Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases.

It's challenging work to identify disease-causing genes from the next-generation sequencing (NGS) data of patients with Mendelian disorders. To improve this situation, researchers have developed many phenotype-driven gene prioritization methods using a patient's genotype and phenotype information, or phenotype information only as input to rank the candidate's pathogenic genes. Evaluations of these ranking methods provide practitioners with convenience for choosing an appropriate tool for their workflows, but retrospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate. In this research, the performance of ten recognized causal-gene prioritization methods was benchmarked using 305 cases from the Deciphering Developmental Disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results show that methods using Human Phenotype Ontology (HPO) terms and Variant Call Format (VCF) files as input achieved better overall performance than those using phenotypic data alone. Besides, LIRICAL and AMELIE, two of the best methods in our benchmark experiments, complement each other in cases with the causal genes ranked highly, suggesting a possible integrative approach to further enhance the diagnostic efficiency. Our benchmarking provides valuable reference information to the computer-assisted rapid diagnosis in Mendelian diseases and sheds some light on the potential direction of future improvement on disease-causing gene prioritization methods.

What Are the Functional, Radiographic, and Survivorship Outcomes of a Modified Cup-Cage Technique for Pelvic Discontinuity?

BACKGROUND: Pelvic discontinuity (PD) presents a complex challenge in revision hip arthroplasty. The traditional cup-cage construct, which involves a screw-secured porous metal cup and an overlying antiprotrusio cage, has shown promising mid- to long-term results. However, there is limited information on the outcomes of modifications to the original technique. Our study aims to evaluate a modified technique in which the cup position is determined by the placement of the overlying cage, allowing for adjustments to achieve optimal orientation. QUESTIONS/PURPOSES: Among patients treated for PD with a cup-cage construct in which the cup position was dictated by the position of the cage: (1) What are Harris hip scores achieved at a minimum of 2 years of follow-up? (2) What is the Kaplan-Meier survivorship free from aseptic loosening or component migration? (3) What is the Kaplan-Meier survivorship free from revision for any reason? (4) What surgical complications are associated with the procedure? METHODS: Between October 2013 and January 2022, we performed 805 acetabular revisions. Among these, 33 patients with PD confirmed intraoperatively were considered potentially eligible for a cup-cage construct; no other method of surgical management was used. We performed 64% (21 of 33) of these procedures from October 2013 to January 2018, with 6% (2 of 33) of patients lost to follow-up before the minimum study follow-up of 2 years; these 19 patients were monitored over a period ranging from 70 to 115 months. A further 12 patients underwent this procedure from January 2018 to January 2022, with one lost to follow-up before the minimum study follow-up of 2 years; the other patients met the minimum 2-year follow-up requirement. The remaining 30 patients with data analyzed here (10 men, 20 women) had a mean ± SD age of 61 ± 12 years and a median BMI of 29 kg/m2 (range 20 to 33 kg/m2) at the time of revision surgery. Twenty-one patients underwent revision due to aseptic loosening, and nine due to periprosthetic joint infection (PJI). The causes of PD in our patients were as follows: cup aseptic loosening without significant osteolysis in 20% (6 of 30), where the loose cup caused erosion of the host bone, leading to PD; PJI in 30% (9 of 30); intraoperative iatrogenic PD in 3% (1 of 30); and osteolysis in 47% (14 of 30), which also resulted in aseptic loosening. The median follow-up time was 79 months (range 25 to 115 months). The Harris hip score was used to evaluate clinical outcomes, with preoperative values compared with the most recent follow-up. Radiographs were reviewed by two experienced surgeons at each follow-up visit to assess component loosening (defined as migration > 5 mm or the presence of circumferential radiolucent lines) or clear migration. PD was considered healed if bridging callus or trabecular bone was visible across the site of the discontinuity. Complications were assessed through a comprehensive review of electronic medical records. Kaplan-Meier analysis was used to estimate implant survivorship and radiographic loosening, with aseptic loosening or component migration as the endpoint, as well as survivorship free from any reoperation. RESULTS: The Harris hip score improved from a median of 39 (range 30 to 66) preoperatively to a median of 76 (range 30 to 90) postoperatively (median difference 33 [range 2 to 48]; p < 0.01). Within the limitations of two-dimensional (2D) radiographic imaging, successful bone graft integration and the healing of PD were noted in 83% (25 of 30) of patients. Kaplan-Meier survivorship free from radiographic signs of aseptic loosening or component migration was 100% (95% CI 100% to 100%) at 115 months. When any revision related to the acetabular component was considered the endpoint, survivorship free from acetabular component revision at 115 months after revision surgery was 100% (95% CI 100% to 100%). When the need for any reoperation was considered the endpoint, survivorship free from needing reoperation at 115 months after revision surgery was 85% for all patients (95% CI 73% to 100%). When including only patients with a follow-up time of > 4 years (20 of 30), survivorship free from needing reoperation at 115 months after revision surgery was 90% (95% CI 78% to 100%). Postoperative complications during the follow-up period included one early dislocation on the fifth day after surgery, treated with closed reduction and 6 weeks of abduction bracing. One femoral stem loosening occurred at 56 months postoperatively, although the acetabular component remained securely fixed; this patient declined revision surgery. One patient experienced a dislocation 5 months after surgery but refused treatment and opted for prolonged bed rest. Additionally, one patient underwent a debridement, antibiotics, and implant retention procedure 1 week after the revision surgery and subsequently showed no signs of infection at the latest follow-up, 38 months postoperatively. CONCLUSION: Our study highlights the effectiveness of a modified cup-cage technique in complex hip revisions, showing promising results in terms of construct survivorship and low complication rates. Surgeons could consider delaying screw fixation until after positioning the cage within the porous cup to allow for optimal adjustment and using metal augments for severe bone defects to achieve better alignment. Surgeon experience with the cup-cage technique is crucial for achieving optimal outcomes. Future studies should focus on long-term follow-up visits to assess the durability and effectiveness of these modifications and explore the comparative effectiveness versus other methods, such as custom triflange components and jumbo cups with distraction. LEVEL OF EVIDENCE: Level III, therapeutic study.

Efficacy and safety of postoperative single-dose anticoagulant treatment in preventing venous thromboembolism after revision hip arthroplasty: a retrospective cohort study.

PURPOSE: The purpose of the study is to determine the efficacy and safety of postoperative single-dose anticoagulant treatment in preventing venous thromboembolism (VTE) after revision THA, in comparison with a multiple-dose chemoprophylaxis protocol. METHODS: We retrospectively compared 295 patients undergoing revision THA who received multiple-dose chemoprophylaxis protocol (40 mg low-molecular-weight heparin once and oral rivaroxaban for 10 days) or single-dose chemoprophylaxis protocol (40 mg low-molecular-weight heparin once) for VTE. The patients in both groups performed active lower limb exercises. Each group was further stratified into subgroups based on the aetiology of revision. The incidence of VTE, wound complications within three months, hidden blood loss (HBL), transfusion rate, and surgical drainage duration were recorded. RESULTS: The incidence rates of VTE (P = 0.870) did not differ between the two prophylaxis protocols. However, significant differences were observed in wound complications within three months (P = 0.002), HBL (P = 0.015), transfusion rate (P = 0.028). Surgical drainage duration was also shorter in the single-dose chemoprophylaxis group (P = 0.0023). In the subgroup analysis, the use of single-dose chemoprophylaxis protocol cannot significantly reduce HBL and transfusion rate after septic revision THA. The use of multiple-dose chemoprophylaxis protocol (OR = 2.89, P = 0.002) and high BMI (OR = 1.09, P = 0.037) were independent risk factors of wound complications. CONCLUSIONS: Single-dose chemoprophylaxis protocol effectively and safely prevented VTE after revision THA compared with multiple-dose chemoprophylaxis protocol. The effect in reducing HBL and postoperative transfusion rate was limited in septic revision.

Deep insights into the viscosity of deep eutectic solvents by an XGBoost-based model plus SHapley Additive exPlanation.

Deep eutectic solvents (DESs) are emerging as novel green solvents for the processes of mass transport and heat transfer, in which the viscosity of DESs is important for their industrial applications. However, for DESs, the measurement of viscosity is time-consuming, and there are many factors influencing the viscosity, which impedes their wider application. This study aims to develop a data-driven model which could accurately and rapidly predict the viscosity of diverse DESs at different temperatures, and furthermore boost the design and screening of novel DESs. In this work, we collected 107 DESs with 994 experimental values of viscosity from published works. Given the significant effect of water on viscosity, the water content of each collected DES was labeled. The Morgan fingerprint was first employed as a feature to describe the chemical environment of DESs. And four machine learning algorithms were used to train models: support vector regression (SVR), random forest (RF), neural network (NN), and extreme gradient boosting (XGBoost), and XGBoost showed the best predictive performance. In combination with the powerful interpretation method SHapley Additive exPlanation (SHAP), we further revealed the positive or negative effect of features on viscosity. Overall, this work provides a machine learning model which could predict viscosity precisely and facilitate the design and application of DESs.

Mid-Term Outcomes of Cementless Total Hip Arthroplasty in Adult Patients with Childhood Hip Infection.

BACKGROUND Patients with hip joint infections in childhood often have many aftereffects of different degrees, regardless of the kind of treatment or natural course. Total hip arthroplasty is currently the most effective treatment for sequelae of childhood hip septic or tuberculous infection. This is a mid-term follow-up study of treatment results of patients who had undergone total hip arthroplasty (THA) with cementless prostheses. MATERIAL AND METHODS We retrospectively analyzed and followed 45 patients (45 hips) who underwent THA with cementless prostheses between 2010 and 2017. There were 45 patients, including 17 men and 28 women. The average age of the patients was 46 years (range, 18-67 years). All hip infections occurred in early childhood or adolescence, and the mean interval between initial infection and THA was 38.2 years (range, 15-60 years). The mean follow-up was 6.1 years (range, 2.7-9.5 years). RESULTS Two patients underwent revision surgery because of loosening of the prosthesis, and 1 patient underwent revision surgery because of a new infection with no relationship with childhood infection during the follow-up. The average Harris hip scores significantly increased from 43.1 to 86.4 (P<0.01), and the average visual analog scale significantly increased from 4.6 to 1.7 (P<0.01). The hip dysfunction and osteoarthritis outcome scores were also significantly changed (P<0.01) at the final follow-up. There were 2 cases of transient sciatic nerve palsy and intraoperative periprosthetic fractures in 3 cases. During follow-up, single revision was performed after 6 years of primary arthroplasty because of aseptic loosening in 2 cases and prosthesis infection in 1 case, which was not related to childhood pathogens. CONCLUSIONS THA for patients with sequelae of hip joint infection has a satisfactory effect that can effectively relieve joint pain and improve hip function. The recurrence rate of infection after either pyogenic infection or tuberculous is very low. The mid-term outcomes of THA in this setting were satisfactory, with high prosthesis survivorship and hip function scores.

Outcome of Irrigation and Debridement With Topical Antibiotics Delivery for the Management of Periprosthetic Joint Infection Occurring Within 3 Months Since the Primary Total Joint Arthroplasty.

BACKGROUND: Irrigation and debridement with modular component exchange is appealing for surgeons to treat early-stage periprosthetic joint infection (PJI). However, the indication, perioperative protocol, and success rate remain controversial. This study is the first one to present results of debridement, antibiotics, and implant retention (DAIR) with integrated MIT (modular component exchange, povidone-iodine and topical antibiotics delivery) protocol for treating PJI occurring within 3 months since the primary total joint arthroplasty. METHODS: We retrospectively analyzed patients who received DAIR with MIT protocol in our department between January 2011 and May 2018. Topical antibiotics were delivered in all cases. Topical antibiotics infusion was applied for those infected with multidrug-resistant bacteria, fungus, polymicrobial infection, and culture negative one. Failure was defined as additional surgical intervention for infection after DAIR; persistent sinus tract, drainage or excessive joint pain; need for suppressive antibiotics therapy due to the infection; infection relapse with the same pathogen; reinfection with different microorganism; and infection-related death. RESULTS: A total of 73 patients with a mean age of 63.30 ± 10.97 years were included in this study, including 43 men and 30 women. There are 41 knees and 32 hips. Thirty patients had sinus tract. With a mean follow-up of 63.79 ± 18.57 months, there were 9 failures in total with an overall success rate of 87.67%. The success rate was 88.57% and 86.84% for those receiving topical antibiotics infusion postoperatively and those without. CONCLUSIONS: DAIR with a standard MIT protocol is a viable and safe option for PJI occurring within 3 months since the primary total joint arthroplasty. LEVEL OF EVIDENCE: Level 4, therapeutic study.

Detection of structural variation using target captured next-generation sequencing data for genetic diagnostic testing.

PURPOSE: Structural variation (SV) is associated with inherited diseases. Next-generation sequencing (NGS) is an efficient method for SV detection because of its high-throughput, low cost, and base-pair resolution. However, due to lack of standard NGS protocols and a limited number of clinical samples with pathogenic SVs, comprehensive standards for SV detection, interpretation, and reporting are to be established. METHODS: We performed SV assessment on 60,000 clinical samples tested with hereditary cancer NGS panels spanning 48 genes. To evaluate NGS results, NGS and orthogonal methods were used separately in a blinded fashion for SV detection in all samples. RESULTS: A total of 1,037 SVs in coding sequence (CDS) or untranslated regions (UTRs) and 30,847 SVs in introns were detected and validated. Across all variant types, NGS shows 100% sensitivity and 99.9% specificity. Overall, 64% of CDS/UTR SVs were classified as pathogenic/likely pathogenic, and five deletions/duplications were reclassified as pathogenic using breakpoint information from NGS. CONCLUSION: The SVs presented here can be used as a valuable resource for clinical research and diagnostics. The data illustrate NGS as a powerful tool for SV detection. Application of NGS and confirmation technologies in genetic testing ensures delivering accurate and reliable results for diagnosis and patient care.

Correction: DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes.

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DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes.

PURPOSE: Gross duplications are ambiguous in terms of clinical interpretation due to the limitations of the detection methods that cannot infer their context, namely, whether they occur in tandem or are duplicated and inserted elsewhere in the genome. We investigated the proportion of gross duplications occurring in tandem in breast cancer predisposition genes with the intent of informing their classifications. METHODS: The DNA breakpoint assay (DBA) is a custom, paired-end, next-generation sequencing (NGS) method designed to capture and detect deep-intronic DNA breakpoints in gross duplications in BRCA1, BRCA2, ATM, CDH1, PALB2, and CHEK2. RESULTS: DBA allowed us to ascertain breakpoints for 44 unique gross duplications from 147 probands. We determined that the duplications occurred in tandem in 114 (78%) carriers from this cohort, while the remainder have unknown tandem status. Among the tandem gross duplications that were eligible for reclassification, 95% of them were upgraded to pathogenic. CONCLUSION: DBA is a novel, high-throughput, NGS-based method that informs the tandem status, and thereby the classification of, gross duplications. This method revealed that most gross duplications in the investigated genes occurred in tandem and resulted in a pathogenic classification, which helps to secure the necessary treatment options for their carriers.

The fate of immunocompromised patients in the treatment of chronic periprosthetic joint infection: a single-centre experience.

PURPOSE: Immunocompromised patients with periprosthetic joint infection (PJI) are rare and currently there are no reliable guidelines according to which these infections can be successfully managed. The purpose of this study was to report the clinical course of different strategies for treatment of PJI in frail patients. METHODS: A retrospective analysis between 2004 and 2015 included 29 immunocompromised patients (13 hips and 16 knees) with chronic PJI who underwent one-stage revision or debridement, antibiotics and implant retention (DAIR). Patients were stratified according to the Musculoskeletal Infection Society (MSIS) staging system and the clinical course included recurrence of infection and functional outcomes which were extracted from patients' charts. The average follow-up was 68 months (range, 26-149 months). RESULTS: Sixteen of the 29 patients had recurrent infections. At last follow-up, 13 patients were on chronic suppressive antibiotic therapy, three patients died but not one death was considered to be related to the infection. A recurrent infection was observed in 13 of the 24 medically compromised hosts (MSIS type B). Sixteen of the 24 patients underwent one-stage revision; another eight of them underwent DAIR. The infection recurred in three of the five patients (60%) with the worst host grades (MSIS type C). One-stage revision was performed in one of the five patients and the remaining four patients received DAIR. CONCLUSION: Our results show that we should compromise our expectation and intemperate treatment for such a population. The goals of PJI treatment in these patients should take into account their preferences and may pay more attention to the concept of disease control rather than cure, especially for patients with severe comorbidities (MSIS C). LEVEL OF EVIDENCE: Therapeutic Level IV.

Single-Stage Revision for Chronic Fungal Periprosthetic Joint Infection: An Average of 5 Years of Follow-Up.

BACKGROUND: Periprosthetic infections caused by fungal pathogens are a rare entity, and there exist no definite guidelines according to which these infections can be successfully managed. In these situations, we wondered whether patients could be treated successfully for their fungal infections with single-stage revision. METHODS: A retrospective analysis between January 2004 and October 2014 included 11 patients (4 hips and 7 knees) with chronic fungal periprosthetic joint infection who underwent single-stage revision, including aggressive soft-tissue debridement, thorough removal of infected components and cement, pouring powdered vancomycin into the medullary cavity and direct intra-articular injection of fungus-sensitive antibiotics, and a reasonable combination of antifungal agents and antibacterial medications. Recurrence of infection and clinical outcomes were evaluated. The average follow-up was 5 years (range, 2-10 years). RESULTS: There were 3 failures during the study period; 1 patient died during the perioperative period because of acute heart failure on the eighth postoperative day. Of the 11 patients, 7 patients had satisfactory outcomes and required no additional surgical or medical treatment for recurrence of infection. The mean postoperative Harris hip score and Hospital for Special Surgery knee score was 77 points (67-88 points; P < .05) and 78 points (73-84 points; P < .05), respectively, at the most recent assessment. CONCLUSION: Treatment of chronic fungal periprosthetic joint infection with single-stage revision can be fairly effective for achieving acceptable functional outcomes, which indicated that this may be a feasible alternative strategy in selected patients.

Retention of the well-fixed implant in the single-stage exchange for chronic infected total hip arthroplasty: an average of five years of follow-up.

PURPOSE: Removal of an infected prosthesis was considered the gold standard for eradication of infection. However, removal of well-fixed components can result in structural bone damage and compromised reconstruction. In these situations we questioned whether the infection after the total hip arthroplasty could be treated effectively and retain the well-fixed implant in a single-stage exchange. METHODS: A retrospective analysis which included 31 patients with chronic infected THA who underwent major partial single-stage revision, including routinely exchanged femoral head and liner components, aggressive soft tissue debridement, removal of the femoral stem or acetabular cup and retention of the well-fixed component, thorough exposed component brushing, and adequate surgical soaking. Powdered Vancomycin was poured into the surgical area and the infection control rate and clinical outcomes were evaluated. The failure to treat the infection was defined as a recurrence of infection in the same hip. The average follow-up was five years (2-15 years). RESULT: There were four (12.9 %) failures during the study period at an average of 15 months (9-21 months) after partial single-stage revision. Of the 31 patients, 27 (87.1 %) patients had a satisfactory outcome and required no additional surgical or medical treatment for recurrence of infection. Acetabular cups were revised in 22 patients and femoral stems in nine patients. The mean post-operative Harris hip score at the most recent assessment was 74.6 (68-82). CONCLUSIONS: Treatment of chronic infected THA with retention of the well-fixed implant in a single-stage exchange can be fairly effective in the treatment of infection and achieving acceptable functional outcomes, which indicated that this may be an attractive alternative in highly selected patients. LEVEL OF EVIDENCE: Level IV, therapeutic study.

Linking the genetic architecture of cytosine modifications with human complex traits.

Interindividual variation in cytosine modifications could contribute to heterogeneity in disease risks and other complex traits. We assessed the genetic architecture of cytosine modifications at 283,540 CpG sites in lymphoblastoid cell lines (LCLs) derived from independent samples of European and African descent. Our study suggests that cytosine modification variation was primarily controlled in local by single major modification quantitative trait locus (mQTL) and additional minor loci. Local genetic epistasis was detectable for a small proportion of CpG sites, which were enriched by more than 9-fold for CpG sites mapped to population-specific mQTL. Genetically dependent CpG sites whose modification levels negatively (repressive sites) or positively (facilitative sites) correlated with gene expression levels significantly co-localized with transcription factor binding, with the repressive sites predominantly associated with active promoters whereas the facilitative sites rarely at active promoters. Genetically independent repressive or facilitative sites preferentially modulated gene expression variation by influencing local chromatin accessibility, with the facilitative sites primarily antagonizing H3K27me3 and H3K9me3 deposition. In comparison with expression quantitative trait loci (eQTL), mQTL detected from LCLs were enriched in associations for a broader range of disease categories including chronic inflammatory, autoimmune and psychiatric disorders, suggesting that cytosine modification variation, while possesses a degree of cell linage specificity, is more stably inherited over development than gene expression variation. About 11% of unique single-nucleotide polymorphisms reported in the Genome-Wide Association Study Catalog were annotated, 78% as mQTL and 31% as eQTL in LCLs, which covered 37% of the investigated diseases/traits and provided insights to the biological mechanisms.

Midterm Outcome of Cementless Total Hip Arthroplasty in Crowe IV-Hartofilakidis Type III Developmental Dysplasia of the Hip.

BACKGROUND: Developmental dysplasia of the hip (DDH) is widespread in developing countries, and treating Crowe IV-Hartofilakidis Type III DDH in adults requires the use of a highly demanding technique. METHODS: We sought to determine the outcome of cementless total hip arthroplasty using Zweymüller components to treat Crowe IV-Hartofilakidis Type III DDH. Fifty-eight patients (71 hips) with a mean age of 35.8 years at time of index operation were included in our study. The average duration of follow-up was 70.5 months. The acetabular component was placed in the true acetabulum in all cases, and subtrochanteric shortening osteotomy was performed in 61 hips. RESULTS: With any component revision for any reason as the end point, Kaplan-Meier survivorship analysis at 98 months revealed a cumulative survival rate for implanted components of 91.40%. The mean Harris Hip Score improved from 35.6 preoperatively to 82.9 postoperatively. There were 20 cases of intraoperative fracture, 1 case of complete nerve palsy, and 7 cases of transient nerve palsy. Revision surgery was performed in 7 patients because of cup loosening in 1, severe polyethylene wear in 4, cup breakage in 1, and dislocation in 1. CONCLUSIONS: Midterm results for cementless total hip arthroplasty in patients with Crowe IV-Hartofilakidis Type III DDH was satisfactory; however, intraoperative fracture and polyethylene wear were major complications.

Cytochrome P450 2C epoxygenases mediate photochemical stress-induced death of photoreceptors.

Degenerative loss of photoreceptors occurs in inherited and age-related retinal degenerative diseases. A chemical screen facilitates development of new testing routes for neuroprotection and mechanistic investigation. Herein, we conducted a mouse-derived photoreceptor (661W cell)-based high throughput screen of the Food and Drug Administration-approved Prestwick drug library to identify putative cytoprotective compounds against light-induced, synthetic visual chromophore-precipitated cell death. Different classes of hit compounds were identified, some of which target known genes or pathways pathologically associated with retinitis pigmentosa. Sulfaphenazole (SFZ), a selective inhibitor of human cytochrome P450 (CYP) 2C9 isozyme, was identified as a novel and leading cytoprotective compound. Expression of CYP2C proteins was induced by light. Gene-targeted knockdown of CYP2C55, the homologous gene of CYP2C9, demonstrated viability rescue to light-induced cell death, whereas stable expression of functional CYP2C9-GFP fusion protein further exacerbated light-induced cell death. Mechanistically, SFZ inhibited light-induced necrosis and mitochondrial stress-initiated apoptosis. Light elicited calcium influx, which was mitigated by SFZ. Light provoked the release of arachidonic acid from membrane phospholipids and production of non-epoxyeicosatrienoic acid metabolites. Administration of SFZ further stimulated the production of non-epoxyeicosatrienoic acid metabolites, suggesting a metabolic shift of arachidonic acid under inhibition of the CYP2C pathway. Together, our findings indicate that CYP2C genes play a direct causative role in photochemical stress-induced death of photoreceptors and suggest that the CYP monooxygenase system is a risk factor for retinal photodamage, especially in individuals with Stargardt disease and age-related macular degeneration that deposit condensation products of retinoids.

Culture-negative periprosthetic joint infections: Do we have an issue?

Culture-negative periprosthetic joint infection (PJI) poses a significant challenge in clinical settings. The lack of information on causative organism(s) leads to uncertainties regarding the choice of antimicrobial treatment, which can potentially adversely influence the outcome. Recent advances in molecular-based diagnostic methods have the potential to address the difficulties associated with culture-negative PJIs. These technologies offer a solution to the existing clinical dilemma by providing identification of pathogens and guiding appropriate antimicrobial treatment. In this narrative review, we provide information regarding: 1) incidence and risk factors for culture-negative PJI; 2) the optimal antimicrobial therapy and duration of treatment for culture-negative PJI; 3) outcome comparison between culture-positive and culture-negative PJI; and 4) utilization of novel molecular diagnostic methods in culture-negative PJI, including pathogen identification, and the implementation of an antibiotic stewardship program.

Optogenetically modified human embryonic stem cell-derived otic neurons establish functional synaptic connection with cochlear nuclei.

Spiral ganglia neurons (SGNs) impairment can cause deafness. One important therapeutic approach involves utilizing stem cells to restore impaired auditory circuitry. Nevertheless, the inadequate implementation of research methodologies poses a challenge in accurately assessing the functionality of derived cells within the circuit. Here, we describe a novel method for converting human embryonic stem cells (hESCs) into otic neurons (ONs) and assess their functional connectivity using an optogenetic approach with cells or an organotypic slice of rat cochlear nucleus (CN) in coculture. Embryonic stem cell-derived otic neurons (eONs) exhibited SGN marker expression and generated functional synaptic connection when cocultured with cochlear nucleus neurons (CNNs). Synapsin 1 and VGLUT expression are found in the cochlear nucleus of brain slices, where eONs projected processes during the coculture of eONs and CN brain slices. Action potential spikes and INa+/IK+ of CNNs increased in tandem with light stimulations to eONs. These findings provide further evidence that eONs may be a candidate source to treat SGN-deafness.

A novel molecular signature for elevated tricuspid regurgitation velocity in sickle cell disease.

RATIONALE: An increased tricuspid regurgitation jet velocity (TRV > 2.5 m/s) and pulmonary hypertension defined by right heart catheterization both independently confer increased mortality in sickle cell disease (SCD). OBJECTIVES: We explored the usefulness of peripheral blood mononuclear cell-derived gene signatures as biomarkers for an elevated TRV in SCD. METHODS: Twenty-seven patients with SCD underwent echocardiography and peripheral blood mononuclear cell isolation for expression profiling and 112 patients with SCD were genotyped for single-nucleotide polymorphisms. MEASUREMENTS AND MAIN RESULTS: Genome-wide gene and miRNA expression profiles were correlated against TRV, yielding 631 transcripts and 12 miRNAs. Support vector machine analysis identified a 10-gene signature including GALNT13 (encoding polypeptide N-acetylgalactosaminyltransferase 13) that discriminates patients with and without increased TRV with 100% accuracy. This finding was then validated in a cohort of patients with SCD without (n = 10) and with pulmonary hypertension (n = 10, 90% accuracy). Increased TRV-related miRNAs revealed strong in silico binding predictions of miR-301a to GALNT13 corroborated by microarray analyses demonstrating an inverse correlation between their expression. A genetic association study comparing patients with an elevated (n = 49) versus normal (n = 63) TRV revealed five significant single-nucleotide polymorphisms within GALNT13 (P < 0.005), four trans-acting (P < 2.1 × 10(-7)) and one cis-acting (P = 0.6 × 10(-4)) expression quantitative trait locus upstream of the adenosine-A2B receptor gene (ADORA2B). CONCLUSIONS: These studies validate the clinical usefulness of genomic signatures as potential biomarkers and highlight ADORA2B and GALNT13 as potential candidate genes in SCD-associated elevated TRV.

A local genetic algorithm for the identification of condition-specific microRNA-gene modules.

Transcription factor and microRNA are two types of key regulators of gene expression. Their regulatory mechanisms are highly complex. In this study, we propose a computational method to predict condition-specific regulatory modules that consist of microRNAs, transcription factors, and their commonly regulated genes. We used matched global expression profiles of mRNAs and microRNAs together with the predicted targets of transcription factors and microRNAs to construct an underlying regulatory network. Our method searches for highly scored modules from the network based on a two-step heuristic method that combines genetic and local search algorithms. Using two matched expression datasets, we demonstrate that our method can identify highly scored modules with statistical significance and biological relevance. The identified regulatory modules may provide useful insights on the mechanisms of transcription factors and microRNAs.

Single-stage revision for chronic periprosthetic joint infection after knee and hip arthroplasties: indications and treatments.

Single-stage revision for chronic periprosthetic joint infection has been introduced 40 years ago. This option is gaining more and more attention as well as popularity. It is a reliable treatment for the chronic periprosthetic joint infection after knee and hip arthroplasties when implemented by an experienced multi-disciplinary team. However, its indications and corresponding treatments remain controversial. This review focused on the indications and specific treatments related to the option, with an attempt to help surgeons to use this method with more favorable outcomes.