Landmark Series: The Cancer Genome Atlas and the Study of Breast Cancer Disparities.

Race-related variation in breast cancer incidence and mortality are well-documented in the United States. The effect of genetic ancestry on disparities in tumor genomics, risk factors, treatment, and outcomes of breast cancer is less understood. The Cancer Genome Atlas (TCGA) is a publicly available resource that has allowed for the recent emergence of genome analysis research seeking to characterize tumor DNA and protein expression by ancestry as well as the social construction of race and ethnicity. Results from TCGA based studies support previous clinical evidence that demonstrates that American women with African ancestry are more likely to be afflicted with breast cancers featuring aggressive biology and poorer outcomes compared with women with other backgrounds. Data from TCGA based studies suggest that Asian women have tumors with favorable immune microenvironments and may experience better disease-free survival compared with white Americans. TCGA contains limited data on Hispanic/Latinx patients due to small sample size. Overall, TCGA provides important opportunities to define the molecular, biologic, and germline genetic factors that contribute to breast cancer disparities.

The accuracy of race & ethnicity data in US based healthcare databases: A systematic review.

BACKGROUND: The availability and accuracy of data on a patient's race/ethnicity varies across databases. Discrepancies in data quality can negatively impact attempts to study health disparities. METHODS: We conducted a systematic review to organize information on the accuracy of race/ethnicity data stratified by database type and by specific race/ethnicity categories. RESULTS: The review included 43 studies. Disease registries showed consistently high levels of data completeness and accuracy. EHRs frequently showed incomplete and/or inaccurate data on the race/ethnicity of patients. Databases had high levels of accurate data for White and Black patients but relatively high levels of misclassification and incomplete data for Hispanic/Latinx patients. Asians, Pacific Islanders, and AI/ANs are the most misclassified. Systems-based interventions to increase self-reported data showed improvement in data quality. CONCLUSION: Data on race/ethnicity that is collected with the purpose of research and quality improvement appears most reliable. Data accuracy can vary by race/ethnicity status and better collection standards are needed.

Suicidal ideation and sobriety: Should acute alcohol intoxication be taken into account for psychiatric evaluation?

BACKGROUND: When evaluating an emergency department (ED) patient who presents with suicidal ideation, it is a common practice to wait until the patient's ethanol level is known or calculated to be less than 80 mg/dl to evaluate patient safety. We know of no study that establishes an association between the degree of alcohol intoxication based on a blood alcohol level (BAL) and reported suicidal ideation (SI) upon recovery. METHODS: We conducted a retrospective review of patients evaluated in a Midwestern ED for the calendar year 2017. Cases were selected if they had a psychiatric social work consult and a blood alcohol level drawn while in the ED. Patients were selected on the same 2 days each week throughout the year to meet the sample size requirements of the study, resulting in 1084 cases for review. Chi-square analysis was used to evaluate the relationship between suicidal ideation and alcohol intoxication as defined by a BAL ≥80 mg/dl. RESULTS: Among patients presenting with suicidal ideation and a concurrent BAL ≥80 mg/dl, 69% no longer reported suicidal ideation when their BAL was <80 mg/dl, compared to 38% for patients without a positive BAL on presentation (chi-square, p = 0.000012). CONCLUSION: Our data show that patients presenting to the ED with complaints related to suicidal behavior who have a BAL ≥80 mg/dl are more likely to no longer endorse having suicidal ideation once their BAL is < 80 mg/dl than patients with similar presenting complaints and no alcohol intoxication. This finding supports the common ED practice of re-assessing suicidal ideation among individuals who are initially intoxicated once their BAL has decreased below 80 mg/dl.

Genital anatomy and copulatory interactions in the broad snouted Caiman (Caiman latirostris).

The broad snouted caiman is a crocodylian native to South America that is subject to extensive conservation management in both wild and farming environments. Although reproductive behaviors like egg laying and clutch care have been examined in this species, little else is known about their copulatory system. We examined the anatomy of male and female cloacal and genital tissues ex vivo to build hypotheses of their interactions during copulation and the effects of that interaction on insemination. Male phallic glans tissues were artificially inflated to expand into their copulatory state, allowing the examination and quantification of structural changes at the gross and tissue levels. Digital reconstruction of MRI stacks yielded three-dimensional tissue compartment specific glans models of the inflated state. Silicone molds of female cloacae and oviducts in conjunction with dissection and diceCT analysis allowed us to assess internal geometry and infer how male and female features interact in copulo. We observed glans expansion within the female proctodeum would result in a copulatory lock limiting deeper intromission or retraction. Intromission and subsequent creation of the copulatory lock produces extensive clitoral compression, providing a possible mechanism for female assessment of male copulatory performance. Further, glans expansion forms a distal lumen that positions the glans tip in or near the vaginal openings. A coiled, muscular vagina provides a possible mechanism for postcopulatory sexual selection by excluding semen. Together, the complex male-female interaction supports evidence for cryptic selection by female choice, which can act as a driver of genital coevolution.

Investigating trace metal precipitation in highly concentrated cell culture media with Pourbaix diagrams.

Commercial production of therapeutic proteins using mammalian cells requires complex process solutions, and consistency of these process solutions is critical to maintaining product titer and quality between batches. Inconsistencies between process solutions prepared at bench and commercial scale may be due to differences in mixing time, temperature, and pH which can lead to precipitation and subsequent removal via filtration of critical solution components such as trace metals. Pourbaix diagrams provide a useful tool to model the solubility of trace metals and were applied to troubleshoot the scale-up of nutrient feed preparation after inconsistencies in product titer were observed between bench- and manufacturing-scale batches. Pourbaix diagrams modeled the solubility of key metals in solution at various stages of the nutrient feed preparation and identified copper precipitation as the likely root cause of inconsistent medium stability at commercial scale. Copper precipitation increased proportionally with temperature in bench-scale preparations of nutrient feed and temperature was identified as the root cause of copper precipitation at the commercial scale. Additionally, cell culture copper titration studies performed in bench-scale bioreactors linked copper-deficient mammalian cell culture to inconsistent titers at the commercial scale. Pourbaix diagrams can predict when trace metals are at risk of precipitating and can be used to mitigate risk during the scale-up of complex medium preparations.

Glans inflation morphology and female cloaca copulatory interactions of the male American alligator phallus†.

The phallic glans of the American alligator (Alligator mississippiensis) is the distal termination of the semen-conducting sulcus spermaticus and during copulation has the closest, most intimate mechanical interactions with the female urodeum, the middle cloacal chamber that contains the opening to the vaginal passages and oviducts. However, the details of this interface leading to insemination and gamete uptake are unclear. Here, we: (1) histologically characterize the underlying tissue types and morphologically quantify the shape changes associated with glans inflation into the copulatory conformation, (2) digitally reconstruct from MRI the 3D shape of functional tissue compartments, and (3) diffusible iodine-based contrast-enhanced computed tomography image the copulatory fit between male phallus and female cloaca. We discuss these results in relation to tissue type material properties, the transfer on intromittent forces, establishing potential copulatory lock, inflated glans volume scaling with body mass/length, the mechanics of semen targeting and insemination, and potential female cryptic choice impacting multiple clutch paternity. In part, this study further clarifies the phallic morphological variation observed among crocodylians and begins to investigate the role(s) these divergent male forms play during copulation interacting with female cloacal forms to increase reproductive success.

Low oxygen: A (tough) way of life for Okavango fishes.

Botswana's Okavango Delta is a World Heritage Site and biodiverse wilderness. In 2016-2018, following arrival of the annual flood of rainwater from Angola's highlands, and using continuous oxygen logging, we documented profound aquatic hypoxia that persisted for 3.5 to 5 months in the river channel. Within these periods, dissolved oxygen rarely exceeded 3 mg/L and dropped below 0.5 mg/L for up to two weeks at a time. Although these dissolved oxygen levels are low enough to qualify parts of the Delta as a dead zone, the region is a biodiversity hotspot, raising the question of how fish survive. In association with the hypoxia, histological samples, collected from native Oreochromis andersonii (threespot tilapia), Coptodon rendalli (redbreast tilapia), and Oreochromis macrochir (greenhead tilapia), exhibited widespread hepatic and splenic inflammation with marked granulocyte infiltration, melanomacrophage aggregates, and ceroid and hemosiderin accumulations. It is likely that direct tissue hypoxia and polycythemia-related iron deposition caused this pathology. We propose that Okavango cichlids respond to extended natural hypoxia by increasing erythrocyte production, but with significant health costs. Our findings highlight seasonal hypoxia as an important recurring stressor, which may limit fishery resilience in the Okavango as concurrent human impacts rise. Moreover, they illustrate how fish might respond to hypoxia elsewhere in the world, where dead zones are becoming more common.

Morphological changes associated with Nile crocodile (Crocodylus niloticus) phallic glans inflation.

The crocodylian phallic glans is the distal inflatable structure that makes the most direct contact with the female cloacal and associated reproductive tract openings during copulation. Therefore, its form and function directly impact female tissue sensory interactions and insemination mechanics. Compared to mammals, less is known about glans functional anatomy among other amniotes, including crocodylians. Therefore, we paired an ex vivo inflation technique with magnetic resonance imaging 3D-reconstructions and corresponding histological analyses to better characterize the morphological glans restructuring occurring in the Nile crocodile (Crocodylus niloticus) at copulation. The expansion of contiguous inflatable spongiform glans tissues is variably constrained by adjacent regions of dense irregular collagen-rich tissues. Therefore, expansion shows regional differences with greater lateral inflation than dorsal and ventral. Furthermore, this enlargement elaborates the cup-like glans lumen, dorsally reorients the glans ridge, stiffens the blunt and bifid glans tip, and putatively works to seal the ventral sulcus spermaticus semen conduit groove. We suggest how these dynamic male structures may interact with structures of the female cloacal urodeum and how these morphological changes, in concert with the varying material properties of the structural tissue compartments visualized in this study, aid copulatory gamete transfer and resulting fecundity. RESEARCH HIGHLIGHTS: Nile crocodile glans inflation produces a reproductively relevant copulatory structure directing insemination and female tissue interactions. Pairing magnetic resonance imaging 3D reconstruction with corresponding histology effectively studies functional anatomy.

Elemental metal variance in cell culture raw materials for process risk profiling.

Elemental metals are critical raw material attributes which can impact cell culture performance and associated therapeutic protein product quality profiles. Metals such as copper and manganese act as cofactors and reagents for numerous metabolic pathways which govern cell growth, protein expression, and glycosylation, thus mandating elemental monitoring. The growing complexity of modern cell culture media formulations adds additional opportunities for elemental variance and its associated impact risks. This article describes an analytical technique applying inductively coupled plasma mass spectrometry to characterize a list of common raw materials and media powders used in mammalian cell culture and therapeutic protein production. We aim to describe a method qualification approach suitable for biopharmaceutical raw materials. Furthermore, we present detailed profiles of many common raw materials and discuss trends in raw material subtypes. Finally, a case study demonstrating the impact of an unexpected source of raw material variation is presented along with recommendations for raw material elemental risk profiling and control.

Crocodylian conservation and evolution insights from an anatomical and histological examination of phalli from male false gharial (Tomistoma schlegelii).

As wild population threats for the endangered false gharial (Tomistoma schlegelii) persist, conservation breeding programs, including developing semen collection techniques for subsequent artificial insemination, are becoming important species conservation measures. Developing reproductive biology understanding of a species is important to developing best practices and hopefully maximizing reproductive successes. However, information on crocodylians functional copulatory anatomy in general is lacking. To that end, zoological facilities and conservation centres have the exceptional opportunity to contribute new understandings that may not otherwise be attainable regarding crocodylian reproductive anatomy, particularly during routine physical examinations or post-mortem necropsies. Therefore, to better understand T. schlegelii reproductive biology, to contribute knowledge in support of zoo breeding conservation efforts and to contribute to what is known overall about crocodylian reproduction, we investigated phallic anatomy of adult male Tomistoma from two zoological populations, the St. Louis Zoo, USA and Sungai Dusun Wildlife Reserve, Peninsular Malaysia. Here, we present the gross anatomical features and histological analysis of underlying tissue-level details in pursuit of a better understanding of copulatory function and associated gamete transfer mechanisms. While much of the overall Tomistoma phallic morphology and inferred function corresponds to that of other crocodylian species and speaks to conserved aspects of functional anatomy across taxa, species-specific aspects of glans and glans tip morphology are also identified. These novelties are discussed in a general function and overall broader evolutionary contexts.

Correlation between increased postpubertal phallic growth and the initiation of cranial sexual dimorphisms in male Morelet's crocodile.

While puberty is an animal commonality, little is known of its timing or process in crocodylians. Males copulate with an intromittent phallus that has a distinct glans morphology which directly interacts with the female cloaca, putatively effecting effective semen transfer and ultimately increased fecundity. Here we present, during the Morelet's crocodile lifecycle, a well-defined body length (65 cm snout-vent length) inflection point that marks a subsequent increase of phallic glans growth rates. Putatively, this postpubescent growth produces a copulatory-effective phallus. While not as robust of a trend as snout-vent length, this growth inflection concomitantly begins with a body condition index (CI = BM/SVL3 ) between 2.0 and 2.5 and is most distinct above a CI of 2.5. Also, in males, this 65 cm size threshold also aligns with the initiation of more robust growth in caniniform alveoli associated with prominent maxillary and mandibular teeth. This inflection was not observed in females, thus marking a sexual dimorphism that begins to present with the onset of puberty. This bodily manifestation of puberty other than those changes observed in the reproductive tracts is a novel observation for crocodylians and lays a foundation for further study among species of how changing endocrine signaling within sexually maturing males may also influence a broader range of secondary sex characteristics.

Case study: The characterization and implementation of dielectric spectroscopy (biocapacitance) for process control in a commercial GMP CHO manufacturing process.

Dielectric spectroscopy (biocapacitance) is an up-and-coming technology for real time monitoring of biomass in cell culture processes and has opened the door for next-generation cell culture process control techniques such as automated on-demand nutrient feeding. In this case study we empirically demonstrate the lower limit of quantitation (LOQ), probe-to-probe consistency, and scalability of in situ biocapacitance probes using data generated from small- and large-scale Chinese hamster ovary (CHO) bioreactor cultures. The process understanding experiments culminated in the use of biocapacitance for process control in the current good manufacturing practices (GMP) manufacturing environment, first to automate the dilution of seed train cultures during scale-up stages and later as a method of predicting future glucose demand. The automated biomass-probe-based inoculation strategy yielded consistent results in six consecutive seed trains in the GMP manufacturing suite. In the process of improving our understanding of the technology we determined that biocapacitance could additionally be used as an indicator of a shift in the salt balance of a cell culture, and that collecting real time biomass data via biocapacitance has the potential to reduce the total timeline for feed strategy development by providing additional insights into culture performance which are not otherwise apparent using conventional optical cell counting methods.

Spiking Suppression Precedes Cued Attentional Enhancement of Neural Responses in Primary Visual Cortex.

Attending to a visual stimulus increases its detectability, even if gaze is directed elsewhere. This covert attentional selection is known to enhance spiking across many brain areas, including the primary visual cortex (V1). Here we investigate the temporal dynamics of attention-related spiking changes in V1 of macaques performing a task that separates attentional selection from the onset of visual stimulation. We found that preceding attentional enhancement there was a sharp, transient decline in spiking following presentation of an attention-guiding cue. This disruption of V1 spiking was not observed in a task-naïve subject that passively observed the same stimulus sequence, suggesting that sensory activation is insufficient to cause suppression. Following this suppression, attended stimuli evoked more spiking than unattended stimuli, matching previous reports of attention-related activity in V1. Laminar analyses revealed a distinct pattern of activation in feedback-associated layers during both the cue-induced suppression and subsequent attentional enhancement. These findings suggest that top-down modulation of V1 spiking can be bidirectional and result in either suppression or enhancement of spiking responses.

Cortical projections to the two retinotopic maps of primate pulvinar are distinct.

Comprised of at least five distinct nuclei, the pulvinar complex of primates includes two large visually driven nuclei; one in the dorsal (lateral) pulvinar and one in the ventral (inferior) pulvinar, that contain similar retinotopic representations of the contralateral visual hemifield. Both nuclei also appear to have similar connections with areas of visual cortex. Here we determined the cortical connections of these two nuclei in galagos, members of the stepsirrhine primate radiation, to see if the nuclei differed in ways that could support differences in function. Injections of different retrograde tracers in each nucleus produced similar patterns of labeled neurons, predominately in layer 6 of V1, V2, V3, MT, regions of temporal cortex, and other visual areas. More complete labeling of neurons with a modified rabies virus identified these neurons as pyramidal cells with apical dendrites extending into superficial cortical layers. Importantly, the distributions of cortical neurons projecting to each of the two nuclei were highly overlapping, but formed separate populations. Sparse populations of double-labeled neurons were found in both V1 and V2 but were very low in number (<0.1%). Finally, the labeled cortical neurons were predominately in layer 6, and layer 5 neurons were labeled only in extrastriate areas. Terminations of pulvinar projections to area 17 was largely in superficial cortical layers, especially layer 1.

Efficacy of vaporized hydrogen peroxide for repeated sterilization of a single-use single-incision laparoscopic surgery port.

OBJECTIVE: To determine the ability of vaporized hydrogen peroxide (VHP) to sterilize a single-use single-incision laparoscopic surgery port and its associated components after repeated simulated uses. STUDY DESIGN: Prospective in vitro experimental study. SAMPLE POPULATION: Six single-use single-incision laparoscopic surgery ports with associated cannulas and insufflation tubing. METHODS: Ports, cannulas, and tubing were subjected to 10 cycles of simulated use, bacterial inoculation with Staphylococcus pseudintermedius and Escherichia coli, decontamination and sterilization, and testing via culture based on their treatment group designation. Bacteriological scores were compared among the negative control, positive control, and 4 treated ports and components. RESULTS: There was no difference in bacteriological scores between treated ports, cannulas, and insufflation tubing and the negative control port and components. Bacteriological scores of ports and components undergoing 6-10 cycles were not significantly different from scores of ports and components undergoing 5 or fewer sterilization cycles. No difference was found in detection of bacteria from treated ports by biopsy of the foam versus sampling via wash. CONCLUSION: This study suggests that a single-use single-incision laparoscopic port and its associated components can be effectively sterilized after multiple simulated uses by using VHP. CLINICAL SIGNIFICANCE: Reuse of a single-use single-incision laparoscopic port is a safe and effective method of cost reduction in veterinary patients.

On the Significance of Systolic Flow Waveform on Aortic Valve Energy Loss.

This study aims to quantitatively and qualitatively assess energy dissipation in the aortic valve as a function of systolic aortic flow waveform representing pathologies where flow time-to-peak is delayed. A bioprosthetic valve was tested in the aortic position of a left-heart simulator under physiological pressure and flow conditions. The flow loop piston pump was programmed to generate three different flow waveforms each with a different peak time annotated as early peak (EP) with a rapid acceleration, mid peak (MP) and late peak (LP) with a rapid deceleration. Energy dissipation was calculated from flow and pressure measurements while sinus vorticity dynamics were evaluated using time-resolved planar particle image velocimetry. Average pressure gradients during systole are found 30.2 ± 0.19, 30.7 ± 0.25 and 32.9 ± 0.29 mmHg and average dissipation over systole is found 0.95 ± 0.026, 1.05 ± 0.034 and 1.25 ± 0.043 W for EP, MP and LP respectively. As systole's acceleration phase is slower, sinus vortices are more likely to form, necessitating more energy exchange from shear layers inducing more viscous dissipation. EP found in healthy individuals is superior in terms of reducing energy dissipation and increasing aortic valve efficiency. In the context of possible left ventricular dysfunction and aortic stenosis, this means that delayed time-to-peak in the aortic flow waveform seen is not compensatory.

Hydrogen peroxide plasma sterilization of a waterproof, high-definition video camera case for intraoperative imaging in veterinary surgery.

OBJECTIVE: To evaluate the safety and usability of a wearable, waterproof high-definition camera/case for acquisition of surgical images by sterile personnel. STUDY DESIGN: An in vitro study to test the efficacy of biodecontamination of camera cases. Usability for intraoperative image acquisition was assessed in clinical procedures. METHODS: Two waterproof GoPro Hero4 Silver camera cases were inoculated by immersion in media containing Staphylococcus pseudointermedius or Escherichia coli at ≥5.50E+07 colony forming units/mL. Cases were biodecontaminated by manual washing and hydrogen peroxide plasma sterilization. Cultures were obtained by swab and by immersion in enrichment broth before and after each contamination/decontamination cycle (n = 4). The cameras were then applied by a surgeon in clinical procedures by using either a headband or handheld mode and were assessed for usability according to 5 user characteristics. RESULTS: Cultures of all poststerilization swabs were negative. One of 8 cultures was positive in enrichment broth, consistent with a low level of contamination in 1 sample. Usability of the camera was considered poor in headband mode, with limited battery life, inability to control camera functions, and lack of zoom function affecting image quality. Handheld operation of the camera by the primary surgeon improved usability, allowing close-up still and video intraoperative image acquisition. CONCLUSION: Vaporized hydrogen peroxide sterilization of this camera case was considered effective for biodecontamination. Handheld operation improved usability for intraoperative image acquisition. CLINICAL SIGNIFICANCE: Vaporized hydrogen peroxide sterilization and thorough manual washing of a waterproof camera may provide cost effective intraoperative image acquisition for documentation purposes.

No Seasonal Changes in Cognitive Functioning Among High School Football Athletes: Implementation of a Novel Electrophysiological Measure and Standard Clinical Measures.

OBJECTIVE: To evaluate neuroelectric and cognitive function relative to a season of football participation. Cognitive and neuroelectric function declines are hypothesized to be present in football athletes. DESIGN: Observational. SETTING: Athletic fields and research laboratory. PATIENTS (OR PARTICIPANTS): Seventy-seven high school athletes (15.9 + 0.9 years, 178.6 + 7.2 cm, 74.4 + 14.7 kg, and 0.8 + 0.8 self-reported concussions) participating in football (n = 46) and noncontact sports (n = 31). INTERVENTIONS (OR ASSESSMENT OF RISK FACTORS): All athletes completed preseason, midseason, and postseason assessments of cognitive and neuroelectric function, self-reported symptoms, and quality of life. All athletes participated in their respective sports without intervention, while head impact exposure in football athletes was tracked using the Head Impact Telemetry System. MAIN OUTCOME MEASURES: Cognitive performance was based on Cogstate computerized cognitive assessment tool processing speed, attention, learning, working memory speed, and working memory accuracy scores. ElMindA brain network activation amplitude, synchronization, timing and connectivity brain network activation scores demarcated neuroelectric performance. Quality of life was assessed on the Health Behavior Inventory and Satisfaction with Life Scale and symptoms on the SCAT3 inventory. RESULTS: Football and control sport athletes did not show declines in cognitive or neuroelectric function, quality-of-life measures, or symptom reports across a season of sport participation. CONCLUSIONS: These findings refute the notion that routine football participation places athletes at risk for acute cognitive declines. The lack of impairment may be associated with no association with head impacts and cognitive function, increased physical activity offsetting any declines, and/or test sensitivity. How these findings are associated with long-term cognitive function is unknown.

Antigen-Presenting Intratumoral B Cells Affect CD4+ TIL Phenotypes in Non-Small Cell Lung Cancer Patients.

Effective immunotherapy options for patients with non-small cell lung cancer (NSCLC) are becoming increasingly available. The immunotherapy focus has been on tumor-infiltrating T cells (TILs); however, tumor-infiltrating B cells (TIL-Bs) have also been reported to correlate with NSCLC patient survival. The function of TIL-Bs in human cancer has been understudied, with little focus on their role as antigen-presenting cells and their influence on CD4+ TILs. Compared with other immune subsets detected in freshly isolated primary tumors from NSCLC patients, we observed increased numbers of intratumoral B cells relative to B cells from tumor-adjacent tissues. Furthermore, we demonstrated that TIL-Bs can efficiently present antigen to CD4+ TILs and alter the CD4+ TIL phenotype using an in vitro antigen-presentation assay. Specifically, we identified three CD4+ TIL responses to TIL-Bs, which we categorized as activated, antigen-associated, and nonresponsive. Within the activated and antigen-associated CD4+ TIL population, activated TIL-Bs (CD19+CD20+CD69+CD27+CD21+) were associated with an effector T-cell response (IFNγ+ CD4+ TILs). Alternatively, exhausted TIL-Bs (CD19+CD20+CD69+CD27-CD21-) were associated with a regulatory T-cell phenotype (FoxP3+ CD4+ TILs). Our results demonstrate a new role for TIL-Bs in NSCLC tumors in their interplay with CD4+ TILs in the tumor microenvironment, establishing them as a potential therapeutic target in NSCLC immunotherapy. Cancer Immunol Res; 5(10); 898-907. ©2017 AACR.