Tag: nevin manimala

Vector Borne Zoonotic Dis. 2023 Jun 15. doi: 10.1089/vbz.2023.0008. Online ahead of print.

ABSTRACT

Background: Cryptosporidium spp. are a type of protozoan parasite responsible for causing diarrheal illness worldwide. They infect a broad range of vertebrate hosts, including both non-human primates (NHPs) and humans. In fact, zoonotic transmission of cryptosporidiosis from NHPs to humans is frequently facilitated by direct contact between the two groups. However, there is a need to enhance the information available on the subtyping of Cryptosporidium spp. in NHPs in the Yunnan province of China. Materials and Methods: Thus, the study investigated the molecular prevalence and species of Cryptosporidium spp. from 392 stool samples of Macaca fascicularis (n = 335) and Macaca mulatta (n = 57) by using nested PCR targeting the large subunit of nuclear ribosomal RNA (LSU) gene. Of the 392 samples, 42 (10.71%) were tested Cryptosporidium-positive. Results: All the samples were identified as Cryptosporidium hominis. Further, the statistical analysis revealed that age is a risk factor for the infection of C. hominis. The probability of detecting C. hominis was found to be higher (odds ratio = 6.23, 95% confidence interval 1.73-22.38) in NHPs aged between 2 and 3 years, as compared with those younger than 2 years. Sequence analysis of the 60 kDa glycoprotein (gp60) identified six (IbA9 n = 4, IiA17 n = 5, InA23 n = 1, InA24 n = 2, InA25 n = 3, and InA26 n = 18) C. hominis subtypes with “TCA” repeats. Among these subtypes, it has been previously reported that the Ib family subtypes are also capable of infecting humans. Conclusion: The findings of this study highlight the genetic diversity of C. hominis infection among M. fascicularis and M. mulatta in Yunnan province. Further, the results confirm that both these NHPs are susceptible to C. hominis infection, posing a potential threat to humans.

PMID:37326984 | DOI:10.1089/vbz.2023.0008

Bioinformatics. 2023 Jun 16:btad383. doi: 10.1093/bioinformatics/btad383. Online ahead of print.

ABSTRACT

MOTIVATION: The shape of a cell is tightly controlled, and reflects important processes including actomyosin activity, adhesion properties, cell differentiation and polarization. Hence, it is informative to link cell shape to genetic and other perturbations. However, most currently used cell shape descriptors capture only simple geometric features such as volume and sphericity. We propose FlowShape, a new framework to study cell shapes in a complete and generic way.

RESULTS: In our framework a cell shape is represented by measuring the curvature of the shape and mapping it onto a sphere in a conformal manner. This single function on the sphere is next approximated by a series expansion: the spherical harmonics decomposition. The decomposition facilitates many analyses, including shape alignment and statistical cell shape comparison. The new tool is applied to perform a complete, generic analysis of cell shapes, using the early Caenorhabditis elegans embryo as a model case. We distinguish and characterize the cells at the seven-cell stage. Next, a filter is designed to identify protrusions on the cell shape to highlight lamellipodia in cells. Further, the framework is used to identify any shape changes following a gene knockdown of the Wnt pathway. Cells are first optimally aligned using the fast Fourier transform, followed by calculating an average shape. Shape differences between conditions are next quantified and compared to an empirical distribution. Finally, we put forward a highly performant implementation of the core algorithm, as well as routines to characterize, align and compare cell shapes, through the open-source software package FlowShape.

AVAILABILITY: The data and code needed to recreate the results are freely available at https://doi.org/10.5281/zenodo.7778752. The most recent version of the software is maintained at https://bitbucket.org/pgmsembryogenesis/flowshape/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:37326982 | DOI:10.1093/bioinformatics/btad383

Bioinformatics. 2023 Jun 16:btad385. doi: 10.1093/bioinformatics/btad385. Online ahead of print.

ABSTRACT

SUMMARY: Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become supply-limited large clusters. In stochastic simulations, such clusters display a wide range of sizes and compositions. We have developed a Python package, MolClustPy, which performs multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator); MolClustPy characterizes and visualizes the distribution of cluster sizes, molecular composition, and bonds across molecular clusters. The statistical analysis offered by MolClustPy is readily applicable to other stochastic simulation software, such as SpringSaLaD and Readdy.

AVAILABILITY AND IMPLEMENTATION: The software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide and examples are freely available at https://molclustpy.github.io/.

SUPPLEMENTARY INFORMATION: Available at https://molclustpy.github.io/.

PMID:37326981 | DOI:10.1093/bioinformatics/btad385

Neurol Sci. 2023 Jun 16. doi: 10.1007/s10072-023-06883-w. Online ahead of print.

ABSTRACT

OBJECTIVE: The aim of the present study was to assess emergency neurology management in Italy by comparing patients admitted to the hub and spoke hospitals.

METHODS: Data obtained from the annual Italian national survey (NEUDay) investigating the activity and facilities of neurology in the emergency room conducted in November 2021 were considered. Information for each patient who received a neurologic consultation after accessing the emergency room was acquired. Data on facilities were also gathered, including hospital classification (hub vs spoke), number of consultations, presence of neurology and stroke unit, number of beds, availability of neurologist, radiologist, neuroradiologist, and instrumental diagnostic accessibility.

RESULTS: Overall, 1,111 patients were admitted to the emergency room and had neurological consultation across 153 facilities (out of the 260 Italian ones). Hub hospitals had significantly more beds, availability of neurological staff, and instrumental diagnostic accessibility. Patients admitted to hub hospital had a greater need for assistance (higher number of yellow/red codes at neurologist triage). A higher propensity to be admitted to hub centers for cerebrovascular problems and to receive a diagnosis of stroke was observed.

CONCLUSIONS: The identification of hub and spoke hospitals is strongly characterized by the presence of beds and instrumentation mainly dedicated to acute cerebrovascular pathologies. Moreover, the similarity in the number and type of accesses between hub and spoke hospitals suggests the need to look for adequate identification of all the neurological pathologies requiring urgent treatment.

PMID:37326936 | DOI:10.1007/s10072-023-06883-w

Updates Surg. 2023 Jun 16. doi: 10.1007/s13304-023-01560-1. Online ahead of print.

ABSTRACT

New tracers for sentinel lymph node biopsy (SLNB), as indocyanine green (ICG), superparamagnetic iron oxide (SPIO) and micro bubbles, have been recently introduced in clinical practice showing promising but variable results. We reviewed the available evidence comparing these new techniques with the standard tracers to evaluate their safety. To identify all available studies, a systematic search was performed in all electronic databases. Data regarding sample size, mean number of SLN harvested for patient, number of metastatic SLN and SLN identification rate of all studies were extracted. No significant differences were found in terms of SLNs identification rates between SPIO, RI and BD but with a higher identification rate with the use of ICG. No significant differences were also found for the number of metastatic lymph nodes identified between SPIO, RI and BD and the mean number of SLNs identified between SPIO and ICG versus conventional tracers. A statistically significant differences in favor of ICG was reported for the comparison between ICG and conventional tracers for the number of metastatic lymph nodes identified. Our meta-analysis demonstrates that the use of both ICG and SPIO for the pre-operative mapping of sentinel lymph nodes in breast cancer treatment is adequately effective.

PMID:37326934 | DOI:10.1007/s13304-023-01560-1

Updates Surg. 2023 Jun 16. doi: 10.1007/s13304-023-01559-8. Online ahead of print.

ABSTRACT

Intestinal malrotation (IM) results from an altered or incomplete rotation of the fetal midgut around the superior mesenteric artery axis. The abnormal anatomy of IM is associated with risk of acute midgut volvulus which can lead to catastrophic clinical consequences. The upper gastro-intestinal series (UGI) is addressed as the gold standard diagnosis procedure, but a variable failure degree has been described in literature. The aim of the study was to analyze the UGI exam and describe which features are the most reproducible and reliable in diagnosing IM. Medical records of patients surgically treated for suspected IM between 2007 and 2020 at a single pediatric tertiary care center were retrospectively reviewed. UGI inter-observer agreement and diagnostic accuracy were statistically calculated. Images obtained with antero-posterior (AP) projections were the most significant in terms of IM diagnosis. Duodenal-Jejunal Junction (DJJ) abnormal position resulted to be the most reliable parameter (Se = 0.88; Sp = 0.54) as well as the most readable, with an inter-reader agreement of 83% (k = 0.70, CI 0.49-0.90). The First Jejunal Loops (FJL), caecum altered position and duodenal dilatation could be considered additional data. Lateral projections demonstrated an overall low sensitivity (Se = 0.80) and specificity (Sp = 0.33) with a PPV of 0.85 and a NPV of 0.25. UGI on the sole AP projections ensures a good diagnostic accuracy. The position of the third portion of the duodenum on lateral views showed an overall low reliability, therefore it was not helpful but rather deceiving in diagnosing IM.

PMID:37326933 | DOI:10.1007/s13304-023-01559-8

Health Promot J Austr. 2023 Jun 16. doi: 10.1002/hpja.762. Online ahead of print.

ABSTRACT

ISSUE ADDRESSED: Cervical screening rates for young women aged between 25 and 35 are lower than older Australian women, however, little research has been conducted to understand why. This study aimed to identify and explore the barriers and enablers faced by young Victorians with a cervix to regular cervical screening.

METHODS: This study used a mixed method exploratory design consisting of qualitative focus groups and a quantitative online survey. Four focus groups were conducted with 24 Victorians with a cervix aged between 25 and 35. Barriers, enablers and knowledge of cervical screening were explored. Focus groups were recorded and transcribed for thematic analysis of common themes. A supporting online survey was completed by 98 respondents. Summary statistics were analysed for differences in age.

RESULTS: Focus groups and the online survey revealed four main factors that influence young people’s cervical screening behaviour. These include past negative screening experiences, practitioner factors, priority placed on cervical screening, and cervical screening knowledge. These factors differ to the opinions of people older than 35, with young people focusing more on the psychological elements of cervical screening compared with practical factors.

CONCLUSIONS: This research provides a unique insight into cervical screening barriers faced by women and people with a cervix aged between 25 and 35 as well as what factors motivate them to screen. SO WHAT?: These findings should be utilised to inform the design of public health campaign messaging targeting this age demographic. Findings can also assist practitioners to improve how they communicate with young people in a clinical setting.

PMID:37326914 | DOI:10.1002/hpja.762

Psychometrika. 2023 Jun 16. doi: 10.1007/s11336-023-09916-7. Online ahead of print.

ABSTRACT

Lyu et al. (Psychometrika, 2023) demonstrated that item-specific factors can cause spurious effects on the structural parameters of IRTree models for multiple nested response processes per item. Here, we discuss some boundary conditions and argue that person selection effects on item parameters are not unique to item-specific factors and that the effects presented by Lyu et al. (Psychometrika, 2023) may not generalize to the family of IRTree models as a whole. We conclude with the recommendation that IRTree model specification should be guided by theoretical considerations, rather than driven by data, in order to avoid misinterpretations of parameter differences.

PMID:37326912 | DOI:10.1007/s11336-023-09916-7

J Digit Imaging. 2023 Jun 16. doi: 10.1007/s10278-023-00863-4. Online ahead of print.

ABSTRACT

To evaluate the consistency in the performance of Artificial Intelligence (AI)-based diagnostic support software in short-term digital mammography reimaging after core needle biopsy. Of 276 women who underwent short-term (<3 mo) serial digital mammograms followed by breast cancer surgery from Jan. to Dec. 2017, 550 breasts were included. All core needle biopsies for breast lesions were performed between serial exams. All mammography images were analyzed using a commercially available AI-based software providing an abnormality score (0-100). Demographic data for age, interval between serial exams, biopsy, and final diagnosis were compiled. Mammograms were reviewed for mammographic density and finding. Statistical analysis was performed to evaluate the distribution of variables according to biopsy and to test the interaction effects of variables with the difference in AI-based score according to biopsy. AI-based score of 550 exams (benign or normal in 263 and malignant in 287) showed significant difference between malignant and benign/normal exams (0.48 vs. 91.97 in first exam and 0.62 vs. 87.13 in second exam, P<0.0001). In comparison of serial exams, no significant difference was found in AI-based score. AI-based score difference between serial exams was significantly different according to biopsy performed or not (-0.25 vs. 0.07, P = 0.035). In linear regression analysis, there was no significant interaction effect of all clinical and mammographic characteristics with mammographic examinations performed after biopsy or not. The results from AI-based diagnostic support software for digital mammography was relatively consistent in short-term reimaging even after core needle biopsy.

PMID:37326891 | DOI:10.1007/s10278-023-00863-4

Rheumatology (Oxford). 2023 Jun 16:kead281. doi: 10.1093/rheumatology/kead281. Online ahead of print.

ABSTRACT

OBJECTIVE: To evaluate belimumab addition to standard of care (SoC) in patents with refractory Idiopathic Inflammatory Myopathy (IIM).

METHODS: We conducted a 40-week multicentre randomized, double-blind, placebo-controlled trial with 1:1 IV belimumab 10 mg/kg or placebo randomization and a 24-week open-label extension. Clinical responses were measured by the Definition of Improvement (DOI) and Total Improvement Score (TIS). Flow cytometry analyses were performed on available samples before randomization, at 24 and 60-64wk. Descriptive statistics, t test, Fisher’s exact test and ANOVA tests were used.

RESULTS: 17 patients were randomized, 15 received ≥ 5 doses of belimumab or placebo and were included in the intention -to-treat analysis. More belimumab patients vs placebo attained TIS ≥ 40 (55.5% vs 33.3%; p=NS) and achieved DOI (33.3% vs 16.7%; p = NS) at Wk40 and Wk64; mean TIS was similar among groups. Two patients achieved major responses (TIS= 72.5) after Wk40 in the belimumab arm, none in the placebo arm. No improvement in placebo arm after switching to the open label phase was observed. There was no steroid-sparing effect. No new safety signals were detected.Although total B-cells were not reduced, belimumab induced naïve B-cells depletion while enhancing memory B cells number and frequency.

CONCLUSION: The study did not meet the primary end point and no statistically significant differences were observed in clinical responses between arms. More patients achieved sustained TIS ≥ 40 and reached DOI. Most patients who received belimumab longer than 40 weeks had clinical improvement. Phenotypic changes in B cell populations were not associated with clinical responses.

CLINICAL TRIAL REGISTRATION NUMBER: Clinicaltrials.gov, https://clinicaltrials.gov/, NCT02347891.

PMID:37326854 | DOI:10.1093/rheumatology/kead281