Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires

An individual's T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.

Patient ratings in exercise therapy for the management of tendinopathy: a systematic review with meta-analysis

OBJECTIVE

To synthesise exercise therapy intervention data investigating patient rating outcomes for the management of tendinopathy.

DESIGN

A systematic review and meta-analysis of randomized controlled trials investigating exercise therapy interventions and reporting patient rating outcomes.

SETTING

Any setting in any country listed as very high on the human development index.

PARTICIPANTS

People with a diagnosis of any tendinopathy of any severity or duration.

INTERVENTIONS

Exercise therapy for the management of tendinopathy comprising five different therapy classes: 1) resistance; 2) plyometric; 3) vibration; 4) flexibility, and 5) movement pattern retraining modalities, were considered for inclusion.

MAIN OUTCOME MEASURES

Outcomes measuring patient rating of condition, including patient satisfaction and Global Rating of Change (GROC).

RESULTS

From a total of 124 exercise therapy studies, 34 (Achilles: 41%, rotator cuff: 32%, patellar: 15%, elbow: 9% and gluteal: 3%) provided sufficient information to be meta-analysed. The data were obtained across 48 treatment arms and 1246 participants. The pooled estimate for proportion of satisfaction was 0.63 [95%CrI: 0.53-0.73], and the pooled estimate for percentage of maximum GROC was 53 [95%CrI: 38-69%]. The proportion of patients reporting positive satisfaction and perception of change increased with longer follow-up periods from treatment onset.

CONCLUSION

Patient satisfaction and GROC appear similar and are ranked moderately high demonstrating that patients generally perceive exercise therapies positively. Further research including greater consistency in measurement tools is required to explore and where possible, identify patient- and exercise-related moderating factors that can be used to improve person-centred care.

SYSTEMATIC REVIEW REGISTRATION NUMBER

PROSPERO ID=CRD42020168187 CONTRIBUTION OF PAPER.

[DEVELOPMENT OF THE HEALTHCARE SYSTEM BASED ON THE CLUSTER APPROACH]

The study substantiates the possibility of the cluster approach for the development of the healthcare system in Russia. The analysis of foreign experience in the functioning of medical clusters made it possible to identify factors that contribute to their successful development. Based on the assessment of the domestic practice of creating clusters in the healthcare sector, their typification was carried out with the identification of groups of high-tech clusters of biomedical technologies and innovations, medical clusters of drug provision and specialized equipment, clusters of medical services, internships and transfer of medical innovations. The grouping of clusters in the healthcare sector operating in the Russian Federation according to the proposed types showed that there are practically no clusters of medical services that are able to bring the quality of medical care to the population to a higher level in the country. The article identifies the problems that prevent the formation of clusters of medical services on the territory of the regions. To solve these problems, an approach was proposed to create a medical technology park on the basis of public-private partnership, which will serve as the basis for a cluster of medical services and built its structural and functional model.

Water-soluble triazole chitin derivative and its based nanoparticles: Synthesis, characterization, catalytic and antibacterial properties

In this work, we treated chitin with 2-(azidomethyl)oxirane and successfully involved the resultant azido chitin derivatives in the ultrasound-assisted Cu(I)-catalyzed azido-alkyne click (CuAAC) reaction with propargylic ester of N,N,N-trimethyl glycine. Thus, we obtained novel water-soluble triazole chitin derivatives. The triazole chitin derivatives and their nanoparticles are characterized by a high in vitro antibacterial activity, which is the same or even higher than that of commercial antibiotics ampicillin and gentamicin. The obtained derivatives are non-toxic. Moreover, the obtained water-soluble polymers are highly efficient green catalysts for the aldol reaction in green solvent water. The catalysts can be easily extracted from the reaction mixture by its precipitation with green solvent ethanol followed by centrifugation and they can be reused at least 10 times.

Motor development in infancy and spine shape in early old age: Findings from a British birth cohort study

Spine shape changes dramatically in early life, influenced by attainment of developmental milestones such as independent walking. Whether these associations persist across life is unknown. Therefore, we investigated associations between developmental milestones and spine shape, as determined using statistical shape models (SSMs) of lumbar spine from dual-energy X-ray absorptiometry scans in 1327 individuals (688 female) at 60 to 64 years in the MRC National Survey of Health and Development. Lumbar lordosis angle (L4 inferior endplate to T12 superior endplate) was measured using the two-line Cobb method. In analyses adjusted for sex, height, lean and fat mass, socioeconomic position, and birthweight, later walking age was associated with greater lordosis described by SSM1 (regression coefficient, 0.023; 95% CI, 0.000-0.047; P = .05) and direct angle measurement. Modest associations between walking age and less variation in anterior-posterior vertebral size caudally (SSM6) were also observed (0.021; 95% CI, -0.002 to 0.044; P = .07). Sex interactions showed that later walking was associated with larger relative vertebral anterior-posterior dimensions in men (SSM3; -0.043; 95% CI, -0.075 to 0.01; P = .01) but not women (0.018; 95% CI, -0.0007 to 0.043; P = .17). Similar associations were observed between age at independent standing and SSMs but there was little evidence of association between sitting age and spine shape. Unadjusted associations between walking age and SSMs 1 and 6 remained similar after adjustment for potential confounders and mediators. This suggests that these associations may be explained by altered mechanical loading of the spine during childhood growth, although other factors could contribute. Early life motor development, particularly walking, may have a lasting effect on the features of spine morphology with clinical significance.

Is intrinsic lumbar spine shape associated with lumbar disc degeneration? An exploratory study

Background

Lumbar disc degeneration (LDD) is a condition associated with recurrent low back pain (LBP). Knowledge regarding effective management is limited. As a step towards the identification of risk, prognostic or potentially modifiable factors in LDD patients, the aim of this study was to explore the hypothesis that intrinsic lumbar spine shape is associated with LDD and clinical outcomes in symptomatic adults.

Methods

3 T MRI was used to acquire T2-weighted sagittal images (L1-S1) from 70 healthy controls and LDD patients (mean age 49 years, SD 11, range 31–71 years). Statistical Shape Modelling (SSM) was used to describe lumbar spine shape. SSM identified variations in lumbar shape as ‘modes’ of variation and quantified deviation from the mean. Intrinsic shape differences were determined between LDD groups using analysis of variance with post-hoc comparisons. The relationship between intrinsic shape and self-reported function, mental health and quality of life were also examined.

Results

The first 7 modes of variation explained 91% of variance in lumbar shape. Higher LDD sum scores correlated with a larger lumbar lordosis (Mode 1 (55% variance), P = 0.02), even lumbar curve distribution (Mode 2 (12% variance), P = 0.05), larger anterior-posterior (A-P) vertebral diameter (Mode 3 (10% variance), P = 0.007) and smaller L4-S1 disc spaces (Mode 7 (2% variance), P ≤ 0.001). In the presence of recurrent LBP, LDD was associated with a larger A-P vertebral diameter (Mode 3) and a more even lumbar curvature with smaller L5/S1 disc spaces (Mode 4), which was significantly associated with patient quality of life (P = 0.002–0.04, r_p = 0.43–0.61)).

Conclusions

This exploratory study provides new evidence that intrinsic shape phenotypes are associated with LDD and quality of life in patients. Longitudinal studies are required to establish the potential role of these risk or prognostic shape phenotypes.

Perinatal factors associate with vertebral size and shape but not lumbar lordosis in 10-year-old children

The intrauterine environment is known to influence foetal development and future health. Low birthweight has been linked to smaller vertebral canals in children and decreased adulthood spine bone mineral content. Perinatal factors affecting lumbar spine curvature have not yet been considered but could be important for adult spinal health, as lumbar movement during lifting, a risk factor for backpain, is associated with lordosis. To investigate this, lumbar spine magnetic resonance images at age 10 years and perinatal and maternal data (birthweight, placental weight, gestation length, crown-heel length, maternal age, height, weight and smoking status) from 161 children born in Aberdeen in 1988-1989 were acquired. Statistical shape modelling, using principal component analysis, quantified variations in lumbar spine shape and resulting modes of variation were assessed in combination with perinatal data using correlations and analyses of covariance, adjusted for potential confounders. Spine modes 1-3 (SM1-SM3) captured 75% of the variation in lumbar spine shape. The first and third modes described the total amount (SM1) and evenness of curvature distribution (SM3). SM2 accounted for variations in antero-posterior vertebral diameter relative to vertebral height, increasing positive scores representing a larger relative diameter. Adjusting for gestation length and sex, SM2 positively correlated with birthweight (r = 0.25, P < 0.01), placental weight (r = 0.20, P = 0.04), crown-heel length (r = 0.36, P < 0.001) and maternal weight (r = 0.19, P = 0.04), and negatively with maternal age (r = -0.22, P = 0.02). SM2 scores were lower in girls (P < 0.001) and in the low birthweight group (P = 0.02). There were no significant differences in SM1 and SM3 scores between birthweight groups, boys and girls or children of smokers (31%) and non-smokers (69%). In conclusion, some perinatal factors were associated with vertebral body morphology but had little effect on lumbar curvature.

Age at Onset of Walking in Infancy Is Associated With Hip Shape in Early Old Age

Bones' shapes and structures adapt to the muscle and reaction forces they experience during everyday movements. Onset of independent walking, at approximately 12 months, represents the first postnatal exposure of the lower limbs to the large forces associated with bipedal movements; accordingly, earlier walking is associated with greater bone strength. However, associations between early life loading and joint shape have not been explored. We therefore examined associations between walking age and hip shape at age 60 to 64 years in 1423 individuals (740 women) from the MRC National Survey of Health and Development, a nationally representative British birth cohort. Walking age in months was obtained from maternal interview at age 2 years. Ten modes of variation in hip shape (HM1 to HM10), described by statistical shape models, were ascertained from DXA images. In sex-adjusted analyses, earlier walking age was associated with higher HM1 and HM7 scores; these associations were maintained after further adjustment for height, body composition, and socioeconomic position. Earlier walking was also associated with lower HM2 scores in women only, and lower HM4 scores in men only. Taken together, this suggests that earlier walkers have proportionately larger (HM4) and flatter (HM1, HM4) femoral heads, wider (HM1, HM4, HM7) and flatter (HM1, HM7) femoral necks, a smaller neck-shaft angle (HM1, HM4), anteversion (HM2, HM7), and early development of osteophytes (HM1). These results suggest that age at onset of walking in infancy is associated with variations in hip shape in older age. Early walkers have a larger femoral head and neck and smaller neck-shaft angle; these features are associated with reduced hip fracture risk, but also represent an osteoarthritic-like phenotype. Unlike results of previous studies of walking age and bone mass, associations in this study were not affected by adjustment for lean mass, suggesting that associations may relate directly to skeletal loading in early life when joint shape changes rapidly. © 2018 American Society for Bone and Mineral Research.

Variation in lifting kinematics related to individual intrinsic lumbar curvature: an investigation in healthy adults

Objective

Lifting postures are frequently implicated in back pain. We previously related responses to a static load with intrinsic spine shape, and here we investigate the role of lumbar spine shape in lifting kinematics.

Methods

Thirty healthy adults (18-65 years) performed freestyle, stoop and squat lifts with a weighted box (6-15 kg, self-selected) while being recorded by Vicon motion capture. Internal spine shape was characterised using statistical shape modelling (SSM) from standing mid-sagittal MRIs. Associations were investigated between spine shapes quantified by SSM and peak flexion angles.

Results

Two SSM modes described variations in overall lumbar curvature (mode 1 (M1), 55% variance) and the evenness of curvature distribution (mode 2 (M2), 12% variance). M1 was associated with greater peak pelvis (r=0.38, p=0.04) and smaller knee flexion (r=-0.40, p=0.03) angles; individuals with greater curviness preferred to lift with a stooped lifting posture. This was confirmed by analysis of those individuals with very curvy or very straight spines (|M1|>1 SD). There were no associations between peak flexion angles and mode scores in stoop or squat trials (p>0.05). Peak flexion angles were positively correlated between freestyle and squat trials but not between freestyle and stoop or squat and stoop, indicating that individuals adjusted knee flexion while maintaining their preferred range of lumbar flexion and that 'squatters' adapted better to different techniques than 'stoopers'.

Conclusion

Spinal curvature affects preferred lifting styles, and individuals with curvier spines adapt more easily to different lifting techniques. Lifting tasks may need to be tailored to an individual's lumbar spine shape.

[The pilot studies for the development of the combined methods of rehabilitation of the patients as exemplified by the application of phyto- and physiotherapeutic modalities]

Under the modern market conditions, the process of development of the methods for the combined rehabilitation of the patients is becoming increasingly more complicated. For the reduction of potential risks and leveling the factors responsible for the uncertain market situation influencing the creation of new methods, it is necessary to carry out the full-scale pilot studies with the use of the marketing analysis methods. The objective of the present work was to create and elaborate the rationale for the graphological structure (the scheme) of the process of exploratory research with a view to the development of the combined rehabilitation methods as exemplified by phyto- and physiotherapeutic modalities. The work is based on the application of the existing approaches to the structural, comparative, systemic, and situational analyses. The proposed graphological structure (scheme) of the exploratory research process consists of 6 stages. Its distinctive features are as follows: a fractional stage by stage evaluation of a variety of issues including the study of physical factors, characteristic of the means of herbal medicine with special reference to the mechanisms of their production and application under the current market conditions, monitoring the marketing environment with the constant focus on the trends and behavior of the target market, the parallel pursuing of serial studies with the application of the iterative procedures; the use of the previously created data bank to expand medical services at the stages of development and maturation of the life cycle, the evaluation of the possibility of establishment of the industry of parapharmaceutical products.

Endonuclease Activity of MutL Protein of the Rhodobacter sphaeroides Mismatch Repair System

We have purified the MutL protein from Rhodobacter sphaeroides mismatch repair system (rsMutL) for the first time. rsMutL demonstrated endonuclease activity in vitro, as predicted by bioinformatics analysis. Based on the alignment of 1483 sequences of bacterial MutL homologs with presumed endonuclease activity, conserved functional motifs and amino acid residues in the rsMutL sequence were identified: five motifs comprising the catalytic site responsible for DNA cleavage were found in the C-terminal domain; seven conserved motifs involved in ATP binding and hydrolysis and specific to the GHKL family of ATPases were found in the N-terminal domain. rsMutL demonstrated the highest activity in the presence of Mn2+. The extent of plasmid DNA hydrolysis declined in the row Mn2+ > Co2+ > Mg2+ > Cd2+; Ni²⁺ and Ca2+ did not activate rsMutL. Divalent zinc ions inhibited rsMutL endonuclease activity in the presence of Mn2+ excess. ATP also suppressed plasmid DNA hydrolysis by rsMutL. Analysis of amino acid sequences and biochemical properties of five studied bacterial MutL homologs with endonuclease activity revealed that rsMutL resembles the MutL proteins from Neisseria gonorrhoeae and Pseudomonas aeruginosa.

[The marketing evaluation of the consumers' preference as regards the use of medicinal and medicinal table mineral waters]

The development of modern technologies in physiotherapy with the use of mineral waters, the expansion of the assortment of the medicinal and medicinal table waters as well as increasing the competitive advantages of domestic products require the more extensive marketing survey of the consumers' preferences in the market of mineral waters.

AIM

The objective of the present study was the marketing evaluation of the consumers' preference in the segment of medicinal and medicinal table mineral waters in the city of Moscow.

MATERIALS AND METHODS

The survey involved 697 consumers of medicinal and medicinal table mineral waters. The sampling was carried out by the deterministic quota method. The field research was conducted by means of personal verbal interviews (32%) and the CATI to Web method (phone recruiting and on-line questioning) (68%) with the use of the structured questionnaire. Positioning was carried out making use of the two-dimensional schematic map and scoring assessment on an individual basis with calculation of integrated indicators.

RESULTS

The marketing evaluation has demonstrated that the principal motive for purchasing mineral waters in more than 40% of respondents was the treatment and prevention of various diseases including disturbances in the urogenital system as well as digestive and respiratory disorders that appear to be the most frequent reasons for the consumption of mineral waters. The main factors that form the preferences of the consumers as regards the use of a concrete variety of mineral waters were elucidated. Of crucial importance for approximately 40% of the consumers (p<0.01) proved to be their health condition, the medical indications, and the available information about the therapeutic effectiveness of one or another type of mineral waters. Other factors were the quality of mineral water, its cost, the manufacturer and/or place of production, the attractiveness of the packaging, etc.

CONCLUSION

The evaluation of the positioning of the mineral water consumers' preferences made it possible to identify the most preferable products in the group of medicinal mineral waters and in the group of medicinal table mineral waters. The mechanisms governing the formation of the consumers' preferences as regards the use of various mineral waters have been clarified in the course of the present study.

Associations between body mass index across adult life and hip shapes at age 60 to 64: Evidence from the 1946 British birth cohort

OBJECTIVE

To examine the associations of body mass index (BMI) across adulthood with hip shapes at age 60-64years.

METHODS

Up to 1633 men and women from the MRC National Survey of Health and Development with repeat measures of BMI across adulthood and posterior-anterior dual-energy X-ray absorptiometry bone mineral density images of the proximal femur recorded at age 60-64 were included in analyses. Statistical shape modelling was applied to quantify independent variations in hip mode (HM), of which the first 6 were examined in relation to: i) BMI at each age of assessment; ii) BMI gain during different phases of adulthood; iii) age first overweight.

RESULTS

Higher BMI at all ages (i.e. 15 to 60-64) and greater gains in BMI were associated with higher HM2 scores in both sexes (with positive HM2 values representing a shorter femoral neck and a wider and flatter femoral head). Similarly, younger age first overweight was associated with higher HM2 scores but only in men once current BMI was accounted for. In men, higher BMI at all ages was also associated with lower HM4 scores (with negative HM4 values representing a flatter femoral head, a wider neck and smaller neck shaft angle) but no associations with BMI gain or prolonged exposure to high BMI were found. Less consistent evidence of associations was found between BMI and the other four HMs.

CONCLUSION

These results suggest that BMI across adulthood may be associated with specific variations in hip shapes in early old age.

Statistical shape modelling of hip and lumbar spine morphology and their relationship in the MRC National Survey of Health and Development

The anatomical shape of bones and joints is important for their proper function but quantifying this, and detecting pathological variations, is difficult to do. Numerical descriptions would also enable correlations between joint shapes to be explored. Statistical shape modelling (SSM) is a method of image analysis employing pattern recognition statistics to describe and quantify such shapes from images; it uses principal components analysis to generate modes of variation describing each image in terms of a set of numerical scores after removing global size variation. We used SSM to quantify the shapes of the hip and the lumbar spine in dual-energy x-ray absorptiometry (DXA) images from 1511 individuals in the MRC National Survey of Health and Development at ages 60-64 years. We compared shapes of both joints in men and women and hypothesised that hip and spine shape would be strongly correlated. We also investigated associations with height, weight, body mass index (BMI) and local (hip or lumber spine) bone mineral density. In the hip, all except one of the first 10 modes differed between men and women. Men had a wider femoral neck, smaller neck-shaft angle, increased presence of osteophytes and a loss of the femoral head/neck curvature compared with women. Women presented with a flattening of the femoral head and greater acetabular coverage of the femoral head. Greater weight was associated with a shorter, wider femoral neck and larger greater and lesser trochanters. Taller height was accompanied by a flattening of the curve between superior head and neck and a larger lesser trochanter. Four of the first eight modes describing lumbar spine shape differed between men and women. Women tended to have a more lordotic spine than men with relatively smaller but caudally increasing anterior-posterior (a-p) vertebral diameters. Men were more likely to have a straighter spine with larger vertebral a-p diameters relative to vertebral height than women, increasing cranially. A weak correlation was found between body weight and a-p vertebral diameter. No correlations were found between shape modes and height in men, whereas in women there was a weak positive correlation between height and evenness of spinal curvature. Linear relationships between hip and spine shapes were weak and inconsistent in both sexes, thereby offering little support for our hypothesis. In conclusion, men and women entering their seventh decade have small but statistically significant differences in the shapes of their hips and their spines. Associations with height, weight, BMI and BMD are small and correspond to subtle variations whose anatomical significance is not yet clear. Correlations between hip and spine shapes are small.

The lumbar spine has an intrinsic shape specific to each individual that remains a characteristic throughout flexion and extension

PURPOSE

We have previously shown that the lumbar spine has an intrinsic shape specific to the individual and characteristic of sitting, standing and supine postures. The purpose of this study was to test the hypothesis that this intrinsic shape is detectable throughout a range of postures from extension to full flexion in healthy adults.

METHODS

Sagittal images of the lumbar spine were taken using a positional MRI with participants (n = 30) adopting six postures: seated extension, neutral standing, standing with 30, 45 and 60° and full flexion. Active shape modelling (ASM) was used to identify and quantify 'modes' of variation in the shape of the lumbar spine.

RESULTS

ASM showed that 89.5% of the variation in the shape of the spine could be explained by the first two modes; describing the overall curvature and the distribution of curvature of the spine. Mode scores were significantly correlated between all six postures (modes 1-9, r = 0.4-0.97, P < 0.05), showing that an element of intrinsic shape was maintained when changing postures. The spine was most even in seated extension (P < 0.001) and most uneven between 35 and 45° flexion (P < 0.05).

CONCLUSIONS

This study shows that an individual's intrinsic lumbar spine shape is quantifiable and detectable throughout lumbar flexion and extension. These findings will enable the role of lumbar curvature in injury and low back pain to be assessed in the clinic and in the working and recreational environments.

Synthesis and beta-lactamase inhibitory activity of new 6 beta-sulfonamidopenicillanic acids

New 6 beta-aryl(alkyl)sulfonamidopenicillanic acids and their sulfoxides were synthesized by sulfonylation of 6 beta-aminopenicilanic acid or its beta-sulfoxide with an appropriate sulfonyl chloride. The corresponding 6 beta-sulfonamidopenicillanic acids sulfones were prepared by oxidation of the sulfoxides with potassium permanganate in aqueous medium. The obtained compounds reduced the minimum inhibitory concentrations of ampicillin against 8 reference and 7 clinically isolated strains.