Single-Molecule Surface-Enhanced Raman Spectroscopy: Challenges, Opportunities, and Future Directions.

Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) is a powerful experimental technique for label-free sensing, imaging, and chemical analysis. Although Raman spectroscopy itself is an extremely "feeble" phenomenon, the intense interaction of optical fields with metallic nanostructures in the form of plasmonic hotspots can generate Raman signals from single molecules. While what constitutes a true single-molecule signal has taken some years for the scientific community to establish, many SERS experiments, even those not specifically attempting single-molecule sensitivity, have observed fluctuation in both the SERS intensity and spectral features. In this Perspective, we discuss the impact that fluctuating SERS signals have had on the continuing advancement of SM-SERS, along with challenges and current and potential future applications.

Noninvasive brain stimulation during EEG improves machine learning classification in chronic stroke.

BACKGROUND: In individuals with chronic stroke and hemiparesis, noninvasive brain stimulation (NIBS) may be used as an adjunct to therapy for improving motor recovery. Specific states of movement during motor recovery are more responsive to brain stimulation than others, thus a system that could auto-detect movement state would be useful in correctly identifying the most effective stimulation periods. The aim of this study was to compare the performance of different machine learning models in classifying movement periods during EEG recordings of hemiparetic individuals receiving noninvasive brain stimulation. We hypothesized that transcranial direct current stimulation, a form of NIBS, would modulate brain recordings correlating with movement state and improve classification accuracies above those receiving sham stimulation. METHODS: Electroencephalogram data were obtained from 10 participants with chronic stroke and 11 healthy individuals performing a motor task while undergoing transcranial direct current stimulation. Eight traditional machine learning algorithms and five ensemble methods were used to classify two movement states (a hold posture and an arm reaching movement) before, during and after stimulation. To minimize compute times, preprocessing and feature extraction were limited to z-score normalization and power binning into five frequency bands (delta through gamma). RESULTS: Classification of disease state produced significantly higher accuracies in the stimulation (versus sham) group at 78.9% (versus 55.6%, p < 0.000002). We observed significantly higher accuracies when classifying stimulation state in the chronic stroke group (77.6%) relative to healthy controls (64.1%, p < 0.0095). In the chronic stroke cohort, classification of hold versus reach was highest during the stimulation period (75.2%) as opposed to the pre- and post-stimulation periods. Linear discriminant analysis, logistic regression, and decision tree algorithms classified movement state most accurately in participants with chronic stroke during the stimulation period (76.1%). For the ensemble methods, the highest classification accuracy for hold versus reach was achieved using low gamma frequency (30-50 Hz) as a feature (74.5%), although this result did not achieve statistical significance. CONCLUSIONS: Machine learning algorithms demonstrated sufficiently high movement state classification accuracy in participants with chronic stroke performing functional tasks during noninvasive brain stimulation. tDCS improved disease state and movement state classification in participants with chronic stroke.

C-L Case Conference: The interaction between emotional dysregulation and chronic critical illness in a patient with a terminal personality disorder.

We present a case of a patient who presented for endocarditis and subsequently had a prolonged and challenging hospital course, with much of it spent in the intensive care unit (ICU). Throughout their hospitalization, personality factors, combined with impaired communication and pain in severe medical illness, led to challenging behaviors of disengagement, impulsivity, splitting, agitation, and suicidal statements. Experts in critical care psychiatry review the case and its key elements, including principles of critical care psychiatry and pharmacologic management of ICU patients; communication problems in ICU patients and associated psychiatric distress; the benefits of proactive consultation for challenging patients; and the construct of post-intensive care syndrome. Patients with personality disorders often struggle to cope with severe medical illness, leading to challenging, self-defeating behaviors. Such acts are even more difficult to manage in intensive care, where a patient's tenuous medical status depends on smooth interactions between them and the medical team. We address how these challenges may be mitigated in collaboration with a psychiatric consult team.

Incidence and risk factors for invasive fungal infections in patients initiating TNF-alpha inhibitors for inflammatory bowel disease and rheumatoid arthritis.

In a commercial claims database analysis, <0.5% of patients with inflammatory bowel disease or rheumatoid arthritis developed an IFI within one year of initiating TNF-alpha therapy. Histoplasmosis was the most common IFI type. Overall IFI incidence varied based on region, underlying conditions, and use of certain immunosuppressive medications.

Endothelial ß1 Integrins are Necessary for Microvascular Function and Glucose Uptake.

Microvascular insulin delivery to myocytes is rate limiting for the onset of insulin-stimulated muscle glucose uptake. The structural integrity of capillaries of the microvasculature is regulated, in part, by a family of transmembrane adhesion receptors known as integrins, which are composed of an α and ß subunit. The integrin ß1 (itgß1) subunit is highly expressed in endothelial cells (EC). EC itgß1 is necessary for the formation of capillary networks during embryonic during development and its knockdown in adult mice blunts the reactive hyperemia that manifests during ischemia reperfusion. In this study we investigated the contribution of skeletal muscle EC itgß1 in microcirculatory function and glucose uptake. We hypothesized that loss of EC itgß1 would impair microvascular hemodynamics and glucose uptake during insulin stimulation, creating 'delivery'-mediated insulin resistance. An itgß1 knockdown mouse model was developed to avoid lethality of embryonic gene knockout and the deteriorating health resulting from early post-natal inducible gene deletion. We found that mice with (itgß1fl/flSCLcre) and without (itgß1fl/fl) inducible stem cell leukemia cre recombinase (SLCcre) expression at 10 days post cre induction have comparable exercise tolerance and pulmonary and cardiac functions. We quantified microcirculatory hemodynamics using intravital microscopy and the ability of mice to respond to the high metabolic demands of insulin-stimulated muscle using a hyperinsulinemic-euglycemia clamp. We show that itgß1fl/flSCLcre mice compared to itgß1fl/fl littermates have, i) deficits in capillary flow rate, flow heterogeneity, and capillary density; ii) impaired insulin-stimulated glucose uptake despite sufficient transcapillary insulin efflux; and iii) reduced insulin-stimulated glucose uptake due to perfusion-limited glucose delivery. Thus, EC itgß1 is necessary for microcirculatory function and to meet the metabolic challenge of insulin stimulation.

Links between fecal microplastics and parameters related to metabolic dysfunction-associated steatotic liver disease (MASLD) in humans: An exploratory study.

Microplastics (MPs) can persist in the environment and human body. Murine studies showed that exposure to MPs could cause metabolic dysregulation, contributing metabolic dysfunction-associated steatotic liver disease (MASLD) or steatohepatitis (MASH). However, research on the role of MPs in humans is limited. Thus, we aimed to assess links between human fecal MPs and liver histology, gene expression, immune cells and intestinal microbiota (IM). We included 6 lean healthy liver donors and 6 normal liver (obese) and 11 MASH patients. Overall, pre-BSx, we observed no significant differences in fecal MPs between groups. However, fecal MP fibers and total MPs positively correlated with portal and total macrophages and total killer T cells while total fecal MPs were positively correlated with natural killer cells. Additionally, 19 genes related to immune system and apoptosis correlated with fecal MPs at baseline. Fecal MP fibers correlated positively with fecal Bifidobacterium and negatively with Lachnospiraceae. Patients with MASH (n = 11) were re-assessed 12-months post-bariatric surgery (BSx) and we found that those with persistent disease (n = 4) had higher fecal MP fragments than those with normalized liver histology (n = 7). At 12-month post-BSx, MP fragments positively correlated with helper T cells and total MPs positively correlated with natural killer T cells and B cells. Our study is the first to look at 1) the role of MPs in MASH and its association with IM, immune cells and hepatic gene expression and 2) look at the role of MPs longitudinally in MASH persistence following BSx. Future research should further explore this relationship.

Spatial Transcriptomics Analysis: Maternal Obesity Impairs Myogenic Cell Migration and Differentiation during Embryonic Limb Development.

Limb muscle is responsible for physical activities and myogenic cell migration during embryogenesis is indispensable for limb muscle formation. Maternal obesity (MO) impairs prenatal skeletal muscle development, but the effects of MO on myogenic cell migration remain to be examined. C57BL/6 mice embryos were collected at E13.5. The GeoMx DSP platform was used to customize five regions along myogenic cell migration routes (myotome, dorsal/ventral limb, limb stroma, limb tip), and data were analyzed by GeomxTools 3.6.0. A total of 2224 genes were down-regulated in the MO group. The GO enrichment analysis showed that MO inhibited migration-related biological processes. The signaling pathways guiding myogenic migration such as hepatocyte growth factor signaling, fibroblast growth factor signaling, Wnt signaling and GTPase signaling were down-regulated in the MO E13.5 limb tip. Correspondingly, the expression levels of genes involved in myogenic cell migration, such as Pax3, Gab1, Pxn, Tln2 and Arpc, were decreased in the MO group, especially in the dorsal and ventral sides of the limb. Additionally, myogenic differentiation-related genes were down-regulated in the MO limb. MO impedes myogenic cell migration and differentiation in the embryonic limb, providing an explanation for the impairment of fetal muscle development and offspring muscle function due to MO.

Borafluorene-Mediated Sulfur Activation: Isolation of Boryl-Linked S7 and S8 Catenates and Related Chalcogenide Molecules.

Although the activation of elemental sulfur by main group compounds is well-documented in the literature, the products of such reactions are often heterocyclic in nature. However, the isolation and characterization of sulfur catenates (i.e., acyclic sulfur chains) is significantly less common. In this study, we report the activation of elemental sulfur by the 9-CAAC-9-borafluorene radical (1) and anion (2) (CAAC = (2,6-diisopropylphenyl)-4,4-diethyl-2,2-dimethyl-pyrrolidin-5-ylidene) to form boron-sulfur catenates (3-6). From the isolation of the octasulfide-bridged compound 3, a sulfur extrusion reaction using 1,3,4,5-tetramethylimidazol-2-ylidene (IMe4) was used to decrease the sulfide chain length from eight to seven (4). Bonding analysis of compounds 3-6 was performed using density functional theory, which elucidated the nature of the sulfur-sulfur bonding observed within these compounds. We also report the synthesis of a series of borafluorene-chalcogenide species (7-9), via diphenyl dichalcogenide activation, which portray characteristics described by an internal heavy atom effect. Compounds 7-9 each exhibit blue fluorescence, with the lowest energy emissive process (S2 → S0) at 436 nm (7 and 8) and 431 nm (9). The S1 → S0 emission is not observed experimentally due to a Laporte forbidden transition. Density functional theory was employed to investigate the frontier molecular orbitals and absorption and emission profiles of compounds 7-9.

Ulnar shaft diameter as it relates to plate osteosynthesis: A cadaveric study.

Background: Ulnar shaft fractures are common and the standard of care treatment is with 3.5 â€‹mm plating. The purpose of this study was to measure diameters along the length of the ulna to provide information on screw length and appropriateness of 3.5 â€‹mm screws and plate location. Methods: Ten embalmed cadaveric ulnas were dissected free of all soft tissues. The length of the ulna was measured and then divided by four. Transverse osteotomies were performed along the length of the ulna at », ½ and ¾ its full length. The diameter of the ulna at these locations was then measured in a radio-ulnar direction as well as a volar-dorsal direction. Results: There were five female and five male specimens with an average age of 83.6 and 78.8 respectively. The smallest diameter in both the female and male specimens was in the distal ¾ shaft measured in a volar-dorsal direction with an average of 9.1 â€‹mm and 12 â€‹mm. The average volar-dorsal measurement was less than radio-ulnar measurement at all locations. The diameters increased along the ulna heading proximally. Conclusion: This study provides information pertinent to screw width and length with respect to the ulnar shaft and calls in to question the use of 3.5 â€‹mm screws in the distal and midshaft ulnar diaphysis in females. Removal of 3.5 â€‹mm screws in the mid and distal ulnar shaft in females can leave a hole corresponding to 23% and 27% of the bone which can be concerning for a stress riser.

Association Between Intraoperative Cataract Surgical Complications and Mortality.

PURPOSE: To evaluate the association between intraoperative complications of cataract surgery and postoperative mortality. METHODS: A retrospective review of patients who underwent cataract surgery at our institution from 2014 to 2020 was conducted. Intraoperative complications included choroidal hemorrhage, posterior capsule rupture, vitreous loss, retained lens, and/or severe zonular dialysis in either eye. All-cause mortality statistics were obtained through a collaborative agreement with the Colorado Department of Public Health and Environment. Hazard ratios (HRs) from Cox proportional hazard models were used to estimate survival following cataract surgery. RESULTS: Among 8,054 patients, the mean follow-up time was 4.4 (SD = 2.3) years and the mortality rate was 15% (n = 1,175). The overall complication rate was 2.2% (n = 181), and the rate of retained lens was 0.7% (n = 58). In univariate analysis, retained lens (HR: 1.86, 95% CI: 1.08-3.21, p = 0.026), severe zonular dialysis (HR: 2.00, 95% CI: 1.29-3.12, p = 0.002), and any intraoperative complication (HR: 1.51, 95% CI: 1.09-2.11, p = 0.015) were associated with higher hazard of mortality. When adjusted for demographic factors, comorbid medical conditions, and pre-operative visual acuity, intraoperative complications were not associated with mortality. CONCLUSION: Intraoperative cataract surgery complications were associated with mortality in univariate analysis. However, this association was not significant in the multivariable analysis as it is confounded by other factors such as pre-operative visual acuity.

Lower Extremity Hockey Puck Impaction Fractures in Professional Hockey Players: A Case Series and Review of the Literature.

Hockey is a contact sport notorious for injuries. The hockey puck is a projectile that can impart substantial energy when it impacts a player. Hockey puck impact is a frequent and underreported cause of injury. This case report describes the clinical course of 3 professional hockey players who sustained injuries to the lower leg and ankle from projectile hockey pucks. Each player sustained a unique injury with associated complications affecting return to play. We aim to bring attention to this injury mechanism that can cause significant morbidity among players.Levels of Evidence: IV.

Malignant Rhabdoid Tumor and Related Pediatric Tumors: Multimodality Imaging Review with Pathologic Correlation.

Malignant rhabdoid tumors (MRTs) are rare but lethal solid neoplasms that overwhelmingly affect infants and young children. While the central nervous system is the most common site of occurrence, tumors can develop at other sites, including the kidneys and soft tissues throughout the body. The anatomic site of involvement dictates tumor nomenclature and nosology. While the clinical and imaging manifestations of MRTs and other more common entities may overlap, there are some site-specific distinctive imaging characteristics. Irrespective of the site of occurrence, somatic and germline mutations in SMARCB1, and rarely in SMARCA4, underlie the entire spectrum of rhabdoid tumors. MRTs have a simple and remarkably stable genome but can demonstrate considerable molecular and biologic heterogeneity. Related neoplasms encompass an expanding category of phenotypically dissimilar (nonrhabdoid tumors driven by SMARC-related alterations) entities. US, CT, MRI, and fluorodeoxyglucose PET/CT or PET/MRI facilitate diagnosis, initial staging, and follow-up, thus informing therapeutic decision making. Multifocal synchronous or metachronous rhabdoid tumors occur predominantly in the context of underlying rhabdoid tumor predisposition syndromes (RTPSs). These autosomal dominant disorders are driven in most cases by pathogenic variants in SMARCB1 (RTPS type 1) and rarely by pathogenic variants in SMARCA4 (RTPS type 2). Genetic testing and counseling are imperative in RTPS. Guidelines for imaging surveillance in cases of RTPS are based on age at diagnosis. ©RSNA, 2024 Supplemental material is available for this article.

Implementation of single high-dose liposomal amphotericin B based induction therapy for treatment of HIV-associated cryptococcal meningitis in Uganda: a comparative prospective cohort study.

BACKGROUND: In 2022, the World Health Organization (WHO) recommended a single 10mg/kg dose of liposomal amphotericin B in combination with 14 days of flucytosine and fluconazole (AMBITION-cm regimen) for induction therapy of HIV-associated cryptococcal meningitis, based on the results of the multisite AMBITION-cm trial. We evaluated outcomes after real-world implementation of this novel regimen in Uganda. METHODS: We enrolled Ugandan adults with cryptococcal meningitis into an observational cohort receiving the AMBITION-cm regimen with therapeutic lumbar punctures in routine care during 2022-2023. We compared 10-week survival and CSF early fungicidal activity with the outcomes observed in the AMBITION-cm clinical trial conducted at the same sites. RESULTS: During 2022-2023, 179 adults were treated with the AMBITION-cm regimen via routine care and compared to the 171 adults randomized to the AMBITION-cm trial interventional arm in Uganda from 2018-2021. No significant difference in 10-week survival occurred between the observational cohort (68.6%; 95%CI 61.6%-76.3%) and AMBITION-cm trial participants in the intervention arm (71.7%; 95%CI 65.2%-78.8%; absolute risk difference = -3.1%; 95%CI -13.1% to 6.9%; p=.61). Early fungicidal activity did not differ (0.42 vs 0.39 log10CFU/mL/day; p=.80) between groups. Among observational cohort participants discharged alive initially and for whom follow up data were available, the incidence of re-hospitalizations due to persistently elevated intracranial pressure was 2.8% (4/144). CONCLUSION: The AMBITION-cm regimen for cryptococcal meningitis resulted in similar outcomes as observed in the AMBITION-cm clinical trial when implemented in routine care. Intracranial pressure management during hospitalization and awareness after discharge are key components of optimizing outcomes.

Methods for constructing and evaluating consensus genomic interval sets.

The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing regions across experiments, but also by necessity lose precision in region definitions. We require methods to assess this loss of precision and build optimal consensus region sets. Here, we introduce the concept of flexible intervals and propose three novel methods for building consensus region sets, or universes: a coverage cutoff method, a likelihood method, and a Hidden Markov Model. We then propose three novel measures for evaluating how well a proposed universe fits a collection of region sets: a base-level overlap score, a region boundary distance score, and a likelihood score. We apply our methods and evaluation approaches to several collections of region sets and show how these methods can be used to evaluate fit of universes and build optimal universes. We describe scenarios where the common approach of merging regions to create consensus leads to undesirable outcomes and provide principled alternatives that provide interoperability of interval data while minimizing loss of resolution.

Concurrent tDCS-fMRI after stroke reveals link between attention network organization and motor improvement.

Restoring motor function after stroke necessitates involvement of numerous cognitive systems. However, the impact of damage to motor and cognitive network organization on recovery is not well understood. To discover correlates of successful recovery, we explored imaging characteristics in chronic stroke subjects by combining noninvasive brain stimulation and fMRI. Twenty stroke survivors (6 months or more after stroke) were randomly assigned to a single session of transcranial direct current stimulation (tDCS) or sham during image acquisition. Twenty healthy subjects were included as controls. tDCS was limited to 10 min at 2 mA to serve as a mode of network modulation rather than therapeutic delivery. Fugl-Meyer Assessments (FMA) revealed significant motor improvement in the chronic stroke group receiving active stimulation (p = 0.0005). Motor changes in this group were correlated in a data-driven fashion with imaging features, including functional connectivity (FC), surface-based morphometry, electric field modeling and network topology, focusing on relevant regions of interest. We observed stimulation-related changes in FC in supplementary motor (p = 0.0029), inferior frontal gyrus (p = 0.0058), and temporo-occipital (p = 0.0095) areas, though these were not directly related to motor improvement. The feature most strongly associated with FMA improvement in the chronic stroke cohort was graph topology of the dorsal attention network (DAN), one of the regions surveyed and one with direct connections to each of the areas with FC changes. Chronic stroke subjects with a greater degree of motor improvement had lower signal transmission cost through the DAN (p = 0.029). While the study was limited by a small stroke cohort with moderate severity and variable lesion location, these results nevertheless suggest a top-down role for higher order areas such as attention in helping to orchestrate the stroke recovery process.

Extent of Radiolytic Damage from Liquid Cell TEM Experiments on Metal-Organic Frameworks via Post-Mortem 4D-STEM.

We report a systematic analysis of electron beam damage of the zeolitic imidazolate framework (ZIF-8) during liquid cell transmission electron microscopy (LCTEM). Our analysis reveals ZIF-8 morphology is strongly affected by solvent used (water vs dimethylformamide), electron flux applied, and imaging mode (i.e., TEM vs STEM), while ZIF-8 crystallinity is primarily affected by accumulated electron fluence. Our observations indicate that the stability of ZIF-8 morphology is higher in dimethylformamide (DMF) than in water. However, in situ electron diffraction indicates that ZIF-8 nanocrystals lose crystallinity at critical fluence of ∼80 e-Å-2 independent of the presence of solvent. Furthermore, 4D-STEM analysis as a post-mortem method reveals the extent of electron beam damage beyond the imaging area and indicates that radiolytic reactions are more pronounced in TEM mode than in STEM mode. These results illustrate the significance of radiolysis occurring while imaging ZIF-8 and present a workflow for assessing damage in LCTEM experiments.

Dynamics of indirect protection against SARS-CoV-2 infection through vaccine and infection-acquired immunity.

Early investigation revealed that COVID-19 vaccines confer indirect protection to fully susceptible and unvaccinated persons, defined as a reduced risk of SARS-CoV-2 infection among social contacts of vaccinated individuals. However, indirect protection from infection-acquired immunity and its comparative strength and durability to vaccine-derived indirect protection in the current epidemiologic context of high levels of vaccination, prior infection, and novel variants are not well characterized. Here, we show that both infection-acquired and vaccine-derived immunity independently yield indirect protection to close social contacts with key differences in their strength and waning. Analyzing anonymized data from a system-wide SARS-CoV-2 surveillance program of 177,319 residents across 35 California state prisons from December 2021 to December 2022, we find that vaccine-derived indirect protection against Omicron SARS-CoV-2 infection is strongest within three months post-vaccination [30% (95% confidence interval: 20-38%)], whereas infection-acquired immunity provides 39% (25-51%) indirect protection to roommates for 6 months after SARS-CoV-2 infection, with moderate indirect protection persisting for over one year. Variant-targeted vaccines (bivalent formulation including Omicron subvariants BA.4/BA.5) confer strong indirect protection for at least three months [51% (18-70%)]. These results have important implications for understanding the long-term transmission dynamics of SARS-CoV-2 and can guide vaccine policy and public health measures, especially in high-risk environments such as prisons.

Geographical distribution of the Cryptococcus gattii species complex: a systematic review.

The taxonomy of the Cryptococcus gattii species complex continues to evolve, and has been divided into five pathogenic species. The objective of this systematic review was to summarise the geographical distribution of the C gattii species complex and the species within the C gattii species complex. We searched PubMed for articles related to human, animal, ecological, or laboratory-based studies of C gattii species complex isolates with traceable geographical origin published from January, 1970, until September, 2021. Having extracted their geographical origin, we used ArcMap to construct maps according to the highest degree of resolution allowed by their reported taxonomy, to reflect the most likely area of transmission on the basis of published reports of human isolates. 604 such articles were included in the study. This review indicated that although C gattii species complex isolates have been reported globally, understanding their heterogeneous geographical distribution by species can have implications for researchers and clinicians in formulating research questions and considering diagnostic quandaries.

Conformational modulation and polymerization-induced folding of proteomimetic peptide brush polymers.

Peptide-brush polymers generated by graft-through living polymerization of peptide-modified monomers exhibit high proteolytic stability, therapeutic efficacy, and potential as functional tandem repeat protein mimetics. Prior work has focused on polymers generated from structurally disordered peptides that lack defined conformations. To obtain insight into how the structure of these polymers is influenced by the folding of their peptide sidechains, a set of polymers with varying degrees of polymerization was prepared from peptide monomers that adopt α-helical secondary structure for comparison to those having random coil structures. Circular dichroism and nuclear magnetic resonance spectroscopy confirm the maintenance of the secondary structure of the constituent peptide when polymerized. Small-angle X-ray scattering (SAXS) studies reveal the solution-phase conformation of PLPs in different solvent environments. In particular, X-ray scattering shows that modulation of solvent hydrophobicity, as well as hydrogen bonding patterns of the peptide sidechain, plays an important role in the degree of globularity and conformation of the overall polymer, with polymers of helical peptide brushes showing less spherical compaction in conditions where greater helicity is observed. These structural insights into peptide brush folding and polymer conformation inform the design of these proteomimetic materials with promise for controlling and predicting their artificial fold and morphology.

Methods for evaluating unsupervised vector representations of genomic regions.

Representation learning models have become a mainstay of modern genomics. These models are trained to yield vector representations, or embeddings, of various biological entities, such as cells, genes, individuals, or genomic regions. Recent applications of unsupervised embedding approaches have been shown to learn relationships among genomic regions that define functional elements in a genome. Unsupervised representation learning of genomic regions is free of the supervision from curated metadata and can condense rich biological knowledge from publicly available data to region embeddings. However, there exists no method for evaluating the quality of these embeddings in the absence of metadata, making it difficult to assess the reliability of analyses based on the embeddings, and to tune model training to yield optimal results. To bridge this gap, we propose four evaluation metrics: the cluster tendency score (CTS), the reconstruction score (RCS), the genome distance scaling score (GDSS), and the neighborhood preserving score (NPS). The CTS and RCS statistically quantify how well region embeddings can be clustered and how well the embeddings preserve information in training data. The GDSS and NPS exploit the biological tendency of regions close in genomic space to have similar biological functions; they measure how much such information is captured by individual region embeddings in a set. We demonstrate the utility of these statistical and biological scores for evaluating unsupervised genomic region embeddings and provide guidelines for learning reliable embeddings.