bluuebunny/crossref_metadata_2025_split huggingface dataset:
Current evidence for suction in endourological procedures: comprehensive review of literature
Authors: Quhal Fahad , Zeng Guohua , Seitz Christian 
Published: November 2022

Purpose of review
To identify the latest advances on the utilization of suctioning devices in the surgical treatment of urinary stones.

Recent findings
Advances are being made to incorporate suction and pressure control capabilities in percutaneous and ureteroscopic lithotripsy. Multiple retrospective studies and few prospective studies have shown that suctioning with minimally invasive percutaneous nephrolithotomy, commonly referred to as Super MiniPerc, can lead to better stone-free rates (SFR) and shorter operative time with lower incidence of infectious complications. Suctioning during retrograde intrarenal surgery (RIRS) has mainly been achieved through suctioning ureteral access sheath. Here as well, the incorporation of suction improved the SFR, but most importantly, reduced the risk of postoperative infectious complications.

Summary
Theoretically suction in endourological procedures could facilitate stone debris removal and could reduce intrarenal pressure at the same time allowing for increased irrigation flow potentially decreasing operation time and infectious complications. These claims are supported in contemporary clinical studies, reporting superior SFR and reduced postoperative infectious complications in both percutaneous nephrolithotomy and RIRS.
68Ga-FAPI and 18F-FDG PET/CT Images of a Patient With Rosai-Dorfman Disease With Liver Involvement
Authors: Chen Zhenying , Xue Qianqian , Yang Yun , Shun Hu , Miao Weibing 
Published: November 2022

Abstract
Rosai-Dorfman disease is a rare non-Langerhans cell histiocytosis that is histopathologically characterized by the accumulation of CD68-positive and S100-positive histiocytes. The pathological changes are mostly discovered in lymph nodes. We report a case of Rosai-Dorfman disease with liver and bone marrow involvement. In this case, 18F-FDG PET/CT revealed FDG avidity in multiple lymph nodes, liver, and bone marrow. 68Ga-FAPI PET/CT showed higher uptake of 68Ga-FAPI than that of 18F-FDG in the same lesions. The findings of 68Ga-FAPI PET/CT in this patient highlighted the potential value of 68Ga-FAPI for staging in Rosai-Dorfman disease.
FDG PET/CT Aiding in Early Diagnosis of Central Pontine Myelinolysis
Authors: Dhull Varun Singh , Shinde Suraj , Sane Nikhil , Bhavsar Sandeep Avinash , Chowhan Manoranjan 
Published: November 2022

Abstract
We report a 70-year-old man with central pontine myelinolysis who presented in the emergency department with recent onset altered sensorium and tremors (Glasgow Coma Scale score, 13). Laboratory findings revealed hyponatremia and hypokalemia. MRI brain was unremarkable. Subsequently, patient was referred for FDG PET/CT to rule out malignancy or paraneoplastic syndrome. FDG PET revealed focal radiotracer uptake in the pons without any underlying CT abnormality consistent with central pontine myelinolysis, thus aiding in early diagnosis where conventional imaging modality was unremarkable.
Fast-forward scaling theory
Authors: Masuda S. , Nakamura K. 
Published: November 2022

Speed is the key to further advances in technology. For example, quantum technologies, such as quantum computing, require fast manipulations of quantum systems in order to overcome the effect of decoherence. However, controlling the speed of quantum dynamics is often very difficult due to both the lack of a simple scaling property in the dynamics and the infinitely large parameter space to be explored. Therefore, protocols for speed control based on understanding of the dynamical properties of the system, such as non-trivial scaling property, are highly desirable. Fast-forward scaling theory (FFST) was originally developed to provide a way to accelerate, decelerate, stop and reverse the dynamics of quantum systems. FFST has been extended in order to accelerate quantum and classical adiabatic dynamics of various systems including cold atoms, internal state of molecules, spins and solid-state artificial atoms. This paper describes the basic concept of FFST and reviews the recent developments and its applications such as fast state-preparations, state protection and ion sorting. We introduce a method, called inter-trajectory travel, recently derived from FFST. We also point out the significance of deceleration in quantum technology.
This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
Effective non-adiabatic holonomic quantum computation of cavity modes via invariant-based reverse engineering
Authors: Kang Yi-Hao , Shi Zhi-Cheng , Song Jie , Xia Yan 
Published: November 2022

In this paper, we propose a protocol to realize non-adiabatic holonomic quantum computation (NHQC) of cavity modes via invariant-based reverse engineering. Coupling cavity modes with an auxiliary atom trapped in a cavity, we derive effective Hamiltonians with the help of laser pulses. Based on the derived Hamiltonians, invariant-based reverse engineering is used to find proper evolution paths for NHQC. Moreover, the systematic-error-sensitivity nullified optimal control method is considered in the parameter selections, making the protocol insensitive to the influence of systematic errors of pulses. We also estimate the imperfections induced by random noise and decoherence. Numerical results show that the protocol holds robustness against these imperfections. Therefore, the protocol may provide useful perspectives to quantum computation with optical qubits in cavity quantum electrodynamics systems.
This article is part of the theme issue ‘Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives’.
HssS activation by membrane heme defines a paradigm for 2-component system signaling inStaphylococcus aureus
Authors: Saillant Vincent , Morey Léo , Lipuma Damien , Boëton Pierre , Arnoux Pascal , Lechardeur Delphine 
Published: November 2022

AbstractStrict management of intracellular heme pools, which are both toxic and beneficial, can be crucial for bacterial survival during infection. The human pathogenStaphylococcus aureususes a two-component heme sensing system (HssRS), which counteracts environmental heme toxicity by triggering expression of the efflux transporter HrtBA. The HssS heme sensor is a HisKA-type histidine kinase, characterized as a membrane-bound homodimer containing an extracellular sensor and a cytoplasmic conserved catalytic domain. To elucidate HssS heme sensing mechanism, a structural simulation of the HssS dimer based on Alphafold2 was docked with heme. In this model, heme is embedded in the membrane bilayer with its 2 protruding porphyrin propionates interacting with 2 conserved Arg94 and Arg163 that are located extracellularly. Mutagenesis of these arginines and of 2 highly conserved phenylalanines, Phe25 and Phe128, in the predicted hydrophobic heme binding pocket abolished the ability of HssS to induce HrtBA synthesis. This study gives evidence that exogenous heme interacts with HssS at the membrane/extracellular interface to initiate HssS activation to induce HrtBA-mediated heme extrusion from the membrane. This “gatekeeper” mechanism could limit intracellular diffusion of exogenous heme inS. aureus, and may serve as a paradigm for how efflux transporters control detoxification of exogenous hydrophobic stressors.ImportanceIn the host blood, pathogenic bacteria are exposed to the red pigment heme that concentrates in their lipid membranes, generating cytotoxicity. To overcome heme toxicity,Staphylococcus aureusexpresses a membrane sensor protein, HssS. Activation of HssS by heme triggers a phosphorelay mechanism leading to the expression of a heme efflux system, HrtBA. This detoxification system prevents intracellular accumulation of heme. Our structural and functional data reveal a heme-binding hydrophobic cavity in HssS within the TM helices at the interface with the extracellular domain. This structural pocket is important for the function of HssS as a heme sensor. Our findings provide a new basis for the elucidation of pathogen sensing mechanisms as a prerequisite to the discovery of inhibitors.
COVID-19 (Omicron strain) hospital admissions from a virtual ward – who required further care?
Authors: Mackay Ian , France Megan , McAuley Duncan , Wing Sean , Wheeldon Mary , Britton Susan , Todd Catherine , Pitiris Alexandra , Barrett-Beck Leah , Rushbrook Elizabeth , Bennett Cameron , McCarthy Kate 
Published: November 2022

AbstractBackgroundThe COVID-19 virtual ward was created to provide care for people at home with COVID-19. Only a small proportion required hospital admission during their care. Given this was a new model of care, little was known about the clinical characteristics and outcomes of patients requiring admission to hospital from the virtual ward platform.AimA retrospective observational study with the aim to characterise hospital admission volume, patient epidemiology, clinical characteristics and outcome form a virtual ward in the setting of an Omicron BA.1 and BA.2 outbreak.MethodsA retrospective observational study was performed for all virtual ward patients admitted from 1stJanuary 2022 to 25thMarch 2022. Patients had to be at least 16 years old to be included. Epidemiological, clinical and laboratory data was reviewed on all patients who required admission to hospital. This was analysed to describe this patient cohort.ResultsA total of 7021 patients were cared for on the virtual ward over the study period with 473 referred to hospital for assessment. Twenty-six (0.4%) patients were admitted to hospital during their care on the ward. Twenty-two (84.6%) admissions were COVID-19 related. Fifty three percent of the hospitalised patients were fully vaccinated, and 11 had received prior therapeutics for COVID-19 in the community. There was one ICU admission, and one in-hospital mortality. Shortness of breath was the most common reason for escalation to hospital. Chest pain was the second most common reason and the most common diagnosis after investigation was non-cardiac chest pain that spontaneously resolved.ConclusionsFew patients required admission from the virtual ward in the setting of the Omicron variant (BA.1, BA.2) as a direct result of COVID-19 disease and virtual ward care. Shortness of breath and chest pain were the most common symptoms driving further clinical care.What does this paper add to the literature?This paper describes the patient cohort with COVID-19 (Omicron variant) who are unable to be cared for by the virtual model of care and required escalation for hospital admission. It assists in health service planning in the setting of large numbers of cases.
Opi1-mediated transcriptional modulation orchestrates genotoxic stress response in budding yeast
Authors: Panessa Giovanna Marques , Tassoni-Tsuchida Eduardo , Pires Marina Rodrigues , Felix Rodrigo Rodrigues , Jekabson Rafaella , de Souza-Pinto Nadja Cristhina , da Cunha Fernanda Marques , Brandman Onn , Cussiol José Renato Rosa 
Published: November 2022

AbstractIn budding yeast, the transcriptional repressor Opi1 regulates phospholipid biosynthesis by repressing expression of genes containing inositol-sensitive upstream activation sequences (UASINO). Upon genotoxic stress, cells activate the DNA Damage Response (DDR) to coordinate a complex network of signaling pathways aimed at preserving genomic integrity. Here, we reveal that Opi1 is important to modulate transcription in response to genotoxic stress. We find that cells lacking Opi1 exhibit hypersensitivity to genotoxins, along with a delayed G1 to S-phase transition and decreased gamma-H2A levels. Transcriptome analysis using RNA-seq reveals that Opi1 plays a central role in modulating essential biological processes during genotoxic stress induced by methyl methanesulfonate, including repression of phospholipid biosynthesis and transduction of mating signaling. Moreover, Opi1 induces sulfate assimilation and amino acid metabolic processes, such as arginine and histidine biosynthesis and glycine catabolism. Furthermore, we observe increased mitochondrial DNA instability inopi1Δcells upon MMS treatment. Notably, we show that constitutive activation of the transcription factors Ino2-Ino4 is responsible for genotoxin sensitivity in Opi1-deficient cells, and the production of inositol pyrophosphates by Kcs1 counteracts Opi1 function specifically during MMS-induced genotoxic stress. Overall, our findings highlight Opi1 as a critical sensor of genotoxic stress in budding yeast, orchestrating gene expression to facilitate appropriate DNA damage response.
Snake River alfalfa virus, a tentative endornavirus infecting alfalfa (Medicago sativaL.) in Washington State, USA
Authors: Postnikova Olga A. , Irish Brian M. , Eisenback Jonathan , Nemchinov Lev G. 
Published: November 2022

AbstractHere we report, for the first time, an occurrence of Snake River alfalfa virus (SRAV) in Washington state, USA. SRAV was recently identified in alfalfa (Medicago sativaL.) plants and western flower thrips in south-central Idaho and proposed to be a first flavi-like virus identified in a plant host. We argue that the SRAV, based on its abundance in alfalfa plants, genome structure, presence in alfalfa seeds, and seed-mediated transmission is a member of theEndornaviridaefamily.
Enrichment of charge-absent regions in phase separated proteins
Authors: Nicolaou Sonia T. , Verma Chandra S. , Warwicker Jim 
Published: November 2022

AbstractMany studies focus on the relationship between protein charge and liquid-liquid phase separation (LLPS), generally finding that a large degree of charge neutralisation is involved for condensate formation. Here, sequences within human proteins that lack the charge-bearing residues Asp, Glu, Lys, and Arg (termed charge-absent) are analysed alongside annotation for involvement in LLPS. Scaffold proteins, central to condensate formation, on average possess longer charge-absent regions than those not key for LLPS. Charge-absent regions tend to have relatively high hydropathy scores. Overall, they are enriched in Ala, Gly, Pro, and Ser with more specific groupings evident when the subset is clustered by amino acid composition. For several proteins, segments with charge-absent regions have been identified as modulators of LLPS. It is hypothesised that for at least some of the charge-absent regions, a lack of charged group desolvation energy, together with a relatively hydrophobic sequence composition, may facilitate condensation through homomeric interactions. If this is the case, it should be relatively easy to modulate through incorporation of charge through engineering, potentially including pH-sensing.
An integrated Bayesian framework for multi-omics prediction and classification
Authors: Mallick Himel , Porwal Anupreet , Saha Satabdi , Basak Piyali , Svetnik Vladimir , Paul Erina 
Published: November 2022

AbstractWith the growing commonality of multi-omics datasets, there is now increasing evidence that integrated omics profiles lead to the more efficient discovery of clinically actionable biomarkers that enable better disease outcome prediction and patient stratification. Several methods exist to perform host phenotype prediction from crosssectional, single-omics data modalities but decentralized frameworks that jointly analyze multiple time-dependent omics data to highlight the integrative and dynamic impact of repeatedly measured biomarkers are currently limited. In this article, we propose a novel Bayesian ensemble method to consolidate prediction by combining information across several longitudinal and cross-sectional omics data layers. Unlike existing frequentist paradigms, our approach enables uncertainty quantification in prediction as well as interval estimation for a variety of quantities of interest based on posterior summaries. We apply our method to four published multi-omics datasets and demonstrate that it recapitulates known biology in addition to providing novel insights while also outperforming existing methods in estimation, prediction, and uncertainty quantification. Our open-source software is publicly available athttps://github.com/himelmallick/IntegratedLearner.
C-low threshold mechanoreceptor activation becomes sufficient to trigger affective pain in spinal cord-injured mice in association with increased respiratory rates
Authors: Noble Donald J. , Dongmo Rochinelle , Parvin Shangrila , Martin Karmarcha K. , Garraway Sandra M. 
Published: November 2022

AbstractThe mechanisms of neuropathic pain after spinal cord injury (SCI) are not fully understood. In addition to the plasticity that occurs within the injured spinal cord, peripheral processes, such as hyperactivity of primary nociceptors, are critical to the expression of pain after SCI. In adult rats, truncal stimulation within the tuning range of C-low threshold mechanoreceptors (C-LTMRs) contributes to pain hypersensitivity and elevates respiratory rates (RRs) after SCI. This suggests that C-LTMRs, which normally encode pleasant, affiliative touch, undergo plasticity to transmit pain sensation following injury. Because tyrosine hydroxylase (TH) expression is a specific marker of C-LTMRs, in the periphery, here we used Th-Cre adult mice to investigate more specifically the involvement of C-LTMRs in at-level pain after thoracic contusion SCI. Using a modified light-dark chamber conditioned place aversion (CPA) paradigm, we assessed chamber preferences and transitions between chambers at baseline, and in response to mechanical and optogenetic stimulation of C-LTMRs. In parallel, at baseline and select post-surgical timepoints, mice underwent non-contact RR recordings and von Frey assessment of mechanical hypersensitivity. The results showed that SCI mice avoided the chamber associated with C-LTMR stimulation, an effect that was more pronounced with optical stimulation. They also displayed elevated RRs at rest and during CPA training sessions. Importantly, these changes were restricted to chronic post-surgery timepoints, when hindpaw mechanical hypersensitivity was also evident. Together, these results suggest that C-LTMR afferent plasticity, coexisting with a potentially facilitatory state of sympathetic activation, drives at-level affective pain following SCI in adult mice.Contribution to the field statementPreclinical studies have only recently sought to understand biological mechanisms connecting peripheral afferent neuron hypersensitivity to pain. Using mechanical brush and selective optogenetic activation in transgenic mice, this study investigated the role of an implicated subpopulation of sensory afferents, the C-low threshold mechanoreceptors (C-LTMRs), that may be transformed from pleasurable touch- to pain-encoding neurons after spinal cord injury (SCI). C-LTMR activation after SCI evoked at-level conditioned pain responses associated with sympathetic activation (increased respiratory rates). These studies provide a foundation for research into the peripheral afferent mechanisms of pain that is expected to translate into new options for pain control in humans.
Awakening adult neural stem cells: NOX signalling as a positive regulator of quiescence to proliferation transition in theXenopusretina
Authors: Donval A. , Hernandez Puente CV , Lainé A. , Roman D. , Vessely R. , Leclercq J. , Perron M. , Locker M. 
Published: November 2022

AbstractReactive oxygen species (ROS) are both harmful molecules sustaining the pathogenesis of several diseases and essential modulators of cell behaviours. In particular, a growing wealth of data suggest that ROS-dependent signalling pathways might be critical in conferring embryonic or adult stem cells their specific properties. However, how stem cells control ROS production and scavenging, and how ROS in turn contribute to stemness remain poorly understood. Using theXenopusretina as a model system, we first investigated the redox status of retinal stem cells (RSCs). We discovered that they exhibit higher ROS levels compared to progenitors and retinal neurons and express a set of specific antioxidant genes. We next addressed the question of ROS functional involvement in these cells. Using pharmacological or genetic tools, we demonstrate that inhibition of NADPH oxidase (NOX)-dependent ROS production increases the proportion of quiescent RSCs. This is surprisingly accompanied by an apparent acceleration of the mean division speed within the remaining proliferating pool. Our data further unveil that such impact on RSC cell cycling is achieved by modulation of the Wnt/Hedgehog signalling balance. Altogether, we highlight that RSCs exhibit distinctive redox characteristics and exploit NOX signalling to limit quiescence and fine-tune their proliferation rate.
The Cousa objective: a long working distance air objective for multiphoton imagingin vivo
Authors: Yu Che-Hang , Yu Yiyi , Adsit Liam M. , Chang Jeremy T. , Barchini Jad , Moberly Andrew H. , Benisty Hadas , Kim Jinkyung , Young Brent K. , Heng Kathleen , Farinella Deano M. , Leikvoll Austin , Pavan Rishaab , Vistein Rachel , Nanfito Brandon R. , Hildebrand David G. C. , Otero-Coronel Santiago , Vaziri Alipasha , Goldberg Jeffrey L. , Ricci Anthony J. , Fitzpatrick David , Cardin Jessica A. , Higley Michael J. , Smith Gordon B. , Kara Prakash , Nielsen Kristina J. , Smith Ikuko T. , Smith Spencer LaVere 
Published: November 2022

AbstractMultiphoton microscopy can resolve fluorescent structures and dynamics deep in scattering tissue, but applying this techniquein vivocan be limited by short working distance water-immersion objectives. Here we present an ultra long working distance (20 mm) air objective called the Cousa objective. It is optimized for performance across multiphoton imaging wavelengths, offers a > 4 mm2field-of-view with submicron lateral resolution, and is compatible with commonly used multiphoton imaging systems. We share the full optical prescription, and report performance includingin vivo2-photon and 3-photon imaging in a range of species and preparations.
A jasmonate-responsive ERF transcription factor regulates steroidal glycoalkaloid biosynthesis genes in eggplant
Authors: Shoji Tsubasa , Saito Kazuki 
Published: November 2022

AbstractSteroidal glycoalkaloids (SGAs) are a class of cholesterol-derived anti-nutritional defense compounds that are produced in species of the genusSolanum, such as tomato (S. lycopersicum), potato (S. tuberosum), and eggplant (S. melongena). However, the regulation of defense-related metabolites in eggplant remains underexplored. In tomato and potato, the JASMONATE-RESPONSIVE ETHYLENE RESPONSE FACTOR 4 (JRE4) transcription factor positively regulates a large number of genes involved in SGA biosynthesis. Here, we report that overexpression of eggplantJRE4(SmJRE4) induces numerous metabolic genes involved in SGA biosynthesis in leaves. We demonstrate jasmonate-dependent induction ofSmJRE4and its downstream metabolic genes and show that ethylene treatment attenuates this induction. Our findings thus provide molecular insights into SGA biosynthesis and its regulation in this major crop.