bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement-induced collective vibrational quantum coherence under spontaneous Raman scattering in a liquid
Authors: Vento Valeria , Tarrago Velez Santiago , Pogrebna Anna , Galland Christophe 
Published: May 2023

AbstractSpontaneous vibrational Raman scattering is a ubiquitous form of light–matter interaction whose description necessitates quantization of the electromagnetic field. It is usually considered as an incoherent process because the scattered field lacks any predictable phase relationship with the incoming field. When probing an ensemble of molecules, the question therefore arises: What quantum state should be used to describe the molecular ensemble following spontaneous Stokes scattering? We experimentally address this question by measuring time-resolved Stokes–anti-Stokes two-photon coincidences on a molecular liquid consisting of several sub-ensembles with slightly different vibrational frequencies. When spontaneously scattered Stokes photons and subsequent anti-Stokes photons are detected into a single spatiotemporal mode, the observed dynamics is inconsistent with a statistical mixture of individually excited molecules. Instead, we show that the data are reproduced if Stokes–anti-Stokes correlations are mediated by a collective vibrational quantum, i.e. a coherent superposition of all molecules interacting with light. Our results demonstrate that the degree of coherence in the vibrational state of the liquid is not an intrinsic property of the material system, but rather depends on the optical excitation and detection geometry.
Elucidating the molecular programming of a nonlinear non-ribosomal peptide synthetase responsible for fungal siderophore biosynthesis
Authors: Jenner Matthew , Hai Yang , Nguyen Hong H. , Passmore Munro , Skyrud Will , Kim Junyong , Garg Neil K. , Zhang Wenjun , Ogorzalek Loo Rachel R. , Tang Yi 
Published: May 2023

AbstractSiderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) enzymes remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin. In vitro reconstitution of purified SidC reveals its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovers several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.
Rubisco deactivation and chloroplast electron transport rates co-limit photosynthesis above optimal leaf temperature in terrestrial plants
Authors: Scafaro Andrew P. , Posch Bradley C. , Evans John R. , Farquhar Graham D. , Atkin Owen K. 
Published: May 2023

AbstractNet photosynthetic CO2 assimilation rate (An) decreases at leaf temperatures above a relatively mild optimum (Topt) in most higher plants. This decline is often attributed to reduced CO2 conductance, increased CO2 loss from photorespiration and respiration, reduced chloroplast electron transport rate (J), or deactivation of Ribulose-1,5-bisphosphate Carboxylase Oxygenase (Rubisco). However, it is unclear which of these factors can best predict species independent declines in An at high temperature. We show that independent of species, and on a global scale, the observed decline in An with rising temperatures can be effectively accounted for by Rubisco deactivation and declines in J. Our finding that An declines with Rubisco deactivation and J supports a coordinated down-regulation of Rubisco and chloroplast electron transport rates to heat stress. We provide a model that, in the absence of CO2 supply limitations, can predict the response of photosynthesis to short-term increases in leaf temperature.
Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9
Authors: Martin Gregory M. , Fernández-Quintero Monica L. , Lee Wen-Hsin , Pholcharee Tossapol , Eshun-Wilson Lisa , Liedl Klaus R. , Pancera Marie , Seder Robert A. , Wilson Ian A. , Ward Andrew B. 
Published: May 2023

AbstractA primary objective in malaria vaccine design is the generation of high-quality antibody responses against the circumsporozoite protein of the malaria parasite, Plasmodium falciparum (PfCSP). To enable rational antigen design, we solved a cryo-EM structure of the highly potent anti-PfCSP antibody L9 in complex with recombinant PfCSP. We found that L9 Fab binds multivalently to the minor (NPNV) repeat domain, which is stabilized by a unique set of affinity-matured homotypic, antibody-antibody contacts. Molecular dynamics simulations revealed a critical role of the L9 light chain in integrity of the homotypic interface, which likely impacts PfCSP affinity and protective efficacy. These findings reveal the molecular mechanism of the unique NPNV selectivity of L9 and emphasize the importance of anti-homotypic affinity maturation in protective immunity against P. falciparum.
A randomized clinical trial assessing the effect of automated medication-targeted alerts on acute kidney injury outcomes
Authors: Wilson F. Perry , Yamamoto Yu , Martin Melissa , Coronel-Moreno Claudia , Li Fan , Cheng Chao , Aklilu Abinet , Ghazi Lama , Greenberg Jason H. , Latham Stephen , Melchinger Hannah , Mansour Sherry G. , Moledina Dennis G. , Parikh Chirag R. , Partridge Caitlin , Testani Jeffrey M. , Ugwuowo Ugochukwu 
Published: May 2023

AbstractAcute kidney injury is common among hospitalized individuals, particularly those exposed to certain medications, and is associated with substantial morbidity and mortality. In a pragmatic, open-label, National Institutes of Health-funded, parallel group randomized controlled trial (clinicaltrials.gov NCT02771977), we investigate whether an automated clinical decision support system affects discontinuation rates of potentially nephrotoxic medications and improves outcomes in patients with AKI. Participants included 5060 hospitalized adults with AKI and an active order for any of three classes of medications of interest: non-steroidal anti-inflammatory drugs, renin-angiotensin-aldosterone system inhibitors, or proton pump inhibitors. Within 24 hours of randomization, a medication of interest was discontinued in 61.1% of the alert group versus 55.9% of the usual care group (relative risk 1.08, 1.04 – 1.14, p = 0.0003). The primary outcome – a composite of progression of acute kidney injury, dialysis, or death within 14 days - occurred in 585 (23.1%) of individuals in the alert group and 639 (25.3%) of patients in the usual care group (RR 0.92, 0.83 – 1.01, p = 0.09). Trial Registration Clinicaltrials.gov NCT02771977.
The experience of Anxiety for people with Parkinson’s disease
Authors: Blundell Emma. K. , Grover Laura. E. , Stott Joshua , Schrag Anette 
Published: May 2023

AbstractAnxiety is a common non-motor symptom of Parkinson’s disease (PD) associated with increased disability and reduced quality of life. However, anxiety is poorly understood, underdiagnosed, and undertreated. To date, little research has explored how anxiety is experienced by patients themselves. This study explored the experience of anxiety for people with Parkinson’s (PWP) to inform future research and interventions. Semi-structured interviews with 22 PWP (aged 43-80, 50% female) were conducted and analysed using inductive thematic analysis. Four main themes were extracted: conceptualising anxiety; anxiety and the body; anxiety and social identity; and coping with anxiety. Sub-themes revealed inconsistent perceptions: anxiety was in body and mind, part of disease and human nature, part of self-identity and a threat to it. The symptoms described were diverse. Many perceived their anxiety as more incapacitating than motor symptoms or capable of amplifying them, and described that anxiety restricted their lifestyle. All perceived anxiety as connected to PD, and ultimately persistent: dominant aspirations were coping and acceptance rather than cures, with medications strongly resisted. Findings highlight the complexity and high importance of anxiety for PWP. Implications for therapeutic approaches are discussed.
The genetic spectrum of a cohort of patients clinically diagnosed as Parkinson’s disease in mainland China
Authors: Sun Yi-Min , Zhou Xin-Yue , Liang Xiao-Niu , Lin Jin-Ran , Xu Yi-Dan , Chen Chen , Wei Si-Di , Chen Qi-Si , Liu Feng-Tao , Zhao Jue , Tang Yi-Lin , Shen Bo , Gan Lin-Hua , Lu Boxun , Ding Zheng-Tong , An Yu , Wu Jian-Jun , Wang Jian 
Published: May 2023

AbstractSo far, over 20 causative genes of monogenic Parkinson’s disease (PD) have been identified. Some causative genes of non-parkinsonian entities may also manifest with parkinsonism mimicking PD. This study aimed to investigate the genetic characteristics of clinically diagnosed PD with early onset age or family history. A total of 832 patients initially diagnosed with PD were enrolled, of which, 636 were classified into the early-onset group and 196 were classified into the familial late-onset group. The genetic testing included the multiplex ligation-dependent probe amplification and next generation sequencing (target sequencing or whole-exome sequencing). The dynamic variants of spinocerebellar ataxia were tested in probands with family history. In the early-onset group, 30.03% of patients (191/636) harbored pathogenic/likely pathogenic (P/LP) variants in known PD-related genes (CHCHD2, DJ-1, GBA (heterozygous), LRRK2, PINK1, PRKN, PLA2G6, SNCA and VPS35). Variants in PRKN were the most prevalent, accounting for 15.72% of the early-onset patients, followed by GBA (10.22%), and PLA2G6 (1.89%). And 2.52% (16/636) had P/LP variants in causative genes of other diseases (ATXN3, ATXN2, GCH1, TH, MAPT, GBA (homozygous)). In the familial late-onset group, 8.67% of patients (17/196) carried P/LP variants in known PD-related genes (GBA (heterozygous), HTRA2, SNCA) and 2.04% (4/196) had P/LP variants in other genes (ATXN2, PSEN1, DCTN1). Heterozygous GBA variants (7.14%) were the most common genetic cause found in familial late-onset patients. Genetic testing is of vital importance in differential diagnosis especially in early-onset and familial PD. Our findings may also provide some clues to the nomenclature of genetic movement disorders.
Th1-dominant cytokine responses in kidney patients after COVID-19 vaccination are associated with poor humoral responses
Authors: den Hartog Yvette , Malahe S. Reshwan K. , Rietdijk Wim J. R. , Dieterich Marjolein , Gommers Lennert , Geers Daryl , Bogers Susanne , van Baarle Debbie , Diavatopoulos Dimitri A. , Messchendorp A. Lianne , van der Molen Renate G. , Remmerswaal Ester B. M. , Bemelman Frederike J. , Gansevoort Ron T. , Hilbrands Luuk B. , Sanders Jan-Stephan , GeurtsvanKessel Corine H. , Kho Marcia M. L. , Reinders Marlies E. J. , de Vries Rory D. , Baan Carla C. ,   on behalf of RECOVAC Consortium
Published: May 2023

AbstractCytokines are regulators of the immune response against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, the contribution of cytokine-secreting CD4+ and CD8+ memory T cells to the SARS-CoV-2-specific humoral immune response in immunocompromised kidney patients is unknown. Here, we profiled 12 cytokines after stimulation of whole blood obtained 28 days post second 100 μg mRNA-1273 vaccination with peptides covering the SARS-CoV-2 spike (S)-protein from patients with chronic kidney disease (CKD) stage 4/5, on dialysis, kidney transplant recipients (KTR), and healthy controls. Unsupervised hierarchical clustering analysis revealed two distinct vaccine-induced cytokine profiles. The first profile was characterized by high levels of T-helper (Th)1 (IL-2, TNF-α, and IFN-γ) and Th2 (IL-4, IL-5, IL-13) cytokines, and low levels of Th17 (IL-17A, IL-22) and Th9 (IL-9) cytokines. This cluster was dominated by patients with CKD, on dialysis, and healthy controls. In contrast, the second cytokine profile contained predominantly KTRs producing mainly Th1 cytokines upon re-stimulation, with lower levels or absence of Th2, Th17, and Th9 cytokines. Multivariate analyses indicated that a balanced memory T cell response with the production of Th1 and Th2 cytokines was associated with high levels of S1-specific binding and neutralizing antibodies mainly at 6 months after second vaccination. In conclusion, seroconversion is associated with the balanced production of cytokines by memory T cells. This emphasizes the importance of measuring multiple T cell cytokines to understand their influence on seroconversion and potentially gain more information about the protection induced by vaccine-induced memory T cells.
Succession of bacterial biofilm communities following removal of chloramine from a full-scale drinking water distribution system
Authors: Rosenqvist Tage , Danielsson Mikael , Schleich Caroline , Ahlinder Jon , Brindefalk Björn , Pullerits Kristjan , Dacklin Ingrid , Salomonsson Emelie N. , Sundell David , Forsman Mats , Keucken Alexander , Rådström Peter , Paul Catherine J. 
Published: May 2023

AbstractMonochloramine is used to regulate microbial regrowth in drinking water distribution systems (DWDS) but produces carcinogenic disinfection byproducts and constitutes a source of energy for nitrifying bacteria. This study followed biofilm-dispersed microbial communities of a full-scale DWDS distributing ultrafiltered water over three years, before and after removal of monochloramine. Communities were described using flow cytometry and amplicon sequencing, including full-length 16S rRNA gene sequencing. Removal of monochloramine increased total cell counts by up to 440%. Increased abundance of heterotrophic bacteria was followed by emergence of the predatory bacteriaBdellovibrio, and a community potentially metabolizing small organic compounds replaced the nitrifying core community. No increased abundance ofMycobacteriumorLegionellawas observed. Co-occurrence analysis identified a network ofNitrosomonas,Nitrospira,SphingomonasandHyphomicrobium, suggesting that monochloramine supported this biofilm community. While some species expanded into the changed niche, no immediate biological risk to consumers was indicated within the DWDS.
Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma
Authors: Naghavian Reza , Faigle Wolfgang , Oldrati Pietro , Wang Jian , Toussaint Nora C. , Qiu Yuhan , Medici Gioele , Wacker Marcel , Freudenmann Lena K. , Bonté Pierre-Emmanuel , Weller Michael , Regli Luca , Amigorena Sebastian , Rammensee Hans-Georg , Walz Juliane S. , Brugger Silvio D. , Mohme Malte , Zhao Yingdong , Sospedra Mireia , Neidert Marian C. , Martin Roland 
Published: May 2023

AbstractMicrobial organisms have key roles in numerous physiological processes in the human body and have recently been shown to modify the response to immune checkpoint inhibitors1,2. Here we aim to address the role of microbial organisms and their potential role in immune reactivity against glioblastoma. We demonstrate that HLA molecules of both glioblastoma tissues and tumour cell lines present bacteria-specific peptides. This finding prompted us to examine whether tumour-infiltrating lymphocytes (TILs) recognize tumour-derived bacterial peptides. Bacterial peptides eluted from HLA class II molecules are recognized by TILs, albeit very weakly. Using an unbiased antigen discovery approach to probe the specificity of a TIL CD4+ T cell clone, we show that it recognizes a broad spectrum of peptides from pathogenic bacteria, commensal gut microbiota and also glioblastoma-related tumour antigens. These peptides were also strongly stimulatory for bulk TILs and peripheral blood memory cells, which then respond to tumour-derived target peptides. Our data hint at how bacterial pathogens and bacterial gut microbiota can be involved in specific immune recognition of tumour antigens. The unbiased identification of microbial target antigens for TILs holds promise for future personalized tumour vaccination approaches.
Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days
Authors: Gillon Colleen J. , Lecoq Jérôme A. , Pina Jason E. , Ahmed Ruweida , Billeh Yazan N. , Caldejon Shiella , Groblewski Peter , Henley Timothy M. , Kato India , Lee Eric , Luviano Jennifer , Mace Kyla , Nayan Chelsea , Nguyen Thuyanh V. , North Kat , Perkins Jed , Seid Sam , Valley Matthew T. , Williford Ali , Bengio Yoshua , Lillicrap Timothy P. , Zylberberg Joel , Richards Blake A. 
Published: May 2023

AbstractThe apical dendrites of pyramidal neurons in sensory cortex receive primarily top-down signals from associative and motor regions, while cell bodies and nearby dendrites are heavily targeted by locally recurrent or bottom-up inputs from the sensory periphery. Based on these differences, a number of theories in computational neuroscience postulate a unique role for apical dendrites in learning. However, due to technical challenges in data collection, little data is available for comparing the responses of apical dendrites to cell bodies over multiple days. Here we present a dataset collected through the Allen Institute Mindscope’s OpenScope program that addresses this need. This dataset comprises high-quality two-photon calcium imaging from the apical dendrites and the cell bodies of visual cortical pyramidal neurons, acquired over multiple days in awake, behaving mice that were presented with visual stimuli. Many of the cell bodies and dendrite segments were tracked over days, enabling analyses of how their responses change over time. This dataset allows neuroscientists to explore the differences between apical and somatic processing and plasticity.
Characterizing amblyopic perception under non-rivalrous viewing conditions
Authors: Meier Kimberly , Tarczy-Hornoch Kristina , Boynton Geoffrey M. , Fine Ione 
Published: May 2023

AbstractCurrent assessments of interocular interactions in amblyopia often use rivalrous stimuli, with conflicting stimuli in each eye, which does not reflect vision under typical circumstances. Here we measure interocular interactions in observers with amblyopia, strabismus with equal vision, and controls using a non-rivalrous stimulus. Observers used a joystick to continuously report the perceived binocular contrast of dichoptic grating stimuli, identical except that the stimulus was contrast-modulated independently in each eye over time. Consistent with previous studies, a model predicting the time-course of perceived contrast found increased amblyopic eye attenuation, and reduced contrast normalization of the fellow eye by the amblyopic eye, in amblyopic participants compared to controls. However, these suppressive interocular effects were weaker than those found in previous studies, suggesting that rivalrous stimuli may overestimate the effects of amblyopia on interocular interactions during naturalistic viewing conditions.
Effects of folic acid supplementation in pregnant mice on glucose metabolism disorders in male offspring induced by lipopolysaccharide exposure during pregnancy
Authors: Sun Wan-Xiao , Shu Yi-Ping , Yang Xin-Yu , Huang Wei , Chen Jing , Yu Ning-Ning , Zhao Mei 
Published: May 2023

AbstractThe DOHaD theory suggests that adverse environmental factors in early life may lead to the development of metabolic diseases including diabetes and hypertension in adult offspring through epigenetic mechanisms such as DNA methylation. Folic acid (FA) is an important methyl donor in vivo and participates in DNA replication and methylation. The preliminary experimental results of our group demonstrated that lipopolysaccharide (LPS, 50 µg/kg/d) exposure during pregnancy could lead to glucose metabolism disorders in male offspring, but not female offspring; however, the effect of folic acid supplementation on glucose metabolism disorders in male offspring induced by LPS exposure remains unclear. Therefore, in this study, pregnant mice were exposed to LPS on gestational day (GD) 15–17 and were given three doses of FA supplementation (2 mg/kg, 5 mg/kg, or 40 mg/kg) from mating to lactation to explore its effect on glucose metabolism in male offspring and the potential mechanism. This study confirmed that FA supplementation of 5 mg/kg in pregnant mice improved glucose metabolism in LPS-exposed offspring during pregnancy by regulating gene expression.
Effect of cetrimonium carrier micelles on bacterial membranes and extracellular DNA, an in silico study
Authors: Puelles Jhonatan Soto , Ghorbani Mahdi , Tuck Benjamin , Machuca Laura L. , Ackland M. Leigh , Chen Fangfang , Somers Anthony E. , Forsyth Maria 
Published: May 2023

AbstractMicroorganisms do not live as dispersed single cells but rather they form aggregates with extracellular polymeric substances at interfaces. Biofilms are considered efficient life forms because they shield bacteria from biocides and collect dilute nutrients. This is a big concern in industry since the microorganisms can colonize a wide range of surfaces, accelerating material deterioration, colonizing medical devices, contaminating ultrapure drinking water, increasing energy costs and creating focus of infection. Conventional biocides that target a specific component of the bacteria are not effective in the presence of biofilms. Efficient biofilm inhibitors are based on a multitarget approach interacting with the bacteria and the biofilm matrix. Their rationale design requires a thorough understanding of inhibitory mechanisms that are still largely lacking today. Herein we uncover via molecular modelling the inhibition mechanism of cetrimonium 4-OH cinnamate (CTA-4OHcinn). Simulations show that CTA-4OH micelles can disrupt symmetric and asymmetric bilayers, representative of inner and outer bacterial membranes, following three stages: adsorption, assimilation, and defect formation. The main driving force for micellar attack is electrostatic interactions. In addition to disrupting the bilayers, the micelles work as carriers facilitating the trapping of 4OH cinnamate anions within the bilayer upper leaflet and overcoming electrostatic repulsion. The micelles also interact with extracellular DNA (e-DNA), which is one of the main components of biofilms. It is observed that CTA-4OHcinn forms spherical micelles on the DNA backbone; which hinders their ability to pack. This is demonstrated by modelling the DNA along the hbb histone-like protein, showing that in the presence of CTA-4OHcinn, DNA does not pack properly around hbb. The abilities of CTA-4OHcinn to cause cell death through membrane disruption and to disperse a mature, multi-species biofilm are also confirmed experimentally.