bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decision trees for COVID-19 prognosis learned from patient data: Desaturating the ER with Artificial Intelligence
Authors: Bernaola Nikolas , de Lima Guillermo , Riaño Miguel , Llanos Lucia , Heili-Frades Sarah , Sanchez Olga , Lara Antonio , Plaza Guillermo , Carballo Cesar , Gallego Paloma , Larrañaga Pedro , Bielza Concha 
Published: May 2022

AbstractObjectivesTo present a model that enhances the accuracy of clinicians when presented with a possibly critical Covid-19 patient.MethodsA retrospective study was performed with information of 5,745 SARS-CoV2 infected patients admitted to the Emergency room of 4 public Hospitals in Madrid belonging to Quirón Salud Health Group (QS) from March 2020 to February 2021. Demographics, clinical variables on admission, laboratory markers and therapeutic interventions were extracted from Electronic Clinical Records. Traits related to mortality were found through difference in means testing and through feature selection by learning multiple classification trees with random initialization and selecting the ones that were used the most. We validated the model through cross-validation and tested generalization with an external dataset from 4 hospitals belonging to Sanitas Hospitals Health Group. The usefulness of two different models in real cases was tested by measuring the effect of exposure to the model decision on the accuracy of medical professionals.ResultsOf the 5,745 admitted patients, 1,173 died. Of the 110 variables in the dataset, 34 were found to be related with our definition of criticality (death in <72 hours) or all-cause mortality. The models had an accuracy of 85% and a sensitivity of 50% averaged through 5-fold cross validation. Similar results were found when validating with data from the 4 hospitals from Sanitas. The models were found to have 11% better accuracy than doctors at classifying critical cases and improved accuracy of doctors by 12% for non-critical patients, reducing the cost of mistakes made by 17%.
Remote self-report and speech-in-noise measures predict clinical audiometric thresholds
Authors: Motlagh Zadeh Lina , Brennan Veronica , Swanepoel De Wet , Lin Li , Moore David R. 
Published: May 2022

AbstractDevelopments in smartphone technology and the COVID-19 pandemic have highlighted the feasibility and need for remote, but reliable hearing tests. Previous studies used remote testing but did not directly compare results in the same listeners with standard lab or clinic testing. This study investigated reliability of remote, self-administered digits-in-noise (remote-DIN) compared with lab-based, supervised (lab-DIN) testing. Predictive validity was further examined in relation to a commonly used self-report, Speech, Spatial, and Qualities of Hearing (SSQ-12), and lab-based, pure tone audiometry. DIN speech reception thresholds (SRTs) of adults (18-64 y/o) with normal-hearing (NH, N=16) and hearing loss (HL, N=18), were measured using English-language digits (0-9), binaurally presented as triplets in one of four speech-shaped noise maskers (broadband, low-pass filtered at 2, 4, 8 kHz) and two digit phases (diotic, antiphasic). High, significant intraclass correlation coefficients indicated strong internal consistency of remote-DIN SRTs, which also correlated significantly with lab-DIN SRTs. There was no significant mean difference between remote- and lab-DIN on any tests. NH listeners had significantly higher SSQ scores, and remote- and lab-DIN SRTs than listeners with HL. All versions of remote-DIN SRTs correlated significantly with pure-tone-average (PTA), with the 2-kHz filtered test the best predictor, explaining 50% of variance in PTA. SSQ total score also significantly and independently predicted PTA (17% of variance) and all test versions of the remote-DIN, except the antiphasic BB test. This study shows that remote SSQ-12 and remote-DIN are sensitive tools for capturing important aspects of auditory function.
Assessing the impacts of timing on the health benefits, cost-effectiveness and relative affordability of COVID-19 vaccination programmes in 27 African Countries
Authors: Liu Yang , Pearson Carl AB , Madriz Montero Andrés , Torres-Rueda Sergio , Asfaw Elias , Uzochukwu Benjamin , Drake Tom , Bergren Eleanor , Eggo Rosalind M , Ruiz Francis , Ndembi Nicaise , Nonvignon Justice , Jit Mark , Vassall Anna 
Published: May 2022

AbstractBackgroundThe COVID-19 vaccine supply shortage in 2021 constrained rollout efforts in Africa while populations experienced waves of epidemics. As supply picks up, a key question becomes if vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.MethodsWe assessed the impact of timing using an epidemiological and economic model. We fitted our mathematical epidemiological model to reported COVID-19 deaths in 27 African countries to estimate the existing immunity (resulting from infection) before substantial vaccine rollout. We then projected health outcomes for different programme start dates (2021-01-01 to 2021-12-01, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/ million population-day, respectively) for viral vector and mRNA vaccines. Rollout rates used were derived from observed uptake trajectories. We collected data on vaccine delivery costs by country income group. Lastly, we calculated incremental cost-effectiveness ratios and relative affordability.FindingsVaccination programmes with early start dates incur the most health benefits and are most cost-effective. While incurring the most health benefits, fast vaccine roll-outs are not always the most cost-effective. At a willingness-to-pay threshold of 0.5xGDP per capita, vaccine programmes starting in August 2021 using mRNA and viral vector vaccines were cost-effective in 6-10 and 17-18 of 27 countries, respectively.InterpretationAfrican countries with large proportions of their populations unvaccinated by late 2021 may find vaccination programmes less cost-effective than they could have been earlier in 2021. Lower vaccine purchasing costs and/or the emergence of new variants may improve cost-effectiveness.FundingBill and Melinda Gates Foundation, World Health Organization, National Institute of Health Research (UK), Health Data Research (UK)
Aggregated genomic data as cohort-specific allelic frequencies can boost variants and genes prioritization in non-solved cases of inherited retinal dystrophies
Authors: Iancu Ionut-Florin , Perea-Romero Irene , Núñez-Moreno Gonzalo , de la Fuente Lorena , Romero Raquel , Ávila-Fernandez Almudena , José Trujillo-Tiebas María , Riveiro-Álvarez Rosa , Almoguera Berta , Martín-Mérida Inmaculada , Del Pozo-Valero Marta , Damián-Verde Alejandra , Cortón Marta , Ayuso Carmen , Minguez Pablo 
Published: May 2022

AbstractThe introduction of NGS in genetic diagnosis has increased the repertoire of variants and genes involved and the amount of genomic information produced. We built an allelic-frequency (AF) database for a heterogeneous cohort of genetic diseases to explore the aggregated genomic information and boost diagnosis in inherited retinal dystrophies (IRD). We retrospectively selected 5683 index-cases with clinical exome sequencing tests available, 1766 with IRD and the rest, with diverse genetic diseases. We calculated subcohort’s IRD specific AF and compare it with suitable pseudocontrols. For non-solved IRD cases, we prioritized variants with a significant increment of frequencies, with 8 variants that may contribute to explain the phenotype, and 10/11 of uncertain significance that were reclassified as likely-pathogenic according to ACMG. Besides, we developed a method to highlight genes with more frequent pathogenic variants in IRD cases than in pseudocontrols weighted by the increment of benign variants in the same comparison. We identified 18 genes for further studies that provided new insights in five cases. This resource can also help to calculate the carrier-frequency in IRD genes. A cohort-specific AF database assist with variants and genes prioritization and operate as an engine that provides new hypothesis in non-solved cases, augmenting diagnosis rate.
Qualitative hepatitis C virus RNA assay identifies active infection with sufficient viral load for treatment among Phetchabun residents in Thailand
Authors: Pratedrat Pornpitra , Nilyanimit Pornjarim , Wasitthankasem Rujipat , Posuwan Nawarat , Auphimai Chompoonut , Hansoongnern Payuda , Pimsing Napaporn , Ngamnimit Saranya , Thongmai Chaiwat , Phaengkha Wijittra , Wanlapakorn Nasamon , Vongpunsawad Sompong , Poovorawan Yong 
Published: May 2022

AbstractThe World Health Organization envisions the elimination of viral hepatitis by 2030 through reducing prevalence and transmission, increasing diagnostic screening, and expanding treatment coverage. Efforts to micro-eliminate hepatitis in Phetchabun province in Thailand, a region where the prevalence of hepatitis C virus (HCV) infection and liver cancer is higher than elsewhere in the country, began with evaluating the province-wide burden of HCV. Here, we describe a feasibility study to assess active HCV infection by screening Phetchabun residents ages 35 to 69 years for anti-HCV antibodies by using a rapid diagnostic test (RDT) at the point of care. Positive anti-HCV results were further evaluated for active infection using qualitative HCV RNA assay, followed by quantitative HCV viral load determination in a subset of samples. Currently, we have identified 6.2% (10,621/170,163) anti-HCV positive individuals, of whom 74.9% (3,930/5,246) demonstrated detectable viral RNA. Quantitative test found that 97.5% (1,001/1,027) had HCV viral load ≥5,000 IU/mL. Thus, primary screening with anti-HCV RDT followed by qualitative HCV RNA evaluation could identify active and chronic HCV infection in almost all individuals with a viral load ≥5,000 IU/mL, which is the current threshold for the National Health Security Office treatment in Thailand. Our data suggest that qualitative HCV RNA evaluation may obviate the need for the more expensive quantitative HCV viral load test and reduce a significant barrier toward HCV elimination in a middle-income country.
Characterization of Childhood Trauma, Hippocampal Mediation and Cannabis Use in a Large Dataset of Psychosis and Non-Psychosis Individuals
Authors: del Re Elisabetta C. , Yassin Walid , Zeng Victor , Keedy Sarah , Alliey-Rodriguez Ney , Ivleva Elena , Hill Scott , Rychagov Nicole , McDowell Jennifer E. , Bishop Jeffrey R. , Mesholam-Gately Raquelle , Merola Giovanni , Lizano Paulo , Gershon Elliot , Pearlson Godfrey , Sweeney John A. , Clementz Brett , Tamminga Carol , Keshavan Matcheri 
Published: May 2022

AbstractBackgroundCannabis use (CA) and childhood trauma (CT) independently increase the risk of earlier psychosis onset; but their interaction in relation to psychosis risk and association with endocannabinoid-receptor rich brain regions, i.e. the hippocampus (HP), remains unclear. The objective was to determine whether lower age of psychosis onset (AgePsyOnset) is associated with CA and CT through mediation by the HP, and genetic risk, as measured by schizophrenia polygene scores (SZ-PGRS).MethodsCross- sectional, case-control, multicenter sample from 5 metropolitan US regions. Participants (n=1185) included 397 controls not affected by psychosis (HC); 209 participants with bipolar disorder type-1; 279 with schizoaffective disorder; and 300 with schizophrenia (DSM IV-TR). CT was assessed using the Childhood Trauma Questionnaire (CTQ); CA was assessed by self-reports and trained clinical interviewers. Assessment included neuroimaging, symptomatology, cognition and calculation of the SZ polygenic risk score (SZ-PGRS).OutcomesIn survival analysis, low CT and CA are associated with lower AgePsyOnset. At high CT or CA, CT or CA are individually sufficient to affect AgePsyOnset. CT relation with AgePsyOnset is mediated in part by the HP in CA users before AgePsyOnset. CA before AgePsyOnset is associated with higher SZ-PGRS and correlated with younger age at CA usage.InterpretationCA and CT interact to increase risk when moderate; while severe CT and/or CA abuse/dependence are each sufficient to affect AgePsyOnset, indicating a ceiling effect. Probands with/out CA before AgePsyOnset differ on biological variables, suggesting divergent pathways to psychosis.FundingMH077945; MH096942; MH096913; MH077862; MH103368; MH096900; MH122759.Research in contextEvidence before this studyCannabis use (CA) and childhood trauma (CT) independently increase the risk of earlier development of psychosis. Scarce evidence exists on the interaction between CA and CT and the neurobiological substrate of their interaction.Added value of this studyAnalysis of a large transdiagnostic sample of psychosis probands and controls (N=1288) indicates synergy of CT and CA and small but significant contribution of the posterior hippocampus. Data further indicate existence of two populations of probands with psychosis, those with and those without CA after CT before psychosis onset. CT and CA before psychosis onset interact according to a stepwise increase up to reaching a ceiling effect.Implications of all the available evidenceClinically, youth with low, medium CT need to be targeted for intervention before CA onset.
Prevalence and risk factors of Pseudomonas aeruginosa colonization
Authors: Vy Tran Nguyen Bao , Truong Quang Minh , Anh Nguyen Lam Que , Huong Nguyen Ngoc My , Tran Quang Hung , Phuong Dinh Thi Tuyet , Hua Vinh Son , Lambert Peter A. , Nguyen Thi Thu Hoai 
Published: May 2022

AbstractPseudomonas aeruginosa (P. aeruginosa) is one of the most concerning pathogens due to its multidrug resistance. P. aeruginosa can be a part of the normal commensal flora of humans but can also cause a wide range of infections. In this study, we investigated the prevalence of commensal P. aeruginosa in 609 Vietnamese participants (310 females and 299 males, age range of 2 to 73 years) who had no acute infection or disease symptoms at the time of sample collection. Samples were taken from the throat, naris and outer ears. As a result, 19 were positive with P. aeruginosa (3.12%, 95% CI: 0.017-0.045) which came mostly from throat (11/19, 57.89%). Participants with a history of sinusitis were 11.57 times more likely to be colonized with P. aeruginosa than participants without a history of sinusitis (OR: 11.57, 95% CI: 4.08-32.76, p-value< 0.0001). Age and gender were not significantly associated with P. aeruginosa colonization. The commensal P. aeruginosa isolates were tested for biofilm formation, pyocyanin, siderophore, lipase, protease and gelatinase production. Among 16 P. aeruginosa isolates used for these tests, 100% (16/16) were positive for biofilm, pyocyanin and siderophores; 93.75% (15/16) isolates were positive for gelatinase and protease; and 50% (8/16) isolates were positive for lipase. There were no differences in the pattern and range of virulence factors of P. aeruginosa isolates taken from participants with and without sinusitis history. In summary, P. aeruginosa colonized 3.12% of participants, and its presence was clearly associated with sinusitis history. Most commensal P. aeruginosa isolates can produce biofilm, pyocyanin, siderophores, gelatinase and protease.Author summaryP. aeruginosa is both a common opportunistic pathogen which causes various infections in humans, such as blood, lung, and skin infections and a commensal bacterium which can be found normal human flora. In this study, we showed that the P. aeruginosa colonized 3.12% participants and resided mostly in human throat. Interestingly, we found that people with sinusitis history were more likely to be P. aeruginosa carriers. On the other hand, age and gender did not significantly affect P. aeruginosa colonization. Most tested P. aeruginosa isolates expressed various virulence factors, including biofilm, siderophores, pyocyanin, gelatinase, protease, and lipase.
Tle4 controls both developmental acquisition and postnatal maintenance of corticothalamic projection neuron identity
Authors: Galazo Maria J. , Sweetser David , Macklis Jeffrey D. 
Published: May 2022

SummaryIdentities, circuitry, and function of distinct neuron subtypes are specified during embryonic development, then maintained during postnatal maturation and potential plasticity. Mechanisms that control early acquisition of neuron subtype identities, encompassing circuitry and function, in the cerebral cortex have become increasingly understood. However, mechanisms controlling maintenance of identity, and accompanying regulation of plasticity, are largely unexplored and unknown.Here, we identify two novel functions of the co-repressor Tle4 in both acquisition and maintenance of neuron subtype identity of corticothalamic projection neurons. Embryonically, Tle4 promotes acquisition of corticothalamic molecular and cellular identity, and blocks emergence of core characteristics of subcerebral / corticospinal projection neuron identity, including morphology, gene expression, axonal connectivity, and circuitry. Postnatally, Tle4 is required to maintain corticothalamic molecular and projection identity during circuit maturation, avoiding potentially disruptive plasticity, but also limiting potentially beneficial plasticity.We identify an epigenetic mechanism by which TLE4 controls the activation state of loci regulating the level of Fezf2 expression by corticothalamic neurons during embryonic and postnatal development. This mechanism contributes importantly to distinction of cortical output (corticofugal) subtypes, and ensures appropriate maturation and maintenance of CThPN.HighlightsTle4 promotes CThPN identity and blocks SCPN identity in early-born cortical neuronsTle4 is necessary to maintain CThPN identity during circuit maturationTLE4-FEZF2 complex epigenetically regulates Fezf2 expression in developing CThPNTLE4-FEZF2 regulates corticofugal subtypes distinction and maturation of CThPN
Reduced contrast surround suppression associated with schizophrenia depends on visual acuity and scene context
Authors: Pokorny Victor J. , Schallmo Michael-Paul , Sponheim Scott R. , Olman Cheryl 
Published: May 2022

AbstractPerceptual distortions are core features of psychosis. Weakened surround suppression has been proposed as a neural mechanism of such atypical perceptual experiences. While previous work has measured suppression by asking participants to report the perceived contrast of a low-contrast target surrounded by a high-contrast surround, it is possible to modulate perceived contrast solely by manipulating the orientation of a matched-contrast center and surround. Removing the bottom-up segmentation cue of contrast difference and isolating the orientation-dependent suppression may clarify the neural processes responsible for atypical surround suppression in psychosis. We examined surround suppression across a spectrum of psychotic psychopathology including people with schizophrenia (PSZ; N=31) and bipolar disorder (PBD; N=29), first-degree biological relatives of these patient groups (PBDrel, PSZrel; N=28, N=21, respectively), and healthy controls (N=29). Surround suppression deficits in PSZ, while observable under many stimulus conditions, were absent under the condition that produced the strongest suppression. PBD and PSZrel exhibited intermediate suppression, while PBDrel performed most similarly to controls. Intriguingly, group differences in surround suppression magnitude were moderated by visual acuity. We propose a potential model by which visual acuity and/or focal attention interact with untuned gain control that reproduces the observed pattern of results including the lack of group differences when orientation of center and surround are the same. Our findings further elucidate perceptual mechanisms of impaired center-surround processing in psychosis and provide insights into the effects of visual acuity on orientation-dependent suppression in PSZ.
Inhaled CO2 concentration while wearing face masks: a pilot study using capnography
Authors: Martellucci Cecilia Acuti , Flacco Maria Elena , Martellucci Mosè , Violante Francesco Saverio , Manzoli Lamberto 
Published: May 2022

ABSTRACTNone of the available evaluations of the inhaled air carbon dioxide (CO2) concentration, while wearing face masks, used professional, real-time capnography with water-removal tubing. We measured the end-tidal CO2 using professional side-stream capnography, with water-removing tubing (Rad-97™ capnograph), at rest, (1) without masks, (2) wearing a surgical mask, and (3) wearing a FFP2 respirator, in 102 healthy volunteers aged 10-90 years, from the general population of Ferrara province, Italy. The inhaled air CO2 concentration was then computed as: ((mask volume × end-tidal CO2) + ((tidal volume - mask volume) × ambient air CO2)) / tidal volume).The mean CO2 concentration was 4965±1047 ppm with surgical masks, and 9396±2254 ppm with FFP2 respirators. The proportion of the sample showing a CO2 concentration higher than the 5000 ppm acceptable exposure threshold recommended for workers was 40.2% while wearing surgical masks, 99.0% while wearing FFP2 respirators. The mean blood oxygen saturation remained >96%, and the mean end-tidal CO2 <33 mmHg. Adjusting for age, gender, BMI, and smoking, the inhaled air CO2 concentration significantly increased with increasing respiratory rate (with a mean of 10,143±2782 ppm among the participants taking 18 or more breaths per minute, while wearing FFP2 respirators), and was higher among the minors, who showed a mean CO2 concentration of 12,847±2898 ppm, while wearing FFP2 respirators. If these results will be confirmed, the current guidelines on mask-wearing could be updated to integrate recommendations for slow breathing and a more targeted use when contagion risk is low.
Polygenic resilience scores capture protective genetic effects for Alzheimer’s disease
Authors: Hou Jiahui , Hess Jonathan L. , Armstrong Nicola , Bis Joshua C. , Grenier-Boley Benjamin , Karlsson Ida K. , Leonenko Ganna , Numbers Katya , O’Brien Eleanor K. , Shadrin Alexey , Thalamuthu Anbupalam , Yang Qiong , Andreassen Ole A. , Brodaty Henry , Gatz Margaret , Kochan Nicole A. , Lambert Jean-Charles , Laws Simon M. , Masters Colin L. , Mather Karen A. , Pedersen Nancy L. , Posthuma Danielle , Sachdev Perminder S. , Williams Julie ,   the Alzheimer’s Disease Neuroimaging Initiative, Fan Chun Chieh , Faraone Stephen V. , Fennema-Notestine Christine , Lin Shu-Ju , Escott-Price Valentina , Holmans Peter , Seshadri Sudha , Tsuang Ming T. , Kremen William S. , Glatt Stephen J. 
Published: May 2022

AbstractPolygenic risk scores (PRSs) can boost risk-prediction in late-onset Alzheimer’s disease (LOAD) beyond apolipoprotein E (APOE)but have not been leveraged to identify genetic resilience factors. Here, we sought to identify resilience-conferring common genetic variants in 1) unaffected individuals having high PRSs for LOAD, and 2) unaffectedAPOE-ε4 carriers also having high PRSs for LOAD. We used genome-wide association study (GWAS) to contrast “resilient” unaffected individuals at the highest genetic risk for LOAD with LOAD cases at comparable risk. From GWAS results, we constructed polygenic resilience scores to aggregate the addictive contributions of risk-orthogonal common variants that promote resilience to LOAD. Replication of resilience scores was undertaken in eight independent studies. We successfully replicated two polygenic resilience scores that reduce genetic-risk penetrance for LOAD. We also showed that polygenic resilience scores positively correlate with polygenic risk scores in unaffected individuals, perhaps aiding in staving off disease. Our findings align with the hypothesis that a combination of risk-independent common variants mediates resilience to LOAD by moderating genetic disease risk.