Tag: statistics

J Microbiol Methods. 2021 Nov 21:106378. doi: 10.1016/j.mimet.2021.106378. Online ahead of print.

ABSTRACT

Listeria monocytogenes belongs to the category of facultative anaerobic bacteria, and is the pathogen of listeriosis, potentially lethal disease for humans. There are many similarities between L. monocytogenes and other non-pathogenic Listeria species, which causes great difficulties for their correct identification. The level of L. monocytogenes contamination in food remains high according to statistics from the Food and Drug Administration. This situation leads to food recall and destruction, which has caused huge economic losses to the food industry. Therefore, the identification of Listeria species is very important for clinical treatment and food safety. This work aims to explore an efficient classification algorithm which could easily and reliably distinguish Listeria species. We attempted to classify Listeria species by incorporating denoising autoencoder (DAE) and machine learning algorithms in matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition, convolutional neural networks were used to map the high dimensional original mass spectrometry data to low dimensional core features. By analyzing MALDI-TOF MS data via incorporating DAE and support vector machine (SVM), the identification accuracy of Listeria species was 100%. The proposed classification algorithm is fast (range of seconds), easy to handle, and, more importantly, this method also allows for extending the identification scope of bacteria. The DAE model used in our research is an effective tool for the extraction of MALDI-TOF mass spectrometry features. Despite the fact that the MALDI-TOF MS dataset examined in our research had high dimensionality, the DAE + SVM algorithm was still able to exploit the hidden information embedded in the original MALDI-TOF mass spectra. The experimental results in our work demonstrated that MALDI-TOF mass spectrum combined with DAE + SVM could easily and reliably distinguish Listeria species.

PMID:34818574 | DOI:10.1016/j.mimet.2021.106378

Prim Care Companion CNS Disord. 2021 Nov 24;23(6):21m02927. doi: 10.4088/PCC.21m02927.

ABSTRACT

Objective: To compare the safety and efficacy of conventional anticoagulants with new oral anticoagulants (NOACs) for management of cerebral venous sinus thrombosis (CVST).

Methods: This was a retrospective, prospective cohort study of patients who presented with CVST to a tertiary stroke center in the Middle East from January 2012 to October 2019. Patients with a diagnosis of CVST were identified, and data were analyzed for demographic characteristics. Specific consideration was given to compare the efficacy and safety of different anticoagulation treatments.

Results: A total of 36 patients were included in the final analysis, with 15 (41%) men and 21 (59%) women and a male to female ratio of 1:1.4. Most of the patients (n = 22, 61%) were Saudi. Their ages ranged between 15 and 82 years (mean ± SD age of 34.22 ± 13.16 years). Headache was the most common feature, present in 22 (61%) of the patients, followed by unilateral weakness in 15 (41%) and cranial nerve palsies in 11 (30%). The most common etiology was prothrombotic state (both hereditary and acquired thrombophilia: n = 16, 45%). Other etiologies were postpartum state/oral contraceptive pill usage in 7 (19%), infections in 7 (19%), and trauma in 3 (8%). Most of the patients (n = 24, 67%) still received conventional anticoagulation (warfarin/low molecular weight heparin), but 9 (25%) of the patients consented to start NOACs. Efficacy (as measured by clinical improvement plus rate of recanalization of previously thrombosed venous sinuses) showed no statistically significant difference, although it proved to be better tolerated, as none of the patients stopped the treatment due to adverse events and risk of major bleeding was significantly low in the NOAC group. Nine patients in the warfarin group stopped medication, while none in the NOAC group did so (P = .034).

Conclusion: NOACs were found to be at least as good as conventional anticoagulation for the management of CVST. However, efficacy was almost similar, a finding that is consistent with most of the published case series and the few recently published prospective studies. Larger prospective and population-based studies are needed to clarify our preliminary results.

PMID:34818472 | DOI:10.4088/PCC.21m02927

J Speech Lang Hear Res. 2021 Nov 24:1-15. doi: 10.1044/2021_JSLHR-20-00464. Online ahead of print.

ABSTRACT

PURPOSE: This study examined the relationship between utterance length, syntactic complexity, and the probability of making an error at the utterance level.

METHOD: The participants in this study included 830 Spanish-speaking first graders who were learning English at school. Story retells in both Spanish and English were collected from all children. Generalized mixed linear models were used to examine within-child and between-children effects of utterance length and subordination on the probability of making an error at the utterance level.

RESULTS: The relationship between utterance length and grammaticality was found to differ by error type (omission vs. commission), language (Spanish vs. English), and level of analysis (within-child vs. between-children). For errors of commission, the probability of making an error increased as a child produced utterances that were longer relative to their average utterance length (within-child effect). Contrastively, for errors of omission, the probability of making an error decreased when a child produced utterances that were longer relative to their average utterance length (within-child effect). In English, a child who produced utterances that were, on average, longer than the average utterance length for all children produced more errors of commission and fewer errors of omission (between-children effect). This between-children effect was similar in Spanish for errors of commission but nonsignificant for errors of omission. For both error types, the within-child effects of utterance length were moderated by the use of subordination.

CONCLUSION: The relationship between utterance length and grammaticality is complex and varies by error type, language, and whether the frame of reference is the child’s own language (within-child effect) or the language of other children (between-children effect). Supplemental Material https://doi.org/10.23641/asha.17035916.

PMID:34818505 | DOI:10.1044/2021_JSLHR-20-00464

Asia Pac J Clin Oncol. 2021 Nov 24. doi: 10.1111/ajco.13639. Online ahead of print.

ABSTRACT

AIM: The effects of diabetes mellitus (DM) on the outcomes of colorectal cancer (CRC) are controversial. This retrospective study evaluated the effects of DM on American Joint Committee on Cancer (AJCC, 7th) Stages II and III CRC patients who received curative surgery.

METHODS: We reviewed the records of CRC patients who were treated from January 2008 to December 2014 and identified the presence of DM and hypertension prior to CRC diagnosis. Cox proportional hazards analyses were used for prognostic factor determination, and survival was analyzed using the Kaplan-Meier method with the log-rank test.

RESULTS: Total of 1066 consecutive eligible patients with stage II/III CRC were enrolled. There were 326 (30.6%) patients diagnosed with DM, and 311 (29.2%) CRC patients had recurrence. Patients with DM did not have a higher recurrence risk (p = 0.183) but had higher mortality (adjusted hazard ratio [aHR] = 1.381; 95% conference interval [CI], 1.069-1.782). In addition, HbA1c (≥7 vs. <7) was not associated with recurrence (p = 0.365). Patients with DM had more hypertension than patients without DM (69.1% vs. 37.6%, p < 0.001). A lower recurrence risk was noted in patients with hypertension (p = 0.002), but the overall survival (OS) did not reach statistical significance (aHR = 0.910; 95% CI, 0.707-1.169).

CONCLUSION: In our study, DM was a poor prognostic factor for survival in curative CRC patients. More studies are required to elucidate the effects that DM and other metabolic disorders, such as hypertension, have on the prognosis of patients with CRC.

PMID:34818458 | DOI:10.1111/ajco.13639

Psychophysiology. 2021 Nov 24:e13972. doi: 10.1111/psyp.13972. Online ahead of print.

ABSTRACT

This study aims to use structural equation modeling (SEM) to investigate the role of error processing in behavioral adaptation in children by testing relationships between error-related and stimulus-related event-related potentials (ERPs) obtained from two sessions of a speeded Eriksen flanker task. First, path models of averaged ERP components and mean response times (N1 → P2 → N2 → P3 → RTs) while controlling for trait effects, age, and sex, on each was examined separately for correct and incorrect trials from each session. While the model demonstrated acceptable fit statistics, the four models yielded diverse results. Next, path models for correct and incorrect trials were tested using latent variables defined by factoring together respective measures of ERP component amplitudes from each session. Comparison of correct and incorrect models revealed significant differences in the relationships between the successive measures of neural processing after controlling for trait effects. Moreover, latent variable models controlling for both trait and session-specific state variables yielded excellent model fit while models without session-specific state variables did not. In the final model, the error-related neural activity (i.e., the ERN and Pe) from incorrect trials was found to significantly relate to the stream of neural processes contributing to trials with the correct behavior. Importantly, the relationship between RT and error detection in the final model signifies a brain-and-behavior feedback loop. These findings provided empirical evidence that supports the adaptive orienting theory of error processing by demonstrating how the neural signals of error processing influence behavioral adaptations that facilitate correct behavioral performance.

PMID:34818441 | DOI:10.1111/psyp.13972

Clin Pharmacol Ther. 2021 Nov 24. doi: 10.1002/cpt.2477. Online ahead of print.

ABSTRACT

Even modest improvements in the probability of success of selecting drug targets which are ultimately approved can substantially reduce the costs of research and development. Drug targets with human genetic evidence of disease association are twice as likely to lead to approved drugs. A key enabler of identifying and validating these genetically validated targets is access to association results from genome-wide genotyping, whole-exome sequencing, and whole-genome sequencing studies with observable traits (often diseases) across large numbers of individuals. Today, linkage between genotype and real-world data (RWD) provides significant opportunities to not only increase the statistical power of genome-wide association studies by ascertaining additional cases for diseases of interest, but also to improve diversity and coverage of association studies across the disease phenome. As RWD-genetics linked resources continue to grow in diversity of participants, breadth of data captured, length of observation, and number of participants, there is a greater need to leverage the experience of RWD experts, clinicians, and highly experienced geneticists together to understand which lessons and frameworks from general research using RWD sources are relevant to improve genetics-driven drug discovery and development. This paper describes new challenges and opportunities for phenotypes enabled by diverse RWD sources, considerations in the use of RWD phenotypes for disease gene identification across the disease phenome, and challenges and opportunities in leveraging RWD phenotypes in target validation. The paper concludes with views on the future directions for phenotype development using RWD, and key questions requiring further research and development to advance this nascent field.

PMID:34818443 | DOI:10.1002/cpt.2477

ALTEX. 2021 Nov 24. doi: 10.14573/altex.2105251. Online ahead of print.

ABSTRACT

Animal testing has been the corner stone for chemical safety assessments, but fish embryo assays now represent an alternative. Increases in omics studies offers unparalleled access to examine early molecular responses in organisms in response to environmental stressors and yet reduction in animal usage within this context has been overlooked. For proteomics, there is significant disparity and variability in organismal pool size ranging from 1-2000 embryos per replicate for zebrafish alone. However, it is unknown if varying sample pool size results in higher protein identifications. To examine whether the proteome changes are dependent on this variable, 3 pool sizes (5, 10 or 20 embryos per replicate) were examined using the two most common fish models with appropriate biological replicate number determined based on statistical power analysis (n=7). Samples were analysed by data-independent acquisition (DIA), resulted in 1,946 and 2,770 protein groups identified (1 % FDR) for the fathead minnow and zebrafish, respectively. Proteins were not differentially expressed among pool sizes, and no significant difference was observed among the protein groups identified. However, for the fathead minnow, a decrease in the number of proteins identified was observed with increasing pool size, while only a modest increase of 110 protein identifications was observed in zebrafish between the lowest and highest pool size. Taken together, our observations suggests that a proteome characterization experiment using these fish models can achieve comparable protein identifications using pool sizes of less than 5 per replicate assuming a protein requirement of 50µg or less.

PMID:34818429 | DOI:10.14573/altex.2105251

J Clin Ultrasound. 2021 Sep 7. doi: 10.1002/jcu.23062. Online ahead of print.

ABSTRACT

PURPOSE: Despite continued efforts, a majority of patients with valvular heart disease (VHD) remain undiagnosed and untreated. This study aimed to assess the adoptability and accuracy of point-of-care handheld echocardiographic assessments (POCE) in the primary care setting.

METHODS: Eleven previously untrained primary care providers were trained to use the Vscan Extend (GE, WI) POCE to assess VHD, left ventricular function (LVEF), and major extra-cardiac findings. Their assessments were compared to those of three blinded expert readers. A total of 175 patients underwent POCE assessments which were evaluated using Kappa statistics (κ) together with their estimated standard error, p value, and 95% CI bounds.

RESULTS: Each patient had a mean of 3.3 ± 1.1 (±SD) assessments performed. Identical or nearly identical agreement between previously untrained primary providers and expert readers was evident for the diagnosis of tricuspid regurgitation, mitral regurgitation, pericardial effusion, and volume status. These agreements were strongest in apical long axis (κ = 1, p < 0.001) and parasternal long and short axis views (κ > =0.82 p < 0.001), though agreement remained robust in apical 4-chamber views (κ ≥ 0.76). The agreements in LVEF assessment were identical in the apical long axis view (κ = 1, p < 0.001) and robust in the remaining 3 views (κ > =0.66, p < 0.001). The assessments of aortic stenosis (parasternal/long, κ = 0.42, and parasternal/short, κ = 0.47, both p < 0.001) were weak in their agreement.

CONCLUSION: Compared to expert echocardiography readers, the untrained providers’ use of POCE for VHD shows high user adoptability and diagnostic accuracies in the primary care setting.

PMID:34818437 | DOI:10.1002/jcu.23062

Acta Cir Bras. 2021 Oct 25;36(9):e360902. doi: 10.1590/ACB360902. eCollection 2021.

ABSTRACT

PURPOSE: To investigate experimentally the effects of Tropifexor, a farnesoid X receptor agonist, on liver injury in rats with obstructive jaundice.

METHODS: Forty healthy Wistar albino female rats were divided randomly in selected groups. These groups were the sham group, control group, vehicle solution group, Ursodeoxycholic acid group and Tropifexor group. Experimental obstructive jaundice was created in all groups, except the sham one. In the blood samples obtained, aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), gamma-glutamyl transferase (GGT), total bilirubin and direct bilirubin levels were established and recorded. Additionally, liver malondialdehyde, myeloperoxidase and catalase enzyme activity in the tissue samples were studied. Histopathological analysis was also performed.

RESULTS: No statistical difference was found between the control group and the Tropifexor group when AST, ALT and ALP values were compared. However, it was found that the Tropifexor group had statistically significant decreases in the values of GGT, total bilirubin and direct bilirubin (p < 0.05). Additionally, Tropifexor decreased the median values of malondialdehyde and myeloperoxidase, but this difference was not statistically significant compared to the control group. Finally, the Tropifexor group was statistically significant in recurring histopathological liver damage indicators (p < 0.05).

CONCLUSIONS: Tropifexor reduced liver damage due to obstructive jaundice.

PMID:34818403 | DOI:10.1590/ACB360902

Int J Periodontics Restorative Dent. 2021 Nov-Dec;41(6):895-900. doi: 10.11607/prd.5039.

ABSTRACT

This study aimed to determine the impact of implant placement depth (bone-level [BL] and subcrestal [SC]) on soft-tissue inflammatory parameters bleeding on probing (BOP), probing depth (PD), and crestal bone resorption (CBR) in moderate cigarette-smokers and nonsmokers at 5 years postplacement. Patient details were recorded, including sex, age, smoking history, duration of implants in function, implant arch location, and daily toothbrushing and flossing habits. Peri-implant BOP, PD, and CBR were measured in all groups, and group comparisons were done; a probability score < .05 was selected as a value for statistical significance. Fifty-three patients (27 smokers, 26 nonsmokers) had BL implants, and 55 patients (28 smokers, 27 nonsmokers) had SC implants. Among all patients, PD was higher in smokers than nonsmokers (P < .05). The peri-implant sites that demonstrated BOP were higher (P < .05) in nonsmokers than smokers. Among smokers, the CBR was higher in those with BL implants than those with SC implants (P < .05). Among nonsmokers, there was a difference in BOP, PD, and CBR at the 5-year follow-up. At 5 years, SC implants demonstrated less CBR than BL implants. Peri-implant PD is higher in smokers than nonsmokers, irrespective of the implant placement depth.

PMID:34818397 | DOI:10.11607/prd.5039