cssi/SciSciGPT-SciSciNet huggingface dataset:
The interaction of lead exposure and arylsulfatase A genotype affects sulfatide catabolism in human fibroblasts

Abstract Lead exposure causes cognitive and behavioral deficits in some affected children. We propose that a contributing mechanism for the neurological damage is that lead induces critically low levels of arylsulfatase A (ASA) at sensitive stages of nervous system development. It is hypothesized that the combined effects of a single nucleotide polymorphism (SNP) in human ASA which results in reduced levels of the enzyme, and lead concentrations which decrease ASA activity culminate in cellular enzymic activity that is below a critical threshold required for the maintenance of normal nervous system function. Human fibroblasts grown in the presence of 20 microM lead acetate exhibit a more than 60% decrease of cellular ASA enzyme protein. Lead treatment of cells from individuals with the SNP(s) of pseudodeficient ASA, but not those from subjects with the normal gene, results in a significant decrease in ability of the cells to desulfate sulfatide, the substrate of ASA. The decrease in the degree of sulfatide catabolism is consistent with possible enhanced lead-induced neurobehavioral effects in individuals homozygous for the pseudodeficiency polymorphism(s) of ASA.
Geologic and hydrologic aspects of brine disposal intervals in the Appalachian Basin

Many different rock intervals are used for brine disposal injection in the Appalachian Basin. The study area was defined as eastern Kentucky, Ohio, Pennsylvania, and West Virginia. Brine injection in the study area has increased from approximately 6–7 million barrels (bbl) per year in the early 2000s to 17.6 million bbl in 2012, mostly due to shale gas activity. A review of geologic properties and subsurface distribution of rock formations used for injection is useful to understand brine disposal operations in the region. Operational data on injection rates and pressures were compiled for 2008–2012 for more than 300 class II brine disposal wells. Several class II brine disposal wells were monitored with continuous wellhead pressure loggers to estimate reservoir properties and understand injection operations. Project results provide a catalog of injection rates for the various formations, which range from hundreds to more than 100,000 bbl per month per well. Hydrologic analysis of depleted hydrocarbon reservoirs and deep saline formations in the study area indicates that there is a large capacity for brine disposal, but the characteristics of the rock formations may limit injection rates. Based on hydrocarbon production and brine injection volumes from 2008 to 2012, approximately 9984 bbl of brine were routed to class II brine disposal wells per billion cubic feet gas production, which suggests ultimate demand of up to 706–2290 million bbl brine disposal related to unconventional Marcellus and Utica plays. Understanding the geology and operational history of the injection zones is critical to support safe, reliable, and environmentally responsible brine disposal in the region.
Magnetic Behaviour of RCu4Al (R = Rare Earth) Intermetallic Compounds II

Intermetallic compounds of the general formula RCu4Al, where R = La,Ce,Pr,Nd,Sm,Gd,Tb,Dy,Ho,Er and Tm, have been prepared and are found to crystallize in the hexagonal CaCu5 type structure. Magnetization measurements on these compounds have been carried out in the temperature range 4.2 to 300 K. The compounds with Gd, Tb,Dy and Ho have been reported earlier (1) to order antiferromagnetically at low temperatures. There is no conclusive evidence about magnetic ordering in the remaining RCu4Al compounds from magnetization measurements in 21 k0e applied field. Deviation from Curie-Weiss behaviour, at low temperatures, is observed in Er and Tm compounds and is attributed to crystal field effects. The effective paramagnetic moments are close to free ion value except for the Ce and Pr compounds. The paramagnetic Curie temperatures are negative for Ce,Pr and Gd compounds and positive for the remaining compounds. The results are discussed and compared with those on RCU5 and RCu4Ag compounds.
Genetic Approaches for Signaling Pathways and Proteins

This chapter discusses some genetic approaches for studying signaling pathways and for elucidating the molecular mechanisms of information processing by modular signaling proteins. Bacteria live in precarious environments. Nutrient and toxin levels, acidity, temperature, osmolarity, humidity, and many other conditions can change rapidly and unexpectedly. Bacterial signaling systems are amenable to detailed genetic and biochemical analyses. In this chapter, some general strategies for using genetic methods to study sensory pathways and signaling proteins are discussed. Many signaling proteins, from both gram-positive and gram-negative bacteria, contain characteristic "transmitters" and "receivers" domains that promote information transfer within and between proteins. Transmitters and receivers are ideally suited as circuit elements for assembling signaling pathways. The only demonstrated mechanisms of transmitter-receiver communication involve phosphorylation and dephosphorylation reactions. With caution, the logic of epistatic analysis can be extended to more elaborate signaling pathways that have branches, feedback loops, and so on. Genetic approaches can provide considerable insight into the operation of signaling pathways and proteins. Even though actual signaling circuits are unlikely to be as simple as the two-component examples in the chapter, the same basic principles should apply.
Anthracobia, Ascodesmis, Pyronema, and Trichophaea in Culture

Brief descriptions of apothecia, asexual states present, and cultural characteristics of operculate Discomycetes, Anthracobia muelleri, Ascodesmis sphaerospora, Pyronema domesticum, and Trichophaea...
Trunk implantations of dicrotophos for cone-insect control in slash pine seed production stands.

Presented are the results of 4 years of research in north Florida on dicrotophos trunk implantation to control Dioryctria spp. coneworms and the slash pine seedworm, Laspeyresia anaranjada Miller, on 2nd-year cones of slash pine, Pinus elliottii var elliotti Engelm. Dicrotophos technical liquid (1.08 kg active ingredient (AI) per liter) was implanted in early May into holes drilled in the tree stems. Dosage rates of 0.8–2.0 g AI per cm of tree diameter at waist height gave 86–94% control of Dioryctria spp. and 94–100% control of M L. anaranjada on mature cones harvested in mid-September of the year of treatment. Dicrotophos implanted by Mauget® injectors at dosages of 0.6–1.4 g/cm diameter resulted in 30–81% control of Dioryctria spp. and 56–97% control of slash pine seedworm. Date of treatment may be advanced to early April and good control of both insects still be obtained. Foliage of trees implanted with dicrotophos in early May showed no phytotoxic symptoms at the dosages tested. Seeds from trees implanted with a 1.4 g per cm-diameter dosage of dicrotophos for 3 consecutive years showed no decrease in full-seed germination percentage when compared with seeds from untreated trees. Seed losses caused by the hemipteran seed bugs Leptoglossus corculus (Say) and Tetyra bipunctata (Herrich-Schaeffer) were also reduced with dicrotophos implants.
Complex Primary Total Knee Arthroplasty: Management of Flexion Contracture

For successful execution of total knee arthroplasty, the surgeon must be able to manage preoperative flexion contracture to ensure adequate postoperative motion, function, and patient satisfaction. The case presented highlights the steps taken to appropriately balance the flexion and extension space in a knee with a 20° preoperative flexion contracture. Consideration is given to coronal plane balancing, osteophyte resection, posterior capsular releasing, and additional femoral bone resection.
Enhanced phagocytic capacity endows chondrogenic progenitor cells with a novel scavenger function within injured cartilage

Summary Objective Articular cartilage harbors chondrogenic progenitor cells (CPCs), a population that responds chemotactically to cell death. Because this behavior is reminiscent of macrophages, we hypothesized that CPCs have macrophage-like capabilities for scavenging cell and tissue debris through phagocytosis. Design CPCs, chondrocytes, synoviocytes, and macrophages were cultured with fluorophore-labeled chondrocyte debris for 3, 6, 12, or 24 h. Debris internalization was quantified by confocal microscopy and flow cytometry. Confocal microscopy was also used to test CPCs and chondrocytes for uptake of fluorophore-labeled fibronectin fragments (Fn-fs), a form of extracellular matrix debris. Lysosome activity and mass in CPCs and chondrocytes were measured using fluorescent probes. The relative expression of phagocytosis-related genes and proteins was evaluated by polymerase chain reaction (PCR) and immunoblotting, respectively. Pulse-chase experiments were performed to determine if the debris internalized by CPCs and chondrocytes was cleared, and if clearance was affected by a cathepsin B inhibitor. Results More macrophages, synoviocytes, and CPCs internalized cell debris than chondrocytes at all time points. While uptake remained flat in chondrocytes at ∼10%, in the other cell types it peaked at more than 60% after 12–24 h. Relative to chondrocytes, CPCs showed significantly higher rates of Fn-fs engulfment, greater lysosome activity and mass, and over-expressed phagocytosis-related genes and proteins. Pulse-chase experiments revealed time- and cathepsin B-dependent clearance of cell debris in CPCs, but not in chondrocytes. Conclusions CPCs phagocytized cell and matrix debris much more efficiently than chondrocytes, supporting the hypothesis that they play a macrophage-like role in injured cartilage.
Abstract B24: ATDC (Trim29) drives invasive bladder cancer formation

Bladder cancer is a common and deadly malignancy, but incomplete understanding of the molecular events driving tumor development and metastasis has limited development of effective treatments. Ataxia-Telangiectasia Group D Complementing (ATDC; also named TRIM29) is highly expressed in many cancer types, including bladder and pancreas. To determine the role of ATDC in tumorigenesis, we developed a novel transgenic mouse model in which ATDC was overexpressed in multiple tissue types. The dominant phenotype in these mice was the development of both papillary and invasive bladder carcinoma beginning at approximately 8 months of age. In this model, invasive bladder tumors were histologically indistinguishable and shared a similar gene expression signature with human invasive bladder cancers. We also found that ATDC was highly expressed in ~70% human bladder cancers where it marked invasive tumors and correlated with worse survival after chemotherapy (p = 0.002). Furthermore, ATDC knockdown decreased proliferation, invasion and tumor growth in multiple human bladder cancer cell lines and in an in vivo orthotopic bladder tumor model. ATDC-induced bladder tumorigenesis was mediated by upregulation of DNA methyltransferase 3A (DNMT3A), which drove PTEN promoter methylation and silencing, events which promoted invasion and proliferation in both transgenic mice and human bladder cancers. These findings establish ATDC as a novel driver and therapeutic target in bladder cancer. In addition, the ATDC transgenic mouse model should serve as an important and unique new model to study bladder cancer development, progression and therapeutic responses. Citation Format: Phillip Palmbos, Lidong Wang, Huibin Yang, Jake LeFlein, John E. Wilkinson, Chandan Kumar-Sinha, L. Priya Kunju, Stephanie Daignault, Xue-Ru Wu, Yair Lotan, Monica Liebert, Mats Ljungman, Diane Simeone. ATDC (Trim29) drives invasive bladder cancer formation. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr B24.
Metabolism of dynorphin A1-13 in human CSF.

In-vitro incubation of human cerebrospinal fluid (CSF) obtained from patients ranging from 22–78 years with 10 μM of dynorphin A1–13 (Dyn A1–13) resulted in several cleavage products. Dyn A1–12 and A2–13 were identified as the major CSF metabolites by matrix-assisted laser desorption mass spectrometry (LD-MS). Further metabolites were Dyn A1–6, A2–12 and A4–12. LD-MS further suggested the formation of Dyn A1–8, A1–7, A1–10, A7–10, A3–12, A7–12, A3–13, A7–13 and A8–13. The metabolic half-life of Dyn A1–13 at 37°C was approximately 2.5 h (range 1.75–8.5 h), compared to less than one minute in plasma. The half-life of Dyn A1–13 decreased markedly with age or age-associated processes (n=20, r2=0.498). Noncompartmental kinetic analysis in the absence or presence of enzyme inhibitors (leucinethiol 10 μM, captopril 100 μM and GEMSA 20 μM) suggested that Dyn A1–13 is mainly metabolized by carboxypeptidase to A1–12 (51%) and by aminopeptidases to A2–13 (35%). The generation of A1–6 (13%) was only detected under enzyme inhibition. The extent of conversion into the main metabolites did not follow an age-associated trend, thus over-all enzyme levels but no specific enzymatic systems are elevated with age.
An increased initial follicle-stimulating hormone/luteinizing hormone ratio does not affect ovarian responses and the outcomes of in vitro fertilization *

The tenet that a combination of human follicle-stimulating hormone (hFSH)/human menopausal gonadotropin (hMG) improves follicular recruitment was assessed by randomly treating ovulatory women either with hFSH/hMG on days 3 and 4 of the cycle followed by two ampules of hMG daily or with a constant daily dose of 2 ampules of hMG. Estradiol (E2) levels on the day of human chorionic gonadotropin (hCG) and the mean number of mature, immature and atretic oocytes per cycle did not differ between the two groups. Likewise, fertilization, cleavage, and pregnancy rates were similar for the two treatments. When daily hormone levels were compared in 11 patients during two successive treatment cycles with both stimulation protocols, the temporal pattern of FSH accumulation was repeated in both cycles, but FSH levels were significantly higher when patients received hFSH/hMG. Nevertheless, during both cycles, E2 reached similar peak levels and the mean number of follicles per cycle on the day of hCG administration was not different. We conclude that routine use of hFSH/hMG does not improve the success of an in vitro fertilization (IVF) program and that higher FSH levels do not change the individuality of ovarian response in the same woman.
Hyperthermia and exercise.

The paper emphasizes fluid and electrolyte parameters that affect the hyperthermia of physical exercise (metabolic heat production). The major hypothesis discussed is that fluid and electrolyte changes influence thermal regulation within the fine control boundaries. A second working hypothesis is that the elevation of core temperature during exercise is a regulated phenomenon that is beneficial to the organism in terms of efficiency and potential for survival and is not merely a failure of the thermoregulatory control system. The central thermoregulatory mechanism seems more responsive to the hypothermic effect of calcium than to the hyperthermic effect of sodium. The mechanisms controlling plasma fluid-electrolyte shifts, particularly during exercise and recovery from exercise, may play an important part in exercise thermoregulation.
Neural Coding of Interaural Time Differences with Bilateral Cochlear Implants in Unanesthetized Rabbits.

Although bilateral cochlear implants (CIs) provide improvements in sound localization and speech perception in noise over unilateral CIs, bilateral CI users9 sensitivity to interaural time differences (ITDs) is still poorer than normal. In particular, ITD sensitivity of most CI users degrades with increasing stimulation rate and is lacking at the high carrier pulse rates used in CI processors to deliver speech information. To gain a better understanding of the neural basis for this degradation, we characterized ITD tuning of single neurons in the inferior colliculus (IC) for pulse train stimuli in an unanesthetized rabbit model of bilateral CIs. Approximately 73% of IC neurons showed significant ITD sensitivity in their overall firing rates. On average, ITD sensitivity was best for pulse rates near 80–160 pulses per second (pps) and degraded for both lower and higher pulse rates. The degradation in ITD sensitivity at low pulse rates was caused by strong, unsynchronized background activity that masked stimulus-driven responses in many neurons. Selecting synchronized responses by temporal windowing revealed ITD sensitivity in these neurons. With temporal windowing, both the fraction of ITD-sensitive neurons and the degree of ITD sensitivity decreased monotonically with increasing pulse rate. To compare neural ITD sensitivity to human performance in ITD discrimination, neural just-noticeable differences (JNDs) in ITD were computed using signal detection theory. Using temporal windowing at lower pulse rates, and overall firing rate at higher pulse rates, neural ITD JNDs were within the range of perceptual JNDs in human CI users over a wide range of pulse rates. SIGNIFICANCE STATEMENT Many profoundly deaf people wearing cochlear implants (CIs) still face challenges in everyday situations, such as understanding conversations in noise. Even with CIs in both ears, they have difficulty making full use of subtle differences in the sounds reaching the two ears [interaural time difference (ITD)] to identify where the sound is coming from. This problem is especially acute at the high stimulation rates used in clinical CI processors. This study provides a better understanding of ITD processing with bilateral CIs and shows a parallel between human performance in ITD discrimination and neural responses in the auditory midbrain. The present study is the first report on binaural properties of auditory neurons with CIs in unanesthetized animals.
Engineering optimization of stellarator coils lead to improvements in device maintenance

As part of an early PPPL pilot plant study an engineering exercise was undertaken to straighten the stellarator modular coil (MC) back legs to provide greater access to plasma components. Saddle coils were located within separate enclosures and configured to reconstitute changes in the magnetic fields caused by straightening the MC back legs. A follow on lab directed research study looked to further improve stellarator maintenance by considering higher aspect ratio plasmas along with improving the MC defining metrics by adding engineering maintenance requirements to the physics code used in defining the modular coil winding configuration. The physics design code (COILOPT) was upgraded to provide coil solutions with straightened MC back legs and to receive inputs of engineering constraints on the MC surface geometry and winding centers. Several improvements and extensions of COILOPT++ were made which include: the ability to target coil penalties and freeze coil geometry for individual coils; adding torsion constraints on the geometry of the space curve defining the MC winding; allowing freedom to straighten MC back legs over asymmetric distances above and below the outboard midplane; the inclusion of nested saddles with enforced minimum coil-to-coil separation distances and adding the ability to accept coil winding surface geometry from Pro- E. These changes along with a number of other features have substantially improved our ability to achieve better self-consistency between engineering maintenance requirements and plasma surface reconstructions with targeted physics. Using the new COILOPT++ code, a first pass design of an improved maintenance stellarator device has been developed. The code details and the ensuing device design will be presented.
Aberrant right subclavian artery (arteria lusoria) diagnosed during transradial coronary catheterization.

Aberrant right subclavian artery, or arteria lusoria, is the most common aortic arch anomaly. It is an uncommon condition, with an incidence of 0.2–1.7% (1). In this disorder four vessels arise sequentially from the aortic arch: the right common carotid artery, the left common carotid artery, the left subclavian artery and the aberrant right subclavian artery, which crosses upwards and to the right in the posterior mediastinum. It results from a disruption in the complex remodeling of the paired branchial arches, typically of the right dorsal aorta distal to the sixth cervical intersegmental artery (2,3).
In-Hospital Vital Status and Heart Transplants After Intervention for Congenital Heart Disease in the Pediatric Cardiac Care Consortium: Completeness of Ascertainment Using the National Death Index and United Network for Organ Sharing Datasets.

Background The long‐term outcomes of patients undergoing interventions for congenital heart disease (CHD) remain largely unknown. We linked the Pediatric Cardiac Care Consortium (PCCC) with the National Death Index (NDI) and the United Network for Organ Sharing Dataset (UNOS) registries to study mortality and transplant occurring up to 32 years postintervention. The objective of the current analysis was to determine the sensitivity of this linkage in identifying patients who are known to have died or undergone heart transplant. Methods and Results We used direct identifiers from 59 324 subjects registered in the PCCC between 1982 and 2003 to test for completeness of case ascertainment of subjects with known vital and heart transplant status by linkage with the NDI and UNOS registries. Of the 4612 in‐hospital deaths, 3873 were identified by the NDI as “true” matches for a sensitivity of 84.0% (95% CI, 82.9–85.0). There was no difference in sensitivity across 25 congenital cardiovascular conditions after adjustment for age, sex, race, presence of first name, death year, and residence at death. Of 455 known heart transplants in the PCCC, there were 408 matches in the UNOS registry, for a sensitivity of 89.7% (95% CI, 86.9–92.3). An additional 4851 deaths and 363 transplants that occurred outside the PCCC were identified through 2014. Conclusions The linkage of the PCCC with the NDI and UNOS national registries is feasible with a satisfactory sensitivity. This linkage provides a conservative estimate of the long‐term death and heart transplant events in this cohort.
Strategically Mean: Extending the Study of Relational Aggression in Communication

In this chapter we draw connections between current research on relational aggression in psychology, education, new media studies, and communication to make a case for extending the study of relational aggression by communication scholars. We also challenge the prevailing conceptualization of relational aggression as a pathological trait specific to young girls, arguing that it should be studied as a situation-specific communication strategy, employed by individuals of all ages for particular purposes and toward specific ends, using multiple modes of communication. We conclude with four recommendations for future research on relational aggression in the field of communication.
Publish or Perish

This article looks at ways to effectively use time and resources to achieve a level of productive scholarship.
Innovation Dynamics of Large, Complex, Technological Products in a Monopsony: The Case of ESA Science Missions

The roles of actors in a particular class of complex technological system - the ESA science mission - are mapped onto a competitive functional framework in order to identify key differences imposed by the market structure. Three general results are observed: there is no clear separation between "buyers" and "sellers," the governing driver is an explicitly defined need-based "pull" and a high level of technological maturity is required before a new capability can be incorporated into the product development process. They are explained in terms of the incremental impacts of the complexity of the system, in a monopsony market structure with the government as monopsonist. A preliminary model is proposed and policy implications discussed.
Location of the natural knee axis for internal–external tibial rotation

Abstract Background Rotating hinge and mobile bearing tray knee replacement designs utilize a single fixed axis for tibial rotation, yet there is little published information regarding the natural internal–external axis (IEA) for tibial rotation. Identifying the IEA should provide an opportunity for reproducing normal knee kinematics and maintaining the balance of forces in the soft tissues that help control rotation of the tibia. Methods The location and orientation of the IEA relative to the tibial plateau were calculated in 46 fresh frozen human cadaveric specimens using an instant center of rotation analysis at fixed knee flexion angles ranging from five degrees to 105°. Results IEA location ranged from 4.0 to 4.9 mm medial and 1.7 to 5.5 mm posterior to the center of the tibial plateau (from 5° to 105° of knee flexion). IEA orientation was reported relative to a reference axis perpendicular to the plane of the tibial plateau. In the frontal plane, the IEA was not significantly different from the reference axis from five degrees to 45° flexion, and 2.0° to 2.7° valgus to the reference axis from 60° to 105° flexion. In the sagittal plane, the IEA was not significantly different from the reference axis from 5° to 15° flexion, and 3.0° to 7.0° extended from the reference axis from 30° to 105° flexion. Conclusions The IEA moves posteriorly with increasing knee flexion on the tibial plateau. Placement of the IEA relative to the tibial plateau for a rotating hinge or mobile bearing tray implant may represent a compromise between design objectives for moderate and deeper knee flexion. Clinical relevance This study has relevance for future knee implant designs.
Idiotype Interactions between T Cells

Interactions between T cells mediated by their clonotypic receptors (idiotype interactions) have long been postulated as an extension of network concepts (1,2). Moreover, the possibility that these interactions may mediate different aspects of the complex regulation of T cells, as part of an integrated system, has been considered (3,4).
Mechanisms of Immunosuppression By FVIII-Specific TCR Engineered Human Regulatory T Cells

Abstract Expanded antigen-specific engineered regulatory T cells (Tregs) have been proposed for potential clinical application for the treatment of undesirable immune responses, such as inhibitor responses in hemophilia A patients and autoimmune diseases. By providing an antigen-specific T-cell receptor (TCR) to polyclonal natural Tregs, we suggested that antigen-specific engineered Tregs would migrate specifically to particular target tissues and induce antigen-specific immune tolerance in the local milieu. Previously, we developed FVIII C2-specific Tregs using a long-term stabilization protocol in vitro and demonstrated that these stabilized engineered Tregs successfully modulated FVIII-specific T-cell- and B-cell immune responses. Herein, we examined the mechanism of suppression by antigen-specific engineered Tregs compared to polyclonal normal natural Tregs. Initially, we tested whether these FVIII-specific engineered Tregs were able to suppress neighboring activated T-cell effectors locally. We found that FVIII C2-specific Tregs strongly suppressed myelin basic protein (MBP)-specific T effectors by presentation of both specific antigens in same APC population. However, we also observed that C2-specific Tregs could suppress MBP-specific T effectors presented on different APCs. These results imply contactless suppressive function of C2-specific engineered Tregs. Using a modified trans-well suppression assay, in which physical distance and clear separation between Tregs and a set of T effectors was created, we found that C2-specific activated Tregs showed significant contactless suppression only when T effectors were also present. In addition, and confirming previous studies with polyclonal Tregs, suppression by FVIII-specific engineered Tregs could be overcome by increasing the dose of IL-2 in co-culture media. This suggests that Tregs act, in part, by usurping IL-2 needed by T effectors to proliferate. Surprisingly, neutralization of CTLA-4 did not interfere with FVIII C2-specific suppression of engineered Tregs in contrast to the reversal seen with anti-CD3e-driven non-specific immunosuppression. Our data strongly suggest that suppressive function of FVIII-specific engineered Tregs is not restricted to cell-to-cell contact. Rather cross-talk of engineered Tregs and T effectors potentially generate a contactless suppressive mechanism to suppress other FVIII-specific multiple effector cells in the local milieu for effective immune tolerance. Understanding the mechanism of contactless suppression mechanism should provide critical clues to develop more effective engineered Tregs as a therapeutic tool in hemophilia A. (Supported by NIH grants HL061883 and HL126727) Disclosures Kim: Henry Jackson Foundation: Other: patent filed. Zhang: Henry Jackson Foundation: Other: patent filed. Scott: Henry Jackson Foundation: Other: patent filed.
Models as Partial Explanations

Models incorporate idealizations that do not hold in natural systems, and yet models elucidate natural systems. How can a model explain a natural system’s operation despite a failure to represent the system accurately? This chapter presents an answer to this question. It argues that an explanatory model, despite idealizations, offers a partial explanation of a phenomenon by displaying the operation of some factors behind the phenomenon’s production. The first section presents this view, the second compares it to rival views, and the third shows how it guides construction of models.
Recognition-induced forgetting of faces in visual long-term memory

Despite more than a century of evidence that long-term memory for pictures and words are different, much of what we know about memory comes from studies using words. Recent research examining visual long-term memory has demonstrated that recognizing an object induces the forgetting of objects from the same category. This recognition-induced forgetting has been shown with a variety of everyday objects. However, unlike everyday objects, faces are objects of expertise. As a result, faces may be immune to recognition-induced forgetting. However, despite excellent memory for such stimuli, we found that faces were susceptible to recognition-induced forgetting. Our findings have implications for how models of human memory account for recognition-induced forgetting as well as represent objects of expertise and consequences for eyewitness testimony and the justice system.
Photonic Band Gap Cavities for a Future ADMX

The coupling of the ‘Standard Model Axion’ exists within a finite band, the mass is only bounded by experiment and observation. This leads to the need for multiple experiments dedicated to searching specific mass regions. The current ADMX run plan uses cylindrical microwave cavities to act as a detector in the frequency range of 500 MHz–10 GHz. Beyond 10 GHz the relative performance of microwave cavities is reduced and therefore new technology is needed. Photonic bandgap cavities act like conventional cavities but they can operate in the 10–100 GHz with little degradation in performance. A crucial aspect of the haloscope technique employed in ADMX is the ability to tune the frequency of the cavity. In this report it will be shown that PBGs are tuneable within 10% of the fundamental frequency while retaining a high Quality factor.
Dynamics of Dissociation and Reactions of Cluster Ions

Under certain conditions following the ionization of a cluster, reactions proceed between various moieties with the cluster ion that, in terms of products, parallel those resulting from bimolecular gas-phase ion-molecule reactions. In addition, the exothermicity of these reactions and the dielectric relaxation that occurs in newly ionized clusters lead to metastability and dissociation of the clusters. Studies with time-of-flight techniques that have been made on clusters of ammonia, methanol, xenon, and p-xylene • trimethylamine exemplify some of these processes. Fast-flow reaction techniques are used to study the association kinetics of metal ions with neutral ligands. A model for angular momentum coupling which involves vibrational relaxation is consistent with the results. Work on the photodissociation of CO3 − hydrates and (S02)2 − has revealed the channels and processes of energy redistribution in clusters.
Acupuncture in the Management of Head and Neck Pain: An Introduction

The treatment of medical disorders with the insertion of needles into various parts of the body originated thousands of years ago. The earliest acupuncture needles, small shards of stone, date to Neolithic times (8000–3500 BC). An ice age mummy discovered in Southern Tyrol in 1988, and estimated to have lived around 3200 BC, was found to bear numerous tattoo scars, many corresponding to known acupuncture points (Samadelli et al., J Cultural Heritage 16(5):753–758, 2015). By contrast, the earliest Western medical document, the Edwin Smith Papyrus from Egypt, dates to 1600 BC, and the works attributed to Hippocrates were written even more recently, around 470–360 BC.
Designing a Cooperative Mixed-Reality Game About Reconciliation

‘Wall Mounted Level’ is a cooperative mixed-reality game that leverages multimodal interactions to support its narrative of ‘reconciliation’. In it, players control their digitally projected characters and navigate them across a hand-drawn physical sculpture as they collaborate towards a shared goal: finding one another. The digital and physical characteristics of the game are further reflected in the ways in which players interact with the software and one another through ‘touch’. This paper discusses the design choices we made in creating the varying modes of player collaboration through both digital and physical engagement.
A Reliable Wave Convention for Oppositely Traveling Waves

Care must be taken representing waves traveling in opposite directions. Erroneous results can occur when combining waves with the popular convention where a wave traveling to the right is ψR(x,t) = A sin (kx–ωt) and a left-traveling wave is ψL(x,t) = A sin (kx + ωt). An easily overlooked pitfall is pointed out and a way to avoid it with a secure convention is presented. As an exercise in critical thinking, students can be presented with the pitfall and asked to find a way out.
Sensing the invisible: Understanding the perception of indoor air quality among children in low-income families

Abstract Indoor air pollution is a leading indoor environmental risk factor, especially to individuals already at risk, such as children in low-income families. While studies have shown that occupants’ perceptions plays a significant role in improving indoor air quality (IAQ), little is known about how at-risk, low-income populations perceive and engage in IAQ. In this paper, we sought to understand how low-income families, especially children, perceive and assess IAQ. Findings show that the air quality of the indoor environment is perceived and assessed primarily through sensory responses relating to perceived comfort or discomfort, such as a sense of smell, visual cleanliness, and thermal comfort. We discuss how our findings could be applied to the future design of persuasive IAQ monitoring technologies.
Effect of Fabrication Technique on the Marginal Discrepancy and Resistance of Lithium Disilicate Crowns: An In Vitro Study.

Purpose To evaluate the impact of fabrication technique on the marginal fit and resistance of lithium disilicate crowns. Materials and methods Twelve ivorine molars were prepared to receive lithium disilicate crowns. The preparations were digitally recorded using an intraoral scanner, and the crowns were designed following the anatomy of an unprepared tooth using a design software. The designed crowns were fabricated using 3 techniques: (1) milling from lithium disilicate blocks using a 3-axis milling machine (3XM), (2) milling from lithium disilicate blocks using a 5-axis milling machine (5XM), and (3) milling from resin-wax billet using a 5-axis milling machine, followed by heat-pressing the pattern into lithium disilicate (5XWP). For the control group, the wax patterns were fabricated by one lab technician, and the crowns were fabricated by heat-pressing the pattern into lithium disilicate (CWP). After sintering, the crowns were secured on their associated preparations using an elastomeric material. The marginal gap of each crown was then measured at 14 defined locations through analyses of 20× images captured with a stereomicroscope. The marginal integrity and resistance to rotation of each crown were assessed by 2 calibrated practitioners. Differences in outcomes by fabrication technique were assessed using Wilcoxon, Kruskal Wallis, and Fisher's exact tests, as appropriate (α = 0.05). Results Crowns fabricated using digital workflows (3XM, 5XM, 5XWP) had significantly smaller mean marginal gaps compared to the CWP group (p = 0.0001, p = 0.0002, p = 0.0001, respectively); however, 3XM group was the only group to exhibit significantly better marginal integrity than the CWP group (p = 0.0004). No significant difference (p = 0.6004) in the resistance to rotation of crowns was observed between groups. Conclusions Choice of fabrication technique and instrument may impact the marginal discrepancy of lithium disilicate crowns; however, all fabrication techniques analyzed produced crowns with acceptable marginal discrepancies.
Genetic diversity of Chamaecrista fasciculata (Fabaceae) from the USDA germplasm collection

Chamaecrista fasciculata is a widespread annual legume across Eastern North America, with potential as a restoration planting, biofuel crop, and genetic model for non-papillinoid legumes. As a non-Papilinoid, C. fasciculata, belongs to the Caesalpiniod group in which nodulation likely arose independently of the nodulation in Papilinoid and Mimosoid legumes. Thus, C. fasciculata is an attractive model system for legume evolution. In this study, we describe population structure and genetic diversity among 32 USDA germplasm accessions of C. fasciculata using 317 AFLP markers developed from 12 primer pairs, to assess where geographically there is the most genetic variation. We found that the C. fasciculata germplasm collection fall into four clusters with admixture among them. After correcting for outliers, our analysis shows two primary groups across Eastern and Central North America. To better understand the population biology of this species, further sampling of the full range of this widespread species is needed across North America, as well as the development of a larger set of markers providing denser coverage of the genome. Further sampling will help clarify geographical relationships in this widespread temperate species.
A study of rock pillar behaviors in laboratory and in-situ scales using combined finite-discrete element method models

Abstract With advances in numerical modeling techniques, the combined finite-discrete-element-method (FDEM) is increasingly being used to study the mechanical behavior and failure processes of brittle geomaterials under various loading conditions. The progressive rock fracturing process from initial formation to subsequent propagation can be simulated explicitly in FDEM models where the corresponding mechanical response in the simulations is governed by a set of microparameters. Previous studies have calibrated these microparameters by comparing the macroscopic results of simulated laboratory tests with those obtained in physical tests or by comparing larger-scale model results to observed field performance of engineered structures. Very few studies, however, have calibrated models at both the laboratory and field scales, and there is, therefore, a lack of understanding of the scale-dependency of FDEM material parameter inputs. To explore this scale issue, this study presents a series of calibrated laboratory-scale models of Creighton granite. Next, models of 8 m-wide pillars with different width-to-height ratios are calibrated against the strength trends predicted by empirical relationships. In the context of the pillar models developed, the effects of each input parameter on the macroscopic pillar stress-strain behavior are presented, considering the yield stress, peak strength, and post-yield behaviors. Ultimately, it is found that while the same set of input parameters can be used to reproduce both the expected laboratory specimen behavior and the expected pillar peak strengths at different width-to-height ratios, the post-yield behavior of the pillar models obtained using the laboratory parameters is much more brittle than would be expected in reality.
Methodological considerations for near-infrared spectroscopy to assess mitochondrial capacity after spinal cord injury

Background: Skeletal muscle mitochondrial activity is reduced by ∼ 50–60% after SCI, resulting in impaired energy expenditure, glucose utilization and insulin sensitivity. Near infra-red spectrosco...
IRESpy: an XGBoost model for prediction of internal ribosome entry sites

Internal ribosome entry sites (IRES) are segments of mRNA found in untranslated regions that can recruit the ribosome and initiate translation independently of the 5′ cap-dependent translation initiation mechanism. IRES usually function when 5′ cap-dependent translation initiation has been blocked or repressed. They have been widely found to play important roles in viral infections and cellular processes. However, a limited number of confirmed IRES have been reported due to the requirement for highly labor intensive, slow, and low efficiency laboratory experiments. Bioinformatics tools have been developed, but there is no reliable online tool. This paper systematically examines the features that can distinguish IRES from non-IRES sequences. Sequence features such as kmer words, structural features such as QMFE, and sequence/structure hybrid features are evaluated as possible discriminators. They are incorporated into an IRES classifier based on XGBoost. The XGBoost model performs better than previous classifiers, with higher accuracy and much shorter computational time. The number of features in the model has been greatly reduced, compared to previous predictors, by including global kmer and structural features. The contributions of model features are well explained by LIME and SHapley Additive exPlanations. The trained XGBoost model has been implemented as a bioinformatics tool for IRES prediction, IRESpy (https://irespy.shinyapps.io/IRESpy/), which has been applied to scan the human 5′ UTR and find novel IRES segments. IRESpy is a fast, reliable, high-throughput IRES online prediction tool. It provides a publicly available tool for all IRES researchers, and can be used in other genomics applications such as gene annotation and analysis of differential gene expression.
Chemical contamination and associated liver diseases in two species of fish from San Francisco Bay and Bodega Bay

Starry flounder (Platichthys stellatus), white croaker (Genyonemus lineatus) and sediments were collected annually from selected sites within San Francisco Bay, and a reference site in Bodega Bay between 1984--1991. Fish livers were examined for toxicopathic lesions and analysed for selected chlorinated hydrocarbons (CHs) such as PCBs, DDTs, chlordanes and dieldrin; sediment and fish stomach contents were analysed for polycyclic aromatic hydrocarbons (PAHs) and CHs; and bile was analysed for PAH metabolites. Sediment concentrations of PAHs, PCBs and DDTs; bile concentrations of PAH metabolites; and liver concentrations of PCBs, dieldrin and chlordanes were generally significantly higher at all San Francisco Bay sites compared to the Bodega Bay reference site. For both species, hydropic vacuolation of biliary epithelial cells was the most prevalent liver lesion detected and was statistically associated with sediment and tissue concentrations of PAHs or their metabolites, PCBs, DDTs, chlordanes and dieldrin. Temporal trends analyses showed that at Hunters Point, sediment PAHs and CHs increased between 1984--1991, while liver concentrations of CHs decreased. Liver concentrations of dieldrin in starry flounder decreased at all three San Francisco Bay sites
U-loss associated with laser-heating of hematite and goethite in vacuum during (U-Th)/He dating and prevention using high O2 partial pressure

Abstract Single-aliquot (U–Th)/He dating of hematite has been used to study iron-oxide precipitation in various environments, but we show there is an important challenge to the method: highly retentive hematite samples require temperatures of >1000 °C to be completely degassed, whereas the temperature for major U-loss is ∼ 980 °C. This leads to erroneously high (U–Th)/He ages. Through the analysis of U, Th, and Sm of hematite and goethite samples, we establish the degree of U-loss at this temperature and demonstrate that prolonged heating at temperatures of 950 °C can lead to U-loss. We show that loss of U in goethite and hematite samples is associated with phase change from hematite to magnetite as Fe is reduced. The onset temperature of vacuum reduction of hematite can be increased from about 800–900 °C in vacuum to approximately 1250 °C in an oxygen partial pressure of 100 mbar. We demonstrate that samples can be outgassed to extract helium at 1150 °C without U-loss in an O2-rich atmosphere during heating, which does not increase the analytical blanks. We describe our implementation and automation of the procedure. An average age calculated on a reference hematite sample from replicate aliquots ( n = 12 ), which were analyzed using this procedure, has a relative uncertainty of 2% (1 σ ), and is within uncertainty of the previously measured two-aliquot age. We suggest this O2 degassing procedure as a way to precisely and reproducibly determine single-aliquot hematite and goethite (U–Th)/He ages.
Calculating Engine Designed by Charles Babbage

Many credit Charles Babbage (1791 - 1871) as the father of the computer. A copy of the American Magazine of Useful and Entertaining Knowledge, which originally published an article in Volume 1, 183...
The Impacts of Additive Noise and 1-bit Quantization on the Correlation Coefficient in the Low-SNR Regime

This paper analyzes the impact of 2-level (1-bit) quantization on the correlation of Gaussian sources and of binary sources in the presence of additive noise, with a focus on the low-SNR regime. In this regime, in which the correlation vanishes as the SNR tends to zero, 1-bit symmetric-threshold quantization of Gaussian sources and of equiprobable, antipodal binary sources degrades the correlation by $\frac{2}{\pi}$ (-1.96 dB), a result first established by Van Vleck for correlated Gaussian sources. Symmetric quantization of these sources also reduces the channel capacity per unit-energy by the same factor. However, asymmetric-threshold quantization of a class of binary source distributions known as flash signaling can avoid the $\frac{2}{\pi}$ penalty in channel capacity, as shown by Koch and Lapidoth. In this paper, we show how flash signaling with asymmetric quantization can not only avoid the $\frac{2}{\pi}$ penalty in correlation, but as the SNR tends to zero, the quantized correlation can approach the noise-free source correlation.