bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal muscle thickness as an independent prognostic imaging marker in newly diagnosed glioblastoma patients: A validation study
Authors: Broen Martinus P G , Beckers Rueben , Willemsen Anna C H , Huijs Sandra M H , Pasmans Raphael C O S , Eekers Daniëlle B P , Ackermans Linda , Beckervordersandforth Jan , van Raak Elisabeth P M , Verduin Maikel , Anten Monique H M E , Hoeben Ann , Postma Alida A
Published: March 2022

Background

Previous studies have recognized temporal muscle thickness (TMT) as a prognostic marker in glioblastoma, but clinical implementation is hampered due to studies’ heterogeneity and lack of established cutoff values. The aim of this study was to assess the validity of recent proposed sex-specific TMT cutoff values in a real-world population of genotyped primary glioblastoma patients.

Methods

We measured TMT in preoperative MR images of 328 patients. Sex-specific TMT cutoff values were used to divide patients into “at risk of sarcopenia” or “normal muscle status”. Kaplan-Meier analyses and stepwise multivariate Cox-Regression analyses were used to assess the association with overall survival (OS) and progression-free survival (PFS). The association with occurrence of complications and discontinuation of glioblastoma treatment was investigated using odds ratios (OR).

Results

Patients at risk of sarcopenia had a significantly higher risk of progression and death than patients with normal muscle status, which remained significant in the multivariate analyses (OS HR = 1.437; 95%CI: 1.046–1.973; P = .025 and PFS HR = 1.453; 95%CI: 1.037–2.036; P = .030). Patients at risk of sarcopenia also had a significantly higher risk of early discontinuation of treatment (OR = 2.45; 95%CI: 1.011–5.952; P = .042) and a significantly lower chance of receiving second-line treatment (OR = 0.23; 95%CI: 0.09–0.60; P = .001). There was no association with the occurrence of complications.

Conclusions

Our study confirms external validity of the use of proposed sex-specific TMT cutoff values as an independent prognostic marker in newly diagnosed glioblastoma patients. This simple, noninvasive marker could improve patient counseling and aid in treatment decision processes or trial stratification.
Atypical Conjunctival Lesion as the Initial Presentation of Granulomatosis With Polyangiitis in an Adolescent Male
Authors: Sripawadkul Wathanee , Zein Mike , Galor Anat , Rivas-Chacon Rafael , Khzam Rayan Abou , Dubovy Sander R. , Karp Carol L.
Published: March 2022

Purpose:

The purpose of this study was to report the first case of a conjunctival granulomatous lesion as the presenting sign of granulomatous polyangiitis (GPA) in a pediatric patient.

Methods:

This study is a case report.

Results:

A 14-year-old Hispanic boy presented with a conjunctival lesion on the inferior bulbar conjunctiva of the right eye associated with diffuse conjunctival injection. The mass progressively grew and became painful over the course of 6 weeks. No retinal or orbital abnormalities were noted on examination. The lesion was excised, and histopathological analysis was consistent with granulomatous inflammation. The lesion recurred after 15 months, and a second excisional biopsy was performed. The lesion again slowly recurred, and on presentation to our clinic, an elevated lesion in the inferior limbal/bulbar conjunctiva of the right eye was noted from 4 to 8 o'clock with accompanying forniceal shortening. Five months after the second excision, the patient developed flu-like symptoms with polyarthralgia. A full diagnostic workup revealed multiple pulmonary nodules on chest imaging, proteinuria on urinalysis, and a positive c-antineutrophil cytoplasmic antibody on serological studies. Based on these findings, the patient underwent a kidney biopsy which showed pauci-immune crescentic glomerulonephritis, consistent with a diagnosis of GPA. The patient achieved disease remission with rituximab. Despite treatment, the conjunctival lesion did not regress and remained unchanged in size for 3 years with periodic episodes of inflammation.

Conclusions:

This is the first documented case of a conjunctival mass as the initial presenting feature of pediatric GPA. The presence of granulomatous inflammation on histopathology and recurrences after excision should raise suspicion for GPA in children and adults.
Guiding Fellows to Independent Practice
Authors: Kou Maybelle , Baghdassarian Aline , Khanna Kajal , Jamal Nazreen , Carney Michele , Fein Daniel M. , Kim In , Langhan Melissa L. , Rose Jerri A. , Zuckerbraun Noel S. , Roskind Cindy G. ,   On behalf of the AAP Section on Emergency Medicine Fellowship Program Director's Committee
Published: March 2022

Background

Recent studies highlight the importance of physician readiness to practice beyond graduate training. The Accreditation Council for Graduate Medical Education mandates that pediatric emergency medicine (PEM) fellows be prepared for independent practice by allowing “progressive responsibility for patient care.” Prior unpublished surveys of program directors (PDs) indicate variability in approaches to provide opportunities for more independent practice during fellowship training.

Objectives

The aims of the study were to describe practices within PEM fellowship programs allowing fellows to work without direct supervision and to identify any barriers to independent practice in training.

Design/Methods

An anonymous electronic survey of PEM fellowship PDs was performed. Survey items were developed using an iterative modified Delphi process and pilot tested. Close-ended survey responses and demographic variables were summarized with descriptive statistics. Responses to open-ended survey items were reviewed and categorized by theme.

Results

Seventy two of 84 PDs (88%) responded to the survey; however, not all surveys were completed. Of the 68 responses to whether fellows could work without direct supervision (as defined by the Accreditation Council for Graduate Medical Education) during some part of their training, 31 (45.6%) reported that fellows did have this opportunity. In most programs, clinical independence was conditional on specific measures including the number of clinical hours completed, milestone achievement, and approval by the clinical competency committee. Reported barriers to fellow practice without direct oversight included both regulatory and economic constraints.

Conclusions

Current training practices that provide PEM fellows with conditional clinical independence are variable. Future work should aim to determine best practices of entrustment, identify ideal transition points, and mitigate barriers to graduated responsibility.
Deimplementation of Polycythemia Screening in Asymptomatic Infants in a Level 1 Nursery
Authors: Johnson Scarlett C. , Bigus Elizabeth , Thompson Patricia L. , Bundy David G. , Amaya Michelle I.
Published: March 2022

Introduction:

Polycythemia (venous hematocrit >65%) is rare in healthy newborns (incidence: 0.4%–5%), with serious outcomes (stroke, bowel ischemia) of unknown incidence in asymptomatic infants. No national guidelines address screening or management of asymptomatic infants with polycythemia. Our nursery screened “high risk” (HR) newborns (small for gestational age, large for gestational age, twin, infant of diabetic mother) with poor adherence and low yield. We aimed to decrease polycythemia screening of asymptomatic HR infants by 80% within 6 months.

Methods:

We conducted an improvement project at a tertiary children’s hospital using the Model for Improvement. Eligible infants had an HR ICD-10 code on their problem list, were asymptomatic, over 35 weeks gestational age, and remained in the nursery for >6 hrs. Interventions included discontinuation of prior protocol, education for staff, bimonthly feedback on project performance, and visual reminders. Our primary outcome measure was the proportion of asymptomatic infants who received a hematocrit screen. Secondary measures were screening costs. Balancing measures were the length of stay, detected/symptomatic polycythemia, transfers to ICU/wards, and readmissions within 1 week of discharge.

Results:

The Nursery unit screened 80% of HR infants at baseline. This decreased to 7.3% after PDSA1, 0% after PDSA2, and 1% after PDSA3. There was no symptomatic polycythemia or statistically significant increase in readmissions/transfers. One month of monitoring revealed persistent changes.

Conclusion:

Simple quality improvement interventions such as education, reminders, and feedback can facilitate the deimplementation of low-value practices.
Effect of a Multispecialty Faculty Handoff Initiative on Safety Culture and Handoff Quality
Authors: Fitzgerald Katie M. , Banerjee Taruna R. , Starmer Amy J. , Caplan Gregory H. , Alkuwari Mohammed , Hillier Debra F. , Stack Anne M.
Published: March 2022

Introduction:

Structured handoffs at transitions of care are vital components of patient safety. A safety culture survey showed that “handoffs and transitions” were among the lowest scoring dimensions at our hospital. We sought to improve physician handoffs and safety culture scores by implementing standardized handoff communication across multiple divisions of an academic pediatric department.

Methods:

We used a modified learning collaborative model to implement an I-PASS program, including training, standardized verbal handoff processes, observation and feedback, and sustainment. The setting was the Department of Pediatrics (DoP) within a tertiary academic children’s hospital encompassing 13 clinical divisions. The primary outcome was a change in the DoP staff physician “handoffs and transitions” score on the Agency for Healthcare Quality (AHRQ) Hospital Survey on Patient Safety Culture. Process measures included handoff duration and proportion of handoffs using the complete I-PASS mnemonic.

Results:

Five hundred sixty-seven physicians from clinical divisions participated over 14 months. One hundred percent of eligible physicians completed an introductory online I-PASS training module. The “handoffs and transitions” score improved from 46% to 54% from 2018 to 2020. From May 2019 to February 2020, the proportion of observed handoffs with all five elements of the I-PASS mnemonic improved from 62% to 100%, and the duration of handoffs per patient did not change.

Conclusions:

We successfully implemented an I-PASS program across an academic department of pediatrics. The departmental staff physician safety culture “handoff and transitions” score improved. The adherence to the I-PASS mnemonic improved. The duration of handoffs did not change over the study period.
Engagement and Bundle Compliance during COVID-19: A Virtual Strategy
Authors: Reinhart Richelle M. , Fink Alia , Bhattarai Sopnil , Cheng Jenhao Jacob , Saha Anit , Worten Katherine , Cronin Jessica , Shah Rahul
Published: March 2022

Introduction:

COVID-19 forced industries to change work processes; this was no different for those working to improve patient outcomes in healthcare. Due to competing priorities, many hospitals struggled with the upkeep of hospital-acquired condition (HAC) auditing and engagement. Children’s National hospital developed a three-pronged approach for virtual engagement and sustainment of the processes necessary to achieve and maintain goal auditing and bundle compliance in three HACs: unplanned extubation, central line-associated bloodstream infections, and employee staff safety overexertion injuries.

Methods:

The overall goal was to create a flexible approach to maintaining engagement while relying on virtual communication.

Aim:

To maintain, without a decrease of more than 20%, the baseline bundle compliance per month for each HAC (unplanned extubation, central line-associated bloodstream infections, and employee staff safety) from March 2020 to March 2021. Our approach to increasing bundle compliance (primary outcome measure) and audits (process measure) included: regular leadership meetings using multiple virtual modalities, improving the audit process, and ensuring fidelity to bundle elements.

Results:

Qualitatively, we have found that microsystem leaders regularly engage with quality improvement staff and their teams using virtual touchpoints and ongoing communication. We exceeded the goal of maintaining our monthly bundle compliance, and we saw a significant positive change in the rate of audits after COVID-19.

Conclusions:

In a time of change during a pandemic, increased engagement in HAC work can adapt structure and processes. Our results are generalizable by increasing touchpoints using multiple virtual modalities.
Ectopic Gallbladder in the Left Upper Abdomen Shown on Hepatobiliary Scintigraphy
Authors: Bai Xia , Zhuang Hongming
Published: March 2022

The gallbladder is normally located in the right upper abdomen below the undersurface of the liver. We reported an ectopically located gallbladder, which was located in the left upper abdomen on hepatobiliary scintigraphy in an 18-year-old woman.
Heterogeneous Head and Neck Paraganglioma With Distinct Features on 123I-MIBG and 68Ga-DOTATATE Images
Authors: Lu Yang
Published: March 2022

A 37-year-old man has palpable bilateral carotid body paragangliomas, larger on the right. The right-sided tumor is avid on both 123I-MIBG and 68Ga-DOTATATE PET/CT images. The left-sided tumor is only avid on 68Ga-DOTATATE PET/CT, but not 123I-MIBG scan. This case illustrates the heterogeneous features of carotid body paragangliomas.
Hormone analysis and candidate genes identification associated with seed size in
Camellia oleifera
Authors: Ji Ke , Song Qiling , Yu Xinran , Tan Chuanbo , Wang Linkai , Chen Le , Xiang Xiaofeng , Gong Wenfang , Yuan Deyi
Published: March 2022

Camellia oleifera
is an important woody oil species in China. Its seed oil has been widely used as a cooking oil. Seed size is a crucial factor influencing the yield of seed oil. In this study, the horizontal diameter, vertical diameter and volume of
C. oleifera
seeds showed a rapid growth tendency from 235 days after pollination (DAP) to 258 DAP but had a slight increase at seed maturity. During seed development, the expression of genes related to cell proliferation and expansion differ greatly. Auxin plays an important role in
C. oleifera
seeds;
YUC4
and
IAA17
were significantly downregulated. Weighted gene co-expression network analysis screened 21 hub transcription factors for
C. oleifera
seed horizontal diameter, vertical diameter and volume. Among them,
SPL4
was significantly decreased and associated with all these three traits, while
ABI4
and
YAB1
were significantly increased and associated with horizontal diameter of
C. oleifera
seeds. Additionally,
KLU
significantly decreased (2040-fold). Collectively, our data advances the knowledge of factors related to seed size and provides a theoretical basis for improving the yield of
C. oleifera
seeds.
Effects of poly(vinyl alcohol) blending with Ag/alginate solutions to form nanocomposite fibres for potential use as antibacterial wound dressings
Authors: Vidovic Srdjan , Stojkovska Jasmina , Stevanovic Milan , Balanc Bojana , Vukasinovic-Sekulic Maja , Marinkovic Aleksandar , Obradovic Bojana
Published: March 2022

In this work, nanocomposite fibres and microfibres based on alginate and poly(vinyl alcohol) (PVA) with silver nanoparticles (AgNPs) were produced and characterized for potential application as antibacterial wound dressings. PVA/Ag/Na-alginate colloid solution was used for the preparation of the fibres by a simple extrusion technique followed by freezing–thawing cycles. UV–Visible spectroscopy confirmed successful preservation of AgNPs in fibres while Fourier transform infrared spectroscopy has shown a balanced combined effect on the Ca-alginate spatial arrangement with the addition of both AgNPs and PVA. The presence of PVA in fibres induced an increase in the swelling degree as compared with that of Ag/Ca-alginate fibres (approx. 28 versus approx. 14). Still, the initially produced PVA/Ca-alginate fibres were mechanically weaker than Ca-alginate fibres, but after drying and rehydration exhibited better mechanical properties. Also, the obtained fibres released AgNPs and/or silver ions at the concentration of approximately 2.6 µg cm
−3
leading to bacteriostatic effects against
Staphylococcus aureus
and
Escherichia coli
. These results are relevant for practical utilization of the fibres, which could be stored and applied in the dry form with preserved mechanical stability, sorption capacity and antibacterial activity.
Demographic variation in space and time: implications for conservation targeting
Authors: Morrison Catriona A. , Butler Simon J. , Clark Jacquie A. , Arizaga Juan , Baltà Oriol , Cepák Jaroslav , Nebot Arantza Leal , Piha Markus , Thorup Kasper , Wenninger Thomas , Robinson Robert A. , Gill Jennifer A.
Published: March 2022

The dynamics of wild populations are governed by demographic rates which vary spatially and/or temporally in response to environmental conditions. Conservation actions for widespread but declining populations could potentially exploit this variation to target locations (or years) in which rates are low, but only if consistent spatial or temporal variation in demographic rates occurs. Using long-term demographic data for wild birds across Europe, we show that productivity tends to vary between sites (consistently across years), while survival rates tend to vary between years (consistently across sites), and that spatial synchrony is more common in survival than productivity. Identifying the conditions associated with low demographic rates could therefore facilitate spatially targeted actions to improve productivity or (less feasibly) forecasting and temporally targeting actions to boost survival. Decomposing spatio-temporal variation in demography can thus be a powerful tool for informing conservation policy and for revealing appropriate scales for actions to influence demographic rates.
Fast model-free standardization and integration of single-cell transcriptomics data
Authors: Xu Yang , Kramann Rafael , McCord Rachel Patton , Hayat Sikander
Published: March 2022

Single-cell transcriptomics datasets from the same anatomical sites generated by different research labs are becoming mainstream. However, fast, and computationally inexpensive tools for standardization of cell-type annotation and data integration are still needed to increase research inclusivity. To standardize cell-type annotation and integrate single-cell transcriptomics datasets, we have built a fast, model-free integration method called MASI (Marker-Assisted Standardization and Integration). MASI can run integrative annotation on a personal laptop for approximately one million cells, providing a cheap computational alternative for the single-cell data analysis community. MASI has an average macro F1/overall accuracy of 0.79/0.89 over the 4 benchmark datasets. We demonstrate that MASI outperforms other methods based on speed, and its performance for the tasks of data integration and cell-type annotation is comparable or even superior to other existing methods. We apply MASI for integrative lineage analysis and show that it preserves the underlying biological signal in datasets tested. Finally, to harness knowledge from single-cell atlases, we demonstrate three case studies that cover integration across research groups, biological conditions, and surveyed participants, respectively.
Profiling the proximal proteome of the mu opioid receptor identifies novel regulators of receptor signaling and trafficking
Authors: Polacco Benjamin J. , Lobingier Braden T. , Blythe Emily E. , Abreu Nohely , Khare Prachi , Howard Matthew K. , Gonzalez-Hernandez Alberto J. , Xu Jiewei , Li Qiongyu , Novy Brandon , Chi Naing Zun Zar , Shoichet Brian K. , Coyote-Maestas Willow , Levitz Joshua , Krogan Nevan J. , Zastrow Mark Von , Hüttenhain Ruth
Published: March 2022

The mu opioid receptor (μOR), a prototypic member of the large G protein-coupled receptor (GPCR) family, represents an important target of therapeutic and abused drugs. To date, most of our understanding of μOR activity has focused on signal transducers and regulatory molecules including G proteins, GPCR kinases, and beta-arrestins. Yet it is clear that signaling through the μOR is coordinated by additional proteins recruited into the proximal interaction network of the activated receptor, which have largely remained invisible given the lack of technologies to interrogate these networks systematically.

Here, we implement a quantitative proteomics pipeline leveraging the chemical diversity of μOR agonists and APEX-based proximity labeling to investigate the protein networks that underlie μOR signaling. We leverage a novel computational framework to extract subcellular location, trafficking, and functional partners of GPCR activity from the proximity labeling datasets. Applying this unbiased, systematic approach to the μOR, we demonstrate that opioid agonists exert differences in the μOR proximal proteome mediated by endocytosis and subsequent endosomal sorting, exemplified by VPS35 and COMMD3. Moreover, we identify two novel μOR network components, EYA4 and KCTD12, that are recruited into the receptor proximal network irrespective of the activating ligand and independent of receptor trafficking but based on receptor-triggered G protein activation. We provide functional evidence that these network components form a previously unrecognized buffering system for G protein activity which broadly modulates cellular GPCR signaling.
Reference-based cell type matching of spatial transcriptomics data
Authors: Zhang Yun , Miller Jeremy A. , Park Jeongbin , Lelieveldt Boudewijn P. , Long Brian , Abdelaal Tamim , Aevermann Brian D. , Biancalani Tommaso , Comiter Charles , Dzyubachyk Oleh , Eggermont Jeroen , Langseth Christoffer Mattsson , Petukhov Viktor , Scalia Gabriele , Vaishnav Eeshit Dhaval , Zhao Yilin , Lein Ed S. , Scheuermann Richard H.
Published: March 2022

With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly. Spatial transcriptomics provides spatial location and pattern information about cells in tissue sections at single cell resolution. Cell type classification of spatially-resolved cells can also be inferred by matching the spatial transcriptomics data to reference single cell RNA-sequencing (scRNA-seq) data with cell types determined by their gene expression profiles. However, robust cell type matching of the spatial cells is challenging due to the intrinsic differences in resolution between the spatial and scRNA-seq data. In this study, we systematically evaluated six computational algorithms for cell type matching across four spatial transcriptomics experimental protocols (MERFISH, smFISH, BaristaSeq, and ExSeq) conducted on the same mouse primary visual cortex (VISp) brain region. We find that while matching results of individual algorithms vary to some degree, they also show agreement to some extent. We present two ensembl meta-analysis strategies to combine the individual matching results and share the consensus matching results in the Cytosplore Viewer (https://viewer.cytosplore.org) for interactive visualization and data exploration. The consensus matching can also guide spot-based spatial data analysis using SSAM, allowing segmentation-free cell type assignment.
A DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci
Authors: Doi Akiko , Suarez Gianmarco D. , Droste Rita , Horvitz H. Robert
Published: March 2022

How cells regulate gene expression in a precise spatiotemporal manner during organismal development is a fundamental question in biology. Recent studies have demonstrated the role of transcriptional condensates in gene regulation1–5. However, little is known about the function and regulation of these transcriptional condensates in the context of animal development and physiology. We found that the evolutionarily conserved DEAD-box helicase DDX-23 controls stem cell fate in C. elegans at least in part by binding to and facilitating the condensation of MAB-10, the C. elegans homolog of mammalian NAB protein. MAB-10 is a transcriptional cofactor that functions with the EGR protein LIN-29 to regulate the transcription of genes required for exiting the cell cycle, terminal differentiation, and the larval-to-adult transition6. We suggest that DEAD-box helicase proteins function more generally during animal development to control the condensation of NAB proteins important in cell-fate decisions and that this mechanism is evolutionarily conserved. In mammals, a comparable mechanism might underlie terminal cell differentiation and when misregulated might promote cancerous growth.
Application of B cell immortalization for the isolation of antibodies and B cell clones from vaccine and infection settings
Authors: Boswell Kristin L. , Watkins Timothy , Cale Evan M. , Samsel Jakob , Andrews Sarah F. , Ambrozak David R. , Driscoll Jefferson I. , Messina Michael A. , Narpala Sandeep , Hopp Christine S. , Cagigi Alberto , Casazza Joseph P. , Yamamoto Takuya , Zhou Tongqing , Schief William R. , Crompton Peter D. , Ledgerwood Julie E. , Connors Mark , Gama Lucio , Kwong Peter D. , McDermott Adrian , Mascola John R. , Koup Richard A.
Published: March 2022

The isolation and characterization of neutralizing antibodies from infection and vaccine settings will inform future vaccine design, and methodologies that streamline the isolation of antibodies and the generation of B cell clones are of great interest. Retroviral transduction to express Bcl-6 and Bcl-xL in primary B cells has been shown to promote long-term B cell survival and antibody secretion in vitro, and can be used to isolate antibodies from memory B cells. The application of this methodology to B cell subsets from tissues and to B cells from individuals with chronic infection has not been extensively characterized. Here, we characterize Bcl-6/Bcl-xL B cell immortalization across multiple tissue types and B cell subsets in healthy and HIV-1 infected individuals, as well as individuals recovering from malaria. In HIV-1- and malaria-uninfected donors, naïve and memory B cell subsets from PBMC and tonsil tissue transformed with similar efficiencies, and displayed similar characteristics after transformation with respect to their longevity and immunoglobulin secretion. In HIV-1-viremic individuals or in individuals after malaria infection, the CD27-CD21- memory B cell subsets transformed with lower efficiencies compared to the CD27+CD21+ populations, but following transformation B cells expanded and secreted IgG with similar efficiency. Using B cells from HIV-1-infected individuals, we combined Bcl-6/Bcl-xL B cell immortalization with a HIV-1 microneutralization assay to isolate broadly neutralizing antibodies related to VRC13 and VRC38.01. Overall, Bcl-6/Bcl-xL B cell immortalization can be used to isolate antibodies and generate B cell clones from multiple different B cell populations, albeit with different efficiencies.
The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer’s fields in western Burkina Faso
Authors: Barro Mariam , Wonni Issa , Simonin Marie , Kassankogno Abalo Itolou , Klonowska Agnieszka , Moulin Lionel , Béna Gilles , Somda Irénée , Brunel Caroline , Tollenaere Charlotte
Published: March 2022

As a consequence of its potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer’s fields from irrigated and rainfed lowlands in western Burkina Faso, using an amplicon metabarcoding approach 16S (Prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure according to the root compartment (root vs. rhizosphere) and geographical zones, we show that the rice production system is a major driver of microbiome structure, both for prokaryotes and fungi. In irrigated systems, we found a higher diversity of prokaryotic communities from rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands. Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae and Bradyrhizobiaceae families in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, phylotypes assigned to putative phytobeneficial and pathogen species were found. Mycorrhizal fungi Glomeromycetes abundance was higher in rainfed lowlands. Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for potential microbial engineering applications.
Toward a first principles understanding of the activation and deactivation mechanisms of class A G-protein coupled receptors and voltage-gated cation channels
Authors: Wan Hongbin , Pearlstein Robert A.
Published: March 2022

We previously reported a first principles multi-scale theory called Biodynamics that attributes cellular functions to sets of coupled molecular and ionic fluxes operating in the non-equilibrium/non-linear dynamic regime. Fluxes build and decay over time and undergo dynamic non-covalent intra- and intermolecular state transitions powered principally by the storage and release of free energy to/from the H-bond networks of external and internal solvation (that we refer to as solvation dynamics) at rates governed by the desolvation and resolvation costs incurred during their entry and exit, respectively. We have thus far examined the functional state transitions of cereblon and COVID Mproin this context, and now turn to the agonist-induced activating and deactivating state transitions of class A G-protein coupled receptors (GPCRs) and membrane potential-/dipole potential-induced activating and deactivating state transitions of voltage-gated cation channels (VGCCs). We analyzed crystal structures of the activated and deactivated forms of the human β2-adrenergic receptor (β2-AR) and cryo-EM structures of the activated and deactivated forms of Nav1.7 channels. We postulate that activation and deactivation of the β2-AR is conveyed by switchable changes in transmembrane helix (TMH) orientations relative to extracellular loop 2 (ECL2) and curvature of TMH6 and TMH7, all of which are powered by solvation free energy and kickstarted by agonist binding. The known activation and deactivation mechanisms of Nav1.7 consist of S4 translations toward and away from the extracellular membrane surface, respectively, resulting in S4-S5 linker repositioning, followed by rearrangements of the S5 and S6 helices. The latter TMH conveys channel opening and closing by respectively curving away from and toward the central pore axis. We postulate that all of these rearrangements are likewise powered by solvation free energy and kickstarted by changes in the membrane and dipole potentials. The results of our study may facilitate structure-based design of GPCR agonists/antagonists and mitigation of drug-induced ion channel blockade.
Automated identification and registration of anatomical landmarks inC. elegans
Authors: Laird Nicolette M. , Pincus Zachary
Published: March 2022

The physiology of the nematodeC. eleganscan be visualized with many microscopy techniques. However, quantitative microscopy ofC. elegansis complicated by the flexible and deformable nature of the nematode. These differences in posture and shape must be addressed in some fashion in any automated or manual analysis. Manual approaches are time intensive and require hand-labeling anatomical regions of interest. Automated tools exist, but generally rely on high-magnification imaging using labeled nuclei as fiducial markers. Here we describe a suite of new tools that allows for high-throughput analysis of whole-body images, aligned using anatomical landmarks identified from brightfield images. We show how these tools can be used in basic morphometric tasks and examine anatomical variation and morphological changes in a population over time.
Induction of Bacteriophage PinR Facilitates the Evolution of Antibiotic Resistance
Authors: Zhang Le , Guan Yunpeng , Su Qian Peter , Liao Yan , Duggin Iain , Jin Dayong
Published: March 2022

A recent work reports that the single treatment of β-lactams can cause a SOS-independent superfast evolution of multi-drug resistance in the DNA repair deficiency Escherichia coli (E. coli), but the mechanism is not yet clear. Here, we find that the induction of PinR, a lambdoid prophage Rac, is involved in this process and facilitates the evolution of antibiotic resistance in DNA repair deficiency bacteria through the repression on the transcription of antioxidative genes and the thereafter ROS burst in cells. It is highlighted that the bacteriophage PinR can orchestrate the mutagenesis induced by the overaccumulation of ROS in cells. More importantly, we for the first time demonstrate that the deletion of pinR can avoid the rapid evolution of antibiotic resistance induced by either the single or long-term exposure to antibiotics, while strategies to target RecA, e.g., the inactivation on RecA, can be safely implemented to disarm the bacterial resistance to other antibiotics. Therefore, from a drug development perspective, our work suggests future studies on the “evolutionary potentiators” towards a safe and more effective strategy to be developed for infectious disease treatment.
THRONCAT: Efficient metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog
Authors: Ignacio Bob J. , Dijkstra Jelmer , Garcia Natalia Mora , Slot Erik F.J. , van Weijsten Margot J. , Storkebaum Erik , Vermeulen Michiel , Bonger Kimberly M.
Published: March 2022

Profiling the nascent cellular proteome and capturing early proteomic changes in response to external stimuli provides valuable insight into cellular physiology. Existing metabolic protein labeling approaches based on bioorthogonal methionine-or puromycin analogs allow for the selective visualization and enrichment of the newly synthesized proteins. However, their applications are limited as they require methionine-free conditions, auxotrophic cells and/or are toxic to cells. Here, we introduce THRONCAT, a novel threonine-derived non-canonical amino acid tagging method based on bioorthogonal threonine analog β-ethynylserine (βES) that enables efficient and non-toxic labeling of the nascent proteome in complete growth media within minutes. We used THRONCAT for the visualization and enrichment of nascent proteins in bacteria, mammalian cells and Drosophila melanogaster. We profiled immediate proteome dynamics of Ramos B-cells in response to receptor activation, demonstrating the ease-of-use of the method and its potential to address diverse biological questions. In addition, using a Drosophila model of Charcot-Marie-Tooth peripheral neuropathy, we show that THRONCAT enables visualization and quantification of relative protein synthesis rates in vivo.
A machine learning method for estimating the probability of presence using presence-background data
Authors: Wang Yan , Samarasekara Chathuri L. , Stone Lewi
Published: March 2022

Estimating the prevalence or the absolute probability of presence of a species from presence-background data has become a controversial topic in species distribution modelling. In this paper we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with unfounded model assumptions would render fragile estimation/prediction of the desired probabilities. Rather we propose the local knowledge condition, which relaxes the pre-determined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the CLK method utilising the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence without absence data in species distribution modelling.
Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly towards kinetically-trapped morphologies
Authors: Pak Alexander J. , Gupta Manish , Yeager Mark , Voth Gregory A.
Published: March 2022

During the late stages of the HIV-1 lifecycle, immature virions are produced by the concerted activity of Gag polyproteins, primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains, which assemble into a spherical lattice, package viral genomic RNA, and deform the plasma membrane. Recently, inositol hexakisphosphate (IP6) has been identified as an essential assembly cofactor that efficiently produces both immature virions in vivo and immature virus-like particles in vitro. To date, however, several distinct mechanistic roles for IP6 have been proposed on the basis of independent functional, structural, and kinetic studies. In this work, we investigate the molecular influence of IP6 on the structural outcomes and dynamics of CA/SP1 assembly using coarse-grained (CG) molecular dynamics (MD) simulations and free energy calculations. Here, we derive a bottom-up, low-resolution, and implicit-solvent CG model of CA/SP1 and IP6, and simulate their assembly under conditions that emulate both in vitro and in vivo systems. Our analysis identifies IP6 as an assembly accelerant that promotes curvature generation and fissure-like defects throughout the lattice. Our findings suggest that IP6 induces kinetically-trapped immature morphologies, which may be physiologically important for later stages of viral morphogenesis and potentially useful for virus-like particle technologies.
Optimal inference of molecular interactions in live FRET imaging
Authors: Kamino Keita , Kadakia Nirag , Aoki Kazuhiro , Shimizu Thomas S. , Emonet Thierry
Published: March 2022

Intensity-based live-cell fluorescence resonance energy transfer (FRET) imaging converts otherwise unobservable molecular interactions inside cells into fluorescence time-series signals. However, inferring the degree of molecular interactions from these observables is challenging, due to experimental complications such as spectral crosstalk, photobleaching, and measurement noise. Conventional methods solve this inverse problem through algebraic manipulations of the observables, but such manipulations inevitably accumulate measurement noise, limiting the scope of FRET analysis. Here, we introduce a Bayesian inference framework, B-FRET, which estimates molecular interactions from FRET data in a statistically optimal manner. B-FRET requires no additional measurements beyond those routinely conducted in standard 3-cube FRET imaging methods, and yet, by using the information contained in the data more efficiently, dramatically improves the signal-to-noise ratio (SNR). We validate B-FRET using simulated data, and then apply it to FRET data measured from single bacterial cells, a system with notoriously low SNR, to reveal signaling dynamics that are otherwise hidden in noise.
Predicting Protein Function and Orientation on a Gold Nanoparticle Surface Using a Residue-Based Affinity Scale
Authors: Xu Joanna Xiuzhu , Alom Md Siddik , Yadav Rahul , Fitzkee Nicholas C.
Published: March 2022

The orientation adopted by proteins on nanoparticle surfaces determines the nanoparticle’s bioactivity and its interactions with living systems. Here, we present a residue-based affinity scale for predicting protein orientation on citrate-gold nanoparticles (AuNPs). Competitive binding between protein variants accounts for thermodynamic and kinetic aspects of adsorption in this scale. For hydrophobic residues, the steric considerations dominate, whereas electrostatic interactions are critical for hydrophilic residues. The scale rationalizes the well-defined binding orientation of the small GB3 protein, and it subsequently predicts the orientation and active site accessibility of two enzymes on AuNPs. Additionally, our approach accounts for the AuNP-bound activity of five out of six additional enzymes from the literature. The model developed here enables high-throughput predictions of protein behavior on nanoparticles, and it enhances our understanding of protein orientation in the biomolecular corona, which should greatly enhance the performance and safety of nanomedicines used in vivo.
scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq
Authors: Valdez Giovanni Quinones , Fu Ting , Chan Tracey , Xiao Xinshu (Grace)
Published: March 2022

Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq data set, scAllele identified variants with strong allelic linkage to alternative splicing, some of which being cancer-specific. scAllele represents a versatile tool to uncover multi-layer information and novel biological insights from scRNA-seq data.
More than names on a roster: the many meanings behind Sgaw Karen names
Authors: Gilhooly Daniel , Htoo Chris Mu
Published: March 2022

Purpose

The purpose of this paper is to demonstrate how teachers can use their Sgaw Karen students’ names as a means to gaining awareness of their students’ home culture, language and personal stories.

Design/methodology/approach

This case study uses interviews with four Karen families to explore the meanings behind the names and nicknames given to Karen individuals.

Findings

The findings of this study reveal that Karen names can provide teachers important insights into Karen culture, history and language. Moreover, Karen names can also provide important biographical information about the student.

Research limitations/implications

This study only focuses on Sgaw Karen names and does not include other Karen subgroups like the Pwo Karen, who are also resettling in the USA. This study does not include all Sgaw Karen names, but the authors have made efforts to include Karen names from various regions of Burma and of different religious backgrounds.

Practical implications

Teachers and others working with culturally and linguistically diverse students like the Karen will gain a better understanding of the various ways that names are given across cultures. While this paper focuses on one particular ethnic group, it is believed that teachers need to expand their notions about how other non-European groups name their children and how these names may reveal something about the student’s heritage culture, history, language and the unique lived experiences of their students.

Social implications

Too often teachers and others working cross-culturally do not realize that other cultures follow different naming practices than those used in the USA. Teachers often mispronounce or misunderstand students’ names when the student comes from a cultural group unfamiliar to them. This paper helps a general audience better realize the unique approach Karen culture takes to naming children and how these names are often transformed to fit American naming conventions. As the title suggests, Karen students often feel embarrassed and take on a negative opinion of their given name as a result of a lack of awareness by teachers and others.

Originality/value

This paper provides a unique perspective in the literature on the ways cultural naming conventions can serve teachers aspiring to incorporate biography-driven instruction into their classroom practices.
Study on the dyeing process of fast-growing fir veneer with reactive dyes
Authors: Guan Xuemei , Li Wenfeng , Huang Jingyi
Published: March 2022

Purpose

The purpose of this paper is to improve the dyeing effect of fast-growing fir wood dyed with reactive dyes.

Design/methodology/approach

In this study, five factors including temperature, the dosage of dye accelerator, dyeing time, the dosage of fixing agent and fixing time were investigated. Then, the color difference and light resistance of the wood surface after dyeing were used as the evaluation indicators; the best dyeing process under the two indicators was obtained through the range analysis. Finally, the two indicators were considered comprehensively, and the fuzzy comprehensive evaluation method was used to obtain the best dyeing process under the comprehensive indicators.

Findings

The results show that when the comprehensive index was used as the evaluation index, the optimal dyeing process for reactive red X-3B dyeing fast-growing fir veneer was that the dyeing temperature was 65°C; the amount of dye accelerator was 25 g L−1; the dyeing time was 2 h; the amount of fixing agent was 15 g L−1; and the fixing time was 35 min.

Originality/value

The technique of wood dyeing is an important method to increase the value of wood products. When using different kinds of dyes or dyeing substrates for wood dyeing, the dyeing process is different. This study determined the best process for reactive dye dyeing of fast-growing fir veneer and provided a solution for improving the value of fast-growing fir wood.
Discovery of 3‐(2‐aminoethyl)‐thiazolidine‐2,4‐diones as a novel chemotype of sigma‐1 receptor ligands
Authors: Elkholy Nada , Abdelwaly Ahmad , Mohamed Karim , Amata Emanuele , Lombino Jessica , Cosentino Giuseppe , Intagliata Sebastiano , Helal Mohamed A.
Published: March 2022

Sigma receptor is a transmembrane non‐GPCR protein expressed mainly in the endoplasmic reticulum membrane associated with mitochondria. It is classified into two types: Sigma‐1 (S1R) and Sigma‐2 (S2R) based on their biological functions. S1R has been implicated in many neurological disorders such as anxiety, schizophrenia, and depression. Therefore, S1R ligands possess a variety of potential clinical applications with a great interest in the treatment of neuropathic pain. In this study, we report the discovery of a novel lead compound for S1R binding, based on the thiazolidine‐2,4‐dione nucleus. We have explored hydrophobic groups of different sizes on both sides of the five‐membered ring scaffold guided by the crystal structure of S1R. Six compounds showed more than 50% displacement of the radioligand at 10 µM concentration with compound 6c resulting in 100% displacement and a Ki of 95.5 nM. Moreover, compounds 6c and 6e showed a significant selectivity over S2R. In addition, molecular docking predicted that all the compounds showed the critical salt bridge with Glu172 with variable degrees of π‐stacking interaction with Tyr103. Upon optimization, this series of compounds could represent potential clinically useful S1R ligands for pain management.