bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deamidated TPI is an efficacious target for cell-selective therapy in triple-negative breast cancer
Authors: Enríquez-Flores Sergio , Flores- López Luis A. , Mora-De la Mora Ignacio De la , García-Torres Itzhel , Gracia-Mora Isabel , Gutiérrez-Castrellón Pedro , Fernández-Lainez Cynthia , Martínez-Pérez Yoalli , Olaya-Vargas Alberto , de Vos Paul , López-Velázquez Gabriel 
Published: November 2021

AbstractHuman TPI (HsTPI) is a central and essential glycolytic enzyme for energy supply and is overexpressed in cancer cells. Here, we investigated HsTPI as a potential target for inducing cell death in triple-hormone receptor-negative breast cancer, which is highly dependent on glycolysis, and therapies for its treatment are limited. We found endogenous accumulation of deamidated HsTPI in human breast cancer cells, which might be caused by the lower activity of the HsTPI-degrading caspase-1 in breast cancer cells.In silicoandin vitroanalyses of deamidated HsTPI demonstrated the efficacy of thiol-reactive drugs in blocking enzyme activity. The cancer cells were selectively programmed to undergo apoptosis with thiol-reactive drugs by inducing the production of methylglyoxal (MGO) and advanced glycation-end products (AGEs).In vivoin mice, the thiol-reactive drug effectively inhibited the growth of human tumors by targeting HsTPI as underlying mechanism. Our findings demonstrate deamidated HsTPI as a novel target to develop therapeutic strategies for treating cancers and other pathologies in which this post-translationally modified protein accumulates.
Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator
Authors: Abdelfattah Ahmed S , Zheng Jihong , Reep Daniel , Tsegaye Getahun , Tsang Arthur , Arthur Benjamin J , Rehorova Monika , Olson Carl VL , Huang Yi-Chieh , Shuai Yichun , Koyama Minoru , Moya Maria V , Weber Timothy D , Lemire Andrew L , Baker Christopher A , Falco Natalie , Zheng Qinsi , Grimm Jonathan B , Yip Mighten C , Walpita Deepika , Forest Craig R , Chase Martin , Campagnola Luke , Murphy Gabe , Wong Allan M , Mertz Jerome , Economo Michael N , Turner Glenn , Lin Bei-Jung , Chen Tsai-Wen , Novak Ondrej , Lavis Luke D , Svoboda Karel , Korff Wyatt , Schreiter Eric R , Hasseman Jeremy P , Kolb Ilya 
Published: November 2021

AbstractThe ability to optically image cellular transmembrane voltage at millisecond-timescale resolution can offer unprecedented insight into the function of living brains in behaving animals. The chemigenetic voltage indicator Voltron is bright and photostable, making it a favorable choice for long in vivo imaging of neuronal populations at cellular resolution. Improving the voltage sensitivity of Voltron would allow better detection of spiking and subthreshold voltage signals. We performed site saturation mutagenesis at 40 positions in Voltron and screened for increased ΔF/F0 in response to action potentials (APs) in neurons. Using a fully automated patch-clamp system, we discovered a Voltron variant (Voltron.A122D) that increased the sensitivity to a single AP by 65% compared to Voltron. This variant (named Voltron2) also exhibited approximately 3-fold higher sensitivity in response to sub-threshold membrane potential changes. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, with lower baseline fluorescence. Introducing the same A122D substitution to other Ace2 opsin-based voltage sensors similarly increased their sensitivity. We show that Voltron2 enables improved sensitivity voltage imaging in mice, zebrafish and fruit flies. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.
VALIS: Virtual Alignment of pathoLogy Image Series
Authors: Gatenbee Chandler D. , Baker Ann-Marie , Prabhakaran Sandhya , Slebos Robbert J. C. , Mandal Gunjan , Mulholland Eoghan , Leedham Simon , Conejo-Garcia Jose R. , Chung Christine H. , Robertson-Tessi Mark , Graham Trevor A. , Anderson Alexander R.A. 
Published: November 2021

AbstractSpatial analyses can reveal important interactions between and among cells and their microenvironment. However, most existing staining methods are limited to a handful of markers per slice, thereby limiting the number of interactions that can be studied. This limitation is frequently overcome by registering multiple images to create a single composite image containing many markers. While there are several existing image registration methods for whole slide images (WSI), most have specific use cases. Here, we present the Virtual Alignment of pathoLogy Image Series (VALIS), a fully automated pipeline that opens, registers (rigid and/or non-rigid), and saves aligned slides in the ome.tiff format. VALIS has been tested with 273 immunohistochemistry (IHC) samples and 340 immunofluorescence (IF) samples, each of which contained between 2-69 images per sample. The registered WSI tend to have low error and are completed within a matter of minutes. In addition to registering slides, VALIS can also using the registration parameters to warp point data, such as cell centroids previously determined via cell segmentation and phenotyping. VALIS is written in Python and requires only few lines of code for execution. VALIS therefore provides a free, opensource, flexible, and simple pipeline for rigid and non-rigid registration of IF and/or IHC that can facilitate spatial analyses of WSI from novel and existing datasets.
Audiovisual task switching rapidly modulates sound encoding in mouse auditory cortex
Authors: Morrill Ryan J. , Bigelow James , DeKloe Jefferson , Hasenstaub Andrea R. 
Published: November 2021

AbstractIn everyday behavior, sensory systems are in constant competition for attentional resources, but the cellular and circuit-level mechanisms of modality-selective attention remain largely uninvestigated. We conducted translaminar recordings in mouse auditory cortex (AC) during an audiovisual (AV) attention shifting task. Attending to sound elements in an AV stream reduced both pre-stimulus and stimulus-evoked spiking activity, primarily in deep layer neurons. Despite reduced spiking, stimulus decoder accuracy was preserved, suggesting improved sound encoding efficiency. Similarly, task-irrelevant probe stimuli during intertrial intervals evoked fewer spikes without impairing stimulus encoding, indicating that these attention influences generalized beyond training stimuli. Importantly, these spiking reductions predicted trial-to-trial behavioral accuracy during auditory attention, but not visual attention. Together, these findings suggest auditory attention facilitates sound discrimination by filtering sound-irrelevant spiking in AC, and that the deepest cortical layers may serve as a hub for integrating extramodal contextual information.
A novel cryo-electron microscopy support film based on 2D crystal of HFBI protein
Authors: Fan Hongcheng , Wang Bo , Zhang Yan , Zhu Yun , Song Bo , Xu Haijin , Zhai Yujia , Qiao Mingqiang , Sun Fei 
Published: November 2021

AbstractCryo-electron microscopy (cryo-EM) has become the most powerful tool to resolve the high-resolution structures of biomacromolecules in solution. However, the air-water interface induced preferred orientation, dissociation or denaturation of biomacromolecules during cryo-vitrification is still a major limitation factor for many specimens. To solve this bottleneck, we developed a new type of cryo-EM support film using the 2D crystal of hydrophobin I (HFBI) protein. The HFBI-film utilizes its hydrophilic side to adsorb protein particles via electrostatic interactions and keep air-water interface away, allowing thin-enough ice and high-quality data collection. The particle orientation distribution can be optimized by changing the buffer pH. We, for the first time, solved the cryo-EM structure of catalase (2.28-Å) that exhibited strong preferred orientation using conventional cryo-vitrification protocol. We further proved the HFBI-film is suitable to solve the high-resolution structures of small proteins including aldolase (150 kDa, 3.34-Å) and hemoglobin (64 kDa, 3.6-Å). Our work implied that the HFBI-film will have a wide application in the future to increase the successful rate and efficiency of cryo-EM.
Cortico-striatal activity characterizes human safety learning via Pavlovian conditioned inhibition
Authors: Laing Patrick A.F. , Steward Trevor , Davey Christopher G. , Felmingham Kim L. , Fullana Miguel Angel , Vervliet Bram , Greaves Matthew D. , Moffat Bradford , Glarin Rebecca K. , Harrison Ben J. 
Published: November 2021

AbstractSafety learning generates associative links between neutral stimuli and the absence of threat, promoting the inhibition of fear and security-seeking behaviours. Precisely how safety learning is mediated at the level of underlying brain systems, particularly in humans, remains unclear. Here, we integrated a novel Pavlovian conditioned inhibition task with ultra-high field (UHF) fMRI to examine the neural basis of inhibitory safety learning in 49 healthy participants. In our task, participants were conditioned to two safety signals: a conditioned inhibitor that predicted threat-omission when paired with a known threat signal (A+/AX-), and a standard safety signal that generally predicted threat-omission (BC-). Both safety signals evoked equivalent autonomic and subjective learning responses but diverged strongly in terms of underlying brain activation. The conditioned inhibitor was characterized by more prominent activation of the dorsal striatum, anterior insular and dorsolateral prefrontal cortex compared to the standard safety signal, whereas the latter evoked greater activation of the ventromedial prefrontal cortex, posterior cingulate and hippocampus, among other regions. Further analyses of the conditioned inhibitor indicated that its initial learning was characterized by consistent engagement of dorsal striatal, midbrain, thalamic, premotor, and prefrontal subregions. These findings suggest that safety learning via conditioned inhibition involves a distributed cortico-striatal circuitry, separable from broader cortical regions involved with processing standard safety signals (e.g., CS-). This cortico-striatal system could represent a novel neural substrate of safetylearning, underlying the initial generation of ‘stimulus-safety’ associations, distinct from wider cortical correlates of safety processing, which facilitate the behavioraloutcomesof learning.Significance statementIdentifying safety is critical for maintaining adaptive levels of anxiety, but the neural mechanisms of human safety learning remain unclear. Using ultra-high field fMRI, we compared learning-related brain activity for a conditioned inhibitor, which actively predicted threat-omission, and a standard safety signal (CS-), which was passively unpaired with threat. The inhibitor engaged an extended circuitry primarily featuring the dorsal striatum, along with thalamic, midbrain, and premotor/prefrontal cortex regions. The CS-exclusively involved cortical safety-related regions observed in basic safety conditioning, such as the vmPFC. These findings extend current models to include learning-specific mechanisms for encoding stimulus-safety associations, which might be distinguished from expression-related cortical mechanisms. These insights may suggest novel avenues for targeting dysfunctional safety learning in psychopathology.
An evolutionary divergent thermodynamic brake in ZAP-70 fine-tunes the kinetic proofreading in T cell
Authors: Gangopadhyay Kaustav , Roy Arnab , Chandradasan Athira C. , Roy Swarnendu , Debnath Olivia , SenGupta Soumee , Chowdhury Subhankar , Das Dipjyoti , Das Rahul 
Published: November 2021

AbstractT cell signaling starts with assembling several tyrosine kinases and adaptor proteins to the T cell receptor (TCR), following the antigen binding. The lifetime of the TCR: antigen complex and the time delay between the recruitment and activation of each kinase determines the T cell response. The mechanism by which the time delays are implemented in TCR signaling is not fully understood. Combining experiments and kinetic modeling, we here report a thermodynamic-brake in the regulatory module of ZAP-70, which determines the ligand selectivity, and may delay the ZAP-70 activation in TCR. Phylogenetic analysis revealed that the evolution of the thermodynamic-brake coincides with the divergence of the adaptive immune system to the cell-mediated and humoral responses. Paralogous kinase Syk expressed in B cells, does not possess such a functional thermodynamic brake, which may explain higher basal activation and lack of ligand selectivity by Syk.
Aspergillus fumigatus drives tissue damage via iterative assaults upon mucosal integrity and immune homeostasis
Authors: Okaa Uju Joy , Bertuzzi Margherita , Fortune-Grant Rachael , Thomson Darren D. , Moyes David L. , Naglik Julian R. , Bignell Elaine 
Published: November 2021

ABSTRACTThe human lung is constantly exposed to Aspergillus fumigatus spores, the most prevalent worldwide cause of fungal respiratory disease. Pulmonary tissue damage is a unifying feature of Aspergillus-related diseases; however, the mechanistic basis of damage is not understood. In the lungs of susceptible hosts A. fumigatus undergoes an obligatory morphological switch involving spore germination and hyphal growth. We modelled A. fumigatus infection in cultured A549 human pneumocytes, capturing phosphoactivation status of five host signalling pathways, nuclear translocation & DNA binding of eight host transcription factors, and expression of nine host response proteins over six time points encompassing exposures to live fungus and the secretome thereof. The resulting dataset, comprised of more than 1000 data points, reveals that pneumocytes mount differential responses to A. fumigatus spores, hyphae and soluble secreted products via the NF-kB, JNK, and JNK + p38 pathways respectively. Importantly, via selective degradation of host pro-inflammatory (IL-6 and IL-8) cytokines and growth factors (FGF-2), fungal secreted products reorchestrate the host response to fungal challenge as well as driving multiparametric epithelial damage, culminating in cytolysis. Dysregulation of NF-kB signalling, involving iterative stimulation of canonical and non-canonical signalling, was identified as a significant feature of host damage both in vitro and in a mouse model of invasive aspergillosis. Our data demonstrate that composite tissue damage results from iterative exposures to different fungal morphotypes and secreted products and suggest that modulation of host responses to fungal challenge might represent a unified strategy for therapeutic control of pathologically distinct types of Aspergillus-related disease.IMPORTANCEPulmonary aspergillosis is a spectrum of diseases caused primarily by Aspergillus fumigatus. This fungus is ubiquitous in the environment and grows as a mold, which harbors and disperses spores into the environment. Like other airborne pathogens, the lung mucosa is the first point of contact with the fungus post inhalation. The outcome and severity of disease depends on the host-fungal interaction at the lung interface. We studied how the human lung interacts with spore, germ tube and hyphae growth forms to understand the sequence and dynamics of the early events, which are critical drivers of disease development and progression. Our work is significant in identifying, in response to fungal secreted products, non-canonical NF-kB activation via RelB as being a driving factor in fungus-mediated lung damage. This process could be modulated therapeutically to protect the integrity of infected lung mucosae.
Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in infliximab- and vedolizumab-treated patients
Authors: Lin Simeng , Kennedy Nicholas A , Saifuddin Aamir , Sandoval Diana Muñoz , Reynolds Catherine J , Seoane Rocio Castro , Kottoor Sherine H , Pieper Franziska P , Lin Kai-Min , Butler David K. , Chanchlani Neil , Nice Rachel , Chee Desmond , Bewshea Claire , Janjua Malik , McDonald Timothy J , Sebastian Shaji , Alexander James L , Constable Laura , Lee James C , Murray Charles D , Hart Ailsa L , Irving Peter M , Jones Gareth-Rhys , Kok Klaartje B , Lamb Christopher A , Lees Charlie W , Altmann Daniel M , Boyton Rosemary J , Goodhand James R , Powell Nick , Ahmad Tariq ,   Contributors of the CLARITY IBD study
Published: November 2021

AbstractWe report SARS-CoV-2 vaccine-induced immunity and risk of breakthrough infections in patients with inflammatory bowel disease treated with infliximab, a commonly used anti-TNF drug and those treated with vedolizumab, a gut-specific antibody targeting integrin a4b7 that does not impact systemic immunity. In infliximab-treated patients, the magnitude of anti-SARS-CoV2 antibodies was reduced 4-6-fold. One fifth of both infliximab- and vedolizumab-treated patients did not mount a T cell response. Antibody half-life was shorter in infliximab-treated patients. Breakthrough SARS-CoV-2 infections occurred more frequently in infliximab-treated patients and the risk was predicted by the level of antibody response after second vaccine dose. Overall, recipients of two doses of the BNT162b2 vaccine had higher anti-SARS-CoV-2 antibody concentrations, higher seroconversion rates, shorter antibody half-life and less breakthrough infections compared to ChAdOx1 nCoV-19 vaccine recipients. Irrespective of biologic treatment, higher, more sustained antibody levels were observed in patients with a history of SARS-CoV-2 infection prior to vaccination. Patients treated with anti-TNF therapy should be offered third vaccine doses.
DiagnosisQA: A semi-automated pipeline for developing clinician validated diagnosis specific QA datasets
Authors: Mishra Shreya , Awasthi Raghav , Papay Frank , Maheshawari Kamal , Cywinski Jacek B , Khanna Ashish , Mathur Piyush 
Published: November 2021

AbstractQuestion answering (QA) is one of the oldest research areas of AI and Computational Linguistics. QA has seen significant progress with the development of state-of-the-art models and benchmark datasets over the last few years. However, pre-trained QA models perform poorly for clinical QA tasks, presumably due to the complexity of electronic healthcare data. With the digitization of healthcare data and the increasing volume of unstructured data, it is extremely important for healthcare providers to have a mechanism to query the data to find appropriate answers. Since diagnosis is central to any decision-making for the clinicians and patients, we have created a pipeline to develop diagnosis-specific QA datasets and curated a QA database for the Cerebrovascular Accident (CVA). CVA, also commonly known as Stroke, is an important and commonly occurring diagnosis amongst critically ill patients. Our method when compared to clinician validation achieved an accuracy of 0.90(with 90% CI [0.82,0.99]). Using our method, we hope to overcome the key challenges of building and validating a highly accurate QA dataset in a semiautomated manner which can help improve performance of QA models.
Depth-targeted intracortical microstroke by two-photon photothrombosis in rodent brain
Authors: Fukuda Masahiro , Matsumura Takayoshi , Suda Toshio , Hirase Hajime 
Published: November 2021

AbstractSignificancePhotothrombosis is a widely used model of ischemic stroke in rodent experiments. In the photothromboris model, the photosensitizer Rose Bengal is systemically introduced to the blood stream and activated by green light to induce aggregation of platelets that eventually cause vessel occlusion. Since the activation of Rose Bengal is a one-photon phenomenon and the molecules in the illuminated area (light path) are subject to excitation, targeting of thrombosis is unspecific especially in the depth dimension. We have developed a photothrombosis protocol that can target a single vessel in the cortical parenchyma by two-photon excitation.AimWe aim to induce a thrombotic stroke in the cortical parenchyma by two-photon activation of Rose Bengal so that we confine photothrombosis within a vessel of a target depth.ApproachFITC-dextran is injected into the blood stream to visualize the cerebral blood flow in anesthetized adult mice with a cranial window. After a target vessel is chosen by two-photon imaging (950 nm), Rose Bengal is injected into the blood stream. The scanning wavelength is changed to 720 nm and photothrombosis was induced by scanning the target vessel.ResultsTwo-photon depth-targeted single vessel photothrombosis was achieved with a success rate of 84.9±1.7% within 80 s. Attempts without Rose Bengal (i.e., only with FITC) did not result in photothrombosis at the excitation wavelength of 720 nm.ConclusionsWe described a protocol that achieves depth-targeted single vessel photothrombosis by two-photon excitation. Simultaneous imaging of blood flow in the targeted vessel using FITC dextran enabled the confirmation of vessel occlusion and prevention of excess irradiation that possibly induces unintended photodamage.
Increased frequency of CD4+ and CD8+ follicular helper T cells in human lymph node biopsies during the earliest stages of rheumatoid arthritis
Authors: Anang Dornatien C. , Ramwadhdoebe Tamara H. , Hahnlein Janine , van Kuijk Bo , Smits N. , van Lienden Krijn P. , Maas Mario , Gerlag Danielle M. , Tak Paul P. , de Vries Niek , van Baarsen Lisa G. 
Published: November 2021

ABSTRACTObjectivesFollicular helper T cells (Tfh cells) provide key B cell help, and are essential in germinal center (GC) formation and (auto) antibody generation. To gain more insight into their role during the earliest phase of rheumatoid arthritis (RA) we analyzed their frequencies, phenotype and cytokine profile in peripheral blood and lymphoid tissues.MethodsUsing flow cytometry, we studied the frequency of Tfh and B cells in peripheral blood and lymph node (LN) needle biopsies. Three donor groups were included and compared: healthy controls (HCs), autoantibody positive individuals at risk for developing RA (RA-risk individuals), and early RA patients. Ex vivo stimulation of lymphocytes with PMA/ionomycin was performed to assess cytokine secretion by Tfh cells.ResultsIn blood, the frequency of circular Tfh cells (cTfh) did not differ between study groups. In lymphoid tissue, the frequency of Tfh cells correlated strongly with the frequency of CD19+ B cells. Compared to healthy controls, LN samples of RA patients and RA-risk individuals showed more CD19+ B cells and more CD4+CXCR5+ and CD8+CXCR5+ Tfh cells. These Tfh cells from LNs expressed less IL-21 upon ex vivo stimulation.ConclusionLN tissue of early RA patients as well as part of RA-risk individuals exhibit increased frequencies of Tfh cells correlating with increased numbers of B cells. Interestingly, IL-21 production is already aberrant in the very early at risk phase of the disease. This suggests that Tfh cells may present a novel rationale for therapeutic targeting during the preclinical stage of the disease to prevent further disease progression.