profiles in the presence of even modest changes in dNTP pools. Furthermore, we identified broader sequence contexts and specific nucleotide motifs that influenced variant profiles in differentrnr1backgrounds, which allowed us to make specific mechanistic predictions about the impact of altered dNTP pools on replication fidelity.
ESCRT recruitment by the inner nuclear membrane protein Heh1 is regulated by Hub1-mediated alternative splicing
Authors: Capella Matías , Caballero Lucía Martín , Pfander Boris , Braun Sigurd , Jentsch Stefan
Published: June 2020

Misassembled nuclear pore complexes (NPCs) are removed by sealing off the surrounding nuclear envelope (NE), which is mediated by members of the ESCRT (endosomalsortingcomplexesrequired fortransport) machinery. Recruitment of ESCRT proteins to the NE is mediated by the interaction between the ESCRT member Chm7 and the inner nuclear membrane protein Heh1, which belongs to the conserved LEM family. Increased ESCRT recruitment results in excessive membrane scission at damage sites but its regulation remains poorly understood. Here, we show that Hub1-mediated alternative splicing ofHEH1pre-mRNA, resulting into its shorter form Heh1-S, is critical for the integrity of the NE. ESCRT-III mutants lacking Hub1 or Heh1-S display severe growth defects and accumulate improperly assembled NPCs. This depends on the interaction of Chm7 with the conserved MSC domain only present in the longer spliced variant Heh1-L. Heh1 variants assemble into heterodimers and we demonstrate that a unique splice segment in Heh1-S suppresses growth defects associated with uncontrolled interaction between Heh1-L and Chm7. Together, our findings reveal that Hub1-mediated splicing generates Heh1-S to regulate ESCRT recruitment to the nuclear envelope.

Summary statement

Heh1-S, the Hub1-mediated spliced version ofHEH1pre-mRNA, contributes to nuclear envelope maintenance by preventing excessive recruitment of Chm7.
A single cell atlas of the healthy breast tissues reveal clinically relevant clusters of breast epithelial cells
Authors: Bhat-Nakshatri Poornima , Gao Hongyu , McGuire Patrick C. , Xuei Xiaoling , Sheng Liu , Wan Jun , Liu Yunlong , Althouse Sandra K. , Colter Austyn , Sandusky George , Storniolo Anna Maria , Nakshatri Harikrishna
Published: June 2020

Single cell RNA sequencing is an evolving field to elucidate cellular architecture of adult organs. Using normal breast tissues from healthy volunteers and a rapid procurement/processing/sequencing protocol, 13 breast epithelial cell clusters were identified. Approximately 90% of breast cancers were enriched for cell-of-origin signatures derived from differentiated luminal clusters and two minor luminal progenitor clusters. Expression of cell cycle and chromosome segregation-related genes were higher in one of the minor clusters and breast tumors with this cluster signature displayed the highest mutation rate and poor outcome. We identified TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts and their expression analyses in >550 breast cancers enabled prognostically relevant cell-of-origin based subclassification of ER+ breast cancers.

Significance

This study elucidates different epithelial cell types of the normal breasts and identifies a minor subpopulation of cells from which the majority of breast cancers may originate. This observation should help to develop methods to characterize breast tumors based on cell-of-origin. Although it was suggested that intrinsic subtypes of breast cancers have distinct cells of origins, this study suggests multiple cell-of-origin for an intrinsic subtype of breast cancer, including for hormone responsive breast cancers. Cell-of-origin signatures allowed survival-associated subclassification of intrinsic subtypes. Critically, this normal breast cell atlas would allow for the classification of genes differentially expressed in a breast tumor compared to normal breast due to the cell-of-origin of tumor and those that are acquired due to genomic aberrations.
Tsetse salivary glycoproteins are modified with paucimannosidicN-glycans, are recognised by C-type lectins and bind to trypanosomes
Authors: Kozak Radoslaw P. , Mondragon-Shem Karina , Williams Christopher , Rose Clair , Perally Samirah , Caljon Guy , Van Den Abbeele Jan , Wongtrakul-Kish Katherine , Gardner Richard , Spencer Daniel , Lehane Michael J. , Acosta-Serrano Alvaro
Published: June 2020

African sleeping sickness is caused byTrypanosoma brucei,a parasite transmitted by the bite of a tsetse fly. Trypanosome infection induces a severe transcriptional downregulation of tsetse genes encoding for salivary proteins, which reduces its anti-hemostatic and anti-clotting properties. To better understand trypanosome transmission and the possible role of glycans in insect bloodfeeding, we characterized theN-glycome of tsetse saliva glycoproteins. Tsetse salivaryN-glycans were enzymatically released, tagged with either 2-aminobenzamide (2-AB) or procainamide, and analyzed by HILIC-UHPLC-FLR coupled online with positive-ion ESI-LC-MS/MS. We found that theN-glycan profiles ofT. brucei-infected and naïve tsetse salivary glycoproteins are almost identical, consisting mainly (>50%) of highly processed Man3GlcNAc2 in addition to several other paucimannose, high mannose, and few hybrid-type glycans. In overlay assays, these sugars were differentially recognized by the C-type lectins mannose receptor and DC-SIGN. We also show that salivary glycoproteins bind strongly to the surface of transmissible metacyclic trypanosomes. We suggest that although the repertoire of tsetse salivaryN-glycans does not change during a trypanosome infection, the interactions with mannosylated glycoproteins may influence parasite transmission into the vertebrate host.
The Evolution of Insect Metallothioneins
Authors: Luo Mei , Finet Cédric , Cong Haosu , Wei Hong-yi , Chung Henry
Published: June 2020

Metallothioneins (MTs) are a family of cysteine-rich metal-binding proteins that are important in the chelating and detoxification of toxic heavy metals. Until now, the short length and the low sequence complexity of MTs has hindered the possibility of any phylogenetic reconstruction, hampering the study of their evolution. To answer this longstanding question, we developed an iterative BLAST search pipeline that allowed us to build a unique dataset of more than 300 MT sequences in insects. By combining phylogenetics and synteny analysis, we reconstructed the evolutionary history of MTs in insects. We show that the MT content in insects has been shaped by lineage-specific tandem duplications from a single ancestral MT. Strikingly, we also uncovered a sixth MT,MtnF, in the model organismDrosophila melanogaster.MtnFevolves faster than other MTs and is characterized by a non-canonical length and higher cysteine content. Our methodological framework not only paves the way for future studies on heavy metal detoxification but also can allow us to identify other previously unidentified genes and other low complexity genomic features.