cssi/SciSciGPT-SciSciNet huggingface dataset:
Alignment algorithm for homology modeling and threading

A DNA/protein sequence comparison is a popular computational tool for molecular biologists. Finding a good alignment implies an evolutionary and/or functional relationship between proteins or genomic loci. Sequential similarity between two proteins indicates their structural resemblance, providing a practical approach for structural modeling, when structure of one of these proteins is known. The first step in the homology modeling is a construction of an accurate sequence alignment. The commonly used alignment algorithms do not provide an adequate treatment of the structurally mismatched residues in locally dissimilar regions. We propose a simple modification of the existing alignment algorithm which treats these regions properly and demonstrate how this modification improves sequence alignments in real proteins.
On facilitating the use of HARDI in population studies by creating rotation-invariant markers.

Abstract We design and evaluate a novel method to compute rotationally invariant features using High Angular Resolution Diffusion Imaging (HARDI) data. These measures quantify the complexity of the angular diffusion profile modeled using a higher order model, thereby giving more information than classical diffusion tensor-derived parameters. The method is based on the spherical harmonic (SH) representation of the angular diffusion information, and is generalizable to a range of HARDI reconstruction models. These scalars are obtained as homogeneous polynomials of the SH representation of a HARDI reconstruction model. We show that finding such polynomials is equivalent to solving a large linear system of equations, and present a numerical method based on sparse matrices to efficiently solve this system. Among the solutions, we only keep a subset of algebraically independent polynomials, using an algorithm based on a numerical implementation of the Jacobian criterion. We compute a set of 12 or 25 rotationally invariant measures representative of the underlying white matter for the rank-4 or rank-6 spherical harmonics (SHs) representation of the apparent diffusion coefficient (ADC) profile, respectively. Synthetic data was used to investigate and quantify the difference in contrast. Real data acquired with multiple repetitions showed that within subject variation in the invariants was less than the difference across subjects – facilitating their use to study population differences. These results demonstrate that our measures are able to characterize white matter, especially complex white matter found in regions of fiber crossings and hence can be used to derive new biomarkers for HARDI and can be used for HARDI-based population analysis.
Characteristic features of actinomycin D-induced paw inflammation of the rat.

Abstract Features of paw edema induced by subplantar injection of actinomycin D (act D) were investigated in rats. The paw edema was produced as early as the 1st day and reached a maximal level on the 3rd or the 4th day. Thereafter, it began to subside progressively and was considerably reduced by the 16th day following act D (20 μgm) injection. A direct dose response relationship between the amount of act D injected and the intensity of the paw edema was obtained. No difference in β-glucuronidase and acid phosphatase activity was found between saline and act D-injected paws on the 2nd day. This was followed by an increase in the activity of both enzymes on the 4th, 8th, and 16th days after injection. The histamine content of the saline and act D-injected paws remained unchanged during the early phase of inflammation. A marked increase in the histamine content was noted during the late phase in the drug-injected paw. The effects of act D treatment on capillary permeability to Evans blue dye (EBD) and the edema formation of the paw revealed that a maximal increase in vascular permeability to EBD occurred on the 1st day and was maintained until the 8th day. In contrast to permeability, the paw edema on the 1st day was minimal and increased progressively until the 3rd or 4th day. Thereafter, both the permeability and the paw edema began to diminish and were considerably reduced on the 16th day. Aspirin and hydrocortisone treatment were ineffective in suppressing the act D-induced paw inflammation. Indomethacin produced a somewhat dose-related anti-inflammatory effect against the inflammation caused by this drug.
Model for a three-dimensional optical illusion

A homogeneous coordinate system is used to describe the transformation from a real three-dimensional stimulus to an illusory three-dimensional perceptual object. The model comprises a series of transformations of which one acts as an illusion operator. The illusion operator is specified by a single parameter whose value determines whether the real or the illusory object is perceived. An experiment to test one prediction derived from the model was performed. The results confirm the prediction.
Hepatic iron and nonalcoholic fatty liver disease

Increased iron is suspected to enhance hepatic injury associated with nonalcoholic fatty liver disease (NAFL). We evaluated the impact of iron accumulation on the outcome of NAFL. Patients with NAFL were identified from our database. Twenty-two clinicodemographic and 19 pathological features were available for each patient. Histological staining (Perls' Prussian blue), hepatic iron concentration (HIC), and hepatic iron index (HII) were determined. Data on follow-up, mortality, and cause of death were analyzed. In 65 patients with available liver biopsy blocks, HIC and HII were 1,171 ± 717 μg/g dry weight and 0.43 ± 0.30 μmol/g/yr, respectively. Males had more iron accumulation (HIC: 1,514 ± 836 vs. 859 ± 389, P = .0001; and HII: 0.58 ± 0.35 vs. 0.29 ± 0.16, P =.0001). In type II diabetics, both HIC (977 ± 769 vs. 1,301 ± 659; P < .05) and HII (0.30 ± 0.23 vs. 0.52 ± 0.32; P < .05) were lower. Iron accumulation was not related to other variables analyzed. Increased iron was not seen in those with higher grades of fibrosis or other pathological features associated with the aggressive form of NAFL (hepatocyte necrosis, fibrosis, ballooning degeneration, and Mallory hyaline). Iron accumulation was not associated with increased overall mortality, liver-related mortality, or development of cirrhosis. In summary, in most patients with NAFL, significant iron accumulation is not seen. Additionally, in our series of patients with NAFL, iron is not associated with poor clinical or pathological outcomes.
High-temperature solution growth of intermetallic single crystals and quasicrystals

Solution growth continues to be one of the most powerful techniques for the production of single crystals for basic and applied research. It is a versatile technique that allows for the growth of congruently and incongruently melting materials with equal ease. The primary requirement for growth is that there be an exposed primary solidification surface in the appropriate equilibrium alloy phase diagram. In this paper, we will review some of the systems that we have applied this technique to over the past several years. These range from binary and ternary intermetallic compounds such as RFe 2 (R= Rare earth) and RT 2 Ge 2 (T= Ni and Cu) to the refractory RNi 2 B 2 C family of magnetic superconductors to several families of quasicrystals. In each case, specific nuances of the relatively simple growth technique will be discussed.
Novel peroxisome clustering mutants and peroxisome biogenesis mutants of Saccharomyces cerevisiae

The goal of this research is to identify and characterize the protein machinery that functions in the intracellular translocation and assembly of peroxisomal proteins in Saccharomyces cerevisiae. Several genes encoding proteins that are essential for this process have been identified previously by Kunau and collaborators, but the mutant collection was incomplete. We have devised a positive selection procedure that identifies new mutants lacking peroxisomes or peroxisomal function. Immunofluorescence procedures for yeast were simplified so that these mutants could be rapidly and efficiently screened for those in which peroxisome biogenesis is impaired. With these tools, we have identified four complementation groups of peroxisome biogenesis mutants, and one group that appears to express reduced amounts of peroxisomal proteins. Two of our mutants lack recognizable peroxisomes, although they might contain peroxisomal membrane ghosts like those found in Zellweger syndrome. Two are selectively defective in packaging peroxisomal proteins and moreover show striking intracellular clustering of the peroxisomes. The distribution of mutants among complementation groups implies that the collection of peroxisome biogenesis mutants is still incomplete. With the procedures described, it should prove straightforward to isolate mutants from additional complementation groups.
Settlement assistance and intermarriage for immigrants to Canada

Canada initiated a points‐based admission system in 1967 to select immigrants, regardless of racial or ethnic origin, who were most likely to prosper economically and assimilate into the host society. If the points‐based admission system achieved its goal of selecting ‘assimilable ‘ immigrants, those persons admitted under the policy should be just as likely to marry outside of their nationality group as within it. Using data from the Longitudinal Study of Economic and Social Adaptation of Immigrants to Life in Canada, multinomial logistic regression models of spousal choice were estimated for the 3,984 respondents who were single upon arrival in Canada. Nominated immigrants (those persons admitted with promises of settlement assistance) were found to have greater odds of intramarriage than independent immigrants.
Self-consistent modelling of the mechanical behaviour of viscoplastic polycrystals incorporating intragranular field fluctuations

We present a detailed description of the numerical implementation, within the widely used viscoplastic self-consistent (VPSC) code, of a rigorous second-order (SO) homogenization procedure for non-linear polycrystals. The method is based on a linearization scheme, making explicit use of the covariance of the fluctuations of the local fields in a certain linear comparison material, whose properties are, in turn, determined by means of a suitably designed variational principle. We discuss the differences between this second-order approach and several first-order self-consistent (SC) formulations (secant, tangent and affine approximations) by comparing their predictions with exact full-field solutions. We do so for crystals with different symmetries, as a function of anisotropy, number of independent slip systems and degree of non-linearity. In this comparison, the second-order estimates show the best overall agreement with the full-field solutions. Finally, the different SC approaches are applied to simulat...
Staphylococcal nuclease makes a single non-random cut in the simian virus 40 viral minichromosome.

Abstract When compact simian virus 40 (SV40) minichromosomes are treated with staphylococcal nuclease at 0 °C under limit-digest conditions, about one-third of the minichromosomes remain resistant to nuclease, a third of them are nicked, while the remaining third suffer one and only one double-stranded cut. Results show that each cleaved minichromosome is cut only once and afterwards becomes resistant to further fragmentation. This is in marked contrast to the action of staphylococcal nuclease at 37 °C, which leads to a rapid fragmentation of all minichromosomes to oligo- and mononucleosomes. The SV40 linear DNA III produced by low-temperature nuclease digestion of minichromosomes was redigested with single-cut restriction endonucleases. By this mapping procedure it was determined that the location of the staphylococcal nuclease cut is neither unique nor random; it occurs at a number of discrete sites on the DNA, half of all cuts being concentrated at the origin of replication and nearby in the “late” portion of the SV40 genome. Control experiments have shown that when staphylococcal nuclease digests naked SV40 DNA at 0 °C it does not “hesitate” after the first cut. Although initial cuts in the purified DNA are non-random in location, their distribution is quite different from that generated by a low-temperature nuclease digestion of compact SV40 minichromosomes. Possible interpretations of these results are discussed in view of the recent finding that a specific region of the SV40 genome is uniquely exposed in the minichromosome (Varshavsky et al. , 1978, 1979; Scott & Wigmore, 1978).
Diagnostics of high-brightness short-pulse lasers and the plasmas they generate

The properties of a laser influence the interaction of the intense laser light with materials. The authors will describe some of the diagnostics that they have implemented at the Los Alamos Bright Source to correlate the changes in the x-ray spectrum and temporal history of a laser generated silicon plasmas with the changes of the incident XeCl laser light. One property is of special interest, the existence of a short prepulse. They find that the prepulse enhances the generation of the x-rays from a later pulse.
A CRISPR Way to Move Things Around

When chromosomal parts are exchanged between nonhomologous chromosomes, a translocation is born. This is a very common event involved in the development of several cancers, especially hematological malignancies and sarcomas. The exact mechanism is unknown, but the starting event is thought to be DNA damage, which causes double-strand breaks, followed by “illegitimate joining” of elements from two different chromosomes. Engineering these translocations into cell models has been limited by the availability of flexible and user-friendly genome editing tools. The recent expansion of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems, which can cut the genome at any desired location, gave Torres et al . an opportunity to recreate two translocations with this method. The first was the t(11;22)(q24;q12) chromosomal translocation, which generates the EWSR1-FLI1 fusion gene, a driving event for Ewing’s sarcoma. The second translocation they generated was t(8;21)(q22;q22), which joins the RUNX1 gene on chromosome 21 with the ETO gene on chromosome 8 in acute myeloid leukemia. The authors started by targeting the gene partners in the t(11;22) translocation with small guiding RNAs and confirmed that the RNA-guided endonuclease induced double-strand breaks at the sites of selected genes on two different chromosomes. The investigators transfected human embryonic kidney (HEK) 293A cells with different small guiding RNA combinations and were able to show that a translocation occurred using fluorescence in situ hybridization (FISH) with an EWSR1 single-fusion probe. A polymerase chain reaction also confirmed the production of a fusion gene. The resulting fusion protein was functional and affected the transcription of known target genes. The team then successfully used the same CRISPR/Cas9 strategy to generate the t(11;22) translocation in genetically unmodified human mesenchymal stem cells, showing the effectiveness of this technique in noncancerous human cells, which will allow future studies of the early effects of these translocations. The same technique was used to induce t(8;21) translocations, first in HEK293A cells and then in human CD34+ human hematopoietic/progenitor stem cells. With this method of recreating translocations common in human cancers, researchers now have a new and “user-friendly” tool to study both the mechanisms and the effects of these translocations in oncogenesis. R. Torres et al ., Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR–Cas9 system. Nat. Commun. 5 , 3964 (2014). [[Abstract]][1] [1]: http://www.nature.com/ncomms/2014/140603/ncomms4964/abs/ncomms4964.html
Kidney Transplant Donor Glomerular Filtration Rate by Iohexol Clearance During Computerized Tomographic Angiography of the Kidneys

Abstract Background Pre-transplantation living-donor kidney function determines remaining donor kidney function and significantly affects post-transplantation allograft function in the recipient. Few transplantation centers perform donor kidney function measurement owing to patient burden. A simplified method of glomerular filtration rate (GFR) measurement after angiographic procedures may facilitate more precise measurement of donor kidney function. Methods We evaluated the agreement between a simplified method of GFR measurement after renal computerized tomographic (CT) angiography (index GFR, 100 mL iohexol [350 mg/mL iodine]) and the reference GFR measurement with the use of iodinated radiocontrast media (5 mL bolus of iohexol [300 mg/mL iodine]) among 19 potential living kidney transplant donors. The 24-hour creatinine clearance and GFR estimation equations were additionally examined. Kidney lengths and total and segmented cortical kidney volumes were also measured. Results The index CT angiography GFR performed best with respect to the reference GFR with minimal bias (mean difference, −4 mL/min/1.73 m 2 ), good precision (SD of the difference, 9.8 mL/min/1.73 m 2 ), coefficient of determination ( R 2 ) of 0.74, narrow mean coefficient of variation (5% [range 1%–15%]), and high accuracy, with 100% of the values for the index test within 30% of the reference test. The 24-hour urine creatinine clearance values performed poorly. Kidney volumes and length did not significantly correlate with measured GFR. Conclusions The CT angiographic GFR measurement could be a useful and more convenient method of donor kidney function evaluation and maintains minimal bias, high precision, and accuracy compared with the reference GFR measurement.
Give or Take: Foreign Aid and Foreign Policy Substitutability*

The article attempts to explain state donations of foreign aid with the application of a general theory of foreign policy. This places foreign aid within the context of a state's creation of a foreign-policy portfolio. The general theory is based upon the assumption that states pursue two goods: 'change', defined as the ability to alter the status quo in desirable ways, and 'maintenance', the ability to prevent changes in favored aspects of the status quo. By applying the 'two-good' model of foreign policy toward an explanation of foreign aid, we are able to derive hypotheses regarding the relationship between state power and foreign aid donations, as well as further implications regarding foreign policy substitutability. The two-good model posits a more complex but better specified conception of foreign policy substitutability, and it implies that state donations of foreign aid are substitutable for other foreign policy choices, such as the initiation of interstate conflict and participation in certain types of alliances, that are directed toward the same goal, namely change. We test these hypotheses using data on official development assistance obtained from the OECD, and additional data from the Correlates of War (COW) Project for 21 states over the 1966-92 period. Our findings indicate that aid allocation is affected by other aspects of a state's foreign policy portfolio. The application of a general framework of foreign policy to the study of foreign aid is fruitful.
Atherosclerosis, serum cholesterol and the homocysteine theory: a study of 194 consecutive autopsies.

ABSTRACT A retrospective study examined 194 consecutive autopsies to determine the proportion of cases of atherosclerosis without elevated serum cholesterol, diabetes mellitus, or hypertension. The study cases were classified into four groups, according to the cause of death and the degree of atherosclerosis. Cases in Group 1, in which death resulted from complications of severe atherosclerosis, have a mean serum cholesterol of 186.7 ± 41.8 mg/dL, and the cholesterol is less than 200 in 65% and less than 250 In 92% of cases. Cases in Group 2, with severe atherosclerosis dying of other diseases, have a mean serum cholesterol of 174.6 ± 60.4 mg/dL, and the cholesterol is less than 200 in 79% of cases and less than 250 in 89% of cases. Cases in Groups 3 and 4, with moderate and minimal atherosclerosis, respectively, have mean serum cholesterol values of 172.3 ± 54.8 and 143.5 ± 47.8 mg/dL, and the cholesterol is less than 200 in 71% and 92% and less than 250 in 92% and 96% of cases, respectively. Serum cholesterol is significantly associated with severity of atherosclerosis in the total sample (P = 0.01). Three fourths of all cases (147/194) have neither diabetes nor hypertension, and in 74% of these cases (109/147) the cholesterol is less than 200 and in 92% (135/147) the cholesterol is less than 250. In 66% (80/122) of the cases with severe atherosclerosis, the disease developed without evidence of elevated serum cholesterol, diabetes, or hypertension. Blood homocysteine, which has been shown by other studies to be an independent risk factor for atherosclerosis, is recommended for assessing prognosis in these cases.
Impersonator identification through dynamic fingerprinting

Tracking the source of impersonation attacks is a difficult challenge for investigators. The attacks are frequently launched from botnets comprised of infected, innocent users and web servers compromised by malware. Current investigative techniques focus on tracking these components. In this paper, we propose the Automated Impersonator Image Identification System (AIIIS), which allows investigators to track images used in impersonation attacks back to the original download from the source. AIIIS accomplishes this by digitally encoding the IP address, server, and time of the image download into the image itself through a digital watermark. AIIIS differs from other image fingerprinting techniques in its combination of dynamic fingerprinting and spread spectrum data hiding. Additionally, the intended goal of AIIIS is tracking impersonation attacks, where the image is a tool used, whereas in most digital rights management techniques, the misuse of the content itself is the primary concern. Our experiments show that the AIIIS system permits recovery even after post-acquisition manipulation of the image, making it a significant addition to the fight against impersonators. The deployment of a pilot of AIIIS was successful in identifying the source of an impersonation attack, and further success is expected with full deployment.
REPLICATION OF CHLORELLA VIRUS PBCV‐1 AND HOST KARYOTYPE DETERMINATION STUDIED WITH PULSED‐FIELD GEL ELECTROPHORESIS

We demonstrated the time-course of DNA replication of the 330-kbp Chlorella virus PBCV-1 by pulsed-field gel electrophoresis. Viral DNA replication began between 90 and 120 min postinfeclion in cell samples produced without first removing cell walls. The host nuclear genome was degraded beginning almost immediately after infection, but some host DNA remained even after 360 min postinfection. The karyotype of the host alga consisted of nine resolvable bands that we presume to represent 13 chromosomes based on band intensity. The chromosomes ranged in size from 1.1 to 6.5 megabase pairs (Mbp). A summation of the sizes of the bands predicts a genome size of 39–45 Mbp of DNA.
The significance of disulfide bonding in biological activity of HB-EGF, a mutagenesis approach

A site-directed mutagenesis approach was taken to disrupt each of 3 disulfide bonds within human HB-EGF by substituting serine for both cysteine residues that contribute to disulfide bonding. Each HB-EGF disulfide analogue (HB-EGF-Cys/Ser(108/121), HB-EGF-Cys/Ser(116/132), and HB-EGF-Cys/Ser(134/143)) was cloned under the regulation of the mouse metallothionein (MT) promoter and stably expressed in mouse fibroblasts. HB-EGF immunoreactive proteins with M(r) of 6.5, 21 and 24 kDa were observed from lysates of HB-EGF and each HB-EGF disulfide analogue. HB-EGF immunohistochemical analyses of each HB-EGF stable cell line demonstrated ubiquitous protein expression except HB-EGF-Cys/Ser(108/121) and HB-EGF-Cys/Ser(116/132) stable cell lines which exhibited accumulated expression immediately outside the nucleus. rHB-EGF, HB-EGF, and HB-EGF(134/143) proteins competed with 125I-EGF in an A431 competitive binding assay, whereas HB-EGF-Cys/Ser(108/121) and HB-EGF-Cys/Ser(116/132) failed to compete. Each HB-EGF disulfide analogue lacked the ability to stimulate tyrosine phosphorylation of the 170 kDa EGFR. These results suggest that HB-EGF-Cys/Ser(134/143) antagonizes EGFRs.
Use of high level procedural languages in dynamics

Abstract The solution of complex problems concerning wave propagation in plane and axisymmetric continua can be obtained through the use of discrete methods of analysis. Invariably these methods introduce mathematical models involving thousands of degrees of freedom. Programming the solution to these problems in a standard procedural language such as FORTRAN generally results in a large lag time between problem inception and program completion. In many instances a shorter development time which results in a moderately efficient program is a more economical and hence, a more desirable approach. The purpose of this paper is to demonstrate that a high level procedural language such as POST is a much more natural language than FORTRAN in which to express the solution of wave propagation problems. The lumped parameter method of analysis is used to determine the solution.
NEUTRINO FLAVOR AND CP/T VIOLATION

We investigate the implications of direct flavor-violating interactions in addition to neutrino oscillations for neutrino oscillations for neutrino oscillation experiments. We show that MINOS and neutrino factories could achieve at least order of magnitude improvements in constraining neutrino flavor-violating parameters.
Detecting dynamical change in nonlinear time series

Abstract We present a robust, model-independent technique for measuring changes in the dynamics underlying nonlinear time-serial data. After constructing discrete density distributions of phase-space points on the attractor for time-windowed data sets, we measure the dissimilarity between density distributions via L 1 -distance and χ 2 statistics. The discriminating power of the new measures is first tested on the Lorenz model and then applied to EEG data to detect the transition between non-seizure and epileptic activity. We find a clear superiority of the new measures in comparison to traditional nonlinear measures as discriminators of changing dynamics.
Locational factors in automobile ownership decisions

An economic utility theory model specifying automobile ownership decision-making in terms of intra-urban locational factors is presented. The long-range objective of the research is to provide an improvement in urban transportation planners' understanding of the relationships between automobile ownership by families residing within urban environments and the supply of transportation system facilities and services. Determinant variables in the model are: the spatial locations of trip destinations accessible to urban travellers with and without use of an automobile and at various times of day, the respective travel times to these destinations by auto and by alternate public transit modes, and the yearly capital and operating cost of automobile ownership in excess of cost by the alternate mode(s). Explicitly evaluated factors in the theory of decision-making proposed include the perceived benefits to tripmakers of travelling to destinations at various times, and the values placed on leisure time and consumption of all other goods. Emphasis is placed on decisions to purchase a second car, predictions of which are particularly relevant to urban transportation planning. Empirical tests for application with traditional transportation planning data are developed for various model hypotheses. These hypotheses are interpreted in terms of future research needs and directions.
Hippocampal Connexin 43 Expression in Human Complex Partial Seizure Disorder

An increase in the cellular production of gap junction proteins and increased numbers of gap junctions in the neuronoglial syncytium of an epileptic focus have been proposed as a possible mechanism underlying synchronization of discharge. To study this issue, both Northern and Western blot analyses of the gap junction protein connexin 43 mRNA and protein abundance were performed on hippocampal tissue resected from patients presenting with a complex partial seizure disorder arising from the medial temporal area and the hippocampus in particular. Samples from 15 patients with medically intractable seizures were compared to those from 5 nonepileptic patients requiring temporal lobectomy in life-threatening situations. Six of the 15 epileptic patients underwent noninvasive electrographic recording, whereas the remaining 9 patients required intracerebral electrodes for extraoperative recording and therefore showed a more discrete focality than the noninvasive recordings. A decline in the mean levels of connexin 43 mRNA expressed predominantly in astrocytes was noted in the epileptic patient groups, particularly for those cases requiring intracranial electrode placement where ictal onset was more clearly established to be intrahippocampal. Quantitation of connexin 43 protein in both epileptogenic and nonepileptogenic hippocampal tissues showed no significant differences in expression. Although mean values for mRNA showed a decline, clinical outcomes postoperatively showed no correlation with either mRNA or protein expression individually in our epileptic population. The findings indicate that there is effectively no upregulation of mRNA and no increased production of connexin 43 protein in response to the development of epileptogenicity. Rather it appears the influence of gap junctions as a substrate of epileptogenicity in any mechanism(s) underlying synchrony or electrical propagation may be a function of the dynamic state (open versus closed) of the membrane-bound gap junction.
Cultural Transition and Infant-Feeding Practices among Somali Immigrant Women in San Diego, California

Cultural Transition and Infant-Feeding Practices among Somali Immigrant Women in San Diego, California
Factors associated with sources, transport, and fate of chloroform and three other trihalomethanes in untreated groundwater used for drinking water

Multiple lines of evidence for indicating factors associated with the sources, transport, and fate of chloroform and three other trihalomethanes (THMs) in untreated groundwater were revealed by evaluating low-level analytical results and logistic regression results for THMs. Samples of untreated groundwater from wells used for drinking water were collected from 1996–2007 from 2492 wells across the United States and analyzed for chloroform, bromodichloromethane, dibromochloromethane, and bromoform by a low-level analytical method implemented in April 1996. Using an assessment level of 0.02 μg/L, chloroform was detected in 36.5% of public-well samples and 17.6% of domestic-well samples, with most concentrations less than 1 μg/L. Brominated THMs occurred less frequently than chloroform but more frequently in public-well samples than domestic-well samples.For both public and domestic wells, THMs occurred most frequently in urban areas. Logistic regression analyses showed that the occurrence of THMs was relate...
Self-Help and Upper Extremity Changes in 36 Children with Cerebral Palsy Subsequent to Selective Posterior Rhizotomy and Intensive Occupational and Physical Therapy

In this descriptive study we evaluated the impact of selective posterior rhizotomy surgery and intensive physical and occupation therapy six weeks post-surgery on 36 children with cerebral palsy. T...
Robustness and the cycle of phosphorylation and dephosphorylation in a two-component regulatory system

The EnvZ/OmpR system in Escherichia coli, which regulates the expression of the porins OmpF and OmpC, is one of the simplest and best-characterized examples of two-component signaling. Like many other histidine kinases, EnvZ is bifunctional; it phosphorylates and dephosphorylates the response regulator OmpR. We have analyzed a mathematical model of the EnvZ-mediated cycle of OmpR phosphorylation and dephosphorylation. The model predicts that when EnvZ is much less abundant than OmpR, as is the case in E. coli, the steady-state level of phosphorylated OmpR (OmpR-P) is insensitive to variations in the concentration of EnvZ. The model also predicts that the level of OmpR-P is insensitive to variations in the concentration of OmpR when the OmpR concentration is sufficiently high. To test these predictions, we have perturbed the porin regulatory circuit in E. coli by varying the expression levels of EnvZ and OmpR. We have constructed two-color fluorescent reporter strains in which ompF and ompC transcription can be easily measured in the same culture. Using these strains we have shown that, consistent with the predictions of our model, the transcription of ompC and ompF is indeed robust or insensitive to a wide range of expression levels of both EnvZ and OmpR.
Amplification of N-myc in human neuroblastomas

Abstract Enhanced expression consequent to amplification of the N- myc gene may contribute to malignant progression of human neuroblastomas. Cytogenetic analyses of human neuroblastomas provide evidence for specific chromosomal abnormalities and have presented an opening for the study of the molecular biology of various forms of human cancer including neuroblastoma, small-cell lung cancer and retinoblastoma. A previously unknown human gene, N- myc , seems to contribute to the growth control of cells and according to contemporary definition can be regarded as a cellular oncogene. A prominent feature is its abnormally high expression due to amplification in numerous human neuroblastomas, several cases of small-cell lung cancer and some retinoblastomas.
Waves, Currents, Sediments, and Sand Bars Associated with Low-Energy Coastal Environments: ABSTRACT

ABSTRACT Low energy beaches are often characterized by a particular series of offshore sand bars which differ markedly, both in shape and sediment characteristics, from the classic offshore bar of high and moderate energy environments. This study reports on the physical interactions of waves and currents with low energy bathymetric features that result in producing a distinct areal distribution of sediment parameters are well correlated with the subtle bathymetric features of the offshore area and thereby may provide a method of determining low energy environments in ancient deposits. Prominent features in low energy environments are subtle digital sand bars which trend perpendicular or at a high angle to the beach face. These bars are called transverse bars. These bars have maximum relief of approximately 0.5 meters, lengths varying between 100 meters and 3,350 meters, and a quasi-regular spacing varying between 300 and 2000 meters. Investigations by several authors indicate that these bars act as avenues for onshore or offshore sediment transport. Recent study by the present author has determined that the sediment is transported as a result of a nearshore current component caused by the transfer of momentum from unstable nearshore waves to the currents. The current component is characterized by a narrow relatively high velocity current directed along the axis of the bars with sluggish return currents between the bars. This results in producing relatively coarse, well sorted sediments along the crest of the bar and finer, less sorted sediments between the bars. The scale of these features as well as the obvious differences in sediment parameters should permit their recognition in ancient deposits. Their presence allows inference to be made about ancient wave energy levels and average wave approach directions.
DNA-Functionalized MFe2O4 (M = Fe, Co, or Mn) Nanoparticles and Their Hybridization to DNA-Functionalized Surfaces

Magnetic MFe2O4 (M = Fe, Co, or Mn) nanoparticles with uniform diameters in the 4−20 nm range and with excellent material properties, reported previously, can be rendered soluble in water or aqueous buffers using a combination of alkylphosphonate surfactants and other surfactants such as ethoxylated fatty alcohols or phospholipids. Surfactant-modified oligonucleotides can be incorporated into the particles' organic shell. The particles can withstand salt concentrations up to 0.3 M, temperatures up to 90 °C, and various operations such as concentration to dryness, column or membrane separations, and electrophoresis. The particles can be selectively hybridized to DNA-functionalized gold surfaces with high coverages using a two-story monolayer structure. These particles may find valuable applications involving the magnetic detection of small numbers of biomolecules using spin valves, magnetic tunnel junctions, or other sensors.
On the Role of Shock Waves and Adiabatic Cooling in the Nucleation of Ice Crystals by the Lightning Discharge

Abstract A cloud of small supercooled water droplets was subjected to shock waves of reproducible intensity in the laboratory. Nucleation of freezing occurred only when the gas driving the shock waves was cooled to −37C or below by adiabatic expansion and subsequently mixed with the droplet-bearing air. Passage of the shock wave did not produce nucleation of the cloud. Results of a numerical model of a lightning discharge show, in the pressure wave from a lightning discharge, that the degree of cooling by adiabatic expansion is probably too small to produce ice crystals by homogeneous nucleation.
The attentional field revealed by single-voxel modeling of fMRI time courses

The spatial topography of visual attention is a distinguishing and critical feature of many theoretical models of visuospatial attention. Previous fMRI-based measurements of the topography of attention have typically been too crude to adequately test the predictions of different competing models. This study demonstrates a new technique to make detailed measurements of the topography of visuospatial attention from single-voxel, fMRI time courses. Briefly, this technique involves first estimating a voxel's population receptive field (pRF) and then “drifting” attention through the pRF such that the modulation of the voxel's fMRI time course reflects the spatial topography of attention. The topography of the attentional field (AF) is then estimated using a time-course modeling procedure. Notably, we are able to make these measurements in many visual areas including smaller, higher order areas, thus enabling a more comprehensive comparison of attentional mechanisms throughout the full hierarchy of human visual cortex. Using this technique, we show that the AF scales with eccentricity and varies across visual areas. We also show that voxels in multiple visual areas exhibit suppressive attentional effects that are well modeled by an AF having an enhancing Gaussian center with a suppressive surround. These findings provide extensive, quantitative neurophysiological data for use in modeling the psychological effects of visuospatial attention.
Advances in electronic structure methods for defects and impurities in solids

Defects and impurities are often decisive in determining the physical properties of most materials. The process of defect identification and characterization is typically difficult and indirect, usually requiring an ingenious combination of different experimental techniques. First-principles calculations have emerged as a powerful microscopic tool that complements experiments or sometimes even serves as the sole source of atomistic information due to experimental limitations. Still, first-principles calculations based on density functional theory in the local density or generalized gradient approximations suffer from serious limitations when describing defects in solids. Recent advances in electronic structure methods, rapid increases in computing power, and the development of efficient algorithms indicate a promising future for computational defect physics. We review recent advances in the theory of defects in solids from the perspective of first-principles calculations. We focus in particular on methods that improve the description of band gaps, leading to results that can be directly compared to experiments on a quantitative level. We discuss the use of LDA+U in wide-band-gap materials, screened hybrid functionals, the quasiparticle GW method, and the use of modified pseudopotentials. Advantages and limitations of these methods are illustrated with examples.
Market segmentation analysis of potential inter-city rail travelers

This paper reports on one aspect of a study conducted to support the analysis of the performance of a proposed intercity rail passenger service in the Piedmont region of North Carolina. In particular, this paper describes a market segmentation study of potential rail travelers on the basis of the responses of 333 participants in a computer-based, mall-intercept, market research survey.
Description of the triple-Regge region with a very large triple-Pomeron coupling and a bare Pomeron

A description of data in the triple-Regge region up to CERN ISR energies is proposed. The description utilizes a very large $\mathrm{PPP}$ (triple-Pomeron) coupling ${g}_{P}$ and assumes that the "bare" or "unrenormalized" Pomeron controls the region near $x=1$. The "bare" Pomeron intercept is ${\stackrel{^}{\ensuremath{\alpha}}}_{0}=0.85$. One secondary term is employed to extend the description to $x=0.7$. This term is chosen to be of the form $\ensuremath{\pi}\ensuremath{\pi}P$. We use a modified ABFST (Amati-Bertocchi-Fubini-Stanghellini-Tonin) model to roughly constrain ${g}_{P}$ and ${\stackrel{^}{\ensuremath{\alpha}}}_{0}$. The number of unconstrained parameters otherwise is one. Other phenomenological applications utilizing the bare Pomeron as the definition of diffraction at intermediate energies are discussed, and the total cross section with and without diffraction is discussed in the context of the ABFST model.
Right Atrial Isolation After Maze Procedure Discovered at the Time of Pacemaker Implantation

This article describes the case of a gentleman who required a permanent pacemaker after mitral valve replacement and a modified maze procedure, with an unusual observation after right atrial lead insertion.
Murine Guanylate-binding Protein: Incomplete Geranylgeranyl Isoprenoid Modification of an Interferon-γ–inducible Guanosine Triphosphate-binding Protein

Farnesylation of Ras proteins is necessary for transforming activity. Although farnesyl transferase inhibitors show promise as anticancer agents, prenylation of the most commonly mutated Ras isoform, K-Ras4B, is difficult to prevent because K-Ras4B can be alternatively modified with geranylgeranyl (C20). Little is known of the mechanisms that produce incomplete or inappropriate prenylation. Among non-Ras proteins with CaaX motifs, murine guanylate-binding protein (mGBP1) was conspicuous for its unusually low incorporation of [(3)H]mevalonate. Possible problems in cellular isoprenoid metabolism or prenyl transferase activity were investigated, but none that caused this defect was identified, implying that the poor labeling actually represented incomplete prenylation of mGBP1 itself. Mutagenesis indicated that the last 18 residues of mGBP1 severely limited C20 incorporation but, surprisingly, were compatible with farnesyl modification. Features leading to the expression of mutant GBPs with partial isoprenoid modification were identified. The results demonstrate that it is possible to alter a protein's prenylation state in a living cell so that graded effects of isoprenoid on function can be studied. The C20-selective impairment in prenylation also identifies mGBP1 as an important model for the study of substrate/geranylgeranyl transferase I interactions.
Reflux symptoms are associated with psychiatric disease.

Methods: To evaluate the frequency of reflux symptoms in patients with a diagnosed psychiatric disorder and to assess potential risk factors for symptom occurrence. Methods: The presence of reflux symptoms was compared between a case population of 94 psychiatric patients and a control population of 198 non-psychiatric patients. Results: Heartburn, exercise-induced heartburn, cough and dysphagia were all reported significantly more frequently by subjects with psychiatric disorders than by control subjects. The presence of any psychiatric diagnosis exerted an increased risk for both heartburn (odds ratio, 2.71; 95% confidence interval, 1.01–7.30) and exercise-induced heartburn (3.34; 1.12–9.96). The type of psychiatric disorder, the type of psychotropic medication and the lifestyle did not influence the presence of reflux symptoms. Conclusions: Reflux symptoms occur more frequently in patients with than without a diagnosed psychiatric disorder. The reflux symptoms are not associated with any specific type of medication and may reflect a generally reduced threshold for or distorted perception of symptoms.
Effects of Applied Potential on Friction of a Piezoelectric Material

Effects of the piezoelectricity of polyvinylidene fluoride (PVDF) on sliding friction against itself are investigated in this research. The piezoelectricity is the response of a piezoelectric material, such as PVDF, to an applied electrical voltage in terms of stress or physical dimension. Such a response is found to influence the sliding-frictional behavior. This research is beneficial in terms of understanding fundamental friction. The applications of this research are in wide areas, such as the design of a microgripper used for surgeries, microassembly, and micromanipulation.
Saudi Arabian seismic-refraction profile: A traveltime interpretation of crustal and upper mantle structure

Abstract The crustal and upper mantle compressional-wave velocity structure across the southwestern Arabian Shield has been investigated by a 1000-km-long seismic refraction profile. The profile begins in Mesozoic cover rocks near Riyadh on the Arabian Platform, trends southwesterly across three major Precambrian tectonic provinces, traverses Cenozoic rocks of the coastal plain near Jizan, and terminates at the outer edge of the Farasan Bank in the southern Red Sea. More than 500 surveyed recording sites were occupied, and six shot points were used, including one in the Red Sea. Two-dimensional ray-tracing techniques, used to analyze amplitude-normalized record sections indicate that the Arabian Shield is composed, to first order, of two layers, each about 20 km thick, with average velocities of about 6.3 km/s and 7.0 km/s, respectively. West of the Shield-Red Sea margin, the crust thins to a total thickness of less than 20 km, beyond which the Red Sea shelf and coastal plain are interpreted to be underlain by oceanic crust. A major crustal inhomogeneity at the northeast end of the profile probably represents the suture zone between two crustal blocks of different composition. Elsewhere along the profile, several high-velocity anomalies in the upper crust correlate with mapped gneiss domes, the most prominent of which is the Khamis Mushayt gneiss. Based on their velocities, these domes may constitute areas where lower crustal rocks have been raised some 20 km. Two intracrustal reflectors in the center of the Shield at 13 km depth probably represent the tops of mafic intrusives. The Mohorovicic discontinuity beneath the Shield varies from a depth of 43 km and mantle velocity of 8.2 km/s in the northeast to a depth of 38 km and mantle velocity of 8.0 km/s depth in the southwest near the Shield-Red Sea transition. Two velocity discontinuities occur in the upper mantle, at 59 and 70 km depth. The crustal and upper mantle velocity structure of the Arabian Shield is interpreted as revealing a complex crust derived from the suturing of island arcs in the Precarnbrian. The Shield is currently flanked by the active spreading boundary in the Red Sea.
Coupling of edge-sharing bioctahedral dirhenium(II) units through the agency of [N(CN)(2)](-), [C(CN)(3)](-), and [Ni(CN)(4)](2-) linkages.

Synthetic strategies have been developed for the synthesis of complexes of the types {[Re2Cl3(μ-dppm)2(CO)2]2[μ-Y]}+, where dppm = Ph2PCH2PPh2 and Y = [N(CN)2] or [C(CN)3], and [Re2Cl3(μ-PP)(CO)(L)]2[μ-Ni(CN)4] (see structure), where PP = dppm or Ph2PC(CH2)PPh2 (dppE) and L = CO or XylNC. The pairs of edge-sharing bioctahedral dirhenium(II) units are linked by single [N(CN)2]-, [C(CN)3]-, or [Ni(CN)4]2- units which allow for electronic communication between the dimetal centers as shown by CV and DPV electrochemical studies.