Category: Statistics

PLoS One. 2022 Feb 11;17(2):e0263849. doi: 10.1371/journal.pone.0263849. eCollection 2022.

ABSTRACT

The most advanced D-Wave Advantage quantum annealer has 5000+ qubits, however, every qubit is connected to a small number of neighbors. As such, implementation of a fully-connected graph results in an order of magnitude reduction in qubit count. To compensate for the reduced number of qubits, one has to rely on special heuristic software such as qbsolv, the purpose of which is to decompose a large quadratic unconstrained binary optimization (QUBO) problem into smaller pieces that fit onto a quantum annealer. In this work, we compare the performance of the open-source qbsolv which is a part of the D-Wave Ocean tools and a new Mukai QUBO solver from Quantum Computing Inc. (QCI). The comparison is done for solving the electronic structure problem and is implemented in a classical mode (Tabu search techniques). The Quantum Annealer Eigensolver is used to map the electronic structure eigenvalue-eigenvector equation to a QUBO problem, solvable on a D-Wave annealer. We find that the Mukai QUBO solver outperforms the Ocean qbsolv with one to two orders of magnitude more accurate energies for all calculations done in the present work, both the ground and excited state calculations. This work stimulates the further development of software to assist in the utilization of modern quantum annealers.

PMID:35148343 | DOI:10.1371/journal.pone.0263849

PLoS One. 2022 Feb 11;17(2):e0263928. doi: 10.1371/journal.pone.0263928. eCollection 2022.

ABSTRACT

Transcriptional regulator PEAPOD (PPD) and its binding partners comprise a complex that is conserved throughout many core eudicot plants with regard to protein domain sequence and the function of controlling organ size and shape. Orthologues of PPD also exist in the basal angiosperm Amborella trichopoda, various gymnosperm species, the lycophyte Selaginella moellendorffii and several monocot genera, although until now it was not known if these are functional sequences. Here we report constitutive expression of orthologues from species representing diverse taxa of plant phylogeny in the Arabidopsis Δppd mutant. PPD orthologues from S. moellendorffii, gymnosperm Picea abies, A. trichopoda, monocot Musa acuminata, and dicot Trifolium repens were able to complement the mutant and return it to the wild-type phenotype, demonstrating the conserved functionality of PPD throughout vascular plants. In addition, analysis of bryophyte genomes revealed potential PPD orthologues in model liverwort and moss species, suggesting a more primitive lineage for this conserved regulator. The Poaceae (grasses) lack the genes for the PPD module and the reason for loss of the complex from this economically significant family is unclear, given that grasses were the last of the flowering plants to evolve. Bioinformatic analyses identified putative PPD orthologues in close relatives of the Poaceae, indicating that the explanation for absence of PPD in the grasses may be more complex than previously considered. Understanding the mechanisms which led to loss of PPD from the grasses will provide insight into evolution of the Poaceae.

PMID:35148336 | DOI:10.1371/journal.pone.0263928

PLoS One. 2022 Feb 11;17(2):e0262735. doi: 10.1371/journal.pone.0262735. eCollection 2022.

ABSTRACT

PURPOSE: We aimed to evaluate the long-term outcome of carotid endarterectomy (CEA) and carotid artery stenting (CAS) in patients who underwent both procedures on different sides.

METHODS: In this single-center retrospective study (2001-2019), 117 patients (men, N = 78; median age at CEA, 64.4 [interquartile range {IQR}, 57.8-72.2] years; median age at CAS, 68.8 [IQR, 61.0-76.0] years) with ≥50% internal carotid artery stenosis who had CEA on one side and CAS on the other side were included. The risk of restenosis was estimated by treatment adjusted for patient and lesion characteristics.

RESULTS: Neurological symptoms were significantly more common (41.9% vs 16.2%, P<0.001) and patients had a significantly shorter mean duration of smoking (30.2 [standard deviation {SD}, 22.2] years vs 31.8 [SD, 23.4] years, P<0.001), hypertension (10.1 [SD, 9.8] years vs 13.4 [SD, 9.1] years, P<0.001), hyperlipidemia (3.6 [SD, 6.6] years vs 5.0 [SD, 7.3] years, P = 0.001), and diabetes mellitus (3.9 [SD, 6.9] years vs 5.7 [SD, 8.9] years, P<0.001) before CEA compared to those before CAS. While the prevalence of heavily calcified stenoses on the operated side (25.6% vs 6.8%, P<0.001), the incidence of predominantly echogenic/echogenic plaques (53.0% vs 70.1%, P = 0.011) and suprabulbar lesions (1.7% vs 22.2%, P<0.001) on the stented side was significantly higher. Restenosis rates were 10.4% at 1 year, 22.3% at 5 years, and 33.7% at the end of the follow-up (at 11 years) for CEA, while these were 11.4%, 14.7%, and 17.2%, respectively, for CAS. Cox regression analysis revealed a significantly higher risk of restenosis (hazard ratio [HR], 1.80; 95% confidence interval [CI], 1.05-3.10; P = 0.030) for CEA compared to that for CAS. After adjusting for relevant confounding factors (smoking, hypertension, diabetes mellitus, calcification severity, plaque echogenicity, and lesion location), the estimate effect size materially did not change, although it did not remain statistically significant (HR, 1.85; 95% CI, 0.95-3.60; P = 0.070).

CONCLUSION: Intra-patient comparison of CEA and CAS in terms of restenosis tilts the balance toward CAS.

PMID:35148323 | DOI:10.1371/journal.pone.0262735

PLoS One. 2022 Feb 11;17(2):e0262828. doi: 10.1371/journal.pone.0262828. eCollection 2022.

ABSTRACT

BACKGROUND: A community-based occupational therapy intervention for people with mild to moderate dementia and their family carers: the Community Occupational Therapy in Dementia-UK version (COTiD-UK); and Treatment as usual (TAU) were randomly assigned to 468 pairs (each comprising a person with dementia and a family carer) in the Valuing Active Life in Dementia (VALID) randomised controlled trial (RCT).

OBJECTIVES: To compare the cost-utility of the COTiD-UK intervention compared to TAU, using data from the VALID RCT.

METHODS: We performed a cost-utility analysis estimating mean costs and quality adjusted life years (QALYs) per person with dementia and carer for both treatments over a 26 weeks’ time horizon based on resource use data and utility values collected in the trial.

RESULTS: Taking the National Health Service and Personal Social Services perspective, including costs and benefits to the person with dementia only, measuring Health Related Quality of Life based on Dementia Quality of Life scale (DEMQOL), accounting for missing data and adjusting for baseline values, there was a significant difference in costs between COTiD-UK and TAU (mean incremental cost for COTiD-UK £784 (95% CI £233 to £1334)), but no significant difference in outcomes (mean QALYs gained 0.00664 (95% CI -0.00404, 0.01732)). The Incremental Net Monetary Benefit (INMB) for COTiD-UK versus TAU was negative at a maximum willingness to pay for a QALY of £20000 (mean -£651, 95% CI -£878 to -£424) or £30000 (mean -£585, 95% CI -£824 to -£345). Extensive sensitivity analyses confirmed the results.

CONCLUSIONS: This community-based occupational therapy intervention has a very low probability of being cost-effective.

PMID:35148329 | DOI:10.1371/journal.pone.0262828

PLoS One. 2022 Feb 11;17(2):e0262305. doi: 10.1371/journal.pone.0262305. eCollection 2022.

ABSTRACT

BACKGROUND: Widespread vaccination coverage is essential for reducing the COVID-19 havoc and regarded as a crucial tool in restoring normal life on university campuses. Therefore, our research aimed to understand the intention to be vaccinated for COVID-19 among Pakistani university students.

METHODS: This cross-sectional study was conducted in five administrative units of Pakistan, i.e., Punjab, Sindh, Balochistan, Azad Jammu and Kashmir, and Khyber Pakhtunkhwa. We obtained data from 2,865 university students between 17th January and 2nd February, 2021, using a semi-structured and self-administered questionnaire. We used Stata (version 16.1, StataCorp LLC) for data management and analysis.

RESULTS: The majority (72.5%) of our respondents were willing to take COVID-19 vaccine. The current level of education had a statistically significant relationship with the intention to be vaccinated (p < 0.05). Respondents answered 11 questions encompassing five different domains of the Health Belief Model (HBM). All the items of HBM were significantly associated with the positive intention towards receiving the vaccine (p < 0.05). We conducted a multivariable logistic regression analysis to assess the relative contribution of different factors towards the intention to receive COVID-19 vaccine. Multiple factors such as belief that vaccination should be mandatory for everyone (AOR: 3.99, 95% CI: 3.20-4.98) and willingness to take vaccine even if it is not free (AOR: 3.91, 95% CI: 3.18-4.81) were observed to be associated with high odds of showing willingness to be vaccinated against COVID-19.

CONCLUSION: Most of our study participants intended to take vaccines based on their belief regarding the high effectiveness of COVID-19 vaccine. But as rumor-mongers are generating and spreading conspiracy theories daily, the health department and policymakers need to undertake evidence-based campaigns through electronic and social media to ensure expected countrywide vaccination coverage. In this case, our study findings can serve as a foundation for them to ensure mass vaccination coverage among university students, which is crucial now to reopen the dormitories and restore everyday life on campuses.

PMID:35148317 | DOI:10.1371/journal.pone.0262305

Nurse Educ. 2022 Feb 9. doi: 10.1097/NNE.0000000000001173. Online ahead of print.

ABSTRACT

BACKGROUND: It is essential to explore virtual learning experiences to identify their impact on nursing students’ learning.

PURPOSE: The purpose of this study was to investigate the relationship between the virtual delivery of a health assessment laboratory course and nursing students’ clinical judgment.

METHODS: Using a mixed-methods explanatory sequential design, the investigators appraised the final laboratory examinations of both in-person and virtual delivery cohorts using the Lasater Clinical Judgment Rubric (LCJR) and then interviewed faculty members.

RESULTS: The LCJR total mean scores (mean = 10.64) and mean scores for Effective Noticing (mean = 3.48) were higher for the virtual delivery students. The faculty reported that virtual delivery advances students’ critical appraisal skills related to subjective assessment but advocated for in-person delivery to develop physical examination techniques.

CONCLUSION: Although the mean clinical judgment scores were higher for the students whose course delivery was virtual, in-person experiences are necessary to develop psychomotor techniques to prepare students for clinical practice.

PMID:35148304 | DOI:10.1097/NNE.0000000000001173

PLoS Comput Biol. 2022 Feb 11;18(2):e1009832. doi: 10.1371/journal.pcbi.1009832. eCollection 2022 Feb.

ABSTRACT

Applying information theoretic measures to neuronal activity data enables the quantification of neuronal encoding quality. However, when the sample size is limited, a naïve estimation of the information content typically contains a systematic overestimation (upward bias), which may lead to misinterpretation of coding characteristics. This bias is exacerbated in Ca2+ imaging because of the temporal sparsity of elevated Ca2+ signals. Here, we introduce methods to correct for the bias in the naïve estimation of information content from limited sample sizes and temporally sparse neuronal activity. We demonstrate the higher accuracy of our methods over previous ones, when applied to Ca2+ imaging data recorded from the mouse hippocampus and primary visual cortex, as well as to simulated data with matching tuning properties and firing statistics. Our bias-correction methods allowed an accurate estimation of the information place cells carry about the animal’s position (spatial information) and uncovered the spatial resolution of hippocampal coding. Furthermore, using our methods, we found that cells with higher peak firing rates carry higher spatial information per spike and exposed differences between distinct hippocampal subfields in the long-term evolution of the spatial code. These results could be masked by the bias when applying the commonly used naïve calculation of information content. Thus, a bias-free estimation of information content can uncover otherwise overlooked properties of the neural code.

PMID:35148310 | DOI:10.1371/journal.pcbi.1009832

Endocr Connect. 2022 Feb 1:EC-21-0546.R2. doi: 10.1530/EC-21-0546. Online ahead of print.

ABSTRACT

OBJECTIVE: The association between insulin therapy and the risk of biliary tract cancer (BTC) is uncertain, we aimed to assess this risk in type 2 diabetic patients.

METHODS: Using electronic medical data from the Shanghai Hospital Link database, 202,557 patients with type 2 diabetes (164,997 insulin never-users and 37,560 insulin ever-users) were identified in this study between January 1, 2013, and December 31, 2016, with follow-up until December 31, 2019. By propensity score matching, an ever-user was matched with a never-user. Cox proportional hazards regression analysis was used to estimate risk ratios (HRs) and 95% confidence intervals (CIs) for three subtypes of BTC (intrahepatic cholangiocarcinoma (ICC), extrahepatic cholangiocarcinoma (ECC), and gallbladder cancer (GBC)).

RESULTS: At a mean follow-up of 5.33 years, 143 cases of BTC were observed. The crude incidence rates (per 100,000 person-years) of ECC, ICC, and GBC in ever-users: never-users were 10.22: 3.63, 2.04: 2.04, and 8.17: 6.01, respectively. Insulin therapy was associated with an increased risk of ECC (HR, 4.10; 95% CI, 1.54-10.92; p = 0.005) compared to patients who never used insulin. No statistically significant results were observed for insulin and ICC/GBC. Consistent results were also found in the original cohort.

CONCLUSIONS: The relationship between insulin therapy and biliary tract cancer is type-specific, further studies are warranted to provide evidence on the identification of ECC risk groups among type 2 diabetic patients.

PMID:35148280 | DOI:10.1530/EC-21-0546

JMIR Med Educ. 2022 Feb 11. doi: 10.2196/33612. Online ahead of print.

ABSTRACT

BACKGROUND: Since the closure of university campuses due to COVID-19 in Spring 2020 necessitated a quick transition to online courses, medical students were isolated from hospitals and universities, negatively impacting their education. During this time, medical students had no opportunity to participate in academic discussions and were also socially isolated. Furthermore, medical doctors and professors of the medical schools were given additional responsibilities during the pandemic because they were the front-liners in the fight against COVID-19. As a result, they did not have enough time to contribute effectively to medical student education.

OBJECTIVE: This paper describes the establishment of the Cerrahpasa Neuroscience Society Journal Clubs, a group of entirely student-run online journal clubs at Istanbul University-Cerrahpasa – Cerrahpasa Faculty of Medicine.

METHODS: The website, mass emailing, and social media accounts were used to announce the online journal clubs. Only medical students were made eligible to apply. Journal clubs included psychiatry, neuroradiology, neurosurgery, neurology, and neuroscience. Following the last journal club meeting, a questionnaire created by the society’s board was distributed to the participants. SPSS Statistics was used for statistical analysis (version 26).

RESULTS: Since 15 March 2021, synchronous online journal club meetings have been held every two weeks on a weekday using Google Meet, Microsoft Teams, or Zoom. Meetings of each journal club lasted about an hour on average. Inter-student interaction across multiple institutions was achieved since a total of 45 students from 11 different universities attended the meetings on a regular basis. Students on the society’s board served as academic mentors for the clubs. The clubs received excellent feedback from participants, with an overall contentment score of 4.32 out of 5.

CONCLUSIONS: By establishing these clubs, we have created a venue for academic discussions, which helps to reduce the negative impact of the pandemic on education. In addition, we believe it greatly aided students in staying in touch with their peers, thereby reducing the sense of isolation. We realize that traditional journal clubs are run by faculty; however, we believe that this experience demonstrated that medical students could run a journal club on their own since the feedback from participants was excellent. Additionally, as a medical student, being a journal club academic mentor is a challenging responsibility; however, having this responsibility significantly improved our academic mentors’ leadership abilities.

PMID:35148270 | DOI:10.2196/33612

Minerva Urol Nephrol. 2022 Feb 11. doi: 10.23736/S2724-6051.21.04587-0. Online ahead of print.

ABSTRACT

INTRODUCTION: The aim of this systematic review and meta-analysis is to provide an updated comparison between the currently available minimally invasive approaches (PCNL, laparoscopic [LP] and robotic pyelolithotomy [RP]) for the management of large renal stones.

EVIDENCE ACQUISITION: An electronic search of the current literature was conducted through the Medline and NCBI PubMed, Embase, Scopus and Cochrane Collaboration Central Register of Controlled Clinical Trials databases in March 2021. Studies about minimally-invasive treatment for kidney stones were considered. Inclusion criteria were: studies evaluating patients with large renal calculi (≥2 cm); the comparison of at least two of the three approaches (PCNL, LP, RP), reporting data suitable for meta-analysis evaluation. Patients with concomitant management for ureteropelvic junction obstruction (UPJ-O) were excluded.

EVIDENCE SYNTHESIS: Overall, 17 reports were considered for qualitative and quantitative synthesis, for a total cohort of 1079 patients, of which 534 with PCNL, 525 treated with LP, and 20 with RP. Of those, 16 compared PCNL with LP, while only 1 study compared LP with RP. PCNL mean operative time was statistically significantly shorter than LP and RP while mean estimated blood loss was statistically significantly higher for PNCL. No statistically significant differences were recorded among the three surgical approaches. Finally, PCNL demonstrated slightly, albeit statistically significant lower stone free rate when compared with LP.

CONCLUSIONS: PCNL, LP and RP may be safely and efficiently used to manage large renal stones. All three procedures showed reasonably low rate of complications with a satisfactory stone clearance rate.

PMID:35147384 | DOI:10.23736/S2724-6051.21.04587-0