cssi/SciSciGPT-SciSciNet huggingface dataset:
Latency-Associated Nuclear Antigen of Kaposi's Sarcoma-Associated Herpesvirus Up-Regulates Transcription of Human Telomerase Reverse Transcriptase Promoter through Interaction with Transcription Factor Sp1

Telomerase is required for the maintenance of telomere length and is an important determinant for cell immortalization. In human cells, telomerase activity is due to the expression of its enzymatic subunit, human telomerase reverse transcriptase (hTERT). The expression of hTERT is not typically detectable in healthy somatic human cells but is present in cancerous tissues and immortalized cells. We have previously shown that hTERT promoter activity is up-regulated by the Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded latency-associated nuclear antigen (LANA). LANA is expressed in all forms of human malignancies associated with KSHV. The hTERT promoter sequence located at positions -130 to +5 contains several Sp1 binding motifs and was shown be important for up-regulation by LANA. In this report, we demonstrate that hTERT promoter activity is due to the direct interaction of LANA with Sp1. The interaction of LANA with Sp1 was demonstrated through in vitro binding experiments and coimmunoprecipitation and is supported by the colocalization of these two molecules in the nuclei of KSHV-infected cells. Moreover, LANA modulates Sp1-mediated transcription in transient GAL4 fusion reporter assays. Mapping of the regions involved in binding and transcriptional activation showed that the amino terminus of LANA is the major site for interaction and up-regulation but that it can cooperate with the carboxy terminus to enhance these functions. An analysis of Sp1 binding to its cognate sequence corroborated the binding data. Together, our results suggest that the interaction of LANA with Sp1 up-regulates the telomerase promoter, potentially contributing to the immortalization of KSHV-infected cells.
Two-dimensional extrusion of crushed ice. Part 1: experimental

Abstract A study of flowing crushed ice behaviour is described in this paper. Extrusion of crushed ice often occurs during ice indentation. An understanding of this problem is needed in order to determine the stress distribution between indentor and ice. The experiments examined two-dimensional flow between two converging flat platens. Local and average normal stresses, as well as displacements were measured. Flow patterns were also observed through transparent side walls. The study examined the role of platen surface roughness, ice particle size distribution and velocity. Stresses were found to depend strongly on current layer thickness, and the spatial stress distributions had pointed and concave shapes with slope discontinuities at the centre. These results are very different from what is predicted from modelling crushed ice as a linear viscous material. The measurements were also sensitive to platen surface roughness. For the present range of test parameters, velocity and particles size showed negligible influence on the results.
Uplink CDMA systems with diverse QoS guarantees for heterogeneous traffic

Addressed is the uplink access control problem for cellular CDMA systems that service heterogeneous traffic with various types of quality-of-service (&OS) and use Multi-Code CDMA (MC-CDMA) t o support variable bit rates. Considering its distinct QoS requirements, class-1 real-time traffic (e.g., voice and video) is differentiated from class-11 nonreal-time traffic (e.g., data). Connection-oriented transmission is achieved by assigning transmitter-oriented code channels for class-1 traffic where each corresponding mobile client needs to pass an admission test. Class-II traffic is transmitted in a best-effort manner using the bandwidth left unused by class-1 traffic and a transmission-rate request access scheme: whenever a mobile has class-11 messages to transmit, the mobile requests code channels via a receiveroriented transmission-request code channel, then, according to the base station scheduling, the transmission is scheduled and permitted. Addressed are the admission test for class-1 connections, power control, and how to maximize the aggregate throughput for class-11 trafiic. The admission region of voice and video connections and the optimum target signalto-interference ratio (SIR) of class-11 traftic are derived numerically. The performance of class-11 traffic transmissions in terms of average delay is also evaluated and discussed based on simulations. Indezz Terms-CDMA systems, wireless/mobile communication, Multi-Code CDMA, admission control, power control, QoS guarantees, transmission-rate request access protocol, Reed-Solomon/convolutional concatenated code, Automatic Retransmission reQuest (ARQ).
Crystal structure of cesium zeolite A prepared by complete aqueous exchange

Abstract The complete exchange of zeolite 4A with Cs + has been achieved by the reaction of a single crystal of hydrated NH 4 + -A with a modest excess of CsOH slush. Its structure was determined by X-ray crystallographic methods. Up to one additional molecule of CsOH is taken up per sodalite cavity. To avoid close Cs + -Cs + contacts through 6-rings, four Cs + ions per large cavity are found nearly opposite 4-rings rather than opposite 6-rings as is usually seen. The hydroxide ion is presumed to be between the two Cs + ions found in each sodalite cavity.
NOTCH1: prognostic factor or molecular target?

Comment on Breit et al, page [1151][1] In this issue, Breit and colleagues report that NOTCH1 mutations, present in approximately 50% of T-ALLs, are associated with an excellent early response to therapy and outcome, raising important questions about how clinical trials should be designed to
Interlocking of plasmid DNAs due to Lac repressor-operator interaction.

Abstract The presence of a single lac repressor binding sequence on plasmid DNAs is shown to mediate the formation of interlocked dimers in E. coli . The presence of both homo- and hetero-interlocked dimers suggests that the lac repressor complex can bring together randomly two plasmid DNA molecules to facilitate gyrase-mediated interlocking. The exclusive formation of multiply intertwined dimers also suggests that the lac repressor complex may bind simultaneously to a pair of replicated daughter plasmid molecules prior to their segregation. The formation of interlocked plasmid DNAs can be indicative of interaction between two DNA bound proteins in vivo .
Pharmacokinetic Profile of Progabide, a New γ-Aminobutyric Acid-Mimetic Drug, in Rhesus Monkey

The pharmacokinetic profile of progabide was investigated in five chronically catheterized male rhesus monkeys. The experimental design included single-dose intravenous bolus and oral administration at two dose levels (50 and 100 mg) and zero-order intravenous infusion for 7 days. Plasma samples were analyzed by electron-capture-GLC. Protein binding of the drug was determined by equilibrium dialysis (4°). A one-compartment open model with monoexponential decay was proposed to describe the pharmacokinetics. The mean parameters (± SEM) of the 50- and 100-mg iv bolus were: total body clearance, 2.09 (± 0.15) and 1.53 (± 0.18) liter/hr/kg; half-life, 0.656 (± 0.054) and 0.789 (± 0.079) hr; distribution volume, 1.97 (± 0.08) and 1.79 (± 0.2fa1) liter/kg. Progabide was highly bound to plasma proteins and also to erythrocytes. The drug was rapidly absorbed (Tmax < 1 hr at both doses). The mean bioavailability was attributed principally to a first-pass effect. In the constant rate infusion study, systemic clearance was larger than that of the single dose studies.
MR imaging of epidural hematoma in the lumbar spine.

Abstract Objective. To bring attention to the MR imaging appearance of epidural hematoma (EDH) in the lumbar spine as a small mass often associated with disk herniation or an acute event. This paper will show our experience with this entity and describe criteria for its MR imaging appearance. Design and patients. Thirteen cases of prospectively diagnosed EDH of the lumbar spine were compared with 12 cases of prospectively diagnosed prominent epidural extrusion. Our criteria were retrospectively evaluated by the two authors for their presence or absence in each case. The chi-square test for nominal data was applied. MR imaging criteria utilized to distinguish EDH from disk herniation at our institution include: (1) signal different from disk, (2) high signal on T1-weighted images, either centrally or peripherally, (3) teardrop- or egg-shaped mass, in the sagittal plane, (4) size greater than half the vertebral body height in a craniocaudal dimension, (5) primarily retrosomatic epidural location, (6) plasticity – the mass is seen to conform closely to the contours of bone (e.g., in the lateral recess), (7) little or no disk space narrowing unless associated with disc herniation. Results. Chi-square analysis demonstrated each criterion to significantly differentiate between EDH and extrusion. Only six of 13 EDH cases went to surgery in spite of their relatively large size. Two of six patients were diagnosed as having epidural clot consistent with hematoma at the time of surgery. The four patients who were not diagnosed at surgery revealed only small disk herniations or fragments of disk. Conclusions. The occurrence of EDH is more frequent than previously suspected. Spontaneous EDH is frequently associated with disk herniation and acute events such as sneezing or coughing. Most cases of spontaneous EDH will resolve prior to surgery with only the minority becoming chronic in order to be seen at surgery as an encapsulated mass. MR imaging can reliably identify EDH and distinguish between EDH and large disk extrusions.
Hydrodynamic Analysis of the Flow in a Rotary Lip Seal Using Flow Factors

The flow field in the lubricating film of a rotary lip seal is analyzed numerically by solving the Reynolds equation with flow factors. The behavior of such a flow field is dominated by the asperities on the lip surface. Since previous analyses treated those asperities deterministically, they required very large computation times. The present approach is much less computationally intensive because the asperities are treated statistically. Since cavitation and asperity orientation play important roles, these are taken into account in the computation of the flow factors. Results of the analysis show how the operating parameters of the seal and the characteristics of the asperities affect such seal characteristics as the pressure distribution in the film, the pumping rate and the load support.
Late Cenozoic volcanism of the southeastern Colorado Plateau: I. Volcanic geology of the Lucero area, New Mexico

The Lucero area is a region of isolated, lava-capped mesas and buttes located in the transition zone of the southeastern Colorado Plateau adjacent to the central Rio Grande rift. Basaltic volcanism (basanites, alkali-olivine basalts, tholeiites, and evolved alkalic basaltic rocks) in the area began 8.3 m.y. ago and continued into Quaternary time, coinciding with much of the classic Basin and Range deformation and with the latest phase of rifting. Volcanism occurred in 3 distinct pulses 8.3−6.2, 4.3−3.3, and 1.1−0 m.y. ago. Compositions of rocks erupted during each cycle comprise distinctly different, although partially overlapping, populations. They define a trend (from oldest to youngest) toward relatively larger volumes of tholeiites and an increasingly bimodal distribution with respect to alkalis versus silica. The alkaline basalts could have been derived from significantly deeper (50–70 km) than were the tholeiites (40–50 km) and thus suggest that the depth from which magmas were derived became shallower with time. Alternatively, the alkaline magmas may have been derived from the same depths as were the tholeiites by smaller amounts of partial melting. In either case, the relatively large volumes of tholeiites erupted during the intermediate and youngest cycles and the (relatively) low alkali content of the youngest tholeiites require an increase of melting at shallow mantle depths through time beginning ∼8 m.y. ago, accompanying the late Cenozoic reactivation of rifting. A lull in magmatism from ∼7 to 4 m.y. ago between the oldest and intermediate cycles was widespread on the southeastern Colorado Plateau and in the central Rio Grande rift, although not on the Great Plains. A second period of quiescence 3−1 m.y. ago was of only local importance, correlating with a shift in the locus of volcanism to the Mount Taylor area. Such shifts in volcanism probably occur in response to local stresses in the lithosphere in an overall extensional stress field. The temporal and compositional patterns that we observe in the Lucero area, although not yet understood, will provide constraints on models of rift evolution and guide future studies of volcanic rocks in this region.
Pseudo-Cabibbo structure in a gauge theory of weak interactions and electromagnetism

Abstract We present an alternative to the Cabibbo theory in the context of a renormalizable gauge model of weak and electromagnetic interactions. The strangeness-changing hadronic weak current is assumed to be V+A.
Heterogenized polymetallic catalysts. Part I. Catalytic air oxidation of 3,5-di-t-butylphenol by Cu(II) and Fe(III) complexed to a polyphenylene polymer containing β-di-and tri-ketone surface ligands

Abstract Catalysis preparation involves the cyclic trimerization polymerization of acetylated aromatics. The polymer is coated on a high surface area support, Celite, and cured to give insoluble high molecular weight polymer. Reaction of the remaining acetyl end groups with base and methyl acetate gave β-diketone groups on the surface of the polymer. A second reaction with base and methyl acetate places β-triketones on the surface. The β-triketones can bind two metal ions in a known geometry. The chemically modified surfaces containing β-diketone and β-triketone surface ligands were reacted with Cu(OAc)2 and FeCl3 to give mono- and bi-metallic surface complexes. The oxidation of 3,5-di-t-butylcatechol was studied with all the surfaces. The monometallic catalysts gave only the ortho-quinone as product. The bimetallic catalysts absorbed about twice as much dioxygen as the monometallic catalysts and gave ring cleaved products. Both gave induction periods before dioxygen uptake began. With the bimetallic catalysts the dioxygen uptake stopped at about the ratio: 2 O 2 1 catechol . This is twice as much dioxygen as that required for ring cleavage so H2O2 may be the dioxygen reduction product rather than water. The monomeric Cu(OAc)2 dioxygen uptake curve reached a maximum and then released gas. This could result from Cu(II) catalyzed decomposition of H2O2.
Chipnet: an optical network of terminals and workstations

Abstract An experimental network is described which utilizes a novel optical link technology. Packets are transmitted using light in free space. This technology is particularly useful where workstations and terminals are to be interconnected in large rooms. The physical location of stations may easily be changed without disrupting the network. In addition to the optical link, Chipnet uses a broadband cable for medium range communication. This paper presents link and physical level hardware and a short outline of networking software.
Printer identification based on graylevel co-occurrence features for security and forensic applications

In today's digital world securing different forms of content is very important in terms of protecting copyright and verifying authenticity. Many techniques have been developed to protect audio, video, digital documents, images, and programs (executable code). One example is watermarking of digital audio and images. We believe that a similar type of protection for printed documents is very important. The goals of our work are to securely print and trace documents on low cost consumer printers such as inkjet and electrophotographic (laser) printers. We will accomplish this through the use of intrinsic and extrinsic features obtained from modelling the printing process. In this paper we describe the use of image texture analysis to identify the printer used to print a document. In particular we will describe a set of features that can be used to provide forensic information about a document. We will demonstrate our methods using 10 EP printers.
Effect of hexachlorophene and related bisphenolic compounds on the dehydrogenases and cytochrome system of Bacillus subtilis and Escherichia coli.

Abstract A study has been made of the effect of hexachlorophene (2, 2′-methylenebis [3,4,6-trichlorophenol]) and certain related compounds on the dehydrogenases and cytochrome oxidase systems of Bacillus subtilis and Escherichia coli . Hexachlorophene (G-11), the dichloro analog (G-4), and the compound G-11S, which contains a sulfur bridge rather than a CH 2 -bridge, all at very low concentrations effectively inhibit the glucose, lactic, and succinic dehydrogenases as well as the cytochrome oxidase systems of both organisms. The absence of chlorine from the molecule results in a profound decrease in inhibitory power against the dehydrogenases with a lesser decrease in activity against the cytochrome oxidase. The inhibitory action of these compounds does not appear to be exerted through their action on the sulfhydryl groups of the enzymes nor could evidence be obtained that they compete with the cytochrome system as hydrogen acceptors. Both organisms bind relatively large amounts of inhibitor.
Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function.

The crystal structure of the hypothetical protein MPN555from Mycoplasma pneumoniae (gi pbar 1673958) has been determined to a resolution of 2.8 Angstrom using anomalous diffraction data at the Sepeak wavelength. Structure determination revealed a mostly alpha-helical protein with a three-lobed shape. The three lobes or fingers delineate a central binding groove and additional grooves between lobes 1 and 3, and between lobes 2 and 3. For one of the molecules in the asymmetric unit,the central binding pocket was filled with a peptide from the uncleaved N-terminal affinity tag. The MPN555 structure has structural homology to two bacterial chaperone proteins, SurA and trigger factor from Escherichia coli. The structural data and the homology to other chaperone for MPN555.
Preparation of scanning tunneling microscopy tips using pulsed alternating current etching

An electrochemical method using pulsed alternating current etching (PACE) to produce atomically sharp scanning tunneling microscopy (STM) tips is presented. An Arduino Uno microcontroller was used to control the number and duration of the alternating current (AC) pulses, allowing for ready optimization of the procedures for both Pt:Ir and W tips using a single apparatus. W tips prepared using constant and pulsed AC power were compared. Tips fashioned using PACE were sharper than those etched with continuous AC power alone. Pt:Ir tips were prepared with an initial coarse etching stage using continuous AC power followed by fine etching using PACE. The number and potential of the finishing AC pulses was varied and scanning electron microscope imaging was used to compare the results. Finally, tip quality using the optimized procedures was verified by UHV-STM imaging. With PACE, at least 70% of the W tips and 80% of the Pt:Ir tips were of sufficiently high quality to obtain atomically resolved images of HOPG or Ni(111).
The automated acquisition of topic signatures for text summarization

In order to produce a good summary, one has to identify the most relevant portions of a given text. We describe in this paper a method for automatically training topic signatures-sets of related words, with associated weights, organized around head topics and illustrate with signatures we created with 6,194 TREC collection texts over 4 selected topics. We describe the possible integration of topic signatures with outologies and its evaluaton on an automated text summarization system.
Enamel Microhardness Change and Plaque pH Measurements in an Intra-oral Model in Humans

Changes in plaque pH and microhardness of bovine enamel slabs were evaluated with a seven-day intra-oral cariogenicity test (ICT). The test enamel slabs were mounted in prosthetic appliances with a Dacron mesh cover for enhancement of microbial colonization. Three percent solutions of sucrose, sorbitol, and xylitol were evaluated as four daily extra-oral immersions of 10 min each, for seven days, and the results were compared with baseline experiments (no daily immersions). The pH was measured with antimony electrodes on one-day and seven-day ICT plaque samples that were challenged with a one-minute immersion in the studied substrates. Plaque samples in the baseline experiments were challenged with 3% sucrose. The enamel softening was assessed with measurements of microhardness. Sucrose challenge caused pH depression with both the baseline and the sucrose-immersed plaque. Sorbitol and xylitol challenge did not depress the plaque pH. Compared with the baseline, sucrose immersions caused enamel softening; sorbitol and xylitol did not.
JAK inhibitors in myeloproliferative neoplasms: rationale, current data and perspective.

Abstract JAK-STAT is an appealing but also problematic drug target in BCR-ABL1 -negative myeloproliferative neoplasms (MPN) – it is appealing because the majority of patients with MPN harbor gain-of-function JAK2 or MPL mutations – it is problematic because currently available JAK inhibitors do not distinguish between oncogenic and physiologic JAK-STAT activation. Furthermore, JAK-STAT-relevant mutations in MPN do not always constitute the predominant or ancestral mutant clone. Such complexities undermine the value of JAK-STAT as a robust drug target in MPN and partly explain the hitherto lack of histologic or molecular remissions associated with currently available JAK inhibitors. Most of these drugs were, however, effective in alleviating constitutional symptoms and reducing spleen size; the mechanism of action in this instance includes drug-induced down-regulation of inflammatory cytokine activity. In addition, non-specific myelosuppression contributes to both their salutary and detrimental effects on peripheral blood count. Non-hematologic side effects include gastrointestinal disturbances, asymptomatic elevation of liver and pancreatic enzymes, peripheral neuropathy and hyperacute relapse of symptoms during treatment interruption. It is our impression that many more JAK inhibitors need to be evaluated in order to identify the best-in-class in terms of efficacy, toxicity and suitability for future combination treatment programs.
The tissue origins of serum and urinary α-amylase

Abstract Past claims for α-amylase produced in the liver have been based on the lack of inhibition of enzyme activity by antiserum produced against salivary amylase, quantitated with a starch-iodine assay. This study represents a reevaluation of amylase inhibition in human tissues and fluids using purified antibodies to salivary amylase. Amylase activity was assessed by monitoring both the disappearance of starch (amyloclastic assay) and the production of reducing sugar (saccharogenic assay). Essentially complete inhibition of enzyme activity assessed by both methods was achieved in those tissues and fluids not containing albumin. The presence of albumin resulted in false activity in the starch-iodine assay and consequently lower inhibitions of activity by antisalivary amylase antibodies than could be obtained in the saccharogenic assay. In addition, saccharogenic activity not inhibited by antisalivary amylase antibodies in liver extracts was found to be due to α-1,4-glucosidase. These results suggest that no immunologically unique amylase is produced in the liver, a finding supported by electrophoretic studies.
UX design with international teams: challenges and best practices

International UX collaboration has become the necessity for producing great global products. Microsoft Windows Intune, an IT management and security product in the cloud, consists of engineering groups in different parts of the world. Being a UX designer leading projects with multiple stakeholders, vendors and contractors from U.S., China and Israel, I would like to share my insights on the challenges and best practices - organizing seeding and recurring visits; having key remote UX champions; utilizing the right communication channels; sharing works early; and be sensitive of time zone and cultural differences.
Photo-hall effect in CdSe sintered photoconductors

Abstract Measurements of the photo-Hall effect in sintered layers of CdSe were made. The mobility was found to vary as the 0.15 to the 0.49 power of the density of carriers per unit area depending on the sample and the temperature. Measurements of the mobility as a function of wave length indicate that the carriers do not appreciably diffuse away from the surface and there is evidence that some of the decrease of the photoresponse on the short wave length side of the absorption edge is due to a change in mobility, possibly resulting from surface scattering.
Pharmacologic Approaches to the Prevention of Type 2 Diabetes in High Risk Pediatric Patients

The past generation has witnessed a surge in the number of children, adolescents, and young adults with type 2 diabetes (1–3). In most cases the illness begins with excess weight gain, insulin resistance, and dyslipidemia and progresses through a stage of fasting or postprandial hyperglycemia [impaired glucose tolerance (IGT)] before the emergence of clinical symptoms (4). IGT, dyslipidemia, and overt type 2 diabetes predispose to hepatic steatosis and microvascular and macrovascular complications, which may arise early in the course of the illness (5–9). The threat of vascular and hepatic complications makes the prevention of type 2 diabetes of paramount importance. Recent studies delineate risk factors for the development of type 2 diabetes in children and young adults. Chief among these are poorly defined genetic factors, ethnic background, and obesity (1–3). Rates of type 2 diabetes increase with age, as puberty is associated with a decline in insulin sensitivity (1–4). In the prodromal state, the risk of diabetes is highest among obese patients with severe insulin resistance and fasting or postprandial hyperglycemia. Emerging evidence suggests that lifestyle intervention and pharmacotherapy may reduce the rates of development of type 2 diabetes in subjects at highest risk (see below). This manuscript summarizes current views of the pathogenesis of type 2 diabetes in children and adolescents and discusses potential roles for pharmacological agents in the prevention of diabetes in high risk subjects.
BIM Mediates EGFR Tyrosine Kinase Inhibitor-Induced Apoptosis in Lung Cancers with Oncogenic EGFR Mutations

Background Epidermal growth factor receptor (EGFR) mutations are present in the majority of patients with non-small cell lung cancer (NSCLC) responsive to the EGFR tyrosine kinase inhibitors (TKIs) gefitinib or erlotinib. These EGFR-dependent tumors eventually become TKI resistant, and the common secondary T790M mutation accounts for half the tumors with acquired resistance to gefitinib. However, the key proapoptotic proteins involved in TKI-induced cell death and other secondary mutations involved in resistance remain unclear. The objective of this study was to identify the mechanism of EGFR TKI-induced apoptosis and secondary resistant mutations that affect this process. Methods and Findings To study TKI-induced cell death and mechanisms of resistance, we used lung cancer cell lines (with or without EGFR mutations), Ba/F3 cells stably transfected with EGFR mutation constructs, and tumor samples from a gefitinib-resistant patient. Here we show that up-regulation of the BH3-only polypeptide BIM (also known as BCL2-like 11) correlated with gefitinib-induced apoptosis in gefitinib-sensitive EGFR-mutant lung cancer cells. The T790M mutation blocked gefitinib-induced up-regulation of BIM and apoptosis. This blockade was overcome by the irreversible TKI CL-387,785. Knockdown of BIM by small interfering RNA was able to attenuate apoptosis induced by EGFR TKIs. Furthermore, from a gefitinib-resistant patient carrying the activating L858R mutation, we identified a novel secondary resistant mutation, L747S in cis to the activating mutation, which attenuated the up-regulation of BIM and reduced apoptosis. Conclusions Our results provide evidence that BIM is involved in TKI-induced apoptosis in sensitive EGFRmutant cells and that both attenuation of the up-regulation of BIM and resistance to gefitinibinduced apoptosis are seen in models that contain the common EGFR T790M and the novel L747S secondary resistance mutations. These findings also suggest that induction of BIM may have a role in the treatment of TKI-resistant tumors.
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

The advent of next generation sequencing has coincided with a growth in interest in using these approaches to better understand the role of the structure and function of the microbial communities in human, animal, and environmental health. Yet, use of next generation sequencing to perform 16S rRNA gene sequence surveys has resulted in considerable controversy surrounding the effects of sequencing errors on downstream analyses. We analyzed 2.7×106 reads distributed among 90 identical mock community samples, which were collections of genomic DNA from 21 different species with known 16S rRNA gene sequences; we observed an average error rate of 0.0060. To improve this error rate, we evaluated numerous methods of identifying bad sequence reads, identifying regions within reads of poor quality, and correcting base calls and were able to reduce the overall error rate to 0.0002. Implementation of the PyroNoise algorithm provided the best combination of error rate, sequence length, and number of sequences. Perhaps more problematic than sequencing errors was the presence of chimeras generated during PCR. Because we knew the true sequences within the mock community and the chimeras they could form, we identified 8% of the raw sequence reads as chimeric. After quality filtering the raw sequences and using the Uchime chimera detection program, the overall chimera rate decreased to 1%. The chimeras that could not be detected were largely responsible for the identification of spurious operational taxonomic units (OTUs) and genus-level phylotypes. The number of spurious OTUs and phylotypes increased with sequencing effort indicating that comparison of communities should be made using an equal number of sequences. Finally, we applied our improved quality-filtering pipeline to several benchmarking studies and observed that even with our stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially confound the interpretation of microbial community data.
The STD and HIV Epidemics in African American Youth: Reconceptualizing Approaches to Risk Reduction:

Sexually transmitted infections, including human immunodeficiency virus (HIV), disproportionately affect African American adolescents and young adults. Many of our current strategies and approaches...
Noise modeling of Stokes parameters in division of focal plane polarization imagers

In this paper we present both theoretical modeling and experimental data on the noise performance of two different division of focal plane polarization imaging sensors. Theoretical estimations of the Stokes parameter signal-to-noise ratios for CCD polarization imaging sensors with both 4-polarizer and 2-polarizer micropolarization filter arrays are derived. The theoretical derivation is verified with measurements from an integrated polarization imaging sensor composed of CCD imaging array and aluminum nanowire polarization filters.
Melanocytic nevi with spitz differentiation: Diagnosis and management†‡§

Objectives: Melanocytic proliferations with Spitz differentiation present a difficult clinicopathologic dilemma, as their spectrum ranges from benign to malignant. Distinct entities include Spitz nevus, atypical Spitz nevus, and Spitzoid melanoma. Their histopathologic differentiation can be challenging, and cases of Spitzoid melanoma initially diagnosed as benign Spitz nevi are reported in the literature. The goal of this article is to discuss the diagnostic tools (including comparative genomic hybridization), which may be helpful in differentiating benign Spitz nevi from malignant melanoma with Spitzoid features, and to propose an appropriate management strategy for each entity. Study Design: Retrospective case reports. Methods: Medical records of patients referred for suspicious nevi were reviewed. Data regarding demographics, site, pathology reports, and treatment were reviewed. Results: Four patients with three distinct diagnoses involving Spitz differentiation were identified. The pathologic interpretation of these biopsies was difficult and multiple dermatopathologists were involved. All four patients underwent excision with or without sentinel node biopsy. Conclusions: Otolaryngologists, plastic surgeons and dermatopathologists will encounter patients who have melanocytic lesions with Spitz differentiation at some point in their career. The management of these patients is significantly impacted by the histopathologic diagnosis, and should not be undertaken until it is confirmed, possibly with comparative genomic hybridization. In our experience, it is not unusual to have multiple independent pathologic examinations. We believe that a team approach between the surgeon and the dermatopathologist is crucial when diagnosing and managing patients with Spitz lesions. Laryngoscope, 2010
Prolate Filters for Nonadaptive Multitaper Spectral Estimators With High Spectral Dynamic Range

This letter presents a new prospect of selection of taper windows (prolate filters) in the multitaper spectral estimators for applications where very wide spectral dynamic range are of interest. Previous works have emphasized on the use of an adaptive approach to deal with such cases. However, the adaptive approach is computationally very expensive. The novel approach proposed in this letter avoids the need for adaptation, by suggesting a modification to the design of the taper windows.
Hydroelectric Development and Road Paving in Brazil's Transamazon Area

There are renewed signs that the Brazilian government has retaken the path of large-scale development in the Amazon and that the strategy has been defined with practically no input from society. Among many other development projects for the region, the federal government recently announced two new projects that will profoundly affect the Transamazon Highway area around the town of Altamira. One of the projects is the development of a major hydroelectric power plant on the Xingu River (Belo Monte) and the other is the paving of the Transamazon between the towns of Maraba and Altamira in eastern Amazonia. The evidence suggests that although these projects are not outright environmental disasters, they will have considerable environmental and social consequences for the area. In addition, the decision-making process that has brought about these projects was practically devoid of public participation.
Building the Case for Novel Clinical Trials in Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) is characterized by increased pulmonary vascular resistance caused by remodeling of distal pulmonary arterioles that occurs as a consequence of a complex interplay between molecular and genetic factors.1 The incidence of PAH is estimated at 7 to 10 individuals per million people,2 with a prevalence of ≤50 cases per million.3 The most recent World Health Organization clinical classification of pulmonary hypertension4 distinguishes group 1 pulmonary hypertension from pulmonary vascular disease related to lung disease, left atrial hypertension or venothromboemoblism by including PAH in association with anorexigen exposure, connective tissue disease, HIV, or portal hypertension, among other specific comorbidities. In turn, idiopathic PAH is diagnosed in patients without a hereditary or other identifiable cause of PAH. Because of the diversity of diseases implicated in the pathogenesis of PAH, an evolving goal among pulmonary hypertension care centers5 is pathophenotyping patients with pulmonary vascular disease to calibrate suitable therapy.6 Before PAH-specific drug treatment availability, diagnosing PAH functioned principally to inform (a dismal) patient prognosis as treatment was relegated primarily to the careful use of warfarin, digoxin, diuretics, and oxygen.7 The discovery of calcium channel blocker efficacy in this disease was a breakthrough, but this therapy was considered to be appropriate for only a minority of patients, which remains true today.8,9 However, subsequent seminal discoveries of key signaling pathways implicated in the pathogenesis of PAH in some patients exposed for the first time disease-specific treatment targets.10 In turn, results from conventional randomized clinical trials (RCTs) validated their translational relevance and introduced 4 novel drug classes to clinical practice that improve incrementally quality of life or longevity in patients with PAH.8,11–17 Even in the era of contemporary PAH therapies, however, progressive heart failure and diminished …
Tunable polymer lens

A new type of solid-state variable focal length lens is described. It is based on shape changes in an elastomeric membrane driven by compression of a reservoir of a polymer gel. A novel fabrication process based on individual lens components allows for customization of lens power based on the desired application. The lens shape as a function of applied compressive strain is measured using direct surface profile measurements. The focal length of a solid state lens was reversibly changed by a factor of 1.9. Calculated back focal lengths of the lens were consistent with experimental measurements.
Recombination between two identical sequences within the same retroviral RNA molecule.

As a consequence of being diploid viruses, members of the Retroviridae have a high recombination rate. To measure recombination between two identical sequences within the same RNA molecule per round of retroviral replication cycle, a murine leukemia virus based vector (JZ442 + 3′ Hyg) has been constructed. It carries a drug resistance gene, hyg , and a 290-bp repeat sequence of the 3′ hyg gene inserted into the 3′ untranslated region of the green fluorescent protein gene ( gfp ). Under fluorescence microscopy, Hyg r cells containing the recombinant proviruses were clear, while a green color was observed in the drug-resistant cells carrying the parental proviruses. The rate of recombination was determined by the ratio of the number of clear colonies to the total number of Hyg r colonies (green and clear colonies). The rate of recombination was found to be 62% by this method. The intermolecular recombination rate between an infectious virus bearing two copies of the 290-bp segment and a noninfectious chimeric RNA virus containing only a single copy of this sequence was also measured.
Human intestinal monoacylglycerol acyltransferase: differential features in tissue expression and activity

Acyl CoA-monoacylglycerol acyltransferase (MGAT) catalyzes the first step in triacyglycerol resynthesis involved in dietary absorption in enterocytes. Despite its potentially important role in diet...
Standard Market Design in Wholesale Electricity Markets: Can FERC’s Proposed Structure Adapt to the Unknown?

Abstract The SMD proposal focuses on wholesale markets and transmission in isolation, not on ways to encourage a more market-based retail approach. As long as it remains so supply-focused, policy will be like one hand clapping, leading to potential overinvestment in transmission and costly future revisions of institutions.
A Multiscale Model for Avascular Tumor Growth

The desire to understand tumor complexity has given rise to mathematical models to describe the tumor microenvironment. We present a new mathematical model for avascular tumor growth and development that spans three distinct scales. At the cellular level, a lattice Monte Carlo model describes cellular dynamics (proliferation, adhesion, and viability). At the subcellular level, a Boolean network regulates the expression of proteins that control the cell cycle. At the extracellular level, reaction-diffusion equations describe the chemical dynamics (nutrient, waste, growth promoter, and inhibitor concentrations). Data from experiments with multicellular spheroids were used to determine the parameters of the simulations. Starting with a single tumor cell, this model produces an avascular tumor that quantitatively mimics experimental measurements in multicellular spheroids. Based on the simulations, we predict: 1), the microenvironmental conditions required for tumor cell survival; and 2), growth promoters and inhibitors have diffusion coefficients in the range between 10−6 and 10−7 cm2/h, corresponding to molecules of size 80–90 kDa. Using the same parameters, the model also accurately predicts spheroid growth curves under different external nutrient supply conditions.
The structure of the stomatogastric neuromuscular system in Callinectes sapidus, Homarus americanus and Panulirus argus (Decapoda Crustacea).

The stomatogastric nervous system of the reptantian Decapoda Crustacea, particularly the small isolated stomatogastric ganglion containing the 25-30 motor neurons that control the muscles of the gastric mill and the pyloric filter of the stomach, is an important preparation for research in comparative neurophysiology. Unfortunately there are no comprehensive descriptions of the neuromuscular system of the stomach in these animals. Therefore, since the stomatogastric motor neurons are identified by reference to the muscles they innervate, it has been difficult to identify neurons within or between species. The most important features for classifying the muscles of the decapod stomach are the ossicles to which the muscles attach. In the latter part of the last century Mocquard demonstrated that the stomach ossicles of the decapods could be compared in different groups despite the large variations from group to group. A summary of Mocquard’s (1883) classification scheme, with some modifications, is given. The scheme recognizes 33 ossicles in seven categories (cardiac gastric mill, I—VII; lateral supporting cardiac ossicles, VIII-XV ; ossicles of the cardio-pyloric valve, XVI-XVIII; supporting ossicles of the dorsal pyloric stomach, XIX -XXI; supporting ossicles of the ventral pylorus and ampullae, XXII-XXVII; supra-ampullary ossicles, XXVIII-XXX ; supporting ossicles of the lateral pylorus, XXXI-XXXIII). Where necessary, comments are then made on the ossicles of the three divergent species studied, the blue crab, Callinectes sapidus (Brachyura); the lobster, Homarus americanus (Macrura) and the spiny lobster Panulirus argus (Palinura). Most of the thirty-three ossicles are found in each of the species, but there are some major differences between species. Callinectes , for example, has the most complex ossicle system and Panulirus the most reduced.
Why is “Bad” Parenting Criminogenic? Implications From Rival Theories

This article tests two rival theories: low self-control and differential association and social learning and their competing accounts of why bad parenting matters. The analysis revealed that several dimensions of parenting (including monitoring and caring and parental reinforcement of aggression) affected both low self-control and aggressive attitudes. Both low self-control and aggressive attitudes predicted delinquent involvement and were found to partially mediate the effect of parenting measures on delinquency. The influence of self-control on delinquent involvement was found to vary across levels of aggressive attitudes—adolescents who had aggressive attitudes and little self-control were especially likely to engage in criminal behavior. The results indicate that ineffective parenting is likely to produce low self-control and aggressive attitudes through not only direct control (e.g., monitoring and punishment) but also through modeling. Thus, the findings question the claim by Gottfredson and Hirschi...
FOOD HABITS OF NYCTINOMOPS MACROTIS AT A MATERNITY ROOST IN NEW MEXICO, AS INDICATED BY ANALYSIS OF GUANO

Abstract We examined 56 fecal pellets from under a maternity colony of big free-tailed bats (Nyctinomops macrotis) in the Jemez Mountains of northern New Mexico. The most important food items, listed in order of decreasing percent volume, were Cicadellidae, leafhoppers (26.7% volume, 58.9% frequency); Ichneumonidae, Ichneumon wasps (19.3% volume, 35.7% frequency); and Lepidoptera, moths (17.2% volume, 82.1% frequency). Overall, the most important orders as prey consumed, listed by decreasing percent volume, were Homoptera (27.6% volume, 62.5% frequency), Hymenoptera (19.5% volume, 37.5% frequency), Lepidoptera (17.2% volume, 82.1% frequency), Hemiptera (11.7% volume, 37.5% frequency), and Diptera (10.6% volume, 50.0% frequency). Our study documents an unusually varied diet, as previous studies indicated that these bats fed almost exclusively on moths.
Parameter estimation and anomaly detection while cutting insulation during telerobotic satellite servicing

For satellite servicing, it is necessary to remove a patch of multi-layer insulation (MLI) that covers the access panel. We consider the case where this patch is secured by tape and desire to use ground-based teleoperation to carefully cut the tape on three sides of the patch. Communication delays of several seconds motivate the development of an online method to enable failure detection by the remote (on-orbit) robot system, so that cutting can be stopped without having to wait several seconds for the ground-based operator to observe the failure. This method is based on a model that predicts the force in the direction of cutting. The model parameters are provided by a recursive least squares estimator, with vector-like forgetting factors, that also includes a throttling mechanism to ensure that the estimator is used only when operating conditions and measurements enable reasonable outcomes. During cutting, the predicted force is compared to the measured force to detect various types of failures. Experiments are conducted on a ground-based platform to demonstrate that the proposed estimation system can reliably detect these failures.
Discussion: The Food Potential of Developing Nations

tation of India's water resources for intensive agriculture will be necessary to sustain a high rate. But it will be difficult for India to do more, especially in the next few years. Economic growth has been interrupted, largely as a result of the drought disaster. Resources are thin and priority for those resources has been given to agricultural development. If there is to be an additional push given to agriculture, it will have to come mostly from outside
Local Economic Consequences of Stock Market Listings

When a firm goes public there is, on average, a positive spillover effect on the local economy where the firm’s headquarters is. We estimate this effect is an incremental 30 to 50 basis points increase in the growth rate of local per capita income. We mitigate concerns about unobserved heterogeneity with judicious subsample tests, MSA fixed effects, and a matching procedure. We provide evidence that our result is not due to reverse causality, and show that it is the listing decision, rather than raising capital, that induces the growth. The channel for the growth effect appears to be through employment.