Nevin Manimala

Nucleic Acids Res. 2022 Nov 18:gkac1068. doi: 10.1093/nar/gkac1068. Online ahead of print.

ABSTRACT

Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.

PMID:36399503 | DOI:10.1093/nar/gkac1068

PLoS One. 2022 Nov 18;17(11):e0277917. doi: 10.1371/journal.pone.0277917. eCollection 2022.

ABSTRACT

After a major upper limb amputation, the use of myoelectric prosthesis as assistive devices is possible. However, these prostheses remain quite difficult to control for grasping and manipulation of daily life objects. The aim of the present observational case study is to document the kinematics of grasping in a group of 10 below-elbow amputated patients fitted with a myoelectric prosthesis in order to describe and better understand their compensatory strategies. They performed a grasping to lift task toward 3 objects (a mug, a cylinder and a cone) placed at two distances within the reaching area in front of the patients. The kinematics of the trunk and upper-limb on the non-amputated and prosthetic sides were recorded with 3 electromagnetic Polhemus sensors placed on the hand, the forearm (or the corresponding site on the prosthesis) and the ipsilateral acromion. The 3D position of the elbow joint and the shoulder and elbow angles were calculated thanks to a preliminary calibration of the sensor position. We examined first the effect of side, distance and objects with non-parametric statistics. Prosthetic grasping was characterized by severe temporo-spatial impairments consistent with previous clinical or kinematic observations. The grasping phase was prolonged and the reaching and grasping components uncoupled. The 3D hand displacement was symmetrical in average, but with some differences according to the objects. Compensatory strategies involved the trunk and the proximal part of the upper-limb, as shown by a greater 3D displacement of the elbow for close target and a greater forward displacement of the acromion, particularly for far targets. The hand orientation at the time of grasping showed marked side differences with a more frontal azimuth, and a more “thumb-up” roll. The variation of hand orientation with the object on the prosthetic side, suggested that the lack of finger and wrist mobility imposed some adaptation of hand pose relative to the object. The detailed kinematic analysis allows more insight into the mechanisms of the compensatory strategies that could be due to both increased distal or proximal kinematic constraints. A better knowledge of those compensatory strategies is important for the prevention of musculoskeletal disorders and the development of innovative prosthetics.

PMID:36399487 | DOI:10.1371/journal.pone.0277917

Am J Physiol Heart Circ Physiol. 2022 Nov 18. doi: 10.1152/ajpheart.00482.2022. Online ahead of print.

ABSTRACT

AIMS: This study compared differences in cardiovascular (CV) risk factor responses between males and females following endurance (END) and resistance (RES) training. We present the frequency of responders to each training modality, and the magnitude of response.

METHODS: Using a randomized cross-over design, 68 healthy adults (age: F: 24.5±4.6; M: 27.3±6.6) completed 3-months of RES and END, with 3-months washout. Peak oxygen consumption (VO₂peak), strength, body composition, blood pressure, glucose, insulin, and lipids were measured.

RESULTS: VO₂peak (L/min) significantly increased in both sexes following END, but not RES. The magnitude of change was larger in males (F: +0.20 L/min; M: +0.32 L/min), although this did not achieve statistical significance (P=0.051). Strength significantly increased in both sexes following RES (P<0.01), with a larger increase in males (Leg press: F: +39kg; M: +63kg; P<0.05). Lean mass significantly increased in both sexes (P<0.01) following RES and fat mass decreased in females following END (P=0.019). The change in C-reactive protein following END was significantly different between sexes (F: -0.4 mg/L; M: +0.5 mg/L; P=0.035). There were no differences between sexes in the proportion of individuals who responded positively to any variable following RES or END; differences between sexes were due to the magnitude of change.

CONCLUSIONS: Males had a larger increase in VO₂peak following END, and strength following RES. There were no sex differences in other CV risk factors. This suggests differences in physiological responses to strength and VO₂peak may not translate to changes in CV risk in healthy subjects.

PMID:36399383 | DOI:10.1152/ajpheart.00482.2022

J Med Internet Res. 2022 Nov 18;24(11):e39248. doi: 10.2196/39248.

ABSTRACT

BACKGROUND: An automated virtual reality cognitive therapy (gameChange) has demonstrated its effectiveness to treat agoraphobia in patients with psychosis, especially for high or severe anxious avoidance. Its economic value to the health care system is not yet established.

OBJECTIVE: In this study, we aimed to estimate the potential economic value of gameChange for the UK National Health Service (NHS) and establish the maximum cost-effective price per patient.

METHODS: Using data from a randomized controlled trial with 346 patients with psychosis (ISRCTN17308399), we estimated differences in health-related quality of life, health and social care costs, and wider societal costs for patients receiving virtual reality therapy in addition to treatment as usual compared with treatment as usual alone. The maximum cost-effective prices of gameChange were calculated based on UK cost-effectiveness thresholds. The sensitivity of the results to analytical assumptions was tested.

RESULTS: Patients allocated to gameChange reported higher quality-adjusted life years (0.008 QALYs, 95% CI -0.010 to 0.026) and lower NHS and social care costs (-£105, 95% CI -£1135 to £924) compared with treatment as usual (£1=US $1.28); however, these differences were not statistically significant. gameChange was estimated to be worth up to £341 per patient from an NHS and social care (NHS and personal social services) perspective or £1967 per patient from a wider societal perspective. In patients with high or severe anxious avoidance, maximum cost-effective prices rose to £877 and £3073 per patient from an NHS and personal social services perspective and societal perspective, respectively.

CONCLUSIONS: gameChange is a promising, cost-effective intervention for the UK NHS and is particularly valuable for patients with high or severe anxious avoidance. This presents an opportunity to expand cost-effective psychological treatment coverage for a population with significant health needs.

TRIAL REGISTRATION: ISRCTN Registry ISRCTN17308399; https://www.isrctn.com/ISRCTN17308399.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1136/bmjopen-2019-031606.

PMID:36399379 | DOI:10.2196/39248

JMIR Public Health Surveill. 2022 Nov 18;8(11):e34908. doi: 10.2196/34908.

ABSTRACT

BACKGROUND: Peripheral arterial disease (PAD) causes blood vessel narrowing that decreases blood flow to the lower extremities, with symptoms such as leg pain, discomfort, and intermittent claudication. PAD increases risks for amputation, poor health-related quality of life, and mortality. It is estimated that more than 200 million people worldwide have PAD, although the paucity of PAD research in the East detracts from knowledge on global PAD epidemiology. There are few national data-based analyses or health care utilization investigations. Thus, a national data analysis of PAD incidence and prevalence would provide baseline data to enable health promotion strategies for patients with PAD.

OBJECTIVE: This study aims to identify South Korean trends in the incidence and prevalence of PAD and PAD treatment, in-hospital deaths, and health care utilization.

METHODS: This was a retrospective analysis of South Korean national claims data from 2009 to 2018. The incidence of PAD was determined by setting the years 2010 and 2011 as a washout period to exclude previously diagnosed patients with PAD. The study included adults aged ≥20 and <90 years who received a primary diagnosis of PAD between 2011 and 2018; patients were stratified according to age, sex, and insurance status for the incidence and prevalence analyses. Descriptive statistics were used to assess incidence, prevalence, endovascular revascularization (EVR) events, amputations, in-hospital deaths, and the health care utilization characteristics of patients with PAD.

RESULTS: Based on data from 2011 to 2018, there were an average of 124,682 and 993,048 incident and prevalent PAD cases, respectively, in 2018. PAD incidence (per 1000 persons) ranged from 2.68 to 3.09 during the study period. From 2012 to 2018, the incidence rate in both sexes showed an increasing trend. PAD incidence continued to increase with age. PAD prevalence (per 1000 persons) increased steadily, from 3.93 in 2011 to 23.55 in 2018. The number of EVR events varied between 933 and 1422 during the study period, and both major and minor amputations showed a decreasing trend. Health care utilization characteristics showed that women visited clinics more frequently than men, whereas men used tertiary and general hospitals more often than women.

CONCLUSIONS: The number of incident and prevalent PAD cases generally showed an increasing trend. Visits to tertiary and general hospitals were higher among men than women. These results indicate the need for attention not only to Western and male patients, but also to Eastern and female patients with PAD. The results are generalizable, as they are based on national claims data from the entire South Korean population, and they can promote preventive care and management strategies for patients with PAD in clinical and public health settings.

PMID:36399371 | DOI:10.2196/34908

Augment Altern Commun. 2022 Nov 18:1-12. doi: 10.1080/07434618.2022.2138780. Online ahead of print.

ABSTRACT

The communicative behavior of young children with significant cognitive and motor developmental delays is generally considered to be limited, idiosyncratic and non-intentional. At present, changes between and within children over time regarding their communicative behavior are hard to detect. This article describes an exploratory observational study that draws on data from the first data point of 38 children who are participating in a longitudinal project on the developmental trajectories of children with significant cognitive and motor developmental delays. The aims of this study were to (a) describe the participants’ communicative behavior in detail with communication-related variables that reflect differences across individuals, (b) create summarizing variables and (c) explore whether subgroups of children can be detected. A self-developed coding scheme and descriptive statistics combined with correlational analyses were used, followed by a principal component analysis and visual inspection of the outcome of this analysis. The within-group differences related to communicative behavior was characterized using 16 variables. Based on these variables, three overarching components were formulated: communication proficiency, Expressions of Discomfort and Rejection and Differentiation According to Focus. All participating children were found to be unique in terms of their component scores and the relationship among their component scores.

PMID:36399357 | DOI:10.1080/07434618.2022.2138780

J Periodontol. 2022 Nov 18. doi: 10.1002/JPER.22-0511. Online ahead of print.

ABSTRACT

OBJECTIVE: To investigate the clinical and radiographic significance of using a mixture of mineralized and demineralized allografts in combination (M) or not (NM) with a resorbable cross-linked barrier membrane in the reconstructive therapy of peri-implantitis defects.

METHODS: A two-arm randomized clinical trial was performed in patients diagnosed with peri-implantitis that exhibited contained defects. Clinical parameters were recorded at baseline (T₀ ), 6 months (T₁ ) and 12 months (T₂ ). Radiographic parameters were recorded at T₀ and T₂ . A composite criteria for disease resolution was defined a priori. A generalized linear model (GLM) of repeated measures with generalized estimation equations (GEE) statistical methods were used.

RESULTS: Overall, 33 patients (n_implants = 48) completed the study. At T₂ , mean disease resolution was 77.1%. The use of a barrier membrane did not enhance the probability of disease resolution at T₂ (OR = 1.55, p = 0.737). Conversely, the odds of disease resolution were statistically associated with modified plaque index (mPI) recorded at T₀ (OR = 0.13, p = 0.006) and keratinized mucosa (KM) width (OR = 2.10, p = 0.035). Moreover, women exhibited greater odds to show disease resolution (OR = 5.56, p = 0.02).

CONCLUSION: Reconstructive therapy by means of a mixture of mineralized and demineralized allografts is effective in clinically resolving peri-implantitis and in gaining radiographic marginal bone level. The addition of a barrier membrane to reconstructive therapy of peri-implantitis does not seem to enhance the outcomes of contained bone defects (NCT05282667). This article is protected by copyright. All rights reserved.

PMID:36399349 | DOI:10.1002/JPER.22-0511

Ir J Med Sci. 2022 Nov 18. doi: 10.1007/s11845-022-03215-3. Online ahead of print.

ABSTRACT

AIM: The aim of this study is to determine accurately the localization of the adenoma with the imaging methods in the patients, who are planned to be operated on with prediagnosis of parathyroid adenoma.

METHOD: In our study, the files of the patients who were considered to have parathyroid adenoma and underwent operation between 2012 and 2020 with the methods such as Tc99m-MIBI SPECT/CT, 18F-fluorocholine PET/CT, and ultrasound, and biochemical examinations were examined retrospectively.

RESULTS: In this study, 31 (18.2%) male and 139 (81.8%) female adult patients were included. The sensitivities of localization methods were 82.6% for ultrasound and 78.4% for scintigraphy. Adenoma was localised in the right place in 14 of 15 (93.3%) patients with the 18F-fluorocholine PET/CT method. A statistically significant correlation was found between the sensitivity of scintigraphy, the gland weights (p: 0.002), and phosphor values (p: 0.039). A statistically significant improvement was observed in the intact PTH value (p: 0.001) 15 min after the removal of adenoma. A statistically significant improvement was observed in the serum PTH value (p: 0.001), the serum phosphorus value (p: 0.001), and the serum calcium (p: 0.001) in the first 3 months after the operation.

CONCLUSION: Determining localization accurately for the patients enables performing operations with minimally invasive surgery successfully in a shorter time. Also, fewer complications and faster recovery are seen in the patients. It was concluded that studying intraoperative intact PTH and using 18F-fluorocholine PET/CT method for localization give more accurate results for localization and allow having more successful operation outcomes.

PMID:36399322 | DOI:10.1007/s11845-022-03215-3

J Assist Reprod Genet. 2022 Nov 18. doi: 10.1007/s10815-022-02645-3. Online ahead of print.

ABSTRACT

PURPOSE: Can the risk factors that cause first trimester pregnancy loss in good-quality frozen-thawed embryo transfer (FET) cycles be predicted using machine learning algorithms?

METHODS: This is a retrospective cohort study conducted at Sisli Memorial Hospital, ART and Reproductive Genetics Center, between January 2011 and May 2021. A total of 3805 good-quality FET cycles were included in the study. First trimester pregnancy loss rates were evaluated according to female age, paternal age, body mass index (BMI), diagnosis of infertility, endometrial preparation protocols (natural/artificial), embryo quality (top/good), presence of polycystic ovarian syndrome (PCOS), history of recurrent pregnancy loss (RPL), recurrent implantation failure (RIF), severe male infertility, adenomyosis and endometriosis.

RESULTS: The first trimester pregnancy loss rate was 18.2% (693/ 3805). The presence of RPL increased first trimester pregnancy loss (OR = 7.729, 95%CI = 5.908-10.142, P = 0.000). BMI, which is > 30, increased first trimester pregnancy loss compared to < 25 (OR = 1.418, 95%CI = 1.025-1.950, P = 0.033). Endometrial preparation with artificial cycle increased first trimester pregnancy loss compared to natural cycle (OR = 2.101, 95%CI = 1.630-2.723, P = 0.000). Female age, which is 35-37, increased first trimester pregnancy loss compared to < 30 (OR = 1.617, 95%CI = 1.120-2.316, P = 0.018), and female age, which is > 37, increased first trimester pregnancy loss compared to < 30 (OR = 2.286, 95%CI = 1.146-4,38, P = 0.016). The presence of PCOS increased first trimester pregnancy loss (OR = 1.693, 95%CI = 1.198-2.390, P = 0.002). The number of previous IVF cycles, which is > 3, increased first trimester pregnancy loss compared to < 3 (OR = 2.182, 95%CI = 1.708-2.790, P = 0.000).

CONCLUSIONS: History of RPL, RIF, advanced female age, presence of PCOS, and high BMI (> 30 kg/m²) were the factors that increased first trimester pregnancy loss.

PMID:36399255 | DOI:10.1007/s10815-022-02645-3

Clin Oral Investig. 2022 Nov 18. doi: 10.1007/s00784-022-04771-9. Online ahead of print.

ABSTRACT

OBJECTIVES: The purpose of this in vitro reliability study was to determine the intra- and inter-examiner agreement of the revised FDI criteria including the categories “fracture of material and retention” (F1) and “caries at restoration margin” (B1).

MATERIALS AND METHODS: Forty-nine photographs of direct tooth-coloured posterior (n = 25) and anterior (n = 24) restorations with common deficiencies were included. Ten dental experts repeated the assessment in three blinded rounds. Later, the experts re-evaluated together all photographs and agreed on a reference standard. Statistical analysis included the calculation of Cohen’s (Cκ), Fleiss’ (Fκ), and weighted Kappa (wκ), the development of a logistic regression with a backward elimination model and Bland/Altman plots.

RESULTS: Intra- and inter-examiner reliability exhibited mostly moderate to substantial Cκ, Fκ, and wκ values for posterior restorations (e.g. Intra: F1 Cκ = 0.57, wκ = 0.74; B1 Cκ = 0.57, wκ = 0.73/Inter F1 Fκ = 0.32, wκ = 0.53; B1 Fκ = 0.41, wκ = 0.64) and anterior restorations (e.g. Intra F1 Cκ = 0.63, wκ = 0.76; B1 Cκ = 0.48, wκ = 0.68/Inter F1 Fκ = 0.42, wκ = 0.57; B1 Fκ = 0.40, wκ = 0.51). Logistic regression analyses revealed significant differences between the evaluation rounds, examiners, categories, and tooth type. Both the intra- and inter-examiner reliability increased along with the evaluation rounds. The overall agreement was higher for anterior restorations compared to posterior restorations.

CONCLUSIONS: The overall reliability of the revised FDI criteria set was found to be moderate to substantial.

CLINICAL RELEVANCE: If properly trained, the revised FDI criteria set are a valid tool to evaluate direct and indirect restorations in a standardized way. However, training and calibration are needed to ensure reliable application.

PMID:36399211 | DOI:10.1007/s00784-022-04771-9