bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical Challenges When Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials
Authors: Moser Carlee B , Chew Kara W , Giganti Mark J , Li Jonathan Z , Aga Evgenia , Ritz Justin , Greninger Alexander L , Javan Arzhang Cyrus , Bender Ignacio Rachel , Daar Eric S , Wohl David A , Currier Judith S , Eron Joseph J , Smith Davey M , Hughes Michael D ,   for the ACTIV-2/A5401 Study Team, Hosey Lara , Roa Jhoanna , Patel Nilam , Aldrovandi Grace , Murtaugh William , Science Frontier , Cooper Marlene , Gutzman Howard , Knowles Kevin , Bosch Ronald , Harrison Linda , Erhardt Bill , Adams Stacey 
Published: August 2023

Abstract
Most clinical trials evaluating coronavirus disease 2019 (COVID-19) therapeutics include assessments of antiviral activity. In recently completed outpatient trials, changes in nasal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA levels from baseline were commonly assessed using analysis of covariance (ANCOVA) or mixed models for repeated measures (MMRM) with single imputation for results below assay lower limits of quantification (LLoQ). Analyzing changes in viral RNA levels with singly imputed values can lead to biased estimates of treatment effects. In this article, using an illustrative example from the ACTIV-2 trial, we highlight potential pitfalls of imputation when using ANCOVA or MMRM methods, and illustrate how these methods can be used when considering values &lt;LLoQ as censored measurements. Best practices when analyzing quantitative viral RNA data should include details about the assay and its LLoQ, completeness summaries of viral RNA data, and outcomes among participants with baseline viral RNA ≥ LLoQ, as well as those with viral RNA &lt; LLoQ.
Clinical Trials Registration. NCT04518410.
Long COVID After Bamlanivimab Treatment
Authors: Evering Teresa H , Moser Carlee B , Jilg Nikolaus , Yeh Eunice , Sanusi Busola , Wohl David A , Daar Eric S , Li Jonathan Z , Klekotka Paul , Javan Arzhang Cyrus , Eron Joseph J , Currier Judith S , Hughes Michael D , Smith Davey M , Chew Kara W ,   for the ACTIV-2/A5401 Study Team, Hosey Lara , Roa Jhoanna , Patel Nilam , Coombs Robert , Greninger Alexander , Degli-Angeli Emily , Goecker Erin , Daza Glenda , Harb Socorro , Dragavon Joan , Aldrovandi Grace , Murtaugh William , Cooper Marlene , Gutzman Howard , Knowles Kevin , Bowman Rachel , Erhardt Bill , Waring Lorraine , Hessinger Diane , Adams Stacey , Kallianpur Asha R 
Published: August 2023

Abstract

Background
Prospective evaluations of long COVID in outpatients with coronavirus disease 2019 (COVID-19) are lacking. We aimed to determine the frequency and predictors of long COVID after treatment with the monoclonal antibody bamlanivimab in ACTIV-2/A5401.

Methods
Data were analyzed from participants who received bamlanivimab 700 mg in ACTIV-2 from October 2020 to February 2021. Long COVID was defined as the presence of self-assessed COVID symptoms at week 24. Self-assessed return to pre-COVID health was also examined. Associations were assessed by regression models.

Results
Among 506 participants, median age was 51 years. Half were female, 5% Black/African American, and 36% Hispanic/Latino. At 24 weeks, 18% reported long COVID and 15% had not returned to pre-COVID health. Smoking (adjusted risk ratio [aRR], 2.41 [95% confidence interval {CI}, 1.34– 4.32]), female sex (aRR, 1.91 [95% CI, 1.28–2.85]), non-Hispanic ethnicity (aRR, 1.92 [95% CI, 1.19–3.13]), and presence of symptoms 22–28 days posttreatment (aRR, 2.70 [95% CI, 1.63–4.46]) were associated with long COVID, but nasal severe acute respiratory syndrome coronavirus 2 RNA was not.

Conclusions
Long COVID occurred despite early, effective monoclonal antibody therapy and was associated with smoking, female sex, and non-Hispanic ethnicity, but not viral burden. The strong association between symptoms 22–28 days after treatment and long COVID suggests that processes of long COVID start early and may need early intervention.

Clinical Trials Registration
NCT04518410.
Association Between Anterior Nasal and Plasma SARS-CoV-2 RNA Levels and Hospitalization or Death in Nonhospitalized Adults With Mild-to-Moderate COVID-19
Authors: Giganti Mark J , Chew Kara W , Eron Joseph J , Li Jonathan Z , Pinilla Mauricio , Moser Carlee , Javan Arzhang Cyrus , Fischer William A , Klekotka Paul , Margolis David , Wohl David Alain , Coombs Robert W , Daar Eric S , Smith Davey M , Currier Judith S , Hughes Michael D ,   for the ACTIV-2/A5401 Study Team, Hosey Lara , Roa Jhoanna , Patel Nilam , Greninger Alexander , Degli-Angeli Emily , Goecker Erin , Daza Glenda , Harb Socorro , Dragavon Joan , Aldrovandi Grace , Murtaugh William , Science Frontier , Cooper Marlene , Gutzman Howard , Knowles Kevin , Bowman Rachel , Erhardt Bill , Waring Lorraine , Hessinger Diane , Adams Stacey 
Published: August 2023

Abstract

Background
There is little information regarding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as a predictor for clinical outcomes in outpatients with mild-to-moderate coronavirus disease 2019 (COVID-19).

Methods
Anterior nasal (AN) and plasma SARS-CoV-2 RNA data from 2115 nonhospitalized adults who received monoclonal antibodies (mAbs) or placebo in the ACTIV-2/A5401 trial were analyzed for associations with hospitalization or death.

Results
One hundred two participants were hospitalized or died through 28 days of follow-up. Higher day 0 (pretreatment) AN RNA was associated with increasing risk of hospitalization/death (risk ratio [RR], 1.24 per log10 copies/mL [95% confidence interval {CI}, 1.04–1.49]) among placebo recipients, ranging from 3% to 16% for &lt;2 to ≥6 log10 copies/mL. Although only 1% had quantifiable levels, there was a similar trend across day 0 plasma RNA categories. Higher day 3 AN RNA was associated with subsequent hospitalization/death among placebo recipients (RR, 1.42 per log10 copies/mL [95% CI, 1.00–2.03]), but not mAb recipients (RR, 1.02 per log10 copies/mL [95% CI, 0.68–1.56]). The proportion of treatment effect (reduction in hospitalizations/deaths after day 3 for mAb vs placebo) explained by day 3 AN RNA was 8%.

Conclusions
SARS-CoV-2 RNA levels are predictive of hospitalization/death in the natural history setting, but AN RNA levels may not be a reliable surrogate marker of mAb treatment effect in COVID-19 trials.
Clinical Trials Registration. NCT04518410.
Validity and Characterization of Time to Symptom Resolution Outcome Measures in the ACTIV-2/A5401 Outpatient COVID-19 Treatment Trial
Authors: Chew Kara W , Moser Carlee , Yeh Eunice , Wohl David A , Daar Eric S , Ritz Justin , Javan Arzhang Cyrus , Eron Joseph J , Currier Judith S , Smith Davey M , Hughes Michael D ,   for the ACTIV-2/A5401 Study Team
Published: August 2023

Abstract

Background
Time to symptom resolution measures were used in outpatient coronavirus disease 2019 (COVID-19) treatment trials without prior validation.

Methods
ACTIV-2/A5401 trial participants completed a COVID-19 diary assessing 13 targeted symptoms and global experience (overall COVID-19 symptoms, return to pre–COVID-19 health) daily for 29 days. We evaluated concordance of time to sustained (2 days) resolution of all targeted symptoms (TSR) with resolution of overall symptoms and return to health in participants receiving placebo.

Results
The analysis included 77 high-risk and 81 standard-risk participants with overall median 6 days of symptoms at entry and median age 47 years, 50% female, 82% white, and 31% Hispanic/Latino. Correlation between TSR and resolution of overall symptoms was 0.80 and 0.68, and TSR and return to health, 0.66 and 0.57 for high- and standard-risk groups, respectively. Of the high- and standard-risk participants, 61% and 79%, respectively, achieved targeted symptom resolution, of which 47% and 43%, respectively, reported symptom recurrence. Requiring &gt;2 days to define sustained resolution reduced the frequency of recurrences.

Conclusions
There was good internal consistency between TSR and COVID-19–specific global outcomes, supporting TSR as a trial end point. Requiring &gt;2 days of symptom resolution better addresses natural symptom fluctuations but must be balanced against the potential influence of non-COVID-19 symptoms.

Clinical Trials Registration
NCT04518410.
Dengue virus infection in mice induces bone marrow myeloid cell differentiation and generates Ly6Glow immature neutrophils with modulated functions
Authors: Duggal Shweta , Rawat Surender , Siddqui Gazala , Vishwakarma Preeti , Samal Sweety , Banerjee Arup , Vrati Sudhanshu 
Published: August 2023

Abstract
While neutrophil activation during dengue virus infection is known, the effect of dengue virus infection on neutrophil biogenesis has not been studied. We demonstrate that dengue virus serotype 2 induces the differentiation of mice progenitor cells ex vivo toward the CD11b+Ly6C+Ly6G+ granulocyte population. We further observed an expansion of CD11b+Ly6CintLy6Glow myeloid cells in the bone marrow of dengue virus serotype 2–infected AG129 mice with low CXCR2 expression, implying an immature population. Additionally, dengue virus serotype 2 alone could induce the differentiation of promyelocyte cell line HL-60 into neutrophil-like cells, as evidenced by increased expression of CD10, CD66b, CD16, CD11b, and CD62L, corroborating the preferential shift toward neutrophil differentiation by dengue virus serotype 2 in the mouse model of dengue infection. The functional analysis showed that dengue virus serotype 2–induced neutrophil-like cells exhibited reduced phagocytic activity and enhanced NETosis, as evidenced by the increased production of myeloperoxidase, citrullinated histones, extracellular DNA, and superoxide. These neutrophil-like cells lose their ability to proliferate irreversibly and undergo arrest in the G0 to G1 phase of the cell cycle. Further studies show that myeloperoxidase-mediated signaling operating through the reactive oxygen species axis may be involved in dengue virus serotype 2–induced proliferation and differentiation of bone marrow cells as ABAH, a myeloperoxidase inhibitor, limits cell proliferation in vitro and ex vivo, affects the cell cycle, and reduces reactive oxygen species production. Additionally, myeloperoxidase inhibitor reduced NETosis and vascular leakage in dengue virus serotype 2–infected AG129 mice. Our study thus provides evidence that dengue virus serotype 2 can accelerate the differentiation of bone marrow progenitor cells into neutrophils through myeloperoxidase and modulate their functions.
Macrophage extracellular traps promote tumor-like biologic behaviors of fibroblast-like synoviocytes through cGAS-mediated PI3K/Akt signaling pathway in patients with rheumatoid arthritis
Authors: Weng Weizhen , Liu Yan , Hu Zuoyu , Li Zhihui , Peng Xiaohua , Wang Manli , Dong Bo , Zhong Shuyuan , Jiang Yutong , Pan Yunfeng 
Published: August 2023

Abstract
Rheumatoid arthritis is an autoimmune disease characterized by synovium hyperplasia and bone destruction. Macrophage extracellular traps are released from macrophages under various stimuli and may generate stable autoantigen–DNA complexes, as well as aggravate autoantibody generation and autoimmune responses. We aimed to investigate the role of macrophage extracellular traps on the biologic behaviors of rheumatoid arthritis fibroblast-like synoviocytes. Synovial tissues and fibroblast-like synoviocytes were obtained from patients with rheumatoid arthritis. Extracellular traps in synovium and synovial fluids were detected by immunofluorescence, immunohistochemistry, and SYTOX Green staining. Cell viability, migration, invasion, and cytokine expression of rheumatoid arthritis fibroblast-like synoviocytes were assessed by CCK-8, wound-healing assay, Transwell assays, and quantitative real-time polymerase chain reaction, respectively. RNA sequencing analysis was performed to explore the underlying mechanism, and Western blot was used to validate the active signaling pathways. We found that extracellular trap formation was abundant in rheumatoid arthritis and positively correlated to anti-CCP. Rheumatoid arthritis fibroblast-like synoviocytes stimulated with purified macrophage extracellular traps demonstrated the obvious promotion in tumor-like biologic behaviors. The DNA sensor cGAS in rheumatoid arthritis fibroblast-like synoviocytes was activated after macrophage extracellular trap stimuli. RNA sequencing revealed that differential genes were significantly enriched in the PI3K/Akt signaling pathway, and cGAS inhibitor RU.521 effectively reversed the promotion of tumor-like biologic behaviors in macrophage extracellular trap–treated rheumatoid arthritis fibroblast-like synoviocytes and downregulated the PI3K/Akt activation. In summary, our study demonstrates that macrophage extracellular traps promote the pathogenically biological behaviors of rheumatoid arthritis fibroblast-like synoviocytes through cGAS-mediated activation of the PI3K/Akt signaling pathway. These findings provide a novel insight into the pathogenesis of rheumatoid arthritis and the mechanisms of macrophages in modulating rheumatoid arthritis fibroblast-like synoviocyte tumor-like behaviors.
Thoracic spinal extradural arachnoid cyst causing Brown-Sequard-like syndrome: a rare case report and review of literature
Authors: Ajoku Uchenna , Nwekeala Bright Uche 
Published: August 2023

Abstract
Spinal extradural arachnoid cysts are rare benign lesions occurring along the cerebrospinal axis. They may be associated with pain or varying degrees of neurological compressive symptoms. Brown-Sequard syndrome is a rare sequalae, where there is ipsilateral upper motor neuron paralysis with loss of proprioception as well as contralateral loss of pain and temperature sensation below the lesion. We present a 33-year-old female with a 6-month history of worsening right lower limb weakness and a 2-month history of right lower limb pain. Motor examination revealed right lower limb weakness as well as exaggerated knee and ankle jerk reflexes. A magnetic resonance imaging (MRI) was done, which showed an eccentrically located T4–7 cystic extradural mass causing severe cord compression. She had T4–7 laminectomies with total excision of the cyst and disconnection of the fistulous tract between the cyst and the subarachnoid space. She made full neurologic recovery with no complications.
De Novo Mutation Rates in Sticklebacks
Authors: Zhang Chaowei , Reid Kerry , Sands Arthur F , Fraimout Antoine , Schierup Mikkel Heide , Merilä Juha 
Published: August 2023

Abstract
Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (&gt;50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10−9 and µ = 4.29 × 10−9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.
Bacillus subtilis NrnB is expressed during sporulation and acts as a unique 3′-5′ exonuclease
Authors: Myers Tanner M , Ingle Shakti , Weiss Cordelia A , Sondermann Holger , Lee Vincent T , Bechhofer David H , Winkler Wade C 
Published: August 2023

Abstract
All cells employ a combination of endo- and exoribonucleases to degrade long RNA polymers to fragments 2–5 nucleotides in length. These short RNA fragments are processed to monoribonucleotides by nanoRNases. Genetic depletion of nanoRNases has been shown to increase abundance of short RNAs. This deleteriously affects viability, virulence, and fitness, indicating that short RNAs are a metabolic burden. Previously, we provided evidence that NrnA is the housekeeping nanoRNase for Bacillus subtilis. Herein, we investigate the biological and biochemical functions of the evolutionarily related protein, B. subtilis NrnB (NrnBBs). These experiments show that NrnB is surprisingly different from NrnA. While NrnA acts at the 5′ terminus of RNA substrates, NrnB acts at the 3′ terminus. Additionally, NrnA is expressed constitutively under standard growth conditions, yet NrnB is selectively expressed during endospore formation. Furthermore, NrnA processes only short RNAs, while NrnB unexpectedly processes both short RNAs and longer RNAs. Indeed, inducible expression of NrnB can even complement the loss of the known global 3′-5′ exoribonucleases, indicating that it acts as a general exonuclease. Together, these data demonstrate that NrnB proteins, which are widely found in Firmicutes, Epsilonproteobacteria and Archaea, are fundamentally different than NrnA proteins and may be used for specialized purposes.
TPIA2: an updated tea plant information archive for Camellia genomics
Authors: Gao Qijuan , Tong Wei , Li Fangdong , Wang Yanli , Wu Qiong , Wan Xiaochun , Xia Enhua 
Published: August 2023

Abstract
The genus Camellia consists of about 200 species, which include many economically important species widely used for making tea, ornamental flowers and edible oil. Here, we present an updated tea plant information archive for Camellia genomics (TPIA2; http://tpia.teaplants.cn) by integrating more novel large-scale genomic, transcriptomic, metabolic and genetic variation datasets as well as a variety of useful tools. Specifically, TPIA2 hosts all currently available and well assembled 10 Camellia genomes and their comprehensive annotations from three major sections of Camellia. A collection of 15 million SNPs and 950 950 small indels from large-scale genome resequencing of 350 diverse tea accessions were newly incorporated, followed by the implementation of a novel ‘Variation’ module to facilitate data retrieval and analysis of the functionally annotated variome. Moreover, 116 Camellia transcriptomes were newly assembled and added, leading to a significant extension of expression profiles of Camellia genes to 13 developmental stages and eight abiotic/biotic treatments. An updated ‘Expression’ function has also been implemented to provide a comprehensive gene expression atlas for Camellia. Two novel analytic tools (e.g. Gene ID Convert and Population Genetic Analysis) were specifically designed to facilitate the data exchange and population genomics in Camellia. Collectively, TPIA2 provides diverse updated valuable genomic resources and powerful functions, and will continue to be an important gateway for functional genomics and population genetic studies in Camellia.
HapX-mediated H2B deub1 and SreA-mediated H2A.Z deposition coordinate in fungal iron resistance
Authors: Sun Kewei , Li Yiqing , Gai Yunpeng , Wang Jingrui , Jian Yunqing , Liu Xin , Wu Liang , Shim Won-Bo , Lee Yin-Won , Ma Zhonghua , Haas Hubertus , Yin Yanni 
Published: August 2023

Abstract
Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism through which pathogens counteract iron stress is unclear. Here, we found that Fusarium graminearum encounters iron excess during the colonization of wheat heads. Deletion of heme activator protein X (FgHapX), siderophore transcription factor A (FgSreA) or both attenuated virulence. Further, we found that FgHapX activates iron storage under iron excess by promoting histone H2B deubiquitination (H2B deub1) at the promoter of the responsible gene. Meanwhile, FgSreA is shown to inhibit genes mediating iron acquisition during iron excess by facilitating the deposition of histone variant H2A.Z and histone 3 lysine 27 trimethylation (H3K27 me3) at the first nucleosome after the transcription start site. In addition, the monothiol glutaredoxin FgGrx4 is responsible for iron sensing and control of the transcriptional activity of FgHapX and FgSreA via modulation of their enrichment at target genes and recruitment of epigenetic regulators, respectively. Taken together, our findings elucidated the molecular mechanisms for adaptation to iron excess mediated by FgHapX and FgSreA during infection in F. graminearum and provide novel insights into regulation of iron homeostasis at the chromatin level in eukaryotes.
Unidirectional trans-cleaving behavior of CRISPR-Cas12a unlocks for an ultrasensitive assay using hybrid DNA reporters containing a 3′ toehold
Authors: Mohammad Noor , Talton Logan , Hetzler Zach , Gongireddy Megha , Wei Qingshan 
Published: August 2023

Abstract
CRISPR-Cas12a can induce nonspecific trans-cleavage of dsDNA substrate, including long and stable λ DNA. However, the mechanism behind this is still largely undetermined. In this study, we observed that while trans-activated Cas12a didn’t cleave blunt-end dsDNA within a short reaction time, it could degrade dsDNA reporters with a short overhang. More interestingly, we discovered that the location of the overhang also affected the susceptibility of dsDNA substrate to trans-activated Cas12a. Cas12a trans-cleaved 3′ overhang dsDNA substrates at least 3 times faster than 5′ overhang substrates. We attributed this unique preference of overhang location to the directional trans-cleavage behavior of Cas12a, which may be governed by RuvC and Nuc domains. Utilizing this new finding, we designed a new hybrid DNA reporter as nonoptical substrate for the CRISPR-Cas12a detection platform, which sensitively detected ssDNA targets at sub picomolar level. This study not only unfolded new insight into the trans-cleavage behavior of Cas12a but also demonstrated a sensitive CRISPR-Cas12a assay by using a hybrid dsDNA reporter molecule.
Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements
Authors: Trauernicht Max , Rastogi Chaitanya , Manzo Stefano G , Bussemaker Harmen J , van Steensel Bas 
Published: August 2023

Abstract
TP53 is a transcription factor that controls multiple cellular processes, including cell cycle arrest, DNA repair and apoptosis. The relation between TP53 binding site architecture and transcriptional output is still not fully understood. Here, we systematically examined in three different cell lines the effects of binding site affinity and copy number on TP53-dependent transcriptional output, and also probed the impact of spacer length and sequence between adjacent binding sites, and of core promoter identity. Paradoxically, we found that high-affinity TP53 binding sites are less potent than medium-affinity sites. TP53 achieves supra-additive transcriptional activation through optimally spaced adjacent binding sites, suggesting a cooperative mechanism. Optimally spaced adjacent binding sites have a ∼10-bp periodicity, suggesting a role for spatial orientation along the DNA double helix. We leveraged these insights to construct a log-linear model that explains activity from sequence features, and to identify new highly active and sensitive TP53 reporters.