cssi/SciSciGPT-SciSciNet huggingface dataset:
The role of extracellular signal-regulated kinase in cognitive and motor deficits following experimental traumatic brain injury

Traumatic brain injury (TBI) causes neuronal death and alters the plasticity (e.g. morphology) of surviving neurons. Both of these events contribute to TBI-associated neurological deficits, such as memory dysfunction. Although a majority of current research is directed towards identifying biochemical cascades responsible for cell death, little is known about mechanisms of altered neuronal plasticity following TBI. Extracellular signal-regulated kinases (Erk1 and 2) play a critical role in growth and have been implicated in long-lasting neuronal plasticity and memory storage. The activation of Erk following TBI was investigated utilizing an antibody that specifically binds to dually phosphorylated Erk. Using this antibody, we report that lateral cortical impact injury in rats increases Erk phosphorylation both in the cortex and the hippocampus as early as 10 min post-injury. Double immunostaining experiments using either a neuron-specific or an astroglial-specific marker show that the active Erk is localized almost exclusively in neuronal cells. Furthermore, the increase in phospho-Erk immunoreactivity was initially localized to axons and at later time points was observed to be predominantly in the cell soma. This suggests that Erk redistributed over time and may play a role in retrograde signaling. Administration of inhibitors of the Erk cascade worsened retrograde amnesia, impaired performances in hippocampus- and amygdala-dependent memory tasks, and exacerbated motor deficits following TBI. Furthermore, inhibition of this cascade did not have any overt effects on cell survival, but altered neuronal morphology as detected by a dendritic-specific marker. These findings suggest that the Erk cascade plays an essential role for the maintenance of neuronal function and plasticity following TBI.
Gene expression profiling of lymphoblasts from autistic and nonaffected sib pairs: Altered pathways in neuronal development and steroid biosynthesis

Despite the identification of numerous autism susceptibility genes, the pathobiology of autism remains unknown. The present “case-control” study takes a global approach to understanding the molecular basis of autism spectrum disorders based upon large-scale gene expression profiling. DNA microarray analyses were conducted on lymphoblastoid cell lines from over 20 sib pairs in which one sibling had a diagnosis of autism and the other was not affected in order to identify biochemical and signaling pathways which are differentially regulated in cells from autistic and nonautistic siblings. Bioinformatics and gene ontological analyses of the data implicate genes which are involved in nervous system development, inflammation, and cytoskeletal organization, in addition to genes which may be relevant to gastrointestinal or other physiological symptoms often associated with autism. Moreover, the data further suggests that these processes may be modulated by cholesterol/steroid metabolism, especially at the level of androgenic hormones. Elevation of male hormones, in turn, has been suggested as a possible factor influencing susceptibility to autism, which affects ∼4 times as many males as females. Preliminary metabolic profiling of steroid hormones in lymphoblastoid cell lines from several pairs of siblings reveals higher levels of testosterone in the autistic sibling, which is consistent with the increased expression of two genes involved in the steroidogenesis pathway. Global gene expression profiling of cultured cells from ASD probands thus serves as a window to underlying metabolic and signaling deficits that may be relevant to the pathobiology of autism.
A comparison of serum and vaginal dialysate concentration of 13,14-dihydro-15-keto-PGF2α in women undergoing 1st trimester therapeutic abortions

Abstract 13,14-Dihydro-15-keto-PGF2α(PGFM) levels in serum and vaginal secretion, before, one hour, and 24 hours post abortion were measured in 13 women from 8 to 12 weeks pregnant. The mean metabolite levels in the blood were 61.2 pg/ml pre-termination, 73.1 pg/ml and 121.4 pg/ml one hour and 24 hours post-termination. The vaginal dialysate means were 136.7 pg/ml, 425.7 pg/ml, and 211.7 pg/ml respectively.
Image cytometric HER2 in gastric carcinoma: Is a new algorithm needed?

BACKGROUND Algorithms for quantitation of HER2 immunohistochemistry were developed for breast carcinoma, where the membranous stain must be entirely around the cell membrane. For gastric carcinoma, although assessment of intensity of immunostain (0 to 3) is similar, the site and percentage of stain differs by lacking the requirement of entire cell membrane positivity (complete, basolateral, or lateral membranous reactivity is sufficient for a positive result). We quantitated HER2 in gastric cancer specimens visually and by image cytometry, comparing results, and where available, with fluorescence in situ hybridization (FISH). The goal was to assess whether lack of concordance among results, might suggest a requirement for changing the image cytometric algorithm. DESIGN All gastric carcinoma biopsies, resections, and cell blocks studied for HER2 expression/amplification in the past 2 years were included. Immunostain intensity, percentage, and score 0 to 3+ (0, 1+ negative, 2+ equivocal, 3+ positive), were evaluated visually, and by image cytometry with the ACIS score 0 to 3 (0, 1 negative, 2 equivocal, 3 positive). FISH ( 2.2 amplified) was performed on all specimens with scores 2 and 3 by image cytometry. Results were compared. RESULTS Sixty-eight specimens were studied, including 43 (63.2%) biopsies, 17 (25%) resections, and 8 (11.8%) cell blocks. Forty-seven (69.1%) were primary gastric, esophageal, or gastroesophageal junction adenocarcinoma; 19 (27.9%) were metastatic; 3 (4.4%) were well, 14 (20.6%) moderately (17, 25% tubular), and 51 (75%) poorly differentiated (poorly cohesive). Fourteen (20.6%) of cases were HER2 IHC positive with no significant difference in frequency based on type of specimen, site of carcinoma, or differentiation. Of the 14 visually HER2 IHC positive, 13 were positive by image cytometry (93% concordance), all 13 were amplified by HER2 FISH (100% concordance). Of the 3 cases equivocal both visually and by image cytometry, only 1 was FISH amplified. Fifty-one were negative by IHC visually and 52 by image cytometry (98% concordance). None of the 5 HER2 IHC negative were amplified by FISH. CONCLUSIONS Despite different recommendations for interpretation of HER2 in gastric versus breast cancer, equivocal and positive/amplified results visually, and by image cytometry, and where FISH was performed, are similar. This concordance is noted for biopsy, resection, and cell block specimens, for primary versus metastatic, and for moderately versus poorly differentiated carcinoma; HER2 positivity/amplification is most frequent with poor differentiation, but not significantly so. There seems to be no need for the HER2 image cytometric algorithm used for breast cancer, to be changed when used for assessment of gastric cancers.
Enhancing Freedom to Operate for Plant Breeders and Farmers through Open Source Plant Breeding

The Open Source Seed Initiative (OSSI) (www. osseeds.org) seeks to address the dramatic transition over the past 100 yr in how plant germplasm is distributed, developed, and released: from a freely available resource primarily located in the public sector to proprietary structures managed largely by the private sector. OSSI was developed by a group of plant breeders, farmers, seed companies, nonprofit organizations, and policymakers with the goal of promoting and maintaining open access to plant genetic resources worldwide. OSSI seeks to provide an alternative to pervasive intellectual property rights agreements that restrict freedom to use plant germplasm through the development and promulgation of a Pledge which is intended both to raise awareness of these issues and to ensure that germplasm can be freely exchanged now and into the future. In this paper we discuss the historical forces and trends that have led to various types of biological and intellectual property protections and how this has potentially limited plant breeders’ “freedom to operate” and farmers’ sovereignty over seed. We then discuss how OSSI is providing an alternative to increasingly restrictive intellectual property rights for plants and working to maintain open access to plant germplasm. C.H. Luby and I.L. Goldman, Dep. of Horticulture, Univ. of WisconsinMadison, 1575 Linden Dr., Madison, WI 53706; J. Kloppenburg, Dep. of Community and Environmental Sociology, Univ. of WisconsinMadison, 1450 Linden Dr., Madison, WI 53706; T.E. Michaels, Dep. of Horticultural Science, Univ. of Minnesota, 456 Alderman Hall, Saint Paul, MN 55108. Received 16 Oct. 2014. Accepted 17 Dec. 2014. *Corresponding author (cluby@wisc.edu). Abbreviations: FOSS, free and open source software; IPR, intellectual property rights; MTA, material transfer agreement; NPGS, National Plant Germplasm System; OSSI, Open Source Seed Initiative; PVP, Plant Variety Protection; PVPA, Plant Variety Protection Act; UPOV, Union for the Protection of New Varieties of Plants. Published in Crop Sci. 55:2481–2488 (2015). doi: 10.2135/cropsci2014.10.0708 Freely available online through the author-supported open-access option. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Published October 19, 2015
Software development for design of illumination systems

Optical design software is developed that includes the capability to model illumination systems. The software enables predicting the intensity distribution of radiation at a plane located at some distance from the source. An illumination system comprising an ellipsoidal reflector and a spherical source is modeled and the results of the analysis are compared to those achieved experimentally.
Cell-cycle-dependent repair of damage in alpha and bulk DNA on monkey cells

Abstract Excision repair of bulky chemical adducts in alpha DNA of confluent cultures of African green monkey cells has previously been shown to be deficient relative to that in the overall genome. We have compared the removal of adducts produced by treatment with aflatoxin B1 (AFB1) and N-acetoxy-2-acetylaminofluorene (NA-AAF) from alpha DNA sequences in synchronized and exponentially and exponentially growing cultures of monkey cells. Proficient removal of AFB1 adducts in alpha DNA was observed in exponentially growing cultures. However, as the cultures approached confluence, adduct removal from alpha DNA became deficient. Cells synchronized by subculturing confluent cultures exhibited proficient removal of adducts from both alpha and bulk DNA when treated in early G1 or late S/G2 while those cells treated in early S phase did not remove adducts from either alpha or bulk DNA. We conclude that the accessibility of chemical adducts to repair in alpha chromatin is influenced by the growth state and the cell cycle stage.
Beyond the New Deal: Ideological Differences Between Eleven State Democratic Parties, 1956-1980

HE conventional interpretation of the breakup of the Democratic coalition in the post-New Deal era emphasizes the emergence of new issues and a new class structure in the 1960s and 1970s (Dawson 1973; Sundquist 1973; Nie, Verba, Petrocik 1976; Ladd and Hadley 1978; Shafer 1985). According to this view, Democrats in the New Deal era built a heterogeneous lower-class coalition around the theme of government nationalism. By the 1960s and 1970s, however, the economic-dominated agenda of the New Deal was supplanted by a multi-issue agenda that included not only economic issues but a vast array of social and cultural issues. This, coupled with changes in the class structure associated with postindustrial society, resulted in a fracturing of the New Deal Democratic coalition. Despite the fact that one of the most distinguishing features of the American party system is its decentralization, little systematic research has examined the agendas of state Democratic organizations during the period of decline in the New Deal party system. Realignment theorists suggest that when there is general agreement on what constitutes the central thrust of the policy agenda, stable, long-term electoral groupings develop (Burnham 1970; Sundquist 1973; Campbell and Trilling 1980). When the component parts of the national party (the state parties) disagree on and about the central thrust of the political agenda, the potential exists for the breakup of the old party system. Did state Democratic organizations in the 1960s and 1970s address the social and cultural issues that, many say, contributed to the ultimate breakup of the New Deal system? If so, did such issues create higher intraparty disagreement than the economic issues of the New Deal? This study employs a content analysis of Democratic platforms from eleven states during the period 1956-80 in an attempt to address these two questions.
EFFECT OF INHIBITORS OF PROTEIN KINASE C(PKC) AND PROTEIN TYROSINE KINASE(PTK) ON THE CEREBROVASCULAR RESPONSE TO ADENOSINE 2276

Adenosine is an important factor in cerebrovascular regulation in the newborn especially under conditions low cerebral oxygen availability. Post receptor signaling associated with adenosine receptor(s) in the newborn cerebral circulation are poorly understood. Recent studies suggest that certain adenosine receptors are coupled to PKC-and/or PTK-dependent signal transduction pathways. We evaluated the hypothesis that activation of PKC modulates the cerebrovascular response to adenosine in vivo by examining the effect of staurosporine, an inhibitor of PKC, using the closed cranial window preparation in twelve newborn piglets. In that paradigm, staurosporine (9 nM) treatment augmented by 4-fold the increase pial arteriolar diameter induced by 1 μM exogenous adenosine (Δdiameter control = 4±2%[79±4 μm to 82±3 μm]; Δdiameter staurosporine = 17±3%[56±3 μm to 101±5 μm]). In addition, the adenosine-induced vasodilation was prolonged in staurosporine-treated preparations. Recent experiments show a similar effect, i.e., enhanced the dose-dependent relaxation response to adenosine in isolated, newborn lamb middle cerebral artery (MCA) preparations in tissue bath. An inhibitor of PTK (genistein, 20 μM) showed similar trend but was not statistically significant. The data suggest that activation of staurosporine-sensitive signal transduction pathways such as PKC may play a role in the ultimate expression of contractile properties of cerebral arteries from newborn animal models. We propose that certain adenosine receptors activate PKC which modulate the contraction/relaxation response and/or modify adenosine uptake and metabolism. (Supported by the American Heart Association national council, #95009270)
Growth response of Pinus taeda L. to herbicide, prescribed fire, and fertilizer

Abstract The purpose of this study was to determine the relative effects of selected combinations of herbicide, fire, and fertilizer treatments on the growth of mid-rotational loblolly pine (Pinus taeda L.) at two East Texas sites, and to evaluate possible mechanisms responsible for the effects. Specifically, the first objective was to determine if fire and herbicide, with and without fertilizer, increased growth of mid-rotation loblolly pine, as assessed from measurements of the change in basal area following treatment. The second objective was to evaluate the roles of crown area and available growing space as possible mechanisms explaining potential increases in tree growth. Herbicide treatment produced an increase of 5% in basal area of unfertilized trees at both sites between 1999 and 2001 (P
Maximum entropy model parameterization with TF∗IDF weighted vector space model

Maximum entropy (MaxEnt) models have been used in many spoken language tasks. The training of a MaxEnt model often involves an iterative procedure that starts from an initial parameterization and gradually updates it towards the optimum. Due to the convexity of its objective function (hence a global optimum on a training set), little attention has been paid to model initialization in MaxEnt training. However, MaxEnt model training often ends early before convergence to the global optimum, and prior distributions with hyper-parameters are often added to the objective function to prevent over-fitting. This paper shows that the initialization and regularization hyper-parameter setting may significantly affect the test set accuracy. It investigates the MaxEnt initialization/regularization based on an n-gram classifier and a TF*IDF weighted vector space model. The theoretically motivated TF*IDF initialization/regularization has achieved significant improvements over the baseline flat initialization/regularization, especially when training data are sparse. In contrast, the n-gram based initialization/ regularization does not exhibit significant improvements.
Synthesis and characterization of asymmetric electrochemical capacitive deionization materials using nanoporous silicon dioxide and magnesium doped aluminum oxide

New capacitive deionization (CDI) materials based on using nanoporous silicon dioxide or alumina surface-doped with magnesium were shown to remove a wide range of cations having different valent states and hydrated radii. The use of the asymmetric insulating oxide nanoparticles as CDI materials increased removal rates due to their small size and opposite surface potentials. This system can be regenerated electrochemically by reversing the potential of the electrodes in order to drive the ions off the electrodes. Unique to this system is that ions do not adsorb onto the opposite electrode during regeneration due to the inherent surface potential of the nanoporous oxide which repels the ions under the conditions employed for these tests. As might be expected, the maximum allowable regeneration voltage was directly related to the zeta potential of the nanoporous coating on the working electrode under the specific test conditions.
TABASCO: A single molecule, base-pair resolved gene expression simulator.

Experimental studies of gene expression have identified some of the individual molecular components and elementary reactions that comprise and control cellular behavior. Given our current understanding of gene expression, and the goals of biotechnology research, both scientists and engineers would benefit from detailed simulators that can explicitly compute genome-wide expression levels as a function of individual molecular events, including the activities and interactions of molecules on DNA at single base pair resolution. However, for practical reasons including computational tractability, available simulators have not been able to represent genome-scale models of gene expression at this level of detail. Here we develop a simulator, TABASCO http://openwetware.org/wiki/TABASCO , which enables the precise representation of individual molecules and events in gene expression for genome-scale systems. We use a single molecule computational engine to track individual molecules interacting with and along nucleic acid polymers at single base resolution. Tabasco uses logical rules to automatically update and delimit the set of species and reactions that comprise a system during simulation, thereby avoiding the need for a priori specification of all possible combinations of molecules and reaction events. We confirm that single molecule, base-pair resolved simulation using TABASCO (Tabasco) can accurately compute gene expression dynamics and, moving beyond previous simulators, provide for the direct representation of intermolecular events such as polymerase collisions and promoter occlusion. We demonstrate the computational capacity of Tabasco by simulating the entirety of gene expression during bacteriophage T7 infection; for reference, the 39,937 base pair T7 genome encodes 56 genes that are transcribed by two types of RNA polymerases active across 22 promoters. Tabasco enables genome-scale simulation of transcription and translation at individual molecule and single base-pair resolution. By directly representing the position and activity of individual molecules on DNA, Tabasco can directly test the effects of detailed molecular processes on system-wide gene expression. Tabasco would also be useful for studying the complex regulatory mechanisms controlling eukaryotic gene expression. The computational engine underlying Tabasco could also be adapted to represent other types of processive systems in which individual reaction events are organized across a single spatial dimension (e.g., polysaccharide synthesis).
Sirtuin 1 signaling and alcoholic fatty liver disease

Alcoholic fatty liver disease (AFLD) is one of the most prevalent forms of liver disease worldwide and can progress to inflammation (hepatitis), fibrosis/cirrhosis, and ultimately lead to end stage liver injury. The mechanisms, by which ethanol consumption leads to AFLD, are complicated and multiple, and remain incompletely understood. Nevertheless, understanding its pathogenesis will facilitate the development of effective pharmacological or nutritional therapies for treating human AFLD. Chronic ethanol consumption causes steatosis and inflammation in rodents or humans by disturbing several important hepatic transcriptional regulators, including AMP-activated kinase (AMPK), lipin-1, sterol regulatory element binding protein 1 (SREBP-1), PPARγ co-activator-1α (PGC-1α), and nuclear transcription factor-κB (NF-κB). Remarkably, the effects of ethanol on these regulators are mediated in whole or in part by inhibition of a central signaling molecule, Sirtuin 1 (SIRT1), which is a nicotinamide adenine dinucleotide (NAD+)-dependent class III protein deacetylase. In recent years, SIRT1 has emerged as a pivotal molecule controlling the pathways of hepatic lipid metabolism, inflammatory responses and in the development of AFLD in rodents and in humans. Ethanol-mediated SIRT1 inhibition suppresses or stimulates the activities of above described transcriptional regulators and co-regulators, thereby deregulating diverse lipid metabolism and inflammatory response pathways including lipogenesis, fatty acid β-oxidation, lipoprotein uptake and secretion and expression of pro-inflammatory cytokines in the liver. This review aims to highlight our current understanding of SIRT1 regulatory mechanisms and its response to ethanol-induced toxicity, thus, affirming significant role of SIRT1 signaling in the development of AFLD.
Refining a pedogenic-carbonate CO2 paleobarometer to quantify a middle Miocene greenhouse spike

Abstract Estimates of respired soil CO2 concentration in paleosols are needed to calculate past atmospheric CO2 levels from the difference between organic and carbonate carbon isotopic values in paleosols. A new compilation of CO2 concentrations late in the growing season in modern calcareous soils can be used to estimate respired soil CO2 by subtracting atmospheric CO2 concentrations. Furthermore, respired CO2 shows a significant relationship with depth to calcic horizon, and this relationship can be used to estimate respired CO2 concentrations in paleosols. These values, as well as estimates of δ13C of atmospheric CO2 from δ13C of soil organic matter, and of paleotemperature from Bw horizon chemical composition, refine the Cerling CO2 paleobarometer. These refinements are applied to quantify the middle Miocene greenhouse, which has been controversial because it was not detected by marine alkenone and boron paleobarometers. New estimates of middle Miocene atmospheric CO2 from paleosols in Railroad Canyon, Idaho, reveal levels at 16 Ma of 852 ± 86 ppmv. This is similar to predicted values by 2100, and 3 times pre-industrial values (PIL = 280 ppmv).
Fifty years of DNA “Breathing”: Reflections on old and new approaches

The coding sequences for genes, and much other regulatory information involved in genome expression, are located 'inside' the DNA duplex. Thus the "macromolecular machines" that read-out this information from the base sequence of the DNA must somehow access the DNA "interior." Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative "melting phase transition" at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome 'melts' in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural ("breathing") fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be "readable" and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA "opening." Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this "Reflections" article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde, and simple DNA "melting" proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in "real time."
Residence Restrictions and the Association With Registered Sex Offender Clustering

This study examined whether sex offender residence restriction policies were associated with the clustering of registered sex offender (RSO) residences in 3,056 upstate New York block groups. RSO c...
Requirements of a Group I Intron for Reactions at the 3′ Splice Site

Abstract Structural elements of the Tetrahymena group I intron have been implicated in directing the exon-ligation transesterification reaction (the second step of self-splicing) to the correct 3′ splice site. The 3′ splice site also serves as the reaction site in a distinct transesterification reaction known as G-exchange and in a specific hydrolysis reaction. The dependence of the reactions on the internal guide sequence (IGS), an exon-binding element, was examined. Hydrolysis did not require the IGS, while G-exchange did, suggesting that one of the guanosine-binding sites employed during G-exchange requires the IGS. For the exon ligation reaction, the specification of the 3′ splice site is thought to be influenced by the 3′ exon-IGS pairing P10 and three structural elements in the intron:the universally conserved guanosine residue preceding the 3′ splice site, the long-range pairing P9.0, and the triple stem-loop region composed of P9, P9.1 and P9.2. A systematic mutational study of the three structural elements was performed in order to clarify the mechanism of the specification of the 3′ splice site for the reactions. For both transesterification reactions, the elements are important, with some superfluity in function. The specific hydrolysis reaction, however, shows even more dependence on the individual elements, especially the conserved guanosine. The results are discussed in terms of models for the mechanism of self-splicing.
Effects of a pre-and post-workout protein-carbohydrate supplement in trained crossfit individuals

Purpose: The purpose was to assess effects of a pre- and a post-workout protein-carbohydrate supplement on CrossFit-specific performance and body composition.
Spatial resolution enhancement of SSM/I data: vegetation studies of the Amazon Basin

The relatively low resolution of the Special Sensor Microwave/Imager (SSM/I) radiometer limits its utility in vegetation studies. However, resolution enhancement techniques can be used to ameliorate this limitation. To this end the Backus Gilbert inversion (BGI) technique and a modified form of the Scatterometer Image Reconstruction (SIR) algorithm are investigated as methods to create enhanced spatial resolution images from SSM/I data. A new method for generating cloud-free composite images is presented. The utility of the composite images is illustrated through a tropical vegetation discrimination study of general vegetation classes. An overall discrimination accuracy of 81.4% is achieved for 14 classes with most of the misclassification within broader vegetation categories.
Widespread promiscuous genetic information transfer from DNA to RNA.

### Widespread RNA and DNA Sequence Differences in the Human Transcriptome Li et al Science . 2011;333:53–58. New genomic studies show that the transfer of genetic information from DNA to RNA within humans is not very faithful. If true, frequent, or purposeful, then the implications for human health and disease are significant, but the burden of proof required is significant. Commentary: Molecular biology and genetics has a “central dogma.” First postulated by Francis Crick1,2 in 1958, shortly after the discovery of the double helix, it states that the molecular transfer or flow of genetic information occurs only as DNA→RNA→ protein. This argument is intrinsic to our understanding of genotypes, phenotypes, and human disease. The central “dogma,” a word whose precise meaning Crick acknowledged he did not precisely know3 and that could have been given the less glamorous moniker “hypothesis,” is frequently misunderstood as also implying high accuracy or even inflexibility.2 We now know that genetic information flow can be sometimes corrupted and can also occur in other directions in particular biological systems. A recent study by Li and colleagues,4 from the laboratory of Vivian Cheung at the University of Pennsylvania, now demonstrates apparent widespread DNA→RNA sequence differences in humans. The experiments they conducted involved sequencing reverse-transcribed RNA from cultured B cells isolated from 27 different humans and comparing them with their host genome sequences. Surprisingly, after appropriate quality controls, they discovered numerous base positions at which the RNA sequence was different from the DNA sequence in multiple molecules, a phenomenon they refer to as RDD (RNA-DNA difference). Specifically, they identified 28766 RDDs in the 27 individuals at 10210 exonic sites within 4741 genes. Each individual had high-quality RNA-based sequence data at 9.8 million sites: so, RDD was detected at a rate of 1.1×10−4 per exonic site (base) across human genes. Interestingly, they observed all 12 types …
The Inherent Mechanical Properties of Allograft Fascia Lata

Autogenous tendon and fascia are the most commonly used grafts for anterior cruciate ligament (ACL) reconstruction. Allografts, however, are now being used in selected patients. Allografts offer the advantage of decreased surgicaltime and morbidity, and a wider choice of graft type, size, and shape. The purpose of this study was to determine the inherent mechanical properties of sterilely procured/ freeze-dried (SP/FD), ethylene oxide/freeze-dried (ETO/FD), and irradiated/ freeze-dried (IRR/FD) fascia lata specimens and to compare the results to freshfrozen (FF) fascia data from our previous study (Noyes et al. 1984).
Semantic Roles for Nominal Predicates: Building a Lexical Resource

The linguistic annotation of noun-verb complex predicates (also termed as light verb constructions) is challenging as these predicates are highly productive in Hindi. For semantic role labelling, each argument of the noun-verb complex predicate must be given a role label. For complex predicates, frame files need to be created specifying the role labels for each noun-verb complex predicate. The creation of frame files is usually done manually, but we propose an automatic method to expedite this process. We use two resources for this method: Hindi PropBank frame files for simple verbs and the annotated Hindi Treebank. Our method perfectly predicts 65% of the roles in 3015 unique noun-verb combinations, with an additional 22% partial predictions, giving us 87% useful predictions to build our annotation resource.
Indigenous environmental knowledge and climate change adaptation

Certain climate change impacts are now unavoidable. The importance of adapting to climate change impacts has become increasingly clear, particularly at the local and regional scales. Many entities are looking to community-based adaptation as a place-based response, and a vehicle for empowering individuals, families and peoples. In regions across the world, including the Pacific, an appeal to indigenous environmental knowledge (IEK) is also emerging. This chapter explores the possible integration of IEK into the laws governing climate change adaptation.Integration of IEK, in the adaptation context, describes at least two different phenomena. It describes the indigenous methods used to respond to historical extremes that climate forecasts portend with greater frequency and severity – such as floods and drought – and suggests proven adaptations. It can also describe a lens, or worldview, with which decisions should be made that might facilitate long-range, multigenerational adaptive governance.While there have been multi-scalar efforts to support IEK methods on an ad hoc basis, few have attempted to harmonize core indigenous worldviews with discrete methods used in the Western context. In other words, Western researchers and practitioners generally investigate and employ specific management strategies without also exploring and introducing the relevant worldviews that have fostered such strategies. Moreover, there has been even less discussion of how to integrate these worldviews into the emerging legal adaptation framework to foster climate resilience in indigenous communities and beyond.Water resource management in Hawaii serves as one example of how such integration might work, while furthering resource resilience in the face of additional climate change-related stressors. By charting the evolution of the public trust doctrine and water management in Hawaii – from the Hawaiian Kingdom to contemporary Hawaii jurisprudence – ways in which the emerging law of adaptation can support IEK and how IEK can strengthen climate law become clearer.
California Draining: Lining the American Canal

The Ninth Circuit Court of Appeals' decision in Consejo de Desarrollo Economico De Mexicali v. U.S. epitomizes Congress' use of preemptive federal laws to impact the environment in the face of well established environmental regulations; specifically water resource allocation from the Colorado River's All-American Canal and its trans-national impacts. In Consejo, the two long running antagonistic forces of environmental resource allocation and increased population water needs coupled with industrial development came into conflict. However, before the Ninth Circuit could decide the issues of first impression presented by Consejo, it was precluded from reaching the merits of the controversy by Congressional action, namely Congress' eleventh-hour passage of the Tax Relief and Health Care Act of 2006. While purporting not to direct a result to the court, the act in fact precluded a judicial determination through the clever use of statutory language. Unsurprisingly, the court made clear that development was the victor. Congressional intent embodied in the plain language of the statute only served to bolster economic development and underscored objectives of the Tax Relief Act. As a result, judicial determination of the merits of Consejo (e.g., Equal Protection in water resource allocation, statutory conflict with other environmental regulations) must wait for either a California state court ruling or Congressional action that does not endorse water overindulgence from one community to the detriment of non-American users of the Colorado River basin water supply.
Bilateral internal thoracic artery grafting: Does graft configuration affect outcome?

Abstract Background Despite evidence that bilateral internal thoracic arteries (ITAs) improve long-term survival after coronary artery bypass grafting (CABG), uptake of this technique remains low. We directly compared bilateral ITA graft configurations and examined long-term outcomes. Methods We reviewed 762 patients who underwent CABG using bilateral ITA grafts at our institution between 1997 and 2014. The outcomes were mortality and a composite revascularization end point defined as need for percutaneous coronary intervention or repeat CABG. Adjusted subgroup analyses were performed using propensity score-adjusted Cox proportional hazards modeling. Results The cohort was divided into 4 groups: in situ (left ITA [LITA] anastomosed to the left anterior descending artery [LAD] with in situ right ITA [RITA] anastomosed to the left coronary circulation [239 patients]); in situ LITA-LAD and in situ RITA-right coronary circulation (239 patients); in situ RITA-LAD with in situ LITA-left coronary circulation (185 patients); and in situ LITA-LAD with a free RITA as a composite graft with inflow from the LITA or a saphenous vein graft (99 patients). Over a median follow-up of 1128 days, there were 47 deaths, 58 late percutaneous coronary interventions, and 7 repeat CABG procedures. Unadjusted Kaplan-Meier analysis revealed a difference in need for repeat revascularization among the 4 groups (log rank P = .049). However, after statistical adjustment, graft configuration was not an independent predictor of repeat revascularization or death. Conclusions Bilateral ITA graft configuration has no independent effect on need for repeat revascularization or long-term survival. Therefore, the simplest technique, determined by individual patient characteristics, should be selected.
Gold-Coated M13 Bacteriophage as a Template for Glucose Oxidase Biofuel Cells with Direct Electron Transfer.

Glucose oxidase-based biofuel cells are a promising source of alternative energy for small device applications, but still face the challenge of achieving robust electrical contact between the redox enzymes and the current collector. This paper reports on the design of an electrode consisting of glucose oxidase covalently attached to gold nanoparticles that are assembled onto a genetically engineered M13 bacteriophage using EDC-NHS chemistry. The engineered phage is modified at the pIII protein to attach onto a gold substrate and serves as a high-surface-area template. The resulting “nanomesh” architecture exhibits direct electron transfer (DET) and achieves a higher peak current per unit area of 1.2 mA/cm2 compared to most other DET attachment schemes. The final enzyme surface coverage on the electrode was calculated to be approximately 4.74 × 10–8 mol/cm2, which is a significant improvement over most current glucose oxidase (GOx) DET attachment methods.
A Mathematical Framework to Assess Vulnerabilities in Codependent Infrastructure and Natural System Networks

The objective of this paper is to understand how flow and topology affect resilience and robustness of co-dependent infrastructure and natural system networks. This paper represents these co-dependent infrastructure and natural systems as an integrated network system (INS) and develops metrics to measure resilience and robustness based on the understanding of network connections and flow characteristics. The paper presents a mathematical framework founded in system dynamics and viability theory that can be used to formulate metrics of robustness and resilience for an INS. As each of these factors are a function of the system “structure”, a graph theoretic approach is used to represent and analyze the INS. The research builds on recent work indicating that the topology of a network determines its vulnerabilities. The immediate contribution of this paper is that it lays the mathematical foundations for measuring robustness and resilience of the INS, and identifies methods to characterize its topology and flow through it. In the long run, this research is likely to support a platform that will pro-actively identify and prepare for unexpected disruptions to infrastructure services while reducing undesirable environmental hazards.
WRINKLING AXISYMMETRIC MEMBRANES

A statical-geometric analysis of axisymmetric wrinkling membranes is presented. The major premise of the underlying theory is preservation of one array of geodesics. It is found that the spatial shape of a wrinkled membrane is defined solely by the type of load and is independent of the original membrane geometry. The extent of the wrinkled zone is controlled by the invariant lengths of the preserving geodesics. The obtained closed form first integral reduces the analysis to forward integration or, in certain cases, to equations in elliptic integrals.
Developmentally Regulated Production of meso-Zeaxanthin in Chicken Retinal Pigment Epithelium/Choroid and Retina.

PURPOSE meso-Zeaxanthin is a carotenoid that is rarely encountered in nature outside of the vertebrate eye. It is not a constituent of a normal human diet, yet this carotenoid comprises one-third of the primate macular pigment. In the current study, we undertook a systematic approach to biochemically characterize the production of meso-zeaxanthin in the vertebrate eye. METHODS Fertilized White Leghorn chicken eggs were analyzed for the presence of carotenoids during development. Yolk, liver, brain, serum, retina, and RPE/choroid were isolated, and carotenoids were extracted. The samples were analyzed on C-30 or chiral HPLC columns to determine the carotenoid composition. RESULTS Lutein and zeaxanthin were found in all studied nonocular tissues, but no meso-zeaxanthin was ever detected. Among the ocular tissues, the presence of meso-zeaxanthin was consistently observed starting at embryonic day 17 (E17) in the RPE/choroid, several days before its consistent detection in the retina. If RPE/choroid of an embryo was devoid of meso-zeaxanthin, the corresponding retina was always negative as well. CONCLUSIONS This is the first report of developmentally regulated synthesis of meso-zeaxanthin in a vertebrate system. Our observations suggest that the RPE/choroid is the primary site of meso-zeaxanthin synthesis. Identification of meso-zeaxanthin isomerase enzyme in the developing chicken embryo will facilitate our ability to determine the biochemical mechanisms responsible for production of this unique carotenoid in other higher vertebrates, such as humans.
Teamwork at 35,000 feet: Enhancing safety through team training

The aviation industry has been commended for its ability to maintain a high level of safety despite operating in a mission critical, high impact work environment. This commitment to mindfulness and safely has led to the aviation community's transition to a high reliability organisation (HRO). A key factor in this transition was its commitment to team training and belief that collaboration among crew-members can be used as a key strategy by which errors can be managed. This recognition led to the development of a highly successful team training program (i.e., crew resource management, CRM). CRM's touted success within aviation has led to its adoption by many industries outside CRM. Therefore, it becomes important to delineate how aviation made this progression through the use of CRM as well as identify areas that have posed key challenges in making this transition. Therefore, the purpose of this paper is twofold. First, to review how aviation has used CRM to become a mindful HRO. In doing this, we briefly review the theoretical drivers behind CRM. Second, to provide principles concerning how organisations outside of aviation can use lessons learned within aviation to move towards becoming an HRO. In highlighting principles we also identify those areas that continue to pose challenges in aviation's quest to maintain HRO status and continually improve.
TAK1 regulates Paneth cell integrity partly through blocking necroptosis

Paneth cells reside at the base of crypts of the small intestine and secrete antimicrobial factors to control gut microbiota. Paneth cell loss is observed in the chronically inflamed intestine, which is often associated with increased reactive oxygen species (ROS). However, the relationship between Paneth cell loss and ROS is not yet clear. Intestinal epithelial-specific deletion of a protein kinase Tak1 depletes Paneth cells and highly upregulates ROS in the mouse model. We found that depletion of gut bacteria or myeloid differentiation factor 88 (Myd88), a mediator of bacteria-derived cell signaling, reduced ROS but did not block Paneth cell loss, suggesting that gut bacteria are the cause of ROS accumulation but bacteria-induced ROS are not the cause of Paneth cell loss. In contrast, deletion of the necroptotic cell death signaling intermediate, receptor-interacting protein kinase 3 (Ripk3), partially blocked Paneth cell loss. Thus, Tak1 deletion causes Paneth cell loss in part through necroptotic cell death. These results suggest that TAK1 participates in intestinal integrity through separately modulating bacteria-derived ROS and RIPK3-dependent Paneth cell loss.
Research on material performance of TBM disk cutter rings

Disc cutter rings are the principal TBM parts for rock breaking.The common forms of failure of the cutter rings were analyzed.Two different cutter rings were selected to analyze the chemical composition by direct reading spectrometer,the microstructure of which were compared by OM and TEM,the hardness was measured by Vickers hardness meter and the impact energy was measured by the impact test.For ring 1,the hardness was about 700 HV,and the impact energy 2-3 J.For ring 2,hardness530 HV,impact energy 30-40 J.Caparison was made between the technological processes of the two different rings.By improvement in purification,homogenization and grain refinement of the material and optimization of the heat treatment,high toughness of the rings could be obtained while maintaining high hardness.
PREMRATION OF NANOCRYSTALLINE SnO2 POWDERS

Tin dioxide powders were prepared by solution method using inorganic salt as a starting material. By well controlling precipitation rate, the homogeneous and condensed precipitates were obtained which were in the form of nearly transparent monolith. These tin hydroxide precipitates were calcinated at 450, 600, 750, 900 and 1050℃ for 2h to form pure SnO2 powders which have very small crystallite sizes. X-ray powder diffraction results showed that the crystallite sizes are in the range of 10～30 nm as the calcination temperature increased from 450 to 1050℃, which indicates that the crystallite size of as synthesized powders is not very sensitive to temperature.
Negative Slope of Exhaled CO2 Profile

In the course of studying gas exchange during partial liquid ventilation (PLV) in healthy and injured piglets, we noted a reversal in the profile of exhaled CO2 (PECO2) versus time. Rather than a positive slope, the CO2 expirogram often reached a peak early in expiration and fell toward the end of the breath. In addition to a change in sign, the absolute value of the slope was very large. The change in profile led us to question the generally accepted practice of using “end-tidal” PECO2 to represent average alveolar PACO2 during PLV. Given the steep rate of change of PECO2 over a breath, the use of a single point on the CO2 expirogram to represent alveolar gas during PLV seemed in error. We hypothesized that a combination of increased ventilation heterogeneity and diffusion limitation could account for the reversal in sign and exaggeration of the slopes. To further investigate this problem we explicitly measured PECO2 vs. exhaled volume in two additional experiments and compared these findings to 40 previously studied animals.