A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers.

Urine is a rich source of nucleic acid biomarkers including cell-free DNA (cfDNA) and RNA for monitoring the health of kidney allografts. In this study, we aimed to evaluate whether urine filtration can serve as an alternative to the commonly used method of centrifugation to collect urinary fluid and cell pellets for isolating cfDNA and cellular messenger RNA (mRNA). We collected urine specimens from kidney allograft recipients and obtained the urine supernatant and cell pellet from each specimen using both filtration and centrifugation for paired analyses. We performed DNA sequencing to characterize the origin and properties of cfDNA, as well as quantitative PCR of mRNAs extracted from cell fractions. Our results showed that the biophysical properties of cfDNA, the microbial DNA content, and the tissues of origin of cfDNA were comparable between samples processed using filtration and centrifugation method. Similarly, mRNA quality and quantity obtained using both methods met our criteria for downstream application and the Ct values for each mRNA were comparable between the two techniques.The Ct values demonstrated a high degree of correlation. These findings suggest that urine filtration is a viable alternative to urine centrifugation for isolation of nucleic acid biomarkers from urine specimens.

Self-perceived upper extremity motor function predicts health-related quality of life in chronic stroke survivors.

PURPOSE: To examine whether the Upper Extremity Functional Index (UEFI) score independently contributes to the Stroke Impact Scale (SIS) score and quantified its relative contribution to SIS scores in chronic stroke survivors. MATERIALS AND METHODS: A cross-sectional study in a university-based rehabilitation centre with people with chronic stroke (N = 95) aged ≥ 50 years. The outcome measures included paretic hand grip strength, Fugl-Meyer Upper Extremity Assessment (FMA-UE), Wolf Motor Function Test (WMFT), UEFI, and SIS. RESULTS: Correlation analysis revealed that paretic hand grip strength, FMA-UE, UEFI, and WMFT scores exhibited a significant moderate positive correlation with SIS scores (r = 0.544-0.687, p < 0.001). The results of a regression model indicated that after adjustment for demographic factors and stroke-related impairments, the UEFI scores remained independently associated with SIS scores, accounting for 18.8% of the variance. The entire model explained 60.3% of the variance in SIS scores. CONCLUSIONS: Self-perceived UE motor function is a crucial component to be included in rehabilitation programmes aimed at enhancing quality of life and participation among chronic stroke survivors.

Observation-based outcome measures, e.g., Fugl­Meyer Assessment for Upper Extremity (FMA-UE), Wolf Motor Function Test (WMFT) could not predict the health-related quality of life (Stroke Impact scale (SIS)) in chronic stroke survivors in our study, which was contradictory with current studies.A self-perceived outcome measure to evaluate upper extremity function (Upper Extremity Functional Index (UEFI)) could independently predict the health-related quality of life (SIS), accounting for 18.8% of the variance.Our study demonstrated that self-perceived UE motor function would be an important component to optimize the rehabilitation programmes aimed at enhancing quality of life and social participation among chronic stroke survivors.

Surgical Management of Pediatric Obstructive Sleep Apnea Beyond T&A - Tongue Base and Larynx.

Pediatric patients with persistent obstructive sleep apnea (OSA) after adenotonsillectomy often have additional sites of upper airway obstruction such as the tongue base or larynx. Sleep endoscopy and cross-sectional, dynamic imaging can be used to direct the surgical management of persistent OSA. The tongue base is one of the most common sites of obstruction in children with persistent OSA, especially for patients with Trisomy 21. Lingual tonsillectomy, tongue suspension, and/or posterior midline glossectomy may be used to address lingual tonsil hypertrophy and tongue base obstruction. Epiglottopexy and/or supraglottoplasty may be used to address laryngomalacia and epiglottic prolapse resulting in OSA. Evidence shows that surgery can lead to significant improvement in postoperative polysomnographic outcomes. Important considerations following surgery of the tongue base and larynx include bleeding, edema, oropharyngeal stenosis, and dysphagia.

Surgical Management of Pediatric Obstructive Sleep Apnea Beyond Tonsillectomy & Adenoidectomy: Tongue Base and Larynx.

Pediatric patients with persistent obstructive sleep apnea (OSA) after adenotonsillectomy often have additional sites of upper airway obstruction such as the tongue base or larynx. Sleep endoscopy and cross-sectional, dynamic imaging can be used to direct surgical management of persistent OSA. The tongue base is one of the most common sites of obstruction in children with persistent OSA, especially for patients with Trisomy 21. Lingual tonsillectomy, tongue suspension, and/or posterior midline glossectomy may be used to address lingual tonsil hypertrophy and tongue base obstruction. Epiglottopexy and/or supraglottoplasty may be used to address laryngomalacia and epiglottic prolapse resulting in OSA.

Effects of mirror therapy with electrical stimulation for upper limb recovery in people with stroke: a systematic review and meta-analysis.

PURPOSE: To provide updated evidence about the effects of MT with ES for recovering upper extremities motor function in people with stroke. METHODS: Systematic review and meta-analysis were completed. Methodological quality was assessed using the version 2 of the Cochrane risk-of-bias tool. The GRADE approach was employed to assess the certainty of evidence. RESULTS: A total of 16 trials with 773 participants were included in this review. The results demonstrated that MT with ES was more effective than sham (standardized mean difference [SMD], 1.89 [1.52-2.26]) and ES alone (SMD, 0.42 [0.11-0.73]) with low quality of evidence, or MT alone (SMD, 0.47[0.04-0.89]) with low quality of evidence for improving upper extremity motor control assessed using Fugl-Meyer Assessment. MT with ES had significant improvement of (MD, 6.47 [1.92-11.01]) the upper extremity gross gripping function assessed using the Action Research Arm Test compared with MT alone with low quality of evidence. MT combined with ES was more effective than sham group (SMD, 1.17 [0.42-1.93) for improving the ability to perform activities of daily living with low quality of evidence assessed using Motor Activity Log. CONCLUSION: MT with ES may be effective in improving upper limb motor recovery in people with stroke.

Combining Mirror Therapy (MT) and Electrical Stimulation (ES) modality could improve upper limb motor control, gross gripping function, and performance in ADLs based on ICF for people with stroke.Those individuals with subacute stroke are recommended as the optimal target group for the combined MT and ES.

RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell-mediated Rejection.

BACKGROUND: Delineation of T-cell genes, gene sets, pathways, and T-cell subtypes associated with acute T cell-mediated rejection (TCMR) may improve its management. METHODS: We performed bulk RNA-sequencing of 34 kidney allograft biopsies (16 Banff TCMR and 18 no rejection [NR] biopsies) from 34 adult recipients of human kidneys. Computational analysis was performed to determine the differential intragraft expression of T-cell genes at the level of single-gene, gene set, and pathways. RESULTS: T-cell signaling pathway gene sets for plenary T-cell activation were overrepresented in TCMR biopsies compared with NR biopsies. Heightened expression of T-cell signaling genes was validated using external TCMR biopsies. Pro- and anti-inflammatory immune gene sets were enriched, and metabolism gene sets were depleted in TCMR biopsies compared with NR biopsies. Gene signatures of regulatory T cells, Th1 cells, Th2 cells, Th17 cells, T follicular helper cells, CD4 tissue-resident memory T cells, and CD8 tissue-resident memory T cells were enriched in TCMR biopsies compared with NR biopsies. T-cell exhaustion and anergy were also molecular attributes of TCMR. Gene sets associated with antigen processing and presentation, and leukocyte transendothelial migration were overexpressed in TCMR biopsies compared with NR biopsies. Cellular deconvolution of graft infiltrating cells by gene expression patterns identified CD8 T cell to be the most abundant T-cell subtype infiltrating the allograft during TCMR. CONCLUSIONS: Our delineation of intragraft T-cell gene expression patterns, in addition to yielding new biological insights, may help prioritize T-cell genes and T-cell subtypes for therapeutic targeting.

Transcriptomic signatures of chronic active antibody-mediated rejection deciphered by RNA sequencing of human kidney allografts.

Natural killer (NK) cells mediate spontaneous cell-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity. This dual functionality could enable their participation in chronic active antibody-mediated rejection (CA-ABMR). Earlier microarray profiling studies have not subcategorized antibody-mediated rejection into CA-ABMR and active-ABMR, and the gene expression pattern of CA-ABMR has not been compared with that of T cell-mediated rejection (TCMR). To fill these gaps, we RNA sequenced human kidney allograft biopsies categorized as CA-ABMR, active-ABMR, TCMR, or No Rejection (NR). Among the 15,910 genes identified in the biopsies, 60, 114, and 231 genes were uniquely overexpressed in CA-ABMR, TCMR, and active-ABMR, respectively; compared to NR, 50 genes were shared between CA-ABMR and active-ABMR, and 164 genes between CA-ABMR and TCMR. The overexpressed genes were annotated to NK cells and T cells in CA-ABMR and TCMR, and to neutrophils and monocytes in active-ABMR. The NK cell cytotoxicity and allograft rejection pathways were enriched in CA-ABMR. Genes encoding perforin, granzymes, and death receptor were overexpressed in CA-ABMR versus active-ABMR but not compared to TCMR. NK cell cytotoxicity pathway gene set variation analysis score was higher in CA-ABMR compared to active-ABMR but not in TCMR. Principal component analysis of the deconvolved immune cellular transcriptomes separated CA-ABMR and TCMR from active-ABMR and NR. Immunohistochemistry of kidney allograft biopsies validated a higher proportion of CD56+ NK cells in CA-ABMR than in active-ABMR. Thus, CA-ABMR was exemplified by the overexpression of the NK cell cytotoxicity pathway gene set and, surprisingly, molecularly more like TCMR than active-ABMR.

Neurologic and Neuromuscular Sequelae of COVID-19.

It is known that there can be neurologic complications related to acute infection with SARS-CoV-2, the virus that causes COVID-19. Currently, there is a growing body of evidence that postacute sequelae of SARS-CoV-2 infection can manifest as neurologic sequelae as a result of direct neuroinvasion, autoimmunity, and possibly lead to chronic neurodegenerative processes. Certain complications can be associated with worse prognosis, lower functional outcome, and higher mortality. This article provides an overview of the known pathophysiology, symptoms presentation, complications and treatment approaches of the post-acute neurologic and neuromuscular sequelae of SARS-CoV-2 infection.

Evaluation of Immunocompetence and Biomarkers of Tolerance in Chimeric and Immunosuppression-free Kidney Allograft Recipients.

BACKGROUND: Thirty-seven patients have received a living-donor kidney transplant in a phase 2 study designed to induce tolerance with facilitated allogeneic hematopoietic stem cell transplant. The study protocol is based on tolerogenic CD8 + /T-cell receptor - facilitating cells (FCR001; also including hematopoietic stem cells and αß-T-cell receptor + T cells) and low-dose, nonmyeloablative conditioning. Persistent chimerism allowing full immunosuppression (IS) withdrawal was achieved in 26 patients (time off IS 36-123 mo). METHODS: We evaluated biomarkers of tolerance through urinary cell mRNA profiling and immunocompetence to respond to vaccination in these patients. We also assessed kidney function and metabolic parameters compared with standard-of-care patients on IS. RESULTS: Persistently chimeric patients retained chimerism after removal of IS and remained rejection free without donor HLA-specific antibody development. The presence of donor chimerism at >50% correlated with a signature of tolerance in urinary cell mRNA profiles, with a uniquely elevated increase in the ratio of cytotoxic T lymphocyte-associated protein 4 to granzyme B mRNA. Tolerance was associated with protection from recurrence of immune-mediated causes of kidney disease. Tolerant participants were safely vaccinated, developed protective immune responses, and did not lose chimerism after vaccination. When compared with kidney transplant recipients treated with standard IS, tolerant participants showed stable kidney function and reduced medication use for hypertension and hyperlipidemia. CONCLUSIONS: These results suggest that elimination of IS has distinct advantages in living-donor kidney allograft recipients.

A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients.

Rationale & Objective: The nasal passages harbor both commensal and pathogenic bacteria. In this study, we sought to characterize the anterior nasal microbiota in PD patients using 16S rRNA gene sequencing. Study Design: Cross-sectional. Setting & Participants: We recruited 32 PD patients, 37 kidney transplant (KTx) recipients, 22 living donor/healthy control (HC) participants and collected anterior nasal swabs at a single point in time. Predictors: We performed 16S rRNA gene sequencing of the V4-V5 hypervariable region to determine the nasal microbiota. Outcomes: Nasal microbiota profiles were determined at the genus level as well as the amplicon sequencing variant level. Analytical Approach: We compared nasal abundance of common genera among the 3 groups using Wilcoxon rank sum testing with Benjamini-Hochberg adjustment. DESeq2 was also utilized to compare the groups at the ASV levels. Results: In the entire cohort, the most abundant genera in the nasal microbiota included: Staphylococcus, Corynebacterium, Streptococcus , and Anaerococcus . Correlational analyses revealed a significant inverse relationship between the nasal abundance of Staphylococcus and that of Corynebacterium . PD patients have a higher nasal abundance of Streptococcus than KTx recipients and HC participants. PD patients have a more diverse representation of Staphylococcus and Streptococcus than KTx recipients and HC participants. PD patients who concurrently have or who developed future Staphylococcus peritonitis had a numerically higher nasal abundance of Staphylococcus than PD patients who did not develop Staphylococcus peritonitis. Limitations: 16S RNA gene sequencing provides taxonomic information to the genus level. Conclusions: We find a distinct nasal microbiota signature in PD patients compared to KTx recipients and HC participants. Given the potential relationship between the nasal pathogenic bacteria and infectious complications, further studies are needed to define the nasal microbiota associated with these infectious complications and to conduct studies on the manipulation of the nasal microbiota to prevent such complications.

Pulmonary function in patients with transfusion-dependent thalassemia and its associations with iron overload.

In patients with transfusion-dependent thalassemia (TDT), pulmonary function impairment has been reported but data are conflicting. Moreover, it remains unclear whether pulmonary dysfunction is associated with iron overload. This study aimed to evaluate the pulmonary function in patients with TDT and to investigate the associations between pulmonary dysfunction and iron overload. It was a retrospective observational study. 101 patients with TDT were recruited for lung function tests. The most recent ferritin levels (pmol/L) and the magnetic resonance imaging (MRI) measurements of the myocardial and liver iron status, as measured by heart and liver T2* relaxation time (millisecond, ms) respectively, were retrieved from the computerized medical records. Only data within 12 months from the lung function measurement were included in the analysis. The serum ferritin, and the cardiac and liver T2* relaxation time were the surrogate indexes of body iron content. The threshold of abnormality in lung function was defined as under 80% of the predicted value. 101 subjects were recruited with a mean age of 25.1 years (standard deviation (SD) 7.9 years). Thirty-eight (38%) and five (5%) demonstrated restrictive and obstructive lung function deficits, respectively. A weak correlation of FVC %Predicted and TLC %Predicted with MRI myocardial T2* relaxation time (rho = 0.32, p = 0.03 and rho = 0.33, p = 0.03 respectively) was observed. By logistic regression, MRI cardiac T2* relaxation time was negatively associated with restrictive lung function deficit (B - 0.06; SE 0.03; Odds ratio 0.94; 95% confidence interval (CI) 0.89-0.99; p = 0.023) after adjusting for age, sex and body mass index. Restrictive pulmonary function deficit was commonly observed in patients with TDT, and the severity potentially correlates with myocardial iron content. Monitoring of lung function in this group of patients, particularly for those with iron overload, is important.

Selective modulation of gene expression in activated normal human peripheral blood mononuclear cells by store-operated calcium entry blocker BTP2.

Calcium is a critical signaling molecule in many cell types including immune cells. The calcium-release activated calcium channels (CRAC) responsible for store-operated calcium entry (SOCE) in immune cells are gated by STIM family members functioning as sensors of Ca2+ store content in the endoplasmic reticulum. We investigated the effect of SOCE blocker BTP2 on human peripheral blood mononuclear cells (PBMC) stimulated with the mitogen phytohemagglutinin (PHA). We performed RNA sequencing (RNA-seq) to query gene expression at the whole transcriptome level and identified genes differentially expressed between PBMC activated with PHA and PBMC activated with PHA in the presence of BTP2. Among the differentially expressed genes, we prioritized genes encoding immunoregulatory proteins for validation using preamplification enhanced real time quantitative PCR assays. We performed multiparameter flow cytometry and validated by single cell analysis that BTP2 inhibits cell surface expression CD25 at the protein level. BTP2 reduced significantly PHA-induced increase in the abundance of mRNAs encoding proinflammatory proteins. Surprisingly, BTP2 did not reduce significantly PHA-induced increase in the abundance of mRNAs encoding anti-inflammatory proteins. Collectively, the molecular signature elicited by BTP2 in activated normal human PBMC appears to be tipped towards tolerance and away from inflammation.

Neurologic Complications of Patients With COVID-19 Requiring Extracorporeal Membrane Oxygenation: A Systematic Review and Meta-Analysis.

In COVID-19 patients requiring extracorporeal membrane oxygenation (ECMO), our primary objective was to determine the frequency of intracranial hemorrhage (ICH). Secondary objectives were to estimate the frequency of ischemic stroke, to explore association between higher anticoagulation targets and ICH, and to estimate the association between neurologic complications and in-hospital mortality. DATA SOURCES: We searched MEDLINE, Embase, PsycINFO, Cochrane, and MedRxiv databases from inception to March 15, 2022. STUDY SELECTION: We identified studies that described acute neurological complications in adult patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requiring ECMO. DATA EXTRACTION: Two authors independently performed study selection and data extraction. Studies with 95% or more of its patients on venovenous or venoarterial ECMO were pooled for meta-analysis, which was calculated using a random-effects model. DATA SYNTHESIS: Fifty-four studies (n = 3,347) were included in the systematic review. Venovenous ECMO was used in 97% of patients. Meta-analysis of ICH and ischemic stroke on venovenous ECMO included 18 and 11 studies, respectively. The frequency of ICH was 11% (95% CI, 8-15%), with intraparenchymal hemorrhage being the most common subtype (73%), while the frequency of ischemic strokes was 2% (95% CI, 1-3%). Higher anticoagulation targets were not associated with increased frequency of ICH (p = 0.06). In-hospital mortality was 37% (95% CI, 34-40%) and neurologic causes ranked as the third most common cause of death. The risk ratio of mortality in COVID-19 patients with neurologic complications on venovenous ECMO compared with patients without neurologic complications was 2.24 (95% CI, 1.46-3.46). There were insufficient studies for meta-analysis of COVID-19 patients on venoarterial ECMO. CONCLUSIONS: COVID-19 patients requiring venovenous ECMO have a high frequency of ICH, and the development of neurologic complications more than doubled the risk of death. Healthcare providers should be aware of these increased risks and maintain a high index of suspicion for ICH.

Sleep Endoscopy and Cine Magnetic Resonance Imaging Evaluation of Children With Persistent Obstructive Sleep Apnea.

OBJECTIVE: To compare findings of same-day cine magnetic resonance imaging (MRI) and drug-induced sleep endoscopy (DISE) and examine how each technique uniquely contributes to the evaluation of persistent obstructive sleep apnea following adenotonsillectomy. STUDY DESIGN: Retrospective cohort study. SETTING: Quaternary care center. METHODS: Chart review was performed for consecutive patients who underwent same-day cine MRI and DISE between 2015 and 2020. Descriptive statistics are reported, and Cohen kappa coefficients were calculated to evaluate the agreement between cine MRI and DISE for obstruction at the adenoids, lingual tonsils, and tongue base. RESULTS: There were 137 patients, the mean age was 10.4 years (95% CI, 3.2-16.7), and 62.8% were male. The most common sites of obstruction on DISE were the tongue base (86.9%), velum (78.7%), epiglottis (74.5%), inferior turbinate (68.6%), and lingual tonsil (61.3%). The most common sites of obstruction on cine MRI were the hypopharynx (56.3%), tongue base (44.8%), lingual tonsil (38.0%), and macroglossia (37.6%). There was moderate agreement for adenoid hypertrophy (κ = 0.53) and poor agreement for lingual tonsil hypertrophy (κ = 0.15) and tongue base obstruction (κ = 0.09). DISE identified more instances of multilevel obstruction when compared with cine MRI (94.9% vs 48.2%). CONCLUSION: DISE offered a better examination of nasal and supraglottic obstruction and is sensitive to partial vs complete collapse, while cine MRI offered better soft tissue resolution for lymphoid tissue hypertrophy and provided a global view of primary and secondary airway obstruction. Cine MRI and DISE are complementary modalities in the evaluation of children with persistent obstructive sleep apnea.

Urinary cell mRNA profiling of kidney allograft recipients: Development of a portable protocol for noninvasive diagnosis of T cell mediated rejection and BK virus nephropathy.

BACKGROUND: We developed urinary cell mRNA profiling for noninvasive diagnosis of acute T cell mediated rejection (TCMR) and BK virus nephropathy (BKVN), two significant post-transplant complications. Our profiling protocol for the multicenter Clinical Trial of Transplantation-04 (CTOT-04) study consisted of centrifugation of urine to prepare cell pellets, washes, addition of an RNA preservative, storage at 800C and shipment in cold containers to our Gene Expression Monitoring (GEM) Core for RNA isolation and quantification of mRNA in RT-qPCR assays. To simplify profiling, we developed a filter-based protocol (ZFBP) that eliminated the need for centrifugation, RNA preservative, storage at 800C, and shipment in cold containers for mRNA profiling. Furthermore, we trained kidney allograft recipients to perform the filtration of urine at home using the filter and post the urinary cell lysate containing the RNA at ambient temperature to our GEM Core for profiling. Here, we report our refinement of ZFBP and investigation of its diagnostic performance characteristics. METHODS: Total RNA was isolated from kidney allograft biopsy-matched urines using a filter-based protocol complemented by a silica-membrane-based cartridge for mRNA enrichment, the Weill Cornell Hybrid Protocol (WCHP). Absolute copy numbers of CD3ε mRNA, CXCL10 mRNA, and 18S rRNA, components of the CTOT-04 three-gene TCMR diagnostic signature, and urinary cell BKV VP 1 mRNA copy number were measured using RT-qPCR assays. Mann-Whitney test, Fischer exact test, and receiver operating characteristic (ROC) curve analysis were used for data analyses. RESULTS: Urinary cell three-gene TCMR diagnostic signature scores in urines processed using the WCHP discriminated kidney allograft recipients with TCMR (12 TCMR biopsies from 11 patients) from those without TCMR or BKVN (29 No TCMR/No BKVN biopsies from 29 patients). The median (25th and 75th percentiles) score of the CTOT-04 three-gene TCMR diagnostic signature was -0.448 (-1.664, 0.204) in the TCMR group and - 2.542 (-3.267, -1.365) in the No TCMR/ No BKVN group (P = 0.0005, Mann-Whitney test). ROC curve analysis discriminated the TCMR group from the No TCMR/ No BKVN group; the area under the ROC curve (AUROC) was 0.84 (95% Confidence Intervals [CI], 0.69 to 0.98) (P < 0.001), and TCMR was diagnosed with a sensitivity of 67% (95% CI, 35 to 89) at a specificity of 86% (95% CI, 67 to 95) using the CTOT-04 validated cutpoint of -1.213 (P = 0.0016, Fisher exact test). BKV VP1 mRNA copy number in urines processed using the WCHP discriminated patients with BKVN (n = 7) from patients without TCMR or BKVN (n = 29) and the AUROC was 1.0 (95% CI, 1.00 to 1.00) (P < 0.0001) and BKVN was diagnosed with a sensitivity of 86% (95% CI, 42 to 99) at a specificity of 100% (95% CI, 85 to 100) with the previously validated cutpoint of 6.5 × 108 BKV-VP1 mRNA copies per microgram of RNA (P < 0.0001, Fisher exact test). CONCLUSION: Urine processed using the WCHP predicted TCMR and BKVN in kidney allograft recipients. WCHP represents not only a significant advance toward the portability of urinary cell mRNA profiling but also improved patient management by minimizing their visits for urine collection.