bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic epidemiology revealed the emergence and worldwide dissemination of ST383 carbapenem-resistant hypervirulent Klebsiella pneumoniae and hospital acquired infections of ST196 Klebsiella quasipneumoniae in Qatar
Authors: Tsui Clement Kin-Ming , Abid Fatma Ben , McElheny Christi Lee , Almuslamani Muna , Omrani Ali S. , Doi Yohei 
Published: June 2022

AbstractThe emergence of carbapenem-resistant (CR) hypervirulent Klebsiella pneumoniae (hvKp) is a new threat to healthcare. In this study, we studied the molecular epidemiology of CR Klebsiella isolates in Qatar using whole genome sequence data. We also characterised the prevalence and genetic basis of hypervirulent phenotypes, and established the virulence potential using a Galleria mellonella model. One hundred CR Klebsiella isolates were recovered, and NDM and OXA-48 were the most common carbapenemases. Phylogenetic analysis indicated the presence of diverse sequence types and clonal lineages; one of them belonged to K. quaisipneumoniae ST196 that may be disseminated among several health care centres. Ten K. pneumoniae isolates carrying rmpA and/or rmpA2, and 2 isolates belonged to KL2, indicating the prevalence of classical hypervirulent (hv) isolates was not high. Isolates carrying CR and hv genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated the blaNDM was located on an IncHI1B type plasmid (pFQ61_ST383_NDM-5), which also harbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from inversion and recombination events. In contrast, blaOXA-48 was located in an IncL-type plasmid. Comparative genomes indicated the recent evolution and emergence of CR-hv Kp ST383 via the acquisition of hybrid plasmids with both carbapenemase and virulence genes. CR-hv K. pneumoniae ST383 pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.
Characterization of prohibitins as novel target to block asexual and sexual stage growth of Plasmodium falciparum
Authors: Saini Monika , Ngwa Che Julius , Marothia Manisha , Vandana  , Pandey Kailash C. , Pati Soumya , Ranganathan Anand , Pradel Gabriele , Singh Shailja 
Published: June 2022

ABSTRACTProhibitins (PHBs) are highly conserved pleiotropic proteins as they have been shown to mediate key cellular functions. Here, we characterize PHBs encoding putative genes of Plasmodium falciparum by exploiting different orthologous models. We demonstrated that PfPHB1 (PF3D7_0829200) and PfPHB2 (PF3D7_1014700) are expressed in asexual and sexual blood stages of the parasite. Immunostaining indicated these proteins as mitochondrial residents as they were found to be localized as punctate foci. We further validated PfPHBs as organellar proteins residing in the Plasmodium mitochondria, where they interact with each other. Functional characterization was done in Saccharomyces cerevisiae orthologous model by expressing PfPHB1 and PfPHB2 in cells harboring respective mutants. The PfPHBs functionally complemented the yeast PHB1 and PHB2 mutants, where the proteins were found to be involved in stabilizing the mitochondrial DNA, retaining mitochondrial integrity and rescuing yeast cell growth. Further, Rocaglamide (Roc-A), a known inhibitor of PHBs and anti-cancerous agent, was tested against PfPHBs and as an antimalarial. Roc-A treatment retarded the growth of PHB1, PHB2, and ethidium bromide petite yeast mutants. Moreover, Roc-A inhibited growth of yeast PHBs mutants that were functionally complemented with PfPHBs, validating P. falciparum PHBs as one of the molecular targets for Roc-A. Roc-A treatment led to growth inhibition of artemisinin-sensitive (3D7), artemisinin-resistant (R539T) and chloroquine-resistant (RKL-9) parasites in nanomolar ranges. The compound was able to retard gametocyte growth with significant morphological aberrations. Based on our findings, we propose the presence of functional mitochondrial PfPHB1 and PfPHB2 in P. falciparum and their druggability to block parasite growth.
An Analysis of PCR Ct Scores and Distributions from the ONS Community Infection Survey during the COVID Second Wave in the UK
Authors: Johnson Keith , Hammer Steven J , Klymenko Tanya 
Published: June 2022

AbstractThis work presents an analysis of PCR cycle threshold (Ct) scores and their distributions, i.e. the probabilities that a test is positive with a score Ct, P(Ct), derived from the survey during the second COVID wave in the UK. Their relation to gene target breakdown is exemplified. Thus a significant parameter for tracking the course of COVID in the second wave is the percentage of positive tests with Ct < 25, %Ct <25, which is obtained by plotting weekly percentiles from the survey against Ct to construct the ogive or cumulative frequency curve (CMF). The biological basis for studying this parameter is the strong correlation between %Ct < 25 and the percentage of positive tests comprising target genes ORF1ab+N and ORF1ab+N+S, or %Inf.Furthermore, the probability distributions, obtained by differentiating the ogives, were found to be predominantly bimodal with a hot peak at Ct = 20.31+/- 4.65 and a cold peak with Ct = 32.95+/-1.11. These closely match the peaks found for the target genes ORF1ab+N, viz. Ct=18.54+/-2.31 and Ct=32.02+/-0.49 as well as in Walker et al [12]. Similar results were found in [13] and [14]. The cold peak seems likely to be associated with residue from a previous infection. The distributions for gene targets in cfvroc Pillar 2 [15,16] are also bimodal but the peaks occur at lower values of Ct. This suggests the results are machine/sample dependent and emphasises the need for calibration, if quality control in PCR testing is to be improved.
A cross-sectional analysis of factors associated with the development of refeeding syndrome in children 0 – 59 months diagnosed with severe acute malnutrition in a South African setting
Authors: Heydenrych Natalie , De Maayer Tim , Nel Mariette , van den Berg Louise 
Published: June 2022

AbstractBackgroundRefeeding syndrome (RFS) is a life-threatening, underdiagnosed, and under-researched complication in treating children with severe acute malnutrition (SAM). This study aimed to determine the incidence and onset of RFS and identify biochemical abnormalities, clinical signs, and complications associated with RFS development in children 0–59 months treated in a South African public hospital setting.MethodsA retrospective cohort study was performed on hospital files of children diagnosed with SAM at Rahima Moosa Mother and Child Hospital, Johannesburg, from 1/10/2014 to 31/12/2018. A total of 148 files could be retrieved from the hospital archives. The diagnosis of SAM based on the World Health Organization definition was confirmed in 126 of these children, and they were included in the study. The onset of RFS among the children included in the study was diagnosed based on published criteria for RFS. Children who developed RFS and those who did not were compared concerning biochemistry and clinical signs and symptoms on admission.ResultsThe median age of the 126 children (63% male) with confirmed SAM was 34 months (IQR: 26.0 to 48.4 months). The mortality rate was 18.2%. Of these children, 8.7% were retrospectively diagnosed as having developed RFS during their recorded hospital stay, despite implementing the WHO treatment guidelines for SAM. A significantly higher percentage of the children that developed RFS presented on admission with hypophosphatemia (p=0.04), severe hypokalemia (p=0.0005), hyponatremia (p=0.004), an international normalized ratio (INR) of above 1.7 (p=0.049), diarrhea (p=0.04), dehydration (p=0.02) and urinary tract infection (UTI) (p=0.04) than those that did not. Edema was more prevalent on admission in children who developed RFS than those who did not (63.6% vs 39.1%), though the difference was not statistically significant (p=0.20). Children who developed RFS stayed in hospital significantly longer than those who did not (18 vs 12 days) (p=0.003).ConclusionIn this population of children with SAM treated in a South African public hospital setting, the presence on hospital admission of low levels of electrolytes, elevated INR, dehydration, diarrhea, and UTI was significantly associated with developing RFS. Recognizing these as possible red flags for developing RFS in children admitted with SAM might contribute to improved outcomes and needs further investigation.
Climate change and the rising incidence of dengue in Argentina
Authors: López MS , Gómez A , Müller G , Walker E , Robert MA , Estallo EL 
Published: June 2022

BACKGROUNDOne of the most important consequences of climate change is the increased spread of dengue from tropical and subtropical regions to temperate areas around the world. Climate variables such as temperature and precipitation influence the dengue vector’s biology, physiology, abundance, and life cycle. Thus, an analysis is needed of climate changes and their possible links with the growing occurrence of epidemics recorded in recent decades.OBJECTIVESTo assess the increasing incidence of dengue driven by climate change at the southern limits of dengue virus transmission in South America.METHODSWe analyze the evolution of climate, epidemiological, and biological variables, comparing a period without the presence of dengue cases to a more recent period with the occurrence of cases and, consequently, of important epidemics. Temperature and precipitation are the climate variables evaluated, the total number of cases and incidence of dengue are the epidemiological variables, and finally, the optimal temperature ranges for transmission of the dengue vector is the biological variable.RESULTSThe presence of dengue cases and epidemic outbreaks are observed to be consistent with positive temperature trends and anomalies. Dengue cases do not seem to be associated with precipitation trends and anomalies. The number of days with optimal temperatures for dengue transmission increased from the period without dengue cases to the period with the presence of dengue cases. However, the number of months with optimal transmission temperatures was the same in both periods.CONCLUSIONSThe higher incidence of dengue virus (DENV) and its expansion to different regions of Argentina seem to be associated with temperature increases in the country during the past decades. The active surveillance of both the vector and associated arboviruses will make it possible to assess and predict the occurrence of epidemics, based on the accelerated changes in climate. Such surveillance should go hand in hand with efforts to improve the understanding of the mechanisms driving the geographic expansion of dengue and other arboviruses beyond the current limits.
Cortical activation predicts posttraumatic improvement in youth treated with TF-CBT or CCT
Authors: Espil Flint M. , Balters Stephanie , Li Rihui , McCurdy Bethany H. , Kletter Hilit , Piccirilli Aaron , Cohen Judith A. , Weems Carl F. , Reiss Allan L. , Carrion Victor G. 
Published: June 2022

AbstractBackgroundIdentifying neural activation patterns that predict youths’ treatment response may aid in the development of imaging-based assessment of emotion dysregulation following trauma and foster tailored intervention. Changes in cortical hemodynamic activity measured with functional near-infrared spectroscopy (fNIRS) may provide a time and cost-effective option for such work. We examined youths’ PTSD symptom change following treatment and tested if previously identified activation patterns would predict treatment response.MethodsYouth (N = 73, mean age = 12.97, SD = 3.09 years) were randomly assigned to trauma-focused cognitive behavioral therapy (TF-CBT), cue-centered therapy (CCT), or treatment as usual (TAU). Parents and youth reported on youth’s PTSD symptoms at pre-intervention, post-intervention, and follow-up. Neuroimaging data (N = 31) assessed at pre-intervention were obtained while youth engaged in an emotion expression task. Treatment response slopes were calculated for youth’s PTSD symptoms.ResultsOverall, PTSD symptoms decreased from pre-intervention through follow-up across conditions, with some evidence of relative benefit of TF-CBT and CCT over TAU but significant individual variation in treatment response. Cortical activation patterns were correlated with PTSD symptom improvement slopes (r = 0.53). In particular, cortical responses to fearful and neutral facial stimuli in six fNIRS channels in the bilateral dlPFC were important predictors of PTSD symptom improvement.ConclusionsThe use of fNIRS provides a method of monitoring and assessing cortical activation patterns in a relatively inexpensive and portable manner. Associations between functional activation and youths’ PTSD symptoms improvement may be a promising avenue for understanding emotion dysregulation in clinical populations.
Recovery of clinical, cognitive and cortical activity measures following mild traumatic brain injury (mTBI): a longitudinal investigation
Authors: Coyle Hannah L. , Bailey Neil W. , Ponsford Jennie , Hoy Kate E. 
Published: June 2022

AbstractThe mechanisms that underpin recovery following mild traumatic brain injury (mTBI) remain poorly understood. Identifying neurophysiological markers and their functional significance is necessary to develop diagnostic and prognostic indicators of recovery. The current study assessed 30 participants in the subacute phase of mTBI (10-31 days post-injury) and 28 demographically matched controls. Participants also completed 3 month (mTBI: N = 21, control: N = 25) and 6 month (mTBI: N = 15, control: N = 25) follow up sessions to track recovery. At each time point, a battery of clinical, cognitive, and neurophysiological assessments was completed. Neurophysiological measures included resting-state electroencephalography (EEG) and transcranial magnetic stimulation combined with EEG (TMS-EEG). Outcome measures were analysed using mixed linear models (MLM). Group differences in mood, post-concussion symptoms and resting-state EEG resolved by 3 months, and recovery was maintained at 6 months. On TMS-EEG derived neurophysiological measures of cortical reactivity, group differences ameliorated at 3 months but re-emerged at 6 months, while on measures of fatigue, group differences persisted across all time points. Persistent neurophysiological changes and greater fatigue in the absence of measurable cognitive impairment may suggest the impact of mTBI on neuronal communication may leads to increased neural effort to maintain efficient function. Neurophysiological measures to track recovery may help identify both temporally optimal windows and therapeutic targets for the development of new treatments in mTBI.
Characterization of non-human primate dura in health and neurodegeneration
Authors: Janson Christopher , Hauser Kyle , Muller Scott , Hansen Eric , Lam Cornelius , Kordower Jeffrey , Romanova Liudmila 
Published: June 2022

AbstractBrain meninges and associated vasculature participate in brain clearance and are implicated in many neurological conditions such as Alzheimer’s disease, meningitis, multiple sclerosis, stroke, and traumatic brain injury. However, most of our knowledge concerning brain clearance via meninges is based on rodent data, and relevance to human disease remains unclear. One of the technical barriers in studies of meningeal physiology in health and disease is that existing imaging modalities are suboptimal for large and optically non-transparent meningeal tissue of humans and non-human primate (NHP) animal models. To address this barrier, we performed first characterization of NHP dura by high resolution confocal microscopy of clarified tissue. We investigated vascular structures and resident cells in normal monkeys and primate models of tauopathy and synucleinopathy. We demonstrated the presence of an extensive meningeal vascular network covering the entire tissue surface with resolution to the smallest capillaries. This is also the first work to map lymphatic vessels in the dura of non-human primate (NHP). Overall, the NHP lymphatic meningeal system resembles the anatomy found in rat dura, but it is more complex. Analysis of dura from NPH models of tauopathy and synucleinopathy revealed an association with disease-specific biomarkers (amyloid, tau, α-synuclein) with both the blood and lymphatic vasculature. This work has broad relevance to many brain diseases where solute accumulation and abnormal macromolecular clearance is a part of the pathogenesis.
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
Authors: Ravindran Vandana , Wagoner Jessica , Athanasiadis Paschalis , Den Hartigh Andreas B. , Sidorova Julia M. , Ianevski Aleksandr , Fink Susan L. , Frigessi Arnoldo , White Judith , Polyak Stephen J. , Aittokallio Tero 
Published: June 2022

ABSTRACTThe ongoing coronavirus disease 2019 (COVID-19) pandemic has highlighted the need to better understand virus-host interactions. We developed a network-based algorithm that expands the SARS-CoV-2-host protein interaction network and identifies host targets that modulate viral infection. To disrupt the SARS-CoV-2 interactome, we systematically probed for potent compounds that selectively target the identified host proteins with high expression in cells relevant to COVID-19. We experimentally tested seven chemical inhibitors of the identified host proteins for modulation of SARS-CoV-2 infection in human cells that express ACE2 and TMPRSS2. Inhibition of the epigenetic regulators bromodomain-containing protein 4 (BRD4) and histone deacetylase 2 (HDAC2), along with ubiquitin specific peptidase (USP10), enhanced SARS-CoV-2 infection. Such proviral effect was observed upon treatment with compounds JQ1, vorinostat, romidepsin, and spautin-1, when measured by cytopathic effect and validated by viral RNA assays, suggesting that HDAC2, BRD4 and USP10 host proteins have antiviral functions. Mycophenolic acid and merimepodib, two inhibitors of inosine monophosphate dehydrogenase (IMPDH 1 and IMPDH 2), showed modest antiviral effects with no toxicity in mock-infected control cells. The network-based approach enables systematic identification of host-targets that selectively modulate the SARS-CoV-2 interactome, as well as reveal novel chemical tools to probe virus-host interactions that regulate virus infection.SynopsisViruses exploit host machinery and therefore it is important to understand the virus-host dependencies to gain better insight of the key regulators of viral infection.Using a context-specific SARS-COV-2 PPI network, a computational framework was developed to identify host modulators of viral infection.Chromatin modifying host proteins HDAC2 and BRD4, along with deubiquitinating enzyme USP10, act as antiviral proteins.IMPDH inhibitors mycophenolic acid and merimipodib showed modest antiviral response to SARS-COV-2 infection, and no toxic effects.Cell context specificity is a critical factor when identifying selective modulators of viral infection and potential antiviral therapeutics.Topology-based network models cannot distinguish between host-proteins, the inhibition of which leads to either virus suppressive or enhancing effects.
Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage
Authors: Martínez-García Belén , Dyson Sílvia , Segura Joana , Gutierrez-Escribano Pilar , Aragón Luís , Roca Joaquim 
Published: June 2022

SUMMARYCondensin extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain DNA positive supercoils. However, in experimental conditions that sustain DNA loop extrusion, condensin restrains negative supercoils. Namely, upon ATP-mediated loading onto DNA, each condensin constrains a DNA linking number difference (ΔLk) of -0.4. This ΔLk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. These ΔLk values reflect the transient formation of a short left-handed loop of DNA, which is not the extruding loop. We conclude that, upon condensin ATPase-head engagement, a segment of DNA is pinched to form a short negatively supercoiled loop, which can be subsequently merged with the extruding loop. Such “pinch and merge” mechanism implies that the DNA is transferred between two dynamic DNA-binding sites while anchored at a third site.
Use of Solentim verified in-situ plate seeding (VIPS™) enhances single-cell cloning efficiency
Authors: Ilyayev Nadia , Martel Catherine , Mazumder Mostafizur , Singh Nishi , Rahbar Ramtin 
Published: June 2022

AbstractThe primary goal in cell line development is to establish high-producer recombinant cell line(s) of single-cell origin. Traditionally, these cell lines are developed using limiting dilution cloning (LDC) method of single cell isolation, a rate-limiting, lengthy and labor-intensive process.The Verified-In-Situ-Plate-Seeding (VIPS™) is an automated single-cell seeding and imaging equipment designed to accelerate cell line development workflow. In this study, VIPS™ was tested for efficiency and accuracy of single cell seeding in parallel with limiting dilution cloning (LDC). Three Chinese hamster ovary (CHO) derived cell lines with known clonal properties were tested under six different growth conditions (three growth media and two different kinds of microplates). Data showed VIPS™ and limiting dilution (LDC) have comparable cloning efficiency when CHO-M cells were tested. By contrast, the Verified In-Situ Plate Seeding (VIPS™) produced 6-8-fold more clones of single-cell origin than LDC when CHO-K1 or CHO-S cells were tested. Moreover, the verified In-Situ Plate Seeding (VIPS™) correctly identified single-cell and multiple-cells seeded wells with 65-72% and 52-81% accuracy, respectively. Taken together, the high throughput imaging and single-cell seeding capabilities of VIPS™ outperformed the rate-limiting LDC method and, therefore, has the potential to accelerate cell line development workflow.
Designed allosteric protein logic
Authors: Plaper Tjaša , Merljak Estera , Fink Tina , Lainšček Duško , Satler Tadej , Jazbec Vid , Benčina Mojca , Jerala Roman 
Published: June 2022

SUMMARYRegulation of the activity of proteins enables control of complex cellular processes. Allosteric regulation has been introduced individually into few natural proteins. Here, we present a generally applicable regulation of diverse proteins called INSRTR (inserted peptide structure regulator), based on inserting a short unstructured peptide into a solvent-accessible loop that retains protein function. Function of the target protein can be inactivated by the addition of a peptide that forms a rigid coiled-coil dimer. This platform enables the construction of ON/OFF protein switches, their regulation by small molecules, and Boolean logic functions with a rapid response in mammalian cells. INSRTR can be used to regulate a wide range of proteins, as demonstrated on ten members of protein families with diverse biological activities including enzymes, signaling mediators, DNA binders/transcriptional regulators, fluorescent protein, and antibodies regulating chimeric antigen receptor. INSRTR platform presents an extraordinary potential for regulating biological systems and applications.One sentence summaryAuthors have designed a widely applicable system to activate or inactivate function of diverse proteins or form Boolean logic gates based on formation of a coiled-coil dimer within protein loops and demonstrated its implementation on a range of 10 diverse proteins.