bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical and biological sources of unreliability of Infinium probes on Illumina Methylation microarrays
Authors: Nazarenko Tatiana , Vavourakis Charlotte D. , Jones Allison , Evans Iona , Schreiberhuber Lena , Kastner Christine , Ishaq-Parveen Isma , Redl Elisa , Watson Antony W. , Brandt Kirsten , Carter Clive , Zaikin Alexey , Herzog Chiara , Widschwendter Martin 
Published: March 2023

ABSTRACTThe Illumina Methylation array platform has facilitated countless epigenetic studies on DNA methylation (DNAme) in health and disease, yet relatively few studies have so studied its reliability, i.e., the consistency of repeated measures. Here we focus on the reliability of both type I and type II Infinium probes. We propose a method for excluding unreliable probes based on dynamic thresholds for mean intensity (MI) and ‘unreliability’, estimated by probe-level simulation of the influence of technical noise on methylation β-values using the background intensities of negative control probes. We validate our method in several datasets, including Illumina MethylationEPIC BeadChip v1.0 data from paired whole blood samples taken six weeks apart. Our analysis revealed that specifically probes with low MI exhibit higher β-value variability between repeated samples. MI was associated with the number of C-bases in the respective probe sequence and correlated negatively with unreliability scores. The unreliability scores were substantiated through validation in a new EPIC v1.0 (blood and cervix) and a publicly available 450k (blood) dataset, as they effectively captured the variability observed in β-values between technical replicates. Finally, despite promising higher robustness, the newer version v2.0 of the MethylationEPIC BeadChip retained a substantial number of probes with poor unreliability scores. To enhance current pre-processing pipelines, we developed an R package to calculate MI and unreliability scores and provide guidance on establishing optimal dynamic score thresholds for a given data set.
Behavioral, molecular and neuronal mechanisms involved in recognition memory retrieval under degraded spatial cues in the rat hippocampus
Authors: Miranda Magdalena , Silva Azul , Morici Juan Facundo , Coletti Marcos Antonio , Belluscio Mariano , Bekinschtein Pedro 
Published: March 2023

AbstractIn a constantly changing environment, organisms face the challenge of adapting their behavior by retrieving previous experiences or acquiring new information. Previous research has postulated that this balance between memory generalization and differentiation manifests in a dichotomic manner. When environmental information exceeds a given threshold, activation of a stored representation could initiate retrieval, but below this threshold, a novel event could be encoded with a concomitant remapping of the internal representation in the hippocampus. Here, we examined the hippocampal molecular and neuronal mechanisms underlying retrieval in a cue-degraded environment by combining in vivo electrophysiological recordings and pharmacological manipulations. We developed a memory recognition task that allows a graded decrease in the contextual cues present during retrieval. We found that the manipulation of the number of visual cues was consistent with the activation or not of the contextual memory trace. Retrieval of a specific context memory was reflected by the level of CA3 remapping, demonstrating a clear relationship between remapping and contextual recognition. Also, manipulation of NMDAR activity in the DG-CA3 circuit bidirectionally modulated contextual memory retrieval. The blockade of NMDAR in CA3 impaired recognition in a cue-degraded, but not in a full-cue context, while their activation has the opposite effect. Conversely, blockade of NMDAR in the DG promoted retrieval under an even more cue-degraded environment, while activation had the opposite effect. Our results provide evidence for a flexible interaction between environmental cues and information stored in the hippocampus and give new insights into the biological mechanisms that balance memory encoding and retrieval.
State-dependent GABAergic regulation of striatal spiny projection neuron excitability
Authors: Day Michelle , Belal Marziyeh , Surmeier William C. , Melendez Alexandra , Wokosin David , Tkatch Tatiana , Clarke Vernon R. J. , Surmeier D. James 
Published: March 2023

AbstractSynaptic transmission mediated by GABAAreceptors (GABAARs) in adult, principal striatal spiny projection neurons (SPNs) can suppress ongoing spiking, but its effect on synaptic integration at sub-threshold membrane potentials is less well characterized, particularly those near the resting down-state. To fill this gap, a combination of molecular, optogenetic, optical and electrophysiological approaches were used to study SPNs in mouseex vivobrain slices, and computational tools were used to model somatodendritic synaptic integration. Activation of GABAARs, either by uncaging of GABA or by optogenetic stimulation of GABAergic synapses, evoked currents with a reversal potential near -60 mV in perforated patch recordings from both juvenile and adult SPNs. Molecular profiling of SPNs suggested that this relatively positive reversal potential was not attributable to NKCC1 expression, but rather to a dynamic equilibrium between KCC2 and Cl-/HCO3-cotransporters. Regardless, from down-state potentials, optogenetic activation of dendritic GABAergic synapses depolarized SPNs. This GABAAR-mediated depolarization summed with trailing ionotropic glutamate receptor (iGluR) stimulation, promoting dendritic spikes and increasing somatic depolarization. Simulations revealed that a diffuse dendritic GABAergic input to SPNs effectively enhanced the response to coincident glutamatergic input. Taken together, our results demonstrate that GABAARs can work in concert with iGluRs to excite adult SPNs when they are in the resting down-state, suggesting that their inhibitory role is limited to brief periods near spike threshold. This state-dependence calls for a reformulation of the role intrastriatal GABAergic circuits.
MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters
Authors: Chattaraj Aniruddha , Nalagandla Indivar , Loew Leslie M. , Blinov Michael L 
Published: March 2023

AbstractSummaryLow-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become extra-large clusters. Characterizing the physical properties of these clusters is important in recent biophysical research. Due to weak interactions such clusters are highly stochastic, demonstrating a wide range of sizes and compositions. We have developed a Python package to perform multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator), characterize and visualize the distribution of cluster sizes, molecular composition, and bonds across molecular clusters and individual molecules of different types.Availability and implementationThe software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide and examples are freely available athttps://molclustpy.github.io/Contactachattaraj007@gmail.com,blinov@uchc.eduSupplementary informationAvailable athttps://molclustpy.github.io/
Regulatable assembly of synthetic microtubule architectures using engineered MAP-IDR condensates
Authors: Chang Chih-Chia , Coyle Scott M. 
Published: March 2023

SummaryMicrotubules filaments are assembled into higher-order structures and machines critical for cellular processes using microtubule-associated proteins (MAPs). However, the design of synthetic MAPs that direct the formation of new structures in cells is challenging, as nanoscale biochemical activities must be organized across micron length-scales. Here we develop synthetic MAP-IDR condensates (synMAPs) that provide tunable and regulatable assembly of higher-order microtubule structuresin vitroand in mammalian cells. synMAPs harness a small microtubule-binding domain from oligodendrocytes (TPPP) whose activity can be synthetically rewired by interaction with condensate-forming IDR sequences. This combination allows synMAPs to self-organize multivalent structures that bind and bridge microtubules into synthetic architectures. Regulating the connection between the microtubule-binding and condensate-forming components allows synMAPs to act as nodes in more complex cytoskeletal circuits in which the formation and dynamics of the microtubule structure can be controlled by small molecules or cell-signaling inputs. By systematically testing a panel of synMAP circuit designs, we define a two-level control scheme for dynamic assembly of microtubule architectures at the nanoscale (via microtubule-binding) and microscale (via condensate formation). synMAPs provide a compact and rationally engineerable starting point for the design of more complex microtubule architectures and cellular machines.
Therapeutic immune cell engineering with an mRNA : AAV-Sleeping Beautycomposite system
Authors: Ye Lupeng , Lam Stanley Z. , Yang Luojia , Suzuki Kazushi , Zou Yongji , Lin Qianqian , Zhang Yueqi , Clark Paul , Peng Lei , Chen Sidi 
Published: March 2023

AbstractAdoptive cell therapy has shown clinical success in patients with hematological malignancies. Immune cell engineering is critical for production, research, and development of cell therapy; however, current approaches for generation of therapeutic immune cells face various limitations. Here, we establish a composite gene delivery system for the highly efficient engineering of therapeutic immune cells. This system, termed MAJESTIC (mRNAAAV-Sleeping-BeautyJointEngineering ofStableTherapeuticImmuneCells), combines the merits of mRNA, AAV vector, and transposon into one composite system. In MAJESTIC, the transient mRNA component encodes a transposase that mediates permanent genomic integration of theSleeping Beauty(SB) transposon, which carries the gene-of-interest and is embedded within the AAV vector. This system can transduce diverse immune cell types with low cellular toxicity and achieve highly efficient and stable therapeutic cargo delivery. Compared with conventional gene delivery systems, such as lentiviral vector, DNA transposon plasmid, or minicircle electroporation, MAJESTIC shows higher cell viability, chimeric antigen receptor (CAR) transgene expression, therapeutic cell yield, as well as prolonged transgene expression. CAR-T cells generated by MAJESTIC are functional and have strong anti-tumor activityin vivo. This system also demonstrates versatility for engineering different cell therapy constructs such as canonical CAR, bi-specific CAR, kill switch CAR, and synthetic TCR; and for CAR delivery into various immune cells, including T cells, natural killer cells, myeloid cells, and induced pluripotent stem cells.
Perturbomics of tumor-infiltrating NK cells
Authors: Peng Lei , Renauer Paul A. , Ye Lupeng , Yang Luojia , Park Jonathan J. , Chow Ryan D. , Zhang Yueqi , Lin Qianqian , Bai Meizhu , Sanchez Angelica , Zhang Yongzhan , Lam Stanley Z. , Chen Sidi 
Published: March 2023

AbstractNatural killer (NK) cells are an innate immune cell type that serves at the first level of defense against pathogens and cancer. NK cells have clinical potential, however, multiple current limitations exist that naturally hinder the successful implementation of NK cell therapy against cancer, including their effector function, persistence, and tumor infiltration. To unbiasedly reveal the functional genetic landscape underlying critical NK cell characteristics against cancer, we perform perturbomics mapping of tumor infiltrating NK cells by jointin vivoAAV-CRISPR screens and single cell sequencing. We establish a strategy with AAV-SleepingBeauty(SB)- CRISPR screening leveraging a custom high-density sgRNA library targeting cell surface genes, and perform four independentin vivotumor infiltration screens in mouse models of melanoma, breast cancer, pancreatic cancer, and glioblastoma. In parallel, we characterize single-cell transcriptomic landscapes of tumor-infiltrating NK cells, which identifies previously unexplored sub-populations of NK cells with distinct expression profiles, a shift from immature to mature NK (mNK) cells in the tumor microenvironment (TME), and decreased expression of mature marker genes in mNK cells.CALHM2,a calcium homeostasis modulator that emerges from both screen and single cell analyses, shows bothin vitroandin vivoefficacy enhancement when perturbed in chimeric antigen receptor (CAR)-NK cells. Differential gene expression analysis reveals thatCALHM2knockout reshapes cytokine production, cell adhesion, and signaling pathways in CAR- NKs. These data directly and systematically map out endogenous factors that naturally limit NK cell function in the TME to offer a broad range of cellular genetic checkpoints as candidates for future engineering to enhance NK cell-based immunotherapies.
CTLA-4 tail fusion enhances CAR-T anti-tumor immunity
Authors: Zhou Xiaoyu , Cao Hanbing , Fang Shao-Yu , Chow Ryan D. , Tang Kaiyuan , Majety Medha , Bai Meizhu , Dong Matthew B. , Renauer Paul A. , Shang Xingbo , Suzuki Kazushi , Levchenko Andre , Chen Sidi 
Published: March 2023

AbstractChimeric antigen receptor (CAR) T cells are powerful therapeutics; however, their efficacy is often hindered by critical hurdles. Here, utilizing the endocytic feature of the cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) cytoplasmic tail (CT), we reprogram CAR function and substantially enhance CAR-T efficacyin vivo. CAR-T cells with monomeric, duplex, or triplex CTLA-4 CTs (CCTs) fused to the C-terminus of CAR exhibit a progressive increase in cytotoxicity under repeated stimulation, accompanied by reduced activation and production of pro-inflammatory cytokines. Further characterization reveals that CARs with increasing CCT fusion show a progressively lower surface expression, regulated by their constant endocytosis, recycling and degradation under steady state. The molecular dynamics of reengineered CAR with CCT fusion results in reduced CAR-mediated trogocytosis, loss of tumor antigen, and improved CAR-T survival. CARs with either monomeric (CAR-1CCT) or duplex CCTs (CAR-2CCT) have superior anti-tumor efficacy in a relapsed leukemia model. Single-cell RNA sequencing and flow cytometry analysis reveal that CAR-2CCT cells retain a stronger central memory phenotype and exhibit increased persistence. These findings illuminate a unique strategy for engineering therapeutic T cells and improving CAR-T function through synthetic CCT fusion, which is orthogonal to other cell engineering techniques.
In vivotracking of adenoviral-transduced iron oxide-labeled bone marrow-derived dendritic cells using magnetic particle imaging
Authors: Fink Corby , Gevaert Julia J. , Barrett John W. , Dikeakos Jimmy D. , Foster Paula J. , Dekaban Gregory A. 
Published: March 2023

ABSTRACTBackgroundDespite widespread study of dendritic cell (DC)-based cancer immunotherapies, thein vivopost-injection fate of DC remains largely unknown. Due in part to a lack of quantifiable imaging modalities, this is troubling as the amount of DC migration to secondary lymphoid organs correlates with therapeutic efficacy. Preliminary studies have identified magnetic particle imaging (MPI) as a suitable modality to quantifyin vivomigration of superparamagnetic iron oxide-(SPIO)-labeled DC. Herein, we describe a lymph node- (LN)-focused MPI scan to quantify DCin vivomigration accurately and consistently.MethodsBoth adenovirus (Ad)-transduced SPIO+(Ad SPIO+) and SPIO+C57BL/6 bone marrow-derived DC were generated and assessed for viability and phenotype using flow cytometry. Ad SPIO+and SPIO+DC were fluorescently-labeled and injected into C57BL/6 mouse hind footpads (n=6). Two days later,in vivoDC migration was quantified using whole animal, popliteal LN- (pLN)-focused, andex vivopLN MPI scans.ResultsNo significant differences in viability, phenotype andin vivopLN migration were noted for Ad SPIO+and SPIO+DC. Day 2 pLN-focused MPI successfully quantified DC migration in all instances while whole animal MPI only quantified pLN migration in 75% of cases.Ex vivoMPI and fluorescence microscopy confirmed MPI signal was pLN-localized and due to originally-injected Ad SPIO+and SPIO+DC.ConclusionsWe overcame a reported limitation of MPI by using a pLN-focused MPI scan to quantify pLN-migrated Ad SPIO+and SPIO+DC in 100% of cases. With this improved method, we detected as few as 1000 DC (4.4 ng Fe)in vivo. MPI is a suitable pre-clinical imaging modality to assess DC-based cancer immunotherapeutic efficacy.
School performance and mortality in young adulthood: a register-based population study
Authors: Reme Bjørn-Atle , Torvik Fartein Ask 
Published: March 2023

AbstractBackgroundThe social gradient in mortality among young adults is well-documented, but poorly understood. This study contrasts the role of parental income and education versus own school performance as predictors of early death.MethodsWe estimated the prospective association between grade point average from lower secondary education and mortality between age 16 and 30 for the Norwegian birth cohorts 1985-2002 (N = 986,573). This association was compared to the associations between measures of family socioeconomic status and young adult mortality in the offspring. We also estimated hazard ratios in models including both school performance, parental income, and education. Sibling comparison analyses were also estimated to assess the importance of within-family variation. Last, we used the cause of death register to estimate the hazard ratio of different causes of death among individuals with poor school performance.FindingsDuring the observational period, we observed 1300 deaths in the lowest quartile of school performance (0·06%) and 413 deaths in the highest quartile of school performance (0·02%). The risk of early death among boys in the lowest quartile of school performance compared to the highest quartile was larger for boys [HR = 3·68, 95% CI 3·54-3·81] than for girls [HR = 2·82, 95% CI 2·62-3·01]. The corresponding hazard ratios across parental income quartiles were 1·79 [95% CI 1·67-1·1·91] for boys, and 1·63 [95% CI 1·43-1·82] for girls. Across parental education level, the hazard ratio was 2·03 [95% CI 1·85-2·21] for boys, and 1·64 [95% CI 1·35-1·93] for girls. When jointly including school performance, parental income and education in the same model, parental income and education were insignificant, while the association school performance remained strong: HR = 3·57 [95% CI 3·44-3·71] for boys, and 2·98 [95% CI 2·78-3·18] for girls. With regards to causes of death, the highest hazard ratio among those in the lowest quartile of school performance was for drug-related poisoning, with 6·47 [95% CI 2·78-3·18] for boys and 7·3 [95% CI 4·93-10·80] for girls. The results were consistent in sibling comparison analyses.InterpretationSchool performance is a substantially stronger predictor of early death than common measures of socioeconomic background. School performance absorbs the social gradient in early death.FundingThis work was supported by the Research Council of Norway (grant number 273659). This work was partly supported by the Research Council of Norway through its Centers of Excellence funding scheme (grant number 262700).
Post-COVID-19 syndrome and related dysautonomia affect patients’ life and work productivity
Authors: Galanis Petros , Katsiroumpa Aglaia , Vraka Irene , Kosiara Katerina , Siskou Olga , Konstantakopoulou Olympia , Katsoulas Theodoros , Gallos Parisis , Kaitelidou Daphne 
Published: March 2023

AbstractBackgroundA significant percentage of COVID-19 patients experience post-COVID-19 symptoms and signs. Post-COVID-19 syndrome affects physical and mental health of patients in several ways.AimTo investigate the impact of post-COVID-19 syndrome and related dysautonomia on patients’ life and work productivity.MethodsWe conducted a cross-sectional study in Greece using an online questionnaire. Study population included 108 workers over 18 years old that have been diagnosed with post-COVID-19 syndrome. Patients were recruited from the Long COVID Greece patients’ society. We measured demographic and clinical characteristics of patients, resilience, and social support.ResultsAmong patients, 68.5% stated that post-COVID-19 syndrome affected their daily life to a great extent, 25% to a moderate level, and 6.5% to a small extent. Moreover, 56.5% stated that post-COVID-19 syndrome affected their work productivity to a great extent, 27.8% to a moderate level, and 15.7% to a small extent. Multivariable analysis identified that females and patients with post-COVID-19 dysautonomia had more problems in their daily life. Moreover, increased duration of COVID-19 symptoms was associated with increased daily problems. Increased resilience was related with fewer problems in daily life. Also, we found that patients with post-COVID-19 dysautonomia had less work productivity. Moreover, increased duration of COVID-19 symptoms was associated with more problems in work. Resilience was related with increased work productivity.ConclusionsPost-COVID-19 syndrome and related dysautonomia affect significantly patients’ daily and work life. Also, resilience is an important preventive factor improving patients’ life. Policy makers should develop and implement educational programs to improve patients’ life. Healthcare professionals should be aware of the post-COVID-19 syndrome and its consequences in order to understand post-COVID-19 patients and their problems.
Repurposing The Dark Genome. I - Antisense Proteins
Authors: Garg Mohit , Dhar Pawan K. 
Published: March 2023

AbstractFrom the functional standpoint, the genome may be considered a collection of three types of sequences: protein encoding, RNA encoding, and non-expressing. Based on the standard sequencing and annotation work, it is now well accepted that a small proportion of the genome has been allocated the job of encoding proteins, while most of the genome encodes RNA, and some DNA sequences are not used for expression. The exact ratio among these three types of sequences varies based on the organism. We asked: Is it possible to artificially encode protein and peptide sequences from naturally non-expressing (dark genome) sequences? This led to proof of the concept of making functional proteins from the intergenic sequences of E.coli (Dhar et al 2009). This study is an extension of the original concept and has been organized around antisense DNA sequences. The full-length antisense gene equivalents in forward and reverse orientations were computationally studied for their structural, cellular location, and functional properties, leading to many interesting observations. The current study points to a huge untapped genomic space that needs to be examined from cell physiology, evolutionary, and application perspectives.