Automated profiling of gene function during embryonic development.

Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C. elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features-including germ layer cell numbers, tissue position, and tissue shape-to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.

A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions.

Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here, we describe a small RNA-Argonaute pathway that ensures early embryonic divisions in C. elegans by employing catalytic slicing activity to broadly tune, instead of silence, germline gene expression. Misregulation of one target, a kinesin-13 microtubule depolymerase, underlies a major phenotype associated with pathway loss. Tuning of target transcript levels is guided by the density of homologous small RNAs, whose generation must ultimately be related to target sequence. Thus, the tuning action of a small RNA-catalytic Argonaute pathway generates oocytes capable of supporting embryogenesis. We speculate that the specialized nature of germline chromatin led to the emergence of small RNA-catalytic Argonaute pathways in the female germline as a post-transcriptional control layer to optimize oocyte composition.

A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue.

High-content screening for gene profiling has generally been limited to single cells. Here, we explore an alternative approach-profiling gene function by analyzing effects of gene knockdowns on the architecture of a complex tissue in a multicellular organism. We profile 554 essential C. elegans genes by imaging gonad architecture and scoring 94 phenotypic features. To generate a reference for evaluating methods for network construction, genes were manually partitioned into 102 phenotypic classes, predicting functions for uncharacterized genes across diverse cellular processes. Using this classification as a benchmark, we developed a robust computational method for constructing gene networks from high-content profiles based on a network context-dependent measure that ranks the significance of links between genes. Our analysis reveals that multi-parametric profiling in a complex tissue yields functional maps with a resolution similar to genetic interaction-based profiling in unicellular eukaryotes-pinpointing subunits of macromolecular complexes and components functioning in common cellular processes.

Cytokinesis in animal cells.

Cytokinesis, the final step in cell division, partitions the contents of a single cell into two. In animal cells, cytokinesis occurs through cortical remodeling orchestrated by the anaphase spindle. Cytokinesis relies on a tight interplay between signaling and cellular mechanics and has attracted the attention of both biologists and physicists for more than a century. In this review, we provide an overview of four topics in animal cell cytokinesis: (a) signaling between the anaphase spindle and cortex, (b) the mechanics of cortical remodeling, (c) abscission, and (d) regulation of cytokinesis by the cell cycle machinery. We report on recent progress in these areas and highlight some of the outstanding questions that these findings bring into focus.

PROMISE Registry: A prostate cancer registry of outcomes and germline mutations for improved survival and treatment effectiveness.

BACKGROUND: Recently approved treatments and updates to genetic testing recommendations for prostate cancer have created a need for correlated analyses of patient outcomes data via germline genetic mutation status. Genetic registries address these gaps by identifying candidates for recently approved targeted treatments, expanding clinical trial data examining specific gene mutations, and understanding effects of targeted treatments in the real-world setting. METHODS: The PROMISE Registry is a 20-year (5-year recruitment, 15-year follow-up), US-wide, prospective genetic registry for prostate cancer patients. Five thousand patients will be screened through an online at-home germline testing to identify and enroll 500 patients with germline mutations, including: pathogenic or likely pathogenic variants and variants of uncertain significance in genes of interest. Patients will be followed for 15 years and clinical data with real time patient reported outcomes will be collected. Eligible patients will enter long-term follow-up (6-month PRO surveys and medical record retrieval). As a virtual study with patient self-enrollment, the PROMISE Registry may fill gaps in genetics services in underserved areas and for patients within sufficient insurance coverage. RESULTS: The PROMISE Registry opened in May 2021. 2114 patients have enrolled to date across 48 US states and 23 recruiting sites. 202 patients have met criteria for long-term follow-up. PROMISE is on target with the study's goal of 5000 patients screened and 500 patients eligible for long-term follow-up by 2026. CONCLUSIONS: The PROMISE Registry is a novel, prospective, germline registry that will collect long-term patient outcomes data to address current gaps in understanding resulting from recently FDA-approved treatments and updates to genetic testing recommendations for prostate cancer. Through inclusion of a broad nationwide sample, including underserved patients and those unaffiliated with major academic centers, the PROMISE Registry aims to provide access to germline genetic testing and to collect data to understand disease characteristics and treatment responses across the disease spectrum for prostate cancer with rare germline genetic variants.

Predictors of Invasive Bacterial Infection in Febrile Infants Aged 2 to 6 Months in the Emergency Department.

Our goal was to identify predictors of invasive bacterial infection (ie, bacteremia and bacterial meningitis) in febrile infants aged 2-6 months. In our multicenter retrospective cohort, older age and lower temperature identified infants at low risk for invasive bacterial infection who could safely avoid routine testing.

Contaminant Organism Growth in Febrile Infants at Low Risk for Invasive Bacterial Infection.

In this multicenter, cross-sectional, secondary analysis of 4042 low-risk febrile infants, nearly 10% had a contaminated culture obtained during their evaluation (4.9% of blood cultures, 5.0% of urine cultures, and 1.8% of cerebrospinal fluid cultures). Our findings have important implications for improving sterile technique and reducing unnecessary cultures.

Consolidation trends in vascular surgery.

BACKGROUND: Practice consolidation by vertical and horizontal integration is a growing trend in surgery. Practice consolidation has not been previously examined in vascular surgery. METHODS: The Medicare Provider Enrollment, Chain, and Ownership System data were used to identify vascular providers and vascular surgery practices in the United States in 2015 and 2020. Practices were categorized as solo (1 surgeon), small (2), medium (3-5), and large (≥6). The number of providers and the number of practices in each size group were determined. The Hirfendahl-Hirshman index (HHI), a measure of market consolidation, was calculated. Provider count, practice size, and HHI were additionally analyzed by urban and rural regions. All values were calculated for each time point and compared. RESULTS: Vascular providers increased in number from 2929 to 3154 (7.7%) from 2015 to 2020. The number of practices decreased from 1351 to 1090 (19.3%). The number of large practices increased by 49.4%; the number of small or solo practices decreased by 42.1%. The mean HHI increased from 0.486 in 2015 to 0.498 in 2020. Both urban and rural regions had a decrease in solo practices (43.3% and 2.3%, respectively) and an increase in HHI (from 0.499 to 0.509 and 0.793 to 0.818, respectively). All changes were statistically significant. CONCLUSIONS: From 2015 to 2020, there is a trend toward vascular providers working in larger practice groups and a corresponding increase in measures of market consolidation.

Perioperative Outcomes After Adrenalectomy for Secondary Adrenal Malignancy.

INTRODUCTION: The risk of adverse outcomes after adrenal metastasectomy is not well defined. Knowledge of these risks is essential to guide patient counseling. METHODS: The 2015-2020 National Surgical Quality Improvement Program datasets were combined. Patients who underwent adrenalectomy for secondary adrenal malignancy (SM) and benign nonfunctional (BNF) adrenal neoplasms were identified; BNF neoplasms were chosen as a comparison as functional neoplasms can contribute to comorbidity. Patients who had additional surgery at the time of adrenalectomy were excluded. Patient demographics, comorbidities, perioperative factors, and outcomes were compared between groups. Multivariable logistic regression analysis was performed. RESULTS: Of 3496 adrenalectomy patients, 332 had SM and 3164 had BNF neoplasms. Patients with SM were older (65 versus 54 y) and more often had chronic obstructive pulmonary disease (7.5% versus 4.4%), chronic steroid use (10.5% versus 3.8%), and bleeding disorders (4.5% versus 2.2%) than patients with BNF, respectively (P < 0.01 for all). Laparoscopic adrenalectomy was the most common operative approach for both groups (74.7% versus 88.3%). Rates of mortality, morbidity, reoperation, readmission, and nonhome discharge did not differ significantly between groups. Patients with SM had higher rates of postoperative bleeding than patients with BNF (6.3% versus 2.6%, P < 0.001). This persisted on multivariable regression analysis that adjusted for demographics, comorbidities, and operative approach (odds ratio 2.34, 95% confidence interval 1.19-4.64). CONCLUSIONS: Adrenalectomy for SM is associated with an increased risk of postoperative bleeding compared to adrenalectomy for BNF adrenal neoplasms. Patients with SM that meet criteria for adrenal metastasectomy should be counseled appropriately.

Adrenalectomy Outcome Variations Across Different Functional Adrenal Tumors.

INTRODUCTION: Adrenalectomy generally has favorable outcomes. It is unknown if patients with functional adrenal tumors experience different clinical outcomes than those with benign adrenal tumors, due to the presence of comorbid conditions secondary to the functional tumor. We investigated outcomes following open and laparoscopic adrenalectomy for benign nonfunctional (BNF) versus functional adrenal masses. METHODS: Patients undergoing adrenalectomy were identified in the 2015-2020 National Surgical Quality Improvement Program database, then categorized as BNF, hyperaldosteronism, hypercortisolism, and pheochromocytoma. The primary outcome of interest was 30-d morbidity and secondary outcomes included 30-d mortality, 30-d readmission, and postoperative length of stay (LOS). Subgroup analysis was performed based upon surgical approach. Univariate analysis was performed, followed by multivariable logistic regression for individual outcomes that differed significantly between patients with BNF and functional neoplasm, factoring in patient demographics and operative approach with statistical significance on univariate analysis. Descriptive statistics and outcomes were analyzed using Pearson's χ2 test and Mann-Whitney U-test as appropriate. RESULTS: There were 3291 patients with BNF while 484 had hyperaldosteronism, 263 hypercortisolism, and 46 pheochromocytomas. Within the laparoscopic group of 3615 (88.5%) of adrenalectomy patients, compared to BNF patients, patients with hyperaldosteronism had lower rates of postoperative morbidity (1.9% versus 5.2%, P < 0.001) and shorter LOS (1 d, interquartile range (IQR) [1-1] versus 1d IQR [1-2], P = 0.003); these persisted on multivariate analysis (OR 0.32, 95% confidence interval [CI] 0.14-0.74 and odds ratio 0.47, 95% CI 0.36-0.60, P < 0.001). Patients with hypercortisolism had higher morbidity (7.3% versus 5.2%, P < 0.001), 30-d readmission rates (5.3% versus 2.9%, P = 0.042) and longer LOS (2d, IQR [1-3] versus 1d, IQR [1-2, P < 0.001). On multivariate analysis, presence of hypercortisolism was independently associated with increased likelihood of readmission within 30 d (OR 2.20, 95% CI 1.11-2.99, P = 0.012) and longer LOS (>1 d) (OR 1.79, 95% CI 1.33-2.40, P < 0.001). Compared to BNF patients, patients with pheochromocytoma had higher rates of postoperative morbidity (6.2% versus 5.2%, P < 0.001). Within the open group of 469 (11.5% of adrenalectomy patients), there were no statistically significant differences in outcomes between patients with BNF and functional adrenal masses. CONCLUSIONS: Outcomes after adrenalectomy performed for functional neoplasms differ based on surgical indication.

Wilms Tumor With Raised Serum Alpha-Fetoprotein: Highlighting the Need for Novel Circulating Biomarkers.

Wilms tumor (WT) is the commonest cause of renal cancer in children. In Europe, a diagnosis is made for most cases on typical clinical and radiological findings, prior to pre-operative chemotherapy. Here, we describe a case of a young boy presenting with a large abdominal tumor, associated with raised serum alpha-fetoprotein (AFP) levels at diagnosis. Given the atypical features present, a biopsy was taken, and histology was consistent with WT, showing triphasic WT, with epithelial, stromal, and blastemal elements present, and positive WT1 and CD56 immunohistochemical staining. During pre-operative chemotherapy, serial serum AFP measurements showed further increases, despite a radiological response, before a subsequent fall to normal following nephrectomy. The resection specimen was comprised of ~55% and ~45% stromal and epithelial elements, respectively, with no anaplasia, but immunohistochemistry using AFP staining revealed positive mucinous intestinal epithelium, consistent with the serum AFP observations. The lack of correlation between tumor response and serum AFP levels in this case highlights a more general clinical unmet need to identify WT-specific circulating tumor markers.

A case of restrictive dermopathy in a Hutterite newborn: Diagnosis and creative skin-directed management.

Restrictive dermopathy is a lethal autosomal recessive disease characterized by tightly adherent skin, distinctive facial dysmorphisms, arthrogryposis, and pulmonary hypoplasia. While clinical findings are unique, histopathology and genetic analysis are critical for early diagnostic confirmation and to initiate appropriate management for this lethal disease. We report on a preterm Hutterite male neonate with biallelic ZMPSTE24 mutations to highlight the clinical and histopathological features of restrictive dermopathy and share our skin-directed management strategies.

Mendelian randomization identifies blood metabolites previously linked to midlife cognition as causal candidates in Alzheimer's disease.

There are currently no disease-modifying treatments for Alzheimer's disease (AD), and an understanding of preclinical causal biomarkers to help target disease pathogenesis in the earliest phases remains elusive. Here, we investigated whether 19 metabolites previously associated with midlife cognition-a preclinical predictor of AD-translate to later clinical risk, using Mendelian randomization (MR) to tease out AD-specific causal relationships. Summary statistics from the largest genome-wide association studies (GWASs) for AD and metabolites were used to perform bidirectional univariable MR. Bayesian model averaging (BMA) was additionally performed to address high correlation between metabolites and identify metabolite combinations that may be on the AD causal pathway. Univariable MR indicated four extra-large high-density lipoproteins (XL.HDL) on the causal pathway to AD: free cholesterol (XL.HDL.FC: 95% CI = 0.78 to 0.94), total lipids (XL.HDL.L: 95% CI = 0.80 to 0.97), phospholipids (XL.HDL.PL: 95% CI = 0.81 to 0.97), and concentration of XL.HDL particles (95% CI = 0.79 to 0.96), significant at an adjusted P < 0.009. MR-BMA corroborated XL.HDL.FC to be among the top three causal metabolites, in addition to total cholesterol in XL.HDL (XL.HDL.C) and glycoprotein acetyls (GP). Both XL.HDL.C and GP demonstrated suggestive univariable evidence of causality (P < 0.05), and GP successfully replicated within an independent dataset. This study offers insight into the causal relationship between metabolites demonstrating association with midlife cognition and AD. It highlights GP in addition to several XL.HDLs-particularly XL.HDL.FC-as causal candidates warranting further investigation. As AD pathology is thought to develop decades prior to symptom onset, expanding on these findings could inform risk reduction strategies.

Overcoming NMR line broadening of nitrogen containing compounds: A simple solution.

This study presents a straightforward solution to the challenge of elucidating the structures of nitrogen containing compounds undergoing isomerization. When spectral line broadening occurs related to isomerization, be it prototropic tautomerism or bond rotations, this poses a significant obstacle to structural elucidation. By adding acids, we demonstrate a simple approach to overcome this issue and effectively sharpen NMR signals for acid stable prototropic tautomers as well as the conformational isomers containing a morpholine or piperazine ring.

Common infections and neuroimaging markers of dementia in three UK cohort studies.

INTRODUCTION: We aimed to investigate associations between common infections and neuroimaging markers of dementia risk (brain volume, hippocampal volume, white matter lesions) across three population-based studies. METHODS: We tested associations between serology measures (pathogen serostatus, cumulative burden, continuous antibody responses) and outcomes using linear regression, including adjustments for total intracranial volume and scanner/clinic information (basic model), age, sex, ethnicity, education, socioeconomic position, alcohol, body mass index, and smoking (fully adjusted model). Interactions between serology measures and apolipoprotein E (APOE) genotype were tested. Findings were meta-analyzed across cohorts (Nmain  = 2632; NAPOE-interaction  = 1810). RESULTS: Seropositivity to John Cunningham virus associated with smaller brain volumes in basic models (ß = -3.89 mL [-5.81, -1.97], Padjusted  < 0.05); these were largely attenuated in fully adjusted models (ß = -1.59 mL [-3.55, 0.36], P = 0.11). No other relationships were robust to multiple testing corrections and sensitivity analyses, but several suggestive associations were observed. DISCUSSION: We did not find clear evidence for relationships between common infections and markers of dementia risk. Some suggestive findings warrant testing for replication.

Differential Effects of an Emergency Department-to-Home Care Transitions Intervention in an Older Adult Population: A Latent Class Analysis.

BACKGROUND: Older adults frequently return to the emergency department (ED) within 30 days of a visit. High-risk patients can differentially benefit from transitional care interventions. Latent class analysis (LCA) is a model-based method used to segment the population and test intervention effects by subgroup. OBJECTIVES: We aimed to identify latent classes within an older adult population from a randomized controlled trial evaluating the effectiveness of an ED-to-home transitional care program and test whether class membership modified the intervention effect. RESEARCH DESIGN: Participants were randomized to receive the Care Transitions Intervention or usual care. Study staff collected outcomes data through medical record reviews and surveys. We performed LCA and logistic regression to evaluate the differential effects of the intervention by class membership. SUBJECTS: Participants were ED patients (age 60 y and above) discharged to a community residence. MEASURES: Indicator variables for the LCA included clinically available and patient-reported data from the initial ED visit. Our primary outcome was ED revisits within 30 days. Secondary outcomes included ED revisits within 14 days, outpatient follow-up within 7 and 30 days, and self-management behaviors. RESULTS: We interpreted 6 latent classes in this study population. Classes 1, 4, 5, and 6 showed a reduction in ED revisit rates with the intervention; classes 2 and 3 showed an increase in ED revisit rates. In class 5, we found evidence that the intervention increased outpatient follow-up within 7 and 30 days (odds ratio: 1.81, 95% CI: 1.13-2.91; odds ratio: 2.24, 95% CI: 1.25-4.03). CONCLUSIONS: Class membership modified the intervention effect. Population segmentation is an important step in evaluating a transitional care intervention.

Missed Opportunities to Diagnose and Treat Tertiary Hyperparathyroidism After Transplant.

INTRODUCTION: Tertiary hyperparathyroidism (3HPT) is common after renal transplant. However, guidelines for diagnosis are not clear and few patients are treated surgically. This study aims to determine rates of diagnosis and treatment of 3HPT in renal transplant patients with hypercalcemia. MATERIALS AND METHODS: This retrospective chart review identified all renal transplant recipients at a single tertiary care institution between 2011 and 2021. Patients with post-transplant hypercalcemia (> 10.2 mg/dL) were identified. The time in months of index hypercalcemia was noted. Measurement of parathyroid hormone (PTH) levels after index hypercalcemia was determined and noted as elevated if > 64 pg/mL at least 6 mo after transplant. Documentation of symptoms of hyperparathyroidism, a diagnosis of hyperparathyroidism in the electronic medical record, and medical or surgical management of patients with classic 3HPT (elevated calcium and PTH) were determined. RESULTS: Of 383 renal transplant recipients, hypercalcemia was identified in 132 patients. The majority of hypercalcemic patients had PTH levels measured (127, 96.2%). PTH was elevated in 109 (82.6%). Among the 109 patients with classic 3HPT, 54 (49.5%) had a documented diagnosis of hyperparathyroidism in the electronic medical record (P = 0.01). Kidney stones or abnormal DEXA scan were present in 16 (14.7%) and 18 (16.5%), respectively. Most patients were managed non-surgically (101, 92.6%); calcimimetics were prescribed for 42 (38.5%, P = 0.01). Eight (7.3%) patients with classic 3HPT were referred to a surgeon (P = 0.35); all were initially prescribed calcimimetics (P = 0.001). CONCLUSIONS: 3HPT is underdiagnosed in patients with elevated calcium and PTH levels post-transplant. A significant percentage of these patients go without surgical referral and curative treatment.

From Debt to Dollars: Assessing a General Surgeon's Career Value.

INTRODUCTION: Surgical residents make decisions that may have a dramatic impact on career earnings based off conceptions regarding future income potential. This study examines the effect of debt burden, repayment plan, and practice setting on a general surgeon's career value. METHODS: Debt levels, repayment plans, and practice setting were considered to model a surgeon's career value using net present value (NPV) across 35 scenarios. The NPV was calculated using salary, education debt, yearly spending, and a discount rate of 5%. Salary data were obtained from the Medical Group Management Association, student debt information from the Association of American Medical Colleges, and tax and household spending data from U.S. government records. Assumptions included no gaps in training, no prior debt, single-person household, and career duration of 35 y. RESULTS: A general surgeon's salary adequately repays debt burdens from $100,000-$300,000 over 10-25 y, regardless of repayment plan or practice setting. Practice setting decreased career value for academic surgeons when debt burden and repayment plan were held constant: the NPV for an academic surgeon was $382,000 compared to $500,000 for a nonacademic surgeon with the same debt and repayment plan. Debt burden repaid through unsubsidized and income-based repayment plans reduced NPV for all surgeons, while subsidized plans increased NPV. The projected NPV for all scenarios ranged $2.35M-$2.87 M. CONCLUSIONS: Though the modeled scenarios do not account for prior debt burden, major expenditures, or increases in yearly household spending beyond national averages, surgery residents should be aware that general surgery remains a financially feasible career.

Mega-disturbances cause rapid decline of mature conifer forest habitat in California.

Mature forests provide important wildlife habitat and support critical ecosystem functions globally. Within the dry conifer forests of the western United States, past management and fire exclusion have contributed to forest conditions that are susceptible to increasingly severe wildfire and drought. We evaluated declines in conifer forest cover in the southern Sierra Nevada of California during a decade of record disturbance by using spatially comprehensive forest structure estimates, wildfire perimeter data, and the eDaRT forest disturbance tracking algorithm. Primarily due to the combination of wildfires, drought, and drought-associated beetle epidemics, 30% of the region's conifer forest extent transitioned to nonforest vegetation during 2011-2020. In total, 50% of mature forest habitat and 85% of high density mature forests either transitioned to lower density forest or nonforest vegetation types. California spotted owl protected activity centers (PAC) experienced greater canopy cover decline (49% of 2011 cover) than non-PAC areas (42% decline). Areas with high initial canopy cover and without tall trees were most vulnerable to canopy cover declines, likely explaining the disproportionate declines of mature forest habitat and within PACs. Drought and beetle attack caused greater cumulative declines than areas where drought and wildfire mortality overlapped, and both types of natural disturbance far outpaced declines attributable to mechanical activities. Drought mortality that disproportionately affects large conifers is particularly problematic to mature forest specialist species reliant on large trees. However, patches of degraded forests within wildfire perimeters were larger with greater core area than those outside burned areas, and remnant forest habitats were more fragmented within burned perimeters than those affected by drought and beetle mortality alone. The percentage of mature forest that survived and potentially benefited from lower severity wildfire increased over time as the total extent of mature forest declined. These areas provide some opportunity for improved resilience to future disturbances, but strategic management interventions are likely also necessary to mitigate worsening mega-disturbances. Remaining dry mature forest habitat in California may be susceptible to complete loss in the coming decades without a rapid transition from a conservation paradigm that attempts to maintain static conditions to one that manages for sustainable disturbance dynamics.

Coupling-Condensation Strategy for the Convergent Synthesis of an Imidazole-Fused 2-Aminoquinoline NLRP3 Agonist.

The development of a convergent route to the NLRP3 (nucleotide-binding domain and leucine-rich repeat-containing protein 3) agonist BMS-986299 is reported. The synthesis relies on a key Miyaura borylation and a tandem Suzuki-Miyaura coupling between an iodoimidazole and an o-aminochloroarene, followed by acid-mediated cyclization to afford the aminoquinoline core. The subsequent Boc cleavage and regioselective acylation afford the target compound. Two routes to the iodoimidazole intermediate are presented, along with the synthesis of the o-aminochloroarene via Negishi coupling. The convergent six-step route leads to an 80% reduction in process mass intensity compared to the linear enabling synthesis.