Classification of PTEN missense VUS through exascale simulations.

Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer. SIGNIFICANCE STATEMENT: Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.

Using Portuguese BRCA pathogenic variation as a model to study the impact of human admixture on human health.

BACKGROUND: Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide. It provides a valuable model to study the impact of admixture on human health. BRCA1 and BRCA2 (BRCA) are two of the important tumor suppressor genes. The pathogenic variation (PV) in BRCA is well determined to cause high risk of hereditary breast and ovarian cancer. Tracing the distribution of Portuguese BRCA PV in Portuguese-heritage population will help to understand the impact of admixture on cancer susceptibility in modern humans. In this study, we analyzed the distribution of the Portuguese-originated BRCA variation in Brazilian population, which has high degree Portuguese-heritage. METHODS: By comprehensive data mining, standardization and annotation, we generated a Portuguese-derived BRCA variation dataset and a Brazilian-derived BRCA variation dataset. We compared the two BRCA variation datasets to identify the BRCA variants shared between the two populations. RESULTS: The Portuguese-derived BRCA variation dataset consists of 220 BRCA variants including 78 PVs from 11,482 Portuguese cancer patients, 93 (42.2%) in BRCA1 and 127 (57.7%) in BRCA2. Of the 556 Portuguese BRCA PV carriers carrying the 78 PVs, 331 (59.5%) carried the three Portuguese-BRCA founder PVs of BRCA1 c.2037delinsCC, BRCA1 c.3331_3334del and BRCA2 c.156_157insAlu. The Brazilian-derived BRCA variation dataset consists of 255 BRCA PVs from 7,711 cancer patients, 136 (53.3%) in BRCA1 and 119 (46.6%) in BRCA2. We developed an open database named dbBRCA-Portuguese ( https://genemutation.fhs.um.edu.mo/dbbrca-portuguese/ ) and an open database named dbBRCA-Brazilian ( https://genemutation.fhs.um.edu.mo/dbbrca-brazilian ) to host the BRCA variation data from Portuguese and Brazilian populations. We compared the BRCA PV datasets between Portuguese and Brazilian populations, and identified 29 Portuguese-specific BRCA PVs shared between Portuguese and Brazilian populations, 14 in BRCA1 including the Portuguese founder BRCA1 c.3331_3334del and BRCA1 c.2037delinsCC, and 15 in BRCA2 including the Portuguese founder BRCA2 c.156_157insAlu. Searching the 78 Portuguese BRCA PVs in over 5,000 ancient human genomes identified evolution origin for only 8 PVs in Europeans dated between 37,470 and 3,818 years before present, confirming the Portuguese-specificity of Portuguese BRCA PVs; comparing the 78 Portuguese BRCA PVs Portuguese, 255 Brazilian BRCA PVs, and 134 African BRCA PVs showed little overlapping, ruling out the possibility that the BRCA PVs shared between Portuguese and Brazilian may also be contributed by African. CONCLUSION: Our study provides evidence that the admixture in recent human history contributed to cancer susceptibility in modern humans.

Pathogenic variants in human DNA damage repair genes mostly arose in recent human history.

BACKGROUND: Genome stability is maintained by the DNA damage repair (DDR) system composed of multiple DNA repair pathways of hundreds of genes. Germline pathogenic variation (PV) in DDR genes damages function of the affected DDR genes, leading to genome instability and high risk of diseases, in particular, cancer. Knowing evolutionary origin of the PVs in human DDR genes is essential to understand the etiology of human diseases. However, answer to the issue remains largely elusive. In this study, we analyzed evolutionary origin for the PVs in human DDR genes. METHODS: We identified 169 DDR genes by referring to various databases and identified PVs in the DDR genes of modern humans from ClinVar database. We performed a phylogenetic analysis to analyze the conservation of human DDR PVs in 100 vertebrates through cross-species genomic data comparison using the phyloFit program of the PHAST package and visualized the results using the GraphPad Prism software and the ggplot module. We identified DDR PVs from over 5000 ancient humans developed a database to host the DDR PVs ( https://genemutation.fhs.um.edu.mo/dbDDR-AncientHumans ). Using the PV data, we performed a molecular archeological analysis to compare the DDR PVs between modern humans and ancient humans. We analyzed evolution selection of DDR genes across 20 vertebrates using the CodeML in PAML for phylogenetic analysis. RESULTS: Our phylogenic analysis ruled out cross-species conservation as the origin of human DDR PVs. Our archeological approach identified rich DDR PVs shared between modern and ancient humans, which were mostly dated within the last 5000 years. We also observed similar pattern of quantitative PV distribution between modern and ancient humans. We further detected a set of ATM, BRCA2 and CHEK2 PVs shared between human and Neanderthals. CONCLUSIONS: Our study reveals that human DDR PVs mostly arose in recent human history. We propose that human high cancer risk caused by DDR PVs can be a by-product of human evolution.

Early evaluation of a natural language processing tool to improve access to educational resources for surgical patients.

PURPOSE: Accessible patient information sources are vital in educating patients about the benefits and risks of spinal surgery, which is crucial for obtaining informed consent. We aim to assess the effectiveness of a natural language processing (NLP) pipeline in recognizing surgical procedures from clinic letters and linking this with educational resources. METHODS: Retrospective examination of letters from patients seeking surgery for degenerative spinal disease at a single neurosurgical center. We utilized MedCAT, a named entity recognition and linking NLP, integrated into the electronic health record (EHR), which extracts concepts and links them to systematized nomenclature of medicine-clinical terms (SNOMED-CT). Investigators reviewed clinic letters, identifying words or phrases that described or identified operations and recording the SNOMED-CT terms as ground truth. This was compared to SNOMED-CT terms identified by the model, untrained on our dataset. A pipeline linking clinic letters to patient-specific educational resources was established, and precision, recall, and F1 scores were calculated. RESULTS: Across 199 letters the model identified 582 surgical procedures, and the overall pipeline after adding rules a total of 784 procedures (precision = 0.94, recall = 0.86, F1 = 0.91). Across 187 letters with identified SNOMED-CT terms the integrated pipeline linking education resources directly to the EHR was successful in 157 (78%) patients (precision = 0.99, recall = 0.87, F1 = 0.92). CONCLUSIONS: NLP accurately identifies surgical procedures in pre-operative clinic letters within an untrained subspecialty. Performance varies among letter authors and depends on the language used by clinicians. The identified procedures can be linked to patient education resources, potentially improving patients' understanding of surgical procedures.

Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method.

Pathogenic variation in DNA mismatch repair (MMR) gene MLH1 is associated with Lynch syndrome (LS), an autosomal dominant hereditary cancer. Of the 3798 MLH1 germline variants collected in the ClinVar database, 38.7% (1469) were missense variants, of which 81.6% (1199) were classified as Variants of Uncertain Significance (VUS) due to the lack of functional evidence. Further determination of the impact of VUS on MLH1 function is important for the VUS carriers to take preventive action. We recently developed a protein structure-based method named "Deep Learning-Ramachandran Plot-Molecular Dynamics Simulation (DL-RP-MDS)" to evaluate the deleteriousness of MLH1 missense VUS. The method extracts protein structural information by using the Ramachandran plot-molecular dynamics simulation (RP-MDS) method, then combines the variation data with an unsupervised learning model composed of auto-encoder and neural network classifier to identify the variants causing significant change in protein structure. In this report, we applied the method to classify 447 MLH1 missense VUS. We predicted 126/447 (28.2%) MLH1 missense VUS were deleterious. Our study demonstrates that DL-RP-MDS is able to classify the missense VUS based solely on their impact on protein structure.

Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.

Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.

Butterfly gliomas: a time for stratified management?

Butterfly glioblastomas (bGBM) are a rare subset of WHO grade IV tumours that carry a poor prognosis with a median survival ranging between 3.3 to 6 months. Given their poor prognosis, there is debate over whether histological diagnosis with a biopsy or any surgical or oncological intervention alters disease progression. With this in mind, we reviewed our experience as a high-volume unit to evaluate management decisions and outcomes. A retrospective analysis was undertaken (January 2009 to June 2021) of the electronic patient records of a large neurosurgical centre. We assessed patient demographics, initial clinical presentation, tumour characteristics, clinical management and overall survival (Kaplan-Meier estimator, log-rank analysis and cox proportional hazard analysis). Eighty cases of bGBM were identified. These patients were managed with biopsy ± adjuvant therapy (36), with radiotherapy alone without biopsy (3), or through surgical resection (3). Thirty-eight cases of suspected bGBM were managed conservatively, receiving no oncological treatment or surgical resection/biopsy for histological diagnosis. Those managed conservatively and with radiotherapy without biopsy were diagnosed at neuro-oncology multidisciplinary meeting (MDT) based on clinical presentation and radiological imaging. No significant difference in survival was seen between conservative management compared with single adjuvant treatment (p = 0.69). However, survival was significantly increased when patients received dual adjuvant chemoradiotherapy following biopsy or resection (p = 0.002). A Cox Proportional Hazards model found that survival was significantly impacted by the oncology treatment (p < 0.001), but was not significantly related to potential confounding variables such as the patient's age (p = 0.887) or KPS (p = 0.057). Butterfly glioblastoma have a poor prognosis. Our study would suggest that unless a patient is planned for adjuvant chemoradiotherapy following biopsy, they should be managed conservatively. This avoids unnecessary procedural interventions with the associated morbidities and costs.

Surgical management and outcomes in spinal intradural arachnoid cysts: the experience from two tertiary neurosurgical centres.

PURPOSE: Evaluation of the presentation and outcomes of different surgical treatment approaches for spinal intradural arachnoid cysts (SIAC). METHODS: Cases were identified from electronic records of two major neurosurgical centres in London over the last 10 years (October 2009-October 2019) that have been surgically treated in both institutions. Clinical findings, surgical technique, and recurrence by procedure were statistically analysed. Statistical analysis was performed with STATA 13.1 Software. RESULTS: A total of 42 patients with SIAC were identified for this study with a mean age at the time of surgery of 53.6 years and a male:female ratio of 8:13. There were 31 patients with primary SIACs and 11 with secondary SIACs. The most common presenting symptom was paraesthesia (n = 27). The most common location of the cyst was in the thoracic region (n = 33). Syrinx was present in 26.2% of SIACs (n = 11). Resection was associated with significantly better postoperative pain compared to other surgical techniques (p = 0.01), significantly poorer postoperative urinary function (p = 0.029), and lower rates of sensory recovery in patients who presented preoperatively with sensory deficit (p = 0.041). No significant difference was seen in symptomatic outcomes between patients with primary and secondary SIACs. CONCLUSION: Resection and drainage are both effective methods of managing SIACs. In this observational study, resection was associated with significantly reduced pain postoperatively when compared with drainage, however also with significantly less improvement in postoperative urinary function. Therefore, resection should be the gold standard management option for SIACs, with drainage as an option where resection is unsafe, and drainage should also be considered in patients presenting with urinary dysfunction.

Twelve tips to organise a mock OSCE.

The objective structured clinical examination (OSCE) is central to assessing clinical competence in undergraduate and postgraduate exams for medical and allied healthcare professions. A mock OSCE on the other hand is a simulation of the OSCE and a unique learning experience for the examinee. They benefit in a variety of ways; from enhancing their time management skills to receiving feedback that can improve their clinical skills. Unfortunately, opportunities to participate in simulated OSCEs remain limited. Reasons include difficulty in fulfilling organisational requirements and equipment-related costs. Mock OSCEs can be set up by undergraduate students or junior trainees for peers, without senior supervision or direct guidance. This article will discuss 12 tips regarding the arrangement of mock OSCEs to guide organisers, including accessing resources and establishing the content of the exam.

Comprehensive Identification of Deleterious TP53 Missense VUS Variants Based on Their Impact on TP53 Structural Stability.

TP53 plays critical roles in maintaining genome stability. Deleterious genetic variants damage the function of TP53, causing genome instability and increased cancer risk. Of the large quantity of genetic variants identified in TP53, however, many remain functionally unclassified as variants of unknown significance (VUS) due to the lack of evidence. This is reflected by the presence of 749 (42%) VUS of the 1785 germline variants collected in the ClinVar database. In this study, we addressed the deleteriousness of TP53 missense VUS. Utilizing the protein structure-based Ramachandran Plot-Molecular Dynamics Simulation (RPMDS) method that we developed, we measured the effects of missense VUS on TP53 structural stability. Of the 340 missense VUS tested, we observed deleterious evidence for 193 VUS, as reflected by the TP53 structural changes caused by the VUS-substituted residues. We compared the results from RPMDS with those from other in silico methods and observed higher specificity of RPMDS in classification of TP53 missense VUS than these methods. Data from our current study address a long-standing challenge in classifying the missense VUS in TP53, one of the most important tumor suppressor genes.

Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition.

BACKGROUND: Core promoter controls transcription initiation. However, little is known for core promoter diversity in the human genome and its relationship with diseases. We hypothesized that as a functional important component in the genome, the core promoter in the human genome could be under evolutionary selection, as reflected by its highly diversification in order to adjust gene expression for better adaptation to the different environment. RESULTS: Applying the "Exome-based Variant Detection in Core-promoters" method, we analyzed human core-promoter diversity by using the 2682 exome data sets of 25 worldwide human populations sequenced by the 1000 Genome Project. Collectively, we identified 31,996 variants in the core promoter region (- 100 to + 100) of 12,509 human genes ( https://dbhcpd.fhs.um.edu.mo ). Analyzing the rich variation data identified highly ethnic-specific patterns of core promoter variation between different ethnic populations, the genes with highly variable core promoters, the motifs affected by the variants, and their involved functional pathways. eQTL test revealed that 12% of core promoter variants can significantly alter gene expression level. Comparison with GWAS data we located 163 variants as the GWAS identified traits associated with multiple diseases, half of these variants can alter gene expression. CONCLUSION: Data from our study reals the highly diversified nature of core promoter in the human genome, and highlights that core promoter variation could play important roles not only in gene expression regulation but also in disease predisposition.

Germline variation in BRCA1/2 is highly ethnic-specific: Evidence from over 30,000 Chinese hereditary breast and ovarian cancer patients.

BRCA1 and BRCA2 play essential roles in maintaining the genome stability. Pathogenic germline mutations in these two genes disrupt their function, lead to genome instability and increase the risk of developing breast and ovarian cancers. BRCA mutations have been extensively screened in Caucasian populations, and the resulting information are used globally as the standard reference in clinical diagnosis, treatment and prevention of BRCA-related cancers. Recent studies suggest that BRCA mutations can be ethnic-specific, raising the question whether a Caucasian-based BRCA mutation information can be used as a universal standard worldwide, or whether an ethnicity-based BRCA mutation information system need to be developed for the corresponding ethnic populations. In this study, we used Chinese population as a model to test ethnicity-specific BRCA mutations considering that China has one of the latest numbers of breast cancer patients therefore BRCA mutation carriers. Through comprehensive data mining, standardization and annotation, we collected 1,088 distinct BRCA variants derived from over 30,000 Chinese individuals, one of the largest BRCA data set from a non-Caucasian population covering nearly all known BRCA variants in the Chinese population (https://dbBRCA-Chinese.fhs.umac.mo). Using this data, we performed multi-layered analyses to determine the similarities and differences of BRCA variation between Chinese and non-Chinese ethnic populations. The results show the substantial differences of BRCA data between Chinese and non-Chinese ethnicities. Our study indicates that the current Caucasian population-based BRCA data is not adequate to represent the BRCA status in non-Caucasian populations. Therefore, ethnic-based BRCA standards need to be established to serve for the non-Caucasian populations.

Simulation Based Investigation of Deleterious nsSNPs in ATXN2 Gene and Its Structural Consequence Toward Spinocerebellar Ataxia.

Spinocerebellar degeneration, termed as ataxia is a neurological disorder of central nervous system, characterized by limb in-coordination and a progressive gait. The patient also demonstrates specific symptoms of muscle weakness, slurring of speech, and decreased vibration senses. Expansion of polyglutamine trinucleotide (CAG) within ATXN2 gene with 35 or more repeats, results in spinocerebellar ataxia type-2. Protein ataxin-2 coded by ATXN2 gene has been reported to have a crucial role in translation of the genetic information through sequestering the histone acetyl transferases (HAT) resulting in a state of hypo-acetylation. In the present study, we have evaluated the outcome for 122 non synonymous single nucleotide polymorphisms (nsSNPs) reported within ATXN2 gene through computational tools such as SIFT, PolyPhen 2.0, PANTHER, I-mutant 2.0, Phd-SNP, Pmut, MutPred. The apo and mutant (L305V and Q339L) form of structures for the ataxin-2 protein were modeled for gaining insights toward 3D spatial arrangement. Further, molecular dynamics simulations and structural analysis were performed to observe the brunt of disease associated nsSNPs toward the strength and secondary properties of ataxin-2 protein structure. Our results showed that, L305V is a highly deleterious and disease causing point substitution. Analysis based on RMSD, RMSF, Rg, SASA, number of hydrogen bonds (NH bonds), covariance matrix trace, projection analysis for eigen vector demonstrated a significant instability and conformation along with rise in mutant flexibility values in comparison to the apo form of ataxin-2 protein. The study provides a blue print of computational methodologies to examine the ataxin-blend SNPs. J. Cell. Biochem. 119: 499-510, 2018. © 2017 Wiley Periodicals, Inc.

Mechanistic Principles Behind Molecular Mechanism of Rifampicin Resistance in Mutant RNA Polymerase Beta Subunit of Mycobacterium tuberculosis.

Evolution of drug-resistant Mycobacterium strains threatens the TB treatment and control programs globally. Rifampicin (RIF) is an important first line antitubercular drug. Resistance to Rifampicin is caused mainly by mutations in its target RNA polymerase beta subunit protein (RpoB). RpoB contains a Rifampicin resistance determining region (RRDR) and has several potent sites for mutations. In this study, we have investigated mutations of a single site (H451) to eight different amino acids, involved in RIF resistance. Long-term molecular dynamics simulations were performed on wild type (WT) and mutant protein structures and various structural analysis were carried out to elucidate the dynamic behavior of WT and mutant forms. Essential dynamics uncovered the difference in conformational flexibility and collective modes of motions between WT and mutants. MMPBSA calculations and interaction pattern analysis revealed the binding site relocation in some mutants. This study presents an exhaustive analysis of RIF binding to the WT and mutant RpoB and clearly highlights structural mechanism for differences in stable binding of Rifampicin with WT than the mutant targets. J. Cell. Biochem. 118: 4594-4606, 2017. © 2017 Wiley Periodicals, Inc.

Mapping patient education encounters in elective surgery: a cohort study and cross-sectional survey.

OBJECTIVE: Develop a process map of when patients learn about their proposed surgery and what resources patients use to educate themselves. DESIGN: A mixed methods design, combining semistructured stakeholder interviews, quantitative validation using electronic healthcare records (EHR) in a retrospective cohort and a cross-sectional patient survey. SETTING: A single surgical centre in the UK. PARTICIPANTS: Fourteen members of the spinal multidisciplinary team were interviewed to develop the process map.This process map was validated using the EHR of 50 patients undergoing elective spine surgery between January and June 2022. Postprocedure, feedback was gathered from 25 patient surveys to identify which resources they used to learn about their spinal procedure. Patients below the age of 18 or who received emergency surgery were excluded. INTERVENTIONS: Elective spine surgery and patient questionnaires given postoperatively either on the ward or in follow-up clinic. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was the percentage of the study cohort that was present at encounters on the process map. Key timepoints were defined if >80% of patients were present. The secondary outcome was the percentage of the study cohort that used educational resources listed in the patient questionnaire. RESULTS: There were 342 encounters which occurred across the cohort, with 16 discrete event categories identified. The initial surgical clinic (88%), anaesthetic preoperative assessment (96%) and admission for surgery (100%) were identified as key timepoints. Surveys identified that patients most used verbal information from their surgeon (100%) followed by written information from their surgeon (52%) and the internet (40%) to learn about their surgery. CONCLUSIONS: Process mapping is an effective method of illustrating the patient pathway. The initial surgical clinic, anaesthetic preoperative assessment and surgical admission are key timepoints where patients receive information. This has future implications for guiding patient education interventions to focus at key timepoints.

Impact of Preoperative Mapping and Intraoperative Neuromonitoring in Minimally Invasive Parafascicular Surgery for Deep-Seated Lesions.

BACKGROUND: Transsulcal tubular retractor-assisted minimally invasive parafascicular surgery changes the surgical strategy for deep-seated lesions by promoting a deficit-sparing approach. When integrated with preoperative brain mapping and intraoperative neuromonitoring (IONM), this approach may potentially improve patient outcomes. In this study, we assessed the impact of preoperative brain mapping and IONM in tubular retractor-assisted neuro-oncological surgery. METHODS: This retrospective single-center cohort study included patients who underwent transsulcal tubular retractor-assisted minimally invasive parafascicular surgery for resection of deep-seated brain tumors from 2016 to 2022. The cohort was divided into 3 groups: group 1, no preoperative mapping or IONM (17 patients); group 2, IONM only (25 patients); group 3, both preoperative mapping and IONM (38 patients). RESULTS: We analyzed 80 patients (33 males and 47 females) with a median age of 46.5 years (range: 1-81 years). There was no significant difference in mean tumor volume (26.2 cm3 [range 1.07-97.4 cm3]; P = 0.740) and mean preoperative depth of the tumor (31 mm [range 3-65 mm], P = 0.449) between the groups. A higher proportion of high-grade gliomas and metastases was present within group 3 (P = 0.003). IONM was related to fewer motor (P = 0.041) and language (P = 0.032) deficits at hospital discharge. Preoperative mapping and IONM were also related to shorter length of stay (P = 0.008). CONCLUSIONS: Preoperative and intraoperative brain mapping and monitoring enhance transsulcal tubular retractor-assisted minimally invasive parafascicular surgery in neuro-oncology. Patients had a reduced length of stay and prolonged overall survival. IONM alone reduces postoperative neurological deficit.

The Fate of Nonoperative Management in Patients with Lytic Spondylolisthesis.

BACKGROUND: There is a lack of consensus within the current literature about the role of nonoperative management in lytic spondylolisthesis. Our objective was to assess the fate that nonoperative management plays in patients diagnosed with lytic spondylolisthesis. METHODS: Data were collected between May 2015 and February 2020 from 41 patients who were initially referred specifically for instrumented lumbar fixation but were instead planned for nonoperative management as they opted to avoid surgery. Magnetic resonance imaging (MRI) scans were used to determine spondylolisthesis grade, type of deformity, and radiologic features. Patient notes were reviewed to establish management plans. Furthermore, patients were also contacted via telephone to assess their symptoms and disease progression. RESULTS: Twenty-six of the 41 patients had lytic spondylolisthesis (63.4%). Of these patients, the male-to-female ratio was 10:16. The median age was 60 (range: 22-76) years. A total of 12 patients were managed nonoperatively for 5 years or longer, with 2 patients showing progression from grade I to II. CONCLUSION: Nonoperative management of lytic spondylolisthesis is a reasonable option in a selected cohort of patients. The longer in duration patients are managed conservatively, the less likely they are to require a surgical intervention. Even severe radiologic foraminal stenosis without radicular pain does not seem to push patients toward surgery. Management decisions must be made on an individual basis. These data can give some reassurance to patients who wish to consider nonoperative management and help guide clinicians.

Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations.

Large quantity of variants of uncertain significance (VUS) has been identified in cancer predisposition genes, but classification of VUS remains a big challenge. We proposed that the impact of VUS on protein structure stability can be used to identify these with deleterious effects by using molecular dynamics simulation (MDS)-based approach and developed a MDS-based method for missense VUS classification. In the current study, we applied the system to classify the missense VUS in BRCA2. BRCA2 plays an important role in maintaining genome stability by repairing double-strand DNA damage through homologous recombination. BRCA2 BRC repeats bring RAD51 from cytoplasm to the break sites in nucleus to initiate the repairing process. Missense variants in BRCA2 BRC repeats can interfere the interaction between BRCA2 and RAD51, impair double-strand break repair, cause genome instability and increase cancer risk. We characterized the missense VUS in BRCA2 BRC4 repeat, the primary site of BRCA2 interacting with RAD51. Based on the well-determined BRC4 structure, we applied MDS to measure the impact of BRC4 missense VUS on the stability of BRC4 structure by testing the equilibrium state, flexibility, compactness, hydrogen bonds and surface accessibility. Of the 46 missense VUS analyzed, we were able to differentiate them into 24 Deleterious and 22 Tolerated variants. Comparison between the MDS-based and other 24 existing computational methods for variant classification showed that the MDS-based approach is highly sensitive and specific for classifying missense VUS in cancer predisposition genes.

Applications of Molecular Dynamics Simulation in Protein Study.

Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein-protein interaction, enzymatic reactions and drug-protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.

Experiences with Cyclical User-Centered Design for Patient and Clinician Facing Medication Reconciliation mHealth Applications.

Accurate medication lists are essential data required to make clinically informed decisions. Obtaining a comprehensive, up-to-date medication list is difficult for clinicians. Patients have limited input into reviewing and reconciling their own medication data. Ideally, a medication list would comprise a 360-degree view of all prescribed, dispensed, purchased medications and would seamlessly connect patients and providers to medication data from multiple sources. While an ideal medication list would capture every aspect of medication management, in reality a Best-Possible Medication History (BPMH) is a more achievable goal. In an effort to realize a BPMH and to facilitate the goals of the State of Connecticut's Office of Health Strategy's Medication Reconciliation and Polypharmacy Committee (MRPC), we engaged stakeholders (patients, clinicians, advocates) in focus-groups and interviews to solicit feedback on the user interface requirements for a BPMH. Feedback was obtained via facilitated discussions that occurred in-person, via virtual meetings, and through online surveys.