Tag: statistics

Biophys J. 2023 Feb 3:S0006-3495(23)00093-0. doi: 10.1016/j.bpj.2023.02.001. Online ahead of print.

ABSTRACT

Cell motility on flat substrates exhibits coexisting steady and oscillatory morphodynamics, the biphasic adhesion-velocity relation, and the universal correlation between speed and persistence (UCSP) as simultaneous observations common to many cell types. Their universality and concurrency suggest a unifying mechanism causing all three of them. Stick-slip models for cells on 1dimensional lanes suggest multistability to arise from the non-linear friction of retrograde flow. This study suggests a mechanical mechanism controlled by integrin signalling on the basis of a biophysical model and analysis of trajectories of MDA-MB-231 cells on Fibronectin lanes which additionally explains the constitutive relations. The experiments exhibit cells with steady or oscillatory morphodynamics and either spread or moving with spontaneous transitions between the dynamic regimes, spread and moving and spontaneous direction reversals. Our biophysical model is based on the force balance at the protrusion edge, the noisy clutch of retrograde flow and a response function of friction and membrane drag to integrin signaling. The theory reproduces the experimentally observed cell states, characteristics of oscillations and state probabilities. Analysis of experiments with the biophysical model establishes a stick-slip oscillation mechanism, explains multistability of cell states and the statistics of state transitions. It suggests protrusion competition to cause direction reversal events, the statistics of which explain the UCSP. The effect of integrin signalling on drag and friction explains the adhesion-velocity relation and cell behavior at Fibronectin density steps. The dynamics of our mechanism are non-linear flow mechanics driven by F-actin polymerization and shaped by the noisy clutch of retrograde flow friction, protrusion competition via membrane tension and drag forces. Integrin signalling controls the parameters of the mechanical system.

PMID:36739476 | DOI:10.1016/j.bpj.2023.02.001

Sci Data. 2023 Feb 4;10(1):73. doi: 10.1038/s41597-023-01987-6.

ABSTRACT

Since the early 2000s, sea ice has experienced an increased rate of decline in thickness, extent and age. This new regime, coined the ‘New Arctic’, is accompanied by a reshuffling of energy flows at the surface. Understanding of the magnitude and nature of this reshuffling and the feedbacks therein remains limited. A novel database is presented that combines satellite observations, model output, and reanalysis data with sea ice parcel drift tracks in a Lagrangian framework. This dataset consists of daily time series of sea ice parcel locations, sea ice and snow conditions, and atmospheric states, including remotely sensed surface energy budget terms. Additionally, flags indicate when sea ice parcels travel within cyclones, recording cyclone intensity and distance from the cyclone center. The quality of the ice parcel database was evaluated by comparison with sea ice mass balance buoys and correlations are high, which highlights the reliability of this database in capturing the seasonal changes and evolution of sea ice. This database has multiple applications for the scientific community; it can be used to study the processes that influence individual sea ice parcel time series, or to explore generalized summary statistics and trends across the Arctic.

PMID:36739456 | DOI:10.1038/s41597-023-01987-6

Sci Rep. 2023 Feb 4;13(1):2053. doi: 10.1038/s41598-023-28904-6.

ABSTRACT

To investigate differences in clinical features based on magnetic resonance imaging (MRI) in idiopathic isolated optic neuritis patients. We retrospectively analyzed 68 eyes of 59 patients diagnosed with optic neuritis and showed inflammatory findings indicative of optic neuritis on MRI. We investigated clinical features, such as the presence of accompanying pain, visual acuity, and optic disc swelling. Optic disc swelling was classified as normal, mild, or severe. The MRI results were divided into intraorbital, intracanalicular, and whole optic nerve according to the lesion, and these were compared and analyzed with clinical features. The study included 29 men and 30 women, with a mean age of 42.6 ± 16.6 years. Among 59 patients, 48 (81.4%) complained of pain. Optic disc swelling was not observed in 48.5% of patients (33 eyes). Inflammatory changes were the most common in the intraorbital region (33 eyes), intracanalicular region (20 eyes), and the entire optic nerve (15 eyes). There was no statistical difference in the pain pattern according to the location of the lesion (p = .677), but when inflammation was present in the entire optic nerve, optic disc swelling was severe (p = .023). The initial and final visual acuity did not significantly correlate with the MRI pattern, presence of pain, or optic disc swelling (p = .156, p = .714, and p = .436). The MRI contrast enhancement pattern was associated with optic disc swelling but was not associated with pain or initial visual acuity. It should be noted that it is insufficient to judge the clinical features of optic neuritis based on MRI findings.

PMID:36739455 | DOI:10.1038/s41598-023-28904-6

Epigenetics Chromatin. 2023 Feb 4;16(1):5. doi: 10.1186/s13072-023-00479-6.

ABSTRACT

BACKGROUND: With the advance of bisulfite sequencing technologies, massive amount of methylation data have been generated, which provide unprecedented opportunities to study the epigenetic mechanism and its relationship to other biological processes. A commonly seen feature of the methylation data is the correlation between nearby CpG sites. Although such a spatial correlation was utilized in several epigenetic studies, its interaction to other characteristics of the methylation data has not been fully investigated.

RESULTS: We filled this research gap from an information theoretic perspective, by exploring the impact of the spatial correlation on the methylation entropy (ME). With the spatial correlation taken into account, we derived the analytical relation between the ME and another key parameter, the methylation probability. By comparing it to the empirical relation between the two corresponding statistics, the observed ME and the mean methylation level, genomic loci under strong epigenetic control can be identified, which may serve as potential markers for cell-type specific methylation. The proposed method was validated by simulation studies, and applied to analyze a published dataset of mouse brain methylome.

CONCLUSIONS: Compared to other sophisticated methods developed in literature, the proposed method provides a simple but effective way to detect CpG segments under strong epigenetic control (e.g., with bipolar methylation pattern). Findings from this study shed light on the identification of cell-type specific genes/pathways based on methylation data from a mixed cell population.

PMID:36739438 | DOI:10.1186/s13072-023-00479-6

Anim Microbiome. 2023 Feb 4;5(1):7. doi: 10.1186/s42523-023-00229-9.

ABSTRACT

BACKGROUND: Anthropogenic disturbance has the potential to negatively affect wildlife health by altering food availability and diet composition, increasing the exposure to agrochemicals, and intensifying the contact with humans, domestic animals, and their pathogens. However, the impact of these factors on the fecal microbiome composition of wildlife hosts and its link to host health modulation remains barely explored. Here we investigated the composition of the fecal bacterial microbiome of the insectivorous bat Kuhl’s pipistrelle (Pipistrellus kuhlii) dwelling in four environmental contexts with different levels of anthropogenic pressure. We analyzed their microbiome composition, structure and diversity through full-length 16S rRNA metabarcoding using the nanopore long-read sequencer MinION™. We hypothesized that the bacterial community structure of fecal samples would vary across the different scenarios, showing a decreased diversity and richness in samples from disturbed ecosystems.

RESULTS: The fecal microbiomes of 31 bats from 4 scenarios were sequenced. A total of 4,829,302 reads were obtained with a taxonomic assignment percentage of 99.9% at genus level. Most abundant genera across all scenarios were Enterococcus, Escherichia/Shigella, Bacillus and Enterobacter. Alpha diversity varied significantly between the four scenarios (p < 0.05), showing the lowest Shannon index in bats from urban and intensive agriculture landscapes, while the highest alpha diversity value was found in near pristine landscapes. Beta diversity obtained by Bray-Curtis distance showed weak statistical differentiation of bacterial taxonomic profiles among scenarios. Furthermore, core community analysis showed that 1,293 genera were shared among localities. Differential abundance analyses showed that the highest differentially abundant taxa were found in near pristine landscapes, with the exception of the family Alcaligenaceae, which was also overrepresented in urban and intensive agriculture landscapes.

CONCLUSIONS: This study suggests that near pristine and undisturbed landscapes could promote a more resilient gut microbiome in wild populations of P. kuhlii. These results highlight the potential of the fecal microbiome as a non-invasive bioindicator to assess insectivorous bats’ health and as a key element of landscape conservation strategies.

PMID:36739423 | DOI:10.1186/s42523-023-00229-9

Biomed Eng Online. 2023 Feb 4;22(1):8. doi: 10.1186/s12938-023-01069-z.

ABSTRACT

OBJECTIVE: The probability density analysis was applied to automatically characterize the center of pressure (COP) data for evaluation of the stroke patients’ balance ability.

METHODS: The real-time COP coordinates of 38 stroke patients with eyes open and closed during quiet standing were obtained, respectively, from a precision force platform. The COP data were analyzed and characterized by the commonly used parameters: total sway length (SL), sway radius (SR), envelope sway area (EA), and the probability density analysis based parameters: projection area (PA), skewness (SK) and kurtosis (KT), and their statistical correlations were analyzed. The differences of both conventional parameters and probability density parameters under the conditions of eyes open (EO) and eyes closed (EC) were compared.

RESULTS: The PA from probability density analysis is strongly correlated with SL and SR. Both the traditional parameters and probability density parameters in the EC state are significantly different from those in the EO state. The obtained various statokinesigrams were calculated and categorized into typical sway types through probability density function for clinical evaluation of the balance ability of stroke patients.

CONCLUSIONS: The probability density analysis of COP data can be used to characterize the posturography for evaluation of the balance ability of stroke patients.

PMID:36739411 | DOI:10.1186/s12938-023-01069-z

J Transl Med. 2023 Feb 4;21(1):79. doi: 10.1186/s12967-023-03924-y.

ABSTRACT

BACKGROUND: The systemic immune-inflammation index (SII) is a novel biomarker to predict the prognosis of some malignant tumors based on neutrophil, platelet, and lymphocyte counts. Evidence is scarce about the prognostic value of SII for prostate cancer patients. This systematic review and meta-analysis was conducted to explore the prognostic value of the SII in prostate cancer.

METHODS: The PubMed, Embase, Web of Science, and Cochrane Library (CENTRAL) databases were searched to determine eligible studies from inception to August 15, 2022. Hazard ratios (HRs) with 95% confidence intervals (CIs) were extracted to pool the results. Statistical analyses were conducted by using Stata 17.0 software.

RESULTS: A total of 12 studies with 8083 patients were included. The quantitative synthesis showed that a high SII was related to poor overall survival (OS) (HR = 1.44, 95% CI 1.23-1.69, p < 0.001). Furthermore, a subgroup analysis showed that a high SII was associated with poor OS in the groups of any ethnicity, tumor type, and cutoff value. An increased SII was also associated with inferior progression-free survival (PFS) (HR = 1.80, 95% CI 1.27-2.56, p = 0.001). In the subgroup analysis, a high SII value was related to poor PFS in Asian patients (HR = 4.03, 95% CI 1.07-15.17, p = 0.04) and a cutoff value > 580 (HR = 1.19, 95% CI 1.04-1.36, p = 0.01).

CONCLUSION: Based on the current evidence, a high pretreatment SII may be associated with poor OS and PFS. The SII may serve as an important prognostic indicator in patients with prostate cancer. More rigorously designed studies are needed to explore the SII and the prognosis of prostate cancer.

PMID:36739407 | DOI:10.1186/s12967-023-03924-y

BMC Oral Health. 2023 Feb 4;23(1):71. doi: 10.1186/s12903-023-02732-6.

ABSTRACT

BACKGROUND: Cancer treatment-induced bone loss (CTIBL) is the most common adverse event experienced by patients affected by breast cancer (BC) patients, without bone metastases. Bone modifying agents (BMAs) therapy is prescribed for the prevention of CTIBL, but it exposes patients to the risk of MRONJ.

METHODS: This multicentre hospital-based retrospective study included consecutive non-metastatic BC patients affected by MRONJ related to exposure to low-dose BMAs for CTIBL prevention. Patients’ data were retrospectively collected from the clinical charts of seven recruiting Italian centres.

RESULTS: MRONJ lesions were found in fifteen females (mean age 67.5 years), mainly in the mandible (73.3%). The mean duration of BMAs therapy at MRONJ presentation was 34.9 months. The more frequent BMAs was denosumab (53.3%). Ten patients (66.7%) showed the following local risk factors associated to MRONJ development: periodontal disease (PD) in three cases (20%) and the remaining six (40%) have undergone PD-related tooth extractions. One patient presented an implant presence-triggered MRONJ (6.7%). In five patients (33.3%) no local risk factors were observed.

CONCLUSIONS: This is the first case series that investigated BC patients under BMAs for CTIBL prevention suffering from MRONJ. These patients seem to have similar probabilities of developing MRONJ as osteo-metabolic ones. Breast cancer patients under BMAs for CTIBL prevention need a regular prevention program for MRONJ, since they may develop bone metastases and be treated with higher doses of BMAs, potentially leading to a high-risk of MRONJ.

PMID:36739399 | DOI:10.1186/s12903-023-02732-6

BMC Med Imaging. 2023 Feb 4;23(1):23. doi: 10.1186/s12880-023-00980-0.

ABSTRACT

BACKGROUND: The variability in the maxillary sinus anatomy makes dental implant planning challenging. One of the anatomical landmarks that could affect the decision for implant placement around the maxillary sinus is the sinus septa. This study aimed to retrospectively determine the prevalence, anatomical distribution, and morphology of the maxillary sinus septa.

MATERIALS AND METHODS: This study included 309 CBCT images that were analyzed to determine the prevalence, height, location, and orientation of the maxillary sinus septa. Descriptive statistics, Mann‒Whitney U tests, and Kruskal‒Wallis tests were used for data analysis.

RESULTS: A total of 618 maxillary sinuses were analyzed. Maxillary septa were present in 30% (n = 188) of the sinuses and in approximately 45% of the analyzed images. The mean height of the septa was 5.09 mm. The presence of bilateral septa was evident in 49 subjects (35.25%). Female subjects were significantly more likely to have only one septum (n = 67, 53.6%, p < 0.05).

CONCLUSION: The presence of septa is very common, found in one-third to approximately half of the evaluated cases, which warrants careful examination before any surgical interventions to avoid possible complications.

PMID:36739395 | DOI:10.1186/s12880-023-00980-0

Parasit Vectors. 2023 Feb 4;16(1):53. doi: 10.1186/s13071-023-05666-8.

ABSTRACT

BACKGROUND: Opportunistic infections are a ubiquitous complication in human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) patients. Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are common opportunistic intestinal pathogens in humans. In China, despite the number of HIV/AIDS patients being extremely large, only a few studies have investigated opportunistic infections caused by intestinal pathogens in this patient population. The aims of this study were to elucidate the occurrence and genetic characteristics of Cryptosporidium spp., G. duodenalis, and E. bieneusi in HIV/AIDS patients.

METHODS: We collected fecal specimens from 155 HIV/AIDS patients (one from each patient). All of the specimens were examined for the presence of the pathogens by genotyping using polymerase chain reaction and sequencing of the small subunit ribosomal RNA gene for Cryptosporidium spp.; the triosephosphate isomerase, β-giardin and glutamate dehydrogenase genes for G. duodenalis; and the internal transcribed spacer region of the rRNA gene for E. bieneusi. The Cryptosporidium-positive specimens were further subtyped by polymerase chain reacion and sequencing of the 60-kDa glycoprotein gene.

RESULTS: Six (3.9%), three (1.9%), and eight (5.2%) HIV/AIDS patients were positive for Cryptosporidium spp., G. duodenalis, and E. bieneusi, respectively. No statistical differences were observed in occurrence rate between the groups by gender, clinical symptom (diarrhea), and CD4⁺ cell count. Four Cryptosporidium species were identified: Cryptosporidium hominis (n = 2), Cryptosporidium parvum (n = 1), Cryptosporidium meleagridis (n = 1), and Cryptosporidium andersoni (n = 2). Furthermore, two C. hominis subtypes (IeA12G3T3 and IaA28R4) were detected. Three G. duodenalis-positive specimens were successfully amplified and sequenced at the triosephosphate isomerase and β-giardin loci, which led to the identification of assemblages C and B, respectively. Seven genotypes (D, Type IV, EbpC, Peru11, EbpD, A, and I) were identified in E. bieneusi-positive specimens.

CONCLUSIONS: Our findings should increase awareness of AIDS-related opportunistic intestinal pathogens, and indicate the need for routine examination in clinical practice for the detection of Cryptosporidium spp., G. duodenalis, and E. bieneusi. Homology analyses of the three intestinal pathogens at the nucleotide and/or amino acid levels indicated their zoonotic potential.

PMID:36739387 | DOI:10.1186/s13071-023-05666-8