cssi/SciSciGPT-SciSciNet huggingface dataset:
Saturated fat intake and prostate cancer aggressiveness: results from the population-based North Carolina-Louisiana Prostate Cancer Project.

BACKGROUND Epidemiologic and laboratory evidence supports a role for cholesterol in prostate cancer (PC). Dietary saturated fat content impacts serum cholesterol levels. However, epidemiologic associations between saturated fat and PC aggressiveness are inconsistent. We hypothesized that high saturated fat intake would be associated with increased PC aggressiveness, and that statin use would modify this association. METHODS Of 1854 PC cases in the North Carolina-Louisiana PC Project, 321 (17%) were classified as high aggressive (Gleason sum ⩾8, PSA>20 ng ml-1, or Gleason sum ⩾7 and clinical stage T3-4) or low/intermediate aggressive (all other cases). Using low/intermediate aggressive cases as the referent group, we examined the association between tertiles of total fat-adjusted saturated fat intake and high aggressive PC using logistic regression, overall and stratified by race and statin use. We examined total fat-adjusted polyunsaturated and monounsaturated fatty acids (PUFA and MUFA, respectively), trans fat and cholesterol intake in secondary analysis. RESULTS High total fat-adjusted saturated fat intake was associated with an elevated odds ratio (OR) for aggressive PC (ORT3vsT1 1.51; 95% CI 1.10-2.06; P-trend=0.009), with an attenuated association in statin users (ORT3vsT1 1.16; 95% CI 0.67-2.01; P-trend=0.661) compared with non-users (ORT3vsT1 1.71; 95% CI 1.16-2.51; P-trend=0.053). High total fat-adjusted cholesterol intake was associated with aggressive PC in European Americans (ORT3vsT1 1.62; 95% CI 1.02-2.58; P-trend=0.056), but not African Americans (ORT3vsT1 0.92; 95% CI 0.60-1.42; P-trend=0.750). High total fat-adjusted PUFA was inversely associated with PC aggressiveness (ORT3vsT1 0.75; 95% CI 0.55-1.03), although this was not significant. No associations were found between total fat-adjusted MUFA or trans fat and PC aggressiveness. CONCLUSIONS High total fat-adjusted saturated fat intake was associated with increased PC aggressiveness, with a suggestion of a stronger effect in men not using statins. The association between total fat-adjusted cholesterol intake and PC aggressiveness was most pronounced in European Americans.
RadMAP: The Radiological Multi-sensor Analysis Platform

Abstract The variability of gamma-ray and neutron background during the operation of a mobile detector system greatly limits the ability of the system to detect weak radiological and nuclear threats. The natural radiation background measured by a mobile detector system is the result of many factors, including the radioactivity of nearby materials, the geometric configuration of those materials and the system, the presence of absorbing materials, and atmospheric conditions. Background variations tend to be highly non-Poissonian, making it difficult to set robust detection thresholds using knowledge of the mean background rate alone. The Radiological Multi-sensor Analysis Platform (RadMAP) system is designed to allow the systematic study of natural radiological background variations and to serve as a development platform for emerging concepts in mobile radiation detection and imaging. To do this, RadMAP has been used to acquire extensive, systematic background measurements and correlated contextual data that can be used to test algorithms and detector modalities at low false alarm rates. By combining gamma-ray and neutron detector systems with data from contextual sensors, the system enables the fusion of data from multiple sensors into novel data products. The data are curated in a common format that allows for rapid querying across all sensors, creating detailed multi-sensor datasets that are used to study correlations between radiological and contextual data, and develop and test novel techniques in mobile detection and imaging. In this paper we will describe the instruments that comprise the RadMAP system, the effort to curate and provide access to multi-sensor data, and some initial results on the fusion of contextual and radiological data.
BRAIN TUMORS AND INFANTILE SPASMS

Two patients, aged 6 and 7 months, with brain tumors who presented with infantile spasms and hypsarrhythmia are reported from Sapporo and Asahikawa Medical Universities, Japan.
Spatiotemporal Mobility Prediction in Proactive Self-Organizing Cellular Networks

Mobility prediction, one of the key enablers of proactive self-organizing networks, aims at efficient management of future cellular networks, which are envisaged to be extremely dense and complex due to conglomeration of diverse technologies. This paves the way for resource reservation prior to actual handover for seamless handover experience and for forecasting user traffic distribution. In this letter, we have utilized semi-Markov model for spatiotemporal mobility prediction coupled with steady state and gain analysis in cellular networks. Maximum prediction accuracy of 90% is achieved in the experimental evaluation leveraging on the real network traces generated by smartphone application.
Genetic aspects of cutaneous malignant melanoma

For those of us engaged in studying familial cancer in general, and familial melanoma in particular, it is both fitting and fascinating to learn that the first patient with malignant melanoma of the skin described in the English language literature was a member of a melanoma-prone family (Norris 1820). Writing in 1820, describing a patient he had treated 3 years earlier, Dr. William Norris (an eminent Scottish surgeon of the day) reported in graphic detail the now all-too-familiar downhill course of far-advanced, widely disseminated melanoma. At the end of his vivid clinical case report, Norris noted “It is remarkable that this gentleman’s father, about thirty years ago, died of a similar disease.... This tumor originated in a mole, and it will be worth mentioning that not only my patient and his children had many moles on various parts of their bodies, but also his own father and brothers had many of them.... These facts, together with a case that has come under my notice rather similar, would incline me to believe that this disease is hereditary.” Thus, Norris both described the first melanoma-prone kindred and raised the hypothesis that its melanoma susceptibility was related to the presence of numerous moles.
Carcinoma mamário metastático em uma vaca: relato de caso

Introducao: O carcinoma mamario e a proliferacao ati- pica de celulas epiteliais da glândula mamaria, que tende a invadir tecidos adjacentes e originar metastases. Pode ocorrer em qualquer especie, porem e comumente encontrado em cadelas, associado ao uso de medicamentos hormonais e animais nao castrados. Ja nos bovinos, o carcinoma de mama e raro. Pode estar associado ao uso de hormonios reprodutivos e de crescimento, normalmente em animais acima dos oito anos de idade (Sonja et al. 2013). Nos bovinos, os sinais clinicos associados sao aumento de volume da glândula mamaria, mastites cronicas e nao responsivas a tratamentos clinicos. O presente trabalho tem como objetivo relatar um caso de carcinoma tubulo-papilar metastatico de glândula mamaria em um bovino de leite, enfatizando os achados clinicos, necroscopicos, histopatologicos e imuno-histoquimicos.
The Sub-Committees

Two important sub-committees were established during the Evian Conference, as this chapter outlines. The first was established for the purpose of hearing out the representatives of the many refugee organizations that had come to Evian to present their respective cases to the delegates. The second was a technical sub-committee that would gather information as to the number and type of immigrants each country was prepared to accept. This chapter outlines the ways in which the two sub-committees functioned, including the representations made by the League of Nations High Commissioner for Refugees, Sir Neill Malcolm, to the conference plenary. Finally, the chapter evaluates the effectiveness of the two sub-committees, in which it was held by many that the “real” work of the conference took place.
Bentu – Chinese Artists in a Time of Turbulence and Transformation: Suzanne Pagé, Laurence Bossé, Philip Tinari, and Claire Staebler, eds.

Review of Page, Suzanne, Laurence Bosse, Philip Tinari, and Claire Staebler, eds. Bentu - Chinese Artists in a Time of Turbulence and Transformation: Cao Fei, Hao Liang, Hu Xiangqian, Liu Chuang, Liu Shiyuan, Liu Wei, Liu Xiaodong, Qiu Zhijie, Tao Hui, Xu Qu, Xu Zhen, Yang Fudong, exh. cat. Paris: Fondation Louis Vuitton, 2016. Texts by Suzanne Page, Laurence Bosse, Philip Tinari, Pierre Haski, Lu Minjun, Nikita Yingqian Cai, Sun Dongdong, Claire Staebler, Venus Lau, Sasha Zhao, Robin Peckham, Jerome Sans, Liu Tian, Yang Zi, Zhang Xiyuan, Philip Tinari, and Aimee Lin. 179 pp., 83 color ills., Paperback €35 (978 0 300 22238 8)
Prevalence of Shiga-toxigenic Escherichia coli in House Flies (Diptera: Muscidae) in an Urban Environment.

House flies (Musca domestica L. [Diptera: Muscidae]) can act as a mechanical vector for food-borne pathogens including Shiga toxin-producing Escherichia coli (Migula; Enterobacteriales: Enterobacteriaceae) (STEC) in and around cattle feedlots. The present study assessed the prevalence of STEC in house flies from a restaurant area of a town in northeastern Kansas. Two hundred twenty-four house flies were collected over 10 wk, surface sterilized, individually homogenized, and cultured by a multifaceted approach of direct plating on selective media and an enrichment broth, followed by the immunomagnetic separation. Bacterial isolates were screened for eight serogroups of E. coli: O103, O104, O26, O111, O45, O145, O121, and O157 using multiplex polymerase chain reaction (PCR). Furthermore, O-serogroup-positive isolates were tested for virulence genes stx1, stx2, eae, and ehxA by PCR. The majority (91.5%) of flies carried enteric bacteria, and the mean value of enteric concentration on the modified Posse agar was 6.7 ± 1.1 × 106 colony forming units per fly. Thirty-nine of the 224 flies (17.4%) were positive for one or more E. coli serogroup of interest; with the majority O103 (10.7%), followed by O26 (3.1%), O121 (1.3%), O45 (1.3%), and O104 (0.9%). However, none of the serogroup-positive isolates carried any of the virulence genes tested. Results of our study show that house flies in the urban environment do not carry STEC. Nevertheless, detection of E. coli O-serogroups with the potential to acquire virulence traits indicates that house flies in an urban environment represent a public health risk.
High Internal Quantum Efficiency Ultraviolet Emission from Phase-Transition Cubic GaN Integrated on Nanopatterned Si(100)

Ultraviolet emission characteristics of cubic (c-) GaN enabled through hexagonal-to-cubic phase transition are reported. Substrate patterning and material growth are shown to affect phase purity and emission characteristics of c-GaN as studied by electron backscatter diffraction, and photo- and cathodoluminescence, respectively. Raman study shows a tensile strain in the c-GaN. Time-resolved photoluminescence reveals c-GaN band edge emission decay time of 11 ps. The ultraviolet emissions from both phases of GaN are linearly polarized in the same direction, which is along the ⟨1120⟩ and ⟨110⟩ directions of hexagonal GaN and c-GaN, respectively. Temperature-dependent (5.7 to 280 K) cathodoluminescence studies reveal an internal quantum efficiency of ∼29% at room temperature along with intrinsic and extrinsic defect energy levels of ∼124 and ∼344 meV, respectively, of the phase-transition c-GaN. Using the IQE value and carrier decay lifetime, a radiative lifetime of 38 ps is extracted. Overall, photonic prop...
Psychiatric Case Review and Treatment Intensification in Collaborative Care Management for Depression in Primary Care

Objective:This study examined whether psychiatric case review was associated with depression medication modification in a large implementation program of collaborative care for depression in safety...
ATP and Odor Mixture Activate TRPM5-Expressing Microvillous Cells and Potentially Induce Acetylcholine Release to Enhance Supporting Cell Endocytosis in Mouse Main Olfactory Epithelium.

The main olfactory epithelium (MOE) functions to detect odor molecules, provide an epithelial surface barrier, and remove xenobiotics from inhaled air. Mechanisms coordinating the activities of different cell types within the MOE to maintain these functions are poorly understood. Previously, we showed that superficially located microvillous cells (MCs) in the MOE expressing transient receptor potential channel M5 (TRPM5) are cholinergic and chemoresponsive and that they play an important role in maintaining odor responses and olfactory-guided behavior under challenging chemical conditions. Here we investigated TRPM5-MC activation and subsequent paracrine regulation. Ca2+ imaging showed that TRPM5-MCs dose-dependently increase their intracellular Ca2+ in response to ATP, an important signaling molecule for airway mucociliary movement, and to an odor mixture. Pharmacological examination showed that the ATP responses are primarily mediated by P2X purinergic receptors. Interestingly, using the endocytosis dye pHrodo Red dextran, we found that chemical-activated TRPM5-MCs significantly increase the number of pHrodo-labeled puncta compared to controls without stimulation and compared to cells that do not respond to ATP or to the odor mixture. These results indicate potential vesicle recycling after release of the signaling molecule acetylcholine (ACh). Interestingly, TRPM5 knockout results in a decrease in ATP-induced pHrodo internalization. We further investigated cholinergic regulation of neighboring supporting cells (SCs). We found that ACh strongly elevates intracellular Ca2+ and potentiates pHrodo endocytosis in SCs. The ACh effects are diminished in the presence of atropine or M3 muscarinic receptor antagonist and in SCs lacking M3 receptors. Collectively, these data suggest that TRPM5-MCs may regulate the MOE’s multicellular network activity via cholinergic paracrine signaling for functional maintenance and adaptive plasticity.
Conservation of Mannan Synthesis in Fungi of the Zygomycota and Ascomycota Reveals a Broad Diagnostic Target

Ascomycetes and zygomycetes account for the majority of (i) fungi responsible for cutaneous, subcutaneous, and invasive human fungal infections, (ii) plant fungal pathogens, (iii) fungi that threaten global biodiversity, (iv) fungal agents of agricultural spoilage, and (v) fungi in water-damaged buildings. Rapid recognition of fungal infection (or contamination) enables early treatment (or remediation). A bioinformatics search found homologues of Saccharomyces cerevisiae Mnn9p present in members of the Zygomycota and Ascomycota phyla and absent in members of the Chytridiomycota and Basidiomycota. Mnn9p is a component of the yeast mannan polymerization complex and is necessary for α-1,6 mannan production. A monoclonal antibody (2DA6) was produced that was reactive with purified mannans of Mucor, Rhizopus, Aspergillus, Fusarium, and Candida species. Experimentation using a 2DA6 antigen capture enzyme-linked immunosorbent assay (ELISA) and extracts of fungi from the four phyla found agreement between the presence or absence of Mnn9p homologues and production or lack of production of mannan reactive with 2DA6. Studies of cell extracts from yeast mannan mutants identified α-1,6 mannan as the epitope recognized by 2DA6. To translate this finding into a point-of-use diagnostic, a 2DA6 lateral flow immunoassay was constructed that detected mannan in (i) extracts of dermatophytes and fungi that produce trauma-related infection and (ii) tissue from plants infected with Grosmannia clavigera or Sclerotium cepivorum These studies (i) revealed that the conservation of α-1,6-linked mannan in fungi of the Zygomycota and Ascomycota can be exploited as a broad diagnostic target and (ii) have provided a means to detect that target in an immunoassay platform that is well suited for clinic or field use.IMPORTANCE A key question asked when faced with an infection, an infestation, or environmental damage is whether it is a fungus. Identification of fungi as the cause of the problem can lead to remediation or treatment. Zygomycetes and ascomycetes account for the vast majority of fungal causes of human, animal, and plant disease, large-scale biodiversity loss, agricultural spoilage, and contamination of water-damaged buildings. These studies revealed the conservation of a common cell wall structural component of zygomycetes and ascomycetes to be a diagnostic target applicable to multiple pathogenic fungi and have leveraged that insight for practical use. Monoclonal antibodies reactive with this pan-fungal structure were produced and used to construct immunoassays (including ELISA and lateral flow assay) for detection of a broad range of pathogenic fungi.
Blue Cone Monochromacy

Blue cone monochromacy (BCM) is an X-linked ocular disorder in which affected males have normal short-wavelength-sensitive (blue) cone and rod function but lack medium-(green) and long-wavelength-sensitive (red) cone function. Affected males characteristically have visual acuities of 20/100 to 20/200, myopia, nystagmus, and minimal foveal granularity with otherwise normal fundus findings.1
Quality Oversight: Patient Satisfaction Surveys

It is likely that health care providers will increasingly compete on the basis of value (the quality of care in relation to the total cost of care) and that health plan members (not patients) and purchasers of care (not third-party payers) will be viewed as the main customers of the health care system. Whether or not this comes to pass, the attitudes and satisfactions of patients will continue to be paramount.
The Bidirectional Effect of Inflammation on Bacterial Growth: A New Insight into the Role of Glucocorticoids in the Resolution of Severe Infections

The ability to generate and respond to signaling molecules establishes a mechanism for regulated cell-to-cell communication. Cells coordinate their growth and proliferation with autocrine and paracrine signaling by means of low molecular weight polypeptides called cytokines. Innate or natural immunity is a highly conserved defense mechanism against infections found in all multicellular organisms (1). The inflammatory reaction is a fundamental component of the innate immune response, and its most proximal expression is characterized by the elaboration of proinflammatory cytokines—tumor necrosis factor (TNF)-α and interleukin (IL)-1β. Response to cytokines is generally viewed as exclusive to cells containing a defined nucleus, since cytokines are intended to work on well-defined eukaryotic cells with consequent signal transduction events.
Export-Oriented International Joint Venture: Endogenous Set-Up Costs and Information Gathering

We analyze the formation of an export-oriented international joint venture (IJV) between a multinational corporation (MNC) and a domestic firm under demand uncertainty and in a principal-agent framework. The MNC possesses a superior production technology and is better at predicting foreign market demand. The domestic firm can reduce set-up costs of the IJV with effort levels that is endogenously determined. We examine how the MNC's preference for, and the ownership structure of, a joint venture depend on the efficiency of information gathering and of cost reduction, and on the nature of credit markets. We find, inter alia, that when the credit constraint is severe the MNC does not push the domestic firm to its reservation profit level. A relaxation of the credit constraint facing the domestic firm never makes it better off and in fact makes the domestic firm worse off when the credit constraint is severe.
Glioma cell proliferation is enhanced in the presence of tumor-derived cilia vesicles

The mechanisms by which primary cilia affect glioma pathogenesis are unclear. Depending on the glioma cell line, primary cilia can promote or inhibit tumor development. Here, we used piggyBac-mediated transgenesis to generate patient-derived glioblastoma (GBM) cell lines that stably express Arl13b:GFP in their cilia. This allowed us to visualize and analyze the behavior of cilia and ciliated cells during live GBM cell proliferation. Time-lapse imaging of Arl13b:GFP+ cilia revealed their dynamic behaviors, including distal tip excision into the extracellular milieu. Recent studies of non-cancerous cells indicate that this process occurs during the G0 phase, prior to cilia resorption and cell cycle re-entry, and requires ciliary recruitment of F-actin and actin regulators. Similarly, we observed ciliary buds associated with Ki67− cells as well as scattered F-actin+ cilia, suggesting that quiescent GBM cells may also utilize an actin network-based mechanism for ciliary tip excision. Notably, we found that the proliferation of ciliated GBM cells was promoted by exposing them to conditioned media obtained from ciliated cell cultures when compared to conditioned media collected from cilia-defective cell cultures (depleted in either KIF3A or IFT88 using CRISPR/Cas9). These results suggest that GBM cilia may release mitogenic vesicles carrying factors that promote tumor cell proliferation. Although Arl13b is implicated in tumor growth, our data suggest that Arl13b released from GBM cilia does not mediate tumor cell proliferation. Collectively, our results indicate that ciliary vesicles may represent a novel mode of intercellular communication within tumors that contributes to GBM pathogenesis. The mitogenic capacity of GBM ciliary vesicles and the molecular mediators of this phenomenon requires further investigation.
Analysis of Malpractice Claims Involving Diagnostic and Interventional Neuroradiology.

Abstract Background Radiologists are increasingly the subject of costly medical malpractice claims. As the field continues to expand to include numerous minimally invasive procedures and diagnostic studies, radiologists are more exposed than ever to medical malpractice. Despite this, little is known on the outcomes of these litigations. Methods A retrospective investigation of the VerdictSearch legal claims database was performed, examining litigations involving radiologists’ interpretation of neuro-imaging and neurological procedures performed by radiologists (including interventional radiologists and diagnostic neuroradiologists). Allegations, outcomes, and payouts were examined. Results In total, 126 cases were analyzed. Mean age of plaintiffs was 45 ± 18.8 years; 64 (50.8%) plaintiffs were men. Fifty-two (41%) cases listed irreversible brain damage as a complication. Paralysis and death were listed in 40 (32%) and 34 (27%) cases, respectively. In total, 44% (55) resulted in a defendant ruling, 25% (25) in a plaintiff ruling, 26% (33) in a settlement, and 5% (7) in a mixed decision. Total liabilities of the 126 cases were $390,329,929, with individual awards ranging from $50,000 to $45,000,000. Median plaintiff award was $2,877,847 (interquartile range: $1,250,000-$6,412,159; mean: $8,446,547 ± $13,036,244). Median settlement amount was $1,950,000 (interquartile range: $934,250-$3,625,000; mean: $2,455,250 ± $1,951,549). Conclusions This study is the first examination of legal claims involving neuroradiology. Over 50% of claims against radiologists end in provider loss, which is both financially costly and detrimental to physicians, practices, and institutions. This information may inform physicians regarding common diagnostic and interventional errors, and potentially minimize medicolegal risk.
Dielectric waveguides with embedded graphene nanoribbons for all-optical broadband modulation

All-optical processing offers low power consumption and fast operation speed and is a promising approach to high-bit-rate communication. Realization of all-optical integrated photonics requires core materials that strongly mediate photon–photon interaction. Recently, it was shown that, in the long-wavelength limit, graphene nanoribbons (GNRs) have a very strong Kerr optical nonlinearity in the telecom wavelength range (1.3−1.6μm). We propose a dielectric waveguide with embedded GNRs for all-optical self-amplitude-modulation applications. By implanting a van der Waals (vdW) heterostructure consisting of GNRs and hexagonal boron nitride into a rib silicon waveguide, we maximize the optical concentration near the GNRs and enhance nonlinear optical effects. Different-width GNRs incorporated in the vdW heterostructure provide strong self-sustaining broadband modulation over the telecom frequency range, without a need for dynamical tuning. The compact footprint and self-sustaining, broad-bandwidth saturable absorption make the proposed device a suitable component for ultrafast nanophotonic applications.
Robust Face Verification via Disentangled Representations.

We introduce a robust algorithm for face verification, i.e., deciding whether twoimages are of the same person or not. Our approach is a novel take on the idea ofusing deep generative networks for adversarial robustness. We use the generativemodel during training as an online augmentation method instead of a test-timepurifier that removes adversarial noise. Our architecture uses a contrastive loss termand a disentangled generative model to sample negative pairs. Instead of randomlypairing two real images, we pair an image with its class-modified counterpart whilekeeping its content (pose, head tilt, hair, etc.) intact. This enables us to efficientlysample hard negative pairs for the contrastive loss. We experimentally show that, when coupled with adversarial training, the proposed scheme converges with aweak inner solver and has a higher clean and robust accuracy than state-of-the-art-methods when evaluated against white-box physical attacks.
Global Fits of B Decay Anomalies

I summarize the current status of the anomalies that are observed in decays of b hadrons based on the charged current \(b \rightarrow c \ell \nu \) transition and the neutral current \(b \rightarrow s \ell \ell \) transition. After a quick review of the experimental situation I discuss the results of a recent global fit in the context of the weak effective theory at the b-quark scale, in the Standard Model effective theory above the electroweak scale, and in a simplified \(Z^\prime \) model. The experimental data continues to consistently point to new physics in semi-leptonic Wilson coefficients with high significance.
A note on knot Floer homology and fixed points of monodromy

Using an argument of Baldwin--Hu--Sivek, we prove that if $K$ is a hyperbolic fibered knot with fiber $F$ in a closed, oriented $3$--manifold $Y$, and $\widehat{HFK}(Y,K,[F], g(F)-1)$ has rank $1$, then the monodromy of $K$ is freely isotopic to a pseudo-Anosov map with no fixed points. In particular, this shows that the monodromy of a hyperbolic L-space knot is freely isotopic to a map with no fixed points.
Deconvolving signals of the stretched exponential form.

A solution is presented for parametrically deconvolving an axisymmetric intrinsic field signal when it is expected to conform to the stretched exponential family of functions (SEF). Except for the Gaussian SEF, computable analytical models for the forward Abel transform of SEFs did not exist until recently. I will highlight a novel mathematical identity that has facilitated this calculation and show how to use the 2D models for the Abel transform to reconstruct the 3D signal to an accuracy of ∼10−6 (or better) under noise-free conditions (possibly even with zero error). Several deconvolution techniques have tested their reconstructions using a noise-free projection of the Gaussian. Under similar conditions, our reconstruction produces errors ∼1950 times lower than 10 other techniques; we get significantly lower errors for other SEFs as well using fewer computing resources. Additionally, unlike other methods, our approach works on unequally spaced data and does not encounter the problem of increasing errors with radii in the outer parts as seen in all other methods. I will describe applications in the imaging of diverse astrophysical and biological systems where SEFs have been used and also highlight the possibility of using the projection of SEFs as basis functions in image deconvolution algorithms.
Tree Variable Selection for Paired Case–Control Studies with Application to Microbiome Data

When case–control studies involve paired samples, tree analyses based on traditional splitting rules are suboptimal as they ignore the paired nature of the data. Paired samples occur in microbiome studies when they are collected from different locations of the same individual or when they are collected from paired individuals with familial ties. Borrowing concepts from tree splitting, we propose a novel approach that accommodates the paired structure in the data for fast and effective nonparametric variable ranking. Importantly, this method allows detangling of different types of associations at play with structured correlated outcomes such as host genotype and environmental exposure effects. Another technique for variable selection are variable importance measures. In this chapter, we describe two types of measures useful for paired data analysis. The methodology is illustrated on the microbiota of paired samples from a case–control study of obesity.
A Hybrid EM Algorithm for Linear Two-Way Interactions with Missing Data

We study an EM algorithm for estimating product-term regression models with missing data. The study of such problems in the likelihood tradition has thus far been restricted to an EM algorithm method using full numerical integration. However, under most missing data patterns, we show that this problem can be solved analytically, and numerical approximations are only needed under specific conditions. Thus we propose a hybrid EM algorithm, which uses analytic solutions when available and approximate solutions only when needed. The theoretical framework of our algorithm is described herein, along with two numerical experiments using both simulated and real data. We show that our algorithm confers higher accuracy to the estimation process, relative to the existing full numerical integration method. We conclude with a discussion of applications, extensions, and topics of further research.
Avidense: advanced video analysis system for colonoscopy semantics

Colonoscopy is an important screening tool for colorectal cancer. During a colonoscopic procedure, a tiny video camera at the tip of the endoscope generates a video signal of the internal mucosa of the colon. The video data are displayed on a monitor for real-time analysis by the endoscopist. We call videos captured from colonoscopic procedures "colonoscopy videos". To the best of our knowledge, they are not captured for post procedural review or analysis in the current practice. Because of the unique characteristics of colonoscopy videos, new types of semantic units and new image/video analyzing techniques are required. In this dissertation, we aim to develop new image/video analysis techniques for these videos to extract important semantic units, such as colonoscopic scenes, operation shots, and appendix images. Our contributions include two parts: (a) new definitions of semantic units (colonoscopic scene, operation shot, and appendix image); and (b) novel image/video analysis algorithms, including novel scene segmentation algorithms using audio and visual information to recognize scene boundaries, new computer-aided detection approaches for operation shot detection, and new image analysis methods for appendix image classification. The new image processing and content-based video analysis algorithms can be extended to videos from other endoscopic procedures, such as upper gastrointestinal endoscopy, EGD, enteroscopy, bronchoscopy, cystoscopy, and laparoscopy. Our research is very useful for the following platforms and resources: (a) platforms for new methods to discover unknown patterns of diseases and cancers; (b) platforms for improving and assessing endoscopists procedural skills; and (c) education resources for endoscopic research.
Molecular orientation in quantasomes. I. Electric dichroism and electric birefringence of quantasomes from spinach chloroplasts.

Quantasomes (lamella subunits) isolated from spinach chloroplasts have been shown to exhibit both intrinsic electric birefringence (Kerr effect) and intrinsic electric dichroism. Measurements of Kerr constants and of rotational relaxation times suggest that the birefringence arises primarily from the proteins in the preparations. The smallest particles studied give rise to rotational relaxation times in the range 20 to 200 μsec. The shortest times may be associated with a particle having a permanent dipole moment. The spherical chromatophore subunits from Rhodospirillum rubrum do not exhibit detectable electric birefringence, as measured in the apparatus of this study. The dichroic ratio spectrum from 330 to 730 mμ of spinach quantasomes has been determined by electric dichroism measurements. The measured dichroic ratios of 1·03 to 1·10 throughout most of the spectrum suggest that the chlorophyll and carotenoid molecules in the quantasome are largely unoriented. A pronounced peak occurs in the dichroic ratio spectrum at 695 mμ, about 17 mμ to the long wavelength side of the strong chlorophyll a absorption maximum in this region. The dichroic ratio increment is at least five times greater at 695 than at 678 mμ. The dichroism anomaly is interpreted as resulting from a small fraction (∼5%) of the chlorophyll a which is strongly oriented at a particular site (the quantatrope) in the quantasome. It is suggested that an oriented cytochrome and one or more bound acceptor molecules are present at this site as well. A mechanism is postulated whereby electronic excitation energy resulting from the absorption of light by the pigments of the quantasome is converted at the quantatrope to chemical potential associated with electron transport processes.
Seeing through obscure glass

Obscure glass is textured glass designed to separate spaces and "obscure" visibility between the spaces. Such glass is used to provide privacy while still allowing light to flow into a space, and is often found in homes and offices. We propose and explore the challenge of "seeing through" obscure glass, using both optical and digital techniques. In some cases - such as when the textured surface is on the side of the observer - we find that simple household substances and cameras with small apertures enable a surprising level of visibility through the obscure glass. In other cases, where optical techniques are not usable, we find that we can model the action of obscure glass as convolution of spatially varying kernels and reconstruct an image of the scene on the opposite side of the obscure glass with surprising detail.
Triornithine-resistant strains of Escherichia coli. Isolation, definition, and genetic studies.

Abstract Triornithine-resistant (TOR) mutants were isolated from several strains of Escherichia coli K-12. All of the mutants were found to be oligopeptide transport-deficient (Opp-). The dipeptide transport system (or systems) was not altered. The rate of growth of these mutants, the morphology of the cells and their colonies and the sensitivity to the phages T1, T4, P1, and φ80 were similar to the parental strains, indicating no dramatic changes at the cell envelope. All Opp- mutants tested showed 98% linkage to trp in sexual recombination, and 80 to 95% P1-mediated co-transduction frequencies. The opp gene is therefore the closest marker to the trp operon. A mutant with a deletion in the region att φ80, tonB, trp still contained the opp gene (or genes), indicating its appearance on the cysB side of the trp operon.
Anatomy of the Breast

The term breast includes a variety of anatomical structures lying on the anterior aspect of the thorax. Contained within it is the mammary gland, a highly specialized cutaneous glandular structure, composed of elements involved in the secretion and ejection of milk. This gland is a well-defined dermal structure which has become too large to remain within the skin itself and has, therefore, invaded the underlying subcutaneous and fascial elements. The gland is peculiar to mammals and its development and structure are strikingly similar in even the lowest of this class. In the human, the gland is composed of some 15 to 20 lobules which originate from the nipple and areola, and radiate along the anterior and lateral thoracic wall (Fig. I).1 The mammary gland is only one component of the breast; other components include a variable quantity of fat, connective tissue, vessels, nerves, and lymphatics.
This Land, This Nation: Conservation, Rural America, and the New Deal

This 2007 book combines political with environmental history to present conservation policy as a critical arm of New Deal reform, one that embodied the promises and limits of midcentury American liberalism. It interprets the natural resource programs of the 1930s and 1940s as a set of federal strategies aimed at rehabilitating the economies of agricultural areas. The New Dealers believed that the country as a whole would remain mired in depression as long as its farmers remained poorer than its urban residents, and these politicians and policymakers set out to rebuild rural life and raise rural incomes with measures tied directly to conservation objectives - land retirement, soil restoration, flood control, and affordable electricity for homes and industries. In building new constituencies for the environmental initiatives, resource administrators and their liberal allies established the political justification for an enlarged federal government and created the institutions that shaped the contemporary rural landscape.
Putting the romance back into sex: Sexuality in romantic relationships

Recent media attention on romantic relationships and sexual behavior in emerging adulthood has portrayed hooking up as a primary means of sexual interaction among young people. Popular books on adolescent and emerging adult sexuality include titles such as Hooking Up: Sex, Dating, and Relationships on College Campuses (Bogle, 2008) and Unhooked: How Young Women Pursue Sex, Delay Love, and Lose at Both (Stepp, 2007); recent articles in the New York Times include scintillating titles like “The Demise of Dating” (Blow, 2008) and “Friends with Benefits, and Stress Too” (Carey, 2007). Popular media frequently portray emerging adults similarly, whether through movies like American Pie 2 or “reality” television like MTV's The Real World . However, as we describe later, these portrayals do not capture the reality of emerging adults' experiences, only presenting a small piece of a very complex picture. THEORIES OF SEXUALITY Mirroring limitations in the media, theories of sexuality do not adequately address emerging adults' sexual behaviors within romantic relationships. Theories about sex tend to fall into four categories. First, biological theories focus on pubertal development and hormonal activation and therefore are more relevant for adolescents than for emerging adults (Rodgers & Rowe, 1993; Udry, Billy, Morris, Gruff, & Raj, 1985). Second, problem behavior theories describe adolescent sexual behaviors within a constellation of other problem behaviors that share antecedents (e.g., Jessor & Jessor, 1975; Newcomb, Huba, & Bentler, 1986). Emerging adults obviously engage in some sexual behaviors with potentially negative physical or psychological consequences.
Effect of clay on the dielectric relaxation of ethylene propylene rubber using thermally stimulated discharge current measurements

Clay filler in EPR (ethylene propylene rubber) causes a peak in the TSDC (thermally stimulated discharge current) spectra at about 40 /spl deg/C. The peak displays dipole behavior and has an activation of 0.48eV. It seems to consist of one single relaxation peak and two smaller peaks which have not yet been analyzed. Reducing the clay concentration and particle size reduces the size of the peak. The polarization mechanism which causes this peak is not clear. It is possible that aggregation of the clay, adhesion of the clay to the polymer, or particle-particle interactions may affect this mechanism. >
Studies on Succinate Dehydrogenase

1 Succinate dehydrogenase flavocoenzyme (“SD-flavin”), previously shown to be an 8α-substituted riboflavin derivative containing a tertiary nitrogen homoconjugated to the flavin nucleus, was subjected to further hydrolysis and to reduction under acid conditions. Both conditions resulted in the liberation of 1 mole of histidine per mole of flavin. This proves histidine to be the covalent link between flavin and peptide backbone in succinate dehydrogenase and imidazole to be the tertiary nitrogen function homoconjugated to the flavin. 2 8α-Histidyl-riboflavin has been synthesized starting from riboflavin chemically and shown to be completely identical with the natural product in optical, ESR and NMR spectra, pH-fluorescence curve and behavior on thin-layer and paper chromatography, as well as paper electrophoresis. 3 Both the natural compound isolated by acid hydrolysis of flavin peptide and the synthetic one contain two isomers, which may be separated by high voltage electrophoresis. The isomers appear to be the N(1)-and N(3)-imidazole substituted compounds. Digestion of the flavin peptide with aminopeptidase M yields only one isomer but on treatment with 6-N HCl this is gradually converted to a mixture of the two isomers. The absolute assignment of the natural isomer is suggested as 8α-[N(3)-histidyl]-riboflavin on the basis of imidazole quaternization with CH3I, reductive cleavage of the flavin-imidazole bond and identification of the methyl-histidine liberated as 1-methyl-histidine.
Stars and Keys: Folktales and Creolization in the Southwest Indian Ocean

Reviewed Medium: book Authors: Lee Haring Translators: Claudie Ricaud, Dawood Auleear Year: 2007 Pages: 392 Publisher: Indiana University Press ISBN: 978-0-253-34868-5 (hard cover). Prices: $65.00 USD(hard cover).
What Is Paleobiogeography

The field of paleobiogeography is derived in direct lineage from its close intellectual cousin, biogeography, a scientific discipline that had its birth in the adventurous and exploratory urges of humankind. When people traveled to far-off lands centuries ago they discovered, much to their surprise, that the plants and animals of these lands, as well as the fossils preserved in their strata, were often very different from those they were familiar with in their own countries. Indeed, it “ … might have been anticipated (that there would be) an almost perfect identity in the animals and plants which inhabit corresponding parallels of latitude” (Lyell, 1832, p. 66), i.e., similar climates. Instead, the travelers’ senses were enriched with the sounds of new bird songs, the smells of new plants, and the sights of different peoples and cultures. The motivations for these explorations were often both base and noble: the will to power or to dominate a local people by controlling their resources, but also the desire to know and to understand. As this is a scientific text, rather than a sociological one, I am going to focus on what are best perceived as the more noble intentions of humanity. Specifically, how the quest for knowledge about our world is related to the establishment of a tradition in paleobiogeographical and biogeographical research.
Knowledge of hepatitis among active drug injectors at a syringe exchange program

Injecting drug users (IDUs) are at high risk for contracting and spreading viral hepatitis through nonsterile injection practices, unprotected sexual contact, and unsanitary living conditions. We sought to characterize hepatitis knowledge, prior testing, and vaccination history among IDUs at a New York City syringe exchange program (SEP). IDU subjects generally had a poor understanding of viral hepatitis transmission and prevention. We also found low vaccination rates: only 8% reported receiving hepatitis A vaccine and 11%, hepatitis B vaccine. Educating IDUs about risky behaviors and medical preventive interventions, such as vaccines for hepatitis A and B and treatment for hepatitis C, may help prevent disease and reduce transmission. Stronger linkages between health-care centers and SEPs, drug treatment programs, and other service delivery centers where IDUs are encountered may promote hepatitis education and vaccination.
On the rank of an elliptic surface

Nagao has recently given a conjectural limit formula for the rank of an elliptic surface E in terms of a weighted average of fibral Frobenius trace values. We show that Tate's conjecture on the order of vanishing of L2(E,s) essentially implies Nagao's formula; in particular, we prove Nagao's formula for rational elliptic surfaces. In the case that E is a twist, we reduce Nagao's and Tate's conjectures to the case of products of curves, and we verify the conjectures for many new classes of elliptic surfaces of Kodaira dimension 0 and 1.
Determinants of nest repair in laughing gulls

Abstract Laughing gulls Larus atricilla , nesting in saltmarshes subject to tidal inundations, build substantial nests and continue adding material throughout the reproductive cycle. Under normal conditions, nest size increased until gulls had 5-day-old chicks. I manipulated nests at various stages in the reproductive cycle. Until their chicks reached 14 days of age, gulls added material to artificially wetted nests, making them significantly deeper and wider than before treatment. During all reproductive stages examined, gulls repaired nests having half of the material removed. The adaptive significances of nest building and relative nest size are discussed in terms of washouts and the requirements of the eggs and chicks at different stages in the reproductive cycle.
Biotic enhancement of weathering and the habitability of Earth

AN important question in the Earth sciences is the role of the biota in the chemical weathering of silicate rocks, which affects atmospheric CO2 and therefore climate1-10. No comprehensive study of biotic influences, however, has quantitatively examined the climatic consequences were weathering to take place under completely abiotic conditions. Here we calculate that if today's weathering is 10, 100 or 1,000 times the abiotic weathering rate, then an abiotic Earth would be, respectively, ∼15, 30 or 45 °C warmer than today. The upper two temperatures are preferred estimates because of the probable almost complete absence of soil under abiotic conditions, suggesting that without a biota that significantly enhances weathering rates, the Earth today would be uninhabitable for nearly all but the most primitive microbes. Life may have been crucial in cooling early Earth and maintaining relatively cool conditions.
Multiple relational equilibria: Polymorphism, metamorphosis and other possibly similar phenomena

In a preceding paper (Rashevsky, 1969. “Outline of a Unified Approach to Physics, Biology and Sociology.”Bulletin of Mathematical Biophysics,31, 159–198) certain isomorphisms between biological and social systems on the one hand and physical systems on the other were studied. The notion or relational forces, of which ordinary physical forces are a particular case, was introduced. In the present paper an attempt is made to establish analogies between stable equilibria in physical systems, equilibria due to physical forces, and stable equilibria in biological and social systems which are due to purely relational forces. The notion of relational forces causing multiple equilibria similar to multiple equilibria in some physical systems is studied, and it is outlined how this notion may possibly help the understanding of such phenomena as polymorphism, metamorphosis and the existence of rudimentary organs or rudimentary functions.
System-level performance optimization and benchmarking for on-chip graphene interconnects

In this paper, graphene interconnects are analyzed and benchmarked against conventional copper wires, indicating the advantage of using graphene at a short wire length or being driven by a device with a large output resistance. For the first time, a system-level optimization of graphene interconnects is performed for both single- and multi-core chips. It is found that under the same power density and die size area, an optimized multi-core processor using graphene as short interconnects can provide up to 25 % and 55% improvements in throughput and energy × execution time per instruction, respectively.