bluuebunny/crossref_metadata_2025_split huggingface dataset:
Historical Contingency Drives Compensatory Evolution and Rare Reversal of Phage Resistance
Authors: Debray Reena , De Luna Nina , Koskella Britt 
Published: August 2022

AbstractBacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, whereas others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each individual mutant in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, whereas others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with the same resistance gene acquired more parallel sets of mutations than populations with different resistance genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria–phage coevolution and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides a new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.
Inhibition of YAP/TAZ-TEAD activity induces cytotrophoblast differentiation into syncytiotrophoblast in human trophoblast
Authors: Mizutani Tetsuya , Orisaka Makoto , Miyazaki Yumiko , Morichika Ririko , Uesaka Miki , Miyamoto Kaoru , Yoshida Yoshio 
Published: August 2022

Abstract
During placentation, placental cytotrophoblast (CT) cells differentiate into syncytiotrophoblast (ST) cells and extravillous trophoblast (EVT) cells. In the placenta, the expression of various genes is regulated by the Hippo pathway through a transcription complex, Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ)-TEA domain transcription factor (TEAD) (YAP/TAZ-TEAD) activity. YAP/TAZ-TEAD activity is controlled by multiple factors and signaling, such as cAMP signaling. cAMP signaling is believed to be involved in the regulation of trophoblast function but is not yet fully understood. Here we showed that YAP/TAZ-TEAD expressions and their activities were altered by cAMP stimulation in BeWo cells, a human choriocarcinoma cell line. The repression of YAP/TAZ-TEAD activity induced the expression of ST-specific genes without cAMP stimulation, and transduction of constitutively active YAP, i.e. YAP-5SA, resulted in the repression of 8Br-cAMP-induced expressions of ST-specific genes in a TEAD-dependent manner. We also investigated the role of YAP/TAZ-TEAD in maintaining CT cells and their differentiation into ST and EVT cells using human trophoblast stem (TS) cells. YAP/TAZ-TEAD activity was involved in maintaining the stemness of TS cells. Induction or repression of YAP/TAZ-TEAD activity resulted in marked changes in the expression of ST-specific genes. Using primary CT cells, which spontaneously differentiate into ST-like cells, the effects of YAP-5SA transduction were investigated, and the expression of ST-specific genes was found to be repressed. These results indicate that the inhibition of YAP/TAZ-TEAD activity, with or without cAMP stimulation, is essential for the differentiation of CT cells into ST cells.
Glucocorticoids in the treatment of IgG4-related disease—Prospects for new international treatment guidelines
Authors: Yoshifuji Hajime , Umehara Hisanori 
Published: August 2022

ABSTRACT
Immunoglobulin G4-related disease (IgG4-RD) is a chronic fibro-inflammatory disease that may cause dysfunction in various organs. Worldwide multidisciplinary experts attending the Fourth International Symposium on IgG4-Related Disease in Japan in 2021 discussed treatments for IgG4-RD, especially glucocorticoid (GC) therapy. This review describes the efficacy, safety, and cost of treatments for IgG4-RD based on findings presented at the international symposium. A medium dose of GC was considered appropriate for the initial treatment of IgG4-RD. A randomized controlled trial and an open-label prospective study have shown that long-term maintenance GC therapy (prednisolone ≥ 5 mg/day) could prevent disease relapse. In addition, two open-label randomized controlled trials reported the effects of combinational use of GC and synthetic immunosuppressive agents, mycophenolate mofetil and leflunomide, on relapse prevention. Moreover, an open-label single-arm study showed an excellent rate of clinical response to rituximab. Many observational studies have shown the efficacy of an appropriate GC regimen in patients with IgG4-RD. Synthetic immunosuppressive agents and a molecular-targeted agent can be potent alternatives to GCs, but additional studies are required comparing their efficacy, risk of infection, and costs.
Lymphoid follicular hyperplasia in patients with systemic lupus erythematosus after multiple cycles of rituximab
Authors: Ruiz-Ordóñez Ingrid , Santos Víctor A , Bonilla-Abadía Fabio , Silva Nhora , Sánchez Aura , Tobón Gabriel J , Cañas Carlos A 
Published: August 2022

ABSTRACTRituximab is indicated in some patients with refractory systemic lupus erythematosus (SLE). Occasionally, this medication is required in chronic form to maintain control of the disease. We described two patients who developed lymphoid follicular hyperplasia (LFH) after multiple cycles of rituximab and evaluated the expression of B cell activating factor belonging to the tumor necrosis factor (TNF) family (BAFF) and its receptors [BAFF-receptor (BAFF-R) and B cell maturation antigen (BCMA)], as possible factors related to lymphoid node enlargement. Two patients with SLE completed six and nine cycles of rituximab (1 g every 2 weeks) indicated each 9 months, achieving remission for 5 and 7 years, respectively, when developed prominent lymphadenopathies. Biopsies showed LFH. Haematological neoplasms were ruled out. Immunohistochemistry showed BAFF overexpression in the follicles, and moderate expression of BAFF-R confined to the mantle zone and BCMA to the germinal centre. Belimumab B cell activating factor belonging to the TNF family (anti-BAFF therapy) was started with positive effects on the clinical condition. LFH can develop in patients with SLE who received multiple cycles of rituximab. BAFF overexpression and moderate expression of BAFF-R and BCMA in lymph nodes were seen. These findings added to the improvement with the change to belimumab could suggest that LFH after cluster of differentiation (CD20) depletion therapy may be associated with a compensatory overexpression of BAFF and its receptors.
Prp43/DHX15 exemplify RNA helicase multifunctionality in the gene expression network
Authors: Bohnsack Katherine E , Kanwal Nidhi , Bohnsack Markus T 
Published: August 2022

Abstract
Dynamic regulation of RNA folding and structure is critical for the biogenesis and function of RNAs and ribonucleoprotein (RNP) complexes. Through their nucleotide triphosphate-dependent remodelling functions, RNA helicases are key modulators of RNA/RNP structure. While some RNA helicases are dedicated to a specific target RNA, others are multifunctional and engage numerous substrate RNAs in different aspects of RNA metabolism. The discovery of such multitasking RNA helicases raises the intriguing question of how these enzymes can act on diverse RNAs but also maintain specificity for their particular targets within the RNA-dense cellular environment. Furthermore, the identification of RNA helicases that sit at the nexus between different aspects of RNA metabolism raises the possibility that they mediate cross-regulation of different cellular processes. Prominent and extensively characterized multifunctional DEAH/RHA-box RNA helicases are DHX15 and its Saccharomyces cerevisiae (yeast) homologue Prp43. Due to their central roles in key cellular processes, these enzymes have also served as prototypes for mechanistic studies elucidating the mode of action of this type of enzyme. Here, we summarize the current knowledge on the structure, regulation and cellular functions of Prp43/DHX15, and discuss the general concept and implications of RNA helicase multifunctionality.
The influenza A virus genome packaging network — complex, flexible and yet unsolved
Authors: Jakob Celia , Paul-Stansilaus Rithu , Schwemmle Martin , Marquet Roland , Bolte Hardin 
Published: August 2022

Abstract
The genome of influenza A virus (IAV) consists of eight unique viral RNA segments. This genome organization allows genetic reassortment between co-infecting IAV strains, whereby new IAVs with altered genome segment compositions emerge. While it is known that reassortment events can create pandemic IAVs, it remains impossible to anticipate reassortment outcomes with pandemic prospects. Recent research indicates that reassortment is promoted by a viral genome packaging mechanism that delivers the eight genome segments as a supramolecular complex into the virus particle. This finding holds promise of predicting pandemic IAVs by understanding the intermolecular interactions governing this genome packaging mechanism. Here, we critically review the prevailing mechanistic model postulating that IAV genome packaging is orchestrated by a network of intersegmental RNA–RNA interactions. Although we find supporting evidence, including segment-specific packaging signals and experimentally proposed RNA–RNA interaction networks, this mechanistic model remains debatable due to a current shortage of functionally validated intersegmental RNA–RNA interactions. We speculate that identifying such functional intersegmental RNA–RNA contacts might be hampered by limitations of the utilized probing techniques and the inherent complexity of the genome packaging mechanism. Nevertheless, we anticipate that improved probing strategies combined with a mutagenesis-based validation could facilitate their discovery.
Cryo-EM structure of the Smc5/6 holo-complex
Authors: Hallett Stephen T , Campbell Harry Isabella , Schellenberger Pascale , Zhou Lihong , Cronin Nora B , Baxter Jonathan , Etheridge Thomas J , Murray Johanne M , Oliver Antony W 
Published: August 2022

Abstract
The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication. Here, we report the cryogenic EM (cryo-EM) structure of the six-subunit budding yeast Smc5/6 holo-complex, reconstituted from recombinant proteins expressed in insect cells – providing both an architectural overview of the entire complex and an understanding of how the Nse1/3/4 subcomplex binds to the hetero-dimeric SMC protein core. In addition, we demonstrate that a region within the head domain of Smc5, equivalent to the ‘W-loop’ of Smc4 or ‘F-loop’ of Smc1, mediates an important interaction with Nse1. Notably, mutations that alter the surface-charge profile of the region of Nse1 which accepts the Smc5-loop, lead to a slow-growth phenotype and a global reduction in the chromatin-associated fraction of the Smc5/6 complex, as judged by single molecule localisation microscopy experiments in live yeast. Moreover, when taken together, our data indicates functional equivalence between the structurally unrelated KITE and HAWK accessory subunits associated with SMC complexes.
A photochemically covalent lock stabilizes aptamer conformation and strengthens its performance for biomedicine
Authors: Zhou Fang , Wang Peng , Chen Jianghuai , Zhu Zhijia , Li Youshan , Wang Sujuan , Wu Shanchao , Sima Yingyu , Fu Ting , Tan Weihong , Zhao Zilong 
Published: August 2022

Abstract
Aptamers’ vast conformation ensemble consisting of interconverting substates severely impairs their performance and applications in biomedicine. Therefore, developing new chemistries stabilizing aptamer conformation and exploring the conformation–performance relationship are highly desired. Herein, we developed an 8-methoxypsoralen-based photochemically covalent lock to stabilize aptamer conformation via crosslinking the inter-stranded thymine nucleotides at TpA sites. Systematical studies and molecular dynamics simulations were performed to explore the conformation–performance relationship of aptamers, revealing that conformation-stabilized aptamers displayed better ability to bind targets, adapt to physiological environment, resist macrophage uptake, prolong circulation half-life, accumulate in and penetrate into tumor than their counterparts. As expected, conformation-stabilized aptamers efficiently improved the therapeutic efficacy of aptamer-drug conjugation on tumor-bearing mice. Collectively, our study has developed a general, simple and economic strategy to stabilize aptamer conformation and shed light on the conformation–performance relationship of aptamers, laying a basis for promoting their basic researches and applications in biomedicine.
The Effect of Biomarker Use on the Speed and Duration of Clinical Trials for Cancer Drugs
Authors: Mohamed Luqmaan , Manjrekar Siddhi , Ng Derek P , Walsh Alec , Lopes Gilberto , Parker Jayson L 
Published: August 2022

Abstract

Background
The purpose of this study was to explore the effects biomarkers have on the duration and speed of clinical trials in oncology.

Materials and Methods
Clinical trial data was pooled from www.clinicaltrials.gov within the 4 cancer indications of non-small cell lung cancer, breast cancer, melanoma, and colorectal cancer. Heatmaps of clinical timelines were used to display differences in the frequency and timing of clinical trials across trials that used or did not use biomarkers, for all 4 indications.

Results
Screening of 8630 clinical trials across the 4 indications yielded 671 unique drugs corresponding to 1224 eligible trials used in our analysis. The constructed heatmaps visually represented that biomarkers did not have an effect on the time gap between trial phases for non-small cell lung cancer and melanoma but did for colorectal and breast cancer trials, reducing the speed of trial timelines. It was also observed that biomarker trials were more often concurrent over shorter periods of time and began later in the timeline for non-small cell lung and colorectal cancers.

Conclusion
The novel visualization method revealed longer gaps between trial phases, later clinical trial start times, and shorter periods of concurrently run trials for drugs that used biomarkers. The study highlights that biomarker-driven trials might impact drug approval timelines and need to be considered carefully in clinical development plan.
Les anomalies vasculaires pendant l’enfance : quand traiter les patients et quand les diriger vers une ressource spécialisée
Authors: Zwicker Kelley , Powell Julie , Cummings Carl 
Published: August 2022

Abstract
Les anomalies vasculaires sont des affections hétérogènes qui touchent les vaisseaux sanguins ou lymphatiques. Les enfants atteints peuvent éprouver de la douleur ou une perte fonctionnelle, présenter une infection ou une coagulopathie ou être confrontés à des difficultés psychologiques. Le diagnostic et la prise en charge exigent souvent une approche interdisciplinaire. Sept cliniques d’anomalies vasculaires au Canada offrent des soins interdisciplinaires. Le présent point de pratique propose une approche thérapeutique des anomalies vasculaires pédiatriques les plus fréquentes (hémangiomes). On y passe en revue les indications de diriger les patients vers une clinique spécialisée, en s’attardant sur les anomalies vasculaires complexes, et notamment les hémangiomes infantiles, qui peuvent provoquer des complications.
Vascular anomalies in childhood: When to treat and when to refer
Authors: Zwicker Kelley , Powell Julie , Cummings Carl 
Published: August 2022

Abstract
Vascular anomalies are heterogeneous conditions that affect blood and/or lymphatic vessels. Affected children may experience pain, functional loss, infection, coagulopathies, and psychological challenges. Diagnosis and management often warrant an interdisciplinary approach. There are seven vascular anomalies clinics in Canada that offer interdisciplinary care. This practice point outlines a treatment approach for the most common paediatric vascular anomaly (hemangioma). It reviews indications for referral to a specialized clinic, with focus on complex vascular anomalies, specifically infantile hemangioma, which can pose complications.
The trans-Golgi-localized protein BICAT3 regulates manganese allocation and matrix polysaccharide biosynthesis
Authors: He Jie , Yang Bo , Hause Gerd , Rössner Nico , Peiter-Volk Tina , Schattat Martin H , Voiniciuc Cătălin , Peiter Edgar 
Published: August 2022

AbstractManganese (Mn2+) is essential for a diversity of processes, including photosynthetic water splitting and the transfer of glycosyl moieties. Various Golgi-localized glycosyltransferases that mediate cell wall matrix polysaccharide biosynthesis are Mn2+ dependent, but the supply of these enzymes with Mn2+ is not well understood. Here, we show that the BIVALENT CATION TRANSPORTER 3 (BICAT3) localizes specifically to trans-cisternae of the Golgi. In agreement with a role in Mn2+ and Ca2+ homeostasis, BICAT3 rescued yeast (Saccharomyces cerevisiae) mutants defective in their translocation. Arabidopsis (Arabidopsis thaliana) knockout mutants of BICAT3 were sensitive to low Mn2+ and high Ca2+ availability and showed altered accumulation of these cations. Despite reduced cell expansion and leaf size in Mn2+-deficient bicat3 mutants, their photosynthesis was improved, accompanied by an increased Mn content of chloroplasts. Growth defects of bicat3 corresponded with an impaired glycosidic composition of matrix polysaccharides synthesized in the trans-Golgi. In addition to the vegetative growth defects, pollen tube growth of bicat3 was heterogeneously aberrant. This was associated with a severely reduced and similarly heterogeneous pectin deposition and caused diminished seed set and silique length. Double mutant analyses demonstrated that the physiological relevance of BICAT3 is distinct from that of ER-TYPE CA2+-ATPASE 3, a Golgi-localized Mn2+/Ca2+-ATPase. Collectively, BICAT3 is a principal Mn2+ transporter in the trans-Golgi whose activity is critical for specific glycosylation reactions in this organelle and for the allocation of Mn2+ between Golgi apparatus and chloroplasts.
The cell biology of charophytes: Exploring the past and models for the future
Authors: Domozych David S , Bagdan Kaylee 
Published: August 2022

AbstractCharophytes (Streptophyta) represent a diverse assemblage of extant green algae that are the sister lineage to land plants. About 500–600+ million years ago, a charophyte progenitor successfully colonized land and subsequently gave rise to land plants. Charophytes have diverse but relatively simple body plans that make them highly attractive organisms for many areas of biological research. At the cellular level, many charophytes have been used for deciphering cytoskeletal networks and their dynamics, membrane trafficking, extracellular matrix secretion, and cell division mechanisms. Some charophytes live in challenging habitats and have become excellent models for elucidating the cellular and molecular effects of various abiotic stressors on plant cells. Recent sequencing of several charophyte genomes has also opened doors for the dissection of biosynthetic and signaling pathways. While we are only in an infancy stage of elucidating the cell biology of charophytes, the future application of novel analytical methodologies in charophyte studies that include a broader survey of inclusive taxa will enhance our understanding of plant evolution and cell dynamics.
Retracted: Effect of Sham Acupuncture on Chronic Pain: A Bayesian Network Meta-Analysis
Authors: Zhou Rui , Zhu Yan-juan , Chen Xian , Ma Hao-chuan , Liu Yi-hong , Chang Xue-song , Chen Ya-dong , Yu Ya-ya , Xiao Zhen-zhen , Liu Li-rong , Li Yong , Zhang Hai-bo 
Published: August 2022

AbstractBackgroundAlong with increasing research on acupuncture for chronic pain, the validity of sham acupuncture (SA) has also been argued.MethodsNine databases were searched for randomized controlled trials (RCTs) from the inception dates of the databases to July 5, 2022. With Markov Chain Monte Carlo methods, a Bayesian multiple-treatment network meta-analysis (NMA) with random-effects model was conducted.ResultsA total of 62 RCTs with 6,806 patients and four kinds of treatments (real acupuncture [RA], non-acupuncture [NA], penetrative SA [PSA], and non-penetrative SA [NPSA]) were included. The results indicated that both NPSA and PSA were not superior to NA in improving chronic pain (NPSA: mean difference [MD]= –4.77, 95% confidence interval [CI] –11.09 to 1.52; PSA: MD= –4.96, 95% CI –10.38 to 0.48). After NPSA and PSA were combined into the SA group, the weak trend of pain relief from SA was still not statistically significant (MD= –4.91, 95% CI –9.93 to 0.05). NPSA and PSA had similar effects (MD= 0.18, 95% CI –5.45 to 5.81). RA was significantly associated with pain relief, compared with NPSA and PSA (NPSA: MD= –12.03, 95% CI –16.62 to –7.41; PSA: MD= –11.85, 95% CI –15.48 to –8.23). The results were generally consistent regardless of pain phenotype, frequency, duration, acupuncture methods, analgesic intake, or detection bias.ConclusionThese results suggested that acupuncture was significantly associated with reduced chronic pain. The two kinds of placebo acupuncture, NPSA and PSA, have similar effects. Both NPSA and PSA, with a weak but not significant effect, are appropriate to be inert placebo controls in RCTs for chronic pain.
Prevalence of undiagnosed axial spondyloarthritis in inflammatory bowel disease patients with chronic back pain: secondary care cross-sectional study
Authors: Lim Chong Seng Edwin , Tremelling Mark , Hamilton Louise , Kim Matthew , Macgregor Alexander , Turmezei Tom , Gaffney Karl 
Published: August 2022

AbstractObjectiveTo elucidate the prevalence of undiagnosed rheumatology-verified diagnosis of axial spondyloarthritis (RVD-axSpA) in patients attending routine secondary care IBD clinics with chronic back pain.MethodsScreening questionnaires were sent to consecutive patients attending IBD clinics in a university teaching hospital. Patients fulling the eligibility criteria (gastroenterologist-verified diagnosis, 18–80 years old, biologic therapy naive, no previous diagnosis of axSpA); and a moderate diagnostic probability of axSpA [self-reported chronic back pain (CBP) &gt;3 months, onset &lt;45 years] were invited for rheumatology assessment. This included medical review, physical examination, patient reported outcome measures, human leucocyte antigen B27, C-reactive protein, pelvic radiograph and axSpA protocol magnetic resonance imaging. A diagnosis of RVD-axSpA was made by a panel of rheumatologists.ResultsOf the 470 patients approached, 91 had self-reported CBP &gt;3 months, onset &lt;45 years, of whom 82 were eligible for clinical assessment. The prevalence of undiagnosed RVD-axSpA in patients attending IBD clinics in a secondary care setting, with self-reported CBP, onset &lt;45 years is estimated at 5% (95% CI 1.3, 12.0) with a mean symptom duration of 12 (s.d. 12.4) years.ConclusionThere is a significant hidden disease burden of axSpA among IBD patients. Appropriate identification and referral from gastroenterology is needed to potentially shorten the delay to diagnosis and allow access to appropriate therapy.