bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal phenotype of PNKP-related primary microcephaly associated with variants in the FHA and Phosphatase domain
Authors: Neuser Sonja , Krey Ilona , Schwan Annemarie , Jamra Rami Abou , Bartolomaeus Tobias , Döring Jan , Syrbe Steffen , Plassmann Margit , Rohde Stefan , Roth Christian , Rehder Helga , Radtke Maximilian , Le Duc Diana , Schubert Susanna , Bermúdez-Guzmán Luis , Leal Alejandro , Schoner Katharina , Popp Bernt 
Published: September 2021

ABSTRACTBiallelic PNKP variants cause heterogeneous disorders ranging from neurodevelopmental disorder with microcephaly/seizures to adult-onset Charcot-Marie-Tooth disease. To date, only postnatal descriptions exist.We present the first prenatal diagnosis of PNKP-related primary microcephaly. Detailed pathological examination of a male fetus revealed micrencephaly with extracerebral malformations and thus presumed syndromic microcephaly. A recessive disorder was suspected because of previous pregnancy termination for similar abnormalities in a sibling fetus. Prenatal trio exome sequencing identified compound-heterozygosity for the PNKP variants c.498G>A, p.[(=),0?] and c.302C>T, p.(Pro101Leu). Segregation confirmed both variants in the sibling fetus. Through RNA analyses, we characterized skipping of exon 4 affecting the PNKP Forkhead-associated (FHA) and Phosphatase domains (p.Leu67_Lys166del) as the predominant effect of the c.498G>A variant. We retrospectively investigated two unrelated individuals diagnosed with biallelic PNKP-variants to compare prenatal/postnatal phenotypes. Both carry the same splice-donor variant c.1029+2T>C in trans with a variant in the FHA domain (c.311T>C, p.(Leu104Pro) and c.151G>C, p.(Val51Leu), respectively). RNA-seq showed complex splicing events for c.1029+2T>C and c.151G>C. Computational modelling and structural analysis revealed significant clustering of missense variants in the FHA domain, with some variants potentially generating structural damage.Our detailed clinical description extends the PNKP-continuum to the prenatal stage. Investigating possible PNKP-variant effects using RNA and structural modelling, we highlight the mutational complexity and exemplify a framework for variant characterization in this multi-domain protein.
Donor clonal hematopoiesis and recipient outcomes after transplantation
Authors: Gibson Christopher J. , Kim Haesook T. , Zhao Lin , Murdock H. Moses , Hambley Bryan , Ogata Alana , Madero-Marroquin Rafael , Wang Shiyu , Green Lisa , Fleharty Mark , Dougan Tyler , Cheng Chi-An , Blumenstiel Brendan , Cibulskis Carrie , Tsuji Junko , Duran Madeleine , Gocke Christopher D. , Antin Joseph H. , Nikiforow Sarah , DeZern Amy E. , Chen Yi-Bin , Ho Vincent T. , Jones Richard J. , Lennon Niall J. , Walt David R. , Ritz Jerome , Soiffer Robert J. , Gondek Lukasz P. , Lindsley R. Coleman 
Published: September 2021

BackgroundClonal hematopoiesis (CH) can be transmitted from donor to recipient during allogeneic hematopoietic cell transplantation. Exclusion of candidate donors with CH is controversial since its impact on recipient outcomes and graft alloimmune function is uncertain.MethodsWe performed targeted error-corrected sequencing on samples from 1727 donors aged 40 or older and assessed the effect of donor CH on recipient clinical outcomes. We measured long-term engraftment of 102 donor clones and cytokine levels in 256 recipients at 3 and 12 months after transplant.ResultsCH was present in 22.5% of donors, withDNMT3A(14.6%) andTET2(5.2%)mutations being most common; 85% of donor clones showed engraftment in recipients after transplantation, including clones with variant allele fraction (VAF)<0.01.DNMT3A-CH with VAF≥0.01, but not smaller clones, was associated with improved recipient overall (HR 0.79, P=0.042) and progression-free survival (HR 0.72, P=0.003) after adjustment for significant clinical variables. In patients receiving calcineurin-based GVHD prophylaxis, donorDNMT3A-CH was associated with reduced relapse (sHR 0.59, P=0.014), increased chronic GVHD (sHR 1.36, P=0.042), and higher IL-12p70 levels in recipients. No recipient of sole DNMT3A orTET2-CH developed donor cell leukemia (DCL). In 7 of 8 cases, DCL evolved from donor CH with rareTP53or splicing factor mutations or from donors carrying germlineDDX41mutations.ConclusionDonor CH is associated with clinical outcomes in transplant recipients, with differential impact on alloimmune function and potential for leukemic transformation related to mutated gene and clonal abundance.DNMT3A-CH is associated with improved recipient survival due to reduced relapse risk and an augmented network of inflammatory cytokines in recipients. Risk of DCL is driven by pre-existing somatic MDS-associated mutations or germline predisposition in donors.
CD14 Positive Extracellular Vesicles in Broncho-Alveolar Lavage Fluid as a New Biomarker of Acute Respiratory Distress Syndrome
Authors: Mahida Rahul Y. , Price Joshua , Lugg Sebastian T. , Li Hui , Parekh Dhruv , Scott Aaron , Harrison Paul , Matthay Michael A. , Thickett David R. 
Published: September 2021

ABSTRACTRecent studies have indicated that extracellular vesicles (EV) may play a role in the pathogenesis of Acute Respiratory Distress Syndrome (ARDS). EV have been identified as potential biomarkers of disease severity and prognosis in other pulmonary diseases. We sought to characterize the EV phenotype within ARDS patient broncho-alveolar lavage fluid (BAL), and to determine whether BAL EV could be utilized as a potential biomarker in ARDS. BAL was collected from sepsis patients with and without ARDS, and from esophagectomy patients post-operatively (of whom a subset later developed ARDS during hospital admission). BAL EV were characterized with regards to size, number and cell of origin. Sepsis patients with ARDS had significantly higher numbers of CD14+/CD81+ monocyte-derived BAL EV than sepsis patients without ARDS (p=0.015). However, the converse was observed in esophagectomy patients who later developed ARDS (p=0.003). Esophagectomy patients who developed ARDS also had elevated CD31+/CD63+ and CD31+/CD81+ endothelial-derived BAL EV (p≤0.02) compared to esophagectomy patients who did not develop ARDS. Further studies are required to determine whether CD31+ BAL EV may be a predictive biomarker for ARDS in esophagectomy patients. CD14+/CD81+ BAL EV numbers were significantly higher in those patients with sepsis-related ARDS who died during the 30 days following ICU admission (p=0.027). Thus, CD14+/CD81+ BAL EV are a potential biomarker for disease severity and mortality in sepsis-related ARDS. These findings provide the impetus to further elucidate the contribution of these EV to ARDS pathogenesis.
A prevaccination validated network that drives the breadth of the protective neutralizing antibody response following Dengue Vaccine TV003 immunization
Authors: Pelletier Adam Nicolas , Sanchez Gabriela , Watson Mark , Izmirly Abdullah , Di Pucchio Tiziana , Haddad Elias , Paramithiotis Eustache , Khalil Jorge , Diamond Michael , Kallas Esper , Sekaly Rafick Pierre 
Published: September 2021

ABSTRACTDevelopment of fully protective dengue virus (DV) vaccines has been problematic as infection with DV requires a broad antibody immune response that targets all 4 possible serotypes. Herein, we used an integrated systems vaccinology approach to identify prevaccination features that allow the development of fully protective DV-specific antibody responses. This approach allowed us to identify a transcription network in a subset of monocytes defined by the expression of CD68 and downstream of specific pro- and anti-inflammatory cytokines. Moreover, we identified metabolites as drivers of an immune response that induced neutralizing antibodies to the 4 DV serotypes. Specifically, PC/PE drove the production of TGF-B in CD68 low monocytes, which was a positive correlate of the protective antibody response. In contrast, primary and secondary bile acids triggered a proinflammatory response downstream of TGR5 signaling and inflammasome activation in CD68 high monocytes, which was associated to a non-protective antibody response. These features were validated in vitro in primary myeloid cells. Our results highlight the role of cell and systemic metabolism as regulators of protective immune responses to vaccination, and that systems vaccinology is a key tool to identify such mechanisms.
Practices for Measuring 3D Organelle Morphology and Generating Surfaces with Amira
Authors: Lopez Edgar Garza , Vue Zer , Katti Prasanna , Neikirk Kit , Biete Michelle , Lam Jacob , Beasley Heather K. , Marshall Andrea G. , Rodman Taylor , Christensen Trace , Salisbury Jeffrey , Vang Larry , Mungai Margaret , AshShareef Salma , Murray Sandra , Shao Jianqiang , Streeter Jennifer , Glancy Brian , Pereira Renata O. , Abel E. Dale , Hinton Antentor 
Published: September 2021

ABSTRACTAnalysis of 3D structures is of paramount importance in cellular biology. Although light microscopy and transmission electron microscopy (TEM) have remained staples for imaging cellular structures, they lack the ability to image in 3D. However, recent technological advances, such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM), have allowed researchers to observe cellular ultrastructure in 3D. Here, we propose a standardized protocol using the visualization software Amira to quantify organelle morphologies in 3D; this method allows researchers to produce accurate and reproducible measurements of cellular structure characteristics. We demonstrate this applicability by utilizing SBF-SEM and Amira to quantify mitochondria and endoplasmic reticulum (ER) structures.GRAPHICAL ABSTRACT
CD19 B cell repopulation after ocrelizumab, alemtuzumab and cladribine: Implications for SARS-CoV-2 vaccinations in multiple sclerosis
Authors: Baker David , MacDougall Amy , Kang Angray S. , Schmierer Klaus , Giovannoni Gavin , Dobson Ruth 
Published: September 2021

AbstractBackgroundCD20 depletion is a highly-effective treatment for relapsing multiple sclerosis that maintains B cells at low levels through six monthly dosing of 600mg ocrelizumab. This dosing schedule is associated with inhibition of seroconversion following SARS-CoV-2 vaccination, in contrast to the high levels of seroconversion following treatment with alemtuzumab and cladribine tablets. A number of emerging reports suggest that repopulation of 1-3% B cells facilitates seroconversion after CD20-depletion. The frequency of this occurring following repeated ocrelizumab treatment, after other DMT, and after treatment cessation is largely unknown.MethodsRelapse data, lymphocyte and CD19 B cell numbers were extracted from phase II ocrelizumab extension study (NCT00676715) data supplied by the manufacturer via the Vivli Inc, trial data-request portal. Repopulation data of oral cladribine from the phase III CLARITY study (NCT00213135) was supplied by the European Medicines Agency; and the alemtuzumab phase III CARE-MS I (NCT00530348) and CARE-MS II (NCT00548405) trial data were supplied by the manufacturer via theclinicalstudydatarequest.comportal.ResultsOnly 3-5% of people with MS exhibit 1% B cells at 6 months after the last infusion following 3-4 cycles of ocrelizumab, compared to 50-55% at 9 months, and 85-90% at 12 months. During this time relapses occurred at consistent disease breakthrough rates compared to people during standard therapy. In contrast most people (90-100%) exhibited more than 1% B cells during treatment with either cladribine or alemtuzumab.ConclusionsFew people repopulate peripheral B cells with standard ocrelizumab dosing, however an extending the dosing interval by 3-6 months may allow many more people to potentially seroconvert in the relative absence of excess relapse-activity. Most people demonstrate B cell repletion within 3 months of the last treatment of alemtuzumab and cladribine. This may help protect against severe COVID-19.
Bayesian approach to comparing the left ventricular volume in myocardial infarction and in normal cases
Authors: Hernowo A.T. 
Published: September 2021

AbstractIntroductionPost-contrast delayed-enhancement MRI helps to show the extent of myocardial infarction (MI), as well as allowing the morphometric analysis of the heart structure, e.g., left ventricular volume (LVV). Here the author deployed Bayesian implementation of statistical inference to determine the difference between the LVV in MI cases and in normal controls.MethodsSixty-seven MI patients and thirty-three controls from the EMIDEC dataset challenge were used. These were acquired at the University Hospital of Dijon (France). A cardiologist with 10 years of experience in cardiology and MRI and a biophysicist with 20 years of experience of cardiovascular MRI supervised the acquisition and annotated the images. ITK-Snap was used to extract the LVV and Bayesian inference were used to investigate the data.ResultsPatients with MI were younger than the controls (58.3 ± 11.5 vs. 66.5 ± 12.9 years; BF10 = 17.9). With age taken into consideration, the patients showed larger LVV relative to the controls (128.1 ± 46.3 vs. 83.4 ± 24.4 cm3; post-hoc BF10 = 12663.8).SummaryUsing Bayesian approach, we can conclude decisively that there is volumetric difference or remodeling in individuals with MI.
Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States
Authors: Mallela Abhishek , Neumann Jacob , Miller Ely F. , Chen Ye , Posner Richard G. , Lin Yen Ting , Hlavacek William S. 
Published: September 2021

AbstractAlthough many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number ℛ0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of ℛ0 relates to a herd immunity threshold (HIT), which is given by 1 − 1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level ℛ0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. ℛ0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21-January-2020 to 21-June-2020. Our ℛ0 estimates characterize infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we find that no state has achieved herd immunity as of 20-September-2021.Significance StatementCOVID-19 will continue to threaten non-immune persons in the presence of ongoing disease transmission. We can estimate when sustained disease transmission will end by calculating the population-specific basic reproduction number ℛ0, which relates to a herd immunity threshold (HIT), given by 1 − 1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely. Here, we report state-level ℛ0 estimates indicating that disease transmission varies considerably across states. Our ℛ0 estimates can also be used to determine HITs for the Delta variant of COVID-19. On the basis of Delta-adjusted HITs, vaccination data, and serological survey results, we find that no state has yet achieved herd immunity.
Prime-seq, efficient and powerful bulk RNA-sequencing
Authors: Janjic Aleksandar , Wange Lucas E. , Bagnoli Johannes W. , Geuder Johanna , Nguyen Phong , Richter Daniel , Vieth Beate , Vick Binje , Jeremias Irmela , Ziegenhain Christoph , Hellmann Ines , Enard Wolfgang 
Published: September 2021

AbstractWith the advent of Next Generation Sequencing, RNA-sequencing (RNA-seq) has become the major method for quantitative gene expression analysis. Reducing library costs by early barcoding has propelled single-cell RNA-seq, but has not yet caught on for bulk RNA-seq. Here, we optimized and validated a bulk RNA-seq method we call prime-seq. We show that with respect to library complexity, measurement accuracy, and statistical power it performs equivalent to TruSeq, a standard bulk RNA-seq method, but is four-fold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step that further improves cost and time-efficiency, show that intronic reads are derived from RNA, validate that prime-seq performs optimal with only 1,000 cells as input, and calculate that prime-seq is the most cost-efficient bulk RNA-seq method currently available. We discuss why many labs would profit from a cost-efficient early barcoding RNA-seq protocol and argue that prime-seq is well suited for setting up such a protocol as it is well validated, well documented, and requires no specialized equipment.
Admixture of evolutionary rates across a hybrid zone
Authors: Xiong Tianzhu , Li Xueyan , Yago Masaya , Mallet James 
Published: September 2021

AbstractHybridization is a major evolutionary force that can erode genetic differentiation between species, whereas reproductive isolation maintains such differentiation. In studying a hybrid zone between the swallowtail butterflies Papilio syfanius and Papilio maackii, we made the unexpected discovery that genomic substitution rates are unequal between the parental species. This phenomenon creates a novel process in hybridization, where genomic regions most affected by gene flow evolve at similar rates, while genomic regions with greater reproductive isolation evolve at divergent rates. Thus, hybridization mixes evolutionary rates in a way similar to its effect on ancestry. Using coalescent theory, we show that the rate-mixing process provides distinct information about levels of gene flow across different parts of genomes, and that maintenance of divergent substitution rates can be predicted quantitatively from relative sequence divergence (FST) between the hybridizing species at equilibrium. A corollary is that divergent rates will be maintained in regions linked to barrier loci. Overall, we demonstrate that reproductive isolation maintains not only the final outcome of genomic differentiation, but also the rate at which differentiation accumulates. This new information also suggests that the separation of evolutionary rates co-localizes with the separation of gene pools between genomes of incipient species.
Quantitative single-cell transcriptome-based ranking of engineered AAVs in human retinal explants
Authors: Xi Zhouhuan , Öztürk Bilge E. , Johnson Molly E. , Stauffer William R. , Byrne Leah C. 
Published: September 2021

AbstractGene therapy is a rapidly developing field, and adeno-associated virus (AAV) is a leading viral vector candidate for therapeutic gene delivery. Newly engineered AAVs with improved abilities are now entering the clinic. It has proven challenging, however, to predict the translational potential of gene therapies developed in animal models, due to cross-species differences. Human retinal explants are the only available model of fully developed human retinal tissue, and are thus important for the validation of candidate AAV vectors. In this study, we evaluated 18 wildtype and engineered AAV capsids in human retinal explants using a recently developed single-cell RNA-Seq AAV engineering pipeline (scAAVengr). Human retinal explants retained the same major cell types as fresh retina, with similar expression of cell-specific markers, except for a cone population with altered expression of cone-specific genes. The efficiency and tropism of AAVs in human explants were quantified, with single-cell resolution. The top performing serotypes, K91, K912, and 7m8, were further validated in non-human primate and human retinal explants. Together, this study provides detailed information about the transcriptome profiles of retinal explants, and quantifies the infectivity of leading AAV serotypes in human retina, accelerating the translation of retinal gene therapies to the clinic.Graphic abstract
Regional and clonal T cell dynamics at single cell resolution in immune checkpoint blockade
Authors: Pai Joy A. , Chow Andrew , Sauter Jennifer L. , Mattar Marissa , Rizvi Hira , Woo Hyung Jun , Shah Nisargbhai , Uddin Fathema , Quintanal-Villalonga Alvaro , Chan Joseph M. , Manoj Parvathy , Allaj Viola , Baine Marina , Chaft Jamie , Plodkowski Andrew J. , Won Helen , Wells Daniel , Donoghue Mark T.A. , de Stanchina Elisa , Sen Triparna , Wolchok Jedd D. , Houck-Loomis Brian , Merghoub Taha , Rudin Charles M. , Satpathy Ansuman T. , Hellmann Matthew D. 
Published: September 2021

ABSTRACTPaired T cell receptor and RNA single cell sequencing (scTCR/RNA-seq) has allowed for enhanced resolution of clonal T cell dynamics in cancer. Here, we report a scTCR/RNA-seq dataset of 162,062 single T cells from 31 tissue regions, including tumor, adjacent normal tissues, and lymph nodes (LN), from three patients who underwent resections for progressing lung cancers after immune checkpoint blockade (ICB). We found marked regional heterogeneity in tumor persistence that was associated with heterogeneity in CD4 and CD8 T cell phenotypes; regions with persistent cancer cells were enriched for follicular helper CD4 T cells (TFH), regulatory T cells (Treg), and exhausted CD8 T cells. Clonal analysis demonstrated that highly-expanded T cell clones were predominantly of the CD8 subtype, were ubiquitously present across all sampled regions, found in the peripheral circulation, and expressed gene signatures of ‘large’ and ‘dual-expanded’ clones that have been predictive of response to ICB. Longitudinal tracking of CD8 T cell clones in the peripheral blood revealed that the persistence of ubiquitous CD8 T cell clones, as well as phenotypically distinct clones with tumor-reactive features, correlated with systemic tumor control. Finally, tracking CD8 T cell clones across tissues revealed the presence of TCF-1+precursor exhausted CD8 T cells in tumor draining LNs that were clonally linked to expanded exhausted CD8 T cells in tumors. Altogether, this comprehensive scTCR/RNA-seq dataset with regional, longitudinal, and clonal resolution provides fundamental insights into the tissue distribution, persistence, and differentiation trajectories of ICB-responsive T cells that underlie clinical responses to ICB.