bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emotions and Conscious Interiority
Authors: McVeigh Brian J. 
Published: June 2022

AbstractThis chapter takes as its theoretical linchpin Jaynes’s two-tiered theory of emotions, i.e., a layer of feelings culturally constructed over basic affects from mammalian evolution. This conscious interiorization of basic affects has both advantages and disadvantages. Meta-emotions grant us the benefit of having a larger menu of more precise, nuanced feelings that enhance interpersonal communication. But the drawback is that such an extensive list of choices can complicate our reactions by obscuring the original affect. Moreover, meta-framed emotions become more intense and prolonged since our narratizing selves project them into the past or “futurize” them, turning them into never-dying ghosts with sentiments and old resentments that haunt our psychoscape. In order to look at affects from a clinical perspective, this chapter examines emotionally focused therapy (EFT), which aims to expand and reorganize emotional reactions; strengthen the bond between individuals; and encourage patients to reframe emotional assumptions and establish healthier interrelations.
Hypnosis and Meditation
Authors: McVeigh Brian J. 
Published: June 2022

AbstractTaken together, the various manifestations of mentality—conscious interiority, hypnosis, and meditation—are like a colorful tapestry with different patterns but woven together with the same threads. The challenge is disentangling the threads so as to understand the psychological processes behind these phenomena. This is the goal of this chapter. Understanding hypnosis and meditation improves one’s understanding of cognition and conscious interiority, as well as allowing the development of better therapeutic techniques. Importantly for any therapeutic implications, meditative practices provide an effective method of gaining control over automatic processes. This chapter adopts a Jaynesian perspective on hypnosis and views meditation as a type of meta-framing (regulating conscious interiority to promote insight): the collective cognitive imperative; suspending FOCI through induction; trancing as a diminution of FOCI. Suggestibility is conceptualized as a therapeutic communication granting and receiving authorization to change oneself.
Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast
Authors: LaPeruta Amber J , Micic Jelena , Woolford Jr. John L 
Published: June 2022

Abstract
During eukaryotic ribosome biogenesis, pre-ribosomes travel from the nucleolus, where assembly is initiated, to the nucleoplasm and then are exported to the cytoplasm, where assembly concludes. Although nuclear export of pre-ribosomes has been extensively investigated, the release of pre-ribosomes from the nucleolus is an understudied phenomenon. Initial data indicate that unfolded rRNA interacts in trans with nucleolar components and that, when rRNA folds due to ribosomal protein (RP) binding, the number of trans interactions drops below the threshold necessary for nucleolar retention. To validate and expand on this idea, we performed a bioinformatic analysis of the protein components of the Saccharomyces cerevisiae ribosome assembly pathway. We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs. We also analyzed cryo-EM structures of ribosome assembly intermediates to determine how nucleolar pre-ribosomes differ from post-nucleolar pre-ribosomes, specifically the capacity of RPs, RiBi factors, and rRNA components to interact in trans. We observed a significant decrease in the theoretical trans-interacting capability of pre-ribosomes between nucleolar and post-nucleolar stages of assembly due to the release of RiBi factors from particles and the folding of rRNA. Here, we provide a mechanism for the release of pre-ribosomes from the nucleolus.
Insights into the product release mechanism of dengue virus NS3 helicase
Authors: Adler Natalia S , Cababie Leila A , Sarto Carolina , Cavasotto Claudio N , Gebhard Leopoldo G , Estrin Darío A , Gamarnik Andrea V , Arrar Mehrnoosh , Kaufman Sergio B 
Published: June 2022

Abstract
The non-structural protein 3 helicase (NS3h) is a multifunctional protein that is critical in RNA replication and other stages in the flavivirus life cycle. NS3h uses energy from ATP hydrolysis to translocate along single stranded nucleic acid and to unwind double stranded RNA. Here we present a detailed mechanistic analysis of the product release stage in the catalytic cycle of the dengue virus (DENV) NS3h. This study is based on a combined experimental and computational approach of product-inhibition studies and free energy calculations. Our results support a model in which the catalytic cycle of ATP hydrolysis proceeds through an ordered sequential mechanism that includes a ternary complex intermediate (NS3h-Pi-ADP), which evolves releasing the first product, phosphate (Pi), and subsequently ADP. Our results indicate that in the product release stage of the DENV NS3h a novel open-loop conformation plays an important role that may be conserved in NS3 proteins of other flaviviruses as well.
AtNusG, a chloroplast nucleoid protein of bacterial origin linking chloroplast transcriptional and translational machineries, is required for proper chloroplast gene expression in Arabidopsis thaliana
Authors: Xiong Hai-Bo , Pan Hui-Min , Long Qiao-Ying , Wang Zi-Yuan , Qu Wan-Tong , Mei Tong , Zhang Nan , Xu Xiao-Feng , Yang Zhong-Nan , Yu Qing-Bo 
Published: June 2022

Abstract
In Escherichia coli, transcription-translation coupling is mediated by NusG. Although chloroplasts are descendants of endosymbiotic prokaryotes, the mechanism underlying this coupling in chloroplasts remains unclear. Here, we report transcription-translation coupling through AtNusG in chloroplasts. AtNusG is localized in chloroplast nucleoids and is closely associated with the chloroplast PEP complex by interacting with its essential component PAP9. It also comigrates with chloroplast ribosomes and interacts with their two components PRPS5 (uS5c) and PRPS10 (uS10c). These data suggest that the transcription and translation machineries are coupled in chloroplasts. In the atnusg mutant, the accumulation of chloroplast-encoded photosynthetic gene transcripts, such as psbA, psbB, psbC and psbD, was not obviously changed, but that of their proteins was clearly decreased. Chloroplast polysomic analysis indicated that the decrease in these proteins was due to the reduced efficiency of their translation in this mutant, leading to reduced photosynthetic efficiency and enhanced sensitivity to cold stress. These data indicate that AtNusG-mediated coupling between transcription and translation in chloroplasts ensures the rapid establishment of photosynthetic capacity for plant growth and the response to environmental changes. Therefore, our study reveals a conserved mechanism of transcription-translation coupling between chloroplasts and E. coli, which perhaps represents a regulatory mechanism of chloroplast gene expression. This study provides insights into the underlying mechanisms of chloroplast gene expression in higher plants.
TRIM25 inhibits influenza A virus infection, destabilizes viral mRNA, but is redundant for activating the RIG-I pathway
Authors: Choudhury Nila Roy , Trus Ivan , Heikel Gregory , Wolczyk Magdalena , Szymanski Jacek , Bolembach Agnieszka , Dos Santos Pinto Rute Maria , Smith Nikki , Trubitsyna Maryia , Gaunt Eleanor , Digard Paul , Michlewski Gracjan 
Published: June 2022

AbstractThe E3 ubiquitin ligase TRIM25 is a key factor in the innate immune response to RNA viruses. TRIM25 has been shown to play a role in the retinoic-acid-inducible gene-1 (RIG-I) pathway, which triggers expression of type 1 interferons upon viral infection. We and others have shown that TRIM25 is an RNA-binding protein; however, the role of TRIM25 RNA-binding in the innate immune response to RNA viruses is unclear. Here, we demonstrate that influenza A virus (IAV A/PR/8/34_NS1(R38A/K41A)) infection is inhibited by TRIM25. Surprisingly, previously identified RNA-binding deficient mutant TRIM25ΔRBD and E3 ubiquitin ligase mutant TRIM25ΔRING, which lack E3 ubiquitin ligase activity, still inhibited IAV replication. Furthermore, we show that in human-derived cultured cells, activation of the RIG-I/interferon type 1 pathway mediated by either an IAV-derived 5′-triphosphate RNA or by IAV itself does not require TRIM25 activity. Additionally, we present new evidence that instead of TRIM25 directly inhibiting IAV transcription it binds and destabilizes IAV mRNAs. Finally, we show that direct tethering of TRIM25 to RNA is sufficient to downregulate the targeted RNA. In summary, our results uncover a potential mechanism that TRIM25 uses to inhibit IAV infection and regulate RNA metabolism.
LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis
Authors: Yang Jen-Hao , Chang Ming-Wen , Tsitsipatis Dimitrios , Yang Xiaoling , Martindale Jennifer L , Munk Rachel , Cheng Aiwu , Izydore Elizabeth , Pandey Poonam R , Piao Yulan , Mazan-Mamczarz Krystyna , De Supriyo , Abdelmohsen Kotb , Gorospe Myriam 
Published: June 2022

Abstract
Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) modulate gene expression programs in physiology and disease. Here, we report a noncoding RNA regulatory network that modulates myoblast fusion into multinucleated myotubes, a process that occurs during muscle development and muscle regeneration after injury. In early stages of human myogenesis, the levels of lncRNA OIP5-AS1 increased, while the levels of miR-7 decreased. Moreover, OIP5-AS1 bound and induced miR-7 decay via target RNA-directed miRNA decay; accordingly, loss of OIP5-AS1 attenuated, while antagonizing miR-7 accelerated, myotube formation. We found that the OIP5-AS1-mediated miR-7 degradation promoted myoblast fusion, as it derepressed the miR-7 target MYMX mRNA, which encodes the fusogenic protein myomixer (MYMX). Remarkably, an oligonucleotide site blocker interfered with the OIP5-AS1-directed miR-7 degradation, allowing miR-7 to accumulate, lowering MYMX production and suppressing myotube formation. These results highlight a mechanism whereby lncRNA OIP5-AS1-mediated miR-7 decay promotes myotube formation by stimulating a myogenic fusion program.
Olivine in Kimberlites: Magma Evolution from Deep Mantle to Eruption
Authors: Abersteiner Adam , Kamenetsky Vadim S , Goemann Karsten , Golovin Alexander , Kamenetsky Maya 
Published: June 2022

Abstract
Elucidating the origin, composition and physical properties of primary kimberlite melts is crucial to our understanding of their source, petrogenesis, ascent mechanisms and ultimately the origin of diamonds. Recently, there has been a growing interest in the study of olivine, which is one of the most abundant minerals in kimberlites with xenocrystic, metamorphic (mantle) and magmatic origins. Olivine is one of the earliest minerals to crystallise in kimberlite magmas, and the presence of ubiquitous zoning (e.g. cores, internal zones, transitional zones, rims, rinds, outmost rinds) and different generations (i.e. primary, pseudosecondary and secondary) of crystal/melt/fluid inclusions in euhedral olivine grains has been shown to provide fundamental insights into the composition and evolution of kimberlite melts. In this contribution, we review and evaluate the following: (1) the widely accepted notion that kimberlite olivine has two distinct origins—xenocrystic and magmatic. We present detailed electron microprobeX-ray element maps of well-preserved and zoned euhedral olivine microcrysts from the Koala and Mark (Lac de Gras, Canada) and Udachnaya-East (Siberia, Russia) kimberlites to show that the cores of olivine occasionally adopt euhedral shapes, which is commonly defined by the distribution of Ni. We present a scenario in which mantle olivine was recrystallised by the early (or proto-) kimberlite melt/fluid infiltrating through the lithospheric mantle to form euhedral ‘pyrocrysts’ (i.e. olivine that formed via re-crystallisation in the mantle in the presence of a melt), which in turn become cores for the subsequent crystallisation of magmatic olivine during kimberlite magma ascent and emplacement. (2) The evolution of ideas using different geochemical, petrological, experimental and melt inclusion approaches to constrain the composition of the primary/parental kimberlite melt. Based on our assessment of available data, in particular using melt inclusions, we propose that kimberlites originated from melts that were initially Si-poor, and Na-K-F-Cl-P-S-bearing and Ca-Mg-carbonate-rich. With this model composition for the primary/parental kimberlite melt considered, we emphasise the implications for the evolution of olivine and its role in the kimberlite petrogenesis. Furthermore, we present a comprehensive model outlining the key stages involved in the petrogenesis of kimberlites, ranging from the generation of the proto kimberlite melt in the mantle, its interaction with mantle silicates during ascent, the role of liquid immiscibility in driving magma differentiation and CO2 degassing and its emplacement and modification in the crust. Finally, we discuss prospective directions that may further guide the future of kimberlite petrological research.
Phosphorylation-mediated inactivation of C3H14 by MPK4 enhances bacterial-triggered immunity in Arabidopsis
Authors: Wang Dian , Chai Guohua , Xu Li , Yang Kangkang , Zhuang Yamei , Yang Aiguo , Liu Shengyi , Kong Yingzhen , Zhou Gongke 
Published: June 2022

Abstract
Perception of pathogen-associated molecular patterns (PAMPs) triggers mitogen-activated protein (MAP) kinase 4 (MPK4)-mediated phosphorylation and induces downstream transcriptional reprogramming, but the mechanisms of the MPK4 defense pathway are poorly understood. Here, we showed that phosphorylation-mediated inactivation of the CCCH protein C3H14 by MPK4 positively regulates the immune response in Arabidopsis (Arabidopsis thaliana). Compared with wild-type plants, loss-of-function mutations in C3H14 and its paralog C3H15 resulted in enhanced defense against Pst DC3000 in infected leaves and the development of systemic acquired resistance (SAR), whereas C3H14 or C3H15 overexpression enhanced susceptibility to this pathogen and failed to induce SAR. The functions of C3H14 in PAMP-triggered immunity (PTI) and SAR were dependent on MPK4-mediated phosphorylation. Challenge with Pst DC3000 or the flagellin peptide flg22 enhanced the phosphorylation of C3H14 by MPK4 in the cytoplasm, relieving C3H14-inhibited expression of PTI-related genes and attenuating C3H14-activated expression of its targets NIM1-INTERACTING1 (NIMIN1) and NIMIN2, two negative regulators of SAR. Salicylic acid (SA) affected the MPK4–C3H14–NIMIN1/2 cascades in immunity, but SA signaling mediated by the C3H14-NIMIN1/2 cascades was independent of MPK4 phosphorylation. Our study suggests that C3H14 might be a negative component of the MPK4 defense signaling pathway.
Efficacy of Skin-to-Skin Care versus Swaddling for Pain Control Associated with Vitamin K Administration in Full-Term Neonates: A Randomized Controlled Trial
Authors: Patel Dipen V , Soni Sarthak N , Shukla Vivek V , Phatak Ajay G , Shinde Mayur K , Nimbalkar Archana S , Nimbalkar Somashekhar M 
Published: June 2022

ABSTRACT

Objective
The objective of the study was to assess the efficacy of immediate skin-to-skin care (SSC) versus swaddling in pain response to intramuscular injection of vitamin K at 30 min of birth in neonates.

Methods
Healthy full-term newborns were enrolled immediately after normal vaginal delivery and randomized in two groups, SSC and swaddling. Neonatal Infant Pain Scale (NIPS) was measured before, immediately after and at 2 min after the injection.

Results
Total 100 newborns were enrolled in the study (50 in each group). The mean (SD) birth weight of newborns in the SSC and swaddling group was 2668 (256) and 2730 (348) g, respectively. NIPS was comparable between the SSC and swaddling at before [1.78 (0.58) vs. 1.96 (0.83), p = 0.21], and immediately after the injection [4.82 (0.72) vs. 5.08 (0.75), p = 0.08]. NIPS at 2 min after the injection was significantly low in the SSC group compared to the swaddling group [1.38 (0.70) vs. 2.88 (1.00), p &lt; 0.001]. At 2 min after injection, the NIPS score was significantly lower than baseline in the SSC group (p = 0.002), while it was significantly higher in the swaddling group (p &lt; 0.001). A significantly higher proportion of newborns had a NIPS score of more than three at 2 min after injection in the swaddling group as compared to the SSC group (22% vs. 2%, p &lt; 0.001).

Conclusion
Immediate SSC was more efficacious as compared to swaddling as a pain control intervention while giving vitamin K injection.

Clinical Trial Registration
The trial is registered with the Clinical Trial Registry of India with Registration number: CTRI/2020/01/022984.
Pressure Injuries Due to Prone Positioning in Patients with COVID-19
Authors: Todd Betsy 
Published: June 2022

Preemptive interventions are needed to prevent pressure injuries in patients with COVID-19 who are placed in the prone position.Risk factors for pressure injuries in these patients include severe obesity, a long duration of prone positioning, male sex, a high D-dimer level, and the use of commercial endotracheal tube holders.
Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study
Authors: Tamarelle Jeanne , Shardell Michelle D. , Ravel Jacques , Brotman Rebecca M. 
Published: June 2022

Background
We sought to assess time-independent and time-varying factors associated with incidence and spontaneous clearance of molecular-bacterial vaginosis (BV; without treatment).

Methods
Midvaginal samples were self-collected daily by 100 participants recruited at the University of Alabama Birmingham for 10 weeks (4778 samples). Vaginal microbiota was characterized by 16S rRNA gene amplicon sequencing and clustered into community state types (CSTs). A low-Lactobacillus CST defined the molecular-BV outcome in this study. Factors associated with molecular-BV incidence and spontaneous clearance were modeled using Andersen-Gill recurrent event Cox models. Community class identified the predominant CST of a participant during follow-up.

Results
Menstruations (adjusted odds ratio [aHR], 2.09 [95% confidence interval, 1.51–2.89] in the prior 24 hours) and CST III (Lactobacillus iners dominated) at the previous sample (aHR, 2.25 [1.48–3.40]) were associated with increased molecular-BV incidence. Participants with a majority of L. iners–dominated samples longitudinally (community class LI) displayed less stable patterns of vaginal microbiota. In LI participants, reduced molecular-BV spontaneous clearance was observed in African American participants (aHR, 0.44 [0.26–0.75]) compared with White participants, older participants (age, 40–49 years [aHR, 0.38; 0.23–0.61]; age, 30–39 years [aHR, 0.48; 0.28–0.83]) compared with participants aged 18 to 29 years, and after douching (0.45 [0.28–0.73] within prior 72 hours).

Conclusions
Although it is now well documented that vaginal microbiota are dynamic, there are few available data on factors associated with spontaneous clearance of molecular-BV. Lactobacillus iners–dominated vaginal microbiota are more likely to be dynamic and associated with different risk factors for incidence and clearance of BV. Among L. iners–dominated participants, age, race, and douching were linked to reduced clearance. Most transitions to molecular-BV during menstruations were short-lived.
Prognostic Value of Optical Coherence Tomography Characteristics in Anterior Visual Pathway Meningiomas
Authors: Kapelushnik Noa , Dror Shai , Huna-Baron Ruth 
Published: June 2022

Background:
Anterior visual pathway meningiomas (AVPM) represent 2.5%–18% of all meningiomas. They may affect visual function, including visual acuity (VA) and visual field (VF). The principal modes of treatment are surgery and radiotherapy. The prognostic value of macular ganglion cell complex count (GCC) thickness has not been assessed in the literature thus far. The purpose of this study was to evaluate the prognostic value of pre-treatment optical coherence tomography (OCT) parameters (retinal nerve fiber layer and GCC) for visual outcomes in patients with AVPM.

Methods:
We retrospectively reviewed the medical records of all patients with AVPM who were treated in the Sheba Medical Center between 2011 and 2020. Included were patients with valid data containing preintervention OCT findings on the CIRRUS device and a minimum follow-up of 6 months. Preintervention and postintervention data on comprehensive ophthalmic examinations and OCT parameters of the affected eyes were retrieved. The correlation between preintervention OCT parameters and the visual outcome was assessed. The patients were also divided into 2 groups according to preintervention GCC (thin vs normal), and the visual outcome was compared between groups.

Results:
In total, 186 patients' medical records were analyzed, and 38 patients who met the inclusion criteria were included in the study (mean age at diagnosis 52.8 ± 12.2 years, 28 women). Twenty-nine patients had 1 affected eye, and 9 had bilateral insult. A higher preinterventional average GCC was associated with better VA at 6 months, 1 year, and 2 years after intervention (r = −0.5, P ≤ 0.004, 0.005, and 0.03, respectively). There was a significant correlation between preinterventional GCC and VF mean deviation 2 years after intervention (r = 0.7, P ≤ 0.001). The thinner the GCC, the more prominent was the change in VA from before intervention to 2 years after intervention (P ≤ 0.008). Correction for multiple comparisons with the Benjamini–Hochberg procedure did not change the significance of our findings.

Conclusions:
OCT parameters (GCC) have a predictive value in AVPM. There is strong correlation between preinterventional GCC and VA shortly after the intervention. Although a thin GCC is generally considered a negative prognostic factor, improvement in clinical parameters was also evident in patients with thin GCC. The potential of improvement despite preinterventional GCC thinning can add to the clinical discussion of the prognosis, and therefore, we recommend the patients with AVPM to undergo OCT and to be advised that GCC thinning alone should not be used as a major criterion in deciding whether treatment should be pursued.