bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5 Umbilical Cord Blood Treatment to Improve Gross Motor Function in Individuals with Cerebral Palsy: Results from an Individual Participant Data Meta-Analysis
Authors: Finch-Edmondson Megan , Paton Madison , Webb Annabel , Ashrafi Mahmoud , Blatch-Williams Remy , Cox, Jr. Charles , Crompton Kylie , Griffin Alexandra , Kim MinYoung , Kosmach Steven , Kurtzberg Joanne , Nouri Masoumeh , Sun Jessica , Zarrabi Morteza , Novak Iona 
Published: September 2023

Abstract

Introduction
Umbilical cord blood (UCB) is a novel treatment for cerebral palsy (CP) with clinical trials indicating UCB is safe and can improve gross motor function. However, heterogeneity across research design, participant selection and treatment protocols has limited the ability to interpret overall treatment effect, identify best responders and dosing thresholds.

Objectives
We sought to conduct a systematic review and individual participant data meta-analysis (IPDMA) to 1) determine the effect of UCB treatment measured by Gross Motor Function Measure (GMFM) in individuals with CP, and 2) determine the effect of UCB cell dose on clinical improvement.

Methods
CENTRAL, Embase and Medline were systematically searched for clinical studies administering UCB to individuals with CP with or without a control group/comparator, collecting GMFM scores at baseline and 1, 3, 6 and/or 12 months. Individual de-identified participant data were obtained before being cleaned and coded. A one-stage IPDMA was conducted in R to obtain the pooled effect of UCB and the pooled cell dose effect via linear mixed models, including random effects terms to investigate between-study heterogeneity.

Results
Individual participant data from nine published and two unpublished studies (seven RCTs and four single-arm studies) were obtained, comprising 285 UCB (+/- erythropoietin, EPO)- treated participants and 171 controls for analysis. Median baseline age was 43 months (range 8-227). Most UCB infusions were allogeneic (80%), and 10/11 studies applied UCB intravenously. The median pre-thaw dose of intravenous-infused UCB was 46.7x10^6 total nucleated cells/kg (range 7.7-210.3).
The pooled effect at 6 months post-intravenous UCB was an average change from baseline GMFM-66 of 0.93 (95% CI: 0.12, 1.75; p=0.027) points greater among UCB-treated participants (+/- EPO) compared to controls. There was also a statistically significant positive pooled cell dose effect at 6 months post-intervention (p=0.005), indicating that higher cell doses were associated with greater GMFM-66 increases. There was negligible between-study heterogeneity in both the treatment effect and the cell dose effect at 6 months.

Discussion
UCB improves gross motor function, and higher dose is beneficial. Future exploration of additional timepoints in addition to co-variates including age at infusion, severity, and etiology is underway and may elucidate responder subgroups and reveal increased efficacy.
Abstract 9 Identification of Effective Changes to Workflow Triaging Criteria and Production Planning
Authors: Shields Sara , Walker Molly , Laster Candice , DeDino Faith , Wood Bridget , Bobik-Kurz Kathy , Thut Dawn , Vincent Kim 
Published: September 2023

Abstract

Introduction
The Cleveland Cord Blood Center (CCBC) analyzes fresh incoming cord blood units for the total nucleated cell (TNC) count. Units that meet the TNC criteria are processed for clinical banking and units not meeting the defined criteria are made available for research collaborations. CCBC sought to understand if adding additional pre-screening criteria would reduce post-manufacturing deferral rates and increase production of licensed units.

Objectives
To identify the main failure modes resulting in cord blood unit deferral for clinical banking post-manufacturing. To identify key factors resulting in unlicensed status of processed cord blood units. To implement changes to pre-screening strategies to reduce deferral rates and increase production of licensed units.

Methods
CCBC created four cross-departmental teams to evaluate the main reasons for deferrals post-manufacturing and to evaluate travel-risk history. Each committee had representation from collections, quality, and laboratory staff. Data was evaluated that was collected between January and June 2022.

Results
The committees identified that 19% of all deferrals post-manufacturing were related to low CD34 count and/or viability and that 17% of all processed units were unlicensed due to travel to Zika related areas. In March 2023, pre-screening criteria was updated to include a pre-processed CD34 count and viability and a pre-screening of the donating mother for travel history after consenting and prior to manufacturing. Units that fulfilled both the TNC and CD34 cut offs and did not have a high-risk travel history were processed for clinical banking. Data evaluated from March and April 2023 indicated that the deferral rates for low viable CD34 counts post-manufacturing went from 19% down to 0% and the percentage of high-risk travel units manufactured was reduced from 17% to 7%.

Discussion
Review of failure modes identified two main factors to guide improved triage efficiency. By implementing a pre-processing CD34 count, the larger TNC and CD34 cord blood units were identified for banking for clinical use. By using a pre-screening process at collection sites, high-risk travel donations were identified prior to processing. In the two-month timeframe evaluated, the overall deferral rates were reduced by roughly 7% and post-manufacturing licensure status increased from 83% to 93%.
Abstract 10 Experience with Enrollments and Releases Within a Medical Needs Program at a Large U.S. Private Cord Blood Bank
Authors: Fernekes Michelle , Brown Heather , Pandolfi Erica , Stroh Eliza , Isley Lauren 
Published: September 2023

Abstract

Introduction
Medical Needs / Directed Donor programs provide families with access to cord blood for potential future use. In situations where a diagnosis, potentially treatable with cord blood, exists in an immediate relative of the newborn, these programs often allow families to preserve newborn stem cells at little to no cost.

Objectives
The objective of this study was to examine indications for enrollment and unit releases in a medical needs program at a large U.S. private newborn stem cell bank.

Methods
Enrollment data over a 24-year period was analyzed. Data was categorized by indications for enrollment and indications for which units were released.

Results
There was a total of 7,034 enrollments within the specified timeframe. Most enrollments were for indications treatable by hematopoietic stem cell transplant given the program did not include experimental indications until 2019. Approximately one-third of enrollments (33.4%) for transplant indications were for various types of leukemia. The experimental indications most frequently represented in enrollments were autism (44.3%) and cerebral palsy (38.4%).
For all cord blood units stored under the medical needs program, the majority (70%) of releases were intended for use in transplant medicine. The most frequently represented transplant indication for releases was hemoglobinopathies including sickle cell anemia and beta thalassemia (44.6%). Approximately one-third (36.1%) of transplant releases were related to leukemia. Autism and cerebral palsy were the two most frequently represented experimental indications for units released at 39% and 36%, respectively.

Discussion
Clinical indications were mostly consistent between enrollments and releases through this cohort. This suggests the structure of the program is effective in identifying families who have a higher likelihood of utilizing their cord blood unit for a transplant or experimental infusion.
Cord blood banks should continue to re-evaluate the eligibility criteria for their medical needs programs in light of relevant updates in the potential utility of newborn stem cells including changes in transplant medicine indications and treatment procedures, as well as clinical trials and experimental protocols using related cord blood units. Future research related to pathways of referral to medical needs programs may inform education gaps among women’s health providers.
Abstract 13 Long-Term Stability of Dus Cord Blood Units After &gt;29 Years of Cryopreservation: Follow-Up Data from the José Carreras Cord Blood Bank
Authors: Liedtke Stefanie , Többen Sabine , Gressmann Holger , Meyer Andrea , Gluckman Eliane , Kögler Gesine 
Published: September 2023

Abstract

Introduction
The José Carreras Cord Blood Bank (CBB) located in Düsseldorf stores 21215 active cryopreserved cord blood units (CBUs) and has released 1476 CBUs for allogeneic transplantation. The success of transplantations, but also the generation of cells for regenerative medicine for e.g. iPSC reprogramming, significantly depends on the quality of the cryopreserved CBUs after thaw.

Objectives
Therefore, typical parameters like cell count, recovery and viability are analysed from thawed CBUs yearly by a stability monitoring program according to the FACT standards. The longest cryopreservation period in liquid nitrogen tested to date is 338 months (&gt;29 years) for unseparated units and 300 months (25 years) for volume-reduced units that are licensed by the Paul-Ehrlich Institute.

Methods
A retrospective analysis of unseparated CBUs processed from 1993-1997, CBUs processed from 1998-2005 by manual volume-reduction and CBUs processed since 2005 by automated volume-reduction applying the Sepax100 system was performed. In consideration of the distinct processing methods, storage time and existing follow-up data of released transplants, this approach should demonstrate the high CBU quality and proof the long-term engrafting capability of CBUs cryopreserved in liquid nitrogen.

Results
According to the CBB stability program means of TNC count (16.32±2.61 x 108), TNC recovery after thaw (106.8±13.91%, above 100% due to earlier applied cell-count method), TNC viability (88.91±5.01%), CD34+7AAD- viability (90.73±3.69%), CD45+7AAD- viability (69.09±5.38%) and CFC count (7.10±2.45 x 106) were determined after &gt;29 years of cryopreservation for unseparated CBUs. In volume-reduced CBUs the mean TNC count (9.37±2.14 x 108), TNC recovery (97.78±3.70%), TNC viability (84.22±10.02%), CD34+7AAD- viability (88.11±5.16%), CD45+7AAD- viability (73.67±8.31%) and CFC count (1.37±0.59 x 106) were determined after 25 years of cryopreservation.

Discussion
In addition, these relevant parameters were retrospectively analyzed for released transplants in correlation to the storage time. The follow-up data of recipients from CBUs demonstrate an earlier engraftment of volume-reduced CBUs as compared to unseparated CBUs in accordance to an increased TNC count over time. With regard to applied processing methods, engraftment time and patient age (children and adults) this retrospective analysis confirms the high quality of old CBUs stored in the liquid phase at -196°C.
Abstract 16 Insights into Highly Engraftable Hematopoietic Cells from 27-Year Cryopreserved Umbilical Cord Blood
Authors: Broxmeyer Hal , Luchsinger Larry , Weinberg Rona , Jimenez Alexandra , Frenet Emeline Masson , Hof Wouter van't , Capitano Maegan , Hillyer Christopher , Kaplan Mark , Cooper Scott , Ropa James 
Published: September 2023

Abstract

Introduction
Cord blood banking has consistently outpaced the utilization of cord blood units (CBUs). Thus, the average duration of cryopreservation among banked CBUs will likely continue to increase. It remains unclear how long cryopreserved CBUs remain functional, and it is critical to determine whether duration of cryopreservation should be used as an exclusionary criterion during selection for clinical use or if alternative post-thaw metrics can identify potent cryopreserved CBUs regardless of age.

Objectives
Our goal was to determine whether long-term (27-year) cryopreserved CBUs retain viable and functional hematopoietic stem (HSCs) and progenitor cells (HPCs). We further sought to leverage differences in HSC/HPC function (measured by in vivo engraftment) to demonstrate the utility of using omics approaches to identify candidate genes for use as molecular potency markers.

Methods
We performed comprehensive ex vivo, in vivo, and molecular analyses on the numbers, viability, and function of three 27-year cryopreserved CBUs using 3-year cryopreserved and fresh CBUs for comparison. Assays included viability staining, immunophenotyping by flow cytometry, primary and secondary colony forming unit (CFU) assays, ex vivo expansion of immunophenotypic HSCs/HPCs/CFUs, limiting dilution transplantations into immune-deficient mice, secondary transplantations, and RNA-sequencing of sorted HSCs and multipotent progenitor cells.

Results
Compared to fresh and recently cryopreserved CBU controls, long-term cryopreserved CBUs yield statistically similar numbers of viable immunophenotypic HSCs, multipotent HPCs, and committed myeloid and lymphoid HPCs. They retain highly functional cells, demonstrating similar primary and secondary CFU numbers and expansion capacity compared to controls, as well as robust engraftment, SCID repopulating cell frequency, and secondary engraftment capacity in mouse models of transplantation. Transcriptomic modelling revealed 18 genes, including MALT1 and MAP2K1, and several gene programs, including lineage determination programs and oxidative stress responses, that are strongly enriched in high engrafting HSCs/HPCs.

Discussion
CBUs cryopreserved for up to 27 years retain highly functional HSCs/HPCs. Thus, duration of cryopreservation alone is not an ideal exclusionary criteria for selection of CBUs. Preserving older CBUs may help to maintain a large and diverse pool of donors for clinical selection. Further, transcriptomics can identify candidate genes associated with engraftment for elucidation of possible CBU potency markers regardless of the duration of cryopreservation.
Abstract 19 CD34+ Cell Isolation from Cord Blood: A Novel Option for Faster, More Consistent Outcomes
Authors: Fedenko Shannon , Sherouse Hallie , Messer Jonathan , Dailey Jordan , Namin Shabnam 
Published: September 2023

Abstract

Introduction
Immunomagnetic isolation of cells has been long established but still suffers from drawbacks when used for hemopoietic stem cells (HSCs) in cord blood. [Kekarainen et al., 2006] Limitations with HSC isolation from cord blood include steep learning curves, time consuming manual labor, and inconsistent outcomes. [de Wynter et al., 1999; Perdomo-Arciniegas and Vernot, 2011] FerroBioTM has developed a semi-automated system for CD34+ cell isolation from unmodified cord blood (Fig 1A) as a means to provide fast, effective, and consistent isolations.

Objectives
The purpose of this work is to explore process improvements for the FerroBioTM system. Additionally, this work aims to characterize the resulting cell isolates.

Methods
The cell isolation protocol was evaluated by flow cytometry for cell counts, viability, and purity (total n=195). Protocol modification included incubation time at various steps, magnetic bead dosing, temperatures, and volumes. The ‘percent of cells captured’ was calculated as the difference between starting CD34 and non-captured CD34 cells. Cryopreservation tolerance was evaluated by freeze-thawing cells in a dimethyl sulfoxide-based media and measuring viability via hemocytometry (n=3). Sterility testing on cell isolates was performed via BacT/ALERT iNST & iAST (n=2).

Results
Incubation time did not have a significant effect on the efficiency of bead-cell binding (Fig 1B). As the FerroBioTM protocol progressed, final cell purity and viability increased and became more consistent (Fig 1C, D). Additionally, over the same phases of process development, final cell recovery increased 4-fold, from 6.5%±5.9% to 28.1%±9.7%. Post-cryopreservation viability was 78.8%±3.3%. Sterility tests were negative for anaerobic and aerobic bacteria.

Discussion
By establishing that bead-cell incubation duration did not significantly influence outcomes, the incubation time was considerably reduced, bringing the total processing time to ~3hrs. That said, if an overnight incubation is preferable for an operator’s workflow, the data suggests the process could be flexible to meet such needs. Iterations of the process have also resulted in significant improvements to final cell recovery while maintaining high purity and viability. Additional work is being done to further improve recovery. The initial investigation of sterility and cryopreservation was encouraging, and assays for cell functionality are underway.

Figure 1. (A) The FerroBioTM hardware, shown with a cartridge in which cell isolation occurs. (B) The proportion of cells that successfully bound magnetic beads as a function of bead-cell incubation time. Final cell (C) purity and (D) viability, shown at different phases of chronological process development. Statistics: GraphPad Prism 9, 1-way ANOVA followed by a Tukey’s HSD. * p &lt; 0.05, **** p &lt; 0.0001. Each data point corresponds to one CBU.
Abstract 21 Machine Learning Approach for Automatic Enumeration of Cord Blood Stem Cells by Flow Cytometry
Authors: Trépanier Patrick , Simard Carl , Fournier Diane 
Published: September 2023

Abstract

Introduction
Stem cell laboratories measure the number of viable CD34+ and CD45+ cells in their products by flow cytometry following a standard protocol (ISHAGE). Although the ISHAGE protocol is well documented, its correct application can be challenging. Automated gating algorithms have been created to address this issue, but they have limitations and can only be used in certain conditions. Recent developments in artificial intelligence (AI) and machine learning (ML) have made these approaches more accessible and practical to use. For flow cytometry data, the Cytobank platform now offers the Automatic Gating Algorithm (AGA), an AI-ML-based feature allowing users to easily implement their own gating strategies.

Objectives
The performance of the AGA based on the ISHAGE protocol gating was evaluated using cord blood post-thaw flow cytometry data.

Methods
In this study, the AGA was trained using 29 flow cytometry cord blood data files analyzed according to the ISHAGE gating strategy. Using the model, an inference analysis was conducted on two series of 12 data samples acquired from two independent operators. The enumeration of viable CD34+ cells was manually performed and compared to the AI analyses.

Results
The mean differences and standard deviation in vCD34+ counts between the manual and the automatic gating are 6.0% ± 2.7 for Operator #1 and 7.7% ± 2.1 for Operator #2. The correlation coefficients between vCD34+ results are 0.9981 for Operator #1 vs AI, and 0.9699 for Operator #2 vs AI. These results show that the AI inference provides results comparable to human manual gating, and are within the accepted difference of 10% between duplicates as defined by ISHAGE convention.

Discussion
This study provides a testing ground for using AI-ML-based automatic gating and supports its use in stem cell laboratories with acceptable performance and accuracy. The application of AI and ML for vCD34+ enumeration can potentially lead to the development of more widely applicable automatic gating algorithms. This could improve standardization by providing a common tool for analyzing flow cytometry data.
Abstract 22 Anomalous HLA-A Typing Found in Patient Using PacBio Sequencing Technology
Authors: Peavy Lydia , Norvell Brian , Liu Haipeng , Steege Eline , Williams Jon 
Published: September 2023

Abstract

Introduction
Labcorp’s DNA Identification division offers HLA typing at various levels of resolution using commercially available kits as well as lab developed assays. A patient sample was received by the lab requiring HLA typing for a disease association screen, and was found to have anomalous HLA-A results.

Objectives
To investigate a patient typing with results initially showing multiple variants to any known reference sequence.

Methods
This sample was sequenced using a lab developed whole gene assay that utilizes Pacific Biosciences’s® (PacBio) SMRT® NGS sequencing technology on a Sequel® I with LAA2 contig generation. Due to ambiguous results, the sample was repeated for confirmation using the same test, but a more sensitive data pipeline was used. Subreads coming off of the sequencer were converted to high fidelity or Closed Circular Consensus (CCS) reads using the PBAA tool from PacBio®. The sample was also processed with the GenDx NGSgo®-MX11-3 HLA typing kit with Illumina® sequencing, and the results were sent to GenDx for analysis.

Results
Initial testing yielded a high resolution fourth field result for HLA Class I, though the result remained ambiguous. Repeat sequencing resulted three HLA-A alleles with a similar number of CCS reads. The sample was typed as A*01:01:01:01, A*02:01:01:01, and A*02:New which contained a large exonic deletion compared to the A*02:01:01:01 reference. GenDX output confirmed previous findings, indicating a clear first allele of A*01:01:01:01, and reads for the second allele split between A*02:01:01:01 and A*02:New.

Discussion
Using Pacbio® sequencing technology with CCS analysis, and confirmation with GenDx technology, it was determined that this individual possesses 3 HLA-A alleles. When aligned with 02:01:01:01, both Pacbio® and GenDx assays determined the A*02:New allele to have a 34bp deletion in exon 2 (position 196-229). As a result of the frame shift caused by this deletion, a premature stop codon was found 43bp downstream from the anomaly, potentially rendering this allele null. Possible explanations for the presence of three HLA-A alleles in one patient include partial allele loss during an autoimmune event, a mutation within a chromosomal duplication of the region, or the patient has undergone a hematopoietic stem cell transplant.