cssi/SciSciGPT-SciSciNet huggingface dataset:
Metastasis-related genes in prostate cancer: the role of caveolin-1.

Prostate cancer continues to be a significant cause of death in U.S. men despite screening of asymptomatic men and extensive treatment with potentially curative therapies, predominantly radical prostatectomy and irradiation therapy. The reason for the persistent mortality resides in part in the presence of occult metastases at the time of treatment. Currently there are no curative therapies for metastatic prostate cancer. To better understand the metastatic phenotype in prostate cancer, we developed a strategy to compare and isolate mRNAs that are expressed differentially in cell lines derived from primary versus metastatic mouse prostate cancer using differential display-PCR. This strategy has proven to be successful and multiple gene sequences associated with metastasis in this model are being investigated. One of the genes isolated by this method was caveolin-1. Caveolin-1 was found to be overexpressed not only in metastatic mouse prostate cancer, but also human metastatic disease. Recent studies have indicated that suppression of caveolin expression induces androgen sensitivity in high-caveolin, androgen-insensitive mouse prostate cancer cells derived from metastases. Overexpression of caveolin leads to androgen insensitivity in low-caveolin, androgen-sensitive mouse prostate cancer cells. Caveolin-1, therefore, is a metastasis-related gene and a candidate gene for hormone-resistant prostate cancer in man.
Modeling of lithium granule injection in NSTX using M3D-C1

In this paper, we present simulations of pedestal control by lithium granule injection (LGI) in NSTX. A model for small granule ablation has been implemented in the M3D-C1 code (Jardin et al 2012 Comput. Sci. Discovery 5 014002), allowing the simulation of realistic lithium granule injections. 2D and 3D simulations of Li injections in NSTX H-mode plasmas are performed and the effect of granule size, injection angle and velocity on the pedestal gradient increase is studied. The amplitude of the local pressure perturbation caused by the granules is found to be highly dependent on the solid granule size. Adjusting the granule injection velocity allows one to inject more particles at the pedestal top. 3D simulations show the destabilization of high order MHD modes whose amplitude is directly linked to the localized pressure perturbation, which is found to depend on the toroidal localization of the granule density source.
Development and Validation of the Metacognitive Strategies for Library Research Skills Scale (MS-LRSS)

Abstract The possession of metacognitive strategies can contribute to successful library research experiences. Accordingly, these skills should be explicitly taught during library instruction. In order to facilitate further examination of student metacognitive strategies, the Metacognitive strategies for Library Research Skills Scale (MS-LRSS) was developed and deployed to 224 graduate and undergraduate students at two post-secondary institutions. Development and validation of this instrument is described in this article. Overall, this instrument demonstrated to be a valid and reliable measure of metacognitive strategies in the context of information literacy and library research.
Polar Opinion Dynamics in Social Networks

For decades, scientists have studied opinion formation in social networks, where information travels via word of mouth. The particularly interesting case is when polar opinions—Democrats versus Republicans or iOS versus Android—compete in the network. The central problem is to design and analyze a model that captures how polar opinions evolve in the real world. In this paper, we propose a general nonlinear model of polar opinion dynamics , rooted in several theories of sociology and social psychology. The model's key distinguishing trait is that unlike in the existing linear models, such as DeGroot and Friedkin–Johnsen models, an individual's susceptibility to persuasion is a function of his or her current opinion . For example, a person holding a neutral opinion may be rather malleable, while “extremists” may be strongly committed to their current beliefs. We also study three specializations of our general model, whose susceptibility functions correspond to different sociopsychological theories. We provide a comprehensive theoretical analysis of our nonlinear models’ behavior using several tools from nonsmooth analysis of dynamical systems. To study convergence, we use nonsmooth max–min Lyapunov functions together with the generalized Invariance Principle. For our general model, we derive a general sufficient condition for the convergence to consensus. For the specialized models, we provide a full theoretical analysis of their convergence—whether to consensus or disagreement. Our results are rather general and easily apply to the analysis of other nonlinear models defined over directed networks, with Lyapunov functions constructed out of convex components.
Expressed parental concern regarding childhood stuttering and the Test of Childhood Stuttering.

Abstract Purpose The purpose of the present study was to determine whether the Test of Childhood Stuttering observational rating scales (TOCS; Gillam et al., 2009) (1) differed between parents who did versus did not express concern (independent from the TOCS) about their child’s speech fluency; (2) correlated with children’s frequency of stuttering measured during a child-examiner conversation; and (3) correlated with the length and complexity of children’s utterances, as indexed by mean length of utterance (MLU). Method Participants were 183 young children ages 3:0–5:11. Ninety-one had parents who reported concern about their child’s stuttering (65 boys, 26 girls) and 92 had parents who reported no such concern (50 boys, 42 girls). Participants’ conversational speech during a child-examiner conversation was analyzed for (a) frequency of occurrence of stuttered and non-stuttered disfluencies, and (b) MLU. Besides expressing concern or lack thereof about their child’s speech fluency, parents completed the TOCS observational rating scales documenting how often they observe different disfluency types in speech of their children, as well as disfluency-related consequences. Results There were three main findings. First, parents who expressed concern (independently from the TOCS) about their child’s stuttering reported significantly higher scores on the TOCS Speech Fluency and Disfluency-Related Consequences rating scales. Second, children whose parents rated them higher on the TOCS Speech Fluency rating scale produced more stuttered disfluencies during a child-examiner conversation. Third, children with higher scores on the TOCS Disfluency-Related Consequences rating scale had shorter MLU during child-examiner conversation, across age and level of language ability. Conclusions Findings support the use of the TOCS observational rating scales as one documentable, objective means to determine parental perception of and concern about their child’s stuttering. Findings also support the notion that parents are reasonably accurate, if not reliable, judges of the quantity and quality (i.e., stuttered vs. non-stuttered) of their child’s speech disfluencies. Lastly, findings that some children may decrease their verbal output in attempts to minimize instances of stuttering – as indexed by relatively low MLU and a high TOCS Disfluency-Related Consequences scores – provides strong support for sampling young children’s speech and language across various situations to obtain the most representative index possible of the child’s MLU and associated instances of stuttering.
What Neuroscience Will Tell Us About Moral Responsibility

The essay is a reflection on determinism, moral and legal responsibility and punishment from the perspective of neuroscience. The author argues that compatibilist free will gives us everything we need to be morally responsible and allows us to maintain a moderately retributivist line of thinking.
Alectinib for advanced ALK-positive non-small-cell lung cancer.

Purpose The pharmacology, pharmacokinetics, clinical efficacy, safety and tolerability, dosage and administration, and place in therapy of alectinib for treatment of patients with non-small-cell lung cancer (NSCLC) are reviewed. Summary In patients with NSCLC driven by mutations of ALK , the gene coding for anaplastic lymphoma kinase (ALK), treatment with the ALK inhibitor crizotinib has been found to provide median progression-free survival (PFS) of 10.9 months; however, therapeutic failures and tumor progression to brain metastases are common with crizotinib use, prompting research to find more potent and tolerable ALK inhibitors that target major oncogenic drivers of NSCLC. Alectinib is a next-generation ALK inhibitor initially approved by the Food and Drug Administration for use in patients with metastatic ALK -positive NSCLC who are intolerant of or have disease progression during crizotinib therapy. In clinical trials, alectinib was found effective for delaying disease progression and, more importantly, reducing brain metastases in patients with NSCLC who developed resistance or intolerance to previous crizotinib therapy. Published data from clinical trials indicate that the most common grade 1 and 2 adverse effects associated with alectinib use are fatigue, constipation, peripheral edema, and myalgia; the most common grade 3 or 4 reactions include increases in creatine phosphokinase, alanine aminotransferase, and aspartate aminotransferase levels. Conclusion Alectinib appears to be effective and safe for use in patients with metastatic ALK -positive NSCLC, with demonstrated superiority over crizotinib in terms of PFS rates. Research to better define ALK inhibitor resistance mechanisms and alectinib’s place in therapy is ongoing.
Tin-gallium-oxide-based UV-C detectors

The emergence of conductive gallium oxide single crystal substrates offers the potential for vertical Schottky detectors operating in the UV-C spectral region. We report here on our recent work in the development of Tin Gallium oxide (TGO) thin film metal-semiconductor-metal (MSM) and Schottky detectors using plasma-assisted molecular beam epitaxy on c plane sapphire and bulk Ga2O3 substrates. Tin alloying of gallium oxide thin films was found to systematically reduce the optical band gap of the compound, providing tunability in the UV-C spectral region. Tin concentration in the TGO epilayers was found to be highly dependent on growth conditions, and Ga flux in particular. First attempts to demonstrate vertical Schottky photodetectors using TGO epilayers on bulk n-type Ga2O3 substrates were successful. Resultant devices showed strong photoresponse to UV-C light with peak responsivities clearly red shifted in comparison to Ga2O3 homoepitaxial Schottky detectors due to TGO alloying.
The Theory of a Single Linear Transformation

The main topic of this chapter is an introduction to the theory of a single linear transformation T ∈L (V,V). The goal is to find a basis of the vector space V such that the matrix of the linear transformation T with respect to this basis is as simple as possible. Since the end result, often called a normal form, is used in different ways, there are several versions of what the normal form of the matrix should be. Some are given in this chapter, and others, for orthogonal and unitary transformations, etc., in Chapter 9.
Time, Space, and Transnational Flows: Critical Historical Conjunctures and Explaining Change in Northern Nigerian Agriculture

In this chapter Lennihan presents us with an approach to the understanding of historical change that centers on the examination of the intersection of social and environmental events. In this example, she accounts for the progressive adoption of wage labor among the rural Hausa of Northern Nigeria in the first part of the twentieth century. The puzzle presented to historians by this case is that wage labor was established even though the rural population was not deprived of its land, and continues to this day to maintain widespread individual land ownership. Nevertheless, landowners found themselves obliged to obtain wage labor through cash payment. Lennihan traces the progressive development of dependence upon cash itself in what was formerly an economy and society where labor, to a large extent, was provided by the household, sometimes including slaves, and neighbors. This arose through a series of political, economic, and environmental crises that are directly related to the region’s interactions with distant regions through colonialism and trade. Initially, local farmers are obliged to grow export commodities such as cotton in order to pay taxes imposed by British colonial authorities; the values of their crops vary with international trade conditions, which themselves reflect a variety of local situations elsewhere. At the same time, their own local conditions vary with the weather. When two or more such shifts—such as a drop in the price of cotton and several successive years of drought—occur together, farmers are forced to adopt wage labor even though they own land. Lennihan refers to such intersections of social, political, economic, and environmental events as “critical historical conjunctures” that should provide useful keys to historical investigation.
Mechanisms of Cell Cycle Regulation by TGF-β Disabled in Cancer

Disabling the TGF-β signaling pathway is a widespread means by which carcinoma cells subvert the normally potent growth arresting effect of TGF-β to enable cancer cell growth. We have shown disrupted TGF-β signaling concomitant with loss of growth inhibition by TGF-β occurs early in endometrial carcinogenesis. As an effector of cell cycle arrest, TGF-β inhibits synthesis of certain cyclin/cdks and directly induces cdk inhibitors (CDKI), such as p15Ink4b(p15) and p21Waf1/Cip1(p21), to inhibit phosphorylation of Rb, thereby preventing progression to S phase. Although the level of the CDKI, p27Kip1(p27) is increased in a variety of TGF-β treated cells, evidence for the regulation of p27 by TGF-β in epithelial cells has largely been indirect. Now, we show that TGF-β dosedependently increases both nuclear and cytoplasmic levels of p27 in primary cultures of normal endometrial epithelial cells (EECs) by preventing its degradation through the downregulation of Skp2 and cks1, critical components of the SCFskp2 complex, that target p27 for ubiquitin-mediated degradation. Thus, the levels of p27 and Cks1/Skp2 are inversely regulated by TGF-β to achieve normal cell cycle arrest in late G1. In contrast, the lack of TGF-β signaling in primary endometrial carcinoma (ECA) cells promotes rapid proteasomal degradation of p27 for uncontrolled cell growth. The increase in p27 and decrease in Cks1/Skp2 is recapitulated in vivo in normal secretory phase endometrium (SE) compared to all grades of ECA, which show the reverse. Transient transfection of Smad2 into a TGF-β-responsive ECA cell line, HEC-1A, decreased the levels of cks1 and a small molecule inhibitor of TGF-β receptor I kinase (SD-208) blocked the ability of TGF-β to decrease cks1 and increase p27 indicating that these effects result from direct classic TGF-β signaling. Importantly, knocking down p27 with a siRNA approach blocked TGF-β mediated growth inhibition in HEC-1A, further substantiating that TGF-β mediates growth inhibition through p27 in these cells. In addition, we further show that estrogen causes MAPK-driven ubiquitin-mediated degradation of p27 for proliferation and that progesterone induces marked accumulation of p27 to block cell growth. Thus, our results suggest that TGF-β and ovarian hormones converge on the regulation of intracellular p27 levels as a major target for endometrial growth. Because ECA is an estrogen-induced cancer, related to unopposed estrogen, and progesterone is therapeutic for this disease, we propose that the pathogenesis of ECA may be related to both the lack of TGF-β signaling and the absence of progesterone (as in menopause and anovulation), causing continuous estrogen-driven proteasomal degradation of p27. Finally, soluble mediators derived from stromal cells in the ECA tumor microenvironment, but not from normal stromal cells, decrease the levels of p27 and increase the levels of cks1, while increasing growth of HEC-1A cells, implicating a role for stromal cells in endometrial carcinogenesis.
A Weakly Supervised Learning Framework for Detecting Social Anxiety and Depression

Although social anxiety and depression are common, they are often underdiagnosed and undertreated, in part due to difficulties identifying and accessing individuals in need of services. Current assessments rely on client self-report and clinician judgment, which are vulnerable to social desirability and other subjective biases. Identifying objective, nonburdensome markers of these mental health problems, such as features of speech, could help advance assessment, prevention, and treatment approaches. Prior research examining speech detection methods has focused on fully supervised learning approaches employing strongly labeled data. However, strong labeling of individuals high in symptoms or state affect in speech audio data is impractical, in part because it is not possible to identify with high confidence which regions of a long speech indicate the person's symptoms or affective state. We propose a weakly supervised learning framework for detecting social anxiety and depression from long audio clips. Specifically, we present a novel feature modeling technique named NN2Vec that identifies and exploits the inherent relationship between speakers' vocal states and symptoms/affective states. Detecting speakers high in social anxiety or depression symptoms using NN2Vec features achieves F-1 scores 17% and 13% higher than those of the best available baselines. In addition, we present a new multiple instance learning adaptation of a BLSTM classifier, named BLSTM-MIL. Our novel framework of using NN2Vec features with the BLSTM-MIL classifier achieves F-1 scores of 90.1% and 85.44% in detecting speakers high in social anxiety and depression symptoms.
Studies of Growth Kinetics on Surfaces with Diffraction

It is common to study a system under the assumption that it has been properly equilibrated. Phenomena occurring at equilibrium can be described by thermodynamics and the parameters that are measured correspond to minimum free-energy states. Most experimental work on surface phases has been done with the assumption of “equilibrium” with the only caveat being that true equilibrium might not be achievable due to kinetic limitations.
Abstract LB-225: Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient

Introduction: Precision medicine approaches to guide therapy selection require routine sampling of tumors. However, tumor biopsies are not always accessible and may be confounded by spatial heterogeneity. Liquid biopsies, including analysis of cell-free DNA (cfDNA), present a non-invasive alternative which may reflect multiple tumors in the body. Previous studies have demonstrated exome-wide concordance between single-site tumor biopsies and cfDNA, but little is known about how cfDNA reflects multiple lesions within a patient. Here we sought to determine how cfDNA reflects the body-wide tumor phylogeny, which will inform the use of cfDNA for cancer precision medicine. Methods: We identified 20 patients with pancreatic cancer who had undergone rapid autopsy. We then screened cfDNA tumor fraction and performed whole-exome sequencing of cfDNA and multiple tumor biopsies for 3 patients with cfDNA tumor fraction >10%. We inferred the tumor phylogeny and then developed a statistical approach to deconvolute the contributions to cfDNA from tumor phylogenetic nodes. Finally, we determined whether shared trunk mutations could be detected in cfDNA and tumor biopsies. Results: For each patient, we found mutations shared between all sites and cfDNA, including putative driver mutations. We found mutations which were clonal in multiple regions were detectable in cfDNA, whereas mutations private to individual sites were never clonal in cfDNA. Through our deconvolution analysis, we found that cfDNA could not be modeled as a simple linear combination of individual sites, but rather that cfDNA represented multiple nodes in the inferred phylogeny. For two pancreatic adenocarcinoma patients, the inferred ancestor of the metastases had high estimated contribution (>70%) to cfDNA, while the ancestors of the primaries had lower contributions ( Conclusions: Through analyzing cfDNA and synchronous tumor biopsies from the same patient, we find trunk mutations are enriched in cfDNA as compared to the average single-site biopsy. We also predict that cfDNA represents multiple nodes in the inferred phylogeny. In cases where tumor biopsies are inaccessible, we demonstrate that cfDNA might be a promising alternative to detect trunk SSNVs. These results suggest that cfDNA may be complementary to tumor biopsies for disease monitoring and treatment selection in personalized medicine. Citation Format: Samuel S. Freeman, Ziao Lin, Gavin Ha, Ignaty Leshchiner, Justin Rhoades, Dimitri Livitz, Daniel Rosebrock, Sarah C. Reed, Gregory Gydush, Christopher Lo, Denisse Rotem, Atish D. Choudhury, Daniel G. Stover, Heather A. Parsons, Jesse S. Boehm, J Christopher Love, Matthew Meyerson, Paul Grandgenett, Michael A. Hollingsworth, Viktor A. Adalsteinsson, Gad Getz. Liquid biopsies identify trunk mutations and reflect multiple tumors in a patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-225.
Mutations present in a low-passage Zika virus isolate result in attenuated pathogenesis in mice

Zika virus (ZIKV) infection can result in neurological disorders including Congenital Zika Syndrome in infants exposed to the virus in utero. Pregnant women can be infected by mosquito bite as well as by sexual transmission from infected men. Herein, the variants of ZIKV within the male reproductive tract and ejaculates were assessed in inoculated mice. We identified two non-synonymous variants at positions E-V330L and NS1-W98G. These variants were also present in the passage three PRVABC59 isolate and infectious clone relative to the patient serum PRVABC59 sequence. In subsequent studies, ZIKV E-330L was less pathogenic in mice than ZIKV E-330V as evident by increased average survival times. In Vero cells, ZIKV E-330L/NS1-98G outcompeted ZIKV E-330V/NS1-98W within 3 passages. These results suggest that the E-330L/NS1-98G variants are attenuating in mice and were enriched during cell culture passaging. Cell culture propagation of ZIKV could significantly affect animal model development and vaccine efficacy studies.
Analysis of bioinspired non-interlocking geometrically patterned interfaces under predominant mode I loading.

Abstract Geometrically patterned interfaces seem to be a common motif in Nature. In particular, geometry plays an important role in increasing the strength, toughness and damage tolerance among different species. Here, we investigate the role of the shape of the opening crack behind the crack tip as the crack propagates along the interface. In particular, we studied the shape of the interface behind the crack tip for different amplitude-to-wavelength aspect ratios with two analytical models and compared with finite element simulations through the J-integral. Additionally, we explore the role of material length scale by investigating the relationship between the geometrical characteristic lengths and the emerging material length scale using a finite element-based cohesive zone model. The results suggest that geometrical toughening is influenced by a size effect, but it is bounded between two extreme conditions.
Twelve tips for running an effective session with standardized patients

The incorporation of actors as standardized patients (SPs) to help students achieve learning goals across a range of topics has become widespread in medical education. SPs are integrated into formative and summative objective structured clinical examinations by medical educators and by licensing boards for assessment of competence. While SPs are useful for assessment of dynamic skills, they also have significant utility as an engaging instructional method. Few tools in teaching allow for the breadth of instruction, practice, and assessment offered by workshops involving SPs. A simulated encounter with an SP may be a trainee's only opportunity to experience working through a particular clinical scenario in an environment that carries no risk of significant harm. Thus, there is immense potential for educational innovation with SPs. The following Twelve Tips piece provides suggestions for harnessing this potential based on available literature and educational experiences of the authors.
Connecting Population, Health and Place with Geospatial Tools and Data

This chapter traces how the growth of geographic information science and the potential for using the accompanying geospatial tools and data to advance our understanding of disease prevalence, etiology, transmission, and treatment. Two major and interrelated topics are addressed. The first describes current geospatial tools and data along with a framework for their use in health applications, and the second documents several conceptual and methodological challenges that are likely to frustrate our efforts to use these geospatial tools and data to connect population, health and place in meaningful ways. The chapter closes by noting some new opportunities and predictions for the future.
Place and progress in the works of Elizabeth Gaskell

The editors of Place and Progress in the Works of Elizabeth Gaskell position their volume as an expansion of Gaskell’s location “within the narrative of British letters and national identity” (2–3)...
Results on Semileptonic D 0 and D s Decays and Evidence for Non- D D Decays of the ψ (3770)

The spectator picture of charm decays and the assumption of isospin symmetry allows us to conclude that the partial widths (Γ i ) for the semileptonic decays of any species of charmed particle are identical: $$ {\Gamma _{{D^0}}}(c \to s\ell v) = {\Gamma _{{D^ + }}}(c \to s\ell v) = {\Gamma _{{D_s}}}(c \to s\ell v) $$ Since the lifetimes of charmed particles (τ i ) are well-known (see Table I), this can be approximately tested by measurements of their individual semileptonic branching ratios B SL i : $$ {\Gamma _{{D_i}}}(c \to s\ell v) \approx B_{SL/\tau {D_i}}^i = B({D_i} \to \ell + X)/{\tau _{{D_i}}} $$ We see in Table I[1] that Tsl(D +) and Γ sl (D 0) are remarkably close, and that the B sl (Ds) is expected to be about (7.8±1.0)% when averaging D 0 and D + partial widths.
Correction to: A community‑engaged approach to transdisciplinary doctoral training in urban ecosystem services

In the original publication of the article, two of the contributors’ names (Darrell Brown, Kim Heavener) were missing in the acknowledgement section. The correct acknowledgement is provided below.
The effect of cooling conditions on Ti 6%Al 4%V microstructure observed using high-temperature in-situ scanning electron microscopy

This study focuses on continuous imaging of microstructural changes in Ti 6% Al 4% V when cooling from the β transus of ~ 995 °C or above. A range of microstructures were obtained by accessing different cooling rates. With cooling rates of 0.1–0.5 °C/s, lamellar microstructures were observed, which initiate in a colony microstructure below temperatures of ~ 930 °C. When the lamellar microstructure began forming at grain boundaries, cooling was interrupted to further observe the kinetics in the system. Lamellae changed in projected length from 40 µm to ~ 160–320 µm over three minutes at ~ 930 °C, within the α + β mixed phase. On further time at temperature, the lengthening of lamellae stagnated. With further cooling at 0.1 °C/s, lamellae grew in projected width, while the projected length remained the same. In addition, a surface topography formed at elevated temperatures (around 800 °C), evolved during the α to β heating transition, and persisted upon cooling.
Adult female urinary incontinence guidelines: a systematic review of evaluation guidelines across clinical specialties

To systematically review evaluation guidelines of uncomplicated urinary incontinence (UI) in community-dwelling adult women to assess guidance available to the full range of providers treating UI. Systematic literature search of eight bibliographic databases. We included UI evaluation guidelines written for medical providers in English after January 1, 2008. Exclusion criteria: guidelines for children, men, institutionalized women, peripartum- and neurologic-related UI. A quantitative scoring system included assessed components and associated recommendation level and clarity. Twenty-two guidelines met the criteria. All guidelines included: history taking, UI characterization, physical examination (PE) performance, urinalysis, and post-void residual volume assessment. At least 75% included medical and surgical history assessment, other disease process exclusion, medication review, impact on quality of life ascertainment, observing stress UI, mental status assessment, performing a pelvic examination, urine culture, bladder diary, and limiting more invasive diagnostics procedures. Fifty to 75% included other important evaluation components (i.e., assessing obstetric history, bowel symptoms, fluid intake, patient expectations/preferences/values, obesity, physical functioning/mobility, other PE [abdominal, rectal, pelvic muscle, and neurologic], urethral hypermobility, and pad testing. Less than 50% of guidelines included discussing patient treatment goals. Guidelines varied in level of detail and clarity, with several instances of unclear or inconsistent recommendations within the same guideline and evaluation components identified only by inference from treatment recommendations. Non-specialty guidelines reported fewer components with a lesser degree of clarity, but this difference was not statistically significant (p = 0.20). UI evaluation guidelines varied in level of comprehensiveness, detail, and clarity. This variability may lead to inconsistent evaluations in the work-up of UI, contributing to missed opportunities for individualized care.
Optimal dimensionality selection for independent component analysis of transcriptomic data

Abstract Independent Component Analysis (ICA) is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, ICA effectively reveals the source signals of the transcriptome as groups of co-regulated genes and their corresponding activities across diverse growth conditions. Two major variables that affect the output of ICA are the diversity and scope of the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. Here, we introduce a new method, called OptICA, for effectively finding the optimal dimensionality that consistently maximizes the number of biologically relevant components revealed while minimizing the potential for over-decomposition. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.
CHAPTER 34 – The Laparoscopic Management of Adnexal Masses and Ovarian Cancer

The potential of laparoscopic approach for management of various benign gynecologic problems is well recognized. This chapter highlights the role and risks of laparoscopy in treatment of adnexal masses and ovarian cancer. The laparoscopic approach offers several distinct advantages over laparotomy that includes magnified pelvic and abdominal anatomy allowing precise diagnosis, and improved identification of subtle changes representing metastatic disease. Additional benefits of laparoscopy in gynecologic oncology include: lower morbidity, improved post-operative recovery, and reduced cost. Numerous procedures in gynecologic oncology can be accomplished by endoscopic approach. It is also used in management of benign or suspicious adnexal masses in pre and postmenopausal women, staging of early ovarian cancer, and staging of selected cases of advanced cancer of the ovary. Formal training program within the subspecialty of gynecologic oncology is needed to establish and propagate skills necessary to perform advanced laparoscopic surgery. The competency of a larger number of gynecologic oncologists in operative laparoscopy can thus facilitate organization of large, prospective trials, needed to objectively assess the utility and safety endoscopic procedures.
The Effect of Resuspension on Primary Production

In a physically-forced environment, the rate of net areal production may be driven by resuspension of benthic algae and sediment. Short-term (hourly) shifts in the number of photosynthetic organisms and in the attenuation of light may be greater than variation between days. The effect of resuspension on net areal production can be described by a simple model derived from that developed by Tailing (New Phytologist 56:133–149, 1957). The model is based on four dimensionless parameters: relative changes in suspended chlorophyll (Chl’) and the diffuse attenuation coefficient (k’); the ratio of total incident light to that saturating photosynthesis (Io/Ik); and the relative photosynthetic capacities of benthic and suspended algae (BP/SP). Chl’ and k’ are not dependent; their relationship depends on the relative suspensibility of benthic algae and sediment. Where benthic algae are more easily suspended than the sediment, resuspension enhances net areal production. Otherwise, the decrease in light penetration as sediment is suspended outweighs the effect of the increase in the number of potential primary producers and production drops. The sensitivity of net areal production to resuspension is highest when Io/Ik and BP/SP are high and is lowest when Io/Ik and BPSP are low. The relationships described by the model are compared to experimental data of fluxes of chlorophyll, attenuation, incident light, and the photosynthesis-irradiance parameters of suspended and benthic algae.
Results readiness in social protection and labor operations : technical guidance notes for social funds task teams

Social funds represent a diverse universe of World Bank projects. Social funds are defined as agencies or programs that channel grants to communities for small scale development projects. Social funds typically finance some mixture of socio economic infrastructure (e.g. building or rehabilitating schools, health centers, water supply systems,), productive investments (e.g. micro?finance and income generating projects), social services (e.g. supporting nutrition campaigns, literacy programs, youth training, support to the elderly and disabled), and capacity building programs (e.g., training for community based organizations, nongovernmental organizations, and local governments). Social Fund programs are demand driven and aim to involve the active participation of several local actors, often using a community driven development approach. The main goal is usually to address the needs of poor and vulnerable communities while building social capital and empowerment at the local level. Social funds have several features that place them in the social protection (SP) realm. They typically target poor communities and/or vulnerable households. They finance social risk management interventions like temporary employment generation and expanded access to basic services by the poorest. Social funds are often employed to address immediate post?conflict needs and responses to natural disasters.
Altered behavior in experimental cortical dysplasia

SUMMARY Purpose: Developmental delay and cognitive impairment are common comorbidities in people with epilepsy associated with malformations of cortical development (MCDs). We studied cognition and behavior in an animal model of diffuse cortical dysplasia (CD), in utero irradiation, using a battery of behavioral tests for neuromuscular and cognitive function. Methods: Fetal rats were exposed to 2.25 Gy external radiation on embryonic day 17 (E17). At 1 month of age they were tested using an open field task, a grip strength task, a grid walk task, inhibitory avoidance, an object recognition task, and the Morris water maze task. Key Findings: Rats with CD showed reduced nonlocomotor activity in the open field task and impaired motor coordination for grid walking but normal grip strength. They showed a reduced tendency to recognize novel objects and reduced retention in an inhibitory avoidance task. Water maze testing showed that learning and memory were impaired in irradiated rats for both cue discrimination and spatially oriented tasks. These results demonstrate significant deficits in cortexand hippocampus-dependent cognitive functions associated with the diffuse abnormalities of cortical and hippocampal development that have been documented in this model. Significance: This study documents multimodal cognitive deficits associated with CD and can serve as the foundation for future investigations into the mechanisms of and possible therapeutic interventions for this problem.
Buckling of Cantilever Bars on Elastic Foundations

Legendre polynomials in conjunction with the Galerkin procedure are used to determine the buckling loads of cantilever bars supported laterally by an elastic foundation. The numerical results of example problems converge rapidly, and the use of the Legendre polynomials to represent the buckled deformation is found to be very desirable. Although the example problem considers only the axial compression to vary along the length of the bar, the general procedure can be extended to account for cases having variable cross sections or foundation stiffness, or both.
Highly sensitive airborne measurements of formaldehyde employing a tunable infrared diode laser spectrometer

Formaldehyde (CH2O) is a ubiquitous component of both the remote background atmosphere as well as the polluted urban atmosphere. This important trace gas is directly emitted from hydrocarbon combustion sources and from oxidation of natural hydrocarbons emitted by plants and trees. Once in the atmosphere, CH2O decomposes by several mechanisms to produce the important hydrogen radical HO2 and carbon monoxide (CO). In producing HO2, CH2O affects the partitioning among odd hydrogen radicals (HOx = [H] + [OH] + [HO2]), which through rapid reactions with hydrocarbons, control the oxidation capacity of the atmosphere. As many hydrocarbon oxidation reactions proceed through CH2O as an intermediate, CH2O also becomes important in further testing our understanding of hydrocarbon reaction mechanisms. Highly accurate measurements of CH2O throughout the mid to upper troposphere are thus critical for improving our understanding of tropospheric photochemistry.
Fretting wear study of surface modified Ni-Ti shape memory alloy

A combination of shape memory characteristics, pseudoelasticity, and good damping properties make near-equiatomic nickel-titanium (Ni-Ti) alloy a desirable candidate material for certain biomedical device applications. The alloy has moderately good wear resistance, however, further improvements in this regard would be beneficial from the perspective of reducing wear debris generation, improving biocompatibility, and preventing failure during service. Fretting wear tests of Ni-Ti in both austenitic and martensitic microstructural conditions were performed with the goal of simulating wear which medical devices such as stents may experience during surgical implantation or service. The tests were performed using a stainless steel stylus counter-wearing surface under dry conditions and also with artificial plasma containing 80 g/L albumen protein as lubricant. Additionally, the research explores the feasibility of surface modification by sequential ion implantation with argon and oxygen to enhance the wear characteristics of the Ni-Ti alloy. Each of these implantations was performed to a dose of 3 x 10(17) atom/cm(2) and an energy of 50 kV, using the plasma source ion implantation process. Improvements in wear resistance were observed for the austenitic samples implanted with argon and oxygen. Ion implantation with argon also reduced the surface Ni content with respect to Ti due to differential sputtering rates of the two elements, an effect that points toward improved biocompatibility.
Protozoa in Water

Protozoa are eukaryotic unicellular animals that possess membrane-bound genetic material and other cellular organelles that carry out various life functions (1). They are colorless and lack cell walls. These motile Eukarya obtain food by ingesting other organisms or organic particles. The uptake of these macromolecules occurs by a process called pinocytosis (2), whereby fluid is sucked into a channel formed by cell membrane invagination and enclosing the fluid within a membrane-bound vacuole. Particulate matter such as bacteria may also be ingested by phagocytosis. Protozoa may be found in a variety of freshwater and marine habitats and in soil. Keywords: protozoa; Giardia lamblia; Entamoeba histolytica; Cryptosporidium parvum; Paramecium; Balantidium coli; Acanthamoeba; Toxoplasma; flagellate; ciliate; amoeba; Microsporidia; Sporozoa
Current status of antimonide-based mid-IR lasers

Summary form only given. Antimonide-based semiconductor lasers, either electrically or optically pumped, have made significant progress in the past few years. Near 2 /spl mu/m, GaInAsSb/AlGaAsSb quantum-well (QW) diode lasers have exhibited excellent performance, with room-temperature threshold current density as low as 50 A/cm/sup 2/, CW output power more than 1 W from 100-/spl mu/m aperture, and diffraction-limited CW power of 600 mW from tapered structures. Recently, room-temperature CW operation has been extended to 2.7 /spl mu/m by increasing the In content in GaInAsSb while limiting the As content to avoid the miscibility gap. The maximum CW power at 10/spl deg/C from a 100-/spl mu/m aperture was 500, 250 and 160 mW for 2.3, 2.5 and 2.6 /spl mu/m, respectively.
Low-temperature spectral studies on the biosynthesis of cytochromes in Baker's yeast.

Abstract The time course of the biosynthesis of the cytochrome system was studied during aeration of anaerobically grown baker's yeast, spectrophotometrically at liquid-air temperature, and by measuring the rate of oxygen consumption with a polarized platinum electrode. Using cells harvested in the stationary phase of growth, the increase in Q o 2 values as well as the spectral transition from cytochrome b 1 to cytochromes b, C 1 , and c was linear from the beginning of aeration, while in exponential phase cells a lag period of about an hour was observed. The lag was attributed in these cells to a lack of an oxygen-binding compound that serves as the inducer in the cytochrome-forming system. The low-temperature spectrum of reduced cytochrome b 1 in intact anaerobically grown yeast cells was shown to have two α bands, at 557.5 and 551.0 mμ, and to be similar to that of reduced cytochrome b 2 , a purified enzyme from brewer's yeast, with bands of 557.5 and 552.5 mμ.
Thorotrast-induced cancer in man

The case history is presented of a malignant tumor in man attributed to the injection of Thorotrast. 55 references. (C.H.)
The molecular biology of Euglena gracilis. I. Growth conditions and cellular composition.

Abstract A new minimal medium, and growth conditions for the exponential growth of Euglena gracilis are described. Cell mass, elemental and molecular composition of the cells are also reported.
Minding Our Ps and Qs: An Adventure in Reclassification

In spring 2007, the Carnegie Mellon University Libraries began the switch from using the Dewey Decimal Classification to the Library of Congress Classification. This article includes the reason for the changeover and describes the process by which the change was made. The project, done mostly in-house, involved members of all units of the libraries, with outside workers hired only to label, sort, and shift books. Various teams or working groups took the lead on different portions of the project, which included mapping the library, hiring and training, supervising the workers, and publicity. The difficulties encountered and solutions to resolve them are discussed, as are the lessons learned from the project.
Invertebrate Neurobiology: Polymorphic neural networks

Recent work on small invertebrate nervous systems provides new insights into the way in which neurons are organized into functional networks to generate behavior.
Cognitive performance is associated with macronutrient intake in healthy young and middle-aged adults.

Abstract Primary objective: The objective was to examine whether dietary intakes of macronutrients are associated with neuropsychological performance. Research design and method: Study participants were 3960 adults aged 20–59 years, who completed three neuropsychological tests and a 24-hour dietary recall as a part of the Third National Health and Nutrition Examination Survey, 1988–1994. Poor performance was defined as the test score below gender-specific 15th percentile. Main outcomes and results: While holding the energy percentages from different macronutrients, additional 100 kcal intake of energy was associated with a reduced odds of poor performance on serial digital learning test (OR = 0.98, 95%CI = 0.96, 0.99) and symbol digital substitution test (OR = 0.97, 95%CI = 0.96, 0.99). Compared with equivalent energy from carbohydrates, each 5% of energy from poly-unsaturated fatty acids (PUFA) or total fat was associated with a reduced OR of poor performance on simple reaction time test (PUFA: OR = 0.77...
Evaluation and diagnosis of noncardiac chest pain.

By far, GERD is the most common cause of NCCP, accounting for up to 60% of the patients. 3 Among patients with non-GERD-related NCCP, up to 30% have an esophageal motor disorder. 4‐6 However, 70% of those with non-GERD-related NCCP have normal esophageal motility but may demonstrate alteration in esophageal pain perception (visceral hyperalgesia). Thus, the main esophageal underlying mechanisms for NCCP include GERD, esophageal motility abnormalities, and visceral hypersensitivity. Differentiating between the underlying mechanisms of NCCP on a clinical basis has not been a gratifying experience. A recent study could not find a significant difference when comparing the quality and characteristics of chest pain between patients with and without GERD-related NCCP. 7 That included chest pain site, radiation, and relationship to food, exercise, and sleep. Only chest pain that was relieved by antacids and the presence of classic GERD symptoms (heartburn and acid regurgitation) were predictive of GERDrelated NCCP. The latter findings were recently supported by another study from Korea demonstrating increased GERD-related findings on invasive diagnostic tools in patients with GERD-related symptoms as compared with those without GERD-related symptoms. 8 Presently, diagnosis of the underlying cause of NCCP is driven by availability of treatment and diagnostic
Deep ecology and radical environmentalism

Abstract The principles of deep ecology and its philosophical critique of reform environmentalism are reviewed, and the relationship between deep ecology and radical environmentalism is described. Major radical environmental groups such as Earth First!, Greenpeace, Sea Shepherd Society, and the Rainforest Action Network are analyzed in terms of their organization, strategies, and tactics. The last section includes a discussion of the mounting environmental “counter‐movement”; and possible changes in the radical environmental movement.