Tag: statistics

Biom J. 2021 Dec 16. doi: 10.1002/bimj.202000334. Online ahead of print.

ABSTRACT

Zeros in compositional data are very common and can be classified into rounded and essential zeros. The rounded zero refers to a small proportion or below detection limit value, while the essential zero refers to the complete absence of the component in the composition. In this article, we propose a new framework for analyzing compositional data with zero entries by introducing a stochastic representation. In particular, a new distribution, namely the Dirichlet composition distribution, is developed to accommodate the possible essential-zero feature in compositional data. We derive its distributional properties (e.g., its moments). The calculation of maximum likelihood estimates via the Expectation-Maximization (EM) algorithm will be proposed. The regression model based on the new Dirichlet composition distribution will be considered. Simulation studies are conducted to evaluate the performance of the proposed methodologies. Finally, our method is employed to analyze a dataset of fluorescence in situ hybridization (FISH) for chromosome detection.

PMID:34914842 | DOI:10.1002/bimj.202000334

Transbound Emerg Dis. 2021 Dec 16. doi: 10.1111/tbed.14424. Online ahead of print.

ABSTRACT

African swine fever virus (ASFV) is a global threat to swine production and sustainable pork supply. Without a commercially available vaccine, prevention of ASFV entry and spread is reliant on biosecurity and early detection of infection. Although ASFV ingestion in swill or feed by naïve pigs is a likely route of initial introduction, controlled experimental studies rarely utilize natural consumption as the infection route. In the current study, we utilized biological samples collected from pigs 5 days after natural consumption of ASFV in feed and liquid to assess diagnostic sensitivity for early detection of virus infection. Biological samples (serum, spleen, lymph nodes, tonsils, and feces) were assessed for the presence of ASFV using quantitative PCR and virus isolation. Statistical methods modeled the detection sensitivity of each sample type with each diagnostic assay in individual samples. Our results provide important information that can be incorporated into ASFV surveillance programs. This article is protected by copyright. All rights reserved.

PMID:34914859 | DOI:10.1111/tbed.14424

J Exp Med. 2022 Feb 7;219(2):e20211381. doi: 10.1084/jem.20211381. Epub 2021 Dec 16.

ABSTRACT

In rare instances, pediatric SARS-CoV-2 infection results in a novel immunodysregulation syndrome termed multisystem inflammatory syndrome in children (MIS-C). We compared MIS-C immunopathology with severe COVID-19 in adults. MIS-C does not result in pneumocyte damage but is associated with vascular endotheliitis and gastrointestinal epithelial injury. In MIS-C, the cytokine release syndrome is characterized by IFNγ and not type I interferon. Persistence of patrolling monocytes differentiates MIS-C from severe COVID-19, which is dominated by HLA-DRlo classical monocytes. IFNγ levels correlate with granzyme B production in CD16+ NK cells and TIM3 expression on CD38+/HLA-DR+ T cells. Single-cell TCR profiling reveals a skewed TCRβ repertoire enriched for TRBV11-2 and a superantigenic signature in TIM3+/CD38+/HLA-DR+ T cells. Using NicheNet, we confirm IFNγ as a central cytokine in the communication between TIM3+/CD38+/HLA-DR+ T cells, CD16+ NK cells, and patrolling monocytes. Normalization of IFNγ, loss of TIM3, quiescence of CD16+ NK cells, and contraction of patrolling monocytes upon clinical resolution highlight their potential role in MIS-C immunopathogenesis.

PMID:34914824 | DOI:10.1084/jem.20211381

J Clin Psychol. 2021 Dec 16. doi: 10.1002/jclp.23292. Online ahead of print.

ABSTRACT

Feature heterogeneity and diagnostic overlap occur regularly among patients in clinical settings. In interpersonal reconstructive therapy (IRT), a case formulation focused on patterns learned in close attachment relationships guides intervention choices. This study illustrates how IRT formulation and treatment proceed, and how it may also fail when there is not close adherence to underlying principles. Don is a music professor in his 40’s with a significant trauma history and complex diagnostic profile that includes many hospitalizations and suicide attempts. He qualified for several diagnostic and statistical manual of mental disorders personality disorders via formal diagnostic interviews (obsessive-compulsive, avoidant, passive-aggressive, narcissistic), as well as major depression, generalized anxiety, and substance abuse. Don’s formulation demonstrates how self-destruction can function as a “gift of love” to internalized representations of important caregivers. Data from work with patients like Don confirm the usefulness of Benjamin’s IRT lens for navigating comorbidity, as well as the importance of underlying principles of change.

PMID:34914841 | DOI:10.1002/jclp.23292

PLoS One. 2021 Dec 16;16(12):e0261437. doi: 10.1371/journal.pone.0261437. eCollection 2021.

ABSTRACT

BACKGROUND AND OBJECTIVES: At present, the focus of the fighting against COVID-19 in China is shifting to strictly prevent the entrance of cases from abroad and disease transmission. Therefore, it is extremely urgent to better understand the clinical features of imported cases from overseas countries, which is conductive to formulate the corresponding countermeasures. This study aimed to describe the clinical features of COVID-19 cases imported from Russia through the Suifenhe port, in order to identify baseline and clinical data associated with disease progression and present corresponding countermeasures.

METHODS: All COVID-19 cases imported from Russia through the Suifenhe port were included in this retrospective study. According to the “Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (seventh edition)”, imported COVID-19 cases were divided into asymptomatic infection, mild, moderate, severe, and critical groups. Baseline and clinical data, including age, gender, comorbidities, disease severity, symptoms at onset, body temperature, white blood cell (WBC) count, lymphocyte (LYMPH) count, lymphocyte percentage (LYM%), C-reactive protein (CRP), oxygenation index (OI), and the use therapeutic modalities were obtained on admission, and then compared between groups.

RESULTS: A total of 375 COVID-19 cases imported from Russia through Suifenhe port were included, of whom the asymptomatic infection, mild, moderate, severe, and critical groups accounted for 4.0%, 13.9%, 75.5%, 5.3%, and 1.3%, respectively. The majority of the imported COVID-19 cases were men (61.9%) with a median age of 38.72 years who had no comorbidity (87.7%). Nearly one-third of them (33.1%) were asymptomatic at onset, and common initial symptoms included fever (36.5%), cough (36.0%), pharyngeal discomfort (12.3%), expectoration (8.0%), and chest tightness (5.3%). In total, 180 (48%) and 4 (1.1%) enrolled imported cases received nasal tube oxygen inhalation therapy and high-flow oxygen absorption, respectively; the remaining patients did not undergo oxygen therapy. The values of age, body temperature, WBC, LYMPH, LYM%, CRP, and OI were 38.72 ± 10.50, 35.10 ± 7.92, 5.59 ± 1.97, 1.67 ± 0.68, 31.05 ± 10.22, 8.00 ± 14.75, and 389.03 ± 74.07, respectively. Gender, age, LYMPH, LYM%, symptoms at onset, cough, fever, other rare symptoms, and oxygen therapy showed significant differences between groups (P = 0.036, < 0.001, < 0.001, < 0.001, < 0.001, < 0.001, < 0.001, = 0.045, < 0.001, respectively).

CONCLUSIONS: Compared with domestic confirmed patients, COVID-19 patients who arrived at China from Russia through the Suifenhe port had significantly different clinical features, and the differences in gender, age, LYMPH, LYM%, symptoms at onset, cough, fever, other rare symptoms, and oxygen therapy between groups were statistically significant. Therefore, detailed and comprehensive countermeasures were developed to manage and prevent another outbreak based on these clinical features.

PMID:34914808 | DOI:10.1371/journal.pone.0261437

PLoS One. 2021 Dec 16;16(12):e0261300. doi: 10.1371/journal.pone.0261300. eCollection 2021.

ABSTRACT

BACKGROUND: Heart failure (HF) imposes a substantial burden on patients and healthcare systems. Hospital-to-home transitional care, involving time-limited interventions delivered predominantly by nurses, was introduced to lighten this burden. This study aimed to examine the effectiveness and dose-response of nurse-led transitional care interventions (TCIs) on healthcare utilization among patients with HF.

METHODS: Health-related databases were systematically searched for articles published from January 2000 to June 2020. We included randomized controlled trials (RCTs) that compared nurse-led TCIs with usual care for adults hospitalized with HF and reported the following healthcare utilization outcomes: all-cause readmissions, HF-specific readmissions, emergency department visits, or length of hospital stay. Random-effects meta-analysis, meta-regression analysis, and dose-response analysis were performed to estimate the treatment effects and explain the heterogeneity.

RESULTS: Twenty-five RCTs including 8422 patients with HF were included. Nurse-led TCIs for patients with HF resulted in a mean 9% (RR = 0.91; 95% CI = 0.82 to 0.99; p = 0.04; I2 = 46%) and 29% (RR = 0.71; 95% CI = 0.60 to 0.84; p < 0.0001; I2 = 0%) reduction in all-cause and HF-specific readmission risks respectively compared to usual care. The interventions were also effective in shortening the length of hospital stay (MD = -2.37; 95% CI = -3.16 to -1.58; p < 0.0001; I2 = 14%). However, no significant reduction was found for emergency department visits (RR = 0.96; 95% CI = 0.84 to 1.10; p = 0.58; I2 = 0%). The effect of meta-regression coefficients on all-cause and HF-specific readmissions was not statistically significant for any prespecified trial-level characteristic. Dose-response analysis revealed that the HF-specific readmission risk decreased in a dose-dependent manner with the complexity and intensity of nurse-led TCIs.

CONCLUSIONS: Nurse-led TCIs were effective in decreasing all-cause and HF-specific readmission risks, as well as in reducing the length of hospital stay; however, the interventions were not effective in reducing the frequency of emergency department visits.

PMID:34914810 | DOI:10.1371/journal.pone.0261300

PLoS One. 2021 Dec 16;16(12):e0261301. doi: 10.1371/journal.pone.0261301. eCollection 2021.

ABSTRACT

Infant and young child feeding is a key area to improve child survival and promote healthy growth and development. Nepal government has developed and implemented different programs to improve infant and young child feeding practice. However, the practice remains poor and is a major cause of malnutrition in Nepal. This study aims to identify infant and young child feeding practices and its associated factors among mothers of children aged less than two years in western hilly region of Nepal. A descriptive cross-sectional study was carried out among 360 mothers of under two years’ children in Syangja district. A semi structural questionnaire was used. Data was entered in EpiData and analyzed using IBM SPSS version 21. Descriptive statistics were used to report the feeding practices and other independent variables. Bivariate and multivariate logistic regression model was used to establish the factors associated with infant and young child feeding practices. The prevalence of breastfeeding, timely initiation of breastfeeding, exclusive breastfeeding, timely initiation of complementary feeding, minimum dietary diversity, minimum meal frequency and minimum acceptable diet (MAD) were 95.6%, 69.2%, 47.6%, 53.3%, 61.5%, 67.3% and 49.9% respectively. Normal delivery (AOR 6.1, 95% CI 1.2-31.3) and higher maternal autonomy (AOR 5.2, 95% CI 1.8-14.6) were significantly associated with exclusive breastfeeding. Similarly, crop production and food security (AOR 3.8, 95% CI 1.9-7.7), maternal knowledge on MAD (AOR 2.5, 95% CI 1.0-6.2) and maternal autonomy (AOR 4.2, 95% CI 2.1-8.4) were significantly associated with minimum acceptable diet. Factors such as maternal education, maternal health services utilization, maternal knowledge, and maternal autonomy were associated with infant and young child feeding practices, which warrants further attention to these factors to reduce malnutrition.

PMID:34914802 | DOI:10.1371/journal.pone.0261301

PLoS One. 2021 Dec 16;16(12):e0261278. doi: 10.1371/journal.pone.0261278. eCollection 2021.

ABSTRACT

As part of a wider reform to scaffold quantitative and research skills throughout the biology major, we introduced course-based undergraduate research experiences (CURE) in sections of a large-enrollment introductory biology laboratory course in a mid-level, public, minority-serving institution. This initiative was undertaken as part of the in the National Science Foundation / Council for Undergraduate Research Transformations Project. Student teams performed two or three experiments, depending on semester. They designed, implemented, analyzed, revised and iterated, wrote scientific paper-style reports, and gave oral presentations. We tested the impact of CURE on student proficiency in experimental design and statistical reasoning, and student research confidence and attitudes over two semesters. We found that students in the CURE sections met the reformed learning objectives for experimental design and statistical reasoning. CURE students also showed higher levels of experimental design proficiency, research self-efficacy, and more expert-like scientific mindsets compared to students in a matched cohort with the traditional design. While students in both groups described labs as a positive experience in end-of-semester reflections, the CURE group showed a high level of engagement with the research process. Students in CURE sections identified components of the research process that were difficult, while also reporting enjoying and valuing research. This study demonstrates improved learning, confidence, and attitudes toward research in a challenging CURE laboratory course where students had significant autonomy combined with appropriate support at a diverse public university.

PMID:34914796 | DOI:10.1371/journal.pone.0261278

PLoS One. 2021 Dec 16;16(12):e0261373. doi: 10.1371/journal.pone.0261373. eCollection 2021.

ABSTRACT

BACKGROUND: Celiac disease (CD) is now viewed as a systemic disease with multifaceted clinical manifestations. Among the extra-intestinal features, neurological and neuropsychiatric symptoms are still a diagnostic challenge, since they can precede or follow the diagnosis of CD. In particular, it is well known that some adults with CD may complain of cognitive symptoms, that improve when the gluten-free diet (GFD) is started, although they may re-appear after incidental gluten intake. Among the neurophysiological techniques, motor evoked potentials (MEPs) to transcranial magnetic stimulation (TMS) can non-invasively probe in vivo the excitation state of cortical areas and cortico-spinal conductivity, being also able to unveil preclinical impairment in several neurological and psychiatric disorders, as well as in some systemic diseases affecting the central nervous system (CNS), such as CD. We previously demonstrated an intracortical disinhibition and hyperfacilitation of MEP responses to TMS in newly diagnosed patients. However, no data are available on the central cholinergic functioning indexed by specific TMS measures, such as the short-latency afferent inhibition (SAI), which might represent the neurophysiological correlate of cognitive changes in CD patients, also at the preclinical level.

METHODS: Cognitive and depressive symptoms were screened by means of the Montreal Cognitive Assessment (MoCA) and the 17-item Hamilton Depression Rating Scale (HDRS), respectively, in 15 consecutive de novo CD patients and 15 healthy controls. All patients were on normal diet at the time of the enrolment. Brain computed tomography (CT) was performed in all patients. SAI, recorded at two interstimulus intervals (2 and 8 ms), was assessed as the percentage amplitude ratio between the conditioned and the unconditioned MEP response. Resting motor threshold, MEP amplitude and latency, and central motor conduction time were also measured.

RESULTS: The two groups were comparable for age, sex, anthropometric features, and educational level. Brain CT ruled out intracranial calcifications and clear radiological abnormalities in all patients. Scores at MoCA and HDRS were significantly worse in patients than in controls. The comparison of TMS data between the two groups revealed no statistically significant difference for all measures, including SAI at both interstimulus intervals.

CONCLUSIONS: Central cholinergic functioning explored by the SAI of the motor cortex resulted to be not affected in these de novo CD patients compared to age-matched healthy controls. Although the statistically significant difference in MoCA, an overt cognitive impairment was not clinically evident in CD patients. Coherently, to date, no study based on TMS or other diagnostic techniques has shown any involvement of the central acetylcholine or the cholinergic fibers within the CNS in CD. This finding might add support to the vascular inflammation hypothesis underlying the so-called “gluten encephalopathy”, which seems to be due to an aetiology different from that of the cholinergic dysfunction. Longitudinal studies correlating clinical, TMS, and neuroimaging data, both before and after GFD, are needed.

PMID:34914787 | DOI:10.1371/journal.pone.0261373

PLoS One. 2021 Dec 16;16(12):e0261271. doi: 10.1371/journal.pone.0261271. eCollection 2021.

ABSTRACT

This study aimed to validate the recently developed Occupational Depression Inventory (ODI) in South Africa. A total of 327 employees (60% female) participated in the study. Bifactor exploratory structural equation modeling analysis indicated that the ODI can be considered essentially unidimensional. The ODI displayed strong scalability (e.g., scale-level H = 0.657). No monotonicity violation was detected. The reliability of the instrument, as indexed by Cronbach’s alpha, McDonald’s omega-total, Guttman’s λ2, and the Molenaar-Sijtsma statistic, was highly satisfactory. Measurement invariance was observed across age groups, sexes, and ethnicities, as well as between our sample and the ODI’s original validation sample. As expected, the ODI showed both a degree of convergent validity and a degree of discriminant validity vis-à-vis a measure of “cause-neutral” depressive symptoms. Moreover, the ODI manifested substantial associations, in the anticipated directions, with measures of work engagement, job satisfaction, and life satisfaction. Overall, the ODI exhibited excellent structural and psychometric properties within the South African context. Consistent with previous research, this study suggests that occupational health specialists can confidently rely on the ODI to investigate job-related distress.

PMID:34914772 | DOI:10.1371/journal.pone.0261271