bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of factors associated with reproductive health seeking behaviours among adolescent mothers in Dodoma region
Authors: Mbwambo Eliwedi , Gibore Nyasiro 
Published: May 2024

ABSTRACTBackgroundAdolescent pregnancy poses a significant public health concern due to its association with high levels of maternal morbidity and mortality, particularly in sub-Saharan countries. For early detection and management of obstetric danger signs, appropriate health seeking behaviour on reproductive health among adolescent mother is highly recommended so as to decrease maternal mortality and morbidity related to pregnancy. This study aims to assess the factors influencing reproductive health-seeking behaviours among adolescent pregnant mothers in Dodoma region.MethodsA community cross-sectional analytical study will be conducted, involving multistage sampling to recruit 604 adolescent pregnant mothers. Face-to-face interviews using structured questionnaires will be utilized to assess predisposing, enabling, and need factors, as well as knowledge and attitudes regarding obstetric danger signs. Data analysis will be performed using SPSS software version 25. Descriptive statistics will be used to analyse background information, while inferential statistics, including chi-square and logistic regression, will determine associations between variables.ResultsThis study will display the trend in utilization of reproductive health as well as predisposing, need and enabling factor associated with health seeking behaviour. A statistically significant variable in the final model will be identified with a 95% confidence interval and a p-value of < 0.05.ConclusionsThis study will provide a clear picture of the level of knowledge, attitude, and health-seeking behaviour which is crucial for preventing delay number one of seeking health care immediately after experiencing complications also gives a picture of the role of healthcare workers in promoting health among vulnerable populations.
Review of publicly available state reimbursement policies for removal and reinsertion of Long-Acting Reversible Contraception
Authors: Okoroh Ekwutosi M. , Kroelinger Charlan D. , Sappenfield Olivia R. , Howland Julia F. , Romero Lisa M. , Uesugi Keriann , Cox Shanna 
Published: May 2024

AbstractWe examined reimbursement policies for the removal and reinsertion of long-acting reversible contraception (LARC). We conducted a standardized, web-based review of publicly available state policies for language on reimbursement of LARC removal and reinsertion. We also summarized policy language on barriers to reimbursement for LARC removal and reinsertion. Twenty-six (52%) of the 50 states had publicly available policies that addressed reimbursement for LARC removal. Of these, 14 (28%) included language on reimbursement for LARC reinsertion. Eleven states included language on barriers for reimbursement for removal and/or reinsertion: five state policies included language with other requirements for removal only, three policies included language with additional requirements for reinsertion only, and three included language with additional requirements for both. Three state policies specified no barriers be placed on reimbursement for removal and one specified no barriers be placed on reimbursement for reinsertion. Half of the states in the U.S. do not have publicly available policies on reimbursement for the removal and reinsertion of LARC devices. Inclusion of unrestricted access to these services is important for reproductive autonomy.
Functional role of myosin-binding protein H in thick filaments of developing vertebrate fast-twitch skeletal muscle
Authors: Mead Andrew F. , Wood Neil B. , Nelson Shane R. , Palmer Bradley M. , Yang Lin , Previs Samantha Beck , Ploysangngam Angela , Kennedy Guy G. , McAdow Jennifer F. , Tremble Sarah M. , Cipolla Marilyn J. , Ebert Alicia M. , Johnson Aaron N. , Gurnett Christina A. , Previs Michael J. , Warshaw David M. 
Published: May 2024

AbstractMyosin-binding protein H (MyBP-H) is a component of the vertebrate skeletal muscle sarcomere with sequence and domain homology to myosin-binding protein C (MyBP-C). Whereas skeletal muscle isoforms of MyBP-C (fMyBP-C, sMyBP-C) modulate muscle contractility via interactions with actin thin filaments and myosin motors within the muscle sarcomere “C-zone,” MyBP-H has no known function. This is in part due to MyBP-H having limited expression in adult fast-twitch muscle and no known involvement in muscle disease. Quantitative proteomics reported here reveal MyBP-H is highly expressed in prenatal rat fast-twitch muscles and larval zebrafish, suggesting a conserved role in muscle development, and promoting studies to define its function. We take advantage of the genetic control of the zebrafish model and a combination of structural, functional, and biophysical techniques to interrogate the role of MyBP-H. Transgenic, FLAG-tagged MyBP-H or fMyBP-C both localize to the C-zones in larval myofibers, whereas genetic depletion of endogenous MyBP-H or fMyBP-C leads to increased accumulation of the other, suggesting competition for C-zone binding sites. Does MyBP-H modulate contractility from the C-zone? Globular domains critical to MyBP-C’s modulatory functions are absent from MyBP-H, suggesting MyBP-H may be functionally silent. However, our results suggest an active role. Small angle x-ray diffraction of intact larval tails revealed MyBP-H contributes to the compression of the myofilament lattice accompanying stretch or contraction, whilein vitromotility experiments indicate MyBP-H shares MyBP-C’s capacity as a molecular “brake”. These results provide new insights and raise questions about the role of the C-zone during muscle development.
A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons
Authors: Szabó Dominik , Franke Vedran , Bianco Simona , Batiuk Mykhailo Y. , Paul Eleanor J. , Kukalev Alexander , Pfisterer Ulrich G. , Irastorza-Azcarate Ibai , Chiariello Andrea M. , Demharter Samuel , Zea-Redondo Luna , Lopez-Atalaya Jose P. , Nicodemi Mario , Akalin Altuna , Khodosevich Konstantin , Ungless Mark A. , Winick-Ng Warren , Pombo Ana 
Published: May 2024

AbstractMidbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage1–3. As the synaptic and transcriptional changes that follow an acute cocaine exposure are mostly resolved within a few days4,5, the molecular changes that encode the long-term cellular memory of the exposure within DNs remain unknown. To investigate whether a single cocaine exposure induces long-term changes in the 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in the mouse midbrain. We found extensive rewiring of 3D genome architecture at 24 hours past exposure which remains or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. A single cocaine exposure triggers extensive long-lasting changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding ofRbfox1which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a specific DN sub-type characterized by low expression of the dopamine auto-receptorDrd2, a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.
CD13 Activation Assembles Signaling Complexes that Promote the Formation of Tunneling Nanotubes in Endothelial Cells
Authors: Meredith Emily , Aguilera Brian , McGurk Fraser , Zong Pengyu , Yue Lixia , Ghosh Mallika , Shapiro Linda H 
Published: May 2024

AbstractTransmembrane CD13 assembles protein complexes at the plasma membrane to enable diverse cellular processes such as cell-cell adhesion, focal adhesion turnover, endocytosis and recycling of cell surface proteins. In this study, we demonstrate a novel CD13-dependent assembly platform that regulates phosphoinositide (PI) signal transduction during the formation of Tunneling Nanotubes (TNTs). TNTs are actin-based, membrane-delimited bridges that facilitate intercellular communication by connecting distant cells to physically transfer subcellular cargoes. TNTs form between various cell types under stress conditions, but few molecular TNT-inducers exist. Human Kaposi’s sarcoma-derived endothelial cells (KSECs) readily form stress-induced TNTs capable of transferring Ca2+and membrane molecules between cells, with clear accumulation of CD13 and actin at the base of the protrusions. Alternatively, CD13-null KSECs form fewer TNTs and Ca2+transfer is markedly reduced. Mechanistically, CD13-mediated TNT formation requires activation of CD13, Src, FAK and Cdc42 to allow tethering of the IQGAP1 and ARF6 complex at the membrane to activate the phosphatidylinositol-4-phosphate-5-kinase PI5K. This increases local phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) levels to promote the actin-polymerization and membrane protrusion necessary for TNT formation. Therefore, CD13 is a novel molecular PIP regulator and TNT trigger that will facilitate the dissection of downstream pathways and mechanisms regulating TNT formation.
Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust
Authors: Lunde China , Seong Kyungyong , Kumar Rakesh , Deatker Andrew , Chhabra Bhavit , Wang Meinan , Kaur Shivreet , Song Sarah , Palayur Ann , Davies Cole , Cumberlich William , Gill Upinder , Rawat Nidhi , Chen Xianming , Aoun Meriem , Mundt Christopher , Krasileva Ksenia V 
Published: May 2024

AbstractTetraploid durum wheatTriticum turgidumsubsp.durumcv ‘Kronos’ has extensive genetic variation resources, including a sequenced and cataloged ethyl methanesulfonate (EMS) mutagenized population. To utilize this allelic diversity, we screened over 2,000 mutant lines and identified over 30 enhanced disease resistance (EDR) mutants in a forward genetic field screen against stripe rust. Sixteen of the EDR lines have persistent resistance to stripe rust after four years, and several mutants showed differential disease responses against other fungal pathogens, indicating that the lines possess diverse alleles that affect multiple routes of pathogen suppression. Five of these 16 lines showed spontaneous lesion formation in the absence of pathogens. Only one showed a reduction in kernel weight under pathogen pressure, a testimony to the high mutational density that wheat can tolerate. Phenotypic selection for resistance at the adult stage identified useful EMS alleles for stripe rust resistance. The mutations in the 16 EDR lines were newly mapped to a recently released long-read Kronos genome to enhance their utility in molecular breeding for fungal resistance and for fundamental studies of plant-pathogen interactions.
Disulfide constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM
Authors: Kung Jennifer E. , Johnson Matthew C. , Jao Christine C. , Arthur Christopher P. , Tegunov Dimitry , Rohou Alexis , Sudhamsu Jawahar 
Published: May 2024

ABSTRACTHigh-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure determination of large proteins and their complexes1, but a vast majority of proteins that underlie human diseases are small (< 50 kDa) and usually beyond its reach due to low signal-to-noise images and difficulties in particle alignment2. Current strategies to overcome this problem increase the overall size of small protein targets using scaffold proteins that bind to the target, but are limited by inherent flexibility and not being bound to their targets in a rigid manner, resulting in the target being poorly resolved compared to the scaffolds3–11. Here we present an iteratively engineered molecular design for transforming Fabs (antibody fragments), into conformationally rigid scaffolds (Rigid-Fabs) that, when bound to small proteins (∼20 kDa), can enable high-resolution structure determination using cryo-EM. This design introduces multiple disulfide bonds at strategic locations, generates a well-folded Fab constrained into a rigid conformation and can be applied to Fabs from various species, isotypes and chimeric Fabs. We present examples of the Rigid Fab design enabling high-resolution (2.3–2.5 Å) structures of small proteins, Ang2 (26 kDa) and KRAS (21 kDa) by cryo-EM. The strategies for designing disulfide constrained Rigid Fabs in our work thus establish a general approach to overcome the target size limitation of single particle cryo-EM.
MAST-Decon: Smooth Cell-type Deconvolution Method for Spatial Transcriptomics Data
Authors: Luo Tianyou , Chen Jiawen , Wu Wenrong , Zhao Jinying , Yao Huaxiu , Zhu Hongtu , Li Yun 
Published: May 2024

AbstractSpatial transcriptomics (ST) technologies have gained increasing popularity due to their ability to provide positional context of gene expressions in a tissue. One major limitation of current commercially available ST methods such as the 10X Genomics Visium platform is the lack of single cell resolution. Cell type deconvolution for ST data is critical in order to fully reveal underlying biological mechanisms. Existing ST data deconvolution methods share two common limitations: first, few of them utilize spatial neighborhood information. Existing methods such as RCTD and SPOTlight intrinsically treat each spatial spot as independent of neighboring spots, although we anticipate nearby spots to share similar cell type compositions based on clinical evidence of tissue structures. Such limitation could be amplified when sequencing depths at single spots are relatively low so that borrowing information from neighboring spots is necessary in order to obtain reliable deconvolution results. Second, although Visium data provide us with a histological image which could add additional information regarding spot heterogeneity, most existing methods do not utilize this H&E image. To solve these two limitations, we developed Multiscale Adaptive ST Deconvolution (MAST-Decon), a smooth deconvolution method for ST data. MAST-Decon uses a weighted likelihood approach and incorporates both gene expression data, spatial neighborhood information and H&E image features by constructing different kernel functions to obtain a smooth deconvolution result. We showcased the strength of MAST-Decon through simulations based on real data, including a single-cell dataset of mouse brain primary visual cortex, and real-world Visium datasets to demonstrate its robust and superior performance compared with other state-of-the-art methods.
Arabidopsis Apoplast TET8 Positively Correlates to Leaf Senescence andtet3tet8Double Mutants are Delayed in Leaf Senescence
Authors: Zimmerman Jayde A. , Verboonen Benjamin , Harrison Hanson Andrew P. , Brusslan Judy A. 
Published: May 2024

AbstractExtracellular vesicles (EVs) are membrane-bound exosomes secreted into the apoplast. Two distinct populations of EVs have been described in Arabidopsis: PEN1-associated and TET8-associated. We previously noted early leaf senescence in thepen1single andpen1pen3double mutant. Both PEN1 and PEN3 are abundant in EV proteomes suggesting EVs might regulate leaf senescence in soil-grown plants. We observed that TET8 is more abundant in the apoplast of early senescingpen1andpen1pen3mutant rosettes and in older WT rosettes. The increase in apoplast TET8 in thepen1mutant did not correspond to increasedTET8mRNA levels. In addition, apoplast TET8 was more abundant in the early leaf senescencemyb59mutant, meaning the increase in apoplast TET8 protein during leaf senescence is not dependent onpen1orpen3. Genetic analysis showed a significant delay in leaf senescence intet3tet8double mutants after six weeks of growth suggesting that these two tetraspanin paralogs operate additively and are positive regulators of leaf senescence. This is opposite of the effect ofpen1andpen1pen3mutants that show early senescence and suggest PEN1 to be a negative regulator of leaf senescence. Our work provides initial support that PEN1-associated EVs and TET8-associated EVs may have opposite effects on soil-grown plants undergoing age-related leaf senescence.
Robotic Imaging and Machine Learning Analysis of Seed Germination: Dissecting the Influence of ABA and DOG1 on Germination Uniformity
Authors: Eckhardt James , Xing Zenan , Subramanian Vish , Vaidya Aditya , Cutler Sean 
Published: May 2024

AbstractSeed germination research has evolved over the years, increasingly incorporating technology. Recent advances in phenotyping platforms have increased the accessibility of high throughput phenotyping technologies to more labs, leading to valuable insights into germination biology. These platforms benefit researchers by limiting manual labor and increasing the temporal resolution of imaging. Each of the platforms developed presents unique benefits and challenges, from scalability to price to computing resources. Performing experiments involving thousands of seeds remains a daunting task due to the limitations of current phenotyping platforms and image analysis pipelines. To overcome these challenges, we introduce SPENCER (Seed Phenotype Evaluation and Germination Curve Estimation Robot), a high-throughput phenotyping platform. SPENCER accommodates 32 rectangular petri plates, capable of assessing up to 8000 Arabidopsis seeds per experiment. Our design allows for high quality images while maintaining optimal humidity, crucial for precise germination assessment over longer experiments. The image analysis workflow incorporates advanced image analysis using semantic segmentation models trained for Arabidopsis and lettuce, providing researchers with accessible, reproducible, and efficient tools. We applied SPENCER to investigate the relative roles of DELAY OF GERMINATION 1 (DOG1) and abscisic acid (ABA) in Arabidopsis dormancy. DOG1 mutants exhibited rapid germination, whereas ANT application had a greater impact on the slower-germinating Ler ecotype. Our findings suggest that DOG1 plays a significant role in dormancy, particularly in non-dormant accessions, while ABA’s influence is more pronounced under stress conditions. Additionally, we explored germination uniformity, another agriculurally relevant trait, observing parallels with germination timing. SPENCER offers a powerful and accessible tool for dissecting complex biological traits in conjunction with chemical and genetic manipulations. Its scalability and versatility make it suitable for large-scale genetic and chemical germination screens.
Biological S0reduction at neutral (pH 6.9) and acidic (pH 3.8) conditions: Performance and microbial community shifts in a H2/CO2-fed bioreactor
Authors: Hidalgo-Ulloa Adrian , van der Graaf Charlotte M. , Sánchez-Andrea Irene , Weijma Jan , Buisman Cees J.N. 
Published: May 2024

AbstractSulfidogenesis is a promising technology for the selective recovery of chalcophile bulk metals (e.g. Cu, Zn, and Co) from metal-contaminated waters such as acid mine drainage (AMD) and metallurgy waste streams. The use of elemental sulfur (S0) instead of sulfate (SO42-) as electron acceptor reduces electron donor requirements four-fold, lowering process costs, and expands the range of operating conditions to more acidic pH. We previously reported autotrophic S0reduction using an industrial mesophilic granular sludge as inoculum under thermoacidophilic conditions. Here, we examined the effect of pH on the S0reduction performance of the same inoculum, in a continuously fed gas-lift reactor run at 30 °C under neutral (pH 6.9) and acidic (pH 3.8) conditions. Steady-state volumetric sulfide production rates (VSPR) dropped 2.3-fold upon transition to acidic pH, from 1.79 ± 0.18 g·L-1·d-1S2-·to 0.71 ± 0.07 g·L-1·d-1S2-· Microbial community analysis via 16S rRNA gene amplicon sequencing showed that at pH 6.9, the S0-reducing generaSulfurospirillum, Sulfurovum, Desulfurella, andDesulfovibriowere present at the highest relative abundance, while at pH 3.9Desulfurelladominated the sequenced reads. The detection of acetic acid and the relative abundance ofAcetobacteriumat pH 6.9 pointed towards acetogenesis, explaining the dominance of the heterotrophic genusSulfurospirillumin this H2and CO2–fed bioreactor.
Genetics, energetics and allostery during a billion years of hydrophobic protein core evolution
Authors: Escobedo Albert , Voigt Gesa , Faure Andre J , Lehner Ben 
Published: May 2024

AbstractProtein folding is driven by the burial of hydrophobic amino acids in a tightly-packed core that excludes water. The genetics, biophysics and evolution of hydrophobic cores are not well understood, in part because of a lack of systematic experimental data on sequence combinations that do - and do not - constitute stable and functional cores. Here we randomize protein hydrophobic cores and evaluate their stability and function at scale. The data show that vast numbers of amino acid combinations can constitute stable protein cores but that these alternative cores frequently disrupt protein function because of allosteric effects. These strong allosteric effects are not due to complicated, highly epistatic fitness landscapes but rather, to the pervasive nature of allostery, with many individually small energy changes combining to disrupt function. Indeed both protein stability and ligand binding can be accurately predicted over very large evolutionary distances using additive energy models with a small contribution from pairwise energetic couplings. As a result, energy models trained on one protein can accurately predict core stability across hundreds of millions of years of protein evolution, with only rare energetic couplings that we experimentally identify limiting the transplantation of cores between highly diverged proteins. Our results reveal the simple energetic architecture of protein hydrophobic cores and suggest that allostery is a major constraint on sequence evolution.
A real-time biochemical assay for quantitative analyses of APOBEC-catalyzed DNA deamination
Authors: Belica Christopher A. , Carpenter Michael A. , Chen Yanjun , Brown William L. , Moeller Nicholas H. , Boylan Ian T. , Harris Reuben S. , Aihara Hideki 
Published: May 2024

AbstractOver the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a need for biochemical tools that can be used to identify and characterize potential inhibitors of this enzyme family. In response to this challenge, we have developed a Real-time APOBEC3-mediated DNA Deamination (RADD) assay. This assay offers a single-step set-up and real-time fluorescent read-out, and it is capable of providing insights into enzyme kinetics and also offering a high-sensitivity and easily scalable method for identifying APOBEC3 inhibitors. This assay serves as a crucial addition to the existing APOBEC3 biochemical and cellular toolkit and possesses the versatility to be readily adapted into a high-throughput format for inhibitor discovery.