bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces
Authors: Ameruoso Andrea , Villegas Kcam Maria Claudia , Cohen Katherine Piper , Chappell James 
Published: July 2022

Abstract
The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an urgent need to discover new antibiotics. Natural products derived from the genus Streptomyces represent a rich and diverse repertoire of chemical molecules from which new antibiotics are likely to be found. However, a major challenge is that the biosynthetic gene clusters (BGCs) responsible for natural product synthesis are often poorly expressed under laboratory culturing conditions, thus preventing the isolation and screening of novel chemicals. To address this, we describe a novel approach to activate silent BGCs through rewiring endogenous regulation using synthetic gene regulators based upon CRISPR-Cas. First, we refine CRISPR interference (CRISPRi) and create CRISPR activation (CRISPRa) systems that allow for highly programmable and effective gene repression and activation in Streptomyces. We then harness these tools to activate a silent BGC by perturbing its endogenous regulatory network. Together, this work advances the synthetic regulatory toolbox for Streptomyces and facilitates the programmable activation of silent BGCs for novel chemical discovery.
Structural analysis of the basal state of the Artemis:DNA-PKcs complex
Authors: Watanabe Go , Lieber Michael R , Williams Dewight R 
Published: July 2022

Abstract
Artemis nuclease and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are key components in nonhomologous DNA end joining (NHEJ), the major repair mechanism for double-strand DNA breaks. Artemis activation by DNA-PKcs resolves hairpin DNA ends formed during V(D)J recombination. Artemis deficiency disrupts development of adaptive immunity and leads to radiosensitive T- B- severe combined immunodeficiency (RS-SCID). An activated state of Artemis in complex with DNA-PK was solved by cryo-EM recently, which showed Artemis bound to the DNA. Here, we report that the pre-activated form (basal state) of the Artemis:DNA-PKcs complex is stable on an agarose-acrylamide gel system, and suitable for cryo-EM structural analysis. Structures show that the Artemis catalytic domain is dynamically positioned externally to DNA-PKcs prior to ABCDE autophosphorylation and show how both the catalytic and regulatory domains of Artemis interact with the N-HEAT and FAT domains of DNA-PKcs. We define a mutually exclusive binding site for Artemis and XRCC4 on DNA-PKcs and show that an XRCC4 peptide disrupts the Artemis:DNA-PKcs complex. All of the findings are useful in explaining how a hypomorphic L3062R missense mutation of DNA-PKcs could lead to insufficient Artemis activation, hence RS-SCID. Our results provide various target site candidates to design disruptors for Artemis:DNA-PKcs complex formation.
Regulated dicing of pre-mir-144 via reshaping of its terminal loop
Authors: Shang Renfu , Kretov Dmitry A , Adamson Scott I , Treiber Thomas , Treiber Nora , Vedanayagam Jeffrey , Chuang Jeffrey H , Meister Gunter , Cifuentes Daniel , Lai Eric C 
Published: July 2022

Abstract
Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2). We provide further evidence that this regulatory switch involves reshaping of the pre-mir-144 apical loop into a structure that is appropriate for Dicer cleavage. In light of our recent findings that mir-144 promotes the nuclear biogenesis of its neighbor mir-451, these data extend the complex hierarchy of nuclear and cytoplasmic regulatory events that can control the maturation of clustered miRNAs.
The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10
Authors: Xiao Yao , MacRae Ian J 
Published: July 2022

Abstract
Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential gene regulators for plant and animal development. The loading of sRNA duplexes into the proper ARGONAUTE (AGO) protein is a key step to forming a functional silencing complex. In Arabidopsis thaliana, the specific loading of miR166/165 into AGO10 (AtAGO10) is critical for the maintenance of the shoot apical meristem, the source of all shoot organs, but the mechanism by which AtAGO10 distinguishes miR166/165 from other cellular miRNAs is not known. Here, we show purified AtAGO10 alone lacks loading selectivity towards miR166/165 duplexes. However, phosphate and HSP chaperone systems reshape the selectivity of AtAGO10 to its physiological substrates. A loop in the AtAGO10 central cleft is essential for recognizing specific mismatches opposite the guide strand 3′ region in miR166/165 duplexes. Replacing this loop with the equivalent loop from Homo sapiens AGO2 (HsAGO2) changes AtAGO10 miRNA loading behavior such that 3′ region mismatches are ignored and mismatches opposite the guide 5′ end instead drive loading, as in HsAGO2. Thus, this study uncovers the molecular mechanism underlying the miR166/165 selectivity of AtAGO10, essential for plant development, and provides new insights into how miRNA duplex structures are recognized for sRNA sorting.
Strand annealing and motor driven activities of SMARCAL1 and ZRANB3 are stimulated by RAD51 and the paralog complex
Authors: Halder Swagata , Ranjha Lepakshi , Taglialatela Angelo , Ciccia Alberto , Cejka Petr 
Published: July 2022

Abstract
SMARCAL1, ZRANB3 and HLTF are required for the remodeling of replication forks upon stress to promote genome stability. RAD51, along with the RAD51 paralog complex, were also found to have recombination-independent functions in fork reversal, yet the underlying mechanisms remained unclear. Using reconstituted reactions, we build upon previous data to show that SMARCAL1, ZRANB3 and HLTF have unequal biochemical capacities, explaining why they have non-redundant functions. SMARCAL1 uniquely anneals RPA-coated ssDNA, which depends on its direct interaction with RPA, but not on ATP. SMARCAL1, along with ZRANB3, but not HLTF efficiently employ ATPase driven translocase activity to rezip RPA-covered bubbled DNA, which was proposed to mimic elements of fork reversal. In contrast, ZRANB3 and HLTF but not SMARCAL1 are efficient in branch migration that occurs downstream in fork remodeling. We also show that low concentrations of RAD51 and the RAD51 paralog complex, RAD51B–RAD51C–RAD51D–XRCC2 (BCDX2), directly stimulate the motor-driven activities of SMARCAL1 and ZRANB3 but not HLTF, and the interplay is underpinned by physical interactions. Our data provide a possible mechanism explaining previous cellular experiments implicating RAD51 and BCDX2 in fork reversal.
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition
Authors: Kim Dongha , Kim Junil , Yu Young Suk , Kim Yong Ryoul , Baek Sung Hee , Won Kyoung-Jae 
Published: July 2022

AbstractAutophagy, a catabolic process to remove unnecessary or dysfunctional organelles, is triggered by various signals including nutrient starvation. Depending on the types of the nutrient deficiency, diverse sensing mechanisms and signaling pathways orchestrate for transcriptional and epigenetic regulation of autophagy. However, our knowledge about nutrient type-specific transcriptional regulation during autophagy is limited. To understand nutrient type-dependent transcriptional mechanisms during autophagy, we performed single cell RNA sequencing (scRNAseq) in the mouse embryonic fibroblasts (MEFs) with or without glucose starvation (GS) as well as amino acid starvation (AAS). Trajectory analysis using scRNAseq identified sequential induction of potential transcriptional regulators for each condition. Gene regulatory rules inferred using TENET newly identified CCAAT/enhancer binding protein γ (C/EBPγ) as a regulator of autophagy in AAS, but not GS, condition, and knockdown experiment confirmed the TENET result. Cell biological and biochemical studies validated that activating transcription factor 4 (ATF4) is responsible for conferring specificity to C/EBPγ for the activation of autophagy genes under AAS, but not under GS condition. Together, our data identified C/EBPγ as a previously unidentified key regulator under AAS-induced autophagy.
Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants
Authors: Rivière Quentin , Corso Massimiliano , Ciortan Madalina , Noël Grégoire , Verbruggen Nathalie , Defrance Matthieu 
Published: July 2022

Abstract
The identification of transcription factor (TF) target genes is central in biology. A popular approach is based on the location by pattern matching of potential cis-regulatory elements (CREs). During the last few years, tools integrating next-generation sequencing data have been developed to improve the performance of pattern matching. However, such tools have not yet been comprehensively evaluated in plants. Hence, we developed a new streamlined method aiming at predicting CREs and target genes of plant TFs in specific organs or conditions. Our approach implements a supervised machine learning strategy, which allows decision rule models to be learnt using TF ChIP-chip/seq experimental data. Different layers of genomic features were integrated in predictive models: the position on the gene, the DNA sequence conservation, the chromatin state and various CRE footprints. Among the tested features, the chromatin features were crucial for improving the accuracy of the method. Furthermore, we evaluated the transferability of predictive models across TFs, organs and species. Finally, we validated our method by correctly inferring the target genes of key TFs controlling metabolite biosynthesis at the organ level in Arabidopsis. We developed a tool—Wimtrap—to reproduce our approach in plant species and conditions/organs for which ChIP-chip/seq data are available. Wimtrap is a user-friendly R package that supports an R Shiny web interface and is provided with pre-built models that can be used to quickly get predictions of CREs and TF gene targets in different organs or conditions in Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa and Zea mays.
Class and culture in the making of an assisted living market
Authors: Altomonte Guillermina 
Published: July 2022

AbstractThis article examines the growing industry of elite assisted living in Chile, which represents a break with a longstanding culture of care provided at home by family members and domestic workers. How does this market, locally associated with deprivation, abandonment and standardization, become a legitimate option for the rich clientele it caters to? Drawing on 40 interviews with consumers and providers of institutional care, I show that the market for assisted living is moralized through material and symbolic continuities with forms of class privilege that residents feel slipping away. Respondents interpret assisted living as an extension of the domestic work previously consumed in clients’ homes, they reframe care as an exclusive commodity and they highlight residents’ entitlement to bend organizational structures and retain authority over space and labor. These findings shed light on the relationship of class to processes of cultural legitimation by revealing the extent to which not only the affective meanings of ‘home’, but its social hierarchies, play a role in moralizing markets of care.
XIThe Eighteenth Century
Authors: Lyons-Mcfarland Michelle , Milne Fiona , Carver Dylan , Distel Kristin M 
Published: July 2022

AbstractThis chapter has four sections: 1. General and Prose; 2. The Novel; 3. Poetry; 4. Drama. Section 1 is by Michelle Lyons-McFarland; section 2 is by Fiona Milne; section 3 is by Dylan Carver; section 4 is by Kristin M. Distel.
Responsiveness and Minimally Important Differences of the Traditional Chinese Version of PROMIS Paediatric-25 Profile in Chinese Children With Cancer
Authors: Chan Stephen W. W. , Wong Arnold Y. L. , Chien C. W. , Pang Marco Y. C. 
Published: July 2022

Background:
Although the Patient-Reported Outcomes Measurement Information System Paediatric-25 Profile version 2.0 (PROMIS-25) has shown good reliability and validity in assessing HRQOL in Chinese children with cancer, its responsiveness (ie, the ability of the instrument to identify temporal changes in the construct to be measured) in detecting clinically meaningful changes in these children remains unclear.

Objective:
To evaluate the responsiveness and minimally important difference (MID) of the traditional Chinese PROMIS-25 for Chinese children with cancer.

Design:
Prospective study.

Methods:
The responsiveness of traditional Chinese PROMIS-25 domains before and after cancer treatment was evaluated by testing 24 a priori hypotheses of the correlations between changes in the domain scores and the corresponding changes in domain/total scores of the traditional Chinese Patient Health Questionnaire-9, traditional Chinese Paediatric Quality of Life Inventory 4.0, and 11-point numeric pain rating scale. The MID for each domain was determined by anchored-based method (MID-A), receiver operating characteristic curve analysis method, and distribution-based method (MID-D).

Results:
A total of 103 children with cancer (13.1 ± 1.8 years) were recruited. The traditional Chinese PROMIS-25 demonstrated moderate to high responsiveness. As all MID-As were higher than the MID-Ds, MID-As were recommended to determine domain changes. The MID-As were Physical Function = 12.3; Anxiety = 17.2; Depression = 15.4; Fatigue = 13.6; Peer Relationships = 6.5; and Pain Interference = 13.0.

Limitations:
This study excluded children with cognitive or visual impairments, as well as those requiring end-of-life care.

Conclusions:
The traditional Chinese PROMIS-25 is a responsive instrument to detect health-related quality of life changes among Chinese children with cancer. Our results provided important references for using PROMIS-25 in clinical practice and research.
Transcutaneous Electrical Nerve Stimulation for Post–Cesarean Birth Pain Control
Authors: Kurata Nicole B. , Ghatnekar Reema J. , Mercer Elizabeth , Chin Jennifer M. , Kaneshiro Bliss , Yamasato Kelly S. 
Published: July 2022

OBJECTIVE:
To evaluate whether transcutaneous electrical nerve stimulation (TENS) reduces opioid use after cesarean birth.

METHODS:
We conducted a randomized, double-blind, placebo-controlled trial of TENS after cesarean birth, with the primary outcome of opioid use during the first 60 hours postoperatively. Secondary outcomes included pain scores and satisfaction with pain control on each postoperative day, duration of postoperative hospitalization, and adverse effects of TENS. We estimated 60 patients in each arm for 80% power to detect a 25% decrease in opioid use, assuming 10% attrition. To assess for a placebo effect, an additional 60 patients were randomized to no TENS during recruitment for secondary analyses comparing opioid use, pain scores, and pain control satisfaction between no TENS and placebo TENS. Analysis was by intention-to-treat.

RESULTS:
From January 2020 through March 2021, we enrolled 180 participants—60 per group. Baseline characteristics were similar across groups. Median (interquartile range) opioid consumption in the first 60 hours postoperatively, in morphine milligram equivalents, was 7.5 (0–30) with active TENS and 0 (0–22.5) with placebo TENS (P=.31). There were no significant differences in pain scores, satisfaction with pain control, or postoperative length of stay. In the no TENS group, median (interquartile range) opioid consumption in the first 60 hours postoperatively was 7.5 (0–21.9), similar to that in the placebo group (P=.57). There were also no significant differences in pain scores or pain control satisfaction between participants allocated to no TENS and those allocated to placebo TENS.

CONCLUSION:
Use of TENS after cesarean birth did not change hospital opioid consumption, pain scores, or length of postoperative stay. There was no evidence for a placebo effect of TENS on opioid use or pain scores.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov: NCT04399707.

FUNDING SOURCE:
Cardinal Health.
High-Dose Inhaled Nitric Oxide for the Treatment of Spontaneously Breathing Pregnant Patients With Severe Coronavirus Disease 2019 (COVID-19) Pneumonia
Authors: Valsecchi Carlo , Winterton Dario , Safaee Fakhr Bijan , Collier Ai-ris Y. , Nozari Ala , Ortoleva Jamel , Mukerji Shivali , Gibson Lauren E. , Carroll Ryan W. , Shaefi Shahzad , Pinciroli Riccardo , La Vita Carolyn , Ackman Jeanne B. , Hohmann Elizabeth , Arora Pankaj , Barth William H. , Kaimal Anjali , Ichinose Fumito , Berra Lorenzo ,   for the DELiverly oF iNO (DELFiNO) Network Collaborators
Published: July 2022

OBJECTIVE:
To evaluate whether the use of inhaled nitric oxide (iNO)200 improves respiratory function.

METHODS:
This retrospective cohort study used data from pregnant patients hospitalized with severe bilateral coronavirus disease 2019 (COVID-19) pneumonia at four teaching hospitals between March 2020 and December 2021. Two cohorts were identified: 1) those receiving standard of care alone (SoC cohort) and 2) those receiving iNO200 for 30 minutes twice daily in addition to standard of care alone (iNO200 cohort). Inhaled nitric oxide, as a novel therapy, was offered only at one hospital. The prespecified primary outcome was days free from any oxygen supplementation at 28 days postadmission. Secondary outcomes were hospital length of stay, rate of intubation, and intensive care unit (ICU) length of stay. The multivariable-adjusted regression analyses accounted for age, body mass index, gestational age, use of steroids, remdesivir, and the study center.

RESULTS:
Seventy-one pregnant patients were hospitalized for severe bilateral COVID-19 pneumonia: 51 in the SoC cohort and 20 in the iNO200 cohort. Patients receiving iNO200 had more oxygen supplementation–free days (iNO200: median [interquartile range], 24 [23–26] days vs standard of care alone: 22 [14–24] days, P=.01) compared with patients in the SoC cohort. In the multivariable-adjusted analyses, iNO200 was associated with 63.2% (95% CI 36.2–95.4%; P<.001) more days free from oxygen supplementation, 59.7% (95% CI 56.0–63.2%; P<.001) shorter ICU length of stay, and 63.6% (95% CI 55.1–70.8%; P<.001) shorter hospital length of stay. No iNO200-related adverse events were reported.

CONCLUSION:
In pregnant patients with severe bilateral COVID-19 pneumonia, iNO200 was associated with a reduced need for oxygen supplementation and shorter hospital stay.
Quality-Improvement Initiative for Expedited Partner Therapy Provision in an Obstetrics and Gynecology Office
Authors: Vasudeva Isha , Hartnett Janice , Bondi Laura , Newmark Alexis , Lindsay Sarah 
Published: July 2022

OBJECTIVE:
To perform a quality-improvement project to increase the rate at which expedited partner therapy is offered and prescribed at our clinic, in line with Connecticut Department of Public Health regulations.

METHODS:
We conducted quality-improvement interventions at an urban hospital-based outpatient clinic in Hartford, Connecticut, to improve prescribing of expedited partner therapy to at least 70% of eligible patients. We defined appropriate provision of expedited partner therapy by infection type (gonorrhea or chlamydia only per Centers for Disease Control and Prevention guidelines) and method of prescription per Connecticut Department of Public Health regulations (paper prescription or in-clinic dispensing).

RESULTS:
Rates of appropriate provision of expedited partner therapy improved with our interventions (21.6% vs 75.5%). We found an unexpected decrease in acceptance by patients after initiation of our interventions (81.3% vs 50.5%).

CONCLUSION:
We achieved our goal of improvement of rates of appropriate provision of expedited partner therapy to greater than 70% and have maintained this improvement over time. Future work should investigate potential barriers to expedited partner therapy acceptance, including type of infection, the effect of Department of Public Health regulation of prescribing options, and standard workflow in patient counseling.
Coaching for Surgeons: A Scoping Review of the Quantitative Evidence
Authors: Skinner Sarah C. , Mazza Stéphanie , Carty Matthew J. , Lifante Jean-Christophe , Duclos Antoine 
Published: July 2022

Objective:
To characterize quantitative studies on coaching interventions for professional surgeons to understand how surgical coaching is defined; examine how different coaching programs are designed, implemented, and evaluated; and identify any relevant research gaps.

Background:
Surgical coaching is gaining attention as an approach that could help surgeons optimize performance and improve overall wellbeing. However, surgical coaching programs and definitions of coaching vary widely between studies.

Methods:
A systematic literature search of PubMed, Scopus, Web of Science, CENTRAL, clinicaltrials.gov, and WHO ICTRP was conducted according to the PRISMA-ScR framework to identify studies and registered clinical trials written in English. Original quantitative studies on coaching interventions for professional surgeons were included. Characteristics of the coachees, coaching programs, study designs, outcomes, and findings were charted and analyzed.

Results:
From 2589 references, 8 studies (6 published; 2 registered trials) met inclusion criteria. Published studies targeted technical or nontechnical skills, included 2–26 surgeons as coachees, and used coaches who were surgeons. Two studies demonstrated that surgeons react positively to coaching. Studies showed inconsistent effects on technical/nontechnical skills. Only two studies measured patient adverse events and reported no significant positive impacts. The registered randomized trials targeted surgeons’ physiological parameters or wellbeing and used professional coaches. These trials measure surgeon and patient outcomes.

Conclusions:
There is an emerging interest in coaching programs to improve surgeons’ performance by targeting their professional skills and personal factors. However, more randomized trials are needed to evaluate the impact of coaching interventions on patient outcomes and surgeon wellness.