cssi/SciSciGPT-SciSciNet huggingface dataset:
Adherence of Pharmaceutical Advertisements in Medical Journals to FDA Guidelines and Content for Safe Prescribing

Background Physician-directed pharmaceutical advertising is regulated in the United States by the Food and Drug Administration (FDA); adherence to current FDA guidelines is unknown. Our objective was to determine adherence rates of physician-directed print advertisements in biomedical journals to FDA guidelines and describe content important for safe prescribing. Methods and Findings Cross-sectional analysis of November 2008 pharmaceutical advertisements within top U.S.-based biomedical journals publishing original research. We excluded advertisements for devices, over the counter medications, and disease awareness. We utilized FDA guideline items identifying unique forms of advertisement bias to categorize advertisements as adherent to FDA guidelines, possibly non-adherent to at least 1 item, or non-adherent to at least 1 item. We also evaluated advertisement content important for safe prescribing, including benefit quantification, risk information and verifiable references. All advertisements were evaluated by 2 or more investigators, with differences resolved by discussion. Twelve journals met inclusion criteria. Nine contained pharmaceutical advertisements, including 192 advertisements for 82 unique products; median 2 per product (range 1–14). Six “teaser” advertisements presented only drug names, leaving 83 full unique advertisements. Fifteen advertisements (18.1%) adhered to all FDA guidelines, 41 (49.4%) were non-adherent with at least one form of FDA-described bias, and 27 (32.5%) were possibly non-adherent due to incomplete information. Content important for safe prescribing was often incomplete; 57.8% of advertisements did not quantify serious risks, 48.2% lacked verifiable references and 28.9% failed to present adequate efficacy quantification. Study limitations included its focus on advertisements from a single month, the subjectivity of FDA guidelines themselves, and the necessary subjectivity of determinations of adherence. Conclusions Few physician-directed print pharmaceutical advertisements adhere to all FDA guidelines; over half fail to quantify serious risks. The FDA could better protect public health by creating new more objective advertisement guidelines requiring transparent presentation of basic safety and efficacy information.
Transactions Letters - Random Redundant Iterative Soft-in Soft-out Decoding

This letter presents an iterative soft-in soft-out (SISO) decoding algorithm based on redundant Tanner graphs that is applicable to arbitrary linear block codes. The proposed algorithm utilizes the permutation group of a code in order to efficiently and randomly generate redundant parity-checks.
Pharmacological manipulation of human working memory

Rationale The goal of this paper is to briefly overview human studies that have examined pharmacological agents designed to enhance working memory function, with the idea of providing clues as to promising avenues to follow for the development of drugs likely to enhance working memory and other cognitive processes in individuals with schizophrenia.
Characterization of a flocculation-like phenotype in Cryptococcus neoformans and its effects on pathogenesis

We investigated the phenomenon of cell-cell aggregation (flocculation) in a serotype D strain of Cryptococcus neoformans (ATCC 24067, isolate RC-2). Cell aggregation into clumps of 5-40 cells (clump+ cells) occurred during the early log phase and disappeared in the beginning of the stationary phase (clump- cells). The cell aggregation phenomenon was medium dependent. Clump+ cells could be dispersed by either vortexing or proteinase K digestion. Most importantly, the transient change in cellular phenotype changed several important host-pathogen interactions. Adherence of clump+ cells to murine macrophage-like cells J774.16 was significantly (P < 0.001) enhanced compared with adherence of clump- cells. Furthermore, complement-mediated phagocytosis efficacy of dispersed clump+ cells was significantly higher (P < 0.001) compared with clump- cells. Similar findings were documented with an in vivo phagocytosis assay. Infection of mice with a low inoculum (10(4)) of clump+ cells resulted in lower fungal burden when compared with mice infected with clump- cells. Accordingly, mice infected with clump+ cells survived significantly longer than mice infected with clump- cells. These results indicate that the cellular phenotype undergoes significant changes that result in a transient flocculation-like phenotype. We hypothesize that this cell-cell aggregation is the result of changes in protein content in the polysaccharide capsule. We conclude from our data that the change in cellular phenotype has a dramatic effect on cell adherence, and on complement-mediated phagocytosis, both of which can affect the pathogenesis of the disease in the host. Our results underscore the complexity of studies that investigate host pathogen interactions and may explain differences and inconsistencies observed in in vitro and in vivo assays.
Supercontinuum coherent anti-Stokes Raman scattering (CARS) spectroscopy

We investigate broad-band CARS spectroscopy in supercontinuum optical trap. Methods for suppressing or smoothing non-resonant background are demonstrated.
Serum bilirubin levels at 72 hours by selected characteristics in breastfed and formula-fed term infants delivered by cesarean section.

UNLABELLED: The present multicenter study analysed the relative impact of maternal and infant factors on serum bilirubin levels at 72 +/- 12 h in exclusively breastfed vs formula-fed term infants. End-tidal carbon monoxide levels corrected for ambient air (ETCOc), an index of bilirubin production, were measured in exclusively breastfed (B = 66) or formula-fed (F = 210) term infants at 2-8 h of age. Inclusion criteria included cesarean section to ensure a 3 d hospitalization, birthweight > or = 2,500 g, gestational age >37 wk and absence of any illness. The ETCOc for B infants and F infants did not differ significantly (1.3 +/- 0.7 ppm vs 1.3 +/- 0.8 ppm). The serum bilirubin level at 72 +/- 12 h was significantly higher in B infants than in F infants (8.5 +/- 3.4mg dl(-1) vs 6.7 +/- 3.4mg dl(-1) p < 0.001), as was the percentage weight loss from birthweight. Serum bilirubin levels were significantly higher in infants who were male, who did not have meconium-stained amniotic fluid, and in those whose mothers were insulin-dependent diabetics or hypertensive. There was no difference between groups in the need for phototherapy or exchange transfusion. CONCLUSION: Although higher bilirubin levels were observed in group B at 72 +/- 12 h compared with group F, this finding was not of clinical or therapeutic consequence in this study. The lack of difference in ETCOc between the groups may be a factor of the timing of ETCOc measurement in this study, or may suggest that early increased bilirubin production is not a significant contributor to jaundice observed in exclusively breastfed infants. Key words: bilirubin, breastfeeding, jaundice
Lincoln, Machiavelli, and American Political Thought

The author argues that Machiavelli's political theory provides us with a framework that can be used to illuminate the words and deeds of Abraham Lincoln. He draws primarily on the competing interpretations of Machiavelli offered by J.G.A. Pocock, on one hand, and Harvey Mansfield on the other. According to the author, Pocock's and Mansfield's very different readings of Machiavelli can both be employed to shed light on Lincoln's multifaceted statesmanship. This conclusion is at odds with the interpretation of Lincoln offered by John Patrick Diggins in The Lost Soul of American Politics. According to Diggins, there may be some similarities between Lincoln and Machiavelli, but “such similarities… are far less telling than the contrasts.” The author hopes to convince the reader that a Machiavellian interpretation of Lincoln is, in fact, far more compelling than Diggins would have us believe.
THE MINIMUM TIME PROBLEM IN BATCH RADICAL POLYMERIZATION: A COMPARISON OF TWO POLICIES

The minimum time problem for the batch radical polymerization of styrene is formulated with a realistic kinetic model. A policy that minimizes the time to reach a desired conversion is compared with another policy including a number average molecular weight as an additional requirement. The performance of solution methods is discussed.
Further notes on electromagnetic field behavior near homogeneous anisotropic wedges

The behavior of fields near a wedge of anisotropic material is an important electromagnetic computation problem. Such fields may, under certain conditions, become infinite near the wedge. As a result, standard numerical methods such as finite elements and finite differences will introduce significant errors in the solution. This paper uses an approach first suggested by Beker (1991). We attempt to find a solution for a general anisotropic wedge and show the radial behavior of the resulting fields as a function of the angle of the wedge as well as the choice of media. Without any loss of generality we limit ourselves to a tensor dielectric permittivity of unity. Using duality, the results can be extended to magnetically anisotropic wedges. We investigate the rate at which the solution becomes infinite near the wedge. Since singular behavior occurs just at the tip of the wedge, the analysis is limited to distances much smaller than a wavelength.
Scalp Reconstruction: An Algorithmic Approach and Systematic Review

Importance Reconstruction of the scalp after acquired defects remains a common challenge for the reconstructive surgeon, especially in a patient with a history of radiation to the area. Objective To review the current literature and describe a novel algorithm to help guide the reconstructive surgeon in determining the optimal reconstruction from a cosmetic and functional standpoint. Pertinent surgical anatomy, considerations for patient and technique selection, reconstructive goals, as well as the reconstructive ladder, are also discussed. Evidence Review A PubMed and Medline search was performed of the entire English literature with respect to scalp reconstruction. Priority of review was given to those studies with higher-quality levels of evidence. Findings Size, location, radiation history, and potential for hairline distortion are important factors in determining the ideal reconstruction. The tighter and looser areas of the scalp play a major role in the potential for primary or local flap closure. Patients with medium to large defects and a history of radiation will likely benefit from free tissue transfer. Conclusions and Relevance Ideal reconstruction of scalp defects relies on a comprehensive understanding of scalp anatomy, a full consideration of the armamentarium of surgical techniques, and a detailed appraisal of patient factors and expectations. The simplest reconstruction should be used whenever possible to provide the most functional and aesthetic scalp reconstruction, with the least amount of complexity. Level of Evidence NA.
Tissue-Restricted Transcription from a Conserved Intragenic CpG Island in the Klf1 Gene in Mice

Beyond Mendelian inheritance, an understanding of the complexities and consequences of the transfer of nonhereditary information to successive generations is at an early stage. Such epigenetic functionality is exemplified by DNA methylation and, as genome-wide high-throughput methodologies emerge, is increasingly being considered in the context of conserved intragenic and intergenic CpG islands that function as alternate sites of transcription initiation. Here we characterize an intragenic CpG island in exon 2 of the protein-coding mouse Klf1 gene, from which clustered transcription initiation sites yield positive-strand, severely truncated, capped and spliced RNAs. Expression from this CpG island in the testis begins between Postnatal Days 14–20, increases during development, and is temporally correlated with the maturation of secondary spermatocytes as they become the dominant cell population in the seminiferous epithelium. Only full-length KLF1-encoding mRNAs are detected in the hematopoietic tissue, spleen; thus, expression from the exon 2 CpG island is both developmentally regulated and tissue restricted. DNA methylation analysis indicates that spatiotemporal expression from the Klf1 CpG island is not associated with hypermethylation. Finally, our computational analysis from multiple species confirms intragenic transcription initiation and indicates that the KLF1 CpG island is evolutionarily conserved. Currently we have no evidence that these truncated RNAs can be translated via nonconventional mechanisms such as in-frame, conserved non-AUG-dependent Kozak consensus sequences; however, high-quality carboxyl-terminal antibodies will more effectively address this issue.
The uses of disease activity scoring and the physician global assessment of disease activity for managing rheumatoid arthritis in rheumatology practice.

Objective. To evaluate the uses of quantitative disease activity scoring and a physician global assessment of disease activity for managing rheumatoid arthritis (RA) in rheumatology practice. Methods. The Global Arthritis Score (GAS) and a physician global assessment (Physician Global) were determined during each office visit for a community practice RA population. The GAS was calculated from patients’ self-reported pain, functional assessment, and tender joint count. The Physician Global was recorded on a 10-point visual analog scale. The correlation of these 2 disease activity measures was determined for the most recent office visit of 185 patients with RA, and the reasons for discordant results were identified by chart review. Results. The GAS and Physician Global were concordant for active or inactive disease in 126 of 185 patients (68%) and were discordant in 59 (32%). Forty-five of these discordant patients had a high GAS while their Physician Global indicated inactive disease. Their GAS values were high because of osteoarthritis, back pain, soft tissue rheumatism, and/or prior joint damage rather than active RA. The other 14 patients had a low GAS with an uncontrolled Physician Global for a variety of reasons. Conclusion. (1) An RA disease activity score and a quantitative Physician Global can be measured during rheumatology office visits to document patients’ disease status. (2) Disease activity scoring contributes valuable information, but should not replace the Physician Global in guiding RA patient management or reimbursement decisions.
Control of Transcriptional Elongation

Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified. Among the factors we describe are the pausing factors--NELF (negative elongation factor) and DSIF (DRB sensitivity-inducing factor)--and P-TEFb (positive elongation factor b), which is the key player in pause release. We also describe the high-resolution view of Pol II pausing and propose nonexclusive models for how pausing is achieved. We then discuss Pol II elongation through the bodies of genes and the roles of FACT and SPT6, factors that allow Pol II to move through nucleosomes.
Properties of spectra

It is often useful to ask of a point in the spectrum of an operator how it got there. To say that A is in the spectrum of A means that A — λ is not invertible. The question reduces therefore to this: why is a non-invertible operator not invertible? There are several possible ways of answering the question; they have led to several (confusingly overlapping) classifications of spectra.
Modifying the design of ongoing trials without unblinding

Conventional group sequential designs provide an objective basis for reducing the sample size of a trial if the difference between the treatments is much more or much less than anticipated. The flexibility of group sequential designs can be enhanced by allowing the sample size to increase when the variability turns out greater than expected. This can be accomplished by examining the variability before unblinding the data at the first stage of the trial. Depending on the result of this examination, the trial may continue as planned, or the design may change in various ways, for example, by increasing the sample size or by changing the number of stages or the scheduling of the interim analyses. The effect of this adaptive flexibility on the error rates turns out as one would expect from the findings for fixed-sample designs: no material impact on the type I error rate and an effect on the power that depends on the final total sample size.
Electron paramagnetic resonance line shifts and line shape changes due to spin exchange of nitroxide free radicals in liquids. 7. Singly charged surfactant nitroxide.

EPR spectra of aqueous solutions of the singly charged surfactant nitroxide 4-[N,N-dimethyl-N-(ndodecyl)ammonium]-2,2,6,6-tetramethylpiperidinyl-N-oxy bromide-d16 (DCAT12) are studied as functions of the molar concentration, c ) 0.1-8 mM, and the temperature from 273 to 353 K. This concentration range is below the critical micelle concentration, cmc, at which DCAT12 forms micelles. Spin-spin broadening of the EPR lines averaged over the three lines is separated into contributions due to spin exchange, 〈Be〉, and dipolar, 〈Bdip〉, interactions yielding values of the fractional broadening by spin exchange, Ω(T), that vary from near unity at 353 K to approximately 50% at 273 K. This compares with a variation from unity to approximately 77% for a neutral spin probe perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (PDT) over the same range. Unlike PDT and the Stokes-Einstein prediction, the broadening constant by spin exchange, d〈Be〉/dc, is not linear with T/η, where η is the shear viscosity, instead following a quadratic dependence. Nevertheless, d〈Be〉/dc is remarkably close to a hydrodynamic prediction using the Stokes-Einstein equation modified to take the spin probe charge into account. Compared with PDT, values of d〈Be〉/dc are decreased and d〈Bdip〉/dc increased at all temperatures, while the values of the re-encounter rate, τRE1 , deduced from line shifts, are reduced. Interestingly, values of d〈Bdip〉/dc, Ω(T), and τRE1 are comparable for PDT and DCAT12 when compared at the same rotational diffusion rates.
Comparison of bipA alleles within and across Bordetella species.

The Bordetella BvgAS signal transduction system controls the expression of at least three phenotypic phases, the Bvg+ or virulent phase, the Bvg− or avirulent phase, and the Bvgi or Bvg intermediate phase, which has been hypothesized to be important for transmission. bipA, the first identified Bvgi-phase gene, encodes a protein with similarity to the well-characterized bacterial adhesins intimin and invasin. Proteins encoded by the bipA genes present in Bordetella pertussis Tohama I and Bordetella bronchiseptica RB50 differ in the number of 90-amino-acid repeats which they possess and in the sequence of the C-terminal domain. To investigate the possibility that bipA alleles segregate according to host specificity and to gain insight into the role of BipA and the Bvgi phase in the Bordetella infectious cycle, we compared bipA alleles across members of the B. bronchiseptica cluster, which includes both human-infective (B. pertussis and B. parapertussishu) and non-human-infective (B. bronchiseptica and B. parapertussisov) strains. bipA genes were present in most, but not all, strains. All bipA genes present in B. bronchiseptica strains were identical to bipA of RB50 (at least with regard to the DNA sequence of the 3′ C-terminal-domain-encoding region, the number of 90-amino-acid repeats encoded, and expression patterns). Although all bipA genes present in the other Bordetella strains were identical in the 3′ C-terminal-domain-encoding region to bipA of B. pertussis Tohama I, they varied in the number of 90-amino-acid repeats that they encoded and in expression level. Notably, the genes present in B. parapertussishu strains were pseudogenes, and the genes present in B. parapertussisov strains were expressed at significantly reduced levels compared with the levels in B. pertussis and B. bronchiseptica strains. Our results indicate that there is a correlation between specific bipA alleles and specific hosts. They also support the hypothesis that both horizontal gene transfer and fine-tuning of gene expression patterns contribute to the evolution of host adaptation in lineages of the B. bronchiseptica cluster.
New Thermocouple-Based Microwave/Millimeter-Wave Power Sensor MMIC Techniques in GaAs

We describe a new RF and microwave power sensor monolithic microwave integrated circuit design. The circuit incorporates a number of advances over existing designs. These include a III-V epitaxial structure optimized for sensitivity, the figure-of-merit applicable to the optimization, a mechanism for in-built detection of load ageing and damage to extend calibration intervals, and a novel symmetrical structure to linearize the high-power end of the scale.
Intra-abdominal pressure and abdominal wall muscular function: Spinal unloading mechanism

article i nfo Article history: Received 22 January 2010 Accepted 28 June 2010 Background: The roles of antagonistic activation of abdominal muscles and of intra-abdominal pressurization remain enigmatic, but are thought to be associated with both spinal unloading and spinal stabilization in activities such as lifting. Biomechanical analyses are needed to understand the function of intra-abdominal pressurization because of the anatomical and physiological complexity, but prior analyses have been over- simplified. Methods: To test whether increased intra-abdominal pressure was associated with reduced spinal compression forces for efforts that generated moments about each of the principal axis directions, a previously published biomechanical model of the spine and its musculature was modified by the addition of anatomically realistic three-layers of curved abdominal musculature connected by fascia to the spine. Published values of muscle cross-sectional areas and the active and passive stiffness properties were assigned. The muscle activations were calculated assuming minimized muscle stress and stretch for the model loaded with flexion, extension, lateral bending and axial rotation moments of up to 60 Nm, along with intra-abdominal pressurization of 5 or 10 kPa (37.5 or 75 mm Hg) and partial bodyweight (340 N). Findings: The analysis predicted a reduction in spinal compressive force with increase in intra-abdominal pressurization from 5 to 10 kPa. This reduction at 60 Nm external effort was 21% for extension effort, 18% for flexion effort, 29% for lateral bending and 31% for axial rotation. Interpretation: This analysis predicts that intra-abdominal pressure produces spinal unloading, and shows likely muscle activation patterns that achieve this.
Three-dimensional ultrasound imaging using multiple magnetic tracking systems and miniature magnetic sensors

The authors have used several configurations of a commercial 6D magnetic position and orientation measurement system to track an ultrasound scanhead and reconstruct 2D ultrasound images in 3D space. They have measured precision and accuracy with two magnetic sensors working in parallel, and with a miniaturized magnetic sensor. The use of two standard size sensors has shown limited improvement in precision (1.5 mm RMS uncertainty compared with 1.8 mm for a single sensor). The miniature sensor has an average precision of 2.1 mm over its operating range. The miniature sensor has been calibrated with an imaging system and has been used in 3D reconstructions of the stomach and the carotid artery.
Designer Reagents for Mass Spectrometry-Based Proteomics: Clickable Cross-Linkers for Elucidation of Protein Structures and Interactions

We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein–protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enri...
CD4+CD25+ Invariant Natural Killer T Cells Are Enriched in Cord Blood: Implication on Immune-Regulation

unstimulated control. The surface expression of CCR5 was measured separately by flow cytometry. Results: Twenty-four reduced-intensity alloSCT recipients received MVC 300 mg b.i.d. orally from day -3 to day +90 on an ongoing phase II study. Recipient bloodwas tested on days -6 (beforeMVC), 0 and 14, and donor bloodwas tested on day 0. We observed significant variability in surface CCR5 expression on T-cells in donors (range 0e9%) and recipients (range 0e49%). Recipient surface CCR5 expression increased from d-6 to d0 on both CD4 (mean 3.6 to 7.3%, p1⁄40.005) and CD8 (mean 13.5 to 30.6%, p1⁄40.005) T-cells, consistent with blockade of receptor internalization. CD8 T-cell pCCR5 levels increased in response to CCL4 stimulation on d -6 (p1⁄40.01) and decreased in response to MVC (p1⁄40.002), compared to unstimulated blood (Fig. 2). A decrease in pCCR5 levels in response to MVC was observed evenwithout CCL4 stimulation, reflecting loss of background CCR5 activity (p1⁄40.0002). In contrast, d0 pCCR5 levels failed to increase in response to CCL4 (p1⁄40.32), nor did they decrease in response to additional MVC (p1⁄40.13), mirroring effective in vivo blockade of CCR5. The magnitude of increase in CD8 T-cell pCCR5 levels in response to CCL4 stimulation on d-6 correlated with CCR5 surface expression (r1⁄40.55, p1⁄40.02). The same was true of CD4 T-cells (r1⁄40.76, p1⁄40.0004). On d0, however, the ability to stimulate CCR5 inversely correlated with CCR5 surface expression for both CD8 (r1⁄4-0.46, p1⁄40.04) and CD4 (r1⁄4-0.62, p1⁄40.004), suggesting that greater CCR5 surface upregulation may serve as an indicator for complete receptor blockade. Conclusions: Intracellular phosphorylation of CCR5 in response to stimulation is efficiently blocked by MVC in patients undergoing alloSCT, as measured by a novel phosphoflow assay. Upregulation of surface CCR5 may indicate effective CCR5 blockade and should be explored as a biomarker for drug response.
Isolation, characterization, and transcription of the gene encoding mouse mast cell protease 7.

Abstract A gene that encodes mouse mast cell protease (mMCP) 7 (also known as mouse mast cell tryptase 2) was isolated by genomic cloning with a cDNA that encodes mMCP-6, a tryptase in serosal mast cells. cDNAs encoding mMCP-7 were isolated from a bone-marrow-derived mast cell cDNA library. The mMCP-7 gene spans 2.3 kilobases and contains five exons rather than six, as found in the mMCP-6 and human mast cell tryptase I genes. Comparison of the 5' end of the transcript with the genomic sequence indicated that the region corresponding to the first intron in the mMCP-6 and human tryptase I genes is not spliced during transcription of mMCP-7 mRNA because of a point mutation at the intron 1 acceptor splice site; this results in a 5' untranslated region of 195 nucleotides, which is longer than that of any other known mast cell-specific transcript. mMCP-7 is 71-76% homologous with mMCP-6 and with dog and human mast cell tryptases, and it is the most acidic mast cell protease, with an overall net charge of -10. RNA blot analyses revealed that the mMCP-7 gene is transcribed in bone-marrow-derived mast cells but is not transcribed in mature serosal mast cells or in mucosal mast cell-enriched intestinal tissue of Trichinella spiralis-infected mice. Transcription of the mMCP-7 gene by differentiating bone-marrow-derived mast cells occurred within 1 week of bone-marrow culture but decreased dramatically after 3 weeks. Thus, the mMCP-7 gene displays a number of unusual structural characteristics and is distinctive in its transient and selective expression in immature mast cells maintained in interleukin 3-enriched medium.
Robust classification of subcellular location patterns in fluorescence microscope images

The ongoing biotechnology revolution promises a complete understanding of the mechanisms by which cells and tissues carry out their functions. Central to that goal is the determination of the function of each protein that is present in a given cell type, and determining a protein's location within cells is critical to understanding its function. As large amounts of data become available from genome-wide determination of protein subcellular location, automated approaches to categorizing and comparing location patterns are urgently needed. Since subcellular location is most often determined using fluorescence microscopy, we have developed automated systems for interpreting the resulting images. We report here improved numeric features for describing such images that are fairly robust to image intensity binning and spatial resolution. We validate these features by using them to train neural networks that accurately recognize all major subcellular patterns with an accuracy higher than previously reported. Having validated the features by using them for classification, we also demonstrate using them to create Subcellular Location Trees that group similar proteins and provide a systematic framework for describing subcellular location.
Differences between wheat genotypes in damage from freezing temperatures during reproductive growth

Abstract Cereal crops in the reproductive stage of growth are considerably more susceptible to injury from freezing temperatures than during their vegetative growth stage in the fall. While damage resulting from spring-freeze events has been documented, information on genotypic differences in tolerance to spring-freezes is scarce. Ninety wheat genotypes were subjected to a simulated spring-freeze at the mid-boot growth stage under controlled conditions. Spring-freeze tolerance was evaluated as the number of seeds per head at maturity after plants were frozen at −6 °C. Plants that froze, as confirmed by infrared (IR) thermography, died shortly after thawing and consequently the heads did not mature. Only in plants that had no visible freezing (super-cooled) were heads able to reach maturity and produce seeds. In plants that super-cooled four genotypes had significantly higher seed counts after being exposed to freezing than three with the lowest. In addition, significant differences between genotypes were found in whole plant survival among those that had frozen. Genotypes with high whole-plant freezing survival were not necessarily the same as the super-cooled plants with the highest seed counts. Spring-freeze tolerance was not correlated with maturity suggesting that improvement in freezing tolerance could be selected for without affecting heading date. Spring-freeze tolerance was not correlated with freezing tolerance of genotypes of plants in a vegetative state, either under non-acclimated or cold-acclimated conditions indicating that vegetative freezing tolerance is not a good predictor of spring-freeze tolerance.
Abstract 16098: Risk Factors for Frequent Premature Atrial Complexes in a Ten Year Holter Cohort

Introduction: Frequent premature atrial complexes (fPACs) predict increased risk of Atrial Fibrillation (AF). Risk factors for fPACs are not well established. Hypothesis: Patients with fPACs (≥100/day) will differ significantly from those without fPACs (<100/day). Methods: Holter recordings obtained between 2000 and 2010 of 1357 veterans free of AF were analyzed for premature atrial activity. Holter groups with fPACs and infrequent PACs were compared for differences in baseline characteristics obtained from EMR. Statistical comparisons were made using Chi square and student t-tests. Multivariate logistic regression analysis was used adjust for confounders. Results: Mean age of the study population was 64.3 years and 93% were male. Ninety one percent had at least 1 PAC per 24 hour ECG study period. Patients with fPACs were older (mean age 71.4 versus 60.3 years) and had higher mean maximum and a lower mean minimum heart rate. Hypertension, CAD, CHF and COPD were significantly more prevalent in fPAC group. ...
A Multifaceted Approach to Modernizing NASA's Advanced Multi-Mission Operations System (AMMOS) System Architecture

The Advanced Multi-Mission Operations Systems (AMMOS) is NASA's premier space mission operations product line offering for use in deep-space robotic and astrophysics missions. The general approach to AMMOS modernization over the course of its 29-year history exemplifies a continual, evolutionary approach with periods of sponsor investment peaks and valleys in between. Today, the Multimission Ground Systems and Services (MGSS) office-the program office that manages the AMMOS for NASA-actively pursues modernization initiatives and continues to evolve the AMMOS by incorporating enhanced capabilities and newer technologies into its end-user tool and service offerings. Despite the myriad of modernization investments that have been made over the evolutionary course of the AMMOS, pain points remain. These pain points, based on interviews with numerous flight project mission operations personnel, can be classified principally into two major categories: 1) information-related issues, and 2) process-related issues. By information-related issues, we mean pain points associated with the management and flow of MOS data across the various system interfaces. By process-related issues, we mean pain points associated with the MOS activities performed by mission operators (i.e., humans) and supporting software infrastructure used in support of those activities. In this paper, three foundational concepts-Timeline, Closed Loop Control, and Separation of Concerns-collectively form the basis for expressing a set of core architectural tenets that provides a multifaceted approach to AMMOS system architecture modernization intended to address the information- and process-related issues. Each of these architectural tenets will be further explored in this paper. Ultimately, we envision the application of these core tenets resulting in a unified vision of a future-state architecture for the AMMOS-one that is intended to result in a highly adaptable, highly efficient, and highly cost-effective set of multimission MOS products and services.
Two New Species of Stephanothrips from South Carolina and Key to the Known Species (Urothripidae: Thysanoptera)

The two species of Stephanothrips Trybom described below are the only ones of the genus yet found within the bounds of South Carolina. Taxonomically, they are closely related and illustrate a somewhat different type of antenna from that of the other members of the genus. They differ in having segments 4 and 5, i. e., the last two segments, almost completely fused so that they appear as a single segment. Following the descriptions is a key to the known species of the genus.
Does hiring at the “wrong” time pay off?

Research Translation "Contrarian" investment strategies, or courses of action that are in opposition to those of most investors at a given time, have been practiced in the stock market for years. However, contrarian approaches are relatively new to human resource management. Authors Charles Greer of Texas Christian University and Timothy Ireland of Oklahoma State University examined this new practice of hiring to determine whether contrarian human resource practices really work.
The use of a cation exchange resin in decalcification.

Decalcification of 2–3 mm. sections of human ribs by 5–40% concentrations of both formic and nitric acid was subjected to a controlled study. The effect of adding 1 g. of phloroglucinol and of 2.5, 5 and 10 g. of the exchange resin (Win-3000) per 100 ml. of decalcifying solution was observed after staining celloidin sections with hematoxylin and Triosin or with Giemsa stain. Electrolytically decalcified material was included for comparison also. The following conclusions were drawn: (1) The addition of resin did not appreciably shorten the decalcification time nor enhance tissue preservation and staining qualities. (2) Formic acid, 20% or less, gave results superior to nitric acid in any concentration and also superior to those obtained after the electrolytic method. (3) The addition of 1% phloroglucinol to formic acid solution improved both preservation and staining. (4) Helly's fluid fixation with all combinations gave uniformly better results than formalin fixation.
The Present Situation of Centralized Water Supply in Partial Rural Areas of Yongdeng County in 2009

OBJECTIVE To know the present situation of centralized water supply in partial rural areas in Yongdeng County,to provide the scientific basis for further pushing ahead water renovation in Yongdeng,formulating safe drinking water project plan in rural and ensuring farmers' health.METHODS A field investigation was conducted to survey the base situation in 9 spots of centralized water supply in Yongdeng.Water quality test followed the national standard of Standard Examination Methods for Drinking Water(GB/T57502006),results assessment followed the national standard of Standards for Drinking Water Quality(GB/T5749-2006).RESULTS The source of the nine detection points were mainly groundwater,the daily supply capacity of water reached 150~2 000 tons and covered 53 553 population,88.9 of them no any disinfection were made and the water qualification rate were 25.0.There were 9 out of the limits in the 19 measurement indicators and the over-limit ratio of total plate count was the highest(47.2).CONCLUSIONS The sanitary quality of centralized water supply were poor in Yongdeng Rural,the education of sanitation of drinking water for farmers should be strengthened,the water sauce should be protected and the disinfection and water quality monitoring of drinking water also should be enhanced.
Application of Boron-bearing Iron Concentrate to Optimizing Sintering Quality of High Chromium Vanadium-Titanium Magnetite Ore

Experiment on the effects of boron-bearing iron concentrate applied to sintering of high chromium vanadium-titanium magnetic ore was carried out under laboratory conditions. The results showthat,with the increase of boron-bearing iron concentrate addition,vertical sintering speed,sinter yield,tumbler strength,utilization coefficient raise at first then decrease,as well as composite indicator and RDI+ 3. 15. When boron-bearing iron concentrate addition is 5. 0%,the maximum values of the above indexes are 28. 84 mm·min-1,86. 02%,61. 2%,1. 919 t·( m2·h)-1,363 and 90. 76%,respectively. The properties of sinter ore with adding 5. 0% boron-bearing iron concentrate ore are superior to the properties of sinter ore without boron-bearing concentrate. As a result,properties of high chromium vanadium-titanium magnetite sinter ore are optimized with adding balanced amount of boron-bearing iron concentrate,and can meet the higher requirements of blast furnace process.
Coincidence of Opposites in the Thought of Nicolas Cusanus and Niels Bohr

Although they lived nearly 500 years apart, Nicholas of Cusa (Cusanus) and Niels Bohr have a certain commonality. They both maintained that opposite ideas are not always incompatible, but are often complementary. Cusanus called this the coincidence of opposites; Bohr called it complementarity. This essay reviews the lives of these two intellectual leaders and outlines how their devotion to their guiding principle led them to understanding in various fields. For Cusanus, the topic was conciliarism versus papalism. For Bohr, the initial impetus was to resolve the paradox of waves and particles. He later branched into issues such as determinism versus uncertainty, discreet versus continuous models of the nucleus, secrecy versus openness, and objectivity versus subjectivity.
Role of diversity in ICA and IVA: theory and applications

Independent component analysis (ICA) has been the most popular approach for solving the blind source separation problem. Starting from a simple linear mixing model and the assumption of statistical independence, ICA can recover a set of linearly-mixed sources to within a scaling and permutation ambiguity. It has been successfully applied to numerous data analysis problems in areas as diverse as biomedicine, communications, finance, geo- physics, and remote sensing. ICA can be achieved using different types of diversity—statistical property—and, can be posed to simultaneously account for multiple types of diversity such as higher-order-statistics, sample dependence, non-circularity, and nonstationarity. A recent generalization of ICA, independent vector analysis (IVA), generalizes ICA to multiple data sets and adds the use of one more type of diversity, statistical dependence across the data sets, for jointly achieving independent decomposition of multiple data sets. With the addition of each new diversity type, identification of a broader class of signals become possible, and in the case of IVA, this includes sources that are independent and identically distributed Gaussians. We review the fundamentals and properties of ICA and IVA when multiple types of diversity are taken into account, and then ask the question whether diversity plays an important role in practical applications as well. Examples from various domains are presented to demonstrate that in many scenarios it might be worthwhile to jointly account for multiple statistical properties. This paper is submitted in conjunction with the talk delivered for the “Unsupervised Learning and ICA Pioneer Award” at the 2016 SPIE Conference on Sensing and Analysis Technologies for Biomedical and Cognitive Applications. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Paleolithic Diet and the Division of Labor in Mediterranean Eurasia

Hunter-gatherers of the recent era vary in many aspects of culture, yet they display great uniformity in their tendency to divide labor along the lines of gender and age. We argue on the basis of zooarchaeological, technological, and demographic evidence that the complementary economic roles of men and women so typical of ethnographically docu- mented hunter-gatherers did not appear in Eurasia until the beginning of the Upper Paleolithic. The rich archaeological record of Middle Paleolithic cultures in Eurasia suggests, by contrast, that earlier hominins (Neandertals, among others) pursued narrowly focused economies, with women's activities more closely aligned to those of men with respect to schedules and territory use patterns. Hoofed animals were the principal source of meat for virtually all Middle and Upper Paleolithic foragers, but Upper Paleolithic people supplemented diets from large game with a broader spectrum of small animals, leading to considerable expansion in dietary breadth. Parallel trends are apparent in the technological record. Evidence of skill-intensive, time-consuming craft work that normally sup- ports the food quest among recent forager economies also emerged in the early Upper Paleolithic, including indications of dry hide scraping based on lithic micro-wear evidence and widespread use of bone tools suitable for working hide, plant fibers or both. The comparatively narrow reliance on large game animals during the Middle Paleolithic for meat would have constrained the demographic potential of these endemic populations. More broadly based economies, as indicated both by the faunal record and the increasing complexity of foraging and related technologies, appeared earliest in the eastern Mediterranean region and spread (with modification) to the north and west. The behavioral changes associated with the Upper Paleolithic record signal a wider range of economic and technological roles in forager societies, and these changes in adaptation may have provided the expanding Homo sapi- ens populations with a demographic advantage over other hominins in Eurasia. Middle Paleolithic human reproductive units probably were not robust at the micropopulation scale, and localized extinctions were likely to have been common. The demographic robustness of the Upper Paleolithic systems may be explained by the rise of new, diversified strategies for evening-out or sharing risk. When and where Middle and Upper Paleolithic populations first came into contact, the marginal advantages provided by collaborative economies meant that replacement of the Middle Paleolithic groups was only a matter of time.