cssi/SciSciGPT-SciSciNet huggingface dataset:
Narratives Can Motivate Environmental Action: The Whiskey Creek Ocean Acidification Story

Even when environmental data quantify the risks and benefits of delayed responses to rapid anthropogenic change, institutions rarely respond promptly. We propose that narratives complementing environmental datasets can motivate responsive environmental policy. To explore this idea, we relate a case study in which a narrative of economic loss due to regionally rapid ocean acidification—an anthropogenic change—helped connect knowledge with action. We pose three hypotheses to explain why narratives might be particularly effective in linking science to environmental policy, drawing from the literature of economics, environmental policy, and cognitive psychology. It seems that yet-untold narratives may hold similar potential for strengthening the feedback between environmental data and policy and motivating regional responses to other environmental problems.
Differential gene expression analysis during porcine hepatocyte spheroid formation

Primary porcine hepatocytes cultured in suspension self-assemble into multicellular aggregates or spheroids that display enhanced liver-specific functional capability and remain viable for an extended period of time in vitro. The molecular events underlying the process of spheroid formation were explored by differential gene expression analysis. Critical time points in spheroid formation were first identified by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of stress-related gene expression levels at different stages of spheroid formation. Suppression subtractive hybridization was used to identify transcripts up- or down-regulated at different stages of spheroid formation. Subsequently, three sets of reciprocal subtractions, comparing freshly isolated hepatocytes, spheroid-forming hepatocytes, and mature spheroids were carried out, and differentially expressed transcripts were isolated, cloned, sequenced, and annotated. A total of 65 genes and 14 novel transcripts were identified as differentially expressed, and very high sequence conservation between pig and human transcripts was observed. The resultant expressed sequence tags (ESTs) revealed a rapid decrease in the transcript levels of a subset of liver-specific genes, cytochrome P450s, and enzymes involved in heme biosynthesis, as well as up-regulation of genes involved in calcium-dependent vesicle trafficking and a number of acute-phase proteins in mature spheroids. Previous morphological and functional data on hepatocyte spheroid formation support cellular polarization of the hepatocyte into apical and basolateral domains in spheroids. This is important for the re-emergence of differentiated functions in vitro and is reflected by differences in gene expression patterns.
Duality and Regge-Mueller phenomenology for inclusive spectra

Abstract Further predictions are examined of a recently proposed, phenomenologically supported, duality scheme for double Regge-Mueller graphs. It is stressed that these duality constraints should be tested, not only on the non-scaling behaviour at x = 0 of single-particle spectra, but also on the shape (i.e. curvature) of rapidity spectra. Exchange degeneracy constraints for single and double Regge-Mueller expansions are used, together with factorization to investigate two-particle spectra of ( a → d | c | b ) when one particle is near the kinematic boundary and the other is in the central region. A rapid scaling criterion is derived. The relative sizes of the non-scaling part of (p→ π − | c | b ) spectra c = π + , π − , π 0 , b = π + , π − K + ,K − ,p are estimated. An extended pattern of duality constraints for many-particle Regge-Mueller graphs is suggested.
Partitioning of elastic energy in open-cell foams under finite deformations

Abstract The challenges associated with the computational modeling and simulation of solid foams are threefold—namely, the proper representation of an intricate geometry, the capability to accurately describe large deformations, and the extremely arduous numerical detection and enforcement of self-contact during crushing. The focus of this study is to assess and accurately quantify the effects of geometric nonlinearities (i.e. finite deformations, work produced under buckling-type motions) on the predicted mechanical response of open-cell foams of aluminum and polyurethane prior to the onset of plasticity and contact. Beam elements endowed with three-dimensional finite deformation kinematics are used to represent the foam ligaments. Ligament cross-sections are discretized through a fiber-based formulation that provides accurate information regarding the onset of plasticity, given the uniaxial yield stress–strain data for the bulk material. It is shown that the (hyper-) elastic energy partition within ligaments is significantly influenced by kinematic nonlinearities, which frequently cause strong coupling between the axial, bending, shear and torsional deformation modes. This deformation mode-coupling is uniquely obtained as a result of evaluating equilibrium in the deformed configuration, and is undetectable when small deformations are assumed. The relationship between the foam topology and energy partitioning at various stages of moderate deformation is also investigated. Coupled deformation modes are shown to play an important role, especially in perturbed Kelvin structures where over 70% of the energy is stored in coupled axial-shear and axial-bending modes. The results from this study indicate that it may not always be possible to accurately simulate the onset of plasticity (and the response beyond this regime) if finite deformation kinematics are neglected.
Network Architecture and Modulus of Miscible Heteropolymer Blends

The architecture and entanglement density of a multicomponent polymer network composed of miscible, flexible chains is related to the corresponding properties and concentrations of the pure components. It is assumed that the coupling frequency between different chain species is proportional to their fractional participation in the blend and that the entanglement ability of polymers can be affected by the presence of heteropolymer neighbors. The theory, equally applicable to temporary and permanent networks, estimates the molecular weight between entanglements and their total number along a chain in the blend. This information is used in establishing a mixing law for the rubbery plateau modulus of a fluid polymer blend and in deriving a relationship for the equilibrium modulus of an interpenetrating polymer network containing trapped entanglements and dangling segments. The theoretical predictions are compared with experimental results from the literature on several miscible polymer blends.
Thermometric titrations in acetonitrile

Abstract The use of acetonitrile as a medium for thermometric acid-base titrations has been studied. Satisfactory titrations are obtainable for a wide variety of amines and organic acids, but the instability of the solvent in the presence of strong bases greatly limits its practical applicability. Data are given on the heats of neutralisation of various acids in acetonitrile, and the results for m - and p -substituted benzoic acids are shown to correlate well with their Hammett σ-values.
Resveratrol and Malignancies

Carcinogenesis is a multifactorial process, frequently encompassing 3 stages: initiation, promotion and progression. It is characterized by multiple deviations from normal both at the cell and organism levels. Although most people have a small number of cells that present deviations from normal, most of those cells will not cause cancer. However, some will. What tips the balance between normal and abnormal is the subject of intense scientific research as well as unfounded speculations. Chronic inflammation is one of the risk factors for cancer. Resveratrol is consumed by the population as a dietary supplement in the hope of decreasing the risk of inflammation and cancer and other chronic diseases such as diabetes and vascular diseases. There is a discrepancy between the doses used in the animal studies showing that resveratrol decreases all three stages of carcinogenesis, and the doses ingested by the population either as supplements or in the diet. While there is health benefit from using high resveratrol doses, it might be also of practical and scientific benefit to focus future effort in understanding the effects of normal dietary resveratrol levels.
Tukey's gh Distribution for Multiple Imputation

Tukey proposed a class of distributions, the g-and-h family (gh family), based on a transformation of a standard normal variable to accommodate different skewness and elongation in the distribution of variables arising in practical applications. It is easy to draw values from this distribution even though it is hard to explicitly state the probability density function. Given this flexibility, the gh family may be extremely useful in creating multiple imputations for missing data. This article demonstrates how this family, as well as its generalizations, can be used in the multiple imputation analysis of incomplete data. The focus of this article is on a scalar variable with missing values. In the absence of any additional information, data are missing completely at random, and hence the correct analysis is the complete-case analysis. Thus, the application of the gh multiple imputation to the scalar cases affords comparison with the correct analysis and with other model-based multiple imputation methods. C...
Studies on the mechanisms of epinephrine stimulation of lypolysis

The time course for epinephrine stimulation of lypolysis, cyclic AMP accumulation and activation of protein kinase was studied in adipose tissue from hypophysectomized rats. Triglyceride breakdown, as assessed by glycerol release, increased rapidly in response to epinephrine, maintained a constant rate as long as the hormone was present, and decreased rapidly to basal values when the hormone was removed. Cyclic AMP accumulation was transient peaking within 3 min of exposure to epinephrine and then declining to levels indistinguishable from basal by 9 min. Protein kinase activity in extracts also peaked at 3 min and thereafter declined to a level approximately 25% greater than resting activity. Peak levels of cyclic AMP, steady state levels of protein kinase activity and the rate of glycerol production were all related in a dose dependent manner to the concentration of epinephrine. These observations suggest that the spike in cyclic AMP levels may be necessary to trigger the activation of lipolysis, but was not sufficient to sustain an accelerated rate of triglyceride breakdown. Continued activation of protein kinase, however, may be essential to sustained lipolysis.
Chronic methylphenidate treatment enhances striatal dopamine neurotransmission after experimental traumatic brain injury.

Traumatic brain injury (TBI) results in functional deficits that often are effectively treated clinically with the neurostimulant, methylphenidate (MPH). We hypothesized that daily MPH administration would reverse striatal neurotransmission deficits observed in the controlled cortical impact (CCI) model of TBI. CCI or naive rats received daily injections of MPH (5 mg/kg) or saline for 14 days and were assessed on day 15 using fast scan cyclic voltammetry. Dopamine (DA) transporter (DAT) localization, DA-related proteins, and transcription factor (c-fos) expression were also assessed. CCI resulted in reduced electrically evoked overflow of DA and maximal velocity of DA clearance (V(max)). In contrast, CCI was associated with a decrease in the apparent K(M) of DAT. Daily dose of MPH after CCI resulted in robust increases in evoked DA overflow and V(max) as well as increased apparent K(M). Reductions in total striatal DAT expression occurred after CCI and were not further affected by MPH. In contrast, membrane-bound striatal DAT levels were increased in both CCI groups. MPH post-CCI significantly increased striatal c-fos levels compared with saline. These results support the hypothesis that daily MPH improves striatal DA neurotransmission after CCI. DAT expression and transcriptional changes affecting DA protein function may underlie the injury and MPH-induced alterations in neurotransmission observed.
Synthesis and Characterization of Soyamide Ferulate

Ferulic acid (4-hydroxy-3-methoxycinnamic acid) is a phytochemical antioxidant that is widely distributed throughout the plant kingdom. Cinnamic acid derivatives are used as biobased ultraviolet (UV) absorbers in sunscreen formulations. Soybean oil ferulate, a biobased UV absorber, was synthesized by reacting soyamide with ferulic acid. The resulting product was characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy, and gel permeation chromatography (GPC). Spectroscopic studies measured the soyamide-based ferulate maximum absorbance at 327 nm with a molar extinction coefficient of 19,705 L mol−1 cm−1. Soyamide ferulate has potential to be used in coatings.
Trap spectroscopy of a-Si:H diodes using transient current techniques

Transient current techniques have been applied to hydrogenated amorphous silicon (a-Si:H) solar cells to obtain information about the electron traps in the upper half of the band gap. These studies lead to the conclusion that electron trapping occurs in specific regions distributed throughout the a-Si:H. A model based on these trapping regions becoming negatively charged as electrons are captured and thus opposing further capture is presented. Because of this inhomogeneous capture only the lower limit to the density of traps is obtained.
Unmanned aircraft sense and avoid radar: Surrogate flight testing performance evaluation

Unmanned aircraft systems (UAS) have proven to have distinct advantages compared to manned aircraft for a variety of tasks. Current airspace regulations require a capability to sense and avoid other aircraft to replace the ability of a pilot to see and avoid other traffic. A prototype phased-array radar was developed and tested to demonstrate a capability to support the sense and avoid (SAA) requirement and to validate radar performance models. Validated radar models enable evaluation of other radar systems in simulation. This paper provides an overview of the unique radar technology, and focuses on radar performance and model validation as demonstrated through a flight testing campaign. Performance results demonstrate that the prototype SAA radar system can provide sufficient accuracy to sense avoid non-cooperative aircraft.
Capital mobility and monetary adjustment in Western Europe, 1973–1991

The western European experience is perhaps the best known instance of formal exchange rate management and attempted monetary integration on a regional basis. This article examines the role of heightened international capital mobility in accounting for this phenomenon. The behavior of ten industrial western European states during the period 1973–1991 is analyzed in this regard. These states vary in terms of size, membership in the European Community (now the European Union), participation in the exchange rate mechanism of the European Monetary System, and their revealed policy preferences. Nevertheless, all ten states eventually accommodated German monetary policy in an effort to stabilize regional exchange rates around the deutsche mark. The pursuit of increasingly similar policies by states differing in non-trivial ways suggests that, at least by the end of the research period, the external constraint imposed upon each of them as a result of international financial integration had become severe indeed. Recognition of this constraint provides a basis for understanding the nature of the policy choices facing European monetary authorities. Nevertheless, heightened international capital mobility (in isolation from other factors) is found to provide an incomplete explanation of certain key features of the European experience. Suggestions for further research are proposed with this in mind.
On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities

Abstract A 410 base-pair (bp) Sau 3A restriction fragment derived from a Leishmania tarentolae kinetoplast DNA minicircle, which is known to have slower than expected electrophoretic mobilities in polyacrylamide gels, has been cloned in a plasmid and deletions from one end of the cloned segment have been constructed. Analysis of the gel electrophoretic mobility data of a large number of restriction fragments derived from the kinetoplast DNA clone and its deletion subclones has led to the conclusion that two sequences, one in the region bp 100 to 170 and the other bp 190 to 250, both numbered from one end of the 410 bp kinetoplast DNA segment, are important for the abnormal gel electrophoretic behavior of the kinetoplast DNA fragment. One common feature of these sequences is the periodic presence of short runs of A residues (3 to 6 As in each); auto-correlation analysis of these runs of A residues shows a strong harmonic component with a period around 11 bp. These results support and extend the previous analysis of Wu & Crothers (1984). The abnormal electrophoretic behavior is accentuated at low temperature and by the addition of Mg 2+ to the electrophoresis buffer; addition of Na + has the opposite effect. Insertion of sequences derived from the kinetoplast DNA fragment into nicked circular DNA causes no unexpected change in its electrophoretic mobility in agarose gel. suggesting that the 410 bp sequence, or segments of it, has no significant spatial writhe. Abnormal shifts in agarose gel mobilities are observed, however, when certain segments of the kinetoplast DNA are inserted into positively or negatively supercoiled DNA topoisomers. These results are consistent with a bent structure of the kinetoplast DNA in which the bend has zero writhe in its undistorted form but is easily distorted.
The ν1 fundamental of HCCN: evidence for quasilinearity

Abstract The high resolution infrared spectrum of HCCN in the CH stretching region has been observed by infrared kinetic spectroscopy. In addition to the CH stretching fundamental, ν 1 , several hot bands associated with the bending vibrations have been observed. By measuring the intensity of the band, ν 1 + ν 5 − ν 5 , relative to the fundamental, the energy of ν 5 has been found to be 187 ± 20 cm − . This value is intermediate between that expected for a normal linear molecule and that expected for a bent molecule suggesting a very floppy HCX bending potential that is characteristic of a quasilinear molecule.
Staying in touch with normative reality

Ralph Wedgwood has, almost single-handedly, attempted to shoulder the burden that critics of Platonic non-naturalism have laid at its feet for years. If there are irreducible, non-natural normative facts, properties, and relations, critics have pressed, just where are they in the order of things? And if they are outside the natural, causal order, how can we come to know them, or refer to them, or be necessarily moved by them? The standard answer, "These facts are known a priori, by rational intuition", has only deepened the mystery. For, as Kant pointed out, normative truths would have substantive implications for thought and action, and so must be synthetic rather than analytic. But how could purely rational a priori intuition deliver knowledge of such truths? Wedgwood finds the Intuitionists' self-assurance about their contact with normative reality not much better than magical thinking, and therefore seeks to offer a fundamental philosophical explanation of "the nature of normative facts, properties, and relations" that provides an illuminating, recognizably Platonic response to these worries. Aware of the constraints imposed upon metaphysical accounts of the normative by supervenience, Wedgwood also aims to work within the assumptions of what he calls "moderate naturalism", according to which all the contingent facts in the world contingent normative facts included are "realized in facts of the sort that are studied by the natural sciences and physics". No brief commentary can do justice to the full sweep and ingenuity of The Nature of Normativity. Here I will confine myself to some of the issues that are the central focus of Part II, which is presented as the metaphysical portion of the story. However, the intricate, interlocking nature of this story will require me to venture a bit into the semantic and epistemological concerns that take up Parts I and III.
A Descriptive Taxonomy of Couples' Complaint Interactions.

Prior research on couples’ conversational complaints has focused almost exclusively on the types of responses dysfunctional couples manifest; it has failed to provide a complete description of the complaint interaction. This essay offers an overview of couples’ complaint behavior by describing couples’ complaint types, response types, complaint‐response sequencing, and the environment in which such complaining occurs. As well, differences in reported complaint behavior between males and females and between satisfied and dissatisfied couples are examined.
Analysis and optimization of Lipschitz continuous mappings

In this paper, four fundamental theorems for continuously differentiable mappings (the multiplier rule for equality constraints of Caratheodory, the inverse mapping theorem, the implicit mapping theorem, and the general multiplier rule for inequality and equality constraints of Mangasarian and Fromovitz) are shown to have natural extensions valid when the mappings are only Lipschitz continuous. Involved in these extensions is a compact, convex set of linear mappings called the generalized derivative, which can be assigned to any Lipschitz continuous mapping and point of its (open) domain and which reduces to the usual derivative whenever the mapping is continuously differentiable. After a brief calculus for this generalized derivative is presented in Part I, the connection between the ranks of the linear mappings in the generalized derivative and theinteriority of the given mapping is explored in Parts II and IV; this relationship is used in Parts III and IV to prove the extensions of the theorems mentioned above.
Release of calcium-45 from frog nerves during electrical activity.

Shanes and Bianchi1 have demonstrated that stimulation of frog sartorius muscle accelerates the release of calcium-45 loaded on muscles, although Harris2 had failed to observe this effect. Koketsu and Miyamoto3 recently confirmed an increase in the output of calcium-45 during muscle activity. An important problem remains, however, whether acceleration of calcium output during activity is caused by the mechanism specific of the contractile system or actually is responsible for the electrical membrane phenomena. Hodgkin and Keynes4 have reported that no change in calcium efflux can be detected during stimulation of squid axon, concluding that calcium movement during nervous activity is wholly inward. Furthermore, the 30-fold greater influx of calcium per impulse in muscle than in nerve despite the near equality of the resting influxes has been noted as consistent with a special role for calcium in contraction5.
Rapid assay for quantitative measurement of apoptosis in cultured cells and brain tissue

Analysis of apoptosis in brain tissue following ischemia, hypoxia, or oxidative stress has technical limitations. The use of counting cells displaying apoptotic morphology is time intensive, vulnerable to sampling errors, and suffers from low numbers of total recorded events. Other cell death assays such as agarose gel analysis of DNA fragmentation, TUNEL, or ELISA are time intensive, limited to a single endpoint measure, and can be technically difficult to perform or reproduce. To overcome these limitations, we set out to develop a technique using flow cytometry to measure apoptosis based on the physical properties of light scatter produced from isolated nuclei. This dye/marker free approach would bypass many of the inherent encumbrances and reproducibility problems found in other apoptosis assays. Here we demonstrate that this new technique, using flow cytometry performed on isolated nuclei, allows rapid quantitation of apoptosis in a variety of brain tissues without the need for intercalating dyes or fluorescent markers. We conclude that this technique significantly improves currently available protocols to quantify apoptosis from tissue and offers the possibility to perform additional analysis on the same population of nuclei via downstream assays.
Diagnosis of acute right ventricular infarction.

In acute inferior myocardial infarction (MI) due to right coronary artery occlusion, associated right ventricular infarction (RVMI) is best diagnosed by ST-segment elevation in an additional lead-precordial V4R. 1 Many studies and reviews have confirmed the value of lead V4R in recognizing RVMI and in prompting the clinical recognition of important hemodynamic consequences—systemic venous hypertension, clear lungs, and systemic hypoperfusion with low blood pressure. Appropriate therapy with intravenous fluid and inotropic agents is indicated. A variety of electrocardiogram (ECG) lead and display systems have been proposed as effective in capturing STsegment elevations not apparent in the standard 12-lead format. These include calculated epicardial potentials from 80-site body surface maps using a thoracic volume conductor model; a 24-lead system in which each of the standard 12 leads is inverted, producing an additional 12 leads for analysis, and various methods for predicting ECGs at nonrecorded sites from measured ECGs. An entire recent issue of Journal of Electrocardiology (volume 41 no. 3 May/ June 2008) was devoted to the lead system problem. None of the proposed techniques is widely accepted as yet or available in a standard commercial application. The addition of posterior (V7-V9) and right ventricular (V4R to V6R) leads in all suspected acute MI cases increased the sensitivity of diagnosis by 8.4%. In our method to rapidly identify acute RVMI, only a single additional lead (V4R) is recorded and that only if the word “inferior” has appeared in the computer diagnostic statement. Thus, no time is lost before a necessary V4R is
Microbial enzymatic activity and secondary production in sediments affected by the sedimentation pulse following the Deepwater Horizon oil spill

Abstract A large fraction of the spilled oil from the Deepwater Horizon (DwH) blowout in April 2010 reached the seafloor via sinking oil aggregates (oil snow) in a massive sedimentation that continued until late summer 2010 (“Dirty blizzard”). We measured heterotrophic microbial metabolic rates as well as porewater and sedimentary geochemical parameters at sites proximate to and distant from the wellhead to investigate microbial responses to the “Dirty Blizzard”. Lipase activity and rates of bacterial protein production were highest and leucine-aminopeptidase activity was lowest in 0–2 cm sediment layers at the sites proximate to the wellhead. These results suggest that the presence of the oil snow stimulated benthic microbial enzymatic hydrolysis of oil-derived organic matter that was depleted in peptide substrates at the time of our sampling. The strong gradients in porewater DOC, NH 4 + , and HPO 4 3− concentrations in the upper 6 cm of the sediments near the wellhead likewise indicate elevated heterotrophic responses to recently-sedimented organic matter. In addition to enhanced microbial activities in the 0–2 cm sediment layers, we found peaks of total organic carbon and elevated microbial metabolic rates down to 10 cm at the sites closest to the wellhead. Our results indicate distinct benthic metabolic responses of heterotrophic microbial communities, even three months after the ending of the “Dirty Blizzard”. Compared to other deep-sea environments, however, metabolic rates associated with the recently deposited particulate matter around the wellhead were only moderately enhanced. Oil contaminants at the seafloor may therefore have prolonged residence times, enhancing the potential for longer-term ecological consequences in deep-sea environments.
PIR: A Domain Specific Language for Multimedia Retrieval

Multimedia retrieval is a problem domain involving salient features extraction, machine learning, indexing, and retrieval. There are a variety of implementations for these tasks, which are difficult to compose and reuse due to the interface and language incompatibility. Because of this low reusability, researchers often have to implement their experiments from scratch and the resulting programs are not optimized for efficiency and cannot be easily adapted for parallelization. In this paper, we present PIR (Pipeline Information Retrieval), a domain specific language (DSL) for multimedia feature manipulation. The goal is to unify the programming tasks for feature-related programming in multimedia retrieval experiments by hiding the programming details under a flexible layer of domain specific interface. This DSL enables us to optimize the feature-related tasks by compiling the DSL programs into pipeline graphs, which can be executed using a variety of strategies to eliminate redundant computation and enable parallelization and change propagation.
Capuchins’ ( Cebus apella ) sensitivity to others’ goal-directed actions in a helping context

As humans, our ability to help others effectively is at least in part dependent upon our capacity to infer others' goals in a variety of different contexts. Several species of nonhuman primate have demonstrated that they will also help others in some relatively simple situations, but it is not always clear whether this helping is based on an understanding of another agent's goals. Although the results of a number of different studies support the hypothesis that chimpanzees represent others' goals in various helping contexts and are sensitive to these goals when actually helping others, less work has addressed whether more distantly related species actively represent goals when helping. To explore the cognitive mechanisms underlying helping behaviors in species less closely related to humans, we tested whether a species of New World monkey-the brown capuchin (Cebus apella)-would provide an experimenter with a desired out-of-reach object more often than an alternative object when the experimenter attempted to obtain the former object only. We found that capuchins reliably helped by providing the experimenter's goal object (Experiment 1) and that explanations based on the use of several less sophisticated strategies did not account for the overall pattern of data (Experiments 2-4). Results are thus consistent with the hypothesis that capuchins help others based on an understanding of their goals although more work is needed to address the possibility that capuchins may be responding to gestural and postural factors alone.
Fecal egg output of lambs in relationship to Haemonchus contortus burden.

Lejambre L. F., Ractliffe L. H., Uhazy L. S. & Whitlock J. H., 1971. Fecal egg output of lambs in relationship to Haemonchus contortas burden. International Journal for Parasitology, 1: 157–160. Variation among the egg counts of lambs infected with Haemonchus contortus was correlated with variation among the total weights of female worms harbored. The correlation was better than that between egg counts and numbers of worms.
A Novel CDX2 Isoform Regulates Alternative Splicing

Gene expression is a dynamic and coordinated process coupling transcription with pre-mRNA processing. This regulation enables tissue-specific transcription factors to induce expression of specific transcripts that are subsequently amplified by alternative splicing allowing for increased proteome complexity and functional diversity. The intestine-specific transcription factor CDX2 regulates development and maintenance of the intestinal epithelium by inducing expression of genes characteristic of the mature enterocyte phenotype. Here, sequence analysis of CDX2 mRNA from colonic mucosa-derived tissues revealed an alternatively spliced transcript (CDX2/AS) that encodes a protein with a truncated homeodomain and a novel carboxy-terminal domain enriched in serine and arginine residues (RS domain). CDX2 and CDX2/AS exhibited distinct nuclear expression patterns with minimal areas of co-localization. CDX2/AS did not activate the CDX2-dependent promoter of guanylyl cyclase C nor inhibit transcriptional activity of CDX2. Unlike CDX2, CDX2/AS co-localized with the putative splicing factors ASF/SF2 and SC35. CDX2/AS altered splicing patterns of CD44v5 and Tra2-β1 minigenes in Lovo colon cancer cells independent of CDX2 expression. These data demonstrate unique dual functions of the CDX2 gene enabling it to regulate gene expression through both transcription (CDX2) and pre-mRNA processing (CDX2/AS).
Employment‐at‐Will Statements: Perceptions of Job Applicants

Employers in the USA often use employment‐at‐will statements in the employment application process to minimize their vulnerability in post‐discharge litigation. Reports survey results of job seekers′ attitudes towards such statements. The findings suggest that applicants would prefer to join organizations that do not include employment‐at‐will statements in the application process and that job‐seekers′ perceptions of the greater risk involved, greater expectations of employees, and a lack of company concern regarding its employees would significantly influence their views of an employment‐at‐will organization.
Partial Liquid Ventilation(PLV) Reduces Early Inflammation in Hydrocarbon Aspiration Pneumonitis 207

Introduction-PLV has been investigated in a number of laboratory and clinical settings. Those studies demonstrate a general improvement in gas exchange and lung mechanics. We have shown a reduction in early inflammatory events following treatment of experimental acute lung injury (ALI) with PLV. Experimental models frequently do not mimic human disease. Furthermore, the onset of human disease is often more temporally remote than that seen in lab studies. Hydrocarbon aspiration is a clinically important cause of ALI associated with significant morbidity and cost. The timing of onset of injury in hydrocarbon aspiration is usually reliable. We hypothesized that timely intervention with PLV in this clinically relevant model of ALI would reduce the early inflammatory events. Methods-Six NZW rabbits were sedated and the trachea exposed under local anesthesia. The trachea was punctured under direct vision and kerosene (0.15-0.2 cc/kg) was injected. The rabbits were kept in 100% O2 spontaneously breathing until the p aO2 fell below 100 torr. At that point, they were randomized to receive PLV (FC-77, 3M Corp.) or conventional ventilation (CMV). The rabbits were supported with volume expanders and pressors as needed. Following 3 hours support, the animals were sacrificed and lung tissue was frozen at-70°C for subsequent batch analysis. The tissue was homogenized in buffered saline, ultrasonified, freeze thawed and clarified. Protein content was determined by the BCA method. Myeloperoxidase activity (MPO) was determined in the supernatants in conventional fashion with o-dianisidine and H2O2 by spectrophotometry over 1 minute. Blood gases (ABG) were determined throughout the study. Average p aO2 for the last hour is presented. The data were analyzed by t-test. Results- In general, the PLV treated rabbits tended to have a higher paO2. The histologic appearance of the PLV treated lungs indicated less severe injury. Table
Efficacy and safety concerns are important reasons why the FDA requires multiple reviews before approval of new drugs

The regulatory approval of new drugs by the Food and Drug Administration (FDA) is a long and complex process and often requires multiple cycles of review, potentially delaying patients’ access to new and effective therapeutics. We used qualitative methods to characterize the safety and efficacy reasons why applications for novel therapeutics approved by the FDA between 2001 and 2011 required multiple review cycles prior to approval. Among ninety-six applications approved between 2001 and 2011 that required multiple review cycles, safety concerns contributed to seventy-four (77.1 percent) and efficacy concerns to forty-three (44.8 percent). Our study suggests that multiple review cycles appear to play an important role in allowing the FDA to protect public health and in ensuring adequate understanding of clinical benefits and risks prior to approval.
Testicular descent and ascent in the first year of life

Ascent of the intrascrotal testis to an undescended position has been described, but it remains controversial. A case of a 1-year-old with bilateral ascended testes is presented. These testes were documented by a pediatric urologist to have been intrascrotal on two prior occasions. The right testis was intra-abdominal, and the left was peeping at the internal ring. Ascent has generally been seen in older children with a history of retractile testis and has never been reported to result in a testis located in an intra-abdominal position. This represents a rarely reported early testicular ascent, the mechanism of which is different than that of older children.
Correlations between Analyses and Forecasts of Banded Heavy Snow Ingredients and Observed Snowfall

Abstract North American Mesoscale (NAM) model forecasts of the occurrence, magnitude, depth, and persistence of ingredients previously shown to be useful in the diagnosis of banded and/or heavy snowfall potential are examined for a broad range of 25 snow events, with event total snowfall ranging from 10 cm (4 in.) to over 75 cm (30 in.). The ingredients examined are frontogenetical forcing, weak moist symmetric stability, saturation, and microphysical characteristics favorable for the production of dendritic snow crystals. It is shown that these ingredients, previously identified as being critical indicators for heavy and/or banded snowfall in major storms, are often found in smaller snowfall events. It is also shown that the magnitude, depth, and persistence of these ingredients, or combinations of these ingredients, appear to be good predictors of event total snowfall potential. In addition, a relationship is demonstrated between temporal trends associated with one of the ingredients (saturated, geostro...
Nutrient stimulation of spore settlement in the kelpsPterygophora californica andMacrocystis pyrifera

FertilePterygophora californica Rupr. andMacrocystis pyrifera (L.) C.Ag. were collected in California, USA, from 1987 to 1989. Settlement activity of the spores was stimulated by nutrients, but this was not constant over time. Nutrients had no effect on the settlement ofP. californica spores between 2 and 18 h after sunrise, but settlement activity was stimulated by a nutrient mixture between 20 and 24 h after sunrise (14 to 18 h after release). Settlement activity inM. pyrifera spores was unaffected at 2 to 3 h after release, but settlement activity was significantly stimulated from 5 to 12 h after release. A variety of individual nutrients significantly stimulated settlement in 8 to 9 h oldM. pyrifera spores: ammonium, nitrate, glycine, phosphate, manganese-EDTA (18µM), borate, ferrous iron-EDTA, and ferric iron-EDTA. Spores also settled readily in unenriched artificial seawater, and nutrient-stimulated settlement rates were usually ≤150% of the unenriched control levels. Neither EDTA alone, cobalt-EDTA, nor manganese-EDTA (2µM) had significant effects onM. pyrifera spore settlement. The effects of time and of several individual nutrients on spore settlement activity are different from previously reported chemotactic effects of nutrients onP. californica andM. pyrifera spores. It is suggested that nutrient settlement-stimulation is mechanistically different from nutrient chemotaxis. However, like chemotaxis, settlement stimulation is probably an adaptation which increases the likelihood of spore settlement in microhabitats suitable for subsequent growth and reproduction of gametophytes.
Pathological calcifications studied with micro-CT

The microstructure of pathological biomineral deposits has received relatively little attention, perhaps, in part because of the difficulty preparing samples for microscopy. MicroCT avoids these difficulties, and laboratory microCT results are reviewed for aortic valve calcification (human as well as a rabbit model), for human renal calculi (stones) and for calcinoses formed in juvenile dermatomyositis (JDM). In calcified aortic valves of rabbits, numerical analysis of the data shows statistically significant correlation with diet. In a large kidney stone the pattern of mineralization is clearly revealed and may provide a temporal blueprint for stone growth. In JDM calcified deposits, very different microstructures are observed and may be related to processes unique to this disease.
Reducing indirect function call overhead in C++ programs

Modern computer architectures increasingly depend on mechanisms that estimate future control flow decisions to increase performance. Mechanisms such as speculative execution and prefetching are becoming standard architectural mechanisms that rely on control flow prediction to prefetch and speculatively execute future instructions. At the same time, computer programmers are increasingly turning to object-oriented languages to increase their productivity. These languages commonly use run time dispatching to implement object polymorphism. Dispatching is usually implemented using an indirect function call, which presents challenges to existing control flow prediction techniques.We have measured the occurrence of indirect function calls in a collection of C++ programs. We show that, although it is more important to predict branches accurately, indirect call prediction is also an important factor in some programs and will grow in importance with the growth of object-oriented programming. We examine the improvement offered by compile-time optimizations and static and dynamic prediction techniques, and demonstrate how compilers can use existing branch prediction mechanisms to improve performance in C++ programs. Using these methods with the programs we examined, the number of instructions between mispredicted breaks in control can be doubled on existing computers.
Disease candidate gene identification and prioritization using protein interaction networks

Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses. For the first time, extended versions of the PageRank and HITS algorithms, and the K-Step Markov method are applied to prioritize disease candidate genes in a training-test schema. Using a list of known disease-related genes from our earlier study as a training set ("seeds"), and the rest of the known genes as a test list, we perform large-scale cross validation to rank the candidate genes and also evaluate and compare the performance of our approach. Under appropriate settings – for example, a back probability of 0.3 for PageRank with Priors and HITS with Priors, and step size 6 for K-Step Markov method – the three methods achieved a comparable AUC value, suggesting a similar performance. Even though network-based methods are generally not as effective as integrated functional annotation-based methods for disease candidate gene prioritization, in a one-to-one comparison, PPIN-based candidate gene prioritization performs better than all other gene features or annotations. Additionally, we demonstrate that methods used for studying both social and Web networks can be successfully used for disease candidate gene prioritization.
Diverse mechanisms of post‐transcriptional repression by the small RNA regulator of glucose‐phosphate stress

The Escherichia coli small RNA SgrS controls a metabolic stress response that occurs upon accumulation of certain glycolytic intermediates. SgrS base pairs with and represses translation of ptsG and manXYZ mRNAs, which encode sugar transporters, and activates translation of yigL mRNA, encoding a sugar phosphatase. This study defines four new genes as direct targets of E. coli SgrS. These new targets, asd, adiY, folE and purR, encode transcription factors or enzymes of diverse metabolic pathways, including aspartate semialdehyde dehydrogenase, arginine decarboxylase gene activator, GTP cyclohydrolase I and a repressor of purine biosynthesis, respectively. SgrS represses translation of each of the four target mRNAs via distinct mechanisms. SgrS binding sites overlapping the Shine-Dalgarno sequences of adiY and folE mRNAs suggest that SgrS pairing with these targets directly occludes ribosome binding and prevents translation initiation. SgrS binding within the purR coding sequence recruits the RNA chaperone Hfq to directly repress purR translation. Two separate SgrS binding sites were found on asd mRNA, and both are required for full translational repression. Ectopic overexpression of asd, adiY and folE is specifically detrimental to cells experiencing glucose-phosphate stress, suggesting that SgrS-dependent repression of the metabolic functions encoded by these targets promotes recovery from glucose-phosphate stress.
Therapists’ Perceptions of Pediatric Occupational Therapy Interventions in Self-Care

Objectives This study examined the congruence between pediatric occupational therapists' self-care interventions and occupational therapy's philosophical base, which focuses on performance of self-care skills as primary in evaluation and intervention. Method A questionnaire was mailed to 252 therapists serving children ages birth to 6 years. The questionnaire asked for therapists' perceptions about the importance, uniqueness, and frequency of 10 areas of intervention, including self-care. Results Perceived importance of self-care was found to be strongly related to perceived frequency of self-care intervention. Practice setting was significantly associated with perceptions of uniqueness of self-care, and team membership status was significantly associated with importance of self-care. Most respondents perceived self-care intervention to be important (86%) and unique (80%) to occupational therapy. Seventy percent regularly provided intervention for self-care. Conclusions The therapists' perceptions reflected continued regard for self-care as an important and unique area of pediatric occupational therapy but were somewhat discrepant with the actual frequency of self-care interventions.
Redirecting the inactivation pathway of penicillin amidase and increasing amoxicillin production via a thermophilic molecular chaperone.

We have previously shown that a single-subunit thermosome from Methanocaldococcus jannaschii (rTHS) can stabilize enzymes in semi-aqueous media (Bergeron et al., 2008b). In the present study, rTHS was used to stabilize penicillin amidase (PGA) in methanol–water mixtures. Including methanol in the reaction medium for amoxicillin synthesis can suppress unwanted hydrolysis reactions but inactivate PGA. Inactivation and reactivation pathways proposed for PGA illustrate the predictability of enzyme stabilization by rTHS in co-solvents. Calcium was necessary for reversible dissociation of the two PGA subunits in methanol–water and the presence of calcium resulted in an enhancement of chaperone-assisted stabilization. rTHS also acted as a stabilizer in the enzymatic synthesis of the β-lactam antibiotic amoxicillin. rTHS stabilized PGA, increasing its half-life in 35% methanol by fivefold at 37°C. Stabilization by rTHS was enhanced but did not require the presence of ATP. Including rTHS in fed-batch reactions performed in methanol–water resulted in nearly 4 times more amoxicillin than when the reaction was run without rTHS, and over threefold higher selectivity towards amoxicillin synthesis compared to aqueous conditions without rTHS. The thermosome and other thermophilic chaperones may thus be generally useful for stabilizing enzymes in their soluble form and expanding the range of conditions suitable for biocatalysis. Biotechnol. Bioeng. 2009;102: 417–424. © 2008 Wiley Periodicals, Inc.