Category: Statistics

ACM BCB. 2023 Sep;2023:42. doi: 10.1145/3584371.3612982. Epub 2023 Oct 4.

ABSTRACT

In computational biology, $k$-mers and edit distance are fundamental concepts. However, little is known about the metric space of all $k$-mers equipped with the edit distance. In this work, we explore the structure of the $k$-mer space by studying its maximal independent sets (MISs). An MIS is a sparse sketch of all $k$-mers with nice theoretical properties, and therefore admits critical applications in clustering, indexing, hashing, and sketching large-scale sequencing data, particularly those with high error-rates. Finding an MIS is a challenging problem, as the size of a $k$-mer space grows geometrically with respect to $k$. We propose three algorithms for this problem. The first and the most intuitive one uses a greedy strategy. The second method implements two techniques to avoid redundant comparisons by taking advantage of the locality-property of the $k$-mer space and the estimated bounds on the edit distance. The last algorithm avoids expensive calculations of the edit distance by translating the edit distance into the shortest path in a specifically designed graph. These algorithms are implemented and the calculated MISs of $k$-mer spaces and their statistical properties are reported and analyzed for $k$ up to 15. Source code is freely available at https://github.com/Shao-Group/kmerspace.

PMID:38050580 | PMC:PMC10694840 | DOI:10.1145/3584371.3612982

Adv Med Educ Pract. 2023 Nov 29;14:1347-1355. doi: 10.2147/AMEP.S427974. eCollection 2023.

ABSTRACT

PURPOSE: First- and second-year medical students typically have limited exposure to the field of anesthesiology, yet recent match data shows growing interest in the specialty. Early, structured exposure to anesthesiology in the form of a preclinical elective may allow medical students to make more informed decisions on their specialty of choice.

METHODS: The anesthesiology preclinical elective, BIOL 6704: “Anesthesia: Much More than Putting you to Sleep”, is a one-credit course taught at The Warren Alpert Medical School of Brown University. A survey consisting of fifteen questions assessing changes in attitudes, perceptions, and interest in anesthesiology was distributed to first- and second-year medical students before and after course participation. The results were analyzed using the Wilcoxon’s signed-rank test for paired samples.

RESULTS: The biggest impact of the preclinical elective was observed in the students’ subjective understanding of key aspects of the practice of anesthesiology. Statistically significant improvement was seen in the understanding of airway management, anesthetic pharmacology, basics of ultrasound, vascular access, anesthesiology subspecialties, and an understanding of anesthesiology residency. Overall, results were limited by our small sample size.

CONCLUSION: Our elective allows medical students to explore anesthesiology early in their medical school career. After taking this course, students noted more familiarity with various topics in anesthesiology. Peer institutions lacking a similar course may consider using our experience to increase interest about the specialty of anesthesiology for future students.

PMID:38050578 | PMC:PMC10693776 | DOI:10.2147/AMEP.S427974

Basic Clin Neurosci. 2023 Jul-Aug;14(4):511-518. doi: 10.32598/bcn.2021.3369.1. Epub 2023 Jul 1.

ABSTRACT

INTRODUCTION: Since the introduction of the Food and Drug Administration (FDA)-approved repetitive transcranial magnetic stimulation (rTMS) intervention in 2008, a breakthrough has been made in treating major depressive disorder (MDD). However, many sessions of treatment and its cost make it inconvenient for those who seek treatment, especially in large cities as well as in developing countries.

METHODS: A total of 22 patients (out of initial 24 referrals) who met diagnostic and statistical manual of mental disorders, 4^th edition (DSM IV) criteria for MDD were enrolled in the study. All subjects had to fail at least one prior treatment for depression. The patients received the FDA-approved protocol of high-frequency (10 Hz) rTMS over the left dorsolateral prefrontal cortex.

RESULTS: Seventeen out of twenty-two cases showed significant improvements after two weeks of treatment. Only six patients continued their treatments for the next two to four weeks.

CONCLUSION: We have replicated other studies showing that the use of rTMS is effective for many patients with MDD without major side effects and their improvements are measurable mostly after two weeks. Our data highlight the importance of the application of more convenient protocols that require fewer sessions on fewer days to help with compliance and outcome, particularly in large populated cities and countries, such as Iran going through economic hardship.

HIGHLIGHTS: Repetitive transcranial magnetic stimulation (rTMS) is effective for treating major depresion.Improvemens are measurable after 2 weeks of treating with rTMS.Compliance is a major factorto for completing rTMS protocols.

PLAIN LANGUAGE SUMMARY: Major depression is one of the most common psychiatric disorders leading to debilitating course causing significant burden for the society. Many cases with major depression are resistent to treatment as they try multiple interventions with no success. This condition is also called refractory depression. rTMS is a novel intervention introduced first almost two decades ago to treat refractory depression among some other psychiatric disorders. In this intervention pulses generated by magnetic stimulation over the brain leads to improvement is depression. As this treatment is safe with no pain and discomfort there have been much interest in the field to use it more frequently. rTMS is usually done over 15-30 sessions with its maximum effects appearing within the first two weeks of treatment. The number of sessions is a potential factor contributing to poor compliance in some cases especially those living in large metropolitan areas. In this paper we explored compliance and effect of treatment within the first two weeks among a group of patients in a private outpatient clinic of a large metropolitan area.

PMID:38050571 | PMC:PMC10693813 | DOI:10.32598/bcn.2021.3369.1

Clin Ophthalmol. 2023 Nov 29;17:3663-3672. doi: 10.2147/OPTH.S439287. eCollection 2023.

ABSTRACT

PURPOSE: To collate the accuracy of two recently introduced intraocular lens (IOL) formulas (VRF and VRF-G) in cataract patients using a swept-source optical coherence tomography (SS-OCT) biometry (IOL Master 700, Carl Zeiss Meditec AG, Jena, Germany).

PATIENTS AND METHODS: Data records of 295 eyes from 295 patients were included in this scrutiny. The IOLMaster 700 SS-OCT biometer was used for biometric measurements. The VRF and VRF-G formulas were compared with seven 3rd and 4th generation thin and thick-lens formulas: Haigis, Hoffer Q, Holladay 1, Holladay 2, SRK/T, T2, and Barrett Universal II. With optimized lens constants, the mean prediction error (PE) and its standard deviation (SD), the median absolute error (MedAE), the mean absolute error (MAE), and the percentage of eyes with PEs within ±0.25 D, ±0.50 D, ±0.75 D, ±1.00 D, and <±2.00 D were analyzed.

RESULTS: Statistically significant differences were found between formulas in the whole group (Friedman test, P = 0.000). The VRF-G and Haigis formulas showed the lowest SD values (0.464 D and 0.466 D respectively). The VRF and Barrett Universal II formulas were less predictable (SD 0.471 D and SD 0.474 D respectively). The biggest proportion of eyes within ±0.50 D was found with VRF-G (76.27%), Haigis (75.59%), VRF (74.92%), and Barrett Universal II (74.92%) formulas.

CONCLUSION: Based on data achieved from the SS-OCT biometry, the VRF-G and Haigis methods were the more precise predictors of postoperative refraction with the biggest proportion of eyes within ±0.50 D.

PMID:38050557 | PMC:PMC10693751 | DOI:10.2147/OPTH.S439287

Int J Sports Phys Ther. 2023 Dec 1;18(6):1308-1319. doi: 10.26603/001c.89273. eCollection 2023.

ABSTRACT

BACKGROUND: Injuries during elite level competition like the Canada Games, occur frequently and injury history is one of the strongest predictors of future injury; however, this association is unknown in the Canada Games.

PURPOSE: To determine the association between injury history and incidence of lower extremity joint injury during Canada Games competition.

METHODS: Data from the 2009 – 2019 Canada Games (8710 male and 8391 female athletes) competitions were de-identified by the Canada Games Council for analysis. Injury data were cleaned and categorized for previous injury and injury type and location. Injury history was self-reported and included concussion, major surgical procedure, neck and back, trauma to joint or bone, and trauma to ligament or tendon. Injury from the Canada Games competitions were categorized to include ankle, knee, hip, and patellofemoral joint injuries. Chi-Square (χ² ) test of independence determined association between injury history and incidence of lower extremity joint injury during Canada Games competition. IBM SPSS (Version 26) was used for statistical analysis (p-value < 0.05).

RESULTS: Four hundred and seventy-five ankle, 503 knee, 253 hip, and 106 patellofemoral joint injuries were reported during 10 years of Canada Games competitions. There were significant associations between history of neck and back injuries with ankle injuries and knee injuries, history of trauma and overuse of ligament or tendon with hip injuries and history of trauma or overuse of joint or bone with patellofemoral joint injuries.

CONCLUSION: These findings support previous literature suggesting that injury history is associated with future injury.

LEVEL OF EVIDENCE: 3.

PMID:38050547 | PMC:PMC10693481 | DOI:10.26603/001c.89273

Biol Rev Camb Philos Soc. 2023 Dec 4. doi: 10.1111/brv.13034. Online ahead of print.

ABSTRACT

Genetic data show that many nominal species are composed of more than one biological species, and thus contain cryptic species in the broad sense (including overlooked species). When ignored, cryptic species generate confusion which, beyond biodiversity or vulnerability underestimation, blurs our understanding of ecological and evolutionary processes and may impact the soundness of decisions in conservation or medicine. However, very few hypotheses have been tested about factors that predispose a taxon to contain cryptic or overlooked species. To fill this gap, we surveyed the literature on free-living marine metazoans and built two data sets, one of 187,603 nominal species and another of 83 classes or phyla, to test several hypotheses, correcting for sequence data availability, taxon size and phylogenetic relatedness. We found a strong effect of scientific history: the probability of a taxon containing cryptic species was highest for the earliest described species and varied among time periods potentially consistently with an influence of prevailing scientific theories. The probability of cryptic species being present was also increased for species with large distribution ranges. They were more frequent in the north polar and south polar zones, contradicting previous predictions of more cryptic species in the tropics, and supporting the hypothesis that many cryptic species diverged recently. The number of cryptic species varied among classes, with an excess in hydrozoans and polychaetes, and a deficit in actinopterygians, for example, but precise class ranking was relatively sensitive to the statistical model used. For all models, biological traits, rather than phylum, appeared responsible for the variation among classes: there were fewer cryptic species than expected in classes with hard skeletons (perhaps because they provide good characters for taxonomy) and image-forming vision (in which selection against heterospecific mating may enhance morphological divergence), and more in classes with internal fertilisation. We estimate that among marine free-living metazoans, several thousand additional cryptic species complexes could be identified as more sequence data become available. The factors identified as important for marine animal cryptic species are likely important for other biomes and taxa and should aid many areas in biology that rely on accurate species identification.

PMID:38049930 | DOI:10.1111/brv.13034

Rural Remote Health. 2023 Dec;23(4):8372. doi: 10.22605/RRH8372. Epub 2023 Dec 5.

ABSTRACT

INTRODUCTION: The US is currently experiencing a maternal health crisis. Maternal morbidity and mortality in the US are higher than in other developed nations and continue to rise. Infant mortality, likewise, is higher in the US than in other developed nations. Limited availability of maternal health services, particularly in rural areas, contributes to this crisis. Maternal health outcomes are poorer, and maternal care workforce shortages are more severe in rural areas of the US. In rural areas where obstetric specialists are rare, many patients rely on family medicine physicians for maternity care. However, the number of family medicine physicians who provide maternal care services is decreasing, aggravating shortages. Calls have been made to build maternal care capacity in rural areas. The role family medicine will play in addressing the maternal health crisis is not clear. Maternal care shortages are complex issues resulting from multiple factors; likewise, efforts to build maternal health capacity are challenging and require multifaceted approaches.

METHODS: With funding from the Health Resources and Services Administration (HRSA), the University of Utah seeks to address the shortage of quality maternity care in rural and underserved areas of Utah by strengthening partnerships, enhancing maternal care training of family medicine residents and obstetrics fellows, and improving the transition from training to rural practice for residents and fellows. This protocol describes the evaluation of the HRSA-funded project. The evaluation includes three components. Component 1 consists of qualitative interviews with a diverse group of maternal health providers, administrators, educators and academics, patients, and others. Interviews will be analyzed using qualitative content analysis. Component 2 is a survey of family medicine residents and obstetrics fellows, which aims to increase understanding of the factors and circumstances influencing intention to practice in rural or underserved areas and to provide maternal health services. Component 3 involves surveying fellowship alumni and tracking graduates to assess effectiveness of training programs in producing physicians who provide maternal health services in rural and underserved areas. Surveys will be analyzed with descriptive statistics including means, frequencies, and cross-tabulations. If sample size and participation provide sufficient power, statistical tests will be included in analyses.

RESULTS: Evaluation results will help to fill an important gap in research literature concerning outcomes of projects and initiatives designed to build maternal care capacity in rural areas of the US. In addition, results will provide valuable information regarding effective practices for building capacity, which can be adopted elsewhere to address maternal care shortages. Finally, results will help to define the role of family medicine in addressing the maternal health crisis. Amid maternal care shortages, fewer and fewer family medicine physicians are providing maternal care in their practice. Evaluation results will clarify the role of training and preparation of family medicine residents in addressing workforce shortages.

CONCLUSION: This evaluation will provide important contributions, but additional research is needed, including research protocols and studies of project outcomes, to understand how best to resolve the maternal care crisis in the US.

PMID:38049929 | DOI:10.22605/RRH8372

Trop Dis Travel Med Vaccines. 2023 Dec 5;9(1):21. doi: 10.1186/s40794-023-00207-8.

ABSTRACT

BACKGROUND: International Health Regulations (IHR) were developed by the World Health Organization (WHO) to curb the trans-border spread of epidemics. To our knowledge, no airport-based studies have assessed travelers’ health practices against a combination of diseases subject to IHR 2005. Therefore, we aimed to generate and describe the baseline travelers’ pre-travel health practices towards Cholera, Yellow Fever (YF), and Plague at Murtala Muhammed International Airport (MMIA) in Nigeria.

METHODS: A cross-sectional study was employed to collect data from 486 international travelers using a multistage sampling technique. Pre-travel health practices (a combination of pre-travel consultation, pre-travel vaccination, and preventive measures against insect bites) were assessed using an interviewer-administered questionnaire. Logistic regression models were used to estimates the association between selected variables and pre-travel health practices. Statistical significance level was set at 5%.

RESULTS: A total of 479 complete questionnaires were analyzed. The median age of respondents was 34.0 years Interquartile range (IQR) = 28.0, 44.0). Of the total respondents, 311 (64.3%) were aware of pre-travel health consultation and sources of information, amongst others, including friends/relatives in 180 (37.6%) travelers, social media/internet in 155 (32.4%) travelers, and health professionals in 102 (21.3%) travelers. Two hundred and seventy-one (56.6%) had pre-travel consultation, 156 (32.6%) had YF vaccination, and 226 (47.2%) were prepared to use preventive measures against insect bites. Only 10.6% had good pre-travel practices against the diseases subject to 2 International Health Regulations (IHR). Travelers with bachelor/college degrees, when compared to those with secondary/high education, had 2.91 times higher odds of having good practices when adjusting for other factors (95% C.I: 1.10, 7.70; p < 0.03). Also, those traveling to destinations endemic for YF infection, when compared to those who are not traveling to endemic countries/areas, had 48% lower odds of having good practices after adjusting for other factors (95% C.I: 1.41, 7.77; p < 0.01).

CONCLUSIONS: Our study revealed a low prevalence of good pre-travel health practices among participants. Educational level and endemicity of YF at the destination were predictors of pre-travel health practices. Introducing topics on travelers’ health into schools’ curriculums may have a ripple positive effect on health practices among international travelers. Also, there is a need for public enlightenment programs on pre-travel health practices using social media platforms.

PMID:38049921 | DOI:10.1186/s40794-023-00207-8

Adv Rheumatol. 2023 Dec 4;63(1):57. doi: 10.1186/s42358-023-00329-9.

ABSTRACT

BACKGROUND: Many people with non-specific chronic low back pain (NSCLBP) do not recover with current conventional management. Systematic reviews show multidimensional treatment improves pain better than usual active interventions. It is unclear whether multidimensional physiotherapy improves pain better than usual physiotherapy. This study determines the effectiveness of this treatment to reduce pain and disability and improve quality of life, pain cognitions, and electroencephalographic pattern in individuals with NSCLBP.

METHODS: 70 eligible participants aged 18 to 50 years with NSCLBP were randomized into either the experimental group (multidimensional physiotherapy) or the active control group (usual physiotherapy). Pain intensity was measured as the primary outcome. Disability, quality of life, pain Catastrophizing, kinesiophobia, fear Avoidance Beliefs, active lumbar range of motion, and brain function were measured as secondary outcomes. The outcomes were measured at pre-treatment, post-treatment, 10, and 22 weeks. Data were analyzed using intention-to-treat approaches.

RESULTS: There were 17 men and 18 women in the experimental group (mean [SD] age, 34.57 [6.98] years) and 18 men and 17 women in the active control group (mean [SD] age, 35.94 [7.51] years). Multidimensional physiotherapy was not more effective than usual physiotherapy at reducing pain intensity at the end of treatment. At the 10 weeks and 22 weeks follow-up, there were statistically significant differences between multidimensional physiotherapy and usual physiotherapy (mean difference at 10 weeks, -1.54; 95% CI, -2.59 to -0.49 and mean difference at 22 weeks, -2.20; 95% CI, – 3.25 to – 1.15). The standardized mean difference and their 95% confidence intervals (Cohen’s d) revealed a large effect of pain at 22 weeks: (Cohen’s d, -0.89; 95% CI (-1.38 to-0.39)). There were no statistically significant differences in secondary outcomes.

CONCLUSIONS: In this randomized controlled trial, multidimensional physiotherapy resulted in statistically and clinically significant improvements in pain compared to usual physiotherapy in individuals with NSCLBP at 10 and 22 weeks.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04270422; IRCT IRCT20140810018754N11.

PMID:38049905 | DOI:10.1186/s42358-023-00329-9

Trials. 2023 Dec 4;24(1):785. doi: 10.1186/s13063-023-07784-1.

ABSTRACT

BACKGROUND: Irritable bowel syndrome (IBS) is a highly prevalent disorder for which treatment options such as medication, diets, and hypnotherapy either have shown limited effect or relieve symptoms in only a limited subset of patients. Abdominal pain is the key criterion for the diagnosis and is deemed the most distressing IBS symptom, and the most disruptive of everyday life. A growing body of research demonstrates the effect of Eye Movement Desensitization and Reprocessing (EMDR) on chronic pain. EMDR is known as a safe and successful treatment for disorders in which unresolved traumatic memories play a role in the cause or maintenance of symptoms. In IBS, activated memories may increase pain through pain flashbacks and the stress generated by unresolved memories. The aim of this study is to ascertain whether applying EMDR to traumatic memories including pain memories will reduce abdominal pain in IBS patients.

METHODS: This study is a randomized controlled trial which will be conducted at a city hospital in the Netherlands. Adult patients with considerable IBS pain (pain intensity at least 60/100 during at least 5/10 days) will be randomly assigned to either EMDR therapy or the wait list. We aim to include 34 participants. The EMDR condition comprises seven sessions, around 90 min in length delivered weekly, the first of which is a case conceptualization session. All participants will be assessed at baseline, post-treatment, and at 3 months follow-up. The primary outcome measure is pain intensity on a Likert scale which is self-reported daily during a 2-week period. Secondary outcomes include similar daily ratings on other IBS symptoms and reported hindrance of valued activities, and also standardized questionnaires on IBS symptoms and Quality of Life. Data will be analyzed by a Linear Mixed Effects Model for repeated measures.

DISCUSSION: The results are expected to gain insight into the effectiveness of EMDR treatment on abdominal pain in IBS. As there are very few effective treatment options for IBS-related abdominal pain, this study could have important implications for clinical practice.

TRIAL REGISTRATION: Human ethics committee MEC-U NL71740.100.20. International Clinical Trial Registry Platform: NL8894. Prospectively registered on 28 January 2020.

PMID:38049872 | DOI:10.1186/s13063-023-07784-1