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Abstract The detection of cancer-driving mutations is important for understanding cancer pathology and therapeutics development. Prediction tools have been created to streamline the computation process. However, most tools available have heterogeneous sensitivity or specificity. We built a machine learning-derived algorithm, DriverDetect that combines the outputs of seven pre-existing tools to improve the prediction of candidate driver cancer mutations. The algorithm was trained with cancer gene-specific mutation datasets of cancer patients to identify cancer drivers. DriverDetect performed better than the individual tools or their combinations in the validation test. It has the potential to incorporate future novel prediction algorithms and can be retrained with new datasets, offering an expanded application to pan-cancer analysis for cross-cancer study. (115 words).

Background:. Overdevelopment of zygomatic bones often results in protrusion and flaring of the midfacial region. This makes the face appear squarer than the more favorable oval shape. Therefore, zygoma reduction surgery has become a commonly performed procedure in patients seeking to obtain an ideal facial shape. Facial soft-tissue ptosis is one of the main complications of zygoma reduction surgery. Previously, the evaluation of cheek soft-tissue ptosis was subjectively based on patients and surgeons. Our study aimed to provide an objective evaluation of soft-tissue sagging in the cheek region after zygoma reduction surgery using artificial intelligence (AI). Methods:. We used AI to evaluate cheek sagging in a series of patients who underwent zygoma reduction surgery. We used four methods: tracking facial landmarks, detecting changes in the cheek curvature, and examining changes in the nasolabial fold and marionette lines. Then, the obtained numerical results were assessed for statistically significant differences using statistical validation methods. Results:. Use of AI with the four methods demonstrated no statistically significant differences between the pre- and postsurgery evaluations. AI analysis demonstrated that soft-tissue ptosis did not occur in our series of patients. Conclusions:. AI offers objective evaluation for both patients and doctors. Future research could build on this application to examine various influencing factors and develop new tools using machine learning to evaluate and predict the extent of cheek sagging in patients before surgery.

Introduction: Venolymphatic malformations are benign, but rare congenital lesions that can be found throughout the body. They tend to grow in size along with the patient, and thus are especially rare in the pre-adolescent pediatric population. In this article, we present a case of a vulvar lymphatic/vascular malformation in a 3-year-old female. Case Presentation: A 3-year-old, otherwise healthy, female presented with a labial/clitoral mass that had been growing over the past 2 years. A previous biopsy demonstrated benign vascular proliferation with stromal components, concerning for a vascular malformation versus hamartoma. Pelvic MRI was consistent with a lymphatic malformation. She was evaluated by both a pediatric endocrinologist and a genetic counselor who ruled out underlying hormonal abnormalities, such as central puberty or congenital adrenal hyperplasia, or genetic causes, such as neurofibromatosis 1. The 3.6 × 2.1 × 1.7cm mass was surgically excised with a multidisciplinary team with pediatric surgery, gynecologic oncology, and plastic and reconstructive surgery with final pathology demonstrating a lymphatic/vascular malformation. A rotational advancement flap was used to reconstruct the area. At 9 months, the sensation was preserved with good cosmesis. Conclusion: Vulvar venolymphatic malformations in the pediatric population are exceedingly rare. This is a highly sensitive area and should thus be approached both methodically and cautiously with a multidisciplinary approach.

Abstract Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35–2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex.

Background:. Malar/zygoma reduction is an effective procedure to change a broader, flatter facial appearance to an oval facial shape. Of the intraoral and coronal approaches, the intraoral is the more commonly used technique than the coronal, due to the perception that complications with the coronal approach are significant, and intraoral results are satisfactory. We compared the postoperative effects of both approaches. Methods:. From 1994 to 1999, we included the 150 intraoral cases that were followed up for 3 years postoperatively. From 2000 to 2018, we changed our technique to the coronal approach and included the 575 cases that were followed up for 3 years postoperatively. We compared the results of our prior intraoral approach with the more recent coronal approach. Results:. All cases of the intraoral approach resulted in smaller-sized faces horizontally; however, 90 patients (60%) still had resulting flat-shaped faces due to acute angle formation in the resultant zygoma. There were 141 cases (94%) of partial malunion and 138 cases (92%) of midface ptosis. Among the 575 coronal approaches, 518 cases (90%) resulted in an oval facial shape without acute angled zygoma. There were 161 cases (28%) of visible incision scars, 466 cases (81%) of temporary alopecia, 12 cases (2%) of hematoma, and 29 cases (5%) of temporary frontal facial nerve injury. Conclusions:. The intraoral approach led to flat and acute zygomas. The majority of patients experienced midface soft tissue ptosis. In contrast, the coronal approach led to an oval facial shape. The most notable complications of the coronal approach were visible scars and temporary alopecia.

The role of empty lipid nanoparticles in eliciting dendritic cell maturation and innate immune signaling is shown to be impaired in older adults, potentially contributing to lower immune responses to SARS-CoV-2 mRNA-based vaccines.

Importance: Scientific literature currently lacks data on surgical outcomes of single-port robotic sacrocolpopexy compared with traditional multi-port approaches. Objectives: To evaluate feasibility and surgical outcomes for the single-port robotic approach to sacrocolpopexy when compared with traditional multi-port approaches. Study design: Retrospective chart review of fifty patients who underwent minimally invasive sacrocolpopexy with a single urogynecologist between 2018 and 2021 ​at an academic tertiary care hospital. Patients were divided into three cohorts: laparoscopic multi-port (LMP), robotic multi-port (RMP), and robotic single-port (RSP). Outcome measures were operative time, number of adverse events, and severity of adverse events by Clavien-Dindo. Results: All patients underwent at least one concomitant procedure; however, LMP had more concomitant procedures compared to RMP and RSP (p ​

Background: Anti-Asian violence increased during the COVID-19 pandemic. Asian American/Pacific Islanders (AAPI) represent a diverse population experiencing a long history of stereotyping and exclusionism; however, this group is often left out of diversity/inclusion conversations. In academic medicine, AAPI are under-represented in leadership. We characterized the personal/professional experiences of AAPI gynecologic oncology trainees and assessed the impact of a virtual panel discussion with leaders in the field. Methods: An anonymous survey was disseminated online to trainees in/interested in gynecologic oncology fellowship who identified as AAPI, using modified snowball sampling. A virtual session with AAPI leaders in gynecologic oncology discussed themes emerging from survey responses. Session attendees completed an anonymous follow-up survey. Results were assessed quantitatively and qualitatively. Results: 44/59 (75%) respondents participated in the pre-survey; 23 (39%) participated in the virtual session. All session participants (23/23, 100%) completed the post-session survey. Participants reported increased identity-related thoughts with the COVID-19 pandemic (88% during, 61% prior). Sixty-eight percent reported that identity-related thoughts/awareness changed during the pandemic. Presence of AAPI colleagues was associated with higher perceived identity-related support from their department. Of those without AAPI coworkers, none (0%) felt ‘moderately’ or ‘extremely well supported.’ Qualitative analysis demonstrated that the panel discussion created a sense of community and encouragement, combating previously reported isolation and self-consciousness. Participants reported more connection with their heritage and identified more personal/professional topics that might be related to their cultural backgrounds. Discussion: This intervention demonstrates the opportunity to provide a supportive network for mentorship and professional development in a culturally inclusive way.

Abstract Background Taxonomic assignment is a key step in the identification of human viral pathogens. Current tools for taxonomic assignment from sequencing reads based on alignment or alignment-free k-mer approaches may not perform optimally in cases where the sequences diverge significantly from the reference sequences. Furthermore, many tools may not incorporate the genomic coverage of assigned reads as part of overall likelihood of a correct taxonomic assignment for a sample. Results In this paper, we describe the development of a pipeline that incorporates a multi-task learning model based on convolutional neural network (MT-CNN) and a Bayesian ranking approach to identify and rank the most likely human virus from sequence reads. For taxonomic assignment of reads, the MT-CNN model outperformed Kraken 2, Centrifuge, and Bowtie 2 on reads generated from simulated divergent HIV-1 genomes and was more sensitive in identifying SARS as the closest relation in four RNA sequencing datasets for SARS-CoV-2 virus. For genomic region assignment of assigned reads, the MT-CNN model performed competitively compared with Bowtie 2 and the region assignments were used for estimation of genomic coverage that was incorporated into a naïve Bayesian network together with the proportion of taxonomic assignments to rank the likelihood of candidate human viruses from sequence data. Conclusions We have developed a pipeline that combines a novel MT-CNN model that is able to identify viruses with divergent sequences together with assignment of the genomic region, with a Bayesian approach to ranking of taxonomic assignments by taking into account both the number of assigned reads and genomic coverage. The pipeline is available at GitHub via https://github.com/MaHaoran627/CNN_Virus .

Hyperthermic intraperitoneal chemotherapy (HIPEC) with cisplatin when used at the time of interval cytoreductive surgery (ICS) after neoadjuvant chemotherapy (NACT) has been shown to provide a survival advantage compared to interval cytoreduction alone for patients with advanced epithelial ovarian cancer in a cost-effective manner. A recent large multi-center retrospective cohort study showed a survival advantage with HIPEC given during primary debulking surgery compared to surgery alone. While there is an ongoing randomized controlled trial examining HIPEC at the time of primary cytoreductive surgery (PCS) before chemotherapy (OVHIPEC-2), there is currently no study of this practice in the United States or cost data to inform incorporation of this practice. To help guide the use of HIPEC in the upfront setting until the results of the OVHIPEC-2 are available in 2026, a decision-analytic cost-effectiveness model of the US healthcare sector was developed for patients undergoing PCS with or without HIPEC. Effectiveness inputs were extracted from a Chinese retrospective cohort study of 425 patients who underwent PCS with HIPEC and 159 patients who underwent PCS alone. We found incremental cost effectiveness ratios (ICER) of $9,789 per life year saved (LYS) for optimal PCS, $18,164/LYS for suboptimal PCS, and $7,854/LYS for all patients. Our findings provide preliminary data to support that HIPEC at the time of primary cytoreductive surgery can be considered cost-effective regardless of residual disease status when using a standard willingness to pay threshold.

Primary Epstein-Barr virus (EBV)-positive nodal T/NK-cell lymphoma (PTCL-EBV) is a poorly understood disease which shows features resembling extranodal NK/T-cell lymphoma (ENKTL) and is currently not recognized as a distinct entity but categorized as a variant of primary T-cell lymphoma not otherwise specified (PTCL-NOS). Herein, we analyzed copynumber aberrations (n=77) with a focus on global measures of genomic instability and homologous recombination deficiency and performed gene expression (n=84) and EBV miRNA expression (n=24) profiling as well as targeted mutational analysis (n=16) to further characterize PTCL-EBV in relation to ENKTL and PTCL-NOS. Multivariate analysis revealed that patients with PTCL-EBV had a significantly worse outcome compared to patients with PTCL-NOS (P=0.002) but not to those with ENKTL. Remarkably, PTCL-EBV exhibited significantly lower genomic instability and homologous recombination deficiency scores compared to ENKTL and PTCL-NOS. Gene set enrichment analysis revealed that many immune-related pathways, interferon α/γ response, and IL6_JAK_STAT3 signaling were significantly upregulated in PTCLEBV and correlated with lower genomic instability scores. We also identified that NFκB-associated genes, BIRC3, NFKB1 (P50) and CD27, and their proteins are upregulated in PTCL-EBV. Most PTCL-EBV demonstrated a type 2 EBV latency pattern and, strikingly, exhibited downregulated expression of most EBV miRNA compared to ENKTL and their target genes were also enriched in immune-related pathways. PTCL-EBV also showed frequent mutations of TET2, PIK3CD and STAT3, and are characterized by microsatellite stability. Overall, poor outcome, low genomic instability, upregulation of immune pathways and downregulation of EBV miRNA are distinctive features of PTCL-EBV. Our data support the concept that PTCL-EBV could be considered as a distinct entity, provide novel insights into the pathogenesis of the disease and offer potential new therapeutic targets for this tumor.

Objective This study aimed to evaluate the effects of a financial literacy curriculum on resident and fellow's sense of well-being and financial stress. Study Design This single institution pilot study prospectively enrolled obstetrician/gynecologist (OB/GYN) medical trainees (residents and fellows) to take part in a five-part personal financial literacy curriculum during the 2019 to 2020 academic year. Topics covered included the following: financial education and its relationship to personal well-being, overview of financial terms and principles, budgeting, debt planning, and investing and giving. Primary outcomes were the improvement in well-being as measured by the Expanded Well-Being Index (E-WBI) and financial stress as measured by the Financial Stress Scale-College Version (FSS-CV) survey. Results Of the 35 residents and fellows who participated in the study, 21 (60%) completed the postintervention survey. After course completion, there was significant improvement in the individual's E-WBI (p

The systematic identification of genetic events driving cellular transformation and tumor progression in the absence of a highly recurrent oncogenic driver mutation is a challenge in cutaneous oncology. In cutaneous squamous cell carcinoma (cuSCC), the high UV-induced mutational burden poses a hurdle to achieve a complete molecular landscape of this disease. Here, we utilized the Sleeping Beauty transposon mutagenesis system to statistically define drivers of keratinocyte transformation and cuSCC progression in vivo in the absence of UV-IR, and identified both known tumor suppressor genes and novel oncogenic drivers of cuSCC. Functional analysis confirms an oncogenic role for the ZMIZ genes, and tumor suppressive roles for KMT2C, CREBBP and NCOA2, in the initiation or progression of human cuSCC. Taken together, our in vivo screen demonstrates an extremely heterogeneous genetic landscape of cuSCC initiation and progression, which can be harnessed to better understand skin oncogenic etiology and prioritize therapeutic candidates.

BackgroundWhile hand, foot and mouth disease (HFMD) is primarily self-resolving-soaring incidence rate of symptomatic HFMD effectuates economic burden in the Asia-Pacific region. Singapore has seen a conspicuous rise in the number of HFMD cases from 2010s. Here, we aims to identify the serology and genotypes responsible for such outbreaks in hospitals and childcare facilities.MethodsWe studied symptomatic paediatric HFMD cases from 2013 to 2018 in Singapore. Surveillance for subclinical enterovirus infections was also performed in childcares at the same time period.ResultsGenotyping 101 symptomatic HFMD samples revealed CV-A6 as the major etiological agent for recent outbreaks. We detected infections with CV-A6 (41.0%), EV-A71 (7%), CV-A16 (3.0%), coxsackievirus A2, CV-A2 (1.0%) and coxsackievirus A10, CV-A10 (1.0%). Phylogenetic analysis of local CV-A6 strains revealed a high level of heterogeneity compared against others worldwide, dissimilar to other HFMD causative enteroviruses for which the dominant strains and genotypes are highly region specific. We detected sub-clinical enterovirus infections in childcare centres; 17.1% (n = 245) tested positive for enterovirus in saliva, without HFMD indicative symptoms at the point of sample collection.ConclusionsCV-A6 remained as the dominant HFMD causative strain in Singapore. Silent subclinical enteroviral infections were detected and warrant further investigations.

The study of viral diversity is imperative in understanding sequence change and its implications for intervention strategies. The widely used alignment-dependent approaches to study viral diversity are limited in their utility as sequence dissimilarity increases, particularly when expanded to the genus or higher ranks of viral species lineage. Herein, we present an alignment-independent algorithm, implemented as a tool, UNIQmin, to determine the effective viral sequence diversity at any rank of the viral taxonomy lineage. This is done by performing an exhaustive search to generate the minimal set of sequences for a given viral non-redundant sequence dataset. The minimal set is comprised of the smallest possible number of unique sequences required to capture the diversity inherent in the complete set of overlapping k-mers encoded by all the unique sequences in the given dataset. Such dataset compression is possible through the removal of unique sequences, whose entire repertoire of overlapping k-mers can be represented by other sequences, thus rendering them redundant to the collective pool of sequence diversity. A significant reduction, namely ~44%, ~45%, and ~53%, was observed for all reported unique sequences of species Dengue virus, genus Flavivirus, and family Flaviviridae, respectively, while still capturing the entire repertoire of nonamer (9-mer) viral peptidome diversity present in the initial input dataset. The algorithm is scalable for big data as it was applied to ~2.2 million non-redundant sequences of all reported viruses. UNIQmin is open source and publicly available on GitHub. The concept of a minimal set is generic and, thus, potentially applicable to other pathogenic microorganisms of non-viral origin, such as bacteria.

Management of complex chronic diseases such as diabetes requires the assimilation and interpretation of multiple laboratory test results. Traditional electronic health records tend to display laboratory results in a piecemeal and segregated fashion. This makes the assembly and interpretation of results related to diabetes care challenging. We developed a diabetes-specific clinical decision support system (Diabetes Dashboard) interface for displaying glycemic, lipid and renal function results, in an integrated form with decision support capabilities, based on local clinical practice guidelines. The clinical decision support system included a dashboard feature that graphically summarized all relevant laboratory results and displayed them in a color-coded system that allowed quick interpretation of the metabolic control of the patients. An alert module informs the user of tests that are due for repeat testing. An interactive graph module was also developed for better visual appreciation of the trends of the laboratory results of the patient. In a pilot study involving case scenarios administered via an electronic questionnaire, the Diabetes Dashboard, compared to the existing laboratory reporting interface, significantly improved the identification of abnormal laboratory results, of the long-term trend of the laboratory tests and of tests due for repeat testing. However, the Diabetes Dashboard did not significantly improve the identification of patients requiring treatment adjustment or the amount of time spent on each case scenario. In conclusion, we have developed and shown that the use of the Diabetes Dashboard, which incorporates several decision support features, can improve the management of diabetes. It is anticipated that this dashboard will be most helpful when deployed in an outpatient setting, where physicians can quickly make clinical decisions based on summarized information and be alerted to pertinent areas of care that require additional attention.

Background: To avoid a static double-eyelid fold characterized by nonmobile overdepression of the fold, we propose a new surgical approach of using septoaponeurosis junctional thickening (SAJT) to create a dynamic fold. Methods: Six hundred eighty patients underwent double-eyelid surgery using the SAJT fixation technique. The orbital septum was exposed and transversely opened superior to the incision margin. The lower septal stump was trimmed to expose the SAJT. The dermis and orbicularis oculi muscle of the lower flap of the upper eyelid were attached to the SAJT. Patients were followed for 2–8 years (mean, 3.6 y). Anatomic study with 28 upper eyelids from 28 Korean adult cadavers was performed to confirm the histological structure of the SAJT. Results: This technique created a dynamic fold. When the eyes were open, the fold depth was moderate. When the eyes were closed, the fold site was smooth and not depressed. The surgery had a 95% patient satisfaction rate (365 responded as satisfied and 236 responded as very satisfied). Postoperative complications included partial or complete loss of the double-eyelid line in 14 and 4 cases, respectively, hypertrophic scar formation in 7 cases, and asymmetric fold in 8 cases. Conclusions: The authors introduce a double-eyelid surgery technique using the SAJT. This SAJT fixation technique creates a dynamic double-eyelid fold. Our study showed a high patient satisfaction rate and that the resulting fold mimics the movement of the congenital supratarsal fold in Asians.

Gene therapy for HIV-1 infection is a promising alternative to lifelong combination antiviral drug treatment. Chemokine receptor 5 (CCR5) is the coreceptor required for R5-tropic HIV-1 infection of human cells. Deletion of CCR5 renders cells resistant to R5-tropic HIV-1 infection, and the potential for cure has been shown through allogeneic stem cell transplantation with naturally occurring homozygous deletion of CCR5 in donor hematopoietic stem/progenitor cells (HSPC). The requirement for HLA-matched HSPC bearing homozygous CCR5 deletions prohibits widespread application of this approach. Thus, a strategy to disrupt CCR5 genomic sequences in HSPC using zinc finger nucleases was developed. Following discussions with regulatory agencies, we conducted IND-enabling preclinical in vitro and in vivo testing to demonstrate the feasibility and (preclinical) safety of zinc finger nucleases-based CCR5 disruption in HSPC. We report here the clinical-scale manufacturing process necessary to deliver CCR5-specific zinc finger nucleases mRNA to HSPC using electroporation and the preclinical safety data. Our results demonstrate effective biallelic CCR5 disruption in up to 72.9% of modified colony forming units from adult mobilized HSPC with maintenance of hematopoietic potential in vitro and in vivo. Tumorigenicity studies demonstrated initial product safety; further safety and feasibility studies are ongoing in subjects infected with HIV-1 (NCT02500849@clinicaltrials.gov).