scholarly journals IgEvolution: clonal analysis of antibody repertoires

2019 ◽  
Author(s):  
Yana Safonova ◽  
Pavel A. Pevzner
Keyword(s):  
Binding Sites ◽  
Clonal Analysis ◽  
Reconstruction Algorithms ◽  
Tree Reconstruction ◽  
New Approach ◽  
Clonal Development ◽  
Antibody Repertoires ◽  
Complementarity Determining Regions ◽  
Independent Tasks

AbstractConstructing antibody repertoires is an important error-correcting step in analyzing immunosequencing datasets that is important for reconstructing evolutionary (clonal) development of antibodies. However, the state-of-the-art repertoire construction tools typically miss low-abundance antibodies that often represent internal nodes in clonal trees and are crucially important for clonal tree reconstruction. Thus, although repertoire construction is a prerequisite for follow up clonal tree reconstruction, the existing repertoire reconstruction algorithms are not well suited for this task. Since clonal analysis has the potential to reveal errors in the constructed repertoires and contribute to constructing more accurate repertoires, we advocate a tree-guided construction of antibody repertoires that combines error correction and clonal reconstruction as interconnected (rather than independent) tasks. We developed the IgEvolution algorithm for simultaneous repertoire and clonal tree reconstruction and applied it for analyzing multiple immunosequencing datasets representing antigen-specific immune responses. We demonstrate that analysis of clonal trees reveals highly mutable positions that correlate with antigen-binding sites and light-chain contacts in crystallized antibody-antigen complexes. We further demonstrate that this analysis leads to a new approach for identifying complementarity determining regions (CDRs) in antibodies.

Visualization of molecular binding sites at the nanoscale in the lift-up mode by amplitude-modulation atomic force microscopy

Nanoscale ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 4213-4220
Author(s):  
Tatsuhiro Maekawa ◽  
Takashi Nyu ◽  
Evan Angelo Quimada Mondarte ◽  
Hiroyuki Tahara ◽  
Kasinan Suthiwanich ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Recognition ◽  
Amplitude Modulation ◽  
Binding Sites ◽  
Local Distribution ◽  
New Approach ◽  
Molecular Binding ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Sites

We report a new approach to visualize the local distribution of molecular recognition sites with nanoscale resolution by amplitude-modulation atomic force microscopy.

scholarly journals Long-Term Follow-Up of Giant Symptomatic Hepatic Hemangiomas Treated with Direct Sclerotherapy: Introducing a New Approach

2020 ◽  
Author(s):  
Hadi Rokni Yazdi ◽  
Niloofar Ayoobi Yazdi ◽  
Mohammad Mehdi Mehrabinejad ◽  
Habibollah Dashti ◽  
Morteza Ghassed ◽  
...  
Keyword(s):  
New Approach ◽  
Long Term Follow Up ◽  
Hepatic Hemangiomas

scholarly journals Molecular Recognition: Perspective and a New Approach

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2757
Author(s):  
W. Rudolf Seitz ◽  
Casey J. Grenier ◽  
John R. Csoros ◽  
Rongfang Yang ◽  
Tianyu Ren
Keyword(s):  
Molecular Recognition ◽  
Molecularly Imprinted Polymers ◽  
Binding Sites ◽  
Binding Kinetics ◽  
Molecularly Imprinted ◽  
New Approach ◽  
Imprinted Polymers ◽  
High Affinity ◽  
Water Blocking ◽  
High Level

This perspective presents an overview of approaches to the preparation of molecular recognition agents for chemical sensing. These approaches include chemical synthesis, using catalysts from biological systems, partitioning, aptamers, antibodies and molecularly imprinted polymers. The latter three approaches are general in that they can be applied with a large number of analytes, both proteins and smaller molecules like drugs and hormones. Aptamers and antibodies bind analytes rapidly while molecularly imprinted polymers bind much more slowly. Most molecularly imprinted polymers, formed by polymerizing in the presence of a template, contain a high level of covalent crosslinker that causes the polymer to form a separate phase. This results in a material that is rigid with low affinity for analyte and slow binding kinetics. Our approach to templating is to use predominantly or exclusively noncovalent crosslinks. This results in soluble templated polymers that bind analyte rapidly with high affinity. The biggest challenge of this approach is that the chains are tangled when the templated polymer is dissolved in water, blocking access to binding sites.

scholarly journals Innovative method for Amplatzer device implantation in patients with bronchopleural fistulas

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jisong Zhang ◽  
Huihui Hu ◽  
Li Xu ◽  
Shan Xu ◽  
Jihong Zhu ◽  
...  
Keyword(s):  
Present Report ◽  
Rare Complication ◽  
Bronchopleural Fistula ◽  
Rigid Bronchoscopy ◽  
New Approach ◽  
Device Implantation ◽  
Amplatzer Device ◽  
Field Of Vision ◽  
Duration Of Operation

Abstract Background Bronchopleural fistula (BPF) is a relatively rare complication after various types of pulmonary resection. The double-sided mushroom-shaped occluder (Amplatzer device, AD) has been gradually used for BPF blocking due to its reliable blocking effect. We have improved the existing AD implantation methods to facilitate clinical use and named the new approach Sheath-free method (SFM). The aim of the present report was to explore the reliability and advantages of the SFM in AD implantation. Methods We improved the existing implantation methods by abandoning the sheath of the AD and using the working channel of the bronchoscope to directly store or release the AD without general anesthesia, rigid bronchoscopy, fluoroscopy, or bronchography. A total of 6 patients (5 men and 1 woman, aged 66.67 ± 6.19 years [mean ± SD]) had BPF blocking and underwent the SFM in AD implantation. Results AD implantation was successfully performed in all 6 patients with the SFM, 4 persons had a successful closure of the fistula, one person died after few days and one person did not have a successful closure of the fistula. The average duration of operation was 16.17 min (16.17 ± 4.67 min [mean ± SD]). No patients died due to operation complications or BPF recurrence. The average follow-up time was 13.2 months (range 10–17 months). Conclusion We observed that the SFM for AD implantation—with accurate device positioning and a clear field of vision—is efficient and convenient. The AD is effective in BPF blocking, and could contribute to significantly improved symptoms of patients.

Strut remodeling with hypercompliant balloon: A new approach to Y stent-assisted coil embolization in the treatment of complex wide-neck bifurcation aneurysms

2020 ◽  
pp. 159101992098433
Author(s):  
Ali Burak Binboga ◽  
Mehmet Onay ◽  
Cetin Murat Altay
Keyword(s):  
Coil Embolization ◽  
Complication Rates ◽  
Thromboembolic Complications ◽  
New Approach ◽  
Long Term Follow Up ◽  
Safety Effectiveness ◽  
Wide Neck

Background The objective of this study was to present the long-term safety and effectiveness of strand remodelling with a hypercompliant balloon. Methods Patients with complex wide-neck bifurcation aneurysms (WNBAs) who underwent strand remodelling with a hypercompliant balloon via Y-stent-assisted coil embolization (Y-SACE) between September 2016 and January 2020 were included in the study. The feasibility, safety, effectiveness, and complication rates of the strand remodelling technique were investigated. Results A total of 12 patients (6 females, 6 males) were included in this study. Significant expansion was obtained in the intersection zone after remodelling. No regression was observed in the expansion rates during follow-up. There was no additional morbidity or mortality. No delayed thromboembolic complications occurred in our patients during long-term follow-up. Conclusions Performing strand remodelling to reduce thromboembolic complications triggered by structural faults caused by the Y-stent configuration is feasible, safe, and effective. This new approach can aid in the prevention of thromboembolic complications in Y-SACE.

scholarly journals Antigenic diversity and seroprevalences of Torque teno viruses in children and adults by ORF2-based immunoassays

2013 ◽  
Vol 94 (2) ◽  
pp. 409-417 ◽  
Author(s):  
Tingting Chen ◽  
Elina Väisänen ◽  
Petri S. Mattila ◽  
Klaus Hedman ◽  
Maria Söderlund-Venermo
Keyword(s):  
Serum Samples ◽  
Phylogenetic Groups ◽  
Single Strain ◽  
New Approach ◽  
Antiviral Antibody ◽  
Specific Igg ◽  
Species Specific ◽  
Multiple Strains ◽  
Antigenic Relationships

Torque teno viruses (TTVs) circulate widely among humans, causing persistent viraemia in healthy individuals. Numerous TTV isolates with high genetic variability have been identified and segregated into 29 species of five major phylogenetic groups. To date, the diversity of TTV sequences, challenges in protein expression and the subsequent lack of serological assays have hampered TTV seroprevalence studies. Moreover, the antigenic relationships of different TTVs and their specific seroprevalences in humans remain unknown. For five TTV strains – belonging to different species of four genogroups – we developed, using recombinant glutathione S-transferase (GST)-fused TTV ORF2 proteins, glutathione–GST capture enzyme immunoassays (EIAs) detecting antibodies towards conformational epitopes. We then analysed serum samples from 178 healthy adults and 108 children; IgG reactivities were observed either towards a single strain or towards multiple strains, which pointed to antigenic distinction of TTV species. The overall seroprevalence for the five TTVs peaked at 43 % (18 of 42) in children 2–4 years of age, subsequently declined, and again reached 42 % (74 of 178) among adults. TTV6 species-specific IgG predominated in children, whereas that for TTV13 predominated in adults. During a 3 year follow-up of the same children, both species-specific seroconversions and seroreversions occurred. This is the first EIA-based study of different TTVs, providing a new approach for seroepidemiology and diagnosis of TTV infections. Our data suggest that different TTVs in humans may differ in antiviral antibody profiles, infection patterns and epidemiology.

scholarly journals Clonal Salivary Gland Infiltrates Associated With Myoepithelial Sialadenitis (Sjögren's Syndrome) Begin as Nonmalignant Antigen-Selected Expansions

Blood ◽  
1998 ◽  
Vol 91 (6) ◽  
pp. 1864-1872 ◽  
Author(s):  
David W. Bahler ◽  
Steven H. Swerdlow
Keyword(s):  
Salivary Gland ◽  
Gene Segment ◽  
Sequence Motifs ◽  
Antigen Stimulation ◽  
Associated Lesions ◽  
Vh Gene ◽  
Complementarity Determining Regions ◽  
Conserved Amino Acids ◽  
Gene Restriction

Myoepithelial sialadenitis (MESA) is the reactive salivary gland lymphoid infiltrate that occurs in patients with Sjögren's syndrome. Although it is well established that mucosa-associated lymphoid tissue (MALT)-type lymphomas may develop from MESA, the issue of whether monoclonal B-cell populations in early MESA-associated lesions represent MALT lymphomas or more benign types of expansions has been very controversial. In addition, it is unknown whether antigen stimulation plays a role in the development or growth of MESA-associated clones. To investigate these issues, we have analyzed the Ig VH genes used by MESA-associated clones in sequential biopsies obtained from contralateral sites of seven different patients. In three cases, single clones were identified in the follow-up biopsies that were distinct from the single clones identified in the initial specimens, whereas in three other cases, the same clone was identified in both the initial and subsequent specimens. In the remaining case, two clones were identified in the second biopsy specimen, one of which was distinct from the initial clone. Of the 11 distinct clones identified in the 14 specimens that were analyzed, 8 were derived from a V1-69 VH gene segment, whereas the other 3 were derived from a V3-7 VH gene segment. In addition, the MESA clones also showed conserved amino acids sequence motifs in their third complementarity-determining regions (CDR3), some of which were encoded by N nucleotides. The marked VH gene restriction along with the similar CDR3 sequences suggests that MESA-associated clones even from different patients may bind the same or similar antigens and are selected for clonal expansion on that basis. The high rates of ongoing VH gene mutation observed in some of the cases futher suggest that the growth of early MESA clones is still dependent on antigen stimulation. In addition, our finding that different biopsies from the same patient may contain distinct clones indicates that some MESA-associated clones have not yet evolved to malignant lymphomas.

A new approach to managing follow-up patients with sino-nasal disorders: the rhinology panel

2020 ◽  
Vol 26 (3) ◽  
pp. 88-93
Author(s):  
Abdulaziz Abushaala ◽  
Helen Sargent ◽  
Jennifer McLean ◽  
Deborah Grech-Marguerat ◽  
Hisham Khalil
Keyword(s):  
Patient Safety ◽  
Waiting List ◽  
Nurse Specialist ◽  
Review Panel ◽  
Clinical Nurse ◽  
New Approach ◽  
Specialist Registrar ◽  
Face To Face ◽  
Clinical Records

Background/aims There is a growing backlog of patients with sino-nasal disorders waiting for a follow-up appointment. This study aimed to identify rhinology patients on the outpatient follow-up list who could be removed from the waiting list for a face to face follow-up appointment and instead either given a phone consultation by a clinical nurse specialist or discharged from the service. Methods The clinical records of patients on the waiting list for a follow-up appointment at a nasal disorders clinic were reviewed by a panel comprising a consultant rhinologist, a rhinology fellow, a specialist registrar and two nurse specialists. Results A total of 300 clinical records of patients on the follow-up list of the Rhinology clinic were identified, of which 253 were found to have a sino-nasal disorder. Of these, 137 patients (54%) were discharged from the rhinology face to face follow-up clinics, while 116 patients (46%) were given face to face review appointments. Conclusions A multi-professional rhinology review panel is an effective way of managing the waiting list of an outpatient rhinology clinic and providing nurse-led telephone consultations could decrease the strain on resources while maintaining patient safety.

Reconnecting governance configuration variables to enterprises contingency factors for optimizing productivity at the start-up level

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Walter Amedzro St-Hilaire
Keyword(s):  
Structural Design ◽  
Design Methodology ◽  
System Analysis ◽  
System Control ◽  
Ceteris Paribus ◽  
New Approach ◽  
Content Type ◽  
Start Up ◽  
The Future

PurposeThe article broaches the important topic of the relationships between governance operationalizations and productivity at the start-up level. It proposes a new approach to reconnect the contingency factors to the optimization of productivity. This helps us to identify the changing characteristics that influence the determinants of decisions, actions and management of the technological projects of the mainly innovative enterprises.Design/methodology/approachThe study uses techniques that effectively solve unobserved endogeneity and heterogeneity problems in enterprises: an empirical–structural design. With this method, this study enables rich empirical conceptualization and helps with extending theory. However, there is a need to further the research by taking into account the system analysis and the complexity of the research object: one of the options might be to explore a possible follow-up of the research through drawing on ethnostatistics and qualimetrics.FindingsThe analysis reveals that the phenomenon of technological project productivity in operational governance context is thus manifested by the coexistence of the applied governance configuration variables, the contingency factors operationalization, the optimizing productivity mechanisms and this with the secular innovation and stagnation and stagnation. Ceteris paribus, the governance operationalizations have an important role in the productivity of technological projects of the innovative enterprises.Originality/valueThis research is the first to mobilize as major determinants of the operationalization of governance, the oversight of the capital, the dividend strategy and the system control, the managerial follow-up, the detection of opportunistic behaviours and the application of governing incentives (among others) as governance configuration variables in order to highlight their interactions with productivity in the innovative firm technological projects. For this reason alone, the paper will be referenced by other authors in the future.

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