Emergence of the novel sixth Candida auris Clade VI in Bangladesh.

Candida auris, initially identified in 2009, has rapidly become a critical concern due to its antifungal resistance and significant mortality rates in healthcare-associated outbreaks. To date, whole-genome sequencing (WGS) has identified five unique clades of C. auris, with some strains displaying resistance to all primary antifungal drug classes. In this study, we presented the first WGS analysis of C. auris from Bangladesh, describing its origins, transmission dynamics, and antifungal susceptibility testing (AFST) profile. Ten C. auris isolates collected from hospital settings in Bangladesh were initially identified by CHROMagar Candida Plus, followed by VITEK2 system, and later sequenced using Illumina NextSeq 550 system. Reference-based phylogenetic analysis and variant calling pipelines were used to classify the isolates in different clades. All isolates aligned ~90% with the Clade I C. auris B11205 reference genome. Of the 10 isolates, 8 were clustered with Clade I isolates, highlighting a South Asian lineage prevalent in Bangladesh. Remarkably, the remaining two isolates formed a distinct cluster, exhibiting >42,447 single-nucleotide polymorphism differences compared to their closest Clade IV counterparts. This significant variation corroborates the emergence of a sixth clade (Clade VI) of C. auris in Bangladesh, with potential for international transmission. AFST results showed that 80% of the C. auris isolates were resistant to fluconazole and voriconazole, whereas Clade VI isolates were susceptible to azoles, echinocandins, and pyrimidine analogue. Genomic sequencing revealed ERG11_Y132F mutation conferring azole resistance while FCY1_S70R mutation found inconsequential in describing 5-flucytosine resistance. Our study underscores the pressing need for comprehensive genomic surveillance in Bangladesh to better understand the emergence, transmission dynamics, and resistance profiles of C. auris infections. Unveiling the discovery of a sixth clade (Clade VI) accentuates the indispensable role of advanced sequencing methodologies.IMPORTANCECandida auris is a nosocomial fungal pathogen that is commonly misidentified as other Candida species. Since its emergence in 2009, this multidrug-resistant fungus has become one of the five urgent antimicrobial threats by 2019. Whole-genome sequencing (WGS) has proven to be the most accurate identification technique of C. auris which also played a crucial role in the initial discovery of this pathogen. WGS analysis of C. auris has revealed five distinct clades where isolates of each clade differ among themselves based on pathogenicity, colonization, infection mechanism, as well as other phenotypic characteristics. In Bangladesh, C. auris was first reported in 2019 from clinical samples of a large hospital in Dhaka city. To understand the origin, transmission dynamics, and antifungal-resistance profile of C. auris isolates circulating in Bangladesh, we conducted a WGS-based surveillance study on two of the largest hospital settings in Dhaka, Bangladesh.

Functional guilds and drivers of diversity in seaweed-associated bacteria.

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Complete genome sequence of Escherichia phage iGC_PHA_EC001.

Antimicrobial resistance (AMR) in bacteria poses a global health emergency due to limited treatment options. Here, we report a lytic bacteriophage belonging to Stephanstirmvirinae family against an AMR Escherichia coli (ST2089). Escherichia phage iGC_PHA_EC001 is of genus Phapecoctavirus and 148,445 bp in length, encoding 269 predicted protein-coding sequences and 10 tRNAs. The phage encodes two lytic proteins containing phage_lysozyme (PF00959.22) and cell wall hydrolase_2 (PF07486.15) as catalytic domains, respectively.

Model-based image updating in deep brain stimulation with assimilation of deep brain sparse data.

BACKGROUND: Accuracy of electrode placement for deep brain stimulation (DBS) is critical to achieving desired surgical outcomes and impacts the efficacy of treating neurodegenerative diseases. Intraoperative brain shift degrades the accuracy of surgical navigation based on preoperative images. PURPOSE: We extended a model-based image updating scheme to address intraoperative brain shift in DBS surgery and improved its accuracy in deep brain. METHODS: We evaluated 10 patients, retrospectively, who underwent bilateral DBS surgery and classified them into groups of large and small deformation based on a 2 mm subsurface movement threshold and brain shift index of 5%. In each case, sparse brain deformation data were used to estimate whole brain displacements and deform preoperative CT (preCT) to generate updated CT (uCT). Accuracy of uCT was assessed using target registration errors (TREs) at the Anterior Commissure (AC), Posterior Commissure (PC), and four calcification points in the sub-ventricular area by comparing their locations in uCT with their ground truth counterparts in postoperative CT (postCT). RESULTS: In the large deformation group, TREs were reduced from 2.5 mm in preCT to 1.2 mm in uCT (53% compensation); in the small deformation group, errors were reduced from 1.25 to 0.74 mm (41%). Average reduction of TREs at AC, PC and pineal gland were significant, statistically (p ⩽ 0.01). CONCLUSIONS: With more rigorous validation of model results, this study confirms the feasibility of improving the accuracy of model-based image updating in compensating for intraoperative brain shift during DBS procedures by assimilating deep brain sparse data.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes.

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.

Endocrine surgery and the surgeon-scientist: Bridging the gap between a rich history and a bright future.

INTRODUCTION: We evaluate National Institutes of Health (NIH) data to describe endocrine surgical research performed by surgeons in the United States. METHODS: An internal NIH database was queried for endocrine surgery-related grants awarded to surgeons in 2010, 2015, and 2020. The grants were then compared based on cost, grant type, research type, and endocrine topic. RESULTS: Eighteen grants ($6.4 M) focused on endocrine surgery-related research topics were identified in 2020, 17 ($7.3 M) in 2015, and 11 ($3.8 M) in 2010. In 2020, 14 grants were basic science and 4 were clinical outcomes, and pancreatic endocrine disease and thyroid disease each comprised 6 grants. R01 and R21 grants comprised 10 (55.6%) of the grants in 2020, compared to 10 (58.5%) in 2015 and 8 (72.7%) in 2010, while K08 and K23 grants increased to 4 (22.2%) in 2020 from 2 (11.8%) in 2015 and none in 2010. CONCLUSION: There were more K-awards focused on endocrine surgery-related research in 2020 compared to 2015 and 2010, suggesting the pipeline is growing.

Breast Surgical Oncology Fellowship applicant selection and ranking: A survey of Society of Surgical Oncology programs.

BACKGROUND AND OBJECTIVES: In 2003, the Society of Surgical Oncology (SSO) initiated a breast surgical oncology fellowship, which has now grown to 60 SSO accredited programs as of 2021. Limited knowledge exists on the traits of successful applicants and the factors influencing the rank list. METHODS: A web-based, anonymous survey was sent to all SSO Breast Surgical Oncology Fellowship program directors. The survey consisted of 26 questions. Descriptive statistics were used to analyze survey responses and evaluate impact on applicant interview and rank list. RESULTS: Thirty-four programs (57% response rate) completed the survey. Programs received an average of 70 applications and granted 24 interviews. Most programs reported a minimum ABSITE cut-off score (n = 28, 82%) and a defined publication requirement (n = 22, 65%), including a first-author requirement (n = 18, 53%) to extend an invitation to interview. For postinterview rank, applicant interpersonal skills were highly valued. The interview was the most important aspect for the rank list. CONCLUSIONS: Many programs have ABSITE and publication thresholds before offering an interview. Upon receiving interview invitation, the applicant's interview performance, interpersonal skills, and letters of recommendation were the most important aspect in rank list decision making.

COV-RadNet: A Deep Convolutional Neural Network for Automatic Detection of COVID-19 from Chest X-Rays and CT Scans.

With the increase in severity of COVID-19 pandemic situation, the world is facing a critical fight to cope up with the impacts on human health, education and economy. The ongoing battle with the novel corona virus, is showing much priority to diagnose and provide rapid treatment to the patients. The rapid growth of COVID-19 has broken the healthcare system of the affected countries, creating a shortage in ICUs, test kits, ventilation support system. etc. This paper aims at finding an automatic COVID-19 detection approach which will assist the medical practitioners to diagnose the disease quickly and effectively. In this paper, a deep convolutional neural network, 'COV-RadNet' is proposed to detect COVID positive, viral pneumonia, lung opacity and normal, healthy people by analyzing their Chest Radiographic (X-ray and CT scans) images. Data augmentation technique is applied to balance the dataset 'COVID 19 Radiography Dataset' to make the classifier more robust to the classification task. We have applied transfer learning approach using four deep learning based models: VGG16, VGG19, ResNet152 and ResNext 101 to detect COVID-19 from chest X-ray images. We have achieved 97% classification accuracy using our proposed COV-RadNet model for COVID/Viral Pneumonia/Lungs Opacity/Normal, 99.5% accuracy to detect COVID/Viral Pneumonia/Normal and 99.72% accuracy to detect COVID and non-COVID people. Using chest CT scan images, we have found 99.25% accuracy to classify between COVID and non-COVID classes. Among the performance of the pre-trained models, ResNext 101 has shown the highest accuracy of 98.5% for multiclass classification (COVID, viral pneumonia, Lungs opacity and normal).

Predictors of post-operative pancreatic fistula formation in pancreatic neuroendocrine tumors: A national surgical quality improvement program analysis.

BACKGROUND: Post-operative pancreatic fistula (POPF) is a serious complication following pancreas surgery. We aimed to establish factors associated with POPF specifically in patients with pancreatic neuroendocrine tumors (PNET). METHODS: The 2014-2018 American College of Surgeons National Surgical Quality Improvement Program database was querried for patients undergoing resection for PNET. The impact of patient, tumor, and operative factors on POPF formation was evaluated. RESULTS: 3532 patient underwent resections for PNET. The POPF rate was significantly higher in patients with PNET (24.8%) versus non-PNET (16.4%) (p < 0.0001). Male sex (OR 1.45, 95% CI 1.11-1.89), enucleation (OR 3.14, 95% CI 1.10-8.98), pancreaticoduodenectomy (OR 1.51, 95% CI 1.13-2.03), small duct size <3 mm (OR 3.24, 95% CI 1.62-6.48), and soft gland texture (OR 1.81, 95% CI 1.18-2.77) were independently associated with POPF in PNET patients on multivariable analysis. CONCLUSIONS: POPF is more common in patients undergoing resection for PNET and is dictated primarily by surgical approach and gland characteristics.

Follow-up of practiced treatment regimens and health conditions of patients following recovery from COVID-19 residing in Dhaka City: a survey-based, descriptive, cross-sectional study.

Objective: To observe the prognosis of cases of coronavirus 2019 (COVID-19), focusing on symptoms, treatment and post-recovery health conditions. Methodology: The respondents were residents of Dhaka City, Bangladesh who had a reverse transcription polymerase chain reaction (RT-PCR)-confirmed diagnosis of COVID-19 from the Institute of Epidemiology, Disease Control and Research from October to December 2020. They were followed up 1-3 months after diagnosis. Data were collected via Google forms sent directly by e-mail, and were analysed using SPSS. Participation was voluntary, and confidentiality of the respondents was strictly maintained. Results: Five hundred and twenty-two of 3148 patients who had recovered from COVID-19 responded to the survey. The mean (±standard deviation) age and body mass index of the respondents were 39.8±13 years and 26.4±6.5 kg/m2, respectively. More males than females participated in this study (70.3% vs 29.5%). Approximately 39.3% of respondents had comorbidities. The majority (88.5%) of respondents had experienced symptoms, including fever, fatigue, anosmia and aguesia, body pain, headache and dry cough, for 1-5 days. Respondents were treated with antibiotics (72.4%), antiparasitics (47.9%) and antivirals (15.9%). Overall, respondents were RT-PCR positive for a mean of 19.7±7.6 days. Symptoms such as fatigue, anxiety, depression, uneasiness, body pain and dry cough persisted in 76.3% of respondents when they were RT-PCR negative. Conclusion: For most respondents, COVID-19 symptoms extended beyond the period of RT-PCR positivity. Further studies are needed to determine the changing status of COVID-19.

Adjuvant chemotherapy is associated with improved overall survival in select patients with Stage II colon cancer: A National Cancer Database analysis.

BACKGROUND AND OBJECTIVES: Guidelines for Stage II colon cancer recommend adjuvant chemotherapy (AC) only for tumors with high-risk features, but long-term outcomes data are mixed. We aimed to determine if AC was associated with a survival benefit in this population. METHODS: Patients were identified from the National Cancer Database and included if they met the following criteria: diagnosis of Stage II colon cancer, surgery, survival data, and complete data on six high-risk features. The cohort of 57 335 patients was stratified by receipt of AC. Subgroup analysis was performed on patients under the age of 65 years with no comorbidities. Overall survival (OS) was the primary endpoint. RESULTS: An increasing number of high-risk features was associated with significantly decreased median OS. AC was associated with significantly increased OS for patients with 0, 1, 2, and ≥3 high-risk features. On subgroup analysis, receipt of AC was associated with a reduced risk of death (hazard ratio: 0.66; confidence interval: 0.59-0.74). For patients in the subgroup who had a T4 tumor, AC was associated with increased OS (92.7 vs. 83.6 months). CONCLUSIONS: AC should be considered for all younger, healthy patients with Stage II colon cancer and may be associated with a survival benefit for patients with T4 disease.

Patient demographics, clinicopathologic features, and outcomes in wild-type gastrointestinal stromal tumor: a national cohort analysis.

Wild-type KIT and PDGFRA gastrointestinal stromal tumors (GIST) are rare tumors with limited treatment options. We sought to determine the clinicopathologic features of wild-type GIST and identify factors that influence overall survival (OS) using a large national database. Retrospective evaluation of patients with wild-type GIST in the National Cancer Database (NCDB) was performed. Demographic, clinicopathologic, and treatment data were analyzed. Features associated with OS were investigated using Kaplan-Meier analysis and Cox proportional hazards model. 244 patients with median diagnosis age of 59 years (95% CI 57-63) were identified. The stomach was the most common primary site (57%) followed by the small intestine (35%). Surgical resection was performed on 85% of patients and 53% of patients received systemic therapy. Factors associated with decreased OS on multivariable analysis included small intestine primary (HR 2.72, 95% CI 1.13-6.69, P = 0.026) and > 5 mitoses per 50 HPF (HR 4.77, 95% CI 1.86-13.2, P = 0.001). Wild-type GISTs may be identified in older patients, with most arising in the stomach and small bowel. Surgery remains the principal treatment modality. Small intestine primary site and high mitotic count were associated with abbreviated OS.

Molecular dynamic simulation on temperature evolution of SiC under directional microwave radiation.

Silicon carbide (SiC) is widely used as the substrate for high power electronic devices as well as susceptors for microwave (MW) heating. The dynamics of microwave interaction with SiC is not fully understood, especially at the material boundaries. In this paper, we used the molecular dynamics simulation method to study the temperature evolution during the microwave absorption of SiC under various amplitudes and frequencies of the microwave electric field. Directional MW heating of a SiC crystal slab bounded by surfaces along [100] crystallographic direction shows significantly faster melting when the field is applied parallel to the surface compared to when applied perpendicular.