cssi/SciSciGPT-SciSciNet huggingface dataset:
Domain transfer learning for MCI conversion prediction

In recent studies of Alzheimer's disease (AD), it has increasing attentions in identifying mild cognitive impairment (MCI) converters (MCI-C) from MCI non-converters (MCI-NC). Note that MCI is a prodromal stage of AD, with possibility to convert to AD. Most traditional methods for MCI conversion prediction learn information only from MCI subjects (including MCI-C and MCI-NC), not from other related subjects, e.g., AD and normal controls (NC), which can actually aid the classification between MCI-C and MCI-NC. In this paper, we propose a novel domain-transfer learning method for MCI conversion prediction. Different from most existing methods, we classify MCI-C and MCI-NC with aid from the domain knowledge learned with AD and NC subjects as auxiliary domain to further improve the classification performance. Our method contains two key components: (1) the cross-domain kernel learning for transferring auxiliary domain knowledge, and (2) the adapted support vector machine (SVM) decision function construction for cross-domain and auxiliary domain knowledge fusion. Experimental results on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database show that the proposed method can significantly improve the classification performance between MCI-C and MCI-NC, with aid of domain knowledge learned from AD and NC subjects.
Photo-Assembly of the Catalytic Manganese Cluster

The biogenesis of the Photosystem II (PS II) water oxidizing complex is reviewed with emphasis on the sequence and location of assembly of the subunits within the internal membrane systems of prokaryotes and chloroplasts. The uptake and distribution of manganese in cyanobacterial cells are discussed. The role of individual subunits in isolated PS II in light-induced assembly of the inorganic core of the water splitting complex is discussed (photoactivation process). The roles of the inorganic cofactors (Mn2+, Ca2+, Cl and bicarbonate) in water splitting are revealed by examining the effects of their reconstitution with non-native cofactors. Novel instrumentation for the measurement of O2 concentration and the kinetics and mechanism of photoactivation are described.
Emotion–Cognition Interactions

Limbic forebrain regions are anatomically positioned to integrate cortical and subcortical processing streams that mediate cognitive and emotional functions. Feedback projections to sensory cortices bias perceptual systems to process stimuli of high significance. The amygdala is critical for learning contingencies in the environment that predict emotional outcomes and for modulating explicit memory processes in the hippocampus. The anterior cingulate gyrus and ventromedial and orbital prefrontal cortices serve as interfaces that link emotional information processing and attentional control systems to guide goal-directed behavior. Dysregulation of the balance between affective and cognitive systems is a hallmark of anxiety and mood disorders.
Abstract 2695: Quantitative phosphoproteome analysis identifies novel functional pathways of tumor suppressor DLC1 in estrogen receptor-positive breast cancer

Deleted in Liver Cancer-1 (DLC1), a member of the RhoGAP family of proteins, functions as a tumor suppressor in several cancers including breast cancer. However, its clinical relevance is unclear in breast cancer. In this study, expression of DLC1 was correlated with prognosis using publicly available breast cancer gene expression datasets and quantitative polymerase chain reaction (qPCR) in cohorts of Estrogen Receptor-positive (ER+) breast cancer. Mutation and methylation status of DLC1 were assessed in these datasets including The Cancer Genome Atlas (TCGA). To seek further insights in understanding the role of DLC1 in ER+ breast cancer, we developed a knock-in model of DLC1 in T47D breast cancer cells. Label-free global proteomic and TiO2 phosphopeptide enrichment assays were performed and validated using Western blotting. Data are available via ProteomeXchange with identifier PXD008220. Here, we report that low expression of DLC1 correlates with poor prognosis in patients with ER+ breast cancer with further decrease in metastatic lesions. Analysis of the TCGA data showed that down regulation of DLC1 is not due to methylation or mutations. Stable knock-in of DLC1-full-length inhibits cell colony formation significantly in vitro compared to its control counterpart. 6726 phosphopeptides were quantified by phosphoproteomics analysis in both conditons, whereas 205 and 122 were unique to DLC1 knock-in and T47D-control cells, respectively. Pathway analysis using DAVID showed the top three significant clusters of differentially identified phosphopeptides involving cell-cell adhesion, mRNA processing and splicing, and transcription regulation. Decreased phosphorylation of epithelial cell transforming sequence 2 (ECT2) at the residue T359, critical for its active conformational change, was validated. In conclusion, this data suggests that high expression of DLC1 reduces cell growth and is associated with favorable prognosis. Our results document an inverse relation between ECT2 phosphorylation and DLC1 expression, promising a novel strategy for treating ER+ breast cancer. Citation Format: Yesim Gokmen-Polar, Jason D. True, Edyta Vieth, Yuan Gu, Xiaoping Gu, Guihong D. Qi, Amber L. Mosley, Sunil Badve. Quantitative phosphoproteome analysis identifies novel functional pathways of tumor suppressor DLC1 in estrogen receptor-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2695.
Prevalence of traditional, complementary, and alternative medicine use by cancer patients in low income and lower-middle income countries

The use of traditional, complementary, and alternative medicine (TCAM) for cancer may influence the delivery or effectiveness of conventional cancer treatment. In this systematic review, we aimed t...
Characterization of the Esi3/RCI2/PMP3 gene family in the Triticeae.

Members of the Early Salt Induced 3 (Esi3/RCI2/PMP3) gene family in plants have been shown to be induced in response to both biotic and abiotic stresses and to enhance stress tolerance in both transgenic plants and Saccharomyces cerevisiae. Esi3 was first identified as a salt stress induced gene in the salt tolerant wild wheat grass, Lophopyrum elongatum, and subsequently homologous genes in many other species were found to be members of the gene family. These include Arabidopsis thaliana and Oryza sativa where they are referred to as Rare Cold Inducible 2 (RCI2), and Zea mays where they are referred to as Plasma Membrane Protein 3 (PMP3). This study characterizes the Esi3 family members in Triticum aestivum and explores the tissue specific expression patterns of the gene family members as well as their response to a variety of environmental stresses. The Esi3 gene family was found to have a total of 29 family members comprised of ten paralogous groups in the hexaploid T. aestivum. Each paralogous group contains three homeologous copies, one in each of the A, B and D genomes with the exception of Esi3–2 which is missing the B copy. The genes of the Esi3 gene family were also identified in four other monocot species, Aegilops tauschii, Hordeum vulgare, Secale cereale and Sorghum bicolor, and were confirmed or corrected for Brachypodium distachyon, Oryza sativa and Zea mays, as well as the dicot Arabidopsis thaliana. Gene expression of the Esi3s was analyzed using tissue-specific, abiotic and biotic stress RNA-Seq 454 sequence libraries and Affymetrix microarray data for T. aestivum. Members of nearly all paralogous groups of the Esi3 genes in T. aestivum have altered gene expression in response to abiotic or biotic stress conditions. In addition, there are modest differences in gene expression among homeologous members of the gene family. This suggests that the Esi3 gene family plays an important role in the plants response to the stresses presented in this study. The Esi3–9 in T. aestivum has a unique N terminal extension placing it into Group III, a new group for the Esi3/RCI2/PMP3 gene family.
The Impact of Decentralization on Municipalities: Evidence from the Municipal Home Rule Movement

The municipal home rule movement of the late 19th and early 20th centuries decentralized control from the state and gave municipalities the ability to independently draft and adopt a municipal charter. Since not all states adopted home rule, and not all states that adopted home rule did it at the same time, the natural episode presents a rich ground for empirical study. There are several avenues on which to explore the effect of decentralization on outcomes. Previous research has considered the effect of decentralization on expenditures or on types of services provided. In the case of home rule, did the ability for municipalities to write their own charters and determine their own structure and functions result in different outcomes relative to municipalities who were not given the option? As much of the research in fiscal federalism deals with decentralization at the federal level, this paper serves as a nice complement as it investigates decentralization at a sub-national level and thus holds constant important country-level variables. Preliminary evidence seems to indicate that home rule had an effect both on municipal debt and on the composition of the municipal population.
The Community Climate System Model, version 2

Abstract The Community Climate System Model, version 2 (CCSM2) is briefly described. A 1000-yr control simulation of the present day climate has been completed without flux adjustments. Minor modifications were made at year 350, which included all five components using the same physical constants. There are very small trends in the upper-ocean, sea ice, atmosphere, and land fields after year 150 of the control simulation. The deep ocean has small but significant trends; however, these are not large enough that the control simulation could not be continued much further. The equilibrium climate sensitivity of CCSM2 is 2.2 K, which is slightly larger than the Climate System Model, version 1 (CSM1) value of 2.0 K. Several aspects of the control simulation's mean climate and interannual variability are described, and good and bad properties of the control simulation are documented. In particular, several aspects of the simulation, especially in the Arctic region, are much improved over those obtained in CSM1. ...
Creditor Control Rights and Firm Cash Holdings

We examine firm’s cash holdings from the perspective of the agency cost of debt and find that firms with outstanding loans hold significantly less cash than firms without outstanding loans. This relationship is particularly stronger in financially constrained firms with higher hedging needs, suggesting that it the creditor control but not the voluntary reduction that leads to lower level of cash holdings because cash is more valuable to those firms. We show that creditors influence firms’ cash holdings by setting up stricter covenants in those with more excess cash especially when there is higher information opacity, financial constraints with higher hedging needs and higher agency cost of debt. Results also show that covenants are effective in reducing cash holdings. Lastly, we study how cash changes around covenant violation where creditors could exert direct influence on firms’ cash holding policies. We find that while cash increases in the firms that fail to meet financial performance covenants, those with managerial violations actually experience significant cash reductions.
Modulation of intrinsic excitability as a function of learning within the fear conditioning circuit

Experience-dependent neuronal plasticity is a fundamental substrate of learning and memory. Intrinsic excitability is a form of neuronal plasticity that can be altered by learning and indicates the pattern of neuronal responding to external stimuli (e.g. a learning or synaptic event). Associative fear conditioning is one form of learning that alters intrinsic excitability, reflecting an experience-dependent change in neuronal function. After fear conditioning, intrinsic excitability changes are evident in brain regions that are a critical part of the fear circuit, including the amygdala, hippocampus, retrosplenial cortex, and prefrontal cortex. Some of these changes are transient and/or reversed by extinction as well as learning-specific (i.e. they are not observed in neurons from control animals). This review will explore how intrinsic neuronal excitability changes within brain structures that are critical for fear learning, and it will also discuss evidence promoting intrinsic excitability as a vital mechanism of associative fear memories. This work has raised interesting questions regarding the role of fear learning in changes of intrinsic excitability within specific subpopulations of neurons, including those that express immediate early genes and thus demonstrate experience-dependent activity, as well as in neurons classified as having a specific firing type (e.g. burst-spiking vs. regular-spiking). These findings have interesting implications for how intrinsic excitability can serve as a neural substrate of learning and memory, and suggest that intrinsic plasticity within specific subpopulations of neurons may promote consolidation of the memory trace in a flexible and efficient manner.
Constitutive cyclophilin-D ablation in mice increases exercise and cognitive-behavioral performance under normoxic and hypoxic conditions.

Abstract We recently reported that constitutive ablation of cyclophilin-D (Cyp-D) in mice reduces oxygen consumption (VO2) while paradoxically increasing exercise endurance, thereby demonstrating increased O2 utilization efficiency. This response was associated with augmented glucose uptake and glucose utilization, in part mediated through adenosine monophosphate-activated kinase signaling. We now hypothesized that Cyp-D knock-out (KO) mice might also exhibit improved cognitive-behavioral performance and that these favorable adaptive responses may persist under hypoxic conditions. We therefore assessed under normoxic (20.9% O2, simulating ground O2 levels) and hypoxic (8% O2, simulating 7600 m altitude O2 levels) conditions exercise capacity and cognitive-behavioral performance. We used a treadmill test to assess exercise capacity, a pole-test to assess agility, an elevated-plus-maze test to assess anti-anxiety, and a passive avoidance test to assess learning and memory retention. Compared to wild type, Cyp-D KO mice showed comparable treadmill work under normoxia (48 ± 12 vs 47 ± 9 Joules) but increased treadmill work (12 ± 1 vs 8 ± 1 Joules; p = 0.02) under hypoxia. Cyp-D KO mice displayed increased pole-descending time (17 ± 3 vs 8 ± 2 s; p ≤ 0.05) under normoxia but shorter pole-descending time (21 ± 3 vs 37 ± 4 s; p ≤ 0.01) under hypoxia. In addition, the Cyp-D KO mice demonstrated increased elevated plus-maze open arm time (91 ± 31 vs 23 ± 12 s; p ≤ 0.05) under hypoxia and increased latency to enter dark chamber (261 ± 23 vs 185 ± 42 s; p ≤ 0.05) under normoxia. Thus, our experiments showed that under normoxia Cyp-D KO mice displayed anti-anxiety behavior and improved learning and memory retention. Under hypoxia, Cyp-D KO mice displayed increased exercise capacity, increased agility, and increased anti-anxiety consistent with our previously reported findings of increased O2 utilization efficiency. Identifying interventions to elicit these effects could be beneficial in a myriad of physiological and clinical conditions in which increasing O2 utilization efficiency would be advantageous.
Imaging with thick lenses using ABCD matrices and first-order material dispersion

ABCD matrices for a thick lens based on first-order frequency-dependent material dispersion of dielectric permittivity are derived using standard paraxial theory and spherical surfaces. The analysis and results are compared with the non-dispersive problem and used to ascertain imaging behavior for a gray scale 2D object. The possibility of introducing chirality and negative index in the lens material is also discussed.
Nurses' psychological trauma: "They leave me lying awake at night".

Abstract Objective To describe nurses' personal and professional psychological trauma. Methods A content analysis of 372 responses surrounding personal and professional trauma was performed. Results Five themes emerged. A new type of trauma was uncovered, heretofore undescribed in the literature: insufficient resource trauma caused by a lack of resources and staff needed to render quality, safe care. Conclusion Nurses' reports were vivid, frequently indicating they were still recovering from traumatic experiences. Professional sources of trauma were categorized as inherent in the role of the nurse and those that could be mitigated through organizational policy, adequate resources, and oversight.
Dark-rearing uncovers novel gene expression patterns in an obligate cave-dwelling fish.

Extreme environments often result in the evolution of dramatic adaptive features. The Mexican tetra, Astyanax mexicanus, includes 30 different populations of cave-dwelling forms that live in perpetual darkness. As a consequence, many populations have evolved eye loss, reduced pigmentation, and amplification of nonvisual sensory systems. Closely-related surface-dwelling morphs demonstrate typical vision, pigmentation, and sensation. Transcriptomic assessments in this system have revealed important developmental changes associated with the cave morph, however, they have not accounted for photic rearing conditions. Prior studies reared individuals under a 12:12 hr light/dark (LD) cycle. Here, we reared cavefish under constant darkness (DD) for 5+ years. From these experimental individuals, we performed mRNA sequencing and compared gene expression of surface fish reared under LD conditions to cavefish reared under DD conditions to identify photic-dependent gene expression differences. Gene Ontology enrichment analyses revealed a number of previously underappreciated cave-associated changes impacting blood physiology and olfaction. We further evaluated the position of differentially expressed genes relative to QTL positions from prior studies and found several candidate genes associated with these ecologically relevant lighting conditions. In sum, this work highlights photic conditions as a key environmental factor impacting gene expression patterns in blind cave-dwelling fish.
Improving Educational Attainment for Girls: A Case Study of One Rural Kenyan School

The purpose of this qualitative study was to examine one rural Kenyan community’s attempts to improve the educational attainment for primary school girls in the region. Data were gathered through f...
Setting new boundaries with transcription and CTCF.

How do boundary elements divide chromosomes into domains? A new study uses random genomic insertions to show how small genomic fragments can shape chromatin folding through the interplay of loop extrusion and compartmentalization. Spoiler: context matters.
Switchable Asymmetric Moiré Patterns with Strongly Localized States.

Most moire pattern structures are constructed by twisting the angle of two similar 2D materials. The corresponding electronic structures are fixed in device applications. Here we study moire patter...
Exploring Students' Explanations of Energy Transfer and Transformation

The ability to build mechanistic explanations of natural phenomena is highly valued in all scientific disciplines, including chemistry. In this paper, we summarize the results of a qualitative study designed to characterize the nature of the mechanistic explanations built by college General Chemistry students when analyzing a physical process involving energy transfer between parts of a system at different temperatures, and a chemical process involving energy transformation and transfer due to chemical bonding. Prior studies have mostly focused on eliciting “what” students think happens in terms of energy transfer when chemical bonds break or form (e.g., energy is absorbed or released) and in this investigation we provide insights into their reasoning about “how” and “why” it happens. Our findings reveal that many students struggle to build sound mechanistic explanations for energy transfer between objects at different temperatures and for energy transformation and transfer during the formation of chemical bonds.
The Evolution of University Business Incubators: Transnational Hubs for Entrepreneurship:

University business incubators (UBIs) are uniquely positioned to foster transnational entrepreneurship and the evolution of business and technical communication practices on a worldwide basis. UBIs...
Are 'Complementary Policies' Substitutes? Evidence from R&D Subsidies in the UK

Governments often subsidize private R&D using both direct subsidies and tax incentives. In this paper, I develop a framework for studying their interdependence, which also provides a test for detecting capital market imperfections. I implement two quasi-experimental research designs to examine firms in the United Kingdom and show that grants and tax credits are complements for small firms but substitutes for larger firms. Higher tax credit rates substantially enhance the effect of grants on R&D investment for small firms, particularly those facing financial constraints, but they reduce it for larger firms. The productivity of small firms also increases. My findings imply that the innovation policy mix should include both support mechanisms for small firms only.
Inhibition of Anaerobic Sucrose Fermentation Using Novel Adulterants

Several novel material s were added to a standard fermentation reaction mixture. Some compounds were found to compl etel y inhibit the activity and no ethanol and carbon dioxide were formed, whil e certain other compounds had no effect. In particul ar, the sodium salt of 2:1/sal ical dehyde: acetone condensation product, (compound A) compl etel y stopped the fermentation as did the potassium salt. In contrast, neither benzonic acid nor p-toluic acid had an inhabitory effect. A tentative conclusion is that the potency resides in the phenol group.
Using a Critical Hip-Hop School Counseling Framework to Promote Black Consciousness Among Black Boys:

In this article, I outline an approach for critical hip-hop school counseling (CHHSC) for novice and tenured school counselors to use when working with Black boys. Various facets of hip-hop culture...
COVID-19-related policy changes for methadone take-home dosing: A multistate survey of opioid treatment program leadership.

Background: In the United States, methadone for treatment of opioid use disorder is dispensed via highly-regulated accredited opioid treatment programs (OTP). During the COVID-19 pandemic, federal regulations were loosened, allowing for greater use of take-home methadone doses. We sought to understand how OTP leaders responded to these policy changes. Methods: We distributed a multistate electronic survey from September to November 2020 of OTP leadership to members of the American Association for the Treatment of Opioid Dependence (AATOD) who self-identified as leaders of OTPs. We asked study participants about how their OTP(s) implemented COVID-19-related policy changes into their clinical practice focusing on provision of take-home methadone doses, factors used to determine patient stability, and potential concerns about increased take-home doses. We used Chi-square test to compare survey responses between characterizations of the OTPs. Results: Of 170 survey respondents (17% response rate), the majority represented leadership of for-profit OTPs (69%) and were in a Southern state (54%). Routine allowances and practices related to take-home methadone doses varied across OTPs during the COVID-19 pandemic: 80 (47%) reported 14 days for newly enrolled patients (within past 90 days), 89 (52%) reported 14 days for "less stable" patients, and 112 (66%) reported 28 days for "stable" patients. Conclusions: We found that not all eligible OTP leaders adopted the practice of routinely allowing newly enrolled, "less stable," and "stable" patients on methadone to have increased take-home doses up to the limit allowed by federal regulations during COVID-19. The pandemic provides an opportunity to critically re-evaluate long-established methadone and OTP regulations in preparation for future emergencies.
Management of Respiratory Distress and Failure in Morbidly and Super Obese Patients During Critical Care Transport

Abstract Morbidly and super obese patients are a unique patient population that presents critical care transport providers with unique clinical and logistical challenges in the setting of respiratory distress and failure. These patients are more likely to have chronic respiratory issues at baseline, unique anatomic and physiologic abnormalities, and other comorbidities that leave them poorly able to tolerate respiratory illness or injury. This requires specialized understanding of their respiratory mechanics as well as how to tailor standard treatment modalities, such as noninvasive ventilation, to meet their needs. Also, careful and deliberate planning is required to address the specific anatomic and physiologic characteristics of this population if intubation and mechanical ventilation are needed. Finally, their dimensions and weight also have distinct consequences on transport vehicle considerations. This article reviews the pathophysiology, management, and critical care transport considerations for this unique patient population in respiratory distress and failure.
Isolation of a butyrate-utilizing bacterium in coculture with Methanobacterium thermoautotrophicum from a thermophilic digester.

Sludge from a thermophilic, 55 degrees C digester produced methane without a lag period when enriched with butyrate. The sludge was found by most-probable-number enumeration to have ca. 5 x 10 butyrate-utilizing bacteria per ml. A thermophilic butyrate-utilizing bacterium was isolated in coculture with Methanobacterium thermoautotrophicum. This bacterium was a gram-negative, slightly curved rod, occurred singly, was nonmotile, and did not appear to produce spores. When this coculture was incubated with Methanospirillum hungatei at 37 degrees C, the quantity of methane produced was less than 5% of the methane produced when the coculture was incubated at 55 degrees C, the routine incubation temperature. The coculture required clarified digester fluid. The addition of yeast extract to medium containing 5% clarified digester fluid stimulated methane production when a Methanosarcina sp. was present. Hydrogen in the gas phase prevented butyrate utilization. However, when the hydrogen was removed, butyrate utilization began. Penicillin G and d-cycloserine caused the complete inhibition of butyrate utilization by the coculture. The ability of various ecosystems to convert butyrate to methane was studied. Marine sediments enriched with butyrate required a 2-week incubation period before methanogenesis began. Hypersaline sediments did not produce methane after 3 months when enriched with butyrate.
Chronic vulvar pain from a physical therapy perspective

When assessing women with chronic vulvar pain, women's health physical therapists search for comorbid mechanical components (including musculoskeletal, fascial, and visceral) and other disorders that may contribute to or be caused by chronic vulvar pain (CVP). Pelvic floor hypertonicity is a key perpetuating factor for CVP. Comprehensive physical therapy evaluation and suggested physical therapy interventions are described. Anatomy of the pelvis, common evaluative findings, and specifics for pelvic floor muscle rehabilitation are presented. Normalization of pelvic floor muscle function contributes to the reduction of CVP. Successful treatment includes the identification and treatment of co-existing physical abnormalities throughout the trunk and pelvis.
Systems biology of neurodegenerative diseases

Neurodegenerative diseases (NDs) collectively afflict more than 40 million people worldwide. The majority of these diseases lack therapies to slow or stop progression due in large part to the challenge of disentangling the simultaneous presentation of broad, multifaceted pathophysiologic changes. Present technologies and computational capabilities suggest an optimistic future for deconvolving these changes to identify novel mechanisms driving ND onset and progression. In particular, integration of highly multi-dimensional omic analytical techniques (e.g., microarray, mass spectrometry) with computational systems biology approaches provides a systematic methodology to elucidate new mechanisms driving NDs. In this review, we begin by summarizing the complex pathophysiology of NDs associated with protein aggregation, emphasizing the shared complex dysregulation found in all of these diseases, and discuss available experimental ND models. Next, we provide an overview of technological and computational techniques used in systems biology that are applicable to studying NDs. We conclude by reviewing prior studies that have applied these approaches to NDs and comment on the necessity of combining analysis from both human tissues and model systems to identify driving mechanisms. We envision that the integration of computational approaches with multiple omic analyses of human tissues, and mouse and in vitro models, will enable the discovery of new therapeutic strategies for these devastating diseases.
SU-E-J-18: Evaluation of the Effectiveness of Compression Methods in SBRT for Lung.

Purpose: This study aims to evaluate the effectiveness of compression in immobilizing tumor during stereotactic body radiotherapy(SBRT) for lungcancer.Methods: Published data have demonstrated bigger respiratory motion in lower lobe than in upper lobe during normal breathing. We hypothesize that 4DCT‐based patient selection and abdominal compression would immobilize lungtumor volumes effectively, regardless of their location. We retrospectively reviewed 12 SBRTlung cases treated with Trilogy® (Varian Medical System, Palo Alto, CA). Either compression plate or Vac‐LokTM was used as abdomen compression of the SBRT immobilization system (Body Pro‐LokTM, CIVCO) to restrict patients' breathing during CT simulation and treatment delivery. These cases are grouped into 2 categories: lower and upper lobe tumor, each with 6 cases. Records for 33 treatments were studied. On each treatment day, the patient was set up to the bony anatomy using kV‐kV‐match. A CBCT was performed to further set up the patient to the tumor based on the soft tissue information. The shifts from CBCT‐setup were analyzed as displacement vectors demonstrating the magnitude of the tumor motion relative to the bony anatomy.Results: The mean magnitude of displacement vectors for upper lobe and lower lobe were 3.7±2.7 and 4.2±6.3, [1S.D.] mm, respectively. The Wilcoxon rank sum test indicates that the difference in the displacement vector between the two groups is not statistically significant (p‐value = 0.33). Conclusions: The magnitude of shifts from CBCT were small with mean value <5mm in SBRTlungtreatments. No statistically significant difference were observed in the displacement of tumor between lower and upper lobes. With limited sample size, this suggests that our current 4DCT screening/abdominal compression approach is effective in restricting the respiration‐induced tumor motion despite its location within the lung. We plan to confirm this Result in additional patients.
Promoter CpG methylation of Hox-a10 and Hox-a11 in mouse uterus not altered upon neonatal diethylstilbestrol exposure.

Mouse abdominal B–like Hoxa genes are expressed and functionally required in the developing reproductive tracts. Mice lacking either Hoxa-10 or Hoxa-11, two of the AbdB Hoxa genes, exhibit abnormal uterine development similar to that induced by in utero diethylstilbestrol (DES) exposure. Indeed, uterine Hoxa-10 and Hoxa-11 expression is potently repressed by perinatal DES exposure, providing a potential molecular mechanism for DES-induced reproductive tract malformations. We have shown previously that DES can permanently alter uterine lactoferrin gene expression through modulation of the lactoferrin promoter methylation pattern. Here we ask whether a similar mechanism also functions to deregulate uterine Hoxa-10 or Hoxa-11 expression during neonatal DES exposure. We mapped the Hoxa-10 promoter by cloning a 1.485 kb DNA fragment 5′ of the Hoxa-10 exon1a. A 5′ rapid amplification of cDNA ends (RACE) experiment revealed a transcription start site for the a10-1 transcript. Functional analysis of the proximal 200-bp sequences demonstrated significant promoter activity, confirming the location of the Hoxa-10 promoter. Moreover, methylation assays performed on eight CpGs in Hoxa-10 and 19 CpGs in Hoxa-11 proximal promoters demonstrated that all these CpGs were highly unmethylated in both control and DES-dosed mice from postnatal day 5 to day 30. Significant methylation around Hoxa-10 and Hoxa-11 promoters was only observed in DES-induced uterine carcinomas in 18-mo-old mice. Our results suggest that DES-induced downregulations of Hoxa-10 or Hoxa-11 gene expression are not associated with methylation changes in their proximal promoters and that gene imprinting by developmental DES exposure may be a gene-specific phenomenon. Published 2001 Wiley-Liss, Inc.
Clinical variability in ciliary disorders.

The list of genetic diseases associated with dysfunction of primary cilia continues to expand. Two new studies add to this growing body of literature and provide a fascinating example of the clinical variability associated with ciliary disorders.
Translations Between Design Research and Scholarship

Abstract The idea that design for a changing world necessitates active inquiry, whether scientific or gnostic in inspiration, is at least as longstanding as the identification of modernity with critique or revolution. Whether or how such inquiry constitutes research or scholarship is a more specific and recent consternation. Beyond the diverse institutional and disciplinary concerns at stake in this formulation is an interesting challenge: Can design works be critically engaged as a vehicle of knowledge by a wide audience of readers—one extending beyond the designer or her/his immediate community? What are the enabling and limiting conditions for such engagement?
Finding Tracers for Supernova Produced 26Al

We consider the cospatial production of elements in supernova explosions to find observationally detectable proxies for enhancement of 26Al in supernova ejecta and stellar systems. Using four progenitors, we explore a range of one-dimensional explosions at different energies and an asymmetric three-dimensional explosion. We find that the most reliable indicator of the presence of 26Al in unmixed ejecta is a very low S/Si ratio (~0.05). Production of N in O/S/Si-rich regions is also indicative. The biologically important element P is produced at its highest abundance in the same regions. Proxies should be detectable in supernova ejecta with high spatial resolution multiwavelength observations, but the small absolute abundance of material injected into a proto-planetary disk makes detection unlikely in existing or forming stellar/planetary systems.
The impact of seed market access and transaction costs on potato biodiversity and yields in Bolivia

Using data from Bolivia, this paper analyzes seed market participation and how transaction costs in these markets influence intracrop biodiversity and the influence of biodiversity on yields. Results indicate that seed market attributes such as distance and market-level biodiversity have a crucial effect on a farmer's market choice, suggesting that farmers are willing to sacrifice time and income to travel further distances in order to reach markets with a broader range of varieties. This study finds that farmers from this sample who have access to seed markets are more likely to have higher levels of intracrop biodiversity. In addition, for market-integrated farmers, intracrop biodiversity does not seem to have a negative effect on yields, which suggests that improved market access does not threaten biodiversity in contexts with similar characteristics to the study site.
Analyzing sociocultural perspectives on violence in digital games

This article reports the results of a content analysis that tested whether a significant difference in attitude toward violent digital games occurred in the news media as a result of the Columbine school shootings. This article lists attitudinal information about violent game content for more than 30 worldwide news sources, as well as the most frequently mentioned people, institutions, and digital games mentioned by these sources. A one-way ANOVA of authors' attitudes toward violent digital games prior to and after April 20, 1999, as well as ANOVAs testing geographic location, newspaper, and article type, showed no significant attitudinal difference toward violent digital games before and after the Columbine incident. Four cultural themes that relate to the control of violent digital games are also analyzed.
Developing, Marketing, Distributing, and Supporting an Activity‐Based Costing Decision Support System for Schrader Bellows

In this project, you will develop a database system that allows your clients to model different activity‐based costing allocation schemes to calculate product costs. You will also develop a website to market, distribute, and support your system. You will “sell” your system to actual clients, and you will provide user support while the system is in use.
Bootstrap Tests for Distributional Treatment Effects in Instrumental Variable Models

This article considers the problem of assessing the distributional consequences of a treatment on some outcome variable of interest when treatment intake is (possibly) nonrandomized, but there is a binaryinstrument available for the researcher. Such a scenario is common in observational studies and in randomized experiments with imperfect compliance. One possible approach to this problem is to compare the counterfactual cumulative distribution functions of the outcome with and without the treatment. This article shows how to estimate these distributions using instrumental variable methods and a simple bootstrap procedure is proposed to test distributional hypotheses, such as equality of distributions, first-order and second-order stochastic dominance. These tests and estimators are applied to the study of the effects of veteran status on the distribution of civilian earnings. The results show a negative effect of military service during the Vietnam era that appears to be concentrated on the lower tail of ...
Gardner's syndrome: heredofamilial adenomatosis associated with "soft and hard" fibrous tumors and epidermoid cysts.

Familial polyposis of the colon and rectum appears to be a nonsex-linked hereditary disease, due to a single mutant or pleomorphic gene, which is transmitted as a Mendelian dominant with the expectation that approximately 50 per cent of the off-spring of the affected individual will have the same disease.
Intracardiac echocardiography: in vitro and in vivo validation for right ventricular volume and function.

Abstract To determine the feasibility and accuracy of intracardiac ultrasonography (ICUS) for the measurement of right ventricular (RV) volumes and function, a 10 MHz ICUS catheter was used in an in vitro and in vivo model. In the in vitro study, 16 sheep hearts were imaged. Sequential cross-sectional images from RV apex to base were recorded during a calibrated pullback. Volumes were calculated by applying Simpson's algorithm. ICUS-obtained volumes correlated well with actual volumes (standard error of estimated [SEE] = 2.3 ml, r = 0.98). For the in vivo study, a beating-heart canine model was used (31 hemodynamic stages in six dogs). Actual volumes were measured by an intracavitary balloon connected to an external column. Sequential cross-sectional images were recorded during the ICUS catheter pullback from apex to base of the RV, and volumes calculated by Simpson's algorithm. Good correlations were observed between ICUS and actual values for diastolic (SEE = 4.1 ml, r = 0.97), systolic (SEE = 3.4 ml, r = 0.96), and ejection fraction (SEE = 3.1%, r = 0.87) values. This new technique can accurately quantitate RV volumes, can function both in vitro and in vivo, and has the potential for increasing applications to questions of clinical and research interest.
Quantitative analysis of plasma fibrin monomer.

Abstract An assay for plasma fibrin monomer, based upon protein-protein interaction, has been developed. It depends upon the binding of 125I labeled fibrin monomer to plasma fibrinogen and the ability of protamine sulfate to precipitate some fibrin monomer from this complex. If the plasma sample contains no fibrin monomer, essentially all of the 125I-fibrin monomer remains in solution after protamine sulfate treatment. As the amount of endogenous fibrin monomer increases, the amount of 125I-fibrin monomer left in solution decreases.
Experimental comparison of cone beam CT (CBCT) reconstruction and multi-view reconstruction (MVR) for microangiography (MA) detector system

The new Multi-View Reconstruction (MVR) method for generating 3D vascular images was evaluated experimentally. The MVR method requires only a few digital subtraction angiographic (DSA) projections to reconstruct the 3D model of the vessel object compared to 180 or more projections for standard CBCT. Full micro-CBCT datasets of a contrast filled carotid vessel phantom were obtained using a Microangiography (MA) detector. From these datasets, a few projections were selected for use in the MVR technique. Similar projection views were also obtained using a standard x-ray image intensifier (II) system. A comparison of the 2D views of the MVRs (MA and II derived) with reference micro-CBCT data, demonstrated best agreement with the MA MVRs, especially at the curved part of the phantom. Additionally, the full 3D MVRs were compared with the full micro-CBCT 3D reconstruction resulting for the phantom with the smallest diameter (0.75 mm) vessel, in a mean centerline deviation from the micro-CBCT derived reconstructions of 29 μm for the MA MVR and 48 μm for the II MVR. The comparison implies that an MVR may be substituted for a full micro-CBCT scan for evaluating vessel segments with consequent substantial savings in patient exposure and contrast media injection yet without substantial loss in 3D image content. If a high resolution system with MA detector is used, the improved resolution could be well suited for endovascular image guided interventions where visualization of only a small field of view (FOV) is required.
Meta-analysis of published transcriptional and translational fold changes reveals a preference for low-fold inductions.

The goals of this study were to gain a better quantitative understanding of the dynamic range of transcriptional and translational response observed in biological systems and to examine the reporting of regulatory events for trends and biases. A straightforward pattern-matching routine extracted 3,408 independent observations regarding transcriptional fold-changes and 1,125 regarding translational fold-changes from over 15 million MEDLINE abstracts. Approximately 95% of reported changes were ≥2-fold. Further, the historical trend of reporting individual fold-changes is declining in favor of high-throughput methods for transcription but not translation. Where it was possible to compare the average fold-changes in transcription and translation for the same gene/product (203 examples), approximately 53% were a ≤2-fold difference, suggesting a loose tendency for the two to be coupled in magnitude. We found also that approximately three-fourths of reported regulatory events have been at the transcriptional lev...
The effect in the KHT sarcoma of CCNU and MISO on cell cycle progression evaluated by flow-cytometry.

Abstract Previous studies using the KHT sarcoma have shown that misonidazole (MISO) enhances the cytotoxicity of 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea (CCNU) by as much as a factor of 2.0, In the present study flow cytometry was used to monitor the changing DNA distributions of cells dissociated from solid tumors at successive times following treatment with CCNU, applied either alone or in combination with 0.5 mg/g MISO. The proportion of cells in late S and the G 2 M phases of the cell cycle increased gradually after CCNU treatment. MISO did not significantly change this block in cell progression, which persisted for at least 48 hr after treatment in all cases. CCNU shows marked carbamoylating activity, which has been associated with inhibition of RNA processing and with the degree of chemopotentiation achieved with MISO. Consequently, to evaluate whether MISO chemopotentiation was influencing the RNA distributions in tumors, RNA histograms were generated using acridine orange to differentially stain cellular DNA and RNA. By 24 hr after treatment. CCNU clearly altered the distribution of RNA, but no significant differences could be detected between results obtained from drug and drug plus sensitizer treated groups. These studies demonstrate the effect of CCNU on cell cycle progression in vivo . The addition of MISO did not result in further perturbation of the total tumor population, suggesting that cell cycle redistribution does not play a major role in chemopotentiation by MISO.
ICAM-1 upregulation in distant tissues after hepatic ischemia/reperfusion: a clue to the mechanism of multiple organ failure.

Abstract Background/Purpose: Endothelial cell adhesion molecules (ECAMs) are felt to play an important role in ischemia/ reperfusion (I/R) injury by causing adhesion of leukocytes to endothelial cells. It is possible that ECAMs play a role in multiple organ system failure. ICAM-1 is one of the adhesion molecules that has been shown to be upregulated in response to cytokines. This upregulation leads to leukocyte endothelial cell interaction (adhesion) and to neutrophil infiltration of the affected tissue. The purpose of our study was to measure ICAM-1 expression in the liver and other organs after hepatic ischemia/reperfusion (I/R). Methods: A laparotomy was performed on 14 Sprague-Dawley rats; 45 minutes of occlusive ischemia to the left lateral lobe was followed by 5 hours of reperfusion. The rat was injected with I 125 -labeled ICAM-1 MAb and I 131 -labeled nonbinding MAb (to control for nonspecific accumulation of ICAM-1 MAb). Entire organs were harvested and accumulated activity was measured in each organ. ICAM-1 levels were expressed as percent injected dose per gram of tissue. Control animals underwent sham laparotomy. Results: ICAM-1 was upregulated in the ischemic lobe of the liver, nonischemic lobe of the liver, heart, kidney, intestine, and pancreas. Up-regulation in the lung was not significant. Both the lung and liver had high constitutive levels of ICAM-1. Conclusions: These data show that (1) significant hepatic upregulation of ICAM-1 after hepatic ischemia/reperfusion and (2) significant ICAM-1 upregulation in other tissues (heart, kidney, and intestine) after hepatic ischemia/reperfusion. The ICAM-1 upregulation in distant organs is likely mediated by cytokines such as tumor necrosis factor (TNF). These data show that leukocyte endothelial cell interactions in distant organs may be mediated by hepatic ischemia/ reperfusion. This is a possible explanation for how failure of one organ can lead to failure of others in multiple organ system failure.
Electrical linewidth metrology for systematic CD variation characterization and causal analysis

Control of critical dimension (CD) variation is of extreme importance in modern semiconductor manufacturing processes. To be controlled, the nature of CD variation must be understood. This paper outlines a method for characterizing systematic spatial variation by means of dense electrical linewidth measurements, including actual sample data. In addition, since exhaustive sampling is prohibitively expensive for routine use, a method is discussed for finding an optimum economical sampling plan and using this plan to track systematic CD variation over time.