bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robotic Antimicrobial Susceptibility Platform (RASP): A Next Generation Approach to One-Health Surveillance of Antimicrobial Resistance
Authors: Truswell Alec , Abraham Rebecca , O’Dea Mark , Lee Zheng Zhou , Lee Terence , Laird Tanya , Blinco John , Kaplan Shai , Turnidge John , Trott Darren J. , Jordan David , Abraham Sam 
Published: March 2021

AbstractBackgroundSurveillance of antimicrobial resistance (AMR) is critical to reducing its wide-reaching impact. Its reliance on sample size invites solutions to longstanding constraints regarding scalability. A robotic platform (RASP) was developed for high-throughput AMR surveillance in accordance with internationally recognised standards (CLSI and ISO 20776-1:2019) and validated through a series of experiments.MethodsExperiment A compared RASP’s ability to achieve consistent MICs to that of a human technician across eight replicates for fourE. coliisolates. Experiment B assessed RASP’s agreement with human performed MICs across 91E. coliisolates with a diverse range of AMR profiles. Additionally, to demonstrate its real-world applicability, the RASP workflow was then applied to five faecal samples where a minimum of 47E. coliper animal (239 total) were evaluated using an AMR indexing framework.ResultsFor each drug-rater-isolate combination in experiment A, there was a clear consensus of the MIC and deviation from the consensus remained within one doubling-dilution (the exception being gentamicin at two dilutions). Experiment B revealed a concordance correlation coefficient of 0.9670 (95%CI: 0.9670 - 0.9670) between the robot and human performed MICs. RASP’s application to the five faecal samples highlighted the intra-animal diversity of gut commensalE. coli,identifying between five and nine unique isolate AMR phenotypes per sample.ConclusionsWhile adhering to internationally accepted guidelines, RASP was superior in throughput, cost and data resolution when compared to an experienced human technician. Integration of robotics platforms in the microbiology laboratory is a necessary advancement for future One-Health AMR endeavours.
Mechanisms of transforming DNA uptake to the periplasm ofBacillus subtilis
Authors: Hahn Jeanette , DeSantis Micaela , Dubnau David 
Published: March 2021

ABSTRACTWe demonstrate here that the acquisition of DNAase resistance by transforming DNA, often assumed to indicate transport to the cytoplasm, actually reflects uptake to the periplasm, requiring a re-evaluation of conclusions about the roles of several proteins in transformation. The new evidence suggests that the transformation pilus is needed for DNA binding to the cell surface near the cell poles and for the initiation of uptake. The cellular distribution of the membrane-anchored ComEA ofB. subtilisdoes not noticeably change during DNA uptake as does the unanchored ComEA ofVibrioandNeisseria. Instead, our evidence suggests that ComEA stabilizes the attachment of transforming DNA at localized regions in the periplasm and then mediates uptake, probably by a Brownian ratchet mechanism. Following that, the DNA is transferred to periplasmic portions of the channel protein ComEC, which plays a previously unsuspected role in uptake to the periplasm. We show that the transformation endonuclease NucA also facilitates uptake to the periplasm and that the previously demonstrated role of ComFA in the acquisition of DNAase resistance actually derives from the instability of ComGA when ComFA is deleted. These results prompt a new understanding of the early stages of DNA uptake for transformation.IMPORTANCETransformation is a widely distributed mechanism of bacterial horizontal gene transfer that plays a role in the spread of antibiotic resistance and virulence genes and more generally in evolution. Although transformation was discovered nearly a century ago and most, if not all of the proteins required have been identified in several bacterial species, much remains poorly understood about the molecular mechanism of DNA uptake. This study uses epifluorescence microscopy to investigate the passage of labeled DNA into the compartment between the cell wall and the cell membrane ofBacillus subtilis, a necessary early step in transformation. The roles of individual proteins in this process are identified, and their modes of action are clarified.
Impedance scaling for gold and platinum microelectrodes
Authors: Fan Bo , Wolfrum Bernhard , Robinson Jacob T. 
Published: March 2021

AbstractObjectiveElectrical measurement of the activity of individual neurons is a primary goal for many invasive neural electrodes. Making these “single unit” measurements requires that we fabricate electrodes small enough so that only a few neurons contribute to the signal, but not so small that the impedance of the electrode creates overwhelming noise or signal attenuation. Thus, neuroelectrode design often must strike a balance between electrode size and electrode impedance, where the impedance is often assumed to scale linearly with electrode area.Approach and main resultsHere we study how impedance scales with neural electrode area and find that the 1 kHz impedance of Pt electrodes (but not Au electrodes) transitions from scaling with area (r-2) to scaling with perimeter (r-1) when the electrode radius falls below 10 microns. This effect can be explained by the transition from planar to spherical diffusion behavior previously reported for electrochemical microelectrodes.Significance:These results provide important intuition for designing small, single unit recording electrodes. Specifically, for materials where the impedance is dominated by a pseudo-capacitance that is associated with a diffusion limited process, the total impedance will scale with perimeter rather than area when the electrode size becomes comparable with the diffusion layer thickness. For Pt electrodes this transition occurs around 10 um radius electrodes. At even lower frequencies (1 Hz) impedance approaches a constant. This transition to r-1scaling implies that electrodes with a pseudo-capacitance can be made smaller than one might expect before thermal noise or voltage division limits the ability to acquire high-quality single-unit recordings.
Unplanned Hospital Visits after Ambulatory Surgical Care
Authors: Bongiovanni Tasce , Parzynski Craig , Ranasinghe Isuru , Steinman Michael A , Ross Joseph S. 
Published: March 2021

Structured AbstractObjectivesWe sought to assess the rate of unplanned hospital visits among patients undergoing ambulatory surgery.Summary Background DataThe majority of surgeries performed in the United States now take place in outpatient settings. Post-discharge hospital visit rates have been shown to vary widely, suggesting variation in surgical or discharge care quality. Complicating efforts to address quality, most facilities and surgeons are unaware of their patients’ hospital visits after surgery since patients may present to a different hospital.MethodsWe used state-level, administrative data from the Agency for Healthcare Research and Quality’s Healthcare Cost and Utilization Project from California to assess unplanned hospital visits after ambulatory surgery. To compare rates across centers, we determined the age, sex, and procedure-adjusted rates of hospital visits for each facility using 2-level, hierarchical, generalized linear models using methods similar to existing Centers for Medicare and Medicaid Services measures.ResultsAmong a total of 1,260,619 ambulatory same-day surgeries from 440 surgical facilities, the risk adjusted 30-day rate of unplanned hospital visits was 4.8%, with emergency department visits of 3.1% and hospital admissions of 1.7%. Several patient characteristics were associated with increased risk of unplanned hospitals visits, including increased age, increased number of comorbidities (using the Elixhauser score), and type of procedure (p<0.001).ConclusionsThe overall rate unplanned hospital visits within 30 days after same-day surgery is low but variable, suggesting a difference in the quality of care provided. Further, these rates are higher among specific patient populations and procedure types, suggesting areas for targeted improvement.Mini-AbstractThe majority of surgeries performed in the United States now take place in outpatient settings with wide variation of post-discharge hospital visit rates. We used state-level, administrative data to assess the rate of unplanned hospital visits after ambulatory surgery and found a risk adjusted 30-day rate of 4.8%. Increased age, increased number of comorbidities (using the Elixhauser score), and type of procedure were associated with increased risk of unplanned hospitals visits, suggesting areas for targeted improvement.
Spread and sources of information and misinformation about COVID-19 early during the pandemic in a U.S. national cohort study
Authors: Westmoreland Drew A. , Berry Amanda , Zimba Rebecca , Kulkarni Sarah , Parcesepe Angela , Maroko Andrew R , Poehlein Emily , You William , Mirzayi Chloe , Kochhar Shivani , Robertson McKaylee , Waldron Levi , Grov Christian , Nash Denis 
Published: March 2021

ABSTRACTBackgroundEarly in the pandemic, misinformation about COVID-19 was spread on social media. The purpose of this study was to describe trusted sources of COVID-19 information and claims seen and believed about COVID-19 early in the pandemic among U.S. adults. Then, we assessed the impact of believing such claims on engaging in personal protective actions (PPA).MethodsWe used baseline data from the CHASING COVID Cohort (n = 7,070) collected March 28, 2020 to April 20, 2020 to describe trusted sources of COVID-19 information as well as claims circulating on social media that had been seen and believed. We used Poisson regression to determine the association of believing certain claims with engaging in a higher number of PPA.ResultsThe top three trusted sources of COVID-19 information were the CDC (67.9%), the WHO (53.7%), and State Health Departments (53.0%). Several COVID-19 claims circulated on social media had been seen, e.g., that the virus was created in a laboratory (54.8%). Moreover, substantial proportions of participants indicated agreement with some of these claims. In multivariable regression, we found that belief in certain claims was associated with engaging in a higher number of PPA. For example, believing that paper masks would prevent transmission of the virus was associated with engaging in a higher number of protective actions (β = 0.02, 95% CI: 0.004 – 0.046).ConclusionsResults suggest the need for public health leadership on social media platforms to combat misinformation and supports social media as a tool to further public health interventions.
Acceptability of contact management and care of simple cases of COVID-19 at home: a mixed-method study in Senegal
Authors: Ba Mouhamadou Faly , Ridde Valéry , Diallo Amadou Ibra , Tine Jean Augustin Diégane , Kane Babacar , Gaye Ibrahima , Traoré Zoumana , Bonnet Emmanuel , Faye Adama 
Published: March 2021

ABSTRACTIntroductionIn mid-2020, due to the health system challenges from increased COVID-19 cases, the Ministry of Health and Social Action in Senegal opted for contact management and care of simple cases at home. The study’s objective was to determine the acceptability of contact management, home care of simple cases of COVID-19, and its associated factors.MethodThis was a sequential mixed-method study. We collected data from June 11, 2020, to July 10, 2020, for the quantitative survey (N=813) and from August 24 to September 16, 2020, for the qualitative survey (N=30). We carried out a sampling strategy using marginal quotas at the national level. We collected data using a structured questionnaire in a telephone interview for the quantitative survey and using an interview guide formulated from the quantitative survey’s initial results for the qualitative data. We assessed acceptability using binomial logistic regression combined with content analysis.ResultsThe care of simple cases of COVID-19 at home was well accepted (78.5%). This result was justified for some (saturation of the health system) but not for others (risk of contamination). The use of home contact management was less accepted (51.4%), with risk limitation as the main reason given. The acceptability of home-based care for simple cases was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.55 [95%CI: 1.04,2.28]), regular research into COVID-19 (ORaj: 2.12 [95%CI: 1.45,3.12]), belief in the existence of treatment (ORaj: 1.82 [95%CI: 1.19,2.83]), and confidence in institutional information (ORaj: 2.10 [95%CI: 1.43,3.10]). The acceptability of home-based contact management was positively associated with knowledge of the modes of transmission of the virus (ORaj: 1.77 [95%CI: 1.27,2.48]), regular research for information on COVID-19 (ORaj: 2.39 [95%CI: 1.76,3.26]), and confidence in the government in the fight against the epidemic (ORaj: 1.51 [95%CI: 1.10,2.08]).ConclusionRegular information on the disease, knowledge of its mode of transmission and trust in institutions are factors in accepting COVID-19 management at the community level. Authorities should take these factors into account for better communication to improve the acceptability of home-based care.
Individual’s daily behaviour and intergenerational mixing in different social contexts of Kenya
Authors: Del Fava Emanuele , Adema Irene , Kiti Moses C. , Poletti Piero , Merler Stefano , Nokes D. James , Manfredi Piero , Melegaro Alessia 
Published: March 2021

AbstractWhich are the characteristics of contact patterns in diverse social contexts in sub-Saharan Africa, and which types of individuals and daily behaviours may play a pivotal role in infection transmission to the most vulnerable, such as older adults? We address these questions using novel survey data on social contacts and time use from a sample of 1407 individuals from rural, urban, and slum settings in Kenya. In the rural setting, we observed the highest number of daily social contacts (11.56, SD = 0.23) and the highest share of intergenerational mixing with older adults (7.5% vs. around 4% in the urban settings). Intergenerational mixing with older adults was mainly reported by individuals spending their day mostly in the general community (around 8%) or at home (5.1%), rather than at work (1.5%) or at school (3.6%). These results are essential to define effective interventions to control infection transmission in the African context.
The Burden of and Factors Associated with Age-Related Eye Diseases in Arab American Adults
Authors: Yaldo Luke M. , Dallo Florence J. , Ruterbusch Julie J. , Schwartz Kendra , Jamil Hikmet J. 
Published: March 2021

AbstractPurposeTo estimate the age- and sex-adjusted proportions of cataract, diabetic retinopathy, glaucoma, and macular degeneration among the Arab American community, a notably understudied minority that is aggregated under whites.MethodsThe Arab American Eye Study is a multicenter retrospective chart review involving ten years of electronic medical records (1/1/2010 through 1/1/2020). The study sample included 1,390 Arab Americans and 4,950 whites 45 years of age and older, totaling 6,340 subjects. Arab Americans were identified using an Arab American name algorithm. Subjects with race variables other than white or Arab American or those under age 45 were excluded from the study. Age- and sex-adjusted proportions of cataract, diabetic retinopathy, glaucoma, and macular degeneration were determined. Odds ratios with 95% confidence intervals were used to examine the association between race/ethnicity and eye diseases.ResultsOf the 6,340 participants (4,950 whites and 1,390 Arab Americans), males comprised 46.3% and the median age group was 55-64 years. Arab Americans displayed higher age- and sex-adjusted proportions of cataracts (45.4% versus 40.7%), dry age-related macular degeneration (10% versus 8.9%), glaucoma (8% vs 6%), and diabetic retinopathy (11.7% versus 4.2%). Fully adjusted logistic regression revealed that Arab Americans were 19% more likely to have cataracts (OR = 1.19; 95% CI = 1.05, 1.35) and 272% more likely to have diabetic retinopathy (OR = 2.72; 95% CI = 2.17; 3.41).ConclusionsResults from the Arab American Eye Study suggest that the burden of cataract and diabetic retinopathy is significantly higher among Arab Americans in comparison to whites.
Are vaccines safe in patients with Long COVID? A prospective observational study
Authors: Arnold DT , Milne A , Samms E , Stadon L , Maskell NA , Hamilton FW 
Published: March 2021

IntroductionAlthough the efficacy of SARS-CoV-2 vaccination to prevent symptomatic COVID-19 is well established, there are no published studies on the impact on symptoms in patients with Long Covid. Anecdotal reports have suggested both a potential benefit and worsening of symptoms post vaccination with the uncertainty leading to some vaccine hesitancy amongst affected individuals.MethodsPatients initially hospitalised with COVID-19 were prospectively recruited to an observational study with clinical follow-up at 3 months (June-July 2020) and 8 months (Dec 2020-Jan 2021) post-admission. Participants who received the Pfizer-BioNTech (BNT162b2) or Oxford-AstraZeneca (ChAdOx1 nCoV-19) vaccine between January to February 2021 were identified and matched 2:1 (in terms of 8-month symptoms) with participants from the same cohort who were unvaccinated. All were re-assessed at 1 month post vaccination (or matched timepoint for unvaccinated cohort). Validated quality of life (SF-36), mental wellbeing (WEMWBS) and ongoing symptoms were assessed at all timepoints. Formal statistical analysis compared the effect of vaccination on recent quality of life using baseline symptoms, age, and gender in linear regression.ResultsForty-four vaccinated participants were assessed at a median of 32 days (IQR 20-41) post vaccination with 22 matched unvaccinated participants. Most were highly symptomatic of Long Covid at 8 months (82% in both groups had at least 1 persistent symptom), with fatigue (61%), breathlessness (50%) and insomnia (38%) predominating. There was no significant worsening in quality-of-life or mental wellbeing metrics pre versus post vaccination. Nearly two-thirds (n=27) reported transient (<72hr duration) systemic effects (including fever, myalgia and headache).When compared to matched unvaccinated participants from the same cohort, those who had receive a vaccine had a small overall improvement in Long Covid symptoms, with a decrease in worsening symptoms (5.6% vaccinated vs 14.2% unvaccinated) and increase in symptom resolution (23.2% vaccinated vs 15.4% unvaccinated) (p=0.035). No difference in response was identified between Pfizer-BioNTech or Oxford-AstraZeneca vaccines.ConclusionsReceipt of vaccination with either an mRNA or adenoviral vector vaccine was not associated with a worsening of Long Covid symptoms, quality of life, or mental wellbeing. Individuals with prolonged COVID-19 symptoms should receive vaccinations as suggested by national guidance.
Comparison of SARS-CoV-2 detection in Saliva by real-time RT-PCR and RT-PCR/MALDI-TOF Methods
Authors: Hernandez Matthew M. , Banu Radhika , Shrestha Paras , Patel Armi , Chen Feng , Cao Liyong , Fabre Shelcie , Tan Jessica , Lopez Heidi , Chiu Numthip , Shifrin Biana , Zapolskaya Inessa , Flores Vanessa , Lee Pui Yiu , Castañeda Sergio , Ramírez Juan David , Jhang Jeffrey , Osorio Giuliana , Gitman Melissa R. , Nowak Michael D. , Reich David L. , Cordon-Cardo Carlos , Sordillo Emilia Mia , Paniz-Mondolfi Alberto E. 
Published: March 2021

ABSTRACTThe coronavirus disease 2019 (COVID-19) pandemic has accelerated the need for rapid implementation of diagnostic assays for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in respiratory specimens. While multiple molecular methods utilize nasopharyngeal specimens, supply chain constraints and need for easier and safer specimen collection warrant alternative specimen types, particularly saliva. Although saliva has been found to be a comparable clinical matrix for detection of SARS-CoV-2, evaluations of diagnostic and analytic performance across platforms for this specimen type are limited. Here, we compared two methods for SARS-CoV-2 detection in saliva: the Roche cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test and the Agena Biosciences MassARRAY® SARS-CoV-2 Panel/MassARRAY® System. Overall, both systems had high agreement with one another, and both demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of each platform and determined the limit of detection of the Roche assay was four times lower than that of Agena for saliva specimens (390.6 v. 1,562.5 copies/mL). Furthermore, across individual target components of each assay, T2 and N2 targets had the lowest limits of detection for each platform, respectively. Together, we demonstrate that saliva represents an appropriate specimen for SARS-CoV-2 detection in two technologies that have high agreement and differ in analytical sensitivities overall and across individual component targets. The addition of saliva as an acceptable specimen and understanding the sensitivity for testing on these platforms can further inform public health measures for screening and detection to combat the COVID-19 pandemic.
DIP: Natural History Model for Major Depression with Incidence and Prevalence
Authors: Yildirim Melike , Gaynes Bradley N , Keskinocak Pinar , Pence Brian W , Swann Julie 
Published: March 2021

AbstractBackgroundMajor depression is a treatable disease, and untreated depression can lead to serious health complications. Therefore, prevention, early identification, and treatment efforts are essential. Natural history models can be utilized to make informed decisions about interventions and treatments of major depression.MethodsWe propose a natural history model of major depression. We use steady-state analysis to study the discrete-time Markov chain model. For this purpose, we solved differential equations and tested the parameter and transition probabilities empirically.ResultsWe showed that bias in parameters might collectively cause a significant mismatch in a model. If incidence is correct, then lifetime prevalence is 33.2% for females and 20.5% for males, which is higher than reported values. If prevalence is correct, then incidence is .0008 for females and .00065 for males, which is lower than reported values. The model can achieve feasibility if incidence is at low levels and recall bias of the lifetime prevalence is quantified to be 31.9% for females and 16.3% for males.LimitationsModel is limited to major depression, and patients who have other types of depression are assumed healthy. We assume that transition probabilities (except incidence rates) are correct.ConclusionWe constructed a preliminary model for the natural history of major depression. We determine the lifetime prevalence are underestimated. We conclude that the average incidence rates may be underestimated for males. Our findings mathematically prove the arguments around the potential discordance between reported incidence and lifetime prevalence rates.