Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer.

Cyclin E overexpression as a result of CCNE1 amplification is a critical driver of genomic instability in gastric cancer, but its clinical implication is largely unknown. Thus, we integrated genomic, transcriptomic, and immune profiling analysis of 7,083 esophagogastric tumors and investigated the impact of CCNE1 amplification on molecular features and treatment outcomes. We identified CCNE1 amplification in 6.2% of esophageal adenocarcinoma samples, 7.0% of esophagogastric junction carcinoma, 4.2% of gastric adenocarcinoma samples, and 0.8% of esophageal squamous cell carcinoma. Metastatic sites such as lymph node and liver showed an increased frequency of CCNE1 amplification relative to primary tumors. Consistent with a chromosomal instability phenotype, CCNE1 amplification was associated with decreased CDH1 mutation and increased TP53 mutation and ERBB2 amplification. We observed no differences in immune biomarkers such as PD-L1 expression and tumor mutational burden comparing CCNE1-amplified and nonamplified tumors, although CCNE1 amplification was associated with changes in immune populations such as decreased B cells and increased M1 macrophages from transcriptional analysis. Real-world survival analysis demonstrated that patients with CCNE1-amplified gastric cancer had worse survival after trastuzumab for HER2-positive tumors, but better survival after immunotherapy. These data suggest that CCNE1-amplified gastric cancer has a distinct molecular and immune profile with important therapeutic implications, and therefore further investigation of CCNE1 amplification as a predictive biomarker is warranted. SIGNIFICANCE: Advanced gastric cancer has a relatively dismal outcome with a 5-year overall survival of less than 10%. Furthermore, while comprehensive molecular analyses have established molecular subtypes within gastric cancers, biomarkers of clinical relevance in this cancer type are lacking. Overall, this study demonstrates that CCNE1 amplification is associated with a distinct molecular profile in gastric cancer and may impact response to therapy, including targeted therapy and/or immunotherapy.

Multiomic Characterization Reveals a Distinct Molecular Landscape in Young-Onset Pancreatic Cancer.

PURPOSE: Using a real-world database with matched genomic-transcriptomic molecular data, we sought to characterize the distinct molecular correlates underlying clinical differences between patients with young-onset pancreatic cancer (YOPC; younger than 50 years) and patients with average-onset pancreatic cancer (AOPC; 70 years and older). METHODS: We analyzed matched whole-transcriptome and DNA sequencing data from 2,430 patient samples (YOPC, n = 292; AOPC, n = 2,138) from the Caris Life Sciences database (Phoenix, AZ). Immune deconvolution was performed using the quanTIseq pipeline. Overall survival (OS) data were obtained from insurance claims (n = 4,928); Kaplan-Meier estimates were calculated for age- and molecularly defined cohorts. Significance was determined as FDR-corrected P values (Q) < .05. RESULTS: Patients with YOPC had higher proportions of mismatch repair-deficient/microsatellite instability-high, BRCA2-mutant, and PALB2-mutant tumors compared with patients with AOPC, but fewer SMAD4-, RNF43-, CDKN2A-, and SF3B1-mutant tumors. Notably, patients with YOPC demonstrated significantly lower incidence of KRAS mutations compared with patients with AOPC (81.3% v 90.9%; Q = .004). In the KRAS wild-type subset (n = 227), YOPC tumors demonstrated fewer TP53 mutations and were more likely driven by NRG1 and MET fusions, whereas BRAF fusions were exclusively observed in patients with AOPC. Immune deconvolution revealed significant enrichment of natural killer cells, CD8+ T cells, monocytes, and M2 macrophages in patients with YOPC relative to patients with AOPC, which corresponded with lower rates of HLA-DPA1 homozygosity. There was an association with improved OS in patients with YOPC compared with patients with AOPC with KRAS wild-type tumors (median, 16.2 [YOPC-KRASWT] v 10.6 [AOPC-KRASWT] months; P = .008) but not KRAS-mutant tumors (P = .084). CONCLUSION: In this large, real-world multiomic characterization of age-stratified molecular differences in pancreatic ductal adenocarcinoma, YOPC is associated with a distinct molecular landscape that has prognostic and therapeutic implications.

Opposing Roles of SPOP Mutations in Human Prostate and Endometrial Cancers.

PURPOSE: Recurrent gene mutations in speckle-type POZ protein (SPOP), the substrate-binding component of E3 ubiquitin ligase, are associated with tumor progression in prostate and endometrial cancers. Here, we characterized SPOP mutations in these cancers and explored their association with molecular and immune signatures and patient outcomes. METHODS: There were 7,398 prostate cancer and 19,188 endometrial cancer samples analyzed for clinical and molecular profiles at Caris Life Sciences. Overall survival (OS) was analyzed using Kaplan-Meier survival curves. Statistical significance was determined using chi-square and Mann-Whitney U tests, with P values adjusted for multiple comparisons. RESULTS: SPOP mutations were identified in 9.2% of prostate and 4.3% of endometrial cancers. Mutations clustered in the SPOP meprin and TRAF-C homology domain, with no significant overlap between cancer types. SPOP mutation was associated with differential comutation profiles and opposing tumor immune microenvironment signatures for each cancer, with greater immune infiltration in SPOP-mutated endometrial cancer. SPOP-mutated prostate and endometrial cancers displayed altered epigenetic gene expression, including opposite regulation of BRD2 transcripts. In SPOP-mutant prostate cancer, higher expression of androgen receptor-regulated transcripts and improved OS after treatment with hormonal agents were observed. In endometrial cancer, hormone receptor expression was significantly lower in SPOP-mutated tumors and differences in OS were highly dependent on the particular hotspot mutation and histologic subtype. CONCLUSION: These data indicate that SPOP mutations drive opposing molecular and immune landscapes in prostate and endometrial cancers-suggesting a loss-of-function mechanism in prostate cancer and gain-of-function mechanism in endometrial cancer-and provide a rationale for tailored therapeutic approaches.

Comparative Genomic Analysis of Pancreatic Acinar Cell Carcinoma (PACC) and Pancreatic Ductal Adenocarcinoma (PDAC) Unveils New Actionable Genomic Aberrations in PACC.

PURPOSE: Pure pancreatic acinar cell carcinomas (PACC) are rare malignancies with no established treatment. PACC demonstrates significant genetic intertumoral heterogeneity with multiple pathways involved, suggesting using targeted cancer therapeutics to treat this disease. We aggregated one of the largest datasets of pure PACC to examine the genomic variability and explore patient-specific therapeutic targets. EXPERIMENTAL DESIGN: PACC specimens (n = 51) underwent next-generation sequencing of DNA (n = 29) or whole exome (n = 22) and RNA (whole transcriptome, n = 29) at a commercial laboratory. We performed comparative analyses of a genomic cohort of pancreatic ductal adenocarcinomas (PDAC; n = 4,205). In parallel, we conducted a retrospective review of patients with PACC treated at Huntsman Cancer Institute (HCI). RESULTS: The real-world dataset included samples from 51 patients with PACC. We found key molecular differences between pure PACC and PDAC, highlighting the unique characteristics of pure PACC. Major differences in PACC include lower MAPK signaling and less stromal cell abundance compared with PDAC. Pure PACC showed genomic loss-of-heterozygosity to largely coincide with mutations in BRCA1, BRCA2, and PALB2. Of the 7 patients treated at HCI, one had a tumor that harbored a BRAF-V600E mutation. Leveraging precision oncology, this patient is being treated with encorafenib plus binimetinib, achieving an exceptionally durable and ongoing complete response of more than 3 years. CONCLUSIONS: There are major differences between PACC and PDAC, including downregulation of the MAPK signaling pathway, and less stromal cell abundance. In addition, genomic characterization of pure PACC revealed frequent targetable alterations, which can guide patient treatment.

Metastatic Prostate Cancers with BRCA2 versus ATM Mutations Exhibit Divergent Molecular Features and Clinical Outcomes.

PURPOSE: In patients with metastatic prostate cancer (mPC), ATM and BRCA2 mutations dictate differences in PARPi inhibitor response and other therapies. We interrogated the molecular features of ATM- and BRCA2-mutated mPC to explain the divergent clinical outcomes and inform future treatment decisions. EXPERIMENTAL DESIGN: We examined a novel set of 1,187 mPCs after excluding microsatellite-instable (MSI) tumors. We stratified these based on ATM (n = 88) or BRCA2 (n = 98) mutations. As control groups, mPCs with mutations in 12 other homologous recombination repair (HRR) genes were considered non-BRCA2/ATM HRR-deficient (HRDother, n = 193), whereas lack of any HRR mutations were considered HRR-proficient (HRP; n = 808). Gene expression analyses were performed using Limma. Real-world overall survival was determined from insurance claims data. RESULTS: In noncastrate mPCs, only BRCA2-mutated mPCs exhibited worse clinical outcomes to AR-targeted therapies. In castrate mPCs, both ATM and BRCA2 mutations exhibited worse clinical outcomes to AR-targeted therapies. ATM-mutated mPCs had reduced TP53 mutations and harbored coamplification of 11q13 genes, including CCND1 and genes in the FGF family. BRCA2-mutated tumors showed elevated genomic loss-of-heterozygosity scores and were often tumor mutational burden high. BRCA2-mutated mPCs had upregulation of cell-cycle genes and were enriched in cell-cycle signaling programs. This was distinct from ATM-mutated tumors. CONCLUSIONS: Tumoral ATM and BRCA2 mutations are associated with differential clinical outcomes when patients are stratified by treatments, including hormonal or taxane therapies. ATM- and BRCA2-mutated tumors exhibited differences in co-occurring molecular features. These unique molecular features may inform therapeutic decisions and development of novel therapies.

Multi-omic characterization reveals a distinct molecular landscape in young-onset pancreatic cancer.

Purpose: Using a real-world database with matched genomic-transcriptomic molecular data, we sought to characterize the distinct molecular correlates underlying clinical differences between young-onset pancreatic cancer (YOPC; <50-yrs.) and average-onset pancreatic cancer (AOPC; ≥70-yrs.) patients. Methods: We analyzed matched whole-transcriptome and DNA sequencing data from 2430 patient samples (YOPC, n=292; AOPC, n=2138) from the Caris Life Sciences database (Phoenix, AZ). Immune deconvolution was performed using the quanTIseq pipeline. Overall survival (OS) data was obtained from insurance claims (n=4928); Kaplan-Meier estimates were calculated for age-and molecularly-defined cohorts. Significance was determined as FDR-corrected P -values ( Q )<0.05. Results: YOPC patients had higher proportions of mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H), BRCA2 -mutant, and PALB2 -mutant tumors compared with AOPC patients, but fewer SMAD4-, RNF43-, CDKN2A- , and SF3B1- mutant tumors. Notably, YOPC patients demonstrated significantly lower incidence of KRAS mutations compared with AOPC patients (81.3% vs. 90.9%; Q =0.004). In the KRAS- wildtype subset (n=227), YOPC tumors demonstrated fewer TP53 mutations and were more likely driven by NRG1 and MET fusions, while BRAF fusions were exclusively observed in AOPC patients. Immune deconvolution revealed significant enrichment of natural killer (NK) cells, CD8 + T cells, monocytes, and M2 macrophages in YOPC patients relative to AOPC patients, which corresponded with lower rates of HLA-DPA1 homozygosity. There was an association with improved OS in YOPC patients compared with AOPC patients with KRAS -wildtype tumors (median 16.2 [YOPC- KRAS WT ] vs. 10.6 [AOPC- KRAS WT ] months; P =0.008) but not KRAS -mutant tumors ( P =0.084). Conclusion: In this large, real-world multi-omic characterization of age-stratified molecular differences in PDAC, YOPC is associated with a distinct molecular landscape that has prognostic and therapeutic implications.

Characterization of MET Exon 14 Skipping Alterations (in NSCLC) and Identification of Potential Therapeutic Targets Using Whole Transcriptome Sequencing.

Introduction: Genomic alterations in the juxtamembrane exon 14 splice sites in NSCLC lead to increased MET stability and oncogenesis. We present the largest cohort study of MET Exon 14 (METex14) using whole transcriptome sequencing. Methods: A total of 21,582 NSCLC tumor samples underwent complete genomic profiling with next-generation sequencing of DNA (592 Gene Panel, NextSeq, whole exome sequencing, NovaSeq) and RNA (NovaSeq, whole transcriptome sequencing). Clinicopathologic information including programmed death-ligand 1 and tumor mutational burden were collected and RNA expression for mutation subtypes and MET amplification were quantified. Immunogenic signatures and potential pathways of invasion were characterized using single-sample gene set enrichment analysis and mRNA gene signatures. Results: A total of 533tumors (2.47%) with METex14 were identified. The most common alterations were point mutations (49.5%) at donor splice sites. Most alterations translated to increased MET expression, with MET co-amplification resulting in synergistic increase in expression (q < 0.05). Common coalterations were amplifications of MDM2 (19.0% versus 1.8% wild-type [WT]), HMGA2 (13.2% versus 0.98% WT), and CDK4 (10.0% versus 1.5% WT) (q < 0.05). High programmed death-ligand 1 > 50% (52.5% versus 27.3% WT, q < 0.0001) and lower proportion of high tumor mutational burden (>10 mutations per megabase, 8.3% versus 36.7% WT, p < 0.0001) were associated with METex14, which were also enriched in both immunogenic signatures and immunosuppressive checkpoints. Pathways associated with METex14 included angiogenesis and apical junction pathways (q < 0.05). Conclusions: METex14 splicing alterations and MET co-amplification translated to higher and synergistic MET expression at the transcriptomic level. High frequencies of MDM2 and CDK4 co-amplifications and association with multiple immunosuppressive checkpoints and angiogenic pathways provide insight into potential actionable targets for combination strategies in METex14 NSCLC.

TRPV4 Antagonism Prevents Mechanically Induced Myotonia.

OBJECTIVE: Myotonia is caused by involuntary firing of skeletal muscle action potentials and causes debilitating stiffness. Current treatments are insufficiently efficacious and associated with side effects. Myotonia can be triggered by voluntary movement (electrically induced myotonia) or percussion (mechanically induced myotonia). Whether distinct molecular mechanisms underlie these triggers is unknown. Our goal was to identify ion channels involved in mechanically induced myotonia and to evaluate block of the channels involved as a novel approach to therapy. METHODS: We developed a novel system to enable study of mechanically induced myotonia using both genetic and pharmacologic mouse models of myotonia congenita. We extended ex vivo studies of excitability to in vivo studies of muscle stiffness. RESULTS: As previous work suggests activation of transient receptor potential vanilloid 4 (TRPV4) channels by mechanical stimuli in muscle, we examined the role of this cation channel. Mechanically induced myotonia was markedly suppressed in TRPV4-null muscles and in muscles treated with TRPV4 small molecule antagonists. The suppression of mechanically induced myotonia occurred without altering intrinsic muscle excitability, such that myotonia triggered by firing of action potentials (electrically induced myotonia) was unaffected. When injected intraperitoneally, TRPV4 antagonists lessened the severity of myotonia in vivo by approximately 80%. INTERPRETATION: These data demonstrate that there are distinct molecular mechanisms triggering electrically induced and mechanically induced myotonia. Our data indicates that activation of TRPV4 during muscle contraction plays an important role in triggering myotonia in vivo. Elimination of mechanically induced myotonia by TRPV4 inhibition offers a new approach to treating myotonia. ANN NEUROL 2020;88:297-308.

Sustained activation of GABAA receptors in the suprachiasmatic nucleus mediates light-induced phase delays of the circadian clock: a novel function of ionotropic receptors.

The suprachiasmatic nucleus (SCN) contains a circadian clock that generates endogenous rhythmicity and entrains that rhythmicity with the day-night cycle. The neurochemical events that transduce photic input within the SCN and mediate entrainment by resetting the molecular clock have yet to be defined. Because GABA is contained in nearly all SCN neurons we tested the hypothesis that GABA serves as this signal in studies employing Syrian hamsters (Mesocricetus auratus). Activation of GABAA receptors was found to be necessary and sufficient for light to induce phase delays of the clock. Remarkably, the sustained activation of GABAA receptors for more than three consecutive hours was necessary to phase-delay the clock. The duration of GABAA receptor activation required to induce phase delays would not have been predicted by either the prevalent theory of circadian entrainment or by expectations regarding the duration of ionotropic receptor activation necessary to produce functional responses. Taken together, these data identify a novel neurochemical mechanism essential for phase-delaying the 'master' circadian clock within the SCN as well as identifying an unprecedented action of an amino acid neurotransmitter involving the sustained activation of ionotropic receptors.

Association of impaired fasting glucose, diabetes and their management with the presentation and outcome of peripheral artery disease: a cohort study.

BACKGROUND: Pre-diabetes and untreated diabetes are common in patients with peripheral artery disease however their impact on outcome has not been evaluated. We examined the association of impaired fasting glucose, diabetes and their treatment with the presentation, mortality and requirement for intervention in peripheral artery disease patients. METHODS: We prospectively recruited 1637 patients with peripheral artery disease, measured fasting glucose, recorded medications for diabetes and categorised them by diabetes status. Patients were followed for a median of 1.7 years. RESULTS: At entry 22.7% patients were receiving treatment for type 2 diabetes by oral hypoglycaemics alone (18.1%) or insulin (4.6%). 9.2% patients had non-medicated diabetes. 28.1% of patients had impaired fasting glucose (5.6-6.9 mM). Patients with non-medicated diabetes had increased mortality and requirement for peripheral artery intervention (hazards ratio 1.62 and 1.31 respectively). Patients with diabetes prescribed insulin had increased mortality (hazard ratio 1.97). Patients with impaired fasting glucose or diabetes prescribed oral hypoglycaemics only had similar outcomes to patients with no diabetes. CONCLUSIONS: Non-medicated diabetes is common in peripheral artery disease patients and associated with poor outcomes. Impaired fasting glucose is also common but does not increase intermediate term complications. Peripheral artery disease patients with diabetes requiring insulin are at high risk of intermediate term mortality.

Mechanisms of contrast-induced nephropathy reduction for saline (NaCl) and sodium bicarbonate (NaHCO3).

Nephropathy following contrast media (CM) exposure is reduced by administration before, during, and after the contrast procedure of either isotonic sodium chloride solution (Saline) or isotonic sodium bicarbonate solution (IsoBicarb). The reasons for this reduction are not well established for either sodium salt; probable mechanisms are discussed in this paper. For Saline, the mechanism for the decrease in CIN is likely related primarily to the increased tubular flow rates produced by volume expansion and therefore a decreased concentration of the filtered CM during transit through the kidney tubules. Furthermore, increased tubular flow rates produce a slight increase in tubular pH resulting from a fixed acid excretion in an increased tubular volume. The mechanism for the decreased CIN associated with sodium bicarbonate includes the same mechanisms listed for Saline in addition to a renal pH effect. Increased filtered bicarbonate anion raises both tubular pH and tubular bicarbonate anion levels toward blood physiologic levels, thus providing increased buffer for reactive oxygen species (ROS) formed in the tubules as a result of exposure to CM in renal tubular fluid.

Association of chronic kidney disease categories defined with different formulae with major adverse events in patients with peripheral vascular disease.

OBJECTIVE: The aim of this study was to compare the ability of eGFR calculated by modification of diet in renal disease (MDRD), Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) and Lund-Malmö formulae in predicting major adverse events in peripheral vascular disease (PVD) patients. METHODS: We prospectively recruited 2137 patients, measured serum creatinine to calculate eGFR using three different formulae and grouped patients into eGFR categories ≥90, 60-89, 45-59, 30-44, 15-29 and <15 ml/min/1.73 m(2). Patients were followed up for a median of 1.3 (inter-quartile range 0.3-3.6) years. The primary outcome was the combined incidence of myocardial infarction, stroke or death. The ability of eGFR categories defined with the different formulae to predict outcome was assessed using the net reclassification index. RESULTS: 1450 (67.9%), 1515 (70.9%) and 1813 (84.8%) patients had eGFR <90 ml/min/1.73 m(2) according to the CKD-EPI, MDRD and Lund-Malmö formulae, respectively. Using the CKD-EPI formula 276 (12.9%) patients were reclassified to a different eGFR category in comparison to the MDRD formula and the prediction of outcome was improved (net reclassification index 0.106, p < 0.001). Using the Lund-Malmö formula 563 (26.3%) patients were reclassified to a different eGFR category in comparison to the MDRD formula and the prediction of outcome was improved (net reclassification index 0.108, p < 0.001). Classification using the CKD-EPI and Lund-Malmö formulae was equally effective at predicting outcome (net reclassification index - 0.002, p = 0.397). CONCLUSIONS: eGFR categories determined with the CKD-EPI and Lund-Malmö formulae are equally effective at predicting major adverse events in patients with PVD.

Finite-time statistics of scalar diffusion in Lagrangian coherent structures.

We study the variability of passive scalar diffusion via the statistics of stochastic particle dispersion in a chaotic flow. We find that at intermediate times when the statistics of individual trajectories start to exhibit scaling-law behaviors, scalar variance over the entire domain exhibits multimodal structure. We demarcate the domain based on Lagrangian coherent structures and find that the conditional statistics exhibit strong unimodal behavior, indicating coherence of effective diffusion among each Lagrangian partition of the flow.

Bilateral fractures of the scapula: Possible archeological examples of beatings from Europe, Africa and America.

Traumatic injuries to the scapula have received little attention in the paleopathological literature. They are rarely encountered in medical emergencies today due to the overlying muscles that protect the bone; they comprise just 1% of all fractures. This collaborative project brings together five cases of bilateral fractures of the scapulae in four ancient populations from three different time periods and three continents (France, Sudan and USA). It is thus an opportunity to interpret bilateral scapula fracture etiology by suggesting a cause that could have been present in all contexts, namely direct trauma such as might take place during beating with heavy sticks or other blunt force weapons. We also argue that oval defects with rounded margins in scapular bodies are less likely to be congenital anatomical variants than the result of healed trauma.

Identification of group affinity from cross-sectional contours of the human midfacial skeleton using digital morphometrics and 3D laser scanning technology.

Identifying group affinity from human crania is a long-standing problem in forensic and physical anthropology. Many craniofacial differences used in forensic skeletal identification are difficult to quantify, although certain measurements of the midfacial skeleton have shown high predictive value for group classifications. This study presents a new method for analyzing midfacial shape variation between different geographic groups. Three-dimensional laser scan models of 90 crania from three populations were used to obtain cross-sectional midfacial contours defined by three standard craniometric landmarks. Elliptic Fourier transforms of the contours were used to extract Fourier coefficients for statistical analysis. After cross-validation, discriminant functions based on the Fourier coefficients provided an average of 86% correct classifications for crania from the three groups. The high rate of accuracy of this method indicates its usefulness for identifying group affinities among human skeletal remains and demonstrates the advantages of digital 3D model-based analysis in forensic research.

Variation in the measurement of cranial volume and surface area using 3D laser scanning technology.

Three-dimensional (3D) laser scanner models of human crania can be used for forensic facial reconstruction, and for obtaining craniometric data useful for estimating age, sex, and population affinity of unidentified human remains. However, the use of computer-generated measurements in a casework setting requires the measurement precision to be known. Here, we assess the repeatability and precision of cranial volume and surface area measurements using 3D laser scanner models created by different operators using different protocols for collecting and processing data. We report intraobserver measurement errors of 0.2% and interobserver errors of 2% of the total area and volume values, suggesting that observer-related errors do not pose major obstacles for sharing, combining, or comparing such measurements. Nevertheless, as no standardized procedure exists for area or volume measurements from 3D models, it is imperative to report the scanning and postscanning protocols employed when such measurements are conducted in a forensic setting.

Trophy-taking and dismemberment as warfare strategies in prehistoric central California.

We document evidence for trophy-taking and dismemberment with a new bioarchaeological database featuring 13,453 individuals from prehistoric central California sites. Our study reveals 76 individuals with perimortem removal of body parts consistent with trophy-taking or dismemberment; nine of these individuals display multiple types of trophy-taking and dismemberment for a total of 87 cases. Cases span almost 5,000 years, from the Early Period (3000-500 BC) to the Late Period (AD 900-1700). Collectively, these individuals share traits that distinguish them from the rest of the population: a high frequency of young adult males, an increased frequency of associated trauma, and a tendency towards multiple burials and haphazard burial positions. Eight examples of human bone artifacts were also found that appear related to trophy-taking. These characteristics suggest that trophy-taking and dismemberment were an important part of the warfare practices of central Californian tribes. Temporally, the two practices soared in the Early/Middle Transition Period (500-200 BC), which may have reflected a more complex sociopolitical system that encouraged the use of trophies for status acquisition, as well as the migration of outside groups that resulted in intensified conflict. Overall, trophy-taking and dismemberment appear to have been the product of the social geography of prehistoric central California, where culturally differentiated tribes lived in close proximity to their enemies.

Technical note: prediction of sex based on five skull traits using decision analysis (CHAID).

Osteologists commonly assess the sex of skeletal remains found in forensic and archaeological contexts based on ordinal scores of subjectively assessed sexually dimorphic traits. Using known-sex samples, logistic regression (LR) discriminant functions have been recently developed, which allow sex probabilities to be determined. A limitation of LR is that it emphasizes main effects and not interactions. Chi-square automatic interaction detection (CHAID) is an alternative classification strategy that emphasizes the information in variable interactions and uses decision trees to maximize the probability of correct sex determinations. We used CHAID to analyze the predictive value of the 31 possible combinations of five sexually dimorphic skull traits that Walker used previously to develop logistic regression sex determination equations. The samples consisted of 304 individuals of known sex of English, African American, and European American origin. Based on practical considerations, selection criteria for the best sex predictive trait combinations (SPTCs) were set at accuracies for both sexes of 75% or greater and sex biases lower than 5%. Although several of the trees meeting these criteria were produced for the English and European American samples, none met them for the African American sample. In the series of out-of-sample tests we performed, the trees from the English and combined sample of all groups predicted best.

The causes of porotic hyperostosis and cribra orbitalia: a reappraisal of the iron-deficiency-anemia hypothesis.

Porosities in the outer table of the cranial vault (porotic hyperostosis) and orbital roof (cribra orbitalia) are among the most frequent pathological lesions seen in ancient human skeletal collections. Since the 1950s, chronic iron-deficiency anemia has been widely accepted as the probable cause of both conditions. Based on this proposed etiology, bioarchaeologists use the prevalence of these conditions to infer living conditions conducive to dietary iron deficiency, iron malabsorption, and iron loss from both diarrheal disease and intestinal parasites in earlier human populations. This iron-deficiency-anemia hypothesis is inconsistent with recent hematological research that shows iron deficiency per se cannot sustain the massive red blood cell production that causes the marrow expansion responsible for these lesions. Several lines of evidence suggest that the accelerated loss and compensatory over-production of red blood cells seen in hemolytic and megaloblastic anemias is the most likely proximate cause of porotic hyperostosis. Although cranial vault and orbital roof porosities are sometimes conflated under the term porotic hyperostosis, paleopathological and clinical evidence suggests they often have different etiologies. Reconsidering the etiology of these skeletal conditions has important implications for current interpretations of malnutrition and infectious disease in earlier human populations.

Sexing skulls using discriminant function analysis of visually assessed traits.

The accuracy of sex determinations based on visual assessments of the mental eminence, orbital margin, glabellar area, nuchal area, and mastoid process was tested on a series of 304 skulls of known age and sex from people of European American, African American, and English ancestry as well as on an ancient Native American sample of 156 individuals whose sex could be reliably determined based on pelvic morphology. Ordinal scores of these sexually dimorphic traits were used to compute sex determination discriminant functions. Linear, kth-nearest-neighbor, logistic, and quadratic discriminant analysis models were evaluated based on their capacity to minimize both misclassifications and sex biases in classification errors. Logistic regression discriminant analysis produced the best results: a logistic model containing all five cranial trait scores correctly classified 88% of the modern skulls with a negligible sex bias of 0.1%. Adding age at death, birth year, and population affinity to the model did not appreciably improve its performance. For the ancient Native American sample, the best logistic regression model assigned the correct pelvic sex to 78% of the individuals with a sex bias of only 0.2%. Similar cranial trait frequency distributions were found in same-sex comparisons of the modern African American, European American, and English samples. The sexual dimorphism of these modern people contrasts markedly with that of the ancient Native Americans. Because of such population differences, discriminant functions like those presented in this paper should be used with caution on populations other than those for which they were developed.