cssi/SciSciGPT-SciSciNet huggingface dataset:
The hypothalamus in parkinson's disease

It is currently believed that Parkinson disease (PD) is due to a degenerative process that independently damages multiple areas of the central and peripheral nervous system. Loss of nigrostriatal dopamine is now widely recognized as being directly related to the motor symptoms in Parkinson's disease. Parkinsonian patients also exhibit symptoms and signs suggestive of hypothalamic dysfunction (e.g. dysautonomia, impaired heat tolerance). The latter clinical features are supported by pathological, biochemical and endocrinological findings. Lewy body formation has been demonstrated in every nucleus of the hypothalamus, specifically the tuberomamillary and posterior hypothalamic. Preferential involvement of the hypothalamus was also noted in patients after post-encephalitic parkinsonism. Loss of dopamine (30–40%) in the hypothalamus of affected patients has been shown in recent studies, and is compatible with the reported abnormalities of growth hormone release in response to L-dopa administration, elevated plasma levels of MSH, and reduced CSF levels of somatostatin and beta-endorphins in these patients. Deranged immunological mechanisms have been found in PD patients including the presence of autoantibodies against sympathetic ganglia neurons, adrenal medulla and caudate nucleus. On the evidence of on pathological studies demonstrating the early vulnerability of the hypothalamus in aging and PD, and the known role of the hypoth lamus in immune modulation, we expect that it will be shown that primary damage ot the hypothalamus leads to subsequent secondary degeneration of structures receiving direct projections from the hypothalamus. Within this framework, the dopaminergic systems may be damaged, since striatal dopamine synthesis and receptor sensitivity have been shown to be regulated by ACTH and alpha-MSH through direct arcuate nucleus-striatal projections. We also demonstrate that virtually all other areas well known to be impacted upon in Parkinson disease receive significant hypothalamic peptidergic projections.
“Kissing” Vegetation in a Rare Case of Infective Endocarditis by Gemella sanguinis

Infective endocarditis (IE) is usually caused by Streptococcus, Staphylococcus or Enterococcus species or slow-growing HACEK organisms. We report an extremely rare case of IE caused by Gemella sanguinis.
Combustion products of 1,3-butadiene inhibit catalase activity and induce expression of oxidative DNA damage repair enzymes in human bronchial epithelial cells.

1,3-Butadiene, an important petrochemical, is commonly burned off when excess amounts need to be destroyed. This combustion process produces butadiene soot (BDS), which is composed of a complex mixture of polycyclic aromatic hydrocarbons in particulates ranging in size from <1 μm to 1 mm. An organic extract of BDS is both cytotoxic and genotoxic to normal human bronchial epithelial (NHBE) cells. Based on the oxidizing potential of BDS, we hypothesized that an organic extract of this particulate matter would (1) cause enzyme inactivation due to protein amino acid oxidation and (2) induce oxidative DNA damage in NHBE cells. Thus, our aims were to determine the effect of butadiene soot ethanol extract (BSEE) on both enzyme activity and the expression of proteins involved in the repair of oxidative DNA damage. Catalase was found to be sensitive to BDS as catalase activity was potently diminished in the presence of BSEE. Using Western analysis, both the alpha isoform of human 8-oxoguanine DNA glycosylase (α-hOGG1) and human apurinic/apyrimidinic endonuclease (APE-1) were shown to be significantly overexpressed as compared to untreated controls after exposure of NHBE cells to BSEE. Our results indicate that BSEE is capable of effectively inactivating the antioxidant enzyme catalase, presumably via oxidation of protein amino acids. The presence of oxidized biomolecules may partially explain the extranuclear fluorescence that is detected when NHBE cells are treated with an organic extract of BDS. Overexpression of both α-hOGG1 and APE-1 proteins following treatment of NHBE cells with BSEE suggests that this mixture causes oxidative DNA damage.
Assessing behavioral toxicity with Caenorhabditis elegans

Behavior, even in simple metazoans, depends upon integrated processes at the subcellular, cellular, and organismal level, and thus is susceptible to disruption by a broad spectrum of chemicals. Locomotor behavior (movement) of the small free-living nematode Caenorhabditis elegans has proven to be useful in assessing toxicity. Recently reported observations suggest that behavioral change (reduced movement) occurs after 4 h of exposure to heavy metals, and that with abbreviated exposure, the concentration-response relationship for Pb (a known neurotoxic metal) differs from that for Cu. In this study, movement was evaluated after 4-h exposures for nine compounds from three chemical classes: organic pesticides, organic solvents, and heavy metals. Concentration-dependent reduction of movement was observed for all test compounds with the exception of mebendazole, for which test concentrations were limited by solubility. Within each chemical class, movement was more sensitive to the neurotoxic compounds than to substances not believed to be neurotoxic, as evidenced by behavioral effective concentration to reduce average worm movement to 50% of the control movement values (e.g., levamisole and chlorpyrifos < mebendazole, ethanol and acetone < dimethylsulfoxide, and Pb and Al < Cu). These observations are discussed as they relate to the use of acute behavioral tests in assessing general chemical toxicity, and the enhanced value of 4-h testing for the detection of neural toxicants.
ScGaN alloy growth by molecular beam epitaxy: Evidence for a metastable layered hexagonal phase

Alloy formation in $\mathrm{ScGaN}$ is explored using rf molecular beam epitaxy over the $\mathrm{Sc}$ fraction range $x=0--100%$. Optical and structural analysis show separate regimes of growth, namely (I) wurtzitelike but having local lattice distortions in the vicinity of the ${\mathrm{Sc}}_{\mathrm{Ga}}$ substitutions for small $x\phantom{\rule{0.2em}{0ex}}(x\ensuremath{\leqslant}0.17)$, (II) a transitional regime for intermediate $x$, and (III) cubic, rocksaltlike for large $\phantom{\rule{0.2em}{0ex}}x(x\ensuremath{\geqslant}0.54)$. In regimes I and III, the direct optical transition decreases approximately linearly with increasing $x$ but with an offset over region II. Importantly, it is found that for regime I, an anisotropic lattice expansion occurs with increasing $x$ in which $a$ increases much more than $c$. These observations support the prediction of Farrer and Bellaiche [Phys. Rev. B 66, 201203-1 (2002)] of a metastable layered hexagonal phase of $\mathrm{ScN}$, denoted $h\text{\ensuremath{-}}\mathrm{ScN}$.
Monoclonal gammopathies and associated skin disorders

The monoclonal gammopathies are characterized by clonal proliferation of plasma cells and other clonally related cells in the B-cell lineage. These disorders include monoclonal gammopathy of undetermined significance, multiple myeloma, Waldenstrom macroglobulinemia, heavy chain diseases, plasmacytoma, and primary amyloidosis. Many skin disorders have been described in association with monoclonal gammopathies. This article provides an introduction to the definition, detection, natural course, and spectrum of monoclonal gammopathies and a brief discussion of pathogenesis. The article also reviews the skin disorders associated with monoclonal gammopathies, categorizes the association, and evaluates the strength of the association.
Doubts about the uselessness of men and the meaning of the civilizing process

The discussion between de Swaan and Alt bears on but conflates two issues of considerable import. One, the agoraphobia problematic, has importance because it touches on that intimate savagery now blandly described as "the relations between the sexes". The second is the "civilizing process," a term of uncertain irony, with which Norbert Elias characterizes the emergence of our modem era. While connected, the two are scarcely more identical than a cat and dog who become blurred in battle. The civilizing process is, we might say with only a touch of indelicacy, Norbert Elias's somewhat belated entry into the Dijon contest that Rousseau won when, against the common sense of his time and the optimism of its philosophes, Rousseau churlishly insisted that modern progress was not of one piece and that the new burgeoning of the sciences and arts did not necessarily entail a civilizing cultivation of human manners and relationships. Marx was later to submit a convergent report in the idiom of political economy, observing that the advance of technology was accompanied by a growing reserve army of the unemployed and a spreading alienation.
Osteochondroma of the hip with adjacent bursal chondromatosis

It is well established that irregular bursae can form adjacent to an osteochondroma (bursa exostotica) as a result of mechanical irritation and that these bursae can be complicated by inflammation, hemorrhage, or infection. Bursal chondromatosis is a rare complication, with only seven published cases in the literature according to our searches. We present the case of a 53-year-old female who presented with slowly progressive left hip/thigh pain and was found to have an osteochondroma arising from the lesser trochanter with numerous ossified bodies in the adjacent soft tissues. MRI demonstrated osteochondral bodies in a fluid-filled bursa adjacent to the osteochondroma, with several of the bodies noted to be fairly displaced from the osteochondroma cartilaginous cap. At surgery, the osteochondroma was removed and numerous bodies of varying sizes were excised, some of which were noted to be adherent to the bursal lining and others that were separated/distant from the cartilage cap. The question arises as to whether this process represents bursal chondromatosis resulting from benign neoplasia of cells lining the abnormal bursa, “cartilage shedding” from the osteochondromatous cap, or both. The purpose in presenting this case is to introduce a rare complication of an osteochondroma, demonstrate that soft tissue calcification and osteochondral densities displaced from an underlying osteochondroma are not always the result of sarcomatous degeneration, and provide support for the theory that cells lining a bursa in a nonphysiologic location can undergo benign neoplasia with subsequent formation of osteochondral bodies.
Epicuticular lipid composition of the sand cockroach, Arenivaga investigata

Abstract 1. 1. The epicuticular lipids of A. investigata are predominently wax esters and hydrocarbons. 2. 2. The wax esters range from C-40 to C-54 and are all of even chain length. 3. 3. The hydrocarbons range from C-27 to C-32 in chain length with normal alkanes, internally branched alkanes and 5-methyl alkanes present. The predominant hydrocarbons have an odd number of carbons in the chain.
Polygonal cracking in coarse clastics records cold temperatures in the equatorial Fountain Formation (Pennsylvanian–Permian, Colorado)

Abstract Sand- and granule-filled polygonal fractures are present on bedding surfaces within the equatorial Fountain Formation (Pennsylvanian–Permian, Colorado). The surfaces are areally extensive (> 120,000 m2) and occur within inferred braided braided-river deposits. The fractures penetrate downward into coarse sandstone to granule conglomerate and range from 3–55 cm to 13–> 220 cm in width and depth, respectively. At one locality (Manitou Springs), both fracture fill and polygon interiors display a grain-supported texture and contain The polygonal fractures formed as frozen ground experienced thermal contraction induced by repeated cooling events. Owing to the equatorial location of the Fountain Formation, we suggest that diurnal, rather than seasonal, temperature variations provided the repeated cooling mechanism. Alternative causes of polygonal fracturing, such as desiccation of clay-rich sediments or thermal contraction of evaporite minerals, are untenable because the hosting strata contain minimal clay (
Image Intensity Ratio, a Novel Magnetic Resonance-Based Measure for Quantification of Left Atrial Fibrosis, Correlates with the Distribution of Atrial Bipolar Voltage

Background Recurrence of atrial fibrillation (AF) after catheter ablation has been associated with left atrial (LA) fibrosis. However, arbitrary units of measure limit the interpatient comparison of delayed enhancement intensity. We sought to quantify LA fibrosis using a novel normalized measure: the image intensity ratio (IIR) of late-gadolinium enhanced magnetic resonance imaging (LGE-MRI). Methods LGE-MRI images (1.5 Tesla) were obtained in 30 patients (37% female, mean age 62 ± 8) prior to first (60%), second (23%), or third (17%) ablation procedure for AF. Multiplanar reformatted images were reconstructed from the stack of 3-D axial image data. Epicardial and endocardial contours were manually drawn around LA myocardium. The IIR, defined as local LA myocardial signal intensity divided by the mean LA blood pool image intensity, was measured for each of 20 sectors created on contiguous axial planes through the LA. Electroanatomic map (EAM) points were registered to the corresponding LGE-MRI images using custom software. Results A total of 2569 EAM points were analyzed. The average bipolar voltage was 0.9 ± 1.0 mV (0.5 between and 0.9 within patient standard deviation). Local IIR was strongly associated with bipolar voltage (Figure, P P Conclusions Higher IIR values were observed in areas with lower bipolar voltage on EAM. The IIR obtained from LGE-MRI may improve the quantification of LA fibrosis
Role of testosterone in maintaining lean body mass and bone density in HIV-infected patients

Low testosterone levels are common in both men and women with human immunodeficiency virus (HIV) infection and may contribute to loss of lean body mass and AIDS wasting. Causes of low testosterone levels are complex and may include chronic illness, HIV infection and its complications, medications used to treat HIV and opportunistic diseases, and normal aging-related declines. In the majority of studies addressing the use of testosterone treatment in HIV-infected patients, testosterone has been found to help prevent loss of lean body and muscle mass. Whether the combination of exercise and testosterone is more effective in preventing loss of lean body mass than either therapy alone is not yet clear and warrants further study. In addition to its effects on body composition, testosterone treatment results in improved mood and libido in HIV-infected women and increased bone mineral density in HIV-infected men. Testosterone may thus make a valuable contribution to the treatment of HIV-infected individuals.
Scattering Tomography and Its Application to Sooting Diffusion Flames

A new analytical tomographic reconstruction technique was developed for the determination of the extinction and scattering coefficient distributions in axisymmetric media. This method, called [open quotes]scattering tomography,[close quotes] was tested for several particle concentration profiles corresponding to those for diffusion flames. After that, a series of experiments were performed on sooting acetylene flames using an argon-ion laser nephelometer. The experimental results were reduced using both the transmission and scattering tomography techniques to obtain the extinction coefficient profiles. It was shown that in the center of the flame, the results from these two approaches were in good agreement. Scattering tomography can be used to determine both the absorption and scattering coefficient distributions in the medium. In addition to that, it is preferable over the transmission tomography if the medium is optically very thin and particles are predominantly scattering. 20 refs., 10 figs.
`SHG-labels' for detection of molecules by second harmonic generation

Abstract The concept and technique of `SHG-labels' are introduced. SHG-labels are second harmonic-active moieties which can be attached to some molecule or particle of interest that is not SH-active, in order to render the molecule amenable to study at an interface. The labeled molecules may then be studied by surface-selective techniques such as second harmonic generation (SHG) or sum-frequency generation. In the first example of the technique, a protein, cytochrome c, was labeled with sulfhydryl- or amine-specific SH-active dyes. SHG-labels should find use in studying a variety of interfacial reactions.
Mineralization of Bacterial Cell Mass on a Photocatalytic Surface in Air

Whole cells deposited on a titanium dioxide-coated surface have been oxidized in air to carbon dioxide via photocatalysis. This paper provides the first evidence that the organic matter in whole cells can be completely oxidized. Three experimental techniques were employed to monitor this reaction: scanning electron microscopy,14C radioisotope labeling, and batch reactor measurements. The scanning electron microscopy experiments illustrate the disappearance of Escherichia coli cell mass. The 14C radioisotope labeling experiments establish that the carbon content of E. coli is oxidized to form carbon dioxide with substantial closure of the mass balance. The batch reactor experiments corroborate the mass balance and provide a preliminary indication of the rate of the oxidation reaction. These results provide evidence that a photocatalytic surface used for disinfection can also be self-cleaning in an air−solid system.
DIET, NUTRIENTS, AND GASTROINTESTINAL CANCER

Tobacco and alcohol use are strong risk factors for cancer of the upper gastrointestinal tract. Saturated fat and red meat intake also appear to increase the risk of colorectal cancer. The strongest and most consistent dietary protective factors for gastrointestinal cancer are vegetables and fruits. Some micronutrients show beneficial effects, but the degree of protection is less than that observed from whole plant foods. Substantial decreases in the morbidity and mortality from gastrointestinal cancer could occur with more widespread adoption of dietary guidelines designed for cancer prevention.
A dynamic determination of the anisotropy field and the damping constant of thick magnetic films

A new dynamic method for the measurement of H k and the damping constant T of thick magnetic films is presented from both the theoretical and practical standpoint. The method is based on a property of the differential equation (1), which has been found to be adequate if applied to the read cycle. It is found that, if the easy-axis sense signals obtained with linearly rising hard-axis fields of different rise times are plotted vs. the respective hard-axis fields, the maxima of the sense signals lie almost precisely on a straight line. This straight line cuts the field axis at H k . From the slope of this line it is possible to deduce T , which is primarily the eddy-current time constant for thick films. The resistivity of the magnetic material can, in this case, be evaluated directly if the physical dimensions of the film are known. The influence of dispersion and skew is discussed and found to be reasonably small. The further advantages are that no instrumental integration is needed and that the reading is quite precise. Small variations of H k can, therefore, be easily recorded. Practical results obtained with thick magnetic films illustrate this method.
Which physicians are at high risk for needlestick injuries

One thousand fifty-three incidents of needlestick injuries (from hypodermic and suture needles) were reported to the workmen’s compensation insurance at the University of Texas Medical Branch Hospitals in Galveston, Tex., from Nov. 1, 1984, to Jan. 31, 1989 (Table1). The nursing staff was involved in 61.6% of injuries, whereas physicians were involved in 6.7%. The resident staff had 78.9% and the faculty had 21 .l% of the injuries involving physicians. The average annual incidence rate of needleprick injuries per person for residents was 3.1 times that for faculty members. The distribution of needle injuries to physicians, according to department and site of occurrence, was analyzed (Tables 2 and 3). The Department of Anesthesiology reported 22.5% of the cases, followed by the departments of internal medicine (19.2%), surgery (13.7%), radiology (9.6%), and ophthalmology (9.6%). The highest incidence of needle injuries relative to the number of employees was found in the Department of Ophthalmol-
Coupled heat and mass transfer by natural convection from vertical surfaces in porous media.

Abstract Similarity solutions for buoyancy induced heat and mass transfer from a vertical plate embedded in a saturated porous medium are reported for (1) constant wall temperature and concentration, (2) constant wall heat and mass flux. In addition, the effect of flow injection on the heat and mass transfer has also been considered. Governing parameters for the problem under study are the buoyancy ratio, N, and Lewis number, Le. Depending on the sign of the buoyancy ratio, inclusion of a concentration gradient may either assist or suppress the flow induced by thermal buoyancy. The Lewis number is found to have a more pronounced effect on the concentration field than it does on the flow and temperature fields. Results for Nusselt and Sherwood numbers cover a wide range of the governing parameters, −1
Genetic Stratigraphy of Uranium Host Facies, Tordilla Sandstone Member, Upper Jackson Group, Panna Maria, Texas: ABSTRACT

Uranium mineralization in the Panna Maria, Texas, area occurs in the Tordilla Sandstone Member of the Eocene upper Jackson Whitsett Formation on the reduced side of a linear alteration front that extends more than 3 mi (5 km) along strike. Two open-pit mines at Panna Maria expose parts of a strike-oriented sand belt associated with a barrier island-tidal inlet system. The east pit exposes (1) a tidal inlet-embayment entrance, overlain by (2) tidal-channel, and (3) tidal-flat facies. The inlet facies, the uranium host, is dominantly fine to very fine sand End_Page 759------------------------------ with multidirectional trough and planar cross-bedding, Ophiomorpha sp., rounded mud clasts, and mud blocks. The tidal channel cuts through tidal-flat deposits, is approximately 40 m wide and 11 m thick, and contains gently dipping accretion beds of fine to very fine sand, including small-scale cross-stratification, and upwardly decreasing sand bed thickness. The lithology and sedimentary structures of facies 3 strongly resemble classic tidal-flat deposits of the Wadden Sea. The west pit exposes a regressive sequence of (1) tidal-inlet fill, (2) a poorly represented upper shoreface-beach-barrier flat facies, overlain by (3) bay-lagoon deposits. The inlet facies of fine to very fine sand includes large-scale, low-angle planar cross-beds, Ophiomorpha sp., bipolar, planar cross-beds, and has a scoured base. Some zones are highly burrowed. Facies 2 consists of trough and planar cross-bedded fine to very fine sand, with low-angle parallel bedding, root traces, and woody fragments near a hummocky upper surface. Facies 3 includes an ashy, burrowed lignite overlain by a massive, burrowed clayey siltstone containing plant debris. Facies 1 and 2, as well as the base of the lignite bed, are uranium bearing. End_of_Article - Last_Page 760------------
Optical imaging of mitochondrial function uncovers actively propagating waves of mitochondrial membrane potential collapse across intact heart

Polarization of the mitochondrial membrane potential (DeltaPsi(m)) is critical for normal mitochondrial function and cellular energetics. Mitochondrial dysfunction, manifesting as disrupted DeltaPsi(m) polarization (i.e. depolarization or hyperpolarization), underlies several important and highly prevalent diseases, including a variety of cardiac and neurological disorders. As such, DeltaPsi(m) instability might form a unifying mechanism for a class of metabolic disorders affecting excitable tissues. Here, we measured the spatio-temporal kinetics of DeltaPsi(m) changes across the intact heart using high-resolution optical DeltaPsi(m) imaging and uncovered surprisingly complex spatial patterns and dynamically fluctuating changes in DeltaPsi(m) that developed into actively propagating waves of mitochondrial depolarization during global ischemia. Our data further indicated that the recovery of DeltaPsi(m) upon reperfusion is dictated by the duration of the preceding ischemic insult. Post-ischemic electrical and functional recovery was dependent on early DeltaPsi(m) recovery but independent of overall cellular injury measured using a standard assay of lactate dehydrogenase release. These findings reveal a novel mechanism by which instabilities in cellular energetic properties that are independent of irreversible cellular injury can scale to the level of the intact organ via an organized process of active conduction involving the multi-cellular network. This highlights the importance of investigating cellular metabolic properties in the context of the intact organ.
The Effects of Physical Processes on the Hadley Circulation.

The Hadley cell is involved in the energy, momentum and moisture budgets in the atmosphere; it may be expected to change as sources and sinks of these quantities are altered due to climate perturbations. The nature of the Hadley cell change is complicated since alterations in one budget generally result in alterations in the others. Thus, Hadley cell sensitivity needs to be explored in an interactive system. In the GISS GCM (model I), a number of experiments are performed in which physical processes in each of the three budgets are omitted, the system adjusts, and the resultant circulation is compared to that of the control run. This procedure highlights which effects are most important and reveals the nature of the various interactions. The results emphasize the wide variety of processes that appear capable of influencing the mean circulation. The intensity of the circulation is related to the coherence of the thermal forcing, and to the thermal opacity of the atmosphere. When all frictional forcing is removed, the circulation is restricted to the equatorial region. The latitudinal extent appears to be controlled primarily by eddy processes (Ferrel cell intensity). The implications for climate modeling and climate projections (e.g. rainfall changes) are discussed.
Efficient floor-planning methodology for the Jasper Forest SoC on a 45 nanometer process

Floor-planning is usually one of design bottleneck for physical design convergence. For a complex SoC such as Jasper Forest, being concurrently developed and integrated with a leading edge CPU (Nehalem), floor-planning becomes even a bigger challenge to convergence on a very tight schedule. This paper highlights the floor-plan methodology and implementation details for Jasper Forest, with 782 million transistors, optimized for a 45 nm process. The methodology features an abutment LEGO structure floor-plan partitioning, a hybrid look-ahead floor-planning methodology, a semi-custom global clock tree construction, and Correct-by-Construction practices. These unique and innovative floor-planning methods enabled us to appropriately decouple complex design processes, minimize design dependencies, avoid non value added steps, and reduce the number of iterations to achieve the business goal of fast turnaround time with fewer resources1.
Cultivar Preference and Genotype Distribution of the Brown Stem Rot Pathogen Phialophora gregata in the Midwestern United States

ABSTRACT Brown stem rot (BSR), caused by Phialophora gregata f. sp. sojae, is an important yield-limiting disease of soybean (Glycine max) in the midwestern United States. Midwestern populations of P. gregata are separated into genotypes A and B based on intergenic spacer sequences of nuclear ribosomal DNA. Genotype A causes both leaf and stem symptoms, and genotype B typically causes internal stem symptoms only. Data are limited on the geographic distribution of genotypes A and B. It is not well understood whether cultivars may be infected preferentially by a genotype. Field plots were established at five sites in Illinois, three sites in Wisconsin, and two sites in Minnesota in two different years. Soybean cvs. Bell, BSR101, Dwight, Sturdy, Williams 82, LN92-12033, and LN92-12054 were sown with two to four replications at each field site. From each plot, 5 to 10 stems were harvested arbitrarily at the R8 growth stage and assayed by polymerase chain reaction to detect the A and B genotypes. Both pathogen...
Whole-Genome Thermodynamic Analysis Reduces siRNA Off-Target Effects

Small interfering RNAs (siRNAs) are important tools for knocking down targeted genes, and have been widely applied to biological and biomedical research. To design siRNAs, two important aspects must be considered: the potency in knocking down target genes and the off-target effect on any nontarget genes. Although many studies have produced useful tools to design potent siRNAs, off-target prevention has mostly been delegated to sequence-level alignment tools such as BLAST. We hypothesize that whole-genome thermodynamic analysis can identify potential off-targets with higher precision and help us avoid siRNAs that may have strong off-target effects. To validate this hypothesis, two siRNA sets were designed to target three human genes IDH1, ITPR2 and TRIM28. They were selected from the output of two popular siRNA design tools, siDirect and siDesign. Both siRNA design tools have incorporated sequence-level screening to avoid off-targets, thus their output is believed to be optimal. However, one of the sets we tested has off-target genes predicted by Picky, a whole-genome thermodynamic analysis tool. Picky can identify off-target genes that may hybridize to a siRNA within a user-specified melting temperature range. Our experiments validated that some off-target genes predicted by Picky can indeed be inhibited by siRNAs. Similar experiments were performed using commercially available siRNAs and a few off-target genes were also found to be inhibited as predicted by Picky. In summary, we demonstrate that whole-genome thermodynamic analysis can identify off-target genes that are missed in sequence-level screening. Because Picky prediction is deterministic according to thermodynamics, if a siRNA candidate has no Picky predicted off-targets, it is unlikely to cause off-target effects. Therefore, we recommend including Picky as an additional screening step in siRNA design.
An MTANN CAD for detection of polyps in false-negative CT colonography cases in a large multicenter clinical trial: preliminary results

A major challenge in computer-aided detection (CAD) of polyps in CT colonography (CTC) is the detection of "difficult" polyps which radiologists are likely to miss. Our purpose was to develop a CAD scheme incorporating massive-training artificial neural networks (MTANNs) and to evaluate its performance on false-negative (FN) cases in a large multicenter clinical trial. We developed an initial polyp-detection scheme consisting of colon segmentation based on CT value-based analysis, detection of polyp candidates based on morphologic analysis, and quadratic discriminant analysis based on 3D pattern features for classification. For reduction of false-positive (FP) detections, we developed multiple expert 3D MTANNs designed to differentiate between polyps and seven types of non-polyps. Our independent database was obtained from CTC scans of 155 patients with polyps from a multicenter trial in which 15 medical institutions participated nationwide. Among them, about 45% patients received FN interpretations in CTC. For testing our CAD, 14 cases with 14 polyps/masses were randomly selected from the FN cases. Lesion sizes ranged from 6-35 mm, with an average of 10 mm. The initial CAD scheme detected 71.4% (10/14) of "missed" polyps, including sessile polyps and polyps on folds, with 18.9 (264/14) FPs per case. The MTANNs removed 75% (197/264) of the FPs without loss of any true positives; thus, the performance of our CAD scheme was improved to 4.8 (67/14) FPs per case. With our CAD scheme incorporating MTANNs, 71.4% of polyps "missed" by radiologists in the trial were detected correctly, with a reasonable number of FPs.
An evaluation of taxonomic name finding & next steps in Biodiversity Heritage Library (BHL) developments

The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic name strings from the BHL corpus, as well as suggestions for improvement.
ABCG5 and ABCG8 are expressed in gallbladder epithelial cells

Abstract Gallbladder epithelial cells (GBEC) are exposed to high biliary cholesterol concentrations on their apical (AP) surface. The mechanisms of cholesterol absorption and efflux by these cells are not known. We hypothesized that ABCG5 and ABCG8 are expressed in GBEC and mediate AP cholesterol efflux. Human gallbladder cDNA expressed message for ABCG5 and ABCG8. Cultured murine GBEC also expressed abcg5 and abcg8 mRNA and protein, as did cultured canine GBEC. Interestingly, treatment with model bile containing supersaturating concentrations of cholesterol, or treatment with LXRα/RXR ligands, did not lead to differences in expression of ABCG5 or ABCG8 in the murine or the canine cells. The subcellular localization of ABCG5 and ABCG8 did show alterations, with predominantly intracellular localization at baseline and predominantly AP localization following treatment with model bile or LXRα ligand. GBEC therefore express ABCG5 and ABCG8; these sterol transporters may play a role in mediating AP cholesterol efflux in the gallbladder epithelium.
A model of outcomes research: spinal cord injury.

Abstract Meyers AR, Andresen EM, Hagglund KJ. A model of outcomes research: spinal cord injury. Arch Phys Med Rehabil 2000;81 Suppl 2:S81-S90. Objective: To use spinal cord injury (SCI) care and research as a paradigm to illustrate how the principles and practices of outcomes research have been and can be applied to the sequelae of a specific disability. Data Sources: Review of data sources and literature pertaining to outcomes of SCI. Study Selection: English language literature, health status and health services research agencies, academic and governmental research, and surveillance settings. Data Extraction: A critical review of measures that have been and may be used to measure the outcomes of SCI. Special attention was paid to data sources; the need for methodologic accommodations; the research balance between generic and condition-specific methods; and the measurement outcomes that are highly relevant to people with SCIs. Data Synthesis: There is a substantial research record related to the natural history, rehabilitation, survival, and long-term social reintegration of people with SCI, but relatively less addressing widely used generic health outcomes. Conclusion: Contemporary outcomes research is relevant to people with SCI and those who provide treatment. One area of special attention is the occurrence of secondary conditions. To a large extent, SCI outcomes research can use conventional methods and generic instruments. There also is a need to modify research methods and to refine and apply some measures specific to people with SCI. © 2000 by the American Congress of Rehabilitation Medicine
Influence of Adjuvant Chemotherapy on Skeletal Muscle and Fatigue in Women with Breast Cancer

The purpose of this pilot study was to investigate the changes in skeletal muscle size and strength and perception of fatigue in women undergoing adjuvant chemotherapy for breast cancer. The findings of this pilot study suggest that changes in muscle size and strength can occur during chemotherapy. Quadricep muscle size increased for two subjects. These subjects also experienced an increase in muscle strength. This is the first known study to address change in muscle size and fatigue in women during adjuvant chemotherapy for breast cancer from an integrated biobehavioral perspective. Our findings may indicate that muscle size can increase during chemotherapy, but this may not diminish the subjective experiences of fatigue. As the potential for causing serious damage to striated muscle exists, further research into muscle changes and activity during chemotherapy and its role in fatigue is crucial.
Modeling secondary structures and secondary structure linkages of protein sequences

In this paper we model protein secondary structures such as a-helices and b sheets and linkages thereof using passive electrical circuit components and obtain the frequency responses of these circuits. An analysis of the frequency responses of these model circuits shows that putative connections can be made between circuit behavior and known characteristics of biological structures. Potential applications of this research include protein conformational studies and pharmacogenomics.
Deformation mechanisms of polycrystalline MoSi2 alloyed with 1 at.% Nb

Abstract Molybdenum disilicide (MoSi2) is a high Peierls stress material with a strong temperature dependence of the yield stress at low homologous temperatures. We have investigated the effects of alloying with 1 at.% Nb on the mechanisms of deformation of polycrystalline MoSi2 by compression testing from room temperature to 1600 °C. While polycrystalline unalloyed MoSi2 fractured before plastic yield at temperatures ≤900 °C, the Nb-alloyed MoSi2 could be deformed in compression even at room temperature. Transmission electron microscopy (TEM) investigations indicated that the presence of 1 at.% Nb increased the stacking fault width of 1/2〈111〉 dislocations and promoted 1/2〈111〉 slip at low temperatures. The solution softening is interpreted in terms of easier kink nucleation on partial dislocations (especially in the vicinity of solute atoms) with increasing partial spacing. With increasing deformation temperature, thermal activation makes kink nucleation easy, and presumably, kink migration is hindered by the solute atoms leading to the expected solid solution hardening at elevated temperatures. At very high temperatures (∼1600 °C), the yield strengths of Nb-containing alloys may be up to an order of magnitude higher than pure MoSi2; the related hardening mechanisms are discussed.
Development, critical period plasticity, and adult reorganizations of mammalian somatosensory systems

This review covers recent progress in three major areas of investigation in somatosensory systems: development, developmental plasticity and functional reorganization. Important findings relate to the development of periphery-related patterning in thalamic afferents to somatosensory cortex, the controversial role of neural activity in the development and plasticity of periphery-related afferent patterning in the brainstem and cortex, experience-dependent reorganizations in adult somatosensory cortex, and the locus of these changes.
Unit responses to auditory input in the dorsal and median raphe nuclei of the rat

Abstract Neural responsiveness to auditory stimulation in the medial and dorsal raphe nuclei (MR and DR) was investigated in the chronic, awake rat. Two pure tones (1 and 10 Khz, 75 dB, 2 sec duration) and a transient noise from an energized solenoid were used in a test situation in which the stimuli were presented in random order with 1 min interval on the average between presentations. Two hundred and twenty presentations were given for each stimulus over a period of 11 hr. Computer-aided analysis of unit activity for blocks of 50 trials showed that: (1) responses to one or more of the signals were obtained in 94% of the units sampled in the MR and in 88% in the DR; (2) a majority of the responses had short latencies; 60% of the significant responses in both nuclei occurred within the first 12 msec after the onset of the stimulus; (3) most units responded to more than one stimulus; and (4) the responses of DR and MR could be differentiated from one another.
Mnemic neglect is not an artifact of expectancy : The moderating role of defensive pessimism

Research supporting the mnemic neglect model finds that people more easily recall positive than negative personality feedback, even when only asked to imagine that the feedback is real. The same bias is not found when people are asked to recall information about other people. Despite evidence that these findings reflect self-enhancement motives, more research is needed to rule out the possibility that they instead simply reflect expectancies. Results supported the mnemic neglect model, and revealed that expectancies predicted recall only for a subgroup of participants who did not demonstrate the self–other recall bias characteristic of mnemic neglect: defensive pessimists, who are more likely than other people to process social information by comparing it to their expectancies. These findings suggest that mnemic neglect is not an artifact of expectancies, and is not driven by other self-evaluation motives (such as self-verification or self-assessment). Copyright © 2009 John Wiley & Sons, Ltd.
CONVERSATIONAL SKILLS INSTRUCTION FOR COMMUNICATION APPREHENSION AND AVOIDANCE Evaluation of a Treatment Program

This article describes and evaluates a conversational skills program designed for apprehensive communicators. Subjects, all women, were initially assessed on a variety of measures: questionnaires, behavioral samples, peer ratings, and self-monitoring. They were then randomly assigned to either Immediate Treatment or a Self-Monitor-Delay condition. After the Immediate Treatment group completed the program, both groups were assessed again. Comparisons revealed differences between the control and treatment group in subjects' comfort, social behavior, and impact on others. These improvements were evident in questionnaire measures, laboratory assessments, and confederate and coder ratings. Improvements in comfort, social behavior, and impact on others were replicated when Self-Monitor-Delay students were treated. Follow-up conducted 5 months after each group finished the program suggests that the effects of treatment are durable. By incorporating multiple assessments, a control group, and follow-up evaluation,...
Applications and techniques of gastrointestinal intubation

Gastrointestinal intubation has found increasing applications over the past several years. Although usually an uncomplicated procedure, passage of an intestinal tube may be impeded by ineffective peristalsis, obstructing lesions or surgical alteration of the normal anatomy. A variety of techniques are described for passing tubes into the stomach, duodenum and small bowel. These techniques are an out-growth of those initially developed for manipulating tubes through the vascular, biliary and genitourinary systems. The characteristics of the various decompression and alimentation tubes as well as the dangers of gastrointestinal intubation are also discussed.
Waveguide Mixer Sum frequency Termination Considerations in an FM Communication System

In a 6-GHz FM communications system using a mixer with its diode mounted in waveguide, group delay and linearity anomalies were observed which resulted in serious degradation of intermodulation signal-to-noise performance. This paper describes the problem, presents the reasoning and the laboratory tests by which improper termination of the mixergenerated sum frequency was isolated as its source, and describes a waveguide sum frequency absorber located at the mixer to solve the problem. The necessity of giving attention to all the signals generated in a nonlinear device in waveguide is discussed in this paper and has application to all such components in FM systems.
Polyarginine, polylysine, and protamine mimic the effects of high extracellular calcium concentrations on dispersed bovine parathyroid cells

We investigated the effects of the basic peptides polyarginine, protamine, and polylysine on dispersed bovine parathyroid cells. All three peptides produced a dose-dependent inhibition of dopamine-stimulated cAMP accumulation, with half-maximal inhibition at 4 x 10(-8), 1.5 x 10(-7), 3 x 10(-7), and 2 x 10(-6) M, respectively, for polyarginine, protamine, and two preparations of polylysine of molecular weights 10,200 and 3800. The inhibition of cAMP accumulation was reversible and was blocked by preincubating the cells overnight with 0.5 micrograms/ml of pertussis toxin. The same peptides also inhibited PTH release at similar concentrations, markedly stimulated the accumulation of inositol phosphates at two- to threefold higher concentrations, and produced transient increases in the cytosolic Ca2+ concentration (Cai) in fura-2-loaded parathyroid cells. The polylysine-evoked spike in Cai persisted despite the removal of extracellular Ca2+, indicating that it arose from intracellular Ca2+ stores. Exposure of the cells to elevated extracellular magnesium (Mg2+) concentrations elicited a similar spike in Cai but blocked the Cai transient in response to subsequent addition of polylysine, or vice versa. Thus, Mg2+ and polylysine mobilize Ca2+ from the same intracellular store(s). These results indicate that highly basic peptides closely mimic the effects of polyvalent cations on parathyroid function, suggesting that both agents may regulate parathyroid function via similar biochemical pathways.
Teaching evolution using historical arguments in a conceptual change strategy

A historically rich teaching intervention was developed for biological evolution with the intent of promoting a conceptual change from students' initial understanding to a more Darwinian understanding. The intervention was delivered in a small group setting to underprepared, entry–level biology students. Evaluation of the treatment, using pre–post testing, was used to document the general effectiveness of the intervention and specific changes in students' conceptions of evolution. Results indicate the use of historical materials in conjunction with a conceptual change strategy to be promising. Specific strengths and weaknesses in specific areas of biological evolution are documented. © 1995 John Wiley & Sons. Inc.
Changes of adenosine triphosphate- dependent calcium uptake in microsomal fractions of rat liver during sepsis

Abstract Background. Intracellular calcium concentration is an important regulator of cellular metabolism. Endoplasmic reticulum membranes play an important role in the regulation of cytoplasmic calcium in the mammalian liver. The characterization of the changes of calcium uptake in endoplasmic reticulum may contribute to the potential intracellular mechanisms for cellular dysfunction during sepsis. Methods. The effects of sepsis on the calcium uptake in rough endoplasmic reticulum of rat liver were studied. Sepsis was induced by means of cecal ligation and puncture (CLP). The control rats underwent sham operation. Microsomal fractions were isolated from the liver with differential centrifugation. Results. The calcium uptake by liver endoplasmic reticulum was decreased by 30% to 35% (p Conclusions. These data demonstrate that ATP-dependent calcium uptake in rough endoplasmic reticulum of rat liver was impaired during early and late sepsis. Because the low intracellular calcium concentration plays an important role in the regulation of cellular function, an impairment in the ATP-dependent calcium uptake by endoplasmic reticulum during early and late sepsis may have a pathophysiologic significance in contributing to the development of altered hepatic metabolism during sepsis.
Spectral analysis based on the state covariance: the maximum entropy spectrum and linear fractional parametrization

Input spectra, which are consistent with a given state covariance of a linear filter, correspond to solutions of an analytic interpolation problem. We derive an explicit formula for the power spectrum with maximal entropy, and provide a linear fraction parametrization of all solutions.