Category: Statistics

J Vis. 2023 Dec 1;23(15):56. doi: 10.1167/jov.23.15.56.

ABSTRACT

When we enter a dark place like a tunnel from a bright exterior, our visual sensitivities take some time to adapt to the lower light level. However, there have been few reports about how quickly our sensitivities of luminance and chromaticity discrimination recover in this situation. This study aimed to quantify the time course of discrimination sensitivity for luminance and chromaticity directions after an abrupt decrease in background luminance. In each trial, the background luminance dropped from 100 cd/m² to 1 cd/m². Then, one target and three reference stimuli with different colors were presented under four stimulus onset asynchrony (SOA) conditions. The observer was asked to discriminate the target stimulus from the reference stimuli. The results showed that discrimination sensitivity was lowest right after the background luminance change and gradually improved with SOAs. However, sensitivity recovery differed across color directions, with the most improvement in luminance, followed by S, and negligible change in L-M. There was a statistically significant difference between +S and ±(L-M) sensitivities, indicating that the sensitivity recovery after the sudden background luminance change differed between chromaticity directions. Based on the comparison with previous studies, we speculate that both adaptation and masking may contribute to the temporal change of discrimination sensitivities.

PMID:38109592 | DOI:10.1167/jov.23.15.56

J Vis. 2023 Dec 1;23(15):80. doi: 10.1167/jov.23.15.80.

ABSTRACT

When a person views a color sample, they can usually provide a color term for it. But will that color term allow someone else to understand which sample was named? We examined color understanding using a Color Communication Game, in which one person (the “sender”) names 30 color samples as in any color-naming study, then another person (the “receiver”) chooses the sample they think the sender intended to communicate. The receiver cannot always guess the right sample, and no choice strategy will do better than randomly choosing among the samples the receiver called by that term. When 70 English-speaking dyads and 63 Somali-speaking dyads played the game, receivers did not perform randomly. Instead, they systematically chose “focal” samples near the centers of their color term distributions. When the senders’ named samples were compared directly to the receivers’ chosen samples, the systematic distribution of receiver choices revealed color categories, which appeared without any statistical analysis of the players’ terms. Simulation of receiver choices based on senders’ color names showed that both Somali-speaking and English-speaking participants knew more color terms than the ones they used in color-naming. Our Color Communication Game showed that color-naming experiments underestimate color understanding: people understand colors categorically, but they express colors using multiple synonymous color terms that are well-understood by others.

PMID:38109568 | DOI:10.1167/jov.23.15.80

Proc Natl Acad Sci U S A. 2024 Jan 2;121(1):e2304404120. doi: 10.1073/pnas.2304404120. Epub 2023 Dec 18.

ABSTRACT

The dominant paradigm for assessing ecological responses to climate change assumes that future states of individuals and populations can be predicted by current, species-wide performance variation across spatial climatic gradients. However, if the fates of ecological systems are better predicted by past responses to in situ climatic variation through time, this current analytical paradigm may be severely misleading. Empirically testing whether spatial or temporal climate responses better predict how species respond to climate change has been elusive, largely due to restrictive data requirements. Here, we leverage a newly collected network of ponderosa pine tree-ring time series to test whether statistically inferred responses to spatial versus temporal climatic variation better predict how trees have responded to recent climate change. When compared to observed tree growth responses to climate change since 1980, predictions derived from spatial climatic variation were wrong in both magnitude and direction. This was not the case for predictions derived from climatic variation through time, which were able to replicate observed responses well. Future climate scenarios through the end of the 21st century exacerbated these disparities. These results suggest that the currently dominant paradigm of forecasting the ecological impacts of climate change based on spatial climatic variation may be severely misleading over decadal to centennial timescales.

PMID:38109562 | DOI:10.1073/pnas.2304404120

Eur J Cardiothorac Surg. 2023 Dec 18:ezad412. doi: 10.1093/ejcts/ezad412. Online ahead of print.

ABSTRACT

BACKGROUND: This study aimed to evaluate employing the German Registry of Acute Aortic Dissection Type A (GERAADA) score to predict 30-day mortality in an aortic center in the United States.

METHODS: Between January 2010 and June 2021, 689 consecutive patients underwent surgery for acute type A dissection at a single institution. Excluded were patients with missing clinical data (N = 4). The GERAADA risk score was retrospectively calculated via a web-based application. Model discrimination power was calculated with c-statistics from logistic regression and reported as the area under the receiver operating characteristic curve (AUC) with 95% confidence intervals (CIs). The calibration was measured by calculating the observed versus estimated mortality (O/E) ratio. The Brier score was used for the overall model evaluation.

RESULTS: Included were 685 patients [mean age 60.6 years (SD: 13.5), 64.8% male] who underwent surgery for acute Type A aortic dissection. The 30-day mortality rate was 12.0%. The GERAADA score demonstrated very good discrimination power with an AUC of 0.762 (95% CI 0.703-0.821). The entire cohort’s O/E ratio was 0.543 (0.439-0.648), indicating an overestimation of the model-calculated risk. The Brier score was 0.010, thus revealing the model’s acceptable overall performance.

CONCLUSIONS: The GERAADA score is a practical and easily accessible tool for reliably estimating the 30-day mortality risk of patients undergoing surgery for acute Type A aortic dissection. This model may naturally overestimate risk in patients undergoing surgery in experienced aortic centers.

PMID:38109506 | DOI:10.1093/ejcts/ezad412

Plant Physiol. 2023 Dec 18:kiad672. doi: 10.1093/plphys/kiad672. Online ahead of print.

ABSTRACT

Desiccation is typically fatal, but a small number of land plants have evolved vegetative desiccation tolerance (VDT), allowing them to dry without dying through a process called anhydrobiosis. Advances in sequencing technologies have enabled the investigation of genomes for desiccation-tolerant plants over the past decade. However, a dedicated and integrated database for these valuable genomic resources has been lacking. Our prolonged interest in VDT plant genomes motivated us to create the “Drying without Dying” database, which contains a total of 16 VDT-related plant genomes (including ten mosses) and incorporates 10 genomes that are closely related to VDT plants. The database features bioinformatic tools, such as blast and homologous cluster search, sequence retrieval, GO term and metabolic pathway enrichment statistics, expression profiling, co-expression network extraction, and JBrowser exploration for each genome. To demonstrate its utility we conducted tailored PFAM family statistical analyses, and we discovered that the drought-responsive ABA transporter AWPM-19 family is significantly tandemly duplicated in all bryophytes but rarely so in tracheophytes. Transcriptomic investigations also revealed that response patterns following desiccation diverged between bryophytes and angiosperms. Combined, the analyses provided genomic and transcriptomic evidence supporting a possible divergence and lineage-specific evolution of VDT in plants. The database can be accessed at http://desiccation.novogene.com. We expect this initial release of the “Drying without Dying” plant genome database will facilitate future discovery of VDT genetic resources.

PMID:38109500 | DOI:10.1093/plphys/kiad672

J Low Genit Tract Dis. 2023 Dec 18. doi: 10.1097/LGT.0000000000000793. Online ahead of print.

ABSTRACT

OBJECTIVE: This study aimed to investigate the characteristics and screening history of vaginal intraepithelial neoplasia (VaIN) or vaginal cancer and compare the sensitivity of cytology and human papillomavirus (HPV) tests on the cervix against vaginal and cervical high-grade squamous intraepithelial lesion or cancer.

METHODS: This study included patients who underwent colposcopy-directed biopsy and were diagnosed with VaIN or vaginal cancer from February 2013 to November 2022. Clinical information was obtained from the medical records of the department. Statistical analysis was performed on SPSS 26.0 (IBM Corp, Armonk, NY) using t test, chi-square, and Fisher exact tests.

RESULTS: A total of 1,166 patients were included in this study. The median age of VaIN2+ patients was 50.5 years, whereas VaIN1 reported a median age of 42.1 years old, p < .001. This study reported that VaIN was significantly and positively correlated with cervical lesions (r = 0.244). The high-risk HPV (hr-HPV) detection rate was 88.2% (858/973) in VaIN and 95.2% in VaIN2+. Human papillomavirus 16 was the most prevalent HPV type in VaIN2+, which accounted for 54.9%, followed by HPV58 (19.5%), HPV52 (15.2%), HPV51 (12.2%), and HPV18 (11.0%). The sensitivity of hr-HPV and cytology tests on the cervix for detecting VaIN2+ was 94.7% and 83.4%, respectively. Both tests were not significantly different from detecting cervical intraepithelial neoplasia 2+.

CONCLUSIONS: Human papillomavirus 16 is the dominant HPV type in vaginal precancer lesions. Cervical cancer screening has similar sensitivity for VaIN2+ as for cervical intraepithelial neoplasia 2+, with hr-HPV testing showing higher sensitivity than cytology.

PMID:38109483 | DOI:10.1097/LGT.0000000000000793

PLoS Comput Biol. 2023 Dec 18;19(12):e1011722. doi: 10.1371/journal.pcbi.1011722. Online ahead of print.

ABSTRACT

Recent experimental evidence strongly supports that three-dimensional (3D) long-range enhancer-promoter (E-P) interactions have important influences on gene-expression dynamics, but it is unclear how the interaction information is translated into gene expression over time (4D). To address this question, we developed a general theoretical framework (named as a 4D nucleome equation), which integrates E-P interactions on chromatin and biochemical reactions of gene transcription. With this equation, we first present the distribution of mRNA counts as a function of the E-P genomic distance and then reveal a power-law scaling of the expression level in this distance. Interestingly, we find that long-range E-P interactions can induce bimodal and trimodal mRNA distributions. The 4D nucleome equation also allows for model selection and parameter inference. When this equation is applied to the mouse embryonic stem cell smRNA-FISH data and the E-P genomic-distance data, the predicted E-P contact probability and mRNA distribution are in good agreement with experimental results. Further statistical inference indicates that the E-P interactions prefer to modulate the mRNA level by controlling promoter activation and transcription initiation rates. Our model and results provide quantitative insight into both spatiotemporal gene-expression determinants (i.e., long-range E-P interactions) and cellular fates during development.

PMID:38109463 | DOI:10.1371/journal.pcbi.1011722

Pril (Makedon Akad Nauk Umet Odd Med Nauki). 2023 Dec 18;44(3):27-39. doi: 10.2478/prilozi-2023-0044. Print 2023 Dec 1.

ABSTRACT

Introduction: Studies determined that age and associated comorbidities are associated with worse outcomes for COVID-19 patients. The aim of the present study is to examine previous electronic health records of SARS-CoV-2 patients to identify which chronic conditions are associated with in-hospital mortality in a nationally representative sample. Materials and Methods: The actual study is a cross-sectional analysis of SARS-CoV-2 infected patients who were treated in repurposed hospitals. The study includes a cohort of patients treated from 06-11-2020 to 15-03-2021 for COVID-19 associated pneumonia. To examine the presence of comorbidities, electronic health records were examined and analyzed. Results: A total of 1486 in-patients were treated in the specified period, out of which 1237 met the criteria for case. The median age of the sample was 65 years. The overall in-hospital mortality in the sample was 25.5%, while the median length of stay was 11 days. From whole sample, 16.0% of the patients did not have established diagnoses in their electronic records, while the most prevalent coexisting condition was arterial hypertension (62.7%), followed by diabetes mellitus (27.3%). The factors of age, male gender, and the number of diagnoses showed a statistically significant increase in odds ratio (OR) for in-hospital mortality. The presence of chronic kidney injury was associated with the highest increase of OR (by 3.37) for in-hospital mortality in our sample. Conclusion: The study reaffirms the findings that age, male gender, and the presence of comorbidities are associated with in-hospital mortality in COVID-19 treated and unvaccinated patients. Our study suggests that chronic kidney injury showed strongest association with the outcome, when adjusted for age, gender, and coexisting comorbidities.

PMID:38109453 | DOI:10.2478/prilozi-2023-0044

Pril (Makedon Akad Nauk Umet Odd Med Nauki). 2023 Dec 18;44(3):49-55. doi: 10.2478/prilozi-2023-0046. Print 2023 Dec 1.

ABSTRACT

The main goals of this research are to determine the developmental tendency of salmonellosis in the Republic of North Macedonia and to determine the index of dynamics and the rate of decline/increase of salmonellosis in the Republic of North Macedonia. The research covers the period from 01.01.2012 until 31.12.2022. The data used to implement this study were obtained from the Institute of Public Health of the Republic of North Macedonia. The research included 2711 subjects who were sick with salmonellosis from 2012 to 2022. The following statistical methods of work are used: linear trend, dynamic index with a constant base, dynamic index with a variable base (chain index), rate of decline, and rate of increase. The results of the study suggest that in the period 2012-2022, the highest number of patients (n=373) and the highest incidence (18/100000) of salmonellosis were registered in 2018, and the lowest in 2020 (n=119, I=5.8/100000). From the linear trend values, it can be concluded that salmonellosis in the Republic of North Macedonia shows a decreasing tendency. The biggest increase in salmonellosis in the Republic of North Macedonia was in 2015 by 71% compared to 2014. The biggest decrease in salmonellosis in the Republic of North Macedonia was in 2020 by 48% compared to 2019. From the study, it can be concluded that food operators and manufacturers are observing the procedures of the HACCP control system for food safety, leading to a possible decrease in salmonellosis.

PMID:38109452 | DOI:10.2478/prilozi-2023-0046

Pril (Makedon Akad Nauk Umet Odd Med Nauki). 2023 Dec 18;44(3):79-84. doi: 10.2478/prilozi-2023-0050. Print 2023 Dec 1.

ABSTRACT

In psychology, alienation is a condition of being separated or marginalized from other individuals or some larger segment of society. Self-efficacy is an individual’s belief in their capacity to act in ways necessary to reach specific goals. This study was conducted to investigate the possible connectivity between psychological alienation and feelings of self-efficiency among young male and female adults. The study was conducted in April 2023, among 167 young people, aged 18-25 (M=22.28 ± 1.7SD). For this purpose, we used the Scale for psychological alienation and General self-efficacy. Results showed that there is a significant negative correlation between alienation and self-efficacy, meaning that the higher psychological alienation is, the lower self-efficacy is (t=-0.627; <0.001). There is a statistically significant difference between young male and female adults regarding alienation (t=-5.592; <0.001) e. g. males are reporting to be more alienated than females. Also, there is a statistically significant difference between young male and female adults regarding feeling of self-efficacy (t=4.692; <0.001) e.g. males feel less effective than females and in the scale for measuring meaninglessness (t=-2.966; 0.003) e. g. males feel more meaninglessness than females. In conclusion, psychological alienation and self-efficacy are correlated and there are gender differences regarding the two measured variables, in favor of the females.

PMID:38109447 | DOI:10.2478/prilozi-2023-0050