bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacokinetic considerations for optimizing inhaled spray-dried pyrazinoic acid formulations
Authors: Yeshwante Shekhar B. , Hanafin Patrick , Miller Brittany K. , Rank Laura , Murcia Sebastian , Xander Christian , Annis Ayano , Baxter Victoria K. , Anderson Elizabeth J. , Jermain Brian , Konicki Robyn , Schmalstig Alan A. , Stewart Ian , Braunstein Miriam , Hickey Anthony J. , Rao Gauri G. 
Published: April 2023

ABSTRACTTuberculosis (TB), caused byMycobacterium tuberculosis(Mtb), remains a leading cause of death with 1.6 million deaths worldwide reported in 2021. Oral pyrazinamide (PZA) is an integral part of anti-TB regimens, but its prolonged use has the potential to drive development of PZA resistantMtb. PZA is converted to the active moiety pyrazinoic acid (POA) by theMtbpyrazinamidase encoded bypncA, and mutations inpncAare associated with the majority of PZA resistance. Conventional oral and parenteral therapies may result in subtherapeutic exposure in the lung, hence direct pulmonary administration of POA may provide an approach to rescue PZA efficacy for treatingpncA-mutant PZA-resistantMtb.The objectives of the current study were to i) develop novel dry powder POA formulations ii) assess their feasibility for pulmonary delivery using physicochemical characterization, iii) evaluate their pharmacokinetics (PK) in the guinea pig model and iv) develop a mechanism based pharmacokinetic model (MBM) usingin vivoPK data to select a formulation providing adequate exposure in epithelial lining fluid (ELF) and lung tissue.We developed three POA formulations for pulmonary delivery and characterized their PK in plasma, ELF, and lung tissue following passive inhalation in guinea pigs. Additionally, the PK of POA following oral, intravenous and intratracheal administration was characterized in guinea pigs. The MBM was used to simultaneously model PK data following administration of POA and its formulations via the different routes. The MBM described POA PK well in plasma, ELF and lung tissue.Physicochemical analyses and MBM predictions suggested that POA maltodextrin was the best among the three formulations and an excellent candidate for further development as it has: (i) the highest ELF-to-plasma exposure ratio (203) and lung tissue-to-plasma exposure ratio (30.4) compared with POA maltodextrin and leucine (75.7/16.2) and POA leucine salt (64.2/19.3); (ii) the highest concentration in ELF (CmacELF: 171 nM) within 15.5 minutes, correlating with a fast transfer into ELF after pulmonary administration (kPM: 22.6 1/h).The data from the guinea pig allowed scaling, using the MBM to a human dose of POA maltodextrin powder demonstrating the potential feasibility of an inhaled product.Table of Contents (TOC)/Abstract Graphic
In defense of Apocynaceae: inference on evolution of pyrrolizidine alkaloids from evolution of an enzyme in their biosynthetic pathway, homospermidine synthase
Authors: Smith Chelsea R. , Kaltenegger Elisabeth , Teisher Jordan , Moore Abigail J. , Straub Shannon C. K. , Livshultz Tatyana 
Published: April 2023

AbstractPremiseWhen enzymes encoded by paralogous genes produce identical specialized metabolites in distantly related plant lineages, it is strong evidence of parallel phenotypic evolution. Inference of phenotypic homology for metabolites produced by orthologous genes is not so straightforward, however, since orthologs may be recruited in parallel into novel pathways. Prior research on pyrrolizidine alkaloids (PAs), specialized metabolites of Apocynaceae, reconstructed evolution of homospermidine synthase (HSS), an enzyme of PA biosynthesis, and inferred a single origin of PAs because HSS enzymes of all known PA-producing Apocynaceae species are orthologous and descended from an ancestral enzyme with the predicted motif (VXXXD) of an optimized HSS.MethodsWe increased sampling, tested the effect of amino acid motif on HSS function, revisited motif evolution, and tested for selection to infer evolution of HSS function and its correlation with phenotype.Key resultsSome evidence supports a single origin of PAs: an IXXXD HSS, similar in function to VXXXD HSS, evolved in the shared ancestor of all PA-producing species; loss of optimized HSS occurred multiple times via pseudogenization and perhaps via evolution of an IXXXN motif. Other evidence indicates multiple origins: the VXXXD motif, highly correlated with the PA phenotype, evolved two or four times independently; the ancestral IXXXD gene was not under positive selection while some VXXXD genes were; substitutions at sites experiencing positive selection occurred on multiple branches in theHSS-like gene tree.ConclusionsComplexity of the genotype-function-phenotype map confounds inference of PA homology fromHSSevolution in Apocynaceae.
Chromosome-level genome assembly provides insights into adaptive evolution of chromosome and important traits in the geckoGekko japonicus
Authors: Wang Yinwei , Yue Youxia , Li Chao , Chen Zhiyi , Cai Yao , Hu Chaochao , Qu Yanfu , Li Hong , Zhou Kaiya , Yan Jie , Li Peng 
Published: April 2023

AbstractGekko japonicuspossess excellent flexible climbing and detoxification ability under insectivorous habits, and its chromosomes and the genetic evolutionary mechanisms behind these traits are still unclarified. Here, we assembled a chromosome-level genome ofG. japonicuswith a total size of 2.53 Gb contained in 19 pairs of chromosomes. The evolutionary breakpoint regions (EBRs) are significantly enriched for some repetitive elements compared to the rest of genome and the genes located in the EBRs are enriched in defense response pathway.G. japonicusspecific gene families, expanded gene families and positively selected genes are mainly enriched in some pathways related to the immune, sensory and nervous systems. These results from comprehensive comparative genomics and evolutionary genomics analyses indicated that bitter taste receptor type 2 (T2Rs) expanded in different lineages by tandem gene duplication. The expansion and independent duplication events of T2Rs and positively selected branches were predominantly present in insectivorous species, suggests that T2Rs are associate with clearance of bitter toxins in gekkotans. Detoxification genes in detox and biosynthetic cytochrome P450 ofG. japonicashave frequent duplication and loss events, suggests that they undergo more birth and death processes compared to biosynthesis type genes. Pro, Cys, Gly and Ser are the most abundant amino acids in 66 epidermis formation corneous beta proteins (CBPs) ofG. japonicas, the abundance of Gly and Cys in CBPs implying significant effects on the flexibility and setae adhesiveness of gekkotans. Some thermosensitive thermoregulatory transient receptor potential channels under relaxed purifying selection or positive selection inG. japonicus, implying that one of the important factors improve the ability to adapt to climate change.
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Authors: Baldoni Pedro L. , Chen Yunshun , Hediyeh-zadeh Soroor , Liao Yang , Dong Xueyi , Ritchie Matthew E. , Shi Wei , Smyth Gordon K. 
Published: April 2023

AbstractDifferential expression analysis of RNA-seq is one of the most commonly performed bioinformatics analyses. Transcript-level quantifications are inherently more uncertain than gene-level read counts because of ambiguous assignment of sequence reads to transcripts. While sequence reads can usually be assigned unambiguously to a gene, reads are very often compatible with multiple transcripts for that gene, particularly for genes with many isoforms. Software tools designed for gene-level differential expression do not perform optimally on transcript counts because the read-to-transcript ambiguity (RTA) disrupts the mean-variance relationship normally observed for gene level RNA-seq data and interferes with the efficiency of the empirical Bayes dispersion estimation procedures. The pseudoaligners kallisto and Salmon provide bootstrap samples from which quantification uncertainty can be assessed. We show that the overdispersion arising from RTA can be elegantly estimated by fitting a quasi-Poisson model to the bootstrap counts for each transcript. The technical overdispersion arising from RTA can then be divided out of the transcript counts, leading to scaled counts that can be input for analysis by established gene-level software tools with full statistical efficiency. Comprehensive simulations and test data show that an edgeR analysis of the scaled counts is more powerful and efficient than previous differential transcript expression pipelines while providing correct control of the false discovery rate. Simulations explore a wide range of scenarios including the effects of paired vs single-end reads, different read lengths and different numbers of replicates.
Gelation of Uniform Interfacial Diffusant in Embedded 3D Printing
Authors: Shin Sungchul , Brunel Lucia G. , Cai Betty , Kilian David , Roth Julien G. , Seymour Alexis J. , Heilshorn Sarah C. 
Published: April 2023

ABSTRACTWhile the human body has many different examples of perfusable structures with complex geometries, biofabrication methods to replicate this complexity are still lacking. Specifically, the fabrication of self-supporting, branched networks with multiple channel diameters is particularly challenging. Here, we present the Gelation of Uniform Interfacial Diffusant in Embedded 3D Printing (GUIDE-3DP) approach for constructing perfusable networks of interconnected channels with precise control over branching geometries and vessel sizes. To achieve user-specified channel dimensions, this technique leverages the predictable diffusion of crosslinking reaction-initiators released from sacrificial inks printed within a hydrogel precursor. We demonstrate the versatility of GUIDE-3DP to be adapted for use with diverse physiochemical crosslinking mechanisms by designing seven printable material systems. Importantly, GUIDE-3DP allows for the independent tunability of both the inner and outer diameters of the printed channels and the ability to fabricate seamless junctions at branch points. This 3D bioprinting platform is uniquely suited for fabricating lumenized structures with complex shapes characteristic of multiple hollow vessels throughout the body. As an exemplary application, we demonstrate the fabrication of vasculature-like networks lined with endothelial cells. GUIDE-3DP represents an important advance toward the fabrication of self-supporting, physiologically relevant networks with intricate and perfusable geometries.
Importance of Leaf Age in Grapevines Under Salt Stress
Authors: Lupo Yaniv , Prashanth Kakarla , Lazarovitch Naftali , Fait Aaron , Rachmilevitch Shimon 
Published: April 2023

AbstractThe combined effects of salt stress and leaf age on photosynthesis and stomatal conductance are not fully understood. Salt stress develops at different rates in various plant organs and tissues, leading to osmotic and ionic stresses. We studied the development of salt stress (30 mM NaCl) in two grapevine rootstocks by examining the gas exchange, photochemistry, and salt accumulation of leaves at different ages. Our results indicate that leaf age strongly affected photosynthesis but had a minor effect on stomatal conductance in both control and salinity conditions. Surprisingly, salt stress lowered stomatal conductance but had little effect on photosynthesis, opposite to the leaf age effects. Reduction in photosystem II efficiency explained the age-associated decline in photosynthesis, suggesting that the light-dependent phase of photosynthesis is the first process affected by leaf aging. We also found that the sodium exclusion capacity decreased as leaves matured and was age and variety dependent, indicating the importance of leaf age when sampling for salt tolerance studies. Therefore, we suggest that sampling only young leaves is missing critical information in the evaluation of salt-tolerant traits in grapevines.
Mechanism of ADP-inhibited ATP hydrolysis in single proton-pumping FoF1-ATP synthase trapped in solution
Authors: Pérez Iván , Heitkamp Thomas , Börsch Michael 
Published: April 2023

AbstractFoF1-ATP synthases in mitochondria, in chloroplasts and in most bacteria are the proton-driven membrane enzymes supplying the cells with ATP made from ADP and phosphate. To monitor and prevent the reverse chemical reaction of fast wasteful ATP hydrolysis by the enzymes, different control mechanisms exist including mechanical or redox-based blockade of catalysis and ADP inhibition. In general product inhibition is expected to slow down the mean catalytic turnover. However, biochemical assays are ensemble measurements and cannot discriminate between a mechanism affecting all enzymes equally or individually. For example, all enzymes could work slower at a decreasing substrate/product ratio, or more and more individual enzymes are blocked completely. Here, we examined how increasing amounts of ADP affected ATP hydrolysis of singleEscherichia coliFoF1-ATP synthases in liposomes. We observed individual catalytic turnover of the enzymes one after another by monitoring the internal subunit rotation using single-molecule Förster resonance energy transfer (smFRET). Observation times of single FRET-labeled FoF1-ATP synthase in solution were increased up to seconds using a confocal Anti-Brownian electrokinetic trap (ABEL trap). By counting active versus inhibited enzymes we revealed that ADP inhibition did not decrease the catalytic turnover of all FoF1-ATP synthases equally. Instead, increasing ADP in the ADP/ATP mixture reduced the number of the remaining active enzymes which were operating at similar catalytic rates for varying substrate/product ratios.
Machine Learning exploratory technic detected that men might be up to eight times more affected by the control effect and three times more affected by the placebo effect than women
Authors: Nahon Roberto Lohn , Lazzoli José Kawazoe , Verli Marcio Vinícius de Abreu , Gonçalves Luis Carlos Oliveira , Magalhães Neto Aníbal Monteiro de 
Published: April 2023

AbstractBackgroundThe Placebo effect has been historically described since the beginning of Medicine. When the most skeptical researchers say they do not believe in Noetic Science but use a placebo in their research, they generate an apparent contradiction. The present study aimed to understand the noetic influence on high-level athletes, using a sportomics strategy, statistical exploratory techniques of machine learning and holistic analysis.MethodsThe study included 14 volunteer volleyball athletes. Each volunteer was submitted to four running tests of 3,000 meters, on a 400-meter track, with one test each subsequent day. On the first day, the athletes performed the first test of 3,000, aiming to adapt to the trial (ADAPT 1), and on the second day, the same adaptation (ADAPT 2). On the third and fourth days, the placebos were introduced, and on the third day, the athletes received the information that that would be just a placebo, which was called (CONTROL). On the fourth day, when the identical placebo was given, the athletes received the information that it would be a new cutting-edge nutritional supplement being studied (PLACEBO).ResultsMen might be up to eight times more affected by the control effect and three times more by the placebo effect than women. Regarding performance, there was an antagonistic behavior concerning gender for the control effect and an agonistic effect for the placebo effect, but with less impact on women. Men also showed a faster adaptation to the test.ConclusionNoetic science, always considered but never assumed by researchers, is confirmed when the present study reveals that men are more affected by the control effect and the placebo effect than women, with antagonistic behavior concerning gender for the control effect and an agonist effect for the placebo effect, but with less impact on women about performance.
A minimally-invasive method for ancient DNA sampling of Prehistoric bone and antler tools and hunting weapons
Authors: Tejero José-Miguel , Cheronet Olivia , Gelabert Pere , Zagorc Brina , Alvarez Esteban , Averbouh Aline , Bar-Oz Guy , Belfer-Cohen Anna , Bosch Marjolein D. , Brück Florian , Cueto Marián , Dockner Martin , Fullola Josep Maria , Gárate Diego , Giannakoulis Michael , González Cynthia , Jakeli Nino , Mangado Xavier , Meshveliani Tengiz , Neruda Petr , Nigst Philip , Šimková Petra G. , Tapia Jesús , de la Torre Marta Sánchez , Schwab Catherine , Weber Gerhard , Pinhasi Ron 
Published: April 2023

AbstractInternal and external bony tissues from diverse mammalian taxa are one of the primary animal raw materials exploited for technical and symbolic purposes by Eurasian Upper Palaeolithic hunter-gatherers. Identifying the source species used for osseous raw material is critical to gain insights into these populations’ behaviour, technology, and subsistence. The study of osseous tools has advanced in the last few years by combining archaeological and biomolecular methods. Ancient genomics opens many new analytical opportunities. Ancient DNA (aDNA) can provide a wealth of information about the animal sources of these objects. Unfortunately, aDNA analyses often involve destructive sampling. Here, we develop and apply a minimally-invasive aDNA sampling method for an assemblage of 42 prehistoric hunting weapons and tools from various Eurasian archaeological sites. We evaluated the impact of our approach on the specimens visually, microscopically and through Micro-CT scans. The surface impacts are marginal, ranging from 0.3-0.4 mm. Using a custom-made DNA capture kit for 54 mammalian species, we obtained sufficient aDNA to identify the taxa of 33% of the objects. For one of the tools, we recovered enough endogenous aDNA to infer the genetic affinities of the individual. Our results also demonstrate that ancient antler, one of the primary raw materials used during a large part of prehistory, is a reliable source of aDNA. Our minimally-invasive aDNA sampling method is therefore effective while preserving osseous objects for potential further analyses: morphometric, technical, genetic, radiometric and more.
Transcriptomic analyses reveal regional signatures in lung allograft recipients
Authors: Agudelo-Romero Patricia , Ling Kak-Ming , Lavender Melanie A. , Wrobel Jeremy P. , Musk Michael , Stick Stephen M , Kicic Anthony 
Published: April 2023

AbstractBackgroundLong term outcomes of allograft recipients are compromised by the development of chronic lung allograft dysfunction (CLAD) promoting bronchiolitis obliterans syndrome (BOS). We established baseline transcriptomic profiles of both the large and small airway epithelial cells (referred as LAEC and SAEC, respectively) to identify regional differences irrespective of initiating disease.MethodsWe obtained matched primary LAEC and SAEC from lung allograft recipients (n=4, 42.5 ± 4.2 years) and established primary cultures. Bulk RNA sequencing was performed to determine differentially expressed genes.ResultsWe observed differences in the transcriptional program between LAEC and SAEC Transcription factors (TF) were ranked within the top ten differentially regulated genes. The most abundant TF families included C2H2-ZF, homeobox and bHLH. Upstream regulator analyses identified homeobox genes being significantly in LAEC. Protein-protein interaction network analysis emphasised the role of TFs (ISL1, MSX1, HOXA1, GATA6, ZNF423) in airway modulation. Additionally, functional enrichment analysis revealed the activation of chemotaxis, metalloendipeptidase/metallopeptidase activity and pro-inflammatory signatures (IL17 signalling and RAGE), in LAEC, while SAEC were characterised by elevated expression of surfactant metabolism related genes. Moreover, alveolar and club cells-related genes were expressed in SAEC, suggesting a lower airway-specific signature.ConclusionOur analysis shows robust transcriptional differences between LAEC and SAEC. We suggest a potential role for homeobox TF family as well as the activation of the immune system in the biology of LAEC. Conversely, we observed an alveoli-like transcriptional signature in SAEC, including gas-exchange signals and surfactant metabolism; pathways involved in lung homeostasis.
Astrocytic Slc4a4 regulates blood-brain barrier integrity in healthy and stroke brains via a NO-CCL2-CCR2 pathway
Authors: Ye Qi , Jo Juyeon , Wang Chih-Yen , Oh Heavin , Choy Tiffany J. , Kim Kyoungin , D’Alessandro Angelo , Reshetnyak Yana K. , Jung Sung Yun , Chen Zheng , Marrelli Sean P. , Lee Hyun Kyoung 
Published: April 2023

AbstractAstrocytes play vital roles in blood-brain barrier (BBB) maintenance, yet how they support BBB integrity under normal or pathological conditions remains poorly defined. Recent evidence suggests pH homeostasis is a new cellular mechanism important for BBB integrity. In the current study, we investigated the function of an astrocyte-specific pH regulator, Slc4a4, in BBB maintenance and repair. We show that astrocytic Slc4a4 is required for normal astrocyte morphological complexity and BBB function. Multi-omics analyses identified increased astrocytic secretion of CCL2 coupled with dysregulated arginine-NO metabolism after Slc4a4 deletion. Using a model of ischemic stroke, we found that loss of Slc4a4 exacerbates BBB disruption and reactive gliosis, which were both rescued by pharmacological or genetic inhibition of the NO-CCL2 pathwayin vivo.Together, our study identifies the astrocytic Slc4a4-NO-CCL2 axis as a pivotal mechanism controlling BBB integrity and repair, while providing insights for a novel therapeutic approach against BBB-related CNS disorders.
Short-term auditory priming in freely-moving mice
Authors: Sivroni Shir , Sloin Hadas , Stark Eran 
Published: April 2023

AbstractPriming, a change in the mental processing of a stimulus as a result of prior encounter with a related stimulus, has been observed repeatedly and studied extensively. Yet currently there is no behavioral model of short-term priming in lab animals, limiting the study of the neurobiological basis of priming. Here, we describe an auditory discrimination paradigm for studying response priming in freely-moving mice. We find a priming effect in success rate in all mice tested on the task. In contrast to humans, we do not find a priming effect in response times. Compared to non-primed discrimination trials, the addition of incongruent prime stimuli reduces success rate more than congruent prime stimuli, suggesting a cognitive mechanism based on differential interference. The results establish the short-term priming phenomenon in rodents, and the paradigm opens the door to studying the cellular-network basis of priming.