cssi/SciSciGPT-SciSciNet huggingface dataset:
Deriving transcriptional programs and functional processes from gene expression databases

Motivation: A system-wide approach to revealing the underlying molecular state of a cell is a long-standing biological challenge. Developed over the last decade, gene expression profiles possess the characteristics of such an assay. They have the capacity to reveal both underlying molecular events as well as broader phenotypes such as clinical outcomes. To interpret these profiles, many gene sets have been developed that characterize biological processes. However, the full potential of these gene sets has not yet been achieved. Since the advent of gene expression databases, many have posited that they can reveal properties of activities that are not evident from individual datasets, analogous to how the expression of a single gene generally cannot reveal the activation of a biological process. Results: To address this issue, we have developed a high-throughput method to mine gene expression databases for the regulation of gene sets. Given a set of genes, we scored it against each gene expression dataset by looking for enrichment of co-regulated genes relative to an empirical null distribution. After validating the method, we applied it to address two biological problems. First, we deciphered the E2F transcriptional network. We confirmed that true transcriptional targets exhibit a distinct regulatory profile across a database. Second, we leveraged the patterns of regulation across a database of gene sets to produce an automatically generated catalog of biological processes. These demonstrations revealed the power of a global analysis of the data contained within gene expression databases, and the potential for using them to address biological questions. Contact: jeffrey.t.chang@uth.tmc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
The Relationship Between Leadership Behaviors and Group Cohesion in Team Sports

Abstract The relationship between leadership behaviors and team cohesion among baseball and softball players at two school levels was analyzed in relation to predictions based on Chelladurai and Carron's (1978) Multidimensional Model of Leadership (MML). Athletes (n = 307) completed the perceived and preferred versions of the Leadership Scale for Sports (LSS) and the Group Environment Questionnaire (GEQ). Athletes' coaches (n = 23) completed the self-perceived version of the LSS. Task and social cohesion were assessed in relation to the scales of the three individual versions of the LSS and in relation to two types of discrepancy scores: value and perceptual. Although the concept of discrepancy is prominent in MML theory, the perceptual discrepancy score represents an innovation. Results indicated that, in general, team cohesion was most strongly related to the perceived LSS version and the perceptual discrepancy scores.
U.S. Crop Farmers' Use of Market Advisory Services

Abstract This study reports that Market Advisory Services (MAS) are used by about 82% of commercial U.S. crop producers, based on the results of a recent survey. Only 43% of MAS users rely on a single service, while the other 57% subscribe to multiple services. MAS users' profiles in terms of their (1) demographic characteristics, (2) risk attitude, and (3) marketing behavior are presented. The results indicate that MAS users can be differentiated based on their location and use of computers, though not on age and farm size. MAS users are shown to be significantly more risk seeking than non-users. Furthermore, MAS users apply significantly more forward-pricing techniques, but are no different from non-users in terms of marketing frequency.
Search Engine Statistics Beyond the n-Gram: Application to Noun Compound Bracketing

In order to achieve the long-range goal of semantic interpretation of noun compounds, it is often necessary to first determine their syntactic structure. This paper describes an unsupervised method for noun compound bracketing which extracts statistics from Web search engines using a X2 measure, a new set of surface features, and paraphrases. On a gold standard, the system achieves results of 89.34% (baseline 66.80%), which is a sizable improvement over the state of the art (80.70%).
Structural Relaxation around Substitutional Cr3+ Ions in Sapphire

The local structural arrangement of ions around a substitutional Cr 3+ ion in sapphire (ruby) has been studied experimentally using extended X-ray absorption fine structure (EXAFS) in the vicinity of the Cr absorption edge. The findings are compared with an ionic model (Mott-Littleton) computation using two sets of pairwise potentials. Both the EXAFS results and the computations reveal that when Cr substitutes for an Al ion in sapphire, the surrounding ions relax to an arrangement similar to that for Cr in α-Cr 2 O 3 . Also, most of the structural relaxation is accommodated by the first shell of oxygen and aluminum ions around the substituted Cr 3+ ion. The computations also indicate that with applied pressure (tensile and compressive) the ionic positions change self-similarly and in proportion to the macroscopic strain.
Habitat relationships of reptiles in pine beetle disturbed forests of Alabama, U.S.A., with guidelines for a modified drift-fence sampling method

Understanding vertebrate habitat relationships is important to promote management strategies for the longterm con- servation of many species. Using a modified drift fence method, we sampled reptiles and compared habitat variables within the William B. Bankhead National Forest (BNF) in Alabama, U.S.A from April 2005 to June 2006. We captured 226 individual rep- tiles representing 19 species during 564 total trap nights. We used canonical correspondence analysis to examine habitat associa- tions for the reptiles sampled and we detected a distinct habitat gradient ranging from sites with greater litter depth and percent canopy cover to more open sites with greater woody, herbaceous, and coarse woody debris (CWD) coverage, and CWD volume. Little brown skinks Scincella lateralis and eastern worm snakes Carphophis a. amoenus were associated with sites with greater litter depth and canopy cover, whereas eastern fence lizards Sceloporus undulatus, copperheads Agkistrodon contortrix, and gray ratsnakes Pantherophis spiloides were associated with sites possessing greater CWD coverage and volume. We found that distur- bances due to the southern pine beetle Dendroctonus frontalis were likely important for influencing reptile distributions through the creation of canopy gaps and fallen coarse woody debris. Compared to other studies, our modified drift-fence trap technique was successful for sampling larger snake species (66 snakes in 564 trap nights). We have also provided detailed schematics for constructing drift fence array and box traps used in this study (Current Zoology 56 (4): 411-420, 2010).
Cross-document Event Coreference Resolution based on Cross-media Features

In this paper we focus on a new problem of event coreference resolution across television news videos. Based on the observation that the contents from multiple data modalities are complementary, we develop a novel approach to jointly encode effective features from both closed captions and video key frames. Experiment results demonstrate that visual features provided 7.2% absolute F-score gain on stateof-the-art text based event extraction and coreference resolution.
Pancreatic sympathetic nerves contribute to increased glucagon secretion during severe hypoglycemia in dogs

To determine if pancreatic sympathetic nerves can contribute to increased glucagon secretion during hypoglycemia, plasma glucagon and pancreatic glucagon secretion in situ were measured before and during insulin-induced hypoglycemia in three groups of halothane-anesthetized dogs. All dogs were bilaterally vagotomized to eliminate the input from pancreatic parasympathetic nerves. One group of dogs received only vagotomy (VAGX). A second group was vagotomized and adrenalectomized (VAGX + ADX). A third group received vagotomy, adrenalectomy, plus surgical denervation of the pancreas (VAGX + ADX + NERVX) to prevent activation of pancreatic sympathetic nerves. In dogs with VAGX only, hypoglycemia increased plasma epinephrine (Epi), pancreatic norepinephrine (NE) output (+320 +/- 140 pg/min, P < 0.05), arterial plasma glucagon (+28 +/- 12 pg/ml, P < 0.01), and pancreatic glucagon output (+1,470 +/- 370 pg/min, P < 0.01). The addition of ADX eliminated the increase of Epi but did not increase pancreatic NE output (+370 +/- 190 pg/min, P < 0.025), arterial plasma glucagon (+20 +/- 5 pg/ml, P < 0.01), or pancreatic glucagon output (+810 +/- 200 pg/min, P < 0.01). In contrast, the addition of pancreatic denervation eliminated the increase of pancreatic NE output (-20 +/- 40 pg/min, P < 0.05 vs. VAGX), the arterial glucagon (+1 +/- 2 pg/ml, P < 0.01 vs. VAGX), and pancreatic glucagon output responses (+210 +/- 280 pg/min, P < 0.025 vs. VAGX) to hypoglycemia. Thus activation of pancreatic sympathetic nerves can contribute to the increased glucagon secretion during severe insulin-induced hypoglycemia in dogs.
Graphene nanophotonic sensors

Graphene is known to possess a host of remarkable properties such as a zero bandgap at its Dirac point, broadband saturable optical absorption, ballistic carrier transport at room temperature, as well as extremely high stiffness and thermal conductivity. This has in turn made it a material of interest for many applications, ranging from fundamental physics studies to electronic devices. From a photonics perspective, graphene's ability to support surface plasmon-polaritons with extremely small mode volumes in the infrared spectral regime and beyond renders it an ideal platform for strongly enhanced light–matter interactions at deeply subwavelength size scales. Together with its large bandwidth of operation, as well as intrinsic chemical stability and affinity to organic molecules, graphene serves as a natural candidate for numerous optics-based sensing applications. This article reviews recent works that highlight the various advantages of graphene in an optical sensing context. Specifically, it focuses on how the passive functionalization of graphene can improve the performance of existing optical sensors, and how its use as an active signal transduction element could lead to various novel or hybrid devices that extend the functionalities of traditional sensors.
Common Viral Integration Sites Identified in Avian Leukosis Virus-Induced B-Cell Lymphomas

ABSTRACT Avian leukosis virus (ALV) induces B-cell lymphoma and other neoplasms in chickens by integrating within or near cancer genes and perturbing their expression. Four genes— MYC , MYB , Mir-155 , and TERT —have previously been identified as common integration sites in these virus-induced lymphomas and are thought to play a causal role in tumorigenesis. In this study, we employ high-throughput sequencing to identify additional genes driving tumorigenesis in ALV-induced B-cell lymphomas. In addition to the four genes implicated previously, we identify other genes as common integration sites, including TNFRSF1A , MEF2C , CTDSPL , TAB2 , RUNX1 , MLL5 , CXorf57 , and BACH2 . We also analyze the genome-wide ALV integration landscape in vivo and find increased frequency of ALV integration near transcriptional start sites and within transcripts. Previous work has shown ALV prefers a weak consensus sequence for integration in cultured human cells. We confirm this consensus sequence for ALV integration in vivo in the chicken genome. IMPORTANCE Avian leukosis virus induces B-cell lymphomas in chickens. Earlier studies showed that ALV can induce tumors through insertional mutagenesis, and several genes have been implicated in the development of these tumors. In this study, we use high-throughput sequencing to reveal the genome-wide ALV integration landscape in ALV-induced B-cell lymphomas. We find elevated levels of ALV integration near transcription start sites and use common integration site analysis to greatly expand the number of genes implicated in the development of these tumors. Interestingly, we identify several genes targeted by viral insertions that have not been previously shown to be involved in cancer.
Book Review: More than Maoism: Politics and Policies of Insurgency in South Asia and Ordinary People, Extraordinary Violence

Robin Jeffrey, Ronojoy Sen and Pratima Sen, eds, More than Maoism: Politics and Policies of Insurgency in South Asia. New Delhi: Manohar. 2012. 470 pages. ₹ 1,250.Chitralekha, Ordinary People, Extraordinary Violence. New Delhi: Routledge. 2012. 348 pages. ₹ 795.
ALLERGIC REACTIONS TO MILK-CONTAMINATED NONDAIRY PRODUCTS

ADVERSE reactions to cow's milk have been estimated to occur in 0.1 to 7.5 percent of children.1 , 2 A variety of manifestations have been reported, including urticaria, angioedema, atopic dermatitis, rhinitis, wheezing, anaphylactic reactions, various gastrointestinal syndromes, and failure to thrive.3 , 4 Some patients may be extremely sensitive to milk; the ingestion of as little as one drop has been reported to cause generalized reactions.5 In children, repeated exposures to small quantities of food allergens may lead to recurrence of symptoms and delay the resolution of food allergy.2 , 6 , 7 The management of sensitivity to cow's milk is based on the complete elimination of . . .
Three Laboratory Techniques for Screening Small Grains for Resistance to the Cereal Leaf Beetle

Larval growth and oviposition were used to screen winter wheat, Triticum aestivum L.; barley, Hordeum vulgare L.; and oats, Avena sativa L. for resistance to Oulema melanopus (L.). Seedlings of wheat line CI 8519, barley line CI 6671, and oat lines CI 1795 and CI 3393 were least preferred for oviposition, and when gravid females alone or with males were restricted to these specific lines, a significant reduction often occurred in the number of eggs laid. Larval survival on the resistant wheat lines after 3 days was also significantly reduced: only 10% were alive on plants of wheat line CI 8519. Larval Weights were significantly lower on highly resistant wheat (0.41 mg vs. 1.53 mg on susceptible wheat). However, no significant changes in larval mortality or weight occurred on the barley and oat selections.
Jack Nichols, Gay Pioneer: “Have You Heard My Message?”: Campbell, J. Louis III (2007). New York: Harrington Park Press. 315 pp. with Notes, Bibliography, and Index. 43 black-and-white photos. $69.95 (hard) ISBN: 978-1-56023-652-8; $29.95 (soft) ISBN: 978-1-56023-653-5.

Placing the name of Jack Nichols to the left of the colon in the title implies that Nichols is the focus, and this book delivers on that promise. “Have You Heard My Message?” is largely biographica...
Why Not Go Back to the Moon

This chapter explores the reasons why NASA is choosing to go to Mars instead of going back to the Moon. The politics affecting this decision is discussed including initial attempts for financial support by President George H.W. Bush in the late 1980s to President George W. Bush in 2003 and up to current decisions from President Obama’s era. Opposing thoughts still exist whether to set up a lunar base to serve as a space platform to travel to deep space versus moving directly to manned Mars missions.
Attracting unwanted attention: generalization of behavioural adaptation to an invasive predator carries costs

Behavioural responses of animals to environmental cues are often governed by general ‘rules of thumb’. Animals that face novel conditions as a result of global environmental change may alter these behavioural rules to persist. However, adaptation of generalized rules to novel pressures may cause a species to be maladapted to original conditions (e.g. predators) that remain in its environment. Invasive red imported fire ants, Solenopsis invicta, are novel predators of eastern fence lizards, Sceloporus undulatus. Lizards from fire ant-invaded sites break crypsis to flee from fire ants at higher frequencies than fire ant-naive lizards. This shift promotes survival of attacks by these invasive ants but could result in attacks by native visual predators. Generalization of this increase in antipredator behaviour to native species could further increase this cost. We tested whether lizards' increased propensity to flee from fire ants is generalized to native ants and a predatory bird. We found that increased behavioural responsiveness to fire ants was generalized to two native ants but not to a perceived avian predator. We also found that lizards from populations invaded by fire ants had higher prevalence of injuries in the field, likely indicating greater attempted predation. We propose that generalized anti-ant behaviour may improve survival in the presence of fire ants but increase attacks by native visual predators. This study suggests that generalized rules can be maladaptive under novel conditions and highlights the challenges of assessing the costs and benefits of adaptations to rapid environmental change.
Issues in the Management of Esophagogastric Cancer in Geriatric Patients

Esophagogastric cancers predominantly affect older adults; however, older patients are less likely to be recommended for both curative and palliative treatment. Older patients have unique challenges that need to be addressed during their oncologic care. Tools such as complete geriatric assessments may help to better identify fit older adults and stratify patients for aggressive treatment strategies. This review evaluates the current knowledge and the remaining challenges in optimally managing elderly patients with esophagogastric cancers.
Efficient approximation of labeling problems with applications to immune repertoire analysis

Labeling problems are finding increasing applications to optimization problems. They usually get realized into linear or quadratic optimization problems, which are inefficient for large graphs. In this paper we propose an efficient primal-dual solution, ML PD , for a family of labeling problems. We apply this algorithm to the analysis of immune repertoires, and compare it against our baseline approach based on refinement operators. We provide a comparative evaluation both in terms of accuracy and computational efficiency with respect to the baseline model, as well as to quadratic optimization.
Droplet digital PCR for rapid enumeration of viral genomes and particles from cells and animals infected with orthopoxviruses.

Abstract Droplet digital polymerase chain reaction (ddPCR) was adapted for quantifying the number of orthopoxviral genomes in purified virus samples, infected cell lysates and tissues of infected animals. In contrast to the more commonly used qPCR, the newer ddPCR provides absolute numbers of DNA copies in samples without need for standard curves and has the ability to detect rare mutants in a population. The genome/infectious unit ratio for several sucrose gradient-purified orthopoxviruses varied from 5 to 10, which correlated well with values obtained using the Virocyt, a dedicated fluorescence flow cytometer. By employing a nuclease step to digest unencapsulated DNA, the genome/infectious unit ratios of virus in crude cell lysates approached that of purified virus particles. The speed, accuracy, sensitivity, and dynamic range of less than one to millions of infectious units in a sample make this semi-automated method well suited to a variety of laboratory, animal and clinical studies.
Age-related differences in bimanual movements: A systematic review and meta-analysis.

Abstract Background With increasing age motor functions decline. The additional challenges of executing bimanual movements further hinder motor functions in older adults. The current systematic review and meta-analysis determined the effects of healthy aging on performance in bimanual movements as compared to younger adults. Methods Our comprehensive search identified 27 studies that reported bimanual movement performance measures. Each study included a between groups comparison of older (mean age = 68.79 years) and younger adults (mean age = 23.14 years). The 27 qualified studies generated 40 total outcome measure comparisons: (a) accuracy: 18, (b) variability: 14, and (c) movement time: eight. Results Our meta-analysis conducted on a random effects model identified a relatively large negative standardized mean difference effect (ES = − 0.93). This indicates that older adults exhibited more impaired bimanual movement performance in comparison to younger adults in our group of studies. Specifically, a moderator variable analysis revealed large negative effects in both accuracy (ES = − 0.94) and variability (ES = − 1.00), as well as a moderate negative effect (ES = − 0.71) for movement time. These findings indicate that older adults displayed reduced accuracy, greater variability, and longer execution time when executing bimanual movements. Conclusion These meta-analytic findings revealed that aging impairs bimanual movement performance.
Contributions of Kansas rangeland burning to ambient O3: Analysis of data from 2001 to 2016.

Abstract Prescribed range/pasture burning is a common practice in Kansas to enhance the nutritional value of native grasses and control invading weeds, trees, and brush. A major concern associated with the burning is the contribution of smoke to elevated ground level ambient ozone (O3). The objective of this study is to estimate contributions of Kansas rangeland burning to ambient O3 mixing ratios through regression analysis (1) between observed O3 data and available satellite burn activity data from 2001 to 2016; and (2) between observed O3 data and the smoke contributions to PM2.5 which were resolved from receptor modeling. Positive correlations were observed between ambient O3 levels and the acres burned each year estimated from satellite imagery. When burned acres in April were larger than or equal to 1.9 million, O3 > 70 ppb occurred at least at one of the ten monitoring sites in Kansas. Statistical regression models of daily maximum 8-hour O3 mixing ratios were developed at each of the ten monitoring sites using meteorological predictors. The O3 model residuals that were not explained by the meteorological effect models were affected by PM2.5 contributors including sulfate/industrial sources and emissions that generated secondary organic particles, such as rangeland burning, which were derived from receptor modeling. The average O3 model residual on the high O3 days in April was 21 ± 9 ppb, which was likely associated with smoke emissions from burning. Research will continue to obtain daily satellite burn activity data and to correlate burn data with daily O3 data, so that modeling of O3 levels can be improved under influences of daily burn activities. Less frequency of high O3 days was observed in April since 2011, which may be partly due to implementation of the Flint Hills Smoke Management Plan which promoted better timing of burns.
Finite groups with trivial Frattini subgroup

All groups considered are finite. A group has a trivial Frattini subgroup if and only if every nontrivial normal subgroup has a proper supplement.The property is normal subgroup closed, but neither subgroup nor quotient closed. It is subgroup closed if and only if the group is elementary, i.e. all Sylow subgroups are elementary abelian. If G is solvable, then G and all its quotients have trivial Frattini subgroup if and only if every normal subgroup of G has a complement. For a nilpotent group, every nontrivial normal subgroup has a supplement if and only if the group is elementary abelian. Consequently, the center of a group in which every normal subgroup has a supplement is an elementary abelian direct factor.
Effect of Shearing Strain-Rate on the Undrained Strength of Clay

Dynamic testing method is required to determine the strength of soils for problems of dynamic loading. This paper presents an experimental technique for measuring the relationship of undrained shear strength and strain-rate of a clay. Torsion tests were performed on remolded hollow cylinder specimens. The test results show that the undrained shear strength increases initially with strain-rate from the static undrained strength, but subsequently the undrained strength reaches an ultimate value as the strain-rate increases.
Investigational trials of the Hemopump at the Texas Heart Institute: practical issues

When we were first introduced to the Hemopump, we were skeptical about it. We feared that the device would cause hemolysis, as well as other problems. In fact, we told Dr. Wampler that we did not think it would work, but we did the initial animal experiments anyway. To paraphrase the famous Frenchman Claude Bernard, however, “You have to decide on the experiment and hang your ideas outside the laboratory, do the experiment, and see what nature says, not what you think.” We did the animal experiments, and they went very well, as has been reported in the literature (5). We saw no abnormality in plasma-free hemoglobin levels or hematologic profiles (Figs. 1, 2). The animals tolerated the intraventricular device very well.
Comparison of Conventional and Cone-Beam CT for Monitoring and Assessing Pulmonary Microwave Ablation in a Porcine Model.

Abstract Purpose To compare cone-beam computed tomography (CT) with conventional CT for assessing the growth and postprocedural appearance of pulmonary microwave ablation zones. Materials and Methods A total of 17 microwave ablations were performed in porcine lung in vivo by applying 65 W for 5 minutes through a single 17-gauge antenna. Either CT (n = 8) or CBCT (n = 9) was used for guidance and ablation zone monitoring at 1-minute intervals. Postprocedural noncontrast images were acquired with both modalities. Three independent readers measured the length, width, cross-sectional area, and circularity of the ablation zones on gross tissue samples and CT and cone-beam CT images. The measurements were compared via linear mixed-effects models for postprocedural appearance and with a polynomial mixed effects model for ablation zone growth curves. Results On postprocedural images, the differences between cone-beam CT and CT in mean length (3.84 vs 3.86 cm; Δ = −0.02; P = .70), width (2.61 vs 2.56 cm; Δ = 0.06; P = .46), area (7.84 vs 7.65 cm2; Δ = 0.19; P = .35), and circularity (0.85 vs 0.85; Δ = 0.01; P = .62) were not statistically significant after accounting for intersubject and interrater variability. Also, there was no significant difference between CT and cone-beam CT growth curves of the ablation zones during monitoring in terms of length (pInt. = 1.00; pLin.Slope = 0.52; pQuad.Slope = 0.69); width (pInt. = 0.83; pLin.Slope = 0.98; pQuad.Slope = 0.79), area (pInt. = 0.47; pLin.Slope = 0.27; pQuad.Slope = 0.57), or circularity (pInt. = 0.54; pLin.Slope = 0.74; pQuad.Slope = 0.80). Both CT and cone-beam CT overestimated gross pathologic observations of ablation length, width, and area (P Conclusions Cone-beam CT was similar to conventional CT when assessing the growth, final size, and shape of pulmonary microwave ablation zones and may be useful for monitoring and evaluating microwave ablations in the lung.
Accuracy of Dynamic Virtual Articulation: Trueness and Precision

Purpose To study the effects of altering condylar settings and pin openings on the trueness and precision of virtual articulators vs. mechanical articulators. Materials and methods Maxillary and mandibular typodonts with fiducial markers were mounted on a mechanical Artex-CR articulator, and the mandibular teeth were prepared to allow guidance solely by the posterior determinants of the articulator and the incisal table. The relationship of the mounted typodonts was preserved digitally by scanning using manufacturer transfer plate adaptors. On the mechanical articulator, pattern resin was allowed to set between the maxillary and mandibular occlusal surfaces (area #25-30) at the endpoints of dynamic movements at 3 condylar inclinations (SCI): 10°, 30°, and 45°, n = 12/inclination, or at 3 incisal pin openings (2, 5, and 10 mm, n = 12/opening). All other articulator settings were kept constant. Resin specimens attached to the typodonts were scanned within 5 minutes of setting, then removed, and the articulated typodonts rescanned. Fixed dental prostheses (FDPs) #25-30 were designed on the virtual articulator using identical parameters to the mechanical articulator. Dynamic virtual movements were used to sculpt the design, and a file of the design was saved. The files of both types of samples were aligned and overlaid. Interocclusal separation was measured in triplicate at the indentation created by the mesiolabioincisal point angle on the incisal edge of #8 and the mesiobucco-occlusal point angle of #3. Trueness and precision of both types of articulators were calculated and compared using one-way ANOVA, followed by the Tukey HSD test (α = 0.05). Results There was no statistically significant difference at altered pin openings in either trueness (F = 0.202, p = 0.37) or precision (F = 3.134, p = 0.09) for the majority of measurements. The only significant difference was in the precision between the 2 types of articulators at 5 mm incisal opening, and only at the anterior measurement point (F = 15.134, p = 0.0008); however, these differences were less than 100 μm. When the SCI was altered, there was no statistically significant difference (F = 3.624, p > 0.05) between the virtual and mechanical articulators in trueness for 5 of the 6 measurements obtained (F = 3.624, p = 0.07) or for all of the precision measurements (F = 3.529, p = 0.07). The one trueness measurement that was significantly different (F = 9.237, p = 0.006) occured at SCI of 10°, and it was less than 100 µm. Conclusions Dynamic movements on the virtual articulator were shown to be as true and precise as to the mechanical articulator. When there were deviations, these deviations were less than 100 µm and thus, these deviations may not be clinically relevant.
Adjuvant Radiation Improves Recurrence-Free Survival and Overall Survival in Adrenocortical Carcinoma.

Context Adrenocortical carcinoma (ACC) is a rare malignancy with high rates of recurrence and poor prognosis. The role of radiotherapy (RT) in localized ACC has been controversial, and RT is not routinely offered. Objective To evaluate the benefit of adjuvant RT on outcomes in ACC. Design This is a retrospective propensity-matched analysis. Setting All patients were seen through the University of Michigan's Endocrine Oncology program, and all those who underwent RT were treated at the University of Michigan. Participants Of 424 patients with ACC, 78 were selected; 39 patients underwent adjuvant radiation. Intervention Adjuvant RT to the tumor bed and adjacent lymph nodes. Main outcomes measures Time to local failure, distant failure, or death. Results Median follow-up time was 4.21 years (95% CI, 2.79 to 4.94). The median radiation dose was 55 Gy (range, 45 to 60). The 3-year overall survival estimate for patients improved from 48.6% for patients without RT (95% CI, 29.7 to 65.2) to 77.7% (95% CI, 56.3 to 89.5) with RT, with a hazard ratio (HR) of 3.59 (95% CI, 1.60 to 8.09; P = 0.002). RT improved local recurrence-free survival (RFS) from 34.2% (95% CI, 18.8 to 50.3) to 59.5% (95% CI, 39.0 to 75.0), with an HR of 2.67 (95% CI, 1.38 to 5.19; P = 0.0035). RT improved all RFS from 18.3% (95% CI, 6.7 to 34.3) to 46.7% (95% CI, 26.9 to 64.3), with an HR 2.59 (95% CI, 1.40 to 4.79; P = 0.0024). Conclusions In the largest single institution study to date, adjuvant RT after gross resection of ACC improved local RFS, all RFS, and overall survival in this propensity-matched analysis. Adjuvant RT should be considered a part of multidisciplinary management for patients with ACC.
Correction to: Putting Puerto Rico’s best (black) face forward: Ramón Rivero’s “Diplo” and racialized performances of liberation

In the previously published version of this article an error appears in the bibliographic citation (Jimenez-Roman, G. 1995). The author cited should be Jimenez-Munoz, G.
Preservice Teachers' Perceptions of Teacher Leadership: Is It about Compliance or Understanding?.

Little attention has been paid to the leadership experiences of pre-service teachers despite the robust field of teacher leadership research. This study reviews 124 activities in the Teacher Leader Essays, a part our program’s licensure requirements, to understand our pre-service teachers’ experiences and perceptions of leadership. This inquiry informs the literature on teacher leadership by providing a summary of pre-service teachers’ actions and reflections on teacher leadership while noting the constraints of such mandated activities.
Effective Application of Metabolite Profiling in Drug Design and Discovery

At one time, biotransformation was a descriptive activity in pharmaceutical development, viewed simply as structural elucidation of drug metabolites, completed only once compounds entered clinical development. Herein, we present our strategic approach using structural elucidation to enable chemistry design/SAR development. The approach considers four questions that often present themselves to medicinal chemists optimizing their compounds for candidate selection: (1) What are the important clearance mechanisms that mediate the disposition of my molecule? (2) Can metabolic liabilities be modulated in a favorable way? (3) Does my compound undergo bioactivation to a reactive metabolite? (4) Do any of the metabolites possess activity, either on- or off-target? An additional question necessary to support compound development relates to metabolites in safety testing (MIST) and our approach also addresses this question. The value in structural elucidation is derived from its application to better design molecules, guide their clinical development, and underwrite patient safety.
Y chromosome copy number variation and its effects on fertility and other health factors: a review

The Y chromosome is essential for testis development and spermatogenesis. It is a chromosome with the lowest gene density owing to its medium size but paucity of coding genes. The Y chromosome is unique in that the majority of its structure is highly repetitive sequences, with the majority of these limited genes occurring in 9 amplionic sequences throughout the chromosome. The repetitive nature has its benefits as it can be protective against gene loss over many generations, but it can also predispose the Y chromosome to having wide variations of the number of gene copies present in these repeated sequences. This is known as copy number variation. Copy number variation is not unique to the Y chromosome but copy number variation is a well-known cause of male infertility and having effects on spermatogenesis. This is most commonly seen as deletions of the AZF sequences on the Y chromosome. However, there are other implications for copy number variation beyond just the AZF deletions that can affect spermatogenesis and potentially have other health implications. Copy number variations of TSPY1, DAZ, CDY1, RBMY1, the DYZ1 array, along with minor deletions of gr/gr, b1/b3, and b2/b3 have all be implicated in affecting spermatogenesis. UTY copy number variations have been implicated in risk for cardiovascular disease, and other deletions within gr/gr and the AZF sequences have been implicated in cancer and neuropsychiatric diseases. This review sets out to describe the Y chromosome and unique susceptibility to copy number variation and then to examine how this growing body of research impacts spermatogenesis and other health factors.
COVID-19: Outcomes for trauma-impacted nurses and nursing students.

Suppose you wake up one day, and all your plans are hindered, postponed, and potentially suspended. Your future, the future of your family, and life as you know it is changed. Although the COVID-19 pandemic did not occur overnight, the impact on nursing and nursing education appeared to have happened abruptly. During the pandemic, nurses and nursing students voiced concern for themselves, families, patients, communities, and the future (McClunie-Trust, 2020). The actions taken to flatten the curve can have an unprecedented impact on a specific sect of nurses and nursing students who have been survivors of trauma or acute childhood experiences (ACE). Nurses and nursing students as individuals are not immune to traumatic experiences in their formative years. Nursing school is a high stake, stressful environment, and the opportunity to be re-traumatized is high. In addition, cognitive processes impact students who have experienced ACE events. Conversely, practicing professional nurses will be exposed to high-stress events, such as death, patient trauma, and COVID-19, which has the potential to re-traumatize the nurse and influence the care provided.
EDA on the asymptotic normality of the standardized sequential stopping times, Part-II: Distribution-free models

In sequential analysis, an experimenter gathers information regarding an unknown functional (parameter) by observing random samples in successive steps. We discuss a number of distribution-free sce...
Learning Places: Place-Based Learning in an Interdisciplinary Approach to Undergraduate Research

This chapter discusses the faculty toolkit of specific practices with particular effectiveness in student engagement and learning in the twenty-first century, including undergraduate research. While this high-impact practice is most often associated with the sciences, it has wider applicability to undergraduate learning where the methods of research can integrate synergistic strategies that further enhance student engagement and learning: place-based learning and interdisciplinary teaching. In this chapter, these two compelling approaches to higher education are presented as a powerful, interwoven, and integrated approach to undergraduate research. The interdisciplinary general education course Learning Places: Understanding the City provides a case study illustrating undergraduate research using the city as an engaging interdisciplinary laboratory.
Topical Treatment of Human Skin and Cultured Keratinocytes with High-Dose Spironolactone Reduces XPB Expression and Induces Toxicity

Spironolactone (SP) is used to treat a variety of disparate disease states ranging from heart failure to acne through antagonism of the mineralocorticoid and androgen receptors. Although normally taken as an oral medication, recent studies have explored the topical application of SP onto the skin. However, because SP induces the proteolytic degradation of the XPB protein, which plays critical roles in DNA repair and transcription, there may be safety concerns with the use of topical SP. In this study, we show that the topical application of a high concentration of either SP or its metabolite canrenone onto human skin ex vivo lowers XPB protein levels and induces toxic responses in the epidermis. Interestingly, although SP and canrenone both inhibit cell proliferation, induce replication stress responses, and stimulate apoptotic signaling at high concentrations in cultured keratinocytes in vitro, these effects were not correlated with XPB protein loss. Thus, high concentrations of SP and canrenone likely inhibit cell proliferation and induce toxicity through additional mechanisms to XPB proteolytic degradation. This work suggests that care may need to be taken when using high concentrations of SP directly on human skin.
Projected Composition Operators on Pseudoconvex Domains

Let $$\Omega \subset {\mathbb {C}}^n$$ be a smooth bounded pseudoconvex domain and $$A^2 (\Omega )$$ denote its Bergman space. Let $$P:L^2(\Omega )\longrightarrow A^2(\Omega )$$ be the Bergman projection. For a measurable $$\varphi :\Omega \longrightarrow \Omega $$ , the projected composition operator is defined by $$(K_\varphi f)(z) = P(f \circ \varphi )(z), z \in \Omega , f\in A^2 (\Omega ).$$ In 1994, Rochberg studied boundedness of $$K_\varphi $$ on the Hardy space of the unit disk and obtained different necessary or sufficient conditions for boundedness of $$K_\varphi $$ . In this paper we are interested in projected composition operators on Bergman spaces on pseudoconvex domains. We study boundedness of this operator under the smoothness assumptions on the symbol $$\varphi $$ on $${{\overline{\Omega }}}$$ .
Teaching NeuroImages: Dorsal Medullary Lesions in Juvenile-Onset Alexander Disease

A 6-year-old boy presented with dysphagia, vomiting, and weight loss. Early developmental milestones were notable for mild gross motor and speech delay. Hypotonia was present on examination. Brain MRI revealed bilateral enhancing dorsal medullary lesions (figure, contrast not shown). The differential diagnosis included a leukodystrophy or mitochondrial disease. Alexander disease was confirmed genetically (de novo variant in GFAP -targeted testing: p.Arg-376-Gly). Typical features also include hypernasal speech with subsequent motor difficulties and autonomic dysfunction over time.2 GFAP sequencing should be considered in patients with unilateral or bilateral dorsal medullary lesions with localizing symptoms (e.g., vomiting and dysphagia).
Empirical Study and Enhancement of Association and Long Sleep in 802.11 IoT Systems

The 802.11 standard, a.k.a., WiFi, is becoming more popular for IoT connectivity. The three essential operations performed to ensure connectivity in an 802.11 network are association, maintaining association, and periodic beacon reception. Understanding and enhancing the energy efficiency of these operations is essential for building IoT systems. Unfortunately, the overheads of these operations have not been studied considering station’s software and hardware configuration, access point configuration, and link unreliability. In this paper, we show that: (i) association cost depends on multiple factors including probing, key generation, operating system, and network stack, (ii) increasing listen interval to reduce beacon reception wake-up instances may negatively impact energy efficiency, (iii) maintaining association by relying on the poll messages generated by the access point is not reliable, and (iv) key renewal aggravates the chance of disassociation. We also present station- and access point-based solutions that address some of these problems.
Validation of obesity-related diagnosis codes in claims data.

AIM To determine whether body mass index (BMI) can be accurately identified in epidemiological studies using claims databases. MATERIALS AND METHODS Using the Mass General Brigham Research Patient Data Repository-Medicare-linked database, we identified a cohort of patients with a BMI measurement for the periods January 1 to June 31, 2014 or January 1 to June 31, 2016, to capture both the International Classification of Disease (ICD)-9 and ICD-10 eras. Patients were divided into two groups, with or without an obesity-related ICD code in the 6 months before or after the BMI measurement date. We created two binary measures, first for composite overweight, obesity, or severe obesity (BMI ≥25 kg/m2 ), and second for obesity or severe obesity (BMI ≥30 kg/m2 ). We calculated accuracy measures (sensitivity, specificity, positive predictive value [PPV] and negative predictive value [NPV]) for each obesity category for the overall cohort, and stratified by type 2 diabetes and ICD-code era. RESULTS The cohort included 73 644 patients with a BMI measurement in 2014 or 2016, of whom 16 280 had an obesity-related ICD code. The specificity of obesity-related ICD codes (ICD-9 and ICD-10) was 99.7% for underweight/normal weight, 97.4% for overweight, 99.7% for obese and 98.9% for severely obese. For binary categories capturing BMI ≥25 kg/m2 and BMI ≥30 kg/m2 , specificity was 97.0% and 98.2%, and PPV was 86.9% and 97.3%. Sensitivity was low overall (<40%). Codes for patients with type 2 diabetes and codes in the ICD-10 era had higher sensitivity, PPV and NPV. CONCLUSION Obesity-related ICD codes can accurately identify patients with obesity in epidemiological studies using claims databases.
Lack of Transparency and Potential Bias in Artificial Intelligence Data Sets and Algorithms: A Scoping Review.

Importance Clinical artificial intelligence (AI) algorithms have the potential to improve clinical care, but fair, generalizable algorithms depend on the clinical data on which they are trained and tested. Objective To assess whether data sets used for training diagnostic AI algorithms addressing skin disease are adequately described and to identify potential sources of bias in these data sets. Data sources In this scoping review, PubMed was used to search for peer-reviewed research articles published between January 1, 2015, and November 1, 2020, with the following paired search terms: deep learning and dermatology, artificial intelligence and dermatology, deep learning and dermatologist, and artificial intelligence and dermatologist. Study selection Studies that developed or tested an existing deep learning algorithm for triage, diagnosis, or monitoring using clinical or dermoscopic images of skin disease were selected, and the articles were independently reviewed by 2 investigators to verify that they met selection criteria. Consensus process Data set audit criteria were determined by consensus of all authors after reviewing existing literature to highlight data set transparency and sources of bias. Results A total of 70 unique studies were included. Among these studies, 1 065 291 images were used to develop or test AI algorithms, of which only 257 372 (24.2%) were publicly available. Only 14 studies (20.0%) included descriptions of patient ethnicity or race in at least 1 data set used. Only 7 studies (10.0%) included any information about skin tone in at least 1 data set used. Thirty-six of the 56 studies developing new AI algorithms for cutaneous malignant neoplasms (64.3%) met the gold standard criteria for disease labeling. Public data sets were cited more often than private data sets, suggesting that public data sets contribute more to new development and benchmarks. Conclusions and relevance This scoping review identified 3 issues in data sets that are used to develop and test clinical AI algorithms for skin disease that should be addressed before clinical translation: (1) sparsity of data set characterization and lack of transparency, (2) nonstandard and unverified disease labels, and (3) inability to fully assess patient diversity used for algorithm development and testing.
Mucin Expression and Splicing Determine Novel Subtypes and Patient Mortality in Pancreatic Ductal Adenocarcinoma

Purpose: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy demonstrating aberrant and progressive expression of mucins. The contribution of individual mucins has been extensively investigated in PDAC; however, comprehensive mucin profiling including splice variants in PDAC tumors has not been reported. Experimental Design: Using publicly available RNA sequencing (RNA-seq) datasets, we assess the expression of mucin family members and their splice variants (SV) in PDAC tumor samples for the first time. Mucin SVs that are correlated with PDAC patient survival are validated in a cohort of patient tumor samples. Further, we use computational methods to derive novel pancreatic tumor subtypes using mucin expression signatures and their associated activated pathways. Results: Principal component analysis identified four novel mucin-based PDAC subtypes. Pathway analysis implicated specific biological signatures for each subtype, labeled (i) immune activated, (ii) progressive, (iii) pancreatitis-initiated, and (iv) anti-inflammatory/PanIN-initiated. Assessing mucin SVs, significantly longer survival is observed with higher expression of 4 MUC1 and 1 MUC13 SVs, whereas patients expressing 2 MUC4 and 1 MUC16 SVs had shorter survival. Using a whole-transcriptome correlation, a three-gene panel, including ESRP2, PTK6, and MAGEH1, is designated to assess PDAC tumor sample cellularity by PCR. One MUC4 SV and one MUC13 SV are quantified in a separate PDAC patient cohort, and their effects on survival are experimentally validated. Conclusions: Altogether, we demonstrate the unique expression pattern of mucins, four mucin-based PDAC subtypes, and the contribution of MUC1, MUC4, and MUC16 SVs in PDAC patient survival.