bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formalin fixation and paraffin embedding interfere with preservation of optical metabolic assessments based on endogenous NAD(P)H and FAD two photon excited fluorescence
Authors: Sánchez-Hernández Adriana , Polleys Christopher M. , Georgakoudi Irene 
Published: June 2023

AbstractEndogenous NAD(P)H and FAD two-photon excited fluorescence (TPEF) images provide functional metabolic information with high spatial resolution for a wide range of living specimens. Preservation of metabolic function optical metrics upon fixation would facilitate studies which assess the impact of metabolic changes in the context of numerous diseases. However, robust assessments of the impact of formalin fixation, paraffin embedding, and sectioning on the preservation of optical metabolic readouts are lacking. Here, we evaluate intensity and lifetime images at excitation/emission settings optimized for NAD(P)H and FAD TPEF detection from freshly excised murine oral epithelia and corresponding bulk and sectioned fixed tissues. We find that fixation impacts the overall intensity as well as the intensity fluctuations of the images acquired. Accordingly, the depth-dependent variations of the optical redox ratio (defined as FAD/(NAD(P)H + FAD)) across squamous epithelia are not preserved following fixation. This is consistent with significant changes in the 755 nm excited spectra, which reveal broadening upon fixation and additional distortions upon paraffin embedding and sectioning. Analysis of fluorescence lifetime images acquired for excitation/emission settings optimized for NAD(P)H TPEF detection indicate that fixation alters the long lifetime of the observed fluorescence and the long lifetime intensity fraction. These parameters as well as the short TPEF lifetime are significantly modified upon embedding and sectioning. Thus, our studies highlight that the autofluorescence products formed during formalin fixation, paraffin embedding and sectioning overlap highly with NAD(P)H and FAD emission and limit the potential to utilize such tissues to assess metabolic activity.
Dual effects of the small-conductance Ca2+-activated K+current on human atrial electrophysiology and Ca2+-driven arrhythmogenesis: anin silicostudy
Authors: Herrera Nathaniel T. , Zhang Xianwei , Ni Haibo , Maleckar Mary M. , Heijman Jordi , Dobrev Dobromir , Grandi Eleonora , Morotti Stefano 
Published: June 2023

AbstractBy sensing changes in intracellular Ca2+, small-conductance Ca2+-activated K+(SK) channels dynamically regulate the dynamics of the cardiac action potential (AP) on a beat-to-beat basis. Given their predominance in atria vs. ventricles, SK channels are considered a promising atrial-selective pharmacological target against atrial fibrillation (AF), the most common cardiac arrhythmia. However, the precise contribution of SK current (ISK) to atrial arrhythmogenesis is poorly understood, and may potentially involve different mechanisms that depend on species, heart rates, and degree of AF-induced atrial remodeling. Both reduced and enhanced ISKhave been linked to AF. Similarly, both SK channel up- and downregulation have been reported in chronic AF (cAF) vs. normal sinus rhythm (nSR) patient samples. Here, we use our multi-scale modeling framework to obtain mechanistic insights into the contribution of ISKin human atrial myocyte electrophysiology. We simulate several protocols to quantify how ISKmodulation affects the regulation of AP duration (APD), Ca2+transient, refractoriness, and occurrence of alternans and delayed afterdepolarizations (DADs). Our simulations show that ISKactivation shortens the APD and atrial effective refractory period, limits Ca2+cycling, and slightly increases the propensity for alternans in both nSR and cAF conditions. We also show that increasing ISKcounteracts DAD development by reducing the coupling between transmembrane potential and intracellular Ca2+. Taken together, our results suggest that increasing ISKin human atrial myocytes could promote reentry, while protecting against triggered activity. Depending on the leading arrhythmogenic mechanism, ISKinhibition may thus be a beneficial or detrimental anti-AF strategy.
NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration
Authors: Liefeld Ted , Huang Edwin , Wenzel Alexander T. , Yoshimoto Kenneth , Sharma Ashwyn K , Sicklick Jason K , Mesirov Jill P , Reich Michael 
Published: June 2023

AbstractSummaryNon-negative Matrix Factorization (NMF) is an algorithm that can reduce high dimensional datasets of tens of thousands of genes to a handful of metagenes which are biologically easier to interpret. Application of NMF on gene expression data has been limited by its computationally intensive nature, which hinders its use on large datasets such as single-cell RNA sequencing (scRNA-seq) count matrices. We have implemented NMF based clustering to run on high performance GPU compute nodes using CuPy, a GPU backed python library, and the Message Passing Interface (MPI). This reduces the computation time by up to three orders of magnitude and makes the NMF Clustering analysis of large RNA-Seq and scRNA-seq datasets practical. We have made the method freely available through the GenePattern gateway, which provides free public access to hundreds of tools for the analysis and visualization of multiple ‘omic data types. Its web-based interface gives easy access to these tools and allows the creation of multi-step analysis pipelines on high performance computing (HPC) clusters that enable reproduciblein silicoresearch for non-programmers.Availability and ImplementationNMFClustering is freely available on the public GenePattern server athttps://genepattern.ucsd.edu. Code for the NMFClustering is available under a BSD style license on github athttps://github.com/genepattern/nmf-gpu.ContactTed Liefeld,jliefeld@cloud.ucsd.eduSupplementary InformationSupplementary data are available at Bioinformatics online and athttps://datasets.genepattern.org/?prefix=data/test_data/NMFClustering/.
Neuronal modeling of magnetoencephalography responses in auditory cortex to auditory and visual stimuli
Authors: Lankinen Kaisu , Ahveninen Jyrki , Jas Mainak , Raij Tommi , Ahlfors Seppo P. 
Published: June 2023

AbstractPrevious studies have demonstrated that auditory cortex activity can be influenced by crosssensory visual inputs. Intracortical recordings in non-human primates (NHP) have suggested a bottom-up feedforward (FF) type laminar profile for auditory evoked but top-down feedback (FB) type for cross-sensory visual evoked activity in the auditory cortex. To test whether this principle applies also to humans, we analyzed magnetoencephalography (MEG) responses from eight human subjects (six females) evoked by simple auditory or visual stimuli. In the estimated MEG source waveforms for auditory cortex region of interest, auditory evoked responses showed peaks at 37 and 90 ms and cross-sensory visual responses at 125 ms. The inputs to the auditory cortex were then modeled through FF and FB type connections targeting different cortical layers using the Human Neocortical Neurosolver (HNN), which consists of a neocortical circuit model linking the cellular– and circuit-level mechanisms to MEG. The HNN models suggested that the measured auditory response could be explained by an FF input followed by an FB input, and the crosssensory visual response by an FB input. Thus, the combined MEG and HNN results support the hypothesis that cross-sensory visual input in the auditory cortex is of FB type. The results also illustrate how the dynamic patterns of the estimated MEG/EEG source activity can provide information about the characteristics of the input into a cortical area in terms of the hierarchical organization among areas.Significance statementLaminar intracortical profiles of activity characterize feedforward– and feedback-type influences in the inputs to a cortical area. By combining magnetoencephalography (MEG) and biophysical computational neural modeling, we obtained evidence of cross-sensory visual evoked activity in human auditory cortex being of feedback type. The finding is consistent with previous intracortical recordings in non-human primates. The results illustrate how patterns of MEG source activity can be interpreted in the context of the hierarchical organization among cortical areas.
Cortical Surface Area Relates to Distinct Computational Properties in Human Visual Perception
Authors: Murray Scott O. , Kolodny Tamar , Webb Sara Jane 
Published: June 2023

AbstractUnderstanding the relationship between cortical structure and function is essential for elucidating the neural basis of human behavior. However, the impact of cortical structural features on the computational properties of neural circuits remains poorly understood. In this study, we demonstrate that a simple structural feature – cortical surface area (SA) – relates to specific computational properties underlying human visual perception. By combining psychophysical, neuroimaging, and computational modeling approaches, we show that differences in SA in the parietal and frontal cortices are associated with distinct patterns of behavior in a motion perception task. These behavioral differences can be accounted for by specific parameters of a divisive normalization model, suggesting that SA in these regions contributes uniquely to the spatial organization of cortical circuitry. Our findings provide novel evidence linking cortical structure to distinct computational properties and offer a framework for understanding how cortical architecture can impact human behavior.
Expanding the toolkit for genetic manipulation and discovery inCandidaspecies using a CRISPR ribonucleoprotein-based approach
Authors: Gregor Justin B. , Gutierrez-Schultz Victor A. , Hoda Smriti , Baker Kortany M. , Saha Debasmita , Burghaze Madeline G. , Briggs Scott D. 
Published: June 2023

ABSTRACTThe World Health Organization recently published the first list of priority fungal pathogens highlighting multipleCandidaspecies includingC. glabrata,C. albicans, andC. auris. The use of CRISPR-Cas9 and auxotrophicC. glabrataandC. albicansstrains have been instrumental in the study of these fungal pathogens. Dominant drug resistance cassettes are also critical for genetic manipulation and eliminate the concern of altered virulence when using auxotrophic strains. However, genetic manipulation has been mainly limited to the use of two drug resistance cassettes,NatMXandHphMX. Using anin vitroassembled CRISPR-Cas9 ribonucleoprotein (RNP)-based system and 130-150 bp homology regions for directed repair, we expand the drug resistance cassettes forCandidato includeKanMXandBleMX, commonly used inS. cerevisiae. As a proof of principle, we demonstrated efficient deletion ofERGgenes usingKanMXandBleMX. We also showed the utility of the CRISPR-Cas9 RNP system for generating double deletions of genes in the ergosterol pathway and endogenous epitope tagging ofERGgenes using an existingKanMXcassette. This indicates that CRISPR-Cas9 RNP can be used to repurpose theS. cerevisiaetoolkit. Furthermore, we demonstrated that this method is effective at deletingERG3inC. aurisusing a codon optimizedBleMXcassette and effective at deleting the epigenetic factor,SET1, inC. albicansusing a recyclableSAT1.Using this expanded toolkit, we discovered new insights into fungal biology and drug resistance.IMPORTANCEThe increasing problem of drug resistance and emerging pathogens is an urgent global health problem that necessitates the development and expansion of tools for studying fungal drug resistance and pathogenesis. We have demonstrated the effectiveness of an expression-free CRISPR-Cas9 RNP-based approach employing 130-150 bp homology regions for directed repair. Our approach is robust and efficient for making gene deletions inC. glabrata,C. aurisandC. albicansas well as epitope tagging inC. glabrata. Furthermore, we demonstrated thatKanMXandBleMXdrug resistance cassettes can be repurposed inC. glabrataandBleMXinC. auris. Overall, we have expanded the toolkit for genetic manipulation and discovery in fungal pathogens.
The phoretic mite (Arachnida: Acari) assemblage of the Douglas-fir beetle,Dendroctonus pseudotsugaeHopkins (Coleoptera: Curculionidae)
Authors: Browning Laura-Anne , Huber Dezene P.W. 
Published: June 2023

AbstractThe phoretic mite assemblage of the Douglas-fir beetle,Dendroctonus pseudotsugaeHopkins (Coleoptera: Curculionidae) has not been as thoroughly documented as that of some other ecologically and economically important bark beetle species. Phoretic mites can impact individual fitness and population dynamics of their hosts and documenting the mite assemblage associated with a bark beetle may provide information on their ecological and interactive roles. We caught Douglas-fir beetles over two summers in central British Columbia, Canada and sorted the associated mites into morphospecies. Representatives of the morphospecies were DNA barcoded (cytochrome oxidate I barcode region) which indicated at least nine distinct Operational Taxonomic Units (OTUs). There was a mean of 50.5 ± 4.7 mites per beetle with both females and males carrying similar numbers of most mite species. However one OTU (Sarcoptiformes: Hemisarcoptidae) was found in substantially higher numbers than all other OTUs, and was always clustered in large aggregations in an anterior pocket on the sub-elytral surface. When B1 was removed from the mean, there were only 1.3 ± 0.2 mites per beetle. The consistent high numbers of that OTU in conjunction with its consistent anatomical aggregation suggests an important interaction between that mite species and the Douglas-fir beetle.
Changes in ADAR RNA Editing Patterns in CMV and ZIKV Congenital Infections
Authors: Wales-McGrath Benjamin , Mercer Heather , Piontkivska Helen 
Published: June 2023

BackgroundRNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data.ResultsWe found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding.ConclusionsOur findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
Systems engineering ofSaccharomyces cerevisiaefor synthesis and accumulation of vanillin
Authors: Mo Qiwen , Yuan Jifeng 
Published: June 2023

ABSTRACTVanillin represents one of the most widely used flavoring agents in the world. However, microbial synthesis of vanillin is hindered by the host native metabolism that could rapidly degrade vanillin to the byproducts. Here, we report that the industrial workhorseSaccharomyces cerevisiaewas engineered by systematic deletion of oxidoreductases to improve the vanillin accumulation. Subsequently, we harnessed thereduced aromaticaldehydereduction (RARE) yeast platform forde novosynthesis of vanillin from glucose. We investigated multiple coenzyme-A free pathways to improve vanillin production in yeast. The vanillin productivity in yeast was further enhanced by systems engineering to optimize the supply of cofactors (NADPH andS-adenosylmethionine) together with metabolic reconfiguration of yeast central metabolism. The final yeast strain with overall 24 genetic modifications produced 365.55 ± 7.42 mg L−1under shake-flasks, which represents the highest vanillin titer from glucose achieved to date. Taken together, our work lays a foundation for the future implementation of vanillin production from glucose in budding yeast.Abstract FigureTOC
A Two-Filter Adaptation to Achieve Hemodiafiltration with Enhanced Performance
Authors: Chu Kyle , Li Pei , Ausri Irfani , Vasconez Cesar , Tang Xiaowu (Shirley) 
Published: June 2023

ABSTRACTIntroductionAdvancements in hemodialysis (HD) instrumentation have resulted in numerous breakthroughs in technology and significantly enhanced patient outcomes. Today, hemodiafiltration (HDF) which combines HD and hemofiltration has been widely used as an alternative to conventional HD in many countries. HDF is known to outperform conventional HD, offering more effective waste clearance and better fluid balance to patients. However, HDF requires newer-generation machines that are not accessible in many under-resourced geographical regions and societies. This study investigates a facile adaptation of conventional HD machines to achieve HDF. The objectives are to address the premature obsolescence of older but fully functional machines and to advocate for equal access to improved medical care and treatment.MethodsA bench-top experimental setup was established to evaluate the performance of HDF using a two-filter adaptation in comparison to that of standard HD. Urea clearance, human serum album loss, and hemolysis were assessed under identical operational conditions for both configurations.FindingsOur results show that the HDF configuration outperformed the HD configuration, with significantly higher urea clearance (268.31±44.17 mL/min via HDF vs. 53.33±13.20 mL/min via HD), but comparable human serum albumin loss and hemolysis levels.DiscussionThe explored two-filter adaptation presents a cost-effective method to achieve HDF with improved performance using conventional HD machines, with no added risk to patients. Further validation on patients in a hospital setting is necessary.
Nyctinastic leaf folding mimic reduces herbivory byChromacris trogongrasshoppers (Orthoptera:Romaleidae)
Authors: Bell Aidan B. 
Published: June 2023

ABSTRACTArachis pintoi(Fabaceae) is a common relative of the cultivated peanut, and folds its four leaflets up to look like one at night. The adaptive significance of this behavior (foliar nyctinasty) is unknown. To test the hypothesis that leaflet folding alone can deter herbivores, a leaf preference experiment was performed onChromacris trogongrasshoppers. Small oval cutouts were made from leaves of the grasshopper’s preferred food source,Iochroma arborescens(Solanaceae), and were combined with small pieces of tape and dry grass to construct artificial leaves resembling the day and night form ofA. pintoi. In the experiment, groups of three grasshoppers were starved for 24 hours and then placed in petri dishes containing one closed and one open artificial leaf. After 30 six-hour trials, the average herbivory of open leaves was 12.3%, while closed leaves was 5.2% (p = 0.00145), indicating a significant preference for open leaves. This suggests that the folded configuration ofA. pintoileaves can be a defense against herbivory.
Hierarchical design of pseudosymmetric protein nanoparticles
Authors: Dowling Quinton M. , Park Young-Jun , Gerstenmaier Neil , Yang Erin C. , Wargacki Adam , Hsia Yang , Fries Chelsea N. , Ravichandran Rashmi , Walkey Carl , Burrell Anika , Veesler David , Baker David , King Neil P. 
Published: June 2023

AbstractDiscrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions1–3. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry4,5. Inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540, and 960 subunits. At 49, 71, and 96 nm diameter, these nanoparticles are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work represents an important step towards the accurate design of arbitrary self-assembling nanoscale protein objects.