I-JAMM-(I): A survey providing an insight into the practices of isoagglutinin titration in ABO incompatible kidney and liver transplantation.

BACKGROUND AND OBJECTIVES: ABO-incompatible transplantations allow patients to receive timely transplants. Isoagglutinin titration to ascertain levels of incompatible antibodies in the recipient is important in determining patient selection and transplant survivability. To find out the prevalent trends in India, the largest, first of its kind survey was carried out among the transplant centers regarding their practices in isoagglutinin titration. METHODS: The survey was drafted by a working group of Transfusion and Transplant Immunology specialists from six different centers. Data was obtained via the use of an online questionnaire. RESULTS: Results were categorized into four categories, Hospital information, Titration methodology, Role of transfusion specialists and cut-off titers. Most centers had a well-established solid-organ transplant program with considerable number of ABO-incompatible transplantations. Most centers performed isoagglutinin titration in Transfusion Medicine department. Column Agglutination Technique (CAT) was the most common method, using EDTA blood samples and freshly-prepared in-house pooled cells. Most centers had a turn-around time of less than 12 h. While the policy for ascertaining baseline and threshold titers is well-defined in ABO-incompatible renal transplants, variations from center to center still exist for ABO-incompatible liver transplants. Most centers required a Transfusion Medicine consultation for the patients before such transplants. CONCLUSION: With increasing ABO-incompatible kidney and liver transplants across the country, the role of Transfusion medicine specialists has become vital in pre-conditioning regimes enabling the viability and success of such transplants. This was a unique survey that provided a snapshot of current trends and practices of isoagglutinin titration for ABO-incompatible transplants in India.

'Old is gold' does conventional test tube method still reign supreme? An immuno-haematological survey of anti-D detection and titration in ante-natal cases among major hospitals across India.

INTRODUCTION: Anti-D detection and titration plays a major role in RhD negative antenatal cases both, for monitoring maternal as well as fetal status as well as initiation of early therapeutic interventions, such as intra-uterine transfusions (IUT) to improve maternal as well as fetal morbidity and mortality and reduce the adverse effects of haemolytic disease of fetus and newborn (HDFN). We conducted a survey focusing on the policies and procedures of anti-D detection and titration among major tertiary care centres across India. METHODOLOGY: The survey was drafted by a working group of transfusion medicine and immunohematology specialists from six different centres in India. Data were obtained via the use of an online questionnaire. RESULTS: Results were categorised into four categories, Hospital information, immuno-haematological testing methodology, clinical significance of anti-D testing and the role of transfusion medicine specialists. The survey highlighted the modalities as well as the methodologies of anti-D detection and titration in antenatal women across different major tertiary care centres in India. CONCLUSION: This survey provided a unique snapshot of the prevalent methodologies being employed by major tertiary care centres across the country for detection and titration of anti-D levels as well as the important role it plays in the therapy of affected antenatal women to minimise adverse effects on the fetus.

Single-cell transcriptome analysis identifies novel biomarkers involved in major liver cancer subtypes.

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are the two aggressive subtypes of liver cancer (LC). Immense cellular heterogeneity and cross-talk between cancer and healthy cells make it challenging to treat these cancer subtypes. To address these challenges, the study aims to systematically characterize the tumor heterogeneity of LC subtypes using single-cell RNA sequencing (scRNA-seq) datasets. The study combined 51,927 single cells from HCC, ICC, and healthy scRNA-seq datasets. After integrating the datasets, cell groups with similar gene expression patterns are clustered and cluster annotation has been performed based on gene markers. Cell-cell communication analysis (CCA) was implemented to understand the cross-talk between various cell types. Further, differential gene expression analysis and enrichment analysis were carried out to identify unique molecular drivers associated with HCC and ICC. Our analysis identified T cells, hepatocytes, epithelial cells, and monocyte as the major cell types present in the tumor microenvironment. Among them, abundance of natural killer (NK) cells in HCC, epithelial cells, and hepatocytes in ICC was detected. CCA revealed key interaction between T cells to NK cells in HCC and smooth muscle cells to epithelial cells in the ICC. Additionally, SOX4 and DTHD1 are the top differentially expressed genes (DEGs) in HCC, while keratin and CCL4 are in ICC. Enrichment analysis of DEGs reveals major upregulated genes in HCC affect protein folding mechanism and in ICC alter pathways involved in cell adhesion. The findings suggest potential targets for the development of novel therapeutic strategies for the treatment of these two aggressive subtypes of LC.

An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.

MOTIVATION: In the past few years, researchers have proposed numerous indexing schemes for searching large datasets of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes-Mantis, VariMerge and Bifrost-that can serve as colored de Bruijn graph representations in addition to serving as k-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data. RESULTS: In this paper, we show how to build a scalable and updatable exact raw sequence-search index. Specifically, we extend Mantis using the Bentley-Saxe transformation to support efficient updates, called Dynamic Mantis. We demonstrate Dynamic Mantis's scalability by constructing an index of ≈40K samples from SRA by adding samples one at a time to an initial index of 10K samples. Compared to VariMerge and Bifrost, Dynamic Mantis is more efficient in terms of index-construction time and memory, query time and memory and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Dynamic Mantis scaled to more than 39K samples. Queries were over 24× faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Dynamic Mantis indexes were about 2.5× smaller than Bifrost's indexes and about half as big as VariMerge's indexes. AVAILABILITY AND IMPLEMENTATION: Dynamic Mantis implementation is available at https://github.com/splatlab/mantis/tree/mergeMSTs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Immunohematological challenges in COVID infected patients.

BACKGROUND: Several autoimmune disorders have been reported to be related with COVID infection. In continuation to these autoimmune phenomenon, autoimmune hemolytic anaemia (AIHA) also has been noted in COVID infected patients. The aim of the study was to find out the prevalence of red cell alloimmunization, ABO discrepancy and positive direct antiglobulin test (DAT) results in COVID infected patients hospitalised in a tertiary care centre in North India. METHODOLOGY: This was a retrospective observational study done from July 2020 to June 2021. All symptomatic patients admitted to ICU tested positive for SARS CoV-2 whose blood samples were received in the immunohematology laboratory of department of Transfusion Medicine for determination of blood group and issue of packed red cells, and found to have positive antibody screen, blood group discrepancy and positive DAT results, were included in the study. RESULTS: A total of 10,568 tests were run, out of which 4437 were for determination of blood group, 5842 were for antibody screen and 289 were for direct antiglobulin test. Included in this study were 146 patients who either had blood group discrepancy, or had a positive antibody screen or had a positive DAT. Out of 115 positive antibody screen, 66 patients had only alloantibodies, 44 patients had only autoantibodies while only 5 patients had both auto as well as alloantibodies. Total number of positive DAT cases was 50 (50/289 = 17.3 %). There were 26 ABO discrepancies (26/4437 =0.58 %) found. CONCLUSION: Our results also indicate that there is rise in rate of alloimmunization and DAT positivity among COVID patients.

Single center experience of therapeutic plasma exchange in a resource-constrained setting: A study of trends in scope and complications.

BACKGROUND: Therapeutic apheresis procedures are becoming an increasingly integral part of modern medical practice, be it as a part of therapy or pre-conditioning regimes for solid organ transplants. In our center, we follow the American Society for Apheresis (ASFA) guidelines for categorizing these procedures. However, lack of a centralized registry for therapeutic apheresis in India, lack of consolidated data as well as a resource-constrained setting prevent it from being utilized to its full potential. STUDY DESIGN AND METHODS: This study was a retrospective analysis of therapeutic plasma exchange (TPE) procedures performed from January 2015 to October 2022 in the Department of Transfusion Medicine at a large tertiary care hospital in North India. All consecutive TPE procedures were included. Overall and specialty-wise scoring for all patients was performed. Mean scores were calculated. RESULTS: A total of 1434 procedures were performed during the study duration of 7 years. These procedures were performed for 284 different patients. Majority of the procedures were referred from nephrology (895 of 1434, 62.4%), followed by neurology, gastroenterology, and liver transplant teams, hematology, critical care, rheumatology, pediatrics, and internal medicine. Complete response, partial response, and no-response were observed in 1077 (75.1%), 201 (14%), and 156 (10.9%) procedures respectively. Only 14 procedures reported adverse effects. DISCUSSION: Increasing effectiveness of TPE in a number of procedures and a variety of indications has broadened its scope, while the small number of adverse events, when supervised by trained Transfusion Medicine physicians has made TPE a more viable and safer alternative to other treatment modalities.

What are the optimal targeting visualizations for performing surgical navigation of iliosacral screws? A user study.

INTRODUCTION: Complex orthopaedic procedures, such as iliosacral screw (ISS) fixations, can take advantage of surgical navigation technology to achieve accurate results. Although the impact of surgical navigation on outcomes has been studied, no studies to date have quantified how the design of the targeting display used for navigation affects ISS targeting performance. However, it is known in other contexts that how task information is displayed can have significant effects on both accuracy and time required to perform motor tasks, and that this can be different among users with different experience levels. This study aimed to investigate which visualization techniques helped experienced surgeons and inexperienced users most efficiently and accurately align a surgical tool to a target axis. METHODS: We recruited 21 participants and conducted a user study to investigate five proposed 2D visualizations (bullseye, rotated bullseye, target-fixed, tool-fixed in translation, and tool-fixed in translation and rotation) with varying representations of the ISS targets and tool, and one 3D visualization. We measured the targeting accuracy achieved by each participant, as well as the time required to perform the task using each of the visualizations. RESULTS: We found that all 2D visualizations had equivalent translational and rotational errors, with mean translational errors below 0.9 mm and rotational errors below 1.1[Formula: see text]. The 3D visualization had statistically greater mean translational and rotational errors (4.29 mm and 5.47[Formula: see text], p < 0.001) across all users. We also found that the 2D bullseye view allowed users to complete the simulated task most efficiently (mean 30.2 s; 95% CI 26.4-35.7 s), even when combined with other visualizations. CONCLUSIONS: Our results show that 2D bullseye views helped both experienced orthopaedic trauma surgeons and inexperienced users target iliosacral screws accurately and efficiently. These findings could inform the design of visualizations for use in a surgical navigation system for screw insertions for both training and surgical practice.

Electrospun Biomimetic Nanofibrous Scaffolds: A Promising Prospect for Bone Tissue Engineering and Regenerative Medicine.

Skeletal-related disorders such as arthritis, bone cancer, osteosarcoma, and osteoarthritis are among the most common reasons for mortality in humans at present. Nanostructured scaffolds have been discovered to be more efficient for bone regeneration than macro/micro-sized scaffolds because they sufficiently permit cell adhesion, proliferation, and chemical transformation. Nanofibrous scaffolds mimicking artificial extracellular matrices provide a natural environment for tissue regeneration owing to their large surface area, high porosity, and appreciable drug loading capacity. Here, we review recent progress and possible future prospective electrospun nanofibrous scaffolds for bone tissue engineering. Electrospun nanofibrous scaffolds have demonstrated promising potential in bone tissue regeneration using a variety of nanomaterials. This review focused on the crucial role of electrospun nanofibrous scaffolds in biological applications, including drug/growth factor delivery to bone tissue regeneration. Natural and synthetic polymeric nanofibrous scaffolds are extensively inspected to regenerate bone tissue. We focused mainly on the significant impact of nanofibrous composite scaffolds on cell adhesion and function, and different composites of organic/inorganic nanoparticles with nanofiber scaffolds. This analysis provides an overview of nanofibrous scaffold-based bone regeneration strategies; however, the same concepts can be applied to other organ and tissue regeneration tactics.

Versatile and multifaceted CRISPR/Cas gene editing tool for plant research.

The ability to create desirable gene variants through targeted changes offers tremendous opportunities for the advancement of basic and applied plant research. Gene editing technologies have opened new avenues to perform such precise gene modifications in diverse biological systems. These technologies use sequence-specific nucleases, such as homing endonucleases, zinc-finger nucleases, transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (CRISPR/Cas) complexes to enable targeted genetic manipulations. Among these, the CRISPR/Cas system has emerged as a broadly applicable and valued gene editing system for its ease of use and versatility. The adaptability of the CRISPR/Cas system has facilitated rapid and continuous innovative developments to the precision and applications of this technology, since its introduction less than a decade ago. Although developed in animal systems, the simple and elegant CRISPR/Cas gene editing technology has quickly been embraced by plant researchers. From early demonstration in model plants, the CRISPR/Cas system has been successfully adapted for various crop species and enabled targeting of agronomically important traits. Although the approach faces several efficiency and delivery related challenges, especially in recalcitrant crop species, continuous advances in the CRISPR/Cas system to address these limitations are being made. In this review, we discuss the CRISPR/Cas technology, its myriad applications and their prospects for crop improvement.

Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein.

Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.

Clinical outcome of living donor kidney transplantation across simultaneous ABO and HLA incompatibility: Single center experience of first ten cases.

BACKGROUND AND AIMS: Preconditioning using different protocols has been tested to prevent antibody mediated rejection (ABMR) individually for ABO and HLA incompatibility. However, simultaneous presence of both barriers is still less explored. The aim of this study was to report outcomes of institutional desensitization protocol in renal transplant recipients with simultaneous ABO and HLA incompatibility. MATERIALS AND METHODS: This was a retrospective study conducted from October 2015 to December 2018. All patients with a clinical diagnosis of dialysis dependent chronic kidney disease (CKD), who were prospective coexistent HLA and ABO incompatible renal transplant recipients were included in the study. Patients were followed up and graft function and patient survival was assessed at 1 y from the date of transplant. RESULTS: Median and mode baseline anti-A titers were 64, while median and mode baseline anti-B titers were 256. All recipients were discharged by tenth postoperative day. None of the patients had any bleeding complications. Post transplant infection rate was found to be 20 %. A total of 54 therapeutic plasma exchange (TPE) procedures were performed before transplant and 8 were performed after transplant. Graft survival and patient survival was 100 % at 3, 6, 9, and 12 months. Range and mean follow-up period was 15-42 months and 23 months respectively. Mean glomerular filtration rate (GFR) at 1 y using the CKD-EPI equation was 85.25 ± 13.76 mL/min. Biopsy proven ABMR was observed in one case only which was managed with TPE and immunosuppression. CONCLUSION: Simultaneous ABO and HLA incompatibility in renal transplant recipients can be managed successfully with adequate preconditioning and careful monitoring.

Prospective audit of blood transfusion request forms and continuing medical education to optimise compliance of clinicians in a hospital setting.

OBJECTIVES: The aim of this study was to analyse blood requisition forms sent by clinicians in a tertiary care hospital to the transfusion service to ascertain their completeness and correctness. A secondary objective was to study the effect of continuing medical education (CME) in a hospital setting on clinician's behaviour regarding the importance of details that ought to be mentioned on blood requisition forms. BACKGROUND: Transfusion audits are useful tools in the evaluation and education of those requesting blood components. METHODS/MATERIALS: This was a prospective, observational study conducted in the department of Transfusion Medicine at a tertiary-level healthcare centre from June 2019 to December 2019. The study was divided into two phases: pre-CME (P1) and post-CME (P2). In both phases, an audit for assessing completeness and correctness of blood requisition forms, which were divided into four sections, was performed. A scoring system was devised to compare both phases. RESULTS: In the P1 phase, 45.77% of the blood requisition form entries were complete and correct; 23.45% of incomplete entries were generated by emergency and trauma. In the P2 phase, 76.75% of the blood requisition form entries were complete and correct; 35.09% of the incomplete entries were generated by obstetrics and gynaecology. Complete and correct entries increased from 45.7% (P1) to 76.75% (P2). Scores of P1 were found to be lower than scores of P2 for all four sections. Cumulative mean score for P1 (20687) was found to be significantly lower than the mean score for P2 (30870). CONCLUSION: Audit and CME regarding different aspects of transfusion medicine practices play a major role in the improvement of transfusion practices in hospitals.

Outcome of desensitization in human leukocyte antigen and ABO incompatible living donor kidney transplantation: Single center experience of first 200 incompatible transplants.

BACKGROUND AND AIMS: Although desensitization is well established, concerns about graft outcome, patient survival and rejection still exist. The present study aims at comparing outcomes of renal transplant recipients across simultaneous ABO and human leukocyte antigen (HLA) incompatibility barriers to those with ABO or HLA incompatibility alone. MATERIALS AND METHODS: This was a retrospective study conducted from October 2015 to December 2018. All patients with a clinical diagnosis of chronic kidney disease, who were prospective HLA incompatible (HLAi) and/or ABO incompatible (ABOi) renal transplant recipients were included. A total of 400 cases including 36 ABOi transplants, 154 HLAi transplants, 10 simultaneously ABO and HLA incompatible transplants, and 200 ABO (ABOc) and HLA (HLAc) compatible kidney transplants from living donors were included. RESULTS: There were significantly more number of blood transfusions, previous transplants and pregnancies in HLAi transplant recipients relative to the ABOi or the control group. Mean number of therapeutic plasma exchange procedures per patient and mean plasma volume processed per procedure were slightly higher in the ABOi + HLAi category. The incidence of graft dysfunction due to suspected antibody-mediated rejection during first year was highest in the ABOi + HLAi group, followed by ABOc + HLAi and ABOi + HLAc, lowest in the ABOc + HLAc category. Mean time to first episode of graft dysfunction was significantly shorter with incompatible transplants. There were no kidney transplant recipient deaths in the study. CONCLUSION: Patient outcome and graft outcomes observed with incompatible transplants were not worse than those observed with compatible transplants.

Comparative analysis of complement-dependent lymphocytotoxicity crossmatch and flow cytometry crossmatch results versus Luminex single-antigen bead-based donor-specific IgG class I antibody MFI values in live related renal transplant cases; a retrospective observation in 102 cases.

The aim of this study was to compare the results of solid phase assay and cell-based assay, and explore the near-accurate DSA-MFI-cutoff value detected on solid phase assay above which the cell-based assay would show a positive result. In this retrospective study, 102 prospective renal transplant recipients were tested for the presence of donor-specific antibodies (DSAs) by cell-based assay (T-cell-CDC-AHG-XM and T-cell-IgG-FC-XM) and solid phase assay (class-I-IgG-L-SAB) with their corresponding donor. Among the 40 patients in the group first (L-SAB-DSA-MFI<1000), one case was positive in IgG-T-cell-FC-XM while T-cell-CDC-AHG-XM was negative in all the cases. In the second group having L-SAB-DSA-MFI values between 1000 and 3000, 19 cases were positive and the remaining 11 cases were negative in IgG-T-cell-FC-XM. T-cell-CDC-AHG-XM showed a negative reaction in all 30 cases. In the third group having L-SAB-DSA-MFI values between 3000 and 5000, IgG-T-cell-FC-XM was positive in 18 cases while, two were negative. T-cell-CDC-AHG-XM demonstrated a negative result in 14 cases while reaming six cases demonstrated a positive result. In the fourth group having L-SAB-DSA-MFI values >5000, all 12 cases showed a positive result in both IgG-T-cell FC-XM and T-cell-CDC-AHG-XM. Our results indicated that the L-SAB-DSA-MFI values >2215 were significantly (P < .001) correlated with positive IgG-T-cell-FC-XM while L-SAB-DSA-MFI values >4689 were significantly (P < .001) correlated with positive CDC-XM.

Locality-sensitive hashing for the edit distance.

MOTIVATION: Sequence alignment is a central operation in bioinformatics pipeline and, despite many improvements, remains a computationally challenging problem. Locality-sensitive hashing (LSH) is one method used to estimate the likelihood of two sequences to have a proper alignment. Using an LSH, it is possible to separate, with high probability and relatively low computation, the pairs of sequences that do not have high-quality alignment from those that may. Therefore, an LSH reduces the overall computational requirement while not introducing many false negatives (i.e. omitting to report a valid alignment). However, current LSH methods treat sequences as a bag of k-mers and do not take into account the relative ordering of k-mers in sequences. In addition, due to the lack of a practical LSH method for edit distance, in practice, LSH methods for Jaccard similarity or Hamming similarity are used as a proxy. RESULTS: We present an LSH method, called Order Min Hash (OMH), for the edit distance. This method is a refinement of the minHash LSH used to approximate the Jaccard similarity, in that OMH is sensitive not only to the k-mer contents of the sequences but also to the relative order of the k-mers in the sequences. We present theoretical guarantees of the OMH as a gapped LSH. AVAILABILITY AND IMPLEMENTATION: The code to generate the results is available at http://github.com/Kingsford-Group/omhismb2019. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Survey to assess knowledge, attitude and practices for safe and efficient vein-to-vein transfusion practices and effect of educational intervention in a hospital setting.

OBJECTIVES: The primary aim was to assess the knowledge, attitude and practices (KAP) of employees (medical, paramedical and other hospital staff) towards blood donation and transfusion practices in a tertiary care hospital. A secondary objective was to assess and interpret the effect of an educational module on improvement in the KAP of employees in a hospital setting. BACKGROUND: For satisfactory practices, it is essential to initiate KAP studies. METHODS/MATERIALS: This was a prospective, observational study conducted among hospital staff (clinical and non-clinical) from January to December 2019. The study was divided into two phases: pre-educational module (P1) and post-educational module (P2). In both phases, a questionnaire was distributed. Knowledge was assessed by 30 questions, attitude by 20 questions and practice by 30 questions. If any individual had unsatisfactory scores in both the P1 and P2 phases (scores <40; 50%), they had to participate in a mandatory certificate course. RESULTS: A total of 180 individuals participated in the P1 and 172 participated in the P2 phase. Mean score for practice (0.471) was better than that for attitude (0.447) and knowledge (0.43). Factors associated with good scores were younger age group, more than 5 years of employment and clinical field of study. The total score for KAP increased, and a statistically significant difference (P-value < .05) was observed between P1 and P2 scores. Of 172 participants, 27 were asked to attend the 2-week certificate course due to unsatisfactory scores (score < 40) in both P1 and P2 phases. These 27 participants required attending this certificate course a mean of 1.67 ± 0.83 times to obtain satisfactory scores. CONCLUSION: Educational intervention is an important tool for improving KAP among not only physicians but hospital staff as well.

A prospective, observational study for optimization of antibody screening in pretransfusion compatibility testing.

CONCLUSIONS: Despite known use of antibody screening (AS), it has not been adopted uniformly across blood centers in India. Many centers in India are currently using a type and hold policy with subsequent antihuman globulin (AHG) crossmatch when blood units are requested. The main aim of this study was to assess the benefits of a type and screen (TS) policy in which blood grouping and AS are performed simultaneously during the first hospital visit. If the AS is negative, subsequent requests for blood units would require an immediate spin test (IST) crossmatch with release of blood units, followed by an AHG crossmatch. This prospective, observational study was conducted at a tertiary health care center between July 2014 and December 2018 and included only Indian patients. Blood grouping and AS were performed during the first hospital visit on a total of 22,888 patients; the majority of patients were from hemato-oncology and blood marrow transplant, hepatology and liver transplant, cardiothoracic vascular surgery, and medical intensive care units. Demographic parameters were evaluated for risk of alloimmunization, and a record of the same was maintained. Depending on the AS results, a further course of action was chosen. Clinically significant alloantibodies were detected in 145 patients, and autoantibodies were detected in 53 patients. Alloantibodies were mainly against Rh and Kell blood group antigens. A significantly higher proportion of patients in the AS+ group required blood transfusion when compared with the AS- group. In cases wherein the IST crossmatch was compatible but AHG crossmatch was not, follow-up did not demonstrate any clinical or laboratory evidence of hemolysis. AS is a safe, efficient, and beneficial tool for pretransfusion compatibility testing in both AS+ and AS- patients. With a TS policy, AHG crossmatch can be omitted in AS- patients without compromising safety.

Blood component administration to multiple myeloma patients treated with daratumumab: suggesting a novel approach with use of 0.1 M dithiothreitol.

CONCLUSIONS: Storage of dithiothreitol (DTT)-treated red blood cells (RBCs) leads to hemolysis. The aim of this study was to compare 0.1 M DTT with 0.2 M DTT treatment of RBCs and to share our experience of providing components to seven patients on daratumumab (DARA). This prospective, observational study included patients who required RBC transfusion within 6 months of DARA administration. All patients underwent a baseline serologic evaluation followed by a repeat evaluation after DARA administration. In addition, use of 0.1 M DTT was compared with 0.2 M DTT in terms of concordance of results, hemolysis with storage of treated RBCs, and ease of use. A total of 22 RBC requisitions were received for seven patients. Antibody screen was positive for one patient (anti-C) at baseline; it was panreactive for all patients after DARA. Concordance of results between the two concentrations was 98.5 percent. Laboratory personnel found results obtained with use of 0.1 M DTT-treated RBCs easy to interpret. Supernatant hemoglobin was found to be significantly greater for 0.2 M DTT-treated RBCs at the sixth day of storage. In conclusion, component administration to patients on DARA can be done without delay if adequate policies and procedures are in place. Use of 0.1 M DTT-pretreated RBCs can be used to avoid delay in transfusion and reduce the burden on the laboratory of weekly preparation of 0.2 M DTT-treated RBCs.

Significance of Luminex-based single antigen class II bead assay and its mean fluorescence intensity in renal transplant cases; a retrospective observation in 97 cases.

The objective of this study was to determine the mean fluorescence intensity (MFI) values of class II Luminex single antigen bead (L-SAB) assay and compare these MFI values with cell-based complement-dependent cytotoxicity crossmatch with anti-human globulin (CDC-AHG-XM) and IgG-B-cell flow cytometry crossmatch (FC-XM) results and explore the near-accurate MFI-cutoff values of positive cell-based crossmatch results. This retrospective study was an analysis in 97 renal transplant recipients, who were tested for the presence of DSA by CDC-AHG-XM and IgG-B-cell-FC-XM methods with their corresponding donor as well as for anti-human leukocyte antigen (HLA) antibody detection using a sensitive L-SAB assay. In the group having DSA MFI values <1000, none of the patients showed positivity for FC-XM and CDC-AHG-XM; in the group having MFI values between 1000 and 3000, 35.48% showed positivity for FC-XM but none by the CDC-AHG-XM method. However, in the group having MFI values >3000, 83.33% of cases were positive for FC-XM. Further, in those groups with MFI values between 3000 and 6000, 38.09% were positive for CDC-AHG-XM, while 86.66% showed positivity in the group with MFI >6000. Our results indicated that Luminex-DSA MFI value >1995 (P < .0001) significantly correlated with IgG-B-cell-FC-XM positivity while Luminex-DSA MFI value of >4247 (P < .0006) was significantly correlated with positive CDC-AHG-XM. MFI cutoff of 1995 exhibited a diagnostic sensitivity of 97.56% and specificity of 89.29% for predicting positive IgG B-cell FC-XM and MFI cutoff of 4247 exhibited a diagnostic sensitivity of 90.48% and specificity of 97.37% for predicting positive CDC-AHG-XM. However, a cutoff MFI of >5000 and >7000 for SAB assay had a sensitivity and specificity of 100% in detecting a positive IgG B-cell FC-XM and CDC-AHG-XM, respectively.

Squeakr: an exact and approximate k-mer counting system.

Motivation: k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure. We introduce the k-mer-counting/querying system Squeakr (Simple Quotient filter-based Exact and Approximate Kmer Representation), which is based on the counting quotient filter. This off-the-shelf data structure turns out to be an efficient (approximate or exact) representation for sets or multisets of k-mers. Results: Squeakr takes 2×-4.3× less time than the state-of-the-art to count and perform a random-point-query workload. Squeakr is memory-efficient, consuming 1.5×-4.3× less memory than the state-of-the-art. It offers competitive counting performance. In fact, it is faster for larger k-mers, and answers point queries (i.e. queries for the abundance of a particular k-mer) over an order-of-magnitude faster than other systems. The Squeakr representation of the k-mer multiset turns out to be immediately useful for downstream processing (e.g. de Bruijn graph traversal) because it supports fast queries and dynamic k-mer insertion, deletion, and modification. Availability and implementation: https://github.com/splatlab/squeakr available under BSD 3-Clause License. Contact: ppandey@cs.stonybrook.edu. Supplementary information: Supplementary data are available at Bioinformatics online.